deda6f10dedc9b7ae370bc262e8a45aa669b00f6
.DS_Store
BLK.md
| ... | ... | @@ -32,12 +32,14 @@ |
| 32 | 32 | |
| 33 | 33 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BLK_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BLK_protein_hg38.html) |
| 34 | 34 | |
| 35 | - |
|
| 35 | + |
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| 36 | 36 | |
| 37 | 37 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BLK.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BLK_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | + |
|
| 40 | 41 | ## BLK Expression |
| 41 | - |
|
| 42 | + |
|
| 42 | 43 | <!-- ORIGIN: Unknown --> |
| 44 | + |
|
| 43 | 45 | ## References |
BL_DLBCL_FL_sankey_methods-1.png
| ... | ... | Binary files /dev/null and b/BL_DLBCL_FL_sankey_methods-1.png differ |
BMP7.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # BMP7 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2019-09-26 : Panea : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -29,8 +31,6 @@ timeline |
| 29 | 31 | |FL |No |No |1.371 | 0.000 | |
| 30 | 32 | |
| 31 | 33 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468) |
|
| 34 | 34 | |
| 35 | 35 | |
| 36 | 36 | ## BMP7 Hotspots |
| ... | ... | @@ -56,14 +56,16 @@ timeline |
| 56 | 56 | |
| 57 | 57 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BMP7_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BMP7_protein_hg38.html) |
| 58 | 58 | |
| 59 | - |
|
| 59 | + |
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| 60 | 60 | |
| 61 | 61 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BMP7.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BMP7_hg38.html) |
| 62 | 62 | |
| 63 | - |
|
| 63 | + |
|
| 64 | + |
|
| 64 | 65 | ## BMP7 Expression |
| 65 | - |
|
| 66 | + |
|
| 66 | 67 | <!-- ORIGIN: paneaWholeGenomeLandscape2019 --> |
| 67 | 68 | <!-- BL: paneaWholeGenomeLandscape2019 --> |
| 69 | + |
|
| 68 | 70 | ## References |
| 69 | 71 | 1. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019; |
BRAF.md
| ... | ... | @@ -10,6 +10,7 @@ timeline |
| 10 | 10 | 2011-06-16 : Tiacci : DLBCL |
| 11 | 11 | 2012-12-01 : Love : BL |
| 12 | 12 | ``` |
| 13 | + |
|
| 13 | 14 | ## Relevance tier by entity |
| 14 | 15 | |
| 15 | 16 | |Entity|Tier|Description | |
| ... | ... | @@ -39,8 +40,6 @@ timeline |
| 39 | 40 | |FL |No |No |4.680 |0 | |
| 40 | 41 | |
| 41 | 42 | |
| 42 | -> [!NOTE] |
|
| 43 | -> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in DLBCL in 2012 by [Lohr JG](https://pubmed.ncbi.nlm.nih.gov/22343534) |
|
| 44 | 43 | |
| 45 | 44 | |
| 46 | 45 | ## BRAF Hotspots |
| ... | ... | @@ -60,14 +59,14 @@ timeline |
| 60 | 59 | |
| 61 | 60 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BRAF_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BRAF_protein_hg38.html) |
| 62 | 61 | |
| 63 | - |
|
| 62 | + |
|
| 64 | 63 | |
| 65 | 64 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BRAF.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BRAF_hg38.html) |
| 66 | 65 | |
| 67 | - |
|
| 66 | + |
|
| 68 | 67 | |
| 69 | 68 | ## BRAF Expression |
| 70 | - |
|
| 69 | + |
|
| 71 | 70 | |
| 72 | 71 | ## References |
| 73 | 72 | 1. *Tiacci E, Trifonov V, Schiavoni G, Holmes A, Kern W, Martelli MP, Pucciarini A, Bigerna B, Pacini R, Wells VA, Sportoletti P, Pettirossi V, Mannucci R, Elliott O, Liso A, Ambrosetti A, Pulsoni A, Forconi F, Trentin L, Semenzato G, Inghirami G, Capponi M, Di Raimondo F, Patti C, Arcaini L, Musto P, Pileri S, Haferlach C, Schnittger S, Pizzolo G, Foà R, Farinelli L, Haferlach T, Pasqualucci L, Rabadan R, Falini B. BRAF mutations in hairy-cell leukemia. N Engl J Med. 2011 Jun 16;364(24):2305-15. doi: 10.1056/NEJMoa1014209. Epub 2011 Jun 11. PMID: 21663470; PMCID: PMC3689585.* |
BRD4.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # BRD4 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -29,20 +31,20 @@ timeline |
| 29 | 31 | |FL |No |No |0.000 |0 | |
| 30 | 32 | |
| 31 | 33 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597) |
|
| 34 | 34 | |
| 35 | 35 | |
| 36 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BRD4_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BRD4_protein_hg38.html) |
| 37 | 37 | |
| 38 | - |
|
| 38 | + |
|
| 39 | 39 | |
| 40 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BRD4.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BRD4_hg38.html) |
| 41 | 41 | |
| 42 | - |
|
| 42 | + |
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| 43 | + |
|
| 43 | 44 | ## BRD4 Expression |
| 44 | - |
|
| 45 | + |
|
| 45 | 46 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 46 | 47 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 48 | + |
|
| 47 | 49 | ## References |
| 48 | 50 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
BRINP3.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # BRINP3 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup>1</sup> Subsequent exome and genome-wide studies of DLBCL did not reproduce this observation. |
| 4 | 5 | |
| ... | ... | @@ -13,6 +14,7 @@ timeline |
| 13 | 14 | title Publication timing |
| 14 | 15 | 2017-10-10 : Reddy : DLBCL |
| 15 | 16 | ``` |
| 17 | + |
|
| 16 | 18 | ## Relevance tier by entity |
| 17 | 19 | |
| 18 | 20 | |Entity|Tier|Description | |
| ... | ... | @@ -39,13 +41,14 @@ timeline |
| 39 | 41 | |
| 40 | 42 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BRINP3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BRINP3_protein_hg38.html) |
| 41 | 43 | |
| 42 | - |
|
| 44 | + |
|
| 43 | 45 | |
| 44 | 46 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BRINP3.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BRINP3_hg38.html) |
| 45 | 47 | |
| 46 | - |
|
| 48 | + |
|
| 49 | + |
|
| 47 | 50 | ## BRINP3 Expression |
| 48 | - |
|
| 51 | + |
|
| 49 | 52 | |
| 50 | 53 | ## References |
| 51 | 54 | 1. *Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.* |
BTBD3.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # BTBD3 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup>1</sup> Subsequent exome and genome-wide studies of DLBCL did not reproduce this observation. |
| 4 | 5 | |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | title Publication timing |
| 9 | 10 | 2017-10-10 : Reddy : DLBCL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -33,13 +35,14 @@ timeline |
| 33 | 35 | |
| 34 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BTBD3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BTBD3_protein_hg38.html) |
| 35 | 37 | |
| 36 | - |
|
| 38 | + |
|
| 37 | 39 | |
| 38 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BTBD3.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BTBD3_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 43 | + |
|
| 41 | 44 | ## BTBD3 Expression |
| 42 | - |
|
| 45 | + |
|
| 43 | 46 | |
| 44 | 47 | ## References |
| 45 | 48 | 1. *Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.* |
BTG1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # BTG1 |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | BTG1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. These mutations are a feature of the MCD genetic subgroup of DLBCL.<sup>1</sup> Mutations in the BTG1 gene have been implicated in the pathogenesis and progression of diffuse large B-cell lymphoma (DLBCL) through functional exploration in vivo. Knock-out of BTG1 did not lead to spontaneous lymphomagenesis but enhanced the lymphoproliferation induced by VavP-BCL2 and promoted lymphoma dissemination in xenotransplantation experiments.<sup>2</sup> Another study demonstrated that specific BTG1 mutations afford germinal center (GC) B cells with a fitness advantage relative to un-mutated counterparts.<sup>3</sup> |
| 4 | 5 | |
| ... | ... | @@ -10,6 +11,7 @@ timeline |
| 10 | 11 | 2021-04-01 : Sarkozy : PMBL |
| 11 | 12 | 2022-07-06 : Burkhardt : BL |
| 12 | 13 | ``` |
| 14 | + |
|
| 13 | 15 | ## Relevance tier by entity |
| 14 | 16 | |
| 15 | 17 | |Entity|Tier|Description | |
| ... | ... | @@ -77,20 +79,21 @@ timeline |
| 77 | 79 | |
| 78 | 80 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BTG1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BTG1_protein_hg38.html) |
| 79 | 81 | |
| 80 | - |
|
| 82 | + |
|
| 81 | 83 | |
| 82 | 84 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BTG1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BTG1_hg38.html) |
| 83 | 85 | |
| 84 | - |
|
| 86 | + |
|
| 85 | 87 | |
| 86 | 88 | ## BTG1 Expression |
| 87 | - |
|
| 89 | + |
|
| 88 | 90 | |
| 89 | 91 | |
| 90 | 92 | <!-- ORIGIN: morinFrequentMutationHistonemodifying2011 --> |
| 91 | 93 | <!-- DLBCL: morinFrequentMutationHistonemodifying2011 --> |
| 92 | 94 | <!-- BL: burkhardtClinicalRelevanceMolecular2022b --> |
| 93 | 95 | <!-- BL: burkhardtClinicalRelevanceMolecular2022b --> |
| 96 | + |
|
| 94 | 97 | ## References |
| 95 | 98 | |
| 96 | 99 | 1. *Wright GW, Huang DW, Phelan JD, Coulibaly ZA, Roulland S, Young RM, Wang JQ, Schmitz R, Morin RD, Tang J, Jiang A, Bagaev A, Plotnikova O, Kotlov N, Johnson CA, Wilson WH, Scott DW, Staudt LM. A Probabilistic Classification Tool for Genetic Subtypes of Diffuse Large B Cell Lymphoma with Therapeutic Implications. Cancer Cell. 2020 Apr 13;37(4):551-568.e14. doi: 10.1016/j.ccell.2020.03.015. PMID: 32289277; PMCID: PMC8459709.* |
BTG2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # BTG2 |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | BTG2 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. Mutations in the BTG2 gene have been implicated in the pathogenesis of diffuse large B-cell lymphoma (DLBCL), contributing to the development and progression of the disease. These mutations are a feature of the MCD genetic subgroup of DLBCL.<sup>1</sup> The biological function of BTG2 mutations and their role in lymphomagenesis remains poorly understood. A potential prognostic association with BTG2 mutations in primary testicular DLBCL has been reported but this has not yet been reproduced.<sup>2</sup> |
| 4 | 5 | ## History |
| ... | ... | @@ -10,6 +11,7 @@ timeline |
| 10 | 11 | 2011-07-27 : Morin : DLBCL |
| 11 | 12 | 2012-12-01 : Love : BL |
| 12 | 13 | ``` |
| 14 | + |
|
| 13 | 15 | ## Relevance tier by entity |
| 14 | 16 | |
| 15 | 17 | |Entity|Tier|Description | |
| ... | ... | @@ -45,20 +47,18 @@ timeline |
| 45 | 47 | |:--------:|:----------:|:---------:|:----------------------------------------------------------------------------------------------:|:------------------:| |
| 46 | 48 | |chr1 |203274698 |203275778|[intron](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr1%3A203274698%2D203275778)|active_promoter | |
| 47 | 49 | |
| 48 | -> [!NOTE] |
|
| 49 | -> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119) |
|
| 50 | 50 | |
| 51 | 51 | |
| 52 | 52 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BTG2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BTG2_protein_hg38.html) |
| 53 | 53 | |
| 54 | - |
|
| 54 | + |
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| 55 | 55 | |
| 56 | 56 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BTG2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BTG2_hg38.html) |
| 57 | 57 | |
| 58 | - |
|
| 58 | + |
|
| 59 | 59 | |
| 60 | 60 | ## BTG2 Expression |
| 61 | - |
|
| 61 | + |
|
| 62 | 62 | |
| 63 | 63 | ## References |
| 64 | 64 | 1. *Wright GW, Huang DW, Phelan JD, Coulibaly ZA, Roulland S, Young RM, Wang JQ, Schmitz R, Morin RD, Tang J, Jiang A, Bagaev A, Plotnikova O, Kotlov N, Johnson CA, Wilson WH, Scott DW, Staudt LM. A Probabilistic Classification Tool for Genetic Subtypes of Diffuse Large B Cell Lymphoma with Therapeutic Implications. Cancer Cell. 2020 Apr 13;37(4):551-568.e14. doi: 10.1016/j.ccell.2020.03.015. PMID: 32289277; PMCID: PMC8459709.* |
BTK.md
| ... | ... | @@ -8,6 +8,7 @@ timeline |
| 8 | 8 | 2017-01-26 : Krysiak : FL |
| 9 | 9 | 2017-05-01 : Albuquerque : DLBCL |
| 10 | 10 | ``` |
| 11 | + |
|
| 11 | 12 | ## Relevance tier by entity |
| 12 | 13 | |
| 13 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -37,18 +38,19 @@ timeline |
| 37 | 38 | |
| 38 | 39 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BTK_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BTK_protein_hg38.html) |
| 39 | 40 | |
| 40 | - |
|
| 41 | + |
|
| 41 | 42 | |
| 42 | 43 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BTK.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BTK_hg38.html) |
| 43 | 44 | |
| 44 | - |
|
| 45 | + |
|
| 45 | 46 | |
| 46 | 47 | |
| 47 | 48 | ## BTK Expression |
| 48 | - |
|
| 49 | + |
|
| 49 | 50 | <!-- ORIGIN: albuquerqueEnhancingKnowledgeDiscovery2017a --> |
| 50 | 51 | <!-- FL: krysiakRecurrentSomaticMutations2017b --> |
| 51 | 52 | <!-- DLBCL: albuquerqueEnhancingKnowledgeDiscovery2017a --> |
| 53 | + |
|
| 52 | 54 | ## References |
| 53 | 55 | 1. Krysiak K, Gomez F, White BS, Matlock M, Miller CA, Trani L, Fronick CC, Fulton RS, Kreisel F, Cashen AF, Carson KR, Berrien-Elliott MM, Bartlett NL, Griffith M, Griffith OL, Fehniger TA. Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma. Blood. 2017 Jan 26;129(4):473–483. PMCID: PMC5270390 |
| 54 | 56 | 2. Albuquerque MA, Grande BM, Ritch EJ, Pararajalingam P, Jessa S, Krzywinski M, Grewal JK, Shah SP, Boutros PC, Morin RD. Enhancing knowledge discovery from cancer genomics data with Galaxy. Gigascience. 2017 May 1;6(5):1–13. PMCID: PMC5437943 |
C6orf27.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # C6orf27 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -25,18 +27,18 @@ timeline |
| 25 | 27 | | |
| 26 | 28 | |
| 27 | 29 | |
| 28 | -> [!NOTE] |
|
| 29 | -> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597) |
|
| 30 | 30 | |
| 31 | 31 | |
| 32 | 32 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C6orf27_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/C6orf27_protein_hg38.html) |
| 33 | 33 | |
| 34 | 34 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C6orf27.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/C6orf27_hg38.html) |
| 35 | 35 | |
| 36 | - |
|
| 36 | + |
|
| 37 | + |
|
| 37 | 38 | ## C6orf27 Expression |
| 38 | - |
|
| 39 | + |
|
| 39 | 40 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 40 | 41 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 42 | + |
|
| 41 | 43 | ## References |
| 42 | 44 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
CAD.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CAD |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -29,8 +31,6 @@ timeline |
| 29 | 31 | |FL |No |No |0.000 |0 | |
| 30 | 32 | |
| 31 | 33 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597) |
|
| 34 | 34 | |
| 35 | 35 | |
| 36 | 36 | ## CAD Hotspots |
| ... | ... | @@ -41,14 +41,16 @@ timeline |
| 41 | 41 | |
| 42 | 42 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CAD_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CAD_protein_hg38.html) |
| 43 | 43 | |
| 44 | - |
|
| 44 | + |
|
| 45 | 45 | |
| 46 | 46 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CAD.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CAD_hg38.html) |
| 47 | 47 | |
| 48 | - |
|
| 48 | + |
|
| 49 | + |
|
| 49 | 50 | ## CAD Expression |
| 50 | - |
|
| 51 | + |
|
| 51 | 52 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 52 | 53 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 54 | + |
|
| 53 | 55 | ## References |
| 54 | 56 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
CADPS2.md
| ... | ... | @@ -9,6 +9,7 @@ timeline |
| 9 | 9 | title Publication timing |
| 10 | 10 | 2021-05-05 : Hübschmann : DLBCL |
| 11 | 11 | ``` |
| 12 | + |
|
| 12 | 13 | ## Relevance tier by entity |
| 13 | 14 | |
| 14 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -35,13 +36,14 @@ timeline |
| 35 | 36 | |
| 36 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CADPS2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CADPS2_protein_hg38.html) |
| 37 | 38 | |
| 38 | - |
|
| 39 | + |
|
| 39 | 40 | |
| 40 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CADPS2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CADPS2_hg38.html) |
| 41 | 42 | |
| 42 | - |
|
| 43 | + |
|
| 44 | + |
|
| 43 | 45 | ## CADPS2 Expression |
| 44 | - |
|
| 46 | + |
|
| 45 | 47 | |
| 46 | 48 | ## References |
| 47 | 49 | 1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491 |
CARD11.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CARD11 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | |
| 4 | 5 | ```mermaid |
| ... | ... | @@ -11,6 +12,7 @@ timeline |
| 11 | 12 | 2016-06-21 : Wu : MCL |
| 12 | 13 | 2019-09-26 : Panea : BL |
| 13 | 14 | ``` |
| 15 | + |
|
| 14 | 16 | ## Relevance tier by entity |
| 15 | 17 | |
| 16 | 18 | |Entity|Tier|Description | |
| ... | ... | @@ -66,14 +68,14 @@ timeline |
| 66 | 68 | |
| 67 | 69 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CARD11_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CARD11_protein_hg38.html) |
| 68 | 70 | |
| 69 | - |
|
| 71 | + |
|
| 70 | 72 | |
| 71 | 73 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CARD11.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CARD11_hg38.html) |
| 72 | 74 | |
| 73 | - |
|
| 75 | + |
|
| 74 | 76 | |
| 75 | 77 | ## CARD11 Expression |
| 76 | - |
|
| 78 | + |
|
| 77 | 79 | |
| 78 | 80 | |
| 79 | 81 | |
| ... | ... | @@ -82,6 +84,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C |
| 82 | 84 | <!-- MCL: wuGeneticHeterogeneityPrimary2016 --> |
| 83 | 85 | <!-- MZL: yanBCRTLRSignaling2012a --> |
| 84 | 86 | <!-- DLBCL: lenzOncogenicCARD11Mutations2008 --> |
| 87 | + |
|
| 85 | 88 | ## References |
| 86 | 89 | 1. Lenz G, Davis RE, Ngo VN, Lam L, George TC, Wright GW, Dave SS, Zhao H, Xu W, Rosenwald A, Ott G, Müller-Hermelink HK, Gascoyne RD, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Fisher RI, Chan WC, Staudt LM. Oncogenic CARD11 mutations in human diffuse large B cell lymphoma. Science. 2008 Mar;319(5870):1676–1679. |
| 87 | 90 | 2. Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJM, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298–303. PMCID: PMC3210554 |
CARD4.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CARD4 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | |
| 4 | 5 | ```mermaid |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | title Publication timing |
| 8 | 9 | 2012-12-01 : Love : BL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -26,18 +28,18 @@ timeline |
| 26 | 28 | | |
| 27 | 29 | |
| 28 | 30 | |
| 29 | -> [!NOTE] |
|
| 30 | -> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597) |
|
| 31 | 31 | |
| 32 | 32 | |
| 33 | 33 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CARD4_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CARD4_protein_hg38.html) |
| 34 | 34 | |
| 35 | 35 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CARD4.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CARD4_hg38.html) |
| 36 | 36 | |
| 37 | - |
|
| 37 | + |
|
| 38 | + |
|
| 38 | 39 | ## CARD4 Expression |
| 39 | - |
|
| 40 | + |
|
| 40 | 41 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 41 | 42 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 43 | + |
|
| 42 | 44 | ## References |
| 43 | 45 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
CD274.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CD274 |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | the CD274 gene encodes the programmed death-ligand 1 (PD-L1). Mutations in B-cell lymphomas, such as DLBCL, are relatively rare.<sup>1</sup> Although rare, mutations have the potential to impact PD-L1 expression and could be relevant in the context of immune checkpoint inhibitors. |
| 4 | 5 | ## History |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | title Publication timing |
| 9 | 10 | 2011-07-27 : Morin : DLBCL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -32,21 +34,19 @@ timeline |
| 32 | 34 | |FL |No |No |4.631 |42.709 | |
| 33 | 35 | |
| 34 | 36 | |
| 35 | -> [!NOTE] |
|
| 36 | -> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119) |
|
| 37 | 37 | |
| 38 | 38 | |
| 39 | 39 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CD274_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CD274_protein_hg38.html) |
| 40 | 40 | |
| 41 | - |
|
| 41 | + |
|
| 42 | 42 | |
| 43 | 43 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CD274.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CD274_hg38.html) |
| 44 | 44 | |
| 45 | - |
|
| 45 | + |
|
| 46 | 46 | |
| 47 | 47 | |
| 48 | 48 | ## CD274 Expression |
| 49 | - |
|
| 49 | + |
|
| 50 | 50 | |
| 51 | 51 | ## References |
| 52 | 52 |
CDC73.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CDC73 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | Mutations in this gene were first described in BL in 2012 by Love et al<sup>1</sup> and subsequently in DLBCL by Reddy et al.<sup>2</sup> Subsequent exome and genome-wide studies of DLBCL and BL did not reproduce these observations. |
| 4 | 5 | |
| ... | ... | @@ -9,6 +10,7 @@ timeline |
| 9 | 10 | 2012-12-01 : Love : BL |
| 10 | 11 | 2017-10-10 : Reddy : DLBCL |
| 11 | 12 | ``` |
| 13 | + |
|
| 12 | 14 | ## Relevance tier by entity |
| 13 | 15 | |
| 14 | 16 | |Entity|Tier|Description | |
| ... | ... | @@ -38,14 +40,14 @@ timeline |
| 38 | 40 | |
| 39 | 41 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CDC73_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CDC73_protein_hg38.html) |
| 40 | 42 | |
| 41 | - |
|
| 43 | + |
|
| 42 | 44 | |
| 43 | 45 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CDC73.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CDC73_hg38.html) |
| 44 | 46 | |
| 45 | - |
|
| 47 | + |
|
| 46 | 48 | |
| 47 | 49 | ## CDC73 Expression |
| 48 | - |
|
| 50 | + |
|
| 49 | 51 | |
| 50 | 52 | ## References |
| 51 | 53 | 1. *Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561* |
CDH17.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CDH17 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -29,20 +31,20 @@ timeline |
| 29 | 31 | |FL |No |No |0.000 |0.000 | |
| 30 | 32 | |
| 31 | 33 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597) |
|
| 34 | 34 | |
| 35 | 35 | |
| 36 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CDH17_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CDH17_protein_hg38.html) |
| 37 | 37 | |
| 38 | - |
|
| 38 | + |
|
| 39 | 39 | |
| 40 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CDH17.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CDH17_hg38.html) |
| 41 | 41 | |
| 42 | - |
|
| 42 | + |
|
| 43 | + |
|
| 43 | 44 | ## CDH17 Expression |
| 44 | - |
|
| 45 | + |
|
| 45 | 46 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 46 | 47 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 48 | + |
|
| 47 | 49 | ## References |
| 48 | 50 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
CDH8.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CDH8 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | |
| 4 | 5 | ```mermaid |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | title Publication timing |
| 8 | 9 | 2014-05-08 : Zhang : MCL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -28,20 +30,20 @@ timeline |
| 28 | 30 | |FL |No |No |0.000 |0.00 | |
| 29 | 31 | |
| 30 | 32 | |
| 31 | -> [!NOTE] |
|
| 32 | -> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267) |
|
| 33 | 33 | |
| 34 | 34 | |
| 35 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CDH8_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CDH8_protein_hg38.html) |
| 36 | 36 | |
| 37 | - |
|
| 37 | + |
|
| 38 | 38 | |
| 39 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CDH8.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CDH8_hg38.html) |
| 40 | 40 | |
| 41 | - |
|
| 41 | + |
|
| 42 | + |
|
| 42 | 43 | ## CDH8 Expression |
| 43 | - |
|
| 44 | + |
|
| 44 | 45 | <!-- ORIGIN: zhangGenomicLandscapeMantle2014 --> |
| 45 | 46 | <!-- MCL: zhangGenomicLandscapeMantle2014 --> |
| 47 | + |
|
| 46 | 48 | ## References |
| 47 | 49 | 1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996. |
CDH9.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CDH9 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | |
| 4 | 5 | ```mermaid |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | title Publication timing |
| 8 | 9 | 2013-08-15 : Morin : DLBCL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -31,20 +33,20 @@ timeline |
| 31 | 33 | |FL |No |No |0.774 |0 | |
| 32 | 34 | |
| 33 | 35 | |
| 34 | -> [!NOTE] |
|
| 35 | -> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601) |
|
| 36 | 36 | |
| 37 | 37 | |
| 38 | 38 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CDH9_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CDH9_protein_hg38.html) |
| 39 | 39 | |
| 40 | - |
|
| 40 | + |
|
| 41 | 41 | |
| 42 | 42 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CDH9.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CDH9_hg38.html) |
| 43 | 43 | |
| 44 | - |
|
| 44 | + |
|
| 45 | + |
|
| 45 | 46 | ## CDH9 Expression |
| 46 | - |
|
| 47 | + |
|
| 47 | 48 | <!-- ORIGIN: morinMutationalStructuralAnalysis2013 --> |
| 48 | 49 | <!-- DLBCL: morinMutationalStructuralAnalysis2013 --> |
| 50 | + |
|
| 49 | 51 | ## References |
| 50 | 52 | 1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992 |
CDKN2A.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CDKN2A |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | Although CDKN2A aberrations are common in DLBCL, this gene is predominantly affected by copy number alterations. One study found that deletions of the CDKN2A locus occur in about one-third of DLBCL patients.<sup>1</sup> The mutation pattern in DLBCL and FL implies the preferential accumulation of *inactivating mutations*. This gene has some recurrent sites of mutations (hotspots) with the most common mutation causing a truncation at codon 80 (R80*). |
| 4 | 5 | |
| ... | ... | @@ -14,6 +15,7 @@ timeline |
| 14 | 15 | 2016-09-08 : Spina : MZL |
| 15 | 16 | 2019-03-21 : Grande : BL |
| 16 | 17 | ``` |
| 18 | + |
|
| 17 | 19 | ## Relevance tier by entity |
| 18 | 20 | |
| 19 | 21 | |Entity|Tier|Description | |
| ... | ... | @@ -54,15 +56,15 @@ timeline |
| 54 | 56 | |
| 55 | 57 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CDKN2A_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CDKN2A_protein_hg38.html) |
| 56 | 58 | |
| 57 | - |
|
| 59 | + |
|
| 58 | 60 | |
| 59 | 61 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CDKN2A.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CDKN2A_hg38.html) |
| 60 | 62 | |
| 61 | - |
|
| 63 | + |
|
| 62 | 64 | |
| 63 | 65 | ## CDKN2A Expression |
| 64 | 66 | |
| 65 | - |
|
| 67 | + |
|
| 66 | 68 | |
| 67 | 69 | ## References |
| 68 | 70 | 1. *Guney S, Jardin F, Bertrand P, Mareschal S, Parmentier F, Picquenot JM, Tilly H, Bastard C. Several mechanisms lead to the inactivation of the CDKN2A (P16), P14ARF, or CDKN2B (P15) genes in the GCB and ABC molecular DLBCL subtypes. Genes Chromosomes Cancer. 2012 Sep;51(9):858-67. doi: 10.1002/gcc.21970. Epub 2012 May 23. PMID: 22619049.* |
CDKN2C.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CDKN2C |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2023-02-03 : Thomas : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -29,20 +31,20 @@ timeline |
| 29 | 31 | |FL |No |No | 0.000 | 0.000 | |
| 30 | 32 | |
| 31 | 33 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in BL in 2023 by [Thomas N](https://pubmed.ncbi.nlm.nih.gov/36201743) |
|
| 34 | 34 | |
| 35 | 35 | |
| 36 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CDKN2C_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CDKN2C_protein_hg38.html) |
| 37 | 37 | |
| 38 | - |
|
| 38 | + |
|
| 39 | 39 | |
| 40 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CDKN2C.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CDKN2C_hg38.html) |
| 41 | 41 | |
| 42 | - |
|
| 42 | + |
|
| 43 | + |
|
| 43 | 44 | ## CDKN2C Expression |
| 44 | - |
|
| 45 | + |
|
| 45 | 46 | <!-- ORIGIN: thomasGeneticSubgroupsInform2023 --> |
| 46 | 47 | <!-- BL: thomasGeneticSubgroupsInform2023 --> |
| 48 | + |
|
| 47 | 49 | ## References |
| 48 | 50 | 1. Thomas N, Dreval K, Gerhard DS, Hilton LK, Abramson JS, Ambinder RF, Barta S, Bartlett NL, Bethony J, Bhatia K, Bowen J, Bryan AC, Cesarman E, Casper C, Chadburn A, Cruz M, Dittmer DP, Dyer MA, Farinha P, Gastier-Foster JM, Gerrie AS, Grande BM, Greiner T, Griner NB, Gross TG, Harris NL, Irvin JD, Jaffe ES, Henry D, Huppi R, Leal FE, Lee MS, Martin JP, Martin MR, Mbulaiteye SM, Mitsuyasu R, Morris V, Mullighan CG, Mungall AJ, Mungall K, Mutyaba I, Nokta M, Namirembe C, Noy A, Ogwang MD, Omoding A, Orem J, Ott G, Petrello H, Pittaluga S, Phelan JD, Ramos JC, Ratner L, Reynolds SJ, Rubinstein PG, Sissolak G, Slack G, Soudi S, Swerdlow SH, Traverse-Glehen A, Wilson WH, Wong J, Yarchoan R, ZenKlusen JC, Marra MA, Staudt LM, Scott DW, Morin RD. Genetic subgroups inform on pathobiology in adult and pediatric Burkitt lymphoma. Blood. 2023 Feb 23;141(8):904–916. |
CHD1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CHD1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup>1</sup> Subsequent exome and genome-wide studies of DLBCL did not reproduce this observation. |
| 4 | 5 | |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | title Publication timing |
| 9 | 10 | 2017-10-10 : Reddy : DLBCL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -34,14 +36,14 @@ timeline |
| 34 | 36 | |
| 35 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CHD1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CHD1_protein_hg38.html) |
| 36 | 38 | |
| 37 | - |
|
| 39 | + |
|
| 38 | 40 | |
| 39 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CHD1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CHD1_hg38.html) |
| 40 | 42 | |
| 41 | - |
|
| 43 | + |
|
| 42 | 44 | |
| 43 | 45 | ## CHD1 Expression |
| 44 | - |
|
| 46 | + |
|
| 45 | 47 | |
| 46 | 48 | ## References |
| 47 | 49 | 1. *Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.* |
CHD4.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CHD4 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2022-07-06 : Burkhardt : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -29,20 +31,20 @@ timeline |
| 29 | 31 | |FL |No |No |1.815 |0 | |
| 30 | 32 | |
| 31 | 33 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096) |
|
| 34 | 34 | |
| 35 | 35 | |
| 36 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CHD4_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CHD4_protein_hg38.html) |
| 37 | 37 | |
| 38 | - |
|
| 38 | + |
|
| 39 | 39 | |
| 40 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CHD4.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CHD4_hg38.html) |
| 41 | 41 | |
| 42 | - |
|
| 42 | + |
|
| 43 | + |
|
| 43 | 44 | ## CHD4 Expression |
| 44 | - |
|
| 45 | + |
|
| 45 | 46 | <!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b --> |
| 46 | 47 | <!-- BL: burkhardtClinicalRelevanceMolecular2022b --> |
| 48 | + |
|
| 47 | 49 | ## References |
| 48 | 50 | 1. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584 |
CHD8.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CHD8 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | Mutations in this gene were first described in DLBCL in 2017 by Reddy et al<sup>1</sup> and in BL in 2019 by Grande et al.<sup>2</sup> |
| 4 | 5 | |
| ... | ... | @@ -9,6 +10,7 @@ timeline |
| 9 | 10 | 2017-10-10 : Reddy : DLBCL |
| 10 | 11 | 2019-03-21 : Grande : BL |
| 11 | 12 | ``` |
| 13 | + |
|
| 12 | 14 | ## Relevance tier by entity |
| 13 | 15 | |
| 14 | 16 | |Entity|Tier|Description | |
| ... | ... | @@ -40,14 +42,14 @@ timeline |
| 40 | 42 | |
| 41 | 43 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CHD8_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CHD8_protein_hg38.html) |
| 42 | 44 | |
| 43 | - |
|
| 45 | + |
|
| 44 | 46 | |
| 45 | 47 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CHD8.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CHD8_hg38.html) |
| 46 | 48 | |
| 47 | - |
|
| 49 | + |
|
| 48 | 50 | |
| 49 | 51 | ## CHD8 Expression |
| 50 | - |
|
| 52 | + |
|
| 51 | 53 | |
| 52 | 54 | ## References |
| 53 | 55 |
CHST2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CHST2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup>1</sup> Subsequent exome and genome-wide studies of DLBCL did not reproduce this observation. |
| 4 | 5 | |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | title Publication timing |
| 9 | 10 | 2017-10-10 : Reddy : DLBCL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -34,13 +36,14 @@ timeline |
| 34 | 36 | |
| 35 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CHST2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CHST2_protein_hg38.html) |
| 36 | 38 | |
| 37 | - |
|
| 39 | + |
|
| 38 | 40 | |
| 39 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CHST2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CHST2_hg38.html) |
| 40 | 42 | |
| 41 | - |
|
| 43 | + |
|
| 44 | + |
|
| 42 | 45 | ## CHST2 Expression |
| 43 | - |
|
| 46 | + |
|
| 44 | 47 | |
| 45 | 48 | ## References |
| 46 | 49 | 1. *Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.* |
CIITA.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CIITA |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | CIITA encodes the major histocompatibility complex (MHC) class II transactivator. CIITA mutations are frequent in PMBCL. These mutations often include structural genomic rearrangements, missense, nonsense, and frameshift mutations. In PMBCL, these mutations are thought to contribute to loss of MHC expression.<sup>1</sup> Although loss of CIITA and MHC Class II Expression is commonly observed in DLBCL, the role of mutations and methylation affecting this locus remains unclear.<sup>2</sup> CIITA is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. |
| 4 | 5 | |
| ... | ... | @@ -9,6 +10,7 @@ timeline |
| 9 | 10 | 2011-07-27 : Morin : DLBCL |
| 10 | 11 | 2015-11-17 : Mottok : PMBL |
| 11 | 12 | ``` |
| 13 | + |
|
| 12 | 14 | ## Relevance tier by entity |
| 13 | 15 | |
| 14 | 16 | |Entity|Tier|Description | |
| ... | ... | @@ -39,20 +41,18 @@ timeline |
| 39 | 41 | |:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:-------------------------------:| |
| 40 | 42 | |chr16 |10970795 |10975465|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr16%3A10970795%2D10975465)|active_promoter-strong_enhancer| |
| 41 | 43 | |
| 42 | -> [!NOTE] |
|
| 43 | -> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119) |
|
| 44 | 44 | |
| 45 | 45 | |
| 46 | 46 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CIITA_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CIITA_protein_hg38.html) |
| 47 | 47 | |
| 48 | - |
|
| 48 | + |
|
| 49 | 49 | |
| 50 | 50 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CIITA.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CIITA_hg38.html) |
| 51 | 51 | |
| 52 | - |
|
| 52 | + |
|
| 53 | 53 | |
| 54 | 54 | ## CIITA Expression |
| 55 | - |
|
| 55 | + |
|
| 56 | 56 | |
| 57 | 57 | ## References |
| 58 | 58 | 1. *Mottok, A., Woolcock, B., Chan, F., Tong, K., Chong, L., Farinha, P., Telenius, A., Chavez, E., Ramchandani, S., Drake, M., Boyle, M., Ben-Neriah, S., Scott, D., Rimsza, L., Siebert, R., Gascoyne, R., & Steidl, C. (2015). Genomic Alterations in CIITA Are Frequent in Primary Mediastinal Large B Cell Lymphoma and Are Associated with Diminished MHC Class II Expression.. Cell reports, 13 7, 1418-1431 . https://doi.org/10.1016/j.celrep.2015.10.008.* |
CILP.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CILP |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | |
| 4 | 5 | ```mermaid |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | title Publication timing |
| 8 | 9 | 2023-07-26 : Russler : FL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -28,20 +30,20 @@ timeline |
| 28 | 30 | |FL |No |No |0.000 |0 | |
| 29 | 31 | |
| 30 | 32 | |
| 31 | -> [!NOTE] |
|
| 32 | -> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986) |
|
| 33 | 33 | |
| 34 | 34 | |
| 35 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CILP_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CILP_protein_hg38.html) |
| 36 | 36 | |
| 37 | - |
|
| 37 | + |
|
| 38 | 38 | |
| 39 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CILP.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CILP_hg38.html) |
| 40 | 40 | |
| 41 | - |
|
| 41 | + |
|
| 42 | + |
|
| 42 | 43 | ## CILP Expression |
| 43 | - |
|
| 44 | + |
|
| 44 | 45 | <!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a --> |
| 45 | 46 | <!-- FL: russler-germainMutationsAssociatedProgression2023b --> |
| 47 | + |
|
| 46 | 48 | ## References |
| 47 | 49 | 1. Russler-Germain DA, Krysiak K, Ramirez CA, Mosior M, Watkins MP, Gomez F, Skidmore ZL, Trani L, Gao F, Geyer S, Cashen A, Mehta-Shah N, Kahl B, Bartlett N, Alderuccio J, Lossos I, Ondrejka S, Hsi E, Martin P, Leonard J, Griffith M, Griffith O, Fehniger T. Mutations associated with progression in follicular lymphoma predict inferior outcomes at diagnosis: Alliance A151303. Blood Advances. 2023;7:5524–5539. |
CNOT2.md
| ... | ... | @@ -9,6 +9,7 @@ timeline |
| 9 | 9 | title Publication timing |
| 10 | 10 | 2021-05-05 : H : DLBCL |
| 11 | 11 | ``` |
| 12 | + |
|
| 12 | 13 | ## Relevance tier by entity |
| 13 | 14 | |
| 14 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -34,14 +35,14 @@ timeline |
| 34 | 35 | |
| 35 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CNOT2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CNOT2_protein_hg38.html) |
| 36 | 37 | |
| 37 | - |
|
| 38 | + |
|
| 38 | 39 | |
| 39 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CNOT2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CNOT2_hg38.html) |
| 40 | 41 | |
| 41 | - |
|
| 42 | + |
|
| 42 | 43 | |
| 43 | 44 | ## CNOT2 Expression |
| 44 | - |
|
| 45 | + |
|
| 45 | 46 | |
| 46 | 47 | ## References |
| 47 | 48 | 1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491 |
CNTNAP5.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CNTNAP5 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | Mutations in this gene were first described in DLBCL in 2013 by Morin et al.<sup>1</sup> |
| 4 | 5 | |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | title Publication timing |
| 9 | 10 | 2013-08-15 : Morin : DLBCL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -34,13 +36,14 @@ timeline |
| 34 | 36 | |
| 35 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CNTNAP5_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CNTNAP5_protein_hg38.html) |
| 36 | 38 | |
| 37 | - |
|
| 39 | + |
|
| 38 | 40 | |
| 39 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CNTNAP5.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CNTNAP5_hg38.html) |
| 40 | 42 | |
| 41 | - |
|
| 43 | + |
|
| 44 | + |
|
| 42 | 45 | ## CNTNAP5 Expression |
| 43 | - |
|
| 46 | + |
|
| 44 | 47 | |
| 45 | 48 | ## References |
| 46 | 49 | 1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992 |
COL11A1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # COL11A1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | |
| 4 | 5 | ```mermaid |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | title Publication timing |
| 8 | 9 | 2014-05-08 : Zhang : MCL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -28,20 +30,20 @@ timeline |
| 28 | 30 | |FL |No |No |0.628 |0.000 | |
| 29 | 31 | |
| 30 | 32 | |
| 31 | -> [!NOTE] |
|
| 32 | -> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267) |
|
| 33 | 33 | |
| 34 | 34 | |
| 35 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/COL11A1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/COL11A1_protein_hg38.html) |
| 36 | 36 | |
| 37 | - |
|
| 37 | + |
|
| 38 | 38 | |
| 39 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/COL11A1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/COL11A1_hg38.html) |
| 40 | 40 | |
| 41 | - |
|
| 41 | + |
|
| 42 | + |
|
| 42 | 43 | ## COL11A1 Expression |
| 43 | - |
|
| 44 | + |
|
| 44 | 45 | <!-- ORIGIN: zhangGenomicLandscapeMantle2014 --> |
| 45 | 46 | <!-- MCL: zhangGenomicLandscapeMantle2014 --> |
| 47 | + |
|
| 46 | 48 | ## References |
| 47 | 49 | 1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996. |
COL16A1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # COL16A1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | |
| 4 | 5 | ```mermaid |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | title Publication timing |
| 8 | 9 | 2014-05-08 : Zhang : MCL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -28,20 +30,20 @@ timeline |
| 28 | 30 | |FL |No |No |0.000 |0.000 | |
| 29 | 31 | |
| 30 | 32 | |
| 31 | -> [!NOTE] |
|
| 32 | -> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267) |
|
| 33 | 33 | |
| 34 | 34 | |
| 35 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/COL16A1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/COL16A1_protein_hg38.html) |
| 36 | 36 | |
| 37 | - |
|
| 37 | + |
|
| 38 | 38 | |
| 39 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/COL16A1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/COL16A1_hg38.html) |
| 40 | 40 | |
| 41 | - |
|
| 41 | + |
|
| 42 | + |
|
| 42 | 43 | ## COL16A1 Expression |
| 43 | - |
|
| 44 | + |
|
| 44 | 45 | <!-- ORIGIN: zhangGenomicLandscapeMantle2014 --> |
| 45 | 46 | <!-- MCL: zhangGenomicLandscapeMantle2014 --> |
| 47 | + |
|
| 46 | 48 | ## References |
| 47 | 49 | 1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996. |
COL4A2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # COL4A2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | |
| 4 | 5 | ```mermaid |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | title Publication timing |
| 8 | 9 | 2012-12-01 : Love : BL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -30,20 +32,20 @@ timeline |
| 30 | 32 | |FL |No |No |1.043 |0 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597) |
|
| 35 | 35 | |
| 36 | 36 | |
| 37 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/COL4A2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/COL4A2_protein_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | 40 | |
| 41 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/COL4A2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/COL4A2_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | + |
|
| 44 | 45 | ## COL4A2 Expression |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 47 | 48 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 49 | + |
|
| 48 | 50 | ## References |
| 49 | 51 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
COQ7.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # COQ7 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | |
| 4 | 5 | ```mermaid |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | title Publication timing |
| 8 | 9 | 2018-05-01 : Chapuy : DLBCL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -31,20 +33,20 @@ timeline |
| 31 | 33 | |FL |No |No |0.000 |0 | |
| 32 | 34 | |
| 33 | 35 | |
| 34 | -> [!NOTE] |
|
| 35 | -> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087) |
|
| 36 | 36 | |
| 37 | 37 | |
| 38 | 38 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/COQ7_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/COQ7_protein_hg38.html) |
| 39 | 39 | |
| 40 | - |
|
| 40 | + |
|
| 41 | 41 | |
| 42 | 42 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/COQ7.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/COQ7_hg38.html) |
| 43 | 43 | |
| 44 | - |
|
| 44 | + |
|
| 45 | + |
|
| 45 | 46 | ## COQ7 Expression |
| 46 | - |
|
| 47 | + |
|
| 47 | 48 | <!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b --> |
| 48 | 49 | <!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b --> |
| 50 | + |
|
| 49 | 51 | ## References |
| 50 | 52 | 1. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387 |
CPNE8.md
| ... | ... | @@ -9,6 +9,7 @@ timeline |
| 9 | 9 | title Publication timing |
| 10 | 10 | 2021-05-05 : H : FL |
| 11 | 11 | ``` |
| 12 | + |
|
| 12 | 13 | ## Relevance tier by entity |
| 13 | 14 | |
| 14 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -30,19 +31,18 @@ timeline |
| 30 | 31 | |FL |No |No |1.808 |12.601 | |
| 31 | 32 | |
| 32 | 33 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289) |
|
| 35 | 34 | |
| 36 | 35 | |
| 37 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CPNE8_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CPNE8_protein_hg38.html) |
| 38 | 37 | |
| 39 | - |
|
| 38 | + |
|
| 40 | 39 | |
| 41 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CPNE8.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CPNE8_hg38.html) |
| 42 | 41 | |
| 43 | - |
|
| 42 | + |
|
| 43 | + |
|
| 44 | 44 | ## CPNE8 Expression |
| 45 | - |
|
| 45 | + |
|
| 46 | 46 | |
| 47 | 47 | ## References |
| 48 | 48 | 1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491 |
CPXM2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CPXM2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | |
| 4 | 5 | ```mermaid |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | title Publication timing |
| 8 | 9 | 2022-07-06 : Burkhardt : BL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -30,20 +32,20 @@ timeline |
| 30 | 32 | |FL |No |No |1.307 |0 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096) |
|
| 35 | 35 | |
| 36 | 36 | |
| 37 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CPXM2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CPXM2_protein_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | 40 | |
| 41 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CPXM2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CPXM2_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | + |
|
| 44 | 45 | ## CPXM2 Expression |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | <!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b --> |
| 47 | 48 | <!-- BL: burkhardtClinicalRelevanceMolecular2022b --> |
| 49 | + |
|
| 48 | 50 | ## References |
| 49 | 51 | 1. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584 |
CREBBP.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CREBBP |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | CREBBP mutations are highly prevalent in both DLBCL and FL. These mutations often affect the histone acetyltransferase (HAT) domain, crucial for regulating gene expression through chromatin modification, or generate a truncated protein.<sup>1</sup> This gene has some recurrent sites of mutations (hotspots), mostly in the HAT domain. The pattern of mutations in DLBCL is distinct from FL with the latter having more HAT domain mutations relative to truncating mutations.<sup>2</sup> |
| 4 | 5 | |
| ... | ... | @@ -13,6 +14,7 @@ timeline |
| 13 | 14 | 2013-12-13 : Parry : MZL |
| 14 | 15 | 2021-07-15 : Duns : PMBL |
| 15 | 16 | ``` |
| 17 | + |
|
| 16 | 18 | ## Relevance tier by entity |
| 17 | 19 | |
| 18 | 20 | |Entity|Tier|Description | |
| ... | ... | @@ -77,14 +79,14 @@ timeline |
| 77 | 79 | |
| 78 | 80 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CREBBP_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CREBBP_protein_hg38.html) |
| 79 | 81 | |
| 80 | - |
|
| 82 | + |
|
| 81 | 83 | |
| 82 | 84 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CREBBP.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CREBBP_hg38.html) |
| 83 | 85 | |
| 84 | - |
|
| 86 | + |
|
| 85 | 87 | |
| 86 | 88 | ## CREBBP Expression |
| 87 | - |
|
| 89 | + |
|
| 88 | 90 | <!-- ORIGIN: pasqualucciInactivatingMutationsAcetyltransferase2011a --> |
| 89 | 91 | <!-- FL: pasqualucciInactivatingMutationsAcetyltransferase2011a --> |
| 90 | 92 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
CRIP1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CRIP1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | |
| 4 | 5 | ```mermaid |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | title Publication timing |
| 8 | 9 | 2018-05-01 : Chapuy : DLBCL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -31,20 +33,20 @@ timeline |
| 31 | 33 | |FL |No |No |0.000 |0 | |
| 32 | 34 | |
| 33 | 35 | |
| 34 | -> [!NOTE] |
|
| 35 | -> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087) |
|
| 36 | 36 | |
| 37 | 37 | |
| 38 | 38 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CRIP1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CRIP1_protein_hg38.html) |
| 39 | 39 | |
| 40 | - |
|
| 40 | + |
|
| 41 | 41 | |
| 42 | 42 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CRIP1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CRIP1_hg38.html) |
| 43 | 43 | |
| 44 | - |
|
| 44 | + |
|
| 45 | + |
|
| 45 | 46 | ## CRIP1 Expression |
| 46 | - |
|
| 47 | + |
|
| 47 | 48 | <!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b --> |
| 48 | 49 | <!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b --> |
| 50 | + |
|
| 49 | 51 | ## References |
| 50 | 52 | 1. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387 |
CTCF.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CTCF |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | |
| 4 | 5 | ```mermaid |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | title Publication timing |
| 8 | 9 | 2019-09-26 : Panea : BL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -30,20 +32,20 @@ timeline |
| 30 | 32 | |FL |No |No |0.000 |0 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468) |
|
| 35 | 35 | |
| 36 | 36 | |
| 37 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CTCF_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CTCF_protein_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | 40 | |
| 41 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CTCF.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CTCF_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | + |
|
| 44 | 45 | ## CTCF Expression |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | <!-- ORIGIN: paneaWholeGenomeLandscape2019 --> |
| 47 | 48 | <!-- BL: paneaWholeGenomeLandscape2019 --> |
| 49 | + |
|
| 48 | 50 | ## References |
| 49 | 51 | 1. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019; |
CTNNA2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CTNNA2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | |
| 4 | 5 | ```mermaid |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | title Publication timing |
| 8 | 9 | 2014-05-08 : Zhang : MCL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -28,20 +30,20 @@ timeline |
| 28 | 30 | |FL |No |No |2.047 |0.000 | |
| 29 | 31 | |
| 30 | 32 | |
| 31 | -> [!NOTE] |
|
| 32 | -> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267) |
|
| 33 | 33 | |
| 34 | 34 | |
| 35 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CTNNA2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CTNNA2_protein_hg38.html) |
| 36 | 36 | |
| 37 | - |
|
| 37 | + |
|
| 38 | 38 | |
| 39 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CTNNA2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CTNNA2_hg38.html) |
| 40 | 40 | |
| 41 | - |
|
| 41 | + |
|
| 42 | + |
|
| 42 | 43 | ## CTNNA2 Expression |
| 43 | - |
|
| 44 | + |
|
| 44 | 45 | <!-- ORIGIN: zhangGenomicLandscapeMantle2014 --> |
| 45 | 46 | <!-- MCL: zhangGenomicLandscapeMantle2014 --> |
| 47 | + |
|
| 46 | 48 | ## References |
| 47 | 49 | 1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996. |
CTSS.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CTSS |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | |
| 4 | 5 | ```mermaid |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | title Publication timing |
| 8 | 9 | 2020-05-05 : Bararia : FL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -39,14 +41,16 @@ timeline |
| 39 | 41 | |
| 40 | 42 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CTSS_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CTSS_protein_hg38.html) |
| 41 | 43 | |
| 42 | - |
|
| 44 | + |
|
| 43 | 45 | |
| 44 | 46 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CTSS.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CTSS_hg38.html) |
| 45 | 47 | |
| 46 | - |
|
| 48 | + |
|
| 49 | + |
|
| 47 | 50 | ## CTSS Expression |
| 48 | - |
|
| 51 | + |
|
| 49 | 52 | <!-- ORIGIN: barariaCathepsinAlterationsInduce2020c --> |
| 50 | 53 | <!-- FL: barariaCathepsinAlterationsInduce2020c --> |
| 54 | + |
|
| 51 | 55 | ## References |
| 52 | 56 | 1. Bararia D, Hildebrand JA, Stolz S, Haebe S, Alig S, Trevisani CP, Osorio-Barrios F, Bartoschek MD, Mentz M, Pastore A, Gaitzsch E, Heide M, Jurinovic V, Rautter K, Gunawardana J, Sabdia MB, Szczepanowski M, Richter J, Klapper W, Louissaint A, Ludwig C, Bultmann S, Leonhardt H, Eustermann S, Hopfner KP, Hiddemann W, von Bergwelt-Baildon M, Steidl C, Kridel R, Tobin JWD, Gandhi MK, Weinstock DM, Schmidt-Supprian M, Sárosi MB, Rudelius M, Passerini V, Mautner J, Weigert O. Cathepsin S Alterations Induce a Tumor-Promoting Immune Microenvironment in Follicular Lymphoma. Cell Rep. 2020 May 5;31(5):107522. PMID: 32330423 |
CXCR4.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CXCR4 |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | |
| 4 | 5 | CXCR4 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. No notable hot spots have been described in this gene in the context of the cancers listed below. The mutation pattern in DLBCL implies the preferential accumulation of *inactivating mutations*. |
| ... | ... | @@ -15,6 +16,7 @@ timeline |
| 15 | 16 | 2017-01-26 : Krysiak : FL |
| 16 | 17 | 2019-09-26 : Panea : BL |
| 17 | 18 | ``` |
| 19 | + |
|
| 18 | 20 | ## Relevance tier by entity |
| 19 | 21 | |
| 20 | 22 | |Entity|Tier|Description | |
| ... | ... | @@ -51,19 +53,18 @@ timeline |
| 51 | 53 | |:--------:|:----------:|:---------:|:----------------------------------------------------------------------------------------------:|:------------------:| |
| 52 | 54 | |chr2 |136874728 |136875461|[intron](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr2%3A136874728%2D136875461)|weak_promoter | |
| 53 | 55 | |
| 54 | -> [!NOTE] |
|
| 55 | -> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2012 by [Khodabakhshi AH](https://pubmed.ncbi.nlm.nih.gov/23131835). First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289) |
|
| 56 | 56 | |
| 57 | 57 | |
| 58 | 58 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CXCR4_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CXCR4_protein_hg38.html) |
| 59 | 59 | |
| 60 | - |
|
| 60 | + |
|
| 61 | 61 | |
| 62 | 62 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CXCR4.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CXCR4_hg38.html) |
| 63 | 63 | |
| 64 | - |
|
| 64 | + |
|
| 65 | + |
|
| 65 | 66 | ## CXCR4 Expression |
| 66 | - |
|
| 67 | + |
|
| 67 | 68 | |
| 68 | 69 | ## References |
| 69 | 70 | 1. Khodabakhshi AH, Morin RD, Fejes AP, Mungall AJ, Mungall KL, Bolger-Munro M, Johnson NA, Connors JM, Gascoyne RD, Marra MA, Birol I, Jones SJM. Recurrent targets of aberrant somatic hypermutation in lymphoma. Oncotarget. 2012 Nov 12;3(11):1308–1319. PMCID: PMC3717795 |
CXCR5.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CXCR5 |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | CXCR5 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. No notable hot spots have been described in this gene in the context of the cancers listed below. The mutation pattern in DLBCL and FL implies the preferential accumulation of *inactivating mutations*. |
| 4 | 5 | ## History |
| ... | ... | @@ -10,6 +11,7 @@ timeline |
| 10 | 11 | 2018-04-12 : Schmitz : DLBCL |
| 11 | 12 | 2019-09-05 : Mottok : PMBL |
| 12 | 13 | ``` |
| 14 | + |
|
| 13 | 15 | ## Relevance tier by entity |
| 14 | 16 | |
| 15 | 17 | |Entity|Tier|Description | |
| ... | ... | @@ -40,22 +42,22 @@ timeline |
| 40 | 42 | |:--------:|:----------:|:---------:|:--------------------------------------------------------------------------------------------:|:------------------:| |
| 41 | 43 | |chr11 |118754458 |118756514|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr11%3A118754458%2D118756514)|NA | |
| 42 | 44 | |
| 43 | -> [!NOTE] |
|
| 44 | -> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966) |
|
| 45 | 45 | |
| 46 | 46 | |
| 47 | 47 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CXCR5_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CXCR5_protein_hg38.html) |
| 48 | 48 | |
| 49 | - |
|
| 49 | + |
|
| 50 | 50 | |
| 51 | 51 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CXCR5.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CXCR5_hg38.html) |
| 52 | 52 | |
| 53 | - |
|
| 53 | + |
|
| 54 | + |
|
| 54 | 55 | ## CXCR5 Expression |
| 55 | - |
|
| 56 | + |
|
| 56 | 57 | <!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a --> |
| 57 | 58 | <!-- PMBL: mottokIntegrativeGenomicAnalysis2019b --> |
| 58 | 59 | <!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a --> |
| 60 | + |
|
| 59 | 61 | ## References |
| 60 | 62 | 1. Schmitz R, Wright GW, Huang DW, Johnson CA, Phelan JD, Wang JQ, Roulland S, Kasbekar M, Young RM, Shaffer AL, Hodson DJ, Xiao W, Yu X, Yang Y, Zhao H, Xu W, Liu X, Zhou B, Du W, Chan WC, Jaffe ES, Gascoyne RD, Connors JM, Campo E, Lopez-Guillermo A, Rosenwald A, Ott G, Delabie J, Rimsza LM, Tay Kuang Wei K, Zelenetz AD, Leonard JP, Bartlett NL, Tran B, Shetty J, Zhao Y, Soppet DR, Pittaluga S, Wilson WH, Staudt LM. Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma. N Engl J Med. 2018 Apr 12;378(15):1396–1407. PMCID: PMC6010183 |
| 61 | 63 | 2. Mottok A, Hung SS, Chavez EA, Woolcock B, Telenius A, Chong LC, Meissner B, Nakamura H, Rushton C, Viganò E, Sarkozy C, Gascoyne RD, Connors JM, Ben-Neriah S, Mungall A, Marra MA, Siebert R, Scott DW, Savage KJ, Steidl C. Integrative genomic analysis identifies key pathogenic mechanisms in primary mediastinal large B-cell lymphoma. Blood. 2019 Sep 5;134(10):802–813. PMID: 31292115 |
CYB5D1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CYB5D1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | |
| 4 | 5 | ```mermaid |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | title Publication timing |
| 8 | 9 | 2012-12-01 : Love : BL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -30,20 +32,20 @@ timeline |
| 30 | 32 | |FL |No |No |0 |0 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597) |
|
| 35 | 35 | |
| 36 | 36 | |
| 37 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CYB5D1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CYB5D1_protein_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | 40 | |
| 41 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CYB5D1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CYB5D1_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | + |
|
| 44 | 45 | ## CYB5D1 Expression |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 47 | 48 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 49 | + |
|
| 48 | 50 | ## References |
| 49 | 51 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
CYP2A6.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CYP2A6 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | |
| 4 | 5 | ```mermaid |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | title Publication timing |
| 8 | 9 | 2023-07-26 : Russler : FL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -28,20 +30,20 @@ timeline |
| 28 | 30 | |FL |No |No |0.000 |0 | |
| 29 | 31 | |
| 30 | 32 | |
| 31 | -> [!NOTE] |
|
| 32 | -> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986) |
|
| 33 | 33 | |
| 34 | 34 | |
| 35 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CYP2A6_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CYP2A6_protein_hg38.html) |
| 36 | 36 | |
| 37 | - |
|
| 37 | + |
|
| 38 | 38 | |
| 39 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CYP2A6.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CYP2A6_hg38.html) |
| 40 | 40 | |
| 41 | - |
|
| 41 | + |
|
| 42 | + |
|
| 42 | 43 | ## CYP2A6 Expression |
| 43 | - |
|
| 44 | + |
|
| 44 | 45 | <!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a --> |
| 45 | 46 | <!-- FL: russler-germainMutationsAssociatedProgression2023b --> |
| 47 | + |
|
| 46 | 48 | ## References |
| 47 | 49 | 1. Russler-Germain DA, Krysiak K, Ramirez CA, Mosior M, Watkins MP, Gomez F, Skidmore ZL, Trani L, Gao F, Geyer S, Cashen A, Mehta-Shah N, Kahl B, Bartlett N, Alderuccio J, Lossos I, Ondrejka S, Hsi E, Martin P, Leonard J, Griffith M, Griffith O, Fehniger T. Mutations associated with progression in follicular lymphoma predict inferior outcomes at diagnosis: Alliance A151303. Blood Advances. 2023;7:5524–5539. |
CYP4F22.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # CYP4F22 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | |
| 4 | 5 | ```mermaid |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | title Publication timing |
| 8 | 9 | 2012-12-01 : Love : BL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -30,20 +32,20 @@ timeline |
| 30 | 32 | |FL |No |No |0.000 |0.000 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597) |
|
| 35 | 35 | |
| 36 | 36 | |
| 37 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CYP4F22_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CYP4F22_protein_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | 40 | |
| 41 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CYP4F22.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CYP4F22_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | + |
|
| 44 | 45 | ## CYP4F22 Expression |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 47 | 48 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 49 | + |
|
| 48 | 50 | ## References |
| 49 | 51 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
DAZAP1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # DAZAP1 |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | This gene has some recurrent sites of mutations (hot spots). The mutation pattern in DLBCL and FL implies the preferential accumulation of *inactivating mutations* however the pattern is notable. These mutations often result in truncations affecting the DAZAP1 C-terminus, which are predicted to alter protein sub-cellular localization and disrupt protein-protein interactions.<sup>1</sup> |
| 4 | 5 | ## History |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | title Publication timing |
| 9 | 10 | 2020-07-30 : Pararajalingam : MCL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -46,14 +48,14 @@ timeline |
| 46 | 48 | |
| 47 | 49 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/DAZAP1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/DAZAP1_protein_hg38.html) |
| 48 | 50 | |
| 49 | - |
|
| 51 | + |
|
| 50 | 52 | |
| 51 | 53 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/DAZAP1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/DAZAP1_hg38.html) |
| 52 | 54 | |
| 53 | - |
|
| 55 | + |
|
| 54 | 56 | |
| 55 | 57 | ## DAZAP1 Expression |
| 56 | - |
|
| 58 | + |
|
| 57 | 59 | |
| 58 | 60 | ## References |
| 59 | 61 | 1. *Pararajalingam P, Coyle KM, Arthur SE, Thomas N, Alcaide M, Meissner B, Boyle M, Qureshi Q, Grande BM, Rushton C, Slack GW, Mungall AJ, Tam CS, Agarwal R, Dawson SJ, Lenz G, Balasubramanian S, Gascoyne RD, Steidl C, Connors J, Villa D, Audas TE, Marra MA, Johnson NA, Scott DW, Morin RD. Coding and noncoding drivers of mantle cell lymphoma identified through exome and genome sequencing. Blood. 2020 Jul 30;136(5):572-584. doi: 10.1182/blood.2019002385. PMID: 32160292; PMCID: PMC7440974.* |
DCAF6.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # DCAF6 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup>1</sup> Subsequent exome and genome-wide studies of DLBCL did not reproduce this observation. |
| 4 | 5 | |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | title Publication timing |
| 9 | 10 | 2017-10-10 : Reddy : DLBCL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -32,19 +34,18 @@ timeline |
| 32 | 34 | |FL |No |No |0.000 |0 | |
| 33 | 35 | |
| 34 | 36 | |
| 35 | -> [!NOTE] |
|
| 36 | -> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567) |
|
| 37 | 37 | |
| 38 | 38 | |
| 39 | 39 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/DCAF6_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/DCAF6_protein_hg38.html) |
| 40 | 40 | |
| 41 | - |
|
| 41 | + |
|
| 42 | 42 | |
| 43 | 43 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/DCAF6.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/DCAF6_hg38.html) |
| 44 | 44 | |
| 45 | - |
|
| 45 | + |
|
| 46 | + |
|
| 46 | 47 | ## DCAF6 Expression |
| 47 | - |
|
| 48 | + |
|
| 48 | 49 | |
| 49 | 50 | ## References |
| 50 | 51 | 1. *Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.* |
DDX10.md
| ... | ... | @@ -8,6 +8,7 @@ timeline |
| 8 | 8 | title Publication timing |
| 9 | 9 | 2017-10-10 : Reddy : DLBCL |
| 10 | 10 | ``` |
| 11 | + |
|
| 11 | 12 | ## Relevance tier by entity |
| 12 | 13 | |
| 13 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -32,20 +33,20 @@ timeline |
| 32 | 33 | |FL |No |No |0.000 |0.000 | |
| 33 | 34 | |
| 34 | 35 | |
| 35 | -> [!NOTE] |
|
| 36 | -> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567) |
|
| 37 | 36 | |
| 38 | 37 | |
| 39 | 38 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/DDX10_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/DDX10_protein_hg38.html) |
| 40 | 39 | |
| 41 | - |
|
| 40 | + |
|
| 42 | 41 | |
| 43 | 42 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/DDX10.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/DDX10_hg38.html) |
| 44 | 43 | |
| 45 | - |
|
| 44 | + |
|
| 45 | + |
|
| 46 | 46 | ## DDX10 Expression |
| 47 | - |
|
| 47 | + |
|
| 48 | 48 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
| 49 | 49 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 50 | + |
|
| 50 | 51 | ## References |
| 51 | 52 | 1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
DDX3X.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # DDX3X |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | Mutations in the DDX3X gene, which encodes an RNA helicase involved in various aspects of RNA metabolism, have significant implications in B-cell lymphomas, including BL, DLBCL, and other related malignancies and are particularly enriched within MYC-translocated tumors and those expressing the dark zone signature (DZsig).<sup>1</sup> These mutations are predominantly loss-of-function (LOF) mutations, affecting the helicase domain of the protein.<sup>2</sup> Missense mutations are predominantly found in male patients and rarely in females, hence showing a sex-specific pattern.<sup>3</sup> |
| 4 | 5 | ## History |
| ... | ... | @@ -10,6 +11,7 @@ timeline |
| 10 | 11 | 2018-04-12 : Schmitz : DLBCL |
| 11 | 12 | 2019-09-05 : Mottok : PMBL |
| 12 | 13 | ``` |
| 14 | + |
|
| 13 | 15 | ## Relevance tier by entity |
| 14 | 16 | |
| 15 | 17 | |Entity|Tier|Description | |
| ... | ... | @@ -46,17 +48,15 @@ timeline |
| 46 | 48 | |:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------------:|:------------------:| |
| 47 | 49 | |chrX |42800580 |42804184|[intergenic](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chrX%3A42800580%2D42804184)|NA | |
| 48 | 50 | |
| 49 | -> [!NOTE] |
|
| 50 | -> First described in BL in 2012 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/22885699). First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966). First described in FL in 2023 by [Dreval K](https://pubmed.ncbi.nlm.nih.gov/37084389) |
|
| 51 | 51 | |
| 52 | 52 | |
| 53 | 53 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/DDX3X_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/DDX3X_protein_hg38.html) |
| 54 | 54 | |
| 55 | - |
|
| 55 | + |
|
| 56 | 56 | |
| 57 | 57 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/DDX3X.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/DDX3X_hg38.html) |
| 58 | 58 | |
| 59 | - |
|
| 59 | + |
|
| 60 | 60 | |
| 61 | 61 | ## References |
| 62 | 62 | 1. *Ennishi D, Jiang A, Boyle M, Collinge B, Grande BM, Ben-Neriah S, Rushton C, Tang J, Thomas N, Slack GW, Farinha P, Takata K, Miyata-Takata T, Craig J, Mottok A, Meissner B, Saberi S, Bashashati A, Villa D, Savage KJ, Sehn LH, Kridel R, Mungall AJ, Marra MA, Shah SP, Steidl C, Connors JM, Gascoyne RD, Morin RD, Scott DW. Double-Hit Gene Expression Signature Defines a Distinct Subgroup of Germinal Center B-Cell-Like Diffuse Large B-Cell Lymphoma. J Clin Oncol. 2019 Jan 20;37(3):190-201. doi: 10.1200/JCO.18.01583. Epub 2018 Dec 3. PMID: 30523716; PMCID: PMC6804880.* |
| ... | ... | @@ -64,7 +64,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D |
| 64 | 64 | 3. *Gong, C., Krupka, J., Gao, J., Grigoropoulos, N., Giotopoulos, G., Asby, R., Screen, M., Usheva, Z., Cucco, F., Barrans, S., Painter, D., Zaini, N., Haupl, B., Bornelöv, S., Mozos, I., Meng, W., Zhou, P., Blain, A., Forde, S., Matthews, J., Tan, M., Burke, G., Sze, S., Beer, P., Burton, C., Campbell, P., Rand, V., Turner, S., Ule, J., Roman, E., Tooze, R., Oellerich, T., Huntly, B., Turner, M., Du, M., Samarajiwa, S., & Hodson, D. (2021). Sequential inverse dysregulation of the RNA helicases DDX3X and DDX3Y facilitates MYC-driven lymphomagenesis.. Molecular cell. https://doi.org/10.1016/j.molcel.2021.07.041.* |
| 65 | 65 | |
| 66 | 66 | ## DDX3X Expression |
| 67 | - |
|
| 67 | + |
|
| 68 | 68 | <!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 --> |
| 69 | 69 | <!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a --> |
| 70 | 70 | <!-- BL: schmitzBurkittLymphomaPathogenesis2012 --> |
DHDH.md
| ... | ... | @@ -8,6 +8,7 @@ timeline |
| 8 | 8 | title Publication timing |
| 9 | 9 | 2014-05-08 : Zhang : MCL |
| 10 | 10 | ``` |
| 11 | + |
|
| 11 | 12 | ## Relevance tier by entity |
| 12 | 13 | |
| 13 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -29,20 +30,20 @@ timeline |
| 29 | 30 | |FL |No |No |0 |0 | |
| 30 | 31 | |
| 31 | 32 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267) |
|
| 34 | 33 | |
| 35 | 34 | |
| 36 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/DHDH_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/DHDH_protein_hg38.html) |
| 37 | 36 | |
| 38 | - |
|
| 37 | + |
|
| 39 | 38 | |
| 40 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/DHDH.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/DHDH_hg38.html) |
| 41 | 40 | |
| 42 | - |
|
| 41 | + |
|
| 42 | + |
|
| 43 | 43 | ## DHDH Expression |
| 44 | - |
|
| 44 | + |
|
| 45 | 45 | <!-- ORIGIN: zhangGenomicLandscapeMantle2014 --> |
| 46 | 46 | <!-- MCL: zhangGenomicLandscapeMantle2014 --> |
| 47 | + |
|
| 47 | 48 | ## References |
| 48 | 49 | 1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996. |
DHX15.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # DHX15 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | Mutations in this gene were first described in FL in 2021 by Hübschmann et al.<sup>1</sup> |
| 4 | 5 | |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | title Publication timing |
| 9 | 10 | 2021-05-05 : H : FL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -29,23 +31,23 @@ timeline |
| 29 | 31 | |FL |No |No |2.763 |23.133 | |
| 30 | 32 | |
| 31 | 33 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289) |
|
| 34 | 34 | |
| 35 | 35 | |
| 36 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/DHX15_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/DHX15_protein_hg38.html) |
| 37 | 37 | |
| 38 | - |
|
| 38 | + |
|
| 39 | 39 | |
| 40 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/DHX15.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/DHX15_hg38.html) |
| 41 | 41 | |
| 42 | - |
|
| 42 | + |
|
| 43 | + |
|
| 43 | 44 | ## DHX15 Expression |
| 44 | - |
|
| 45 | + |
|
| 45 | 46 | 1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491 |
| 46 | 47 | |
| 47 | 48 | |
| 48 | 49 | <!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b --> |
| 49 | 50 | <!-- FL: hubschmannMutationalMechanismsShaping2021b --> |
| 51 | + |
|
| 50 | 52 | ## References |
| 51 | 53 | 1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491 |
DHX16.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # DHX16 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | Mutations in this gene were first described in DLBCL in 2021 by Hübschmann et al.<sup>1</sup> |
| 4 | 5 | |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | title Publication timing |
| 9 | 10 | 2021-05-05 : H : DLBCL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -32,19 +34,18 @@ timeline |
| 32 | 34 | |FL |No |No |3.825 | 0.00 | |
| 33 | 35 | |
| 34 | 36 | |
| 35 | -> [!NOTE] |
|
| 36 | -> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289) |
|
| 37 | 37 | |
| 38 | 38 | |
| 39 | 39 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/DHX16_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/DHX16_protein_hg38.html) |
| 40 | 40 | |
| 41 | - |
|
| 41 | + |
|
| 42 | 42 | |
| 43 | 43 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/DHX16.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/DHX16_hg38.html) |
| 44 | 44 | |
| 45 | - |
|
| 45 | + |
|
| 46 | + |
|
| 46 | 47 | ## DHX16 Expression |
| 47 | - |
|
| 48 | + |
|
| 48 | 49 | |
| 49 | 50 | ## References |
| 50 | 51 | 1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491 |
DICER1.md
| ... | ... | @@ -8,6 +8,7 @@ timeline |
| 8 | 8 | title Publication timing |
| 9 | 9 | 2017-10-10 : Reddy : DLBCL |
| 10 | 10 | ``` |
| 11 | + |
|
| 11 | 12 | ## Relevance tier by entity |
| 12 | 13 | |
| 13 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -32,8 +33,6 @@ timeline |
| 32 | 33 | |FL |No |No |2.448 |0 | |
| 33 | 34 | |
| 34 | 35 | |
| 35 | -> [!NOTE] |
|
| 36 | -> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567) |
|
| 37 | 36 | |
| 38 | 37 | > [!WARNING] |
| 39 | 38 | > Mutations in this gene were reported to be inflated in the original results according to [Dreval K](https://www.biorxiv.org/content/10.1101/2023.11.21.567983v1) |
| ... | ... | @@ -41,14 +40,16 @@ timeline |
| 41 | 40 | |
| 42 | 41 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/DICER1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/DICER1_protein_hg38.html) |
| 43 | 42 | |
| 44 | - |
|
| 43 | + |
|
| 45 | 44 | |
| 46 | 45 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/DICER1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/DICER1_hg38.html) |
| 47 | 46 | |
| 48 | - |
|
| 47 | + |
|
| 48 | + |
|
| 49 | 49 | ## DICER1 Expression |
| 50 | - |
|
| 50 | + |
|
| 51 | 51 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
| 52 | 52 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 53 | + |
|
| 53 | 54 | ## References |
| 54 | 55 | 1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
DLBCL_FL_BL_MCL_sankey1-1.svg
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class="node"><rect fill="#e15759" width="10" height="7.0512820512822145"/></g><g y="894.294871794871" x="526.6666666666666" transform="translate(526.6666666666666,894.294871794871)" id="node-84" class="node"><rect fill="#76b7b2" width="10" height="14.80769230769215"/></g><g y="919.1025641025632" x="526.6666666666666" transform="translate(526.6666666666666,919.1025641025632)" id="node-85" class="node"><rect fill="#59a14f" width="10" height="4.935897435897459"/></g><g y="951.0897435897429" x="526.6666666666666" transform="translate(526.6666666666666,951.0897435897429)" id="node-86" class="node"><rect fill="#edc949" width="10" height="20.448717948718013"/></g><g y="844.5345771565457" x="0" transform="translate(0,844.5345771565457)" id="node-87" class="node"><rect fill="#af7aa1" width="10" height="78.97435897435912"/></g><g y="825.2718781973838" x="263.3333333333333" transform="translate(263.3333333333333,825.2718781973838)" id="node-88" class="node"><rect fill="#ff9da7" width="10" height="69.1025641025642"/></g><g y="802.4513653768709" x="263.3333333333333" transform="translate(263.3333333333333,802.4513653768709)" id="node-89" class="node"><rect fill="#9c755f" width="10" height="1.410256410256352"/></g><g y="962.7861894400426" x="263.3333333333333" transform="translate(263.3333333333333,962.7861894400426)" id="node-90" class="node"><rect fill="#bab0ab" width="10" height="7.051282051282101"/></g><g y="951.3759330334477" x="263.3333333333333" transform="translate(263.3333333333333,951.3759330334477)" id="node-91" class="node"><rect fill="#4e79a7" width="10" height="1.4102564102565793"/></g></g><g font-size="14" font-family="sans-serif" class="node-labels"><text text-anchor="end" dy="0.35em" y="121.79487179487165" x="520.6666666666666">Lohr 2012</text><text text-anchor="end" dy="0.35em" y="198.63398939508616" x="784">DLBCL Tier 1</text><text text-anchor="end" dy="0.35em" y="101.1980919591887" x="784">DLBCL Tier 2</text><text text-anchor="end" dy="0.35em" y="147.30769230769218" x="520.6666666666666">Morin 2013</text><text text-anchor="end" dy="0.35em" y="287.82051282051276" x="520.6666666666666">Pasqualucci 2001</text><text text-anchor="end" dy="0.35em" y="81.3461538461537" x="520.6666666666666">Schmitz 2018</text><text text-anchor="end" dy="0.35em" y="6.698717948717928" x="520.6666666666666">Chapuy 2018</text><text text-anchor="end" dy="0.35em" y="219.74358974358964" x="520.6666666666666">Arthur 2018</text><text text-anchor="end" dy="0.35em" y="187.40384615384605" x="520.6666666666666">Pasqualucci 2011</text><text text-anchor="end" dy="0.35em" y="237.4999999999999" x="520.6666666666666">Morin 2016</text><text text-anchor="end" dy="0.35em" y="172.46794871794862" x="520.6666666666666">Albuquerque 2017</text><text text-anchor="end" dy="0.35em" y="201.9871794871794" x="520.6666666666666">Mareschal 2016</text><text text-anchor="end" dy="0.35em" y="348.8461538461537" x="520.6666666666666">Morin 2011</text><text text-anchor="end" dy="0.35em" y="44.55128205128196" x="520.6666666666666">Reddy 2017</text><text text-anchor="end" dy="0.35em" y="103.68589743589729" x="520.6666666666666">Zhang 2013</text><text text-anchor="end" dy="0.35em" y="262.3076923076922" x="520.6666666666666">Hubschmann 2021</text><text text-anchor="end" dy="0.35em" y="570.9294871794868" x="520.6666666666666">Pararajalingam 2020</text><text text-anchor="start" dy="0.35em" y="98.1471733326677" x="16">DLBCL</text><text text-anchor="start" dy="0.35em" y="174.42307692307705" x="279.3333333333333">DLBCL-Sanger</text><text text-anchor="start" dy="0.35em" y="133.75000000000006" x="279.3333333333333">DLBCL-WGS</text><text text-anchor="start" dy="0.35em" y="47.243589743589766" x="279.3333333333333">DLBCL-exome</text><text text-anchor="start" dy="0.35em" y="218.044871794872" x="279.3333333333333">DLBCL-RNA-seq/WGS</text><text text-anchor="start" dy="0.35em" y="278.5897435897438" x="279.3333333333333">DLBCL-WGS/exome</text><text text-anchor="end" dy="0.35em" y="299.93589743589735" x="520.6666666666666">Okosun 2016</text><text text-anchor="end" dy="0.35em" y="343.10945405577695" x="784">FL Tier 1</text><text text-anchor="end" dy="0.35em" y="300.47432309610815" x="784">FL Tier 2</text><text text-anchor="end" dy="0.35em" y="317.6923076923076" x="520.6666666666666">Russler-germain 2023</text><text text-anchor="end" dy="0.35em" y="380.70512820512806" x="520.6666666666666">Krysiak 2017</text><text text-anchor="start" dy="0.35em" y="281.4297406742834" x="16">FL</text><text text-anchor="start" dy="0.35em" y="252.37179487179512" x="279.3333333333333">FL-exome</text><text text-anchor="start" dy="0.35em" y="192.53205128205144" x="279.3333333333333">FL-WGS</text><text text-anchor="start" dy="0.35em" y="329.9659195706672" x="279.3333333333333">FL-RNA-seq/WGS</text><text text-anchor="end" dy="0.35em" y="524.0064102564102" x="520.6666666666666">Muppidi 2014</text><text text-anchor="end" dy="0.35em" y="514.7635359549067" x="784">BL Tier 1</text><text text-anchor="end" dy="0.35em" y="441.6545615959323" x="784">BL Tier 2</text><text text-anchor="end" dy="0.35em" y="416.08974358974336" x="520.6666666666666">Panea 2019</text><text text-anchor="end" dy="0.35em" y="464.51923076923055" x="520.6666666666666">Love 2012</text><text text-anchor="end" dy="0.35em" y="504.13461538461524" x="520.6666666666666">Burkhardt 2022</text><text text-anchor="end" dy="0.35em" y="590.8012820512816" x="520.6666666666666">Schmitz 2012</text><text text-anchor="end" dy="0.35em" y="555.9935897435894" x="520.6666666666666">Thomas 2023</text><text text-anchor="end" dy="0.35em" y="609.2628205128201" x="520.6666666666666">Richter 2012</text><text text-anchor="end" dy="0.35em" y="539.6474358974357" x="520.6666666666666">Grande 2019</text><text text-anchor="start" dy="0.35em" y="464.36465958080777" x="16">BL</text><text text-anchor="start" dy="0.35em" y="543.4038609436568" x="279.3333333333333">BL-RNA-seq</text><text text-anchor="start" dy="0.35em" y="510.5074717939219" x="279.3333333333333">BL-WGS</text><text text-anchor="start" dy="0.35em" y="561.8657281897797" x="279.3333333333333">BL-RNA-seq/WGS/exome</text><text text-anchor="start" dy="0.35em" y="385.0237012537016" x="279.3333333333333">BL-RNA-seq/exome</text><text text-anchor="start" dy="0.35em" y="492.9777694102027" x="279.3333333333333">BL-Sanger</text><text text-anchor="start" dy="0.35em" y="473.10597453840774" x="279.3333333333333">BL-panel</text><text text-anchor="start" dy="0.35em" y="433.49058992302326" x="279.3333333333333">BL-exome</text><text text-anchor="end" dy="0.35em" y="610.4447640578153" x="784">MCL Tier 1</text><text text-anchor="end" dy="0.35em" y="645.8045311514483" x="784">MCL Tier 2</text><text text-anchor="end" dy="0.35em" y="651.8269230769224" x="520.6666666666666">Nadeu 2020</text><text text-anchor="end" dy="0.35em" y="673.4615384615378" x="520.6666666666666">Zhang 2014</text><text text-anchor="end" dy="0.35em" y="630.5448717948713" x="520.6666666666666">Bea 2013</text><text text-anchor="start" dy="0.35em" y="639.0659324217646" x="16">MCL</text><text text-anchor="start" dy="0.35em" y="667.9565239564145" x="279.3333333333333">MCL-exome</text><text text-anchor="start" dy="0.35em" y="612.8826020109457" x="279.3333333333333">MCL-WGS/exome</text><text text-anchor="start" dy="0.35em" y="646.3219085717991" x="279.3333333333333">MCL-WGS</text><text text-anchor="end" dy="0.35em" y="695.0961538461531" x="520.6666666666666">Rossi 2011</text><text text-anchor="end" dy="0.35em" y="724.8958797134587" x="784">MZL Tier 1</text><text text-anchor="end" dy="0.35em" y="768.7420335596125" x="784">MZL Tier 2</text><text text-anchor="end" dy="0.35em" y="729.1987179487171" x="520.6666666666666">Spina 2016</text><text text-anchor="end" dy="0.35em" y="707.5641025641017" x="520.6666666666666">Yan 2012</text><text text-anchor="end" dy="0.35em" y="784.8076923076914" x="520.6666666666666">Jallades 2017</text><text text-anchor="end" dy="0.35em" y="757.5320512820504" x="520.6666666666666">Rossi 2012</text><text text-anchor="end" dy="0.35em" y="865.8333333333323" x="520.6666666666666">Vandenbrand 2017</text><text text-anchor="end" dy="0.35em" y="807.147435897435" x="520.6666666666666">Parry 2013</text><text text-anchor="start" dy="0.35em" y="746.0125582688436" x="16">MZL</text><text text-anchor="start" dy="0.35em" y="764.3667803666708" x="279.3333333333333">MZL-exome</text><text text-anchor="start" dy="0.35em" y="702.0590880589785" x="279.3333333333333">MZL-Panel</text><text text-anchor="start" dy="0.35em" y="723.6937034435939" x="279.3333333333333">MZL-exome/panel</text><text text-anchor="start" dy="0.35em" y="814.5667499922555" x="279.3333333333333">MZL-panel</text><text text-anchor="start" dy="0.35em" y="689.5911393410298" x="279.3333333333333">MZL-Sanger</text><text text-anchor="end" dy="0.35em" y="822.0833333333325" x="520.6666666666666">Wienand 2019</text><text text-anchor="end" dy="0.35em" y="891.1966166140156" 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y="549.0550656064898" x="784">MZL Tier 2</text><text text-anchor="end" dy="0.35em" y="600.4934210526314" x="520.6666666666666">Parry 2013</text><text text-anchor="end" dy="0.35em" y="561.7434210526314" x="520.6666666666666">Spina 2016</text><text text-anchor="end" dy="0.35em" y="631.6866445538581" x="784">MZL Tier 1</text><text text-anchor="end" dy="0.35em" y="711.4473684210527" x="520.6666666666666">Yan 2012</text><text text-anchor="end" dy="0.35em" y="636.9736842105262" x="520.6666666666666">Jallades 2017</text><text text-anchor="end" dy="0.35em" y="684.046052631579" x="520.6666666666666">Rossi 2012</text><text text-anchor="end" dy="0.35em" y="726.7434210526317" x="520.6666666666666">Rossi 2011</text><text text-anchor="start" dy="0.35em" y="602.5529133633438" x="16">MZL</text><text text-anchor="start" dy="0.35em" y="613.7626044848902" x="279.3333333333333">MZL-exome</text><text text-anchor="start" dy="0.35em" y="687.0566941459966" x="279.3333333333333">MZL-Panel</text><text 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|
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DLBCL_sankey_verdana-1.png
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FL_sankey-1.png
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HLA-DMB.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # HLA-DMB |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | HLA-DMB, along with HLA-DMA, plays a critical role in the proper functioning of HLA class II molecules. These genes are essential for the loading of antigenic peptides onto HLA class II molecules, facilitating the presentation of these peptides to CD4+ T cells. |
| 4 | 5 | |
| ... | ... | @@ -33,11 +34,14 @@ HLA-DMB, along with HLA-DMA, plays a critical role in the proper functioning of |
| 33 | 34 | |
| 34 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/HLA-DMB_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/HLA-DMB_protein_hg38.html) |
| 35 | 36 | |
| 36 | - |
|
| 37 | + |
|
| 37 | 38 | |
| 38 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/HLA-DMB.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/HLA-DMB_hg38.html) |
| 39 | 40 | |
| 40 | - |
|
| 41 | + |
|
| 42 | + |
|
| 41 | 43 | ## HLA-DMB Expression |
| 42 | - |
|
| 44 | + |
|
| 43 | 45 | <!-- ORIGIN: Unknown --> |
| 46 | + |
|
| 47 | +## References |
HLA-DQA1.md
| ... | ... | @@ -1,6 +1,4 @@ |
| 1 | 1 | # HLA-DQA1 |
| 2 | -> [!NOTE] |
|
| 3 | -Mutations in this gene are relatively rare in DLBCL overall. *Without further support, this gene may be migrated to Tier 2.* |
|
| 4 | 2 | |
| 5 | 3 | ## History |
| 6 | 4 | Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschmann et al.<sup>1</sup> |
| ... | ... | @@ -12,6 +10,7 @@ timeline |
| 12 | 10 | title Publication timing |
| 13 | 11 | 2021-05-05 : Hübschmann : DLBCL |
| 14 | 12 | ``` |
| 13 | + |
|
| 15 | 14 | ## Relevance tier by entity |
| 16 | 15 | |
| 17 | 16 | |Entity|Tier|Description | |
| ... | ... | @@ -38,7 +37,7 @@ timeline |
| 38 | 37 | |
| 39 | 38 | |
| 40 | 39 | ## HLA-DQA1 Expression |
| 41 | - |
|
| 40 | + |
|
| 42 | 41 | |
| 43 | 42 | ## References |
| 44 | 43 | 1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491 |
HLA-DQB1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # HLA-DQB1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2022-07-06 : Burkhardt : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -29,20 +31,20 @@ timeline |
| 29 | 31 | |FL |No |No |0 |0 | |
| 30 | 32 | |
| 31 | 33 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096) |
|
| 34 | 34 | |
| 35 | 35 | |
| 36 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/HLA-DQB1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/HLA-DQB1_protein_hg38.html) |
| 37 | 37 | |
| 38 | - |
|
| 38 | + |
|
| 39 | 39 | |
| 40 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/HLA-DQB1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/HLA-DQB1_hg38.html) |
| 41 | 41 | |
| 42 | - |
|
| 42 | + |
|
| 43 | + |
|
| 43 | 44 | ## HLA-DQB1 Expression |
| 44 | - |
|
| 45 | + |
|
| 45 | 46 | <!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b --> |
| 46 | 47 | <!-- BL: burkhardtClinicalRelevanceMolecular2022b --> |
| 48 | + |
|
| 47 | 49 | ## References |
| 48 | 50 | 1. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584 |
HNF1B.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # HNF1B |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2011-07-31 : Pasqualucci : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,20 +32,20 @@ timeline |
| 30 | 32 | |FL |No |No |2.652 |0 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in DLBCL in 2011 by [Pasqualucci L](https://pubmed.ncbi.nlm.nih.gov/21804550) |
|
| 35 | 35 | |
| 36 | 36 | |
| 37 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/HNF1B_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/HNF1B_protein_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | 40 | |
| 41 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/HNF1B.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/HNF1B_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | + |
|
| 44 | 45 | ## HNF1B Expression |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | <!-- ORIGIN: pasqualucciAnalysisCodingGenome2011 --> |
| 47 | 48 | <!-- DLBCL: pasqualucciAnalysisCodingGenome2011 --> |
| 49 | + |
|
| 48 | 50 | ## References |
| 49 | 51 | 1. Pasqualucci L, Trifonov V, Fabbri G, Ma J, Rossi D, Chiarenza A, Wells VA, Grunn A, Messina M, Elliot O, Chan J, Bhagat G, Chadburn A, Gaidano G, Mullighan CG, Rabadan R, Dalla-Favera R. Analysis of the coding genome of diffuse large B-cell lymphoma. Nat Genet. 2011 Jul 31;43(9):830–837. PMCID: PMC3297422 |
HNRNPD.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # HNRNPD |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | hnRNPs are a family of RNA-binding proteins that play crucial roles in RNA processing, including splicing, stability, transport, and translation. They are involved in the regulation of gene expression at multiple levels. HNRNPD mutations are rare in DLBCL. The mutation pattern in DLBCL and FL implies the preferential accumulation of *inactivating mutations*. *Without further support, this gene may be migrated to Tier 2.* |
| 4 | 5 | |
| ... | ... | @@ -31,14 +32,17 @@ hnRNPs are a family of RNA-binding proteins that play crucial roles in RNA proce |
| 31 | 32 | |
| 32 | 33 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/HNRNPD_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/HNRNPD_protein_hg38.html) |
| 33 | 34 | |
| 34 | - |
|
| 35 | + |
|
| 35 | 36 | |
| 36 | 37 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/HNRNPD.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/HNRNPD_hg38.html) |
| 37 | 38 | |
| 38 | - |
|
| 39 | + |
|
| 40 | + |
|
| 39 | 41 | ## HNRNPD Expression |
| 40 | - |
|
| 42 | + |
|
| 41 | 43 | |
| 42 | 44 | |
| 43 | 45 | <!-- FLAGGED FOR TIER 2 --> |
| 44 | 46 | <!-- ORIGIN: Unknown --> |
| 47 | + |
|
| 48 | +## References |
HNRNPH1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # HNRNPH1 |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | Non-coding mutations, including synonymous and intronic mutations, are enriched at splicing signals in exon 4 of HNRNPH1. These result in deregulated splicing and increased expression of the hnRNP H1 protein. This overexpression is linked to enhanced cell proliferation and survival, contributing to the aggressive nature of MCL. <sup>1,2</sup> Although initially characterized in MCL, the same pattern of mutations appears in a small number of DLBCLs. |
| 4 | 5 | |
| ... | ... | @@ -9,6 +10,7 @@ timeline |
| 9 | 10 | title Publication timing |
| 10 | 11 | 2020-07-30 : Pararajalingam : MCL |
| 11 | 12 | ``` |
| 13 | + |
|
| 12 | 14 | ## Relevance tier by entity |
| 13 | 15 | |
| 14 | 16 | |Entity|Tier|Description | |
| ... | ... | @@ -42,14 +44,14 @@ timeline |
| 42 | 44 | |
| 43 | 45 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/HNRNPH1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/HNRNPH1_protein_hg38.html) |
| 44 | 46 | |
| 45 | - |
|
| 47 | + |
|
| 46 | 48 | |
| 47 | 49 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/HNRNPH1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/HNRNPH1_hg38.html) |
| 48 | 50 | |
| 49 | - |
|
| 51 | + |
|
| 50 | 52 | |
| 51 | 53 | ## HNRNPH1 Expression |
| 52 | - |
|
| 54 | + |
|
| 53 | 55 | |
| 54 | 56 | |
| 55 | 57 | ## References |
HNRNPU.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # HNRNPU |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | |
| 4 | 5 | ```mermaid |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | 2017-10-10 : Reddy : DLBCL |
| 9 | 10 | 2019-09-26 : Panea : BL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -43,11 +45,11 @@ timeline |
| 43 | 45 | |
| 44 | 46 | View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HNRNPU_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HNRNPU_protein_hg38.html) |
| 45 | 47 | |
| 46 | - |
|
| 48 | + |
|
| 47 | 49 | |
| 48 | 50 | View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HNRNPU.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HNRNPU_hg38.html) |
| 49 | 51 | |
| 50 | - |
|
| 52 | + |
|
| 51 | 53 | |
| 52 | 54 | |
| 53 | 55 | ## References |
HRAS.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # HRAS |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2017-07-27 : Jallades : MZL |
| 8 | 9 | 2017-10-10 : Reddy : DLBCL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -32,22 +34,22 @@ timeline |
| 32 | 34 | |FL |No |No |0 |0 | |
| 33 | 35 | |
| 34 | 36 | |
| 35 | -> [!NOTE] |
|
| 36 | -> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567) |
|
| 37 | 37 | |
| 38 | 38 | |
| 39 | 39 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/HRAS_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/HRAS_protein_hg38.html) |
| 40 | 40 | |
| 41 | - |
|
| 41 | + |
|
| 42 | 42 | |
| 43 | 43 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/HRAS.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/HRAS_hg38.html) |
| 44 | 44 | |
| 45 | - |
|
| 45 | + |
|
| 46 | + |
|
| 46 | 47 | ## HRAS Expression |
| 47 | - |
|
| 48 | + |
|
| 48 | 49 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
| 49 | 50 | <!-- MZL: jalladesExomeSequencingIdentifies2017 --> |
| 50 | 51 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 52 | + |
|
| 51 | 53 | ## References |
| 52 | 54 | 1. Jallades L, Baseggio L, Sujobert P, Huet S, Chabane K, Callet-Bauchu E, Verney A, Hayette S, Desvignes JP, Salgado D, Levy N, Béroud C, Felman P, Berger F, Magaud JP, Genestier L, Salles G, Traverse-Glehen A. Exome sequencing identifies recurrent BCOR alterations and the absence of KLF2, TNFAIP3 and MYD88 mutations in splenic diffuse red pulp small B-cell lymphoma. Haematologica. 2017 Oct;102(10):1758–1766. PMCID: PMC5622860 |
| 53 | 55 | 2. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
HVCN1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # HVCN1 |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | HVCN1, a voltage-gated proton channel, has been identified as recurrently mutated in follicular lymphoma and mutations also appear in some DLBCL.<sup>1</sup> HVCN1 mutations disrupt its normal function, affecting B-cell receptor (BCR) signaling pathways.<sup>1</sup> This gene has some recurrent sites of mutations (hot spots) but the function of these mutations is not well understood. The mutation pattern in DLBCL and FL implies the preferential accumulation of *inactivating mutations*. |
| 4 | 5 | ## History |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | title Publication timing |
| 9 | 10 | 2017-01-26 : Krysiak : FL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -49,15 +51,15 @@ timeline |
| 49 | 51 | |
| 50 | 52 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/HVCN1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/HVCN1_protein_hg38.html) |
| 51 | 53 | |
| 52 | - |
|
| 54 | + |
|
| 53 | 55 | |
| 54 | 56 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/HVCN1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/HVCN1_hg38.html) |
| 55 | 57 | |
| 56 | - |
|
| 58 | + |
|
| 57 | 59 | |
| 58 | 60 | ## References |
| 59 | 61 | 1. *Krysiak, K., Gomez, F., White, B., Matlock, M., Miller, C., Trani, L., Fronick, C., Fulton, R., Kreisel, F., Cashen, A., Carson, K., Berrien-Elliott, M., Bartlett, N., Griffith, M., Griffith, O., & Fehniger, T. (2017). Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma.. Blood, 129 4, 473-483 . https://doi.org/10.1182/blood-2016-07-729954.* |
| 60 | 62 | ## HVCN1 Expression |
| 61 | - |
|
| 63 | + |
|
| 62 | 64 | <!-- ORIGIN: krysiakRecurrentSomaticMutations2017b --> |
| 63 | 65 | <!-- FL: krysiakRecurrentSomaticMutations2017b --> |
ICK.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # ICK |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -29,18 +31,18 @@ timeline |
| 29 | 31 | |FL |No |No |0.000 |0 | |
| 30 | 32 | |
| 31 | 33 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597) |
|
| 34 | 34 | |
| 35 | 35 | |
| 36 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ICK_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ICK_protein_hg38.html) |
| 37 | 37 | |
| 38 | 38 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ICK.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ICK_hg38.html) |
| 39 | 39 | |
| 40 | - |
|
| 40 | + |
|
| 41 | + |
|
| 41 | 42 | ## ICK Expression |
| 42 | - |
|
| 43 | + |
|
| 43 | 44 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 44 | 45 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 46 | + |
|
| 45 | 47 | ## References |
| 46 | 48 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
ID3.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # ID3 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ID3 was first reported as mutated in BL in 2012 by Richter et al.<sup>1</sup> The existence of mutations in DLBCL were described in 2012 by Schmitz et al<sup>2</sup> and later in MZL by Spina et al.<sup>3</sup> |
| 4 | 5 | |
| ... | ... | @@ -10,6 +11,7 @@ ID3 was first reported as mutated in BL in 2012 by Richter et al.<sup>1</sup> Th |
| 10 | 11 | 2012-11-11 : Richter : BL |
| 11 | 12 | 2016 : Spina : MZL |
| 12 | 13 | ``` |
| 14 | + |
|
| 13 | 15 | ## Relevance tier by entity |
| 14 | 16 | |
| 15 | 17 | |Entity|Tier|Description | |
| ... | ... | @@ -47,13 +49,14 @@ ID3 was first reported as mutated in BL in 2012 by Richter et al.<sup>1</sup> Th |
| 47 | 49 | |
| 48 | 50 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ID3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ID3_protein_hg38.html) |
| 49 | 51 | |
| 50 | - |
|
| 52 | + |
|
| 51 | 53 | |
| 52 | 54 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ID3.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ID3_hg38.html) |
| 53 | 55 | |
| 54 | - |
|
| 56 | + |
|
| 57 | + |
|
| 55 | 58 | ## ID3 Expression |
| 56 | - |
|
| 59 | + |
|
| 57 | 60 | |
| 58 | 61 | ## References |
| 59 | 62 | 1. *Richter J, Schlesner M, Hoffmann S, Kreuz M, Leich E, Burkhardt B, Rosolowski M, Ammerpohl O, Wagener R, Bernhart SH, Lenze D, Szczepanowski M, Paulsen M, Lipinski S, Russell RB, Adam-Klages S, Apic G, Claviez A, Hasenclever D, Hovestadt V, Hornig N, Korbel JO, Kube D, Langenberger D, Lawerenz C, Lisfeld J, Meyer K, Picelli S, Pischimarov J, Radlwimmer B, Rausch T, Rohde M, Schilhabel M, Scholtysik R, Spang R, Trautmann H, Zenz T, Borkhardt A, Drexler HG, Möller P, MacLeod RAF, Pott C, Schreiber S, Trümper L, Loeffler M, Stadler PF, Lichter P, Eils R, Küppers R, Hummel M, Klapper W, Rosenstiel P, Rosenwald A, Brors B, Siebert R, ICGC MMML-Seq Project. Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing. Nat Genet. 2012 Dec;44(12):1316–1320. PMID: 23143595* |
IER2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # IER2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2013-08-15 : Morin : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,11 +32,10 @@ timeline |
| 30 | 32 | |FL |No |No |0.000 |0 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601) |
|
| 35 | 35 | ## IER2 Expression |
| 36 | - |
|
| 36 | + |
|
| 37 | 37 | <!-- ORIGIN: morinMutationalStructuralAnalysis2013 --> |
| 38 | 38 | <!-- DLBCL: morinMutationalStructuralAnalysis2013 --> |
| 39 | + |
|
| 39 | 40 | ## References |
| 40 | 41 | 1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992 |
IFNGR1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # IFNGR1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2013-08-15 : Morin : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,20 +32,20 @@ timeline |
| 30 | 32 | |FL |No |No |0.000 |0 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601) |
|
| 35 | 35 | |
| 36 | 36 | |
| 37 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IFNGR1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IFNGR1_protein_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | 40 | |
| 41 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IFNGR1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IFNGR1_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | + |
|
| 44 | 45 | ## IFNGR1 Expression |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | <!-- ORIGIN: morinMutationalStructuralAnalysis2013 --> |
| 47 | 48 | <!-- DLBCL: morinMutationalStructuralAnalysis2013 --> |
| 49 | + |
|
| 48 | 50 | ## References |
| 49 | 51 | 1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992 |
IGLL5.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # IGLL5 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | 2019-09-26 : Panea : BL |
| 9 | 10 | 2023-07-26 : Russler : FL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -44,19 +46,18 @@ timeline |
| 44 | 46 | |:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:| |
| 45 | 47 | |chr22 |23229554 |23232042|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr22%3A23229554%2D23232042)|NA | |
| 46 | 48 | |
| 47 | -> [!NOTE] |
|
| 48 | -> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986) |
|
| 49 | 49 | |
| 50 | 50 | |
| 51 | 51 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IGLL5_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IGLL5_protein_hg38.html) |
| 52 | 52 | |
| 53 | - |
|
| 53 | + |
|
| 54 | 54 | |
| 55 | 55 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IGLL5.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IGLL5_hg38.html) |
| 56 | 56 | |
| 57 | - |
|
| 57 | + |
|
| 58 | + |
|
| 58 | 59 | ## IGLL5 Expression |
| 59 | - |
|
| 60 | + |
|
| 60 | 61 | |
| 61 | 62 | ## References |
| 62 | 63 | 1. Desch AK, Hartung K, Botzen A, Brobeil A, Rummel M, Kurch L, Georgi T, Jox T, Bielack S, Burdach S, Classen CF, Claviez A, Debatin KM, Ebinger M, Eggert A, Faber J, Flotho C, Frühwald M, Graf N, Jorch N, Kontny U, Kramm C, Kulozik A, Kühr J, Sykora KW, Metzler M, Müller HL, Nathrath M, Nüßlein T, Paulussen M, Pekrun A, Reinhardt D, Reinhard H, Rössig C, Sauerbrey A, Schlegel PG, Schneider DT, Scheurlen W, Schweigerer L, Simon T, Suttorp M, Vorwerk P, Schmitz R, Kluge R, Mauz-Körholz C, Körholz D, Gattenlöhner S, Bräuninger A. Genotyping circulating tumor DNA of pediatric Hodgkin lymphoma. Leukemia. 2020 Jan;34(1):151–166. PMID: 31431735 |
IKBKB.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # IKBKB |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | 2017-10-10 : Reddy : DLBCL |
| 9 | 10 | 2019-12-10 : Wienand : PMBL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -34,23 +36,23 @@ timeline |
| 34 | 36 | |FL |No |No |3.189 |0 | |
| 35 | 37 | |
| 36 | 38 | |
| 37 | -> [!NOTE] |
|
| 38 | -> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567) |
|
| 39 | 39 | |
| 40 | 40 | |
| 41 | 41 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IKBKB_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IKBKB_protein_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | 44 | |
| 45 | 45 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IKBKB.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IKBKB_hg38.html) |
| 46 | 46 | |
| 47 | - |
|
| 47 | + |
|
| 48 | + |
|
| 48 | 49 | ## IKBKB Expression |
| 49 | - |
|
| 50 | + |
|
| 50 | 51 | <!-- ORIGIN: rossiAlterationBIRC3Multiple2011a --> |
| 51 | 52 | <!-- MZL: rossiAlterationBIRC3Multiple2011a --> |
| 52 | 53 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 53 | 54 | <!-- PMBL: wienandGenomicAnalysesFlowsorted2019b --> |
| 55 | + |
|
| 54 | 56 | ## References |
| 55 | 57 | 1. Rossi D, Deaglio S, Dominguez-Sola D, Rasi S, Vaisitti T, Agostinelli C, Spina V, Bruscaggin A, Monti S, Cerri M, Cresta S, Fangazio M, Arcaini L, Lucioni M, Marasca R, Thieblemont C, Capello D, Facchetti F, Kwee I, Pileri SA, Foà R, Bertoni F, Dalla-Favera R, Pasqualucci L, Gaidano G. Alteration of BIRC3 and multiple other NF-κB pathway genes in splenic marginal zone lymphoma. Blood. 2011 Nov 3;118(18):4930–4934. PMID: 21881048 |
| 56 | 58 | 2. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
IKBKE.md
| ... | ... | @@ -9,6 +9,7 @@ timeline |
| 9 | 9 | title Publication timing |
| 10 | 10 | 2021-05-05 : H : DLBCL |
| 11 | 11 | ``` |
| 12 | + |
|
| 12 | 13 | ## Relevance tier by entity |
| 13 | 14 | |
| 14 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -36,13 +37,14 @@ timeline |
| 36 | 37 | |
| 37 | 38 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IKBKE_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IKBKE_protein_hg38.html) |
| 38 | 39 | |
| 39 | - |
|
| 40 | + |
|
| 40 | 41 | |
| 41 | 42 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IKBKE.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IKBKE_hg38.html) |
| 42 | 43 | |
| 43 | - |
|
| 44 | + |
|
| 45 | + |
|
| 44 | 46 | ## IKBKE Expression |
| 45 | - |
|
| 47 | + |
|
| 46 | 48 | |
| 47 | 49 | |
| 48 | 50 | ## References |
IKZF3.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # IKZF3 |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | IKZF3 (IKAROS family zinc finger 3, also known as AIOLOS) is a transcription factor involved in regulating B-cell development and function. Mutations in IKZF3 can lead to transcriptional dysregulation and contribute to the pathogenesis of B-cell neoplasms. IKZF3 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. IKZF3 has multiple hot spot mutations in DLBCL. The most common, L162R, has been identified as a driver in CLL. In that context, it alters DNA binding specificity and causes hyperactivation of B-cell receptor (BCR) signaling and overexpression of NF-κB target genes.<sup>1</sup> While primarily studied in CLL, the functional effects of IKZF3 mutations could have implications for other B-cell malignancies, including DLBCL |
| 4 | 5 | ## History |
| ... | ... | @@ -9,6 +10,7 @@ timeline |
| 9 | 10 | 2013-08-15 : Morin : DLBCL |
| 10 | 11 | 2019-09-26 : Panea : BL |
| 11 | 12 | ``` |
| 13 | + |
|
| 12 | 14 | ## Relevance tier by entity |
| 13 | 15 | |
| 14 | 16 | |Entity|Tier|Description | |
| ... | ... | @@ -43,8 +45,6 @@ timeline |
| 43 | 45 | |chr17 |37928959 |37940119|[TSS-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr17%3A37928959%2D37940119)|NA | |
| 44 | 46 | |chr17 |38015776 |38024832|[TSS-2](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr17%3A38015776%2D38024832)|NA | |
| 45 | 47 | |
| 46 | -> [!NOTE] |
|
| 47 | -> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601) |
|
| 48 | 48 | |
| 49 | 49 | ## IKZF3 Hotspots |
| 50 | 50 | |
| ... | ... | @@ -70,16 +70,16 @@ timeline |
| 70 | 70 | |
| 71 | 71 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IKZF3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IKZF3_protein_hg38.html) |
| 72 | 72 | |
| 73 | - |
|
| 73 | + |
|
| 74 | 74 | |
| 75 | 75 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IKZF3.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IKZF3_hg38.html) |
| 76 | 76 | |
| 77 | - |
|
| 77 | + |
|
| 78 | 78 | |
| 79 | 79 | ## References |
| 80 | 80 | 1. *Lazarian, G., Yin, S., Hacken, E., Sewastianik, T., Uduman, M., Font-Tello, A., Gohil, S., Li, S., Kim, E., Joyal, H., Billington, L., Witten, E., Zheng, M., Huang, T., Severgnini, M., Lefebvre, V., Rassenti, L., Gutierrez, C., Georgopoulos, K., Ott, C., Wang, L., Kipps, T., Burger, J., Livak, K., Neuberg, D., Baran-Marszak, F., Cymbalista, F., Carrasco, R., & Wu, C. (2021). A hotspot mutation in transcription factor IKZF3 drives B cell neoplasia via transcriptional dysregulation.. Cancer cell, 39 3, 380-393.e8 . https://doi.org/10.1016/j.ccell.2021.02.003.* |
| 81 | 81 | ## IKZF3 Expression |
| 82 | - |
|
| 82 | + |
|
| 83 | 83 | <!-- ORIGIN: morinMutationalStructuralAnalysis2013 --> |
| 84 | 84 | <!-- DLBCL: morinMutationalStructuralAnalysis2013 --> |
| 85 | 85 | <!-- BL: paneaWholeGenomeLandscape2019 --> |
IL16.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # IL16 |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | The IL16 gene, which encodes a pro-inflammatory cytokine, plays a role in immune responses. IL-16 is highly expressed in the activated B-cell-like (ABC) subtype of DLBCL compared to the germinal center B-cell-like (GCB) subtype. The role of mutations in lymphomagenesis is not understood. Overall, the mutation rate of IL16 is relatively low in DLBCL. *Without further support, this gene may be migrated to Tier 2.* |
| 4 | 5 | ## History |
| ... | ... | @@ -30,15 +31,17 @@ The IL16 gene, which encodes a pro-inflammatory cytokine, plays a role in immune |
| 30 | 31 | |
| 31 | 32 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IL16_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IL16_protein_hg38.html) |
| 32 | 33 | |
| 33 | - |
|
| 34 | + |
|
| 34 | 35 | |
| 35 | 36 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IL16.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IL16_hg38.html) |
| 36 | 37 | |
| 37 | - |
|
| 38 | + |
|
| 38 | 39 | |
| 39 | 40 | ## IL16 Expression |
| 40 | - |
|
| 41 | + |
|
| 41 | 42 | |
| 42 | 43 | <!-- FLAGGED FOR TIER 2 --> |
| 43 | 44 | |
| 44 | 45 | <!-- ORIGIN: Unknown --> |
| 46 | + |
|
| 47 | +## References |
IL4R.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # IL4R |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | Mutations in IL4R have been identified in various types of B-cell lymphomas, particularly primary mediastinal large B-cell lymphoma (PMBCL) and DLBCL. IL4R is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. IL4R mutations are found in approximately 24.2% of primary PMBCL cases. These mutations are commonly single nucleotide variants in exon 8, resulting in the I242N amino acid change. This leads to constitutive activation of the JAK-STAT signaling pathway and upregulation of downstream cytokine expression profiles and B cell-specific antigens.<sup>1,2</sup> In DLBCL, IL4R mutations are more rare and tend to occur within the GCB subgroup.<sup>2</sup> |
| 4 | 5 | ## History |
| ... | ... | @@ -9,6 +10,7 @@ timeline |
| 9 | 10 | 2018-05-03 : Vigan : PMBL |
| 10 | 11 | 2021-07-15 : Duns : DLBCL |
| 11 | 12 | ``` |
| 13 | + |
|
| 12 | 14 | ## Relevance tier by entity |
| 13 | 15 | |
| 14 | 16 | |Entity|Tier|Description | |
| ... | ... | @@ -39,8 +41,6 @@ timeline |
| 39 | 41 | |:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:| |
| 40 | 42 | |chr16 |27322895 |27329423|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr16%3A27322895%2D27329423)|active_promoter | |
| 41 | 43 | |
| 42 | -> [!NOTE] |
|
| 43 | -> First described in DLBCL in 2021 by [Duns G](https://pubmed.ncbi.nlm.nih.gov/33684939) |
|
| 44 | 44 | |
| 45 | 45 | |
| 46 | 46 | ## IL4R Hotspots |
| ... | ... | @@ -51,17 +51,17 @@ timeline |
| 51 | 51 | |
| 52 | 52 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IL4R_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IL4R_protein_hg38.html) |
| 53 | 53 | |
| 54 | - |
|
| 54 | + |
|
| 55 | 55 | |
| 56 | 56 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IL4R.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IL4R_hg38.html) |
| 57 | 57 | |
| 58 | - |
|
| 58 | + |
|
| 59 | 59 | |
| 60 | 60 | ## References |
| 61 | 61 | 1. *Gunawardana, J., Tol, T., Mak, K., Twa, D., Chavez, E., Woolcock, B., Kridel, R., Mottok, A., Healy, S., Telenius, A., Boyle, M., Ben-Neriah, S., Hung, S., Hother, C., Gascoyne, R., & Steidl, C. (2015). Abstract 3941: Recurrent IL4R mutations in primary mediastinal large B cell lymphoma. Cancer Research, 75, 3941-3941. https://doi.org/10.1158/1538-7445.AM2015-3941.* |
| 62 | 62 | 2. *Viganò E, Gunawardana J, Mottok A, Van Tol T, Mak K, Chan FC, Chong L, Chavez E, Woolcock B, Takata K, Twa D, Shulha HP, Telenius A, Kutovaya O, Hung SS, Healy S, Ben-Neriah S, Leroy K, Gaulard P, Diepstra A, Kridel R, Savage KJ, Rimsza L, Gascoyne R, Steidl C. Somatic IL4R mutations in primary mediastinal large B-cell lymphoma lead to constitutive JAK-STAT signaling activation. Blood. 2018 May 3;131(18):2036-2046. doi: 10.1182/blood-2017-09-808907. Epub 2018 Feb 21. PMID: 29467182.* |
| 63 | 63 | ## IL4R Expression |
| 64 | - |
|
| 64 | + |
|
| 65 | 65 | <!-- ORIGIN: viganoSomaticIL4RMutations2018b --> |
| 66 | 66 | <!-- DLBCL: dunsCharacterizationDLBCLPMBL2021b --> |
| 67 | 67 | <!-- PMBL: viganoSomaticIL4RMutations2018b --> |
IL6.md
| ... | ... | @@ -7,6 +7,7 @@ timeline |
| 7 | 7 | title Publication timing |
| 8 | 8 | 2018-05-01 : Chapuy : DLBCL |
| 9 | 9 | ``` |
| 10 | + |
|
| 10 | 11 | ## Relevance tier by entity |
| 11 | 12 | |
| 12 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -31,20 +32,20 @@ timeline |
| 31 | 32 | |FL |No |No |0.000 |0 | |
| 32 | 33 | |
| 33 | 34 | |
| 34 | -> [!NOTE] |
|
| 35 | -> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087) |
|
| 36 | 35 | |
| 37 | 36 | |
| 38 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IL6_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IL6_protein_hg38.html) |
| 39 | 38 | |
| 40 | - |
|
| 39 | + |
|
| 41 | 40 | |
| 42 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IL6.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IL6_hg38.html) |
| 43 | 42 | |
| 44 | - |
|
| 43 | + |
|
| 44 | + |
|
| 45 | 45 | ## IL6 Expression |
| 46 | - |
|
| 46 | + |
|
| 47 | 47 | <!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b --> |
| 48 | 48 | <!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b --> |
| 49 | + |
|
| 49 | 50 | ## References |
| 50 | 51 | 1. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387 |
INO80.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # INO80 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2013-01-01 : Zhang : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,20 +32,20 @@ timeline |
| 30 | 32 | |FL |No |No |0.000 |0.000 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937) |
|
| 35 | 35 | |
| 36 | 36 | |
| 37 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/INO80_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/INO80_protein_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | 40 | |
| 41 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/INO80.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/INO80_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | + |
|
| 44 | 45 | ## INO80 Expression |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | <!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 --> |
| 47 | 48 | <!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 --> |
| 49 | + |
|
| 48 | 50 | ## References |
| 49 | 51 | 1. Zhang J, Grubor V, Love CL, Banerjee A, Richards KL, Mieczkowski PA, Dunphy C, Choi W, Au WY, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers C, Naresh K, Evens A, Gordon LI, Czader M, Gill JI, Hsi ED, Liu Q, Fan A, Walsh K, Jima D, Smith LL, Johnson AJ, Byrd JC, Luftig MA, Ni T, Zhu J, Chadburn A, Levy S, Dunson D, Dave SS. Genetic heterogeneity of diffuse large B-cell lymphoma. 2013 Jan; |
IRAG2.md
| ... | ... | @@ -20,5 +20,7 @@ |
| 20 | 20 | | |
| 21 | 21 | |
| 22 | 22 | ## IRAG2 Expression |
| 23 | - |
|
| 23 | + |
|
| 24 | 24 | <!-- ORIGIN: Unknown --> |
| 25 | + |
|
| 26 | +## References |
IRF1.md
| ... | ... | @@ -9,6 +9,7 @@ timeline |
| 9 | 9 | title Publication timing |
| 10 | 10 | 2021-05-05 : H : DLBCL |
| 11 | 11 | ``` |
| 12 | + |
|
| 12 | 13 | ## Relevance tier by entity |
| 13 | 14 | |
| 14 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -41,13 +42,14 @@ timeline |
| 41 | 42 | |
| 42 | 43 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IRF1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IRF1_protein_hg38.html) |
| 43 | 44 | |
| 44 | - |
|
| 45 | + |
|
| 45 | 46 | |
| 46 | 47 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IRF1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IRF1_hg38.html) |
| 47 | 48 | |
| 48 | - |
|
| 49 | + |
|
| 50 | + |
|
| 49 | 51 | ## IRF1 Expression |
| 50 | - |
|
| 52 | + |
|
| 51 | 53 | |
| 52 | 54 | |
| 53 | 55 | ## References |
IRF4.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # IRF4 |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | IRF4 (Interferon Regulatory Factor 4) encodes a transcription factor that plays a critical role in the regulation of immune response genes and B-cell development. Mutations and rearrangements in the IRF4 gene have been implicated in various B-cell lymphomas, including DLBCL. IRF4-rearranged large B-cell lymphomas (LBCL-IRF4) show a unique molecular profile with strong expression of IRF4/MUM1 and are associated with favorable outcomes. MUM1 staining is also commonly used to assign DLBCLs to one of the two cell-of-origin (COO) subgroups by immunohistochemistry.<sup>1</sup> IRF4 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. There are a few mutation hotspots in this gene. The functional role of mutations in IRF4 in the absence of a rearrangement remains poorly understood. |
| 4 | 5 | ## History |
| ... | ... | @@ -9,6 +10,7 @@ timeline |
| 9 | 10 | 2011-07-27 : Morin : DLBCL |
| 10 | 11 | 2019-09-05 : Mottok : PMBL |
| 11 | 12 | ``` |
| 13 | + |
|
| 12 | 14 | ## Relevance tier by entity |
| 13 | 15 | |
| 14 | 16 | |Entity|Tier|Description | |
| ... | ... | @@ -41,8 +43,6 @@ timeline |
| 41 | 43 | |:--------:|:----------:|:--------:|:-------------------------------------------------------------------------------------:|:------------------:| |
| 42 | 44 | |chr6 |390572 |394093 |[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr6%3A390572%2D394093)|active_promoter | |
| 43 | 45 | |
| 44 | -> [!NOTE] |
|
| 45 | -> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119) |
|
| 46 | 46 | |
| 47 | 47 | |
| 48 | 48 | ## IRF4 Hotspots |
| ... | ... | @@ -56,14 +56,14 @@ timeline |
| 56 | 56 | |
| 57 | 57 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IRF4_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IRF4_protein_hg38.html) |
| 58 | 58 | |
| 59 | - |
|
| 59 | + |
|
| 60 | 60 | |
| 61 | 61 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IRF4.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IRF4_hg38.html) |
| 62 | 62 | |
| 63 | - |
|
| 63 | + |
|
| 64 | 64 | |
| 65 | 65 | # IRF4 Expression |
| 66 | - |
|
| 66 | + |
|
| 67 | 67 | |
| 68 | 68 | ## References |
| 69 | 69 | 1. *Hans CP, Weisenburger DD, Greiner TC, Gascoyne RD, Delabie J, Ott G, Müller-Hermelink HK, Campo E, Braziel RM, Jaffe ES, Pan Z, Farinha P, Smith LM, Falini B, Banham AH, Rosenwald A, Staudt LM, Connors JM, Armitage JO, Chan WC. Confirmation of the molecular classification of diffuse large B-cell lymphoma by immunohistochemistry using a tissue microarray. Blood. 2004 Jan 1;103(1):275-82. doi: 10.1182/blood-2003-05-1545. Epub 2003 Sep 22. PMID: 14504078.* |
IRF8.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # IRF8 |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | IRF8 (Interferon Regulatory Factor 8) is a transcription factor critical for the development and function of B lymphocytes. Mutations in IRF8 have been implicated in various lymphoid malignancies, most predominantly in FL and DLBCL. IRF8 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. Coding and non-coding mutations in IRF8 are associated with the EZB subgroup of DLBCL.<sup>1</sup> There is preliminary evidence that IRF8 mutations contribute to immune evasion by downregulating CD74 and HLA-DM in DLBCL.<sup>2</sup> These are crucial for processing and presentation of self antigens. |
| 4 | 5 | ## History |
| ... | ... | @@ -10,6 +11,7 @@ timeline |
| 10 | 11 | 2019-09-05 : Mottok : PMBL |
| 11 | 12 | 2019-09-26 : Panea : BL |
| 12 | 13 | ``` |
| 14 | + |
|
| 13 | 15 | ## Relevance tier by entity |
| 14 | 16 | |
| 15 | 17 | |Entity|Tier|Description | |
| ... | ... | @@ -62,18 +64,18 @@ timeline |
| 62 | 64 | |
| 63 | 65 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IRF8_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IRF8_protein_hg38.html) |
| 64 | 66 | |
| 65 | - |
|
| 67 | + |
|
| 66 | 68 | |
| 67 | 69 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IRF8.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IRF8_hg38.html) |
| 68 | 70 | |
| 69 | - |
|
| 71 | + |
|
| 70 | 72 | |
| 71 | 73 | ## References |
| 72 | 74 | 1. *Wright GW, Huang DW, Phelan JD, Coulibaly ZA, Roulland S, Young RM, Wang JQ, Schmitz R, Morin RD, Tang J, Jiang A, Bagaev A, Plotnikova O, Kotlov N, Johnson CA, Wilson WH, Scott DW, Staudt LM. A Probabilistic Classification Tool for Genetic Subtypes of Diffuse Large B Cell Lymphoma with Therapeutic Implications. Cancer Cell. 2020 Apr 13;37(4):551-568.e14. doi: 10.1016/j.ccell.2020.03.015. PMID: 32289277; PMCID: PMC8459709.* |
| 73 | 75 | 2. *Qiu Z, Khalife J, Lin AP, Ethiraj P, Jaafar C, Chiou L, Huelgas-Morales G, Aslam S, Arya S, Gupta YK, Dahia PLM, Aguiar RCT. IRF8-mutant B cell lymphoma evades immunity through a CD74-dependent deregulation of antigen processing and presentation in MHC CII complexes. bioRxiv [Preprint]. 2023 Oct 15:2023.10.14.560755. doi: 10.1101/2023.10.14.560755. PMID: 37873241; PMCID: PMC10592808.* |
| 74 | 76 | 3. *Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351. PMID: 21796119; PMCID: PMC3210554.* |
| 75 | 77 | ## IRF8 Expression |
| 76 | - |
|
| 78 | + |
|
| 77 | 79 | <!-- ORIGIN: morinFrequentMutationHistonemodifying2011 --> |
| 78 | 80 | <!-- PMBL: mottokIntegrativeGenomicAnalysis2019b --> |
| 79 | 81 | <!-- FL: morinFrequentMutationHistonemodifying2011 --> |
ITPKB.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # ITPKB |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | The ITPKB gene encodes inositol-trisphosphate 3-kinase B, an enzyme involved in the regulation of intracellular calcium levels and PI3K/Akt signaling pathways. Mutations in ITPKB have been linked to various B-cell lymphomas, including DLBCL, PMBCL and, less commonly, FL.<sup>1</sup> ITPKB is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. These mutations are associated with the **BN2** genetic subgroup of DLBCL. The mutation pattern in ITPKB implies selection for loss-of-function mutations. |
| 4 | 5 | ## History |
| ... | ... | @@ -9,6 +10,7 @@ timeline |
| 9 | 10 | 2015-02-12 : Reichel : PMBL |
| 10 | 11 | 2018-04-12 : Schmitz : DLBCL |
| 11 | 12 | ``` |
| 13 | + |
|
| 12 | 14 | ## Relevance tier by entity |
| 13 | 15 | |
| 14 | 16 | |Entity|Tier|Description | |
| ... | ... | @@ -53,16 +55,16 @@ timeline |
| 53 | 55 | |
| 54 | 56 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ITPKB_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ITPKB_protein_hg38.html) |
| 55 | 57 | |
| 56 | - |
|
| 58 | + |
|
| 57 | 59 | |
| 58 | 60 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ITPKB.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ITPKB_hg38.html) |
| 59 | 61 | |
| 60 | - |
|
| 62 | + |
|
| 61 | 63 | |
| 62 | 64 | ## References |
| 63 | 65 | 1. *Mareschal S, Dubois S, Viailly PJ, Bertrand P, Bohers E, Maingonnat C, Jaïs JP, Tesson B, Ruminy P, Peyrouze P, Copie-Bergman C, Fest T, Jo Molina T, Haioun C, Salles G, Tilly H, Lecroq T, Leroy K, Jardin F. Whole exome sequencing of relapsed/refractory patients expands the repertoire of somatic mutations in diffuse large B-cell lymphoma. Genes Chromosomes Cancer. 2016 Mar;55(3):251-67. doi: 10.1002/gcc.22328. Epub 2015 Nov 26. PMID: 26608593.* |
| 64 | 66 | ## ITPKB Expression |
| 65 | - |
|
| 67 | + |
|
| 66 | 68 | <!-- ORIGIN: reichelFlowSortingExome2015a --> |
| 67 | 69 | <!-- PMBL: reichelFlowSortingExome2015a --> |
| 68 | 70 | <!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a --> |
ITPR3.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # ITPR3 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | 2018-05-31 : Tiacci : PMBL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -34,13 +36,14 @@ timeline |
| 34 | 36 | |
| 35 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ITPR3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ITPR3_protein_hg38.html) |
| 36 | 38 | |
| 37 | - |
|
| 39 | + |
|
| 38 | 40 | |
| 39 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ITPR3.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ITPR3_hg38.html) |
| 40 | 42 | |
| 41 | - |
|
| 43 | + |
|
| 44 | + |
|
| 42 | 45 | ## ITPR3 Expression |
| 43 | - |
|
| 46 | + |
|
| 44 | 47 | |
| 45 | 48 | |
| 46 | 49 |
JAK1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # JAK1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2013-01-01 : Zhang : DLBCL |
| 8 | 9 | 2019-09-05 : Mottok : PMBL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -32,8 +34,6 @@ timeline |
| 32 | 34 | |FL |No |No |0.000 |0 | |
| 33 | 35 | |
| 34 | 36 | |
| 35 | -> [!NOTE] |
|
| 36 | -> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937) |
|
| 37 | 37 | |
| 38 | 38 | |
| 39 | 39 | ## JAK1 Hotspots |
| ... | ... | @@ -44,16 +44,18 @@ timeline |
| 44 | 44 | |
| 45 | 45 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/JAK1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/JAK1_protein_hg38.html) |
| 46 | 46 | |
| 47 | - |
|
| 47 | + |
|
| 48 | 48 | |
| 49 | 49 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/JAK1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/JAK1_hg38.html) |
| 50 | 50 | |
| 51 | - |
|
| 51 | + |
|
| 52 | + |
|
| 52 | 53 | ## JAK1 Expression |
| 53 | - |
|
| 54 | + |
|
| 54 | 55 | <!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 --> |
| 55 | 56 | <!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 --> |
| 56 | 57 | <!-- PMBL: mottokIntegrativeGenomicAnalysis2019b --> |
| 58 | + |
|
| 57 | 59 | ## References |
| 58 | 60 | 1. Zhang J, Grubor V, Love CL, Banerjee A, Richards KL, Mieczkowski PA, Dunphy C, Choi W, Au WY, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers C, Naresh K, Evens A, Gordon LI, Czader M, Gill JI, Hsi ED, Liu Q, Fan A, Walsh K, Jima D, Smith LL, Johnson AJ, Byrd JC, Luftig MA, Ni T, Zhu J, Chadburn A, Levy S, Dunson D, Dave SS. Genetic heterogeneity of diffuse large B-cell lymphoma. 2013 Jan; |
| 59 | 61 | 2. Mottok A, Hung SS, Chavez EA, Woolcock B, Telenius A, Chong LC, Meissner B, Nakamura H, Rushton C, Viganò E, Sarkozy C, Gascoyne RD, Connors JM, Ben-Neriah S, Mungall A, Marra MA, Siebert R, Scott DW, Savage KJ, Steidl C. Integrative genomic analysis identifies key pathogenic mechanisms in primary mediastinal large B-cell lymphoma. Blood. 2019 Sep 5;134(10):802–813. PMID: 31292115 |
MAP4K4.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # MAP4K4 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2017-10-10 : Reddy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,20 +32,20 @@ timeline |
| 30 | 32 | |FL |No |No |0.000 |0.000 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567) |
|
| 35 | 35 | |
| 36 | 36 | |
| 37 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MAP4K4_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MAP4K4_protein_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | 40 | |
| 41 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MAP4K4.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MAP4K4_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | + |
|
| 44 | 45 | ## MAP4K4 Expression |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
| 47 | 48 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 49 | + |
|
| 48 | 50 | ## References |
| 49 | 51 | 1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
MAP7D1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # MAP7D1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2023-07-26 : Russler : FL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -27,20 +29,20 @@ timeline |
| 27 | 29 | |FL |No |No |0.000 |0 | |
| 28 | 30 | |
| 29 | 31 | |
| 30 | -> [!NOTE] |
|
| 31 | -> First described in FL in 2023 by [Kalmbach S](https://pubmed.ncbi.nlm.nih.gov/37563306) |
|
| 32 | 32 | |
| 33 | 33 | |
| 34 | 34 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MAP7D1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MAP7D1_protein_hg38.html) |
| 35 | 35 | |
| 36 | - |
|
| 36 | + |
|
| 37 | 37 | |
| 38 | 38 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MAP7D1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MAP7D1_hg38.html) |
| 39 | 39 | |
| 40 | - |
|
| 40 | + |
|
| 41 | + |
|
| 41 | 42 | ## MAP7D1 Expression |
| 42 | - |
|
| 43 | + |
|
| 43 | 44 | <!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a --> |
| 44 | 45 | <!-- FL: russler-germainMutationsAssociatedProgression2023b --> |
| 46 | + |
|
| 45 | 47 | ## References |
| 46 | 48 | 1. Russler-Germain DA, Krysiak K, Ramirez CA, Mosior M, Watkins MP, Gomez F, Skidmore ZL, Trani L, Gao F, Geyer S, Cashen A, Mehta-Shah N, Kahl B, Bartlett N, Alderuccio J, Lossos I, Ondrejka S, Hsi E, Martin P, Leonard J, Griffith M, Griffith O, Fehniger T. Mutations associated with progression in follicular lymphoma predict inferior outcomes at diagnosis: Alliance A151303. Blood Advances. 2023;7:5524–5539. |
MARK1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # MARK1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2017-10-10 : Reddy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,20 +32,20 @@ timeline |
| 30 | 32 | |FL |No |No |2.768 |0 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567) |
|
| 35 | 35 | |
| 36 | 36 | |
| 37 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MARK1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MARK1_protein_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | 40 | |
| 41 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MARK1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MARK1_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | + |
|
| 44 | 45 | ## MARK1 Expression |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
| 47 | 48 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 49 | + |
|
| 48 | 50 | ## References |
| 49 | 51 | 1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
MCL1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # MCL1 |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | MCL1 (Myeloid Cell Leukemia 1) is a member of the BCL2 family of proteins that play a critical role in inhibiting apoptosis. It is frequently overexpressed and sometimes mutated in DLBCL.<sup>1,2</sup> Recurrent chromosomal gains and amplifications of the MCL1 locus occur are frequent in ABC-DLBCLs.<sup>1</sup> MCL1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. |
| 4 | 5 | ## History |
| ... | ... | @@ -10,6 +11,7 @@ timeline |
| 10 | 11 | 2019-09-26 : Panea : BL |
| 11 | 12 | 2021-07-15 : Duns : PMBL |
| 12 | 13 | ``` |
| 14 | + |
|
| 13 | 15 | ## Relevance tier by entity |
| 14 | 16 | |
| 15 | 17 | |Entity|Tier|Description | |
| ... | ... | @@ -47,14 +49,14 @@ timeline |
| 47 | 49 | |
| 48 | 50 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MCL1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MCL1_protein_hg38.html) |
| 49 | 51 | |
| 50 | - |
|
| 52 | + |
|
| 51 | 53 | |
| 52 | 54 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MCL1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MCL1_hg38.html) |
| 53 | 55 | |
| 54 | - |
|
| 56 | + |
|
| 55 | 57 | |
| 56 | 58 | ## MCL1 Expression |
| 57 | - |
|
| 59 | + |
|
| 58 | 60 | |
| 59 | 61 | |
| 60 | 62 |
MECOM.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # MECOM |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2017-10-10 : Reddy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,20 +32,20 @@ timeline |
| 30 | 32 | |FL |No |No |0.000 |0 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567) |
|
| 35 | 35 | |
| 36 | 36 | |
| 37 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MECOM_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MECOM_protein_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | 40 | |
| 41 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MECOM.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MECOM_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | + |
|
| 44 | 45 | ## MECOM Expression |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
| 47 | 48 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 49 | + |
|
| 48 | 50 | ## References |
| 49 | 51 | 1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
MEF2B.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # MEF2B |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | MEF2B is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. MEF2B mutations are observed in a significant subset of follicular lymphoma cases, as well as in other B-cell lymphomas, including diffuse large B-cell lymphoma (DLBCL) and MCL.<sup>1</sup> MEF2B has known hotspot mutations that affect multiple distinct domains of the protein. |
| 4 | 5 | ## History |
| ... | ... | @@ -9,6 +10,7 @@ timeline |
| 9 | 10 | 2011-07-27 : Morin : DLBCL |
| 10 | 11 | 2013-11-05 : Bea : MCL |
| 11 | 12 | ``` |
| 13 | + |
|
| 12 | 14 | ## Relevance tier by entity |
| 13 | 15 | |
| 14 | 16 | |Entity|Tier|Description | |
| ... | ... | @@ -47,8 +49,6 @@ timeline |
| 47 | 49 | |:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:| |
| 48 | 50 | |chr19 |19279635 |19281441|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr19%3A19279635%2D19281441)|active_promoter | |
| 49 | 51 | |
| 50 | -> [!NOTE] |
|
| 51 | -> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in MCL in 2013 by [Beà S](https://pubmed.ncbi.nlm.nih.gov/24145436) |
|
| 52 | 52 | |
| 53 | 53 | ## MEF2B Hotspots |
| 54 | 54 | |
| ... | ... | @@ -61,6 +61,7 @@ timeline |
| 61 | 61 | **N81 (Asparagine 81)** A mutation hotspot within the transcriptional activation domain. Alterations at this position can enhance the transcriptional activity of MEF2B, contributing to the overexpression of target genes involved in cell survival and proliferation. |
| 62 | 62 | |
| 63 | 63 | ## Functional Impact of MEF2B Mutations |
| 64 | + |
|
| 64 | 65 | ### Altered Transcriptional Activity: |
| 65 | 66 | Mutations in the DNA-binding domain, such as those at R24 and R30, can alter the binding affinity and specificity of MEF2B for its target DNA sequences. This can lead to changes in the expression of genes that are critical for cell growth, differentiation, and survival. |
| 66 | 67 | Mutations in the transcriptional activation domain, like N81, can enhance the ability of MEF2B to activate transcription, which may lead to the upregulation of oncogenes and survival pathways. |
| ... | ... | @@ -79,15 +80,15 @@ Mutations in the transcriptional activation domain, like N81, can enhance the ab |
| 79 | 80 | |
| 80 | 81 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MEF2B_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MEF2B_protein_hg38.html) |
| 81 | 82 | |
| 82 | - |
| 84 | 85 | |
| 85 | 86 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MEF2B.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MEF2B_hg38.html) |
| 86 | 87 | |
| 87 | - |
|
| 88 | + |
|
| 88 | 89 | |
| 89 | 90 | ## MEF2B Expression |
| 90 | - |
|
| 91 | + |
|
| 91 | 92 | |
| 92 | 93 | |
| 93 | 94 | <!-- ORIGIN: morinFrequentMutationHistonemodifying2011 --> |
| ... | ... | @@ -95,6 +96,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M |
| 95 | 96 | <!-- MCL: beaLandscapeSomaticMutations2013 --> |
| 96 | 97 | <!-- FL: morinFrequentMutationHistonemodifying2011 --> |
| 97 | 98 | <!-- BL: 2 --> |
| 99 | + |
|
| 98 | 100 | ## References |
| 99 | 101 | 1. Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJM, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298–303. PMCID: PMC3210554 |
| 100 | 102 | 2. Beà S, Valdés-Mas R, Navarro A, Salaverria I, Martín-Garcia D, Jares P, Giné E, Pinyol M, Royo C, Nadeu F, Conde L, Juan M, Clot G, Vizán P, Croce LD, Puente DA, López-Guerra M, Moros A, Roue G, Aymerich M, Villamor N, Colomo L, Martínez A, Valera A, Martín-Subero JI, Amador V, Hernández L, Rozman M, Enjuanes A, Forcada P, Muntañola A, Hartmann EM, Calasanz MJ, Rosenwald A, Ott G, Hernández-Rivas JM, Klapper W, Siebert R, Wiestner A, Wilson WH, Colomer D, López-Guillermo A, López-Otín C, Puente XS, Campo E. Landscape of somatic mutations and clonal evolution in mantle cell lymphoma. PNAS. 2013 Nov 5;110(45):18250–18255. PMID: 24145436 |
MEF2C.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # MEF2C |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | MEF2C is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. |
| 4 | 5 | ## History |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | title Publication timing |
| 9 | 10 | 2018-10-01 : Arthur : DLBCL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -44,14 +46,14 @@ timeline |
| 44 | 46 | |
| 45 | 47 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MEF2C_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MEF2C_protein_hg38.html) |
| 46 | 48 | |
| 47 | - |
|
| 49 | + |
|
| 48 | 50 | |
| 49 | 51 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MEF2C.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MEF2C_hg38.html) |
| 50 | 52 | |
| 51 | - |
|
| 53 | + |
|
| 52 | 54 | |
| 53 | 55 | ## MEF2C Expression |
| 54 | - |
|
| 56 | + |
|
| 55 | 57 | |
| 56 | 58 | ## References |
| 57 | 59 |
MYH10.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # MYH10 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -32,14 +34,16 @@ timeline |
| 32 | 34 | |
| 33 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MYH10_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MYH10_protein_hg38.html) |
| 34 | 36 | |
| 35 | - |
|
| 37 | + |
|
| 36 | 38 | |
| 37 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MYH10.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MYH10_hg38.html) |
| 38 | 40 | |
| 39 | - |
|
| 41 | + |
|
| 42 | + |
|
| 40 | 43 | ## MYH10 Expression |
| 41 | - |
|
| 44 | + |
|
| 42 | 45 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 43 | 46 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 47 | + |
|
| 44 | 48 | ## References |
| 45 | 49 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
MYO18A.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # MYO18A |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-10-04 : Schmitz : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -29,19 +31,18 @@ timeline |
| 29 | 31 | |FL |No |No |2.227 |0 | |
| 30 | 32 | |
| 31 | 33 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096) |
|
| 34 | 34 | |
| 35 | 35 | |
| 36 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MYO18A_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MYO18A_protein_hg38.html) |
| 37 | 37 | |
| 38 | - |
|
| 38 | + |
|
| 39 | 39 | |
| 40 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MYO18A.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MYO18A_hg38.html) |
| 41 | 41 | |
| 42 | - |
|
| 42 | + |
|
| 43 | + |
|
| 43 | 44 | ## MYO18A Expression |
| 44 | - |
|
| 45 | + |
|
| 45 | 46 | |
| 46 | 47 | ## References |
| 47 | 48 | 1. Schmitz R, Young RM, Ceribelli M, Jhavar S, Xiao W, Zhang M, Wright G, Shaffer AL, Hodson DJ, Buras E, Liu X, Powell J, Yang Y, Xu W, Zhao H, Kohlhammer H, Rosenwald A, Kluin P, Müller-Hermelink HK, Ott G, Gascoyne RD, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Ogwang MD, Reynolds SJ, Fisher RI, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Pittaluga S, Wilson W, Waldmann TA, Rowe M, Mbulaiteye SM, Rickinson AB, Staudt LM. Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics. Nature. 2012 Oct 4;490(7418):116–120. PMCID: PMC3609867 |
MYO1E.md
| ... | ... | @@ -32,12 +32,14 @@ |
| 32 | 32 | |
| 33 | 33 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MYO1E_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MYO1E_protein_hg38.html) |
| 34 | 34 | |
| 35 | - |
|
| 35 | + |
|
| 36 | 36 | |
| 37 | 37 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MYO1E.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MYO1E_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | + |
|
| 40 | 41 | ## MYO1E Expression |
| 41 | - |
|
| 42 | + |
|
| 42 | 43 | <!-- ORIGIN: Unknown --> |
| 44 | + |
|
| 43 | 45 | ## References |
MYOM2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # MYOM2 |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | The prevalence of MYOM2 mutations in DLBCL varies across studies. The role of these mutations in lymphomagenesis has not been thoroughly explored. |
| 4 | 5 | ## History |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | title Publication timing |
| 9 | 10 | 2011-07-31 : Pasqualucci : DLBCL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -32,18 +34,18 @@ timeline |
| 32 | 34 | |FL |No |No |0.649 |12.057 | |
| 33 | 35 | |
| 34 | 36 | |
| 35 | -> [!NOTE] |
|
| 36 | -> First described in DLBCL in 2011 by [Pasqualucci L](https://pubmed.ncbi.nlm.nih.gov/21804550) |
|
| 37 | 37 | |
| 38 | 38 | |
| 39 | 39 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MYOM2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MYOM2_protein_hg38.html) |
| 40 | 40 | |
| 41 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MYOM2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MYOM2_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | + |
|
| 44 | 45 | ## MYOM2 Expression |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | <!-- ORIGIN: pasqualucciAnalysisCodingGenome2011 --> |
| 47 | 48 | <!-- DLBCL: pasqualucciAnalysisCodingGenome2011 --> |
| 49 | + |
|
| 48 | 50 | ## References |
| 49 | 51 | 1. Pasqualucci L, Trifonov V, Fabbri G, Ma J, Rossi D, Chiarenza A, Wells VA, Grunn A, Messina M, Elliot O, Chan J, Bhagat G, Chadburn A, Gaidano G, Mullighan CG, Rabadan R, Dalla-Favera R. Analysis of the coding genome of diffuse large B-cell lymphoma. Nat Genet. 2011 Jul 31;43(9):830–837. PMCID: PMC3297422 |
N2RF2.md
| ... | ... | @@ -9,6 +9,7 @@ timeline |
| 9 | 9 | title Publication timing |
| 10 | 10 | 2021-05-05 : H : DLBCL |
| 11 | 11 | ``` |
| 12 | + |
|
| 12 | 13 | ## Relevance tier by entity |
| 13 | 14 | |
| 14 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -28,9 +29,10 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM |
| 28 | 29 | |
| 29 | 30 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N2RF2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/N2RF2_hg38.html) |
| 30 | 31 | |
| 31 | - |
|
| 32 | + |
|
| 33 | + |
|
| 32 | 34 | ## N2RF2 Expression |
| 33 | - |
|
| 35 | + |
|
| 34 | 36 | |
| 35 | 37 | |
| 36 | 38 | ## References |
NANOG.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # NANOG |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2018-05-01 : Chapuy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -33,14 +35,16 @@ timeline |
| 33 | 35 | |
| 34 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NANOG_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NANOG_protein_hg38.html) |
| 35 | 37 | |
| 36 | - |
|
| 38 | + |
|
| 37 | 39 | |
| 38 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NANOG.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NANOG_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 43 | + |
|
| 41 | 44 | ## NANOG Expression |
| 42 | - |
|
| 45 | + |
|
| 43 | 46 | <!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b --> |
| 44 | 47 | <!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b --> |
| 48 | + |
|
| 45 | 49 | ## References |
| 46 | 50 | 1. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387 |
NAV1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # NAV1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2018-05-01 : Chapuy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -33,14 +35,16 @@ timeline |
| 33 | 35 | |
| 34 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NAV1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NAV1_protein_hg38.html) |
| 35 | 37 | |
| 36 | - |
|
| 38 | + |
|
| 37 | 39 | |
| 38 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NAV1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NAV1_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 43 | + |
|
| 41 | 44 | ## NAV1 Expression |
| 42 | - |
|
| 45 | + |
|
| 43 | 46 | <!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b --> |
| 44 | 47 | <!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b --> |
| 48 | + |
|
| 45 | 49 | ## References |
| 46 | 50 | 1. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387 |
NBEAL1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # NBEAL1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -32,14 +34,16 @@ timeline |
| 32 | 34 | |
| 33 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NBEAL1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NBEAL1_protein_hg38.html) |
| 34 | 36 | |
| 35 | - |
|
| 37 | + |
|
| 36 | 38 | |
| 37 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NBEAL1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NBEAL1_hg38.html) |
| 38 | 40 | |
| 39 | - |
|
| 41 | + |
|
| 42 | + |
|
| 40 | 43 | ## NBEAL1 Expression |
| 41 | - |
|
| 44 | + |
|
| 42 | 45 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 43 | 46 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 47 | + |
|
| 44 | 48 | ## References |
| 45 | 49 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
NCOA3.md
| ... | ... | @@ -32,12 +32,14 @@ |
| 32 | 32 | |
| 33 | 33 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NCOA3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NCOA3_protein_hg38.html) |
| 34 | 34 | |
| 35 | - |
|
| 35 | + |
|
| 36 | 36 | |
| 37 | 37 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NCOA3.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NCOA3_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | + |
|
| 40 | 41 | ## NCOA3 Expression |
| 41 | - |
|
| 42 | + |
|
| 42 | 43 | <!-- ORIGIN: Unknown --> |
| 44 | + |
|
| 43 | 45 | ## References |
NCOR1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # NCOR1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2017-10-10 : Reddy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,20 +32,20 @@ timeline |
| 30 | 32 | |FL |No |No |1.147 |0.000 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567) |
|
| 35 | 35 | |
| 36 | 36 | |
| 37 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NCOR1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NCOR1_protein_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | 40 | |
| 41 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NCOR1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NCOR1_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | + |
|
| 44 | 45 | ## NCOR1 Expression |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
| 47 | 48 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 49 | + |
|
| 48 | 50 | ## References |
| 49 | 51 | 1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
NCOR2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # NCOR2 |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | Mutations in this gene are relatively rare in DLBCL overall but show a pattern of inactivation. *Without further support, this gene may be migrated to Tier 2.* |
| 4 | 5 | ## History |
| ... | ... | @@ -10,6 +11,7 @@ timeline |
| 10 | 11 | 2016-09-08 : Spina : MZL |
| 11 | 12 | 2021-04-01 : Sarkozy : PMBL |
| 12 | 13 | ``` |
| 14 | + |
|
| 13 | 15 | ## Relevance tier by entity |
| 14 | 16 | |
| 15 | 17 | |Entity|Tier|Description | |
| ... | ... | @@ -40,8 +42,6 @@ timeline |
| 40 | 42 | |FL |No |No |0.985 |0.000 | |
| 41 | 43 | |
| 42 | 44 | |
| 43 | -> [!NOTE] |
|
| 44 | -> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096) |
|
| 45 | 45 | |
| 46 | 46 | |
| 47 | 47 | ## NCOR2 Hotspots |
| ... | ... | @@ -51,20 +51,21 @@ timeline |
| 51 | 51 | |
| 52 | 52 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NCOR2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NCOR2_protein_hg38.html) |
| 53 | 53 | |
| 54 | - |
|
| 54 | + |
|
| 55 | 55 | |
| 56 | 56 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NCOR2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NCOR2_hg38.html) |
| 57 | 57 | |
| 58 | - |
|
| 58 | + |
|
| 59 | 59 | |
| 60 | 60 | ## NCOR2 Expression |
| 61 | - |
|
| 61 | + |
|
| 62 | 62 | |
| 63 | 63 | <!-- FLAGGED FOR TIER 2 --> |
| 64 | 64 | <!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 --> |
| 65 | 65 | <!-- MZL: spinaGeneticsNodalMarginal2016b --> |
| 66 | 66 | <!-- BL: schmitzBurkittLymphomaPathogenesis2012 --> |
| 67 | 67 | <!-- BL: schmitzBurkittLymphomaPathogenesis2012 --> |
| 68 | + |
|
| 68 | 69 | ## References |
| 69 | 70 | 1. Schmitz R, Young RM, Ceribelli M, Jhavar S, Xiao W, Zhang M, Wright G, Shaffer AL, Hodson DJ, Buras E, Liu X, Powell J, Yang Y, Xu W, Zhao H, Kohlhammer H, Rosenwald A, Kluin P, Müller-Hermelink HK, Ott G, Gascoyne RD, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Ogwang MD, Reynolds SJ, Fisher RI, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Pittaluga S, Wilson W, Waldmann TA, Rowe M, Mbulaiteye SM, Rickinson AB, Staudt LM. Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics. Nature. 2012 Oct 4;490(7418):116–120. PMCID: PMC3609867 |
| 70 | 71 | 2. Spina V, Khiabanian H, Messina M, Monti S, Cascione L, Bruscaggin A, Spaccarotella E, Holmes AB, Arcaini L, Lucioni M, Tabbò F, Zairis S, Diop F, Cerri M, Chiaretti S, Marasca R, Ponzoni M, Deaglio S, Ramponi A, Tiacci E, Pasqualucci L, Paulli M, Falini B, Inghirami G, Bertoni F, Foà R, Rabadan R, Gaidano G, Rossi D. The genetics of nodal marginal zone lymphoma. Blood. 2016 Sep 8;128(10):1362–1373. |
NEAT1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # NEAT1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2018-10-01 : Arthur : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -34,14 +36,16 @@ timeline |
| 34 | 36 | |
| 35 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NEAT1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NEAT1_protein_hg38.html) |
| 36 | 38 | |
| 37 | - |
|
| 39 | + |
|
| 38 | 40 | |
| 39 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NEAT1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NEAT1_hg38.html) |
| 40 | 42 | |
| 41 | - |
|
| 43 | + |
|
| 44 | + |
|
| 42 | 45 | ## NEAT1 Expression |
| 43 | - |
|
| 46 | + |
|
| 44 | 47 | <!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 --> |
| 45 | 48 | <!-- DLBCL: arthurGenomewideDiscoverySomatic2018 --> |
| 49 | + |
|
| 46 | 50 | ## References |
| 47 | 51 | 1. Arthur SE, Jiang A, Grande BM, Alcaide M, Cojocaru R, Rushton CK, Mottok A, Hilton LK, Lat PK, Zhao EY, Culibrk L, Ennishi D, Jessa S, Chong L, Thomas N, Pararajalingam P, Meissner B, Boyle M, Davidson J, Bushell KR, Lai D, Farinha P, Slack GW, Morin GB, Shah S, Sen D, Jones SJM, Mungall AJ, Gascoyne RD, Audas TE, Unrau P, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma. Nat Commun. 2018 Oct 1;9(1):4001. PMCID: PMC6167379 |
NF1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # NF1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2017-10-10 : Reddy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,20 +32,20 @@ timeline |
| 30 | 32 | |FL |No |No |0.000 |0.000 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567) |
|
| 35 | 35 | |
| 36 | 36 | |
| 37 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NF1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NF1_protein_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | 40 | |
| 41 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NF1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NF1_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | + |
|
| 44 | 45 | ## NF1 Expression |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
| 47 | 48 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 49 | + |
|
| 48 | 50 | ## References |
| 49 | 51 | 1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
NFKB1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # NFKB1 |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | Mutations in this gene are relatively rare in DLBCL overall. Some hotspots have been identified in DLBCL. *Without further support, this gene may be migrated to Tier 2.* |
| 4 | 5 | |
| ... | ... | @@ -38,14 +39,16 @@ Mutations in this gene are relatively rare in DLBCL overall. Some hotspots have |
| 38 | 39 | |
| 39 | 40 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NFKB1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NFKB1_protein_hg38.html) |
| 40 | 41 | |
| 41 | - |
|
| 42 | + |
|
| 42 | 43 | |
| 43 | 44 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NFKB1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NFKB1_hg38.html) |
| 44 | 45 | |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | |
| 47 | 48 | ## NFKB1 Expression |
| 48 | - |
|
| 49 | + |
|
| 49 | 50 | |
| 50 | 51 | <!-- FLAGGED FOR TIER 2 --> |
| 51 | 52 | <!-- ORIGIN: Unknown --> |
| 53 | + |
|
| 54 | +## References |
NFKB2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # NFKB2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2017-10-10 : Reddy : DLBCL |
| 8 | 9 | 2019-09-05 : Mottok : PMBL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -32,22 +34,22 @@ timeline |
| 32 | 34 | |FL |No |No |2.873 |0.00 | |
| 33 | 35 | |
| 34 | 36 | |
| 35 | -> [!NOTE] |
|
| 36 | -> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567) |
|
| 37 | 37 | |
| 38 | 38 | |
| 39 | 39 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NFKB2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NFKB2_protein_hg38.html) |
| 40 | 40 | |
| 41 | - |
|
| 41 | + |
|
| 42 | 42 | |
| 43 | 43 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NFKB2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NFKB2_hg38.html) |
| 44 | 44 | |
| 45 | - |
|
| 45 | + |
|
| 46 | + |
|
| 46 | 47 | ## NFKB2 Expression |
| 47 | - |
|
| 48 | + |
|
| 48 | 49 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
| 49 | 50 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 50 | 51 | <!-- PMBL: mottokIntegrativeGenomicAnalysis2019b --> |
| 52 | + |
|
| 51 | 53 | ## References |
| 52 | 54 | 1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
| 53 | 55 | 2. Mottok A, Hung SS, Chavez EA, Woolcock B, Telenius A, Chong LC, Meissner B, Nakamura H, Rushton C, Viganò E, Sarkozy C, Gascoyne RD, Connors JM, Ben-Neriah S, Mungall A, Marra MA, Siebert R, Scott DW, Savage KJ, Steidl C. Integrative genomic analysis identifies key pathogenic mechanisms in primary mediastinal large B-cell lymphoma. Blood. 2019 Sep 5;134(10):802–813. PMID: 31292115 |
NFKBIA.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # NFKBIA |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | NFKBIA encodes IκBα, an inhibitor of NF-κB, which regulates the NF-κB signaling pathway by preventing the translocation of NF-κB to the nucleus. Mutations in NFKBIA can disrupt this regulation, leading to constitutive activation of NF-κB signaling, which has an important role in a subset of DLBCLs. Mutations and deletions in NFKBIA are observed in DLBCL and are associated with constitutive activation of the NF-κB pathway. These mutations often occur in the ABC subtype and are associated with the **ST2** genetic subgroup of DLBCL.<sup>1</sup> |
| 4 | 5 | ## History |
| ... | ... | @@ -10,6 +11,7 @@ timeline |
| 10 | 11 | 2019-12-10 : Wienand : PMBL |
| 11 | 12 | 2023-07-26 : Russler-Germain : FL |
| 12 | 13 | ``` |
| 14 | + |
|
| 13 | 15 | ## Relevance tier by entity |
| 14 | 16 | |
| 15 | 17 | |Entity|Tier|Description | |
| ... | ... | @@ -37,26 +39,25 @@ timeline |
| 37 | 39 | |FL |No |No |0.000 |28.519 | |
| 38 | 40 | |
| 39 | 41 | |
| 40 | -> [!NOTE] |
|
| 41 | -> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986) |
|
| 42 | 42 | |
| 43 | 43 | |
| 44 | 44 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NFKBIA_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NFKBIA_protein_hg38.html) |
| 45 | 45 | |
| 46 | - |
|
| 46 | + |
|
| 47 | 47 | |
| 48 | 48 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NFKBIA.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NFKBIA_hg38.html) |
| 49 | 49 | |
| 50 | - |
|
| 50 | + |
|
| 51 | 51 | |
| 52 | 52 | ## NFKBIA Expression |
| 53 | - |
|
| 53 | + |
|
| 54 | 54 | |
| 55 | 55 | |
| 56 | 56 | <!-- ORIGIN: lakeMutationsNFKBIAEncoding2009 --> |
| 57 | 57 | <!-- DLBCL: lakeMutationsNFKBIAEncoding2009 --> |
| 58 | 58 | <!-- FL: russler-germainMutationsAssociatedProgression2023b --> |
| 59 | 59 | <!-- PMBL: wienandGenomicAnalysesFlowsorted2019b --> |
| 60 | + |
|
| 60 | 61 | ## References |
| 61 | 62 | 1. Wright GW, Huang DW, Phelan JD, Coulibaly ZA, Roulland S, Young RM, Wang JQ, Schmitz R, Morin RD, Tang J, Jiang A, Bagaev A, Plotnikova O, Kotlov N, Johnson CA, Wilson WH, Scott DW, Staudt LM. A Probabilistic Classification Tool for Genetic Subtypes of Diffuse Large B Cell Lymphoma with Therapeutic Implications. Cancer Cell. 2020 Apr 13;37(4):551-568.e14. doi: 10.1016/j.ccell.2020.03.015. PMID: 32289277; PMCID: PMC8459709. |
| 62 | 63 | 2. Lake A, Shield LA, Cordano P, Chui DTY, Osborne J, Crae S, Wilson KS, Tosi S, Knight SJL, Gesk S, Siebert R, Hay RT, Jarrett RF. Mutations of NFKBIA, encoding IkappaB alpha, are a recurrent finding in classical Hodgkin lymphoma but are not a unifying feature of non-EBV-associated cases. Int J Cancer. 2009 Sep 15;125(6):1334–1342. PMID: 19507254 |
NFKBIE.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # NFKBIE |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | NFKBIE encodes IκBε, a negative regulator of NF-κB. Mutations in NFKBIE can disrupt this regulatory function, leading to constitutive activation of NF-κB signaling.<sup>1</sup> Mutations are relatively common in DLBCL and MCL.<sup>2</sup> |
| 4 | 5 | ## History |
| ... | ... | @@ -11,6 +12,7 @@ timeline |
| 11 | 12 | 2016-12-08 : Mansouri : PMBL |
| 12 | 13 | 2020-07-30 : Pararajalingam : MCL |
| 13 | 14 | ``` |
| 15 | + |
|
| 14 | 16 | ## Relevance tier by entity |
| 15 | 17 | |
| 16 | 18 | |Entity|Tier|Description | |
| ... | ... | @@ -38,20 +40,18 @@ timeline |
| 38 | 40 | |FL |No |No |0.000 |46.628 | |
| 39 | 41 | |
| 40 | 42 | |
| 41 | -> [!NOTE] |
|
| 42 | -> First described in DLBCL in 2016 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/26647218). First described in MCL in 2020 by [Pararajalingam P](https://pubmed.ncbi.nlm.nih.gov/32160292) |
|
| 43 | 43 | |
| 44 | 44 | |
| 45 | 45 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NFKBIE_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NFKBIE_protein_hg38.html) |
| 46 | 46 | |
| 47 | - |
|
| 47 | + |
|
| 48 | 48 | |
| 49 | 49 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NFKBIE.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NFKBIE_hg38.html) |
| 50 | 50 | |
| 51 | - |
|
| 51 | + |
|
| 52 | 52 | |
| 53 | 53 | ## NFKBIE Expression |
| 54 | - |
|
| 54 | + |
|
| 55 | 55 | |
| 56 | 56 | ## References |
| 57 | 57 | 1. *Mansouri, L., Noerenberg, D., Young, E., Mylonas, E., Abdulla, M., Frick, M., Asmar, F., Ljungström, V., Schneider, M., Yoshida, K., Skaftason, A., Pandzic, T., González, B., Tasidou, A., Waldhueter, N., Rivas-Delgado, A., Angelopoulou, M., Ziepert, M., Arends, C., Couronné, L., Lenze, D., Baldus, C., Bastard, C., Okosun, J., Fitzgibbon, J., Dörken, B., Drexler, H., Roos-Weil, D., Schmitt, C., Munch-Petersen, H., Zenz, T., Hansmann, M., Strefford, J., Enblad, G., Bernard, O., Ralfkiaer, E., Erlanson, M., Korkolopoulou, P., Hultdin, M., Papadaki, T., Grønbæk, K., López-Guillermo, A., Ogawa, S., Küppers, R., Stamatopoulos, K., Stavroyianni, N., Kanellis, G., Rosenwald, A., Campo, E., Amini, R., Ott, G., Vassilakopoulos, T., Hummel, M., Rosenquist, R., & Damm, F. (2016). Frequent NFKBIE deletions are associated with poor outcome in primary mediastinal B-cell lymphoma.. Blood, 128 23, 2666-2670 . https://doi.org/10.1182/BLOOD-2016-03-704528.* |
NFKBIZ.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # NFKBIZ |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | The NFKBIZ gene is a significant player in NF-κB signaling, with mutations leading to its deregulation. This pathway is critical in the pathogenesis of ABC DLBCL. NFKBIZ is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. The predominant cluster of mutations in NFKBIZ is in the 3' UTR and not a consequence of aSHM. NFKBIZ 3' UTR mutations confer a selective growth advantage in DLBCL cells by stabilizing NFKBIZ mRNA, resulting in increased protein levels.<sup>1</sup> |
| 4 | 5 | ## History |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | title Publication timing |
| 9 | 10 | 2016-05-01 : Morin : DLBCL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -41,14 +43,14 @@ timeline |
| 41 | 43 | |
| 42 | 44 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NFKBIZ_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NFKBIZ_protein_hg38.html) |
| 43 | 45 | |
| 44 | - |
|
| 46 | + |
|
| 45 | 47 | |
| 46 | 48 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NFKBIZ.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NFKBIZ_hg38.html) |
| 47 | 49 | |
| 48 | - |
|
| 50 | + |
|
| 49 | 51 | |
| 50 | 52 | ## NFKBIZ Expression |
| 51 | - |
|
| 53 | + |
|
| 52 | 54 | |
| 53 | 55 | ## References |
| 54 | 56 | 1. *Arthur SE, Jiang A, Grande BM, Alcaide M, Cojocaru R, Rushton CK, Mottok A, Hilton LK, Lat PK, Zhao EY, Culibrk L, Ennishi D, Jessa S, Chong L, Thomas N, Pararajalingam P, Meissner B, Boyle M, Davidson J, Bushell KR, Lai D, Farinha P, Slack GW, Morin GB, Shah S, Sen D, Jones SJM, Mungall AJ, Gascoyne RD, Audas TE, Unrau P, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma. Nat Commun. 2018 Oct 1;9(1):4001. doi: 10.1038/s41467-018-06354-3. PMID: 30275490; PMCID: PMC6167379.* |
NIN.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # NIN |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2014-05-08 : Zhang : MCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -27,20 +29,20 @@ timeline |
| 27 | 29 | |FL |No |No |4.145 |8.842 | |
| 28 | 30 | |
| 29 | 31 | |
| 30 | -> [!NOTE] |
|
| 31 | -> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267) |
|
| 32 | 32 | |
| 33 | 33 | |
| 34 | 34 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NIN_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NIN_protein_hg38.html) |
| 35 | 35 | |
| 36 | - |
|
| 36 | + |
|
| 37 | 37 | |
| 38 | 38 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NIN.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NIN_hg38.html) |
| 39 | 39 | |
| 40 | - |
|
| 40 | + |
|
| 41 | + |
|
| 41 | 42 | ## NIN Expression |
| 42 | - |
|
| 43 | + |
|
| 43 | 44 | <!-- ORIGIN: zhangGenomicLandscapeMantle2014 --> |
| 44 | 45 | <!-- MCL: zhangGenomicLandscapeMantle2014 --> |
| 46 | + |
|
| 45 | 47 | ## References |
| 46 | 48 | 1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996. |
NLRC5.md
| ... | ... | @@ -27,11 +27,14 @@ |
| 27 | 27 | |
| 28 | 28 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NLRC5_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NLRC5_protein_hg38.html) |
| 29 | 29 | |
| 30 | - |
|
| 30 | + |
|
| 31 | 31 | |
| 32 | 32 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NLRC5.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NLRC5_hg38.html) |
| 33 | 33 | |
| 34 | - |
|
| 34 | + |
|
| 35 | + |
|
| 35 | 36 | ## NLRC5 Expression |
| 36 | - |
|
| 37 | + |
|
| 37 | 38 | <!-- ORIGIN: Unknown --> |
| 39 | + |
|
| 40 | +## References |
NLRP5.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # NLRP5 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2013-08-15 : Morin : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -33,14 +35,16 @@ timeline |
| 33 | 35 | |
| 34 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NLRP5_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NLRP5_protein_hg38.html) |
| 35 | 37 | |
| 36 | - |
|
| 38 | + |
|
| 37 | 39 | |
| 38 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NLRP5.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NLRP5_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 43 | + |
|
| 41 | 44 | ## NLRP5 Expression |
| 42 | - |
|
| 45 | + |
|
| 43 | 46 | <!-- ORIGIN: morinMutationalStructuralAnalysis2013 --> |
| 44 | 47 | <!-- DLBCL: morinMutationalStructuralAnalysis2013 --> |
| 48 | + |
|
| 45 | 49 | ## References |
| 46 | 50 | 1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992 |
NLRP8.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # NLRP8 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | |
| 4 | 5 | ```mermaid |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | title Publication timing |
| 8 | 9 | 2018-05-01 : Chapuy : DLBCL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -33,14 +35,16 @@ timeline |
| 33 | 35 | |
| 34 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NLRP8_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NLRP8_protein_hg38.html) |
| 35 | 37 | |
| 36 | - |
|
| 38 | + |
|
| 37 | 39 | |
| 38 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NLRP8.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NLRP8_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 43 | + |
|
| 41 | 44 | ## NLRP8 Expression |
| 42 | - |
|
| 45 | + |
|
| 43 | 46 | <!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b --> |
| 44 | 47 | <!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b --> |
| 48 | + |
|
| 45 | 49 | ## References |
| 46 | 50 | 1. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387 |
NOA1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # NOA1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2022-07-06 : Burkhardt : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -31,14 +33,16 @@ timeline |
| 31 | 33 | |
| 32 | 34 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NOA1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NOA1_protein_hg38.html) |
| 33 | 35 | |
| 34 | - |
|
| 36 | + |
|
| 35 | 37 | |
| 36 | 38 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NOA1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NOA1_hg38.html) |
| 37 | 39 | |
| 38 | - |
|
| 40 | + |
|
| 41 | + |
|
| 39 | 42 | ## NOA1 Expression |
| 40 | - |
|
| 43 | + |
|
| 41 | 44 | <!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b --> |
| 42 | 45 | <!-- BL: burkhardtClinicalRelevanceMolecular2022b --> |
| 46 | + |
|
| 43 | 47 | ## References |
| 44 | 48 | 1. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584 |
NOL9.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # NOL9 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2016-09-08 : Spina : MZL |
| 8 | 9 | 2018-04-12 : Schmitz : DLBCL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -43,16 +45,18 @@ timeline |
| 43 | 45 | |
| 44 | 46 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NOL9_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NOL9_protein_hg38.html) |
| 45 | 47 | |
| 46 | - |
|
| 48 | + |
|
| 47 | 49 | |
| 48 | 50 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NOL9.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NOL9_hg38.html) |
| 49 | 51 | |
| 50 | - |
|
| 52 | + |
|
| 53 | + |
|
| 51 | 54 | ## NOL9 Expression |
| 52 | - |
|
| 55 | + |
|
| 53 | 56 | <!-- ORIGIN: spinaGeneticsNodalMarginal2016b --> |
| 54 | 57 | <!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a --> |
| 55 | 58 | <!-- MZL: spinaGeneticsNodalMarginal2016b --> |
| 59 | + |
|
| 56 | 60 | ## References |
| 57 | 61 | 1. Spina V, Khiabanian H, Messina M, Monti S, Cascione L, Bruscaggin A, Spaccarotella E, Holmes AB, Arcaini L, Lucioni M, Tabbò F, Zairis S, Diop F, Cerri M, Chiaretti S, Marasca R, Ponzoni M, Deaglio S, Ramponi A, Tiacci E, Pasqualucci L, Paulli M, Falini B, Inghirami G, Bertoni F, Foà R, Rabadan R, Gaidano G, Rossi D. The genetics of nodal marginal zone lymphoma. Blood. 2016 Sep 8;128(10):1362–1373. |
| 58 | 62 | 2. Schmitz R, Wright GW, Huang DW, Johnson CA, Phelan JD, Wang JQ, Roulland S, Kasbekar M, Young RM, Shaffer AL, Hodson DJ, Xiao W, Yu X, Yang Y, Zhao H, Xu W, Liu X, Zhou B, Du W, Chan WC, Jaffe ES, Gascoyne RD, Connors JM, Campo E, Lopez-Guillermo A, Rosenwald A, Ott G, Delabie J, Rimsza LM, Tay Kuang Wei K, Zelenetz AD, Leonard JP, Bartlett NL, Tran B, Shetty J, Zhao Y, Soppet DR, Pittaluga S, Wilson WH, Staudt LM. Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma. N Engl J Med. 2018 Apr 12;378(15):1396–1407. PMCID: PMC6010183 |
NOTCH1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # NOTCH1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | |
| 4 | 5 | ```mermaid |
| ... | ... | @@ -10,6 +11,7 @@ timeline |
| 10 | 11 | 2012-12-01 : Love : BL |
| 11 | 12 | 2013-11-05 : Bea : MCL |
| 12 | 13 | ``` |
| 14 | + |
|
| 13 | 15 | ## Relevance tier by entity |
| 14 | 16 | |
| 15 | 17 | |Entity|Tier|Description | |
| ... | ... | @@ -50,18 +52,20 @@ timeline |
| 50 | 52 | |
| 51 | 53 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NOTCH1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NOTCH1_protein_hg38.html) |
| 52 | 54 | |
| 53 | - |
|
| 55 | + |
|
| 54 | 56 | |
| 55 | 57 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NOTCH1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NOTCH1_hg38.html) |
| 56 | 58 | |
| 57 | - |
|
| 59 | + |
|
| 60 | + |
|
| 58 | 61 | ## NOTCH1 Expression |
| 59 | - |
|
| 62 | + |
|
| 60 | 63 | <!-- ORIGIN: pasqualucciAnalysisCodingGenome2011 --> |
| 61 | 64 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 62 | 65 | <!-- MZL: rossiCodingGenomeSplenic2012c --> |
| 63 | 66 | <!-- MCL: beaLandscapeSomaticMutations2013 --> |
| 64 | 67 | <!-- DLBCL: pasqualucciAnalysisCodingGenome2011 --> |
| 68 | + |
|
| 65 | 69 | ## References |
| 66 | 70 | 1. Pasqualucci L, Trifonov V, Fabbri G, Ma J, Rossi D, Chiarenza A, Wells VA, Grunn A, Messina M, Elliot O, Chan J, Bhagat G, Chadburn A, Gaidano G, Mullighan CG, Rabadan R, Dalla-Favera R. Analysis of the coding genome of diffuse large B-cell lymphoma. Nat Genet. 2011 Jul 31;43(9):830–837. PMCID: PMC3297422 |
| 67 | 71 | 2. Rossi D, Trifonov V, Fangazio M, Bruscaggin A, Rasi S, Spina V, Monti S, Vaisitti T, Arruga F, Famà R, Ciardullo C, Greco M, Cresta S, Piranda D, Holmes A, Fabbri G, Messina M, Rinaldi A, Wang J, Agostinelli C, Piccaluga PP, Lucioni M, Tabbò F, Serra R, Franceschetti S, Deambrogi C, Daniele G, Gattei V, Marasca R, Facchetti F, Arcaini L, Inghirami G, Bertoni F, Pileri SA, Deaglio S, Foà R, Dalla-Favera R, Pasqualucci L, Rabadan R, Gaidano G. The coding genome of splenic marginal zone lymphoma: activation of NOTCH2 and other pathways regulating marginal zone development. J Exp Med. 2012 Aug 27;209(9):1537–1551. PMCID: PMC3428941 |
NOTCH2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # NOTCH2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -9,6 +10,7 @@ timeline |
| 9 | 10 | 2013-11-05 : Bea : MCL |
| 10 | 11 | 2019-09-26 : Panea : BL |
| 11 | 12 | ``` |
| 13 | + |
|
| 12 | 14 | ## Relevance tier by entity |
| 13 | 15 | |
| 14 | 16 | |Entity|Tier|Description | |
| ... | ... | @@ -40,8 +42,6 @@ timeline |
| 40 | 42 | |FL |No |No |0.000 | 0.000 | |
| 41 | 43 | |
| 42 | 44 | |
| 43 | -> [!NOTE] |
|
| 44 | -> First described in MCL in 2013 by [Beà S](https://pubmed.ncbi.nlm.nih.gov/24145436) |
|
| 45 | 45 | |
| 46 | 46 | ## NOTCH2 Hotspots |
| 47 | 47 | |
| ... | ... | @@ -51,18 +51,20 @@ timeline |
| 51 | 51 | |
| 52 | 52 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NOTCH2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NOTCH2_protein_hg38.html) |
| 53 | 53 | |
| 54 | - |
|
| 54 | + |
|
| 55 | 55 | |
| 56 | 56 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NOTCH2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NOTCH2_hg38.html) |
| 57 | 57 | |
| 58 | - |
|
| 58 | + |
|
| 59 | + |
|
| 59 | 60 | ## NOTCH2 Expression |
| 60 | - |
|
| 61 | + |
|
| 61 | 62 | <!-- ORIGIN: 18508802 --> |
| 62 | 63 | <!-- DLBCL: troenNOTCH2MutationsMarginal2008 --> |
| 63 | 64 | <!-- MCL: beaLandscapeSomaticMutations2013 --> |
| 64 | 65 | <!-- MZL: rossiCodingGenomeSplenic2012c --> |
| 65 | 66 | <!-- BL: paneaWholeGenomeLandscape2019 --> |
| 67 | + |
|
| 66 | 68 | ## References |
| 67 | 69 | 1. Trøen G, Wlodarska I, Warsame A, Hernández Llodrà S, De Wolf-Peeters C, Delabie J. NOTCH2 mutations in marginal zone lymphoma. Haematologica. 2008 Jul;93(7):1107–1109. PMID: 18508802 |
| 68 | 70 | 2. Rossi D, Trifonov V, Fangazio M, Bruscaggin A, Rasi S, Spina V, Monti S, Vaisitti T, Arruga F, Famà R, Ciardullo C, Greco M, Cresta S, Piranda D, Holmes A, Fabbri G, Messina M, Rinaldi A, Wang J, Agostinelli C, Piccaluga PP, Lucioni M, Tabbò F, Serra R, Franceschetti S, Deambrogi C, Daniele G, Gattei V, Marasca R, Facchetti F, Arcaini L, Inghirami G, Bertoni F, Pileri SA, Deaglio S, Foà R, Dalla-Favera R, Pasqualucci L, Rabadan R, Gaidano G. The coding genome of splenic marginal zone lymphoma: activation of NOTCH2 and other pathways regulating marginal zone development. J Exp Med. 2012 Aug 27;209(9):1537–1551. PMCID: PMC3428941 |
NRXN2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # NRXN2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -33,14 +35,16 @@ timeline |
| 33 | 35 | |
| 34 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NRXN2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NRXN2_protein_hg38.html) |
| 35 | 37 | |
| 36 | - |
|
| 38 | + |
|
| 37 | 39 | |
| 38 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NRXN2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NRXN2_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 43 | + |
|
| 41 | 44 | ## NRXN2 Expression |
| 42 | - |
|
| 45 | + |
|
| 43 | 46 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 44 | 47 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 48 | + |
|
| 45 | 49 | ## References |
| 46 | 50 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
NSD2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # NSD2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2013-11-05 : Bea : MCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -24,20 +26,20 @@ timeline |
| 24 | 26 | | |
| 25 | 27 | |
| 26 | 28 | |
| 27 | -> [!NOTE] |
|
| 28 | -> First described in MCL in 2013 by [Beà S](https://pubmed.ncbi.nlm.nih.gov/24145436) |
|
| 29 | 29 | |
| 30 | 30 | |
| 31 | 31 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NSD2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NSD2_protein_hg38.html) |
| 32 | 32 | |
| 33 | - |
|
| 33 | + |
|
| 34 | 34 | |
| 35 | 35 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NSD2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NSD2_hg38.html) |
| 36 | 36 | |
| 37 | - |
|
| 37 | + |
|
| 38 | + |
|
| 38 | 39 | ## NSD2 Expression |
| 39 | - |
|
| 40 | + |
|
| 40 | 41 | <!-- ORIGIN: beaLandscapeSomaticMutations2013 --> |
| 41 | 42 | <!-- MCL: beaLandscapeSomaticMutations2013 --> |
| 43 | + |
|
| 42 | 44 | ## References |
| 43 | 45 | 1. Beà S, Valdés-Mas R, Navarro A, Salaverria I, Martín-Garcia D, Jares P, Giné E, Pinyol M, Royo C, Nadeu F, Conde L, Juan M, Clot G, Vizán P, Croce LD, Puente DA, López-Guerra M, Moros A, Roue G, Aymerich M, Villamor N, Colomo L, Martínez A, Valera A, Martín-Subero JI, Amador V, Hernández L, Rozman M, Enjuanes A, Forcada P, Muntañola A, Hartmann EM, Calasanz MJ, Rosenwald A, Ott G, Hernández-Rivas JM, Klapper W, Siebert R, Wiestner A, Wilson WH, Colomer D, López-Guillermo A, López-Otín C, Puente XS, Campo E. Landscape of somatic mutations and clonal evolution in mantle cell lymphoma. PNAS. 2013 Nov 5;110(45):18250–18255. PMID: 24145436 |
ODZ3.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # ODZ3 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2013-08-15 : Morin : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -26,11 +28,10 @@ timeline |
| 26 | 28 | | |
| 27 | 29 | |
| 28 | 30 | |
| 29 | -> [!NOTE] |
|
| 30 | -> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601) |
|
| 31 | 31 | ## ODZ3 Expression |
| 32 | - |
|
| 32 | + |
|
| 33 | 33 | <!-- ORIGIN: morinMutationalStructuralAnalysis2013 --> |
| 34 | 34 | <!-- DLBCL: morinMutationalStructuralAnalysis2013 --> |
| 35 | + |
|
| 35 | 36 | ## References |
| 36 | 37 | 1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992 |
OGDHL.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # OGDHL |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2014-05-08 : Zhang : MCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,14 +32,16 @@ timeline |
| 30 | 32 | |
| 31 | 33 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/OGDHL_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/OGDHL_protein_hg38.html) |
| 32 | 34 | |
| 33 | - |
|
| 35 | + |
|
| 34 | 36 | |
| 35 | 37 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/OGDHL.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/OGDHL_hg38.html) |
| 36 | 38 | |
| 37 | - |
|
| 39 | + |
|
| 40 | + |
|
| 38 | 41 | ## OGDHL Expression |
| 39 | - |
|
| 42 | + |
|
| 40 | 43 | <!-- ORIGIN: zhangGenomicLandscapeMantle2014 --> |
| 41 | 44 | <!-- MCL: zhangGenomicLandscapeMantle2014 --> |
| 45 | + |
|
| 42 | 46 | ## References |
| 43 | 47 | 1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996. |
OR8H2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # OR8H2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2023-07-26 : Russler-Germain : FL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,14 +32,16 @@ timeline |
| 30 | 32 | |
| 31 | 33 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/OR8H2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/OR8H2_protein_hg38.html) |
| 32 | 34 | |
| 33 | - |
|
| 35 | + |
|
| 34 | 36 | |
| 35 | 37 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/OR8H2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/OR8H2_hg38.html) |
| 36 | 38 | |
| 37 | - |
|
| 39 | + |
|
| 40 | + |
|
| 38 | 41 | ## OR8H2 Expression |
| 39 | - |
|
| 42 | + |
|
| 40 | 43 | <!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a --> |
| 41 | 44 | <!-- FL: russler-germainMutationsAssociatedProgression2023b --> |
| 45 | + |
|
| 42 | 46 | ## References |
| 43 | 47 | 1. Russler-Germain DA, Krysiak K, Ramirez CA, Mosior M, Watkins MP, Gomez F, Skidmore ZL, Trani L, Gao F, Geyer S, Cashen A, Mehta-Shah N, Kahl B, Bartlett N, Alderuccio J, Lossos I, Ondrejka S, Hsi E, Martin P, Leonard J, Griffith M, Griffith O, Fehniger T. Mutations associated with progression in follicular lymphoma predict inferior outcomes at diagnosis: Alliance A151303. Blood Advances. 2023;7:5524–5539. |
OSBPL10.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # OSBPL10 |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | OSBPL10 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. |
| 4 | 5 | ## History |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | title Publication timing |
| 9 | 10 | 2018-10-01 : Arthur : DLBCL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -41,14 +43,16 @@ timeline |
| 41 | 43 | |
| 42 | 44 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/OSBPL10_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/OSBPL10_protein_hg38.html) |
| 43 | 45 | |
| 44 | - |
|
| 46 | + |
|
| 45 | 47 | |
| 46 | 48 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/OSBPL10.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/OSBPL10_hg38.html) |
| 47 | 49 | |
| 48 | - |
|
| 50 | + |
|
| 51 | + |
|
| 49 | 52 | ## OSBPL10 Expression |
| 50 | - |
|
| 53 | + |
|
| 51 | 54 | <!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 --> |
| 52 | 55 | <!-- DLBCL: arthurGenomewideDiscoverySomatic2018 --> |
| 56 | + |
|
| 53 | 57 | ## References |
| 54 | 58 | 1. Arthur SE, Jiang A, Grande BM, Alcaide M, Cojocaru R, Rushton CK, Mottok A, Hilton LK, Lat PK, Zhao EY, Culibrk L, Ennishi D, Jessa S, Chong L, Thomas N, Pararajalingam P, Meissner B, Boyle M, Davidson J, Bushell KR, Lai D, Farinha P, Slack GW, Morin GB, Shah S, Sen D, Jones SJM, Mungall AJ, Gascoyne RD, Audas TE, Unrau P, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma. Nat Commun. 2018 Oct 1;9(1):4001. PMCID: PMC6167379 |
P2RX5.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # P2RX5 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2013-08-15 : Morin : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -35,20 +37,20 @@ timeline |
| 35 | 37 | |:--------:|:----------:|:--------:|:----------------------------------------------------------------------------------------:|:------------------:| |
| 36 | 38 | |chr17 |3597616 |3599572 |[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr17%3A3597616%2D3599572)|active_promoter | |
| 37 | 39 | |
| 38 | -> [!NOTE] |
|
| 39 | -> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601) |
|
| 40 | 40 | |
| 41 | 41 | |
| 42 | 42 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P2RX5_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/P2RX5_protein_hg38.html) |
| 43 | 43 | |
| 44 | - |
|
| 44 | + |
|
| 45 | 45 | |
| 46 | 46 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P2RX5.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/P2RX5_hg38.html) |
| 47 | 47 | |
| 48 | - |
|
| 48 | + |
|
| 49 | + |
|
| 49 | 50 | ## P2RX5 Expression |
| 50 | - |
|
| 51 | + |
|
| 51 | 52 | <!-- ORIGIN: morinMutationalStructuralAnalysis2013 --> |
| 52 | 53 | <!-- DLBCL: morinMutationalStructuralAnalysis2013 --> |
| 54 | + |
|
| 53 | 55 | ## References |
| 54 | 56 | 1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992 |
P2RY2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # P2RY2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -29,20 +31,20 @@ timeline |
| 29 | 31 | |FL |No |No |0.000 |0 | |
| 30 | 32 | |
| 31 | 33 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597) |
|
| 34 | 34 | |
| 35 | 35 | |
| 36 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P2RY2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/P2RY2_protein_hg38.html) |
| 37 | 37 | |
| 38 | - |
|
| 38 | + |
|
| 39 | 39 | |
| 40 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P2RY2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/P2RY2_hg38.html) |
| 41 | 41 | |
| 42 | - |
|
| 42 | + |
|
| 43 | + |
|
| 43 | 44 | ## P2RY2 Expression |
| 44 | - |
|
| 45 | + |
|
| 45 | 46 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 46 | 47 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 48 | + |
|
| 47 | 49 | ## References |
| 48 | 50 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
P2RY8.md
| ... | ... | @@ -9,6 +9,7 @@ timeline |
| 9 | 9 | 2012-03-06 : Lohr : DLBCL |
| 10 | 10 | 2014-12-11 : Muppidi : BL |
| 11 | 11 | ``` |
| 12 | + |
|
| 12 | 13 | ## Relevance tier by entity |
| 13 | 14 | |
| 14 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -42,14 +43,14 @@ timeline |
| 42 | 43 | |
| 43 | 44 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P2RY8_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/P2RY8_protein_hg38.html) |
| 44 | 45 | |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | |
| 47 | 48 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P2RY8.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/P2RY8_hg38.html) |
| 48 | 49 | |
| 49 | - |
|
| 50 | + |
|
| 50 | 51 | |
| 51 | 52 | ## P2RY8 Expression |
| 52 | - |
|
| 53 | + |
|
| 53 | 54 | |
| 54 | 55 | ## References |
| 55 | 56 | 1. *Muppidi JR, Schmitz R, Green JA, Xiao W, Larsen AB, Braun SE, An J, Xu Y, Rosenwald A, Ott G, Gascoyne RD, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Vaidehi N, Staudt LM, Cyster JG. Loss of signalling via Gα13 in germinal centre B-cell-derived lymphoma. Nature. 2014 Dec 11;516(7530):254-8. doi: 10.1038/nature13765. Epub 2014 Sep 28. PMID: 25274307; PMCID: PMC4267955.* |
PABPC4L.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PABPC4L |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2019-09-26 : Panea : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -29,20 +31,20 @@ timeline |
| 29 | 31 | |FL |No |No |0.000 |0 | |
| 30 | 32 | |
| 31 | 33 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468) |
|
| 34 | 34 | |
| 35 | 35 | |
| 36 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PABPC4L_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PABPC4L_protein_hg38.html) |
| 37 | 37 | |
| 38 | - |
|
| 38 | + |
|
| 39 | 39 | |
| 40 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PABPC4L.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PABPC4L_hg38.html) |
| 41 | 41 | |
| 42 | - |
|
| 42 | + |
|
| 43 | + |
|
| 43 | 44 | ## PABPC4L Expression |
| 44 | - |
|
| 45 | + |
|
| 45 | 46 | <!-- ORIGIN: paneaWholeGenomeLandscape2019 --> |
| 46 | 47 | <!-- BL: paneaWholeGenomeLandscape2019 --> |
| 48 | + |
|
| 47 | 49 | ## References |
| 48 | 50 | 1. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019; |
PAPOLG.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PAPOLG |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2018-04-12 : Schmitz : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,20 +32,20 @@ timeline |
| 30 | 32 | |FL |No |No |4.497 |0 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966) |
|
| 35 | 35 | |
| 36 | 36 | |
| 37 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PAPOLG_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PAPOLG_protein_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | 40 | |
| 41 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PAPOLG.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PAPOLG_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | + |
|
| 44 | 45 | ## PAPOLG Expression |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | <!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a --> |
| 47 | 48 | <!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a --> |
| 49 | + |
|
| 48 | 50 | ## References |
| 49 | 51 | 1. Schmitz R, Wright GW, Huang DW, Johnson CA, Phelan JD, Wang JQ, Roulland S, Kasbekar M, Young RM, Shaffer AL, Hodson DJ, Xiao W, Yu X, Yang Y, Zhao H, Xu W, Liu X, Zhou B, Du W, Chan WC, Jaffe ES, Gascoyne RD, Connors JM, Campo E, Lopez-Guillermo A, Rosenwald A, Ott G, Delabie J, Rimsza LM, Tay Kuang Wei K, Zelenetz AD, Leonard JP, Bartlett NL, Tran B, Shetty J, Zhao Y, Soppet DR, Pittaluga S, Wilson WH, Staudt LM. Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma. N Engl J Med. 2018 Apr 12;378(15):1396–1407. PMCID: PMC6010183 |
PASK.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PASK |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2013-08-15 : Morin : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,20 +32,20 @@ timeline |
| 30 | 32 | |FL |No |No |1.504 |0 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601) |
|
| 35 | 35 | |
| 36 | 36 | |
| 37 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PASK_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PASK_protein_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | 40 | |
| 41 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PASK.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PASK_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | + |
|
| 44 | 45 | ## PASK Expression |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | <!-- ORIGIN: morinMutationalStructuralAnalysis2013 --> |
| 47 | 48 | <!-- DLBCL: morinMutationalStructuralAnalysis2013 --> |
| 49 | + |
|
| 48 | 50 | ## References |
| 49 | 51 | 1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992 |
PAX5.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PAX5 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2001-07-19 : Pasqualucci : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -39,20 +41,20 @@ timeline |
| 39 | 41 | |chr9 |37382267 |37385854|[distal-enhancer-2](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr9%3A37382267%2D37385854)|enhancer | |
| 40 | 42 | |chr9 |37395932 |37409239|[distal-enhancer-3](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr9%3A37395932%2D37409239)|enhancer | |
| 41 | 43 | |
| 42 | -> [!NOTE] |
|
| 43 | -> First described in DLBCL in 2001 by [Pasqualucci L](https://pubmed.ncbi.nlm.nih.gov/11460166) |
|
| 44 | 44 | |
| 45 | 45 | |
| 46 | 46 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PAX5_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PAX5_protein_hg38.html) |
| 47 | 47 | |
| 48 | - |
|
| 48 | + |
|
| 49 | 49 | |
| 50 | 50 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PAX5.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PAX5_hg38.html) |
| 51 | 51 | |
| 52 | - |
|
| 52 | + |
|
| 53 | + |
|
| 53 | 54 | ## PAX5 Expression |
| 54 | - |
|
| 55 | + |
|
| 55 | 56 | <!-- ORIGIN: pasqualucciHypermutationMultipleProtooncogenes2001a --> |
| 56 | 57 | <!-- DLBCL: pasqualucciHypermutationMultipleProtooncogenes2001a --> |
| 58 | + |
|
| 57 | 59 | ## References |
| 58 | 60 | 1. Pasqualucci L, Neumeister P, Goossens T, Nanjangud G, Chaganti RS, Küppers R, Dalla-Favera R. Hypermutation of multiple proto-oncogenes in B-cell diffuse large-cell lymphomas. Nature. 2001 Jul 19;412(6844):341–346. PMID: 11460166 |
PC.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PC |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -29,20 +31,20 @@ timeline |
| 29 | 31 | |FL |No |No |0.000 |27.654 | |
| 30 | 32 | |
| 31 | 33 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597) |
|
| 34 | 34 | |
| 35 | 35 | |
| 36 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PC_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PC_protein_hg38.html) |
| 37 | 37 | |
| 38 | - |
|
| 38 | + |
|
| 39 | 39 | |
| 40 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PC.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PC_hg38.html) |
| 41 | 41 | |
| 42 | - |
|
| 42 | + |
|
| 43 | + |
|
| 43 | 44 | ## PC Expression |
| 44 | - |
|
| 45 | + |
|
| 45 | 46 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 46 | 47 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 48 | + |
|
| 47 | 49 | ## References |
| 48 | 50 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
PCBP1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PCBP1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-10-04 : Schmitz : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -35,8 +37,6 @@ timeline |
| 35 | 37 | |FL |No |No | 1.401 | 0.000 | |
| 36 | 38 | |
| 37 | 39 | |
| 38 | -> [!NOTE] |
|
| 39 | -> First described in BL in 2015 by [Wagener R](https://pubmed.ncbi.nlm.nih.gov/26173642) |
|
| 40 | 40 | |
| 41 | 41 | |
| 42 | 42 | ## PCBP1 Hotspots |
| ... | ... | @@ -50,14 +50,16 @@ timeline |
| 50 | 50 | |
| 51 | 51 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PCBP1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PCBP1_protein_hg38.html) |
| 52 | 52 | |
| 53 | - |
|
| 53 | + |
|
| 54 | 54 | |
| 55 | 55 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PCBP1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PCBP1_hg38.html) |
| 56 | 56 | |
| 57 | - |
|
| 57 | + |
|
| 58 | + |
|
| 58 | 59 | ## PCBP1 Expression |
| 59 | - |
|
| 60 | + |
|
| 60 | 61 | <!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 --> |
| 61 | 62 | <!-- BL: schmitzBurkittLymphomaPathogenesis2012 --> |
| 63 | + |
|
| 62 | 64 | ## References |
| 63 | 65 | 1. Schmitz R, Young RM, Ceribelli M, Jhavar S, Xiao W, Zhang M, Wright G, Shaffer AL, Hodson DJ, Buras E, Liu X, Powell J, Yang Y, Xu W, Zhao H, Kohlhammer H, Rosenwald A, Kluin P, Müller-Hermelink HK, Ott G, Gascoyne RD, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Ogwang MD, Reynolds SJ, Fisher RI, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Pittaluga S, Wilson W, Waldmann TA, Rowe M, Mbulaiteye SM, Rickinson AB, Staudt LM. Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics. Nature. 2012 Oct 4;490(7418):116–120. PMCID: PMC3609867 |
PCDHA11.md
| ... | ... | @@ -6,6 +6,7 @@ timeline |
| 6 | 6 | title Publication timing |
| 7 | 7 | 2019-09-26 : Panea : BL |
| 8 | 8 | ``` |
| 9 | + |
|
| 9 | 10 | ## Relevance tier by entity |
| 10 | 11 | |
| 11 | 12 | |Entity|Tier|Description | |
| ... | ... | @@ -29,20 +30,20 @@ timeline |
| 29 | 30 | |FL |No |No |0.784 |0 | |
| 30 | 31 | |
| 31 | 32 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468) |
|
| 34 | 33 | |
| 35 | 34 | |
| 36 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PCDHA11_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PCDHA11_protein_hg38.html) |
| 37 | 36 | |
| 38 | - |
|
| 37 | + |
|
| 39 | 38 | |
| 40 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PCDHA11.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PCDHA11_hg38.html) |
| 41 | 40 | |
| 42 | - |
|
| 41 | + |
|
| 42 | + |
|
| 43 | 43 | ## PCDHA11 Expression |
| 44 | - |
|
| 44 | + |
|
| 45 | 45 | <!-- ORIGIN: paneaWholeGenomeLandscape2019 --> |
| 46 | 46 | <!-- BL: paneaWholeGenomeLandscape2019 --> |
| 47 | + |
|
| 47 | 48 | ## References |
| 48 | 49 | 1. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019; |
PCDHB11.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PCDHB11 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2013-08-15 : Morin : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -32,14 +34,16 @@ timeline |
| 32 | 34 | |
| 33 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PCDHB11_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PCDHB11_protein_hg38.html) |
| 34 | 36 | |
| 35 | - |
|
| 37 | + |
|
| 36 | 38 | |
| 37 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PCDHB11.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PCDHB11_hg38.html) |
| 38 | 40 | |
| 39 | - |
|
| 41 | + |
|
| 42 | + |
|
| 40 | 43 | ## PCDHB11 Expression |
| 41 | - |
|
| 44 | + |
|
| 42 | 45 | <!-- ORIGIN: morinMutationalStructuralAnalysis2013 --> |
| 43 | 46 | <!-- DLBCL: morinMutationalStructuralAnalysis2013 --> |
| 47 | + |
|
| 44 | 48 | ## References |
| 45 | 49 | 1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992 |
PCDHB2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PCDHB2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2014-05-08 : Zhang : MCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,14 +32,16 @@ timeline |
| 30 | 32 | |
| 31 | 33 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PCDHB2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PCDHB2_protein_hg38.html) |
| 32 | 34 | |
| 33 | - |
|
| 35 | + |
|
| 34 | 36 | |
| 35 | 37 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PCDHB2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PCDHB2_hg38.html) |
| 36 | 38 | |
| 37 | - |
|
| 39 | + |
|
| 40 | + |
|
| 38 | 41 | ## PCDHB2 Expression |
| 39 | - |
|
| 42 | + |
|
| 40 | 43 | <!-- ORIGIN: zhangGenomicLandscapeMantle2014 --> |
| 41 | 44 | <!-- MCL: zhangGenomicLandscapeMantle2014 --> |
| 45 | + |
|
| 42 | 46 | ## References |
| 43 | 47 | 1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996. |
PCLO.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PCLO |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-03-06 : Lohr : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -44,14 +46,14 @@ timeline |
| 44 | 46 | |
| 45 | 47 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PCLO_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PCLO_protein_hg38.html) |
| 46 | 48 | |
| 47 | - |
|
| 49 | + |
|
| 48 | 50 | |
| 49 | 51 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PCLO.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PCLO_hg38.html) |
| 50 | 52 | |
| 51 | - |
|
| 53 | + |
|
| 52 | 54 | |
| 53 | 55 | ## PCLO Expression |
| 54 | - |
|
| 56 | + |
|
| 55 | 57 | |
| 56 | 58 | ## References |
| 57 | 59 | 1. *Lohr JG, Stojanov P, Lawrence MS, Auclair D, Chapuy B, Sougnez C, Cruz-Gordillo P, Knoechel B, Asmann YW, Slager SL, Novak AJ, Dogan A, Ansell SM, Link BK, Zou L, Gould J, Saksena G, Stransky N, Rangel-Escareño C, Fernandez-Lopez JC, Hidalgo-Miranda A, Melendez-Zajgla J, Hernández-Lemus E, Schwarz-Cruz y Celis A, Imaz-Rosshandler I, Ojesina AI, Jung J, Pedamallu CS, Lander ES, Habermann TM, Cerhan JR, Shipp MA, Getz G, Golub TR. Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing. Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3879-84. doi: 10.1073/pnas.1121343109. Epub 2012 Feb 17. PMID: 22343534; PMCID: PMC3309757.* |
PDCD11.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PDCD11 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-10-04 : Schmitz : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -32,14 +34,16 @@ timeline |
| 32 | 34 | |
| 33 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PDCD11_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PDCD11_protein_hg38.html) |
| 34 | 36 | |
| 35 | - |
|
| 37 | + |
|
| 36 | 38 | |
| 37 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PDCD11.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PDCD11_hg38.html) |
| 38 | 40 | |
| 39 | - |
|
| 41 | + |
|
| 42 | + |
|
| 40 | 43 | ## PDCD11 Expression |
| 41 | - |
|
| 44 | + |
|
| 42 | 45 | <!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 --> |
| 43 | 46 | <!-- BL: schmitzBurkittLymphomaPathogenesis2012 --> |
| 47 | + |
|
| 44 | 48 | ## References |
| 45 | 49 | 1. Schmitz R, Young RM, Ceribelli M, Jhavar S, Xiao W, Zhang M, Wright G, Shaffer AL, Hodson DJ, Buras E, Liu X, Powell J, Yang Y, Xu W, Zhao H, Kohlhammer H, Rosenwald A, Kluin P, Müller-Hermelink HK, Ott G, Gascoyne RD, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Ogwang MD, Reynolds SJ, Fisher RI, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Pittaluga S, Wilson W, Waldmann TA, Rowe M, Mbulaiteye SM, Rickinson AB, Staudt LM. Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics. Nature. 2012 Oct 4;490(7418):116–120. PMCID: PMC3609867 |
PDE4DIP.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PDE4DIP |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2018-05-01 : Chapuy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -32,14 +34,16 @@ timeline |
| 32 | 34 | |
| 33 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PDE4DIP_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PDE4DIP_protein_hg38.html) |
| 34 | 36 | |
| 35 | - |
|
| 37 | + |
|
| 36 | 38 | |
| 37 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PDE4DIP.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PDE4DIP_hg38.html) |
| 38 | 40 | |
| 39 | - |
|
| 41 | + |
|
| 42 | + |
|
| 40 | 43 | ## PDE4DIP Expression |
| 41 | - |
|
| 44 | + |
|
| 42 | 45 | <!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b --> |
| 43 | 46 | <!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b --> |
| 47 | + |
|
| 44 | 48 | ## References |
| 45 | 49 | 1. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387 |
PDS5B.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PDS5B |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | Mutations in this gene were first described in DLBCL in 2013 by Morin et al<sup>1</sup> and in FL in 2021 by Hübschmann et al.<sup>2</sup> |
| 4 | 5 | |
| ... | ... | @@ -9,6 +10,7 @@ timeline |
| 9 | 10 | 2013-08-15 : Morin : DLBCL |
| 10 | 11 | 2021-05-05 : H : FL |
| 11 | 12 | ``` |
| 13 | + |
|
| 12 | 14 | ## Relevance tier by entity |
| 13 | 15 | |
| 14 | 16 | |Entity|Tier|Description | |
| ... | ... | @@ -36,13 +38,14 @@ timeline |
| 36 | 38 | |
| 37 | 39 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PDS5B_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PDS5B_protein_hg38.html) |
| 38 | 40 | |
| 39 | - |
|
| 41 | + |
|
| 40 | 42 | |
| 41 | 43 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PDS5B.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PDS5B_hg38.html) |
| 42 | 44 | |
| 43 | - |
|
| 45 | + |
|
| 46 | + |
|
| 44 | 47 | ## PDS5B Expression |
| 45 | - |
|
| 48 | + |
|
| 46 | 49 | |
| 47 | 50 | ## References |
| 48 | 51 | 1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992 |
PDZRN3.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PDZRN3 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2019-09-26 : Panea : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -29,20 +31,20 @@ timeline |
| 29 | 31 | |FL |No |No |0.935 |0 | |
| 30 | 32 | |
| 31 | 33 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468) |
|
| 34 | 34 | |
| 35 | 35 | |
| 36 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PDZRN3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PDZRN3_protein_hg38.html) |
| 37 | 37 | |
| 38 | - |
|
| 38 | + |
|
| 39 | 39 | |
| 40 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PDZRN3.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PDZRN3_hg38.html) |
| 41 | 41 | |
| 42 | - |
|
| 42 | + |
|
| 43 | + |
|
| 43 | 44 | ## PDZRN3 Expression |
| 44 | - |
|
| 45 | + |
|
| 45 | 46 | <!-- ORIGIN: paneaWholeGenomeLandscape2019 --> |
| 46 | 47 | <!-- BL: paneaWholeGenomeLandscape2019 --> |
| 48 | + |
|
| 47 | 49 | ## References |
| 48 | 50 | 1. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019; |
PHF6.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PHF6 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2017-10-10 : Reddy : DLBCL |
| 8 | 9 | 2023-02-03 : Thomas : BL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -35,22 +37,22 @@ timeline |
| 35 | 37 | |FL |No |No |31.614 | 0.000 | |
| 36 | 38 | |
| 37 | 39 | |
| 38 | -> [!NOTE] |
|
| 39 | -> First described in BL in 2023 by [Thomas N](https://pubmed.ncbi.nlm.nih.gov/36201743). First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567) |
|
| 40 | 40 | |
| 41 | 41 | |
| 42 | 42 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PHF6_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PHF6_protein_hg38.html) |
| 43 | 43 | |
| 44 | - |
|
| 44 | + |
|
| 45 | 45 | |
| 46 | 46 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PHF6.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PHF6_hg38.html) |
| 47 | 47 | |
| 48 | - |
|
| 48 | + |
|
| 49 | + |
|
| 49 | 50 | ## PHF6 Expression |
| 50 | - |
|
| 51 | + |
|
| 51 | 52 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
| 52 | 53 | <!-- BL: thomasGeneticSubgroupsInform2023 --> |
| 53 | 54 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 55 | + |
|
| 54 | 56 | ## References |
| 55 | 57 | 1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
| 56 | 58 | 2. Thomas N, Dreval K, Gerhard DS, Hilton LK, Abramson JS, Ambinder RF, Barta S, Bartlett NL, Bethony J, Bhatia K, Bowen J, Bryan AC, Cesarman E, Casper C, Chadburn A, Cruz M, Dittmer DP, Dyer MA, Farinha P, Gastier-Foster JM, Gerrie AS, Grande BM, Greiner T, Griner NB, Gross TG, Harris NL, Irvin JD, Jaffe ES, Henry D, Huppi R, Leal FE, Lee MS, Martin JP, Martin MR, Mbulaiteye SM, Mitsuyasu R, Morris V, Mullighan CG, Mungall AJ, Mungall K, Mutyaba I, Nokta M, Namirembe C, Noy A, Ogwang MD, Omoding A, Orem J, Ott G, Petrello H, Pittaluga S, Phelan JD, Ramos JC, Ratner L, Reynolds SJ, Rubinstein PG, Sissolak G, Slack G, Soudi S, Swerdlow SH, Traverse-Glehen A, Wilson WH, Wong J, Yarchoan R, ZenKlusen JC, Marra MA, Staudt LM, Scott DW, Morin RD. Genetic subgroups inform on pathobiology in adult and pediatric Burkitt lymphoma. Blood. 2023 Feb 23;141(8):904–916. |
PIK3CD.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PIK3CD |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2017-10-10 : Reddy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -42,14 +44,16 @@ timeline |
| 42 | 44 | |
| 43 | 45 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PIK3CD_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PIK3CD_protein_hg38.html) |
| 44 | 46 | |
| 45 | - |
|
| 47 | + |
|
| 46 | 48 | |
| 47 | 49 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PIK3CD.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PIK3CD_hg38.html) |
| 48 | 50 | |
| 49 | - |
|
| 51 | + |
|
| 52 | + |
|
| 50 | 53 | ## PIK3CD Expression |
| 51 | - |
|
| 54 | + |
|
| 52 | 55 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
| 53 | 56 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 57 | + |
|
| 54 | 58 | ## References |
| 55 | 59 | 1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
PIK3R1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PIK3R1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2013-01-01 : Zhang : DLBCL |
| 8 | 9 | 2019-09-26 : Panea : BL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -35,22 +37,22 @@ timeline |
| 35 | 37 | |FL |No |No |0.000 |14.389 | |
| 36 | 38 | |
| 37 | 39 | |
| 38 | -> [!NOTE] |
|
| 39 | -> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937) |
|
| 40 | 40 | |
| 41 | 41 | |
| 42 | 42 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PIK3R1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PIK3R1_protein_hg38.html) |
| 43 | 43 | |
| 44 | - |
|
| 44 | + |
|
| 45 | 45 | |
| 46 | 46 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PIK3R1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PIK3R1_hg38.html) |
| 47 | 47 | |
| 48 | - |
|
| 48 | + |
|
| 49 | + |
|
| 49 | 50 | ## PIK3R1 Expression |
| 50 | - |
|
| 51 | + |
|
| 51 | 52 | <!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 --> |
| 52 | 53 | <!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 --> |
| 53 | 54 | <!-- BL: paneaWholeGenomeLandscape2019 --> |
| 55 | + |
|
| 54 | 56 | ## References |
| 55 | 57 | 1. Zhang J, Grubor V, Love CL, Banerjee A, Richards KL, Mieczkowski PA, Dunphy C, Choi W, Au WY, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers C, Naresh K, Evens A, Gordon LI, Czader M, Gill JI, Hsi ED, Liu Q, Fan A, Walsh K, Jima D, Smith LL, Johnson AJ, Byrd JC, Luftig MA, Ni T, Zhu J, Chadburn A, Levy S, Dunson D, Dave SS. Genetic heterogeneity of diffuse large B-cell lymphoma. 2013 Jan; |
| 56 | 58 | 2. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019; |
PIM1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PIM1 |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | PIM1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. |
| 4 | 5 | ## History |
| ... | ... | @@ -10,6 +11,7 @@ timeline |
| 10 | 11 | 2021-07-15 : Duns : PMBL |
| 11 | 12 | 2022-07-06 : Burkhardt : BL |
| 12 | 13 | ``` |
| 14 | + |
|
| 13 | 15 | ## Relevance tier by entity |
| 14 | 16 | |
| 15 | 17 | |Entity|Tier|Description | |
| ... | ... | @@ -46,8 +48,6 @@ timeline |
| 46 | 48 | |:--------:|:----------:|:--------:|:-----------------------------------------------------------------------------------------:|:------------------:| |
| 47 | 49 | |chr6 |37138104 |37139804|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr6%3A37138104%2D37139804)|active_promoter | |
| 48 | 50 | |
| 49 | -> [!NOTE] |
|
| 50 | -> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096). First described in DLBCL in 2001 by [Pasqualucci L](https://pubmed.ncbi.nlm.nih.gov/11460166) |
|
| 51 | 51 | |
| 52 | 52 | |
| 53 | 53 | ## PIM1 Hotspots |
| ... | ... | @@ -77,17 +77,19 @@ timeline |
| 77 | 77 | |
| 78 | 78 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PIM1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PIM1_protein_hg38.html) |
| 79 | 79 | |
| 80 | - |
|
| 80 | + |
|
| 81 | 81 | |
| 82 | 82 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PIM1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PIM1_hg38.html) |
| 83 | 83 | |
| 84 | - |
|
| 84 | + |
|
| 85 | + |
|
| 85 | 86 | ## PIM1 Expression |
| 86 | - |
|
| 87 | + |
|
| 87 | 88 | <!-- ORIGIN: pasqualucciHypermutationMultipleProtooncogenes2001a --> |
| 88 | 89 | <!-- BL: burkhardtClinicalRelevanceMolecular2022b --> |
| 89 | 90 | <!-- BL: burkhardtClinicalRelevanceMolecular2022b --> |
| 90 | 91 | <!-- DLBCL: pasqualucciHypermutationMultipleProtooncogenes2001a --> |
| 92 | + |
|
| 91 | 93 | ## References |
| 92 | 94 | 1. Pasqualucci L, Neumeister P, Goossens T, Nanjangud G, Chaganti RS, Küppers R, Dalla-Favera R. Hypermutation of multiple proto-oncogenes in B-cell diffuse large-cell lymphomas. Nature. 2001 Jul 19;412(6844):341–346. PMID: 11460166 |
| 93 | 95 | 2. Duns G, Viganò E, Ennishi D, Sarkozy C, Hung SS, Chavez E, Takata K, Rushton C, Jiang A, Ben-Neriah S, Woolcock BW, Slack GW, Hsi ED, Craig JW, Hilton LK, Shah SP, Farinha P, Mottok A, Gascoyne RD, Morin RD, Savage KJ, Scott DW, Steidl C. Characterization of DLBCL with a PMBL gene expression signature. Blood. 2021 Jul 15;138(2):136–148. PMID: 33684939 |
PIM2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PIM2 |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | PIM2 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. |
| 4 | 5 | ## History |
| ... | ... | @@ -10,6 +11,7 @@ timeline |
| 10 | 11 | 2015-02-12 : Reichel : PMBL |
| 11 | 12 | 2018-10-01 : Arthur : DLBCL |
| 12 | 13 | ``` |
| 14 | + |
|
| 13 | 15 | ## Relevance tier by entity |
| 14 | 16 | |
| 15 | 17 | |Entity|Tier|Description | |
| ... | ... | @@ -43,16 +45,18 @@ timeline |
| 43 | 45 | |
| 44 | 46 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PIM2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PIM2_protein_hg38.html) |
| 45 | 47 | |
| 46 | - |
|
| 48 | + |
|
| 47 | 49 | |
| 48 | 50 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PIM2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PIM2_hg38.html) |
| 49 | 51 | |
| 50 | - |
|
| 52 | + |
|
| 53 | + |
|
| 51 | 54 | ## PIM2 Expression |
| 52 | - |
|
| 55 | + |
|
| 53 | 56 | <!-- ORIGIN: reichelFlowSortingExome2015a --> |
| 54 | 57 | <!-- DLBCL: arthurGenomewideDiscoverySomatic2018 --> |
| 55 | 58 | <!-- PMBL: reichelFlowSortingExome2015a --> |
| 59 | + |
|
| 56 | 60 | ## References |
| 57 | 61 | 1. Reichel J, Chadburn A, Rubinstein PG, Giulino-Roth L, Tam W, Liu Y, Gaiolla R, Eng K, Brody J, Inghirami G, Carlo-Stella C, Santoro A, Rahal D, Totonchy J, Elemento O, Cesarman E, Roshal M. Flow sorting and exome sequencing reveal the oncogenome of primary Hodgkin and Reed-Sternberg cells. Blood. 2015 Feb 12;125(7):1061–1072. PMID: 25488972 |
| 58 | 62 | 2. Arthur SE, Jiang A, Grande BM, Alcaide M, Cojocaru R, Rushton CK, Mottok A, Hilton LK, Lat PK, Zhao EY, Culibrk L, Ennishi D, Jessa S, Chong L, Thomas N, Pararajalingam P, Meissner B, Boyle M, Davidson J, Bushell KR, Lai D, Farinha P, Slack GW, Morin GB, Shah S, Sen D, Jones SJM, Mungall AJ, Gascoyne RD, Audas TE, Unrau P, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma. Nat Commun. 2018 Oct 1;9(1):4001. PMCID: PMC6167379 |
PKD1.md
| ... | ... | @@ -7,6 +7,7 @@ timeline |
| 7 | 7 | title Publication timing |
| 8 | 8 | 2013-08-15 : Morin : DLBCL |
| 9 | 9 | ``` |
| 10 | + |
|
| 10 | 11 | ## Relevance tier by entity |
| 11 | 12 | |
| 12 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -34,14 +35,16 @@ timeline |
| 34 | 35 | |
| 35 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PKD1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PKD1_protein_hg38.html) |
| 36 | 37 | |
| 37 | - |
|
| 38 | + |
|
| 38 | 39 | |
| 39 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PKD1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PKD1_hg38.html) |
| 40 | 41 | |
| 41 | - |
|
| 42 | + |
|
| 43 | + |
|
| 42 | 44 | ## PKD1 Expression |
| 43 | - |
|
| 45 | + |
|
| 44 | 46 | <!-- ORIGIN: morinMutationalStructuralAnalysis2013 --> |
| 45 | 47 | <!-- DLBCL: morinMutationalStructuralAnalysis2013 --> |
| 48 | + |
|
| 46 | 49 | ## References |
| 47 | 50 | 1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992 |
PLCG2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PLCG2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2019-09-26 : Panea : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -39,14 +41,16 @@ timeline |
| 39 | 41 | |
| 40 | 42 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PLCG2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PLCG2_protein_hg38.html) |
| 41 | 43 | |
| 42 | - |
|
| 44 | + |
|
| 43 | 45 | |
| 44 | 46 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PLCG2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PLCG2_hg38.html) |
| 45 | 47 | |
| 46 | - |
|
| 48 | + |
|
| 49 | + |
|
| 47 | 50 | ## PLCG2 Expression |
| 48 | - |
|
| 51 | + |
|
| 49 | 52 | <!-- ORIGIN: paneaWholeGenomeLandscape2019 --> |
| 50 | 53 | <!-- BL: paneaWholeGenomeLandscape2019 --> |
| 54 | + |
|
| 51 | 55 | ## References |
| 52 | 56 | 1. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019; |
PLXNB3.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PLXNB3 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2014-05-08 : Zhang : MCL |
| 8 | 9 | 2016-09-08 : Spina : MZL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -32,16 +34,18 @@ timeline |
| 32 | 34 | |
| 33 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PLXNB3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PLXNB3_protein_hg38.html) |
| 34 | 36 | |
| 35 | - |
|
| 37 | + |
|
| 36 | 38 | |
| 37 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PLXNB3.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PLXNB3_hg38.html) |
| 38 | 40 | |
| 39 | - |
|
| 41 | + |
|
| 42 | + |
|
| 40 | 43 | ## PLXNB3 Expression |
| 41 | - |
|
| 44 | + |
|
| 42 | 45 | <!-- ORIGIN: zhangGenomicLandscapeMantle2014 --> |
| 43 | 46 | <!-- MCL: zhangGenomicLandscapeMantle2014 --> |
| 44 | 47 | <!-- MZL: spinaGeneticsNodalMarginal2016b --> |
| 48 | + |
|
| 45 | 49 | ## References |
| 46 | 50 | 1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996. |
| 47 | 51 | 2. Spina V, Khiabanian H, Messina M, Monti S, Cascione L, Bruscaggin A, Spaccarotella E, Holmes AB, Arcaini L, Lucioni M, Tabbò F, Zairis S, Diop F, Cerri M, Chiaretti S, Marasca R, Ponzoni M, Deaglio S, Ramponi A, Tiacci E, Pasqualucci L, Paulli M, Falini B, Inghirami G, Bertoni F, Foà R, Rabadan R, Gaidano G, Rossi D. The genetics of nodal marginal zone lymphoma. Blood. 2016 Sep 8;128(10):1362–1373. |
PNPO.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PNPO |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschmann et al.<sup>1</sup> |
| 4 | 5 | |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | title Publication timing |
| 9 | 10 | 2021-05-05 : Hübschmann : DLBCL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -34,13 +36,14 @@ timeline |
| 34 | 36 | |
| 35 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PNPO_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PNPO_protein_hg38.html) |
| 36 | 38 | |
| 37 | - |
|
| 39 | + |
|
| 38 | 40 | |
| 39 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PNPO.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PNPO_hg38.html) |
| 40 | 42 | |
| 41 | - |
|
| 43 | + |
|
| 44 | + |
|
| 42 | 45 | ## PNPO Expression |
| 43 | - |
|
| 46 | + |
|
| 44 | 47 | |
| 45 | 48 | ## References |
| 46 | 49 | 1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491 |
POGZ.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # POGZ |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2013-08-15 : Morin : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -33,14 +35,16 @@ timeline |
| 33 | 35 | |
| 34 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/POGZ_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/POGZ_protein_hg38.html) |
| 35 | 37 | |
| 36 | - |
|
| 38 | + |
|
| 37 | 39 | |
| 38 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/POGZ.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/POGZ_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 43 | + |
|
| 41 | 44 | ## POGZ Expression |
| 42 | - |
|
| 45 | + |
|
| 43 | 46 | <!-- ORIGIN: morinMutationalStructuralAnalysis2013 --> |
| 44 | 47 | <!-- DLBCL: morinMutationalStructuralAnalysis2013 --> |
| 48 | + |
|
| 45 | 49 | ## References |
| 46 | 50 | 1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992 |
POLRMT.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # POLRMT |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -31,14 +33,16 @@ timeline |
| 31 | 33 | |
| 32 | 34 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/POLRMT_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/POLRMT_protein_hg38.html) |
| 33 | 35 | |
| 34 | - |
|
| 36 | + |
|
| 35 | 37 | |
| 36 | 38 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/POLRMT.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/POLRMT_hg38.html) |
| 37 | 39 | |
| 38 | - |
|
| 40 | + |
|
| 41 | + |
|
| 39 | 42 | ## POLRMT Expression |
| 40 | - |
|
| 43 | + |
|
| 41 | 44 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 42 | 45 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 46 | + |
|
| 43 | 47 | ## References |
| 44 | 48 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
POR.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # POR |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -32,14 +34,16 @@ timeline |
| 32 | 34 | |
| 33 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/POR_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/POR_protein_hg38.html) |
| 34 | 36 | |
| 35 | - |
|
| 37 | + |
|
| 36 | 38 | |
| 37 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/POR.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/POR_hg38.html) |
| 38 | 40 | |
| 39 | - |
|
| 41 | + |
|
| 42 | + |
|
| 40 | 43 | ## POR Expression |
| 41 | - |
|
| 44 | + |
|
| 42 | 45 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 43 | 46 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 47 | + |
|
| 44 | 48 | ## References |
| 45 | 49 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
POT1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # POT1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | |
| 4 | 5 | ```mermaid |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | title Publication timing |
| 8 | 9 | 2014-05-08 : Zhang : MCL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -28,20 +30,20 @@ timeline |
| 28 | 30 | |FL |No |No |0.000 |18.704 | |
| 29 | 31 | |
| 30 | 32 | |
| 31 | -> [!NOTE] |
|
| 32 | -> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267) |
|
| 33 | 33 | |
| 34 | 34 | |
| 35 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/POT1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/POT1_protein_hg38.html) |
| 36 | 36 | |
| 37 | - |
|
| 37 | + |
|
| 38 | 38 | |
| 39 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/POT1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/POT1_hg38.html) |
| 40 | 40 | |
| 41 | - |
|
| 41 | + |
|
| 42 | + |
|
| 42 | 43 | ## POT1 Expression |
| 43 | - |
|
| 44 | + |
|
| 44 | 45 | <!-- ORIGIN: zhangGenomicLandscapeMantle2014 --> |
| 45 | 46 | <!-- MCL: zhangGenomicLandscapeMantle2014 --> |
| 47 | + |
|
| 46 | 48 | ## References |
| 47 | 49 | 1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996. |
POU2AF1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # POU2AF1 |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | POU2AF1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. |
| 4 | 5 | ## History |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | title Publication timing |
| 9 | 10 | 2017-01-26 : Krysiak : FL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -54,14 +56,16 @@ timeline |
| 54 | 56 | |
| 55 | 57 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/POU2AF1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/POU2AF1_protein_hg38.html) |
| 56 | 58 | |
| 57 | - |
|
| 59 | + |
|
| 58 | 60 | |
| 59 | 61 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/POU2AF1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/POU2AF1_hg38.html) |
| 60 | 62 | |
| 61 | - |
|
| 63 | + |
|
| 64 | + |
|
| 62 | 65 | ## POU2AF1 Expression |
| 63 | - |
|
| 66 | + |
|
| 64 | 67 | <!-- ORIGIN: krysiakRecurrentSomaticMutations2017b --> |
| 65 | 68 | <!-- FL: krysiakRecurrentSomaticMutations2017b --> |
| 69 | + |
|
| 66 | 70 | ## References |
| 67 | 71 | 1. Krysiak K, Gomez F, White BS, Matlock M, Miller CA, Trani L, Fronick CC, Fulton RS, Kreisel F, Cashen AF, Carson KR, Berrien-Elliott MM, Bartlett NL, Griffith M, Griffith OL, Fehniger TA. Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma. Blood. 2017 Jan 26;129(4):473–483. PMCID: PMC5270390 |
POU2F2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # POU2F2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2013-01-01 : Zhang : DLBCL |
| 8 | 9 | 2017-01-26 : Krysiak : FL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -46,16 +48,18 @@ timeline |
| 46 | 48 | |
| 47 | 49 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/POU2F2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/POU2F2_protein_hg38.html) |
| 48 | 50 | |
| 49 | - |
|
| 51 | + |
|
| 50 | 52 | |
| 51 | 53 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/POU2F2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/POU2F2_hg38.html) |
| 52 | 54 | |
| 53 | - |
|
| 55 | + |
|
| 56 | + |
|
| 54 | 57 | ## POU2F2 Expression |
| 55 | - |
|
| 58 | + |
|
| 56 | 59 | <!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 --> |
| 57 | 60 | <!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 --> |
| 58 | 61 | <!-- FL: krysiakRecurrentSomaticMutations2017b --> |
| 62 | + |
|
| 59 | 63 | ## References |
| 60 | 64 | 1. Zhang J, Grubor V, Love CL, Banerjee A, Richards KL, Mieczkowski PA, Dunphy C, Choi W, Au WY, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers C, Naresh K, Evens A, Gordon LI, Czader M, Gill JI, Hsi ED, Liu Q, Fan A, Walsh K, Jima D, Smith LL, Johnson AJ, Byrd JC, Luftig MA, Ni T, Zhu J, Chadburn A, Levy S, Dunson D, Dave SS. Genetic heterogeneity of diffuse large B-cell lymphoma. 2013 Jan; |
| 61 | 65 | 2. Krysiak K, Gomez F, White BS, Matlock M, Miller CA, Trani L, Fronick CC, Fulton RS, Kreisel F, Cashen AF, Carson KR, Berrien-Elliott MM, Bartlett NL, Griffith M, Griffith OL, Fehniger TA. Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma. Blood. 2017 Jan 26;129(4):473–483. PMCID: PMC5270390 |
PPP1R9B.md
| ... | ... | @@ -29,12 +29,13 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM |
| 29 | 29 | |
| 30 | 30 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PPP1R9B.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PPP1R9B_hg38.html) |
| 31 | 31 | |
| 32 | - |
|
| 32 | + |
|
| 33 | 33 | |
| 34 | 34 | ## PPP1R9B Expression |
| 35 | - |
|
| 35 | + |
|
| 36 | 36 | |
| 37 | 37 | <!-- FLAGGED FOR TIER 2 --> |
| 38 | 38 | |
| 39 | 39 | <!-- ORIGIN: Unknown --> |
| 40 | + |
|
| 40 | 41 | ## References |
PPP4C.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PPP4C |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2021-05-05 : H : FL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -35,14 +37,16 @@ timeline |
| 35 | 37 | |
| 36 | 38 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PPP4C_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PPP4C_protein_hg38.html) |
| 37 | 39 | |
| 38 | - |
|
| 40 | + |
|
| 39 | 41 | |
| 40 | 42 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PPP4C.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PPP4C_hg38.html) |
| 41 | 43 | |
| 42 | - |
|
| 44 | + |
|
| 45 | + |
|
| 43 | 46 | ## PPP4C Expression |
| 44 | - |
|
| 47 | + |
|
| 45 | 48 | <!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b --> |
| 46 | 49 | <!-- FL: hubschmannMutationalMechanismsShaping2021b --> |
| 50 | + |
|
| 47 | 51 | ## References |
| 48 | 52 | 1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491 |
PPP6R2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PPP6R2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2022-07-06 : Burkhardt : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -33,14 +35,16 @@ timeline |
| 33 | 35 | |
| 34 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PPP6R2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PPP6R2_protein_hg38.html) |
| 35 | 37 | |
| 36 | - |
|
| 38 | + |
|
| 37 | 39 | |
| 38 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PPP6R2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PPP6R2_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 43 | + |
|
| 41 | 44 | ## PPP6R2 Expression |
| 42 | - |
|
| 45 | + |
|
| 43 | 46 | <!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b --> |
| 44 | 47 | <!-- BL: burkhardtClinicalRelevanceMolecular2022b --> |
| 48 | + |
|
| 45 | 49 | ## References |
| 46 | 50 | 1. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584 |
PRDM1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PRDM1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2006-02-02 : Pasqualucci : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -35,8 +37,6 @@ timeline |
| 35 | 37 | |
| 36 | 38 | |
| 37 | 39 | |
| 38 | -> [!NOTE] |
|
| 39 | -> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601) |
|
| 40 | 40 | |
| 41 | 41 | ## PRDM1 Hotspots |
| 42 | 42 | |
| ... | ... | @@ -52,15 +52,17 @@ timeline |
| 52 | 52 | |
| 53 | 53 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PRDM1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PRDM1_protein_hg38.html) |
| 54 | 54 | |
| 55 | - |
|
| 55 | + |
|
| 56 | 56 | |
| 57 | 57 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PRDM1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PRDM1_hg38.html) |
| 58 | 58 | |
| 59 | - |
|
| 59 | + |
|
| 60 | + |
|
| 60 | 61 | ## PRDM1 Expression |
| 61 | - |
|
| 62 | + |
|
| 62 | 63 | <!-- ORIGIN: pasqualucciInactivationPRDM1BLIMP12006 --> |
| 63 | 64 | <!-- DLBCL: pasqualucciInactivationPRDM1BLIMP12006 --> |
| 64 | 65 | <!-- BL: 2 --> |
| 66 | + |
|
| 65 | 67 | ## References |
| 66 | 68 | 1. Pasqualucci L, Compagno M, Houldsworth J, Monti S, Grunn A, Nandula SV, Aster JC, Murty VV, Shipp MA, Dalla-Favera R. Inactivation of the PRDM1/BLIMP1 gene in diffuse large B cell lymphoma. J Exp Med. 2006 Feb;203(2):311–317. |
PREX1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PREX1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2022-07-06 : Burkhardt : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -33,14 +35,16 @@ timeline |
| 33 | 35 | |
| 34 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PREX1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PREX1_protein_hg38.html) |
| 35 | 37 | |
| 36 | - |
|
| 38 | + |
|
| 37 | 39 | |
| 38 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PREX1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PREX1_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 43 | + |
|
| 41 | 44 | ## PREX1 Expression |
| 42 | - |
|
| 45 | + |
|
| 43 | 46 | <!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b --> |
| 44 | 47 | <!-- BL: burkhardtClinicalRelevanceMolecular2022b --> |
| 48 | + |
|
| 45 | 49 | ## References |
| 46 | 50 | 1. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584 |
PRKCB.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PRKCB |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2013-08-15 : Morin : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -33,14 +35,16 @@ timeline |
| 33 | 35 | |
| 34 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PRKCB_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PRKCB_protein_hg38.html) |
| 35 | 37 | |
| 36 | - |
|
| 38 | + |
|
| 37 | 39 | |
| 38 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PRKCB.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PRKCB_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 43 | + |
|
| 41 | 44 | ## PRKCB Expression |
| 42 | - |
|
| 45 | + |
|
| 43 | 46 | <!-- ORIGIN: morinMutationalStructuralAnalysis2013 --> |
| 44 | 47 | <!-- DLBCL: morinMutationalStructuralAnalysis2013 --> |
| 48 | + |
|
| 45 | 49 | ## References |
| 46 | 50 | 1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992 |
PRKDC.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PRKDC |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2018-04-12 : Schmitz : DLBCL |
| 8 | 9 | 2021-05-05 : H : FL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -34,22 +36,22 @@ timeline |
| 34 | 36 | |FL |No |No |0.000 |7.794 | |
| 35 | 37 | |
| 36 | 38 | |
| 37 | -> [!NOTE] |
|
| 38 | -> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289) |
|
| 39 | 39 | |
| 40 | 40 | |
| 41 | 41 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PRKDC_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PRKDC_protein_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | 44 | |
| 45 | 45 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PRKDC.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PRKDC_hg38.html) |
| 46 | 46 | |
| 47 | - |
|
| 47 | + |
|
| 48 | + |
|
| 48 | 49 | ## PRKDC Expression |
| 49 | - |
|
| 50 | + |
|
| 50 | 51 | <!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a --> |
| 51 | 52 | <!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a --> |
| 52 | 53 | <!-- FL: hubschmannMutationalMechanismsShaping2021b --> |
| 54 | + |
|
| 53 | 55 | ## References |
| 54 | 56 | 1. Schmitz R, Wright GW, Huang DW, Johnson CA, Phelan JD, Wang JQ, Roulland S, Kasbekar M, Young RM, Shaffer AL, Hodson DJ, Xiao W, Yu X, Yang Y, Zhao H, Xu W, Liu X, Zhou B, Du W, Chan WC, Jaffe ES, Gascoyne RD, Connors JM, Campo E, Lopez-Guillermo A, Rosenwald A, Ott G, Delabie J, Rimsza LM, Tay Kuang Wei K, Zelenetz AD, Leonard JP, Bartlett NL, Tran B, Shetty J, Zhao Y, Soppet DR, Pittaluga S, Wilson WH, Staudt LM. Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma. N Engl J Med. 2018 Apr 12;378(15):1396–1407. PMCID: PMC6010183 |
| 55 | 57 | 2. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491 |
PRPS1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PRPS1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2018-05-01 : Chapuy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -34,14 +36,16 @@ timeline |
| 34 | 36 | |
| 35 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PRPS1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PRPS1_protein_hg38.html) |
| 36 | 38 | |
| 37 | - |
|
| 39 | + |
|
| 38 | 40 | |
| 39 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PRPS1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PRPS1_hg38.html) |
| 40 | 42 | |
| 41 | - |
|
| 43 | + |
|
| 44 | + |
|
| 42 | 45 | ## PRPS1 Expression |
| 43 | - |
|
| 46 | + |
|
| 44 | 47 | <!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b --> |
| 45 | 48 | <!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b --> |
| 49 | + |
|
| 46 | 50 | ## References |
| 47 | 51 | 1. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387 |
PRSS22.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PRSS22 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -33,14 +35,16 @@ timeline |
| 33 | 35 | |
| 34 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PRSS22_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PRSS22_protein_hg38.html) |
| 35 | 37 | |
| 36 | - |
|
| 38 | + |
|
| 37 | 39 | |
| 38 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PRSS22.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PRSS22_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 43 | + |
|
| 41 | 44 | ## PRSS22 Expression |
| 42 | - |
|
| 45 | + |
|
| 43 | 46 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 44 | 47 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 48 | + |
|
| 45 | 49 | ## References |
| 46 | 50 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
PTEN.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PTEN |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -37,14 +39,16 @@ timeline |
| 37 | 39 | |
| 38 | 40 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PTEN_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PTEN_protein_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 41 | 43 | |
| 42 | 44 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PTEN.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PTEN_hg38.html) |
| 43 | 45 | |
| 44 | - |
|
| 46 | + |
|
| 47 | + |
|
| 45 | 48 | ## PTEN Expression |
| 46 | - |
|
| 49 | + |
|
| 47 | 50 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 48 | 51 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 52 | + |
|
| 49 | 53 | ## References |
| 50 | 54 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
PTMA.md
| ... | ... | @@ -32,12 +32,14 @@ |
| 32 | 32 | |
| 33 | 33 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PTMA_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PTMA_protein_hg38.html) |
| 34 | 34 | |
| 35 | - |
|
| 35 | + |
|
| 36 | 36 | |
| 37 | 37 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PTMA.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PTMA_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | + |
|
| 40 | 41 | ## PTMA Expression |
| 41 | - |
|
| 42 | + |
|
| 42 | 43 | <!-- ORIGIN: Unknown --> |
| 44 | + |
|
| 43 | 45 | ## References |
PTPN1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PTPN1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2014-02-16 : Gunawardana : PMBL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -39,14 +41,16 @@ timeline |
| 39 | 41 | |
| 40 | 42 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PTPN1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PTPN1_protein_hg38.html) |
| 41 | 43 | |
| 42 | - |
|
| 44 | + |
|
| 43 | 45 | |
| 44 | 46 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PTPN1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PTPN1_hg38.html) |
| 45 | 47 | |
| 46 | - |
|
| 48 | + |
|
| 49 | + |
|
| 47 | 50 | ## PTPN1 Expression |
| 48 | - |
|
| 51 | + |
|
| 49 | 52 | <!-- ORIGIN: gunawardanaRecurrentSomaticMutations2014c --> |
| 50 | 53 | <!-- PMBL: gunawardanaRecurrentSomaticMutations2014c --> |
| 54 | + |
|
| 51 | 55 | ## References |
| 52 | 56 | 1. Gunawardana J, Chan FC, Telenius A, Woolcock B, Kridel R, Tan KL, Ben-Neriah S, Mottok A, Lim RS, Boyle M, Rogic S, Rimsza LM, Guiter C, Leroy K, Gaulard P, Haioun C, Marra MA, Savage KJ, Connors JM, Shah SP, Gascoyne RD, Steidl C. Recurrent somatic mutations of PTPN1 in primary mediastinal B cell lymphoma and Hodgkin lymphoma. Nat Genet. 2014 Apr;46(4):329–335. PMID: 24531327 |
PTPN23.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PTPN23 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2013-08-15 : Morin : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,20 +32,20 @@ timeline |
| 30 | 32 | |FL |No |No |0.000 |0 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601) |
|
| 35 | 35 | |
| 36 | 36 | |
| 37 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PTPN23_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PTPN23_protein_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | 40 | |
| 41 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PTPN23.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PTPN23_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | + |
|
| 44 | 45 | ## PTPN23 Expression |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | <!-- ORIGIN: morinMutationalStructuralAnalysis2013 --> |
| 47 | 48 | <!-- DLBCL: morinMutationalStructuralAnalysis2013 --> |
| 49 | + |
|
| 48 | 50 | ## References |
| 49 | 51 | 1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992 |
PTPN6.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PTPN6 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2017-10-10 : Reddy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -33,14 +35,16 @@ timeline |
| 33 | 35 | |
| 34 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PTPN6_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PTPN6_protein_hg38.html) |
| 35 | 37 | |
| 36 | - |
|
| 38 | + |
|
| 37 | 39 | |
| 38 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PTPN6.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PTPN6_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 43 | + |
|
| 41 | 44 | ## PTPN6 Expression |
| 42 | - |
|
| 45 | + |
|
| 43 | 46 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
| 44 | 47 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 48 | + |
|
| 45 | 49 | ## References |
| 46 | 50 | 1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
PTPRD.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PTPRD |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2016-09-08 : Spina : MZL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -44,14 +46,16 @@ timeline |
| 44 | 46 | |
| 45 | 47 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PTPRD_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PTPRD_protein_hg38.html) |
| 46 | 48 | |
| 47 | - |
|
| 49 | + |
|
| 48 | 50 | |
| 49 | 51 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PTPRD.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PTPRD_hg38.html) |
| 50 | 52 | |
| 51 | - |
|
| 53 | + |
|
| 54 | + |
|
| 52 | 55 | ## PTPRD Expression |
| 53 | - |
|
| 56 | + |
|
| 54 | 57 | <!-- ORIGIN: spinaGeneticsNodalMarginal2016b --> |
| 55 | 58 | <!-- MZL: spinaGeneticsNodalMarginal2016b --> |
| 59 | + |
|
| 56 | 60 | ## References |
| 57 | 61 | 1. Spina V, Khiabanian H, Messina M, Monti S, Cascione L, Bruscaggin A, Spaccarotella E, Holmes AB, Arcaini L, Lucioni M, Tabbò F, Zairis S, Diop F, Cerri M, Chiaretti S, Marasca R, Ponzoni M, Deaglio S, Ramponi A, Tiacci E, Pasqualucci L, Paulli M, Falini B, Inghirami G, Bertoni F, Foà R, Rabadan R, Gaidano G, Rossi D. The genetics of nodal marginal zone lymphoma. Blood. 2016 Sep 8;128(10):1362–1373. |
PTPRK.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PTPRK |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2017-10-10 : Reddy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -34,14 +36,16 @@ timeline |
| 34 | 36 | |
| 35 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PTPRK_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PTPRK_protein_hg38.html) |
| 36 | 38 | |
| 37 | - |
|
| 39 | + |
|
| 38 | 40 | |
| 39 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PTPRK.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PTPRK_hg38.html) |
| 40 | 42 | |
| 41 | - |
|
| 43 | + |
|
| 44 | + |
|
| 42 | 45 | ## PTPRK Expression |
| 43 | - |
|
| 46 | + |
|
| 44 | 47 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
| 45 | 48 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 49 | + |
|
| 46 | 50 | ## References |
| 47 | 51 | 1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
PTPRN.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PTPRN |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -32,14 +34,16 @@ timeline |
| 32 | 34 | |
| 33 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PTPRN_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PTPRN_protein_hg38.html) |
| 34 | 36 | |
| 35 | - |
|
| 37 | + |
|
| 36 | 38 | |
| 37 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PTPRN.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PTPRN_hg38.html) |
| 38 | 40 | |
| 39 | - |
|
| 41 | + |
|
| 42 | + |
|
| 40 | 43 | ## PTPRN Expression |
| 41 | - |
|
| 44 | + |
|
| 42 | 45 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 43 | 46 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 47 | + |
|
| 44 | 48 | ## References |
| 45 | 49 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
PXDNL.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PXDNL |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2019-09-26 : Panea : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -32,14 +34,16 @@ timeline |
| 32 | 34 | |
| 33 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PXDNL_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PXDNL_protein_hg38.html) |
| 34 | 36 | |
| 35 | - |
|
| 37 | + |
|
| 36 | 38 | |
| 37 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PXDNL.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PXDNL_hg38.html) |
| 38 | 40 | |
| 39 | - |
|
| 41 | + |
|
| 42 | + |
|
| 40 | 43 | ## PXDNL Expression |
| 41 | - |
|
| 44 | + |
|
| 42 | 45 | <!-- ORIGIN: paneaWholeGenomeLandscape2019 --> |
| 43 | 46 | <!-- BL: paneaWholeGenomeLandscape2019 --> |
| 47 | + |
|
| 44 | 48 | ## References |
| 45 | 49 | 1. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019; |
PZP.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # PZP |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2023-07-26 : Russler : FL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,14 +32,16 @@ timeline |
| 30 | 32 | |
| 31 | 33 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PZP_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PZP_protein_hg38.html) |
| 32 | 34 | |
| 33 | - |
|
| 35 | + |
|
| 34 | 36 | |
| 35 | 37 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PZP.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PZP_hg38.html) |
| 36 | 38 | |
| 37 | - |
|
| 39 | + |
|
| 40 | + |
|
| 38 | 41 | ## PZP Expression |
| 39 | - |
|
| 42 | + |
|
| 40 | 43 | <!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a --> |
| 41 | 44 | <!-- FL: russler-germainMutationsAssociatedProgression2023b --> |
| 45 | + |
|
| 42 | 46 | ## References |
| 43 | 47 | 1. Russler-Germain DA, Krysiak K, Ramirez CA, Mosior M, Watkins MP, Gomez F, Skidmore ZL, Trani L, Gao F, Geyer S, Cashen A, Mehta-Shah N, Kahl B, Bartlett N, Alderuccio J, Lossos I, Ondrejka S, Hsi E, Martin P, Leonard J, Griffith M, Griffith O, Fehniger T. Mutations associated with progression in follicular lymphoma predict inferior outcomes at diagnosis: Alliance A151303. Blood Advances. 2023;7:5524–5539. |
RAC2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # RAC2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | Mutations in this gene were first described in BL in 2019 by Panea et al<sup>1</sup> and in DLBCL 2021 by Hübschmann et al.<sup>2</sup> |
| 4 | 5 | |
| ... | ... | @@ -9,6 +10,7 @@ timeline |
| 9 | 10 | 2019-09-26 : Panea : BL |
| 10 | 11 | 2021-05-05 : Hübschmann : DLBCL |
| 11 | 12 | ``` |
| 13 | + |
|
| 12 | 14 | ## Relevance tier by entity |
| 13 | 15 | |
| 14 | 16 | |Entity|Tier|Description | |
| ... | ... | @@ -46,13 +48,14 @@ timeline |
| 46 | 48 | |
| 47 | 49 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RAC2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RAC2_protein_hg38.html) |
| 48 | 50 | |
| 49 | - |
|
| 51 | + |
|
| 50 | 52 | |
| 51 | 53 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RAC2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RAC2_hg38.html) |
| 52 | 54 | |
| 53 | - |
|
| 55 | + |
|
| 56 | + |
|
| 54 | 57 | ## RAC2 Expression |
| 55 | - |
|
| 58 | + |
|
| 56 | 59 | |
| 57 | 60 | ## References |
| 58 | 61 |
RAD9A.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # RAD9A |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2018-05-01 : Chapuy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -32,14 +34,16 @@ timeline |
| 32 | 34 | |
| 33 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RAD9A_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RAD9A_protein_hg38.html) |
| 34 | 36 | |
| 35 | - |
|
| 37 | + |
|
| 36 | 38 | |
| 37 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RAD9A.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RAD9A_hg38.html) |
| 38 | 40 | |
| 39 | - |
|
| 41 | + |
|
| 42 | + |
|
| 40 | 43 | ## RAD9A Expression |
| 41 | - |
|
| 44 | + |
|
| 42 | 45 | <!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b --> |
| 43 | 46 | <!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b --> |
| 47 | + |
|
| 44 | 48 | ## References |
| 45 | 49 | 1. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387 |
RANBP6.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # RANBP6 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -32,14 +34,16 @@ timeline |
| 32 | 34 | |
| 33 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RANBP6_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RANBP6_protein_hg38.html) |
| 34 | 36 | |
| 35 | - |
|
| 37 | + |
|
| 36 | 38 | |
| 37 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RANBP6.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RANBP6_hg38.html) |
| 38 | 40 | |
| 39 | - |
|
| 41 | + |
|
| 42 | + |
|
| 40 | 43 | ## RANBP6 Expression |
| 41 | - |
|
| 44 | + |
|
| 42 | 45 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 43 | 46 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 47 | + |
|
| 44 | 48 | ## References |
| 45 | 49 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
RARA.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # RARA |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2017-10-10 : Reddy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -33,14 +35,16 @@ timeline |
| 33 | 35 | |
| 34 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RARA_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RARA_protein_hg38.html) |
| 35 | 37 | |
| 36 | - |
|
| 38 | + |
|
| 37 | 39 | |
| 38 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RARA.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RARA_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 43 | + |
|
| 41 | 44 | ## RARA Expression |
| 42 | - |
|
| 45 | + |
|
| 43 | 46 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
| 44 | 47 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 48 | + |
|
| 45 | 49 | ## References |
| 46 | 50 | 1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
RB1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # RB1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | |
| 4 | 5 | ```mermaid |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | 2013-08-15 : Morin : DLBCL |
| 9 | 10 | 2014-05-08 : Zhang : MCL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -34,22 +36,22 @@ timeline |
| 34 | 36 | |FL |No |No |1.890 | 0.000 | |
| 35 | 37 | |
| 36 | 38 | |
| 37 | -> [!NOTE] |
|
| 38 | -> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601). First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267) |
|
| 39 | 39 | |
| 40 | 40 | |
| 41 | 41 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RB1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RB1_protein_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | 44 | |
| 45 | 45 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RB1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RB1_hg38.html) |
| 46 | 46 | |
| 47 | - |
|
| 47 | + |
|
| 48 | + |
|
| 48 | 49 | ## RB1 Expression |
| 49 | - |
|
| 50 | + |
|
| 50 | 51 | <!-- ORIGIN: morinMutationalStructuralAnalysis2013 --> |
| 51 | 52 | <!-- DLBCL: morinMutationalStructuralAnalysis2013 --> |
| 52 | 53 | <!-- MCL: zhangGenomicLandscapeMantle2014 --> |
| 54 | + |
|
| 53 | 55 | ## References |
| 54 | 56 | 1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992 |
| 55 | 57 | 2. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996. |
RBM6.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # RBM6 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschmann et al.<sup>1</sup> |
| 4 | 5 | |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | title Publication timing |
| 9 | 10 | 2021-05-05 : Hübschmann : FL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -31,13 +33,14 @@ timeline |
| 31 | 33 | |
| 32 | 34 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RBM6_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RBM6_protein_hg38.html) |
| 33 | 35 | |
| 34 | - |
|
| 36 | + |
|
| 35 | 37 | |
| 36 | 38 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RBM6.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RBM6_hg38.html) |
| 37 | 39 | |
| 38 | - |
|
| 40 | + |
|
| 41 | + |
|
| 39 | 42 | ## RBM6 Expression |
| 40 | - |
|
| 43 | + |
|
| 41 | 44 | |
| 42 | 45 | ## References |
| 43 | 46 | 1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491 |
RBP3.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # RBP3 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -32,14 +34,16 @@ timeline |
| 32 | 34 | |
| 33 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RBP3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RBP3_protein_hg38.html) |
| 34 | 36 | |
| 35 | - |
|
| 37 | + |
|
| 36 | 38 | |
| 37 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RBP3.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RBP3_hg38.html) |
| 38 | 40 | |
| 39 | - |
|
| 41 | + |
|
| 42 | + |
|
| 40 | 43 | ## RBP3 Expression |
| 41 | - |
|
| 44 | + |
|
| 42 | 45 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 43 | 46 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 47 | + |
|
| 44 | 48 | ## References |
| 45 | 49 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
RET.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # RET |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -29,20 +31,20 @@ timeline |
| 29 | 31 | |FL |No |No |0.000 |0 | |
| 30 | 32 | |
| 31 | 33 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597) |
|
| 34 | 34 | |
| 35 | 35 | |
| 36 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RET_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RET_protein_hg38.html) |
| 37 | 37 | |
| 38 | - |
|
| 38 | + |
|
| 39 | 39 | |
| 40 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RET.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RET_hg38.html) |
| 41 | 41 | |
| 42 | - |
|
| 42 | + |
|
| 43 | + |
|
| 43 | 44 | ## RET Expression |
| 44 | - |
|
| 45 | + |
|
| 45 | 46 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 46 | 47 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 48 | + |
|
| 47 | 49 | ## References |
| 48 | 50 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
REV3L.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # REV3L |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2022-07-06 : Burkhardt : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -33,14 +35,16 @@ timeline |
| 33 | 35 | |
| 34 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/REV3L_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/REV3L_protein_hg38.html) |
| 35 | 37 | |
| 36 | - |
|
| 38 | + |
|
| 37 | 39 | |
| 38 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/REV3L.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/REV3L_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 43 | + |
|
| 41 | 44 | ## REV3L Expression |
| 42 | - |
|
| 45 | + |
|
| 43 | 46 | <!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b --> |
| 44 | 47 | <!-- BL: burkhardtClinicalRelevanceMolecular2022b --> |
| 48 | + |
|
| 45 | 49 | ## References |
| 46 | 50 | 1. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584 |
RFTN1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # RFTN1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2018-10-01 : Arthur : DLBCL |
| 8 | 9 | 2021-07-15 : Duns : PMBL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -38,22 +40,22 @@ timeline |
| 38 | 40 | |:--------:|:----------:|:--------:|:-----------------------------------------------------------------------------------------:|:-------------------------------:| |
| 39 | 41 | |chr3 |16546433 |16556786|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A16546433%2D16556786)|active_promoter-strong_enhancer| |
| 40 | 42 | |
| 41 | -> [!NOTE] |
|
| 42 | -> First described in DLBCL in 2018 by [Arthur SE](https://pubmed.ncbi.nlm.nih.gov/30275490) |
|
| 43 | 43 | |
| 44 | 44 | |
| 45 | 45 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RFTN1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RFTN1_protein_hg38.html) |
| 46 | 46 | |
| 47 | - |
|
| 47 | + |
|
| 48 | 48 | |
| 49 | 49 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RFTN1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RFTN1_hg38.html) |
| 50 | 50 | |
| 51 | - |
|
| 51 | + |
|
| 52 | + |
|
| 52 | 53 | ## RFTN1 Expression |
| 53 | - |
|
| 54 | + |
|
| 54 | 55 | <!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 --> |
| 55 | 56 | <!-- PMBL: dunsCharacterizationDLBCLPMBL2021b --> |
| 56 | 57 | <!-- DLBCL: arthurGenomewideDiscoverySomatic2018 --> |
| 58 | + |
|
| 57 | 59 | ## References |
| 58 | 60 | 1. Arthur SE, Jiang A, Grande BM, Alcaide M, Cojocaru R, Rushton CK, Mottok A, Hilton LK, Lat PK, Zhao EY, Culibrk L, Ennishi D, Jessa S, Chong L, Thomas N, Pararajalingam P, Meissner B, Boyle M, Davidson J, Bushell KR, Lai D, Farinha P, Slack GW, Morin GB, Shah S, Sen D, Jones SJM, Mungall AJ, Gascoyne RD, Audas TE, Unrau P, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma. Nat Commun. 2018 Oct 1;9(1):4001. PMCID: PMC6167379 |
| 59 | 61 | 2. Duns G, Viganò E, Ennishi D, Sarkozy C, Hung SS, Chavez E, Takata K, Rushton C, Jiang A, Ben-Neriah S, Woolcock BW, Slack GW, Hsi ED, Craig JW, Hilton LK, Shah SP, Farinha P, Mottok A, Gascoyne RD, Morin RD, Savage KJ, Scott DW, Steidl C. Characterization of DLBCL with a PMBL gene expression signature. Blood. 2021 Jul 15;138(2):136–148. PMID: 33684939 |
RFX7.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # RFX7 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | First described as mutated in BL in 2009 by Grande et al.<sup>1</sup> |
| 4 | 5 | |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | title Publication timing |
| 9 | 10 | 2019-03-21 : Grande : BL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -39,14 +41,14 @@ timeline |
| 39 | 41 | |
| 40 | 42 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RFX7_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RFX7_protein_hg38.html) |
| 41 | 43 | |
| 42 | - |
|
| 44 | + |
|
| 43 | 45 | |
| 44 | 46 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RFX7.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RFX7_hg38.html) |
| 45 | 47 | |
| 46 | - |
|
| 48 | + |
|
| 47 | 49 | |
| 48 | 50 | ## RFX7 Expression |
| 49 | - |
|
| 51 | + |
|
| 50 | 52 | |
| 51 | 53 | ## References |
| 52 | 54 | 1. *Grande BM, Gerhard DS, Jiang A, Griner NB, Abramson JS, Alexander TB, Allen H, Ayers LW, Bethony JM, Bhatia K, Bowen J, Casper C, Choi JK, Culibrk L, Davidsen TM, Dyer MA, Gastier-Foster JM, Gesuwan P, Greiner TC, Gross TG, Hanf B, Harris NL, He Y, Irvin JD, Jaffe ES, Jones SJM, Kerchan P, Knoetze N, Leal FE, Lichtenberg TM, Ma Y, Martin JP, Martin MR, Mbulaiteye SM, Mullighan CG, Mungall AJ, Namirembe C, Novik K, Noy A, Ogwang MD, Omoding A, Orem J, Reynolds SJ, Rushton CK, Sandlund JT, Schmitz R, Taylor C, Wilson WH, Wright GW, Zhao EY, Marra MA, Morin RD, Staudt LM. Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma. Blood. 2019 Mar 21;133(12):1313–1324.* |
RFXAP.md
| ... | ... | @@ -27,11 +27,14 @@ |
| 27 | 27 | |
| 28 | 28 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RFXAP_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RFXAP_protein_hg38.html) |
| 29 | 29 | |
| 30 | - |
|
| 30 | + |
|
| 31 | 31 | |
| 32 | 32 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RFXAP.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RFXAP_hg38.html) |
| 33 | 33 | |
| 34 | - |
|
| 34 | + |
|
| 35 | + |
|
| 35 | 36 | ## RFXAP Expression |
| 36 | - |
|
| 37 | + |
|
| 37 | 38 | <!-- ORIGIN: Unknown --> |
| 39 | + |
|
| 40 | +## References |
RHEX.md
| ... | ... | @@ -25,6 +25,7 @@ |
| 25 | 25 | |:--------:|:----------:|:---------:|:-------------------------------------------------------------------------------------------:|:------------------:| |
| 26 | 26 | |chr1 |206285239 |206288105|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr1%3A206285239%2D206288105)|NA | |
| 27 | 27 | ## RHEX Expression |
| 28 | - |
|
| 28 | + |
|
| 29 | 29 | <!-- ORIGIN: Unknown --> |
| 30 | + |
|
| 30 | 31 | ## References |
RHOA.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # RHOA |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2001-07-19 : Pasqualucci : DLBCL |
| 8 | 9 | 2012-11-11 : Richter : BL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -36,8 +38,6 @@ timeline |
| 36 | 38 | |FL |No |No |31.528 |0 | |
| 37 | 39 | |
| 38 | 40 | |
| 39 | -> [!NOTE] |
|
| 40 | -> First described in DLBCL in 2001 by [Pasqualucci L](https://pubmed.ncbi.nlm.nih.gov/11460166) |
|
| 41 | 41 | |
| 42 | 42 | ## RHOA Hotspots |
| 43 | 43 | |
| ... | ... | @@ -53,16 +53,18 @@ timeline |
| 53 | 53 | |
| 54 | 54 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RHOA_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RHOA_protein_hg38.html) |
| 55 | 55 | |
| 56 | - |
|
| 56 | + |
|
| 57 | 57 | |
| 58 | 58 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RHOA.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RHOA_hg38.html) |
| 59 | 59 | |
| 60 | - |
|
| 60 | + |
|
| 61 | + |
|
| 61 | 62 | ## RHOA Expression |
| 62 | - |
|
| 63 | + |
|
| 63 | 64 | <!-- ORIGIN: pasqualucciHypermutationMultipleProtooncogenes2001a --> |
| 64 | 65 | <!-- DLBCL: pasqualucciHypermutationMultipleProtooncogenes2001a --> |
| 65 | 66 | <!-- BL: richterRecurrentMutationID32012a --> |
| 67 | + |
|
| 66 | 68 | ## References |
| 67 | 69 | 1. Pasqualucci L, Neumeister P, Goossens T, Nanjangud G, Chaganti RS, Küppers R, Dalla-Favera R. Hypermutation of multiple proto-oncogenes in B-cell diffuse large-cell lymphomas. Nature. 2001 Jul 19;412(6844):341–346. PMID: 11460166 |
| 68 | 70 | 2. Richter J, Schlesner M, Hoffmann S, Kreuz M, Leich E, Burkhardt B, Rosolowski M, Ammerpohl O, Wagener R, Bernhart SH, Lenze D, Szczepanowski M, Paulsen M, Lipinski S, Russell RB, Adam-Klages S, Apic G, Claviez A, Hasenclever D, Hovestadt V, Hornig N, Korbel JO, Kube D, Langenberger D, Lawerenz C, Lisfeld J, Meyer K, Picelli S, Pischimarov J, Radlwimmer B, Rausch T, Rohde M, Schilhabel M, Scholtysik R, Spang R, Trautmann H, Zenz T, Borkhardt A, Drexler HG, Möller P, MacLeod RAF, Pott C, Schreiber S, Trümper L, Loeffler M, Stadler PF, Lichter P, Eils R, Küppers R, Hummel M, Klapper W, Rosenstiel P, Rosenwald A, Brors B, Siebert R, ICGC MMML-Seq Project. Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing. Nat Genet. 2012 Dec;44(12):1316–1320. PMID: 23143595 |
RHOH.md
| ... | ... | @@ -32,11 +32,14 @@ |
| 32 | 32 | |
| 33 | 33 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RHOH_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RHOH_protein_hg38.html) |
| 34 | 34 | |
| 35 | - |
|
| 35 | + |
|
| 36 | 36 | |
| 37 | 37 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RHOH.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RHOH_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | + |
|
| 40 | 41 | ## RHOH Expression |
| 41 | - |
|
| 42 | + |
|
| 42 | 43 | <!-- ORIGIN: Unknown --> |
| 44 | + |
|
| 45 | +## References |
RNF144B.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # RNF144B |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2019-09-26 : Panea : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -38,14 +40,16 @@ timeline |
| 38 | 40 | |
| 39 | 41 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RNF144B_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RNF144B_protein_hg38.html) |
| 40 | 42 | |
| 41 | - |
|
| 43 | + |
|
| 42 | 44 | |
| 43 | 45 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RNF144B.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RNF144B_hg38.html) |
| 44 | 46 | |
| 45 | - |
|
| 47 | + |
|
| 48 | + |
|
| 46 | 49 | ## RNF144B Expression |
| 47 | - |
|
| 50 | + |
|
| 48 | 51 | <!-- ORIGIN: paneaWholeGenomeLandscape2019 --> |
| 49 | 52 | <!-- BL: paneaWholeGenomeLandscape2019 --> |
| 53 | + |
|
| 50 | 54 | ## References |
| 51 | 55 | 1. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019; |
ROBO2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # ROBO2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2014-05-08 : Zhang : MCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -27,11 +29,10 @@ timeline |
| 27 | 29 | |FL |No |No |3.479 |0.000 | |
| 28 | 30 | |
| 29 | 31 | |
| 30 | -> [!NOTE] |
|
| 31 | -> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267) |
|
| 32 | 32 | ## ROBO2 Expression |
| 33 | - |
|
| 33 | + |
|
| 34 | 34 | <!-- ORIGIN: zhangGenomicLandscapeMantle2014 --> |
| 35 | 35 | <!-- MCL: zhangGenomicLandscapeMantle2014 --> |
| 36 | + |
|
| 36 | 37 | ## References |
| 37 | 38 | 1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996. |
RPL10.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # RPL10 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2022-07-06 : Burkhardt : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -33,14 +35,16 @@ timeline |
| 33 | 35 | |
| 34 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RPL10_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RPL10_protein_hg38.html) |
| 35 | 37 | |
| 36 | - |
|
| 38 | + |
|
| 37 | 39 | |
| 38 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RPL10.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RPL10_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 43 | + |
|
| 41 | 44 | ## RPL10 Expression |
| 42 | - |
|
| 45 | + |
|
| 43 | 46 | <!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b --> |
| 44 | 47 | <!-- BL: burkhardtClinicalRelevanceMolecular2022b --> |
| 48 | + |
|
| 45 | 49 | ## References |
| 46 | 50 | 1. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584 |
RRAGC.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # RRAGC |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2016-02-02 : Okosun : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -32,20 +34,20 @@ timeline |
| 32 | 34 | |FL |No |Yes |163.715 |0 | |
| 33 | 35 | |
| 34 | 36 | |
| 35 | -> [!NOTE] |
|
| 36 | -> First described in DLBCL in 2016 by [Okosun J](https://pubmed.ncbi.nlm.nih.gov/26691987) |
|
| 37 | 37 | |
| 38 | 38 | |
| 39 | 39 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RRAGC_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RRAGC_protein_hg38.html) |
| 40 | 40 | |
| 41 | - |
|
| 41 | + |
|
| 42 | 42 | |
| 43 | 43 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RRAGC.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RRAGC_hg38.html) |
| 44 | 44 | |
| 45 | - |
|
| 45 | + |
|
| 46 | + |
|
| 46 | 47 | ## RRAGC Expression |
| 47 | - |
|
| 48 | + |
|
| 48 | 49 | <!-- ORIGIN: okosunRecurrentMTORC1activatingRRAGC2016a --> |
| 49 | 50 | <!-- DLBCL: okosunRecurrentMTORC1activatingRRAGC2016a --> |
| 51 | + |
|
| 50 | 52 | ## References |
| 51 | 53 | 1. Okosun J, Wolfson RL, Wang J, Araf S, Wilkins L, Castellano BM, Escudero-Ibarz L, Al Seraihi AF, Richter J, Bernhart SH, Efeyan A, Iqbal S, Matthews J, Clear A, Guerra-Assunção JA, Bödör C, Quentmeier H, Mansbridge C, Johnson P, Davies A, Strefford JC, Packham G, Barrans S, Jack A, Du MQ, Calaminici M, Lister TA, Auer R, Montoto S, Gribben JG, Siebert R, Chelala C, Zoncu R, Sabatini DM, Fitzgibbon J. Recurrent mTORC1-activating RRAGC mutations in follicular lymphoma. Nat Genet. 2016 Feb;48(2):183–188. PMCID: PMC4731318 |
RUBCNL.md
| ... | ... | @@ -20,6 +20,7 @@ |
| 20 | 20 | | |
| 21 | 21 | |
| 22 | 22 | ## RUBCNL Expression |
| 23 | - |
|
| 23 | + |
|
| 24 | 24 | <!-- ORIGIN: Unknown --> |
| 25 | + |
|
| 25 | 26 | ## References |
RUNX1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # RUNX1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2017-10-10 : Reddy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,20 +32,20 @@ timeline |
| 30 | 32 | |FL |No |No |0 |0 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567) |
|
| 35 | 35 | |
| 36 | 36 | |
| 37 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RUNX1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RUNX1_protein_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | 40 | |
| 41 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RUNX1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RUNX1_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | + |
|
| 44 | 45 | ## RUNX1 Expression |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
| 47 | 48 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 49 | + |
|
| 48 | 50 | ## References |
| 49 | 51 | 1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
S1PR1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # S1PR1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | |
| 4 | 5 | ```mermaid |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | title Publication timing |
| 8 | 9 | 2020-07-30 : Pararajalingam : MCL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -28,20 +30,20 @@ timeline |
| 28 | 30 | |FL |No |No |0.000 |0 | |
| 29 | 31 | |
| 30 | 32 | |
| 31 | -> [!NOTE] |
|
| 32 | -> First described in MCL in 2020 by [Pararajalingam P](https://pubmed.ncbi.nlm.nih.gov/32160292) |
|
| 33 | 33 | |
| 34 | 34 | |
| 35 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S1PR1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/S1PR1_protein_hg38.html) |
| 36 | 36 | |
| 37 | - |
|
| 37 | + |
|
| 38 | 38 | |
| 39 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S1PR1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/S1PR1_hg38.html) |
| 40 | 40 | |
| 41 | - |
|
| 41 | + |
|
| 42 | + |
|
| 42 | 43 | ## S1PR1 Expression |
| 43 | - |
|
| 44 | + |
|
| 44 | 45 | <!-- ORIGIN: pararajalingamCodingNoncodingDrivers2020 --> |
| 45 | 46 | <!-- MCL: pararajalingamCodingNoncodingDrivers2020 --> |
| 47 | + |
|
| 46 | 48 | ## References |
| 47 | 49 | 1. Pararajalingam P, Coyle KM, Arthur SE, Thomas N, Alcaide M, Meissner B, Boyle M, Qureshi Q, Grande BM, Rushton C, Slack GW, Mungall AJ, Tam CS, Agarwal R, Dawson SJ, Lenz G, Balasubramanian S, Gascoyne RD, Steidl C, Connors J, Villa D, Audas TE, Marra MA, Johnson NA, Scott DW, Morin RD. Coding and noncoding drivers of mantle cell lymphoma identified through exome and genome sequencing. Blood. 2020 Jul 30;136(5):572–584. PMCID: PMC7440974 |
S1PR2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # S1PR2 |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | S1PR2 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. |
| 4 | 5 | ## History |
| ... | ... | @@ -9,6 +10,7 @@ timeline |
| 9 | 10 | 2011-07-27 : Morin : DLBCL |
| 10 | 11 | 2014-12-11 : Muppidi : BL |
| 11 | 12 | ``` |
| 13 | + |
|
| 12 | 14 | ## Relevance tier by entity |
| 13 | 15 | |
| 14 | 16 | |Entity|Tier|Description | |
| ... | ... | @@ -48,16 +50,18 @@ timeline |
| 48 | 50 | |
| 49 | 51 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S1PR2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/S1PR2_protein_hg38.html) |
| 50 | 52 | |
| 51 | - |
|
| 53 | + |
|
| 52 | 54 | |
| 53 | 55 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S1PR2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/S1PR2_hg38.html) |
| 54 | 56 | |
| 55 | - |
|
| 57 | + |
|
| 58 | + |
|
| 56 | 59 | ## S1PR2 Expression |
| 57 | - |
|
| 60 | + |
|
| 58 | 61 | <!-- ORIGIN: 21796119 --> |
| 59 | 62 | <!-- BL: muppidiLossSignalingGa132014b --> |
| 60 | 63 | <!-- DLBCL: morinFrequentMutationHistonemodifying2011 --> |
| 64 | + |
|
| 61 | 65 | ## References |
| 62 | 66 | 1. Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJM, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298–303. PMCID: PMC3210554 |
| 63 | 67 | 2. Muppidi J, Schmitz R, Green JA, Green JA, Xiao W, Larsen AB, Braun S, An J, Xu Y, Rosenwald A, Ott G, Gascoyne R, Rimsza L, Campo E, Jaffe E, Delabie J, Smeland E, Braziel R, Tubbs R, Cook J, Weisenburger D, Chan W, Vaidehi N, Staudt L, Cyster J. Loss of signaling via Gα13 in germinal center B cell-derived lymphoma. Nature. 2014;516:254–258. |
SAL3.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SAL3 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2022-07-06 : Burkhardt : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -26,10 +28,12 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM |
| 26 | 28 | |
| 27 | 29 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SAL3.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SAL3_hg38.html) |
| 28 | 30 | |
| 29 | - |
|
| 31 | + |
|
| 32 | + |
|
| 30 | 33 | ## SAL3 Expression |
| 31 | - |
|
| 34 | + |
|
| 32 | 35 | <!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b --> |
| 33 | 36 | <!-- BL: burkhardtClinicalRelevanceMolecular2022b --> |
| 37 | + |
|
| 34 | 38 | ## References |
| 35 | 39 | 1. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584 |
SALL3.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SALL3 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | 2014-05-08 : Zhang : MCL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -36,16 +38,18 @@ timeline |
| 36 | 38 | |
| 37 | 39 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SALL3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SALL3_protein_hg38.html) |
| 38 | 40 | |
| 39 | - |
|
| 41 | + |
|
| 40 | 42 | |
| 41 | 43 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SALL3.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SALL3_hg38.html) |
| 42 | 44 | |
| 43 | - |
|
| 45 | + |
|
| 46 | + |
|
| 44 | 47 | ## SALL3 Expression |
| 45 | - |
|
| 48 | + |
|
| 46 | 49 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 47 | 50 | <!-- MCL: zhangGenomicLandscapeMantle2014 --> |
| 48 | 51 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 52 | + |
|
| 49 | 53 | ## References |
| 50 | 54 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
| 51 | 55 | 2. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996. |
SAMD9L.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SAMD9L |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2013-08-15 : Morin : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -33,14 +35,16 @@ timeline |
| 33 | 35 | |
| 34 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SAMD9L_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SAMD9L_protein_hg38.html) |
| 35 | 37 | |
| 36 | - |
|
| 38 | + |
|
| 37 | 39 | |
| 38 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SAMD9L.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SAMD9L_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 43 | + |
|
| 41 | 44 | ## SAMD9L Expression |
| 42 | - |
|
| 45 | + |
|
| 43 | 46 | <!-- ORIGIN: morinMutationalStructuralAnalysis2013 --> |
| 44 | 47 | <!-- DLBCL: morinMutationalStructuralAnalysis2013 --> |
| 48 | + |
|
| 45 | 49 | ## References |
| 46 | 50 | 1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992 |
SAPS2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SAPS2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -28,10 +30,12 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM |
| 28 | 30 | |
| 29 | 31 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SAPS2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SAPS2_hg38.html) |
| 30 | 32 | |
| 31 | - |
|
| 33 | + |
|
| 34 | + |
|
| 32 | 35 | ## SAPS2 Expression |
| 33 | - |
|
| 36 | + |
|
| 34 | 37 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 35 | 38 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 39 | + |
|
| 36 | 40 | ## References |
| 37 | 41 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
SARM1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SARM1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2013-08-15 : Morin : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -34,14 +36,16 @@ timeline |
| 34 | 36 | |
| 35 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SARM1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SARM1_protein_hg38.html) |
| 36 | 38 | |
| 37 | - |
|
| 39 | + |
|
| 38 | 40 | |
| 39 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SARM1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SARM1_hg38.html) |
| 40 | 42 | |
| 41 | - |
|
| 43 | + |
|
| 44 | + |
|
| 42 | 45 | ## SARM1 Expression |
| 43 | - |
|
| 46 | + |
|
| 44 | 47 | <!-- ORIGIN: morinMutationalStructuralAnalysis2013 --> |
| 45 | 48 | <!-- DLBCL: morinMutationalStructuralAnalysis2013 --> |
| 49 | + |
|
| 46 | 50 | ## References |
| 47 | 51 | 1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992 |
SBF1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SBF1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -29,20 +31,20 @@ timeline |
| 29 | 31 | |FL |No |No |1.554 |19.971 | |
| 30 | 32 | |
| 31 | 33 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597) |
|
| 34 | 34 | |
| 35 | 35 | |
| 36 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SBF1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SBF1_protein_hg38.html) |
| 37 | 37 | |
| 38 | - |
|
| 38 | + |
|
| 39 | 39 | |
| 40 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SBF1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SBF1_hg38.html) |
| 41 | 41 | |
| 42 | - |
|
| 42 | + |
|
| 43 | + |
|
| 43 | 44 | ## SBF1 Expression |
| 44 | - |
|
| 45 | + |
|
| 45 | 46 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 46 | 47 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 48 | + |
|
| 47 | 49 | ## References |
| 48 | 50 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
SEL1L3.md
| ... | ... | @@ -32,12 +32,14 @@ |
| 32 | 32 | |
| 33 | 33 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SEL1L3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SEL1L3_protein_hg38.html) |
| 34 | 34 | |
| 35 | - |
|
| 35 | + |
|
| 36 | 36 | |
| 37 | 37 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SEL1L3.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SEL1L3_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | + |
|
| 40 | 41 | ## SEL1L3 Expression |
| 41 | - |
|
| 42 | + |
|
| 42 | 43 | <!-- ORIGIN: Unknown --> |
| 44 | + |
|
| 43 | 45 | ## References |
SEPTIN9.md
| ... | ... | @@ -27,5 +27,7 @@ |
| 27 | 27 | |chr17 |75443766 |75451177|[intron-2](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr17%3A75443766%2D75451177)|active_promoter | |
| 28 | 28 | |chr17 |75453203 |75471471|[intron-3](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr17%3A75453203%2D75471471)|active_promoter | |
| 29 | 29 | ## SEPTIN9 Expression |
| 30 | - |
|
| 30 | + |
|
| 31 | 31 | <!-- ORIGIN: Unknown --> |
| 32 | + |
|
| 33 | +## References |
SERPINA9.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SERPINA9 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2018-10-01 : Arthur : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -35,20 +37,20 @@ timeline |
| 35 | 37 | |:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:| |
| 36 | 38 | |chr14 |94940587 |94942549|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr14%3A94940587%2D94942549)|NA | |
| 37 | 39 | |
| 38 | -> [!NOTE] |
|
| 39 | -> First described in DLBCL in 2018 by [Arthur SE](https://pubmed.ncbi.nlm.nih.gov/30275490) |
|
| 40 | 40 | |
| 41 | 41 | |
| 42 | 42 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SERPINA9_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SERPINA9_protein_hg38.html) |
| 43 | 43 | |
| 44 | - |
|
| 44 | + |
|
| 45 | 45 | |
| 46 | 46 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SERPINA9.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SERPINA9_hg38.html) |
| 47 | 47 | |
| 48 | - |
|
| 48 | + |
|
| 49 | + |
|
| 49 | 50 | ## SERPINA9 Expression |
| 50 | - |
|
| 51 | + |
|
| 51 | 52 | <!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 --> |
| 52 | 53 | <!-- DLBCL: arthurGenomewideDiscoverySomatic2018 --> |
| 54 | + |
|
| 53 | 55 | ## References |
| 54 | 56 | 1. Arthur SE, Jiang A, Grande BM, Alcaide M, Cojocaru R, Rushton CK, Mottok A, Hilton LK, Lat PK, Zhao EY, Culibrk L, Ennishi D, Jessa S, Chong L, Thomas N, Pararajalingam P, Meissner B, Boyle M, Davidson J, Bushell KR, Lai D, Farinha P, Slack GW, Morin GB, Shah S, Sen D, Jones SJM, Mungall AJ, Gascoyne RD, Audas TE, Unrau P, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma. Nat Commun. 2018 Oct 1;9(1):4001. PMCID: PMC6167379 |
SESN1.md
| ... | ... | @@ -21,18 +21,18 @@ |
| 21 | 21 | |FL |No |No |0.000 |0 | |
| 22 | 22 | |
| 23 | 23 | |
| 24 | -> [!NOTE] |
|
| 25 | -> First described in FL in 2017 by [Oricchio E](https://pubmed.ncbi.nlm.nih.gov/28659443) |
|
| 26 | 24 | |
| 27 | 25 | |
| 28 | 26 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SESN1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SESN1_protein_hg38.html) |
| 29 | 27 | |
| 30 | - |
|
| 28 | + |
|
| 31 | 29 | |
| 32 | 30 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SESN1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SESN1_hg38.html) |
| 33 | 31 | |
| 34 | - |
|
| 32 | + |
|
| 33 | + |
|
| 35 | 34 | ## SESN1 Expression |
| 36 | - |
|
| 35 | + |
|
| 37 | 36 | <!-- ORIGIN: Unknown --> |
| 37 | + |
|
| 38 | 38 | ## References |
SETD1B.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SETD1B |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2017-10-10 : Reddy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -47,10 +49,12 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM |
| 47 | 49 | |
| 48 | 50 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SETD1B.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SETD1B_hg38.html) |
| 49 | 51 | |
| 50 | - |
|
| 52 | + |
|
| 53 | + |
|
| 51 | 54 | ## SETD1B Expression |
| 52 | - |
|
| 55 | + |
|
| 53 | 56 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
| 54 | 57 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 58 | + |
|
| 55 | 59 | ## References |
| 56 | 60 | 1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
SETD2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SETD2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2013-01-01 : Zhang : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -33,14 +35,16 @@ timeline |
| 33 | 35 | |
| 34 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SETD2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SETD2_protein_hg38.html) |
| 35 | 37 | |
| 36 | - |
|
| 38 | + |
|
| 37 | 39 | |
| 38 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SETD2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SETD2_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 43 | + |
|
| 41 | 44 | ## SETD2 Expression |
| 42 | - |
|
| 45 | + |
|
| 43 | 46 | <!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 --> |
| 44 | 47 | <!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 --> |
| 48 | + |
|
| 45 | 49 | ## References |
| 46 | 50 | 1. Zhang J, Grubor V, Love CL, Banerjee A, Richards KL, Mieczkowski PA, Dunphy C, Choi W, Au WY, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers C, Naresh K, Evens A, Gordon LI, Czader M, Gill JI, Hsi ED, Liu Q, Fan A, Walsh K, Jima D, Smith LL, Johnson AJ, Byrd JC, Luftig MA, Ni T, Zhu J, Chadburn A, Levy S, Dunson D, Dave SS. Genetic heterogeneity of diffuse large B-cell lymphoma. 2013 Jan; |
SETD5.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SETD5 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2017-10-10 : Reddy : DLBCL |
| 8 | 9 | 2018-05-31 : Tiacci : PMBL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -32,8 +34,6 @@ timeline |
| 32 | 34 | |FL |No |No |2.236 | 0.000 | |
| 33 | 35 | |
| 34 | 36 | |
| 35 | -> [!NOTE] |
|
| 36 | -> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567) |
|
| 37 | 37 | |
| 38 | 38 | > [!WARNING] |
| 39 | 39 | > Mutations in this gene were reported to be inflated in the original results according to [Dreval K](https://www.biorxiv.org/content/10.1101/2023.11.21.567983v1) |
| ... | ... | @@ -41,16 +41,18 @@ timeline |
| 41 | 41 | |
| 42 | 42 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SETD5_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SETD5_protein_hg38.html) |
| 43 | 43 | |
| 44 | - |
|
| 44 | + |
|
| 45 | 45 | |
| 46 | 46 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SETD5.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SETD5_hg38.html) |
| 47 | 47 | |
| 48 | - |
|
| 48 | + |
|
| 49 | + |
|
| 49 | 50 | ## SETD5 Expression |
| 50 | - |
|
| 51 | + |
|
| 51 | 52 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
| 52 | 53 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 53 | 54 | <!-- PMBL: tiacciPervasiveMutationsJAKSTAT2018b --> |
| 55 | + |
|
| 54 | 56 | ## References |
| 55 | 57 | 1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
| 56 | 58 | 2. Tiacci E, Ladewig E, Schiavoni G, Penson A, Fortini E, Pettirossi V, Wang Y, Rosseto A, Venanzi A, Vlasevska S, Pacini R, Piattoni S, Tabarrini A, Pucciarini A, Bigerna B, Santi A, Gianni AM, Viviani S, Cabras A, Ascani S, Crescenzi B, Mecucci C, Pasqualucci L, Rabadan R, Falini B. Pervasive mutations of JAK-STAT pathway genes in classical Hodgkin lymphoma. Blood. 2018 May 31;131(22):2454–2465. PMCID: PMC6634958 |
SF3B1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SF3B1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -34,8 +36,6 @@ timeline |
| 34 | 36 | |FL |No |No |2.408 |0.000 | |
| 35 | 37 | |
| 36 | 38 | |
| 37 | -> [!NOTE] |
|
| 38 | -> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597) |
|
| 39 | 39 | |
| 40 | 40 | |
| 41 | 41 | ## SF3B1 Hotspots |
| ... | ... | @@ -48,14 +48,16 @@ timeline |
| 48 | 48 | |
| 49 | 49 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SF3B1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SF3B1_protein_hg38.html) |
| 50 | 50 | |
| 51 | - |
|
| 51 | + |
|
| 52 | 52 | |
| 53 | 53 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SF3B1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SF3B1_hg38.html) |
| 54 | 54 | |
| 55 | - |
|
| 55 | + |
|
| 56 | + |
|
| 56 | 57 | ## SF3B1 Expression |
| 57 | - |
|
| 58 | + |
|
| 58 | 59 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 59 | 60 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 61 | + |
|
| 60 | 62 | ## References |
| 61 | 63 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
SGK1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SGK1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2011-07-27 : Morin : FL |
| 8 | 9 | 2021-07-15 : Duns : PMBL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -39,23 +41,21 @@ timeline |
| 39 | 41 | |:--------:|:----------:|:---------:|:---------------------------------------------------------------------------------------------:|:------------------:| |
| 40 | 42 | |chr6 |134487960 |134499859|[TSS-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr6%3A134487960%2D134499859)|active_promoter | |
| 41 | 43 | |
| 42 | -> [!NOTE] |
|
| 43 | -> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119) |
|
| 44 | 44 | |
| 45 | 45 | |
| 46 | 46 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SGK1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SGK1_protein_hg38.html) |
| 47 | 47 | |
| 48 | - |
|
| 48 | + |
|
| 49 | 49 | |
| 50 | 50 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SGK1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SGK1_hg38.html) |
| 51 | 51 | |
| 52 | - |
|
| 52 | + |
|
| 53 | 53 | |
| 54 | 54 | ## References |
| 55 | 55 | 1. *Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351. PMID: 21796119; PMCID: PMC3210554.* |
| 56 | 56 | |
| 57 | 57 | ## SGK1 Expression |
| 58 | - |
|
| 58 | + |
|
| 59 | 59 | <!-- ORIGIN: morinFrequentMutationHistonemodifying2011 --> |
| 60 | 60 | <!-- FL: morinFrequentMutationHistonemodifying2011 --> |
| 61 | 61 | <!-- PMBL: dunsCharacterizationDLBCLPMBL2021b --> |
SHANK1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SHANK1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -32,14 +34,16 @@ timeline |
| 32 | 34 | |
| 33 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SHANK1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SHANK1_protein_hg38.html) |
| 34 | 36 | |
| 35 | - |
|
| 37 | + |
|
| 36 | 38 | |
| 37 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SHANK1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SHANK1_hg38.html) |
| 38 | 40 | |
| 39 | - |
|
| 41 | + |
|
| 42 | + |
|
| 40 | 43 | ## SHANK1 Expression |
| 41 | - |
|
| 44 | + |
|
| 42 | 45 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 43 | 46 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 47 | + |
|
| 44 | 48 | ## References |
| 45 | 49 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
SHROOM3.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SHROOM3 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2023-07-26 : Russler-Germain : FL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -31,14 +33,16 @@ timeline |
| 31 | 33 | |
| 32 | 34 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SHROOM3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SHROOM3_protein_hg38.html) |
| 33 | 35 | |
| 34 | - |
|
| 36 | + |
|
| 35 | 37 | |
| 36 | 38 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SHROOM3.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SHROOM3_hg38.html) |
| 37 | 39 | |
| 38 | - |
|
| 40 | + |
|
| 41 | + |
|
| 39 | 42 | ## SHROOM3 Expression |
| 40 | - |
|
| 43 | + |
|
| 41 | 44 | <!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a --> |
| 42 | 45 | <!-- FL: russler-germainMutationsAssociatedProgression2023b --> |
| 46 | + |
|
| 43 | 47 | ## References |
| 44 | 48 | 1. Russler-Germain DA, Krysiak K, Ramirez CA, Mosior M, Watkins MP, Gomez F, Skidmore ZL, Trani L, Gao F, Geyer S, Cashen A, Mehta-Shah N, Kahl B, Bartlett N, Alderuccio J, Lossos I, Ondrejka S, Hsi E, Martin P, Leonard J, Griffith M, Griffith O, Fehniger T. Mutations associated with progression in follicular lymphoma predict inferior outcomes at diagnosis: Alliance A151303. Blood Advances. 2023;7:5524–5539. |
SI.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SI |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2014-05-08 : Zhang : MCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,14 +32,16 @@ timeline |
| 30 | 32 | |
| 31 | 33 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SI_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SI_protein_hg38.html) |
| 32 | 34 | |
| 33 | - |
|
| 35 | + |
|
| 34 | 36 | |
| 35 | 37 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SI.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SI_hg38.html) |
| 36 | 38 | |
| 37 | - |
|
| 39 | + |
|
| 40 | + |
|
| 38 | 41 | ## SI Expression |
| 39 | - |
|
| 42 | + |
|
| 40 | 43 | <!-- ORIGIN: zhangGenomicLandscapeMantle2014 --> |
| 41 | 44 | <!-- MCL: zhangGenomicLandscapeMantle2014 --> |
| 45 | + |
|
| 42 | 46 | ## References |
| 43 | 47 | 1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996. |
SIAH2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SIAH2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2015-02-12 : Reichel : PMBL |
| 8 | 9 | 2021-05-05 : Hübschmann : DLBCL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -32,22 +34,22 @@ timeline |
| 32 | 34 | |FL |No |No |4.227 |0 | |
| 33 | 35 | |
| 34 | 36 | |
| 35 | -> [!NOTE] |
|
| 36 | -> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289) |
|
| 37 | 37 | |
| 38 | 38 | |
| 39 | 39 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SIAH2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SIAH2_protein_hg38.html) |
| 40 | 40 | |
| 41 | - |
|
| 41 | + |
|
| 42 | 42 | |
| 43 | 43 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SIAH2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SIAH2_hg38.html) |
| 44 | 44 | |
| 45 | - |
|
| 45 | + |
|
| 46 | + |
|
| 46 | 47 | ## SIAH2 Expression |
| 47 | - |
|
| 48 | + |
|
| 48 | 49 | <!-- ORIGIN: reichelFlowSortingExome2015a --> |
| 49 | 50 | <!-- DLBCL: hubschmannMutationalMechanismsShaping2021b --> |
| 50 | 51 | <!-- PMBL: reichelFlowSortingExome2015a --> |
| 52 | + |
|
| 51 | 53 | ## References |
| 52 | 54 | 1. Reichel J, Chadburn A, Rubinstein PG, Giulino-Roth L, Tam W, Liu Y, Gaiolla R, Eng K, Brody J, Inghirami G, Carlo-Stella C, Santoro A, Rahal D, Totonchy J, Elemento O, Cesarman E, Roshal M. Flow sorting and exome sequencing reveal the oncogenome of primary Hodgkin and Reed-Sternberg cells. Blood. 2015 Feb 12;125(7):1061–1072. PMID: 25488972 |
| 53 | 55 | 2. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491 |
SIN3A.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SIN3A |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | Mutations in this gene were first described in MZL in 2012 by Rossi et al<sup>1</sup> and in BL in 2019 by Grande et al.<sup>2</sup> |
| 4 | 5 | |
| ... | ... | @@ -9,6 +10,7 @@ timeline |
| 9 | 10 | 2012-08-27 : Rossi : MZL |
| 10 | 11 | 2019-03-21 : Grande : BL |
| 11 | 12 | ``` |
| 13 | + |
|
| 12 | 14 | ## Relevance tier by entity |
| 13 | 15 | |
| 14 | 16 | |Entity|Tier|Description | |
| ... | ... | @@ -41,13 +43,14 @@ timeline |
| 41 | 43 | |
| 42 | 44 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SIN3A_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SIN3A_protein_hg38.html) |
| 43 | 45 | |
| 44 | - |
|
| 46 | + |
|
| 45 | 47 | |
| 46 | 48 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SIN3A.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SIN3A_hg38.html) |
| 47 | 49 | |
| 48 | - |
|
| 50 | + |
|
| 51 | + |
|
| 49 | 52 | ## SIN3A Expression |
| 50 | - |
|
| 53 | + |
|
| 51 | 54 | |
| 52 | 55 | ## References |
| 53 | 56 |
SLC29A2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SLC29A2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -33,14 +35,16 @@ timeline |
| 33 | 35 | |
| 34 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SLC29A2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SLC29A2_protein_hg38.html) |
| 35 | 37 | |
| 36 | - |
|
| 38 | + |
|
| 37 | 39 | |
| 38 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SLC29A2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SLC29A2_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 43 | + |
|
| 41 | 44 | ## SLC29A2 Expression |
| 42 | - |
|
| 45 | + |
|
| 43 | 46 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 44 | 47 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 48 | + |
|
| 45 | 49 | ## References |
| 46 | 50 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
SLC34A2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SLC34A2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2021-05-05 : Hübschmann : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -32,14 +34,16 @@ timeline |
| 32 | 34 | |
| 33 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SLC34A2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SLC34A2_protein_hg38.html) |
| 34 | 36 | |
| 35 | - |
|
| 37 | + |
|
| 36 | 38 | |
| 37 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SLC34A2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SLC34A2_hg38.html) |
| 38 | 40 | |
| 39 | - |
|
| 41 | + |
|
| 42 | + |
|
| 40 | 43 | ## SLC34A2 Expression |
| 41 | - |
|
| 44 | + |
|
| 42 | 45 | <!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b --> |
| 43 | 46 | <!-- DLBCL: hubschmannMutationalMechanismsShaping2021b --> |
| 47 | + |
|
| 44 | 48 | ## References |
| 45 | 49 | 1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491 |
SMARCA4.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SMARCA4 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | |
| 4 | 5 | ```mermaid |
| ... | ... | @@ -10,6 +11,7 @@ timeline |
| 10 | 11 | 2017-01-26 : Krysiak : FL |
| 11 | 12 | 2020-09-17 : Nadeu : MCL |
| 12 | 13 | ``` |
| 14 | + |
|
| 13 | 15 | ## Relevance tier by entity |
| 14 | 16 | |
| 15 | 17 | |Entity|Tier|Description | |
| ... | ... | @@ -43,24 +45,24 @@ timeline |
| 43 | 45 | |FL |No |No |11.081 |0.000 | |
| 44 | 46 | |
| 45 | 47 | |
| 46 | -> [!NOTE] |
|
| 47 | -> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937). First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986). First described in MCL in 2020 by [Nadeu F](https://pubmed.ncbi.nlm.nih.gov/32584970) |
|
| 48 | 48 | |
| 49 | 49 | |
| 50 | 50 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SMARCA4_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SMARCA4_protein_hg38.html) |
| 51 | 51 | |
| 52 | - |
|
| 52 | + |
|
| 53 | 53 | |
| 54 | 54 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SMARCA4.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SMARCA4_hg38.html) |
| 55 | 55 | |
| 56 | - |
|
| 56 | + |
|
| 57 | + |
|
| 57 | 58 | ## SMARCA4 Expression |
| 58 | - |
|
| 59 | + |
|
| 59 | 60 | <!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 --> |
| 60 | 61 | <!-- MCL: nadeuGenomicEpigenomicInsights2020a --> |
| 61 | 62 | <!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 --> |
| 62 | 63 | <!-- FL: krysiakRecurrentSomaticMutations2017b --> |
| 63 | 64 | <!-- BL: richterRecurrentMutationID32012a --> |
| 65 | + |
|
| 64 | 66 | ## References |
| 65 | 67 | 1. Richter J, Schlesner M, Hoffmann S, Kreuz M, Leich E, Burkhardt B, Rosolowski M, Ammerpohl O, Wagener R, Bernhart SH, Lenze D, Szczepanowski M, Paulsen M, Lipinski S, Russell RB, Adam-Klages S, Apic G, Claviez A, Hasenclever D, Hovestadt V, Hornig N, Korbel JO, Kube D, Langenberger D, Lawerenz C, Lisfeld J, Meyer K, Picelli S, Pischimarov J, Radlwimmer B, Rausch T, Rohde M, Schilhabel M, Scholtysik R, Spang R, Trautmann H, Zenz T, Borkhardt A, Drexler HG, Möller P, MacLeod RAF, Pott C, Schreiber S, Trümper L, Loeffler M, Stadler PF, Lichter P, Eils R, Küppers R, Hummel M, Klapper W, Rosenstiel P, Rosenwald A, Brors B, Siebert R, ICGC MMML-Seq Project. Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing. Nat Genet. 2012 Dec;44(12):1316–1320. PMID: 23143595 |
| 66 | 68 | 2. Zhang J, Grubor V, Love CL, Banerjee A, Richards KL, Mieczkowski PA, Dunphy C, Choi W, Au WY, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers C, Naresh K, Evens A, Gordon LI, Czader M, Gill JI, Hsi ED, Liu Q, Fan A, Walsh K, Jima D, Smith LL, Johnson AJ, Byrd JC, Luftig MA, Ni T, Zhu J, Chadburn A, Levy S, Dunson D, Dave SS. Genetic heterogeneity of diffuse large B-cell lymphoma. 2013 Jan; |
SMARCB1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SMARCB1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2020-09-17 : Nadeu : MCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -27,20 +29,20 @@ timeline |
| 27 | 29 | |FL |No |No |15.559 |0 | |
| 28 | 30 | |
| 29 | 31 | |
| 30 | -> [!NOTE] |
|
| 31 | -> First described in MCL in 2020 by [Nadeu F](https://pubmed.ncbi.nlm.nih.gov/32584970) |
|
| 32 | 32 | |
| 33 | 33 | |
| 34 | 34 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SMARCB1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SMARCB1_protein_hg38.html) |
| 35 | 35 | |
| 36 | - |
|
| 36 | + |
|
| 37 | 37 | |
| 38 | 38 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SMARCB1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SMARCB1_hg38.html) |
| 39 | 39 | |
| 40 | - |
|
| 40 | + |
|
| 41 | + |
|
| 41 | 42 | ## SMARCB1 Expression |
| 42 | - |
|
| 43 | + |
|
| 43 | 44 | <!-- ORIGIN: nadeuGenomicEpigenomicInsights2020a --> |
| 44 | 45 | <!-- MCL: nadeuGenomicEpigenomicInsights2020a --> |
| 46 | + |
|
| 45 | 47 | ## References |
| 46 | 48 | 1. Nadeu F, Martín-García D, Clot G, Díaz-Navarro A, Duran-Ferrer M, Navarro A, Vilarrasa-Blasi R, Kulis M, Royo R, Gutiérrez-Abril J, Valdés-Mas R, López C, Chapaprieta V, Puiggrós M, Castellano G, Costa D, Aymerich M, Jares P, Espinet B, Muntañola A, Ribera‐Cortada I, Siebert R, Colomer D, Torrents D, Giné E, López-Guillermo A, Küppers R, Martín-Subero J, Puente X, Beà S, Campo E. Genomic and epigenomic insights into the origin, pathogenesis and clinical behavior of mantle cell lymphoma subtypes. Blood. 2020; |
SMC1A.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SMC1A |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2014-05-08 : Zhang : MCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,14 +32,16 @@ timeline |
| 30 | 32 | |
| 31 | 33 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SMC1A_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SMC1A_protein_hg38.html) |
| 32 | 34 | |
| 33 | - |
|
| 35 | + |
|
| 34 | 36 | |
| 35 | 37 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SMC1A.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SMC1A_hg38.html) |
| 36 | 38 | |
| 37 | - |
|
| 39 | + |
|
| 40 | + |
|
| 38 | 41 | ## SMC1A Expression |
| 39 | - |
|
| 42 | + |
|
| 40 | 43 | <!-- ORIGIN: zhangGenomicLandscapeMantle2014 --> |
| 41 | 44 | <!-- MCL: zhangGenomicLandscapeMantle2014 --> |
| 45 | + |
|
| 42 | 46 | ## References |
| 43 | 47 | 1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996. |
SMEK1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SMEK1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2018-05-01 : Chapuy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -32,14 +34,16 @@ timeline |
| 32 | 34 | |
| 33 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SMEK1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SMEK1_protein_hg38.html) |
| 34 | 36 | |
| 35 | - |
|
| 37 | + |
|
| 36 | 38 | |
| 37 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SMEK1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SMEK1_hg38.html) |
| 38 | 40 | |
| 39 | - |
|
| 41 | + |
|
| 42 | + |
|
| 40 | 43 | ## SMEK1 Expression |
| 41 | - |
|
| 44 | + |
|
| 42 | 45 | <!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b --> |
| 43 | 46 | <!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b --> |
| 47 | + |
|
| 44 | 48 | ## References |
| 45 | 49 | 1. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387 |
SNTB2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SNTB2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2019-09-26 : Panea : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -31,14 +33,16 @@ timeline |
| 31 | 33 | |
| 32 | 34 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SNTB2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SNTB2_protein_hg38.html) |
| 33 | 35 | |
| 34 | - |
|
| 36 | + |
|
| 35 | 37 | |
| 36 | 38 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SNTB2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SNTB2_hg38.html) |
| 37 | 39 | |
| 38 | - |
|
| 40 | + |
|
| 41 | + |
|
| 39 | 42 | ## SNTB2 Expression |
| 40 | - |
|
| 43 | + |
|
| 41 | 44 | <!-- ORIGIN: paneaWholeGenomeLandscape2019 --> |
| 42 | 45 | <!-- BL: paneaWholeGenomeLandscape2019 --> |
| 46 | + |
|
| 43 | 47 | ## References |
| 44 | 48 | 1. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019; |
SOCS1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SOCS1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2006-04-27 : Weniger : PMBL |
| 8 | 9 | 2011-07-27 : Morin : DLBCL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -43,16 +45,18 @@ timeline |
| 43 | 45 | |
| 44 | 46 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SOCS1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SOCS1_protein_hg38.html) |
| 45 | 47 | |
| 46 | - |
|
| 48 | + |
|
| 47 | 49 | |
| 48 | 50 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SOCS1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SOCS1_hg38.html) |
| 49 | 51 | |
| 50 | - |
|
| 52 | + |
|
| 53 | + |
|
| 51 | 54 | ## SOCS1 Expression |
| 52 | - |
|
| 55 | + |
|
| 53 | 56 | <!-- ORIGIN: wenigerMutationsTumorSuppressor2006a --> |
| 54 | 57 | <!-- PMBL: wenigerMutationsTumorSuppressor2006a --> |
| 55 | 58 | <!-- DLBCL: morinFrequentMutationHistonemodifying2011 --> |
| 59 | + |
|
| 56 | 60 | ## References |
| 57 | 61 | 1. Weniger MA, Melzner I, Menz CK, Wegener S, Bucur AJ, Dorsch K, Mattfeldt T, Barth TFE, Möller P. Mutations of the tumor suppressor gene SOCS-1 in classical Hodgkin lymphoma are frequent and associated with nuclear phospho-STAT5 accumulation. Oncogene. 2006 Apr 27;25(18):2679–2684. PMID: 16532038 |
| 58 | 62 | 2. Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJM, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298–303. PMCID: PMC3210554 |
SP140.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SP140 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2013-11-05 : Bea : MCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -27,20 +29,20 @@ timeline |
| 27 | 29 | |FL |No |No |0.000 | 0.000 | |
| 28 | 30 | |
| 29 | 31 | |
| 30 | -> [!NOTE] |
|
| 31 | -> First described in MCL in 2020 by [Pararajalingam P](https://pubmed.ncbi.nlm.nih.gov/32160292) |
|
| 32 | 32 | |
| 33 | 33 | |
| 34 | 34 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SP140_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SP140_protein_hg38.html) |
| 35 | 35 | |
| 36 | - |
|
| 36 | + |
|
| 37 | 37 | |
| 38 | 38 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SP140.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SP140_hg38.html) |
| 39 | 39 | |
| 40 | - |
|
| 40 | + |
|
| 41 | + |
|
| 41 | 42 | ## SP140 Expression |
| 42 | - |
|
| 43 | + |
|
| 43 | 44 | <!-- ORIGIN: beaLandscapeSomaticMutations2013 --> |
| 44 | 45 | <!-- MCL: beaLandscapeSomaticMutations2013 --> |
| 46 | + |
|
| 45 | 47 | ## References |
| 46 | 48 | 1. Beà S, Valdés-Mas R, Navarro A, Salaverria I, Martín-Garcia D, Jares P, Giné E, Pinyol M, Royo C, Nadeu F, Conde L, Juan M, Clot G, Vizán P, Croce LD, Puente DA, López-Guerra M, Moros A, Roue G, Aymerich M, Villamor N, Colomo L, Martínez A, Valera A, Martín-Subero JI, Amador V, Hernández L, Rozman M, Enjuanes A, Forcada P, Muntañola A, Hartmann EM, Calasanz MJ, Rosenwald A, Ott G, Hernández-Rivas JM, Klapper W, Siebert R, Wiestner A, Wilson WH, Colomer D, López-Guillermo A, López-Otín C, Puente XS, Campo E. Landscape of somatic mutations and clonal evolution in mantle cell lymphoma. PNAS. 2013 Nov 5;110(45):18250–18255. PMID: 24145436 |
SP3.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SP3 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2019-09-26 : Panea : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -32,14 +34,16 @@ timeline |
| 32 | 34 | |
| 33 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SP3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SP3_protein_hg38.html) |
| 34 | 36 | |
| 35 | - |
|
| 37 | + |
|
| 36 | 38 | |
| 37 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SP3.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SP3_hg38.html) |
| 38 | 40 | |
| 39 | - |
|
| 41 | + |
|
| 42 | + |
|
| 40 | 43 | ## SP3 Expression |
| 41 | - |
|
| 44 | + |
|
| 42 | 45 | <!-- ORIGIN: paneaWholeGenomeLandscape2019 --> |
| 43 | 46 | <!-- BL: paneaWholeGenomeLandscape2019 --> |
| 47 | + |
|
| 44 | 48 | ## References |
| 45 | 49 | 1. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019; |
SPEN.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SPEN |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2012-08-27 : Rossi : MZL |
| 8 | 9 | 2021-04-01 : Sarkozy : PMBL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -44,17 +46,19 @@ timeline |
| 44 | 46 | |
| 45 | 47 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SPEN_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SPEN_protein_hg38.html) |
| 46 | 48 | |
| 47 | - |
|
| 49 | + |
|
| 48 | 50 | |
| 49 | 51 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SPEN.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SPEN_hg38.html) |
| 50 | 52 | |
| 51 | - |
|
| 53 | + |
|
| 54 | + |
|
| 52 | 55 | ## SPEN Expression |
| 53 | - |
|
| 56 | + |
|
| 54 | 57 | <!-- ORIGIN: rossiCodingGenomeSplenic2012c --> |
| 55 | 58 | <!-- DLBCL: rossiCodingGenomeSplenic2012c --> |
| 56 | 59 | <!-- MZL: rossiCodingGenomeSplenic2012c --> |
| 57 | 60 | <!-- PMBL: sarkozyMutationalLandscapeGray2021a --> |
| 61 | + |
|
| 58 | 62 | ## References |
| 59 | 63 | 1. Rossi D, Trifonov V, Fangazio M, Bruscaggin A, Rasi S, Spina V, Monti S, Vaisitti T, Arruga F, Famà R, Ciardullo C, Greco M, Cresta S, Piranda D, Holmes A, Fabbri G, Messina M, Rinaldi A, Wang J, Agostinelli C, Piccaluga PP, Lucioni M, Tabbò F, Serra R, Franceschetti S, Deambrogi C, Daniele G, Gattei V, Marasca R, Facchetti F, Arcaini L, Inghirami G, Bertoni F, Pileri SA, Deaglio S, Foà R, Dalla-Favera R, Pasqualucci L, Rabadan R, Gaidano G. The coding genome of splenic marginal zone lymphoma: activation of NOTCH2 and other pathways regulating marginal zone development. J Exp Med. 2012 Aug 27;209(9):1537–1551. PMCID: PMC3428941 |
| 60 | 64 | 2. Sarkozy C, Hung SS, Chavez EA, Duns G, Takata K, Chong LC, Aoki T, Jiang A, Miyata-Takata T, Telenius A, Slack GW, Molina TJ, Ben-Neriah S, Farinha P, Dartigues P, Damotte D, Mottok A, Salles GA, Casasnovas RO, Savage KJ, Laurent C, Scott DW, Traverse-Glehen A, Steidl C. Mutational landscape of gray zone lymphoma. Blood. 2021 Apr 1;137(13):1765–1776. PMID: 32961552 |
SRRM2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SRRM2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2013-08-15 : Morin : DLBCL |
| 8 | 9 | 2023-07-26 : Russler-Germain : FL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -36,16 +38,18 @@ timeline |
| 36 | 38 | |
| 37 | 39 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SRRM2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SRRM2_protein_hg38.html) |
| 38 | 40 | |
| 39 | - |
|
| 41 | + |
|
| 40 | 42 | |
| 41 | 43 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SRRM2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SRRM2_hg38.html) |
| 42 | 44 | |
| 43 | - |
|
| 45 | + |
|
| 46 | + |
|
| 44 | 47 | ## SRRM2 Expression |
| 45 | - |
|
| 48 | + |
|
| 46 | 49 | <!-- ORIGIN: morinMutationalStructuralAnalysis2013 --> |
| 47 | 50 | <!-- DLBCL: morinMutationalStructuralAnalysis2013 --> |
| 48 | 51 | <!-- FL: russler-germainMutationsAssociatedProgression2023b --> |
| 52 | + |
|
| 49 | 53 | ## References |
| 50 | 54 | 1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992 |
| 51 | 55 | 2. Russler-Germain DA, Krysiak K, Ramirez CA, Mosior M, Watkins MP, Gomez F, Skidmore ZL, Trani L, Gao F, Geyer S, Cashen A, Mehta-Shah N, Kahl B, Bartlett N, Alderuccio J, Lossos I, Ondrejka S, Hsi E, Martin P, Leonard J, Griffith M, Griffith O, Fehniger T. Mutations associated with progression in follicular lymphoma predict inferior outcomes at diagnosis: Alliance A151303. Blood Advances. 2023;7:5524–5539. |
ST6GAL1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # ST6GAL1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2018-10-01 : Arthur : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -41,14 +43,16 @@ timeline |
| 41 | 43 | |
| 42 | 44 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ST6GAL1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ST6GAL1_protein_hg38.html) |
| 43 | 45 | |
| 44 | - |
|
| 46 | + |
|
| 45 | 47 | |
| 46 | 48 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ST6GAL1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ST6GAL1_hg38.html) |
| 47 | 49 | |
| 48 | - |
|
| 50 | + |
|
| 51 | + |
|
| 49 | 52 | ## ST6GAL1 Expression |
| 50 | - |
|
| 53 | + |
|
| 51 | 54 | <!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 --> |
| 52 | 55 | <!-- DLBCL: arthurGenomewideDiscoverySomatic2018 --> |
| 56 | + |
|
| 53 | 57 | ## References |
| 54 | 58 | 1. Arthur SE, Jiang A, Grande BM, Alcaide M, Cojocaru R, Rushton CK, Mottok A, Hilton LK, Lat PK, Zhao EY, Culibrk L, Ennishi D, Jessa S, Chong L, Thomas N, Pararajalingam P, Meissner B, Boyle M, Davidson J, Bushell KR, Lai D, Farinha P, Slack GW, Morin GB, Shah S, Sen D, Jones SJM, Mungall AJ, Gascoyne RD, Audas TE, Unrau P, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma. Nat Commun. 2018 Oct 1;9(1):4001. PMCID: PMC6167379 |
STAB2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # STAB2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2023-07-26 : Russler-Germain : FL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,14 +32,16 @@ timeline |
| 30 | 32 | |
| 31 | 33 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/STAB2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/STAB2_protein_hg38.html) |
| 32 | 34 | |
| 33 | - |
|
| 35 | + |
|
| 34 | 36 | |
| 35 | 37 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/STAB2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/STAB2_hg38.html) |
| 36 | 38 | |
| 37 | - |
|
| 39 | + |
|
| 40 | + |
|
| 38 | 41 | ## STAB2 Expression |
| 39 | - |
|
| 42 | + |
|
| 40 | 43 | <!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a --> |
| 41 | 44 | <!-- FL: russler-germainMutationsAssociatedProgression2023b --> |
| 45 | + |
|
| 42 | 46 | ## References |
| 43 | 47 | 1. Russler-Germain DA, Krysiak K, Ramirez CA, Mosior M, Watkins MP, Gomez F, Skidmore ZL, Trani L, Gao F, Geyer S, Cashen A, Mehta-Shah N, Kahl B, Bartlett N, Alderuccio J, Lossos I, Ondrejka S, Hsi E, Martin P, Leonard J, Griffith M, Griffith O, Fehniger T. Mutations associated with progression in follicular lymphoma predict inferior outcomes at diagnosis: Alliance A151303. Blood Advances. 2023;7:5524–5539. |
STAT3.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # STAT3 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2014-07-01 : Ohgami : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -31,8 +33,6 @@ timeline |
| 31 | 33 | |FL |No |No |34.737 | 0.000 | |
| 32 | 34 | |
| 33 | 35 | |
| 34 | -> [!NOTE] |
|
| 35 | -> First described in DLBCL in 2014 by [Ohgami RS](https://pubmed.ncbi.nlm.nih.gov/24837465) |
|
| 36 | 36 | |
| 37 | 37 | ## STAT3 Hotspots |
| 38 | 38 | |
| ... | ... | @@ -45,14 +45,16 @@ timeline |
| 45 | 45 | |
| 46 | 46 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/STAT3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/STAT3_protein_hg38.html) |
| 47 | 47 | |
| 48 | - |
|
| 48 | + |
|
| 49 | 49 | |
| 50 | 50 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/STAT3.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/STAT3_hg38.html) |
| 51 | 51 | |
| 52 | - |
|
| 52 | + |
|
| 53 | + |
|
| 53 | 54 | ## STAT3 Expression |
| 54 | - |
|
| 55 | + |
|
| 55 | 56 | <!-- ORIGIN: ohgamiSTAT3MutationsAre2014 --> |
| 56 | 57 | <!-- DLBCL: ohgamiSTAT3MutationsAre2014 --> |
| 58 | + |
|
| 57 | 59 | ## References |
| 58 | 60 | 1. Ohgami RS, Ma L, Monabati A, Zehnder JL, Arber DA. STAT3 mutations are present in aggressive B-cell lymphomas including a subset of diffuse large B-cell lymphomas with CD30 expression. Haematologica. 2014 Jul;99(7):e105-107. PMCID: PMC4077094 |
STAT5B.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # STAT5B |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2013-01-01 : Zhang : DLBCL |
| 8 | 9 | 2018-05-31 : Tiacci : PMBL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -35,16 +37,18 @@ timeline |
| 35 | 37 | |
| 36 | 38 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/STAT5B_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/STAT5B_protein_hg38.html) |
| 37 | 39 | |
| 38 | - |
|
| 40 | + |
|
| 39 | 41 | |
| 40 | 42 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/STAT5B.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/STAT5B_hg38.html) |
| 41 | 43 | |
| 42 | - |
|
| 44 | + |
|
| 45 | + |
|
| 43 | 46 | ## STAT5B Expression |
| 44 | - |
|
| 47 | + |
|
| 45 | 48 | <!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 --> |
| 46 | 49 | <!-- PMBL: tiacciPervasiveMutationsJAKSTAT2018b --> |
| 47 | 50 | <!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 --> |
| 51 | + |
|
| 48 | 52 | ## References |
| 49 | 53 | 1. Zhang J, Grubor V, Love CL, Banerjee A, Richards KL, Mieczkowski PA, Dunphy C, Choi W, Au WY, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers C, Naresh K, Evens A, Gordon LI, Czader M, Gill JI, Hsi ED, Liu Q, Fan A, Walsh K, Jima D, Smith LL, Johnson AJ, Byrd JC, Luftig MA, Ni T, Zhu J, Chadburn A, Levy S, Dunson D, Dave SS. Genetic heterogeneity of diffuse large B-cell lymphoma. 2013 Jan; |
| 50 | 54 | 2. Tiacci E, Ladewig E, Schiavoni G, Penson A, Fortini E, Pettirossi V, Wang Y, Rosseto A, Venanzi A, Vlasevska S, Pacini R, Piattoni S, Tabarrini A, Pucciarini A, Bigerna B, Santi A, Gianni AM, Viviani S, Cabras A, Ascani S, Crescenzi B, Mecucci C, Pasqualucci L, Rabadan R, Falini B. Pervasive mutations of JAK-STAT pathway genes in classical Hodgkin lymphoma. Blood. 2018 May 31;131(22):2454–2465. PMCID: PMC6634958 |
STAT6.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # STAT6 |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | The STAT6 gene, which encodes a transcription factor involved in the JAK-STAT signaling pathway, plays a significant role in the pathogenesis of various lymphomas, including diffuse large B-cell lymphoma (DLBCL). Below is a summary of the common mutations in the STAT6 gene identified in DLBCL. Mutations in the DNA binding domain of STAT6 are common in PMBCL and more rare in DLBCL. |
| 4 | 5 | ## History |
| ... | ... | @@ -9,6 +10,7 @@ timeline |
| 9 | 10 | 2009-08-06 : Ritz : PMBL |
| 10 | 11 | 2015-01-22 : Yildiz : DLBCL |
| 11 | 12 | ``` |
| 13 | + |
|
| 12 | 14 | ## Relevance tier by entity |
| 13 | 15 | |
| 14 | 16 | |Entity|Tier|Description | |
| ... | ... | @@ -60,17 +62,17 @@ Recurrent mutations at the D419 amino acid residue are a common feature in DLBCL |
| 60 | 62 | |
| 61 | 63 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/STAT6_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/STAT6_protein_hg38.html) |
| 62 | 64 | |
| 63 | - |
|
| 65 | + |
|
| 64 | 66 | |
| 65 | 67 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/STAT6.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/STAT6_hg38.html) |
| 66 | 68 | |
| 67 | - |
|
| 69 | + |
|
| 68 | 70 | |
| 69 | 71 | ## References |
| 70 | 72 | |
| 71 | 73 | 1. *Morin RD, Assouline S, Alcaide M, Mohajeri A, Johnston RL, Chong L, Grewal J, Yu S, Fornika D, Bushell K, Nielsen TH, Petrogiannis-Haliotis T, Crump M, Tosikyan A, Grande BM, MacDonald D, Rousseau C, Bayat M, Sesques P, Froment R, Albuquerque M, Monczak Y, Oros KK, Greenwood C, Riazalhosseini Y, Arseneault M, Camlioglu E, Constantin A, Pan-Hammarstrom Q, Peng R, Mann KK, Johnson NA. Genetic Landscapes of Relapsed and Refractory Diffuse Large B-Cell Lymphomas. Clin Cancer Res. 2016 May 1;22(9):2290-300. doi: 10.1158/1078-0432.CCR-15-2123. Epub 2015 Dec 8. PMID: 26647218.* |
| 72 | 74 | ## STAT6 Expression |
| 73 | - |
|
| 75 | + |
|
| 74 | 76 | <!-- ORIGIN: yildizActivatingSTAT6Mutations2015c --> |
| 75 | 77 | <!-- PMBL: ritzRecurrentMutationsSTAT62009a --> |
| 76 | 78 | <!-- FL: yildizActivatingSTAT6Mutations2015c --> |
SYK.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SYK |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2017-10-10 : Reddy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -33,14 +35,16 @@ timeline |
| 33 | 35 | |
| 34 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SYK_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SYK_protein_hg38.html) |
| 35 | 37 | |
| 36 | - |
|
| 38 | + |
|
| 37 | 39 | |
| 38 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SYK.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SYK_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 43 | + |
|
| 41 | 44 | ## SYK Expression |
| 42 | - |
|
| 45 | + |
|
| 43 | 46 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
| 44 | 47 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 48 | + |
|
| 45 | 49 | ## References |
| 46 | 50 | 1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
SYNCRIP.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SYNCRIP |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2019-09-26 : Panea : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -32,14 +34,16 @@ timeline |
| 32 | 34 | |
| 33 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SYNCRIP_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SYNCRIP_protein_hg38.html) |
| 34 | 36 | |
| 35 | - |
|
| 37 | + |
|
| 36 | 38 | |
| 37 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SYNCRIP.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SYNCRIP_hg38.html) |
| 38 | 40 | |
| 39 | - |
|
| 41 | + |
|
| 42 | + |
|
| 40 | 43 | ## SYNCRIP Expression |
| 41 | - |
|
| 44 | + |
|
| 42 | 45 | <!-- ORIGIN: paneaWholeGenomeLandscape2019 --> |
| 43 | 46 | <!-- BL: paneaWholeGenomeLandscape2019 --> |
| 47 | + |
|
| 44 | 48 | ## References |
| 45 | 49 | 1. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019; |
SYNE1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SYNE1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2020-09-17 : Nadeu : MCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -27,20 +29,20 @@ timeline |
| 27 | 29 | |FL |No |No |0.000 |0.000 | |
| 28 | 30 | |
| 29 | 31 | |
| 30 | -> [!NOTE] |
|
| 31 | -> First described in MCL in 2020 by [Nadeu F](https://pubmed.ncbi.nlm.nih.gov/32584970) |
|
| 32 | 32 | |
| 33 | 33 | |
| 34 | 34 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SYNE1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SYNE1_protein_hg38.html) |
| 35 | 35 | |
| 36 | - |
|
| 36 | + |
|
| 37 | 37 | |
| 38 | 38 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SYNE1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SYNE1_hg38.html) |
| 39 | 39 | |
| 40 | - |
|
| 40 | + |
|
| 41 | + |
|
| 41 | 42 | ## SYNE1 Expression |
| 42 | - |
|
| 43 | + |
|
| 43 | 44 | <!-- ORIGIN: nadeuGenomicEpigenomicInsights2020a --> |
| 44 | 45 | <!-- MCL: nadeuGenomicEpigenomicInsights2020a --> |
| 46 | + |
|
| 45 | 47 | ## References |
| 46 | 48 | 1. Nadeu F, Martín-García D, Clot G, Díaz-Navarro A, Duran-Ferrer M, Navarro A, Vilarrasa-Blasi R, Kulis M, Royo R, Gutiérrez-Abril J, Valdés-Mas R, López C, Chapaprieta V, Puiggrós M, Castellano G, Costa D, Aymerich M, Jares P, Espinet B, Muntañola A, Ribera‐Cortada I, Siebert R, Colomer D, Torrents D, Giné E, López-Guillermo A, Küppers R, Martín-Subero J, Puente X, Beà S, Campo E. Genomic and epigenomic insights into the origin, pathogenesis and clinical behavior of mantle cell lymphoma subtypes. Blood. 2020; |
SYNGAP1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SYNGAP1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -31,14 +33,16 @@ timeline |
| 31 | 33 | |
| 32 | 34 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SYNGAP1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SYNGAP1_protein_hg38.html) |
| 33 | 35 | |
| 34 | - |
|
| 36 | + |
|
| 35 | 37 | |
| 36 | 38 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SYNGAP1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SYNGAP1_hg38.html) |
| 37 | 39 | |
| 38 | - |
|
| 40 | + |
|
| 41 | + |
|
| 39 | 42 | ## SYNGAP1 Expression |
| 40 | - |
|
| 43 | + |
|
| 41 | 44 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 42 | 45 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 46 | + |
|
| 43 | 47 | ## References |
| 44 | 48 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
SYPL1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # SYPL1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2013-08-15 : Morin : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -33,14 +35,16 @@ timeline |
| 33 | 35 | |
| 34 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SYPL1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SYPL1_protein_hg38.html) |
| 35 | 37 | |
| 36 | - |
|
| 38 | + |
|
| 37 | 39 | |
| 38 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SYPL1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SYPL1_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 43 | + |
|
| 41 | 44 | ## SYPL1 Expression |
| 42 | - |
|
| 45 | + |
|
| 43 | 46 | <!-- ORIGIN: morinMutationalStructuralAnalysis2013 --> |
| 44 | 47 | <!-- DLBCL: morinMutationalStructuralAnalysis2013 --> |
| 48 | + |
|
| 45 | 49 | ## References |
| 46 | 50 | 1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992 |
TAF1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TAF1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2013-08-15 : Morin : DLBCL |
| 8 | 9 | 2016-09-08 : Spina : MZL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -32,22 +34,22 @@ timeline |
| 32 | 34 | |FL |No |No |8.661 |0 | |
| 33 | 35 | |
| 34 | 36 | |
| 35 | -> [!NOTE] |
|
| 36 | -> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601) |
|
| 37 | 37 | |
| 38 | 38 | |
| 39 | 39 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TAF1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TAF1_protein_hg38.html) |
| 40 | 40 | |
| 41 | - |
|
| 41 | + |
|
| 42 | 42 | |
| 43 | 43 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TAF1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TAF1_hg38.html) |
| 44 | 44 | |
| 45 | - |
|
| 45 | + |
|
| 46 | + |
|
| 46 | 47 | ## TAF1 Expression |
| 47 | - |
|
| 48 | + |
|
| 48 | 49 | <!-- ORIGIN: morinMutationalStructuralAnalysis2013 --> |
| 49 | 50 | <!-- MZL: spinaGeneticsNodalMarginal2016b --> |
| 50 | 51 | <!-- DLBCL: morinMutationalStructuralAnalysis2013 --> |
| 52 | + |
|
| 51 | 53 | ## References |
| 52 | 54 | 1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992 |
| 53 | 55 | 2. Spina V, Khiabanian H, Messina M, Monti S, Cascione L, Bruscaggin A, Spaccarotella E, Holmes AB, Arcaini L, Lucioni M, Tabbò F, Zairis S, Diop F, Cerri M, Chiaretti S, Marasca R, Ponzoni M, Deaglio S, Ramponi A, Tiacci E, Pasqualucci L, Paulli M, Falini B, Inghirami G, Bertoni F, Foà R, Rabadan R, Gaidano G, Rossi D. The genetics of nodal marginal zone lymphoma. Blood. 2016 Sep 8;128(10):1362–1373. |
TAP1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TAP1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2018-04-12 : Schmitz : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -34,14 +36,16 @@ timeline |
| 34 | 36 | |
| 35 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TAP1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TAP1_protein_hg38.html) |
| 36 | 38 | |
| 37 | - |
|
| 39 | + |
|
| 38 | 40 | |
| 39 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TAP1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TAP1_hg38.html) |
| 40 | 42 | |
| 41 | - |
|
| 43 | + |
|
| 44 | + |
|
| 42 | 45 | ## TAP1 Expression |
| 43 | - |
|
| 46 | + |
|
| 44 | 47 | <!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a --> |
| 45 | 48 | <!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a --> |
| 49 | + |
|
| 46 | 50 | ## References |
| 47 | 51 | 1. Schmitz R, Wright GW, Huang DW, Johnson CA, Phelan JD, Wang JQ, Roulland S, Kasbekar M, Young RM, Shaffer AL, Hodson DJ, Xiao W, Yu X, Yang Y, Zhao H, Xu W, Liu X, Zhou B, Du W, Chan WC, Jaffe ES, Gascoyne RD, Connors JM, Campo E, Lopez-Guillermo A, Rosenwald A, Ott G, Delabie J, Rimsza LM, Tay Kuang Wei K, Zelenetz AD, Leonard JP, Bartlett NL, Tran B, Shetty J, Zhao Y, Soppet DR, Pittaluga S, Wilson WH, Staudt LM. Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma. N Engl J Med. 2018 Apr 12;378(15):1396–1407. PMCID: PMC6010183 |
TBC1D26.md
| ... | ... | @@ -6,6 +6,7 @@ timeline |
| 6 | 6 | title Publication timing |
| 7 | 7 | 2014-05-08 : Zhang : MCL |
| 8 | 8 | ``` |
| 9 | + |
|
| 9 | 10 | ## Relevance tier by entity |
| 10 | 11 | |
| 11 | 12 | |Entity|Tier|Description | |
| ... | ... | @@ -27,20 +28,20 @@ timeline |
| 27 | 28 | |FL |No |No |0 |0 | |
| 28 | 29 | |
| 29 | 30 | |
| 30 | -> [!NOTE] |
|
| 31 | -> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267) |
|
| 32 | 31 | |
| 33 | 32 | |
| 34 | 33 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TBC1D26_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TBC1D26_protein_hg38.html) |
| 35 | 34 | |
| 36 | - |
|
| 35 | + |
|
| 37 | 36 | |
| 38 | 37 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TBC1D26.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TBC1D26_hg38.html) |
| 39 | 38 | |
| 40 | - |
|
| 39 | + |
|
| 40 | + |
|
| 41 | 41 | ## TBC1D26 Expression |
| 42 | - |
|
| 42 | + |
|
| 43 | 43 | <!-- ORIGIN: zhangGenomicLandscapeMantle2014 --> |
| 44 | 44 | <!-- MCL: zhangGenomicLandscapeMantle2014 --> |
| 45 | + |
|
| 45 | 46 | ## References |
| 46 | 47 | 1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996. |
TBC1D4.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TBC1D4 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2018-10-01 : Arthur : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -38,14 +40,16 @@ timeline |
| 38 | 40 | |
| 39 | 41 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TBC1D4_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TBC1D4_protein_hg38.html) |
| 40 | 42 | |
| 41 | - |
|
| 43 | + |
|
| 42 | 44 | |
| 43 | 45 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TBC1D4.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TBC1D4_hg38.html) |
| 44 | 46 | |
| 45 | - |
|
| 47 | + |
|
| 48 | + |
|
| 46 | 49 | ## TBC1D4 Expression |
| 47 | - |
|
| 50 | + |
|
| 48 | 51 | <!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 --> |
| 49 | 52 | <!-- DLBCL: arthurGenomewideDiscoverySomatic2018 --> |
| 53 | + |
|
| 50 | 54 | ## References |
| 51 | 55 | 1. Arthur SE, Jiang A, Grande BM, Alcaide M, Cojocaru R, Rushton CK, Mottok A, Hilton LK, Lat PK, Zhao EY, Culibrk L, Ennishi D, Jessa S, Chong L, Thomas N, Pararajalingam P, Meissner B, Boyle M, Davidson J, Bushell KR, Lai D, Farinha P, Slack GW, Morin GB, Shah S, Sen D, Jones SJM, Mungall AJ, Gascoyne RD, Audas TE, Unrau P, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma. Nat Commun. 2018 Oct 1;9(1):4001. PMCID: PMC6167379 |
TBC1D9B.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TBC1D9B |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -31,14 +33,16 @@ timeline |
| 31 | 33 | |
| 32 | 34 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TBC1D9B_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TBC1D9B_protein_hg38.html) |
| 33 | 35 | |
| 34 | - |
|
| 36 | + |
|
| 35 | 37 | |
| 36 | 38 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TBC1D9B.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TBC1D9B_hg38.html) |
| 37 | 39 | |
| 38 | - |
|
| 40 | + |
|
| 41 | + |
|
| 39 | 42 | ## TBC1D9B Expression |
| 40 | - |
|
| 43 | + |
|
| 41 | 44 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 42 | 45 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 46 | + |
|
| 43 | 47 | ## References |
| 44 | 48 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
TBL1XR1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TBL1XR1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2012-08-27 : Rossi : MZL |
| 8 | 9 | 2016-03-01 : Mareschal : DLBCL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -50,16 +52,18 @@ timeline |
| 50 | 52 | |
| 51 | 53 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TBL1XR1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TBL1XR1_protein_hg38.html) |
| 52 | 54 | |
| 53 | - |
|
| 55 | + |
|
| 54 | 56 | |
| 55 | 57 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TBL1XR1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TBL1XR1_hg38.html) |
| 56 | 58 | |
| 57 | - |
|
| 59 | + |
|
| 60 | + |
|
| 58 | 61 | ## TBL1XR1 Expression |
| 59 | - |
|
| 62 | + |
|
| 60 | 63 | <!-- ORIGIN: rossiCodingGenomeSplenic2012c --> |
| 61 | 64 | <!-- MZL: rossiCodingGenomeSplenic2012c --> |
| 62 | 65 | <!-- DLBCL: mareschalWholeExomeSequencing2016 --> |
| 66 | + |
|
| 63 | 67 | ## References |
| 64 | 68 | 1. Rossi D, Trifonov V, Fangazio M, Bruscaggin A, Rasi S, Spina V, Monti S, Vaisitti T, Arruga F, Famà R, Ciardullo C, Greco M, Cresta S, Piranda D, Holmes A, Fabbri G, Messina M, Rinaldi A, Wang J, Agostinelli C, Piccaluga PP, Lucioni M, Tabbò F, Serra R, Franceschetti S, Deambrogi C, Daniele G, Gattei V, Marasca R, Facchetti F, Arcaini L, Inghirami G, Bertoni F, Pileri SA, Deaglio S, Foà R, Dalla-Favera R, Pasqualucci L, Rabadan R, Gaidano G. The coding genome of splenic marginal zone lymphoma: activation of NOTCH2 and other pathways regulating marginal zone development. J Exp Med. 2012 Aug 27;209(9):1537–1551. PMCID: PMC3428941 |
| 65 | 69 | 2. Mareschal S, Dubois S, Viailly PJ, Bertrand P, Bohers E, Maingonnat C, Jaïs JP, Tesson B, Ruminy P, Peyrouze P, Copie-Bergman C, Fest T, Jo Molina T, Haioun C, Salles G, Tilly H, Lecroq T, Leroy K, Jardin F. Whole exome sequencing of relapsed/refractory patients expands the repertoire of somatic mutations in diffuse large B-cell lymphoma. Genes Chromosomes Cancer. 2016 Mar;55(3):251–267. PMID: 26608593 |
TCF3.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TCF3 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-10-04 : Schmitz : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,8 +32,6 @@ timeline |
| 30 | 32 | |FL |No |No |0.000 | 0.000 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in BL in 2012 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/22885699) |
|
| 35 | 35 | |
| 36 | 36 | |
| 37 | 37 | ## TCF3 Hotspots |
| ... | ... | @@ -49,14 +49,16 @@ timeline |
| 49 | 49 | |
| 50 | 50 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TCF3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TCF3_protein_hg38.html) |
| 51 | 51 | |
| 52 | - |
|
| 52 | + |
|
| 53 | 53 | |
| 54 | 54 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TCF3.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TCF3_hg38.html) |
| 55 | 55 | |
| 56 | - |
|
| 56 | + |
|
| 57 | + |
|
| 57 | 58 | ## TCF3 Expression |
| 58 | - |
|
| 59 | + |
|
| 59 | 60 | <!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 --> |
| 60 | 61 | <!-- BL: schmitzBurkittLymphomaPathogenesis2012 --> |
| 62 | + |
|
| 61 | 63 | ## References |
| 62 | 64 | 1. Schmitz R, Young RM, Ceribelli M, Jhavar S, Xiao W, Zhang M, Wright G, Shaffer AL, Hodson DJ, Buras E, Liu X, Powell J, Yang Y, Xu W, Zhao H, Kohlhammer H, Rosenwald A, Kluin P, Müller-Hermelink HK, Ott G, Gascoyne RD, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Ogwang MD, Reynolds SJ, Fisher RI, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Pittaluga S, Wilson W, Waldmann TA, Rowe M, Mbulaiteye SM, Rickinson AB, Staudt LM. Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics. Nature. 2012 Oct 4;490(7418):116–120. PMCID: PMC3609867 |
TCL1A.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TCL1A |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2019-03-21 : Grande : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -40,20 +42,18 @@ timeline |
| 40 | 42 | |:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:| |
| 41 | 43 | |chr14 |96179535 |96180366|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr14%3A96179535%2D96180366)|active_promoter | |
| 42 | 44 | |
| 43 | -> [!NOTE] |
|
| 44 | -> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194) |
|
| 45 | 45 | |
| 46 | 46 | |
| 47 | 47 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TCL1A_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TCL1A_protein_hg38.html) |
| 48 | 48 | |
| 49 | - |
|
| 49 | + |
|
| 50 | 50 | |
| 51 | 51 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TCL1A.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TCL1A_hg38.html) |
| 52 | 52 | |
| 53 | - |
|
| 53 | + |
|
| 54 | 54 | |
| 55 | 55 | ## TCL1A Expression |
| 56 | - |
|
| 56 | + |
|
| 57 | 57 | |
| 58 | 58 | ## References |
| 59 | 59 | 1. *Grande BM, Gerhard DS, Jiang A, Griner NB, Abramson JS, Alexander TB, Allen H, Ayers LW, Bethony JM, Bhatia K, Bowen J, Casper C, Choi JK, Culibrk L, Davidsen TM, Dyer MA, Gastier-Foster JM, Gesuwan P, Greiner TC, Gross TG, Hanf B, Harris NL, He Y, Irvin JD, Jaffe ES, Jones SJM, Kerchan P, Knoetze N, Leal FE, Lichtenberg TM, Ma Y, Martin JP, Martin MR, Mbulaiteye SM, Mullighan CG, Mungall AJ, Namirembe C, Novik K, Noy A, Ogwang MD, Omoding A, Orem J, Reynolds SJ, Rushton CK, Sandlund JT, Schmitz R, Taylor C, Wilson WH, Wright GW, Zhao EY, Marra MA, Morin RD, Staudt LM. Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma. Blood. 2019 Mar 21;133(12):1313-1324. doi: 10.1182/blood-2018-09-871418. Epub 2019 Jan 7. PMID: 30617194; PMCID: PMC6428665.* |
TERT.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TERT |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2020-09-17 : Nadeu : MCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -27,20 +29,20 @@ timeline |
| 27 | 29 | |FL |No |No |0.000 |0 | |
| 28 | 30 | |
| 29 | 31 | |
| 30 | -> [!NOTE] |
|
| 31 | -> First described in MCL in 2020 by [Nadeu F](https://pubmed.ncbi.nlm.nih.gov/32584970) |
|
| 32 | 32 | |
| 33 | 33 | |
| 34 | 34 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TERT_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TERT_protein_hg38.html) |
| 35 | 35 | |
| 36 | - |
|
| 36 | + |
|
| 37 | 37 | |
| 38 | 38 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TERT.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TERT_hg38.html) |
| 39 | 39 | |
| 40 | - |
|
| 40 | + |
|
| 41 | + |
|
| 41 | 42 | ## TERT Expression |
| 42 | - |
|
| 43 | + |
|
| 43 | 44 | <!-- ORIGIN: nadeuGenomicEpigenomicInsights2020a --> |
| 44 | 45 | <!-- MCL: nadeuGenomicEpigenomicInsights2020a --> |
| 46 | + |
|
| 45 | 47 | ## References |
| 46 | 48 | 1. Nadeu F, Martín-García D, Clot G, Díaz-Navarro A, Duran-Ferrer M, Navarro A, Vilarrasa-Blasi R, Kulis M, Royo R, Gutiérrez-Abril J, Valdés-Mas R, López C, Chapaprieta V, Puiggrós M, Castellano G, Costa D, Aymerich M, Jares P, Espinet B, Muntañola A, Ribera‐Cortada I, Siebert R, Colomer D, Torrents D, Giné E, López-Guillermo A, Küppers R, Martín-Subero J, Puente X, Beà S, Campo E. Genomic and epigenomic insights into the origin, pathogenesis and clinical behavior of mantle cell lymphoma subtypes. Blood. 2020; |
TET2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TET2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2017-05-01 : Albuquerque : DLBCL |
| 8 | 9 | 2019-09-26 : Panea : BL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -35,22 +37,22 @@ timeline |
| 35 | 37 | |FL |No |No |0.892 |10.949 | |
| 36 | 38 | |
| 37 | 39 | |
| 38 | -> [!NOTE] |
|
| 39 | -> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468) |
|
| 40 | 40 | |
| 41 | 41 | |
| 42 | 42 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TET2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TET2_protein_hg38.html) |
| 43 | 43 | |
| 44 | - |
|
| 44 | + |
|
| 45 | 45 | |
| 46 | 46 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TET2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TET2_hg38.html) |
| 47 | 47 | |
| 48 | - |
|
| 48 | + |
|
| 49 | + |
|
| 49 | 50 | ## TET2 Expression |
| 50 | - |
|
| 51 | + |
|
| 51 | 52 | <!-- ORIGIN: 28327945 --> |
| 52 | 53 | <!-- BL: paneaWholeGenomeLandscape2019 --> |
| 53 | 54 | <!-- DLBCL: albuquerqueEnhancingKnowledgeDiscovery2017a --> |
| 55 | + |
|
| 54 | 56 | ## References |
| 55 | 57 | 1. Albuquerque MA, Grande BM, Ritch EJ, Pararajalingam P, Jessa S, Krzywinski M, Grewal JK, Shah SP, Boutros PC, Morin RD. Enhancing knowledge discovery from cancer genomics data with Galaxy. Gigascience. 2017 May 1;6(5):1–13. PMCID: PMC5437943 |
| 56 | 58 | 2. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019; |
TFAP4.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TFAP4 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | Mutations in BL were first described by Grande et al.<sup>1</sup> |
| 4 | 5 | |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | title Publication timing |
| 9 | 10 | 2019-03-21 : Grande : BL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -33,14 +35,14 @@ timeline |
| 33 | 35 | |
| 34 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TFAP4_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TFAP4_protein_hg38.html) |
| 35 | 37 | |
| 36 | - |
|
| 38 | + |
|
| 37 | 39 | |
| 38 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TFAP4.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TFAP4_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 41 | 43 | |
| 42 | 44 | ## TFAP4 Expression |
| 43 | - |
|
| 45 | + |
|
| 44 | 46 | |
| 45 | 47 | ## References |
| 46 | 48 | 1. *Grande BM, Gerhard DS, Jiang A, Griner NB, Abramson JS, Alexander TB, Allen H, Ayers LW, Bethony JM, Bhatia K, Bowen J, Casper C, Choi JK, Culibrk L, Davidsen TM, Dyer MA, Gastier-Foster JM, Gesuwan P, Greiner TC, Gross TG, Hanf B, Harris NL, He Y, Irvin JD, Jaffe ES, Jones SJM, Kerchan P, Knoetze N, Leal FE, Lichtenberg TM, Ma Y, Martin JP, Martin MR, Mbulaiteye SM, Mullighan CG, Mungall AJ, Namirembe C, Novik K, Noy A, Ogwang MD, Omoding A, Orem J, Reynolds SJ, Rushton CK, Sandlund JT, Schmitz R, Taylor C, Wilson WH, Wright GW, Zhao EY, Marra MA, Morin RD, Staudt LM. Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma. Blood. 2019 Mar 21;133(12):1313-1324. doi: 10.1182/blood-2018-09-871418. Epub 2019 Jan 7. PMID: 30617194; PMCID: PMC6428665.* |
TGFBR2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TGFBR2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2017-10-10 : Reddy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -34,14 +36,16 @@ timeline |
| 34 | 36 | |
| 35 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TGFBR2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TGFBR2_protein_hg38.html) |
| 36 | 38 | |
| 37 | - |
|
| 39 | + |
|
| 38 | 40 | |
| 39 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TGFBR2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TGFBR2_hg38.html) |
| 40 | 42 | |
| 41 | - |
|
| 43 | + |
|
| 44 | + |
|
| 42 | 45 | ## TGFBR2 Expression |
| 43 | - |
|
| 46 | + |
|
| 44 | 47 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
| 45 | 48 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 49 | + |
|
| 46 | 50 | ## References |
| 47 | 51 | 1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
TIGD6.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TIGD6 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -32,14 +34,16 @@ timeline |
| 32 | 34 | |
| 33 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TIGD6_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TIGD6_protein_hg38.html) |
| 34 | 36 | |
| 35 | - |
|
| 37 | + |
|
| 36 | 38 | |
| 37 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TIGD6.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TIGD6_hg38.html) |
| 38 | 40 | |
| 39 | - |
|
| 41 | + |
|
| 42 | + |
|
| 40 | 43 | ## TIGD6 Expression |
| 41 | - |
|
| 44 | + |
|
| 42 | 45 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 43 | 46 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 47 | + |
|
| 44 | 48 | ## References |
| 45 | 49 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
TIPARP.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TIPARP |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2017-10-10 : Reddy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,20 +32,20 @@ timeline |
| 30 | 32 | |FL |No |No |0.000 |0 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567) |
|
| 35 | 35 | |
| 36 | 36 | |
| 37 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TIPARP_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TIPARP_protein_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | 40 | |
| 41 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TIPARP.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TIPARP_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | + |
|
| 44 | 45 | ## TIPARP Expression |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
| 47 | 48 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 49 | + |
|
| 48 | 50 | ## References |
| 49 | 51 | 1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
TLR2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TLR2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2013-11-05 : Bea : MCL |
| 8 | 9 | 2018-05-01 : Chapuy : DLBCL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -41,16 +43,18 @@ timeline |
| 41 | 43 | |
| 42 | 44 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TLR2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TLR2_protein_hg38.html) |
| 43 | 45 | |
| 44 | - |
|
| 46 | + |
|
| 45 | 47 | |
| 46 | 48 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TLR2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TLR2_hg38.html) |
| 47 | 49 | |
| 48 | - |
|
| 50 | + |
|
| 51 | + |
|
| 49 | 52 | ## TLR2 Expression |
| 50 | - |
|
| 53 | + |
|
| 51 | 54 | <!-- ORIGIN: beaLandscapeSomaticMutations2013 --> |
| 52 | 55 | <!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b --> |
| 53 | 56 | <!-- MCL: beaLandscapeSomaticMutations2013 --> |
| 57 | + |
|
| 54 | 58 | ## References |
| 55 | 59 | 1. Beà S, Valdés-Mas R, Navarro A, Salaverria I, Martín-Garcia D, Jares P, Giné E, Pinyol M, Royo C, Nadeu F, Conde L, Juan M, Clot G, Vizán P, Croce LD, Puente DA, López-Guerra M, Moros A, Roue G, Aymerich M, Villamor N, Colomo L, Martínez A, Valera A, Martín-Subero JI, Amador V, Hernández L, Rozman M, Enjuanes A, Forcada P, Muntañola A, Hartmann EM, Calasanz MJ, Rosenwald A, Ott G, Hernández-Rivas JM, Klapper W, Siebert R, Wiestner A, Wilson WH, Colomer D, López-Guillermo A, López-Otín C, Puente XS, Campo E. Landscape of somatic mutations and clonal evolution in mantle cell lymphoma. PNAS. 2013 Nov 5;110(45):18250–18255. PMID: 24145436 |
| 56 | 60 | 2. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387 |
TMEM30A.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TMEM30A |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2011-07-27 : Morin : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -32,8 +34,6 @@ timeline |
| 32 | 34 | |FL |No |No |5.098 | 0.000 | |
| 33 | 35 | |
| 34 | 36 | |
| 35 | -> [!NOTE] |
|
| 36 | -> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119) |
|
| 37 | 37 | |
| 38 | 38 | ## TMEM30A Hotspots |
| 39 | 39 | |
| ... | ... | @@ -45,16 +45,16 @@ timeline |
| 45 | 45 | |
| 46 | 46 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TMEM30A_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TMEM30A_protein_hg38.html) |
| 47 | 47 | |
| 48 | - |
|
| 48 | + |
|
| 49 | 49 | |
| 50 | 50 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TMEM30A.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TMEM30A_hg38.html) |
| 51 | 51 | |
| 52 | - |
|
| 52 | + |
|
| 53 | 53 | |
| 54 | 54 | ## References |
| 55 | 55 | 1. *Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351. PMID: 21796119; PMCID: PMC3210554.* |
| 56 | 56 | ## TMEM30A Expression |
| 57 | - |
|
| 57 | + |
|
| 58 | 58 | <!-- ORIGIN: morinFrequentMutationHistonemodifying2011 --> |
| 59 | 59 | <!-- DLBCL: morinFrequentMutationHistonemodifying2011 --> |
| 60 | 60 | <!-- FL: morinFrequentMutationHistonemodifying2011 --> |
TMSB4X.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TMSB4X |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | TMSB4X is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. |
| 4 | 5 | ## History |
| ... | ... | @@ -9,6 +10,7 @@ timeline |
| 9 | 10 | title Publication timing |
| 10 | 11 | 2017-05-01 : Albuquerque : DLBCL |
| 11 | 12 | ``` |
| 13 | + |
|
| 12 | 14 | ## Relevance tier by entity |
| 13 | 15 | |
| 14 | 16 | |Entity|Tier|Description | |
| ... | ... | @@ -41,20 +43,20 @@ timeline |
| 41 | 43 | |:--------:|:----------:|:--------:|:--------------------------------------------------------------------------------------------:|:------------------:| |
| 42 | 44 | |chrX |12993308 |12994511|[intron](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chrX%3A12993308%2D12994511)|active_promoter | |
| 43 | 45 | |
| 44 | -> [!NOTE] |
|
| 45 | -> First described in DLBCL in 2017 by [Albuquerque MA](https://pubmed.ncbi.nlm.nih.gov/28327945) |
|
| 46 | 46 | |
| 47 | 47 | |
| 48 | 48 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TMSB4X_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TMSB4X_protein_hg38.html) |
| 49 | 49 | |
| 50 | - |
|
| 50 | + |
|
| 51 | 51 | |
| 52 | 52 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TMSB4X.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TMSB4X_hg38.html) |
| 53 | 53 | |
| 54 | - |
|
| 54 | + |
|
| 55 | + |
|
| 55 | 56 | ## TMSB4X Expression |
| 56 | - |
|
| 57 | + |
|
| 57 | 58 | <!-- ORIGIN: albuquerqueEnhancingKnowledgeDiscovery2017a --> |
| 58 | 59 | <!-- DLBCL: albuquerqueEnhancingKnowledgeDiscovery2017a --> |
| 60 | + |
|
| 59 | 61 | ## References |
| 60 | 62 | 1. Albuquerque MA, Grande BM, Ritch EJ, Pararajalingam P, Jessa S, Krzywinski M, Grewal JK, Shah SP, Boutros PC, Morin RD. Enhancing knowledge discovery from cancer genomics data with Galaxy. Gigascience. 2017 May 1;6(5):1–13. PMCID: PMC5437943 |
TNFAIP3.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TNFAIP3 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | 2009-06-04 : Compagno : DLBCL |
| 9 | 10 | 2011-11-03 : Rossi : MZL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -36,8 +38,6 @@ timeline |
| 36 | 38 | |FL |No |No |5.686 |75.953 | |
| 37 | 39 | |
| 38 | 40 | |
| 39 | -> [!NOTE] |
|
| 40 | -> First described in DLBCL in 2009 by [Compagno M](https://pubmed.ncbi.nlm.nih.gov/19412164). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119) |
|
| 41 | 41 | |
| 42 | 42 | ## TNFAIP3 Hotspots |
| 43 | 43 | |
| ... | ... | @@ -49,15 +49,15 @@ timeline |
| 49 | 49 | |
| 50 | 50 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TNFAIP3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TNFAIP3_protein_hg38.html) |
| 51 | 51 | |
| 52 | - |
|
| 52 | + |
|
| 53 | 53 | |
| 54 | 54 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TNFAIP3.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TNFAIP3_hg38.html) |
| 55 | 55 | |
| 56 | - |
|
| 56 | + |
|
| 57 | 57 | |
| 58 | 58 | ## TNFAIP3 Expression |
| 59 | 59 | |
| 60 | - |
|
| 60 | + |
|
| 61 | 61 | |
| 62 | 62 | ## References |
| 63 | 63 | 1. |
TNFRSF14.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TNFRSF14 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2010-11-15 : Cheung : FL |
| 8 | 9 | 2016-09-08 : Spina : MZL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -34,8 +36,6 @@ timeline |
| 34 | 36 | |FL |No |Yes |96.380 |1034.281 | |
| 35 | 37 | |
| 36 | 38 | |
| 37 | -> [!NOTE] |
|
| 38 | -> First described in DLBCL in 2010 by [Cheung KJ](https://pubmed.ncbi.nlm.nih.gov/20884631). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119) |
|
| 39 | 39 | |
| 40 | 40 | ## TNFRSF14 Hotspots |
| 41 | 41 | |
| ... | ... | @@ -56,14 +56,14 @@ timeline |
| 56 | 56 | |
| 57 | 57 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TNFRSF14_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TNFRSF14_protein_hg38.html) |
| 58 | 58 | |
| 59 | - |
|
| 59 | + |
|
| 60 | 60 | |
| 61 | 61 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TNFRSF14.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TNFRSF14_hg38.html) |
| 62 | 62 | |
| 63 | - |
|
| 63 | + |
|
| 64 | 64 | |
| 65 | 65 | ## TNFRSF14 Expression |
| 66 | - |
|
| 66 | + |
|
| 67 | 67 | |
| 68 | 68 | ## References |
| 69 | 69 | 1. *Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Ch$ |
TOP2A.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TOP2A |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-10-04 : Schmitz : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -29,20 +31,20 @@ timeline |
| 29 | 31 | |FL |No |No |0.000 |0 | |
| 30 | 32 | |
| 31 | 33 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096) |
|
| 34 | 34 | |
| 35 | 35 | |
| 36 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TOP2A_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TOP2A_protein_hg38.html) |
| 37 | 37 | |
| 38 | - |
|
| 38 | + |
|
| 39 | 39 | |
| 40 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TOP2A.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TOP2A_hg38.html) |
| 41 | 41 | |
| 42 | - |
|
| 42 | + |
|
| 43 | + |
|
| 43 | 44 | ## TOP2A Expression |
| 44 | - |
|
| 45 | + |
|
| 45 | 46 | <!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 --> |
| 46 | 47 | <!-- BL: schmitzBurkittLymphomaPathogenesis2012 --> |
| 48 | + |
|
| 47 | 49 | ## References |
| 48 | 50 | 1. Schmitz R, Young RM, Ceribelli M, Jhavar S, Xiao W, Zhang M, Wright G, Shaffer AL, Hodson DJ, Buras E, Liu X, Powell J, Yang Y, Xu W, Zhao H, Kohlhammer H, Rosenwald A, Kluin P, Müller-Hermelink HK, Ott G, Gascoyne RD, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Ogwang MD, Reynolds SJ, Fisher RI, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Pittaluga S, Wilson W, Waldmann TA, Rowe M, Mbulaiteye SM, Rickinson AB, Staudt LM. Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics. Nature. 2012 Oct 4;490(7418):116–120. PMCID: PMC3609867 |
TOX.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TOX |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2017-10-10 : Reddy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -42,14 +44,16 @@ timeline |
| 42 | 44 | |
| 43 | 45 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TOX_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TOX_protein_hg38.html) |
| 44 | 46 | |
| 45 | - |
|
| 47 | + |
|
| 46 | 48 | |
| 47 | 49 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TOX.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TOX_hg38.html) |
| 48 | 50 | |
| 49 | - |
|
| 51 | + |
|
| 52 | + |
|
| 50 | 53 | ## TOX Expression |
| 51 | - |
|
| 54 | + |
|
| 52 | 55 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
| 53 | 56 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 57 | + |
|
| 54 | 58 | ## References |
| 55 | 59 | 1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
TP53.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TP53 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | |
| 4 | 5 | ```mermaid |
| ... | ... | @@ -11,6 +12,7 @@ timeline |
| 11 | 12 | 2013-11-05 : Be : MCL |
| 12 | 13 | 2018-05-31 : Tiacci : PMBL |
| 13 | 14 | ``` |
| 15 | + |
|
| 14 | 16 | ## Relevance tier by entity |
| 15 | 17 | |
| 16 | 18 | |Entity|Tier|Description | |
| ... | ... | @@ -48,14 +50,14 @@ timeline |
| 48 | 50 | |
| 49 | 51 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TP53_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TP53_protein_hg38.html) |
| 50 | 52 | |
| 51 | - |
|
| 53 | + |
|
| 52 | 54 | |
| 53 | 55 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TP53.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TP53_hg38.html) |
| 54 | 56 | |
| 55 | - |
|
| 57 | + |
|
| 56 | 58 | |
| 57 | 59 | ## TP53 Expression |
| 58 | - |
|
| 60 | + |
|
| 59 | 61 | |
| 60 | 62 | |
| 61 | 63 | <!-- ORIGIN: wildaInactivationARFMDM2p53Pathway2004 --> |
| ... | ... | @@ -65,6 +67,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T |
| 65 | 67 | <!-- MCL: beaLandscapeSomaticMutations2013 --> |
| 66 | 68 | <!-- MZL: rossiCodingGenomeSplenic2012c --> |
| 67 | 69 | <!-- PMBL: tiacciPervasiveMutationsJAKSTAT2018b --> |
| 70 | + |
|
| 68 | 71 | ## References |
| 69 | 72 | 1. Wilda M, Bruch J, Harder L, Rawer D, Reiter A, Borkhardt A, Woessmann W. Inactivation of the ARF-MDM-2-p53 pathway in sporadic Burkitt’s lymphoma in children. Leukemia. 2004 Mar;18(3):584–588. PMID: 14712292 |
| 70 | 73 | 2. Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJM, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298–303. PMCID: PMC3210554 |
TPP1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TPP1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2021-05-05 : H : FL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -27,20 +29,20 @@ timeline |
| 27 | 29 | |FL |No |No |9.163 |29.516 | |
| 28 | 30 | |
| 29 | 31 | |
| 30 | -> [!NOTE] |
|
| 31 | -> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289) |
|
| 32 | 32 | |
| 33 | 33 | |
| 34 | 34 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TPP1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TPP1_protein_hg38.html) |
| 35 | 35 | |
| 36 | - |
|
| 36 | + |
|
| 37 | 37 | |
| 38 | 38 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TPP1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TPP1_hg38.html) |
| 39 | 39 | |
| 40 | - |
|
| 40 | + |
|
| 41 | + |
|
| 41 | 42 | ## TPP1 Expression |
| 42 | - |
|
| 43 | + |
|
| 43 | 44 | <!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b --> |
| 44 | 45 | <!-- FL: hubschmannMutationalMechanismsShaping2021b --> |
| 46 | + |
|
| 45 | 47 | ## References |
| 46 | 48 | 1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491 |
TPST2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TPST2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -29,20 +31,20 @@ timeline |
| 29 | 31 | |FL |No |No |0.000 |0 | |
| 30 | 32 | |
| 31 | 33 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597) |
|
| 34 | 34 | |
| 35 | 35 | |
| 36 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TPST2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TPST2_protein_hg38.html) |
| 37 | 37 | |
| 38 | - |
|
| 38 | + |
|
| 39 | 39 | |
| 40 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TPST2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TPST2_hg38.html) |
| 41 | 41 | |
| 42 | - |
|
| 42 | + |
|
| 43 | + |
|
| 43 | 44 | ## TPST2 Expression |
| 44 | - |
|
| 45 | + |
|
| 45 | 46 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 46 | 47 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 48 | + |
|
| 47 | 49 | ## References |
| 48 | 50 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
TRAF3.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TRAF3 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | 2011-11-03 : Rossi : MZL |
| 9 | 10 | 2012-06-01 : Otto : PMBL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -37,17 +39,19 @@ timeline |
| 37 | 39 | |
| 38 | 40 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TRAF3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TRAF3_protein_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 41 | 43 | |
| 42 | 44 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TRAF3.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TRAF3_hg38.html) |
| 43 | 45 | |
| 44 | - |
|
| 46 | + |
|
| 47 | + |
|
| 45 | 48 | ## TRAF3 Expression |
| 46 | - |
|
| 49 | + |
|
| 47 | 50 | <!-- ORIGIN: rossiAlterationBIRC3Multiple2011a --> |
| 48 | 51 | <!-- MZL: rossiAlterationBIRC3Multiple2011a --> |
| 49 | 52 | <!-- DLBCL: pasqualucciAnalysisCodingGenome2011 --> |
| 50 | 53 | <!-- PMBL: ottoGeneticLesionsTRAF32012a --> |
| 54 | + |
|
| 51 | 55 | ## References |
| 52 | 56 | 1. Pasqualucci L, Trifonov V, Fabbri G, Ma J, Rossi D, Chiarenza A, Wells VA, Grunn A, Messina M, Elliot O, Chan J, Bhagat G, Chadburn A, Gaidano G, Mullighan CG, Rabadan R, Dalla-Favera R. Analysis of the coding genome of diffuse large B-cell lymphoma. Nat Genet. 2011 Jul 31;43(9):830–837. PMCID: PMC3297422 |
| 53 | 57 | 2. Rossi D, Deaglio S, Dominguez-Sola D, Rasi S, Vaisitti T, Agostinelli C, Spina V, Bruscaggin A, Monti S, Cerri M, Cresta S, Fangazio M, Arcaini L, Lucioni M, Marasca R, Thieblemont C, Capello D, Facchetti F, Kwee I, Pileri SA, Foà R, Bertoni F, Dalla-Favera R, Pasqualucci L, Gaidano G. Alteration of BIRC3 and multiple other NF-κB pathway genes in splenic marginal zone lymphoma. Blood. 2011 Nov 3;118(18):4930–4934. PMID: 21881048 |
TRAF6.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TRAF6 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2021-05-05 : Hübschmann : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -41,14 +43,16 @@ timeline |
| 41 | 43 | |
| 42 | 44 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TRAF6_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TRAF6_protein_hg38.html) |
| 43 | 45 | |
| 44 | - |
|
| 46 | + |
|
| 45 | 47 | |
| 46 | 48 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TRAF6.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TRAF6_hg38.html) |
| 47 | 49 | |
| 48 | - |
|
| 50 | + |
|
| 51 | + |
|
| 49 | 52 | ## TRAF6 Expression |
| 50 | - |
|
| 53 | + |
|
| 51 | 54 | <!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b --> |
| 52 | 55 | <!-- DLBCL: hubschmannMutationalMechanismsShaping2021b --> |
| 56 | + |
|
| 53 | 57 | ## References |
| 54 | 58 | 1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491 |
TRIP12.md
| ... | ... | @@ -27,12 +27,14 @@ |
| 27 | 27 | |
| 28 | 28 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TRIP12_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TRIP12_protein_hg38.html) |
| 29 | 29 | |
| 30 | - |
|
| 30 | + |
|
| 31 | 31 | |
| 32 | 32 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TRIP12.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TRIP12_hg38.html) |
| 33 | 33 | |
| 34 | - |
|
| 34 | + |
|
| 35 | + |
|
| 35 | 36 | ## TRIP12 Expression |
| 36 | - |
|
| 37 | + |
|
| 37 | 38 | <!-- ORIGIN: Unknown --> |
| 39 | + |
|
| 38 | 40 | ## References |
TRRAP.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TRRAP |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2012-08-27 : Rossi : MZL |
| 8 | 9 | 2013-12-13 : Parry : DLBCL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -42,16 +44,18 @@ timeline |
| 42 | 44 | |
| 43 | 45 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TRRAP_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TRRAP_protein_hg38.html) |
| 44 | 46 | |
| 45 | - |
|
| 47 | + |
|
| 46 | 48 | |
| 47 | 49 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TRRAP.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TRRAP_hg38.html) |
| 48 | 50 | |
| 49 | - |
|
| 51 | + |
|
| 52 | + |
|
| 50 | 53 | ## TRRAP Expression |
| 51 | - |
|
| 54 | + |
|
| 52 | 55 | <!-- ORIGIN: rossiCodingGenomeSplenic2012c --> |
| 53 | 56 | <!-- DLBCL: parryWholeExomeSequencing2013 --> |
| 54 | 57 | <!-- MZL: rossiCodingGenomeSplenic2012c --> |
| 58 | + |
|
| 55 | 59 | ## References |
| 56 | 60 | 1. Rossi D, Trifonov V, Fangazio M, Bruscaggin A, Rasi S, Spina V, Monti S, Vaisitti T, Arruga F, Famà R, Ciardullo C, Greco M, Cresta S, Piranda D, Holmes A, Fabbri G, Messina M, Rinaldi A, Wang J, Agostinelli C, Piccaluga PP, Lucioni M, Tabbò F, Serra R, Franceschetti S, Deambrogi C, Daniele G, Gattei V, Marasca R, Facchetti F, Arcaini L, Inghirami G, Bertoni F, Pileri SA, Deaglio S, Foà R, Dalla-Favera R, Pasqualucci L, Rabadan R, Gaidano G. The coding genome of splenic marginal zone lymphoma: activation of NOTCH2 and other pathways regulating marginal zone development. J Exp Med. 2012 Aug 27;209(9):1537–1551. PMCID: PMC3428941 |
| 57 | 61 | 2. Parry M, Rose-Zerilli MJJ, Gibson J, Ennis S, Walewska R, Forster J, Parker H, Davis Z, Gardiner A, Collins A, Oscier DG, Strefford JC. Whole exome sequencing identifies novel recurrently mutated genes in patients with splenic marginal zone lymphoma. PLoS One. 2013;8(12):e83244. PMCID: PMC3862727 |
TTN.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # TTN |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2022-07-06 : Burkhardt : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -37,14 +39,16 @@ timeline |
| 37 | 39 | |
| 38 | 40 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TTN_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TTN_protein_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 41 | 43 | |
| 42 | 44 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/TTN.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/TTN_hg38.html) |
| 43 | 45 | |
| 44 | - |
|
| 46 | + |
|
| 47 | + |
|
| 45 | 48 | ## TTN Expression |
| 46 | - |
|
| 49 | + |
|
| 47 | 50 | <!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b --> |
| 48 | 51 | <!-- BL: burkhardtClinicalRelevanceMolecular2022b --> |
| 52 | + |
|
| 49 | 53 | ## References |
| 50 | 54 | 1. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584 |
UBE2A.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # UBE2A |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2015-02-12 : Reichel : PMBL |
| 8 | 9 | 2017-10-10 : Reddy : DLBCL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -35,16 +37,18 @@ timeline |
| 35 | 37 | |
| 36 | 38 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/UBE2A_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/UBE2A_protein_hg38.html) |
| 37 | 39 | |
| 38 | - |
|
| 40 | + |
|
| 39 | 41 | |
| 40 | 42 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/UBE2A.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/UBE2A_hg38.html) |
| 41 | 43 | |
| 42 | - |
|
| 44 | + |
|
| 45 | + |
|
| 43 | 46 | ## UBE2A Expression |
| 44 | - |
|
| 47 | + |
|
| 45 | 48 | <!-- ORIGIN: reichelFlowSortingExome2015a --> |
| 46 | 49 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 47 | 50 | <!-- PMBL: reichelFlowSortingExome2015a --> |
| 51 | + |
|
| 48 | 52 | ## References |
| 49 | 53 | 1. Reichel J, Chadburn A, Rubinstein PG, Giulino-Roth L, Tam W, Liu Y, Gaiolla R, Eng K, Brody J, Inghirami G, Carlo-Stella C, Santoro A, Rahal D, Totonchy J, Elemento O, Cesarman E, Roshal M. Flow sorting and exome sequencing reveal the oncogenome of primary Hodgkin and Reed-Sternberg cells. Blood. 2015 Feb 12;125(7):1061–1072. PMID: 25488972 |
| 50 | 54 | 2. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
UBE2J1.md
| ... | ... | @@ -32,12 +32,14 @@ |
| 32 | 32 | |
| 33 | 33 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/UBE2J1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/UBE2J1_protein_hg38.html) |
| 34 | 34 | |
| 35 | - |
|
| 35 | + |
|
| 36 | 36 | |
| 37 | 37 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/UBE2J1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/UBE2J1_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | + |
|
| 40 | 41 | ## UBE2J1 Expression |
| 41 | - |
|
| 42 | + |
|
| 42 | 43 | <!-- ORIGIN: Unknown --> |
| 44 | + |
|
| 43 | 45 | ## References |
UBR5.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # UBR5 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2013-01-01 : Zhang : DLBCL |
| 8 | 9 | 2020-07-30 : Pararajalingam : MCL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -34,22 +36,22 @@ timeline |
| 34 | 36 | |FL |No |No |0.918 |6.988 | |
| 35 | 37 | |
| 36 | 38 | |
| 37 | -> [!NOTE] |
|
| 38 | -> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937). First described in MCL in 2020 by [Pararajalingam P](https://pubmed.ncbi.nlm.nih.gov/32160292) |
|
| 39 | 39 | |
| 40 | 40 | |
| 41 | 41 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/UBR5_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/UBR5_protein_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | 44 | |
| 45 | 45 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/UBR5.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/UBR5_hg38.html) |
| 46 | 46 | |
| 47 | - |
|
| 47 | + |
|
| 48 | + |
|
| 48 | 49 | ## UBR5 Expression |
| 49 | - |
|
| 50 | + |
|
| 50 | 51 | <!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 --> |
| 51 | 52 | <!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 --> |
| 52 | 53 | <!-- MCL: pararajalingamCodingNoncodingDrivers2020 --> |
| 54 | + |
|
| 53 | 55 | ## References |
| 54 | 56 | 1. Zhang J, Grubor V, Love CL, Banerjee A, Richards KL, Mieczkowski PA, Dunphy C, Choi W, Au WY, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers C, Naresh K, Evens A, Gordon LI, Czader M, Gill JI, Hsi ED, Liu Q, Fan A, Walsh K, Jima D, Smith LL, Johnson AJ, Byrd JC, Luftig MA, Ni T, Zhu J, Chadburn A, Levy S, Dunson D, Dave SS. Genetic heterogeneity of diffuse large B-cell lymphoma. 2013 Jan; |
| 55 | 57 | 2. Pararajalingam P, Coyle KM, Arthur SE, Thomas N, Alcaide M, Meissner B, Boyle M, Qureshi Q, Grande BM, Rushton C, Slack GW, Mungall AJ, Tam CS, Agarwal R, Dawson SJ, Lenz G, Balasubramanian S, Gascoyne RD, Steidl C, Connors J, Villa D, Audas TE, Marra MA, Johnson NA, Scott DW, Morin RD. Coding and noncoding drivers of mantle cell lymphoma identified through exome and genome sequencing. Blood. 2020 Jul 30;136(5):572–584. PMCID: PMC7440974 |
UNC5B.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # UNC5B |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2021-05-05 : Hübschmann : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -32,14 +34,16 @@ timeline |
| 32 | 34 | |
| 33 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/UNC5B_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/UNC5B_protein_hg38.html) |
| 34 | 36 | |
| 35 | - |
|
| 37 | + |
|
| 36 | 38 | |
| 37 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/UNC5B.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/UNC5B_hg38.html) |
| 38 | 40 | |
| 39 | - |
|
| 41 | + |
|
| 42 | + |
|
| 40 | 43 | ## UNC5B Expression |
| 41 | - |
|
| 44 | + |
|
| 42 | 45 | <!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b --> |
| 43 | 46 | <!-- DLBCL: hubschmannMutationalMechanismsShaping2021b --> |
| 47 | + |
|
| 44 | 48 | ## References |
| 45 | 49 | 1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491 |
UNC5C.md
| ... | ... | @@ -28,11 +28,14 @@ |
| 28 | 28 | |
| 29 | 29 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/UNC5C_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/UNC5C_protein_hg38.html) |
| 30 | 30 | |
| 31 | - |
|
| 31 | + |
|
| 32 | 32 | |
| 33 | 33 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/UNC5C.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/UNC5C_hg38.html) |
| 34 | 34 | |
| 35 | - |
|
| 35 | + |
|
| 36 | + |
|
| 36 | 37 | ## UNC5C Expression |
| 37 | - |
|
| 38 | + |
|
| 38 | 39 | <!-- ORIGIN: Unknown --> |
| 40 | + |
|
| 41 | +## References |
UNC5D.md
| ... | ... | @@ -27,14 +27,15 @@ |
| 27 | 27 | |
| 28 | 28 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/UNC5D_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/UNC5D_protein_hg38.html) |
| 29 | 29 | |
| 30 | - |
|
| 30 | + |
|
| 31 | 31 | |
| 32 | 32 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/UNC5D.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/UNC5D_hg38.html) |
| 33 | 33 | |
| 34 | - |
|
| 34 | + |
|
| 35 | 35 | |
| 36 | 36 | ## UNC5D Expression |
| 37 | - |
|
| 37 | + |
|
| 38 | 38 | |
| 39 | 39 | <!-- ORIGIN: Unknown --> |
| 40 | + |
|
| 40 | 41 | ## References |
USP7.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # USP7 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2019-03-21 : Grande : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -37,14 +39,14 @@ timeline |
| 37 | 39 | |
| 38 | 40 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/USP7_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/USP7_protein_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 41 | 43 | |
| 42 | 44 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/USP7.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/USP7_hg38.html) |
| 43 | 45 | |
| 44 | - |
|
| 46 | + |
|
| 45 | 47 | |
| 46 | 48 | ## USP7 Expression |
| 47 | - |
|
| 49 | + |
|
| 48 | 50 | |
| 49 | 51 | ## References |
| 50 | 52 | 1. *Grande BM, Gerhard DS, Jiang A, Griner NB, Abramson JS, Alexander TB, Allen H, Ayers LW, Bethony JM, Bhatia K, Bowen J, Casper C, Choi JK, Culibrk L, Davidsen TM, Dyer MA, Gastier-Foster JM, Gesuwan P, Greiner TC, Gross TG, Hanf B, Harris NL, He Y, Irvin JD, Jaffe ES, Jones SJM, Kerchan P, Knoetze N, Leal FE, Lichtenberg TM, Ma Y, Martin JP, Martin MR, Mbulaiteye SM, Mullighan CG, Mungall AJ, Namirembe C, Novik K, Noy A, Ogwang MD, Omoding A, Orem J, Reynolds SJ, Rushton CK, Sandlund JT, Schmitz R, Taylor C, Wilson WH, Wright GW, Zhao EY, Marra MA, Morin RD, Staudt LM. Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma. Blood. 2019 Mar 21;133(12):1313-1324. doi: 10.1182/blood-2018-09-871418. Epub 2019 Jan 7. PMID: 30617194; PMCID: PMC6428665.* |
VMA21.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # VMA21 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2021-05-05 : H : FL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -27,20 +29,20 @@ timeline |
| 27 | 29 | |FL |No |Yes |25.632 |598.612 | |
| 28 | 30 | |
| 29 | 31 | |
| 30 | -> [!NOTE] |
|
| 31 | -> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289) |
|
| 32 | 32 | |
| 33 | 33 | |
| 34 | 34 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/VMA21_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/VMA21_protein_hg38.html) |
| 35 | 35 | |
| 36 | - |
|
| 36 | + |
|
| 37 | 37 | |
| 38 | 38 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/VMA21.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/VMA21_hg38.html) |
| 39 | 39 | |
| 40 | - |
|
| 40 | + |
|
| 41 | + |
|
| 41 | 42 | ## VMA21 Expression |
| 42 | - |
|
| 43 | + |
|
| 43 | 44 | <!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b --> |
| 44 | 45 | <!-- FL: hubschmannMutationalMechanismsShaping2021b --> |
| 46 | + |
|
| 45 | 47 | ## References |
| 46 | 48 | 1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491 |
VPS13B.md
| ... | ... | @@ -35,11 +35,14 @@ |
| 35 | 35 | |
| 36 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/VPS13B_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/VPS13B_protein_hg38.html) |
| 37 | 37 | |
| 38 | - |
|
| 38 | + |
|
| 39 | 39 | |
| 40 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/VPS13B.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/VPS13B_hg38.html) |
| 41 | 41 | |
| 42 | - |
|
| 42 | + |
|
| 43 | + |
|
| 43 | 44 | ## VPS13B Expression |
| 44 | - |
|
| 45 | + |
|
| 45 | 46 | <!-- ORIGIN: Unknown --> |
| 47 | + |
|
| 48 | +## References |
VWA7.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # VWA7 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2022-07-06 : Burkhardt : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -29,20 +31,20 @@ timeline |
| 29 | 31 | |FL |No |No |1.950 |0 | |
| 30 | 32 | |
| 31 | 33 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096) |
|
| 34 | 34 | |
| 35 | 35 | |
| 36 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/VWA7_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/VWA7_protein_hg38.html) |
| 37 | 37 | |
| 38 | - |
|
| 38 | + |
|
| 39 | 39 | |
| 40 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/VWA7.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/VWA7_hg38.html) |
| 41 | 41 | |
| 42 | - |
|
| 42 | + |
|
| 43 | + |
|
| 43 | 44 | ## VWA7 Expression |
| 44 | - |
|
| 45 | + |
|
| 45 | 46 | <!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b --> |
| 46 | 47 | <!-- BL: burkhardtClinicalRelevanceMolecular2022b --> |
| 48 | + |
|
| 47 | 49 | ## References |
| 48 | 50 | 1. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584 |
WAC.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # WAC |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2012-08-27 : Rossi : MZL |
| 8 | 9 | 2017-10-10 : Reddy : DLBCL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -32,22 +34,22 @@ timeline |
| 32 | 34 | |FL |No |No |0.000 |0 | |
| 33 | 35 | |
| 34 | 36 | |
| 35 | -> [!NOTE] |
|
| 36 | -> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567) |
|
| 37 | 37 | |
| 38 | 38 | |
| 39 | 39 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/WAC_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/WAC_protein_hg38.html) |
| 40 | 40 | |
| 41 | - |
|
| 41 | + |
|
| 42 | 42 | |
| 43 | 43 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/WAC.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/WAC_hg38.html) |
| 44 | 44 | |
| 45 | - |
|
| 45 | + |
|
| 46 | + |
|
| 46 | 47 | ## WAC Expression |
| 47 | - |
|
| 48 | + |
|
| 48 | 49 | <!-- ORIGIN: rossiCodingGenomeSplenic2012c --> |
| 49 | 50 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 50 | 51 | <!-- MZL: rossiCodingGenomeSplenic2012c --> |
| 52 | + |
|
| 51 | 53 | ## References |
| 52 | 54 | 1. Rossi D, Trifonov V, Fangazio M, Bruscaggin A, Rasi S, Spina V, Monti S, Vaisitti T, Arruga F, Famà R, Ciardullo C, Greco M, Cresta S, Piranda D, Holmes A, Fabbri G, Messina M, Rinaldi A, Wang J, Agostinelli C, Piccaluga PP, Lucioni M, Tabbò F, Serra R, Franceschetti S, Deambrogi C, Daniele G, Gattei V, Marasca R, Facchetti F, Arcaini L, Inghirami G, Bertoni F, Pileri SA, Deaglio S, Foà R, Dalla-Favera R, Pasqualucci L, Rabadan R, Gaidano G. The coding genome of splenic marginal zone lymphoma: activation of NOTCH2 and other pathways regulating marginal zone development. J Exp Med. 2012 Aug 27;209(9):1537–1551. PMCID: PMC3428941 |
| 53 | 55 | 2. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
WDFY3.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # WDFY3 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2013-08-15 : Morin : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,20 +32,20 @@ timeline |
| 30 | 32 | |FL |No |No |2.069 |0.000 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601) |
|
| 35 | 35 | |
| 36 | 36 | |
| 37 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/WDFY3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/WDFY3_protein_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | 40 | |
| 41 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/WDFY3.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/WDFY3_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | + |
|
| 44 | 45 | ## WDFY3 Expression |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | <!-- ORIGIN: morinMutationalStructuralAnalysis2013 --> |
| 47 | 48 | <!-- DLBCL: morinMutationalStructuralAnalysis2013 --> |
| 49 | + |
|
| 48 | 50 | ## References |
| 49 | 51 | 1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992 |
WDR7.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # WDR7 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2019-09-26 : Panea : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -29,20 +31,20 @@ timeline |
| 29 | 31 | |FL |No |No |1.904 |8.746 | |
| 30 | 32 | |
| 31 | 33 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468) |
|
| 34 | 34 | |
| 35 | 35 | |
| 36 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/WDR7_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/WDR7_protein_hg38.html) |
| 37 | 37 | |
| 38 | - |
|
| 38 | + |
|
| 39 | 39 | |
| 40 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/WDR7.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/WDR7_hg38.html) |
| 41 | 41 | |
| 42 | - |
|
| 42 | + |
|
| 43 | + |
|
| 43 | 44 | ## WDR7 Expression |
| 44 | - |
|
| 45 | + |
|
| 45 | 46 | <!-- ORIGIN: paneaWholeGenomeLandscape2019 --> |
| 46 | 47 | <!-- BL: paneaWholeGenomeLandscape2019 --> |
| 48 | + |
|
| 47 | 49 | ## References |
| 48 | 50 | 1. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019; |
WDR90.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # WDR90 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-10-04 : Schmitz : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -33,14 +35,16 @@ timeline |
| 33 | 35 | |
| 34 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/WDR90_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/WDR90_protein_hg38.html) |
| 35 | 37 | |
| 36 | - |
|
| 38 | + |
|
| 37 | 39 | |
| 38 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/WDR90.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/WDR90_hg38.html) |
| 39 | 41 | |
| 40 | - |
|
| 42 | + |
|
| 43 | + |
|
| 41 | 44 | ## WDR90 Expression |
| 42 | - |
|
| 45 | + |
|
| 43 | 46 | <!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 --> |
| 44 | 47 | <!-- BL: schmitzBurkittLymphomaPathogenesis2012 --> |
| 48 | + |
|
| 45 | 49 | ## References |
| 46 | 50 | 1. Schmitz R, Young RM, Ceribelli M, Jhavar S, Xiao W, Zhang M, Wright G, Shaffer AL, Hodson DJ, Buras E, Liu X, Powell J, Yang Y, Xu W, Zhao H, Kohlhammer H, Rosenwald A, Kluin P, Müller-Hermelink HK, Ott G, Gascoyne RD, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Ogwang MD, Reynolds SJ, Fisher RI, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Pittaluga S, Wilson W, Waldmann TA, Rowe M, Mbulaiteye SM, Rickinson AB, Staudt LM. Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics. Nature. 2012 Oct 4;490(7418):116–120. PMCID: PMC3609867 |
WEE1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # WEE1 |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | WEE1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. |
| 4 | 5 | ## History |
| ... | ... | @@ -9,6 +10,7 @@ timeline |
| 9 | 10 | 2015-02-12 : Reichel : PMBL |
| 10 | 11 | 2018-04-12 : Schmitz : DLBCL |
| 11 | 12 | ``` |
| 13 | + |
|
| 12 | 14 | ## Relevance tier by entity |
| 13 | 15 | |
| 14 | 16 | |Entity|Tier|Description | |
| ... | ... | @@ -52,16 +54,18 @@ timeline |
| 52 | 54 | |
| 53 | 55 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/WEE1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/WEE1_protein_hg38.html) |
| 54 | 56 | |
| 55 | - |
|
| 57 | + |
|
| 56 | 58 | |
| 57 | 59 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/WEE1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/WEE1_hg38.html) |
| 58 | 60 | |
| 59 | - |
|
| 61 | + |
|
| 62 | + |
|
| 60 | 63 | ## WEE1 Expression |
| 61 | - |
|
| 64 | + |
|
| 62 | 65 | <!-- ORIGIN: reichelFlowSortingExome2015a --> |
| 63 | 66 | <!-- PMBL: reichelFlowSortingExome2015a --> |
| 64 | 67 | <!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a --> |
| 68 | + |
|
| 65 | 69 | ## References |
| 66 | 70 | 1. Reichel J, Chadburn A, Rubinstein PG, Giulino-Roth L, Tam W, Liu Y, Gaiolla R, Eng K, Brody J, Inghirami G, Carlo-Stella C, Santoro A, Rahal D, Totonchy J, Elemento O, Cesarman E, Roshal M. Flow sorting and exome sequencing reveal the oncogenome of primary Hodgkin and Reed-Sternberg cells. Blood. 2015 Feb 12;125(7):1061–1072. PMID: 25488972 |
| 67 | 71 | 2. Schmitz R, Wright GW, Huang DW, Johnson CA, Phelan JD, Wang JQ, Roulland S, Kasbekar M, Young RM, Shaffer AL, Hodson DJ, Xiao W, Yu X, Yang Y, Zhao H, Xu W, Liu X, Zhou B, Du W, Chan WC, Jaffe ES, Gascoyne RD, Connors JM, Campo E, Lopez-Guillermo A, Rosenwald A, Ott G, Delabie J, Rimsza LM, Tay Kuang Wei K, Zelenetz AD, Leonard JP, Bartlett NL, Tran B, Shetty J, Zhao Y, Soppet DR, Pittaluga S, Wilson WH, Staudt LM. Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma. N Engl J Med. 2018 Apr 12;378(15):1396–1407. PMCID: PMC6010183 |
WHAMM.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # WHAMM |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-10-04 : Schmitz : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -32,14 +34,16 @@ timeline |
| 32 | 34 | |
| 33 | 35 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/WHAMM_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/WHAMM_protein_hg38.html) |
| 34 | 36 | |
| 35 | - |
|
| 37 | + |
|
| 36 | 38 | |
| 37 | 39 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/WHAMM.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/WHAMM_hg38.html) |
| 38 | 40 | |
| 39 | - |
|
| 41 | + |
|
| 42 | + |
|
| 40 | 43 | ## WHAMM Expression |
| 41 | - |
|
| 44 | + |
|
| 42 | 45 | <!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 --> |
| 43 | 46 | <!-- BL: schmitzBurkittLymphomaPathogenesis2012 --> |
| 47 | + |
|
| 44 | 48 | ## References |
| 45 | 49 | 1. Schmitz R, Young RM, Ceribelli M, Jhavar S, Xiao W, Zhang M, Wright G, Shaffer AL, Hodson DJ, Buras E, Liu X, Powell J, Yang Y, Xu W, Zhao H, Kohlhammer H, Rosenwald A, Kluin P, Müller-Hermelink HK, Ott G, Gascoyne RD, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Ogwang MD, Reynolds SJ, Fisher RI, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Pittaluga S, Wilson W, Waldmann TA, Rowe M, Mbulaiteye SM, Rickinson AB, Staudt LM. Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics. Nature. 2012 Oct 4;490(7418):116–120. PMCID: PMC3609867 |
WNK1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # WNK1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -8,6 +9,7 @@ timeline |
| 8 | 9 | 2021-05-05 : Hübschmann : DLBCL |
| 9 | 10 | 2023-02-03 : Thomas : BL |
| 10 | 11 | ``` |
| 12 | + |
|
| 11 | 13 | ## Relevance tier by entity |
| 12 | 14 | |
| 13 | 15 | |Entity|Tier|Description | |
| ... | ... | @@ -46,18 +48,20 @@ timeline |
| 46 | 48 | |
| 47 | 49 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/WNK1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/WNK1_protein_hg38.html) |
| 48 | 50 | |
| 49 | - |
|
| 51 | + |
|
| 50 | 52 | |
| 51 | 53 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/WNK1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/WNK1_hg38.html) |
| 52 | 54 | |
| 53 | - |
|
| 55 | + |
|
| 56 | + |
|
| 54 | 57 | ## WNK1 Expression |
| 55 | - |
|
| 58 | + |
|
| 56 | 59 | |
| 57 | 60 | <!-- ORIGIN: jalladesExomeSequencingIdentifies2017 --> |
| 58 | 61 | <!-- DLBCL: hubschmannMutationalMechanismsShaping2021b --> |
| 59 | 62 | <!-- MZL: jalladesExomeSequencingIdentifies2017 --> |
| 60 | 63 | <!-- BL: thomasGeneticSubgroupsInform2023 --> |
| 64 | + |
|
| 61 | 65 | ## References |
| 62 | 66 | 1. Jallades L, Baseggio L, Sujobert P, Huet S, Chabane K, Callet-Bauchu E, Verney A, Hayette S, Desvignes JP, Salgado D, Levy N, Béroud C, Felman P, Berger F, Magaud JP, Genestier L, Salles G, Traverse-Glehen A. Exome sequencing identifies recurrent BCOR alterations and the absence of KLF2, TNFAIP3 and MYD88 mutations in splenic diffuse red pulp small B-cell lymphoma. Haematologica. 2017 Oct;102(10):1758–1766. PMCID: PMC5622860 |
| 63 | 67 | 2. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491 |
WNK2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # WNK2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2019-09-26 : Panea : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -29,8 +31,6 @@ timeline |
| 29 | 31 | |FL |No |No |0.000 |0 | |
| 30 | 32 | |
| 31 | 33 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468) |
|
| 34 | 34 | |
| 35 | 35 | |
| 36 | 36 | ## WNK2 Hotspots |
| ... | ... | @@ -41,14 +41,16 @@ timeline |
| 41 | 41 | |
| 42 | 42 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/WNK2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/WNK2_protein_hg38.html) |
| 43 | 43 | |
| 44 | - |
|
| 44 | + |
|
| 45 | 45 | |
| 46 | 46 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/WNK2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/WNK2_hg38.html) |
| 47 | 47 | |
| 48 | - |
|
| 48 | + |
|
| 49 | + |
|
| 49 | 50 | ## WNK2 Expression |
| 50 | - |
|
| 51 | + |
|
| 51 | 52 | <!-- ORIGIN: paneaWholeGenomeLandscape2019 --> |
| 52 | 53 | <!-- BL: paneaWholeGenomeLandscape2019 --> |
| 54 | + |
|
| 53 | 55 | ## References |
| 54 | 56 | 1. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019; |
XBP1.md
| ... | ... | @@ -32,12 +32,15 @@ |
| 32 | 32 | |
| 33 | 33 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/XBP1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/XBP1_protein_hg38.html) |
| 34 | 34 | |
| 35 | - |
|
| 35 | + |
|
| 36 | 36 | |
| 37 | 37 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/XBP1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/XBP1_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | + |
|
| 40 | 41 | ## XBP1 Expression |
| 41 | - |
|
| 42 | + |
|
| 42 | 43 | |
| 43 | 44 | <!-- FLAGGED FOR REMOVAL --><!-- ORIGIN: Unknown --> |
| 45 | + |
|
| 46 | +## References |
XIRP2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # XIRP2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2023-07-26 : Russler : FL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -27,8 +29,6 @@ timeline |
| 27 | 29 | |FL |No |No |0.000 |0.000 | |
| 28 | 30 | |
| 29 | 31 | |
| 30 | -> [!NOTE] |
|
| 31 | -> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986) |
|
| 32 | 32 | |
| 33 | 33 | |
| 34 | 34 | ## XIRP2 Hotspots |
| ... | ... | @@ -39,14 +39,16 @@ timeline |
| 39 | 39 | |
| 40 | 40 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/XIRP2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/XIRP2_protein_hg38.html) |
| 41 | 41 | |
| 42 | - |
|
| 42 | + |
|
| 43 | 43 | |
| 44 | 44 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/XIRP2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/XIRP2_hg38.html) |
| 45 | 45 | |
| 46 | - |
|
| 46 | + |
|
| 47 | + |
|
| 47 | 48 | ## XIRP2 Expression |
| 48 | - |
|
| 49 | + |
|
| 49 | 50 | <!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a --> |
| 50 | 51 | <!-- FL: russler-germainMutationsAssociatedProgression2023b --> |
| 52 | + |
|
| 51 | 53 | ## References |
| 52 | 54 | 1. Russler-Germain DA, Krysiak K, Ramirez CA, Mosior M, Watkins MP, Gomez F, Skidmore ZL, Trani L, Gao F, Geyer S, Cashen A, Mehta-Shah N, Kahl B, Bartlett N, Alderuccio J, Lossos I, Ondrejka S, Hsi E, Martin P, Leonard J, Griffith M, Griffith O, Fehniger T. Mutations associated with progression in follicular lymphoma predict inferior outcomes at diagnosis: Alliance A151303. Blood Advances. 2023;7:5524–5539. |
XPO1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # XPO1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2016-03-01 : Mareschal : DLBCL |
| 8 | 9 | 2016-06-01 : Jardin : PMBL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -41,16 +43,18 @@ timeline |
| 41 | 43 | |
| 42 | 44 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/XPO1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/XPO1_protein_hg38.html) |
| 43 | 45 | |
| 44 | - |
|
| 46 | + |
|
| 45 | 47 | |
| 46 | 48 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/XPO1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/XPO1_hg38.html) |
| 47 | 49 | |
| 48 | - |
|
| 50 | + |
|
| 51 | + |
|
| 49 | 52 | ## XPO1 Expression |
| 50 | - |
|
| 53 | + |
|
| 51 | 54 | <!-- ORIGIN: mareschalWholeExomeSequencing2016 --> |
| 52 | 55 | <!-- DLBCL: mareschalWholeExomeSequencing2016 --> |
| 53 | 56 | <!-- PMBL: jardinRecurrentMutationsExportin2016a --> |
| 57 | + |
|
| 54 | 58 | ## References |
| 55 | 59 | 1. Mareschal S, Dubois S, Viailly PJ, Bertrand P, Bohers E, Maingonnat C, Jaïs JP, Tesson B, Ruminy P, Peyrouze P, Copie-Bergman C, Fest T, Jo Molina T, Haioun C, Salles G, Tilly H, Lecroq T, Leroy K, Jardin F. Whole exome sequencing of relapsed/refractory patients expands the repertoire of somatic mutations in diffuse large B-cell lymphoma. Genes Chromosomes Cancer. 2016 Mar;55(3):251–267. PMID: 26608593 |
| 56 | 60 | 2. Jardin F, Pujals A, Pelletier L, Bohers E, Camus V, Mareschal S, Dubois S, Sola B, Ochmann M, Lemonnier F, Viailly PJ, Bertrand P, Maingonnat C, Traverse-Glehen A, Gaulard P, Damotte D, Delarue R, Haioun C, Argueta C, Landesman Y, Salles G, Jais JP, Figeac M, Copie-Bergman C, Molina TJ, Picquenot JM, Cornic M, Fest T, Milpied N, Lemasle E, Stamatoullas A, Moeller P, Dyer MJS, Sundstrom C, Bastard C, Tilly H, Leroy K. Recurrent mutations of the exportin 1 gene (XPO1) and their impact on selective inhibitor of nuclear export compounds sensitivity in primary mediastinal B-cell lymphoma. Am J Hematol. 2016 Sep;91(9):923–930. PMID: 27312795 |
YY1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # YY1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2017-10-10 : Reddy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,22 +32,22 @@ timeline |
| 30 | 32 | |FL |No |No |3.554 |61.850 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567) |
|
| 35 | 35 | |
| 36 | 36 | > [!WARNING] |
| 37 | 37 | > Mutations in this gene were reported to be inflated in the original results according to [Dreval K](https://www.biorxiv.org/content/10.1101/2023.11.21.567983v1) |
| 38 | 38 | |
| 39 | 39 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/YY1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/YY1_protein_hg38.html) |
| 40 | 40 | |
| 41 | - |
|
| 41 | + |
|
| 42 | 42 | |
| 43 | 43 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/YY1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/YY1_hg38.html) |
| 44 | 44 | |
| 45 | - |
|
| 45 | + |
|
| 46 | + |
|
| 46 | 47 | ## YY1 Expression |
| 47 | - |
|
| 48 | + |
|
| 48 | 49 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
| 49 | 50 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 51 | + |
|
| 50 | 52 | ## References |
| 51 | 53 | 1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
YY1AP1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # YY1AP1 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-10-04 : Schmitz : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -29,20 +31,20 @@ timeline |
| 29 | 31 | |FL |No |No |0.000 | 0.000 | |
| 30 | 32 | |
| 31 | 33 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096) |
|
| 34 | 34 | |
| 35 | 35 | |
| 36 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/YY1AP1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/YY1AP1_protein_hg38.html) |
| 37 | 37 | |
| 38 | - |
|
| 38 | + |
|
| 39 | 39 | |
| 40 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/YY1AP1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/YY1AP1_hg38.html) |
| 41 | 41 | |
| 42 | - |
|
| 42 | + |
|
| 43 | + |
|
| 43 | 44 | ## YY1AP1 Expression |
| 44 | - |
|
| 45 | + |
|
| 45 | 46 | <!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 --> |
| 46 | 47 | <!-- BL: schmitzBurkittLymphomaPathogenesis2012 --> |
| 48 | + |
|
| 47 | 49 | ## References |
| 48 | 50 | 1. Schmitz R, Young RM, Ceribelli M, Jhavar S, Xiao W, Zhang M, Wright G, Shaffer AL, Hodson DJ, Buras E, Liu X, Powell J, Yang Y, Xu W, Zhao H, Kohlhammer H, Rosenwald A, Kluin P, Müller-Hermelink HK, Ott G, Gascoyne RD, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Ogwang MD, Reynolds SJ, Fisher RI, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Pittaluga S, Wilson W, Waldmann TA, Rowe M, Mbulaiteye SM, Rickinson AB, Staudt LM. Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics. Nature. 2012 Oct 4;490(7418):116–120. PMCID: PMC3609867 |
ZAN.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # ZAN |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2022-07-06 : Burkhardt : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -25,20 +27,20 @@ timeline |
| 25 | 27 | | |
| 26 | 28 | |
| 27 | 29 | |
| 28 | -> [!NOTE] |
|
| 29 | -> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096) |
|
| 30 | 30 | |
| 31 | 31 | |
| 32 | 32 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZAN_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZAN_protein_hg38.html) |
| 33 | 33 | |
| 34 | - |
|
| 34 | + |
|
| 35 | 35 | |
| 36 | 36 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZAN.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZAN_hg38.html) |
| 37 | 37 | |
| 38 | - |
|
| 38 | + |
|
| 39 | + |
|
| 39 | 40 | ## ZAN Expression |
| 40 | - |
|
| 41 | + |
|
| 41 | 42 | <!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b --> |
| 42 | 43 | <!-- BL: burkhardtClinicalRelevanceMolecular2022b --> |
| 44 | + |
|
| 43 | 45 | ## References |
| 44 | 46 | 1. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584 |
ZBTB7A.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # ZBTB7A |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2017-10-10 : Reddy : DLBCL |
| 8 | 9 | 2022-07-06 : Burkhardt : BL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -35,22 +37,22 @@ timeline |
| 35 | 37 | |FL |No |No |0.000 |0 | |
| 36 | 38 | |
| 37 | 39 | |
| 38 | -> [!NOTE] |
|
| 39 | -> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096). First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567) |
|
| 40 | 40 | |
| 41 | 41 | |
| 42 | 42 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZBTB7A_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZBTB7A_protein_hg38.html) |
| 43 | 43 | |
| 44 | - |
|
| 44 | + |
|
| 45 | 45 | |
| 46 | 46 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZBTB7A.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZBTB7A_hg38.html) |
| 47 | 47 | |
| 48 | - |
|
| 48 | + |
|
| 49 | + |
|
| 49 | 50 | ## ZBTB7A Expression |
| 50 | - |
|
| 51 | + |
|
| 51 | 52 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
| 52 | 53 | <!-- BL: burkhardtClinicalRelevanceMolecular2022b --> |
| 53 | 54 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 55 | + |
|
| 54 | 56 | ## References |
| 55 | 57 | 1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
| 56 | 58 | 2. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584 |
ZC3H12A.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # ZC3H12A |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2017-10-10 : Reddy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -36,15 +38,17 @@ timeline |
| 36 | 38 | |
| 37 | 39 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZC3H12A_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZC3H12A_protein_hg38.html) |
| 38 | 40 | |
| 39 | - |
|
| 41 | + |
|
| 40 | 42 | |
| 41 | 43 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZC3H12A.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZC3H12A_hg38.html) |
| 42 | 44 | |
| 43 | - |
|
| 45 | + |
|
| 46 | + |
|
| 44 | 47 | ## ZC3H12A Expression |
| 45 | - |
|
| 48 | + |
|
| 46 | 49 | <!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 --> |
| 47 | 50 | <!-- DLBCL: arthurGenomewideDiscoverySomatic2018 --> |
| 51 | + |
|
| 48 | 52 | ## References |
| 49 | 53 | 1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996. |
| 50 | 54 | 2. Arthur SE, Jiang A, Grande BM, Alcaide M, Cojocaru R, Rushton CK, Mottok A, Hilton LK, Lat PK, Zhao EY, Culibrk L, Ennishi D, Jessa S, Chong L, Thomas N, Pararajalingam P, Meissner B, Boyle M, Davidson J, Bushell KR, Lai D, Farinha P, Slack GW, Morin GB, Shah S, Sen D, Jones SJM, Mungall AJ, Gascoyne RD, Audas TE, Unrau P, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma. Nat Commun. 2018 Oct 1;9(1):4001. PMCID: PMC6167379 |
ZCCHC7.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # ZCCHC7 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2018-10-01 : Arthur : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -38,20 +40,20 @@ timeline |
| 38 | 40 | |chr9 |37312655 |37328260|[intron-3](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr9%3A37312655%2D37328260)|intron | |
| 39 | 41 | |chr9 |37329706 |37340398|[intron-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr9%3A37329706%2D37340398)|intron | |
| 40 | 42 | |
| 41 | -> [!NOTE] |
|
| 42 | -> First described in DLBCL in 2018 by [Arthur SE](https://pubmed.ncbi.nlm.nih.gov/30275490) |
|
| 43 | 43 | |
| 44 | 44 | |
| 45 | 45 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZCCHC7_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZCCHC7_protein_hg38.html) |
| 46 | 46 | |
| 47 | - |
|
| 47 | + |
|
| 48 | 48 | |
| 49 | 49 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZCCHC7.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZCCHC7_hg38.html) |
| 50 | 50 | |
| 51 | - |
|
| 51 | + |
|
| 52 | + |
|
| 52 | 53 | ## ZCCHC7 Expression |
| 53 | - |
|
| 54 | + |
|
| 54 | 55 | <!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 --> |
| 55 | 56 | <!-- DLBCL: arthurGenomewideDiscoverySomatic2018 --> |
| 57 | + |
|
| 56 | 58 | ## References |
| 57 | 59 | 1. Arthur SE, Jiang A, Grande BM, Alcaide M, Cojocaru R, Rushton CK, Mottok A, Hilton LK, Lat PK, Zhao EY, Culibrk L, Ennishi D, Jessa S, Chong L, Thomas N, Pararajalingam P, Meissner B, Boyle M, Davidson J, Bushell KR, Lai D, Farinha P, Slack GW, Morin GB, Shah S, Sen D, Jones SJM, Mungall AJ, Gascoyne RD, Audas TE, Unrau P, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma. Nat Commun. 2018 Oct 1;9(1):4001. PMCID: PMC6167379 |
ZEB2.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # ZEB2 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2013-01-01 : Zhang : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,20 +32,20 @@ timeline |
| 30 | 32 | |FL |No |No |2.638 | 0.000 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937) |
|
| 35 | 35 | |
| 36 | 36 | |
| 37 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZEB2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZEB2_protein_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | 40 | |
| 41 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZEB2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZEB2_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | + |
|
| 44 | 45 | ## ZEB2 Expression |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | <!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 --> |
| 47 | 48 | <!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 --> |
| 49 | + |
|
| 48 | 50 | ## References |
| 49 | 51 | 1. Zhang J, Grubor V, Love CL, Banerjee A, Richards KL, Mieczkowski PA, Dunphy C, Choi W, Au WY, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers C, Naresh K, Evens A, Gordon LI, Czader M, Gill JI, Hsi ED, Liu Q, Fan A, Walsh K, Jima D, Smith LL, Johnson AJ, Byrd JC, Luftig MA, Ni T, Zhu J, Chadburn A, Levy S, Dunson D, Dave SS. Genetic heterogeneity of diffuse large B-cell lymphoma. 2013 Jan; |
ZFAT.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # ZFAT |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2017-10-10 : Reddy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,20 +32,20 @@ timeline |
| 30 | 32 | |FL |No |No |0.000 |0 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567) |
|
| 35 | 35 | |
| 36 | 36 | |
| 37 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZFAT_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZFAT_protein_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | 40 | |
| 41 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZFAT.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZFAT_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | + |
|
| 44 | 45 | ## ZFAT Expression |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
| 47 | 48 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 49 | + |
|
| 48 | 50 | ## References |
| 49 | 51 | 1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
ZFP36L1.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # ZFP36L1 |
| 2 | + |
|
| 2 | 3 | ## Overview |
| 3 | 4 | ZFP36L1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. |
| 4 | 5 | ## History |
| ... | ... | @@ -10,6 +11,7 @@ timeline |
| 10 | 11 | 2015-02-12 : Reichel : PMBL |
| 11 | 12 | 2019-09-26 : Panea : BL |
| 12 | 13 | ``` |
| 14 | + |
|
| 13 | 15 | ## Relevance tier by entity |
| 14 | 16 | |
| 15 | 17 | |Entity|Tier|Description | |
| ... | ... | @@ -48,13 +50,14 @@ timeline |
| 48 | 50 | |
| 49 | 51 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZFP36L1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZFP36L1_protein_hg38.html) |
| 50 | 52 | |
| 51 | - |
|
| 53 | + |
|
| 52 | 54 | |
| 53 | 55 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZFP36L1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZFP36L1_hg38.html) |
| 54 | 56 | |
| 55 | - |
|
| 57 | + |
|
| 58 | + |
|
| 56 | 59 | ## ZFP36L1 Expression |
| 57 | - |
|
| 60 | + |
|
| 58 | 61 | |
| 59 | 62 | ## References |
| 60 | 63 | 1. Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJM, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298–303. PMCID: PMC3210554 |
ZFX.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # ZFX |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2017-10-10 : Reddy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,8 +32,6 @@ timeline |
| 30 | 32 | |FL |No |No |0.000 |0 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567) |
|
| 35 | 35 | |
| 36 | 36 | > [!WARNING] |
| 37 | 37 | > Mutations in this gene were reported to be inflated in the original results according to [Dreval K](https://www.biorxiv.org/content/10.1101/2023.11.21.567983v1) |
| ... | ... | @@ -39,14 +39,16 @@ timeline |
| 39 | 39 | |
| 40 | 40 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZFX_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZFX_protein_hg38.html) |
| 41 | 41 | |
| 42 | - |
|
| 42 | + |
|
| 43 | 43 | |
| 44 | 44 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZFX.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZFX_hg38.html) |
| 45 | 45 | |
| 46 | - |
|
| 46 | + |
|
| 47 | + |
|
| 47 | 48 | ## ZFX Expression |
| 48 | - |
|
| 49 | + |
|
| 49 | 50 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
| 50 | 51 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 52 | + |
|
| 51 | 53 | ## References |
| 52 | 54 | 1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15. |
ZNF117.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # ZNF117 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2014-05-08 : Zhang : MCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -27,20 +29,20 @@ timeline |
| 27 | 29 | |FL |No |No |0 |0 | |
| 28 | 30 | |
| 29 | 31 | |
| 30 | -> [!NOTE] |
|
| 31 | -> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267) |
|
| 32 | 32 | |
| 33 | 33 | |
| 34 | 34 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZNF117_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZNF117_protein_hg38.html) |
| 35 | 35 | |
| 36 | - |
|
| 36 | + |
|
| 37 | 37 | |
| 38 | 38 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZNF117.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZNF117_hg38.html) |
| 39 | 39 | |
| 40 | - |
|
| 40 | + |
|
| 41 | + |
|
| 41 | 42 | ## ZNF117 Expression |
| 42 | - |
|
| 43 | + |
|
| 43 | 44 | <!-- ORIGIN: zhangGenomicLandscapeMantle2014 --> |
| 44 | 45 | <!-- MCL: zhangGenomicLandscapeMantle2014 --> |
| 46 | + |
|
| 45 | 47 | ## References |
| 46 | 48 | 1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996. |
ZNF217.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # ZNF217 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2015-02-12 : Reichel : PMBL |
| 8 | 9 | 2021-05-05 : H : DLBCL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -32,22 +34,22 @@ timeline |
| 32 | 34 | |FL |No |No |0.000 |0 | |
| 33 | 35 | |
| 34 | 36 | |
| 35 | -> [!NOTE] |
|
| 36 | -> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289) |
|
| 37 | 37 | |
| 38 | 38 | |
| 39 | 39 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZNF217_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZNF217_protein_hg38.html) |
| 40 | 40 | |
| 41 | - |
|
| 41 | + |
|
| 42 | 42 | |
| 43 | 43 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZNF217.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZNF217_hg38.html) |
| 44 | 44 | |
| 45 | - |
|
| 45 | + |
|
| 46 | + |
|
| 46 | 47 | ## ZNF217 Expression |
| 47 | - |
|
| 48 | + |
|
| 48 | 49 | <!-- ORIGIN: reichelFlowSortingExome2015a --> |
| 49 | 50 | <!-- DLBCL: hubschmannMutationalMechanismsShaping2021b --> |
| 50 | 51 | <!-- PMBL: reichelFlowSortingExome2015a --> |
| 52 | + |
|
| 51 | 53 | ## References |
| 52 | 54 | 1. Reichel J, Chadburn A, Rubinstein PG, Giulino-Roth L, Tam W, Liu Y, Gaiolla R, Eng K, Brody J, Inghirami G, Carlo-Stella C, Santoro A, Rahal D, Totonchy J, Elemento O, Cesarman E, Roshal M. Flow sorting and exome sequencing reveal the oncogenome of primary Hodgkin and Reed-Sternberg cells. Blood. 2015 Feb 12;125(7):1061–1072. PMID: 25488972 |
| 53 | 55 | 2. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491 |
ZNF229.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # ZNF229 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2012-12-01 : Love : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -29,20 +31,20 @@ timeline |
| 29 | 31 | |FL |No |No |0.000 |0 | |
| 30 | 32 | |
| 31 | 33 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597) |
|
| 34 | 34 | |
| 35 | 35 | |
| 36 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZNF229_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZNF229_protein_hg38.html) |
| 37 | 37 | |
| 38 | - |
|
| 38 | + |
|
| 39 | 39 | |
| 40 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZNF229.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZNF229_hg38.html) |
| 41 | 41 | |
| 42 | - |
|
| 42 | + |
|
| 43 | + |
|
| 43 | 44 | ## ZNF229 Expression |
| 44 | - |
|
| 45 | + |
|
| 45 | 46 | <!-- ORIGIN: loveGeneticLandscapeMutations2012 --> |
| 46 | 47 | <!-- BL: loveGeneticLandscapeMutations2012 --> |
| 48 | + |
|
| 47 | 49 | ## References |
| 48 | 50 | 1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
ZNF292.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # ZNF292 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2013-01-01 : Zhang : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,20 +32,20 @@ timeline |
| 30 | 32 | |FL |No |No |2.049 | 0.000 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937) |
|
| 35 | 35 | |
| 36 | 36 | |
| 37 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZNF292_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZNF292_protein_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | 40 | |
| 41 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZNF292.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZNF292_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | + |
|
| 44 | 45 | ## ZNF292 Expression |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | <!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 --> |
| 47 | 48 | <!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 --> |
| 49 | + |
|
| 48 | 50 | ## References |
| 49 | 51 | 1. Zhang J, Grubor V, Love CL, Banerjee A, Richards KL, Mieczkowski PA, Dunphy C, Choi W, Au WY, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers C, Naresh K, Evens A, Gordon LI, Czader M, Gill JI, Hsi ED, Liu Q, Fan A, Walsh K, Jima D, Smith LL, Johnson AJ, Byrd JC, Luftig MA, Ni T, Zhu J, Chadburn A, Levy S, Dunson D, Dave SS. Genetic heterogeneity of diffuse large B-cell lymphoma. 2013 Jan; |
ZNF296.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # ZNF296 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2014-05-08 : Zhang : MCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -27,20 +29,20 @@ timeline |
| 27 | 29 | |FL |No |No |0.000 | 0.000 | |
| 28 | 30 | |
| 29 | 31 | |
| 30 | -> [!NOTE] |
|
| 31 | -> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267) |
|
| 32 | 32 | |
| 33 | 33 | |
| 34 | 34 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZNF296_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZNF296_protein_hg38.html) |
| 35 | 35 | |
| 36 | - |
|
| 36 | + |
|
| 37 | 37 | |
| 38 | 38 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZNF296.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZNF296_hg38.html) |
| 39 | 39 | |
| 40 | - |
|
| 40 | + |
|
| 41 | + |
|
| 41 | 42 | ## ZNF296 Expression |
| 42 | - |
|
| 43 | + |
|
| 43 | 44 | <!-- ORIGIN: zhangGenomicLandscapeMantle2014 --> |
| 44 | 45 | <!-- MCL: zhangGenomicLandscapeMantle2014 --> |
| 46 | + |
|
| 45 | 47 | ## References |
| 46 | 48 | 1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996. |
ZNF423.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # ZNF423 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2018-05-01 : Chapuy : DLBCL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -30,20 +32,20 @@ timeline |
| 30 | 32 | |FL |No |No |0.836 |0 | |
| 31 | 33 | |
| 32 | 34 | |
| 33 | -> [!NOTE] |
|
| 34 | -> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087) |
|
| 35 | 35 | |
| 36 | 36 | |
| 37 | 37 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZNF423_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZNF423_protein_hg38.html) |
| 38 | 38 | |
| 39 | - |
|
| 39 | + |
|
| 40 | 40 | |
| 41 | 41 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZNF423.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZNF423_hg38.html) |
| 42 | 42 | |
| 43 | - |
|
| 43 | + |
|
| 44 | + |
|
| 44 | 45 | ## ZNF423 Expression |
| 45 | - |
|
| 46 | + |
|
| 46 | 47 | <!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b --> |
| 47 | 48 | <!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b --> |
| 49 | + |
|
| 48 | 50 | ## References |
| 49 | 51 | 1. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387 |
ZNF608.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # ZNF608 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -7,6 +8,7 @@ timeline |
| 7 | 8 | 2013-01-01 : Zhang : DLBCL |
| 8 | 9 | 2017-01-26 : Krysiak : FL |
| 9 | 10 | ``` |
| 11 | + |
|
| 10 | 12 | ## Relevance tier by entity |
| 11 | 13 | |
| 12 | 14 | |Entity|Tier|Description | |
| ... | ... | @@ -32,22 +34,22 @@ timeline |
| 32 | 34 | |FL |No |No |1.867 |4.218 | |
| 33 | 35 | |
| 34 | 36 | |
| 35 | -> [!NOTE] |
|
| 36 | -> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937) |
|
| 37 | 37 | |
| 38 | 38 | |
| 39 | 39 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZNF608_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZNF608_protein_hg38.html) |
| 40 | 40 | |
| 41 | - |
|
| 41 | + |
|
| 42 | 42 | |
| 43 | 43 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZNF608.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZNF608_hg38.html) |
| 44 | 44 | |
| 45 | - |
|
| 45 | + |
|
| 46 | + |
|
| 46 | 47 | ## ZNF608 Expression |
| 47 | - |
|
| 48 | + |
|
| 48 | 49 | <!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 --> |
| 49 | 50 | <!-- FL: krysiakRecurrentSomaticMutations2017b --> |
| 50 | 51 | <!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 --> |
| 52 | + |
|
| 51 | 53 | ## References |
| 52 | 54 | 1. Zhang J, Grubor V, Love CL, Banerjee A, Richards KL, Mieczkowski PA, Dunphy C, Choi W, Au WY, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers C, Naresh K, Evens A, Gordon LI, Czader M, Gill JI, Hsi ED, Liu Q, Fan A, Walsh K, Jima D, Smith LL, Johnson AJ, Byrd JC, Luftig MA, Ni T, Zhu J, Chadburn A, Levy S, Dunson D, Dave SS. Genetic heterogeneity of diffuse large B-cell lymphoma. 2013 Jan; |
| 53 | 55 | 2. Krysiak K, Gomez F, White BS, Matlock M, Miller CA, Trani L, Fronick CC, Fulton RS, Kreisel F, Cashen AF, Carson KR, Berrien-Elliott MM, Bartlett NL, Griffith M, Griffith OL, Fehniger TA. Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma. Blood. 2017 Jan 26;129(4):473–483. PMCID: PMC5270390 |
ZNF85.md
| ... | ... | @@ -1,4 +1,5 @@ |
| 1 | 1 | # ZNF85 |
| 2 | + |
|
| 2 | 3 | ## History |
| 3 | 4 | ```mermaid |
| 4 | 5 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -6,6 +7,7 @@ timeline |
| 6 | 7 | title Publication timing |
| 7 | 8 | 2022-07-06 : Burkhardt : BL |
| 8 | 9 | ``` |
| 10 | + |
|
| 9 | 11 | ## Relevance tier by entity |
| 10 | 12 | |
| 11 | 13 | |Entity|Tier|Description | |
| ... | ... | @@ -29,20 +31,20 @@ timeline |
| 29 | 31 | |FL |No |No |0.000 |0 | |
| 30 | 32 | |
| 31 | 33 | |
| 32 | -> [!NOTE] |
|
| 33 | -> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096) |
|
| 34 | 34 | |
| 35 | 35 | |
| 36 | 36 | View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZNF85_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZNF85_protein_hg38.html) |
| 37 | 37 | |
| 38 | - |
|
| 38 | + |
|
| 39 | 39 | |
| 40 | 40 | View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ZNF85.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ZNF85_hg38.html) |
| 41 | 41 | |
| 42 | - |
|
| 42 | + |
|
| 43 | + |
|
| 43 | 44 | ## ZNF85 Expression |
| 44 | - |
|
| 45 | + |
|
| 45 | 46 | <!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b --> |
| 46 | 47 | <!-- BL: burkhardtClinicalRelevanceMolecular2022b --> |
| 48 | + |
|
| 47 | 49 | ## References |
| 48 | 50 | 1. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584 |
config.json
| ... | ... | @@ -0,0 +1,13 @@ |
| 1 | +{ |
|
| 2 | + "startOnLoad": true, |
|
| 3 | + "flowchart": { |
|
| 4 | + "useMaxWidth": false, |
|
| 5 | + "htmlLabels": true |
|
| 6 | + }, |
|
| 7 | + "sankey": { |
|
| 8 | + "height": 1000, |
|
| 9 | + "width": 800, |
|
| 10 | + "showValues": false, |
|
| 11 | + "linkColor": "target" |
|
| 12 | + } |
|
| 13 | +} |
config.rb
| ... | ... | @@ -0,0 +1,276 @@ |
| 1 | + # Launch Gollum using a specific git adapter. See https://github.com/gollum/gollum/wiki/Git-adapters |
|
| 2 | + # Default: rugged |
|
| 3 | + # |
|
| 4 | + # Equivalent to --adapter [ADAPTER] |
|
| 5 | + |
|
| 6 | + module Gollum |
|
| 7 | + # to require 'my_adapter': |
|
| 8 | + Gollum::GIT_ADAPTER = "my" |
|
| 9 | + end |
|
| 10 | + |
|
| 11 | + wiki_options = { |
|
| 12 | + |
|
| 13 | + ############################################################################## |
|
| 14 | + #----------------------------------------------------------------------------- |
|
| 15 | + |
|
| 16 | + #----------------------------------------------------------------------------- |
|
| 17 | + # Enable file uploads. If set to 'dir', Gollum will store all uploads in the |
|
| 18 | + # /uploads/ directory in repository root. If set to 'page', Gollum will |
|
| 19 | + # store each upload at the currently edited page. |
|
| 20 | + # Default: false |
|
| 21 | + |
|
| 22 | + # Equivalent to --allow-uploads dir |
|
| 23 | + #allow_uploads: true, |
|
| 24 | + |
|
| 25 | + # Equivalent to --allow-uploads page |
|
| 26 | + #allow_uploads: true, |
|
| 27 | + #per_page_uploads: true, |
|
| 28 | + |
|
| 29 | + #----------------------------------------------------------------------------- |
|
| 30 | + # Set the path to look for static assets. |
|
| 31 | + # |
|
| 32 | + # Equivalent to --assets [PATH] |
|
| 33 | + |
|
| 34 | + #static_assets_path: [PATH] |
|
| 35 | + |
|
| 36 | + #----------------------------------------------------------------------------- |
|
| 37 | + # Tell Gollum that the git repository should be treated as bare. |
|
| 38 | + # |
|
| 39 | + # Equivalent to --bare |
|
| 40 | + |
|
| 41 | + #repo_is_bare: true, |
|
| 42 | + |
|
| 43 | + #----------------------------------------------------------------------------- |
|
| 44 | + # Specify the leading portion of all Gollum URLs (path info). Setting this to |
|
| 45 | + # /wiki will make the wiki accessible under http://localhost:4567/wiki/. |
|
| 46 | + # Default: / |
|
| 47 | + # |
|
| 48 | + # Equivalent to --base-path [PATH] |
|
| 49 | + |
|
| 50 | + #base_path: [PATH], |
|
| 51 | + |
|
| 52 | + #----------------------------------------------------------------------------- |
|
| 53 | + # Enable support for annotations using CriticMarkup. |
|
| 54 | + # |
|
| 55 | + # Equivalent to --critic-markup |
|
| 56 | + |
|
| 57 | + #critic_markup: true, |
|
| 58 | + |
|
| 59 | + #----------------------------------------------------------------------------- |
|
| 60 | + # Tell Gollum to inject custom CSS into each page. Uses custom.css from wiki |
|
| 61 | + # root |
|
| 62 | + # |
|
| 63 | + # Equivalent to --css |
|
| 64 | + |
|
| 65 | + #css: true, |
|
| 66 | + |
|
| 67 | + #----------------------------------------------------------------------------- |
|
| 68 | + # What should the default keybinding be on the edit page? Note: the editor will anyway remember the last choice the user made, so this is only to specify the default. |
|
| 69 | + |
|
| 70 | + #default_keybinding: vim |
|
| 71 | + #default_keybinding: emacs |
|
| 72 | + |
|
| 73 | + #----------------------------------------------------------------------------- |
|
| 74 | + # Parse and interpret emoji tags (e.g. :heart:) except when the leading colon |
|
| 75 | + # is backslashed (e.g. \:heart:). |
|
| 76 | + # |
|
| 77 | + # Equivalent to --emoji |
|
| 78 | + |
|
| 79 | + #emoji: true, |
|
| 80 | + |
|
| 81 | + #----------------------------------------------------------------------------- |
|
| 82 | + # Tell Gollum to use the first <h1> as page title. |
|
| 83 | + # |
|
| 84 | + # Equivalent to --h1-title |
|
| 85 | + |
|
| 86 | + h1_title: true, |
|
| 87 | + |
|
| 88 | + #----------------------------------------------------------------------------- |
|
| 89 | + # Specify the hostname or IP address to listen on. |
|
| 90 | + # Default: '0.0.0.0'. |
|
| 91 | + # |
|
| 92 | + # Equivalent to --host [HOST] |
|
| 93 | + |
|
| 94 | + # ??? |
|
| 95 | + |
|
| 96 | + #----------------------------------------------------------------------------- |
|
| 97 | + # Launch Gollum in "console mode", with a predefined API. |
|
| 98 | + # |
|
| 99 | + # Equivalent to --irb |
|
| 100 | + |
|
| 101 | + # ??? |
|
| 102 | + |
|
| 103 | + #----------------------------------------------------------------------------- |
|
| 104 | + # Tell Gollum to inject custom JS into each page. Uses custom.js from wiki |
|
| 105 | + # root. |
|
| 106 | + # |
|
| 107 | + # Equivalent to --js |
|
| 108 | + |
|
| 109 | + #js: true, |
|
| 110 | + |
|
| 111 | + #----------------------------------------------------------------------------- |
|
| 112 | + # Compatibility with 4.x |
|
| 113 | + # https://github.com/gollum/gollum/wiki/5.0-release-notes#compatibility-option |
|
| 114 | + # |
|
| 115 | + # Internal links resolve case-insensitively, will treat spaces as hyphens, and |
|
| 116 | + # will match the first page found with a certain filename, anywhere in the |
|
| 117 | + # repository. Provides compatibility with Gollum 4.x. |
|
| 118 | + # |
|
| 119 | + # Equivalent to --lenient-tag-lookup |
|
| 120 | + |
|
| 121 | + #hyphened_tag_lookup: true, |
|
| 122 | + #case_insensitive_tag_lookup: true, |
|
| 123 | + #global_tag_lookup: true, |
|
| 124 | + |
|
| 125 | + #----------------------------------------------------------------------------- |
|
| 126 | + # Use the browser's local timezone instead of the server's timezone for displaying dates. |
|
| 127 | + |
|
| 128 | + #show_local_time: true |
|
| 129 | + |
|
| 130 | + #----------------------------------------------------------------------------- |
|
| 131 | + # Equivalent to --math. Set math parsing to either mathjax or katex (default) |
|
| 132 | + |
|
| 133 | + #math: :mathjax, |
|
| 134 | + #math: :katex, |
|
| 135 | + |
|
| 136 | + #----------------------------------------------------------------------------- |
|
| 137 | + # Specify path to a custom MathJax configuration. |
|
| 138 | + # Default: mathjax.config.js file from repository root. |
|
| 139 | + # |
|
| 140 | + # Equivalent to --mathjax-config [FILE] |
|
| 141 | + |
|
| 142 | + #mathjax_config: [FILE], |
|
| 143 | + |
|
| 144 | + #----------------------------------------------------------------------------- |
|
| 145 | + # Do not render metadata tables in pages. |
|
| 146 | + # |
|
| 147 | + # Equivalent to --no-display-metadata |
|
| 148 | + |
|
| 149 | + display_metadata: false, |
|
| 150 | + |
|
| 151 | + #----------------------------------------------------------------------------- |
|
| 152 | + # Disable the feature of editing pages. |
|
| 153 | + # Default: true |
|
| 154 | + # |
|
| 155 | + # Equivalent to --no-edit |
|
| 156 | + |
|
| 157 | + #allow_editing: false, |
|
| 158 | + |
|
| 159 | + #----------------------------------------------------------------------------- |
|
| 160 | + # Specify the subdirectory for all pages. If set, Gollum will only serve pages |
|
| 161 | + # from this directory and its subdirectories. |
|
| 162 | + # Default: repository root. |
|
| 163 | + # |
|
| 164 | + # Equivalent to --page-file-dir [PATH] |
|
| 165 | + |
|
| 166 | + #page_file_dir: [PATH], |
|
| 167 | + |
|
| 168 | + #----------------------------------------------------------------------------- |
|
| 169 | + # Follow pages across renames in the History view. You may set this to `false` to improve performance on wikis with very large histories. |
|
| 170 | + # Default: true. |
|
| 171 | + |
|
| 172 | + #follow_renames: true, |
|
| 173 | + |
|
| 174 | + #----------------------------------------------------------------------------- |
|
| 175 | + # Specify the port to bind Gollum with. |
|
| 176 | + # Default: 4567. |
|
| 177 | + # |
|
| 178 | + # Equivalent to --port [PORT] |
|
| 179 | + |
|
| 180 | + # ??? |
|
| 181 | + |
|
| 182 | + #----------------------------------------------------------------------------- |
|
| 183 | + # Specify the git branch to serve. |
|
| 184 | + # Default: master. |
|
| 185 | + # |
|
| 186 | + # Equivalent to --ref [REF] |
|
| 187 | + |
|
| 188 | + #ref: [REF], |
|
| 189 | + |
|
| 190 | + #----------------------------------------------------------------------------- |
|
| 191 | + # Use static assets. |
|
| 192 | + # Defaults to false in development/test, true in |
|
| 193 | + # production/staging. |
|
| 194 | + |
|
| 195 | + # Equivalent to --static |
|
| 196 | + #static: true, |
|
| 197 | + |
|
| 198 | + # Equivalent to --no-static |
|
| 199 | + #static: false, |
|
| 200 | + |
|
| 201 | + #----------------------------------------------------------------------------- |
|
| 202 | + # Specify custom mustache template directory. |
|
| 203 | + # |
|
| 204 | + # Equivalent to --template-dir [PATH] |
|
| 205 | + |
|
| 206 | + #template_dir: [PATH], |
|
| 207 | + |
|
| 208 | + #----------------------------------------------------------------------------- |
|
| 209 | + # Use _Template in root as a template for new pages. Must be committed. |
|
| 210 | + # |
|
| 211 | + # Equivalent to --template-page |
|
| 212 | + |
|
| 213 | + #template_page: true, |
|
| 214 | + |
|
| 215 | + #----------------------------------------------------------------------------- |
|
| 216 | + # Tell Gollum to use specific user icons for history view. Can be set to |
|
| 217 | + # gravatar, identicon or none. |
|
| 218 | + # Default: none. |
|
| 219 | + # |
|
| 220 | + # Equivalent to --user-icons [MODE] |
|
| 221 | + |
|
| 222 | + #user_icons: [MODE], |
|
| 223 | + |
|
| 224 | + ############################################################################## |
|
| 225 | + # Metadata (front matter) |
|
| 226 | + |
|
| 227 | + #----------------------------------------------------------------------------- |
|
| 228 | + # Header counting |
|
| 229 | + # Default: false |
|
| 230 | + # Can also be a pre-defined counter. See |
|
| 231 | + # https://www.w3.org/TR/css-counter-styles-3/#predefined-counters |
|
| 232 | + |
|
| 233 | + #header_enum: false, |
|
| 234 | + #header_enum: 'decimal-leading-zero', |
|
| 235 | + |
|
| 236 | + #----------------------------------------------------------------------------- |
|
| 237 | + # Global metadata. Arbitrary metadata that will be applied to each page. |
|
| 238 | + |
|
| 239 | + #metadata: { |
|
| 240 | + # monkeyboys: 'are loose in the facility' |
|
| 241 | + #}, |
|
| 242 | + |
|
| 243 | + ############################################################################## |
|
| 244 | + # Tips |
|
| 245 | + |
|
| 246 | + #----------------------------------------------------------------------------- |
|
| 247 | + # Force table of contents tag ([[_TOC_]]) into each page. |
|
| 248 | + # ??? How to set the level in the configuration file? |
|
| 249 | + # https://github.com/gollum/gollum/wiki#table-of-contents-toc-tag |
|
| 250 | + # Default: false |
|
| 251 | + |
|
| 252 | + #universal_toc: false, |
|
| 253 | + |
|
| 254 | + #----------------------------------------------------------------------------- |
|
| 255 | + # Move the sidebar to the left of the page |
|
| 256 | + # https://github.com/gollum/gollum/issues/1450#issuecomment-599124384 |
|
| 257 | + |
|
| 258 | + #sidebar: :left, |
|
| 259 | + |
|
| 260 | + #----------------------------------------------------------------------------- |
|
| 261 | + # Change the home page name |
|
| 262 | + # https://github.com/gollum/gollum/issues/1569#issuecomment-633033895 |
|
| 263 | + |
|
| 264 | + #index_page: 'index', |
|
| 265 | + |
|
| 266 | + #----------------------------------------------------------------------------- |
|
| 267 | + # Change the number of changes in the rss feed |
|
| 268 | + |
|
| 269 | + #pagination_count: 15 |
|
| 270 | + } |
|
| 271 | + |
|
| 272 | + #------------------------------------------------------------------------------- |
|
| 273 | + # Change default markup |
|
| 274 | + #Precious::App.set(:default_markup, :asciidoc) |
|
| 275 | + |
|
| 276 | + Precious::App.set(:wiki_options, wiki_options) |
config1.json
| ... | ... | @@ -0,0 +1,12 @@ |
| 1 | +{ |
|
| 2 | + "theme": "base", |
|
| 3 | + "themeVariables": { |
|
| 4 | + "fontSize": "33px" |
|
| 5 | + }, |
|
| 6 | + "sankey": { |
|
| 7 | + "height": 1000, |
|
| 8 | + "width": 800, |
|
| 9 | + "showValues": false, |
|
| 10 | + "linkColor": "target" |
|
| 11 | + } |
|
| 12 | +} |
config2.json
| ... | ... | @@ -0,0 +1,12 @@ |
| 1 | +{ |
|
| 2 | + "theme": "base", |
|
| 3 | + "themeVariables": { |
|
| 4 | + "fontSize": "33px" |
|
| 5 | + }, |
|
| 6 | + "sankey": { |
|
| 7 | + "height": 700, |
|
| 8 | + "width": 800, |
|
| 9 | + "showValues": false, |
|
| 10 | + "linkColor": "target" |
|
| 11 | + } |
|
| 12 | +} |
images/.DS_Store
images/proteinpaint/.DS_Store
old
| ... | ... | @@ -0,0 +1,12493 @@ |
| 1 | +@article{abateDistinctViralMutational2015a, |
|
| 2 | + title = {Distinct {{Viral}} and {{Mutational Spectrum}} of {{Endemic Burkitt Lymphoma}}}, |
|
| 3 | + author = {Abate, F. and Ambrosio, M. and Mundo, L. and Laginestra, M. and Fuligni, F. and Rossi, M. and Zairis, Sakellarios and Gazaneo, Sara and Falco, G. De and Lazzi, S. and Bellan, C. and Rocca, B. J. and Amato, T. and Marasco, E. and Etebari, Maryam and Ogwang, M. and Calbi, V. and Ndede, I. and Patel, K. and Chumba, D. and Piccaluga, P. and Pileri, S. and Leoncini, L. and Rabadán, R.}, |
|
| 4 | + date = {2015}, |
|
| 5 | + journaltitle = {PLoS Pathogens}, |
|
| 6 | + shortjournal = {PLoS Pathogens}, |
|
| 7 | + volume = {11}, |
|
| 8 | + doi = {10.1371/journal.ppat.1005158}, |
|
| 9 | + file = {/Users/rmorin/Zotero/storage/8CUFAQ4L/Abate et al. - 2015 - Distinct Viral and Mutational Spectrum of Endemic .pdf} |
|
| 10 | +} |
|
| 11 | + |
|
| 12 | +@article{albuquerqueEnhancingKnowledgeDiscovery2017a, |
|
| 13 | + title = {Enhancing Knowledge Discovery from Cancer Genomics Data with {{Galaxy}}}, |
|
| 14 | + author = {Albuquerque, Marco A. and Grande, Bruno M. and Ritch, Elie J. and Pararajalingam, Prasath and Jessa, Selin and Krzywinski, Martin and Grewal, Jasleen K. and Shah, Sohrab P. and Boutros, Paul C. and Morin, Ryan D.}, |
|
| 15 | + date = {2017-05-01}, |
|
| 16 | + journaltitle = {GigaScience}, |
|
| 17 | + shortjournal = {Gigascience}, |
|
| 18 | + volume = {6}, |
|
| 19 | + number = {5}, |
|
| 20 | + eprint = {28327945}, |
|
| 21 | + eprinttype = {pmid}, |
|
| 22 | + pages = {1--13}, |
|
| 23 | + issn = {2047-217X}, |
|
| 24 | + doi = {10.1093/gigascience/gix015}, |
|
| 25 | + abstract = {The field of cancer genomics has demonstrated the power of massively parallel sequencing techniques to inform on the genes and specific alterations that drive tumor onset and progression. Although large comprehensive sequence data sets continue to be made increasingly available, data analysis remains an ongoing challenge, particularly for laboratories lacking dedicated resources and bioinformatics expertise. To address this, we have produced a collection of Galaxy tools that represent many popular algorithms for detecting somatic genetic alterations from cancer genome and exome data. We developed new methods for parallelization of these tools within Galaxy to accelerate runtime and have demonstrated their usability and summarized their runtimes on multiple cloud service providers. Some tools represent extensions or refinement of existing toolkits to yield visualizations suited to cohort-wide cancer genomic analysis. For example, we present Oncocircos and Oncoprintplus, which generate data-rich summaries of exome-derived somatic mutation. Workflows that integrate these to achieve data integration and visualizations are demonstrated on a cohort of 96 diffuse large B-cell lymphomas and enabled the discovery of multiple candidate lymphoma-related genes. Our toolkit is available from our GitHub repository as Galaxy tool and dependency definitions and has been deployed using virtualization on multiple platforms including Docker.}, |
|
| 26 | + langid = {english}, |
|
| 27 | + pmcid = {PMC5437943}, |
|
| 28 | + keywords = {Algorithms,Cancer,Cloud,Driver,Genome,Genomics,Humans,Internet,Lymphoma,Lymphoma Large B-Cell Diffuse,Mutation,Pipeline,Software,Tool,Workflow}, |
|
| 29 | + file = {/Users/rmorin/Zotero/storage/SCLMAU55/Albuquerque et al. - 2017 - Enhancing knowledge discovery from cancer genomics.pdf} |
|
| 30 | +} |
|
| 31 | + |
|
| 32 | +@article{alcaideTargetedErrorsuppressedQuantification2017, |
|
| 33 | + title = {Targeted Error-Suppressed Quantification of Circulating Tumor {{DNA}} Using Semi-Degenerate Barcoded Adapters and Biotinylated Baits.}, |
|
| 34 | + author = {Alcaide, Miguel and Yu, Stephen and Davidson, Jordan and Albuquerque, Marco and Bushell, Kevin and Fornika, Daniel and Arthur, Sarah and Grande, Bruno M and McNamara, Suzan and family=Tertre, given=Mathilde Couetoux, prefix=du, useprefix=false and Batist, Gerald and Huntsman, David G and Cavallone, Luca and Aguilar, Adriana and Basik, Mark and Johnson, Nathalie A and Deyell, Rebecca J and Rassekh, S Rod and Morin, Ryan D}, |
|
| 35 | + date = {2017-09}, |
|
| 36 | + journaltitle = {Scientific reports}, |
|
| 37 | + volume = {7}, |
|
| 38 | + number = {1}, |
|
| 39 | + pages = {10574}, |
|
| 40 | + keywords = {nosource} |
|
| 41 | +} |
|
| 42 | + |
|
| 43 | +@article{alcaideUltrasensitiveDetectionCirculating2019, |
|
| 44 | + title = {Ultrasensitive {{Detection}} of {{Circulating Tumor DNA}} in {{Lymphoma}} via {{Targeted Hybridization Capture}} and {{Deep Sequencing}} of {{Barcoded Libraries}}}, |
|
| 45 | + author = {Alcaide, Miguel and Rushton, Christopher and Morin, Ryan D.}, |
|
| 46 | + date = {2019}, |
|
| 47 | + journaltitle = {Methods in Molecular Biology (Clifton, N.J.)}, |
|
| 48 | + shortjournal = {Methods Mol Biol}, |
|
| 49 | + volume = {1956}, |
|
| 50 | + eprint = {30779047}, |
|
| 51 | + eprinttype = {pmid}, |
|
| 52 | + pages = {383--435}, |
|
| 53 | + issn = {1940-6029}, |
|
| 54 | + doi = {10.1007/978-1-4939-9151-8_20}, |
|
| 55 | + abstract = {Liquid biopsies are rapidly emerging as powerful tools for the early detection of cancer, noninvasive genomic profiling of localized or metastatic tumors, prompt detection of treatment resistance-associated mutations, and monitoring of therapeutic response and minimal residual disease in patients during clinical follow-up. Growing evidence strongly supports the utility of circulating tumor DNA (ctDNA) as a biomarker for the stratification and clinical management of lymphoma patients. However, ctDNA is diluted by variable amounts of cell-free DNA (cfDNA) shed by nonneoplastic cells causing a background signal of wild-type DNA that limits the sensitivity of methods that rely on DNA sequencing. Here, we describe an error suppression method for single-molecule counting that relies on targeted sequencing of cfDNA libraries constructed with semi-degenerate barcode adapters. Custom pools of biotinylated DNA baits for target enrichment can be designed to specifically track somatic mutations in one patient, survey mutation hotspots with diagnostic and prognostic value or be comprised of comprehensive gene panels with broad patient coverage in lymphoma. Such methods are amenable to track ctDNA levels during longitudinal liquid biopsy testing with high specificity and sensitivity and characterize, in real time, the genetic profiles of tumors without the need of standard invasive biopsies. The analysis of ultra-deep sequencing data according to the bioinformatics pipelines also described in this chapter affords to harness lower limits of detection for ctDNA below 0.1\%.}, |
|
| 56 | + langid = {english}, |
|
| 57 | + keywords = {Blood Specimen Collection,Cell-free DNA,Circulating Tumor DNA,DNA Barcoding Taxonomic,DNA damage,DNA Mutational Analysis,Duplex sequencing,Gene Library,High-Throughput Nucleotide Sequencing,Humans,Liquid biopsy,Liquid Biopsy,Lymphoma,Minimal residual disease,Mutation detection,Noninvasive genetic profiling,Nucleic Acid Hybridization,Targeted enrichment,Therapeutic response,Tumor burden} |
|
| 58 | +} |
|
| 59 | + |
|
| 60 | +@article{alduaijMolecularDeterminantsClinical2023, |
|
| 61 | + title = {Molecular Determinants of Clinical Outcomes in a Real-World Diffuse Large {{B-cell}} Lymphoma Population}, |
|
| 62 | + author = {Alduaij, Waleed and Collinge, Brett and Ben-Neriah, Susana and Jiang, Aixiang and Hilton, Laura K. and Boyle, Merrill and Meissner, Barbara and Chong, Lauren and Miyata-Takata, Tomoko and Slack, Graham W. and Farinha, Pedro and Craig, Jeffrey W. and Lytle, Andrew and Savage, Kerry J. and Villa, Diego and Gerrie, Alina S. and Freeman, Ciara L. and Gascoyne, Randy D. and Connors, Joseph M. and Morin, Ryan D. and Sehn, Laurie H. and Mungall, Andrew J. and Steidl, Christian and Scott, David W.}, |
|
| 63 | + date = {2023-05-18}, |
|
| 64 | + journaltitle = {Blood}, |
|
| 65 | + shortjournal = {Blood}, |
|
| 66 | + volume = {141}, |
|
| 67 | + number = {20}, |
|
| 68 | + pages = {2493--2507}, |
|
| 69 | + issn = {0006-4971}, |
|
| 70 | + doi = {10.1182/blood.2022018248}, |
|
| 71 | + url = {https://doi.org/10.1182/blood.2022018248}, |
|
| 72 | + urldate = {2024-01-19}, |
|
| 73 | + abstract = {Molecular heterogeneity of diffuse large B-cell lymphoma (DLBCL) underlies the variable outcomes achieved with immunochemotherapy. However, outcomes of gene expression profiling (GEP)–defined molecular subgroups in a real-world DLBCL population remain unknown. Here we examined the prevalence and outcomes of molecular subgroups in an unselected population of 1149 patients with de novo DLBCL in British Columbia, Canada. Evaluable biopsies were profiled by fluorescence in situ hybridization (FISH), immunohistochemistry, and digital GEP to assign cell-of-origin and the so-called “double-hit signature” (DHITsig)—a signature originally described as being characteristic for high-grade B-cell lymphoma with MYC and BCL2 rearrangements (HGBCL-DH-BCL2). DHITsig was expressed in 21\% of 431 germinal center B-cell-like (GCB)–DLBCL and all 55 Burkitt lymphomas examined. Reflecting this latter finding, DHITsig has been renamed the “dark zone signature” (DZsig). DZsigpos-DLBCL, non-DZsigpos GCB-DLBCL and activated B-cell-like (ABC)–DLBCL were associated with a 2 year overall survival of 57\%, 89\%, and 71\%, respectively. 62\% of DZsigpos tumors were negative for HGBCL-DH-BCL2 by FISH, but were associated with outcomes similar to HGBCL-DH-BCL2. A small group of HGBCL-DH-BCL2 that lacked DZsig expression had different molecular features compared with DZsig-expressing HGBCL-DH-BCL2 and were associated with favorable outcomes comparable to DLBCL, not otherwise specified. DZsigpos and ABC-DLBCL had a shorter diagnosis-to-treatment interval (DTI) than GCB-DLBCL, with this metric being associated with outcome. In conclusion, DZsig expression extends beyond HGBCL-DH-BCL2 and captures a poor-prognosis DLBCL subgroup with short DTI, including patients unidentifiable by routine FISH testing, that should be considered for treatment intensification or novel therapies in prospective trials.}, |
|
| 74 | + file = {/Users/rmorin/Zotero/storage/UXVBGRHE/Alduaij et al. - 2023 - Molecular determinants of clinical outcomes in a r.pdf;/Users/rmorin/Zotero/storage/U6ZLHEF3/Molecular-determinants-of-clinical-outcomes-in-a.html} |
|
| 75 | +} |
|
| 76 | + |
|
| 77 | +@article{algamalGeneSelectionMicroarray2018, |
|
| 78 | + title = {Gene Selection for Microarray Gene Expression Classification Using {{Bayesian Lasso}} Quantile Regression}, |
|
| 79 | + author = {Algamal, Zakariya Yahya and Alhamzawi, Rahim and Mohammad Ali, Haithem Taha}, |
|
| 80 | + date = {2018-01-06}, |
|
| 81 | + journaltitle = {Computers in Biology and Medicine}, |
|
| 82 | + shortjournal = {Comput. Biol. Med.}, |
|
| 83 | + volume = {97}, |
|
| 84 | + eprint = {29729489}, |
|
| 85 | + eprinttype = {pmid}, |
|
| 86 | + pages = {145--152}, |
|
| 87 | + issn = {1879-0534}, |
|
| 88 | + doi = {10.1016/j.compbiomed.2018.04.018}, |
|
| 89 | + abstract = {Gene selection has been proven to be an effective way to improve the results of many classification methods. However, existing gene selection techniques in binary classification regression are sensitive to outliers of the data, heteroskedasticity or other anomalies of the latent response. In this paper, we propose a new Bayesian hierarchical model to overcome these problems in a relatively straightforward way. In particular, we propose a new Bayesian Lasso method that employs a skewed Laplace distribution for the errors and a scaled mixture of uniform distribution for the regression parameters, together with Bayesian MCMC estimation. Comprehensive comparisons between our proposed gene selection method and other competitor methods are performed experimentally, depending on four benchmark gene expression datasets. The experimental results prove that the proposed method is very effective for selecting the most relevant genes with high classification accuracy.}, |
|
| 90 | + langid = {english}, |
|
| 91 | + keywords = {Algorithms,Bayes Theorem,Bayesian hierarchical model,Classification,Computational Biology,Databases Genetic,Gene Expression Profiling,Gene selection,Humans,Lasso,Models Statistical,Neoplasms,Oligonucleotide Array Sequence Analysis,Quantile regression,Regression Analysis,Transcriptome} |
|
| 92 | +} |
|
| 93 | + |
|
| 94 | +@article{alhusainNonparametricApproachesPopulation2018, |
|
| 95 | + title = {Nonparametric Approaches for Population Structure Analysis}, |
|
| 96 | + author = {Alhusain, Luluah and Hafez, Alaaeldin M.}, |
|
| 97 | + date = {2018-05-09}, |
|
| 98 | + journaltitle = {Human Genomics}, |
|
| 99 | + shortjournal = {Hum. Genomics}, |
|
| 100 | + volume = {12}, |
|
| 101 | + number = {1}, |
|
| 102 | + eprint = {29743099}, |
|
| 103 | + eprinttype = {pmid}, |
|
| 104 | + pages = {25}, |
|
| 105 | + issn = {1479-7364}, |
|
| 106 | + doi = {10.1186/s40246-018-0156-4}, |
|
| 107 | + abstract = {The analysis of population structure has many applications in medical and population genetic research. Such analysis is used to provide clear insight into the underlying genetic population substructure and is a crucial prerequisite for any analysis of genetic data. The analysis involves grouping individuals into subpopulations based on shared genetic variations. The most widely used markers to study the variation of DNA sequences between populations are single nucleotide polymorphisms. Data preprocessing is a necessary step to assess the quality of the data and to determine which markers or individuals can reasonably be included in the analysis. After preprocessing, several methods can be utilized to uncover population substructure, which can be categorized into two broad approaches: parametric and nonparametric. Parametric approaches use statistical models to infer population structure and assign individuals into subpopulations. However, these approaches suffer from many drawbacks that make them impractical for large datasets. In contrast, nonparametric approaches do not suffer from these drawbacks, making them more viable than parametric approaches for analyzing large datasets. Consequently, nonparametric approaches are increasingly used to reveal population substructure. Thus, this paper reviews and discusses the nonparametric approaches that are available for population structure analysis along with some implications to resolve challenges.}, |
|
| 108 | + langid = {english}, |
|
| 109 | + pmcid = {PMC5944014}, |
|
| 110 | + keywords = {Allele-sharing distance,Clustering,Dimension reduction,Genetic data,Population genetics,Population structure analysis,Principal component analysis,Single nucleotide polymorphism} |
|
| 111 | +} |
|
| 112 | + |
|
| 113 | +@article{aligDistinctHodgkinLymphoma2024, |
|
| 114 | + title = {Distinct {{Hodgkin}} Lymphoma Subtypes Defined by Noninvasive Genomic Profiling}, |
|
| 115 | + author = {Alig, Stefan K. and Shahrokh Esfahani, Mohammad and Garofalo, Andrea and Li, Michael Yu and Rossi, Cédric and Flerlage, Tim and Flerlage, Jamie E. and Adams, Ragini and Binkley, Michael S. and Shukla, Navika and Jin, Michael C. and Olsen, Mari and Telenius, Adèle and Mutter, Jurik A. and Schroers-Martin, Joseph G. and Sworder, Brian J. and Rai, Shinya and King, Daniel A. and Schultz, Andre and Bögeholz, Jan and Su, Shengqin and Kathuria, Karan R. and Liu, Chih Long and Kang, Xiaoman and Strohband, Maya J. and Langfitt, Deanna and Pobre-Piza, Kristine Faye and Surman, Sherri and Tian, Feng and Spina, Valeria and Tousseyn, Thomas and Buedts, Lieselot and Hoppe, Richard and Natkunam, Yasodha and Fornecker, Luc-Matthieu and Castellino, Sharon M. and Advani, Ranjana and Rossi, Davide and Lynch, Ryan and Ghesquières, Hervé and Casasnovas, Olivier and Kurtz, David M. and Marks, Lianna J. and Link, Michael P. and André, Marc and Vandenberghe, Peter and Steidl, Christian and Diehn, Maximilian and Alizadeh, Ash A.}, |
|
| 116 | + date = {2024-01}, |
|
| 117 | + journaltitle = {Nature}, |
|
| 118 | + shortjournal = {Nature}, |
|
| 119 | + volume = {625}, |
|
| 120 | + number = {7996}, |
|
| 121 | + eprint = {38081297}, |
|
| 122 | + eprinttype = {pmid}, |
|
| 123 | + pages = {778--787}, |
|
| 124 | + issn = {1476-4687}, |
|
| 125 | + doi = {10.1038/s41586-023-06903-x}, |
|
| 126 | + abstract = {The scarcity of malignant Hodgkin and Reed-Sternberg cells hampers tissue-based comprehensive genomic profiling of classic Hodgkin lymphoma (cHL). By contrast, liquid biopsies show promise for molecular profiling of cHL due to relatively high circulating tumour DNA (ctDNA) levels1-4. Here we show that the plasma representation of mutations exceeds the bulk tumour representation in most cases, making cHL particularly amenable to noninvasive profiling. Leveraging single-cell transcriptional profiles of cHL tumours, we demonstrate Hodgkin and Reed-Sternberg ctDNA shedding to be shaped by DNASE1L3, whose increased tumour microenvironment-derived expression drives high ctDNA concentrations. Using this insight, we comprehensively profile 366 patients, revealing two distinct cHL genomic subtypes with characteristic clinical and prognostic correlates, as well as distinct transcriptional and immunological profiles. Furthermore, we identify a novel class of truncating IL4R mutations that are dependent on IL-13 signalling and therapeutically targetable with IL-4Rα-blocking antibodies. Finally, using PhasED-seq5, we demonstrate the clinical value of pretreatment and on-treatment ctDNA levels for longitudinally refining cHL risk prediction and for detection of radiographically occult minimal residual disease. Collectively, these results support the utility of noninvasive strategies for genotyping and dynamic monitoring of cHL, as well as capturing molecularly distinct subtypes with diagnostic, prognostic and therapeutic potential.}, |
|
| 127 | + langid = {english}, |
|
| 128 | + keywords = {Circulating Tumor DNA,Genome Human,Genomics,Hodgkin Disease,Humans,Mutation,Reed-Sternberg Cells,Single-Cell Gene Expression Analysis,Tumor Microenvironment} |
|
| 129 | +} |
|
| 130 | + |
|
| 131 | +@article{alix-panabieresCirculatingTumorCells, |
|
| 132 | + title = {Circulating Tumor Cells and Circulating Tumor {{DNA}}.}, |
|
| 133 | + author = {Alix-Panabières, Catherine and Schwarzenbach, Heidi and Pantel, Klaus}, |
|
| 134 | + journaltitle = {Annual review of medicine}, |
|
| 135 | + volume = {63}, |
|
| 136 | + pages = {199--215}, |
|
| 137 | + keywords = {nosource} |
|
| 138 | +} |
|
| 139 | + |
|
| 140 | +@article{alizadehDistinctTypesDiffuse2000, |
|
| 141 | + title = {Distinct Types of Diffuse Large {{B-cell}} Lymphoma Identified by Gene Expression Profiling.}, |
|
| 142 | + author = {Alizadeh, A A and Eisen, M B and Davis, R E and Ma, C and Lossos, I S and Rosenwald, A and Boldrick, J C and Sabet, H and Tran, T and Yu, X and Powell, J I and Yang, L and Marti, G E and Moore, T and Hudson, J and Lu, L and Lewis, D B and Tibshirani, R and Sherlock, G and Chan, W C and Greiner, T C and Weisenburger, D D and Armitage, J O and Warnke, R and Levy, R and Wilson, W and Grever, M R and Byrd, J C and Botstein, D and Brown, P O and Staudt, L M}, |
|
| 143 | + date = {2000-02}, |
|
| 144 | + journaltitle = {Nature}, |
|
| 145 | + volume = {403}, |
|
| 146 | + number = {6769}, |
|
| 147 | + pages = {503--511}, |
|
| 148 | + keywords = {nosource} |
|
| 149 | +} |
|
| 150 | + |
|
| 151 | +@article{alizadehLymphochipSpecializedCDNA1999, |
|
| 152 | + title = {The Lymphochip: A Specialized {{cDNA}} Microarray for the Genomic-Scale Analysis of Gene Expression in Normal and Malignant Lymphocytes}, |
|
| 153 | + author = {Alizadeh, A and Eisen, M and Davis, R and Ma, C and Sabet, H and Tran, T and Powell, J and Yang, L and Marti, G and Moore, D and Hudson, J and Chan, W and Greiner, T and Weisenburger, D and Armitage, J and Lossos, I and Levy, R and Botstein, D and Brown, P and Staudt, L}, |
|
| 154 | + date = {1999}, |
|
| 155 | + journaltitle = {Cold Spring Harbor symposia on quantitative biology}, |
|
| 156 | + volume = {64}, |
|
| 157 | + pages = {71--78}, |
|
| 158 | + keywords = {nosource} |
|
| 159 | +} |
|
| 160 | + |
|
| 161 | +@article{alizadehNovelClassificationHuman2001, |
|
| 162 | + title = {Towards a Novel Classification of Human Malignancies Based on Gene Expression Patterns}, |
|
| 163 | + author = {Alizadeh, A. A. and Ross, D. T. and Perou, C. M. and family=Rijn, given=M., prefix=van de, useprefix=true}, |
|
| 164 | + date = {2001-09}, |
|
| 165 | + journaltitle = {The Journal of Pathology}, |
|
| 166 | + shortjournal = {J Pathol}, |
|
| 167 | + volume = {195}, |
|
| 168 | + number = {1}, |
|
| 169 | + eprint = {11568890}, |
|
| 170 | + eprinttype = {pmid}, |
|
| 171 | + pages = {41--52}, |
|
| 172 | + issn = {0022-3417}, |
|
| 173 | + doi = {10.1002/path.889}, |
|
| 174 | + abstract = {As a result of progress on the human genome project, approximately 19 000 genes have been identified and tens of thousands more tentatively identified as partial fragments of genes termed expressed sequence tags (ESTs). Most of these genes are only partially characterized and the functions of the vast majority are as yet unknown. It is likely that many genes that might be useful for diagnosis and/or prognostication of human malignancies have yet to be recognized. The advent of cDNA microarray technology now allows the efficient measurement of expression for almost every gene in the human genome in a single overnight hybridization experiment. This genomic scale approach has begun to reveal novel molecular-based sub-classes of tumours in breast carcinoma, colon carcinoma, lymphoma, leukaemia, and melanoma. In several instances, gene microarray analysis has already identified genes that appear to be useful for predicting clinical behaviour. This review discusses some recent findings using gene microarray technology and describes how this and related technologies are likely to contribute to the emergence of novel molecular classifications of human malignancies.}, |
|
| 175 | + langid = {english}, |
|
| 176 | + keywords = {Breast Neoplasms,Cluster Analysis,DNA Fingerprinting,Expressed Sequence Tags,Gene Expression Regulation Neoplastic,Genetic Markers,Genome Human,Humans,Lymphoma,Neoplasms,Oligonucleotide Array Sequence Analysis,Prognosis}, |
|
| 177 | + file = {/Users/rmorin/Zotero/storage/UB5Y6H2N/Alizadeh et al. - 2001 - Towards a novel classification of human malignanci.pdf} |
|
| 178 | +} |
|
| 179 | + |
|
| 180 | +@article{alizadehPredictionSurvivalDiffuse, |
|
| 181 | + title = {Prediction of Survival in Diffuse Large {{B-cell}} Lymphoma Based on the Expression of 2 Genes Reflecting Tumor and Microenvironment}, |
|
| 182 | + author = {Alizadeh, A A and Gentles, A J and Alencar, A J}, |
|
| 183 | + keywords = {nosource} |
|
| 184 | +} |
|
| 185 | + |
|
| 186 | +@article{alkallasMultiomicAnalysisReveals2020, |
|
| 187 | + title = {Multi-Omic Analysis Reveals Significantly Mutated Genes and {{DDX3X}} as a Sex-Specific Tumor Suppressor in Cutaneous Melanoma}, |
|
| 188 | + author = {Alkallas, Rached and Lajoie, Mathieu and Moldoveanu, Dan and Hoang, Karen Vo and Lefrançois, Philippe and Lingrand, Marine and Ahanfeshar-Adams, Mozhdeh and Watters, Kevin and Spatz, Alan and Zippin, Jonathan H. and Najafabadi, Hamed S. and Watson, Ian R.}, |
|
| 189 | + date = {2020-06}, |
|
| 190 | + journaltitle = {Nature Cancer}, |
|
| 191 | + shortjournal = {Nat Cancer}, |
|
| 192 | + volume = {1}, |
|
| 193 | + number = {6}, |
|
| 194 | + pages = {635--652}, |
|
| 195 | + publisher = {Nature Publishing Group}, |
|
| 196 | + issn = {2662-1347}, |
|
| 197 | + doi = {10.1038/s43018-020-0077-8}, |
|
| 198 | + url = {https://www.nature.com/articles/s43018-020-0077-8}, |
|
| 199 | + urldate = {2021-06-01}, |
|
| 200 | + abstract = {The high background tumor mutation burden in cutaneous melanoma limits the ability to identify significantly mutated genes (SMGs) that drive this cancer. To address this, we performed a mutation significance study of over 1,000 melanoma exomes, combined with a multi-omic analysis of 470 cases from The Cancer Genome Atlas. We discovered several SMGs with co-occurring loss-of-heterozygosity and loss-of-function mutations, including PBRM1, PLXNC1 and PRKAR1A, which encodes a protein kinase A holoenzyme subunit. Deconvolution of bulk tumor transcriptomes into cancer, immune and stromal components revealed a melanoma-intrinsic oxidative phosphorylation signature associated with protein kinase A pathway alterations. We also identified SMGs on the X chromosome, including the RNA helicase DDX3X, whose loss-of-function mutations were exclusively observed in males. Finally, we found that tumor mutation burden and immune infiltration contain complementary information on survival of patients with melanoma. In summary, our multi-omic analysis provides insights into melanoma etiology and supports contribution of specific mutations to the sex bias observed in this cancer.}, |
|
| 201 | + issue = {6}, |
|
| 202 | + langid = {english}, |
|
| 203 | + file = {/Users/rmorin/Zotero/storage/93SIU5GI/s43018-020-0077-8.html} |
|
| 204 | +} |
|
| 205 | + |
|
| 206 | +@article{AnalysisCirculatingTumor2001, |
|
| 207 | + title = {Analysis of {{Circulating Tumor DNA}} in {{Plasma}} at {{Diagnosis}} and during {{Follow-Up}} of {{Lung Cancer Patients}}}, |
|
| 208 | + date = {2001-06}, |
|
| 209 | + pages = {1--5}, |
|
| 210 | + keywords = {nosource} |
|
| 211 | +} |
|
| 212 | + |
|
| 213 | +@article{andersHTSeqPythonFramework2015, |
|
| 214 | + title = {{{HTSeq--a Python}} Framework to Work with High-Throughput Sequencing Data}, |
|
| 215 | + author = {Anders, Simon and Pyl, Paul Theodor and Huber, Wolfgang}, |
|
| 216 | + date = {2015-01-15}, |
|
| 217 | + journaltitle = {Bioinformatics (Oxford, England)}, |
|
| 218 | + shortjournal = {Bioinformatics}, |
|
| 219 | + volume = {31}, |
|
| 220 | + number = {2}, |
|
| 221 | + eprint = {25260700}, |
|
| 222 | + eprinttype = {pmid}, |
|
| 223 | + pages = {166--169}, |
|
| 224 | + issn = {1367-4811}, |
|
| 225 | + doi = {10.1093/bioinformatics/btu638}, |
|
| 226 | + abstract = {MOTIVATION: A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard workflows, custom scripts are needed. RESULTS: We present HTSeq, a Python library to facilitate the rapid development of such scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data, such as genomic coordinates, sequences, sequencing reads, alignments, gene model information and variant calls, and provides data structures that allow for querying via genomic coordinates. We also present htseq-count, a tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes. AVAILABILITY AND IMPLEMENTATION: HTSeq is released as an open-source software under the GNU General Public Licence and available from http://www-huber.embl.de/HTSeq or from the Python Package Index at https://pypi.python.org/pypi/HTSeq.}, |
|
| 227 | + langid = {english}, |
|
| 228 | + pmcid = {PMC4287950}, |
|
| 229 | + keywords = {Gene Expression Regulation,Genome Human,Genomics,High-Throughput Nucleotide Sequencing,Humans,Software} |
|
| 230 | +} |
|
| 231 | + |
|
| 232 | +@article{ankoGlobalAnalysisReveals2010, |
|
| 233 | + title = {Global Analysis Reveals {{SRp20-}} and {{SRp75-specific mRNPs}} in Cycling and Neural Cells}, |
|
| 234 | + author = {Ankö, Minna-Liisa and Morales, Lucia and Henry, Ian and Beyer, Andreas and Neugebauer, Karla M.}, |
|
| 235 | + date = {2010-08}, |
|
| 236 | + journaltitle = {Nature Structural \& Molecular Biology}, |
|
| 237 | + shortjournal = {Nat. Struct. Mol. Biol.}, |
|
| 238 | + volume = {17}, |
|
| 239 | + number = {8}, |
|
| 240 | + eprint = {20639886}, |
|
| 241 | + eprinttype = {pmid}, |
|
| 242 | + pages = {962--970}, |
|
| 243 | + issn = {1545-9985}, |
|
| 244 | + doi = {10.1038/nsmb.1862}, |
|
| 245 | + abstract = {Members of the SR protein family of RNA-binding proteins have numerous roles in mRNA metabolism, from transcription to translation. To understand how SR proteins coordinate gene regulation, comprehensive knowledge of endogenous mRNA targets is needed. Here we establish physiological expression of GFP-tagged SR proteins from stable transgenes. Using the GFP tag for immunopurification of mRNPs, mRNA targets of SRp20 and SRp75 were identified in cycling and neurally induced P19 cells. Genome-wide analysis showed that SRp20 and SRp75 associate with hundreds of distinct, functionally related groups of transcripts that change in response to neural differentiation. Knockdown of either SRp20 or SRp75 led to up- or downregulation of specific transcripts, including identified targets, and rescue by the GFP-tagged SR proteins proved their functionality. Thus, SR proteins contribute to the execution of gene-expression programs through their association with distinct endogenous mRNAs.}, |
|
| 246 | + langid = {english}, |
|
| 247 | + keywords = {Animals,Cell Cycle,Cell Differentiation,Cell Line Tumor,Chromosomes Artificial Bacterial,Gene Expression Regulation Neoplastic,Gene Knockdown Techniques,Green Fluorescent Proteins,Immunoprecipitation,Mice,Neurons,Organ Specificity,Protein Binding,Ribonucleoproteins,RNA Messenger,RNA-Binding Proteins,Serine-Arginine Splicing Factors} |
|
| 248 | +} |
|
| 249 | + |
|
| 250 | +@article{ankoRNAbindingLandscapesTwo2012, |
|
| 251 | + title = {The {{RNA-binding}} Landscapes of Two {{SR}} Proteins Reveal Unique Functions and Binding to Diverse {{RNA}} Classes}, |
|
| 252 | + author = {Änkö, Minna-Liisa and Müller-McNicoll, Michaela and Brandl, Holger and Curk, Tomaz and Gorup, Crtomir and Henry, Ian and Ule, Jernej and Neugebauer, Karla M.}, |
|
| 253 | + date = {2012}, |
|
| 254 | + journaltitle = {Genome Biology}, |
|
| 255 | + shortjournal = {Genome Biol.}, |
|
| 256 | + volume = {13}, |
|
| 257 | + number = {3}, |
|
| 258 | + eprint = {22436691}, |
|
| 259 | + eprinttype = {pmid}, |
|
| 260 | + pages = {R17}, |
|
| 261 | + issn = {1474-760X}, |
|
| 262 | + doi = {10.1186/gb-2012-13-3-r17}, |
|
| 263 | + abstract = {BACKGROUND: The SR proteins comprise a family of essential, structurally related RNA binding proteins. The complexity of their RNA targets and specificity of RNA recognition in vivo is not well understood. Here we use iCLIP to globally analyze and compare the RNA binding properties of two SR proteins, SRSF3 and SRSF4, in murine cells. RESULTS: SRSF3 and SRSF4 binding sites mapped to largely non-overlapping target genes, and in vivo consensus binding motifs were distinct. Interactions with intronless and intron-containing mRNAs as well as non-coding RNAs were detected. Surprisingly, both SR proteins bound to the 3' ends of the majority of intronless histone transcripts, implicating SRSF3 and SRSF4 in histone mRNA metabolism. In contrast, SRSF3 but not SRSF4 specifically bound transcripts encoding numerous RNA binding proteins. Remarkably, SRSF3 was shown to modulate alternative splicing of its own as well as three other transcripts encoding SR proteins. These SRSF3-mediated splicing events led to downregulation of heterologous SR proteins via nonsense-mediated decay. CONCLUSIONS: SRSF3 and SRSF4 display unique RNA binding properties underlying diverse cellular regulatory mechanisms, with shared as well as unique coding and non-coding targets. Importantly, CLIP analysis led to the discovery that SRSF3 cross-regulates the expression of other SR protein family members.}, |
|
| 264 | + langid = {english}, |
|
| 265 | + pmcid = {PMC3439968}, |
|
| 266 | + keywords = {3' Untranslated Regions,Alternative Splicing,Animals,Binding Sites,Cell Line Tumor,Gene Expression Regulation,Histones,Introns,Mice,RNA Untranslated,RNA-Binding Proteins,Serine-Arginine Splicing Factors} |
|
| 267 | +} |
|
| 268 | + |
|
| 269 | +@article{ansa-addoRNABindingProtein2020, |
|
| 270 | + title = {{{RNA}} Binding Protein {{PCBP1}} Is an Intracellular Immune Checkpoint for Shaping {{T}} Cell Responses in Cancer Immunity}, |
|
| 271 | + author = {Ansa-Addo, Ephraim A. and Huang, Huai-Cheng and Riesenberg, Brian and Iamsawat, Supinya and Borucki, Davis and Nelson, Michelle H. and Nam, Jin Hyun and Chung, Dongjun and Paulos, Chrystal M. and Liu, Bei and Yu, Xue-Zhong and Philpott, Caroline and Howe, Philip H. and Li, Zihai}, |
|
| 272 | + date = {2020-05-29}, |
|
| 273 | + journaltitle = {Science Advances}, |
|
| 274 | + shortjournal = {Sci Adv}, |
|
| 275 | + volume = {6}, |
|
| 276 | + number = {22}, |
|
| 277 | + eprint = {32523987}, |
|
| 278 | + eprinttype = {pmid}, |
|
| 279 | + pages = {eaaz3865}, |
|
| 280 | + issn = {2375-2548}, |
|
| 281 | + doi = {10.1126/sciadv.aaz3865}, |
|
| 282 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7259945/}, |
|
| 283 | + urldate = {2022-09-28}, |
|
| 284 | + abstract = {RNA binding protein PCBP1 guards effector and antitumor T cell functions., Distinct lineages of T cells can act in response to various environmental cues to either drive or restrict immune-mediated pathology. Here, we identify the RNA binding protein, poly(C)-binding protein 1 (PCBP1) as an intracellular immune checkpoint that is up-regulated in activated T cells to prevent conversion of effector T (Teff) cells into regulatory T (Treg) cells, by restricting the expression of Teff cell–intrinsic Treg commitment programs. This was critical for stabilizing Teff cell functions and subverting immune-suppressive signals. T cell–specific deletion of Pcbp1 favored Treg cell differentiation, enlisted multiple inhibitory immune checkpoint molecules including PD-1, TIGIT, and VISTA on tumor-infiltrating lymphocytes, and blunted antitumor immunity. Our results demonstrate a critical role for PCBP1 as an intracellular immune checkpoint for maintaining Teff cell functions in cancer immunity.}, |
|
| 285 | + pmcid = {PMC7259945}, |
|
| 286 | + file = {/Users/rmorin/Zotero/storage/IWEH8RBR/Ansa-Addo et al. - 2020 - RNA binding protein PCBP1 is an intracellular immu.pdf;/Users/rmorin/Zotero/storage/WFWAV92W/Ansa-Addo et al. - 2020 - RNA binding protein PCBP1 is an intracellular immu.pdf} |
|
| 287 | +} |
|
| 288 | + |
|
| 289 | +@article{aresuPhenotypicalCharacterizationClinical2021, |
|
| 290 | + title = {Phenotypical {{Characterization}} and {{Clinical Outcome}} of {{Canine Burkitt-Like Lymphoma}}}, |
|
| 291 | + author = {Aresu, Luca and Agnoli, Chiara and Nicoletti, Arturo and Fanelli, Antonella and Martini, Valeria and Bertoni, Francesco and Marconato, Laura}, |
|
| 292 | + date = {2021}, |
|
| 293 | + journaltitle = {Frontiers in Veterinary Science}, |
|
| 294 | + shortjournal = {Front. Vet. Sci.}, |
|
| 295 | + volume = {8}, |
|
| 296 | + publisher = {Frontiers}, |
|
| 297 | + issn = {2297-1769}, |
|
| 298 | + doi = {10.3389/fvets.2021.647009}, |
|
| 299 | + url = {https://www.frontiersin.org/articles/10.3389/fvets.2021.647009/full}, |
|
| 300 | + urldate = {2021-05-13}, |
|
| 301 | + abstract = {In dogs, Burkitt-like lymphoma (B-LL) is rare tumour and it is classified as a high-grade B-cell malignancy. The diagnosis is challenging because of the similar histologic appearance with other histotypes, no defined phenotypical criteria and poorly described clinical aspects. The aim of the study was to provide a detailed description of clinical and morphological features, as well as immunophenotypical profile of B-LL in comparison with the human counterpart. Thirteen dogs with histologically proven B-LL, for which a complete staging and follow-up were available, were retrospectively selected. Immunohistochemical expression of CD20, PAX5, CD3, CD10, BCL2, BCL6, MYC and caspase-3 was evaluated. Histologically, all B-LLs showed a diffuse architecture with medium to large-sized cells, high mitotic rate and diffuse starry sky appearance. B-phenotype of neoplastic cells was confirmed both by flow-cytometry and immunohistochemistry. Conversely, B-LLs were negative for BCL2 and MYC, whereas some cases co-expressed BCL6 and CD10, suggesting a germinal centre B-cell origin. Disease stage was advanced in the majority of cases. All dogs received CHOP-based chemotherapy with or without immunotherapy. Despite treatment, prognosis was poor, with a median time to progression and survival of 130 and 228 days, respectively. Nevertheless, approximately 30\% of dogs survived more than one year. An increased apoptotic index, a high turnover index and caspase-3 index correlated with shorter survival. In conclusion, canine B-LL shows phenotypical differences with the human counterpart along with features that might help to differentiate this entity from diffuse large B-cell lymphoma.}, |
|
| 302 | + langid = {english}, |
|
| 303 | + keywords = {apoptic index,Burkitt-like lymphoma,Caspase - 3,dog,MYC,prognosis}, |
|
| 304 | + file = {/Users/rmorin/Zotero/storage/8ZRSBNWC/Aresu et al. - 2021 - Phenotypical Characterization and Clinical Outcome.pdf} |
|
| 305 | +} |
|
| 306 | + |
|
| 307 | +@article{arnedo-pacOncodriveCLUSTLSequencebasedClustering2019, |
|
| 308 | + title = {{{OncodriveCLUSTL}}: A Sequence-Based Clustering Method to Identify Cancer Drivers}, |
|
| 309 | + shorttitle = {{{OncodriveCLUSTL}}}, |
|
| 310 | + author = {Arnedo-Pac, Claudia and Mularoni, Loris and Muiños, Ferran and Gonzalez-Perez, Abel and Lopez-Bigas, Nuria}, |
|
| 311 | + date = {2019-11-01}, |
|
| 312 | + journaltitle = {Bioinformatics (Oxford, England)}, |
|
| 313 | + shortjournal = {Bioinformatics}, |
|
| 314 | + volume = {35}, |
|
| 315 | + number = {22}, |
|
| 316 | + eprint = {31228182}, |
|
| 317 | + eprinttype = {pmid}, |
|
| 318 | + pages = {4788--4790}, |
|
| 319 | + issn = {1367-4811}, |
|
| 320 | + doi = {10.1093/bioinformatics/btz501}, |
|
| 321 | + abstract = {MOTIVATION: Identification of the genomic alterations driving tumorigenesis is one of the main goals in oncogenomics research. Given the evolutionary principles of cancer development, computational methods that detect signals of positive selection in the pattern of tumor mutations have been effectively applied in the search for cancer genes. One of these signals is the abnormal clustering of mutations, which has been shown to be complementary to other signals in the detection of driver genes. RESULTS: We have developed OncodriveCLUSTL, a new sequence-based clustering algorithm to detect significant clustering signals across genomic regions. OncodriveCLUSTL is based on a local background model derived from the simulation of mutations accounting for the composition of tri- or penta-nucleotide context substitutions observed in the cohort under study. Our method can identify known clusters and bona-fide cancer drivers across cohorts of tumor whole-exomes, outperforming the existing OncodriveCLUST algorithm and complementing other methods based on different signals of positive selection. Our results indicate that OncodriveCLUSTL can be applied to the analysis of non-coding genomic elements and non-human mutations data. AVAILABILITY AND IMPLEMENTATION: OncodriveCLUSTL is available as an installable Python 3.5 package. The source code and running examples are freely available at https://bitbucket.org/bbglab/oncodriveclustl under GNU Affero General Public License. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, |
|
| 322 | + langid = {english}, |
|
| 323 | + pmcid = {PMC6853674}, |
|
| 324 | + keywords = {Cluster Analysis,Genomics,Humans,Neoplasms,Software}, |
|
| 325 | + file = {/Users/rmorin/Zotero/storage/K25SVA5Q/Arnedo-Pac et al. - 2019 - OncodriveCLUSTL a sequence-based clustering metho.pdf} |
|
| 326 | +} |
|
| 327 | + |
|
| 328 | +@article{arthurGenomewideDiscoverySomatic2018, |
|
| 329 | + title = {Genome-Wide Discovery of Somatic Regulatory Variants in Diffuse Large {{B-cell}} Lymphoma}, |
|
| 330 | + author = {Arthur, Sarah E. and Jiang, Aixiang and Grande, Bruno M. and Alcaide, Miguel and Cojocaru, Razvan and Rushton, Christopher K. and Mottok, Anja and Hilton, Laura K. and Lat, Prince Kumar and Zhao, Eric Y. and Culibrk, Luka and Ennishi, Daisuke and Jessa, Selin and Chong, Lauren and Thomas, Nicole and Pararajalingam, Prasath and Meissner, Barbara and Boyle, Merrill and Davidson, Jordan and Bushell, Kevin R. and Lai, Daniel and Farinha, Pedro and Slack, Graham W. and Morin, Gregg B. and Shah, Sohrab and Sen, Dipankar and Jones, Steven J. M. and Mungall, Andrew J. and Gascoyne, Randy D. and Audas, Timothy E. and Unrau, Peter and Marra, Marco A. and Connors, Joseph M. and Steidl, Christian and Scott, David W. and Morin, Ryan D.}, |
|
| 331 | + date = {2018-10-01}, |
|
| 332 | + journaltitle = {Nature Communications}, |
|
| 333 | + shortjournal = {Nat Commun}, |
|
| 334 | + volume = {9}, |
|
| 335 | + number = {1}, |
|
| 336 | + eprint = {30275490}, |
|
| 337 | + eprinttype = {pmid}, |
|
| 338 | + pages = {4001}, |
|
| 339 | + issn = {2041-1723}, |
|
| 340 | + doi = {10.1038/s41467-018-06354-3}, |
|
| 341 | + abstract = {Diffuse large B-cell lymphoma (DLBCL) is an aggressive cancer originating from mature B-cells. Prognosis is strongly associated with molecular subgroup, although the driver mutations that distinguish the two main subgroups remain poorly defined. Through an integrative analysis of whole genomes, exomes, and transcriptomes, we have uncovered genes and non-coding loci that are commonly mutated in DLBCL. Our analysis has identified novel cis-regulatory sites, and implicates recurrent mutations in the 3' UTR of NFKBIZ as a novel mechanism of oncogene deregulation and NF-κB pathway activation in the activated B-cell (ABC) subgroup. Small amplifications associated with over-expression of FCGR2B (the Fcγ receptor protein IIB), primarily in the germinal centre B-cell (GCB) subgroup, correlate with poor patient outcomes suggestive of a novel oncogene. These results expand the list of subgroup driver mutations that may facilitate implementation of improved diagnostic assays and could offer new avenues for the development of targeted therapeutics.}, |
|
| 342 | + langid = {english}, |
|
| 343 | + pmcid = {PMC6167379}, |
|
| 344 | + keywords = {3' Untranslated Regions,Adaptor Proteins Signal Transducing,B-Lymphocytes,Cell Line Tumor,Exome,Gene Expression Regulation Neoplastic,Genes Regulator,Genetic Variation,Genome Human,Genome-Wide Association Study,Germinal Center,Humans,I-kappa B Proteins,Lymphoma Large B-Cell Diffuse,Mutation,Nuclear Proteins,Receptors IgG,Sequence Analysis DNA,Transcriptome}, |
|
| 345 | + file = {/Users/rmorin/Zotero/storage/899WLL3X/Arthur et al. - 2018 - Genome-wide discovery of somatic regulatory varian.pdf} |
|
| 346 | +} |
|
| 347 | + |
|
| 348 | +@article{ashrafuzzamanAptamersBothDrugs2014, |
|
| 349 | + title = {Aptamers as {{Both Drugs}} and {{Drug-Carriers}}}, |
|
| 350 | + author = {family=Ashrafuzzaman, given=Md., given-i={{Md}}}, |
|
| 351 | + date = {2014}, |
|
| 352 | + journaltitle = {BioMed Research International}, |
|
| 353 | + shortjournal = {Biomed Res Int}, |
|
| 354 | + volume = {2014}, |
|
| 355 | + eprint = {25295268}, |
|
| 356 | + eprinttype = {pmid}, |
|
| 357 | + pages = {697923}, |
|
| 358 | + issn = {2314-6133}, |
|
| 359 | + doi = {10.1155/2014/697923}, |
|
| 360 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4177733/}, |
|
| 361 | + urldate = {2022-10-14}, |
|
| 362 | + abstract = {Aptamers are short nucleic acid oligos. They may serve as both drugs and drug-carriers. Their use as diagnostic tools is also evident. They can be generated using various experimental, theoretical, and computational techniques. The systematic evolution of ligands by exponential enrichment which uses iterative screening of nucleic acid libraries is a popular experimental technique. Theory inspired methodology entropy-based seed-and-grow strategy that designs aptamer templates to bind specifically to targets is another one. Aptamers are predicted to be highly useful in producing general drugs and theranostic drugs occasionally for certain diseases like cancer, Alzheimer's disease, and so on. They bind to various targets like lipids, nucleic acids, proteins, small organic compounds, and even entire organisms. Aptamers may also serve as drug-carriers or nanoparticles helping drugs to get released in specific target regions. Due to better target specific physical binding properties aptamers cause less off-target toxicity effects. Therefore, search for aptamer based drugs, drug-carriers, and even diagnostic tools is expanding fast. The biophysical properties in relation to the target specific binding phenomena of aptamers, energetics behind the aptamer transport of drugs, and the consequent biological implications will be discussed. This review will open up avenues leading to novel drug discovery and drug delivery.}, |
|
| 363 | + pmcid = {PMC4177733}, |
|
| 364 | + file = {/Users/rmorin/Zotero/storage/YUJURKKQ/Ashrafuzzaman - 2014 - Aptamers as Both Drugs and Drug-Carriers.pdf} |
|
| 365 | +} |
|
| 366 | + |
|
| 367 | +@article{assoulinePhaseStudyPanobinostat2016, |
|
| 368 | + title = {Phase 2 Study of Panobinostat with or without Rituximab in Relapsed Diffuse Large {{B-cell}} Lymphoma.}, |
|
| 369 | + author = {Assouline, Sarit E and Nielsen, Torsten Holm and Yu, Stephen and Alcaide, Miguel and Chong, Lauren and Macdonald, David and Tosikyan, Axel and Kukreti, Vishal and Kezouh, Abbas and Petrogiannis-Haliotis, Tina and Albuquerque, Marco and Fornika, Daniel and Alamouti, Sepideh and Froment, Remi and Greenwood, Celia M T and Oros, Kathleen Klein and Camglioglu, Errol and Sharma, Ayushi and Christodoulopoulos, Rosa and Rousseau, Caroline and Johnson, Nathalie and Crump, Michael and Morin, Ryan D and Mann, Koren K}, |
|
| 370 | + date = {2016-07}, |
|
| 371 | + journaltitle = {Blood}, |
|
| 372 | + volume = {128}, |
|
| 373 | + number = {2}, |
|
| 374 | + pages = {185--194}, |
|
| 375 | + keywords = {nosource} |
|
| 376 | +} |
|
| 377 | + |
|
| 378 | +@article{asterDetectionBCL2Rearrangements2002, |
|
| 379 | + title = {Detection of {{BCL2 Rearrangements}} in {{Follicular Lymphoma}}}, |
|
| 380 | + author = {Aster, Jon C. and Longtine, Janina A.}, |
|
| 381 | + date = {2002-03}, |
|
| 382 | + journaltitle = {The American Journal of Pathology}, |
|
| 383 | + shortjournal = {Am J Pathol}, |
|
| 384 | + volume = {160}, |
|
| 385 | + number = {3}, |
|
| 386 | + eprint = {11891173}, |
|
| 387 | + eprinttype = {pmid}, |
|
| 388 | + pages = {759--763}, |
|
| 389 | + issn = {0002-9440}, |
|
| 390 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867166/}, |
|
| 391 | + urldate = {2023-12-18}, |
|
| 392 | + pmcid = {PMC1867166}, |
|
| 393 | + file = {/Users/rmorin/Zotero/storage/CN6XGEWK/Aster and Longtine - 2002 - Detection of BCL2 Rearrangements in Follicular Lym.pdf} |
|
| 394 | +} |
|
| 395 | + |
|
| 396 | +@article{auweraFastQDataHighConfidence2013, |
|
| 397 | + title = {From {{FastQ Data}} to {{High-Confidence Variant Calls}}: {{The Genome Analysis Toolkit Best Practices Pipeline}}}, |
|
| 398 | + shorttitle = {From {{FastQ Data}} to {{High-Confidence Variant Calls}}}, |
|
| 399 | + author = {family=Auwera, given=Geraldine A. Van, prefix=der, useprefix=false and Carneiro, Mauricio O. and Hartl, Christopher and Poplin, Ryan and family=Angel, given=Guillermo, prefix=del, useprefix=false and Levy‐Moonshine, Ami and Jordan, Tadeusz and Shakir, Khalid and Roazen, David and Thibault, Joel and Banks, Eric and Garimella, Kiran V. and Altshuler, David and Gabriel, Stacey and DePristo, Mark A.}, |
|
| 400 | + date = {2013}, |
|
| 401 | + journaltitle = {Current Protocols in Bioinformatics}, |
|
| 402 | + volume = {43}, |
|
| 403 | + number = {1}, |
|
| 404 | + pages = {11.10.1-11.10.33}, |
|
| 405 | + issn = {1934-340X}, |
|
| 406 | + doi = {10.1002/0471250953.bi1110s43}, |
|
| 407 | + url = {https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471250953.bi1110s43}, |
|
| 408 | + urldate = {2019-12-21}, |
|
| 409 | + abstract = {This unit describes how to use BWA and the Genome Analysis Toolkit (GATK) to map genome sequencing data to a reference and produce high-quality variant calls that can be used in downstream analyses. The complete workflow includes the core NGS data-processing steps that are necessary to make the raw data suitable for analysis by the GATK, as well as the key methods involved in variant discovery using the GATK. Curr. Protoc. Bioinform. 43:11.10.1-11.10.33. © 2013 by John Wiley \& Sons, Inc.}, |
|
| 410 | + langid = {english}, |
|
| 411 | + keywords = {exome,genotyping,NGS,variant detection,WGS}, |
|
| 412 | + file = {/Users/rmorin/Zotero/storage/Y9LV7TXJ/0471250953.html} |
|
| 413 | +} |
|
| 414 | + |
|
| 415 | +@article{ayyadGeneExpressionCancer2019, |
|
| 416 | + title = {Gene Expression Cancer Classification Using Modified {{K-Nearest Neighbors}} Technique}, |
|
| 417 | + author = {Ayyad, Sarah M. and Saleh, Ahmed I. and Labib, Labib M.}, |
|
| 418 | + date = {2019-02-01}, |
|
| 419 | + journaltitle = {Biosystems}, |
|
| 420 | + shortjournal = {Biosystems}, |
|
| 421 | + volume = {176}, |
|
| 422 | + pages = {41--51}, |
|
| 423 | + issn = {0303-2647}, |
|
| 424 | + doi = {10.1016/j.biosystems.2018.12.009}, |
|
| 425 | + url = {http://www.sciencedirect.com/science/article/pii/S0303264718302685}, |
|
| 426 | + urldate = {2020-02-04}, |
|
| 427 | + abstract = {Gene expression microarray classification is a crucial research field as it has been employed in cancer prediction and diagnosis systems. Gene expression data are composed of dozens of samples characterized by thousands of genes. Hence, an accurate and effective classification of such samples is a challenge. Machine learning techniques have been broadly utilized to build substantial and precise classification models. This paper proposes a new classification technique for gene expression data, which is called Modified k-nearest neighbor (MKNN). MKNN is applied in two scenarios namely; smallest modified KNN (SMKNN) and largest modified KNN (LMKNN). Both implementations are undertaken to enhance the performance of KNN. The key idea is to employ robust neighbors from training data by using a new weighting strategy. Several experiments have been performed on six different gene expression datasets. Experiments have shown that MKNN in its both scenarios outperforms traditional as well as recent ones. MKNN has been compared against (i) KNN, (ii) weighted KNN, (iii) support vector machine (SVM), (iv) fuzzy support vector machine, (v) brain emotional learning (BEL) in terms of classification accuracy, precision, and recall. On the other hand, results show that MKNN introduces smaller testing time than both KNN and weighted KNN.}, |
|
| 428 | + langid = {english}, |
|
| 429 | + keywords = {Cancer classification,Data mining,Gene expression,K-Nearest Neighbor,Microarray data classification}, |
|
| 430 | + file = {/Users/rmorin/Zotero/storage/XDA6E8TS/S0303264718302685.html} |
|
| 431 | +} |
|
| 432 | + |
|
| 433 | +@article{balSuperenhancerHypermutationAlters2022, |
|
| 434 | + title = {Super-Enhancer Hypermutation Alters Oncogene Expression in {{B}} Cell Lymphoma}, |
|
| 435 | + author = {Bal, Elodie and Kumar, Rahul and Hadigol, Mohammad and Holmes, Antony B. and Hilton, Laura K. and Loh, Jui Wan and Dreval, Kostiantyn and Wong, Jasper C. H. and Vlasevska, Sofija and Corinaldesi, Clarissa and Soni, Rajesh Kumar and Basso, Katia and Morin, Ryan D. and Khiabanian, Hossein and Pasqualucci, Laura and Dalla-Favera, Riccardo}, |
|
| 436 | + date = {2022-07}, |
|
| 437 | + journaltitle = {Nature}, |
|
| 438 | + shortjournal = {Nature}, |
|
| 439 | + volume = {607}, |
|
| 440 | + number = {7920}, |
|
| 441 | + eprint = {35794478}, |
|
| 442 | + eprinttype = {pmid}, |
|
| 443 | + pages = {808--815}, |
|
| 444 | + issn = {1476-4687}, |
|
| 445 | + doi = {10.1038/s41586-022-04906-8}, |
|
| 446 | + abstract = {Diffuse large B~cell lymphoma (DLBCL) is the most common B cell non-Hodgkin lymphoma and remains incurable in around 40\% of patients. Efforts to sequence the coding genome identified several genes and pathways that are altered in this disease, including potential therapeutic targets1-5. However, the non-coding genome of DLBCL remains largely unexplored. Here we show that active super-enhancers are highly and specifically hypermutated in 92\% of samples from individuals with DLBCL, display signatures of activation-induced cytidine deaminase activity, and are linked to genes that encode B cell developmental regulators and oncogenes. As evidence of oncogenic relevance, we show that the hypermutated super-enhancers linked to the BCL6, BCL2 and CXCR4 proto-oncogenes prevent the binding and transcriptional downregulation of the corresponding target gene by transcriptional repressors, including BLIMP1 (targeting BCL6) and the steroid receptor NR3C1 (targeting BCL2 and CXCR4). Genetic correction of selected mutations restored repressor DNA binding, downregulated target gene expression and led to the counter-selection of cells containing corrected alleles, indicating an oncogenic dependency on the super-enhancer mutations. This pervasive super-enhancer mutational mechanism reveals a major set of genetic lesions deregulating gene expression, which expands the involvement of known oncogenes in DLBCL pathogenesis and identifies new deregulated gene targets of therapeutic relevance.}, |
|
| 447 | + langid = {english}, |
|
| 448 | + pmcid = {PMC9583699}, |
|
| 449 | + keywords = {Down-Regulation,Enhancer Elements Genetic,Gene Expression Regulation Neoplastic,Humans,Lymphoma Large B-Cell Diffuse,Mutation,Oncogenes,Positive Regulatory Domain I-Binding Factor 1,Proto-Oncogene Proteins c-bcl-2,Proto-Oncogene Proteins c-bcl-6,Receptors CXCR4,Receptors Glucocorticoid,Repressor Proteins}, |
|
| 450 | + file = {/Users/rmorin/Zotero/storage/ZR2TF7BL/Bal et al. - 2022 - Super-enhancer hypermutation alters oncogene expre.pdf} |
|
| 451 | +} |
|
| 452 | + |
|
| 453 | +@article{baohuaMutationsPIK3CAGene, |
|
| 454 | + title = {Mutations of the {{PIK3CA Gene}} in {{Diffuse Large B Cell Lymphoma}}}, |
|
| 455 | + author = {Baohua, Yu and Xiaoyan, Zhou and Tiecheng, Zhang and Tao, Qin and Daren, Shi}, |
|
| 456 | + journaltitle = {Diagnostic Molecular Pathology}, |
|
| 457 | + volume = {17}, |
|
| 458 | + number = {3}, |
|
| 459 | + pages = {159--165}, |
|
| 460 | + keywords = {nosource} |
|
| 461 | +} |
|
| 462 | + |
|
| 463 | +@article{baoP53inducedLincRNAp21Derails2015, |
|
| 464 | + title = {The P53-Induced {{lincRNA-p21}} Derails Somatic Cell Reprogramming by Sustaining {{H3K9me3}} and {{CpG}} Methylation at Pluripotency Gene Promoters}, |
|
| 465 | + author = {Bao, Xichen and Wu, Haitao and Zhu, Xihua and Guo, Xiangpeng and Hutchins, Andrew P. and Luo, Zhiwei and Song, Hong and Chen, Yongqiang and Lai, Keyu and Yin, Menghui and Xu, Lingxiao and Zhou, Liang and Chen, Jiekai and Wang, Dongye and Qin, Baoming and Frampton, Jon and Tse, Hung-Fat and Pei, Duanqing and Wang, Huating and Zhang, Biliang and Esteban, Miguel A.}, |
|
| 466 | + date = {2015-01}, |
|
| 467 | + journaltitle = {Cell Research}, |
|
| 468 | + shortjournal = {Cell Res}, |
|
| 469 | + volume = {25}, |
|
| 470 | + number = {1}, |
|
| 471 | + pages = {80--92}, |
|
| 472 | + publisher = {Nature Publishing Group}, |
|
| 473 | + issn = {1748-7838}, |
|
| 474 | + doi = {10.1038/cr.2014.165}, |
|
| 475 | + url = {https://www.nature.com/articles/cr2014165}, |
|
| 476 | + urldate = {2022-09-28}, |
|
| 477 | + abstract = {Recent studies have boosted our understanding of long noncoding RNAs (lncRNAs) in numerous biological processes, but few have examined their roles in somatic cell reprogramming. Through expression profiling and functional screening, we have identified that the large intergenic noncoding RNA p21 (lincRNA-p21) impairs reprogramming. Notably, lincRNA-p21 is induced by p53 but does not promote apoptosis or cell senescence in reprogramming. Instead, lincRNA-p21 associates with the H3K9 methyltransferase SETDB1 and the maintenance DNA methyltransferase DNMT1, which is facilitated by the RNA-binding protein HNRNPK. Consequently, lincRNA-p21 prevents reprogramming by sustaining H3K9me3 and/or CpG methylation at pluripotency gene promoters. Our results provide insight into the role of lncRNAs in reprogramming and establish a novel link between p53 and heterochromatin regulation.}, |
|
| 478 | + issue = {1}, |
|
| 479 | + langid = {english}, |
|
| 480 | + keywords = {DNA methylation,Long non-coding RNAs,Reprogramming}, |
|
| 481 | + file = {/Users/rmorin/Zotero/storage/9PSJMGDI/Bao et al. - 2015 - The p53-induced lincRNA-p21 derails somatic cell r.pdf;/Users/rmorin/Zotero/storage/HGM6T8AR/cr2014165.html} |
|
| 482 | +} |
|
| 483 | + |
|
| 484 | +@article{barariaCathepsinAlterationsInduce2020c, |
|
| 485 | + title = {Cathepsin {{S Alterations Induce}} a {{Tumor-Promoting Immune Microenvironment}} in {{Follicular Lymphoma}}}, |
|
| 486 | + author = {Bararia, Deepak and Hildebrand, Johannes A. and Stolz, Sebastian and Haebe, Sarah and Alig, Stefan and Trevisani, Christopher P. and Osorio-Barrios, Francisco and Bartoschek, Michael D. and Mentz, Michael and Pastore, Alessandro and Gaitzsch, Erik and Heide, Michael and Jurinovic, Vindi and Rautter, Katharina and Gunawardana, Jay and Sabdia, Muhammed B. and Szczepanowski, Monika and Richter, Julia and Klapper, Wolfram and Louissaint, Abner and Ludwig, Christina and Bultmann, Sebastian and Leonhardt, Heinrich and Eustermann, Sebastian and Hopfner, Karl-Peter and Hiddemann, Wolfgang and family=Bergwelt-Baildon, given=Michael, prefix=von, useprefix=true and Steidl, Christian and Kridel, Robert and Tobin, Joshua W. D. and Gandhi, Maher K. and Weinstock, David M. and Schmidt-Supprian, Marc and Sárosi, Menyhárt B. and Rudelius, Martina and Passerini, Verena and Mautner, Josef and Weigert, Oliver}, |
|
| 487 | + date = {2020-05-05}, |
|
| 488 | + journaltitle = {Cell Reports}, |
|
| 489 | + shortjournal = {Cell Rep}, |
|
| 490 | + volume = {31}, |
|
| 491 | + number = {5}, |
|
| 492 | + eprint = {32330423}, |
|
| 493 | + eprinttype = {pmid}, |
|
| 494 | + pages = {107522}, |
|
| 495 | + issn = {2211-1247}, |
|
| 496 | + doi = {10.1016/j.celrep.2020.107522}, |
|
| 497 | + abstract = {Tumor cells orchestrate their microenvironment. Here, we provide biochemical, structural, functional, and clinical evidence that Cathepsin S (CTSS) alterations induce a tumor-promoting immune microenvironment in follicular lymphoma (FL). We found CTSS mutations at Y132 in 6\% of FL (19/305). Another 13\% (37/286) had CTSS amplification, which was associated with higher CTSS expression. CTSS Y132 mutations lead to accelerated autocatalytic conversion from an enzymatically inactive profrom to active CTSS and increased substrate cleavage, including CD74, which regulates major histocompatibility complex class II (MHC class II)-restricted antigen presentation. Lymphoma cells with hyperactive CTSS more efficiently activated antigen-specific CD4+ T~cells in~vitro. Tumors with hyperactive CTSS showed increased CD4+ T~cell infiltration and proinflammatory cytokine perturbation in a mouse model and in human FLs. In mice, this CTSS-induced immune microenvironment promoted tumor growth. Clinically, patients with CTSS-hyperactive FL had better treatment outcomes with standard immunochemotherapies, indicating that these immunosuppressive regimens target both the lymphoma cells and the tumor-promoting immune microenvironment.}, |
|
| 498 | + langid = {english}, |
|
| 499 | + keywords = {Animals,Antigen Presentation,antigen processing and presentation,Antigens Differentiation B-Lymphocyte,cathepsin S,Cathepsins,cysteine-protease,Cytokines,follicular lymphoma,Histocompatibility Antigens Class II,Humans,immune microenvironment,Immunosuppression Therapy,Lymphoma Follicular,Mice,T cell activation,Tumor Microenvironment}, |
|
| 500 | + file = {/Users/rmorin/Zotero/storage/D9BZZT9L/Bararia et al. - 2020 - Cathepsin S Alterations Induce a Tumor-Promoting I.pdf} |
|
| 501 | +} |
|
| 502 | + |
|
| 503 | +@article{barnardPhaseClinicalTrial2014, |
|
| 504 | + title = {Phase {{I}} Clinical Trial and Pharmacodynamic Evaluation of Combination Hydroxychloroquine and Doxorubicin Treatment in Pet Dogs Treated for Spontaneously Occurring Lymphoma}, |
|
| 505 | + author = {Barnard, Rebecca A and Wittenburg, Luke A and Amaravadi, Ravi K and Gustafson, Daniel L and Thorburn, Andrew and Thamm, Douglas H}, |
|
| 506 | + date = {2014-08-01}, |
|
| 507 | + journaltitle = {Autophagy}, |
|
| 508 | + shortjournal = {Autophagy}, |
|
| 509 | + volume = {10}, |
|
| 510 | + number = {8}, |
|
| 511 | + eprint = {24991836}, |
|
| 512 | + eprinttype = {pmid}, |
|
| 513 | + pages = {1415--1425}, |
|
| 514 | + issn = {1554-8627}, |
|
| 515 | + doi = {10.4161/auto.29165}, |
|
| 516 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4203518/}, |
|
| 517 | + urldate = {2021-06-01}, |
|
| 518 | + abstract = {Autophagy is a lysosomal degradation process that may act as a mechanism of survival in a variety of cancers. While pharmacologic inhibition of autophagy with hydroxychloroquine (HCQ) is currently being explored in human clinical trials, it has never been evaluated in canine cancers. Non-Hodgkin lymphoma (NHL) is one of the most prevalent tumor types in dogs and has similar pathogenesis and response to treatment as human NHL. Clinical trials in canine patients are conducted in the same way as in human patients, thus, to determine a maximum dose of HCQ that can be combined with a standard chemotherapy, a Phase I, single arm, dose escalation trial was conducted in dogs with spontaneous NHL presenting as patients to an academic, tertiary-care veterinary teaching hospital. HCQ was administered daily by mouth throughout the trial, beginning 72 h prior to doxorubicin (DOX), which was given intravenously on a 21-d cycle. Peripheral blood mononuclear cells and biopsies were collected before and 3 d after HCQ treatment and assessed for autophagy inhibition and HCQ concentration. A total of 30 patients were enrolled in the trial. HCQ alone was well tolerated with only mild lethargy and gastrointestinal-related adverse events. The overall response rate (ORR) for dogs with lymphoma was 93.3\%, with median progression-free interval (PFI) of 5 mo. Pharmacokinetic analysis revealed a 100-fold increase in HCQ in tumors compared with plasma. There was a trend that supported therapy-induced increase in LC3-II (the cleaved and lipidated form of microtubule-associated protein 1 light chain 3/LC3, which serves as a maker for autophagosomes) and SQSTM1/p62 (sequestosome 1) after treatment. The superior ORR and comparable PFI to single-agent DOX provide strong support for further evaluation via randomized, placebo-controlled trials in canine and human NHL.}, |
|
| 519 | + pmcid = {PMC4203518}, |
|
| 520 | + file = {/Users/rmorin/Zotero/storage/4BFT6QBP/Barnard et al. - 2014 - Phase I clinical trial and pharmacodynamic evaluat.pdf} |
|
| 521 | +} |
|
| 522 | + |
|
| 523 | +@article{barrans1418Associated2003, |
|
| 524 | + title = {The t(14;18) Is Associated with Germinal Center-Derived Diffuse Large {{B-cell}} Lymphoma and Is a Strong Predictor of Outcome.}, |
|
| 525 | + author = {Barrans, Sharon L and Evans, Paul A S and O'Connor, Sheila J M and Kendall, S Jane and Owen, Roger G and Haynes, Andrew P and Morgan, Gareth J and Jack, Andrew S}, |
|
| 526 | + date = {2003-06}, |
|
| 527 | + journaltitle = {Clin Cancer Res}, |
|
| 528 | + volume = {9}, |
|
| 529 | + number = {6}, |
|
| 530 | + pages = {2133--2139}, |
|
| 531 | + keywords = {nosource} |
|
| 532 | +} |
|
| 533 | + |
|
| 534 | +@article{barthOfatumumabExhibitsEnhanced2015, |
|
| 535 | + title = {Ofatumumab {{Exhibits Enhanced In Vitro}} and {{In Vivo Activity Compared}} to {{Rituximab}} in {{Preclinical Models}} of {{Mantle Cell Lymphoma}}}, |
|
| 536 | + author = {Barth, M J and Mavis, C and Czuczman, M S and Hernandez-Ilizaliturri, F J}, |
|
| 537 | + date = {2015-09}, |
|
| 538 | + journaltitle = {Clin Cancer Res}, |
|
| 539 | + volume = {21}, |
|
| 540 | + number = {19}, |
|
| 541 | + pages = {4391--4397}, |
|
| 542 | + keywords = {nosource} |
|
| 543 | +} |
|
| 544 | + |
|
| 545 | +@article{bassoBCL6MasterRegulator2010, |
|
| 546 | + title = {{{BCL6}}: Master Regulator of the Germinal Center Reaction and Key Oncogene in {{B}} Cell Lymphomagenesis}, |
|
| 547 | + shorttitle = {{{BCL6}}}, |
|
| 548 | + author = {Basso, Katia and Dalla-Favera, Riccardo}, |
|
| 549 | + date = {2010}, |
|
| 550 | + journaltitle = {Advances in Immunology}, |
|
| 551 | + shortjournal = {Adv Immunol}, |
|
| 552 | + volume = {105}, |
|
| 553 | + eprint = {20510734}, |
|
| 554 | + eprinttype = {pmid}, |
|
| 555 | + pages = {193--210}, |
|
| 556 | + issn = {1557-8445}, |
|
| 557 | + doi = {10.1016/S0065-2776(10)05007-8}, |
|
| 558 | + abstract = {BCL6 is a transcriptional repressor which has emerged as a critical regulator of germinal centers (GC), the sites where B cells are selected based on the production of antibodies with high affinity for the antigen. BCL6 is also a frequently activated oncogene in the pathogenesis of human B cell lymphomas, most of which derive from the GC B cells. A thorough understanding of the biological role of BCL6 in normal B cell development and lymphomagenesis depends upon the identification of the full set of genes that are targets of its transcriptional regulatory function. Recently, the identification of BCL6 targets has been implemented with the use of genome-wide chromatin immunoprecipitation and gene expression profiling approaches. A large set of promoters have been shown to be physically bound by BCL6, but only a fraction of them appears to be subjected to transcriptional repression in GC B cells. This set of BCL6 targets points to a number of cellular functions which are likely to be directly controlled by BCL6 during GC development, including activation, survival, DNA-damage response, cell cycle arrest, cytokine-, toll-like receptor-, TGFbeta-, WNT-signaling, and differentiation. Overall, BCL6 is revealing its dual role of "safe-keeper" in preventing centroblasts from responding to signals leading to a premature exit from the GC and of contributor to lymphomagenesis by allowing the instauration of conditions favorable to malignant transformation.}, |
|
| 559 | + langid = {english}, |
|
| 560 | + keywords = {B-Lymphocytes,DNA-Binding Proteins,Germinal Center,Humans,Lymphocyte Activation,Lymphoma B-Cell,Proto-Oncogene Proteins c-bcl-6,Somatic Hypermutation Immunoglobulin} |
|
| 561 | +} |
|
| 562 | + |
|
| 563 | +@article{bassoRolesBCL6Normal2012, |
|
| 564 | + title = {Roles of {{BCL6}} in Normal and Transformed Germinal Center {{B}} Cells}, |
|
| 565 | + author = {Basso, Katia and Dalla-Favera, Riccardo}, |
|
| 566 | + date = {2012-05}, |
|
| 567 | + journaltitle = {Immunological Reviews}, |
|
| 568 | + shortjournal = {Immunol Rev}, |
|
| 569 | + volume = {247}, |
|
| 570 | + number = {1}, |
|
| 571 | + eprint = {22500840}, |
|
| 572 | + eprinttype = {pmid}, |
|
| 573 | + pages = {172--183}, |
|
| 574 | + issn = {1600-065X}, |
|
| 575 | + doi = {10.1111/j.1600-065X.2012.01112.x}, |
|
| 576 | + abstract = {BCL6 is a transcriptional repressor required in mature B cells during the germinal center (GC) reaction. Multiple mechanisms act coordinately to timely modulate BCL6 expression at transcriptional and post-transcriptional levels. BCL6 prevents premature activation and differentiation of GC B cells and provides an environment tolerant of the DNA breaks associated with immunoglobulin gene remodeling mechanisms involved in the production of high-affinity antibodies of different isotypes. The critical functions exerted by BCL6 during normal B-cell development can be hijacked by the malignant transformation process. Indeed, BCL6 is targeted by genetic aberrations and acts as an oncogene in GC-derived lymphomas. The aberrations affecting BCL6 interfere with the multiple levels of regulation that grant a fine tuning of BCL6 expression and activity in physiologic conditions. This review summarizes the current knowledge on BCL6 function and its role in lymphomagenesis.}, |
|
| 577 | + langid = {english}, |
|
| 578 | + keywords = {Animals,B-Lymphocytes,Cell Differentiation,Cell Transformation Neoplastic,Germinal Center,Humans,Lymphoma Non-Hodgkin,Proto-Oncogene Proteins c-bcl-6,Transcriptional Activation} |
|
| 579 | +} |
|
| 580 | + |
|
| 581 | +@article{beaDiffuseLargeBcell2005, |
|
| 582 | + title = {Diffuse Large {{B-cell}} Lymphoma Subgroups Have Distinct Genetic Profiles That Influence Tumor Biology and Improve Gene-Expression-Based Survival Prediction.}, |
|
| 583 | + author = {Bea, Silvia and Zettl, Andreas and Wright, George and Salaverria, Itziar and Jehn, Philipp and Moreno, Victor and Burek, Christof and Ott, German and Puig, Xavier and Yang, Liming and López-Guillermo, Armando and Chan, Wing C and Greiner, Timothy C and Weisenburger, Dennis D and Armitage, James O and Gascoyne, Randy D and Connors, Joseph M and Grogan, Thomas M and Braziel, Rita and Fisher, Richard I and Smeland, Erlend B and Kvaloy, Stein and Holte, Harald and Delabie, Jan and Simon, Richard and Powell, John and Wilson, Wyndham H and Jaffe, Elaine S and Montserrat, Emili and Müller-Hermelink, Hans-Konrad and Staudt, Louis M and Campo, Elias and Rosenwald, Andreas and Project, Lymphoma Leukemia Molecular Profiling}, |
|
| 584 | + date = {2005-11}, |
|
| 585 | + journaltitle = {Blood}, |
|
| 586 | + volume = {106}, |
|
| 587 | + number = {9}, |
|
| 588 | + pages = {3183--3190}, |
|
| 589 | + keywords = {nosource} |
|
| 590 | +} |
|
| 591 | + |
|
| 592 | +@article{beaLandscapeSomaticMutations2013, |
|
| 593 | + title = {Landscape of Somatic Mutations and Clonal Evolution in Mantle Cell Lymphoma}, |
|
| 594 | + author = {Beà, Sílvia and Valdés-Mas, Rafael and Navarro, Alba and Salaverria, Itziar and Martín-Garcia, David and Jares, Pedro and Giné, Eva and Pinyol, Magda and Royo, Cristina and Nadeu, Ferran and Conde, Laura and Juan, Manel and Clot, Guillem and Vizán, Pedro and Croce, Luciano Di and Puente, Diana A. and López-Guerra, Mónica and Moros, Alexandra and Roue, Gael and Aymerich, Marta and Villamor, Neus and Colomo, Lluís and Martínez, Antonio and Valera, Alexandra and Martín-Subero, José I. and Amador, Virginia and Hernández, Luis and Rozman, Maria and Enjuanes, Anna and Forcada, Pilar and Muntañola, Ana and Hartmann, Elena M. and Calasanz, María J. and Rosenwald, Andreas and Ott, German and Hernández-Rivas, Jesús M. and Klapper, Wolfram and Siebert, Reiner and Wiestner, Adrian and Wilson, Wyndham H. and Colomer, Dolors and López-Guillermo, Armando and López-Otín, Carlos and Puente, Xose S. and Campo, Elías}, |
|
| 595 | + date = {2013-11-05}, |
|
| 596 | + journaltitle = {Proceedings of the National Academy of Sciences}, |
|
| 597 | + shortjournal = {PNAS}, |
|
| 598 | + volume = {110}, |
|
| 599 | + number = {45}, |
|
| 600 | + eprint = {24145436}, |
|
| 601 | + eprinttype = {pmid}, |
|
| 602 | + pages = {18250--18255}, |
|
| 603 | + issn = {0027-8424, 1091-6490}, |
|
| 604 | + doi = {10.1073/pnas.1314608110}, |
|
| 605 | + url = {https://www.pnas.org/content/110/45/18250}, |
|
| 606 | + urldate = {2019-12-21}, |
|
| 607 | + abstract = {Mantle cell lymphoma (MCL) is an aggressive tumor, but a subset of patients may follow an indolent clinical course. To understand the mechanisms underlying this biological heterogeneity, we performed whole-genome and/or whole-exome sequencing on 29 MCL cases and their respective matched normal DNA, as well as 6 MCL cell lines. Recurrently mutated genes were investigated by targeted sequencing in an independent cohort of 172 MCL patients. We identified 25 significantly mutated genes, including known drivers such as ataxia-telangectasia mutated (ATM), cyclin D1 (CCND1), and the tumor suppressor TP53; mutated genes encoding the anti-apoptotic protein BIRC3 and Toll-like receptor 2 (TLR2); and the chromatin modifiers WHSC1, MLL2, and MEF2B. We also found NOTCH2 mutations as an alternative phenomenon to NOTCH1 mutations in aggressive tumors with a dismal prognosis. Analysis of two simultaneous or subsequent MCL samples by whole-genome/whole-exome (n = 8) or targeted (n = 19) sequencing revealed subclonal heterogeneity at diagnosis in samples from different topographic sites and modulation of the initial mutational profile at the progression of the disease. Some mutations were predominantly clonal or subclonal, indicating an early or late event in tumor evolution, respectively. Our study identifies molecular mechanisms contributing to MCL pathogenesis and offers potential targets for therapeutic intervention.}, |
|
| 608 | + langid = {english}, |
|
| 609 | + keywords = {cancer genetics,cancer heterogeneity,next-generation sequencing}, |
|
| 610 | + file = {/Users/rmorin/Zotero/storage/5HNIUH5H/18250.html} |
|
| 611 | +} |
|
| 612 | + |
|
| 613 | +@article{behrensTranslationalSilencingFunction2018, |
|
| 614 | + title = {A Translational Silencing Function of {{MCPIP1}}/{{Regnase-1}} Specified by the Target Site Context.}, |
|
| 615 | + author = {Behrens, Gesine and Winzen, Reinhard and Rehage, Nina and Dörrie, Anneke and Barsch, Monika and Hoffmann, Anne and Hackermüller, Jörg and Tiedje, Christopher and Heissmeyer, Vigo and Holtmann, Helmut}, |
|
| 616 | + date = {2018-02}, |
|
| 617 | + journaltitle = {Nucleic Acids Res}, |
|
| 618 | + volume = {10}, |
|
| 619 | + pages = {24}, |
|
| 620 | + keywords = {nosource} |
|
| 621 | +} |
|
| 622 | + |
|
| 623 | +@article{benesovaHansAlgorithmFailed, |
|
| 624 | + title = {The {{Hans}} Algorithm Failed to Predict Outcome in Patients with Diffuse Large {{B-cell}} Lymphoma Treated with Rituximab.}, |
|
| 625 | + author = {Benesova, K and Forsterova, K and Votavova, H and Campr, V and Stritesky, J and Velenska, Z and Prochazka, B and Pytlik, R and Trneny, M}, |
|
| 626 | + journaltitle = {Neoplasma}, |
|
| 627 | + volume = {60}, |
|
| 628 | + number = {1}, |
|
| 629 | + pages = {68--73}, |
|
| 630 | + keywords = {nosource} |
|
| 631 | +} |
|
| 632 | + |
|
| 633 | +@article{benhamouCMycMiR1792PTEN2018, |
|
| 634 | + title = {The C-{{Myc}}/{{miR17-92}}/{{PTEN Axis Tunes PI3K Activity}} to {{Control Expression}} of {{Recombination Activating Genes}} in {{Early B Cell Development}}}, |
|
| 635 | + author = {Benhamou, David and Labi, Verena and Getahun, Andrew and Benchetrit, Eli and Dowery, Reem and Rajewsky, Klaus and Cambier, John C. and Melamed, Doron}, |
|
| 636 | + date = {2018}, |
|
| 637 | + journaltitle = {Frontiers in Immunology}, |
|
| 638 | + shortjournal = {Front Immunol}, |
|
| 639 | + volume = {9}, |
|
| 640 | + eprint = {30524445}, |
|
| 641 | + eprinttype = {pmid}, |
|
| 642 | + pages = {2715}, |
|
| 643 | + issn = {1664-3224}, |
|
| 644 | + doi = {10.3389/fimmu.2018.02715}, |
|
| 645 | + abstract = {Appropriate PI3K signals generated by the antigen receptor are essential to promote B cell development. Regulation of recombination activating gene (RAG)-1 and RAG-2 expression is one key process that is mediated by PI3K to ensure developmental progression and selection. When PI3K signals are too high or too low, expression of RAGs does not turn off and B cell development is impaired or blocked. Yet, the mechanism which tunes PI3K activity to control RAG expression during B cell development in the bone marrow is unknown. Recently we showed that a c-Myc/miR17-92/PTEN axis regulates PI3K activity for positive and negative selection of immature B cells. Here, we show that the c-Myc/miR17-92/PTEN axis tunes PI3K activity to control the expression of RAGs in proB cells. Using different genetically engineered mouse models we show that impaired function of the c-Myc/miR17-92/PTEN axis alters the PI3K/Akt/Foxo1 pathway to result in dis-regulated expression of RAG and a block in B cell development. Studies using 38c-13 B lymphoma cells, where RAGs are constitutively expressed, suggest that this regulatory effect is mediated post-translationally through Foxo1.}, |
|
| 646 | + langid = {english}, |
|
| 647 | + pmcid = {PMC6262168}, |
|
| 648 | + keywords = {B cell development,microRNA,PI3K–AKT pathway,PTEN (phosphatase and tensin homolog),recombination activating gene (RAG)} |
|
| 649 | +} |
|
| 650 | + |
|
| 651 | +@article{bettegowdaDetectionCirculatingTumor2014, |
|
| 652 | + title = {Detection of {{Circulating Tumor DNA}} in {{Early-}} and {{Late-Stage Human Malignancies}}}, |
|
| 653 | + author = {Bettegowda, C and Sausen, M and Leary, R J and Kinde, I and Wang, Y and Agrawal, N and Bartlett, B R and Wang, H and Luber, B and Alani, R M and Antonarakis, E S and Azad, N S and Bardelli, A and Brem, H and Cameron, J L and Lee, C C and Fecher, L A and Gallia, G L and Gibbs, P and Le, D and Giuntoli, R L and Goggins, M and Hogarty, M D and Holdhoff, M and Hong, S M and Jiao, Y and Juhl, H H and Kim, J J and Siravegna, G and Laheru, D A and Lauricella, C and Lim, M and Lipson, E J and Marie, S K N and Netto, G J and Oliner, K S and Olivi, A and Olsson, L and Riggins, G J and Sartore-Bianchi, A and Schmidt, K and Shih, l M and Oba-Shinjo, S M and Siena, S and Theodorescu, D and Tie, J and Harkins, T T and Veronese, S and Wang, T L and Weingart, J D and Wolfgang, C L and Wood, L D and Xing, D and Hruban, R H and Wu, J and Allen, P J and Schmidt, C M and Choti, M A and Velculescu, V E and Kinzler, K W and Vogelstein, B and Papadopoulos, N and Diaz, L A}, |
|
| 654 | + date = {2014-02}, |
|
| 655 | + journaltitle = {Science translational medicine}, |
|
| 656 | + volume = {6}, |
|
| 657 | + number = {224}, |
|
| 658 | + pages = {224ra24--224ra24}, |
|
| 659 | + keywords = {nosource} |
|
| 660 | +} |
|
| 661 | + |
|
| 662 | +@article{biffiElevatedLevelsGQuadruplex2014, |
|
| 663 | + title = {Elevated {{Levels}} of {{G-Quadruplex Formation}} in {{Human Stomach}} and {{Liver Cancer Tissues}}}, |
|
| 664 | + author = {Biffi, Giulia and Tannahill, David and Miller, Jodi and Howat, William J. and Balasubramanian, Shankar}, |
|
| 665 | + date = {2014-07-17}, |
|
| 666 | + journaltitle = {PLOS ONE}, |
|
| 667 | + shortjournal = {PLOS ONE}, |
|
| 668 | + volume = {9}, |
|
| 669 | + number = {7}, |
|
| 670 | + pages = {e102711}, |
|
| 671 | + publisher = {Public Library of Science}, |
|
| 672 | + issn = {1932-6203}, |
|
| 673 | + doi = {10.1371/journal.pone.0102711}, |
|
| 674 | + url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0102711}, |
|
| 675 | + urldate = {2022-10-15}, |
|
| 676 | + abstract = {Four-stranded G-quadruplex DNA secondary structures have recently been visualized in the nuclei of human cultured cells. Here, we show that BG4, a G-quadruplex-specific antibody, can be used to stain DNA G-quadruplex structures in patient-derived tissues using immunohistochemistry. We observe a significantly elevated number of G-quadruplex-positive nuclei in human cancers of the liver and stomach as compared to background non-neoplastic tissue. Our results suggest that G-quadruplex formation can be detected and measured in patient-derived material and that elevated G-quadruplex formation may be a characteristic of some cancers.}, |
|
| 677 | + langid = {english}, |
|
| 678 | + keywords = {Breast cancer,Cell staining,DNA structure,Gastric cancer,Hepatocellular carcinoma,Immunohistochemistry techniques,Nuclear staining,Stomach}, |
|
| 679 | + file = {/Users/rmorin/Zotero/storage/CS9GF6FL/Biffi et al. - 2014 - Elevated Levels of G-Quadruplex Formation in Human.pdf;/Users/rmorin/Zotero/storage/8NH9965E/article.html} |
|
| 680 | +} |
|
| 681 | + |
|
| 682 | +@article{blenkGerminalCenterCelllike2007, |
|
| 683 | + title = {Germinal Center {{B}} Cell-like ({{GCB}}) and Activated {{B}} Cell-like ({{ABC}}) Type of Diffuse Large {{B}} Cell Lymphoma ({{DLBCL}}): Analysis of Molecular Predictors, Signatures, Cell Cycle State and Patient Survival.}, |
|
| 684 | + author = {Blenk, S and Engelmann, J and Weniger, M and Schultz, J and Dittrich, M and Rosenwald, A and Muller-Hermelink, H K and Müller, T and Dandekar, T}, |
|
| 685 | + date = {2007}, |
|
| 686 | + journaltitle = {Cancer informatics}, |
|
| 687 | + volume = {3}, |
|
| 688 | + pages = {399--420}, |
|
| 689 | + keywords = {nosource} |
|
| 690 | +} |
|
| 691 | + |
|
| 692 | +@article{blumSnapShotTCGAAnalyzedTumors2018, |
|
| 693 | + title = {{{SnapShot}}: {{TCGA-Analyzed Tumors}}}, |
|
| 694 | + shorttitle = {{{SnapShot}}}, |
|
| 695 | + author = {Blum, Amy and Wang, Peggy and Zenklusen, Jean C.}, |
|
| 696 | + date = {2018-04-05}, |
|
| 697 | + journaltitle = {Cell}, |
|
| 698 | + shortjournal = {Cell}, |
|
| 699 | + volume = {173}, |
|
| 700 | + number = {2}, |
|
| 701 | + eprint = {29625059}, |
|
| 702 | + eprinttype = {pmid}, |
|
| 703 | + pages = {530}, |
|
| 704 | + publisher = {Elsevier}, |
|
| 705 | + issn = {0092-8674, 1097-4172}, |
|
| 706 | + doi = {10.1016/j.cell.2018.03.059}, |
|
| 707 | + url = {https://www.cell.com/cell/abstract/S0092-8674(18)30391-X}, |
|
| 708 | + urldate = {2022-05-23}, |
|
| 709 | + langid = {english}, |
|
| 710 | + file = {/Users/rmorin/Zotero/storage/8J9ITTYW/Blum et al. - 2018 - SnapShot TCGA-Analyzed Tumors.pdf;/Users/rmorin/Zotero/storage/PUKLIKII/S0092-8674(18)30391-X.html} |
|
| 711 | +} |
|
| 712 | + |
|
| 713 | +@article{boevaControlFREECToolAssessing2012, |
|
| 714 | + title = {Control-{{FREEC}}: A Tool for Assessing Copy Number and Allelic Content Using next-Generation Sequencing Data}, |
|
| 715 | + shorttitle = {Control-{{FREEC}}}, |
|
| 716 | + author = {Boeva, Valentina and Popova, Tatiana and Bleakley, Kevin and Chiche, Pierre and Cappo, Julie and Schleiermacher, Gudrun and Janoueix-Lerosey, Isabelle and Delattre, Olivier and Barillot, Emmanuel}, |
|
| 717 | + date = {2012-02-01}, |
|
| 718 | + journaltitle = {Bioinformatics}, |
|
| 719 | + shortjournal = {Bioinformatics}, |
|
| 720 | + volume = {28}, |
|
| 721 | + number = {3}, |
|
| 722 | + pages = {423--425}, |
|
| 723 | + issn = {1367-4803}, |
|
| 724 | + doi = {10.1093/bioinformatics/btr670}, |
|
| 725 | + url = {https://academic.oup.com/bioinformatics/article/28/3/423/189142}, |
|
| 726 | + urldate = {2019-07-08}, |
|
| 727 | + abstract = {Abstract. Summary: More and more cancer studies use next-generation sequencing (NGS) data to detect various types of genomic variation. However, even when rese}, |
|
| 728 | + langid = {english}, |
|
| 729 | + file = {/Users/rmorin/Zotero/storage/694IXV9T/189142.html} |
|
| 730 | +} |
|
| 731 | + |
|
| 732 | +@article{bohersTargetableActivatingMutations, |
|
| 733 | + title = {Targetable Activating Mutations Are Very Frequent in {{GCB}} and {{ABC}} Diffuse Large {{B-cell}} Lymphoma.}, |
|
| 734 | + author = {Bohers, Elodie and Mareschal, Sylvain and Bouzelfen, Abdelilah and Marchand, Vinciane and Ruminy, Philippe and Maingonnat, Catherine and Ménard, Anne-Lise and Etancelin, Pascaline and Bertrand, Philippe and Dubois, Sydney and Alcantara, Marion and Bastard, Christian and Tilly, Hervé and Jardin, Fabrice}, |
|
| 735 | + journaltitle = {Genes Chromosome Canc}, |
|
| 736 | + volume = {53}, |
|
| 737 | + number = {2}, |
|
| 738 | + pages = {144--153}, |
|
| 739 | + keywords = {nosource} |
|
| 740 | +} |
|
| 741 | + |
|
| 742 | +@article{bohleRoleEarlyBcell2013, |
|
| 743 | + title = {Role of Early {{B-cell}} Factor 1 ({{EBF1}}) in {{Hodgkin}} Lymphoma}, |
|
| 744 | + author = {Bohle, V. and Döring, C. and Hansmann, M.-L. and Küppers, R.}, |
|
| 745 | + date = {2013-03}, |
|
| 746 | + journaltitle = {Leukemia}, |
|
| 747 | + shortjournal = {Leukemia}, |
|
| 748 | + volume = {27}, |
|
| 749 | + number = {3}, |
|
| 750 | + eprint = {23174882}, |
|
| 751 | + eprinttype = {pmid}, |
|
| 752 | + pages = {671--679}, |
|
| 753 | + issn = {1476-5551}, |
|
| 754 | + doi = {10.1038/leu.2012.280}, |
|
| 755 | + abstract = {A hallmark of classical Hodgkin lymphoma (cHL) is that the B-cell-derived Hodgkin and Reed-Sternberg (HRS) tumor cells have largely lost the B-cell-typical gene expression program. The factors causing this 'reprogramming' of HRS cells are only partly understood. As early B-cell factor 1 (EBF1), a major B-cell transcription factor, is downregulated in HRS cells, we analyzed whether this downregulation contributes to the lost B-cell phenotype and tested the consequences of EBF1 re-expression in cHL cell lines. EBF1 re-expression caused an upregulation of B-cell genes, such as CD19, CD79A and CD79B, although the B-cell genes FOXO1 and PAX5 remained lowly expressed. The re-expression of CD19, CD79A and CD79B occurred largely without demethylation of promoter CpG motifs of these genes. In the cHL cell line L-1236 fitness decreased after EBF1 re-expression. These data show that EBF1 has the ability to reintroduce part of the B-cell signature in cHL cell lines. Loss of EBF1 expression in HRS cells therefore contributes to their lost B-cell phenotype. Notably, in the cHL cell line KM-H2 destructive mutations were found in one allele of EBF1, indicating that genetic lesions may sometimes have a role in impairing EBF1 expression.}, |
|
| 756 | + langid = {english}, |
|
| 757 | + keywords = {Apoptosis,B-Lymphocytes,Base Sequence,Biomarkers Tumor,Blotting Western,Cell Proliferation,CpG Islands,DNA Methylation,Gene Expression Profiling,Gene Expression Regulation Neoplastic,Hodgkin Disease,Humans,Molecular Sequence Data,Oligonucleotide Array Sequence Analysis,Promoter Regions Genetic,Real-Time Polymerase Chain Reaction,Reed-Sternberg Cells,Reverse Transcriptase Polymerase Chain Reaction,RNA Messenger,Sequence Homology Nucleic Acid,Trans-Activators} |
|
| 758 | +} |
|
| 759 | + |
|
| 760 | +@article{bolotinMiXCRSoftwareComprehensive2015, |
|
| 761 | + title = {{{MiXCR}}: Software for Comprehensive Adaptive Immunity Profiling}, |
|
| 762 | + shorttitle = {{{MiXCR}}}, |
|
| 763 | + author = {Bolotin, Dmitriy A. and Poslavsky, Stanislav and Mitrophanov, Igor and Shugay, Mikhail and Mamedov, Ilgar Z. and Putintseva, Ekaterina V. and Chudakov, Dmitriy M.}, |
|
| 764 | + date = {2015-05}, |
|
| 765 | + journaltitle = {Nature Methods}, |
|
| 766 | + shortjournal = {Nat Methods}, |
|
| 767 | + volume = {12}, |
|
| 768 | + number = {5}, |
|
| 769 | + eprint = {25924071}, |
|
| 770 | + eprinttype = {pmid}, |
|
| 771 | + pages = {380--381}, |
|
| 772 | + issn = {1548-7105}, |
|
| 773 | + doi = {10.1038/nmeth.3364}, |
|
| 774 | + langid = {english}, |
|
| 775 | + keywords = {Adaptive Immunity,Animals,DNA,Gene Expression Regulation,Humans,Mice,RNA,Software} |
|
| 776 | +} |
|
| 777 | + |
|
| 778 | +@article{boseBortezomibTreatmentNonHodgkin2014, |
|
| 779 | + title = {Bortezomib for the Treatment of Non-{{Hodgkin}}'s Lymphoma.}, |
|
| 780 | + author = {Bose, Prithviraj and Batalo, Michael S and Holkova, Beata and Grant, Steven}, |
|
| 781 | + date = {2014-11}, |
|
| 782 | + journaltitle = {Expert opinion on pharmacotherapy}, |
|
| 783 | + volume = {15}, |
|
| 784 | + number = {16}, |
|
| 785 | + pages = {2443--2459}, |
|
| 786 | + keywords = {nosource} |
|
| 787 | +} |
|
| 788 | + |
|
| 789 | +@article{bothamSmallMoleculeProcaspase3Activation2016, |
|
| 790 | + title = {Small-{{Molecule Procaspase-3 Activation Sensitizes Cancer}} to {{Treatment}} with {{Diverse Chemotherapeutics}}}, |
|
| 791 | + author = {Botham, Rachel C. and Roth, Howard S. and Book, Alison P. and Roady, Patrick J. and Fan, Timothy M. and Hergenrother, Paul J.}, |
|
| 792 | + date = {2016-08-24}, |
|
| 793 | + journaltitle = {ACS central science}, |
|
| 794 | + shortjournal = {ACS Cent Sci}, |
|
| 795 | + volume = {2}, |
|
| 796 | + number = {8}, |
|
| 797 | + eprint = {27610416}, |
|
| 798 | + eprinttype = {pmid}, |
|
| 799 | + pages = {545--559}, |
|
| 800 | + issn = {2374-7943}, |
|
| 801 | + doi = {10.1021/acscentsci.6b00165}, |
|
| 802 | + abstract = {Conventional chemotherapeutics remain essential treatments for most cancers, but their combination with other anticancer drugs (including targeted therapeutics) is often complicated by unpredictable synergies and multiplicative toxicities. As cytotoxic anticancer chemotherapeutics generally function through induction of apoptosis, we hypothesized that a molecularly targeted small molecule capable of facilitating a central and defining step in the apoptotic cascade, the activation of procaspase-3 to caspase-3, would broadly and predictably enhance activity of cytotoxic drugs. Here we show that procaspase-activating compound 1 (PAC-1) enhances cancer cell death induced by 15 different FDA-approved chemotherapeutics, across many cancer types and chemotherapeutic targets. In particular, the promising combination of PAC-1 and doxorubicin induces a synergistic reduction in tumor burden and enhances survival in murine tumor models of osteosarcoma and lymphoma. This PAC-1/doxorubicin combination was evaluated in 10 pet dogs with naturally occurring metastatic osteosarcoma or lymphoma, eliciting a biologic response in 3 of 6 osteosarcoma patients and 4 of 4 lymphoma patients. Importantly, in both mice and dogs, coadministration of PAC-1 with doxorubicin resulted in no additional toxicity. On the basis of the mode of action of PAC-1 and the high expression of procaspase-3 in many cancers, these results suggest the combination of PAC-1 with cytotoxic anticancer drugs as a potent and general strategy to enhance therapeutic response.}, |
|
| 803 | + langid = {english}, |
|
| 804 | + pmcid = {PMC4999974}, |
|
| 805 | + file = {/Users/rmorin/Zotero/storage/VZ5A4NKA/Botham et al. - 2016 - Small-Molecule Procaspase-3 Activation Sensitizes .pdf} |
|
| 806 | +} |
|
| 807 | + |
|
| 808 | +@article{boutrosGlobalOptimizationSomatic2014, |
|
| 809 | + title = {Global Optimization of Somatic Variant Identification in Cancer Genomes with a Global Community Challenge}, |
|
| 810 | + author = {Boutros, Paul C. and Ewing, Adam D. and Ellrott, Kyle and Norman, Thea C. and Dang, Kristen K. and Hu, Yin and Kellen, Michael R. and Suver, Christine and Bare, J. Christopher and Stein, Lincoln D. and Spellman, Paul T. and Stolovitzky, Gustavo and Friend, Stephen H. and Margolin, Adam A. and Stuart, Joshua M.}, |
|
| 811 | + date = {2014-04}, |
|
| 812 | + journaltitle = {Nature Genetics}, |
|
| 813 | + shortjournal = {Nat Genet}, |
|
| 814 | + volume = {46}, |
|
| 815 | + number = {4}, |
|
| 816 | + eprint = {24675517}, |
|
| 817 | + eprinttype = {pmid}, |
|
| 818 | + pages = {318--319}, |
|
| 819 | + issn = {1546-1718}, |
|
| 820 | + doi = {10.1038/ng.2932}, |
|
| 821 | + langid = {english}, |
|
| 822 | + pmcid = {PMC4035501}, |
|
| 823 | + keywords = {Computational Biology,Crowdsourcing,Databases Genetic,DNA Mutational Analysis,Genetic Variation,Genome Human,High-Throughput Screening Assays,Humans,Neoplasms,Software}, |
|
| 824 | + file = {/Users/rmorin/Zotero/storage/3NLLBNQG/Boutros et al. - 2014 - Global optimization of somatic variant identificat.pdf} |
|
| 825 | +} |
|
| 826 | + |
|
| 827 | +@article{boutrosGlobalOptimizationSomatic2014a, |
|
| 828 | + title = {Global Optimization of Somatic Variant Identification in Cancer Genomes with a Global Community Challenge}, |
|
| 829 | + author = {Boutros, Paul C. and Ewing, Adam D. and Ellrott, Kyle and Norman, Thea C. and Dang, Kristen K. and Hu, Yin and Kellen, Michael R. and Suver, Christine and Bare, J. Christopher and Stein, Lincoln D. and Spellman, Paul T. and Stolovitzky, Gustavo and Friend, Stephen H. and Margolin, Adam A. and Stuart, Joshua M.}, |
|
| 830 | + date = {2014-04}, |
|
| 831 | + journaltitle = {Nature Genetics}, |
|
| 832 | + shortjournal = {Nat Genet}, |
|
| 833 | + volume = {46}, |
|
| 834 | + number = {4}, |
|
| 835 | + eprint = {24675517}, |
|
| 836 | + eprinttype = {pmid}, |
|
| 837 | + pages = {318--319}, |
|
| 838 | + issn = {1546-1718}, |
|
| 839 | + doi = {10.1038/ng.2932}, |
|
| 840 | + langid = {english}, |
|
| 841 | + pmcid = {PMC4035501}, |
|
| 842 | + keywords = {Computational Biology,Crowdsourcing,Databases Genetic,DNA Mutational Analysis,Genetic Variation,Genome Human,High-Throughput Screening Assays,Humans,Neoplasms,Software}, |
|
| 843 | + file = {/Users/rmorin/Zotero/storage/NKQKYKKS/Boutros et al. - 2014 - Global optimization of somatic variant identificat.pdf} |
|
| 844 | +} |
|
| 845 | + |
|
| 846 | +@article{bowlerMisidentificationMLL3Other2019, |
|
| 847 | + title = {Misidentification of {{MLL3}} and Other Mutations in Cancer Due to Highly Homologous Genomic Regions}, |
|
| 848 | + author = {Bowler, Timothy G. and Pradhan, Kith and Kong, Yu and Bartenstein, Matthias and Morrone, Kerry A. and Sridharan, Ashwin and Kessel, Rachel M. and Shastri, Aditi and Giricz, Orsi and Bhagat, Tushar D. and Gordon-Mitchell, Shanisha and Rohanizadegan, Mersedeh and Hooda, Lauren and Datt, Ishan and Przychodzen, Bartlomiej P. and Parmar, Simrit and Maqbool, Shahina and Maciejewski, Jaroslaw P. and Steidl, Ulrich and Greally, John M. and Verma, Amit}, |
|
| 849 | + date = {2019-12}, |
|
| 850 | + journaltitle = {Leukemia \& Lymphoma}, |
|
| 851 | + shortjournal = {Leuk Lymphoma}, |
|
| 852 | + volume = {60}, |
|
| 853 | + number = {13}, |
|
| 854 | + eprint = {31288594}, |
|
| 855 | + eprinttype = {pmid}, |
|
| 856 | + pages = {3132--3137}, |
|
| 857 | + issn = {1029-2403}, |
|
| 858 | + doi = {10.1080/10428194.2019.1630620}, |
|
| 859 | + abstract = {The MLL3 gene has been shown to be recurrently mutated in many malignancies including in families with acute myeloid leukemia. We demonstrate that many MLL3 variant calls made by exome sequencing are false positives due to misalignment to homologous regions, including a region on chr21, and can only be validated by long-range PCR. Numerous other recurrently mutated genes reported in COSMIC and TCGA databases have pseudogenes and cannot also be validated by conventional short read-based sequencing approaches. Genome-wide identification of pseudogene regions demonstrates that frequency of these homologous regions is increased with sequencing read lengths below 200~bps. To enable identification of poor quality sequencing variants in prospective studies, we generated novel genome-wide maps of regions with poor mappability that can be used in variant calling algorithms. Taken together, our findings reveal that pseudogene regions are a source of false-positive mutations in cancers.}, |
|
| 860 | + langid = {english}, |
|
| 861 | + keywords = {Algorithms,AML,Chromosome Mapping,Databases Genetic,DNA Mutational Analysis,DNA-Binding Proteins,Exons,False Positive Reactions,High-Throughput Nucleotide Sequencing,Humans,Leukemia Myeloid Acute,MLL3,pseudogenes,Pseudogenes,Sequence Homology Nucleic Acid,Whole Exome Sequencing} |
|
| 862 | +} |
|
| 863 | + |
|
| 864 | +@article{bradyMCPIP1Zc3h12aKeeps2013, |
|
| 865 | + title = {{{MCPIP1}} ({{Zc3h12a}}) Keeps Inflammation in Check by Cleaving 3|[Prime]| {{UTRs}}}, |
|
| 866 | + author = {Brady, Brenna L and Muljo, Stefan A}, |
|
| 867 | + date = {2013-05}, |
|
| 868 | + journaltitle = {Immunology and cell biology}, |
|
| 869 | + volume = {91}, |
|
| 870 | + number = {5}, |
|
| 871 | + pages = {331--332}, |
|
| 872 | + keywords = {nosource} |
|
| 873 | +} |
|
| 874 | + |
|
| 875 | +@article{braggioGenomicAnalysisMarginal2012, |
|
| 876 | + title = {Genomic Analysis of Marginal Zone and Lymphoplasmacytic Lymphomas Identified Common and Disease-Specific Abnormalities}, |
|
| 877 | + author = {Braggio, Esteban and Dogan, Ahmet and Keats, Jonathan J. and Chng, Wee J. and Huang, Gaofeng and Matthews, Julie M. and Maurer, Matthew J. and Law, Mark E. and Bosler, David S. and Barrett, Michael and Lossos, Izidore S. and Witzig, Thomas E. and Fonseca, Rafael}, |
|
| 878 | + date = {2012-05}, |
|
| 879 | + journaltitle = {Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc}, |
|
| 880 | + shortjournal = {Mod Pathol}, |
|
| 881 | + volume = {25}, |
|
| 882 | + number = {5}, |
|
| 883 | + eprint = {22301699}, |
|
| 884 | + eprinttype = {pmid}, |
|
| 885 | + pages = {651--660}, |
|
| 886 | + issn = {1530-0285}, |
|
| 887 | + doi = {10.1038/modpathol.2011.213}, |
|
| 888 | + abstract = {Lymphoplasmacytic lymphomas and marginal zone lymphomas of nodal, extra-nodal and splenic types account for 10\% of non-Hodgkin lymphomas. They are similar at the cell differentiation level, sometimes making difficult to distinguish them from other indolent non-Hodgkin lymphomas. To better characterize their genetic basis, we performed array-based comparative genomic hybridization in 101 marginal zone lymphomas (46 MALT, 35 splenic and 20 nodal marginal zone lymphomas) and 13 lymphoplasmacytic lymphomas. Overall, 90\% exhibited copy-number abnormalities. Lymphoplasmacytic lymphomas demonstrated the most complex karyotype (median=7 copy-number abnormalities), followed by MALT (4), nodal (3.5) and splenic marginal zone lymphomas (3). A comparative analysis exposed a group of copy-number abnormalities shared by several or all the entities with few disease-specific abnormalities. Gain of chromosomes 3, 12 and 18 and loss of 6q23-q24 (TNFAIP3) were identified in all entities. Losses of 13q14.3 (MIRN15A-MIRN16-1) and 17p13.3-p12 (TP53) were found in lymphoplasmacytic and splenic marginal zone lymphomas; loss of 11q21-q22 (ATM) was found in nodal, splenic marginal zone and lymphoplasmacytic lymphomas and loss of 7q32.1-q33 was found in MALT, splenic and lymphoplasmacytic lymphomas. Abnormalities affecting the nuclear factor kappa B pathway were observed in 70\% of MALT and lymphoplasmacytic lymphomas and 30\% of splenic and nodal marginal zone lymphomas, suggesting distinct roles of this pathway in the pathogenesis/progression of these subtypes. Elucidation of the genetic alterations contributing to the pathogenesis of these lymphomas may guide to design-specific therapeutic approaches.}, |
|
| 889 | + langid = {english}, |
|
| 890 | + pmcid = {PMC3341516}, |
|
| 891 | + keywords = {Chromosome Aberrations,DNA Neoplasm,Gene Expression Profiling,Gene Expression Regulation Neoplastic,Genomics,Humans,In Situ Hybridization Fluorescence,Lymph Nodes,Lymphoma B-Cell Marginal Zone,Waldenstrom Macroglobulinemia}, |
|
| 892 | + file = {/Users/rmorin/Zotero/storage/6E6IQGNZ/Braggio et al. - 2012 - Genomic analysis of marginal zone and lymphoplasma.pdf} |
|
| 893 | +} |
|
| 894 | + |
|
| 895 | +@article{brazmaMinimumInformationMicroarray2001, |
|
| 896 | + title = {Minimum Information about a Microarray Experiment ({{MIAME}})-toward Standards for Microarray Data}, |
|
| 897 | + author = {Brazma, A. and Hingamp, P. and Quackenbush, J. and Sherlock, G. and Spellman, P. and Stoeckert, C. and Aach, J. and Ansorge, W. and Ball, C. A. and Causton, H. C. and Gaasterland, T. and Glenisson, P. and Holstege, F. C. and Kim, I. F. and Markowitz, V. and Matese, J. C. and Parkinson, H. and Robinson, A. and Sarkans, U. and Schulze-Kremer, S. and Stewart, J. and Taylor, R. and Vilo, J. and Vingron, M.}, |
|
| 898 | + date = {2001-12}, |
|
| 899 | + journaltitle = {Nature Genetics}, |
|
| 900 | + shortjournal = {Nat Genet}, |
|
| 901 | + volume = {29}, |
|
| 902 | + number = {4}, |
|
| 903 | + eprint = {11726920}, |
|
| 904 | + eprinttype = {pmid}, |
|
| 905 | + pages = {365--371}, |
|
| 906 | + issn = {1061-4036}, |
|
| 907 | + doi = {10.1038/ng1201-365}, |
|
| 908 | + abstract = {Microarray analysis has become a widely used tool for the generation of gene expression data on a genomic scale. Although many significant results have been derived from microarray studies, one limitation has been the lack of standards for presenting and exchanging such data. Here we present a proposal, the Minimum Information About a Microarray Experiment (MIAME), that describes the minimum information required to ensure that microarray data can be easily interpreted and that results derived from its analysis can be independently verified. The ultimate goal of this work is to establish a standard for recording and reporting microarray-based gene expression data, which will in turn facilitate the establishment of databases and public repositories and enable the development of data analysis tools. With respect to MIAME, we concentrate on defining the content and structure of the necessary information rather than the technical format for capturing it.}, |
|
| 909 | + langid = {english}, |
|
| 910 | + keywords = {Computational Biology,Gene Expression Profiling,Oligonucleotide Array Sequence Analysis}, |
|
| 911 | + file = {/Users/rmorin/Zotero/storage/82PF3HCQ/Brazma et al. - 2001 - Minimum information about a microarray experiment .pdf} |
|
| 912 | +} |
|
| 913 | + |
|
| 914 | +@article{brazmaMINSEQEMinimumInformation2012, |
|
| 915 | + title = {{{MINSEQE}}: {{Minimum Information}} about a High-Throughput {{Nucleotide SeQuencing Experiment}} - a Proposal for Standards in Functional Genomic Data Reporting}, |
|
| 916 | + shorttitle = {{{MINSEQE}}}, |
|
| 917 | + author = {Brazma, Alvis and Ball, Catherine and Bumgarner, Roger and Furlanello, Cesare and Miller, Michael and Quackenbush, John and Reich, Michael and Rustici, Gabriella and Stoeckert, Chris and Trutane, Stephen Chervitz and Taylor, Ronald C}, |
|
| 918 | + date = {2012-06-01}, |
|
| 919 | + publisher = {Zenodo}, |
|
| 920 | + doi = {10.5281/zenodo.5706412}, |
|
| 921 | + url = {https://zenodo.org/record/5706412}, |
|
| 922 | + urldate = {2022-05-19}, |
|
| 923 | + abstract = {MINSEQE~describes the~Minimum Information about a high-throughput nucleotide SEQuencing Experiment~that is needed to enable the unambiguous interpretation and facilitate reproduction of the results of the~experiment. By analogy to the~MIAME~guidelines for microarray experiments, adherence to the MINSEQE guidelines will improve~integration of multiple experiments across different modalities, thereby maximising the value of high-throughput research.~ The five elements of experimental description considered essential when making data available supporting published high-throughput sequencing experiments are as follows: The description of the biological system, samples, and the experimental variables being studied: “compound” and “dose” in dose-response experiments or “antibody” in ChIP-Seq experiments,~the organism, tissue, and the ~treatment(s) applied. The sequence read data for each assay: read sequences and base-level quality scores for each assay;~FASTQ~format is recommended, with a description of the scale used for quality scores. The ‘final’ processed (or summary) data for the set of assays in the study: the data on which the conclusions in the related publication are based, and~descriptions of the data format. General information about the experiment and sample-data relationships: a summary of the experiment and its goals, contact information, any associated publication, and a~table specifying sample-data relationships. Essential experimental and data processing protocols: how the nucleic acid samples were isolated, purified and processed prior to sequencing,~a summary of the instrumentation used, library preparation strategy, labelling and amplification methodologies, alignment algorithms and data filtering plus data processing \& analysis protocols. The present document contains version 1.0 of the MINSEQE guidelines, which~originated from discussions at an FGED-organized workshop held in Berkeley in March 2008.}, |
|
| 924 | + langid = {english}, |
|
| 925 | + keywords = {nucleotide sequencing genome transcriptome genomics transcriptomics reproducibility standards publication}, |
|
| 926 | + file = {/Users/rmorin/Zotero/storage/3PJ43IHW/Brazma et al. - 2012 - MINSEQE Minimum Information about a high-throughp.pdf} |
|
| 927 | +} |
|
| 928 | + |
|
| 929 | +@article{breenEvolutionarilyConservedCytogenetic2008, |
|
| 930 | + title = {Evolutionarily Conserved Cytogenetic Changes in Hematological Malignancies of Dogs and Humans – Man and His Best Friend Share More than Companionship}, |
|
| 931 | + author = {Breen, Matthew and Modiano, Jaime F.}, |
|
| 932 | + date = {2008-03-01}, |
|
| 933 | + journaltitle = {Chromosome Research}, |
|
| 934 | + shortjournal = {Chromosome Res}, |
|
| 935 | + volume = {16}, |
|
| 936 | + number = {1}, |
|
| 937 | + pages = {145--154}, |
|
| 938 | + issn = {1573-6849}, |
|
| 939 | + doi = {10.1007/s10577-007-1212-4}, |
|
| 940 | + url = {https://doi.org/10.1007/s10577-007-1212-4}, |
|
| 941 | + urldate = {2021-05-28}, |
|
| 942 | + abstract = {The pathophysiological similarities shared by many forms of human and canine disease, combined with the sophisticated genomic resources now available for the dog, have placed ‘man’s best friend’ in a position of high visibility as a model system for a variety of biomedical concerns, including cancer. The importance of nonrandom cytogenetic abnormalities in human leukemia and lymphoma was recognized over 40~years ago, but the mechanisms of genome reorganization remain incompletely understood. The development of molecular cytogenetics, using fluorescence in situ hybridization (FISH) technology, has played a significant role in our understanding of cancer biology by providing a means for ‘interrogating’ tumor cells for a variety of gross genetic changes in the form of either numerical or structural chromosome aberrations. Here, we have identified cytogenetic abnormalities in naturally occurring canine hematopoietic tumors that are evolutionarily conserved compared with those that are considered characteristic of the corresponding human condition. These data suggest that humans and dogs share an ancestrally retained pathogenetic basis for cancer and that cytogenetic evaluation of canine tumors may provide greater insight into the biology of tumorigenesis.}, |
|
| 943 | + langid = {english}, |
|
| 944 | + file = {/Users/rmorin/Zotero/storage/PEGWRRN5/Breen and Modiano - 2008 - Evolutionarily conserved cytogenetic changes in he.pdf} |
|
| 945 | +} |
|
| 946 | + |
|
| 947 | +@article{bresciaMEF2BInstructsGerminal2018, |
|
| 948 | + title = {{{MEF2B Instructs Germinal Center Development}} and {{Acts}} as an {{Oncogene}} in {{B Cell Lymphomagenesis}}}, |
|
| 949 | + author = {Brescia, Paola and Schneider, Christof and Holmes, Antony B. and Shen, Qiong and Hussein, Shafinaz and Pasqualucci, Laura and Basso, Katia and Dalla-Favera, Riccardo}, |
|
| 950 | + date = {2018-09-10}, |
|
| 951 | + journaltitle = {Cancer Cell}, |
|
| 952 | + shortjournal = {Cancer Cell}, |
|
| 953 | + volume = {34}, |
|
| 954 | + number = {3}, |
|
| 955 | + eprint = {30205047}, |
|
| 956 | + eprinttype = {pmid}, |
|
| 957 | + pages = {453-465.e9}, |
|
| 958 | + issn = {1535-6108, 1878-3686}, |
|
| 959 | + doi = {10.1016/j.ccell.2018.08.006}, |
|
| 960 | + url = {https://www.cell.com/cancer-cell/abstract/S1535-6108(18)30366-0}, |
|
| 961 | + urldate = {2019-12-21}, |
|
| 962 | + langid = {english}, |
|
| 963 | + keywords = {B cell,germinal center,lymphoma,MEF2B,mouse model}, |
|
| 964 | + file = {/Users/rmorin/Zotero/storage/XPKUI283/S1535-6108(18)30366-0.html} |
|
| 965 | +} |
|
| 966 | + |
|
| 967 | +@article{breunisCopyNumberVariation2009, |
|
| 968 | + title = {Copy Number Variation at the {{FCGR}} Locus Includes {{FCGR3A}}, {{FCGR2C}} and {{FCGR3B}} but Not {{FCGR2A}} and {{FCGR2B}}.}, |
|
| 969 | + author = {Breunis, Willemijn B and family=Mirre, given=Edwin, prefix=van, useprefix=true and Geissler, Judy and Laddach, Nadja and Wolbink, Gertjan and family=Schoot, given=Ellen, prefix=van der, useprefix=true and family=Haas, given=Masja, prefix=de, useprefix=true and family=Boer, given=Martin, prefix=de, useprefix=true and Roos, Dirk and Kuijpers, Taco W}, |
|
| 970 | + date = {2009-05}, |
|
| 971 | + journaltitle = {Human mutation}, |
|
| 972 | + volume = {30}, |
|
| 973 | + number = {5}, |
|
| 974 | + pages = {E640--50}, |
|
| 975 | + keywords = {nosource} |
|
| 976 | +} |
|
| 977 | + |
|
| 978 | +@article{brooksPanCancerAnalysisTranscriptome2014, |
|
| 979 | + title = {A {{Pan-Cancer Analysis}} of {{Transcriptome Changes Associated}} with {{Somatic Mutations}} in {{U2AF1 Reveals Commonly Altered Splicing Events}}}, |
|
| 980 | + author = {Brooks, Angela N. and Choi, Peter S. and family=Waal, given=Luc, prefix=de, useprefix=false and Sharifnia, Tanaz and Imielinski, Marcin and Saksena, Gordon and Pedamallu, Chandra Sekhar and Sivachenko, Andrey and Rosenberg, Mara and Chmielecki, Juliann and Lawrence, Michael S. and DeLuca, David S. and Getz, Gad and Meyerson, Matthew}, |
|
| 981 | + date = {2014-01-31}, |
|
| 982 | + journaltitle = {PLOS ONE}, |
|
| 983 | + shortjournal = {PLOS ONE}, |
|
| 984 | + volume = {9}, |
|
| 985 | + number = {1}, |
|
| 986 | + pages = {e87361}, |
|
| 987 | + publisher = {Public Library of Science}, |
|
| 988 | + issn = {1932-6203}, |
|
| 989 | + doi = {10.1371/journal.pone.0087361}, |
|
| 990 | + url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0087361}, |
|
| 991 | + urldate = {2020-09-22}, |
|
| 992 | + abstract = {Although recurrent somatic mutations in the splicing factor U2AF1 (also known as U2AF35) have been identified in multiple cancer types, the effects of these mutations on the cancer transcriptome have yet to be fully elucidated. Here, we identified splicing alterations associated with U2AF1 mutations across distinct cancers using DNA and RNA sequencing data from The Cancer Genome Atlas (TCGA). Using RNA-Seq data from 182 lung adenocarcinomas and 167 acute myeloid leukemias (AML), in which U2AF1 is somatically mutated in 3–4\% of cases, we identified 131 and 369 splicing alterations, respectively, that were significantly associated with U2AF1 mutation. Of these, 30 splicing alterations were statistically significant in both lung adenocarcinoma and AML, including three genes in the Cancer Gene Census, CTNNB1, CHCHD7, and PICALM. Cell line experiments expressing U2AF1 S34F in HeLa cells and in 293T cells provide further support that these altered splicing events are caused by U2AF1 mutation. Consistent with the function of U2AF1 in 3′ splice site recognition, we found that S34F/Y mutations cause preferences for CAG over UAG 3′ splice site sequences. This report demonstrates consistent effects of U2AF1 mutation on splicing in distinct cancer cell types.}, |
|
| 993 | + langid = {english}, |
|
| 994 | + keywords = {Acute myeloid leukemia,Adenocarcinoma,Adenocarcinoma of the lung,Alternative splicing,HeLa cells,Lung and intrathoracic tumors,Mutation,Somatic mutation}, |
|
| 995 | + file = {/Users/rmorin/Zotero/storage/HLRC2JZ7/Brooks et al. - 2014 - A Pan-Cancer Analysis of Transcriptome Changes Ass.pdf;/Users/rmorin/Zotero/storage/2ADHZ4MU/article.html} |
|
| 996 | +} |
|
| 997 | + |
|
| 998 | +@article{bruunGlobalIdentificationHnRNP2016, |
|
| 999 | + title = {Global Identification of {{hnRNP A1}} Binding Sites for {{SSO-based}} Splicing Modulation}, |
|
| 1000 | + author = {Bruun, Gitte H. and Doktor, Thomas K. and Borch-Jensen, Jonas and Masuda, Akio and Krainer, Adrian R. and Ohno, Kinji and Andresen, Brage S.}, |
|
| 1001 | + date = {2016-07-05}, |
|
| 1002 | + journaltitle = {BMC Biology}, |
|
| 1003 | + shortjournal = {BMC Biology}, |
|
| 1004 | + volume = {14}, |
|
| 1005 | + number = {1}, |
|
| 1006 | + pages = {54}, |
|
| 1007 | + issn = {1741-7007}, |
|
| 1008 | + doi = {10.1186/s12915-016-0279-9}, |
|
| 1009 | + url = {https://doi.org/10.1186/s12915-016-0279-9}, |
|
| 1010 | + urldate = {2022-10-14}, |
|
| 1011 | + abstract = {Many pathogenic genetic variants have been shown to disrupt mRNA splicing. Besides splice mutations in the well-conserved splice sites, mutations in splicing regulatory elements (SREs) may deregulate splicing and cause disease. A promising therapeutic approach is to compensate for this deregulation by blocking other SREs with splice-switching oligonucleotides (SSOs). However, the location and sequence of most SREs are not well known.}, |
|
| 1012 | + keywords = {Alternative splicing,Cross-linking immunoprecipitation (CLIP),hnRNP A1,iCLIP,Pseudoexons,RNA-seq,Splicing silencer,Splicing splice-switching oligonucleotides (SSOs),Surface plasmon resonance imaging (SPRi)}, |
|
| 1013 | + file = {/Users/rmorin/Zotero/storage/I8XFSHS9/Bruun et al. - 2016 - Global identification of hnRNP A1 binding sites fo.pdf;/Users/rmorin/Zotero/storage/NSS8R7KS/s12915-016-0279-9.html} |
|
| 1014 | +} |
|
| 1015 | + |
|
| 1016 | +@article{buntingNewEffectorFunctions2013, |
|
| 1017 | + title = {New Effector Functions and Regulatory Mechanisms of {{BCL6}} in Normal and Malignant Lymphocytes}, |
|
| 1018 | + author = {Bunting, Karen L. and Melnick, Ari M.}, |
|
| 1019 | + date = {2013-06}, |
|
| 1020 | + journaltitle = {Current opinion in immunology}, |
|
| 1021 | + shortjournal = {Curr Opin Immunol}, |
|
| 1022 | + volume = {25}, |
|
| 1023 | + number = {3}, |
|
| 1024 | + eprint = {23725655}, |
|
| 1025 | + eprinttype = {pmid}, |
|
| 1026 | + pages = {339--346}, |
|
| 1027 | + issn = {0952-7915}, |
|
| 1028 | + doi = {10.1016/j.coi.2013.05.003}, |
|
| 1029 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4075446/}, |
|
| 1030 | + urldate = {2022-10-06}, |
|
| 1031 | + abstract = {The BCL6 oncogenic repressor is a master regulator of humoral immunity and B-cell lymphoma survival. Whereas much research has focused on its regulation and function in germinal center B-cells, its role in other mature lymphoid cell compartments is less clear. A novel role for BCL6 in follicular T helper cell development was recently uncovered. The latest discoveries reveal that BCL6 is also an important regulator of other specialized helper T-cell subsets within germinal centers, pre-germinal center events, and peripheral T-cells effector functions. Here, we review newly discovered roles for BCL6 in lymphocyte subsets residing within and outside of germinal centers, and discuss their implications with respect to the molecular mechanisms of BCL6 regulation and potential links to B and T-cell lymphomas.}, |
|
| 1032 | + pmcid = {PMC4075446}, |
|
| 1033 | + file = {/Users/rmorin/Zotero/storage/AZUT5ZXE/Bunting and Melnick - 2013 - New effector functions and regulatory mechanisms o.pdf} |
|
| 1034 | +} |
|
| 1035 | + |
|
| 1036 | +@article{burkhardtClinicalRelevanceMolecular2022b, |
|
| 1037 | + title = {Clinical Relevance of Molecular Characteristics in {{Burkitt}} Lymphoma Differs According to Age}, |
|
| 1038 | + author = {Burkhardt, Birgit and Michgehl, Ulf and Rohde, Jonas and Erdmann, Tabea and Berning, Philipp and Reutter, Katrin and Rohde, Marius and Borkhardt, Arndt and Burmeister, Thomas and Dave, Sandeep and Tzankov, Alexandar and Dugas, Martin and Sandmann, Sarah and Fend, Falko and Finger, Jasmin and Mueller, Stephanie and Gökbuget, Nicola and Haferlach, Torsten and Kern, Wolfgang and Hartmann, Wolfgang and Klapper, Wolfram and Oschlies, Ilske and Richter, Julia and Kontny, Udo and Lutz, Mathias and Maecker-Kolhoff, Britta and Ott, German and Rosenwald, Andreas and Siebert, Reiner and family=Stackelberg, given=Arend, prefix=von, useprefix=true and Strahm, Brigitte and Woessmann, Wilhelm and Zimmermann, Martin and Zapukhlyak, Myroslav and Grau, Michael and Lenz, Georg}, |
|
| 1039 | + date = {2022-07-06}, |
|
| 1040 | + journaltitle = {Nature Communications}, |
|
| 1041 | + shortjournal = {Nat Commun}, |
|
| 1042 | + volume = {13}, |
|
| 1043 | + number = {1}, |
|
| 1044 | + eprint = {35794096}, |
|
| 1045 | + eprinttype = {pmid}, |
|
| 1046 | + pages = {3881}, |
|
| 1047 | + issn = {2041-1723}, |
|
| 1048 | + doi = {10.1038/s41467-022-31355-8}, |
|
| 1049 | + abstract = {While survival has improved for Burkitt lymphoma patients, potential differences in outcome between pediatric and adult patients remain unclear. In both age groups, survival remains poor at relapse. Therefore, we conducted a comparative study in a large pediatric cohort, including 191 cases and 97 samples from adults. While TP53 and CCND3 mutation frequencies are not age related, samples from pediatric patients showed a higher frequency of mutations in ID3, DDX3X, ARID1A and SMARCA4, while several genes such as BCL2 and YY1AP1 are almost exclusively mutated in adult patients. An unbiased analysis reveals a transition of the mutational profile between 25 and 40 years of age. Survival analysis in the pediatric cohort confirms that TP53 mutations are significantly associated with higher incidence of relapse (25\,±\,4\% versus 6\,±\,2\%, p-value 0.0002). This identifies a promising molecular marker for relapse incidence in pediatric BL which will be used in future clinical trials.}, |
|
| 1050 | + langid = {english}, |
|
| 1051 | + pmcid = {PMC9259584}, |
|
| 1052 | + keywords = {Adult,Burkitt Lymphoma,Cell Cycle Proteins,Child,DNA Helicases,Genes cdc,Humans,Mutation,Mutation Rate,Neoplasm Recurrence Local,Nuclear Proteins,Transcription Factors}, |
|
| 1053 | + file = {/Users/rmorin/Zotero/storage/Q37FNW5K/Burkhardt et al. - 2022 - Clinical relevance of molecular characteristics in.pdf} |
|
| 1054 | +} |
|
| 1055 | + |
|
| 1056 | +@article{burrowsCellDevelopmentDifferentiation1997, |
|
| 1057 | + title = {B Cell Development and Differentiation}, |
|
| 1058 | + author = {Burrows, Peter D and Cooper, Max D}, |
|
| 1059 | + date = {1997-04-01}, |
|
| 1060 | + journaltitle = {Current Opinion in Immunology}, |
|
| 1061 | + shortjournal = {Current Opinion in Immunology}, |
|
| 1062 | + volume = {9}, |
|
| 1063 | + number = {2}, |
|
| 1064 | + pages = {239--244}, |
|
| 1065 | + issn = {0952-7915}, |
|
| 1066 | + doi = {10.1016/S0952-7915(97)80142-2}, |
|
| 1067 | + url = {https://www.sciencedirect.com/science/article/pii/S0952791597801422}, |
|
| 1068 | + urldate = {2022-10-06}, |
|
| 1069 | + abstract = {The initial phases of B cell development depend on interactions between the cell surface molecules and secreted products of stromal cells with their receptor-ligand partners on lymphoid progenitors. Recent research in this area has greatly advanced our understanding of B cell development and differentiation. Antigen receptors on pre-B and B cells play key roles in the progression of this differentiation process, as revealed by targeted and inherited gene mutations that disrupt B cell development and by the transgenic repair of these mutations in mice.}, |
|
| 1070 | + langid = {english}, |
|
| 1071 | + file = {/Users/rmorin/Zotero/storage/QAK5P4NC/Burrows and Cooper - 1997 - B cell development and differentiation.pdf;/Users/rmorin/Zotero/storage/3U4I8F8Z/S0952791597801422.html} |
|
| 1072 | +} |
|
| 1073 | + |
|
| 1074 | +@article{burtonNCIComparativeOncology2018, |
|
| 1075 | + title = {{{NCI Comparative Oncology Program Testing}} of {{Non-Camptothecin Indenoisoquinoline Topoisomerase I Inhibitors}} in {{Naturally Occurring Canine Lymphoma}}}, |
|
| 1076 | + author = {Burton, Jenna H. and Mazcko, Christina and LeBlanc, Amy and Covey, Joseph M. and Ji, Jiuping and Kinders, Robert J. and Parchment, Ralph E. and Khanna, Chand and Paoloni, Melissa and Lana, Sue and Weishaar, Kristen and London, Cheryl and Kisseberth, William and Krick, Erika and Vail, David and Childress, Michael and Bryan, Jeffrey N. and Barber, Lisa and Ehrhart, E. J. and Kent, Michael and Fan, Timothy and Kow, Kelvin and Northup, Nicole and Wilson-Robles, Heather and Tomaszewski, Joseph and Holleran, Julianne L. and Muzzio, Miguel and Eiseman, Julie and Beumer, Jan H. and Doroshow, James H. and Pommier, Yves}, |
|
| 1077 | + date = {2018-12-01}, |
|
| 1078 | + journaltitle = {Clinical Cancer Research}, |
|
| 1079 | + shortjournal = {Clin Cancer Res}, |
|
| 1080 | + volume = {24}, |
|
| 1081 | + number = {23}, |
|
| 1082 | + eprint = {30061364}, |
|
| 1083 | + eprinttype = {pmid}, |
|
| 1084 | + pages = {5830--5840}, |
|
| 1085 | + publisher = {American Association for Cancer Research}, |
|
| 1086 | + issn = {1078-0432, 1557-3265}, |
|
| 1087 | + doi = {10.1158/1078-0432.CCR-18-1498}, |
|
| 1088 | + url = {https://clincancerres.aacrjournals.org/content/24/23/5830}, |
|
| 1089 | + urldate = {2022-01-11}, |
|
| 1090 | + abstract = {Purpose: Only one chemical class of topoisomerase I (TOP1) inhibitors is FDA approved, the camptothecins with irinotecan and topotecan widely used. Because of their limitations (chemical instability, drug efflux-mediated resistance, and diarrhea), novel TOP1 inhibitors are warranted. Indenoisoquinoline non-camptothecin topoisomerase I (TOP1) inhibitors overcome chemical instability and drug resistance that limit camptothecin use. Three indenoisoquinolines, LMP400 (indotecan), LMP776 (indimitecan), and LMP744, were examined in a phase I study for lymphoma-bearing dogs to evaluate differential efficacy, pharmacodynamics, toxicology, and pharmacokinetics. Experimental Design: Eighty-four client-owned dogs with lymphomas were enrolled in dose-escalation cohorts for each indenoisoquinoline, with an expansion phase for LMP744. Efficacy, tolerability, pharmacokinetics, and target engagement were determined. Results: The MTDs were 17.5 mg/m2 for LMP 776 and 100 mg/m2 for LMP744; bone marrow toxicity was dose-limiting; up to 65 mg/m2 LMP400 was well-tolerated and MTD was not reached. None of the drugs induced notable diarrhea. Sustained tumor accumulation was observed for LMP744; γH2AX induction was demonstrated in tumors 2 and 6 hours after treatment; a decrease in TOP1 protein was observed in most lymphoma samples across all compounds and dose levels, which is consistent with the fact that tumor response was also observed at low doses LMP744. Objective responses were documented for all indenoisoquinolines; efficacy (13/19 dogs) was greatest for LMP744. Conclusions: These results demonstrate proof-of-mechanism for indenoisoquinoline TOP1 inhibitors supporting their further clinical development. They also highlight the value of the NCI Comparative Oncology Program (https://ccr.cancer.gov/Comparative-Oncology-Program) for evaluating novel therapies in immunocompetent pets with cancers.}, |
|
| 1091 | + langid = {english}, |
|
| 1092 | + file = {/Users/rmorin/Zotero/storage/2IM96CF9/Burton et al. - 2018 - NCI Comparative Oncology Program Testing of Non-Ca.pdf;/Users/rmorin/Zotero/storage/CR4YP4S7/Burton et al. - 2018 - NCI Comparative Oncology Program Testing of Indeno.pdf;/Users/rmorin/Zotero/storage/6572JTKG/5830.html} |
|
| 1093 | +} |
|
| 1094 | + |
|
| 1095 | +@article{bushellGeneticInactivationTRAF32015, |
|
| 1096 | + title = {Genetic Inactivation of {{TRAF3}} in Canine and Human {{B-cell}} Lymphoma}, |
|
| 1097 | + author = {Bushell, Kevin R. and Kim, Yukyoung and Chan, Fong Chun and Ben-Neriah, Susana and Jenks, Andrew and Alcaide, Miguel and Fornika, Daniel and Grande, Bruno M. and Arthur, Sarah and Gascoyne, Randy D. and Steidl, Christian and Morin, Ryan D.}, |
|
| 1098 | + date = {2015-02-05}, |
|
| 1099 | + journaltitle = {Blood}, |
|
| 1100 | + shortjournal = {Blood}, |
|
| 1101 | + volume = {125}, |
|
| 1102 | + number = {6}, |
|
| 1103 | + eprint = {25468570}, |
|
| 1104 | + eprinttype = {pmid}, |
|
| 1105 | + pages = {999--1005}, |
|
| 1106 | + issn = {1528-0020}, |
|
| 1107 | + doi = {10.1182/blood-2014-10-602714}, |
|
| 1108 | + abstract = {Non-Hodgkin lymphomas (NHLs) are the most common cancer to affect pet dogs. In contrast to the many genes whose mutation contributes to lymphomagenesis in humans, relatively little is known about the acquired genetic alterations that lead to canine B-cell lymphomas (cBCLs). We performed a survey of 84 canine NHL tumors to identify genes affected by somatic point mutations. We found mutations affecting TRAF3, which encodes a negative regulator of nuclear factor (NF)-κB, to be a common feature of cBCLs, with mutations observed in 44\% of tumors including a combination of somatic and rare germ-line variants. Overall, 30\% of the tumors contained ≥1 somatic TRAF3 mutation. The majority of mutations are predicted to cause loss of TRAF3 protein including those impacting reading frame and splicing. To determine whether TRAF3 loss might be relevant to human NHL, we also analyzed 148 human diffuse large B-cell lymphoma (DLBCL) tumors and identified loss of TRAF3 as a common event, affecting ∼9\% of DLBCLs, and reduced expression of TRAF3 among deleted cases. This study implicates mutations affecting NF-κB activity as a novel genetic commonality between human and canine NHLs and supports the potential utility of cBCLs with mutated TRAF3 as a model of the more aggressive activated B-cell subgroup of DLBCL.}, |
|
| 1109 | + langid = {english}, |
|
| 1110 | + keywords = {Animals,B-Lymphocytes,Dogs,Gene Deletion,Gene Expression Regulation Neoplastic,Humans,Lymphoma B-Cell,Lymphoma Large B-Cell Diffuse,Mutation,NF-kappa B,TNF Receptor-Associated Factor 3}, |
|
| 1111 | + file = {/Users/rmorin/Zotero/storage/CHV8WLZH/Bushell et al. - 2015 - Genetic inactivation of TRAF3 in canine and human .pdf} |
|
| 1112 | +} |
|
| 1113 | + |
|
| 1114 | +@article{bustinMIQEGuidelinesMinimum2009, |
|
| 1115 | + title = {The {{MIQE Guidelines}}: {{Minimum Information}} for {{Publication}} of {{Quantitative Real-Time PCR Experiments}}}, |
|
| 1116 | + shorttitle = {The {{MIQE Guidelines}}}, |
|
| 1117 | + author = {Bustin, Stephen A and Benes, Vladimir and Garson, Jeremy A and Hellemans, Jan and Huggett, Jim and Kubista, Mikael and Mueller, Reinhold and Nolan, Tania and Pfaffl, Michael W and Shipley, Gregory L and Vandesompele, Jo and Wittwer, Carl T}, |
|
| 1118 | + date = {2009-04-01}, |
|
| 1119 | + journaltitle = {Clinical Chemistry}, |
|
| 1120 | + shortjournal = {Clinical Chemistry}, |
|
| 1121 | + volume = {55}, |
|
| 1122 | + number = {4}, |
|
| 1123 | + pages = {611--622}, |
|
| 1124 | + issn = {0009-9147}, |
|
| 1125 | + doi = {10.1373/clinchem.2008.112797}, |
|
| 1126 | + url = {https://doi.org/10.1373/clinchem.2008.112797}, |
|
| 1127 | + urldate = {2022-05-19}, |
|
| 1128 | + abstract = {Background: Currently, a lack of consensus exists on how best to perform and interpret quantitative real-time PCR (qPCR) experiments. The problem is exacerbated by a lack of sufficient experimental detail in many publications, which impedes a reader’s ability to evaluate critically the quality of the results presented or to repeat the experiments.Content: The Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines target the reliability of results to help ensure the integrity of the scientific literature, promote consistency between laboratories, and increase experimental transparency. MIQE is a set of guidelines that describe the minimum information necessary for evaluating qPCR experiments. Included is a checklist to accompany the initial submission of a manuscript to the publisher. By providing all relevant experimental conditions and assay characteristics, reviewers can assess the validity of the protocols used. Full disclosure of all reagents, sequences, and analysis methods is necessary to enable other investigators to reproduce results. MIQE details should be published either in abbreviated form or as an online supplement.Summary: Following these guidelines will encourage better experimental practice, allowing more reliable and unequivocal interpretation of qPCR results.}, |
|
| 1129 | + file = {/Users/rmorin/Zotero/storage/C5542MCB/Bustin et al. - 2009 - The MIQE Guidelines Minimum Information for Publi.pdf;/Users/rmorin/Zotero/storage/N2JB4FT2/5631762.html} |
|
| 1130 | +} |
|
| 1131 | + |
|
| 1132 | +@article{butcharReciprocalRegulationActivating2010, |
|
| 1133 | + title = {Reciprocal {{Regulation}} of {{Activating}} and {{Inhibitory Fcγ Receptors}} by {{TLR7}}/8 {{Activation}}: {{Implications}} for {{Tumor Immunotherapy}}}, |
|
| 1134 | + author = {Butchar, J P and Mehta, P and Justiniano, S E and Guenterberg, K D and Kondadasula, S V and Mo, X and Chemudupati, M and Kanneganti, T D and Amer, A and Muthusamy, N and Jarjoura, D and Marsh, C B and Carson, W E and Byrd, J C and Tridandapani, S}, |
|
| 1135 | + date = {2010-03}, |
|
| 1136 | + journaltitle = {Clin Cancer Res}, |
|
| 1137 | + volume = {16}, |
|
| 1138 | + number = {7}, |
|
| 1139 | + pages = {1--12}, |
|
| 1140 | + keywords = {nosource} |
|
| 1141 | +} |
|
| 1142 | + |
|
| 1143 | +@article{callananIgGFcReceptor2000, |
|
| 1144 | + title = {The {{IgG Fc}} Receptor, {{FcγRIIB}}, Is a Target for Deregulation by Chromosomal Translocation in Malignant Lymphoma}, |
|
| 1145 | + author = {Callanan, Mary B. and Baccon, Patricia Le and Mossuz, Pascal and Duley, Samuel and Bastard, Christian and Hamoudi, Rifat and Dyer, Martin J. and Klobeck, Gustav and Rimokh, Ruth and Sotto, Jean Jacques and Leroux, Dominique}, |
|
| 1146 | + date = {2000}, |
|
| 1147 | + journaltitle = {Proceedings of the National Academy of Sciences}, |
|
| 1148 | + volume = {97}, |
|
| 1149 | + number = {1}, |
|
| 1150 | + eprint = {10618414}, |
|
| 1151 | + eprinttype = {pmid}, |
|
| 1152 | + pages = {309--314}, |
|
| 1153 | + issn = {0027-8424}, |
|
| 1154 | + doi = {10.1073/pnas.97.1.309}, |
|
| 1155 | + url = {http://dx.doi.org/10.1073/pnas.97.1.309}, |
|
| 1156 | + abstract = {Rearrangement of chromosomal bands 1q21–23 is one of the most frequent chromosomal aberrations observed in hematological malignancy. The genes affected by these rearrangements remain poorly characterized. Typically, 1q21–23 rearrangements arise during tumor evolution and accompany disease-specific chromosomal rearrangements such as t(14;18) (BCL2) and t(8;14) (MYC), where they are thus thought to play an important role in tumor progression. The pathogenetic basis of this 1q21–23-associated disease progression is currently unknown. In this setting, we surveyed our series of follicular lymphoma for evidence of recurring 1q21–23 breaks and identified three cases in which a t(14;18)(q32;q21) was accompanied by a novel balanced t(1;22)(q22;q11). Molecular cloning of the t(1;22) in a cell line (B593) derived from one of these cases and detailed fluorescent in situ hybridization mapping in the two remaining cases identified the FCGR2B gene, which encodes the immunoreceptor tyrosine-based inhibition motif-bearing IgG Fc receptor, FcγRIIB, as the target gene of the t(1;22)(q22;q11). We demonstrate deregulation of FCGR2B leading to hyperexpression of FcγRIIb2 as the principal consequence of the t(1;22). This is evidence that IgG Fc receptors can be targets for deregulation through chromosomal translocation in lymphoma. It suggests that dysregulation of FCGR2B may play a role in tumor progression in follicular lymphoma.}, |
|
| 1157 | + keywords = {nosource} |
|
| 1158 | +} |
|
| 1159 | + |
|
| 1160 | +@article{camilleri-broetFcgammaRIIBDifferentiallyExpressed2004, |
|
| 1161 | + title = {{{FcgammaRIIB}} Is Differentially Expressed during {{B}} Cell Maturation and in {{B-cell}} Lymphomas.}, |
|
| 1162 | + author = {Camilleri-Broët, Sophie and Cassard, Lydie and Broët, Philippe and Delmer, Alain and Le Touneau, Agnès and Diebold, Jacques and Fridman, Wolf Herman and Molina, Thierry Jo and Sautès-Fridman, Catherine}, |
|
| 1163 | + date = {2004-01}, |
|
| 1164 | + journaltitle = {Br J Haematol}, |
|
| 1165 | + volume = {124}, |
|
| 1166 | + number = {1}, |
|
| 1167 | + pages = {55--62}, |
|
| 1168 | + keywords = {nosource} |
|
| 1169 | +} |
|
| 1170 | + |
|
| 1171 | +@article{campoInternationalConsensusClassification2022, |
|
| 1172 | + title = {The {{International Consensus Classification}} of {{Mature Lymphoid Neoplasms}}: A Report from the {{Clinical Advisory Committee}}}, |
|
| 1173 | + shorttitle = {The {{International Consensus Classification}} of {{Mature Lymphoid Neoplasms}}}, |
|
| 1174 | + author = {Campo, Elias and Jaffe, Elaine S. and Cook, James R. and Quintanilla-Martinez, Leticia and Swerdlow, Steven H. and Anderson, Kenneth C. and Brousset, Pierre and Cerroni, Lorenzo and family=Leval, given=Laurence, prefix=de, useprefix=true and Dirnhofer, Stefan and Dogan, Ahmet and Feldman, Andrew L. and Fend, Falko and Friedberg, Jonathan W. and Gaulard, Philippe and Ghia, Paolo and Horwitz, Steven M. and King, Rebecca L. and Salles, Gilles and San-Miguel, Jesus and Seymour, John F. and Treon, Steven P. and Vose, Julie M. and Zucca, Emanuele and Advani, Ranjana and Ansell, Stephen and Au, Wing-Yan and Barrionuevo, Carlos and Bergsagel, Leif and Chan, Wing C. and Cohen, Jeffrey I. and family=Amore, given=Francesco, prefix=d', useprefix=true and Davies, Andrew and Falini, Brunangelo and Ghobrial, Irene M. and Goodlad, John R. and Gribben, John G. and Hsi, Eric D. and Kahl, Brad S. and Kim, Won-Seog and Kumar, Shaji and LaCasce, Ann S. and Laurent, Camille and Lenz, Georg and Leonard, John P. and Link, Michael P. and Lopez-Guillermo, Armando and Mateos, Maria Victoria and Macintyre, Elizabeth and Melnick, Ari M. and Morschhauser, Franck and Nakamura, Shigeo and Narbaitz, Marina and Pavlovsky, Astrid and Pileri, Stefano A. and Piris, Miguel and Pro, Barbara and Rajkumar, Vincent and Rosen, Steven T. and Sander, Birgitta and Sehn, Laurie and Shipp, Margaret A. and Smith, Sonali M. and Staudt, Louis M. and Thieblemont, Catherine and Tousseyn, Thomas and Wilson, Wyndham H. and Yoshino, Tadashi and Zinzani, Pier-Luigi and Dreyling, Martin and Scott, David W. and Winter, Jane N. and Zelenetz, Andrew D.}, |
|
| 1175 | + date = {2022-09-15}, |
|
| 1176 | + journaltitle = {Blood}, |
|
| 1177 | + shortjournal = {Blood}, |
|
| 1178 | + volume = {140}, |
|
| 1179 | + number = {11}, |
|
| 1180 | + eprint = {35653592}, |
|
| 1181 | + eprinttype = {pmid}, |
|
| 1182 | + pages = {1229--1253}, |
|
| 1183 | + issn = {1528-0020}, |
|
| 1184 | + doi = {10.1182/blood.2022015851}, |
|
| 1185 | + abstract = {Since the publication of the Revised European-American Classification of Lymphoid Neoplasms in 1994, subsequent updates of the classification of lymphoid neoplasms have been generated through iterative international efforts to achieve broad consensus among hematopathologists, geneticists, molecular scientists, and clinicians. Significant progress has recently been made in the characterization of malignancies of the immune system, with many new insights provided by genomic studies. They have led to this proposal. We have followed the same process that was successfully used for the third and fourth editions of the World Health Organization Classification of Hematologic Neoplasms. The definition, recommended studies, and criteria for the diagnosis of many entities have been extensively refined. Some categories considered provisional have now been upgraded to definite entities. Terminology for some diseases has been revised to adapt nomenclature to the current knowledge of their biology, but these modifications have been restricted to well-justified situations. Major findings from recent genomic studies have impacted the conceptual framework and diagnostic criteria for many disease entities. These changes will have an impact on optimal clinical management. The conclusions of this work are summarized in this report as the proposed International Consensus Classification of mature lymphoid, histiocytic, and dendritic cell tumors.}, |
|
| 1186 | + langid = {english}, |
|
| 1187 | + pmcid = {PMC9479027}, |
|
| 1188 | + keywords = {Advisory Committees,Consensus,Hematologic Neoplasms,Humans,Lymphoma,World Health Organization}, |
|
| 1189 | + file = {/Users/rmorin/Zotero/storage/7NE7U3II/Campo et al. - 2022 - The International Consensus Classification of Matu.pdf} |
|
| 1190 | +} |
|
| 1191 | + |
|
| 1192 | +@article{cannellPleiotropicRNABindingProtein2015, |
|
| 1193 | + title = {A {{Pleiotropic RNA-Binding Protein Controls Distinct Cell Cycle Checkpoints}} to {{Drive Resistance}} of P53-Defective {{Tumors}} to {{Chemotherapy}}}, |
|
| 1194 | + author = {Cannell, Ian G and Merrick, Karl A and Morandell, Sandra and Zhu, Chang-Qi and Braun, Christian J and Grant, Robert A and Cameron, Eleanor R and Tsao, Ming-Sound and Hemann, Michael T and Yaffe, Michael B}, |
|
| 1195 | + date = {2015-11-09}, |
|
| 1196 | + journaltitle = {Cancer cell}, |
|
| 1197 | + shortjournal = {Cancer Cell}, |
|
| 1198 | + volume = {28}, |
|
| 1199 | + number = {5}, |
|
| 1200 | + eprint = {26602816}, |
|
| 1201 | + eprinttype = {pmid}, |
|
| 1202 | + pages = {623--637}, |
|
| 1203 | + issn = {1535-6108}, |
|
| 1204 | + doi = {10.1016/j.ccell.2015.09.009}, |
|
| 1205 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4830093/}, |
|
| 1206 | + urldate = {2019-12-21}, |
|
| 1207 | + abstract = {In normal cells p53 is activated by DNA damage checkpoint kinases to simultaneously control the G1/S and G2/M cell cycle checkpoints through transcriptional induction of p21cip1 and Gadd45α. In p53 mutant tumors, cell cycle checkpoints are rewired, leading to dependency on the p38/MK2 pathway to survive DNA-damaging chemotherapy. Here we show that the RNA binding protein hnRNPA0 is the “successor” to p53 for checkpoint control. Like p53, hnRNPA0 is activated by a checkpoint kinase (MK2) and simultaneously controls both cell cycle checkpoints through distinct target mRNAs, but unlike p53 this is through the post-transcriptional stabilization of p27Kip1 and Gadd45α mRNAs. This pathway drives cisplatin resistance in lung cancer demonstrating the importance of post-transcriptional RNA control to chemotherapy response.,}, |
|
| 1208 | + pmcid = {PMC4830093} |
|
| 1209 | +} |
|
| 1210 | + |
|
| 1211 | +@article{cannonEarlyStorageSedentism2006, |
|
| 1212 | + title = {Early {{Storage}} and {{Sedentism}} on the {{Pacific Northwest Coast}}: {{Ancient DNA Analysis}} of {{Salmon Remains}} from {{Namu}}, {{British Columbia}}}, |
|
| 1213 | + shorttitle = {Early {{Storage}} and {{Sedentism}} on the {{Pacific Northwest Coast}}}, |
|
| 1214 | + author = {Cannon, Aubrey and Yang, Dongya Y.}, |
|
| 1215 | + date = {2006-01}, |
|
| 1216 | + journaltitle = {American Antiquity}, |
|
| 1217 | + volume = {71}, |
|
| 1218 | + number = {1}, |
|
| 1219 | + pages = {123--140}, |
|
| 1220 | + issn = {0002-7316, 2325-5064}, |
|
| 1221 | + doi = {10.2307/40035324}, |
|
| 1222 | + url = {https://www.cambridge.org/core/journals/american-antiquity/article/early-storage-and-sedentism-on-the-pacific-northwest-coast-ancient-dna-analysis-of-salmon-remains-from-namu-british-columbia/55BF5175B9F47DCB521786EF5F8EF3BC}, |
|
| 1223 | + urldate = {2018-10-27}, |
|
| 1224 | + abstract = {Ancient DNA identification of salmon remains from the site of Namu on the central coast of British Columbia shows use of a variety of species and an emphasis on pink salmon over the course of the past 7,000 years. These results support arguments that Namu was a permanent village settlement dependent on a salmon storage economy throughout this time. This pattern of subsistence and settlement predates by several millennia the first substantial evidence for population expansion or social differentiation in the region. Periodic salmon shortages in the period after 2000 cal B.C., which are associated with local and regional disruptions in settlement and increased reliance on more marginal resources, appear to be the result of failures in the pink salmon fishery. , Résumé La identificación del ADN antiguo en remanentes de salmón obtenidos en el sitio Namu en la costa central de la Columbia Británica, constituye evidencia de la utilización de una variedad de especies, con preferencia por el salmón rosado, a través de los últimos 7000 años. Dichos resultados vendrían a apoyar la hipótesis de que Namu sería un asentamiento permanente, que dependería económicamente del almacenamiento de salmón. Este patrón de subsistencia y de asentamiento vendría a ser más temprano, por varios milenios, que la importante primera evidencia de una expansión poblacional o de una diferenciación social en esta región. La escasez periódica del salmón en el período posterior al 2000 cal B.C., asociada con trastornos en los asentamientos locales y regionales y con un incremento de la dependencia sobre recursos más marginales, vendrían a ser producto del fracaso en la pesca del salmón rosado.}, |
|
| 1225 | + langid = {english}, |
|
| 1226 | + file = {/Users/rmorin/Zotero/storage/GUJH6LCH/55BF5175B9F47DCB521786EF5F8EF3BC.html} |
|
| 1227 | +} |
|
| 1228 | + |
|
| 1229 | +@article{caoControlAlternativeSplicing2012, |
|
| 1230 | + title = {Control of Alternative Splicing by Forskolin through {{hnRNP K}} during Neuronal Differentiation}, |
|
| 1231 | + author = {Cao, Wenguang and Razanau, Aleh and Feng, Dairong and Lobo, Vincent G. and Xie, Jiuyong}, |
|
| 1232 | + date = {2012-09}, |
|
| 1233 | + journaltitle = {Nucleic Acids Research}, |
|
| 1234 | + shortjournal = {Nucleic Acids Res}, |
|
| 1235 | + volume = {40}, |
|
| 1236 | + number = {16}, |
|
| 1237 | + eprint = {22684629}, |
|
| 1238 | + eprinttype = {pmid}, |
|
| 1239 | + pages = {8059--8071}, |
|
| 1240 | + issn = {0305-1048}, |
|
| 1241 | + doi = {10.1093/nar/gks504}, |
|
| 1242 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439897/}, |
|
| 1243 | + urldate = {2022-09-22}, |
|
| 1244 | + abstract = {The molecular basis of cell signal-regulated alternative splicing at the 3′ splice site remains largely unknown. We isolated a protein kinase A-responsive ribonucleic acid (RNA) element from a 3′ splice site of the synaptosomal-associated protein 25 (Snap25) gene for forskolin-inhibited splicing during neuronal differentiation of rat pheochromocytoma PC12 cells. The element binds specifically to heterogeneous nuclear ribonucleo protein (hnRNP) K in a phosphatase-sensitive way, which directly competes with the U2 auxiliary factor U2AF65, an essential component of early spliceosomes. Transcripts with similarly localized hnRNP K target motifs upstream of alternative exons are enriched in genes often associated with neurological diseases. We show that such motifs upstream of the Runx1 exon 6 also bind hnRNP K, and importantly, hnRNP K is required for forskolin-induced repression of the exon. Interestingly, this exon encodes the peptide domain that determines the switch of the transcriptional repressor/activator activity of Runx1, a change known to be critical in specifying neuron lineages. Consistent with an important role of the target genes in neurons, knocking down hnRNP K severely disrupts forskolin-induced neurite growth. Thus, through hnRNP K, the neuronal differentiation stimulus forskolin targets a critical 3′ splice site component of the splicing machinery to control alternative splicing of crucial genes. This also provides a regulated direct competitor of U2AF65 for cell signal control of 3′ splice site usage.}, |
|
| 1245 | + pmcid = {PMC3439897}, |
|
| 1246 | + file = {/Users/rmorin/Zotero/storage/JY94NGH4/Cao et al. - 2012 - Control of alternative splicing by forskolin throu.pdf} |
|
| 1247 | +} |
|
| 1248 | + |
|
| 1249 | +@article{caputiDeterminationRNABinding2001, |
|
| 1250 | + title = {Determination of the {{RNA Binding Specificity}} of the {{Heterogeneous Nuclear Ribonucleoprotein}} ({{hnRNP}}) {{H}}/{{H}}′/{{F}}/{{2H9 Family}} *}, |
|
| 1251 | + author = {Caputi, Massimo and Zahler, Alan M.}, |
|
| 1252 | + date = {2001-11-23}, |
|
| 1253 | + journaltitle = {Journal of Biological Chemistry}, |
|
| 1254 | + shortjournal = {Journal of Biological Chemistry}, |
|
| 1255 | + volume = {276}, |
|
| 1256 | + number = {47}, |
|
| 1257 | + eprint = {11571276}, |
|
| 1258 | + eprinttype = {pmid}, |
|
| 1259 | + pages = {43850--43859}, |
|
| 1260 | + publisher = {Elsevier}, |
|
| 1261 | + issn = {0021-9258, 1083-351X}, |
|
| 1262 | + doi = {10.1074/jbc.M102861200}, |
|
| 1263 | + url = {https://www.jbc.org/article/S0021-9258(19)82817-X/abstract}, |
|
| 1264 | + urldate = {2022-09-26}, |
|
| 1265 | + abstract = {{$<$}p{$>$}Members of the heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, H, H′, F, and 2H9, are involved in pre-mRNA processing. We analyzed the assembly of these proteins from splicing extracts onto four RNA regulatory elements as follows: a high affinity hnRNP A1-binding site (WA1), a sequence involved in Rev-dependent export (p17gag INS), an exonic splicing silencer from the β-tropomyosin gene, and an intronic splicing regulator (downstream control sequence (DCS) from the c-\emph{src} gene. The entire family binds the WA1, instability (INS), and β-tropomyosin substrates, and the core-binding site for each is a run of three G residues followed by an A. Transfer of small regions containing this sequence to a substrate lacking hnRNP H binding activity is sufficient to promote binding of all family members. The c-\emph{src} DCS has been shown to assemble hnRNP H, not hnRNP F, from HeLa cell extracts, and we show that hnRNP 2H9 does not bind this element. The DCS contains five G residues followed by a C. Mutation of the C to an A changes the specificity of the DCS from a substrate that binds only hnRNP H/H′ to a binding site for all hnRNP H family members. We conclude that the sequence GGGA is recognized by all hnRNP H family proteins.{$<$}/p{$>$}}, |
|
| 1266 | + langid = {english}, |
|
| 1267 | + file = {/Users/rmorin/Zotero/storage/4N5B2FWE/Caputi and Zahler - 2001 - Determination of the RNA Binding Specificity of th.pdf;/Users/rmorin/Zotero/storage/3X5F9TLQ/fulltext.html} |
|
| 1268 | +} |
|
| 1269 | + |
|
| 1270 | +@article{carabetComputerAidedDiscoverySmall2019, |
|
| 1271 | + title = {Computer-{{Aided Discovery}} of {{Small Molecules Targeting}} the {{RNA Splicing Activity}} of {{hnRNP A1}} in {{Castration-Resistant Prostate Cancer}}}, |
|
| 1272 | + author = {Carabet, Lavinia A. and Leblanc, Eric and Lallous, Nada and Morin, Helene and Ghaidi, Fariba and Lee, Joseph and Rennie, Paul S. and Cherkasov, Artem}, |
|
| 1273 | + date = {2019-02-20}, |
|
| 1274 | + journaltitle = {Molecules (Basel, Switzerland)}, |
|
| 1275 | + shortjournal = {Molecules}, |
|
| 1276 | + volume = {24}, |
|
| 1277 | + number = {4}, |
|
| 1278 | + eprint = {30791548}, |
|
| 1279 | + eprinttype = {pmid}, |
|
| 1280 | + pages = {E763}, |
|
| 1281 | + issn = {1420-3049}, |
|
| 1282 | + doi = {10.3390/molecules24040763}, |
|
| 1283 | + abstract = {The heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is a versatile RNA-binding protein playing a critical role in alternative pre-mRNA splicing regulation in cancer. Emerging data have implicated hnRNP A1 as a central player in a splicing regulatory circuit involving its direct transcriptional control by c-Myc oncoprotein and the production of the constitutively active ligand-independent alternative splice variant of androgen receptor, AR-V7, which promotes castration-resistant prostate cancer (CRPC). As there is an urgent need for effective CRPC drugs, targeting hnRNP A1 could, therefore, serve a dual purpose of preventing AR-V7 generation as well as reducing c-Myc transcriptional output. Herein, we report compound VPC-80051 as the first small molecule inhibitor of hnRNP A1 splicing activity discovered to date by using a computer-aided drug discovery approach. The inhibitor was developed to target the RNA-binding domain (RBD) of hnRNP A1. Further experimental evaluation demonstrated that VPC-80051 interacts directly with hnRNP A1 RBD and reduces AR-V7 messenger levels in 22Rv1 CRPC cell line. This study lays the groundwork for future structure-based development of more potent and selective small molecule inhibitors of hnRNP A1⁻RNA interactions aimed at altering the production of cancer-specific alternative splice isoforms.}, |
|
| 1284 | + langid = {english}, |
|
| 1285 | + pmcid = {PMC6413181}, |
|
| 1286 | + keywords = {alternative splicing,Binding Sites,castration-resistant prostate cancer,Cell Line Tumor,Computational Biology,Computer Simulation,computer-aided drug discovery,Drug Discovery,Gene Expression Regulation Neoplastic,Heterogeneous Nuclear Ribonucleoprotein A1,hnRNP A1,Humans,Male,Models Molecular,Molecular Conformation,Prostatic Neoplasms Castration-Resistant,protein–RNA interactions,RNA Splicing,small molecule inhibitors,Structure-Activity Relationship}, |
|
| 1287 | + file = {/Users/rmorin/Zotero/storage/KH45IN8S/Carabet et al. - 2019 - Computer-Aided Discovery of Small Molecules Target.pdf} |
|
| 1288 | +} |
|
| 1289 | + |
|
| 1290 | +@article{carlottiTransformationFollicularLymphoma, |
|
| 1291 | + title = {Transformation of Follicular Lymphoma to Diffuse Large {{B-cell}} Lymphoma May Occur by Divergent Evolution from a Common Progenitor Cell or by Direct Evolution from the Follicular Lymphoma Clone.}, |
|
| 1292 | + author = {Carlotti, Emanuela and Wrench, David and Matthews, Janet and Iqbal, Sameena and Davies, Andrew and Norton, Andrew and Hart, Jason and Lai, Raymond and Montoto, Silvia and Gribben, John G and Lister, T Andrew and Fitzgibbon, Jude}, |
|
| 1293 | + journaltitle = {Blood}, |
|
| 1294 | + volume = {113}, |
|
| 1295 | + number = {15}, |
|
| 1296 | + pages = {3553--3557}, |
|
| 1297 | + keywords = {nosource} |
|
| 1298 | +} |
|
| 1299 | + |
|
| 1300 | +@article{carnetrecessonBCLXLDirectlyModulates2017, |
|
| 1301 | + title = {{{BCL-XL}} Directly Modulates {{RAS}} Signalling to Favour Cancer Cell Stemness}, |
|
| 1302 | + author = {family=Carné Trécesson, given=Sophie, prefix=de, useprefix=false and Souazé, Frédérique and Basseville, Agnès and Bernard, Anne-Charlotte and Pécot, Jessie and Lopez, Jonathan and Bessou, Margaux and Sarosiek, Kristopher A. and Letai, Anthony and Barillé-Nion, Sophie and Valo, Isabelle and Coqueret, Olivier and Guette, Catherine and Campone, Mario and Gautier, Fabien and Juin, Philippe Paul}, |
|
| 1303 | + date = {2017-10-24}, |
|
| 1304 | + journaltitle = {Nature Communications}, |
|
| 1305 | + shortjournal = {Nat Commun}, |
|
| 1306 | + volume = {8}, |
|
| 1307 | + eprint = {29066722}, |
|
| 1308 | + eprinttype = {pmid}, |
|
| 1309 | + pages = {1123}, |
|
| 1310 | + issn = {2041-1723}, |
|
| 1311 | + doi = {10.1038/s41467-017-01079-1}, |
|
| 1312 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5654832/}, |
|
| 1313 | + urldate = {2022-10-04}, |
|
| 1314 | + abstract = {In tumours, accumulation of chemoresistant cells that express high levels of anti-apoptotic proteins such as BCL-XL is thought to result from the counter selection of sensitive, low expresser clones during progression and/or initial treatment. We herein show that BCL-XL expression is selectively advantageous to cancer cell populations even in the absence of pro-apoptotic pressure. In transformed human mammary epithelial cells BCL-XL favours full activation of signalling downstream of constitutively active RAS with which it interacts in a BH4-dependent manner. Comparative proteomic analysis and functional assays indicate that this is critical for RAS-induced expression of stemness regulators and maintenance of a cancer initiating cell (CIC) phenotype. Resistant cancer cells thus arise from a positive selection driven by BCL-XL modulation of RAS-induced self-renewal, and during which apoptotic resistance is not necessarily the directly selected trait., BCL-XL provides a survival advantage to cancer cells even in the absence of apoptotic pressures. In this study, the authors show that BCL-XL interacts with RAS in a BH4-dependent manner and regulates RAS-mediated activation of pathways involved in the stemness feature of breast cancer cells.}, |
|
| 1315 | + pmcid = {PMC5654832}, |
|
| 1316 | + file = {/Users/rmorin/Zotero/storage/VJKDYYVX/Carné Trécesson et al. - 2017 - BCL-XL directly modulates RAS signalling to favour.pdf} |
|
| 1317 | +} |
|
| 1318 | + |
|
| 1319 | +@article{carpenterHeterogeneousNuclearRibonucleoprotein2006, |
|
| 1320 | + title = {Heterogeneous Nuclear Ribonucleoprotein {{K}} Is over Expressed, Aberrantly Localised and Is Associated with Poor Prognosis in Colorectal Cancer}, |
|
| 1321 | + author = {Carpenter, B. and McKay, M. and Dundas, S. R. and Lawrie, L. C. and Telfer, C. and Murray, G. I.}, |
|
| 1322 | + date = {2006-10}, |
|
| 1323 | + journaltitle = {British Journal of Cancer}, |
|
| 1324 | + shortjournal = {Br J Cancer}, |
|
| 1325 | + volume = {95}, |
|
| 1326 | + number = {7}, |
|
| 1327 | + pages = {921--927}, |
|
| 1328 | + publisher = {Nature Publishing Group}, |
|
| 1329 | + issn = {1532-1827}, |
|
| 1330 | + doi = {10.1038/sj.bjc.6603349}, |
|
| 1331 | + url = {https://www.nature.com/articles/6603349}, |
|
| 1332 | + urldate = {2023-01-09}, |
|
| 1333 | + abstract = {Heterogeneous ribonucleoprotein K (hnRNP K) is a member of the hnRNP family which has several different cellular roles including transcription, mRNA shuttling, RNA editing and translation. Several reports implicate hnRNP K having a role in tumorigenesis, for instance hnRNP K increases transcription of the oncogene c-myc and hnRNP K expression is regulated by the p53/MDM 2 pathway. In this study comparing normal colon to colorectal cancer by proteomics, hnRNP K was identified as being overexpressed in this type of cancer. Immunohistochemistry with a monoclonal antibody to hnRNP K (which we developed) on colorectal cancer tissue microarray, confirmed that hnRNP K was overexpressed in colorectal cancer (P{$<$}0.001) and also showed that hnRNP K had an aberrant subcellular localisation in cancer cells. In normal colon hnRNP K was exclusively nuclear whereas in colorectal cancer the protein localised both in the cytoplasm and the nucleus. There were significant increases in both nuclear (P=0.007) and cytoplasmic (P=0.001) expression of hnRNP K in Dukes C tumours compared with early stage tumours. In Dukes C patient's good survival was associated with increased hnRNP K nuclear expression (P=0.0093). To elaborate on the recent observation that hnRNP K is regulated by p53, the expression profiles of these two proteins were also analysed. There was no correlation between hnRNP K and p53 expression, however, patients who presented tumours that were positive for hnRNP K and p53 had a poorer survival outcome (P=0.045).}, |
|
| 1334 | + issue = {7}, |
|
| 1335 | + langid = {english}, |
|
| 1336 | + keywords = {Biomedicine,Cancer Research,Drug Resistance,Epidemiology,general,Molecular Medicine,Oncology}, |
|
| 1337 | + file = {/Users/rmorin/Zotero/storage/H74A5U2D/Carpenter et al. - 2006 - Heterogeneous nuclear ribonucleoprotein K is over .pdf} |
|
| 1338 | +} |
|
| 1339 | + |
|
| 1340 | +@article{castelo-brancoPolypyrimidineTractBinding2004, |
|
| 1341 | + title = {Polypyrimidine {{Tract Binding Protein Modulates Efficiency}} of {{Polyadenylation}}}, |
|
| 1342 | + author = {Castelo-Branco, Pedro and Furger, Andre and Wollerton, Matthew and Smith, Christopher and Moreira, Alexandra and Proudfoot, Nick}, |
|
| 1343 | + date = {2004-05-15}, |
|
| 1344 | + journaltitle = {Molecular and Cellular Biology}, |
|
| 1345 | + volume = {24}, |
|
| 1346 | + number = {10}, |
|
| 1347 | + pages = {4174--4183}, |
|
| 1348 | + publisher = {American Society for Microbiology}, |
|
| 1349 | + doi = {10.1128/MCB.24.10.4174-4183.2004}, |
|
| 1350 | + url = {https://journals.asm.org/doi/full/10.1128/MCB.24.10.4174-4183.2004}, |
|
| 1351 | + urldate = {2022-09-27}, |
|
| 1352 | + file = {/Users/rmorin/Zotero/storage/YP8RIS4D/Castelo-Branco et al. - 2004 - Polypyrimidine Tract Binding Protein Modulates Eff.pdf} |
|
| 1353 | +} |
|
| 1354 | + |
|
| 1355 | +@article{cattorettiDeregulatedBCL6Expression, |
|
| 1356 | + title = {Deregulated {{BCL6}} Expression Recapitulates the Pathogenesis of Human Diffuse Large {{B}} Cell Lymphomas in Mice}, |
|
| 1357 | + author = {Cattoretti, Giorgio and Pasqualucci, Laura and Ballon, Gianna and Tam, Wayne and Nandula, Subhadra V and Shen, Qiong and Mo, Tongwei and Murty, Vundavalli V and Dalla-Favera, Riccardo}, |
|
| 1358 | + journaltitle = {Cancer Cell}, |
|
| 1359 | + volume = {7}, |
|
| 1360 | + number = {5}, |
|
| 1361 | + pages = {445--455}, |
|
| 1362 | + keywords = {nosource} |
|
| 1363 | +} |
|
| 1364 | + |
|
| 1365 | +@article{cattorettiTargetedDisruptionS1P22009, |
|
| 1366 | + title = {Targeted {{Disruption}} of the {{S1P2 Sphingosine}} 1-{{Phosphate Receptor Gene Leads}} to {{Diffuse Large B-Cell Lymphoma Formation}}}, |
|
| 1367 | + author = {Cattoretti, G and Cattoretti, G and Mandelbaum, J and Mandelbaum, J and Lee, N and Lee, N and Chaves, A H and Chaves, A H and Mahler, A M and Mahler, A M and Chadburn, A and Dalla-Favera, R and Pasqualucci, L and MacLennan, A J and MacLennan, A J}, |
|
| 1368 | + date = {2009-11}, |
|
| 1369 | + journaltitle = {Cancer Res}, |
|
| 1370 | + volume = {69}, |
|
| 1371 | + number = {22}, |
|
| 1372 | + pages = {8686--8692}, |
|
| 1373 | + keywords = {nosource} |
|
| 1374 | +} |
|
| 1375 | + |
|
| 1376 | +@online{CellDevelopmentPathways, |
|
| 1377 | + title = {B Cell Development Pathways - {{ProQuest}}}, |
|
| 1378 | + url = {https://www.proquest.com/openview/dd4dd441a1e721485aa871b6e812c2d9/1?casa_token=oL4JXwb4PmAAAAAA:a05XBzPaGKSPDIrAWvwnlVXDB-bn8l3cKX0AQ5lllmjo9zPxpqzckoiCzUkPoAs0C7TDTeBPQuw&cbl=47332&pq-origsite=gscholar&parentSessionId=vkSsFp6eiGXrMO9pT3aWhVFysFqfdTwKAN1ymj7w48c%3D}, |
|
| 1379 | + urldate = {2022-10-06}, |
|
| 1380 | + abstract = {Explore millions of resources from scholarly journals, books, newspapers, videos and more, on the ProQuest Platform.}, |
|
| 1381 | + langid = {english}, |
|
| 1382 | + file = {/Users/rmorin/Zotero/storage/LDNDPEFB/1.html} |
|
| 1383 | +} |
|
| 1384 | + |
|
| 1385 | +@article{cerchiettiPurineScaffoldHsp902009, |
|
| 1386 | + title = {A Purine Scaffold {{Hsp90}} Inhibitor Destabilizes {{BCL-6}} and Has Specific Antitumor Activity in {{BCL-6}}–Dependent {{B}} Cell Lymphomas}, |
|
| 1387 | + author = {Cerchietti, Leandro C. and Lopes, Eloisi C. and Yang, Shao Ning and Hatzi, Katerina and Bunting, Karen L. and Tsikitas, Lucas A. and Mallik, Alka and Robles, Ana I. and Walling, Jennifer and Varticovski, Lyuba and Shaknovich, Rita and Bhalla, Kapil N. and Chiosis, Gabriela and Melnick, Ari}, |
|
| 1388 | + date = {2009-12}, |
|
| 1389 | + journaltitle = {Nature Medicine}, |
|
| 1390 | + shortjournal = {Nat Med}, |
|
| 1391 | + volume = {15}, |
|
| 1392 | + number = {12}, |
|
| 1393 | + pages = {1369--1376}, |
|
| 1394 | + publisher = {Nature Publishing Group}, |
|
| 1395 | + issn = {1546-170X}, |
|
| 1396 | + doi = {10.1038/nm.2059}, |
|
| 1397 | + url = {https://www.nature.com/articles/nm.2059}, |
|
| 1398 | + urldate = {2022-10-04}, |
|
| 1399 | + abstract = {By taking advantage of the direct interaction between heat shock protein 90 (Hsp90) and the transcriptional repressor Bcl-6, a purine-derived inhibitor of Hsp90 selectively kills diffuse large B cell lymphomas that depend on the expression of Bcl-6 for their survival.}, |
|
| 1400 | + issue = {12}, |
|
| 1401 | + langid = {english}, |
|
| 1402 | + keywords = {Biomedicine,Cancer Research,general,Infectious Diseases,Metabolic Diseases,Molecular Medicine,Neurosciences}, |
|
| 1403 | + file = {/Users/rmorin/Zotero/storage/33PWD4NS/Cerchietti et al. - 2009 - A purine scaffold Hsp90 inhibitor destabilizes BCL.pdf;/Users/rmorin/Zotero/storage/AACD4GC7/nm.html} |
|
| 1404 | +} |
|
| 1405 | + |
|
| 1406 | +@article{chadburnImmunophenotypicAnalysisAIDSrelated, |
|
| 1407 | + title = {Immunophenotypic Analysis of {{AIDS-related}} Diffuse Large {{B-cell}} Lymphoma and Clinical Implications in Patients from {{AIDS Malignancies Consortium}} Clinical Trials 010 and 034.}, |
|
| 1408 | + author = {Chadburn, Amy and Chiu, April and Lee, Jeannette Y and Chen, Xia and Hyjek, Elizabeth and Banham, Alison H and Noy, Ariela and Kaplan, Lawrence D and Sparano, Joseph A and Bhatia, Kishor and Cesarman, Ethel}, |
|
| 1409 | + journaltitle = {J Clin Oncol}, |
|
| 1410 | + volume = {27}, |
|
| 1411 | + number = {30}, |
|
| 1412 | + pages = {5039--5048}, |
|
| 1413 | + keywords = {nosource} |
|
| 1414 | +} |
|
| 1415 | + |
|
| 1416 | +@article{changRNAbindingProteinHnRNPLL2015, |
|
| 1417 | + title = {{{RNA-binding}} Protein {{hnRNPLL}} Regulates {{mRNA}} Splicing and Stability during {{B-cell}} to Plasma-Cell Differentiation}, |
|
| 1418 | + author = {Chang, Xing and Li, Bin and Rao, Anjana}, |
|
| 1419 | + date = {2015-04-14}, |
|
| 1420 | + journaltitle = {Proceedings of the National Academy of Sciences}, |
|
| 1421 | + volume = {112}, |
|
| 1422 | + number = {15}, |
|
| 1423 | + pages = {E1888-E1897}, |
|
| 1424 | + publisher = {Proceedings of the National Academy of Sciences}, |
|
| 1425 | + doi = {10.1073/pnas.1422490112}, |
|
| 1426 | + url = {https://www.pnas.org/doi/10.1073/pnas.1422490112}, |
|
| 1427 | + urldate = {2022-10-06}, |
|
| 1428 | + file = {/Users/rmorin/Zotero/storage/BBZQBH54/Chang et al. - 2015 - RNA-binding protein hnRNPLL regulates mRNA splicin.pdf} |
|
| 1429 | +} |
|
| 1430 | + |
|
| 1431 | +@article{changTargetingPanessentialGenes2021, |
|
| 1432 | + title = {Targeting Pan-Essential Genes in Cancer: {{Challenges}} and Opportunities}, |
|
| 1433 | + shorttitle = {Targeting Pan-Essential Genes in Cancer}, |
|
| 1434 | + author = {Chang, Liang and Ruiz, Paloma and Ito, Takahiro and Sellers, William R.}, |
|
| 1435 | + date = {2021-04-12}, |
|
| 1436 | + journaltitle = {Cancer Cell}, |
|
| 1437 | + shortjournal = {Cancer Cell}, |
|
| 1438 | + volume = {39}, |
|
| 1439 | + number = {4}, |
|
| 1440 | + pages = {466--479}, |
|
| 1441 | + issn = {1535-6108}, |
|
| 1442 | + doi = {10.1016/j.ccell.2020.12.008}, |
|
| 1443 | + url = {https://www.sciencedirect.com/science/article/pii/S1535610820306565}, |
|
| 1444 | + urldate = {2023-01-09}, |
|
| 1445 | + abstract = {Despite remarkable successes in the clinic, cancer targeted therapy development remains challenging and the failure rate is disappointingly high. This problem is partly due to the misapplication of the targeted therapy paradigm to therapeutics targeting pan-essential genes, which can result in therapeutics whereby efficacy is attenuated by dose-limiting toxicity. Here we summarize the key features of successful chemotherapy and targeted therapy agents, and use case studies to outline recurrent challenges to drug development efforts targeting pan-essential genes. Finally, we suggest strategies to avoid previous pitfalls for ongoing and future development of pan-essential therapeutics.}, |
|
| 1446 | + langid = {english}, |
|
| 1447 | + keywords = {drug development,pan-essential genes,target identification,target validation,targeted therapies}, |
|
| 1448 | + file = {/Users/rmorin/Zotero/storage/U5A8CXV4/Chang et al. - 2021 - Targeting pan-essential genes in cancer Challenge.pdf;/Users/rmorin/Zotero/storage/4KPPD3NJ/S1535610820306565.html} |
|
| 1449 | +} |
|
| 1450 | + |
|
| 1451 | +@article{chanPathogenesisDiffuseLarge2010, |
|
| 1452 | + title = {Pathogenesis of Diffuse Large {{B}} Cell Lymphoma}, |
|
| 1453 | + author = {Chan, Wing John C}, |
|
| 1454 | + date = {2010-06}, |
|
| 1455 | + journaltitle = {International journal of hematology}, |
|
| 1456 | + volume = {92}, |
|
| 1457 | + number = {2}, |
|
| 1458 | + pages = {219--230}, |
|
| 1459 | + keywords = {nosource} |
|
| 1460 | +} |
|
| 1461 | + |
|
| 1462 | +@article{chapuyDiscoveryCharacterizationSuperEnhancerAssociated2013, |
|
| 1463 | + title = {Discovery and {{Characterization}} of {{Super-Enhancer-Associated Dependencies}} in {{Diffuse Large B Cell Lymphoma}}}, |
|
| 1464 | + author = {Chapuy, Bjoern and McKeown, Michael R and Lin, Charles Y and Monti, Stefano and Roemer, Margaretha G M and Qi, Jun and Rahl, Peter B and Sun, Heather H and Yeda, Kelly T and Doench, John G and Reichert, Elaine and Kung, Andrew L and Rodig, Scott J and Young, Richard A and Shipp, Margaret A and Bradner, James E}, |
|
| 1465 | + date = {2013-12}, |
|
| 1466 | + journaltitle = {Cancer Cell}, |
|
| 1467 | + volume = {24}, |
|
| 1468 | + number = {6}, |
|
| 1469 | + pages = {777--790}, |
|
| 1470 | + keywords = {nosource} |
|
| 1471 | +} |
|
| 1472 | + |
|
| 1473 | +@article{chapuyGenomicAnalysesPMBL2019b, |
|
| 1474 | + title = {Genomic Analyses of {{PMBL}} Reveal New Drivers and Mechanisms of Sensitivity to {{PD-1}} Blockade}, |
|
| 1475 | + author = {Chapuy, Bjoern and Stewart, Chip and Dunford, Andrew J. and Kim, Jaegil and Wienand, Kirsty and Kamburov, Atanas and Griffin, Gabriel K. and Chen, Pei-Hsuan and Lako, Ana and Redd, Robert A. and Cote, Claire M. and Ducar, Matthew D. and Thorner, Aaron R. and Rodig, Scott J. and Getz, Gad and Shipp, Margaret A.}, |
|
| 1476 | + date = {2019-12-26}, |
|
| 1477 | + journaltitle = {Blood}, |
|
| 1478 | + shortjournal = {Blood}, |
|
| 1479 | + volume = {134}, |
|
| 1480 | + number = {26}, |
|
| 1481 | + eprint = {31697821}, |
|
| 1482 | + eprinttype = {pmid}, |
|
| 1483 | + pages = {2369--2382}, |
|
| 1484 | + issn = {1528-0020}, |
|
| 1485 | + doi = {10.1182/blood.2019002067}, |
|
| 1486 | + abstract = {Primary mediastinal large B-cell lymphomas (PMBLs) are aggressive tumors that typically present as large mediastinal masses in young women. PMBLs share clinical, transcriptional, and molecular features with classical Hodgkin lymphoma (cHL), including constitutive activation of nuclear factor κB (NF-κB), JAK/STAT signaling, and programmed cell death protein 1 (PD-1)-mediated immune evasion. The demonstrated efficacy of PD-1 blockade in relapsed/refractory PMBLs led to recent approval by the US Food and Drug Administration and underscored the importance of characterizing targetable genetic vulnerabilities in this disease. Here, we report a comprehensive analysis of recurrent genetic alterations -somatic mutations, somatic copy number alterations, and structural variants-in a cohort of 37 newly diagnosed PMBLs. We identified a median of 9 genetic drivers per PMBL, including known and newly identified components of the JAK/STAT and NF-κB signaling pathways and frequent B2M alterations that limit major histocompatibility complex class I expression, as in cHL. PMBL also exhibited frequent, newly identified driver mutations in ZNF217 and an additional epigenetic modifier, EZH2. The majority of these alterations were clonal, which supports their role as early drivers. In PMBL, we identified several previously uncharacterized molecular features that may increase sensitivity to PD-1 blockade, including high tumor mutational burden, microsatellite instability, and an apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC) mutational signature. The shared genetic features between PMBL and cHL provide a framework for analyzing the mechanism of action of PD-1 blockade in these related lymphoid malignancies.}, |
|
| 1487 | + langid = {english}, |
|
| 1488 | + pmcid = {PMC6933293}, |
|
| 1489 | + keywords = {Adult,Antineoplastic Agents Immunological,Biomarkers Tumor,Cohort Studies,DNA Copy Number Variations,Female,Gene Expression Regulation Neoplastic,Genomics,Humans,Lymphoma Large B-Cell Diffuse,Male,Mediastinal Neoplasms,Mutation,Prognosis,Programmed Cell Death 1 Receptor,Trans-Activators}, |
|
| 1490 | + file = {/Users/rmorin/Zotero/storage/7W7SMIE9/Chapuy et al. - 2019 - Genomic analyses of PMBL reveal new drivers and me.pdf} |
|
| 1491 | +} |
|
| 1492 | + |
|
| 1493 | +@article{chapuyMolecularSubtypesDiffuse2018b, |
|
| 1494 | + title = {Molecular Subtypes of Diffuse Large {{B}} Cell Lymphoma Are Associated with Distinct Pathogenic Mechanisms and Outcomes}, |
|
| 1495 | + author = {Chapuy, Bjoern and Stewart, Chip and Dunford, Andrew J. and Kim, Jaegil and Kamburov, Atanas and Redd, Robert A. and Lawrence, Mike S. and Roemer, Margaretha G. M. and Li, Amy J. and Ziepert, Marita and Staiger, Annette M. and Wala, Jeremiah A. and Ducar, Matthew D. and Leshchiner, Ignaty and Rheinbay, Ester and Taylor-Weiner, Amaro and Coughlin, Caroline A. and Hess, Julian M. and Pedamallu, Chandra S. and Livitz, Dimitri and Rosebrock, Daniel and Rosenberg, Mara and Tracy, Adam A. and Horn, Heike and family=Hummelen, given=Paul, prefix=van, useprefix=true and Feldman, Andrew L. and Link, Brian K. and Novak, Anne J. and Cerhan, James R. and Habermann, Thomas M. and Siebert, Reiner and Rosenwald, Andreas and Thorner, Aaron R. and Meyerson, Matthew L. and Golub, Todd R. and Beroukhim, Rameen and Wulf, Gerald G. and Ott, German and Rodig, Scott J. and Monti, Stefano and Neuberg, Donna S. and Loeffler, Markus and Pfreundschuh, Michael and Trümper, Lorenz and Getz, Gad and Shipp, Margaret A.}, |
|
| 1496 | + date = {2018-05}, |
|
| 1497 | + journaltitle = {Nature Medicine}, |
|
| 1498 | + shortjournal = {Nat Med}, |
|
| 1499 | + volume = {24}, |
|
| 1500 | + number = {5}, |
|
| 1501 | + eprint = {29713087}, |
|
| 1502 | + eprinttype = {pmid}, |
|
| 1503 | + pages = {679--690}, |
|
| 1504 | + issn = {1546-170X}, |
|
| 1505 | + doi = {10.1038/s41591-018-0016-8}, |
|
| 1506 | + abstract = {Diffuse large B cell lymphoma (DLBCL), the most common lymphoid malignancy in adults, is a clinically and genetically heterogeneous disease that is further classified into transcriptionally defined activated B cell (ABC) and germinal center B cell (GCB) subtypes. We carried out a comprehensive genetic analysis of 304 primary DLBCLs and identified low-frequency alterations, captured recurrent mutations, somatic copy number alterations, and structural variants, and defined coordinate signatures in patients with available outcome data. We integrated these genetic drivers using consensus clustering and identified five robust DLBCL subsets, including a previously unrecognized group of low-risk ABC-DLBCLs of extrafollicular/marginal zone origin; two distinct subsets of GCB-DLBCLs with different outcomes and targetable alterations; and an ABC/GCB-independent group with biallelic inactivation of TP53, CDKN2A loss, and associated genomic instability. The genetic features of the newly characterized subsets, their mutational signatures, and the temporal ordering of identified alterations provide new insights into DLBCL pathogenesis. The coordinate genetic signatures also predict outcome independent of the clinical International Prognostic Index and suggest new combination treatment strategies. More broadly, our results provide a roadmap for an actionable DLBCL classification.}, |
|
| 1507 | + langid = {english}, |
|
| 1508 | + pmcid = {PMC6613387}, |
|
| 1509 | + keywords = {DNA Copy Number Variations,Gene Rearrangement,Genes Neoplasm,Genetic Heterogeneity,Humans,Lymphoma Large B-Cell Diffuse,Mutation,Mutation Rate,Treatment Outcome}, |
|
| 1510 | + file = {/Users/rmorin/Zotero/storage/QILRBLTF/Chapuy et al. - 2018 - Molecular subtypes of diffuse large B cell lymphom.pdf} |
|
| 1511 | +} |
|
| 1512 | + |
|
| 1513 | +@article{chaudhuryHeterogeneousNuclearRibonucleoproteins2010, |
|
| 1514 | + title = {Heterogeneous Nuclear Ribonucleoproteins ({{hnRNPs}}) in Cellular Processes: {{Focus}} on {{hnRNP E1}}'s Multifunctional Regulatory Roles}, |
|
| 1515 | + shorttitle = {Heterogeneous Nuclear Ribonucleoproteins ({{hnRNPs}}) in Cellular Processes}, |
|
| 1516 | + author = {Chaudhury, Arindam and Chander, Praveen and Howe, Philip H.}, |
|
| 1517 | + date = {2010-08}, |
|
| 1518 | + journaltitle = {RNA}, |
|
| 1519 | + shortjournal = {RNA}, |
|
| 1520 | + volume = {16}, |
|
| 1521 | + number = {8}, |
|
| 1522 | + eprint = {20584894}, |
|
| 1523 | + eprinttype = {pmid}, |
|
| 1524 | + pages = {1449--1462}, |
|
| 1525 | + issn = {1355-8382}, |
|
| 1526 | + doi = {10.1261/rna.2254110}, |
|
| 1527 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905745/}, |
|
| 1528 | + urldate = {2022-09-28}, |
|
| 1529 | + abstract = {Heterogeneous nuclear ribonucleoproteins (hnRNPs) comprise a family of RNA-binding proteins. The complexity and diversity associated with the hnRNPs render them multifunctional, involved not only in processing heterogeneous nuclear RNAs (hnRNAs) into mature mRNAs, but also acting as trans-factors in regulating gene expression. Heterogeneous nuclear ribonucleoprotein E1 (hnRNP E1), a subgroup of hnRNPs, is a KH-triple repeat containing RNA-binding protein. It is encoded by an intronless gene arising from hnRNP E2 through a retrotransposition event. hnRNP E1 is ubiquitously expressed and functions in regulating major steps of gene expression, including pre-mRNA processing, mRNA stability, and translation. Given its wide-ranging functions in the nucleus and cytoplasm and interaction with multiple proteins, we propose a post-transcriptional regulon model that explains hnRNP E1's widespread functional diversity.}, |
|
| 1530 | + pmcid = {PMC2905745}, |
|
| 1531 | + file = {/Users/rmorin/Zotero/storage/9AJVC6LQ/Chaudhury et al. - 2010 - Heterogeneous nuclear ribonucleoproteins (hnRNPs) .pdf} |
|
| 1532 | +} |
|
| 1533 | + |
|
| 1534 | +@article{chaudhuryTGFbetamediatedPhosphorylationHnRNP2010, |
|
| 1535 | + title = {{{TGF-beta-mediated}} Phosphorylation of {{hnRNP E1}} Induces {{EMT}} via Transcript-Selective Translational Induction of {{Dab2}} and {{ILEI}}}, |
|
| 1536 | + author = {Chaudhury, Arindam and Hussey, George S. and Ray, Partho S. and Jin, Ge and Fox, Paul L. and Howe, Philip H.}, |
|
| 1537 | + date = {2010-03}, |
|
| 1538 | + journaltitle = {Nature Cell Biology}, |
|
| 1539 | + shortjournal = {Nat Cell Biol}, |
|
| 1540 | + volume = {12}, |
|
| 1541 | + number = {3}, |
|
| 1542 | + eprint = {20154680}, |
|
| 1543 | + eprinttype = {pmid}, |
|
| 1544 | + pages = {286--293}, |
|
| 1545 | + issn = {1476-4679}, |
|
| 1546 | + doi = {10.1038/ncb2029}, |
|
| 1547 | + abstract = {Transforming growth factor-beta (TGF-beta) induces epithelial-mesenchymal transdifferentiation (EMT) accompanied by cellular differentiation and migration. Despite extensive transcriptomic profiling, the identification of TGF-beta-inducible, EMT-specific genes has met with limited success. Here we identify a post-transcriptional pathway by which TGF-beta modulates the expression of EMT-specific proteins and of EMT itself. We show that heterogeneous nuclear ribonucleoprotein E1 (hnRNP E1) binds a structural, 33-nucleotide TGF-beta-activated translation (BAT) element in the 3' untranslated region of disabled-2 (Dab2) and interleukin-like EMT inducer (ILEI) transcripts, and represses their translation. TGF-beta activation leads to phosphorylation at Ser 43 of hnRNP E1 by protein kinase Bbeta/Akt2, inducing its release from the BAT element and translational activation of Dab2 and ILEI messenger RNAs. Modulation of hnRNP E1 expression or its post-translational modification alters the TGF-beta-mediated reversal of translational silencing of the target transcripts and EMT. These results suggest the existence of a TGF-beta-inducible post-transcriptional regulon that controls EMT during the development and metastatic progression of tumours.}, |
|
| 1548 | + langid = {english}, |
|
| 1549 | + pmcid = {PMC2830561}, |
|
| 1550 | + keywords = {3' Untranslated Regions,Adaptor Proteins Signal Transducing,Adaptor Proteins Vesicular Transport,Animals,Apoptosis Regulatory Proteins,Cadherins,Carrier Proteins,Cell Line Transformed,Cell Transdifferentiation,Cytokines,DNA-Binding Proteins,Epithelial Cells,Female,Gene Expression,Gene Expression Regulation Neoplastic,Insulin,Mammary Glands Animal,Mesoderm,Mice,Neoplasm Proteins,Phosphorylation,Polyribosomes,Protein Binding,Protein Biosynthesis,Protein Isoforms,Protein Kinase Inhibitors,Proto-Oncogene Proteins c-akt,RNA Messenger,RNA Small Interfering,RNA-Binding Proteins,Signal Transduction,Transforming Growth Factor beta,Vimentin}, |
|
| 1551 | + file = {/Users/rmorin/Zotero/storage/IJ55AK5C/Chaudhury et al. - 2010 - TGF-beta-mediated phosphorylation of hnRNP E1 indu.pdf} |
|
| 1552 | +} |
|
| 1553 | + |
|
| 1554 | +@article{cheahMantleCellLymphoma2016, |
|
| 1555 | + title = {Mantle {{Cell Lymphoma}}}, |
|
| 1556 | + author = {Cheah, Chan Yoon and Seymour, John F. and Wang, Michael L.}, |
|
| 1557 | + date = {2016-04-10}, |
|
| 1558 | + journaltitle = {Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology}, |
|
| 1559 | + shortjournal = {J. Clin. Oncol.}, |
|
| 1560 | + volume = {34}, |
|
| 1561 | + number = {11}, |
|
| 1562 | + eprint = {26755518}, |
|
| 1563 | + eprinttype = {pmid}, |
|
| 1564 | + pages = {1256--1269}, |
|
| 1565 | + issn = {1527-7755}, |
|
| 1566 | + doi = {10.1200/JCO.2015.63.5904}, |
|
| 1567 | + abstract = {Mantle cell lymphoma (MCL) is an uncommon subtype of non-Hodgkin lymphoma previously considered to have a poor prognosis. Large gains were made in the first decade of the new century when clinical trials established the importance of high-dose therapy and autologous stem-cell rescue and high-dose cytarabine in younger patients and the benefits of maintenance rituximab and bendamustine in older patients. In particular, greater depth of understanding of the molecular pathophysiology of MCL has resulted in an explosion of specifically targeted new efficacious agents. In particular, agents recently approved by the Food and Drug Administration include the proteasome inhibitor bortezomib, immunomodulator lenalidomide, and Bruton's tyrosine kinase inhibitor ibrutinib. We review recent advances in the understanding of MCL biology and outline our recommended approach to therapy, including choice of chemoimmunotherapy, the role of stem-cell transplantation, and mechanism-based targeted therapies, on the basis of a synthesis of the data from published clinical trials.}, |
|
| 1568 | + langid = {english}, |
|
| 1569 | + keywords = {Antineoplastic Agents,Antineoplastic Combined Chemotherapy Protocols,Bendamustine Hydrochloride,Bortezomib,Cytarabine,Drug Administration Schedule,Gene Expression Profiling,Gene Expression Regulation Neoplastic,Hematopoietic Stem Cell Transplantation,Humans,Induction Chemotherapy,Lenalidomide,Lymphoma Mantle-Cell,Maintenance Chemotherapy,Molecular Targeted Therapy,Neoplasm Staging,Prognosis,Pyrazoles,Pyrimidines,Risk Factors,Rituximab,Thalidomide,Transplantation Autologous} |
|
| 1570 | +} |
|
| 1571 | + |
|
| 1572 | +@article{chenBenchmarkingLongReadAssemblers2020, |
|
| 1573 | + title = {Benchmarking {{Long-Read Assemblers}} for {{Genomic Analyses}} of {{Bacterial Pathogens Using Oxford Nanopore Sequencing}}}, |
|
| 1574 | + author = {Chen, Zhao and Erickson, David L. and Meng, Jianghong}, |
|
| 1575 | + date = {2020-01}, |
|
| 1576 | + journaltitle = {International Journal of Molecular Sciences}, |
|
| 1577 | + volume = {21}, |
|
| 1578 | + number = {23}, |
|
| 1579 | + pages = {9161}, |
|
| 1580 | + publisher = {Multidisciplinary Digital Publishing Institute}, |
|
| 1581 | + issn = {1422-0067}, |
|
| 1582 | + doi = {10.3390/ijms21239161}, |
|
| 1583 | + url = {https://www.mdpi.com/1422-0067/21/23/9161}, |
|
| 1584 | + urldate = {2022-02-07}, |
|
| 1585 | + abstract = {Oxford Nanopore sequencing can be used to achieve complete bacterial genomes. However, the error rates of Oxford Nanopore long reads are greater compared to Illumina short reads. Long-read assemblers using a variety of assembly algorithms have been developed to overcome this deficiency, which have not been benchmarked for genomic analyses of bacterial pathogens using Oxford Nanopore long reads. In this study, long-read assemblers, namely Canu, Flye, Miniasm/Racon, Raven, Redbean, and Shasta, were thus benchmarked using Oxford Nanopore long reads of bacterial pathogens. Ten species were tested for mediocre- and low-quality simulated reads, and 10 species were tested for real reads. Raven was the most robust assembler, obtaining complete and accurate genomes. All Miniasm/Racon and Raven assemblies of mediocre-quality reads provided accurate antimicrobial resistance (AMR) profiles, while the Raven assembly of Klebsiella variicola with low-quality reads was the only assembly with an accurate AMR profile among all assemblers and species. All assemblers functioned well for predicting virulence genes using mediocre-quality and real reads, whereas only the Raven assemblies of low-quality reads had accurate numbers of virulence genes. Regarding multilocus sequence typing (MLST), Miniasm/Racon was the most effective assembler for mediocre-quality reads, while only the Raven assemblies of Escherichia coli O157:H7 and K. variicola with low-quality reads showed positive MLST results. Miniasm/Racon and Raven were the best performers for MLST using real reads. The Miniasm/Racon and Raven assemblies showed accurate phylogenetic inference. For the pan-genome analyses, Raven was the strongest assembler for simulated reads, whereas Miniasm/Racon and Raven performed the best for real reads. Overall, the most robust and accurate assembler was Raven, closely followed by Miniasm/Racon.}, |
|
| 1586 | + issue = {23}, |
|
| 1587 | + langid = {english}, |
|
| 1588 | + keywords = {bacterial pathogen,benchmarking,genome assembly,genomic analysis,long-read assembler,long-read sequencing,Oxford Nanopore sequencing,whole-genome sequencing}, |
|
| 1589 | + file = {/Users/rmorin/Zotero/storage/FFTQUSPU/Chen et al. - 2020 - Benchmarking Long-Read Assemblers for Genomic Anal.pdf;/Users/rmorin/Zotero/storage/GB3UN4AP/9161.html} |
|
| 1590 | +} |
|
| 1591 | + |
|
| 1592 | +@article{chenBindingHnRNPExonic1999, |
|
| 1593 | + title = {Binding of {{hnRNP H}} to an Exonic Splicing Silencer Is Involved in the Regulation of Alternative Splicing of the Rat β-Tropomyosin Gene}, |
|
| 1594 | + author = {Chen, Charlie Degui and Kobayashi, Ryuji and Helfman, David M.}, |
|
| 1595 | + date = {1999-01-03}, |
|
| 1596 | + journaltitle = {Genes \& Development}, |
|
| 1597 | + shortjournal = {Genes Dev.}, |
|
| 1598 | + volume = {13}, |
|
| 1599 | + number = {5}, |
|
| 1600 | + eprint = {10072387}, |
|
| 1601 | + eprinttype = {pmid}, |
|
| 1602 | + pages = {593--606}, |
|
| 1603 | + publisher = {Cold Spring Harbor Lab}, |
|
| 1604 | + issn = {0890-9369, 1549-5477}, |
|
| 1605 | + url = {http://genesdev.cshlp.org/content/13/5/593}, |
|
| 1606 | + urldate = {2022-09-27}, |
|
| 1607 | + abstract = {In the rat β-tropomyosin (β-TM) gene, exons 6 and 7 are spliced alternatively in a mutually exclusive manner. Exon 6 is included in mRNA encoding nonmuscle TM-1, whereas exon 7 is used in mRNA encoding skeletal muscle β-TM. Previously, we demonstrated that a six nucleotide mutation at the 5′ end of exon 7, designated as ex-1, activated exon 7 splicing in nonmuscle cells. In this study, we show that the activating effect of this mutation is not the result of creating an exonic splicing enhancer (ESE) or disrupting a putative secondary structure. The sequence in exon 7 acts as a bona fide exonic splicing silencer (ESS), which is bound specifically by atrans-acting factor. Isolation and peptide sequencing reveal that this factor is hnRNP H, a member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. Binding of hnRNP H correlates with the ESS activity. Furthermore, addition of antibodies that specifically recognizes hnRNP H to the splicing reactions or partial depletion of hnRNP H from nuclear extract activates exon 7 splicing in vitro and this effect can be reversed by addition of purified recombinant hnRNP H. These results indicate that hnRNP H participates in exclusion of exon 7 in nonmuscle cells. The involvement of hnRNP H in the activity of an ESS may represent a prototype for the regulation of tissue- and developmental-specific alternative splicing.}, |
|
| 1608 | + langid = {english}, |
|
| 1609 | + keywords = {cis-acting element,heterogeneous nuclear ribonucleoproteins,RNA processing,RNA–protein interaction,trans-acting factor}, |
|
| 1610 | + file = {/Users/rmorin/Zotero/storage/TEJRIUE4/Chen et al. - 1999 - Binding of hnRNP H to an exonic splicing silencer .pdf;/Users/rmorin/Zotero/storage/N8I3I97T/593.html} |
|
| 1611 | +} |
|
| 1612 | + |
|
| 1613 | +@article{chenDeregulationFCGR2BExpression2001, |
|
| 1614 | + title = {Deregulation of {{FCGR2B}} Expression by 1q21 Rearrangements in Follicular Lymphomas}, |
|
| 1615 | + author = {Chen, Weiyi and Palanisamy, Nallasivam and Schmidt, Helmut and Teruya-Feldstein, Julie and Jhanwar, Suresh C and Zelenetz, Andrew D and Houldsworth, Jane and Chaganti, R}, |
|
| 1616 | + date = {2001-01}, |
|
| 1617 | + journaltitle = {Oncogene}, |
|
| 1618 | + volume = {20}, |
|
| 1619 | + number = {52}, |
|
| 1620 | + eprint = {11753646}, |
|
| 1621 | + eprinttype = {pmid}, |
|
| 1622 | + pages = {1204989}, |
|
| 1623 | + issn = {1476-5594}, |
|
| 1624 | + doi = {10.1038/sj.onc.1204989}, |
|
| 1625 | + url = {http://dx.doi.org/10.1038/sj.onc.1204989}, |
|
| 1626 | + abstract = {We report here the molecular cloning and characterization of a t(1;14)(q21;q32) in a follicular lymphoma (FL) with an unusual BCL2 aberration. Fluorescence in situ hybridization (FISH) and Southern blot analysis of tumor cells identified the translocation breakpoint within the 5′ switch region of IGHG (Sγ). We cloned the chimeric breakpoint region approximately 1.5 kbp downstream from the HindIII site of 5′Sγ2 on chromosome 14q32 and identified a 360-bp novel segment with homology to the CpG island clone 11h8. Two BAC clones containing this sequence were isolated and mapped to 1q21 by FISH. BAC 342/P13 contained sequences homologous to Fcγ receptors 2A, 3A, 2B, 3B, and a heat shock protein gene HSP70B. The translocation brought the Sγ2 region of a productive IGH allele 20∼30 kbp upstream of FCGR2B. As a result of the translocation, the b2 isoform of FCGR2B was overexpressed in the tumor. Screening of a panel of 76 B-cell lymphomas with 1q21-23 cytogenetic aberrations by Southern blot analysis using breakpoint probes identified an additional FL with a t(14;18)(q32;q21) and a breakpoint in the FCGR2B region. These results suggest that FCGR2B may be deregulated by 1q21 aberration in BCL2 rearranged FLs and possibly play a role in their progression.}, |
|
| 1627 | + keywords = {nosource} |
|
| 1628 | +} |
|
| 1629 | + |
|
| 1630 | +@article{chenIndolentMantleCell2009, |
|
| 1631 | + title = {Indolent {{Mantle Cell Lymphoma}}: {{A Distinct Subgroup Characterized}} by {{Leukemic Phase Disease}} without {{Lymphadenopathy}}.}, |
|
| 1632 | + shorttitle = {Indolent {{Mantle Cell Lymphoma}}}, |
|
| 1633 | + author = {Chen, Dong and Viswanatha, David S. and Zent, Clive S. and Shanafelt, Tait D. and Call, Timothy G. and Kay, Neil E. and Van Dyke, Daniel L. and Ketterling, Rhett P. and Witzig, Thomas E. and Morice, William G. and Hanson, Curtis A.}, |
|
| 1634 | + date = {2009-11-20}, |
|
| 1635 | + journaltitle = {Blood}, |
|
| 1636 | + shortjournal = {Blood}, |
|
| 1637 | + volume = {114}, |
|
| 1638 | + number = {22}, |
|
| 1639 | + pages = {3937--3937}, |
|
| 1640 | + issn = {0006-4971}, |
|
| 1641 | + doi = {10.1182/blood.V114.22.3937.3937}, |
|
| 1642 | + url = {https://ashpublications.org/blood/article/114/22/3937/76125/Indolent-Mantle-Cell-Lymphoma-A-Distinct-Subgroup}, |
|
| 1643 | + urldate = {2019-12-21}, |
|
| 1644 | + langid = {english}, |
|
| 1645 | + file = {/Users/rmorin/Zotero/storage/WKHMK2WV/Indolent-Mantle-Cell-Lymphoma-A-Distinct-Subgroup.html} |
|
| 1646 | +} |
|
| 1647 | + |
|
| 1648 | +@article{chenMantaRapidDetection2016, |
|
| 1649 | + title = {Manta: Rapid Detection of Structural Variants and Indels for Germline and Cancer Sequencing Applications}, |
|
| 1650 | + shorttitle = {Manta}, |
|
| 1651 | + author = {Chen, Xiaoyu and Schulz-Trieglaff, Ole and Shaw, Richard and Barnes, Bret and Schlesinger, Felix and Källberg, Morten and Cox, Anthony J. and Kruglyak, Semyon and Saunders, Christopher T.}, |
|
| 1652 | + date = {2016-04-15}, |
|
| 1653 | + journaltitle = {Bioinformatics (Oxford, England)}, |
|
| 1654 | + shortjournal = {Bioinformatics}, |
|
| 1655 | + volume = {32}, |
|
| 1656 | + number = {8}, |
|
| 1657 | + eprint = {26647377}, |
|
| 1658 | + eprinttype = {pmid}, |
|
| 1659 | + pages = {1220--1222}, |
|
| 1660 | + issn = {1367-4811}, |
|
| 1661 | + doi = {10.1093/bioinformatics/btv710}, |
|
| 1662 | + abstract = {: We describe Manta, a method to discover structural variants and indels from next generation sequencing data. Manta is optimized for rapid germline and somatic analysis, calling structural variants, medium-sized indels and large insertions on standard compute hardware in less than a tenth of the time that comparable methods require to identify only subsets of these variant types: for example NA12878 at 50× genomic coverage is analyzed in less than 20\,min. Manta can discover and score variants based on supporting paired and split-read evidence, with scoring models optimized for germline analysis of diploid individuals and somatic analysis of tumor-normal sample pairs. Call quality is similar to or better than comparable methods, as determined by pedigree consistency of germline calls and comparison of somatic calls to COSMIC database variants. Manta consistently assembles a higher fraction of its calls to base-pair resolution, allowing for improved downstream annotation and analysis of clinical significance. We provide Manta as a community resource to facilitate practical and routine structural variant analysis in clinical and research sequencing scenarios. AVAILABILITY AND IMPLEMENTATION: Manta is released under the open-source GPLv3 license. Source code, documentation and Linux binaries are available from https://github.com/Illumina/manta. CONTACT: csaunders@illumina.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, |
|
| 1663 | + langid = {english}, |
|
| 1664 | + keywords = {DNA Neoplasm,Genome,Genomics,High-Throughput Nucleotide Sequencing,Humans,INDEL Mutation,Neoplasms,Software} |
|
| 1665 | +} |
|
| 1666 | + |
|
| 1667 | +@article{chenSYKdependentTonicBcell, |
|
| 1668 | + title = {{{SYK-dependent}} Tonic {{B-cell}} Receptor Signaling Is a Rational Treatment Target in Diffuse Large {{B-cell}} Lymphoma.}, |
|
| 1669 | + author = {Chen, Linfeng and Monti, Stefano and Juszczynski, Przemyslaw and Daley, John and Chen, Wen and Witzig, Thomas E and Habermann, Thomas M and Kutok, Jeffery L and Shipp, Margaret A}, |
|
| 1670 | + journaltitle = {Blood}, |
|
| 1671 | + volume = {111}, |
|
| 1672 | + number = {4}, |
|
| 1673 | + pages = {2230--2237}, |
|
| 1674 | + keywords = {nosource} |
|
| 1675 | +} |
|
| 1676 | + |
|
| 1677 | +@article{chenThymidinePhosphorylaseMRNA2009, |
|
| 1678 | + title = {Thymidine Phosphorylase {{mRNA}} Stability and Protein Levels Are Increased through {{ERK-mediated}} Cytoplasmic Accumulation of {{hnRNP K}} in Nasopharyngeal Carcinoma Cells}, |
|
| 1679 | + author = {Chen, L.-C. and Liu, H.-P. and Li, H.-P. and Hsueh, C. and Yu, J.-S. and Liang, C.-L. and Chang, Y.-S.}, |
|
| 1680 | + date = {2009-04}, |
|
| 1681 | + journaltitle = {Oncogene}, |
|
| 1682 | + volume = {28}, |
|
| 1683 | + number = {17}, |
|
| 1684 | + pages = {1904--1915}, |
|
| 1685 | + publisher = {Nature Publishing Group}, |
|
| 1686 | + issn = {1476-5594}, |
|
| 1687 | + doi = {10.1038/onc.2009.55}, |
|
| 1688 | + url = {https://www.nature.com/articles/onc200955}, |
|
| 1689 | + urldate = {2022-09-28}, |
|
| 1690 | + abstract = {The cytoplasmic level of heterogeneous nuclear ribonucleoprotein K (hnRNP K) is significantly correlated with the elevated expression of thymidine phosphorylase (TP), and high levels of both proteins are predictive of a poor prognosis in nasopharyngeal carcinoma (NPC). We herein show that TP is highly induced by serum deprivation in NPC cells, and that this is due to an increase in the half-life of the TP mRNA, as shown by nuclear run-on and actinomycin D assays. We further show that the CU-rich element of the TP mRNA directly interacts with hnRNP K, as demonstrated by immunoprecipitation RT–PCR assays, and the nucleus-to-cytoplasm translocation of hnRNP K. Blockade of hnRNP K expression reduces TP expression, suggesting that hnRNP K acts in the upregulation of TP. Mechanistically, both MEK inhibitor and the hnRNP K ERK-phosphoacceptor-site mutant decrease cytoplasmic accumulation of hnRNP K, suggesting that ERK-dependent phosphorylation is critical for TP induction. Furthermore, we found that hnRNP K-mediated TP induction allows NPC cells to resist hypoxia-induced apoptosis. Our results collectively establish the regulation and role of ERK-mediated cytoplasmic accumulation of hnRNP K as an upstream modulator of TP, suggesting that hnRNP K may be an attractive candidate as a future therapeutic target for cancer.}, |
|
| 1691 | + issue = {17}, |
|
| 1692 | + langid = {english}, |
|
| 1693 | + keywords = {Apoptosis,Cell Biology,general,Human Genetics,Internal Medicine,Medicine/Public Health,Oncology}, |
|
| 1694 | + file = {/Users/rmorin/Zotero/storage/PB44PXHW/Chen et al. - 2009 - Thymidine phosphorylase mRNA stability and protein.pdf;/Users/rmorin/Zotero/storage/N2I8V9V4/onc200955.html} |
|
| 1695 | +} |
|
| 1696 | + |
|
| 1697 | +@article{chesonOblimersenTreatmentPatients2007, |
|
| 1698 | + title = {Oblimersen for the Treatment of Patients with Chronic Lymphocytic Leukemia}, |
|
| 1699 | + author = {Cheson, Bruce D}, |
|
| 1700 | + date = {2007-10}, |
|
| 1701 | + journaltitle = {Therapeutics and Clinical Risk Management}, |
|
| 1702 | + shortjournal = {Ther Clin Risk Manag}, |
|
| 1703 | + volume = {3}, |
|
| 1704 | + number = {5}, |
|
| 1705 | + eprint = {18473009}, |
|
| 1706 | + eprinttype = {pmid}, |
|
| 1707 | + pages = {855--870}, |
|
| 1708 | + issn = {1176-6336}, |
|
| 1709 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2376092/}, |
|
| 1710 | + urldate = {2020-09-22}, |
|
| 1711 | + abstract = {Among adults in Western countries, chronic lymphocytic leukemia (CLL) is the most prevalent form of leukemia. CLL primarily affects the elderly and may be associated with multiple comorbidities. A cure has not been identified, and new treatment options are needed. Expression of Bcl-2 protein is associated with the pathogenesis of CLL and chemotherapy resistance. Oblimersen, a Bcl-2 antisense phosphorothioate oligonucleotide, is being evaluated in patients with CLL and other cancers; trials through Phase III have been completed. In the setting of relapsed/refractory CLL, single-agent oblimersen demonstrates modest activity, whereas the addition of oblimersen to fludarabine/cyclophosphamide significantly improves the rate of complete and nodular partial responses; moreover, these responses are durable and associated with clinical benefit. Oblimersen is more efficacious in relapsed rather than refractory patients. The side effect profile of oblimersen, alone or in combination with standard chemotherapy, is favorable compared with currently available chemotherapies. In the first cycle, an infusion reaction with or without tumor lysis syndrome is uncommon, and transient thrombocytopenia is observed. Catheter-related complications are associated with the need for continuous intravenous infusion of oblimersen over several days; other routes of administration are under clinical investigation. Oblimersen is a promising therapeutic approach for patients with relapsed CLL and should be further evaluated in the front-line setting.}, |
|
| 1712 | + pmcid = {PMC2376092}, |
|
| 1713 | + file = {/Users/rmorin/Zotero/storage/8A7RYKLL/Cheson - 2007 - Oblimersen for the treatment of patients with chro.pdf} |
|
| 1714 | +} |
|
| 1715 | + |
|
| 1716 | +@article{cheungAcquiredTNFRSF14Mutations2010a, |
|
| 1717 | + title = {Acquired {{TNFRSF14}} Mutations in Follicular Lymphoma Are Associated with Worse Prognosis}, |
|
| 1718 | + author = {Cheung, K.-John J. and Johnson, Nathalie A. and Affleck, Joslynn G. and Severson, Tesa and Steidl, Christian and Ben-Neriah, Susana and Schein, Jacqueline and Morin, Ryan D. and Moore, Richard and Shah, Sohrab P. and Qian, Hong and Paul, Jessica E. and Telenius, Adele and Relander, Thomas and Lam, Wan and Savage, Kerry and Connors, Joseph M. and Brown, Carolyn and Marra, Marco A. and Gascoyne, Randy D. and Horsman, Douglas E.}, |
|
| 1719 | + date = {2010-11-15}, |
|
| 1720 | + journaltitle = {Cancer Research}, |
|
| 1721 | + shortjournal = {Cancer Res}, |
|
| 1722 | + volume = {70}, |
|
| 1723 | + number = {22}, |
|
| 1724 | + eprint = {20884631}, |
|
| 1725 | + eprinttype = {pmid}, |
|
| 1726 | + pages = {9166--9174}, |
|
| 1727 | + issn = {1538-7445}, |
|
| 1728 | + doi = {10.1158/0008-5472.CAN-10-2460}, |
|
| 1729 | + abstract = {Clinical correlative studies have linked 1p36 deletions with worse prognosis in follicular lymphoma (FL). In this study, we sought to identify the critical gene(s) in this region that is responsible for conferring inferior prognosis. BAC array technology applied to 141 FL specimens detected a minimum region of deletion (MRD) of ∼97 kb within 1p36.32 in 20\% of these cases. Frequent single-nucleotide polymorphism-detected copy-neutral loss of heterozygosity was also found in this region. Analysis of promoter CpGs in the MRD did not reveal differential patterns of DNA methylation in samples that differed in 1p36 status. Exon sequencing of MRD genes identified somatic alterations in the TNFRSF14 gene in 3 of 11 selected cases with matching normal DNA. An expanded cohort consisting of 251 specimens identified 46 cases (18.3\%) with nonsynonymous mutations affecting TNFRSF14. Overall survival (OS) and disease-specific survival (DSS) were associated with the presence of TNFRSF14 mutation in patients whose overall treatment included rituximab. We further showed that inferior OS and DSS were most pronounced in patients whose lymphomas contained both TNFRSF14 mutations and 1p36 deletions after adjustment for the International Prognostic Index [hazard ratios of 3.65 (95\% confidence interval, 1.35-9.878, P=0.011) and 3.19 (95\% confidence interval, 1.06-9.57, P=0.039), respectively]. Our findings identify TNFRSF14 as a candidate gene associated with a subset of FL, based on frequent occurrence of acquired mutations and their correlation with inferior clinical outcomes.}, |
|
| 1730 | + langid = {english}, |
|
| 1731 | + keywords = {Antibodies Monoclonal Murine-Derived,Antineoplastic Combined Chemotherapy Protocols,Chromosome Deletion,Chromosomes Artificial Bacterial,Chromosomes Human Pair 1,Comparative Genomic Hybridization,CpG Islands,Disease-Free Survival,DNA Methylation,Female,Genetic Predisposition to Disease,Humans,In Situ Hybridization Fluorescence,Lymphoma Follicular,Male,Middle Aged,Multivariate Analysis,Mutation,Prognosis,Receptors Tumor Necrosis Factor Member 14,Rituximab}, |
|
| 1732 | + file = {/Users/rmorin/Zotero/storage/VCNZ8JM2/Cheung et al. - 2010 - Acquired TNFRSF14 mutations in follicular lymphoma.pdf} |
|
| 1733 | +} |
|
| 1734 | + |
|
| 1735 | +@article{choiNewImmunostainAlgorithm2009, |
|
| 1736 | + title = {A {{New Immunostain Algorithm Classifies Diffuse Large B-Cell Lymphoma}} into {{Molecular Subtypes}} with {{High Accuracy}}}, |
|
| 1737 | + author = {Choi, W W L and Weisenburger, D D and Greiner, T C and Piris, M A and Banham, A H and Delabie, J and Braziel, R M and Geng, H and Iqbal, J and Lenz, G and Vose, J M and Hans, C P and Fu, K and Smith, L M and Li, M and Liu, Z and Gascoyne, R D and Rosenwald, A and Ott, G and Rimsza, L M and Campo, E and Jaffe, E S and Jaye, D L and Staudt, L M and Chan, W C}, |
|
| 1738 | + date = {2009-08}, |
|
| 1739 | + journaltitle = {Clin Cancer Res}, |
|
| 1740 | + volume = {15}, |
|
| 1741 | + number = {17}, |
|
| 1742 | + pages = {5494--5502}, |
|
| 1743 | + keywords = {nosource} |
|
| 1744 | +} |
|
| 1745 | + |
|
| 1746 | +@article{chongComprehensiveCharacterizationProgrammed2016, |
|
| 1747 | + title = {Comprehensive Characterization of Programmed Death Ligand Structural Rearrangements in {{B-cell}} Non-{{Hodgkin}} Lymphomas}, |
|
| 1748 | + author = {Chong, Lauren C. and Twa, David D. W. and Mottok, Anja and Ben-Neriah, Susana and Woolcock, Bruce W. and Zhao, Yongjun and Savage, Kerry J. and Marra, Marco A. and Scott, David W. and Gascoyne, Randy D. and Morin, Ryan D. and Mungall, Andrew J. and Steidl, Christian}, |
|
| 1749 | + date = {2016-09-01}, |
|
| 1750 | + journaltitle = {Blood}, |
|
| 1751 | + shortjournal = {Blood}, |
|
| 1752 | + volume = {128}, |
|
| 1753 | + number = {9}, |
|
| 1754 | + eprint = {27268263}, |
|
| 1755 | + eprinttype = {pmid}, |
|
| 1756 | + pages = {1206--1213}, |
|
| 1757 | + issn = {1528-0020}, |
|
| 1758 | + doi = {10.1182/blood-2015-11-683003}, |
|
| 1759 | + abstract = {Programmed death ligands (PDLs) are immune-regulatory molecules that are frequently affected by chromosomal alterations in B-cell lymphomas. Although PDL copy-number variations are well characterized, a detailed and comprehensive analysis of structural rearrangements (SRs) and associated phenotypic consequences is largely lacking. Here, we used oligonucleotide capture sequencing of 67 formalin-fixed paraffin-embedded tissues derived from primary B-cell lymphomas and 1 cell line to detect and characterize, at base-pair resolution, SRs of the PDL locus (9p24.1; harboring PDL1/CD274 and PDL2/PDCD1LG2). We describe 36 novel PDL SRs, including 17 intrachromosomal events (inversions, duplications, deletions) and 19 translocations involving BZRAP-AS1, CD44, GET4, IL4R, KIAA0226L, MID1, RCC1, PTPN1 and segments of the immunoglobulin loci. Moreover, analysis of the precise chromosomal breakpoints reveals 2 distinct cluster breakpoint regions (CBRs) within either CD274 (CBR1) or PDCD1LG2 (CBR2). To determine the phenotypic consequences of these SRs, we performed immunohistochemistry for CD274 and PDCD1LG2 on primary pretreatment biopsies and found that PDL SRs are significantly associated with PDL protein expression. Finally, stable ectopic expression of wild-type PDCD1LG2 and the PDCD1LG2-IGHV7-81 fusion showed, in coculture, significantly reduced T-cell activation. Taken together, our data demonstrate the complementary utility of fluorescence in situ hybridization and capture sequencing approaches and provide a classification scheme for PDL SRs with implications for future studies using PDL immune-checkpoint inhibitors in B-cell lymphomas.}, |
|
| 1760 | + langid = {english}, |
|
| 1761 | + keywords = {B7-H1 Antigen,Cell Line Tumor,Chromosome Aberrations,Chromosomes Human,Female,Genetic Loci,Humans,Lymphoma B-Cell,Male,Programmed Cell Death 1 Ligand 2 Protein}, |
|
| 1762 | + file = {/Users/rmorin/Zotero/storage/HXBWZJGD/Chong et al. - 2016 - Comprehensive characterization of programmed death.pdf} |
|
| 1763 | +} |
|
| 1764 | + |
|
| 1765 | +@article{chongHighresolutionArchitecturePartner2018, |
|
| 1766 | + title = {High-Resolution Architecture and Partner Genes of {{MYC}} Rearrangements in Lymphoma with {{DLBCL}} Morphology}, |
|
| 1767 | + author = {Chong, Lauren C. and Ben-Neriah, Susana and Slack, Graham W. and Freeman, Ciara and Ennishi, Daisuke and Mottok, Anja and Collinge, Brett and Abrisqueta, Pau and Farinha, Pedro and Boyle, Merrill and Meissner, Barbara and Kridel, Robert and Gerrie, Alina S. and Villa, Diego and Savage, Kerry J. and Sehn, Laurie H. and Siebert, Reiner and Morin, Ryan D. and Gascoyne, Randy D. and Marra, Marco A. and Connors, Joseph M. and Mungall, Andrew J. and Steidl, Christian and Scott, David W.}, |
|
| 1768 | + date = {2018-10-23}, |
|
| 1769 | + journaltitle = {Blood Advances}, |
|
| 1770 | + shortjournal = {Blood Adv}, |
|
| 1771 | + volume = {2}, |
|
| 1772 | + number = {20}, |
|
| 1773 | + eprint = {30348671}, |
|
| 1774 | + eprinttype = {pmid}, |
|
| 1775 | + pages = {2755--2765}, |
|
| 1776 | + issn = {2473-9537}, |
|
| 1777 | + doi = {10.1182/bloodadvances.2018023572}, |
|
| 1778 | + abstract = {Genomic rearrangements in the MYC locus occur in ∼12\% of lymphomas with diffuse large B-cell lymphoma (DLBCL) morphology and are associated with inferior outcome. Previous studies exploring MYC rearrangements have primarily used fluorescence in situ hybridization (FISH) assays to characterize break-apart status but have rarely examined breakpoint location, and in some cases have not examined partner identity. We performed targeted sequencing of MYC, BCL2, BCL6, and the immunoglobulin (IG) loci in 112 tumors with DLBCL morphology harboring MYC rearrangement. We characterized the location of the MYC rearrangement at base pair resolution and identified the partner in 88 cases. We observed a cluster of breakpoints upstream of the MYC coding region and in intron 1 (the "genic cluster"). Genic cluster rearrangements were enriched for translocations involving IGH (80\%), whereas nongenic rearrangements occurred mostly downstream of the MYC gene with a variety of partners, including IGL and IGK Other recurrent partners included BCL6, ZCCHC7, and RFTN1, which has not previously been described as a MYC partner. We compared 2 commercially available FISH break-apart assays for the MYC locus and observed discordant results in 32\% of cases examined, including some with MYC-IGL and MYC-IGK rearrangements. In cases of high-grade B-cell lymphoma with MYC and BCL2 and/or BCL6 rearrangement (HGBL-DH), so-called "double-hit" lymphomas, the majority of MYC rearrangements had non-IG partners (65\%), with breakpoints outside the genic cluster (72\%). In patients with de novo HGBL-DH of DLBCL morphology, MYC-IG rearrangements showed a trend toward inferior time to progression and overall survival compared with MYC-non-IG rearrangements. Our data reveal clinically relevant architecture of MYC rearrangements in lymphomas with DLBCL morphology.}, |
|
| 1779 | + langid = {english}, |
|
| 1780 | + pmcid = {PMC6199666} |
|
| 1781 | +} |
|
| 1782 | + |
|
| 1783 | +@article{choPolyBindingProtein2013, |
|
| 1784 | + title = {Poly ({{C}})-{{Binding Protein}} 1 {{Regulates}} P63 {{Expression}} through {{mRNA Stability}}}, |
|
| 1785 | + author = {Cho, Seong-Jun and Jung, Yong-Sam and Chen, Xinbin}, |
|
| 1786 | + date = {2013-08-07}, |
|
| 1787 | + journaltitle = {PLOS ONE}, |
|
| 1788 | + shortjournal = {PLOS ONE}, |
|
| 1789 | + volume = {8}, |
|
| 1790 | + number = {8}, |
|
| 1791 | + pages = {e71724}, |
|
| 1792 | + publisher = {Public Library of Science}, |
|
| 1793 | + issn = {1932-6203}, |
|
| 1794 | + doi = {10.1371/journal.pone.0071724}, |
|
| 1795 | + url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0071724}, |
|
| 1796 | + urldate = {2022-09-28}, |
|
| 1797 | + abstract = {p63, a transcription factor and p53 family protein, plays a crucial role in tumor suppression and development of various epithelial tissues. While p63 expression is controlled mostly by post-translational modifications, recent studies indicate that transcriptional and posttranscriptional regulations are essential for proper p63 expression. Here, we investigated the regulation of p63 expression by poly (C)-binding protein 1 (PCBP1, also known as hnRNP-E1 and αCP1). We found that knockdown of PCBP1 decreases the level of p63 transcript and protein. We also found that PCBP1 regulates the stability of p63 mRNA via binding to p63 3’UTR. Additionally, we found that a CU-rich element (CUE) in p63 3′UTR is bound by and responsive to PCBP1. Together, we conclude that PCBP1 regulates p63 expression via mRNA stability.}, |
|
| 1798 | + langid = {english}, |
|
| 1799 | + keywords = {Gene expression,Lentivirus,Luciferase,Messenger RNA,Polymerase chain reaction,Protein translation,Reverse transcriptase-polymerase chain reaction,RNA probes}, |
|
| 1800 | + file = {/Users/rmorin/Zotero/storage/UHK9YXLF/Cho et al. - 2013 - Poly (C)-Binding Protein 1 Regulates p63 Expressio.pdf;/Users/rmorin/Zotero/storage/8W33B99E/article.html} |
|
| 1801 | +} |
|
| 1802 | + |
|
| 1803 | +@article{choPromoterLncRNAGene2018, |
|
| 1804 | + title = {Promoter of {{lncRNA Gene PVT1 Is}} a {{Tumor-Suppressor DNA Boundary Element}}}, |
|
| 1805 | + author = {Cho, Seung Woo and Xu, Jin and Sun, Ruping and Mumbach, Maxwell R. and Carter, Ava C. and Chen, Y. Grace and Yost, Kathryn E. and Kim, Jeewon and He, Jing and Nevins, Stephanie A. and Chin, Suet-Feung and Caldas, Carlos and Liu, S. John and Horlbeck, Max A. and Lim, Daniel A. and Weissman, Jonathan S. and Curtis, Christina and Chang, Howard Y.}, |
|
| 1806 | + date = {2018-05-31}, |
|
| 1807 | + journaltitle = {Cell}, |
|
| 1808 | + shortjournal = {Cell}, |
|
| 1809 | + volume = {173}, |
|
| 1810 | + number = {6}, |
|
| 1811 | + eprint = {29731168}, |
|
| 1812 | + eprinttype = {pmid}, |
|
| 1813 | + pages = {1398-1412.e22}, |
|
| 1814 | + issn = {1097-4172}, |
|
| 1815 | + doi = {10.1016/j.cell.2018.03.068}, |
|
| 1816 | + abstract = {Noncoding mutations in cancer genomes are frequent~but challenging to interpret. PVT1 encodes an oncogenic lncRNA, but recurrent translocations and deletions in human cancers suggest alternative mechanisms. Here, we show that the PVT1 promoter has a tumor-suppressor function that is independent of PVT1 lncRNA. CRISPR interference of PVT1 promoter enhances breast cancer cell competition and growth in~vivo. The promoters of the PVT1 and the MYC oncogenes, located 55 kb apart on chromosome 8q24, compete for engagement with four intragenic enhancers in the PVT1 locus, thereby allowing the PVT1 promoter to regulate pause release of MYC transcription. PVT1 undergoes developmentally regulated monoallelic expression, and the PVT1 promoter inhibits MYC expression only from the same chromosome via promoter competition. Cancer genome sequencing identifies recurrent mutations encompassing the human PVT1 promoter, and genome editing verified that PVT1 promoter mutation promotes cancer cell growth. These results highlight regulatory sequences of lncRNA genes as potential disease-associated DNA elements.}, |
|
| 1817 | + langid = {english}, |
|
| 1818 | + pmcid = {PMC5984165}, |
|
| 1819 | + keywords = {Animals,Breast Neoplasms,Carcinogenesis,Cell Line Tumor,Cell Proliferation,Cell Transformation Neoplastic,Chromatin,CRISPR-Cas Systems,CRISPRi,DNA Neoplasm,enhancer,Enhancer Elements Genetic,Female,Gene Expression Profiling,Gene Expression Regulation Neoplastic,Genes myc,Humans,lncRNA,Mice,Mice Inbred NOD,Mutation,MYC,Neoplasm Transplantation,promoter,Promoter Regions Genetic,PVT1,RNA Long Noncoding,topological domains,Transcription Genetic,transcriptional regulation,tumor suppressor} |
|
| 1820 | +} |
|
| 1821 | + |
|
| 1822 | +@article{choudhurySplicingActivatorDAZAP12014, |
|
| 1823 | + title = {The Splicing Activator {{DAZAP1}} Integrates Splicing Control into {{MEK}}/{{Erk-regulated}} Cell Proliferation and Migration}, |
|
| 1824 | + author = {Choudhury, Rajarshi and Roy, Sreerupa Ghose and Tsai, Yihsuan S. and Tripathy, Ashutosh and Graves, Lee M. and Wang, Zefeng}, |
|
| 1825 | + date = {2014-01-23}, |
|
| 1826 | + journaltitle = {Nature Communications}, |
|
| 1827 | + volume = {5}, |
|
| 1828 | + pages = {3078}, |
|
| 1829 | + issn = {2041-1723}, |
|
| 1830 | + doi = {10.1038/ncomms4078}, |
|
| 1831 | + url = {https://www.nature.com/articles/ncomms4078}, |
|
| 1832 | + urldate = {2018-08-23}, |
|
| 1833 | + abstract = {Alternative splicing of pre-messenger RNA (mRNA) is a critical stage of gene regulation in response to environmental stimuli. Here we show that DAZAP1, an RNA-binding protein involved in mammalian development and spermatogenesis, promotes inclusion of weak exons through specific recognition of diverse cis-elements. The carboxy-terminal proline-rich domain of DAZAP1 interacts with and neutralizes general splicing inhibitors, and is sufficient to activate splicing when recruited to pre-mRNA. This domain is phosphorylated by the MEK/Erk (extracellular signal-regulated protein kinase) pathway and this modification is essential for the splicing regulatory activity and the nuclear/cytoplasmic translocation of DAZAP1. Using mRNA-seq, we identify endogenous splicing events regulated by DAZAP1, many of which are involved in maintaining cell growth. Knockdown or over-expression of DAZAP1 causes a cell proliferation defect. Taken together, these studies reveal a molecular mechanism that integrates splicing control into MEK/Erk-regulated cell proliferation.}, |
|
| 1834 | + langid = {english}, |
|
| 1835 | + file = {/Users/rmorin/Zotero/storage/ZFUNFBRS/ncomms4078.html} |
|
| 1836 | +} |
|
| 1837 | + |
|
| 1838 | +@article{chouHnRNPComponentSplicing1999, |
|
| 1839 | + title = {{{hnRNP H}} Is a Component of a Splicing Enhancer Complex That Activates a C-Src Alternative Exon in Neuronal Cells}, |
|
| 1840 | + author = {Chou, M. Y. and Rooke, N. and Turck, C. W. and Black, D. L.}, |
|
| 1841 | + date = {1999-01}, |
|
| 1842 | + journaltitle = {Molecular and Cellular Biology}, |
|
| 1843 | + shortjournal = {Mol Cell Biol}, |
|
| 1844 | + volume = {19}, |
|
| 1845 | + number = {1}, |
|
| 1846 | + eprint = {9858532}, |
|
| 1847 | + eprinttype = {pmid}, |
|
| 1848 | + pages = {69--77}, |
|
| 1849 | + issn = {0270-7306}, |
|
| 1850 | + doi = {10.1128/MCB.19.1.69}, |
|
| 1851 | + abstract = {The regulation of the c-src N1 exon is mediated by an intronic splicing enhancer downstream of the N1 5' splice site. Previous experiments showed that a set of proteins assembles onto the most conserved core of this enhancer sequence specifically in neuronal WERI-1 cell extracts. The most prominent components of this enhancer complex are the proteins hnRNP F, KSRP, and an unidentified protein of 58 kDa (p58). This p58 protein was purified from the WERI-1 cell nuclear extract by ammonium sulfate precipitation, Mono Q chromatography, and immunoprecipitation with anti-Sm antibody Y12. Peptide sequence analysis of purified p58 protein identified it as hnRNP H. Immunoprecipitation of hnRNP H cross-linked to the N1 enhancer RNA, as well as gel mobility shift analysis of the enhancer complex in the presence of hnRNP H-specific antibodies, confirmed that hnRNP H is a protein component of the splicing enhancer complex. Immunoprecipitation of splicing intermediates from in vitro splicing reactions with anti-hnRNP H antibody indicated that hnRNP H remains bound to the src pre-mRNA after the assembly of spliceosome. Partial immunodepletion of hnRNP H from the nuclear extract partially inactivated the splicing of the N1 exon in vitro. This inhibition of splicing can be restored by the addition of recombinant hnRNP H, indicating that hnRNP H is an important factor for N1 splicing. Finally, in vitro binding assays demonstrate that hnRNP H can interact with the related protein hnRNP F, suggesting that hnRNPs H and F may exist as a heterodimer in a single enhancer complex. These two proteins presumably cooperate with each other and with other enhancer complex proteins to direct splicing to the N1 exon upstream.}, |
|
| 1852 | + langid = {english}, |
|
| 1853 | + pmcid = {PMC83866}, |
|
| 1854 | + keywords = {Alternative Splicing,Dimerization,Enhancer Elements Genetic,Exons,Gene Expression Regulation,HeLa Cells,Heterogeneous-Nuclear Ribonucleoprotein Group F-H,Heterogeneous-Nuclear Ribonucleoproteins,Humans,Neurons,Proto-Oncogene Proteins pp60(c-src),Ribonucleoproteins,RNA Precursors,Spliceosomes} |
|
| 1855 | +} |
|
| 1856 | + |
|
| 1857 | +@article{chunGenomeWideProfilesExtracranial2016, |
|
| 1858 | + title = {Genome-{{Wide Profiles}} of {{Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity}} and {{Dysregulated Developmental Pathways}}}, |
|
| 1859 | + author = {Chun, Hye-Jung E. and Lim, Emilia L. and Heravi-Moussavi, Alireza and Saberi, Saeed and Mungall, Karen L. and Bilenky, Mikhail and Carles, Annaick and Tse, Kane and Shlafman, Inna and Zhu, Kelsey and Qian, Jenny Q. and Palmquist, Diana L. and He, An and Long, William and Goya, Rodrigo and Ng, Michelle and LeBlanc, Veronique G. and Pleasance, Erin and Thiessen, Nina and Wong, Tina and Chuah, Eric and Zhao, Yong-Jun and Schein, Jacquie E. and Gerhard, Daniela S. and Taylor, Michael D. and Mungall, Andrew J. and Moore, Richard A. and Ma, Yussanne and Jones, Steven J. M. and Perlman, Elizabeth J. and Hirst, Martin and Marra, Marco A.}, |
|
| 1860 | + date = {2016-03-14}, |
|
| 1861 | + journaltitle = {Cancer Cell}, |
|
| 1862 | + shortjournal = {Cancer Cell}, |
|
| 1863 | + volume = {29}, |
|
| 1864 | + number = {3}, |
|
| 1865 | + eprint = {26977886}, |
|
| 1866 | + eprinttype = {pmid}, |
|
| 1867 | + pages = {394--406}, |
|
| 1868 | + publisher = {Elsevier}, |
|
| 1869 | + issn = {1535-6108, 1878-3686}, |
|
| 1870 | + doi = {10.1016/j.ccell.2016.02.009}, |
|
| 1871 | + url = {https://www.cell.com/cancer-cell/abstract/S1535-6108(16)30043-5}, |
|
| 1872 | + urldate = {2022-11-23}, |
|
| 1873 | + langid = {english}, |
|
| 1874 | + file = {/Users/rmorin/Zotero/storage/74K8UW9A/Chun et al. - 2016 - Genome-Wide Profiles of Extra-cranial Malignant Rh.pdf;/Users/rmorin/Zotero/storage/544HS26X/S1535-6108(16)30043-5.html} |
|
| 1875 | +} |
|
| 1876 | + |
|
| 1877 | +@article{chungSetNovelConserved1986, |
|
| 1878 | + title = {Set of Novel, Conserved Proteins Fold Pre-Messenger {{RNA}} into Ribonucleosomes}, |
|
| 1879 | + author = {Chung, Su Yun and Wooley, John}, |
|
| 1880 | + date = {1986}, |
|
| 1881 | + journaltitle = {Proteins: Structure, Function, and Bioinformatics}, |
|
| 1882 | + volume = {1}, |
|
| 1883 | + number = {3}, |
|
| 1884 | + pages = {195--210}, |
|
| 1885 | + issn = {1097-0134}, |
|
| 1886 | + doi = {10.1002/prot.340010302}, |
|
| 1887 | + url = {http://onlinelibrary.wiley.com/doi/abs/10.1002/prot.340010302}, |
|
| 1888 | + urldate = {2022-10-06}, |
|
| 1889 | + langid = {english}, |
|
| 1890 | + keywords = {multiple binding sites,oligomeric assembly,protein domains,RNA splicing,RNP core proteins}, |
|
| 1891 | + file = {/Users/rmorin/Zotero/storage/Z2PGHXJ7/prot.html} |
|
| 1892 | +} |
|
| 1893 | + |
|
| 1894 | +@article{ciborowskiNovelClassII2017, |
|
| 1895 | + title = {Novel Class {{II}} Alpha {{MHC}} Variability in a Small Peripheral {{Atlantic}} Salmon Population}, |
|
| 1896 | + author = {Ciborowski, Kate L. and Jordan, William C. and García de Leániz, Carlos and Consuegra, Sofia}, |
|
| 1897 | + date = {2017-06}, |
|
| 1898 | + journaltitle = {Animal Genetics}, |
|
| 1899 | + shortjournal = {Anim. Genet.}, |
|
| 1900 | + volume = {48}, |
|
| 1901 | + number = {3}, |
|
| 1902 | + eprint = {28116806}, |
|
| 1903 | + eprinttype = {pmid}, |
|
| 1904 | + pages = {370--372}, |
|
| 1905 | + issn = {1365-2052}, |
|
| 1906 | + doi = {10.1111/age.12535}, |
|
| 1907 | + langid = {english}, |
|
| 1908 | + keywords = {Amino Acid Sequence,Animals,Genes MHC Class II,Genetic Variation,Genetics Population,Salmo salar} |
|
| 1909 | +} |
|
| 1910 | + |
|
| 1911 | +@article{cifuentesZC3H12AMCPIP1Molecular2010, |
|
| 1912 | + title = {{{ZC3H12A}} ({{MCPIP1}}): {{Molecular}} Characteristics and Clinical Implications}, |
|
| 1913 | + author = {Cifuentes, Ricardo A and Cruz-Tapias, Paola and Rojas-Villarraga, Adriana and Anaya, Juan-Manuel}, |
|
| 1914 | + date = {2010-12}, |
|
| 1915 | + journaltitle = {Clinica Chimica Acta}, |
|
| 1916 | + volume = {411}, |
|
| 1917 | + number = {23-24}, |
|
| 1918 | + pages = {1862--1868}, |
|
| 1919 | + keywords = {nosource} |
|
| 1920 | +} |
|
| 1921 | + |
|
| 1922 | +@article{colganMechanismRegulationMRNA1997, |
|
| 1923 | + title = {Mechanism and Regulation of {{mRNA}} Polyadenylation}, |
|
| 1924 | + author = {Colgan, Diana F. and Manley, James L.}, |
|
| 1925 | + date = {1997-01-11}, |
|
| 1926 | + journaltitle = {Genes \& Development}, |
|
| 1927 | + shortjournal = {Genes Dev.}, |
|
| 1928 | + volume = {11}, |
|
| 1929 | + number = {21}, |
|
| 1930 | + eprint = {9353246}, |
|
| 1931 | + eprinttype = {pmid}, |
|
| 1932 | + pages = {2755--2766}, |
|
| 1933 | + publisher = {Cold Spring Harbor Lab}, |
|
| 1934 | + issn = {0890-9369, 1549-5477}, |
|
| 1935 | + doi = {10.1101/gad.11.21.2755}, |
|
| 1936 | + url = {http://genesdev.cshlp.org/content/11/21/2755}, |
|
| 1937 | + urldate = {2022-10-06}, |
|
| 1938 | + abstract = {A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields}, |
|
| 1939 | + langid = {english}, |
|
| 1940 | + file = {/Users/rmorin/Zotero/storage/GLAGQUL8/Colgan and Manley - 1997 - Mechanism and regulation of mRNA polyadenylation.pdf;/Users/rmorin/Zotero/storage/HSIWISCC/2755.html} |
|
| 1941 | +} |
|
| 1942 | + |
|
| 1943 | +@article{compagnoMutationsMultipleGenes2009a, |
|
| 1944 | + title = {Mutations of Multiple Genes Cause Deregulation of {{NF-kappaB}} in Diffuse Large {{B-cell}} Lymphoma}, |
|
| 1945 | + author = {Compagno, Mara and Lim, Wei Keat and Grunn, Adina and Nandula, Subhadra V. and Brahmachary, Manisha and Shen, Qiong and Bertoni, Francesco and Ponzoni, Maurilio and Scandurra, Marta and Califano, Andrea and Bhagat, Govind and Chadburn, Amy and Dalla-Favera, Riccardo and Pasqualucci, Laura}, |
|
| 1946 | + date = {2009-06-04}, |
|
| 1947 | + journaltitle = {Nature}, |
|
| 1948 | + shortjournal = {Nature}, |
|
| 1949 | + volume = {459}, |
|
| 1950 | + number = {7247}, |
|
| 1951 | + eprint = {19412164}, |
|
| 1952 | + eprinttype = {pmid}, |
|
| 1953 | + pages = {717--721}, |
|
| 1954 | + issn = {1476-4687}, |
|
| 1955 | + doi = {10.1038/nature07968}, |
|
| 1956 | + abstract = {Diffuse large B-cell lymphoma (DLBCL), the most common form of lymphoma in adulthood, comprises multiple biologically and clinically distinct subtypes including germinal centre B-cell-like (GCB) and activated B-cell-like (ABC) DLBCL. Gene expression profile studies have shown that its most aggressive subtype, ABC-DLBCL, is associated with constitutive activation of the NF-kappaB transcription complex. However, except for a small fraction of cases, it remains unclear whether NF-kappaB activation in these tumours represents an intrinsic program of the tumour cell of origin or a pathogenetic event. Here we show that {$>$}50\% of ABC-DLBCL and a smaller fraction of GCB-DLBCL carry somatic mutations in multiple genes, including negative (TNFAIP3, also called A20) and positive (CARD11, TRAF2, TRAF5, MAP3K7 (TAK1) and TNFRSF11A (RANK)) regulators of NF-kappaB. Of these, the A20 gene, which encodes a ubiquitin-modifying enzyme involved in termination of NF-kappaB responses, is most commonly affected, with approximately 30\% of patients displaying biallelic inactivation by mutations and/or deletions. When reintroduced in cell lines carrying biallelic inactivation of the gene, A20 induced apoptosis and cell growth arrest, indicating a tumour suppressor role. Less frequently, missense mutations of TRAF2 and CARD11 produce molecules with significantly enhanced ability to activate NF-kappaB. Thus, our results demonstrate that NF-kappaB activation in DLBCL is caused by genetic lesions affecting multiple genes, the loss or activation of which may promote lymphomagenesis by leading to abnormally prolonged NF-kappaB responses.}, |
|
| 1957 | + langid = {english}, |
|
| 1958 | + pmcid = {PMC2973325}, |
|
| 1959 | + keywords = {Apoptosis,Cell Line Tumor,DNA-Binding Proteins,Gene Expression Regulation Neoplastic,Genes,Humans,Intracellular Signaling Peptides and Proteins,Lymphoma Large B-Cell Diffuse,Mutation,NF-kappa B,Nuclear Proteins,Tumor Necrosis Factor alpha-Induced Protein 3}, |
|
| 1960 | + file = {/Users/rmorin/Zotero/storage/VG8LPAPJ/Compagno et al. - 2009 - Mutations of multiple genes cause deregulation of .pdf} |
|
| 1961 | +} |
|
| 1962 | + |
|
| 1963 | +@article{cooperCellsHitClass2019, |
|
| 1964 | + title = {B {{Cells Hit}} a {{Class Ceiling}} in the {{Germinal Center}}}, |
|
| 1965 | + author = {Cooper, Lucy and Good-Jacobson, Kim L.}, |
|
| 1966 | + date = {2019-08-20}, |
|
| 1967 | + journaltitle = {Immunity}, |
|
| 1968 | + shortjournal = {Immunity}, |
|
| 1969 | + volume = {51}, |
|
| 1970 | + number = {2}, |
|
| 1971 | + eprint = {31433966}, |
|
| 1972 | + eprinttype = {pmid}, |
|
| 1973 | + pages = {206--208}, |
|
| 1974 | + publisher = {Elsevier}, |
|
| 1975 | + issn = {1074-7613}, |
|
| 1976 | + doi = {10.1016/j.immuni.2019.07.004}, |
|
| 1977 | + url = {https://www.cell.com/immunity/abstract/S1074-7613(19)30320-6}, |
|
| 1978 | + urldate = {2020-05-25}, |
|
| 1979 | + langid = {english}, |
|
| 1980 | + file = {/Users/rmorin/Zotero/storage/4WDY3V4E/cooper2019.pdf;/Users/rmorin/Zotero/storage/NAXL9EYC/S1074-7613(19)30320-6.html} |
|
| 1981 | +} |
|
| 1982 | + |
|
| 1983 | +@article{copie-bergmanMYCIGRearrangementsAre2015, |
|
| 1984 | + title = {{{MYC-IG}} Rearrangements Are Negative Predictors of Survival in {{DLBCL}} Patients Treated with Immunochemotherapy: A {{GELA}}/{{LYSA}} Study}, |
|
| 1985 | + shorttitle = {{{MYC-IG}} Rearrangements Are Negative Predictors of Survival in {{DLBCL}} Patients Treated with Immunochemotherapy}, |
|
| 1986 | + author = {Copie-Bergman, Christiane and Cuillière-Dartigues, Peggy and Baia, Maryse and Briere, Josette and Delarue, Richard and Canioni, Danielle and Salles, Gilles and Parrens, Marie and Belhadj, Karim and Fabiani, Bettina and Recher, Christian and Petrella, Tony and Ketterer, Nicolas and Peyrade, Frederic and Haioun, Corinne and Nagel, Inga and Siebert, Reiner and Jardin, Fabrice and Leroy, Karen and Jais, Jean-Philippe and Tilly, Herve and Molina, Thierry Jo and Gaulard, Philippe}, |
|
| 1987 | + date = {2015-11-26}, |
|
| 1988 | + journaltitle = {Blood}, |
|
| 1989 | + volume = {126}, |
|
| 1990 | + number = {22}, |
|
| 1991 | + eprint = {26373676}, |
|
| 1992 | + eprinttype = {pmid}, |
|
| 1993 | + pages = {2466--2474}, |
|
| 1994 | + issn = {0006-4971, 1528-0020}, |
|
| 1995 | + doi = {10.1182/blood-2015-05-647602}, |
|
| 1996 | + url = {http://www.bloodjournal.org/content/126/22/2466}, |
|
| 1997 | + urldate = {2019-07-15}, |
|
| 1998 | + abstract = {Diffuse large B-cell lymphoma (DLBCL) with MYC rearrangement (MYC-R) carries an unfavorable outcome. We explored the prognostic value of the MYC translocation partner gene in a series of MYC-R de novo DLBCL patients enrolled in first-line prospective clinical trials (Groupe d’Etudes des Lymphomes de l’Adulte/Lymphoma Study Association) and treated with rituximab-anthracycline–based chemotherapy. A total of 774 DLBCL cases characterized for cell of origin by the Hans classifier were analyzed using fluorescence in situ hybridization with BCL2, BCL6, MYC, immunoglobulin (IG)K, and IGL break-apart and IGH/MYC, IGK/MYC, and IGL/MYC fusion probes. MYC-R was observed in 51/574 (8.9\%) evaluable DLBCL cases. MYC-R cases were predominantly of the germinal center B-cell–like subtype 37/51 (74\%) with no distinctive morphologic and phenotypic features. Nineteen cases were MYC single-hit and 32 cases were MYC double-hit (MYC plus BCL2 and/or BCL6) DLBCL. MYC translocation partner was an IG gene in 24 cases (MYC-IG) and a non-IG gene (MYC-non-IG) in 26 of 50 evaluable cases. Noteworthy, MYC-IG patients had shorter overall survival (OS) (P = .0002) compared with MYC-negative patients, whereas no survival difference was observed between MYC-non-IG and MYC-negative patients. In multivariate analyses, MYC-IG predicted poor progression-free survival (P = .0051) and OS (P = .0006) independently from the International Prognostic Index and the Hans classifier. In conclusion, we show in this prospective randomized trial that the adverse prognostic impact of MYC-R is correlated to the MYC-IG translocation partner gene in DLBCL patients treated with immunochemotherapy. These results may have an important impact on the clinical management of DLBCL patients with MYC-R who should be routinely characterized according to MYC partner gene. These trials are individually registered at www.clinicaltrials.gov as \#NCT00144807, \#NCT01087424, \#NCT00169143, \#NCT00144755, \#NCT00140660, \#NCT00140595, and \#NCT00135499.}, |
|
| 1999 | + langid = {english}, |
|
| 2000 | + file = {/Users/rmorin/Zotero/storage/BKM25NKU/2466.html} |
|
| 2001 | +} |
|
| 2002 | + |
|
| 2003 | +@online{CopyNumberVariations, |
|
| 2004 | + title = {Copy Number Variations and Cancer | {{Genome Medicine}} | {{Full Text}}}, |
|
| 2005 | + url = {https://genomemedicine.biomedcentral.com/articles/10.1186/gm62}, |
|
| 2006 | + urldate = {2020-05-25}, |
|
| 2007 | + file = {/Users/rmorin/Zotero/storage/LHLMZVSV/gm62.html} |
|
| 2008 | +} |
|
| 2009 | + |
|
| 2010 | +@article{courtsRecurrentInactivationPRDM12008, |
|
| 2011 | + title = {Recurrent Inactivation of the {{PRDM1}} Gene in Primary Central Nervous System Lymphoma}, |
|
| 2012 | + author = {Courts, Cornelius and Montesinos-Rongen, Manuel and Brunn, Anna and Bug, Stefanie and Siemer, Dörte and Hans, Volkmar and Blümcke, Ingmar and Klapper, Wolfram and Schaller, Carlo and Wiestler, Otmar D. and Küppers, Ralf and Siebert, Reiner and Deckert, Martina}, |
|
| 2013 | + date = {2008-07}, |
|
| 2014 | + journaltitle = {Journal of Neuropathology and Experimental Neurology}, |
|
| 2015 | + shortjournal = {J Neuropathol Exp Neurol}, |
|
| 2016 | + volume = {67}, |
|
| 2017 | + number = {7}, |
|
| 2018 | + eprint = {18596541}, |
|
| 2019 | + eprinttype = {pmid}, |
|
| 2020 | + pages = {720--727}, |
|
| 2021 | + issn = {0022-3069}, |
|
| 2022 | + doi = {10.1097/NEN.0b013e31817dd02d}, |
|
| 2023 | + abstract = {Primary lymphomas of the CNS (PCNSLs) show molecular features of the late germinal center exit B-cell phenotype and are impaired in their terminal differentiation as indicated by a lack of immunoglobulin class switching. Because the positive regulatory domain I protein with ZNF domain (PRDM1/BLIMP1) is a master regulator of terminal B-cell differentiation into plasma cells, we investigated a series of 21 PCNSLs for the presence of mutations in the PRDM1 gene and alterations in the expression pattern of the PRDM1 protein. Direct sequencing of all coding exons of the PRDM1 gene identified deleterious mutations associated with abrogation of PRDM1 protein expression in 4 of 21 (19\%) PCNSLs. Thus, similar to systemic diffuse large B-cell lymphomas, PRDM1 may be a tumor suppressor in some PCNSL and contribute to lymphomagenesis by impairing terminal differentiation.}, |
|
| 2024 | + langid = {english}, |
|
| 2025 | + keywords = {Adult,Aged,Aged 80 and over,Central Nervous System Neoplasms,DNA Mutational Analysis,Female,Gene Expression Regulation Neoplastic,Humans,Lymphoma B-Cell,Male,Middle Aged,Positive Regulatory Domain I-Binding Factor 1,Recurrence,Repressor Proteins,Sequence Deletion}, |
|
| 2026 | + file = {/Users/rmorin/Zotero/storage/NC9SUNH2/Courts et al. - 2008 - Recurrent inactivation of the PRDM1 gene in primar.pdf} |
|
| 2027 | +} |
|
| 2028 | + |
|
| 2029 | +@article{coyleSharedDistinctGenetic2022, |
|
| 2030 | + title = {Shared and Distinct Genetic Features in Human and Canine {{B-cell}} Lymphomas}, |
|
| 2031 | + author = {Coyle, Krysta Mila and Hillman, Tiana and Cheung, Matthew and Grande, Bruno M. and Bushell, Kevin R. and Arthur, Sarah E. and Alcaide, Miguel and Thomas, Nicole and Dreval, Kostiantyn and Wong, Stephanie and Campbell, Krishanna and Morin, Ryan D.}, |
|
| 2032 | + date = {2022-06-14}, |
|
| 2033 | + journaltitle = {Blood Advances}, |
|
| 2034 | + shortjournal = {Blood Adv}, |
|
| 2035 | + volume = {6}, |
|
| 2036 | + number = {11}, |
|
| 2037 | + eprint = {35359007}, |
|
| 2038 | + eprinttype = {pmid}, |
|
| 2039 | + pages = {3404--3409}, |
|
| 2040 | + issn = {2473-9537}, |
|
| 2041 | + doi = {10.1182/bloodadvances.2021006429}, |
|
| 2042 | + langid = {english}, |
|
| 2043 | + pmcid = {PMC9198934}, |
|
| 2044 | + keywords = {Animals,Dogs,Humans,Lymphoma B-Cell,Lymphoma T-Cell,Morinlab}, |
|
| 2045 | + file = {/Users/rmorin/Zotero/storage/RF8ECIAE/Coyle et al. - 2022 - Shared and distinct genetic features in human and .pdf} |
|
| 2046 | +} |
|
| 2047 | + |
|
| 2048 | +@article{crumpRandomizedComparisonGemcitabine2014, |
|
| 2049 | + title = {Randomized Comparison of Gemcitabine, Dexamethasone, and Cisplatin versus Dexamethasone, Cytarabine, and Cisplatin Chemotherapy before Autologous Stem-Cell Transplantation for Relapsed and Refractory Aggressive Lymphomas: {{NCIC-CTG LY}}.12}, |
|
| 2050 | + shorttitle = {Randomized Comparison of Gemcitabine, Dexamethasone, and Cisplatin versus Dexamethasone, Cytarabine, and Cisplatin Chemotherapy before Autologous Stem-Cell Transplantation for Relapsed and Refractory Aggressive Lymphomas}, |
|
| 2051 | + author = {Crump, Michael and Kuruvilla, John and Couban, Stephen and MacDonald, David A. and Kukreti, Vishal and Kouroukis, C. Tom and Rubinger, Morel and Buckstein, Rena and Imrie, Kevin R. and Federico, Massimo and Di Renzo, Nicola and Howson-Jan, Kang and Baetz, Tara and Kaizer, Leonard and Voralia, Michael and Olney, Harold J. and Turner, A. Robert and Sussman, Jonathan and Hay, Annette E. and Djurfeldt, Marina S. and Meyer, Ralph M. and Chen, Bingshu E. and Shepherd, Lois E.}, |
|
| 2052 | + date = {2014-11-01}, |
|
| 2053 | + journaltitle = {Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology}, |
|
| 2054 | + shortjournal = {J Clin Oncol}, |
|
| 2055 | + volume = {32}, |
|
| 2056 | + number = {31}, |
|
| 2057 | + eprint = {25267740}, |
|
| 2058 | + eprinttype = {pmid}, |
|
| 2059 | + pages = {3490--3496}, |
|
| 2060 | + issn = {1527-7755}, |
|
| 2061 | + doi = {10.1200/JCO.2013.53.9593}, |
|
| 2062 | + abstract = {PURPOSE: For patients with relapsed or refractory aggressive lymphoma, we hypothesized that gemcitabine-based therapy before autologous stem-cell transplantation (ASCT) is as effective as and less toxic than standard treatment. PATIENTS AND METHODS: We randomly assigned 619 patients with relapsed/refractory aggressive lymphoma to treatment with gemcitabine, dexamethasone, and cisplatin (GDP) or to dexamethasone, cytarabine, and cisplatin (DHAP). Patients with B-cell lymphoma also received rituximab. Responding patients proceeded to stem-cell collection and ASCT. Coprimary end points were response rate after two treatment cycles and transplantation rate. The noninferiority margin for the response rate to GDP relative to DHAP was set at 10\%. Secondary end points included event-free and overall survival, treatment toxicity, and quality of life. RESULTS: For the intention-to-treat population, the response rate with GDP was 45.2\%; with DHAP the response rate was 44.0\% (95\% CI for difference, -9.0\% to 6.7\%), meeting protocol-defined criteria for noninferiority of GDP (P = .005). Similar results were obtained in a per-protocol analysis. The transplantation rates were 52.1\% with GDP and 49.3\% with DHAP (P = .44). At a median follow-up of 53 months, no differences were detected in event-free survival (HR, 0.99; stratified log-rank P = .95) or overall survival (HR, 1.03; P = .78) between GDP and DHAP. Treatment with GDP was associated with less toxicity (P {$<$} .001) and need for hospitalization (P {$<$} .001), and preserved quality of life (P = .04). CONCLUSION: For patients with relapsed or refractory aggressive lymphoma, in comparison with DHAP, treatment with GDP is associated with a noninferior response rate, similar transplantation rate, event-free survival, and overall survival, less toxicity and hospitalization, and superior quality of life.}, |
|
| 2063 | + langid = {english}, |
|
| 2064 | + keywords = {Adolescent,Adult,Aged,Antineoplastic Combined Chemotherapy Protocols,Cisplatin,Cytarabine,Deoxycytidine,Dexamethasone,Female,Hematopoietic Stem Cell Transplantation,Humans,Lymphoma,Male,Middle Aged,Quality of Life,Survival Rate,Transplantation Autologous,Treatment Outcome}, |
|
| 2065 | + file = {/Users/rmorin/Zotero/storage/BJIGNMSC/Crump et al. - 2014 - Randomized comparison of gemcitabine, dexamethason.pdf} |
|
| 2066 | +} |
|
| 2067 | + |
|
| 2068 | +@article{curryPrognosticImpactCREL2009, |
|
| 2069 | + title = {Prognostic Impact of {{C-REL}} Expression in Diffuse Large {{B-cell}} Lymphoma}, |
|
| 2070 | + author = {Curry, Choladda and Ewton, April and Olsen, Randall and Logan, Brent and Preti, Hector and Liu, Yao-Chang and Perkins, Sherrie and Chang, Chung-Che}, |
|
| 2071 | + date = {2009}, |
|
| 2072 | + journaltitle = {Journal of Hematopathology}, |
|
| 2073 | + volume = {2}, |
|
| 2074 | + number = {1}, |
|
| 2075 | + pages = {20--26}, |
|
| 2076 | + keywords = {nosource} |
|
| 2077 | +} |
|
| 2078 | + |
|
| 2079 | +@article{daiCharacterizationMouseDazap12001, |
|
| 2080 | + title = {Characterization of the Mouse {{Dazap1}} Gene Encoding an {{RNA-binding}} Protein That Interacts with Infertility Factors {{DAZ}} and {{DAZL}}}, |
|
| 2081 | + author = {Dai, Tiane and Vera, Yanira and Salido, Eduardo C and Yen, Pauline H}, |
|
| 2082 | + date = {2001-09-26}, |
|
| 2083 | + journaltitle = {BMC Genomics}, |
|
| 2084 | + shortjournal = {BMC Genomics}, |
|
| 2085 | + volume = {2}, |
|
| 2086 | + eprint = {11604102}, |
|
| 2087 | + eprinttype = {pmid}, |
|
| 2088 | + pages = {6}, |
|
| 2089 | + issn = {1471-2164}, |
|
| 2090 | + doi = {10.1186/1471-2164-2-6}, |
|
| 2091 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC57980/}, |
|
| 2092 | + urldate = {2018-08-23}, |
|
| 2093 | + abstract = {Background DAZAP1 (DAZ Associated Protein 1) was originally identified by a yeast two-hybrid system through its interaction with a putative male infertility factor, DAZ (Deleted in Azoospermia). In vitro, DAZAP1 interacts with both the Y chromosome-encoded DAZ and an autosome-encoded DAZ-like protein, DAZL. DAZAP1 contains two RNA-binding domains (RBDs) and a proline-rich C-terminal portion, and is expressed most abundantly in the testis. To understand the biological function of DAZAP1 and the significance of its interaction with DAZ and DAZL, we isolated and characterized the mouse Dazap1 gene, and studied its expression and the subcellular localization of its protein product. Results The human and mouse genes have similar genomic structures and map to syntenic chromosomal regions. The mouse and human DAZAP1 proteins share 98\% identity and their sequences are highly similar to the Xenopus orthologue Prrp, especially in the RBDs. Dazap1 is expressed throughout testis development. Western blot detects a single 45 kD DAZAP1 protein that is most abundant in the testis. Although a majority of DAZAP1 is present in the cytoplasmic fraction, they are not associated with polyribosomes. Conclusions DAZAP1 is evolutionarily highly conserved. Its predominant expression in testes suggests a role in spermatogenesis. Its subcellular localization indicates that it is not directly involved in mRNA translation.}, |
|
| 2094 | + pmcid = {PMC57980} |
|
| 2095 | +} |
|
| 2096 | + |
|
| 2097 | +@article{daiGenomicLandscapePrimary2015, |
|
| 2098 | + title = {Genomic {{Landscape}} of {{Primary Mediastinal B-Cell Lymphoma Cell Lines}}}, |
|
| 2099 | + author = {Dai, Haiping and Ehrentraut, Stefan and Nagel, Stefan and Eberth, Sonja and Pommerenke, Claudia and Dirks, Wilhelm G. and Geffers, Robert and Kalavalapalli, Srilaxmi and Kaufmann, Maren and Meyer, Corrina and Faehnrich, Silke and Chen, Suning and Drexler, Hans G. and MacLeod, Roderick A. F.}, |
|
| 2100 | + date = {2015}, |
|
| 2101 | + journaltitle = {PloS One}, |
|
| 2102 | + shortjournal = {PLoS One}, |
|
| 2103 | + volume = {10}, |
|
| 2104 | + number = {11}, |
|
| 2105 | + eprint = {26599546}, |
|
| 2106 | + eprinttype = {pmid}, |
|
| 2107 | + pages = {e0139663}, |
|
| 2108 | + issn = {1932-6203}, |
|
| 2109 | + doi = {10.1371/journal.pone.0139663}, |
|
| 2110 | + abstract = {Primary mediastinal B-Cell lymphoma (PMBL) is a recently defined entity comprising \textasciitilde 2-10\% non-Hodgkin lymphomas (NHL). Unlike most NHL subtypes, PMBL lacks recurrent gene rearrangements to serve as biomarkers or betray target genes. While druggable, late chemotherapeutic complications warrant the search for new targets and models. Well characterized tumor cell lines provide unlimited material to serve as preclinical resources for verifiable analyses directed at the discovery of new biomarkers and pathological targets using high throughput microarray technologies. The same cells may then be used to seek intelligent therapies directed at clinically validated targets. Four cell lines have emerged as potential PMBL models: FARAGE, KARPAS-1106P, MEDB-1 and U-2940. Transcriptionally, PMBL cell lines cluster near c(lassical)-HL and B-NHL examples showing they are related but separate entities. Here we document genomic alterations therein, by cytogenetics and high density oligonucleotide/SNP microarrays and parse their impact by integrated global expression profiling. PMBL cell lines were distinguished by moderate chromosome rearrangement levels undercutting cHL, while lacking oncogene translocations seen in B-NHL. In total 61 deletions were shared by two or more cell lines, together with 12 amplifications (≥4x) and 72 homozygous regions. Integrated genomic and transcriptional profiling showed deletions to be the most important class of chromosome rearrangement. Lesions were mapped to several loci associated with PMBL, e.g. 2p15 (REL/COMMD1), 9p24 (JAK2, CD274), 16p13 (SOCS1, LITAF, CIITA); plus new or tenuously associated loci: 2p16 (MSH6), 6q23 (TNFAIP3), 9p22 (CDKN2A/B), 20p12 (PTPN1). Discrete homozygous regions sometimes substituted focal deletions accompanied by gene silencing implying a role for epigenetic or mutational inactivation. Genomic amplifications increasing gene expression or gene-activating rearrangements were respectively rare or absent. Our findings highlight biallelic deletions as a major class of chromosomal lesion in PMBL cell lines, while endorsing the latter as preclinical models for hunting and testing new biomarkers and actionable targets.}, |
|
| 2111 | + langid = {english}, |
|
| 2112 | + pmcid = {PMC4657880}, |
|
| 2113 | + keywords = {Aged,Cell Line Tumor,Cluster Analysis,Comparative Genomic Hybridization,Cytogenetic Analysis,DNA Copy Number Variations,Female,Gene Expression Profiling,Gene Expression Regulation Neoplastic,Genetic Loci,Genome Human,Humans,In Situ Hybridization Fluorescence,Loss of Heterozygosity,Lymphoma B-Cell,Mediastinal Neoplasms,Polymorphism Single Nucleotide,Principal Component Analysis,Spectral Karyotyping,Transcription Genetic}, |
|
| 2114 | + file = {/Users/rmorin/Zotero/storage/FNDNDS7W/Dai et al. - 2015 - Genomic Landscape of Primary Mediastinal B-Cell Ly.pdf} |
|
| 2115 | +} |
|
| 2116 | + |
|
| 2117 | +@article{davidHnRNPProteinsControlled2010, |
|
| 2118 | + title = {{{HnRNP}} Proteins Controlled by C-{{Myc}} Deregulate Pyruvate Kinase {{mRNA}} Splicing in Cancer}, |
|
| 2119 | + author = {David, Charles J. and Chen, Mo and Assanah, Marcela and Canoll, Peter and Manley, James L.}, |
|
| 2120 | + date = {2010-01}, |
|
| 2121 | + journaltitle = {Nature}, |
|
| 2122 | + volume = {463}, |
|
| 2123 | + number = {7279}, |
|
| 2124 | + pages = {364--368}, |
|
| 2125 | + publisher = {Nature Publishing Group}, |
|
| 2126 | + issn = {1476-4687}, |
|
| 2127 | + doi = {10.1038/nature08697}, |
|
| 2128 | + url = {https://www.nature.com/articles/nature08697}, |
|
| 2129 | + urldate = {2022-10-06}, |
|
| 2130 | + abstract = {Cancer cells avidly take up glucose and convert it to lactate while eschewing oxidative phosphorylation. This phenomenon is critical for maximal tumorigenicity, and is in part explained by the almost universal reversion of tumours to the embryonic form of pyruvate kinase, PKM2. Here, David et al. now show that aberrant expression of the splicing factors PTB, hnRNPA1 and hnRNPA2, which are themselves regulated by the c-Myc oncogene, is responsible for the PKM1 to PKM2 switch in cancer. This work adds to our understanding of alternative splicing and its role in cancer cell growth.}, |
|
| 2131 | + issue = {7279}, |
|
| 2132 | + langid = {english}, |
|
| 2133 | + keywords = {Humanities and Social Sciences,multidisciplinary,Science}, |
|
| 2134 | + file = {/Users/rmorin/Zotero/storage/2J6EABN8/David et al. - 2010 - HnRNP proteins controlled by c-Myc deregulate pyru.pdf;/Users/rmorin/Zotero/storage/4KEINIXX/nature08697.html} |
|
| 2135 | +} |
|
| 2136 | + |
|
| 2137 | +@article{daviesComparisonMHGDZsig2023, |
|
| 2138 | + title = {Comparison of {{MHG}} and {{DZsig}} Reveals Shared Biology and a Core Overlap Group with Inferior Prognosis in {{DLBCL}}}, |
|
| 2139 | + author = {Davies, John R. and Hilton, Laura K. and Jiang, Aixiang and Barrans, Sharon and Burton, Catherine and Johnson, Peter W. M. and Davies, Andrew J. and Du, Ming-Qing and Tooze, Reuben and Cucco, Francesco and Care, Matthew A. and Morin, Ryan D. and Steidl, Christian and Sha, Chulin and Westhead, David R. and Scott, David W.}, |
|
| 2140 | + date = {2023-10-24}, |
|
| 2141 | + journaltitle = {Blood Advances}, |
|
| 2142 | + shortjournal = {Blood Advances}, |
|
| 2143 | + volume = {7}, |
|
| 2144 | + number = {20}, |
|
| 2145 | + pages = {6156--6162}, |
|
| 2146 | + issn = {2473-9529}, |
|
| 2147 | + doi = {10.1182/bloodadvances.2023010673}, |
|
| 2148 | + url = {https://doi.org/10.1182/bloodadvances.2023010673}, |
|
| 2149 | + urldate = {2023-10-17}, |
|
| 2150 | + abstract = {TO THE EDITOR:Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous disease identified by morphology, immunophenotype, and a typically aggressive clinical course.1 DLBCL has long been stratified based on gene expression profiling (GEP) into activated B-cell–like (ABC) and germinal center B-cell–like (GCB) cell-of-origin (COO) subtypes.2 Recently, several studies stratified DLBCL into genetic subgroups based on the co-occurrence of mutational features with strong associations with COO.3-6 Previously, our 2 groups independently reported gene expression signatures associated with dark-zone–like biology in DLBCL. The molecular high-grade signature (MHG) identifies DLBCLs expressing a Burkitt lymphoma (BL)-like GEP signature,7 whereas the double-hit signature (since renamed dark-zone signature [DZsig]8) identifies DLBCLs with a GEP signature like high-grade B-cell lymphoma with MYC and BCL2 rearrangement (HGBCL-DH-BCL2) (whether the tumors harbor MYC and BCL2 rearrangements or not).9,10 Remarkably, despite the small overlap in the genes that comprise each signature, both classifiers identified a subset of DLBCL tumors enriched for certain genetic aberrations, including concomitant MYC and BCL2 rearrangements.7,9}, |
|
| 2151 | + file = {/Users/rmorin/Zotero/storage/7EEYEALH/Davies et al. - 2023 - Comparison of MHG and DZsig reveals shared biology.pdf;/Users/rmorin/Zotero/storage/JLZMMTJG/Comparison-of-MHG-and-DZsig-reveals-shared-biology.html} |
|
| 2152 | +} |
|
| 2153 | + |
|
| 2154 | +@article{davisChronicActiveBcellreceptor2010, |
|
| 2155 | + title = {Chronic Active {{B-cell-receptor}} Signalling in Diffuse Large {{B-cell}} Lymphoma}, |
|
| 2156 | + author = {Davis, R Eric and Ngo, Vu N and Lenz, Georg and Tolar, Pavel and Young, Ryan M and Romesser, Paul B and Kohlhammer, Holger and Lamy, Laurence and Zhao, Hong and Yang, Yandan and Xu, Weihong and Shaffer, Arthur L and Wright, George and Xiao, Wenming and Powell, John and Jiang, Jian-Kang and Thomas, Craig J and Rosenwald, Andreas and Ott, German and Müller-Hermelink, Hans-Konrad and Gascoyne, Randy D and Connors, Joseph M and Johnson, Nathalie A and Rimsza, Lisa M and Campo, Elias and Jaffe, Elaine S and Wilson, Wyndham H and Delabie, Jan and Smeland, Erlend B and Fisher, Richard I and Braziel, Rita M and Tubbs, Raymond R and Cook, J R and Weisenburger, Dennis D and Chan, Wing C and Pierce, Susan K and Staudt, Louis M}, |
|
| 2157 | + date = {2010-01}, |
|
| 2158 | + journaltitle = {Nature}, |
|
| 2159 | + volume = {463}, |
|
| 2160 | + number = {7277}, |
|
| 2161 | + pages = {88--92}, |
|
| 2162 | + keywords = {nosource} |
|
| 2163 | +} |
|
| 2164 | + |
|
| 2165 | +@article{davisConstitutiveNuclearFactor2001, |
|
| 2166 | + title = {Constitutive Nuclear Factor {{kappaB}} Activity Is Required for Survival of Activated {{B}} Cell-like Diffuse Large {{B}} Cell Lymphoma Cells}, |
|
| 2167 | + author = {Davis, R and Brown, K and Siebenlist, U and Staudt, L}, |
|
| 2168 | + date = {2001}, |
|
| 2169 | + journaltitle = {J Exp Med}, |
|
| 2170 | + volume = {194}, |
|
| 2171 | + number = {12}, |
|
| 2172 | + pages = {1861--1874}, |
|
| 2173 | + keywords = {nosource} |
|
| 2174 | +} |
|
| 2175 | + |
|
| 2176 | +@article{dawsonAnalysisCirculatingTumor2013, |
|
| 2177 | + title = {Analysis of {{Circulating Tumor DNA}} to {{Monitor Metastatic Breast Cancer}}.}, |
|
| 2178 | + author = {Dawson, Sarah-Jane and Tsui, Dana W Y and Murtaza, Muhammed and Biggs, Heather and Rueda, Oscar M and Chin, Suet-Feung and Dunning, Mark J and Gale, Davina and Forshew, Tim and Mahler-Araujo, Betania and Rajan, Sabrina and Humphray, Sean and Becq, Jennifer and Halsall, David and Wallis, Matthew and Bentley, David and Caldas, Carlos and Rosenfeld, Nitzan}, |
|
| 2179 | + date = {2013-03}, |
|
| 2180 | + journaltitle = {N Engl J Med}, |
|
| 2181 | + keywords = {nosource} |
|
| 2182 | +} |
|
| 2183 | + |
|
| 2184 | +@article{decorsiereEssentialRoleInteraction2011, |
|
| 2185 | + title = {Essential Role for the Interaction between {{hnRNP H}}/{{F}} and a {{G}} Quadruplex in Maintaining P53 Pre-{{mRNA}} 3′-End Processing and Function during {{DNA}} Damage}, |
|
| 2186 | + author = {Decorsière, Adrien and Cayrel, Anne and Vagner, Stéphan and Millevoi, Stefania}, |
|
| 2187 | + date = {2011-01-02}, |
|
| 2188 | + journaltitle = {Genes \& Development}, |
|
| 2189 | + shortjournal = {Genes Dev.}, |
|
| 2190 | + volume = {25}, |
|
| 2191 | + number = {3}, |
|
| 2192 | + eprint = {21289067}, |
|
| 2193 | + eprinttype = {pmid}, |
|
| 2194 | + pages = {220--225}, |
|
| 2195 | + publisher = {Cold Spring Harbor Lab}, |
|
| 2196 | + issn = {0890-9369, 1549-5477}, |
|
| 2197 | + doi = {10.1101/gad.607011}, |
|
| 2198 | + url = {http://genesdev.cshlp.org/content/25/3/220}, |
|
| 2199 | + urldate = {2022-09-28}, |
|
| 2200 | + abstract = {Following DNA damage, mRNA 3′-end formation is inhibited, contributing to repression of mRNA synthesis. Here we investigated how DNA-damaged cells accomplish p53 mRNA 3′-end formation when normal mechanisms of pre-mRNA 3′-end processing regulation are inhibited. The underlying mechanism involves the interaction between a G-quadruplex structure located downstream from the p53 cleavage site and hnRNP H/F. Importantly, this interaction is critical for p53 expression and contributes to p53-mediated apoptosis. Our results uncover the existence of a specific rescue mechanism of 3′-end processing regulation allowing stress-induced p53 accumulation and function in apoptosis.}, |
|
| 2201 | + langid = {english}, |
|
| 2202 | + keywords = {DNA damage,hnRNP F,hnRNP H,p53 tumor suppressor,polyadenylation,pre-mRNA 3′-end processing}, |
|
| 2203 | + file = {/Users/rmorin/Zotero/storage/BXKYTK6T/Decorsière et al. - 2011 - Essential role for the interaction between hnRNP H.pdf;/Users/rmorin/Zotero/storage/3GJN53GE/220.html} |
|
| 2204 | +} |
|
| 2205 | + |
|
| 2206 | +@article{deebMachineLearningbasedClassification, |
|
| 2207 | + title = {Machine {{Learning-based Classification}} of {{Diffuse Large B-cell Lymphoma Patients}} by {{Their Protein Expression Profiles}}}, |
|
| 2208 | + author = {Deeb, Sally J and Tyanova, Stefka and Hummel, Michael and Schmidt-Supprian, Marc and Cox, Juergen and Mann, Matthias}, |
|
| 2209 | + journaltitle = {Molecular \& Cellular Proteomics}, |
|
| 2210 | + volume = {14}, |
|
| 2211 | + number = {11}, |
|
| 2212 | + pages = {2947--2960}, |
|
| 2213 | + keywords = {nosource} |
|
| 2214 | +} |
|
| 2215 | + |
|
| 2216 | +@article{delgatto-konczakHnRNPA1Recruited1999, |
|
| 2217 | + title = {{{hnRNP A1 Recruited}} to an {{Exon In Vivo Can Function}} as an {{Exon Splicing Silencer}}}, |
|
| 2218 | + author = {Del Gatto-Konczak, Fabienne and Olive, Michelle and Gesnel, Marie-Claude and Breathnach, Richard}, |
|
| 2219 | + date = {1999-01}, |
|
| 2220 | + journaltitle = {Molecular and Cellular Biology}, |
|
| 2221 | + volume = {19}, |
|
| 2222 | + number = {1}, |
|
| 2223 | + pages = {251--260}, |
|
| 2224 | + publisher = {American Society for Microbiology}, |
|
| 2225 | + doi = {10.1128/MCB.19.1.251}, |
|
| 2226 | + url = {https://journals.asm.org/doi/full/10.1128/MCB.19.1.251}, |
|
| 2227 | + urldate = {2022-09-27}, |
|
| 2228 | + file = {/Users/rmorin/Zotero/storage/Z28YVWQT/Del Gatto-Konczak et al. - 1999 - hnRNP A1 Recruited to an Exon In Vivo Can Function.pdf} |
|
| 2229 | +} |
|
| 2230 | + |
|
| 2231 | +@article{dempseyG4DNABinding1999, |
|
| 2232 | + title = {G4 {{DNA}} Binding by {{LR1}} and Its Subunits, Nucleolin and {{hnRNP D}}, {{A}} Role for {{G-G}} Pairing in Immunoglobulin Switch Recombination}, |
|
| 2233 | + author = {Dempsey, L. A. and Sun, H. and Hanakahi, L. A. and Maizels, N.}, |
|
| 2234 | + date = {1999-01-08}, |
|
| 2235 | + journaltitle = {The Journal of Biological Chemistry}, |
|
| 2236 | + shortjournal = {J Biol Chem}, |
|
| 2237 | + volume = {274}, |
|
| 2238 | + number = {2}, |
|
| 2239 | + eprint = {9873052}, |
|
| 2240 | + eprinttype = {pmid}, |
|
| 2241 | + pages = {1066--1071}, |
|
| 2242 | + issn = {0021-9258}, |
|
| 2243 | + doi = {10.1074/jbc.274.2.1066}, |
|
| 2244 | + abstract = {The immunoglobulin heavy chain switch regions contain multiple runs of guanines on the top (nontemplate) DNA strand. Here we show that LR1, a B cell-specific, duplex DNA binding factor, binds tightly and specifically to synthetic oligonucleotides containing G-G base pairs (KD}, |
|
| 2245 | + langid = {english}, |
|
| 2246 | + keywords = {Antibodies,Base Sequence,DNA,DNA Primers,DNA-Binding Proteins,Heterogeneous-Nuclear Ribonucleoproteins,Immunoglobulin Switch Region,Phosphoproteins,Recombinant Proteins,Recombination Genetic,Ribonucleoproteins,RNA-Binding Proteins,Transcription Factors}, |
|
| 2247 | + file = {/Users/rmorin/Zotero/storage/YFWBE98V/Dempsey et al. - 1999 - G4 DNA binding by LR1 and its subunits, nucleolin .pdf} |
|
| 2248 | +} |
|
| 2249 | + |
|
| 2250 | +@article{deschGenotypingCirculatingTumor2020, |
|
| 2251 | + title = {Genotyping Circulating Tumor {{DNA}} of Pediatric {{Hodgkin}} Lymphoma}, |
|
| 2252 | + author = {Desch, Ann-Kathrin and Hartung, Kristin and Botzen, Ante and Brobeil, Alexander and Rummel, Mathias and Kurch, Lars and Georgi, Thomas and Jox, Theresa and Bielack, Stefan and Burdach, Stefan and Classen, Carl Friedrich and Claviez, Alexander and Debatin, Klaus-Michael and Ebinger, Martin and Eggert, Angelika and Faber, Jörg and Flotho, Christian and Frühwald, Michael and Graf, Norbert and Jorch, Norbert and Kontny, Udo and Kramm, Christof and Kulozik, Andreas and Kühr, Joachim and Sykora, Karl-Walter and Metzler, Markus and Müller, Hermann L. and Nathrath, Michaela and Nüßlein, Thomas and Paulussen, Michael and Pekrun, Arnulf and Reinhardt, Dirk and Reinhard, Harald and Rössig, Claudia and Sauerbrey, Axel and Schlegel, Paul-Gerhardt and Schneider, Dominik T. and Scheurlen, Wolfram and Schweigerer, Lothar and Simon, Thorsten and Suttorp, Meinolf and Vorwerk, Peter and Schmitz, Roland and Kluge, Regine and Mauz-Körholz, Christine and Körholz, Dieter and Gattenlöhner, Stefan and Bräuninger, Andreas}, |
|
| 2253 | + date = {2020-01}, |
|
| 2254 | + journaltitle = {Leukemia}, |
|
| 2255 | + shortjournal = {Leukemia}, |
|
| 2256 | + volume = {34}, |
|
| 2257 | + number = {1}, |
|
| 2258 | + eprint = {31431735}, |
|
| 2259 | + eprinttype = {pmid}, |
|
| 2260 | + pages = {151--166}, |
|
| 2261 | + issn = {1476-5551}, |
|
| 2262 | + doi = {10.1038/s41375-019-0541-6}, |
|
| 2263 | + abstract = {We used hybrid capture-targeted next-generation sequencing of circulating cell-free DNA (ccfDNA) of pediatric Hodgkin lymphoma (PHL) patients to determine pathogenic mechanisms and assess the clinical utility of this method. Hodgkin-Reed/Sternberg (HRS) cell-derived single nucleotide variants, insertions/deletions, translocations and VH-DH-JH rearrangements were detected in pretherapy ccfDNA of 72 of 96 patients. Number of variants per patient ranged from 1 to 21 with allele frequencies from 0.6 to 42\%. Nine translocation breakpoints were detected. Genes involved in JAK/STAT, NFkB and PI3K signaling and antigen presentation were most frequently affected. SOCS1 variants, mainly deletions, were found in most circulating tumor (ct) DNAs, and seven of the nine translocation breakpoints involved SOCS1. Analysis of VH-DH-JH rearrangements revealed an origin of PHL HRS cells from partially selected germinal center B cells. Amounts of pretherapy ctDNA were correlated with metabolic tumor volumes. Furthermore, in all ccfDNA samples of 43 patients with early response assessment quantitative qPET\,{$<$}\,3, indicative of a favorable clinical course, ctDNA was not detectable. In contrast, in five of six patients with qPET\,{$>$}\,3, indicative of an unfavorable clinical course, ctDNA remained detectable. ccfDNA analysis of PHL is thus a suitable approach to determine pathogenic mechanisms and monitor therapy response.}, |
|
| 2264 | + langid = {english}, |
|
| 2265 | + keywords = {Adolescent,Child,Child Preschool,Circulating Tumor DNA,Female,Genotype,Hodgkin Disease,Humans,Male} |
|
| 2266 | +} |
|
| 2267 | + |
|
| 2268 | +@article{desilvaDynamicsCellsGerminal2015, |
|
| 2269 | + title = {Dynamics of {{B}} Cells in Germinal Centres}, |
|
| 2270 | + author = {De Silva, Nilushi S. and Klein, Ulf}, |
|
| 2271 | + date = {2015-03}, |
|
| 2272 | + journaltitle = {Nature Reviews Immunology}, |
|
| 2273 | + shortjournal = {Nat Rev Immunol}, |
|
| 2274 | + volume = {15}, |
|
| 2275 | + number = {3}, |
|
| 2276 | + pages = {137--148}, |
|
| 2277 | + publisher = {Nature Publishing Group}, |
|
| 2278 | + issn = {1474-1741}, |
|
| 2279 | + doi = {10.1038/nri3804}, |
|
| 2280 | + url = {https://www.nature.com/articles/nri3804}, |
|
| 2281 | + urldate = {2022-10-06}, |
|
| 2282 | + abstract = {The germinal centre (GC) of lymphoid organs is the microenvironment in which antigen-activated B cells diversify their immunoglobulin genes by somatic hypermutation (SHM) to generate high-affinity antibodies. A subset of the cells also undergoes class-switch recombination to generate antibodies with specialized effector functions.Early in an immune response, antigen-stimulated B cells form long-lived interactions with antigen-specific T cells at the border between the B cell zone and the T cell zone or the interfollicular region to become fully activated. Antigen-activated B cells and T cells are committed to differentiate into GC B cells and T follicular helper cells (TFH cells), respectively, outside of the follicle. Migration into the follicle is facilitated by B cell lymphoma 6 (BCL-6), which is the master transcriptional regulator of GC B cells.One day after TFH cells have moved into the follicle, GC precursor B cells migrate from the border between the B cell zone and the T cell zone or the interfollicular region into the centre of the follicle to form an early GC. The B cells differentiate into blasts and, over the next several days, rapidly divide and begin to fill the centre of the follicle until they have formed a mature GC that is polarized into two microenvironments known as the dark and light zones.Dark zone B cells, which are GC B cells that undergo active SHM, are programmed to proliferate extremely rapidly and thereby to generate a large number of immunoglobulin mutations in a short time. Dark zone B cells differentiate into light zone B cells, at which stage mutants expressing high-affinity antibodies are selected and instructed to either recirculate to the dark zone to undergo further rounds of SHM or to differentiate into memory B cells or plasma cells.Light zone B cells capture antigen via the B cell receptor (BCR) and present the processed antigen on MHC complexes to TFH cells. Higher BCR affinity is directly associated with greater antigen capture and leads to a higher density of peptide–MHC complex presentation on the surface of the B cell. This results in the greatest share of T cell help, which in turn drives selection.Evidence suggests that the transcription factors MYC and the nuclear factor-κB subunit REL are essential for the maintenance of the GC reaction as they 'license' antigen-selected light zone B cells to recirculate to the dark zone. Inhibition of the terminal differentiation of GC B cells is controlled by multiple mechanisms that include both transcriptional and non-transcriptional regulation.}, |
|
| 2283 | + issue = {3}, |
|
| 2284 | + langid = {english}, |
|
| 2285 | + keywords = {Antibodies,B cells,Germinal centres}, |
|
| 2286 | + file = {/Users/rmorin/Zotero/storage/IU379QHA/De Silva and Klein - 2015 - Dynamics of B cells in germinal centres.pdf;/Users/rmorin/Zotero/storage/JZV583DS/nri3804.html} |
|
| 2287 | +} |
|
| 2288 | + |
|
| 2289 | +@article{DetectionDiffuseLarge2012, |
|
| 2290 | + title = {Detection of {{Diffuse Large B-cell Lymphoma}} in {{Peripheral Blood Using High-Throughput Sequencing Assay}}}, |
|
| 2291 | + date = {2012-12}, |
|
| 2292 | + pages = {1--1}, |
|
| 2293 | + keywords = {nosource} |
|
| 2294 | +} |
|
| 2295 | + |
|
| 2296 | +@article{diaz-munozDeletionAURichElements2015, |
|
| 2297 | + title = {Deletion of {{AU-Rich Elements}} within the {{Bcl2}} 3′{{UTR Reduces Protein Expression}} and {{B Cell Survival In Vivo}}}, |
|
| 2298 | + author = {Díaz-Muñoz, Manuel D. and Bell, Sarah E. and Turner, Martin}, |
|
| 2299 | + date = {2015-02-13}, |
|
| 2300 | + journaltitle = {PLOS ONE}, |
|
| 2301 | + shortjournal = {PLOS ONE}, |
|
| 2302 | + volume = {10}, |
|
| 2303 | + number = {2}, |
|
| 2304 | + pages = {e0116899}, |
|
| 2305 | + publisher = {Public Library of Science}, |
|
| 2306 | + issn = {1932-6203}, |
|
| 2307 | + doi = {10.1371/journal.pone.0116899}, |
|
| 2308 | + url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0116899}, |
|
| 2309 | + urldate = {2022-10-04}, |
|
| 2310 | + abstract = {Post-transcriptional mRNA regulation by RNA binding proteins (RBPs) associated with AU-rich elements (AREs) present in the 3′ untranslated region (3’UTR) of specific mRNAs modulates transcript stability and translation in eukaryotic cells. Here we have functionally characterised the importance of the AREs present within the Bcl2 3’UTR in order to maintain Bcl2 expression. Gene targeting deletion of 300 nucleotides of the Bcl2 3’UTR rich in AREs diminishes Bcl2 mRNA stability and protein levels in primary B cells, decreasing cell lifespan. Generation of chimeric mice indicates that Bcl2-ARE∆/∆ B cells have an intrinsic competitive disadvantage compared to wild type cells. Biochemical assays and predictions using a bioinformatics approach show that several RBPs bind to the Bcl2 AREs, including AUF1 and HuR proteins. Altogether, association of RBPs to Bcl2 AREs contributes to Bcl2 protein expression by stabilizing Bcl2 mRNA and promotes B cell maintenance.}, |
|
| 2311 | + langid = {english}, |
|
| 2312 | + keywords = {3' UTR,B cells,Flow cytometry,Immunoprecipitation,Messenger RNA,Protein expression,Protein extraction,Spleen}, |
|
| 2313 | + file = {/Users/rmorin/Zotero/storage/9SJAXD5H/Díaz-Muñoz et al. - 2015 - Deletion of AU-Rich Elements within the Bcl2 3′UTR.pdf;/Users/rmorin/Zotero/storage/HCC2T5CF/article.html} |
|
| 2314 | +} |
|
| 2315 | + |
|
| 2316 | +@article{diaz-munozUncoveringRoleRNABinding2018, |
|
| 2317 | + title = {Uncovering the {{Role}} of {{RNA-Binding Proteins}} in {{Gene Expression}} in the {{Immune System}}}, |
|
| 2318 | + author = {Díaz-Muñoz, Manuel D. and Turner, Martin}, |
|
| 2319 | + date = {2018}, |
|
| 2320 | + journaltitle = {Frontiers in Immunology}, |
|
| 2321 | + shortjournal = {Front. Immunol.}, |
|
| 2322 | + volume = {9}, |
|
| 2323 | + issn = {1664-3224}, |
|
| 2324 | + doi = {10.3389/fimmu.2018.01094}, |
|
| 2325 | + url = {https://www.frontiersin.org/articles/10.3389/fimmu.2018.01094/full}, |
|
| 2326 | + urldate = {2019-12-21}, |
|
| 2327 | + abstract = {Fighting external pathogens requires an ever-changing immune system that relies on tight regulation of gene expression. Transcriptional control is the first step to build efficient responses while preventing immunodeficiencies and autoimmunity. Post-transcriptional regulation of RNA editing, location, stability and translation are the other key steps for final gene expression and they are all controlled by RNA binding proteins. Nowadays we have a deep understanding of how transcription factors control the immune system but recent evidences suggest that post-transcriptional regulation by RNA binding proteins is equally important for both development and activation of immune responses. Here we review current knowledge about how post-transcriptional control by RNA binding proteins shapes our immune system and we discuss the perspective of RNA binding proteins being the key players of a hidden immune cell epitranscriptome.}, |
|
| 2328 | + langid = {english}, |
|
| 2329 | + keywords = {humoral responses,immune cell activation,immune cell development,immune cell homeostasis,post-transcriptional regulation of gene expression,RNA binding proteins (RBPs),T-cell mediated immunity}, |
|
| 2330 | + file = {/Users/rmorin/Zotero/storage/XKVHJA2T/Díaz-Muñoz and Turner - 2018 - Uncovering the Role of RNA-Binding Proteins in Gen.pdf} |
|
| 2331 | +} |
|
| 2332 | + |
|
| 2333 | +@article{diehlCirculatingMutantDNA2008, |
|
| 2334 | + title = {Circulating Mutant {{DNA}} to Assess Tumor Dynamics.}, |
|
| 2335 | + author = {Diehl, Frank and Schmidt, Kerstin and Choti, Michael A and Romans, Katharine and Goodman, Steven and Li, Meng and Thornton, Katherine and Agrawal, Nishant and Sokoll, Lori and Szabo, Steve A and Kinzler, Kenneth W and Vogelstein, Bert and Diaz, Luis A}, |
|
| 2336 | + date = {2008-09}, |
|
| 2337 | + journaltitle = {Nature Medicine}, |
|
| 2338 | + volume = {14}, |
|
| 2339 | + number = {9}, |
|
| 2340 | + pages = {985--990}, |
|
| 2341 | + keywords = {nosource} |
|
| 2342 | +} |
|
| 2343 | + |
|
| 2344 | +@article{dierlammGainChromosomeRegion2008, |
|
| 2345 | + title = {Gain of Chromosome Region 18q21 Including the {{MALT1}} Gene Is Associated with the Activated {{B-cell-like}} Gene Expression Subtype and Increased {{BCL2}} Gene Dosage and Protein Expression in Diffuse Large {{B-cell}} Lymphoma}, |
|
| 2346 | + author = {Dierlamm, Judith and Murga Penas, Eva M and Bentink, Stefan and Wessendorf, Swen and Berger, Hilmar and Hummel, Michael and Klapper, Wolfram and Lenze, Dido and Rosenwald, Andreas and Haralambieva, Eugenia and Ott, German and Cogliatti, Sergio B and Möller, Peter and Schwaenen, Carsten and Stein, Harald and Löffler, Markus and Spang, Rainer and Trümper, Lorenz and Siebert, Reiner and Lymphomas, Deutsche Krebshilfe Network Project Molecular Mechanisms in Malignant}, |
|
| 2347 | + date = {2008-05}, |
|
| 2348 | + journaltitle = {Haematologica}, |
|
| 2349 | + volume = {93}, |
|
| 2350 | + number = {5}, |
|
| 2351 | + pages = {688--696}, |
|
| 2352 | + keywords = {nosource} |
|
| 2353 | +} |
|
| 2354 | + |
|
| 2355 | +@article{dingConstitutivelyActivatedSTAT32008, |
|
| 2356 | + title = {Constitutively Activated {{STAT3}} Promotes Cell Proliferation and Survival in the Activated {{B-cell}} Subtype of Diffuse Large {{B-cell}} Lymphomas.}, |
|
| 2357 | + author = {Ding, B Belinda and Yu, J Jessica and Yu, Raymond Y-L and Mendez, Lourdes M and Shaknovich, Rita and Zhang, Yonghui and Cattoretti, Giorgio and Ye, B Hilda}, |
|
| 2358 | + date = {2008-02}, |
|
| 2359 | + journaltitle = {Blood}, |
|
| 2360 | + volume = {111}, |
|
| 2361 | + number = {3}, |
|
| 2362 | + pages = {1515--1523}, |
|
| 2363 | + keywords = {nosource} |
|
| 2364 | +} |
|
| 2365 | + |
|
| 2366 | +@article{dobinSTARUltrafastUniversal2013, |
|
| 2367 | + title = {{{STAR}}: Ultrafast Universal {{RNA-seq}} Aligner}, |
|
| 2368 | + shorttitle = {{{STAR}}}, |
|
| 2369 | + author = {Dobin, Alexander and Davis, Carrie A. and Schlesinger, Felix and Drenkow, Jorg and Zaleski, Chris and Jha, Sonali and Batut, Philippe and Chaisson, Mark and Gingeras, Thomas R.}, |
|
| 2370 | + date = {2013-01-01}, |
|
| 2371 | + journaltitle = {Bioinformatics}, |
|
| 2372 | + shortjournal = {Bioinformatics}, |
|
| 2373 | + volume = {29}, |
|
| 2374 | + number = {1}, |
|
| 2375 | + pages = {15--21}, |
|
| 2376 | + issn = {1367-4803}, |
|
| 2377 | + doi = {10.1093/bioinformatics/bts635}, |
|
| 2378 | + url = {https://academic.oup.com/bioinformatics/article/29/1/15/272537}, |
|
| 2379 | + urldate = {2019-12-21}, |
|
| 2380 | + abstract = {Abstract. Motivation: Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript str}, |
|
| 2381 | + langid = {english}, |
|
| 2382 | + file = {/Users/rmorin/Zotero/storage/UYPEK2TR/272537.html} |
|
| 2383 | +} |
|
| 2384 | + |
|
| 2385 | +@article{doyleDiscordantBioinformaticPredictions2020, |
|
| 2386 | + title = {Discordant Bioinformatic Predictions of Antimicrobial Resistance from Whole-Genome Sequencing Data of Bacterial Isolates: An Inter-Laboratory Study}, |
|
| 2387 | + shorttitle = {Discordant Bioinformatic Predictions of Antimicrobial Resistance from Whole-Genome Sequencing Data of Bacterial Isolates}, |
|
| 2388 | + author = {Doyle, Ronan M. and O'Sullivan, Denise M. and Aller, Sean D. and Bruchmann, Sebastian and Clark, Taane and Coello Pelegrin, Andreu and Cormican, Martin and Diez Benavente, Ernest and Ellington, Matthew J. and McGrath, Elaine and Motro, Yair and Phuong Thuy Nguyen, Thi and Phelan, Jody and Shaw, Liam P. and Stabler, Richard A. and family=Belkum, given=Alex, prefix=van, useprefix=true and family=Dorp, given=Lucy, prefix=van, useprefix=true and Woodford, Neil and Moran-Gilad, Jacob and Huggett, Jim F. and Harris, Kathryn A.}, |
|
| 2389 | + date = {2020-02}, |
|
| 2390 | + journaltitle = {Microbial Genomics}, |
|
| 2391 | + shortjournal = {Microb Genom}, |
|
| 2392 | + volume = {6}, |
|
| 2393 | + number = {2}, |
|
| 2394 | + eprint = {32048983}, |
|
| 2395 | + eprinttype = {pmid}, |
|
| 2396 | + issn = {2057-5858}, |
|
| 2397 | + doi = {10.1099/mgen.0.000335}, |
|
| 2398 | + abstract = {Antimicrobial resistance (AMR) poses a threat to public health. Clinical microbiology laboratories typically rely on culturing bacteria for antimicrobial-susceptibility testing (AST). As the implementation costs and technical barriers fall, whole-genome sequencing (WGS) has emerged as a 'one-stop' test for epidemiological and predictive AST results. Few published comparisons exist for the myriad analytical pipelines used for predicting AMR. To address this, we performed an inter-laboratory study providing sets of participating researchers with identical short-read WGS data from clinical isolates, allowing us to assess the reproducibility of the bioinformatic prediction of AMR between participants, and identify problem cases and factors that lead to discordant results. We produced ten WGS datasets of varying quality from cultured carbapenem-resistant organisms obtained from clinical samples sequenced on either an Illumina NextSeq or HiSeq instrument. Nine participating teams ('participants') were provided these sequence data without any other contextual information. Each participant used their choice of pipeline to determine the species, the presence of resistance-associated genes, and to predict susceptibility or resistance to amikacin, gentamicin, ciprofloxacin and cefotaxime. We found participants predicted different numbers of AMR-associated genes and different gene variants from the same clinical samples. The quality of the sequence data, choice of bioinformatic pipeline and interpretation of the results all contributed to discordance between participants. Although much of the inaccurate gene variant annotation did not affect genotypic resistance predictions, we observed low specificity when compared to phenotypic AST results, but this improved in samples with higher read depths. Had the results been used to predict AST and guide treatment, a different antibiotic would have been recommended for each isolate by at least one participant. These challenges, at the final analytical stage of using WGS to predict AMR, suggest the need for refinements when using this technology in clinical settings. Comprehensive public resistance sequence databases, full recommendations on sequence data quality and standardization in the comparisons between genotype and resistance phenotypes will all play a fundamental role in the successful implementation of AST prediction using WGS in clinical microbiology laboratories.}, |
|
| 2399 | + langid = {english}, |
|
| 2400 | + pmcid = {PMC7067211}, |
|
| 2401 | + keywords = {antimicrobial resistance,antimicrobial-susceptibility testing,bioinformatics,carbapenem resistance,whole-genome sequencing}, |
|
| 2402 | + file = {/Users/rmorin/Zotero/storage/8ARAWF7N/Doyle et al. - 2020 - Discordant bioinformatic predictions of antimicrob.pdf} |
|
| 2403 | +} |
|
| 2404 | + |
|
| 2405 | +@article{drevalGeneticSubdivisionsFollicular2023, |
|
| 2406 | + title = {Genetic Subdivisions of Follicular Lymphoma Defined by Distinct Coding and Noncoding Mutation Patterns}, |
|
| 2407 | + author = {Dreval, Kostiantyn and Hilton, Laura K. and Cruz, Manuela and Shaalan, Haya and Ben-Neriah, Susana and Boyle, Merrill and Collinge, Brett and Coyle, Krysta M. and Duns, Gerben and Farinha, Pedro and Grande, Bruno M. and Meissner, Barbara and Pararajalingam, Prasath and Rushton, Christopher K. and Slack, Graham W. and Wong, Jasper and Mungall, Andrew J. and Marra, Marco A. and Connors, Joseph M. and Steidl, Christian and Scott, David W. and Morin, Ryan D.}, |
|
| 2408 | + date = {2023-08-10}, |
|
| 2409 | + journaltitle = {Blood}, |
|
| 2410 | + shortjournal = {Blood}, |
|
| 2411 | + volume = {142}, |
|
| 2412 | + number = {6}, |
|
| 2413 | + eprint = {37084389}, |
|
| 2414 | + eprinttype = {pmid}, |
|
| 2415 | + pages = {561--573}, |
|
| 2416 | + issn = {1528-0020}, |
|
| 2417 | + doi = {10.1182/blood.2022018719}, |
|
| 2418 | + abstract = {Follicular lymphoma (FL) accounts for ∼20\% of all new lymphoma cases. Increases in cytological grade are a feature of the clinical progression of this malignancy, and eventual histologic transformation (HT) to the aggressive diffuse large B-cell lymphoma (DLBCL) occurs in up to 15\% of patients. Clinical or genetic features to predict the risk and timing of HT have not been described comprehensively. In this study, we analyzed whole-genome sequencing data from 423 patients to compare the protein coding and noncoding mutation landscapes of untransformed FL, transformed FL, and de novo DLBCL. This revealed 2 genetically distinct subgroups of FL, which we have named DLBCL-like (dFL) and constrained FL (cFL). Each subgroup has distinguishing mutational patterns, aberrant somatic hypermutation rates, and biological and clinical characteristics. We implemented a machine learning-derived classification approach to stratify patients with FL into cFL and dFL subgroups based on their genomic features. Using separate validation cohorts, we demonstrate that cFL status, whether assigned with this full classifier or a single-gene approximation, is associated with a reduced rate of HT. This implies distinct biological features of cFL that constrain its evolution, and we highlight the potential for this classification to predict HT from genetic features present at diagnosis.}, |
|
| 2419 | + langid = {english}, |
|
| 2420 | + pmcid = {PMC10644066}, |
|
| 2421 | + keywords = {Humans,Lymphoma Follicular,Lymphoma Large B-Cell Diffuse,Morinlab,Mutation}, |
|
| 2422 | + file = {/Users/rmorin/Zotero/storage/8BHQJTBT/Dreval et al. - 2023 - Genetic subdivisions of follicular lymphoma define.pdf} |
|
| 2423 | +} |
|
| 2424 | + |
|
| 2425 | +@article{drevalMinimumInformationReporting2022, |
|
| 2426 | + title = {Minimum {{Information}} for {{Reporting}} a {{Genomics Experiment}}}, |
|
| 2427 | + author = {Dreval, Kostiantyn and Boutros, Paul C. and Morin, Ryan D.}, |
|
| 2428 | + date = {2022-10-11}, |
|
| 2429 | + journaltitle = {Blood}, |
|
| 2430 | + shortjournal = {Blood}, |
|
| 2431 | + eprint = {36219881}, |
|
| 2432 | + eprinttype = {pmid}, |
|
| 2433 | + pages = {blood.2022016095}, |
|
| 2434 | + issn = {1528-0020}, |
|
| 2435 | + doi = {10.1182/blood.2022016095}, |
|
| 2436 | + abstract = {Exome and genome sequencing has facilitated the identification of hundreds of genes and other regions that are recurrently mutated in hematologic neoplasms. The datasets from these studies theoretically provide opportunities. Quality differences between datasets can confound secondary analyses. We explore the consequences of these on the conclusions from some recent studies of B-cell lymphomas. We highlight the need for a minimum reporting standard to increase transparency in genomic research.}, |
|
| 2437 | + langid = {english}, |
|
| 2438 | + keywords = {Morinlab}, |
|
| 2439 | + file = {/Users/rmorin/Zotero/storage/6UVXVG97/Dreval et al. - 2022 - Minimum Information for Reporting a Genomics Exper.pdf} |
|
| 2440 | +} |
|
| 2441 | + |
|
| 2442 | +@online{drevalRevisitingReddyDLBCL2023, |
|
| 2443 | + title = {Revisiting {{Reddy}}: {{A DLBCL Do-over}}}, |
|
| 2444 | + shorttitle = {Revisiting {{Reddy}}}, |
|
| 2445 | + author = {Dreval, Kostiantyn and Cruz, Manuela and Rushton, Christopher and Liuta, Nina and Mirhosseini, Houman Layegh and Brown, Callum and Morin, Ryan D. and Consortium, the GAMBL}, |
|
| 2446 | + date = {2023-11-22}, |
|
| 2447 | + eprinttype = {bioRxiv}, |
|
| 2448 | + eprintclass = {Contradictory Results}, |
|
| 2449 | + pages = {2023.11.21.567983}, |
|
| 2450 | + doi = {10.1101/2023.11.21.567983}, |
|
| 2451 | + url = {https://www.biorxiv.org/content/10.1101/2023.11.21.567983v1}, |
|
| 2452 | + urldate = {2024-01-24}, |
|
| 2453 | + abstract = {The 2017 study by Reddy et al described the comprehensive characterization of somatic drivers of diffuse large B-cell lymphoma using whole exome sequencing.1 After additional large studies relying on exome or whole genome sequencing were published, several oddities unique to the Reddy results have emerged. Seeking to explain the discrepancies, we reanalyzed their data using established open-source pipelines. This revealed thousands of mutations that could not be independently reproduced by these pipelines and a larger set of high-quality mutations that were not reported by Reddy. This caused an artificial under-representation of the mutation prevalence in many genes including clinically relevant hot spots affecting EZH2 and CD79B. More generally, the study had an under-representation of mutations in DLBCL genes that disproportionately affected genes known to have the highest mutation rates. The missing variants and the spurious variants can be attributed to distinct problems with the analytical approaches employed in that study. Our analysis also identified strong associations between mutations and patient outcome including TP53, KMT2D and PIM1, which were not found in the Reddy study. Overall, we demonstrate that this combination of errors influenced many of the central novel findings from their study rendering their results largely non-replicable. The full results of our analyses are included as supplemental items as a resource for other researchers with an interest in the genetics of B-cell lymphomas.}, |
|
| 2454 | + langid = {english}, |
|
| 2455 | + pubstate = {preprint}, |
|
| 2456 | + file = {/Users/rmorin/Zotero/storage/Y46BT7XR/Dreval et al. - 2023 - Revisiting Reddy A DLBCL Do-over.pdf} |
|
| 2457 | +} |
|
| 2458 | + |
|
| 2459 | +@article{dreyfussHeterogeneousNuclearRibonucleoprotein1988, |
|
| 2460 | + title = {Heterogeneous Nuclear Ribonucleoprotein Particles and the Pathway of {{mRNA}} Formation}, |
|
| 2461 | + author = {Dreyfuss, Gideon and Swanson, Maurice S. and Piñol-Roma, Serafin}, |
|
| 2462 | + date = {1988-03-01}, |
|
| 2463 | + journaltitle = {Trends in Biochemical Sciences}, |
|
| 2464 | + shortjournal = {Trends in Biochemical Sciences}, |
|
| 2465 | + volume = {13}, |
|
| 2466 | + number = {3}, |
|
| 2467 | + pages = {86--91}, |
|
| 2468 | + issn = {0968-0004}, |
|
| 2469 | + doi = {10.1016/0968-0004(88)90046-1}, |
|
| 2470 | + url = {https://www.sciencedirect.com/science/article/pii/0968000488900461}, |
|
| 2471 | + urldate = {2022-09-26}, |
|
| 2472 | + abstract = {Heterogeneous nuclear ribonucleoprotein (hnRNP) particles, the structures that package hnRNA, are one of the major constituents of the nucleus. Recent work has led to the immunopurification of hnRNP particles and the identification of their proteins, and demonstrated a role for hnRNP proteins in mRNA splicing. The molecular cloning and sequencing of cDNAs for RNP proteins made possible the discovery of a conserved RNA-binding domain and a RNP consensus sequence.}, |
|
| 2473 | + langid = {english}, |
|
| 2474 | + file = {/Users/rmorin/Zotero/storage/JBPFIZZ8/0968000488900461.html} |
|
| 2475 | +} |
|
| 2476 | + |
|
| 2477 | +@article{duanFBXO11TargetsBCL62011, |
|
| 2478 | + title = {{{FBXO11}} Targets {{BCL6}} for Degradation and Is Inactivated in Diffuse Large {{B-cell}} Lymphomas.}, |
|
| 2479 | + author = {Duan, Shanshan and Cermak, Lukas and Pagan, Julia K and Rossi, Mario and Martinengo, Cinzia and family=Celle, given=Paola Francia, prefix=di, useprefix=true and Chapuy, Bjoern and Shipp, Margaret and Chiarle, Roberto and Pagano, Michele}, |
|
| 2480 | + date = {2011-11}, |
|
| 2481 | + journaltitle = {Nature}, |
|
| 2482 | + keywords = {nosource} |
|
| 2483 | +} |
|
| 2484 | + |
|
| 2485 | +@article{duboisNextGenerationSequencing2016, |
|
| 2486 | + title = {Next {{Generation Sequencing}} in {{Diffuse Large B Cell Lymphoma Highlights Molecular Divergence}} and {{Therapeutic Opportunities}}: A {{LYSA Study}}.}, |
|
| 2487 | + author = {Dubois, Sydney and Viailly, Pierre-Julien and Mareschal, Sylvain and Bohers, Elodie and Bertrand, Philippe and Ruminy, Philippe and Maingonnat, Catherine and Jais, Jean-Philippe and Peyrouze, Pauline and Figeac, Martin and Molina, Thierry J and Desmots, Fabienne and Fest, Thierry and Haioun, Corinne and Lamy, Thierry and Copie-Bergman, Christiane and Briere, Josette and Petrella, Tony and Canioni, Danielle and Fabiani, Bettina and Coiffier, Bertrand and Delarue, Richard and Peyrade, Frederic and Bosly, Andre and Andre, Marc and Ketterer, Nicolas and Salles, Gilles and Tilly, Hervé and Leroy, Karen and Jardin, Fabrice}, |
|
| 2488 | + date = {2016-01}, |
|
| 2489 | + journaltitle = {Clin Cancer Res}, |
|
| 2490 | + pages = {clincanres.2305.2015}, |
|
| 2491 | + keywords = {nosource} |
|
| 2492 | +} |
|
| 2493 | + |
|
| 2494 | +@article{dunleavyBCL2BiomarkerEra2007, |
|
| 2495 | + title = {The {{BCL-2}} Biomarker in the Era of Molecular Diagnosis of Diffuse Large {{B-cell}} Lymphoma}, |
|
| 2496 | + author = {Dunleavy, Kieron and Staudt, Louis M and Wilson, Wyndham H}, |
|
| 2497 | + date = {2007-01}, |
|
| 2498 | + journaltitle = {Leuk lymphoma}, |
|
| 2499 | + volume = {48}, |
|
| 2500 | + number = {6}, |
|
| 2501 | + pages = {1061--1063}, |
|
| 2502 | + keywords = {nosource} |
|
| 2503 | +} |
|
| 2504 | + |
|
| 2505 | +@article{dunsCharacterizationDLBCLPMBL2021b, |
|
| 2506 | + title = {Characterization of {{DLBCL}} with a {{PMBL}} Gene Expression Signature}, |
|
| 2507 | + author = {Duns, Gerben and Viganò, Elena and Ennishi, Daisuke and Sarkozy, Clementine and Hung, Stacy S. and Chavez, Elizabeth and Takata, Katsuyoshi and Rushton, Christopher and Jiang, Aixiang and Ben-Neriah, Susana and Woolcock, Bruce W. and Slack, Graham W. and Hsi, Eric D. and Craig, Jeffrey W. and Hilton, Laura K. and Shah, Sohrab P. and Farinha, Pedro and Mottok, Anja and Gascoyne, Randy D. and Morin, Ryan D. and Savage, Kerry J. and Scott, David W. and Steidl, Christian}, |
|
| 2508 | + date = {2021-07-15}, |
|
| 2509 | + journaltitle = {Blood}, |
|
| 2510 | + shortjournal = {Blood}, |
|
| 2511 | + volume = {138}, |
|
| 2512 | + number = {2}, |
|
| 2513 | + eprint = {33684939}, |
|
| 2514 | + eprinttype = {pmid}, |
|
| 2515 | + pages = {136--148}, |
|
| 2516 | + issn = {1528-0020}, |
|
| 2517 | + doi = {10.1182/blood.2020007683}, |
|
| 2518 | + abstract = {Primary mediastinal large B-cell lymphoma (PMBL) is a type of aggressive B-cell lymphoma that typically affects young adults, characterized by presence of a bulky anterior mediastinal mass. Lymphomas with gene expression features of PMBL have been described in nonmediastinal sites, raising questions about how these tumors should be classified. Here, we investigated whether these nonmediastinal lymphomas are indeed PMBLs or instead represent a distinct group within diffuse large B-cell lymphoma (DLBCL). From a cohort of 325 de novo DLBCL cases, we identified tumors from patients without evidence of anterior mediastinal involvement that expressed a PMBL expression signature (nm-PMBLsig+; n = 16; 5\%). A majority of these tumors expressed MAL and CD23, proteins typically observed in bona fide PMBL (bf-PMBL). Evaluation of clinical features of nm-PMBLsig+ cases revealed close associations with DLBCL, and a majority displayed a germinal center B cell-like cell of origin (GCB). In contrast to patients with bf-PMBL, patients with nm-PMBLsig+ presented at an older age and did not show pleural disease, and bone/bone marrow involvement was observed in 3 cases. However, although clinically distinct from bf-PMBL, nm-PMBLsig+ tumors resembled bf-PMBL at the molecular level, with upregulation of immune response, JAK-STAT, and NF-κB signatures. Mutational analysis revealed frequent somatic gene mutations in SOCS1, IL4R, ITPKB, and STAT6, as well as CD83 and BIRC3, with the latter genes significantly more frequently affected than in GCB DLBCL or bf-PMBL. Our data establish nm-PMBLsig+ lymphomas as a group within DLBCL with distinct phenotypic and genetic features. These findings may have implications for gene expression- and mutation-based subtyping of aggressive B-cell lymphomas and related targeted therapies.}, |
|
| 2519 | + langid = {english}, |
|
| 2520 | + keywords = {Adolescent,Adult,Aged,Aged 80 and over,B-Lymphocytes,DNA Copy Number Variations,DNA Mutational Analysis,Female,Gene Expression Profiling,Gene Expression Regulation Leukemic,HEK293 Cells,Humans,Immune Evasion,Immunophenotyping,Janus Kinases,Lymphoma Large B-Cell Diffuse,Lymphoma Non-Hodgkin,Male,Mediastinal Neoplasms,Middle Aged,Mutation,Receptors Interleukin-4,Somatic Hypermutation Immunoglobulin,STAT Transcription Factors,Young Adult}, |
|
| 2521 | + file = {/Users/rmorin/Zotero/storage/Z9CQEGN7/Duns et al. - 2021 - Characterization of DLBCL with a PMBL gene express.pdf} |
|
| 2522 | +} |
|
| 2523 | + |
|
| 2524 | +@article{dupireTargetedTreatmentNew2010, |
|
| 2525 | + title = {Targeted Treatment and New Agents in Diffuse Large {{B}} Cell Lymphoma}, |
|
| 2526 | + author = {Dupire, Sophie and Coiffier, Bertrand}, |
|
| 2527 | + date = {2010-06}, |
|
| 2528 | + journaltitle = {International journal of hematology}, |
|
| 2529 | + volume = {92}, |
|
| 2530 | + number = {1}, |
|
| 2531 | + pages = {12--24}, |
|
| 2532 | + keywords = {nosource} |
|
| 2533 | +} |
|
| 2534 | + |
|
| 2535 | +@article{durnickExpressionLMO2Associated, |
|
| 2536 | + title = {Expression of {{LMO2}} Is Associated with t(14;18)/{{IGH-BCL2}} Fusion but Not {{BCL6}} Translocations in Diffuse Large {{B-cell}} Lymphoma.}, |
|
| 2537 | + author = {Durnick, David K and Law, Mark E and Maurer, Matthew J and Natkunam, Yasodha and Levy, Ronald and Lossos, Izidore S and Kurtin, Paul J and McPhail, Ellen D}, |
|
| 2538 | + journaltitle = {American journal of clinical pathology}, |
|
| 2539 | + volume = {134}, |
|
| 2540 | + number = {2}, |
|
| 2541 | + pages = {278--281}, |
|
| 2542 | + keywords = {nosource} |
|
| 2543 | +} |
|
| 2544 | + |
|
| 2545 | +@online{DwyerMastCells, |
|
| 2546 | + title = {Dwyer Mast Cells - {{Google Search}}}, |
|
| 2547 | + url = {https://www.google.com/search?q=dwyer+mast+cells&rlz=1C1CHZN_enCA934CA934&sxsrf=ALeKk00ogPFXJ9T4wZxQv49VTN1ebJhTFQ:1629303607472&source=lnms&tbm=isch&sa=X&ved=2ahUKEwiUpIT2_LryAhWTMX0KHbYyCD4Q_AUoAXoECAEQAw&biw=1536&bih=818}, |
|
| 2548 | + urldate = {2021-08-18}, |
|
| 2549 | + file = {/Users/rmorin/Zotero/storage/4TL3V4D2/search.html} |
|
| 2550 | +} |
|
| 2551 | + |
|
| 2552 | +@article{elversExomeSequencingLymphomas2015, |
|
| 2553 | + title = {Exome Sequencing of Lymphomas from Three Dog Breeds Reveals Somatic Mutation Patterns Reflecting Genetic Background}, |
|
| 2554 | + author = {Elvers, Ingegerd and Turner-Maier, Jason and Swofford, Ross and Koltookian, Michele and Johnson, Jeremy and Stewart, Chip and Zhang, Cheng-Zhong and Schumacher, Steven E. and Beroukhim, Rameen and Rosenberg, Mara and Thomas, Rachael and Mauceli, Evan and Getz, Gad and Palma, Federica Di and Modiano, Jaime F. and Breen, Matthew and Lindblad-Toh, Kerstin and Alföldi, Jessica}, |
|
| 2555 | + date = {2015-01-11}, |
|
| 2556 | + journaltitle = {Genome Research}, |
|
| 2557 | + shortjournal = {Genome Res.}, |
|
| 2558 | + volume = {25}, |
|
| 2559 | + number = {11}, |
|
| 2560 | + eprint = {26377837}, |
|
| 2561 | + eprinttype = {pmid}, |
|
| 2562 | + pages = {1634--1645}, |
|
| 2563 | + publisher = {Cold Spring Harbor Lab}, |
|
| 2564 | + issn = {1088-9051, 1549-5469}, |
|
| 2565 | + doi = {10.1101/gr.194449.115}, |
|
| 2566 | + url = {https://genome.cshlp.org/content/25/11/1634}, |
|
| 2567 | + urldate = {2021-04-29}, |
|
| 2568 | + abstract = {Lymphoma is the most common hematological malignancy in developed countries. Outcome is strongly determined by molecular subtype, reflecting a need for new and improved treatment options. Dogs spontaneously develop lymphoma, and the predisposition of certain breeds indicates genetic risk factors. Using the dog breed structure, we selected three lymphoma predisposed breeds developing primarily T-cell (boxer), primarily B-cell (cocker spaniel), and with equal distribution of B- and T-cell lymphoma (golden retriever), respectively. We investigated the somatic mutations in B- and T-cell lymphomas from these breeds by exome sequencing of tumor and normal pairs. Strong similarities were evident between B-cell lymphomas from golden retrievers and cocker spaniels, with recurrent mutations in TRAF3-MAP3K14 (28\% of all cases), FBXW7 (25\%), and POT1 (17\%). The FBXW7 mutations recurrently occur in a specific codon; the corresponding codon is recurrently mutated in human cancer. In contrast, T-cell lymphomas from the predisposed breeds, boxers and golden retrievers, show little overlap in their mutation pattern, sharing only one of their 15 most recurrently mutated genes. Boxers, which develop aggressive T-cell lymphomas, are typically mutated in the PTEN-mTOR pathway. T-cell lymphomas in golden retrievers are often less aggressive, and their tumors typically showed mutations in genes involved in cellular metabolism. We identify genes with known involvement in human lymphoma and leukemia, genes implicated in other human cancers, as well as novel genes that could allow new therapeutic options.}, |
|
| 2569 | + langid = {english}, |
|
| 2570 | + file = {/Users/rmorin/Zotero/storage/MJDYZ346/Elvers et al. - 2015 - Exome sequencing of lymphomas from three dog breed.pdf} |
|
| 2571 | +} |
|
| 2572 | + |
|
| 2573 | +@article{engelsPolypyrimidineTractBinding2012, |
|
| 2574 | + title = {Polypyrimidine {{Tract Binding Protein}} ({{hnRNP I}}) {{Is Possibly}} a {{Conserved Modulator}} of {{miRNA-Mediated Gene Regulation}}}, |
|
| 2575 | + author = {Engels, Bart and Jannot, Guillaume and Remenyi, Judit and Simard, Martin J. and Hutvagner, György}, |
|
| 2576 | + date = {2012-03-09}, |
|
| 2577 | + journaltitle = {PLOS ONE}, |
|
| 2578 | + shortjournal = {PLOS ONE}, |
|
| 2579 | + volume = {7}, |
|
| 2580 | + number = {3}, |
|
| 2581 | + pages = {e33144}, |
|
| 2582 | + publisher = {Public Library of Science}, |
|
| 2583 | + issn = {1932-6203}, |
|
| 2584 | + doi = {10.1371/journal.pone.0033144}, |
|
| 2585 | + url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0033144}, |
|
| 2586 | + urldate = {2022-09-28}, |
|
| 2587 | + abstract = {MiRNAs can regulate gene expression through versatile mechanisms that result in increased or decreased expression of the targeted mRNA and it could effect the expression of thousands of protein in a particular cell. An increasing body of evidence suggest that miRNAs action can be modulated by proteins that bind to the same 3′UTRs that are targeted by miRNAs, suggesting that other factors apart from miRNAs and their target sites determine miRNA-modulation of gene expression. We applied an affinity purification protocol using biotinylated let-7 miRNA inhibitor to isolate proteins that are involved in let-7 mediated gene regulation that resulted in an affinity purification of Polypyrimidine Tract Binding protein (PTB). Here we show that PTB interacts with miRNAs and human Argonaute 2 (hAgo2) through RNA as well as identified potential mammalian cellular targets that are co-regulated by PTB and hAgo2. In addition, using genetic approach, we have demonstrated that PTB genetically interacts with Caenorhabditis elegans let-7 indicating a conserved role for PTB in miRNA-mediated gene regulation.}, |
|
| 2588 | + langid = {english}, |
|
| 2589 | + keywords = {Affinity purification,Caenorhabditis elegans,Gene regulation,HeLa cells,Immunoprecipitation,MicroRNAs,RNA-binding proteins,Small interfering RNA}, |
|
| 2590 | + file = {/Users/rmorin/Zotero/storage/ED3EA9MB/Engels et al. - 2012 - Polypyrimidine Tract Binding Protein (hnRNP I) Is .pdf;/Users/rmorin/Zotero/storage/RFVNZQE8/article.html} |
|
| 2591 | +} |
|
| 2592 | + |
|
| 2593 | +@article{ennishiDoubleHitGeneExpression2019, |
|
| 2594 | + title = {Double-{{Hit Gene Expression Signature Defines}} a {{Distinct Subgroup}} of {{Germinal Center B-Cell-Like Diffuse Large B-Cell Lymphoma}}}, |
|
| 2595 | + author = {Ennishi, Daisuke and Jiang, Aixiang and Boyle, Merrill and Collinge, Brett and Grande, Bruno M. and Ben-Neriah, Susana and Rushton, Christopher and Tang, Jeffrey and Thomas, Nicole and Slack, Graham W. and Farinha, Pedro and Takata, Katsuyoshi and Miyata-Takata, Tomoko and Craig, Jeffrey and Mottok, Anja and Meissner, Barbara and Saberi, Saeed and Bashashati, Ali and Villa, Diego and Savage, Kerry J. and Sehn, Laurie H. and Kridel, Robert and Mungall, Andrew J. and Marra, Marco A. and Shah, Sohrab P. and Steidl, Christian and Connors, Joseph M. and Gascoyne, Randy D. and Morin, Ryan D. and Scott, David W.}, |
|
| 2596 | + date = {2019-01-20}, |
|
| 2597 | + journaltitle = {Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology}, |
|
| 2598 | + shortjournal = {J Clin Oncol}, |
|
| 2599 | + volume = {37}, |
|
| 2600 | + number = {3}, |
|
| 2601 | + eprint = {30523716}, |
|
| 2602 | + eprinttype = {pmid}, |
|
| 2603 | + pages = {190--201}, |
|
| 2604 | + issn = {1527-7755}, |
|
| 2605 | + doi = {10.1200/JCO.18.01583}, |
|
| 2606 | + abstract = {PURPOSE: High-grade B-cell lymphoma with MYC and BCL2 and/or BCL6 rearrangements (HGBL-DH/TH) has a poor outcome after standard chemoimmunotherapy. We sought to understand the biologic underpinnings of HGBL-DH/TH with BCL2 rearrangements (HGBL-DH/TH- BCL2) and diffuse large B-cell lymphoma (DLBCL) morphology through examination of gene expression. PATIENTS AND METHODS: We analyzed RNA sequencing data from 157 de novo germinal center B-cell-like (GCB)-DLBCLs, including 25 with HGBL-DH/TH- BCL2, to define a gene expression signature that distinguishes HGBL-DH/TH- BCL2 from other GCB-DLBCLs. To assess the genetic, molecular, and phenotypic features associated with this signature, we analyzed targeted resequencing, whole-exome sequencing, RNA sequencing, and immunohistochemistry data. RESULTS: We developed a 104-gene double-hit signature (DHITsig) that assigned 27\% of GCB-DLBCLs to the DHITsig-positive group, with only one half harboring MYC and BCL2 rearrangements (HGBL-DH/TH- BCL2). DHITsig-positive patients had inferior outcomes after rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone immunochemotherapy compared with DHITsig-negative patients (5-year time to progression rate, 57\% and 81\%, respectively; P {$<$} .001), irrespective of HGBL-DH/TH- BCL2 status. The prognostic value of DHITsig was confirmed in an independent validation cohort. DHITsig-positive tumors are biologically characterized by a putative non-light zone germinal center cell of origin and a distinct mutational landscape that comprises genes associated with chromatin modification. A new NanoString assay (DLBCL90) recapitulated the prognostic significance and RNA sequencing assignments. Validating the association with HGBL-DH/TH- BCL2, 11 of 25 DHITsig-positive-transformed follicular lymphomas were classified as HGBL-DH/TH- BCL2 compared with zero of 50 in the DHITsig-negative group. Furthermore, the DHITsig was shared with the majority of B-cell lymphomas with high-grade morphology tested. CONCLUSION: We have defined a clinically and biologically distinct subgroup of tumors within GCB-DLBCL characterized by a gene expression signature of HGBL-DH/TH- BCL2. This knowledge has been translated into an assay applicable to routinely available biopsy samples, which enables exploration of its utility to guide patient management.}, |
|
| 2607 | + langid = {english}, |
|
| 2608 | + pmcid = {PMC6804880}, |
|
| 2609 | + keywords = {Adult,Aged,Aged 80 and over,Antibodies Monoclonal Murine-Derived,Antineoplastic Combined Chemotherapy Protocols,Cyclophosphamide,Doxorubicin,Female,Gene Rearrangement,Germinal Center,Humans,Lymphoma B-Cell,Lymphoma Large B-Cell Diffuse,Male,Middle Aged,Morinlab,Prednisone,Prognosis,Proto-Oncogene Proteins c-bcl-2,Proto-Oncogene Proteins c-myc,Rituximab,RNA Neoplasm,Transcriptome,Vincristine,Young Adult}, |
|
| 2610 | + file = {/Users/rmorin/Zotero/storage/U9LQLR2L/Ennishi et al. - 2019 - Double-Hit Gene Expression Signature Defines a Dis.pdf} |
|
| 2611 | +} |
|
| 2612 | + |
|
| 2613 | +@article{ennishiGeneticProfilingMYC2017, |
|
| 2614 | + title = {Genetic Profiling of {{MYC}} and {{BCL2}} in Diffuse Large {{B-cell}} Lymphoma Determines Cell-of-Origin-Specific Clinical Impact.}, |
|
| 2615 | + author = {Ennishi, Daisuke and Mottok, Anja and Ben-Neriah, Susana and Shulha, Hennady P and Farinha, Pedro and Chan, Fong Chun and Meissner, Barbara and Boyle, Merrill and Hother, Christoffer and Kridel, Robert and Lai, Daniel and Saberi, Saeed and Bashashati, Ali and Shah, Sohrab P and Morin, Ryan D and Marra, Marco A and Savage, Kerry J and Sehn, Laurie H and Steidl, Christian and Connors, Joseph M and Gascoyne, Randy D and Scott, David W}, |
|
| 2616 | + date = {2017-05}, |
|
| 2617 | + journaltitle = {Blood}, |
|
| 2618 | + volume = {129}, |
|
| 2619 | + number = {20}, |
|
| 2620 | + pages = {2760--2770}, |
|
| 2621 | + keywords = {nosource} |
|
| 2622 | +} |
|
| 2623 | + |
|
| 2624 | +@article{espinetIncidencePrognosticImpact, |
|
| 2625 | + title = {Incidence and Prognostic Impact of Secondary Cytogenetic Aberrations in a Series of 145 Patients with Mantle Cell Lymphoma.}, |
|
| 2626 | + author = {Espinet, Blanca and Salaverria, Itziar and Bea, Silvia and Ruiz-Xivillé, Neus and Balague, Olga and Salido, Marta and Costa, Dolors and Carreras, Joaquim and Rodríguez-Vicente, Ana Eugenia and Luís García, Juan and Hernández-Rivas, Jesús María and Calasanz, Maria Jose and Siebert, Reiner and Ferrer, Ana and Salar, Antonio and Carrió, Ana and Polo, Natividad and García-Marco, José Antonio and Domingo, Alicia and González-Barca, Eva and Romagosa, Vicenç and Marugan, Isabel and López-Guillermo, Armando and Millá, Fuensanta and Luís Mate, José and Luño, Elisa and Sanzo, Carmen and Collado, Rosa and Oliver, Isabel and Monzó, Sebastià and Palacín, Antonio and González, Teresa and Sant, Francesc and Salinas, Ramon and Ardanaz, María Teresa and Font, Llorenç and Escoda, Lourdes and Florensa, Lourdes and Serrano, Sergi and Campo, Elias and Solé, Francesc}, |
|
| 2627 | + journaltitle = {Genes Chromosome Canc}, |
|
| 2628 | + volume = {49}, |
|
| 2629 | + number = {5}, |
|
| 2630 | + pages = {439--451}, |
|
| 2631 | + keywords = {nosource} |
|
| 2632 | +} |
|
| 2633 | + |
|
| 2634 | +@article{ewingCombiningTumorGenome2015, |
|
| 2635 | + title = {Combining Tumor Genome Simulation with Crowdsourcing to Benchmark Somatic Single-Nucleotide-Variant Detection}, |
|
| 2636 | + author = {Ewing, Adam D. and Houlahan, Kathleen E. and Hu, Yin and Ellrott, Kyle and Caloian, Cristian and Yamaguchi, Takafumi N. and Bare, J. Christopher and P'ng, Christine and Waggott, Daryl and Sabelnykova, Veronica Y. and {ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants} and Kellen, Michael R. and Norman, Thea C. and Haussler, David and Friend, Stephen H. and Stolovitzky, Gustavo and Margolin, Adam A. and Stuart, Joshua M. and Boutros, Paul C.}, |
|
| 2637 | + date = {2015-07}, |
|
| 2638 | + journaltitle = {Nature Methods}, |
|
| 2639 | + shortjournal = {Nat Methods}, |
|
| 2640 | + volume = {12}, |
|
| 2641 | + number = {7}, |
|
| 2642 | + eprint = {25984700}, |
|
| 2643 | + eprinttype = {pmid}, |
|
| 2644 | + pages = {623--630}, |
|
| 2645 | + issn = {1548-7105}, |
|
| 2646 | + doi = {10.1038/nmeth.3407}, |
|
| 2647 | + abstract = {The detection of somatic mutations from cancer genome sequences is key to understanding the genetic basis of disease progression, patient survival and response to therapy. Benchmarking is needed for tool assessment and improvement but is complicated by a lack of gold standards, by extensive resource requirements and by difficulties in sharing personal genomic information. To resolve these issues, we launched the ICGC-TCGA DREAM Somatic Mutation Calling Challenge, a crowdsourced benchmark of somatic mutation detection algorithms. Here we report the BAMSurgeon tool for simulating cancer genomes and the results of 248 analyses of three in silico tumors created with it. Different algorithms exhibit characteristic error profiles, and, intriguingly, false positives show a trinucleotide profile very similar to one found in human tumors. Although the three simulated tumors differ in sequence contamination (deviation from normal cell sequence) and in subclonality, an ensemble of pipelines outperforms the best individual pipeline in all cases. BAMSurgeon is available at https://github.com/adamewing/bamsurgeon/.}, |
|
| 2648 | + langid = {english}, |
|
| 2649 | + pmcid = {PMC4856034}, |
|
| 2650 | + keywords = {Algorithms,Benchmarking,Crowdsourcing,Genome,Humans,Neoplasms,Polymorphism Single Nucleotide}, |
|
| 2651 | + file = {/Users/rmorin/Zotero/storage/6H9S7Z2W/Ewing et al. - 2015 - Combining tumor genome simulation with crowdsourci.pdf} |
|
| 2652 | +} |
|
| 2653 | + |
|
| 2654 | +@article{ewingCombiningTumorGenome2015a, |
|
| 2655 | + title = {Combining Tumor Genome Simulation with Crowdsourcing to Benchmark Somatic Single-Nucleotide-Variant Detection}, |
|
| 2656 | + author = {Ewing, Adam D. and Houlahan, Kathleen E. and Hu, Yin and Ellrott, Kyle and Caloian, Cristian and Yamaguchi, Takafumi N. and Bare, J. Christopher and P'ng, Christine and Waggott, Daryl and Sabelnykova, Veronica Y. and {ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants} and Kellen, Michael R. and Norman, Thea C. and Haussler, David and Friend, Stephen H. and Stolovitzky, Gustavo and Margolin, Adam A. and Stuart, Joshua M. and Boutros, Paul C.}, |
|
| 2657 | + date = {2015-07}, |
|
| 2658 | + journaltitle = {Nature Methods}, |
|
| 2659 | + shortjournal = {Nat Methods}, |
|
| 2660 | + volume = {12}, |
|
| 2661 | + number = {7}, |
|
| 2662 | + eprint = {25984700}, |
|
| 2663 | + eprinttype = {pmid}, |
|
| 2664 | + pages = {623--630}, |
|
| 2665 | + issn = {1548-7105}, |
|
| 2666 | + doi = {10.1038/nmeth.3407}, |
|
| 2667 | + abstract = {The detection of somatic mutations from cancer genome sequences is key to understanding the genetic basis of disease progression, patient survival and response to therapy. Benchmarking is needed for tool assessment and improvement but is complicated by a lack of gold standards, by extensive resource requirements and by difficulties in sharing personal genomic information. To resolve these issues, we launched the ICGC-TCGA DREAM Somatic Mutation Calling Challenge, a crowdsourced benchmark of somatic mutation detection algorithms. Here we report the BAMSurgeon tool for simulating cancer genomes and the results of 248 analyses of three in silico tumors created with it. Different algorithms exhibit characteristic error profiles, and, intriguingly, false positives show a trinucleotide profile very similar to one found in human tumors. Although the three simulated tumors differ in sequence contamination (deviation from normal cell sequence) and in subclonality, an ensemble of pipelines outperforms the best individual pipeline in all cases. BAMSurgeon is available at https://github.com/adamewing/bamsurgeon/.}, |
|
| 2668 | + langid = {english}, |
|
| 2669 | + pmcid = {PMC4856034}, |
|
| 2670 | + keywords = {Algorithms,Benchmarking,Crowdsourcing,Genome,Humans,Neoplasms,Polymorphism Single Nucleotide}, |
|
| 2671 | + file = {/Users/rmorin/Zotero/storage/I3SBB38K/Ewing et al. - 2015 - Combining tumor genome simulation with crowdsourci.pdf} |
|
| 2672 | +} |
|
| 2673 | + |
|
| 2674 | +@article{expert-bezanconHeterogeneousNuclearRibonucleoprotein2002, |
|
| 2675 | + title = {Heterogeneous {{Nuclear Ribonucleoprotein}} ({{hnRNP}}) {{K Is}} a {{Component}} of an {{Intronic Splicing Enhancer Complex That Activates}} the {{Splicing}} of the {{Alternative Exon 6A}} from {{Chicken}} β-{{Tropomyosin Pre-mRNA}} *}, |
|
| 2676 | + author = {Expert-Bezançon, Alain and Caer, Jean Pierre Le and Marie, Joëlle}, |
|
| 2677 | + date = {2002-05-10}, |
|
| 2678 | + journaltitle = {Journal of Biological Chemistry}, |
|
| 2679 | + shortjournal = {Journal of Biological Chemistry}, |
|
| 2680 | + volume = {277}, |
|
| 2681 | + number = {19}, |
|
| 2682 | + eprint = {11867641}, |
|
| 2683 | + eprinttype = {pmid}, |
|
| 2684 | + pages = {16614--16623}, |
|
| 2685 | + publisher = {Elsevier}, |
|
| 2686 | + issn = {0021-9258, 1083-351X}, |
|
| 2687 | + doi = {10.1074/jbc.M201083200}, |
|
| 2688 | + url = {https://www.jbc.org/article/S0021-9258(19)60703-9/abstract}, |
|
| 2689 | + urldate = {2022-09-27}, |
|
| 2690 | + abstract = {{$<$}p{$>$}Splicing of the chicken β-tropomyosin exon 6A is stimulated, both \emph{in vivo} and \emph{in vitro}, by an intronic pyrimidine-rich element (S4) located 37 nucleotides downstream of exon 6A. Several pyrimidine-rich sequences are able to substitute for the natural S4 enhancer with various stimulatory effects. We show that the different enhancer sequences recruit U1 small nuclear ribonucleoprotein (SnRNP) to the exon 6A 5′ splice site, with an efficiency that correlates with the splicing activation. By using RNA affinity and two-dimensional gel electrophoresis, we characterized several proteins that bind to the different enhancer sequences. Heterogeneous nuclear ribonucleoprotein (hnRNP) K and hnRNP I (polypyrimidine track-binding protein, PTB) exhibit a higher level of interaction with the strong enhancer sequences (S4) than with the weakest enhancers. Functional analysis shows that hnRNP K is a component of the enhancer complex that promotes exon 6A splicing through the wild-type S4 sequence. The addition of recombinant hnRNP K to nuclear extracts preincubated with poly(rC) RNA competitor completely restores splicing efficiency to the original level. hnRNP I (PTB) was also found associated with the strong enhancer sequences. Its function in the splicing of exon 6A is discussed.{$<$}/p{$>$}}, |
|
| 2691 | + langid = {english}, |
|
| 2692 | + file = {/Users/rmorin/Zotero/storage/3PY8MDYX/Expert-Bezançon et al. - 2002 - Heterogeneous Nuclear Ribonucleoprotein (hnRNP) K .pdf;/Users/rmorin/Zotero/storage/FZKW9ZBG/fulltext.html} |
|
| 2693 | +} |
|
| 2694 | + |
|
| 2695 | +@article{fabbriAnalysisChronicLymphocytic2011, |
|
| 2696 | + title = {Analysis of the Chronic Lymphocytic Leukemia Coding Genome: Role of {{NOTCH1}} Mutational Activation}, |
|
| 2697 | + shorttitle = {Analysis of the Chronic Lymphocytic Leukemia Coding Genome}, |
|
| 2698 | + author = {Fabbri, Giulia and Rasi, Silvia and Rossi, Davide and Trifonov, Vladimir and Khiabanian, Hossein and Ma, Jing and Grunn, Adina and Fangazio, Marco and Capello, Daniela and Monti, Sara and Cresta, Stefania and Gargiulo, Ernesto and Forconi, Francesco and Guarini, Anna and Arcaini, Luca and Paulli, Marco and Laurenti, Luca and Larocca, Luigi M. and Marasca, Roberto and Gattei, Valter and Oscier, David and Bertoni, Francesco and Mullighan, Charles G. and Foá, Robin and Pasqualucci, Laura and Rabadan, Raul and Dalla-Favera, Riccardo and Gaidano, Gianluca}, |
|
| 2699 | + date = {2011-07-04}, |
|
| 2700 | + journaltitle = {The Journal of Experimental Medicine}, |
|
| 2701 | + shortjournal = {J. Exp. Med.}, |
|
| 2702 | + volume = {208}, |
|
| 2703 | + number = {7}, |
|
| 2704 | + eprint = {21670202}, |
|
| 2705 | + eprinttype = {pmid}, |
|
| 2706 | + pages = {1389--1401}, |
|
| 2707 | + issn = {1540-9538}, |
|
| 2708 | + doi = {10.1084/jem.20110921}, |
|
| 2709 | + abstract = {The pathogenesis of chronic lymphocytic leukemia (CLL), the most common leukemia in adults, is still largely unknown. The full spectrum of genetic lesions that are present in the CLL genome, and therefore the number and identity of dysregulated cellular pathways, have not been identified. By combining next-generation sequencing and copy number analysis, we show here that the typical CLL coding genome contains {$<$}20 clonally represented gene alterations/case, including predominantly nonsilent mutations, and fewer copy number aberrations. These analyses led to the discovery of several genes not previously known to be altered in CLL. Although most of these genes were affected at low frequency in an expanded CLL screening cohort, mutational activation of NOTCH1, observed in 8.3\% of CLL at diagnosis, was detected at significantly higher frequency during disease progression toward Richter transformation (31.0\%), as well as in chemorefractory CLL (20.8\%). Consistent with the association of NOTCH1 mutations with clinically aggressive forms of the disease, NOTCH1 activation at CLL diagnosis emerged as an independent predictor of poor survival. These results provide initial data on the complexity of the CLL coding genome and identify a dysregulated pathway of diagnostic and therapeutic relevance.}, |
|
| 2710 | + langid = {english}, |
|
| 2711 | + pmcid = {PMC3135373}, |
|
| 2712 | + keywords = {Adult,Aged,Disease Progression,Drug Resistance Neoplasm,Female,Gene Dosage,Gene Expression Regulation Neoplastic,Genes Immunoglobulin Heavy Chain,Genome Human,Humans,Leukemia Lymphocytic Chronic B-Cell,Male,Middle Aged,Mutation,Polymorphism Single Nucleotide,Prognosis,Receptor Notch1,Treatment Failure} |
|
| 2713 | +} |
|
| 2714 | + |
|
| 2715 | +@article{fahiminiyaPolyadenylationSiteVariant2015, |
|
| 2716 | + title = {A Polyadenylation Site Variant Causes Transcript-Specific {{BMP1}} Deficiency and Frequent Fractures in Children}, |
|
| 2717 | + author = {Fahiminiya, Somayyeh and Al-Jallad, Hadil and Majewski, Jacek and Palomo, Telma and Moffatt, Pierre and Roschger, Paul and Klaushofer, Klaus and Glorieux, Francis H. and Rauch, Frank}, |
|
| 2718 | + date = {2015-01-15}, |
|
| 2719 | + journaltitle = {Human Molecular Genetics}, |
|
| 2720 | + shortjournal = {Human Molecular Genetics}, |
|
| 2721 | + volume = {24}, |
|
| 2722 | + number = {2}, |
|
| 2723 | + pages = {516--524}, |
|
| 2724 | + issn = {0964-6906}, |
|
| 2725 | + doi = {10.1093/hmg/ddu471}, |
|
| 2726 | + url = {https://doi.org/10.1093/hmg/ddu471}, |
|
| 2727 | + urldate = {2022-10-25}, |
|
| 2728 | + abstract = {We had previously published the clinical characteristics of a bone fragility disorder in children that was characterized mainly by lower extremity fractures and a mineralization defect in bone tissue but not on the growth plate level. We have now performed whole-exome sequencing on four unrelated individuals with this phenotype. Three individuals were homozygous for a nucleotide change in BMP1, affecting the polyadenylation signal of the transcript that codes for the short isoform of BMP1 (BMP1-1) (c.*241T\>C). In skin fibroblasts of these individuals, we found low levels of BMP1-1 transcript and protein. The fourth individual was compound heterozygous for the c.*241T\>C variant in BMP1-1 and a variant in BMP1 exon 15 (c.2107G\>C) that affected splicing in both BMP1-1 and the long isoform of BMP1 (BMP1-3). Both the homozygous 3′UTR variant and the compound heterozygous variants were associated with impaired procollagen type I C-propeptide cleavage, as the amount of free C-propeptide in the supernatant of skin fibroblasts was less than in controls. Peripheral quantitative computed tomography showed that all individuals had elevated volumetric cortical bone mineral density. Assessment of iliac bone samples by histomorphometry and quantitative backscattered electron imaging indicated that the onset of mineralization at bone formation sites was delayed, but that mineralized matrix was hypermineralized. These results show that isolated lack of BMP1-1 causes bone fragility in children.}, |
|
| 2729 | + file = {/Users/rmorin/Zotero/storage/AHSUMGDE/Fahiminiya et al. - 2015 - A polyadenylation site variant causes transcript-s.pdf;/Users/rmorin/Zotero/storage/IIX4GF4C/2901001.html} |
|
| 2730 | +} |
|
| 2731 | + |
|
| 2732 | +@article{fatehchandTolllikeReceptorLigands2016, |
|
| 2733 | + title = {Toll-like {{Receptor}} 4 {{Ligands Down-regulate Fcγ Receptor IIb}} ({{FcγRIIb}}) via {{MARCH3 Protein-mediated Ubiquitination}}.}, |
|
| 2734 | + author = {Fatehchand, Kavin and Ren, Li and Elavazhagan, Saranya and Fang, Huiqing and Mo, Xiaokui and Vasilakos, John P and Dietsch, Gregory N and Hershberg, Robert M and Tridandapani, Susheela and Butchar, Jonathan P}, |
|
| 2735 | + date = {2016-02}, |
|
| 2736 | + journaltitle = {J Biol Chem}, |
|
| 2737 | + volume = {291}, |
|
| 2738 | + number = {8}, |
|
| 2739 | + pages = {3895--3904}, |
|
| 2740 | + keywords = {nosource} |
|
| 2741 | +} |
|
| 2742 | + |
|
| 2743 | +@article{faveroSequenzaAllelespecificCopy2015, |
|
| 2744 | + title = {Sequenza: Allele-Specific Copy Number and Mutation Profiles from Tumor Sequencing Data}, |
|
| 2745 | + shorttitle = {Sequenza}, |
|
| 2746 | + author = {Favero, F. and Joshi, T. and Marquard, A. M. and Birkbak, N. J. and Krzystanek, M. and Li, Q. and Szallasi, Z. and Eklund, A. C.}, |
|
| 2747 | + date = {2015-01}, |
|
| 2748 | + journaltitle = {Annals of Oncology: Official Journal of the European Society for Medical Oncology}, |
|
| 2749 | + shortjournal = {Ann Oncol}, |
|
| 2750 | + volume = {26}, |
|
| 2751 | + number = {1}, |
|
| 2752 | + eprint = {25319062}, |
|
| 2753 | + eprinttype = {pmid}, |
|
| 2754 | + pages = {64--70}, |
|
| 2755 | + issn = {1569-8041}, |
|
| 2756 | + doi = {10.1093/annonc/mdu479}, |
|
| 2757 | + abstract = {BACKGROUND: Exome or whole-genome deep sequencing of tumor DNA along with paired normal DNA can potentially provide a detailed picture of the somatic mutations that characterize the tumor. However, analysis of such sequence data can be complicated by the presence of normal cells in the tumor specimen, by intratumor heterogeneity, and by the sheer size of the raw data. In particular, determination of copy number variations from exome sequencing data alone has proven difficult; thus, single nucleotide polymorphism (SNP) arrays have often been used for this task. Recently, algorithms to estimate absolute, but not allele-specific, copy number profiles from tumor sequencing data have been described. MATERIALS AND METHODS: We developed Sequenza, a software package that uses paired tumor-normal DNA sequencing data to estimate tumor cellularity and ploidy, and to calculate allele-specific copy number profiles and mutation profiles. We applied Sequenza, as well as two previously published algorithms, to exome sequence data from 30 tumors from The Cancer Genome Atlas. We assessed the performance of these algorithms by comparing their results with those generated using matched SNP arrays and processed by the allele-specific copy number analysis of tumors (ASCAT) algorithm. RESULTS: Comparison between Sequenza/exome and SNP/ASCAT revealed strong correlation in cellularity (Pearson's r = 0.90) and ploidy estimates (r = 0.42, or r = 0.94 after manual inspecting alternative solutions). This performance was noticeably superior to previously published algorithms. In addition, in artificial data simulating normal-tumor admixtures, Sequenza detected the correct ploidy in samples with tumor content as low as 30\%. CONCLUSIONS: The agreement between Sequenza and SNP array-based copy number profiles suggests that exome sequencing alone is sufficient not only for identifying small scale mutations but also for estimating cellularity and inferring DNA copy number aberrations.}, |
|
| 2758 | + langid = {english}, |
|
| 2759 | + pmcid = {PMC4269342}, |
|
| 2760 | + keywords = {Algorithms,Alleles,Base Sequence,cancer genomics,copy number alterations,DNA Copy Number Variations,Exome,Gene Dosage,High-Throughput Nucleotide Sequencing,Humans,Mutation,mutations,Neoplasms,next-generation sequencing,Polymorphism Single Nucleotide,Sequence Analysis DNA,software,Software}, |
|
| 2761 | + file = {/Users/rmorin/Zotero/storage/NRNVA4AX/Favero et al. - 2015 - Sequenza allele-specific copy number and mutation.pdf} |
|
| 2762 | +} |
|
| 2763 | + |
|
| 2764 | +@article{fentonFollicularLymphomaNovel2002, |
|
| 2765 | + title = {Follicular Lymphoma with a Novel t(14;18) Breakpoint Involving the Immunoglobulin Heavy Chain Switch Mu Region Indicates an Origin from Germinal Center {{B}} Cells}, |
|
| 2766 | + author = {Fenton, James A. L. and Vaandrager, Jan-Willem and Aarts, Wilhelmina M. and Bende, Richard J. and Heering, Karel and family=Dijk, given=Martin, prefix=van, useprefix=true and Morgan, Gareth and family=Noesel, given=Carel J. M., prefix=van, useprefix=true and Schuuring, Ed and Kluin, Philip M.}, |
|
| 2767 | + date = {2002-01-15}, |
|
| 2768 | + journaltitle = {Blood}, |
|
| 2769 | + shortjournal = {Blood}, |
|
| 2770 | + volume = {99}, |
|
| 2771 | + number = {2}, |
|
| 2772 | + eprint = {11781262}, |
|
| 2773 | + eprinttype = {pmid}, |
|
| 2774 | + pages = {716--718}, |
|
| 2775 | + issn = {0006-4971}, |
|
| 2776 | + doi = {10.1182/blood.v99.2.716}, |
|
| 2777 | + abstract = {With the use of DNA-fiber fluorescent in situ hybridization, a BCL2 protein positive follicular lymphoma with a novel BCL2 breakpoint involving the immunoglobulin heavy chain (IGH) switch mu (S(mu)) region instead of the J(H) or D(H) gene segments was identified. Sequence analysis showed that the genomic breakpoint is localized between the S(mu) region of the IGH complex and the first intron of BCL2. Reverse-transcriptase polymerase chain reaction showed expression of a unique hybrid IGH-BCL2 transcript involving the transcription initiation site I(mu). Sequence analysis of the V(H) region of the functional nontranslocated IGH allele showed multiple shared somatic mutations but also a high intraclonal variation (53 differences in 15 clones), compatible with the lymphoma cells staying in or re-entering the germinal center. This is the first example of a t(14;18) translocation that results from an illegitimate IGH class-switch recombination during the germinal center B-cell stage.}, |
|
| 2778 | + langid = {english}, |
|
| 2779 | + keywords = {Aged,B-Lymphocytes,Base Sequence,Cell Differentiation,Chromosome Breakage,Chromosomes Human Pair 14,Chromosomes Human Pair 16,DNA Neoplasm,Embryonal Carcinoma Stem Cells,Female,Genes bcl-2,Genes Immunoglobulin,Genes Switch,Germinal Center,Humans,Immunoglobulin Heavy Chains,Lymphoma Follicular,Molecular Sequence Data,Neoplastic Stem Cells,Oncogene Proteins Fusion,Reverse Transcriptase Polymerase Chain Reaction,RNA Messenger,RNA Neoplasm,Somatic Hypermutation Immunoglobulin,Translocation Genetic} |
|
| 2780 | +} |
|
| 2781 | + |
|
| 2782 | +@article{fernandez-rodriguezMYD88L265PMutation2014, |
|
| 2783 | + title = {{{MYD88}} ({{L265P}}) Mutation Is an Independent Prognostic Factor for Outcome in Patients with Diffuse Large {{B-cell}} Lymphoma.}, |
|
| 2784 | + author = {Fernández-Rodríguez, C and Bellosillo, B and García-García, M and Sánchez-González, B and Gimeno, E and Vela, M C and Serrano, S and Besses, C and Salar, A}, |
|
| 2785 | + date = {2014-10}, |
|
| 2786 | + journaltitle = {Leukemia}, |
|
| 2787 | + volume = {28}, |
|
| 2788 | + number = {10}, |
|
| 2789 | + pages = {2104--2106}, |
|
| 2790 | + keywords = {nosource} |
|
| 2791 | +} |
|
| 2792 | + |
|
| 2793 | +@article{ferreroKMT2DMutationsTP532019, |
|
| 2794 | + title = {{{KMT2D}} Mutations and {{TP53}} Disruptions Are Poor Prognostic Biomarkers in Mantle Cell Lymphoma Receiving High-Dose Therapy: A {{FIL}} Study}, |
|
| 2795 | + shorttitle = {{{KMT2D}} Mutations and {{TP53}} Disruptions Are Poor Prognostic Biomarkers in Mantle Cell Lymphoma Receiving High-Dose Therapy}, |
|
| 2796 | + author = {Ferrero, Simone and Rossi, Davide and Rinaldi, Andrea and Bruscaggin, Alessio and Spina, Valeria and Eskelund, Christian W. and Evangelista, Andrea and Moia, Riccardo and Kwee, Ivo and Dahl, Christina and Rocco, Alice Di and Stefoni, Vittorio and Diop, Fary and Favini, Chiara and Ghione, Paola and Mahmoud, Abdurraouf Mokhtar and Schipani, Mattia and Kolstad, Arne and Barbero, Daniela and Novero, Domenico and Paulli, Marco and Zamò, Alberto and Jerkeman, Mats and family=Silva, given=Maria Gomez, prefix=da, useprefix=false and Santoro, Armando and Molinari, Annalia and Ferreri, Andres and Grønbæk, Kirsten and Piccin, Andrea and Cortelazzo, Sergio and Bertoni, Francesco and Ladetto, Marco and Gaidano, Gianluca}, |
|
| 2797 | + date = {2019-09-19}, |
|
| 2798 | + journaltitle = {Haematologica}, |
|
| 2799 | + eprint = {31537689}, |
|
| 2800 | + eprinttype = {pmid}, |
|
| 2801 | + issn = {0390-6078, 1592-8721}, |
|
| 2802 | + doi = {10.3324/haematol.2018.214056}, |
|
| 2803 | + url = {http://www.haematologica.org/content/early/2019/09/17/haematol.2018.214056}, |
|
| 2804 | + urldate = {2019-12-24}, |
|
| 2805 | + abstract = {In recent years, the outcome of mantle cell lymphoma has improved, especially in younger patients, receiving cytarabine-containing chemoimmunotherapy and autologous stem cell transplantation. Nevertheless, a proportion of mantle cell lymphoma patients still experience early failure. To identify biomarkers anticipating failure of intensive chemotherapy in mantle cell lymphoma, we performed target resequencing and DNA profiling of purified tumor samples collected from patients enrolled in the prospective FIL-MCL0208 phase III trial (high-dose chemoimmunotherapy followed by autologous transplantation and randomized lenalidomide maintenance). Mutations of KMT2D and disruption of TP53 by deletion or mutation associated with an increased risk of progression and death, both in univariate and multivariate analysis. By adding KMT2D mutations and TP53 disruption to the MIPI-c backbone, we derived a new prognostic index, the MIPI-genetic. The MIPI-g improved the model discrimination ability compared to the MIPI-c alone, defining three risk groups: i) low-risk patients (4-years progression free survival and overall survival of 72.0\% and 94.5\%); ii) intermediate-risk patients (4-years progression free survival and overall survival of 42.2\% and 65.8\%) and iii) high-risk patients (4-years progression free survival and overall survival of 11.5\% and 44.9\%). Our results: i) confirm that TP53 disruption identifies a high-risk population characterized by poor sensitivity to conventional or intensified chemotherapy; ii) provide the pivotal evidence that patients harboring KMT2D mutations share the same poor outcome as patients harboring TP53 disruption; and iii) allow to develop a tool for the identification of high-risk mantle cell lymphoma patients for whom novel therapeutic strategies need to be investigated. (Trial registered at clinicaltrials.gov identifier: NCT02354313)}, |
|
| 2806 | + langid = {english}, |
|
| 2807 | + file = {/Users/rmorin/Zotero/storage/CADICB4V/haematol.2018.214056.html} |
|
| 2808 | +} |
|
| 2809 | + |
|
| 2810 | +@article{filipitsCyclinD3Predictive, |
|
| 2811 | + title = {Cyclin {{D3}} Is a Predictive and Prognostic Factor in Diffuse Large {{B-cell}} Lymphoma}, |
|
| 2812 | + author = {Filipits, Martin and Jaeger, Ulrich and Pohl, Gudrun and Stranzl, Thomas and Simonitsch, Ingrid and Kaider, Alexandra and Skrabs, Cathrin and Pirker, Robert}, |
|
| 2813 | + journaltitle = {Clin Cancer Res}, |
|
| 2814 | + volume = {8}, |
|
| 2815 | + number = {3}, |
|
| 2816 | + pages = {729--733}, |
|
| 2817 | + keywords = {nosource} |
|
| 2818 | +} |
|
| 2819 | + |
|
| 2820 | +@article{fisetteHnRNPA1HnRNP2010, |
|
| 2821 | + title = {{{hnRNP A1}} and {{hnRNP H}} Can Collaborate to Modulate 5′ Splice Site Selection}, |
|
| 2822 | + author = {Fisette, Jean-François and Toutant, Johanne and Dugré-Brisson, Samuel and Desgroseillers, Luc and Chabot, Benoit}, |
|
| 2823 | + date = {2010-01}, |
|
| 2824 | + journaltitle = {RNA}, |
|
| 2825 | + shortjournal = {RNA}, |
|
| 2826 | + volume = {16}, |
|
| 2827 | + number = {1}, |
|
| 2828 | + eprint = {19926721}, |
|
| 2829 | + eprinttype = {pmid}, |
|
| 2830 | + pages = {228--238}, |
|
| 2831 | + issn = {1355-8382}, |
|
| 2832 | + doi = {10.1261/rna.1890310}, |
|
| 2833 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2802032/}, |
|
| 2834 | + urldate = {2022-09-27}, |
|
| 2835 | + abstract = {The mammalian proteins hnRNP A1 and hnRNP H control many splicing decisions in viral and cellular primary transcripts. To explain some of these activities, we have proposed that self-interactions between bound proteins create an RNA loop that represses internal splice sites while simultaneously activating the external sites that are brought in closer proximity. Here we show that a variety of hnRNP H binding sites can affect 5′ splice site selection. The addition of two sets of hnRNP H sites in a model pre-mRNA modulates 5′ splice site selection cooperatively, consistent with the looping model. Notably, binding sites for hnRNP A1 and H on the same pre-mRNA can similarly collaborate to modulate 5′ splice site selection. The C-terminal portion of hnRNP H that contains the glycine-rich domains (GRD) is essential for splicing activity, and it can be functionally replaced by the GRD of hnRNP A1. Finally, we used the bioluminescence resonance energy transfer (BRET) technology to document the existence of homotypic and heterotypic interactions between hnRNP H and hnRNP A1 in live cells. Overall, our study suggests that interactions between different hnRNP proteins bound to distinct locations on a pre-mRNA can change its conformation to affect splicing decisions.}, |
|
| 2836 | + pmcid = {PMC2802032}, |
|
| 2837 | + file = {/Users/rmorin/Zotero/storage/TDMW9PCM/Fisette et al. - 2010 - hnRNP A1 and hnRNP H can collaborate to modulate 5.pdf} |
|
| 2838 | +} |
|
| 2839 | + |
|
| 2840 | +@article{fordGenotypingCopyNumber2020, |
|
| 2841 | + title = {Genotyping and {{Copy Number Analysis}} of {{Immunoglobin Heavy Chain Variable Genes Using Long Reads}}}, |
|
| 2842 | + author = {Ford, Michael and Haghshenas, Ehsan and Watson, Corey T. and Sahinalp, S. Cenk}, |
|
| 2843 | + date = {2020-02-04}, |
|
| 2844 | + journaltitle = {iScience}, |
|
| 2845 | + shortjournal = {iScience}, |
|
| 2846 | + volume = {23}, |
|
| 2847 | + number = {3}, |
|
| 2848 | + eprint = {32109676}, |
|
| 2849 | + eprinttype = {pmid}, |
|
| 2850 | + issn = {2589-0042}, |
|
| 2851 | + doi = {10.1016/j.isci.2020.100883}, |
|
| 2852 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7044747/}, |
|
| 2853 | + urldate = {2020-05-21}, |
|
| 2854 | + abstract = {One of the remaining challenges to describing an individual's genetic variation lies in the highly heterogeneous and complex genomic regions that impede the use of classical reference-guided mapping and assembly approaches. Once such region is the Immunoglobulin heavy chain locus (IGH), which is critical for the development of antibodies and the adaptive immune system. We describe ImmunoTyper, the first PacBio-based genotyping and copy number calling tool specifically designed for IGH V genes (IGHV). We demonstrate that ImmunoTyper's multi-stage clustering and combinatorial optimization approach represents the most comprehensive IGHV genotyping approach published to date, through validation using gold-standard IGH reference sequence. This preliminary work establishes the feasibility of fine-grained genotype and copy number analysis using error-prone long reads in complex multi-gene loci and opens the door for in-depth investigation into IGHV heterogeneity using accessible and increasingly common whole-genome sequence., • We describe ImmunoTyper, a WGS Immunoglobulin Heavy Chain Variable Genotyping tool • Immunotyper is the first such tool to use long reads and call alleles for pseudogenes • We demonstrate high allele call accuracy using simulated and real WGS data , Biological Sciences; Bioinformatics; Computational Bioinformatics; Genomic Analysis}, |
|
| 2855 | + pmcid = {PMC7044747}, |
|
| 2856 | + file = {/Users/rmorin/Zotero/storage/BPEHTZH2/Ford et al. - 2020 - Genotyping and Copy Number Analysis of Immunoglobi.pdf} |
|
| 2857 | +} |
|
| 2858 | + |
|
| 2859 | +@article{frankeAssociationAnalysisCopy2015, |
|
| 2860 | + title = {Association Analysis of Copy Numbers of {{FC-gamma}} Receptor Genes for Rheumatoid Arthritis and Other Immune-Mediated Phenotypes}, |
|
| 2861 | + author = {Franke, Lude and family=Bannoudi, given=Hanane, prefix=el, useprefix=true and Jansen, Diahann T S L and Kok, Klaas and Trynka, Gosia and Diogo, Dorothee and Swertz, Morris and Fransen, Karin and Knevel, Rachel and Gutierrez-Achury, Javier and {rlestig}, Lisbeth Auml and Greenberg, Jeffrey D and Kremer, Joel and Pappas, Dimitrios A and Kanterakis, Alexandros and Weersma, Rinse K and family=Helm-van Mil, given=Annette H M, prefix=van der, useprefix=true and Guryev, Viktor and family=Dahlqvist, given=Solbritt Rantap, prefix=auml auml, useprefix=false and Gregersen, Peter K and Plenge, Robert M and Wijmenga, Cisca and Huizinga, Tom W-J and Ioan-Facsinay, Andreea and Toes, Rene E M and Zhernakova, Alexandra}, |
|
| 2862 | + date = {2015-05}, |
|
| 2863 | + volume = {24}, |
|
| 2864 | + number = {2}, |
|
| 2865 | + pages = {263--270}, |
|
| 2866 | + keywords = {nosource} |
|
| 2867 | +} |
|
| 2868 | + |
|
| 2869 | +@article{fregelMitochondrialDNAHaplogroup2015, |
|
| 2870 | + title = {Mitochondrial {{DNA}} Haplogroup Phylogeny of the Dog: {{Proposal}} for a Cladistic Nomenclature}, |
|
| 2871 | + shorttitle = {Mitochondrial {{DNA}} Haplogroup Phylogeny of the Dog}, |
|
| 2872 | + author = {Fregel, Rosa and Suárez, Nicolás M. and Betancor, Eva and González, Ana M. and Cabrera, Vicente M. and Pestano, José}, |
|
| 2873 | + date = {2015-05}, |
|
| 2874 | + journaltitle = {Mitochondrion}, |
|
| 2875 | + shortjournal = {Mitochondrion}, |
|
| 2876 | + volume = {22}, |
|
| 2877 | + eprint = {25869968}, |
|
| 2878 | + eprinttype = {pmid}, |
|
| 2879 | + pages = {75--84}, |
|
| 2880 | + issn = {1872-8278}, |
|
| 2881 | + doi = {10.1016/j.mito.2015.04.001}, |
|
| 2882 | + abstract = {Canis lupus familiaris mitochondrial DNA analysis has increased in recent years, not only for the purpose of deciphering dog domestication but also for forensic genetic studies or breed characterization. The resultant accumulation of data has increased the need for a normalized and phylogenetic-based nomenclature like those provided for human maternal lineages. Although a standardized classification has been proposed, haplotype names within clades have been assigned gradually without considering the evolutionary history of dog mtDNA. Moreover, this classification is based only on the D-loop region, proven to be insufficient for phylogenetic purposes due to its high number of recurrent mutations and the lack of relevant information present in the coding region. In this study, we design 1) a refined mtDNA cladistic nomenclature from a phylogenetic tree based on complete sequences, classifying dog maternal lineages into haplogroups defined by specific diagnostic mutations, and 2) a coding region SNP analysis that allows a more accurate classification into haplogroups when combined with D-loop sequencing, thus improving the phylogenetic information obtained in dog mitochondrial DNA studies.}, |
|
| 2883 | + langid = {english}, |
|
| 2884 | + keywords = {Animals,Canis lupus familiaris,Cladistic,DNA Mitochondrial,Dog,Dogs,Haplogroup,Haplotypes,Mitochondrial DNA,Nomenclature,Phylogeny,Terminology as Topic} |
|
| 2885 | +} |
|
| 2886 | + |
|
| 2887 | +@article{FrequentCopyNumber2014, |
|
| 2888 | + title = {Frequent Copy Number Variations of {{PI3K}}/{{AKT}} Pathway and Aberrant Protein Expressions of {{PI3K}} Subunits Are Associated with Inferior Survival in Diffuse Large {{B}} Cell Lymphoma}, |
|
| 2889 | + date = {2014-01}, |
|
| 2890 | + pages = {1--11}, |
|
| 2891 | + keywords = {nosource} |
|
| 2892 | +} |
|
| 2893 | + |
|
| 2894 | +@article{fritzRNAbindingProteinPTBP12020, |
|
| 2895 | + title = {The {{RNA-binding}} Protein {{PTBP1}} Promotes {{ATPase-dependent}} Dissociation of the {{RNA}} Helicase {{UPF1}} to Protect Transcripts from Nonsense-Mediated {{mRNA}} Decay}, |
|
| 2896 | + author = {Fritz, Sarah E. and Ranganathan, Soumya and Wang, Clara D. and Hogg, J. Robert}, |
|
| 2897 | + date = {2020-08-14}, |
|
| 2898 | + journaltitle = {Journal of Biological Chemistry}, |
|
| 2899 | + shortjournal = {Journal of Biological Chemistry}, |
|
| 2900 | + volume = {295}, |
|
| 2901 | + number = {33}, |
|
| 2902 | + pages = {11613--11625}, |
|
| 2903 | + issn = {0021-9258}, |
|
| 2904 | + doi = {10.1074/jbc.RA120.013824}, |
|
| 2905 | + url = {https://www.sciencedirect.com/science/article/pii/S0021925817484626}, |
|
| 2906 | + urldate = {2022-10-04}, |
|
| 2907 | + abstract = {The sequence-specific RNA-binding proteins PTBP1 (polypyrimidine tract–binding protein 1) and HNRNP L (heterogeneous nuclear ribonucleoprotein L) protect mRNAs from nonsense-mediated decay (NMD) by preventing the UPF1 RNA helicase from associating with potential decay targets. Here, by analyzing in vitro helicase activity, dissociation of UPF1 from purified mRNPs, and transcriptome-wide UPF1 RNA binding, we present the mechanistic basis for inhibition of NMD by PTBP1. Unlike mechanisms of RNA stabilization that depend on direct competition for binding sites among protective RNA-binding proteins and decay factors, PTBP1 promotes displacement of UPF1 already bound to potential substrates. Our results show that PTBP1 directly exploits the tendency of UPF1 to release RNA upon ATP binding and hydrolysis. We further find that UPF1 sensitivity to PTBP1 is coordinated by a regulatory loop in domain 1B of UPF1. We propose that the UPF1 regulatory loop and protective proteins control kinetic proofreading of potential NMD substrates, presenting a new model for RNA helicase regulation and target selection in the NMD pathway.}, |
|
| 2908 | + langid = {english}, |
|
| 2909 | + keywords = {3′-untranslated region,ATPase,hnRNP L,kinetic proofreading,nonsense-mediated mRNA decay,poly(A)-binding protein,polypyrimidine tract-binding protein 1 (PTBP1),RNA degradation,RNA helicase,RNA metabolism,RNA turnover,RNA–protein interaction,transcriptomics,UPF1}, |
|
| 2910 | + file = {/Users/rmorin/Zotero/storage/DALFG7JK/Fritz et al. - 2020 - The RNA-binding protein PTBP1 promotes ATPase-depe.pdf;/Users/rmorin/Zotero/storage/DVA3U7KY/S0021925817484626.html} |
|
| 2911 | +} |
|
| 2912 | + |
|
| 2913 | +@online{FullArticleNanopore, |
|
| 2914 | + title = {Full Article: {{Nanopore}} Sequencing Detects Structural Variants in Cancer}, |
|
| 2915 | + url = {https://www.tandfonline.com/doi/full/10.1080/15384047.2016.1139236}, |
|
| 2916 | + urldate = {2020-05-21}, |
|
| 2917 | + file = {/Users/rmorin/Zotero/storage/BQTGCI9N/15384047.2016.html} |
|
| 2918 | +} |
|
| 2919 | + |
|
| 2920 | +@article{gagliardiAnalysisUgandanCervical2020, |
|
| 2921 | + title = {Analysis of {{Ugandan}} Cervical Carcinomas Identifies Human Papillomavirus Clade-Specific Epigenome and Transcriptome Landscapes}, |
|
| 2922 | + author = {Gagliardi, Alessia and Porter, Vanessa L. and Zong, Zusheng and Bowlby, Reanne and Titmuss, Emma and Namirembe, Constance and Griner, Nicholas B. and Petrello, Hilary and Bowen, Jay and Chan, Simon K. and Culibrk, Luka and Darragh, Teresa M. and Stoler, Mark H. and Wright, Thomas C. and Gesuwan, Patee and Dyer, Maureen A. and Ma, Yussanne and Mungall, Karen L. and Jones, Steven J. M. and Nakisige, Carolyn and Novik, Karen and Orem, Jackson and Origa, Martin and Gastier-Foster, Julie M. and Yarchoan, Robert and Casper, Corey and Mills, Gordon B. and Rader, Janet S. and Ojesina, Akinyemi I. and Gerhard, Daniela S. and Mungall, Andrew J. and Marra, Marco A.}, |
|
| 2923 | + date = {2020-08}, |
|
| 2924 | + journaltitle = {Nature Genetics}, |
|
| 2925 | + shortjournal = {Nat Genet}, |
|
| 2926 | + volume = {52}, |
|
| 2927 | + number = {8}, |
|
| 2928 | + eprint = {32747824}, |
|
| 2929 | + eprinttype = {pmid}, |
|
| 2930 | + pages = {800--810}, |
|
| 2931 | + issn = {1546-1718}, |
|
| 2932 | + doi = {10.1038/s41588-020-0673-7}, |
|
| 2933 | + abstract = {Cervical cancer is the most common cancer affecting sub-Saharan African women and is prevalent among HIV-positive (HIV+) individuals. No comprehensive profiling of cancer genomes, transcriptomes or epigenomes has been performed in this population thus far. We characterized 118 tumors from Ugandan patients, of whom 72 were HIV+, and performed extended mutation analysis on an additional 89 tumors. We detected human papillomavirus (HPV)-clade-specific differences in tumor DNA methylation, promoter- and enhancer-associated histone marks, gene expression and pathway dysregulation. Changes in histone modification at HPV integration events were correlated with upregulation of nearby genes and endogenous retroviruses.}, |
|
| 2934 | + langid = {english}, |
|
| 2935 | + pmcid = {PMC7498180}, |
|
| 2936 | + keywords = {Adult,Aged,DNA Methylation,Epigenome,Female,Humans,Middle Aged,Papillomaviridae,Papillomavirus Infections,Promoter Regions Genetic,Signal Transduction,Transcriptome,Uganda,Up-Regulation,Uterine Cervical Neoplasms}, |
|
| 2937 | + file = {/Users/rmorin/Zotero/storage/FSL97IPQ/Gagliardi et al. - 2020 - Analysis of Ugandan cervical carcinomas identifies.pdf} |
|
| 2938 | +} |
|
| 2939 | + |
|
| 2940 | +@article{gallardoAberrantHnRNPExpression2016, |
|
| 2941 | + title = {Aberrant {{hnRNP K}} Expression: {{All}} Roads Lead to Cancer}, |
|
| 2942 | + shorttitle = {Aberrant {{hnRNP K}} Expression}, |
|
| 2943 | + author = {Gallardo, Miguel and Hornbaker, Marisa J. and Zhang, Xiaorui and Hu, Peter and Bueso-Ramos, Carlos and Post, Sean M.}, |
|
| 2944 | + date = {2016-04-06}, |
|
| 2945 | + journaltitle = {Cell Cycle}, |
|
| 2946 | + shortjournal = {Cell Cycle}, |
|
| 2947 | + volume = {15}, |
|
| 2948 | + number = {12}, |
|
| 2949 | + eprint = {27049467}, |
|
| 2950 | + eprinttype = {pmid}, |
|
| 2951 | + pages = {1552--1557}, |
|
| 2952 | + issn = {1538-4101}, |
|
| 2953 | + doi = {10.1080/15384101.2016.1164372}, |
|
| 2954 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4934053/}, |
|
| 2955 | + urldate = {2023-01-09}, |
|
| 2956 | + abstract = {The classification of a gene as an oncogene or a tumor suppressor has been a staple of cancer biology for decades. However, as we delve deeper into the biology of these genes, this simple classification has become increasingly difficult for some. In the case of heterogeneous nuclear ribonuclear protein K (hnRNP K), its role as a tumor suppressor has recently been described in acute myeloid leukemia and demonstrated in a haploinsufficient mouse model. In contrast, data from other clinical correlation studies suggest that hnRNP K may be more fittingly described as an oncogene, due to its increased levels in a variety of malignancies. hnRNP K is a multifunctional protein that can regulate both oncogenic and tumor suppressive pathways through a bevy of chromatin-, DNA-, RNA-, and protein-mediated activates, suggesting its aberrant expression may have broad-reaching cellular impacts. In this review, we highlight our current understanding of hnRNP K, with particular emphasis on its apparently dichotomous roles in tumorigenesis.}, |
|
| 2957 | + pmcid = {PMC4934053}, |
|
| 2958 | + file = {/Users/rmorin/Zotero/storage/C7RPJHSB/Gallardo et al. - 2016 - Aberrant hnRNP K expression All roads lead to can.pdf} |
|
| 2959 | +} |
|
| 2960 | + |
|
| 2961 | +@article{gallardoHnRNPHaploinsufficientTumor2015, |
|
| 2962 | + title = {{{hnRNP K}} Is a Haploinsufficient Tumor Suppressor That Regulates Proliferation and Differentiation Programs in Hematologic Malignancies}, |
|
| 2963 | + author = {Gallardo, Miguel and Lee, Hun Ju and Zhang, Xiaorui and Bueso-Ramos, Carlos and Pageon, Laura R. and McArthur, Mark and Multani, Asha and Nazha, Aziz and Manshouri, Taghi and Parker-Thornburg, Jan and Rapado, Inmaculada and Quintas-Cardama, Alfonso and Kornblau, Steven M. and Martinez-Lopez, Joaquin and Post, Sean M.}, |
|
| 2964 | + date = {2015-10-12}, |
|
| 2965 | + journaltitle = {Cancer cell}, |
|
| 2966 | + shortjournal = {Cancer Cell}, |
|
| 2967 | + volume = {28}, |
|
| 2968 | + number = {4}, |
|
| 2969 | + eprint = {26412324}, |
|
| 2970 | + eprinttype = {pmid}, |
|
| 2971 | + pages = {486--499}, |
|
| 2972 | + issn = {1535-6108}, |
|
| 2973 | + doi = {10.1016/j.ccell.2015.09.001}, |
|
| 2974 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4652598/}, |
|
| 2975 | + urldate = {2022-09-25}, |
|
| 2976 | + abstract = {hnRNP K regulates cellular programs and changes in its expression and mutational status have been implicated in neoplastic malignancies. To directly examine its role in tumorigenesis, we generated a mouse model harboring an Hnrnpk knock-out allele (Hnrnpk+/−). Hnrnpk haploinsufficiency resulted in reduced survival, increased tumor formation, genomic instability, and the development of transplantable hematopoietic neoplasms with myeloproliferation. Reduced hnRNP K expression attenuated p21 activation, downregulated C/EBP levels, and activated STAT3 signaling. Additionally, analysis of samples from primary acute myeloid leukemia patients harboring a partial deletion of chromosome 9 revealed a significant decrease in HNRNPK expression. Together, these data implicate hnRNP K in the development of hematological disorders and suggest hnRNP K acts as a tumor suppressor.}, |
|
| 2977 | + pmcid = {PMC4652598}, |
|
| 2978 | + file = {/Users/rmorin/Zotero/storage/CLMIKNCN/Gallardo et al. - 2015 - hnRNP K is a haploinsufficient tumor suppressor th.pdf} |
|
| 2979 | +} |
|
| 2980 | + |
|
| 2981 | +@article{gallardoUncoveringRoleRNABinding2019, |
|
| 2982 | + title = {Uncovering the {{Role}} of {{RNA-Binding Protein hnRNP K}} in {{B-Cell Lymphomas}}}, |
|
| 2983 | + author = {Gallardo, Miguel and Malaney, Prerna and Aitken, Marisa J L and Zhang, Xiaorui and Link, Todd M and Shah, Vrutant and Alybayev, Sanzhar and Wu, Meng-Han and Pageon, Laura R and Ma, Huaxian and Jacamo, Rodrigo and Yu, Li and Xu-Monette, Zijun Y and Steinman, Haley and Lee, Hun Ju and Sarbassov, Dos and Rapado, Inmaculada and Barton, Michelle C and Martinez-Lopez, Joaquin and Bueso-Ramos, Carlos and Young, Ken H and Post, Sean M}, |
|
| 2984 | + date = {2019-05-11}, |
|
| 2985 | + journaltitle = {JNCI Journal of the National Cancer Institute}, |
|
| 2986 | + shortjournal = {J Natl Cancer Inst}, |
|
| 2987 | + volume = {112}, |
|
| 2988 | + number = {1}, |
|
| 2989 | + eprint = {31077320}, |
|
| 2990 | + eprinttype = {pmid}, |
|
| 2991 | + pages = {95--106}, |
|
| 2992 | + issn = {0027-8874}, |
|
| 2993 | + doi = {10.1093/jnci/djz078}, |
|
| 2994 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7489062/}, |
|
| 2995 | + urldate = {2022-09-22}, |
|
| 2996 | + abstract = {Background Heterogeneous nuclear ribonucleoprotein K (hnRNP~K) is an RNA-binding protein that is aberrantly expressed in cancers. We and others have previously shown that reduced hnRNP~K expression downmodulates tumor-suppressive programs. However, overexpression of hnRNP~K is the more commonly observed clinical phenomenon, yet its functional consequences and clinical significance remain unknown. Methods Clinical implications of hnRNP~K overexpression were examined through immunohistochemistry on samples from patients with diffuse large B-cell lymphoma who did not harbor MYC alterations (n\,=\,75). A novel transgenic mouse model that overexpresses hnRNP~K specifically in B cells was generated to directly examine the role of hnRNP~K overexpression in mice (three transgenic lines). Molecular consequences of hnRNP~K overexpression were determined through proteomics, formaldehyde-RNA-immunoprecipitation sequencing, and biochemical assays. Therapeutic response to BET-bromodomain inhibition in the context of hnRNP~K overexpression was evaluated in vitro and in vivo (n\,=\,3 per group). All statistical tests were two-sided. Results hnRNP~K is overexpressed in diffuse large B-cell lymphoma patients without MYC genomic alterations. This overexpression is associated with dismal overall survival and progression-free survival (P\,{$<$}\,.001). Overexpression of hnRNP~K in transgenic mice resulted in the development of lymphomas and reduced survival (P\,{$<$}\,.001 for all transgenic lines; Line 171[n\,=\,30]: hazard ratio [HR]\,=\,64.23, 95\% confidence interval [CI]\,=\,26.1 to 158.0; Line 173 [n\,=\,31]: HR\,=\,25.27, 95\% CI\,=\,10.3 to 62.1; Line 177 [n\,=\,25]: HR\,=\,119.5, 95\% CI\,=\,42.7 to 334.2, compared with wild-type mice). Clinical samples, mouse models, global screening assays, and biochemical studies revealed that hnRNP~K’s oncogenic potential stems from its ability to posttranscriptionally and translationally regulate MYC. Consequently, Hnrnpk overexpression renders cells sensitive to BET-bromodomain-inhibition in both in vitro and transplantation models, which represents a strategy for mitigating hnRNP~K-mediated c-Myc activation in patients. Conclusion Our findings indicate that hnRNP~K is a bona fide oncogene when overexpressed and represents a novel mechanism for c-Myc activation in the absence of MYC lesions.}, |
|
| 2997 | + pmcid = {PMC7489062}, |
|
| 2998 | + file = {/Users/rmorin/Zotero/storage/X8U8RZ5A/Gallardo et al. - 2019 - Uncovering the Role of RNA-Binding Protein hnRNP K.pdf} |
|
| 2999 | +} |
|
| 3000 | + |
|
| 3001 | +@article{gamarnikTwoFunctionalComplexes1997, |
|
| 3002 | + title = {Two Functional Complexes Formed by {{KH}} Domain Containing Proteins with the 5' Noncoding Region of Poliovirus {{RNA}}}, |
|
| 3003 | + author = {Gamarnik, A. V. and Andino, R.}, |
|
| 3004 | + date = {1997-08}, |
|
| 3005 | + journaltitle = {RNA (New York, N.Y.)}, |
|
| 3006 | + shortjournal = {RNA}, |
|
| 3007 | + volume = {3}, |
|
| 3008 | + number = {8}, |
|
| 3009 | + eprint = {9257647}, |
|
| 3010 | + eprinttype = {pmid}, |
|
| 3011 | + pages = {882--892}, |
|
| 3012 | + issn = {1355-8382}, |
|
| 3013 | + abstract = {The 5' noncoding region of the poliovirus genome contains RNA structures important for replication and translation. Here we show that two closely related cellular poly(rC) binding proteins (PCBP1 and PCBP2) bind to the terminal cloverleaf structure and facilitate the interaction of the viral protein 3CD (the uncleaved precursor of the protease-polymerase). In addition, these cellular proteins bind to stem-loop IV of the internal ribosomal entry site. The proteins are cytoplasmic and largely associated with ribosomes; they appear to dimerize in solution and to form heterodimers when binding to stem-loop IV. Initiation of viral translation in Xenopus oocytes is strongly inhibited by co-injection of specific antibodies directed against PCBP1 or PCBP2, indicating that the poly(rC) binding proteins may facilitate this process. Furthermore, PCPB-depleted HeLa extracts translate poliovirus RNA inefficiently and the activity is partially restored by addition of recombinant PCBP proteins.}, |
|
| 3014 | + langid = {english}, |
|
| 3015 | + pmcid = {PMC1369533}, |
|
| 3016 | + keywords = {Animals,Antibodies,Base Sequence,Binding Sites,Cytoplasm,DNA-Binding Proteins,Female,HeLa Cells,Heterogeneous-Nuclear Ribonucleoproteins,Humans,Molecular Sequence Data,Nucleic Acid Conformation,Oocytes,Poliovirus,Protein Biosynthesis,Recombinant Proteins,RNA Viral,RNA-Binding Proteins,Transcription Factors} |
|
| 3017 | +} |
|
| 3018 | + |
|
| 3019 | +@article{ganapathiGeneticLandscapeDural2016, |
|
| 3020 | + title = {The Genetic Landscape of Dural Marginal Zone Lymphomas}, |
|
| 3021 | + author = {Ganapathi, Karthik A. and Jobanputra, Vaidehi and Iwamoto, Fabio and Jain, Preti and Chen, Jinli and Cascione, Luciano and Nahum, Odelia and Levy, Brynn and Xie, Yi and Khattar, Pallavi and Hoehn, Daniela and Bertoni, Francesco and Murty, Vundavalli V. and Pittaluga, Stefania and Jaffe, Elaine S. and Alobeid, Bachir and Mansukhani, Mahesh M. and Bhagat, Govind}, |
|
| 3022 | + date = {2016-05-27}, |
|
| 3023 | + journaltitle = {Oncotarget}, |
|
| 3024 | + volume = {7}, |
|
| 3025 | + number = {28}, |
|
| 3026 | + pages = {43052--43061}, |
|
| 3027 | + publisher = {Impact Journals}, |
|
| 3028 | + issn = {1949-2553}, |
|
| 3029 | + doi = {10.18632/oncotarget.9678}, |
|
| 3030 | + url = {https://www.oncotarget.com/article/9678/text/}, |
|
| 3031 | + urldate = {2024-05-25}, |
|
| 3032 | + abstract = {https://doi.org/10.18632/oncotarget.9678 Karthik A. Ganapathi, Vaidehi Jobanputra, Fabio Iwamoto, Preti Jain, Jinli Chen, Luciano Cascione, Odelia Nahum, Brynn Levy, Yi Xie, Pallavi Khattar, Daniela...}, |
|
| 3033 | + langid = {english}, |
|
| 3034 | + file = {/Users/rmorin/Zotero/storage/3KI8JEJP/Ganapathi et al. - 2016 - The genetic landscape of dural marginal zone lymph.pdf} |
|
| 3035 | +} |
|
| 3036 | + |
|
| 3037 | +@article{gaoIntegrativeAnalysisComplex2013, |
|
| 3038 | + title = {Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the {{cBioPortal}}}, |
|
| 3039 | + author = {Gao, Jianjiong and Aksoy, Bülent Arman and Dogrusoz, Ugur and Dresdner, Gideon and Gross, Benjamin and Sumer, S. Onur and Sun, Yichao and Jacobsen, Anders and Sinha, Rileen and Larsson, Erik and Cerami, Ethan and Sander, Chris and Schultz, Nikolaus}, |
|
| 3040 | + date = {2013-04-02}, |
|
| 3041 | + journaltitle = {Science Signaling}, |
|
| 3042 | + shortjournal = {Sci Signal}, |
|
| 3043 | + volume = {6}, |
|
| 3044 | + number = {269}, |
|
| 3045 | + eprint = {23550210}, |
|
| 3046 | + eprinttype = {pmid}, |
|
| 3047 | + pages = {pl1}, |
|
| 3048 | + issn = {1937-9145}, |
|
| 3049 | + doi = {10.1126/scisignal.2004088}, |
|
| 3050 | + abstract = {The cBioPortal for Cancer Genomics (http://cbioportal.org) provides a Web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. The portal reduces molecular profiling data from cancer tissues and cell lines into readily understandable genetic, epigenetic, gene expression, and proteomic events. The query interface combined with customized data storage enables researchers to interactively explore genetic alterations across samples, genes, and pathways and, when available in the underlying data, to link these to clinical outcomes. The portal provides graphical summaries of gene-level data from multiple platforms, network visualization and analysis, survival analysis, patient-centric queries, and software programmatic access. The intuitive Web interface of the portal makes complex cancer genomics profiles accessible to researchers and clinicians without requiring bioinformatics expertise, thus facilitating biological discoveries. Here, we provide a practical guide to the analysis and visualization features of the cBioPortal for Cancer Genomics.}, |
|
| 3051 | + langid = {english}, |
|
| 3052 | + pmcid = {PMC4160307}, |
|
| 3053 | + keywords = {Gene Expression Profiling,Gene Regulatory Networks,Genetic Predisposition to Disease,Genomics,Humans,Information Storage and Retrieval,Internet,Neoplasms,Reproducibility of Results,Software}, |
|
| 3054 | + file = {/Users/rmorin/Zotero/storage/86ALCFT7/Gao et al. - 2013 - Integrative analysis of complex cancer genomics an.pdf} |
|
| 3055 | +} |
|
| 3056 | + |
|
| 3057 | +@article{garapaty-raoIdentificationEZH2EZH12013, |
|
| 3058 | + title = {Identification of {{EZH2}} and {{EZH1 Small Molecule Inhibitors}} with {{Selective Impact}} on {{Diffuse Large B Cell Lymphoma Cell Growth}}}, |
|
| 3059 | + author = {Garapaty-Rao, Shivani and Nasveschuk, Christopher and Gagnon, Alexandre and Chan, Eric Y and Sandy, Peter and Busby, Jennifer and Balasubramanian, Srividya and Campbell, Robert and Zhao, Feng and Bergeron, Louise and Audia, James E and Albrecht, Brian K and Harmange, Jean-Christophe and Cummings, Richard and Trojer, Patrick}, |
|
| 3060 | + date = {2013-11}, |
|
| 3061 | + journaltitle = {Chemistry \& Biology}, |
|
| 3062 | + volume = {20}, |
|
| 3063 | + number = {11}, |
|
| 3064 | + pages = {1329--1339}, |
|
| 3065 | + keywords = {nosource} |
|
| 3066 | +} |
|
| 3067 | + |
|
| 3068 | +@article{garbatiHistoneAcetyltransferaseP300, |
|
| 3069 | + title = {Histone Acetyltransferase P300 Is a Coactivator for Transcription Factor {{REL}} and Is {{C-terminally}} Truncated in the Human Diffuse Large {{B-cell}} Lymphoma Cell Line {{RC-K8}}}, |
|
| 3070 | + author = {Garbati, Michael and Alço, Gökçen and Gilmore, Thomas}, |
|
| 3071 | + journaltitle = {Cancer Lett}, |
|
| 3072 | + volume = {291}, |
|
| 3073 | + number = {2}, |
|
| 3074 | + pages = {237--245}, |
|
| 3075 | + keywords = {nosource} |
|
| 3076 | +} |
|
| 3077 | + |
|
| 3078 | +@article{garcia-ramirezCrebbpLossCooperates2017, |
|
| 3079 | + title = {Crebbp Loss Cooperates with {{Bcl2}} Overexpression to Promote Lymphoma in Mice}, |
|
| 3080 | + author = {García-Ramírez, Idoia and Tadros, Saber and González-Herrero, Inés and Martín-Lorenzo, Alberto and Rodríguez-Hernández, Guillermo and Moore, Dalia and Ruiz-Roca, Lucía and Blanco, Oscar and Alonso-López, Diego and Rivas, Javier De Las and Hartert, Keenan and Duval, Romain and Klinkebiel, David and Bast, Martin and Vose, Julie and Lunning, Matthew and Fu, Kai and Greiner, Timothy and Rodrigues-Lima, Fernando and Jiménez, Rafael and Criado, Francisco Javier García and Cenador, María Begoña García and Brindle, Paul and Vicente-Dueñas, Carolina and Alizadeh, Ash and Sánchez-García, Isidro and Green, Michael R.}, |
|
| 3081 | + date = {2017-05-11}, |
|
| 3082 | + journaltitle = {Blood}, |
|
| 3083 | + shortjournal = {Blood}, |
|
| 3084 | + volume = {129}, |
|
| 3085 | + number = {19}, |
|
| 3086 | + eprint = {28288979}, |
|
| 3087 | + eprinttype = {pmid}, |
|
| 3088 | + pages = {2645--2656}, |
|
| 3089 | + issn = {1528-0020}, |
|
| 3090 | + doi = {10.1182/blood-2016-08-733469}, |
|
| 3091 | + abstract = {CREBBP is targeted by inactivating mutations in follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL). Here, we provide evidence from transgenic mouse models that Crebbp deletion results in deficits in B-cell development and can cooperate with Bcl2 overexpression to promote B-cell lymphoma. Through transcriptional and epigenetic profiling of these B cells, we found that Crebbp inactivation was associated with broad transcriptional alterations, but no changes in the patterns of histone acetylation at the proximal regulatory regions of these genes. However, B cells with Crebbp inactivation showed high expression of Myc and patterns of altered histone acetylation that were localized to intragenic regions, enriched for Myc DNA binding motifs, and showed Myc binding. Through the analysis of CREBBP mutations from a large cohort of primary human FL and DLBCL, we show a significant difference in the spectrum of CREBBP mutations in these 2 diseases, with higher frequencies of nonsense/frameshift mutations in DLBCL compared with FL. Together, our data therefore provide important links between Crebbp inactivation and Bcl2 dependence and show a role for Crebbp inactivation in the induction of Myc expression. We suggest this may parallel the role of CREBBP frameshift/nonsense mutations in DLBCL that result in loss of the protein, but may contrast the role of missense mutations in the lysine acetyltransferase domain that are more frequently observed in FL and yield an inactive protein.}, |
|
| 3092 | + langid = {english}, |
|
| 3093 | + pmcid = {PMC5428458}, |
|
| 3094 | + keywords = {Animals,B-Lymphocytes,CREB-Binding Protein,Epigenesis Genetic,Gene Deletion,Gene Expression Regulation Neoplastic,Humans,Lymphoma Follicular,Lymphoma Large B-Cell Diffuse,Mice,Mice Transgenic,Mutation,Proto-Oncogene Proteins c-bcl-2}, |
|
| 3095 | + file = {/Users/rmorin/Zotero/storage/98AUYEK7/García-Ramírez et al. - 2017 - Crebbp loss cooperates with Bcl2 overexpression to.pdf} |
|
| 3096 | +} |
|
| 3097 | + |
|
| 3098 | +@article{gargMCPIP1EndoribonucleaseActivity2015, |
|
| 3099 | + title = {{{MCPIP1 Endoribonuclease Activity Negatively Regulates Interleukin-17-Mediated Signaling}} and {{Inflammation}}}, |
|
| 3100 | + author = {Garg, Abhishek V and Amatya, Nilesh and Chen, Kong and Cruz, J Agustin and Grover, Prerna and Whibley, Natasha and Conti, Heather R and Mir, Gerard Hernandez and Sirakova, Tatiana and Childs, Erin C and Smithgall, Thomas E and Biswas, Partha S and Kolls, Jay K and McGeachy, Mandy J and Kolattukudy, Pappachan E and Gaffen, Sarah L}, |
|
| 3101 | + date = {2015-09}, |
|
| 3102 | + journaltitle = {Immunity}, |
|
| 3103 | + volume = {43}, |
|
| 3104 | + number = {3}, |
|
| 3105 | + pages = {475--487}, |
|
| 3106 | + keywords = {nosource} |
|
| 3107 | +} |
|
| 3108 | + |
|
| 3109 | +@article{gaudreauHeterogeneousNuclearRibonucleoprotein2016, |
|
| 3110 | + title = {Heterogeneous {{Nuclear Ribonucleoprotein L}} Is Required for the Survival and Functional Integrity of Murine Hematopoietic Stem Cells}, |
|
| 3111 | + author = {Gaudreau, Marie-Claude and Grapton, Damien and Helness, Anne and Vadnais, Charles and Fraszczak, Jennifer and Shooshtarizadeh, Peiman and Wilhelm, Brian and Robert, François and Heyd, Florian and Möröy, Tarik}, |
|
| 3112 | + date = {2016-06-07}, |
|
| 3113 | + journaltitle = {Scientific Reports}, |
|
| 3114 | + shortjournal = {Sci Rep}, |
|
| 3115 | + volume = {6}, |
|
| 3116 | + number = {1}, |
|
| 3117 | + pages = {27379}, |
|
| 3118 | + publisher = {Nature Publishing Group}, |
|
| 3119 | + issn = {2045-2322}, |
|
| 3120 | + doi = {10.1038/srep27379}, |
|
| 3121 | + url = {https://www.nature.com/articles/srep27379}, |
|
| 3122 | + urldate = {2022-10-04}, |
|
| 3123 | + abstract = {The proliferation and survival of hematopoietic stem cells (HSCs) has to be strictly coordinated to ensure the timely production of all blood cells. Here we report that the splice factor and RNA binding protein hnRNP L (heterogeneous nuclear ribonucleoprotein L) is required for hematopoiesis, since its genetic ablation in mice reduces almost all blood cell lineages and causes premature death of the animals. In agreement with this, we observed that hnRNP L deficient HSCs lack both the ability to self-renew and foster hematopoietic differentiation in transplanted hosts. They also display mitochondrial dysfunction, elevated levels of γH2AX, are Annexin V positive and incorporate propidium iodide indicating that they undergo cell death. Lin-c-Kit+ fetal liver cells from hnRNP L deficient mice show high p53 protein levels and up-regulation of p53 target genes. In addition, cells lacking hnRNP L up-regulated the expression of the death receptors TrailR2 and CD95/Fas and show Caspase-3, Caspase-8 and Parp cleavage. Treatment with the pan-caspase inhibitor Z-VAD-fmk, but not the deletion of p53, restored cell survival in hnRNP L deficient cells. Our data suggest that hnRNP L is critical for the survival and functional integrity of HSCs by restricting the activation of caspase-dependent death receptor pathways.}, |
|
| 3124 | + issue = {1}, |
|
| 3125 | + langid = {english}, |
|
| 3126 | + keywords = {Apoptosis,Haematopoietic stem cells}, |
|
| 3127 | + file = {/Users/rmorin/Zotero/storage/2C778AIZ/Gaudreau et al. - 2016 - Heterogeneous Nuclear Ribonucleoprotein L is requi.pdf;/Users/rmorin/Zotero/storage/RTAMM4IC/srep27379.html} |
|
| 3128 | +} |
|
| 3129 | + |
|
| 3130 | +@article{gautreySRSF3HnRNPH12015, |
|
| 3131 | + title = {{{SRSF3}} and {{hnRNP H1}} Regulate a Splicing Hotspot of {{HER2}} in Breast Cancer Cells}, |
|
| 3132 | + author = {Gautrey, Hannah and Jackson, Claire and Dittrich, Anna-Lena and Browell, David and Lennard, Thomas and Tyson-Capper, Alison}, |
|
| 3133 | + date = {2015-09-14}, |
|
| 3134 | + journaltitle = {RNA Biology}, |
|
| 3135 | + shortjournal = {RNA Biol}, |
|
| 3136 | + volume = {12}, |
|
| 3137 | + number = {10}, |
|
| 3138 | + eprint = {26367347}, |
|
| 3139 | + eprinttype = {pmid}, |
|
| 3140 | + pages = {1139--1151}, |
|
| 3141 | + issn = {1547-6286}, |
|
| 3142 | + doi = {10.1080/15476286.2015.1076610}, |
|
| 3143 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4829299/}, |
|
| 3144 | + urldate = {2022-09-28}, |
|
| 3145 | + abstract = {Overexpression of the oncogene HER2 occurs in 20–30\% of invasive breast cancer and is associated with poor prognosis. A number of different splice variants of HER2 have been identified which produce functionally different proteins. Previously these splice variants have been investigated separately, but in the present study we collectively look at the expression and regulation of a group of HER2 splice variants produced by a splicing hotspot. Initial investigation in a cohort of tumor samples showed large variations in HER2 variant expression between patient samples. RNA interference studies identified 2 splicing factors involved in the regulation of splicing within this region, hnRNP H1 and SRSF3. siRNA targeting hnRNP H1 increases levels of X5 and the oncogenic variant Δ16HER2. Furthermore RNA chromatography assays demonstrated binding of hnRNP H1 to RNA in this region. Additionally the proto-oncogene SRSF3 was also identified as an important regulator of splicing with SRSF3 knockdown resulting in changes in all the splice variants located at the hotspot. Most notably knockdown of SRSF3 resulted in a switch from the oncogenic Δ16HER2 to p100 which inhibits cell proliferation. Binding of SRSF3 to RNA within this region was also demonstrated by RNA chromatography and more specifically 2 SRSF3 binding sites were identified within exon 15. SRSF3 and hnRNP H1 are the first splicing factors identified which regulate the production of these functionally distinct HER2 splice variants and therefore maybe important for the regulation of HER2 signaling.}, |
|
| 3146 | + pmcid = {PMC4829299}, |
|
| 3147 | + file = {/Users/rmorin/Zotero/storage/FH48KJZF/Gautrey et al. - 2015 - SRSF3 and hnRNP H1 regulate a splicing hotspot of .pdf} |
|
| 3148 | +} |
|
| 3149 | + |
|
| 3150 | +@article{gebauerActivatingMutationsAffecting2014, |
|
| 3151 | + title = {Activating Mutations Affecting the {{NF-kappa B}} Pathway and {{EZH2-mediated}} Epigenetic Regulation Are Rare Events in Primary Mediastinal Large {{B-cell}} Lymphoma}, |
|
| 3152 | + author = {Gebauer, Niklas and Hardel, Tim Tristan and Gebauer, Judith and Bernard, Veronica and Merz, Hartmut and Feller, Alfred C. and Rades, Dirk and Biersack, Harald and Lehnert, Hendrik and Thorns, Christoph}, |
|
| 3153 | + date = {2014-10}, |
|
| 3154 | + journaltitle = {Anticancer Research}, |
|
| 3155 | + shortjournal = {Anticancer Res}, |
|
| 3156 | + volume = {34}, |
|
| 3157 | + number = {10}, |
|
| 3158 | + eprint = {25275047}, |
|
| 3159 | + eprinttype = {pmid}, |
|
| 3160 | + pages = {5503--5507}, |
|
| 3161 | + issn = {1791-7530}, |
|
| 3162 | + abstract = {BACKGROUND: Primary mediastinal large B-cell lymphoma (PMBL) is a distinct subtype of diffuse large B-cell lymphoma (DLBCL) frequently observed in young patients. High-dose immunochemotherapy constitutes the current therapeutic gold-standard, despite significant toxicity and serious late effects. Several hotspots harboring oncogenic gain-of-function mutations were recently shown to pose vital hallmarks in activated B-cell like (ABC-) (CD79B, CARD11 and MYD88) and germinal center like (GCB-) DLBCL (EZH2), respectively. Several promising targeted-therapy approaches, derived from these findings, are currently under development. MATERIALS AND METHODS: We thoroughly characterized a cohort of 25 untreated patients with de novo PMBL by immunohistochemical and cytogenetic means and assessed the prevalence of activating mutations affecting EZH2, CD79B and CARD11 utilizing a polymerase chain reaction (PCR)-based capillary sequencing approach. Moreover, the MYD88 p. L265P status was assessed by employing a pyrosequencing approach. RESULTS: PMBLs included in this study did not harbor any of the reported hotspot mutations activating the nuclear factor (NF)-kappa B signaling cascade or the EZH2-mediated epigenetic deregulation of gene expression. Immunohistochemical characterization revealed an ABC phenotype in 44\% (n=11) of cases. CONCLUSION: We report that genetic alterations of these genes are rare events in PMBL unlike other subtypes of DLBCL. Our findings suggest that a substantial subset of PMBL patients may benefit from treatment approaches targeting BCR-mediated activation of NF-kappa B.}, |
|
| 3163 | + langid = {english}, |
|
| 3164 | + keywords = {Adolescent,Adult,Aged,Aged 80 and over,CARD11,CD79B,Enhancer of Zeste Homolog 2 Protein,Epigenesis Genetic,EZH2,Female,Gene Expression Regulation Neoplastic,Humans,Lymphoma Large B-Cell Diffuse,Male,Mediastinal Neoplasms,Middle Aged,Mutation,Mutation Rate,MYD88,NF-kappa B,NFkappaB pathway,Oncogenes,Polycomb Repressive Complex 2,Primary mediastinal large B-cell lymphoma,Signal Transduction,Young Adult} |
|
| 3165 | +} |
|
| 3166 | + |
|
| 3167 | +@online{GENETICSUBGROUPSINFORM, |
|
| 3168 | + title = {{{GENETIC SUBGROUPS INFORM ON PATHOBIOLOGY IN ADULT AND PEDIATRIC BURKITT LYMPHOMA}} | {{Blood}} | {{American Society}} of {{Hematology}}}, |
|
| 3169 | + url = {https://ashpublications.org/blood/article/doi/10.1182/blood.2022016534/486739/GENETIC-SUBGROUPS-INFORM-ON-PATHOBIOLOGY-IN-ADULT}, |
|
| 3170 | + urldate = {2022-10-31}, |
|
| 3171 | + file = {/Users/rmorin/Zotero/storage/43KJ2UVH/GENETIC-SUBGROUPS-INFORM-ON-PATHOBIOLOGY-IN-ADULT.html} |
|
| 3172 | +} |
|
| 3173 | + |
|
| 3174 | +@online{GenomewideMutationalSignatures, |
|
| 3175 | + title = {Genome-Wide Mutational Signatures Revealed Distinct Developmental Paths for Human {{B}} Cell Lymphomas | {{Journal}} of {{Experimental Medicine}} | {{Rockefeller University Press}}}, |
|
| 3176 | + url = {https://rupress.org/jem/article/218/2/e20200573/211517/Genome-wide-mutational-signatures-revealed}, |
|
| 3177 | + urldate = {2023-10-17}, |
|
| 3178 | + file = {/Users/rmorin/Zotero/storage/C5GVZ9TR/Genome-wide-mutational-signatures-revealed.html} |
|
| 3179 | +} |
|
| 3180 | + |
|
| 3181 | +@article{GenomicEpigenomicLandscapes2013, |
|
| 3182 | + title = {Genomic and {{Epigenomic Landscapes}} of {{Adult De Novo Acute Myeloid Leukemia}}}, |
|
| 3183 | + date = {2013-05-30}, |
|
| 3184 | + journaltitle = {New England Journal of Medicine}, |
|
| 3185 | + volume = {368}, |
|
| 3186 | + number = {22}, |
|
| 3187 | + eprint = {23634996}, |
|
| 3188 | + eprinttype = {pmid}, |
|
| 3189 | + pages = {2059--2074}, |
|
| 3190 | + publisher = {Massachusetts Medical Society}, |
|
| 3191 | + issn = {0028-4793}, |
|
| 3192 | + doi = {10.1056/NEJMoa1301689}, |
|
| 3193 | + url = {https://doi.org/10.1056/NEJMoa1301689}, |
|
| 3194 | + urldate = {2022-05-22}, |
|
| 3195 | + abstract = {The molecular pathogenesis of acute myeloid leukemia (AML) has been studied with the use of cytogenetic analysis for more than three decades. Recurrent chromosomal structural variations are well established as diagnostic and prognostic markers, suggesting that acquired genetic abnormalities (i.e., somatic mutations) have an essential role in pathogenesis.1,2 However, nearly 50\% of AML samples have a normal karyotype, and many of these genomes lack structural abnormalities, even when assessed with high-density comparative genomic hybridization or single-nucleotide polymorphism (SNP) arrays3–5 (see Glossary). Targeted sequencing has identified recurrent mutations in FLT3, NPM1, KIT, CEBPA, and TET2.6–8 Massively parallel . . .}, |
|
| 3196 | + file = {/Users/rmorin/Zotero/storage/NF7PD29L/2013 - Genomic and Epigenomic Landscapes of Adult De Novo.pdf;/Users/rmorin/Zotero/storage/UXAM4CRU/nejmoa1301689.html} |
|
| 3197 | +} |
|
| 3198 | + |
|
| 3199 | +@article{geuensHnRNPFamilyInsights2016, |
|
| 3200 | + title = {The {{hnRNP}} Family: Insights into Their Role in Health and Disease}, |
|
| 3201 | + shorttitle = {The {{hnRNP}} Family}, |
|
| 3202 | + author = {Geuens, Thomas and Bouhy, Delphine and Timmerman, Vincent}, |
|
| 3203 | + date = {2016-08}, |
|
| 3204 | + journaltitle = {Human Genetics}, |
|
| 3205 | + shortjournal = {Hum. Genet.}, |
|
| 3206 | + volume = {135}, |
|
| 3207 | + number = {8}, |
|
| 3208 | + eprint = {27215579}, |
|
| 3209 | + eprinttype = {pmid}, |
|
| 3210 | + pages = {851--867}, |
|
| 3211 | + issn = {1432-1203}, |
|
| 3212 | + doi = {10.1007/s00439-016-1683-5}, |
|
| 3213 | + abstract = {Heterogeneous nuclear ribonucleoproteins (hnRNPs) represent a large family of RNA-binding proteins (RBPs) that contribute to multiple aspects of nucleic acid metabolism including alternative splicing, mRNA stabilization, and transcriptional and translational regulation. Many hnRNPs share general features, but differ in domain composition and functional properties. This review will discuss the current knowledge about the different hnRNP family members, focusing on their structural and functional divergence. Additionally, we will highlight their involvement in neurodegenerative diseases and cancer, and the potential to develop RNA-based therapies.}, |
|
| 3214 | + langid = {english}, |
|
| 3215 | + pmcid = {PMC4947485}, |
|
| 3216 | + keywords = {Alternative Splicing,Amyotrophic Lateral Sclerosis Patient,Auxiliary Domain,C9orf72 Repeat Expansion,Heterogeneous-Nuclear Ribonucleoproteins,hnRNP Family,Humans,Neoplasms,Neurodegenerative Diseases,Protein Biosynthesis,RNA Messenger,RNA Stability,RNA-Binding Proteins,Spinal Muscular Atrophy,Transcription Genetic}, |
|
| 3217 | + file = {/Users/rmorin/Zotero/storage/V3ZMNS54/Geuens et al. - 2016 - The hnRNP family insights into their role in heal.pdf} |
|
| 3218 | +} |
|
| 3219 | + |
|
| 3220 | +@article{giganteUsingLongreadSequencing2019, |
|
| 3221 | + title = {Using Long-Read Sequencing to Detect Imprinted {{DNA}} Methylation}, |
|
| 3222 | + author = {Gigante, Scott and Gouil, Quentin and Lucattini, Alexis and Keniry, Andrew and Beck, Tamara and Tinning, Matthew and Gordon, Lavinia and Woodruff, Chris and Speed, Terence P. and Blewitt, Marnie E. and Ritchie, Matthew E.}, |
|
| 3223 | + date = {2019-07-05}, |
|
| 3224 | + journaltitle = {Nucleic Acids Research}, |
|
| 3225 | + shortjournal = {Nucleic Acids Res.}, |
|
| 3226 | + volume = {47}, |
|
| 3227 | + number = {8}, |
|
| 3228 | + eprint = {30793194}, |
|
| 3229 | + eprinttype = {pmid}, |
|
| 3230 | + pages = {e46}, |
|
| 3231 | + issn = {1362-4962}, |
|
| 3232 | + doi = {10.1093/nar/gkz107}, |
|
| 3233 | + abstract = {Systematic variation in the methylation of cytosines at CpG sites plays a critical role in early development of humans and other mammals. Of particular interest are regions of differential methylation between parental alleles, as these often dictate monoallelic gene expression, resulting in parent of origin specific control of the embryonic transcriptome and subsequent development, in a phenomenon known as genomic imprinting. Using long-read nanopore sequencing we show that, with an average genomic coverage of ∼10, it is possible to determine both the level of methylation of CpG sites and the haplotype from which each read arises. The long-read property is exploited to characterize, using novel methods, both methylation and haplotype for reads that have reduced basecalling precision compared to Sanger sequencing. We validate the analysis both through comparison of nanopore-derived methylation patterns with those from Reduced Representation Bisulfite Sequencing data and through comparison with previously reported data. Our analysis successfully identifies known imprinting control regions (ICRs) as well as some novel differentially methylated regions which, due to their proximity to hitherto unknown monoallelically expressed genes, may represent new ICRs.}, |
|
| 3234 | + langid = {english}, |
|
| 3235 | + pmcid = {PMC6486641}, |
|
| 3236 | + keywords = {Alleles,Animals,Chromosome Mapping,CpG Islands,DNA Methylation,Embryo Mammalian,Female,Genome,Genomic Imprinting,Genotyping Techniques,Haplotypes,High-Throughput Nucleotide Sequencing,Male,Mice,Placenta,Pregnancy,Sequence Analysis DNA}, |
|
| 3237 | + file = {/Users/rmorin/Zotero/storage/P9FF9KLW/Gigante et al. - 2019 - Using long-read sequencing to detect imprinted DNA.pdf} |
|
| 3238 | +} |
|
| 3239 | + |
|
| 3240 | +@article{gilletteQuantitativeAnalysisPeptides2012, |
|
| 3241 | + title = {Quantitative Analysis of Peptides and Proteins in Biomedicine by Targeted Mass Spectrometry}, |
|
| 3242 | + author = {Gillette, Michael A and Carr, Steven A}, |
|
| 3243 | + date = {2012-12}, |
|
| 3244 | + journaltitle = {Nature Methods}, |
|
| 3245 | + volume = {10}, |
|
| 3246 | + number = {1}, |
|
| 3247 | + eprint = {23269374}, |
|
| 3248 | + eprinttype = {pmid}, |
|
| 3249 | + pages = {nmeth.2309}, |
|
| 3250 | + issn = {1548-7105}, |
|
| 3251 | + doi = {10.1038/nmeth.2309}, |
|
| 3252 | + url = {http://dx.doi.org/10.1038/nmeth.2309}, |
|
| 3253 | + abstract = {Targeted mass spectrometry (MS) is becoming widely used in academia and in pharmaceutical and biotechnology industries for sensitive and quantitative detection of proteins, peptides and post-translational modifications. Here we describe the increasing importance of targeted MS technologies in clinical proteomics and the potential key roles these techniques will have in bridging biomedical discovery and clinical implementation.}, |
|
| 3254 | + keywords = {nosource} |
|
| 3255 | +} |
|
| 3256 | + |
|
| 3257 | +@article{gintherRaceEthnicityNIH2011, |
|
| 3258 | + title = {Race, Ethnicity, and {{NIH}} Research Awards}, |
|
| 3259 | + author = {Ginther, Donna K. and Schaffer, Walter T. and Schnell, Joshua and Masimore, Beth and Liu, Faye and Haak, Laurel L. and Kington, Raynard}, |
|
| 3260 | + date = {2011-08-19}, |
|
| 3261 | + journaltitle = {Science (New York, N.Y.)}, |
|
| 3262 | + shortjournal = {Science}, |
|
| 3263 | + volume = {333}, |
|
| 3264 | + number = {6045}, |
|
| 3265 | + eprint = {21852498}, |
|
| 3266 | + eprinttype = {pmid}, |
|
| 3267 | + pages = {1015--1019}, |
|
| 3268 | + issn = {1095-9203}, |
|
| 3269 | + doi = {10.1126/science.1196783}, |
|
| 3270 | + abstract = {We investigated the association between a U.S. National Institutes of Health (NIH) R01 applicant's self-identified race or ethnicity and the probability of receiving an award by using data from the NIH IMPAC II grant database, the Thomson Reuters Web of Science, and other sources. Although proposals with strong priority scores were equally likely to be funded regardless of race, we find that Asians are 4 percentage points and black or African-American applicants are 13 percentage points less likely to receive NIH investigator-initiated research funding compared with whites. After controlling for the applicant's educational background, country of origin, training, previous research awards, publication record, and employer characteristics, we find that black applicants remain 10 percentage points less likely than whites to be awarded NIH research funding. Our results suggest some leverage points for policy intervention.}, |
|
| 3271 | + langid = {english}, |
|
| 3272 | + pmcid = {PMC3412416}, |
|
| 3273 | + keywords = {Asian People,Biomedical Research,Black or African American,Black People,Databases Factual,Education Graduate,Ethnicity,Fellowships and Scholarships,Financing Government,Hispanic or Latino,Humans,Likelihood Functions,Models Statistical,National Institutes of Health (U.S.),Peer Review Research,Publishing,Racial Groups,Research Personnel,Research Support as Topic,United States,White People}, |
|
| 3274 | + file = {/Users/rmorin/Zotero/storage/X5GWNSNQ/Ginther et al. - 2011 - Race, ethnicity, and NIH research awards.pdf} |
|
| 3275 | +} |
|
| 3276 | + |
|
| 3277 | +@article{gisselbrechtSalvageRegimensAutologous2010, |
|
| 3278 | + title = {Salvage Regimens with Autologous Transplantation for Relapsed Large {{B-cell}} Lymphoma in the Rituximab Era}, |
|
| 3279 | + author = {Gisselbrecht, Christian and Glass, Bertram and Mounier, Nicolas and Singh Gill, Devinder and Linch, David C. and Trneny, Marek and Bosly, Andre and Ketterer, Nicolas and Shpilberg, Ofer and Hagberg, Hans and Ma, David and Brière, Josette and Moskowitz, Craig H. and Schmitz, Norbert}, |
|
| 3280 | + date = {2010-09-20}, |
|
| 3281 | + journaltitle = {Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology}, |
|
| 3282 | + shortjournal = {J Clin Oncol}, |
|
| 3283 | + volume = {28}, |
|
| 3284 | + number = {27}, |
|
| 3285 | + eprint = {20660832}, |
|
| 3286 | + eprinttype = {pmid}, |
|
| 3287 | + pages = {4184--4190}, |
|
| 3288 | + issn = {1527-7755}, |
|
| 3289 | + doi = {10.1200/JCO.2010.28.1618}, |
|
| 3290 | + abstract = {PURPOSE: Salvage chemotherapy followed by high-dose therapy and autologous stem-cell transplantation (ASCT) is the standard treatment for relapsed diffuse large B-cell lymphoma (DLBCL). Salvage regimens have never been compared; their efficacy in the rituximab era is unknown. PATIENTS AND METHODS: Patients with CD20(+) DLBCL in first relapse or who were refractory after first-line therapy were randomly assigned to either rituximab, ifosfamide, etoposide, and carboplatin (R-ICE) or rituximab, dexamethasone, high-dose cytarabine, and cisplatin (R-DHAP). Responding patients received high-dose chemotherapy and ASCT. RESULTS: The median age of the 396 patients enrolled (R-ICE, n = 202; R-DHAP, n = 194) was 55 years. Similar response rates were observed after three cycles of R-ICE (63.5\%; 95\% CI, 56\% to 70\%) and R-DHAP (62.8\%; 95 CI, 55\% to 69\%). Factors affecting response rates (P {$<$} .001) were refractory disease/relapse less than versus more than 12 months after diagnosis (46\% v 88\%, respectively), International Prognostic Index (IPI) of more than 1 versus 0 to 1 (52\% v 71\%, respectively), and prior rituximab treatment versus no prior rituximab (51\% v 83\%, respectively). There was no significant difference between R-ICE and R-DHAP for 3-year event-free survival (EFS) or overall survival. Three-year EFS was affected by prior rituximab treatment versus no rituximab (21\% v 47\%, respectively), relapse less than versus more than 12 months after diagnosis (20\% v 45\%, respectively), and IPI of 2 to 3 versus 0 to 1 (18\% v 40\%, respectively). In the Cox model, these parameters were significant (P {$<$} .001). CONCLUSION: In patients who experience relapse more than 12 months after diagnosis, prior rituximab treatment does not affect EFS. Patients with early relapses after rituximab-containing first-line therapy have a poor prognosis, with no difference between the effects of R-ICE and R-DHAP.}, |
|
| 3291 | + langid = {english}, |
|
| 3292 | + pmcid = {PMC3664033}, |
|
| 3293 | + keywords = {Adult,Aged,Antibodies Monoclonal,Antibodies Monoclonal Murine-Derived,Antigens CD20,Antineoplastic Combined Chemotherapy Protocols,Australia,Carboplatin,Chemotherapy Adjuvant,Cytarabine,Dexamethasone,Disease-Free Survival,Etoposide,Europe,Female,Humans,Ifosfamide,Israel,Kaplan-Meier Estimate,Lymphoma Large B-Cell Diffuse,Male,Middle Aged,Neoplasm Staging,New York City,Proportional Hazards Models,Recurrence,Risk Assessment,Risk Factors,Rituximab,Salvage Therapy,Stem Cell Transplantation,Time Factors,Transplantation Autologous,Treatment Outcome,Young Adult}, |
|
| 3294 | + file = {/Users/rmorin/Zotero/storage/YDQQLAQ5/Gisselbrecht et al. - 2010 - Salvage regimens with autologous transplantation f.pdf} |
|
| 3295 | +} |
|
| 3296 | + |
|
| 3297 | +@article{golan-gerstlSplicingFactorHnRNP2011, |
|
| 3298 | + title = {Splicing Factor {{hnRNP A2}}/{{B1}} Regulates Tumor Suppressor Gene Splicing and Is an Oncogenic Driver in Glioblastoma}, |
|
| 3299 | + author = {Golan-Gerstl, Regina and Cohen, Michal and Shilo, Asaf and Suh, Sung-Suk and Bakàcs, Arianna and Coppola, Luigi and Karni, Rotem}, |
|
| 3300 | + date = {2011-07-01}, |
|
| 3301 | + journaltitle = {Cancer Research}, |
|
| 3302 | + shortjournal = {Cancer Res.}, |
|
| 3303 | + volume = {71}, |
|
| 3304 | + number = {13}, |
|
| 3305 | + eprint = {21586613}, |
|
| 3306 | + eprinttype = {pmid}, |
|
| 3307 | + pages = {4464--4472}, |
|
| 3308 | + issn = {1538-7445}, |
|
| 3309 | + doi = {10.1158/0008-5472.CAN-10-4410}, |
|
| 3310 | + abstract = {The process of alternative splicing is widely misregulated in cancer, but the contribution of splicing regulators to cancer development is largely unknown. In this study, we found that the splicing factor hnRNP A2/B1 is overexpressed in glioblastomas and is correlated with poor prognosis. Conversely, patients who harbor deletions of the HNRNPA2B1 gene show better prognosis than average. Knockdown of hnRNP A2/B1 in glioblastoma cells inhibited tumor formation in mice. In contrast, overexpression of hnRNP A2/B1 in immortal cells led to malignant transformation, suggesting that HNRNPA2B1 is a putative proto-oncogene. We then identified several tumor suppressors and oncogenes that are regulated by HNRNPA2B1, among them are c-FLIP, BIN1, and WWOX, and the proto-oncogene RON. Knockdown of RON inhibited hnRNP A2/B1 mediated transformation, which implied that RON is one of the mediators of HNRNPA2B1 oncogenic activity. Together, our results indicate that HNRNPA2B1 is a novel oncogene in glioblastoma and a potential new target for glioblastoma therapy.}, |
|
| 3311 | + langid = {english}, |
|
| 3312 | + keywords = {Alternative Splicing,Animals,Brain Neoplasms,Cell Line Tumor,Cell Transformation Neoplastic,Gene Dosage,Gene Expression Regulation Neoplastic,Gene Knockdown Techniques,Genes Tumor Suppressor,Glioblastoma,Heterogeneous-Nuclear Ribonucleoprotein Group A-B,Humans,Mice,NIH 3T3 Cells,Receptor Protein-Tyrosine Kinases,Up-Regulation} |
|
| 3313 | +} |
|
| 3314 | + |
|
| 3315 | +@article{golayGlycoengineeredCD20Antibody2013, |
|
| 3316 | + title = {Glycoengineered {{CD20}} Antibody Obinutuzumab Activates Neutrophils and Mediates Phagocytosis through {{CD16B}} More Efficiently than Rituximab}, |
|
| 3317 | + author = {Golay, Josée and Roit, Fabio and Bologna, Luca and Ferrara, Claudia and Leusen, Jeanette H and Rambaldi, Alessandro and Klein, Christian and Introna, Martino}, |
|
| 3318 | + date = {2013}, |
|
| 3319 | + journaltitle = {Blood}, |
|
| 3320 | + volume = {122}, |
|
| 3321 | + number = {20}, |
|
| 3322 | + eprint = {24106207}, |
|
| 3323 | + eprinttype = {pmid}, |
|
| 3324 | + pages = {3482--3491}, |
|
| 3325 | + issn = {0006-4971}, |
|
| 3326 | + doi = {10.1182/blood-2013-05-504043}, |
|
| 3327 | + url = {http://dx.doi.org/10.1182/blood-2013-05-504043}, |
|
| 3328 | + abstract = {Obinutuzumab (GA101) is a glycoengineered type 2 CD20 antibody with enhanced CD16A-binding and natural killer–mediated cytotoxicity. CD16B is highly homologous to CD16A and a major FcγR on human polymorphonuclear neutrophils (PMNs). We show here that glycoengineered obinutuzumab or rituximab bound CD16B with approximately sevenfold higher affinity, compared with nonglycoengineered wild-type parental antibodies. Furthermore, glycoengineered obinutuzumab activated PMNs, either purified or in chronic lymphoblastic leukemia whole blood, more efficiently than wild-type rituximab. Activation resulted in a 50\% increase in CD11b expression and 70\% down-modulation of CD62L on neutrophils and in release of tumor necrosis factor alpha, IL-6, and IL-8. Activation was not accompanied by generation of reactive oxygen species or antibody-dependent cellular cytotoxicity activity, but led to up to 47\% phagocytosis of glycoengineered anti-CD20 opsonized chronic lymphoblastic leukemia targets by purified PMNs. Significant phagocytosis was observed in whole blood, but only in the presence of glycoengineered antibodies, and was followed by up to 50\% PMN death. Finally we show, using anti-CD16B and anti-CD32A Fab and F(ab’)2 fragments, that both of these receptors are involved in PMN activation, phagocytosis, and cell death induced by glycoengineered antibodies. We conclude that phagocytosis by PMNs is an additional mechanism of action of obinutuzumab mediated through its higher binding affinity for CD16B.}, |
|
| 3329 | + keywords = {nosource} |
|
| 3330 | +} |
|
| 3331 | + |
|
| 3332 | +@article{golubMolecularClassificationCancer1999, |
|
| 3333 | + title = {Molecular {{Classification}} of {{Cancer}}: {{Class Discovery}} and {{Class Prediction}} by {{Gene Expression Monitoring}}}, |
|
| 3334 | + shorttitle = {Molecular {{Classification}} of {{Cancer}}}, |
|
| 3335 | + author = {Golub, T. R. and Slonim, D. K. and Tamayo, P. and Huard, C. and Gaasenbeek, M. and Mesirov, J. P. and Coller, H. and Loh, M. L. and Downing, J. R. and Caligiuri, M. A. and Bloomfield, C. D. and Lander, E. S.}, |
|
| 3336 | + date = {1999-10-15}, |
|
| 3337 | + journaltitle = {Science}, |
|
| 3338 | + volume = {286}, |
|
| 3339 | + number = {5439}, |
|
| 3340 | + eprint = {10521349}, |
|
| 3341 | + eprinttype = {pmid}, |
|
| 3342 | + pages = {531--537}, |
|
| 3343 | + issn = {0036-8075, 1095-9203}, |
|
| 3344 | + doi = {10.1126/science.286.5439.531}, |
|
| 3345 | + url = {https://science.sciencemag.org/content/286/5439/531}, |
|
| 3346 | + urldate = {2020-02-04}, |
|
| 3347 | + abstract = {Although cancer classification has improved over the past 30 years, there has been no general approach for identifying new cancer classes (class discovery) or for assigning tumors to known classes (class prediction). Here, a generic approach to cancer classification based on gene expression monitoring by DNA microarrays is described and applied to human acute leukemias as a test case. A class discovery procedure automatically discovered the distinction between acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) without previous knowledge of these classes. An automatically derived class predictor was able to determine the class of new leukemia cases. The results demonstrate the feasibility of cancer classification based solely on gene expression monitoring and suggest a general strategy for discovering and predicting cancer classes for other types of cancer, independent of previous biological knowledge.}, |
|
| 3348 | + langid = {english} |
|
| 3349 | +} |
|
| 3350 | + |
|
| 3351 | +@article{gomezUltraDeepSequencingReveals2023, |
|
| 3352 | + title = {Ultra-{{Deep Sequencing Reveals}} the {{Mutational Landscape}} of {{Classical Hodgkin Lymphoma}}}, |
|
| 3353 | + author = {Gomez, Felicia and Fisk, Bryan and McMichael, Joshua F. and Mosior, Matthew and Foltz, Jennifer A. and Skidmore, Zachary L. and Duncavage, Eric J. and Miller, Christopher A. and Abel, Haley and Li, Yi-Shan and Russler-Germain, David A. and Krysiak, Kilannin and Watkins, Marcus P. and Ramirez, Cody A. and Schmidt, Alina and Martins Rodrigues, Fernanda and Trani, Lee and Khanna, Ajay and Wagner, Julia A. and Fulton, Robert S. and Fronick, Catrina C. and O'Laughlin, Michelle D. and Schappe, Timothy and Cashen, Amanda F. and Mehta-Shah, Neha and Kahl, Brad S. and Walker, Jason and Bartlett, Nancy L. and Griffith, Malachi and Fehniger, Todd A. and Griffith, Obi L.}, |
|
| 3354 | + date = {2023-11-15}, |
|
| 3355 | + journaltitle = {Cancer Research Communications}, |
|
| 3356 | + shortjournal = {Cancer Res Commun}, |
|
| 3357 | + volume = {3}, |
|
| 3358 | + number = {11}, |
|
| 3359 | + eprint = {37910143}, |
|
| 3360 | + eprinttype = {pmid}, |
|
| 3361 | + pages = {2312--2330}, |
|
| 3362 | + issn = {2767-9764}, |
|
| 3363 | + doi = {10.1158/2767-9764.CRC-23-0140}, |
|
| 3364 | + abstract = {The malignant Hodgkin and Reed Sternberg (HRS) cells of classical Hodgkin lymphoma (cHL) are scarce in affected lymph nodes, creating a challenge to detect driver somatic mutations. As an alternative to cell purification techniques, we hypothesized that ultra-deep exome sequencing would allow genomic study of HRS cells, thereby streamlining analysis and avoiding technical pitfalls. To test this, 31 cHL tumor/normal pairs were exome sequenced to approximately 1,000× median depth of coverage. An orthogonal error-corrected sequencing approach verified {$>$}95\% of the discovered mutations. We identified mutations in genes novel to cHL including: CDH5 and PCDH7, novel stop gain mutations in IL4R, and a novel pattern of recurrent mutations in pathways regulating Hippo signaling. As a further application of our exome sequencing, we attempted to identify expressed somatic single-nucleotide variants (SNV) in single-nuclei RNA sequencing (snRNA-seq) data generated from a patient in our cohort. Our snRNA analysis identified a clear cluster of cells containing a somatic SNV identified in our deep exome data. This cluster has differentially expressed genes that are consistent with genes known to be dysregulated in HRS cells (e.g., PIM1 and PIM3). The cluster also contains cells with an expanded B-cell clonotype further supporting a malignant phenotype. This study provides proof-of-principle that ultra-deep exome sequencing can be utilized to identify recurrent mutations in HRS cells and demonstrates the feasibility of snRNA-seq in the context of cHL. These studies provide the foundation for the further analysis of genomic variants in large cohorts of patients with cHL. SIGNIFICANCE: Our data demonstrate the utility of ultra-deep exome sequencing in uncovering somatic variants in Hodgkin lymphoma, creating new opportunities to define the genes that are recurrently mutated in this disease. We also show for the first time the successful application of snRNA-seq in Hodgkin lymphoma and describe the expression profile of a putative cluster of HRS cells in a single patient.}, |
|
| 3365 | + langid = {english}, |
|
| 3366 | + pmcid = {PMC10648575}, |
|
| 3367 | + keywords = {High-Throughput Nucleotide Sequencing,Hodgkin Disease,Humans,Mutation,Reed-Sternberg Cells,RNA Small Nuclear}, |
|
| 3368 | + file = {/Users/rmorin/Zotero/storage/P9VI9ZGH/Gomez et al. - 2023 - Ultra-Deep Sequencing Reveals the Mutational Lands.pdf} |
|
| 3369 | +} |
|
| 3370 | + |
|
| 3371 | +@article{gongSequentialInverseDysregulation2021, |
|
| 3372 | + title = {Sequential Inverse Dysregulation of the {{RNA}} Helicases {{DDX3X}} and {{DDX3Y}} Facilitates {{MYC-driven}} Lymphomagenesis}, |
|
| 3373 | + author = {Gong, Chun and Krupka, Joanna A. and Gao, Jie and Grigoropoulos, Nicholas F. and Giotopoulos, George and Asby, Ryan and Screen, Michael and Usheva, Zelvera and Cucco, Francesco and Barrans, Sharon and Painter, Daniel and Zaini, Nurmahirah Binte Mohammed and Haupl, Björn and Bornelöv, Susanne and Ruiz De Los Mozos, Igor and Meng, Wei and Zhou, Peixun and Blain, Alex E. and Forde, Sorcha and Matthews, Jamie and Khim Tan, Michelle Guet and Burke, G. A. Amos and Sze, Siu Kwan and Beer, Philip and Burton, Cathy and Campbell, Peter and Rand, Vikki and Turner, Suzanne D. and Ule, Jernej and Roman, Eve and Tooze, Reuben and Oellerich, Thomas and Huntly, Brian J. and Turner, Martin and Du, Ming-Qing and Samarajiwa, Shamith A. and Hodson, Daniel J.}, |
|
| 3374 | + date = {2021-08-25}, |
|
| 3375 | + journaltitle = {Molecular Cell}, |
|
| 3376 | + shortjournal = {Molecular Cell}, |
|
| 3377 | + issn = {1097-2765}, |
|
| 3378 | + doi = {10.1016/j.molcel.2021.07.041}, |
|
| 3379 | + url = {https://www.sciencedirect.com/science/article/pii/S1097276521006250}, |
|
| 3380 | + urldate = {2021-09-15}, |
|
| 3381 | + abstract = {DDX3X is a ubiquitously expressed RNA helicase involved in multiple stages of RNA biogenesis. DDX3X is frequently mutated in Burkitt lymphoma, but the functional basis for this is unknown. Here, we show that loss-of-function DDX3X mutations are also enriched in MYC-translocated diffuse large B cell lymphoma and reveal functional cooperation between mutant DDX3X and MYC. DDX3X promotes the translation of mRNA encoding components of the core translational machinery, thereby driving global protein synthesis. Loss-of-function DDX3X mutations moderate MYC-driven global protein synthesis, thereby buffering MYC-induced proteotoxic stress during early lymphomagenesis. Established lymphoma cells restore full protein synthetic capacity by aberrant expression of DDX3Y, a Y chromosome homolog, the expression of which is normally restricted to the testis. These findings show that DDX3X loss of function can buffer MYC-driven proteotoxic stress and highlight the capacity of male B cell lymphomas to then compensate for this loss by ectopic DDX3Y expression.}, |
|
| 3382 | + langid = {english}, |
|
| 3383 | + keywords = {Burkitt lymphoma,DDX3X,germinal center,MYC,proteotoxic stress,RNA helicase,translation}, |
|
| 3384 | + file = {/Users/rmorin/Zotero/storage/J9YB6XX7/S1097276521006250.html} |
|
| 3385 | +} |
|
| 3386 | + |
|
| 3387 | +@article{gonzalez-perezFunctionalImpactBias2012, |
|
| 3388 | + title = {Functional Impact Bias Reveals Cancer Drivers}, |
|
| 3389 | + author = {Gonzalez-Perez, Abel and Lopez-Bigas, Nuria}, |
|
| 3390 | + date = {2012-11}, |
|
| 3391 | + journaltitle = {Nucleic Acids Research}, |
|
| 3392 | + shortjournal = {Nucleic Acids Res.}, |
|
| 3393 | + volume = {40}, |
|
| 3394 | + number = {21}, |
|
| 3395 | + eprint = {22904074}, |
|
| 3396 | + eprinttype = {pmid}, |
|
| 3397 | + pages = {e169}, |
|
| 3398 | + issn = {1362-4962}, |
|
| 3399 | + doi = {10.1093/nar/gks743}, |
|
| 3400 | + abstract = {Identifying cancer driver genes and pathways among all somatic mutations detected in a cohort of tumors is a key challenge in cancer genomics. Traditionally, this is done by prioritizing genes according to the recurrence of alterations that they bear. However, this approach has some known limitations, such as the difficulty to correctly estimate the background mutation rate, and the fact that it cannot identify lowly recurrently mutated driver genes. Here we present a novel approach, Oncodrive-fm, to detect candidate cancer drivers which does not rely on recurrence. First, we hypothesized that any bias toward the accumulation of variants with high functional impact observed in a gene or group of genes may be an indication of positive selection and can thus be used to detect candidate driver genes or gene modules. Next, we developed a method to measure this bias (FM bias) and applied it to three datasets of tumor somatic variants. As a proof of concept of our hypothesis we show that most of the highly recurrent and well-known cancer genes exhibit a clear FM bias. Moreover, this novel approach avoids some known limitations of recurrence-based approaches, and can successfully identify lowly recurrent candidate cancer drivers.}, |
|
| 3401 | + langid = {english}, |
|
| 3402 | + pmcid = {PMC3505979}, |
|
| 3403 | + keywords = {Genes Neoplasm,Genetic Variation,Genomics,Humans,Mutation} |
|
| 3404 | +} |
|
| 3405 | + |
|
| 3406 | +@article{gorlachDeterminantsRNAbindingSpecificity1994, |
|
| 3407 | + title = {The Determinants of {{RNA-binding}} Specificity of the Heterogeneous Nuclear Ribonucleoprotein {{C}} Proteins.}, |
|
| 3408 | + author = {Görlach, M. and Burd, C. G. and Dreyfuss, G.}, |
|
| 3409 | + date = {1994-09-16}, |
|
| 3410 | + journaltitle = {Journal of Biological Chemistry}, |
|
| 3411 | + shortjournal = {Journal of Biological Chemistry}, |
|
| 3412 | + volume = {269}, |
|
| 3413 | + number = {37}, |
|
| 3414 | + pages = {23074--23078}, |
|
| 3415 | + issn = {0021-9258}, |
|
| 3416 | + doi = {10.1016/S0021-9258(17)31621-6}, |
|
| 3417 | + url = {https://www.sciencedirect.com/science/article/pii/S0021925817316216}, |
|
| 3418 | + urldate = {2022-09-26}, |
|
| 3419 | + abstract = {The hnRNP C proteins (C1/C2) are tenacious nuclear pre-mRNA-binding proteins that belong to the large RNP motif family of RNA-binding proteins. This motif identifies an RNA-binding domain (RBD) that consists of a four-stranded antiparallel beta-sheet packed against two alpha-helices. Despite considerable information on the structure of the hnRNP C RBD, little is known about its RNA-binding properties. To address this we used in vitro selection/amplification from pools of random sequence RNA to determine the RNA-binding specificity of hnRNP C1. After 8 rounds of selection/amplification nearly all RNAs contained contiguous stretches of at least 5 U residues, and filter-binding assays demonstrated that this sequence constitutes a high-affinity (Kd = 170 nM) binding site for hnRNP C1. The highest affinity we measured for hnRNP C1 was for r(U)14 (Kd = 14 nM). An RBD-containing peptide fragment of hnRNP C1 (amino acids 2-94) bound oligoribonucleotides containing an hnRNP C1 high-affinity binding site with nearly equal affinity to that of hnRNP C1. Unlike hnRNP C1, however, this peptide also bound oligoribonucleotides that do not contain high-affinity hnRNP C1-binding sites. We identified a region of 10 amino acids, immediately COOH-terminal to the RNP motif (amino acids 95-104), that prevents the minimal RBD from binding nonspecific RNA ligands. We propose that the highly conserved beta alpha beta beta alpha beta core structure of the RNP motif RBD confers a general RNA binding activity to RNP motif RBDs and that the determinants of RNA-binding specificity reside in the most variable regions, the loops connecting the beta-strands and/or the contiguous NH2 and COOH termini of the RBD.}, |
|
| 3420 | + langid = {english}, |
|
| 3421 | + file = {/Users/rmorin/Zotero/storage/D9US52BJ/Görlach et al. - 1994 - The determinants of RNA-binding specificity of the.pdf;/Users/rmorin/Zotero/storage/T6NUT4I2/S0021925817316216.html} |
|
| 3422 | +} |
|
| 3423 | + |
|
| 3424 | +@article{grabherrFulllengthTranscriptomeAssembly2011, |
|
| 3425 | + title = {Full-Length Transcriptome Assembly from {{RNA-Seq}} Data without a Reference Genome}, |
|
| 3426 | + author = {Grabherr, Manfred G and Haas, Brian J and Yassour, Moran and Levin, Joshua Z and Thompson, Dawn A and Amit, Ido and Adiconis, Xian and Fan, Lin and Raychowdhury, Raktima and Zeng, Qiandong and Chen, Zehua and Mauceli, Evan and Hacohen, Nir and Gnirke, Andreas and Rhind, Nicholas and family=Palma, given=Federica, prefix=di, useprefix=false and Birren, Bruce W and Nusbaum, Chad and Lindblad-Toh, Kerstin and Friedman, Nir and Regev, Aviv}, |
|
| 3427 | + date = {2011-11}, |
|
| 3428 | + journaltitle = {Nature Biotechnology}, |
|
| 3429 | + volume = {29}, |
|
| 3430 | + number = {7}, |
|
| 3431 | + eprint = {21572440}, |
|
| 3432 | + eprinttype = {pmid}, |
|
| 3433 | + pages = {nbt.1883}, |
|
| 3434 | + issn = {1546-1696}, |
|
| 3435 | + doi = {10.1038/nbt.1883}, |
|
| 3436 | + url = {http://dx.doi.org/10.1038/nbt.1883}, |
|
| 3437 | + abstract = {Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here we present the Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available. By efficiently constructing and analyzing sets of de Bruijn graphs, Trinity fully reconstructs a large fraction of transcripts, including alternatively spliced isoforms and transcripts from recently duplicated genes. Compared with other de novo transcriptome assemblers, Trinity recovers more full-length transcripts across a broad range of expression levels, with a sensitivity similar to methods that rely on genome alignments. Our approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome.}, |
|
| 3438 | + keywords = {nosource} |
|
| 3439 | +} |
|
| 3440 | + |
|
| 3441 | +@article{grammatikakisAlternativeSplicingNeuronal2016, |
|
| 3442 | + title = {Alternative {{Splicing}} of {{Neuronal Differentiation Factor TRF2 Regulated}} by {{HNRNPH1}}/{{H2}}}, |
|
| 3443 | + author = {Grammatikakis, Ioannis and Zhang, Peisu and Panda, Amaresh C. and Kim, Jiyoung and Maudsley, Stuart and Abdelmohsen, Kotb and Yang, Xiaoling and Martindale, Jennifer L. and Motiño, Omar and Hutchison, Emmette R. and Mattson, Mark P. and Gorospe, Myriam}, |
|
| 3444 | + date = {2016-05-03}, |
|
| 3445 | + journaltitle = {Cell Reports}, |
|
| 3446 | + shortjournal = {Cell Rep}, |
|
| 3447 | + volume = {15}, |
|
| 3448 | + number = {5}, |
|
| 3449 | + eprint = {27117401}, |
|
| 3450 | + eprinttype = {pmid}, |
|
| 3451 | + pages = {926--934}, |
|
| 3452 | + issn = {2211-1247}, |
|
| 3453 | + doi = {10.1016/j.celrep.2016.03.080}, |
|
| 3454 | + abstract = {During neuronal differentiation, use of an alternative splice site on the rat telomere repeat-binding factor 2 (TRF2) mRNA generates a short TRF2 protein isoform (TRF2-S) capable of derepressing neuronal genes. However, the RNA-binding proteins (RBPs) controlling this splicing event are unknown. Here, using affinity pull-down analysis, we identified heterogeneous nuclear ribonucleoproteins H1 and H2(HNRNPH) as RBPs specifically capable of interacting with the spliced RNA segment (exon 7) of Trf2 pre-mRNA. HNRNPH proteins prevent the production of the short isoform of Trf2 mRNA, as HNRNPH silencing selectively elevates TRF2-S levels. Accordingly, HNRNPH levels decline while TRF2-S levels increase during neuronal differentiation. In addition, CRISPR/Cas9-mediated deletion of hnRNPH2 selectively accelerates the NGF-triggered differentiation of rat pheochromocytoma cells into neurons. In sum, HNRNPH is a splicing regulator of Trf2 pre-mRNA that prevents the expression of TRF2-S, a factor implicated in neuronal differentiation.}, |
|
| 3455 | + langid = {english}, |
|
| 3456 | + pmcid = {PMC4856555}, |
|
| 3457 | + keywords = {alternative splicing,Alternative Splicing,Animals,Base Sequence,Cell Differentiation,Exons,Heterogeneous-Nuclear Ribonucleoprotein Group F-H,HNRNPH,mRNA,Neurons,PC12 Cells,Protein Binding,Proteomics,Rats,ribonucleoprotein complex,RNA,RNA Precursors,Telomeric Repeat Binding Protein 2,TRF2,TRF2-S}, |
|
| 3458 | + file = {/Users/rmorin/Zotero/storage/KVFZUF3C/Grammatikakis et al. - 2016 - Alternative Splicing of Neuronal Differentiation F.pdf} |
|
| 3459 | +} |
|
| 3460 | + |
|
| 3461 | +@article{grandeGenomewideDiscoverySomatic2019, |
|
| 3462 | + title = {Genome-Wide Discovery of Somatic Coding and Noncoding Mutations in Pediatric Endemic and Sporadic {{Burkitt}} Lymphoma}, |
|
| 3463 | + author = {Grande, Bruno M. and Gerhard, Daniela S. and Jiang, Aixiang and Griner, Nicholas B. and Abramson, Jeremy S. and Alexander, Thomas B. and Allen, Hilary and Ayers, Leona W. and Bethony, Jeffrey M. and Bhatia, Kishor and Bowen, Jay and Casper, Corey and Choi, John Kim and Culibrk, Luka and Davidsen, Tanja M. and Dyer, Maureen A. and Gastier-Foster, Julie M. and Gesuwan, Patee and Greiner, Timothy C. and Gross, Thomas G. and Hanf, Benjamin and Harris, Nancy Lee and He, Yiwen and Irvin, John D. and Jaffe, Elaine S. and Jones, Steven J. M. and Kerchan, Patrick and Knoetze, Nicole and Leal, Fabio E. and Lichtenberg, Tara M. and Ma, Yussanne and Martin, Jean Paul and Martin, Marie-Reine and Mbulaiteye, Sam M. and Mullighan, Charles G. and Mungall, Andrew J. and Namirembe, Constance and Novik, Karen and Noy, Ariela and Ogwang, Martin D. and Omoding, Abraham and Orem, Jackson and Reynolds, Steven J. and Rushton, Christopher K. and Sandlund, John T. and Schmitz, Roland and Taylor, Cynthia and Wilson, Wyndham H. and Wright, George W. and Zhao, Eric Y. and Marra, Marco A. and Morin, Ryan D. and Staudt, Louis M.}, |
|
| 3464 | + date = {2019-03-21}, |
|
| 3465 | + journaltitle = {Blood}, |
|
| 3466 | + shortjournal = {Blood}, |
|
| 3467 | + volume = {133}, |
|
| 3468 | + number = {12}, |
|
| 3469 | + pages = {1313--1324}, |
|
| 3470 | + issn = {0006-4971}, |
|
| 3471 | + doi = {10.1182/blood-2018-09-871418}, |
|
| 3472 | + url = {https://ashpublications.org/blood/article/133/12/1313/260486/Genome-wide-discovery-of-somatic-coding-and}, |
|
| 3473 | + urldate = {2019-12-21}, |
|
| 3474 | + langid = {english}, |
|
| 3475 | + keywords = {Morinlab}, |
|
| 3476 | + file = {/Users/rmorin/Zotero/storage/T2KL8BJH/Grande et al. - 2019 - Genome-wide discovery of somatic coding and noncod.pdf;/Users/rmorin/Zotero/storage/LGT5S5FK/Genome-wide-discovery-of-somatic-coding-and.html} |
|
| 3477 | +} |
|
| 3478 | + |
|
| 3479 | +@article{granjaArchRScalableSoftware2021, |
|
| 3480 | + title = {{{ArchR}} Is a Scalable Software Package for Integrative Single-Cell Chromatin Accessibility Analysis}, |
|
| 3481 | + author = {Granja, Jeffrey M. and Corces, M. Ryan and Pierce, Sarah E. and Bagdatli, S. Tansu and Choudhry, Hani and Chang, Howard Y. and Greenleaf, William J.}, |
|
| 3482 | + date = {2021-03}, |
|
| 3483 | + journaltitle = {Nature Genetics}, |
|
| 3484 | + shortjournal = {Nat Genet}, |
|
| 3485 | + volume = {53}, |
|
| 3486 | + number = {3}, |
|
| 3487 | + eprint = {33633365}, |
|
| 3488 | + eprinttype = {pmid}, |
|
| 3489 | + pages = {403--411}, |
|
| 3490 | + issn = {1546-1718}, |
|
| 3491 | + doi = {10.1038/s41588-021-00790-6}, |
|
| 3492 | + abstract = {The advent of single-cell chromatin accessibility profiling has accelerated the ability to map gene regulatory landscapes but has outpaced the development of scalable software to rapidly extract biological meaning from these data. Here we present a software suite for single-cell analysis of regulatory chromatin in R (ArchR; https://www.archrproject.com/ ) that enables fast and comprehensive analysis of single-cell chromatin accessibility data. ArchR provides an intuitive, user-focused interface for complex single-cell analyses, including doublet removal, single-cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing (scRNA-seq). Enabling the analysis of over 1.2 million single cells within 8\,h on a standard Unix laptop, ArchR is a comprehensive software suite for end-to-end analysis of single-cell chromatin accessibility that will accelerate the understanding of gene regulation at the resolution of individual cells.}, |
|
| 3493 | + langid = {english}, |
|
| 3494 | + pmcid = {PMC8012210}, |
|
| 3495 | + keywords = {Animals,Chromatin,Cluster Analysis,Gene Expression Regulation,Genome,Humans,Mice,Sequence Analysis RNA,Single-Cell Analysis,Software,Transcription Factors,User-Computer Interface,Web Browser}, |
|
| 3496 | + file = {/Users/rmorin/Zotero/storage/UNL3GNJT/Granja et al. - 2021 - ArchR is a scalable software package for integrati.pdf} |
|
| 3497 | +} |
|
| 3498 | + |
|
| 3499 | +@article{greenHitandrunLymphomagenesisBcl6, |
|
| 3500 | + title = {Hit-and-Run Lymphomagenesis by the {{Bcl6}} Oncogene.}, |
|
| 3501 | + author = {Green, Michael R and Vicente-Dueñas, Carolina and Alizadeh, Ash A and Sánchez-García, Isidro}, |
|
| 3502 | + journaltitle = {Cell Cycle (Georgetown, Tex.)}, |
|
| 3503 | + volume = {13}, |
|
| 3504 | + number = {12}, |
|
| 3505 | + pages = {1831--1832}, |
|
| 3506 | + keywords = {nosource} |
|
| 3507 | +} |
|
| 3508 | + |
|
| 3509 | +@article{greenTransientExpressionBcl601, |
|
| 3510 | + title = {Transient Expression of {{Bcl6}} Is Sufficient for Oncogenic Function and Induction of Mature {{B-cell}} Lymphoma}, |
|
| 3511 | + author = {Green, Michael R and family=as, given=Carolina Vicente-Due, prefix=ntilde, useprefix=false and Romero-Camarero, Isabel and Liu, Chih Long and Dai, Bo and family=Herrero, given=In eacute s Gonz, prefix=aacute, useprefix=true and family=rez, given=Idoia Garc, prefix=iacute a-Ram iacute, useprefix=false and Alonso-Escudero, Esther and Iqbal, Javeed and Chan, Wing C and Campos-Sánchez, Elena and Orfao, Alberto and family=Pintado, given=Bel, prefix=eacute n, useprefix=false and Flores, Teresa and Blanco, Oscar and family=nez, given=Rafael Jim, prefix=eacute, useprefix=false and family=Climent, given=Jose Angel Mart, prefix=iacute, useprefix=true and family=Criado, given=Francisco Javier Garc, prefix=iacute a, useprefix=false and family=Cenador, given=Mar iacute a Bego ntilde a Garc, prefix=iacute a, useprefix=false and Zhao, Shuchun and Natkunam, Yasodha and Lossos, Izidore S and Majeti, Ravindra and Melnick, Ari and family=Cobaleda, given=C, prefix=eacute sar, useprefix=false and Alizadeh, Ash A and family=a, given=Isidro S, prefix=aacute nchez-Garc iacute, useprefix=false}, |
|
| 3512 | + date = {0001}, |
|
| 3513 | + journaltitle = {Nature communications}, |
|
| 3514 | + volume = {5}, |
|
| 3515 | + pages = {1--13}, |
|
| 3516 | + keywords = {nosource} |
|
| 3517 | +} |
|
| 3518 | + |
|
| 3519 | +@article{greletHnRNPE1Crossroads2019, |
|
| 3520 | + title = {{{hnRNP E1}} at the Crossroads of Translational Regulation of Epithelial-Mesenchymal Transition}, |
|
| 3521 | + author = {Grelet, Simon and Howe, Philip H.}, |
|
| 3522 | + date = {2019-03-11}, |
|
| 3523 | + journaltitle = {Journal of Cancer Metastasis and Treatment}, |
|
| 3524 | + shortjournal = {JCMT}, |
|
| 3525 | + volume = {2019}, |
|
| 3526 | + issn = {2454-2857, 2394-4722}, |
|
| 3527 | + doi = {10.20517/2394-4722.2018.85}, |
|
| 3528 | + url = {https://jcmtjournal.com/article/view/2996}, |
|
| 3529 | + urldate = {2022-09-25}, |
|
| 3530 | + abstract = {The epithelial-mesenchymal transition (EMT), in which cells undergo a switch from a polarized, epithelial phenotype to a highly motile fibroblastic or mesenchymal phenotype is fundamental during embryonic development and can be reactivated in a variety of diseases including cancer. Spatio-temporally-regulated mechanisms are constantly orchestrated to allow cells to adapt to their constantly changing environments when disseminating to distant organs. Although numerous transcriptional regulatory factors are currently wellcharacterized, the post-transcriptional control of EMT requires continued investigation. The hnRNP E1 protein displays a major role in the control of tumor cell plasticity by regulating the translatome through multiple nonredundant mechanisms, and this role is exemplified when E1 is absent. hnRNP E1 binding to RNA molecules leads to direct or indirect translational regulation of specific sets of proteins: (1) hnRNP E1 binding to specific targets has a direct role in translation by preventing elongation of translation; (2) hnRNP E1-dependent alternative splicing can prevent the generation of a competing long non-coding RNA that acts as a decoy for microRNAs (miRNAs) involved in translational inhibition of EMT master regulators; (3) hnRNP E1 binding to the 3’ untranslated region of transcripts can also positively regulate the stability of certain mRNAs to improve their translation. Globally, hnRNP E1 appears to control proteome reprogramming during cell plasticity, either by direct or indirect regulation of protein translation.}, |
|
| 3531 | + langid = {english}, |
|
| 3532 | + file = {/Users/rmorin/Zotero/storage/63RNFMMY/Grelet and Howe - 2019 - hnRNP E1 at the crossroads of translational regula.pdf} |
|
| 3533 | +} |
|
| 3534 | + |
|
| 3535 | +@article{grunewaldEwingSarcoma2018, |
|
| 3536 | + title = {Ewing Sarcoma}, |
|
| 3537 | + author = {Grünewald, Thomas G. P. and Cidre-Aranaz, Florencia and Surdez, Didier and Tomazou, Eleni M. and family=Álava, given=Enrique, prefix=de, useprefix=true and Kovar, Heinrich and Sorensen, Poul H. and Delattre, Olivier and Dirksen, Uta}, |
|
| 3538 | + date = {2018-05-07}, |
|
| 3539 | + journaltitle = {Nature Reviews. Disease Primers}, |
|
| 3540 | + shortjournal = {Nat Rev Dis Primers}, |
|
| 3541 | + volume = {4}, |
|
| 3542 | + number = {1}, |
|
| 3543 | + eprint = {29977059}, |
|
| 3544 | + eprinttype = {pmid}, |
|
| 3545 | + pages = {5}, |
|
| 3546 | + issn = {2056-676X}, |
|
| 3547 | + doi = {10.1038/s41572-018-0003-x}, |
|
| 3548 | + abstract = {Ewing sarcoma is the second most frequent bone tumour of childhood and adolescence that can also arise in soft tissue. Ewing sarcoma is a highly aggressive cancer, with a survival of 70-80\% for patients with standard-risk and localized disease and \textasciitilde 30\% for those with metastatic disease. Treatment comprises local surgery, radiotherapy and polychemotherapy, which are associated with acute and chronic adverse effects that may compromise quality of life in survivors. Histologically, Ewing sarcomas are composed of small round cells expressing high levels of CD99. Genetically, they are characterized by balanced chromosomal translocations in which a member of the FET gene family is fused with an ETS transcription factor, with the most common fusion being EWSR1-FLI1 (85\% of cases). Ewing sarcoma breakpoint region 1 protein (EWSR1)-Friend leukaemia integration 1 transcription factor (FLI1) is a tumour-specific chimeric transcription factor (EWSR1-FLI1) with neomorphic effects that massively rewires the transcriptome. Additionally, EWSR1-FLI1 reprogrammes the epigenome by inducing de novo enhancers at GGAA microsatellites and by altering the state of gene regulatory elements, creating a unique epigenetic signature. Additional mutations at diagnosis are rare and mainly involve STAG2, TP53 and CDKN2A deletions. Emerging studies on the molecular mechanisms of Ewing sarcoma hold promise for improvements in early detection, disease monitoring, lower treatment-related toxicity, overall survival and quality of life.}, |
|
| 3549 | + langid = {english}, |
|
| 3550 | + keywords = {12E7 Antigen,Humans,Neoplasm Metastasis,Proto-Oncogene Protein c-fli-1,Quality of Life,Radiography,Risk Factors,RNA-Binding Protein EWS,Sarcoma Ewing} |
|
| 3551 | +} |
|
| 3552 | + |
|
| 3553 | +@article{guCirclizeImplementsEnhances2014, |
|
| 3554 | + title = {Circlize Implements and Enhances Circular Visualization in {{R}}}, |
|
| 3555 | + author = {Gu, Zuguang and Gu, Lei and Eils, Roland and Schlesner, Matthias and Brors, Benedikt}, |
|
| 3556 | + date = {2014-10-01}, |
|
| 3557 | + journaltitle = {Bioinformatics}, |
|
| 3558 | + shortjournal = {Bioinformatics}, |
|
| 3559 | + volume = {30}, |
|
| 3560 | + number = {19}, |
|
| 3561 | + pages = {2811--2812}, |
|
| 3562 | + issn = {1367-4803}, |
|
| 3563 | + doi = {10.1093/bioinformatics/btu393}, |
|
| 3564 | + url = {https://doi.org/10.1093/bioinformatics/btu393}, |
|
| 3565 | + urldate = {2023-12-16}, |
|
| 3566 | + abstract = {Summary: Circular layout is an efficient way for the visualization of huge amounts of genomic information. Here we present the circlize package, which provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of this package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, circlize gives users more convenience and freedom to design figures for better understanding genomic patterns behind multi-dimensional data. Availability and implementation: ~circlize is available at the Comprehensive R Archive Network (CRAN): http://cran.r-project.org/web/packages/circlize/Contact: ~b.brors@dkfz.deSupplementary information: ~Supplementary data are available at Bioinformatics online.}, |
|
| 3567 | + file = {/Users/rmorin/Zotero/storage/V7Z2NUEL/Gu et al. - 2014 - circlize implements and enhances circular visualiz.pdf;/Users/rmorin/Zotero/storage/BE92YBW6/2422259.html} |
|
| 3568 | +} |
|
| 3569 | + |
|
| 3570 | +@article{gunawardanaRecurrentSomaticMutations2014c, |
|
| 3571 | + title = {Recurrent Somatic Mutations of {{PTPN1}} in Primary Mediastinal {{B}} Cell Lymphoma and {{Hodgkin}} Lymphoma}, |
|
| 3572 | + author = {Gunawardana, Jay and Chan, Fong Chun and Telenius, Adèle and Woolcock, Bruce and Kridel, Robert and Tan, King L. and Ben-Neriah, Susana and Mottok, Anja and Lim, Raymond S. and Boyle, Merrill and Rogic, Sanja and Rimsza, Lisa M. and Guiter, Chrystelle and Leroy, Karen and Gaulard, Philippe and Haioun, Corinne and Marra, Marco A. and Savage, Kerry J. and Connors, Joseph M. and Shah, Sohrab P. and Gascoyne, Randy D. and Steidl, Christian}, |
|
| 3573 | + date = {2014-04}, |
|
| 3574 | + journaltitle = {Nature Genetics}, |
|
| 3575 | + shortjournal = {Nat Genet}, |
|
| 3576 | + volume = {46}, |
|
| 3577 | + number = {4}, |
|
| 3578 | + eprint = {24531327}, |
|
| 3579 | + eprinttype = {pmid}, |
|
| 3580 | + pages = {329--335}, |
|
| 3581 | + issn = {1546-1718}, |
|
| 3582 | + doi = {10.1038/ng.2900}, |
|
| 3583 | + abstract = {Classical Hodgkin lymphoma and primary mediastinal B cell lymphoma (PMBCL) are related lymphomas sharing pathological, molecular and clinical characteristics. Here we discovered by whole-genome and whole-transcriptome sequencing recurrent somatic coding-sequence mutations in the PTPN1 gene. Mutations were found in 6 of 30 (20\%) Hodgkin lymphoma cases, in 6 of 9 (67\%) Hodgkin lymphoma-derived cell lines, in 17 of 77 (22\%) PMBCL cases and in 1 of 3 (33\%) PMBCL-derived cell lines, consisting of nonsense, missense and frameshift mutations. We demonstrate that PTPN1 mutations lead to reduced phosphatase activity and increased phosphorylation of JAK-STAT pathway members. Moreover, silencing of PTPN1 by RNA interference in Hodgkin lymphoma cell line KM-H2 resulted in hyperphosphorylation and overexpression of downstream oncogenic targets. Our data establish PTPN1 mutations as new drivers in lymphomagenesis.}, |
|
| 3584 | + langid = {english}, |
|
| 3585 | + keywords = {Gene Expression Profiling,Gene Knockdown Techniques,Genomics,HEK293 Cells,High-Throughput Nucleotide Sequencing,Hodgkin Disease,Humans,Immunohistochemistry,In Situ Hybridization Fluorescence,Kaplan-Meier Estimate,Laser Capture Microdissection,Lymphoma B-Cell,Mediastinal Neoplasms,Mutation,Phosphorylation,Protein Tyrosine Phosphatase Non-Receptor Type 1,Real-Time Polymerase Chain Reaction,RNA Interference} |
|
| 3586 | +} |
|
| 3587 | + |
|
| 3588 | +@article{haasNovoTranscriptSequence2013, |
|
| 3589 | + title = {De Novo Transcript Sequence Reconstruction from {{RNA-seq}} Using the {{Trinity}} Platform for Reference Generation and Analysis}, |
|
| 3590 | + author = {Haas, Brian J and Papanicolaou, Alexie and Yassour, Moran and Grabherr, Manfred and Blood, Philip D and Bowden, Joshua and Couger, Matthew Brian and Eccles, David and Li, Bo and Lieber, Matthias and MacManes, Matthew D and Ott, Michael and Orvis, Joshua and Pochet, Nathalie and Strozzi, Francesco and Weeks, Nathan and Westerman, Rick and William, Thomas and Dewey, Colin N and Henschel, Robert and LeDuc, Richard D and Friedman, Nir and Regev, Aviv}, |
|
| 3591 | + date = {2013}, |
|
| 3592 | + journaltitle = {Nature Protocols}, |
|
| 3593 | + volume = {8}, |
|
| 3594 | + number = {8}, |
|
| 3595 | + eprint = {23845962}, |
|
| 3596 | + eprinttype = {pmid}, |
|
| 3597 | + pages = {nprot.2013.084}, |
|
| 3598 | + issn = {1750-2799}, |
|
| 3599 | + doi = {10.1038/nprot.2013.084}, |
|
| 3600 | + url = {http://dx.doi.org/10.1038/nprot.2013.084}, |
|
| 3601 | + abstract = {De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-model organisms' of ecological and evolutionary importance, cancer samples or the microbiome. In this protocol we describe the use of the Trinity platform for de novo transcriptome assembly from RNA-seq data in non-model organisms. We also present Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes. In the procedure, we provide a workflow for genome-independent transcriptome analysis leveraging the Trinity platform. The software, documentation and demonstrations are freely available from http://trinityrnaseq.sourceforge.net. The run time of this protocol is highly dependent on the size and complexity of data to be analyzed. The example data set analyzed in the procedure detailed herein can be processed in less than 5 h.}, |
|
| 3602 | + keywords = {nosource} |
|
| 3603 | +} |
|
| 3604 | + |
|
| 3605 | +@article{habibMycStimulatesLymphocyte2007, |
|
| 3606 | + title = {Myc Stimulates {{B}} Lymphocyte Differentiation and Amplifies Calcium Signaling}, |
|
| 3607 | + author = {Habib, Tania and Park, Heon and Tsang, Mark and family=Alborán, given=Ignacio Moreno, prefix=de, useprefix=true and Nicks, Andrea and Wilson, Leslie and Knoepfler, Paul S. and Andrews, Sarah and Rawlings, David J. and Eisenman, Robert N. and Iritani, Brian M.}, |
|
| 3608 | + date = {2007-11-19}, |
|
| 3609 | + journaltitle = {The Journal of Cell Biology}, |
|
| 3610 | + shortjournal = {J Cell Biol}, |
|
| 3611 | + volume = {179}, |
|
| 3612 | + number = {4}, |
|
| 3613 | + eprint = {17998397}, |
|
| 3614 | + eprinttype = {pmid}, |
|
| 3615 | + pages = {717--731}, |
|
| 3616 | + issn = {0021-9525}, |
|
| 3617 | + doi = {10.1083/jcb.200704173}, |
|
| 3618 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2080907/}, |
|
| 3619 | + urldate = {2022-10-06}, |
|
| 3620 | + abstract = {Deregulated expression of the Myc family of transcription factors (c-, N-, and L-myc) contributes to the development of many cancers by a mechanism believed to involve the stimulation of cell proliferation and inhibition of differentiation. However, using B cell–specific c-/N-myc double-knockout mice and Eμ-myc transgenic mice bred onto genetic backgrounds (recombinase-activating gene 2−/− and Btk−/− Tec−/−) whereby B cell development is arrested, we show that Myc is necessary to stimulate both proliferation and differentiation in primary B cells. Moreover, Myc expression results in sustained increases in intracellular Ca2+ ([Ca2+]i), which is required for Myc to stimulate B cell proliferation and differentiation. The increase in [Ca2+]i correlates with constitutive nuclear factor of activated T cells (NFAT) nuclear translocation, reduced Ca2+ efflux, and decreased expression of the plasma membrane Ca2+–adenosine triphosphatase (PMCA) efflux pump. Our findings demonstrate a revised model whereby Myc promotes both proliferation and differentiation, in part by a remarkable mechanism whereby Myc amplifies Ca2+ signals, thereby enabling the concurrent expression of Myc- and Ca2+-regulated target genes.}, |
|
| 3621 | + pmcid = {PMC2080907}, |
|
| 3622 | + file = {/Users/rmorin/Zotero/storage/7KRDRAV7/Habib et al. - 2007 - Myc stimulates B lymphocyte differentiation and am.pdf} |
|
| 3623 | +} |
|
| 3624 | + |
|
| 3625 | +@article{hackenSplicingModulationSensitizes2018, |
|
| 3626 | + title = {Splicing Modulation Sensitizes Chronic Lymphocytic Leukemia Cells to Venetoclax by Remodeling Mitochondrial Apoptotic Dependencies}, |
|
| 3627 | + author = {family=Hacken, given=Elisa, prefix=ten, useprefix=false and Valentin, Rebecca and Regis, Fara Faye D. and Sun, Jing and Yin, Shanye and Werner, Lillian and Deng, Jing and Gruber, Michaela and Wong, Jessica and Zheng, Mei and Gill, Amy L. and Seiler, Michael and Smith, Peter and Thomas, Michael and Buonamici, Silvia and Ghia, Emanuela M. and Kim, Ekaterina and Rassenti, Laura Z. and Burger, Jan A. and Kipps, Thomas J. and Meyerson, Matthew L. and Bachireddy, Pavan and Wang, Lili and Reed, Robin and Neuberg, Donna and Carrasco, Ruben D. and Brooks, Angela N. and Letai, Anthony and Davids, Matthew S. and Wu, Catherine J.}, |
|
| 3628 | + date = {2018-10-04}, |
|
| 3629 | + journaltitle = {JCI Insight}, |
|
| 3630 | + shortjournal = {JCI Insight}, |
|
| 3631 | + volume = {3}, |
|
| 3632 | + number = {19}, |
|
| 3633 | + eprint = {0}, |
|
| 3634 | + eprinttype = {pmid}, |
|
| 3635 | + issn = {0021-9738}, |
|
| 3636 | + doi = {10.1172/jci.insight.121438}, |
|
| 3637 | + url = {https://insight.jci.org/articles/view/121438}, |
|
| 3638 | + urldate = {2019-12-21}, |
|
| 3639 | + langid = {english}, |
|
| 3640 | + file = {/Users/rmorin/Zotero/storage/6G2APFBC/121438.html} |
|
| 3641 | +} |
|
| 3642 | + |
|
| 3643 | +@article{haileAutomatedHighThroughput2017, |
|
| 3644 | + title = {Automated High Throughput Nucleic Acid Purification from Formalin-Fixed Paraffin-Embedded Tissue Samples for next Generation Sequence Analysis}, |
|
| 3645 | + author = {Haile, Simon and Pandoh, Pawan and McDonald, Helen and Corbett, Richard D. and Tsao, Philip and Kirk, Heather and MacLeod, Tina and Jones, Martin and Bilobram, Steve and Brooks, Denise and Smailus, Duane and Steidl, Christian and Scott, David W. and Bala, Miruna and Hirst, Martin and Miller, Diane and Moore, Richard A. and Mungall, Andrew J. and Coope, Robin J. and Ma, Yussanne and Zhao, Yongjun and Holt, Rob A. and Jones, Steven J. and Marra, Marco A.}, |
|
| 3646 | + date = {2017}, |
|
| 3647 | + journaltitle = {PloS One}, |
|
| 3648 | + shortjournal = {PLoS One}, |
|
| 3649 | + volume = {12}, |
|
| 3650 | + number = {6}, |
|
| 3651 | + eprint = {28570594}, |
|
| 3652 | + eprinttype = {pmid}, |
|
| 3653 | + pages = {e0178706}, |
|
| 3654 | + issn = {1932-6203}, |
|
| 3655 | + doi = {10.1371/journal.pone.0178706}, |
|
| 3656 | + abstract = {Curation and storage of formalin-fixed, paraffin-embedded (FFPE) samples are standard procedures in hospital pathology laboratories around the world. Many thousands of such samples exist and could be used for next generation sequencing analysis. Retrospective analyses of such samples are important for identifying molecular correlates of carcinogenesis, treatment history and disease outcomes. Two major hurdles in using FFPE material for sequencing are the damaged nature of the nucleic acids and the labor-intensive nature of nucleic acid purification. These limitations and a number of other issues that span multiple steps from nucleic acid purification to library construction are addressed here. We optimized and automated a 96-well magnetic bead-based extraction protocol that can be scaled to large cohorts and is compatible with automation. Using sets of 32 and 91 individual FFPE samples respectively, we generated libraries from 100 ng of total RNA and DNA starting amounts with 95-100\% success rate. The use of the resulting RNA in micro-RNA sequencing was also demonstrated. In addition to offering the potential of scalability and rapid throughput, the yield obtained with lower input requirements makes these methods applicable to clinical samples where tissue abundance is limiting.}, |
|
| 3657 | + langid = {english}, |
|
| 3658 | + pmcid = {PMC5453589}, |
|
| 3659 | + keywords = {Automation,DNA,Formaldehyde,High-Throughput Nucleotide Sequencing,Paraffin Embedding,RNA,Tissue Fixation}, |
|
| 3660 | + file = {/Users/rmorin/Zotero/storage/CCBC9RAU/Haile et al. - 2017 - Automated high throughput nucleic acid purificatio.pdf} |
|
| 3661 | +} |
|
| 3662 | + |
|
| 3663 | +@article{haileScalableStrandSpecificProtocol2021, |
|
| 3664 | + title = {A {{Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single Cells}}}, |
|
| 3665 | + author = {Haile, Simon and Corbett, Richard D. and LeBlanc, Veronique G. and Wei, Lisa and Pleasance, Stephen and Bilobram, Steve and Nip, Ka Ming and Brown, Kirstin and Trinh, Eva and Smith, Jillian and Trinh, Diane L. and Bala, Miruna and Chuah, Eric and Coope, Robin J. N. and Moore, Richard A. and Mungall, Andrew J. and Mungall, Karen L. and Zhao, Yongjun and Hirst, Martin and Aparicio, Samuel and Birol, Inanc and Jones, Steven J. M. and Marra, Marco A.}, |
|
| 3666 | + date = {2021}, |
|
| 3667 | + journaltitle = {Frontiers in Genetics}, |
|
| 3668 | + shortjournal = {Front Genet}, |
|
| 3669 | + volume = {12}, |
|
| 3670 | + eprint = {34149808}, |
|
| 3671 | + eprinttype = {pmid}, |
|
| 3672 | + pages = {665888}, |
|
| 3673 | + issn = {1664-8021}, |
|
| 3674 | + doi = {10.3389/fgene.2021.665888}, |
|
| 3675 | + abstract = {RNA sequencing (RNAseq) has been widely used to generate bulk gene expression measurements collected from pools of cells. Only relatively recently have single-cell RNAseq (scRNAseq) methods provided opportunities for gene expression analyses at the single-cell level, allowing researchers to study heterogeneous mixtures of cells at unprecedented resolution. Tumors tend to be composed of heterogeneous cellular mixtures and are frequently the subjects of such analyses. Extensive method developments have led to several protocols for scRNAseq but, owing to the small amounts of RNA in single cells, technical constraints have required compromises. For example, the majority of scRNAseq methods are limited to sequencing only the 3' or 5' termini of transcripts. Other protocols that facilitate full-length transcript profiling tend to capture only polyadenylated mRNAs and are generally limited to processing only 96 cells at a time. Here, we address these limitations and present a novel protocol that allows for the high-throughput sequencing of full-length, total RNA at single-cell resolution. We demonstrate that our method produced strand-specific sequencing data for both polyadenylated and non-polyadenylated transcripts, enabled the profiling of transcript regions beyond only transcript termini, and yielded data rich enough to allow identification of cell types from heterogeneous biological samples.}, |
|
| 3676 | + langid = {english}, |
|
| 3677 | + pmcid = {PMC8209500}, |
|
| 3678 | + keywords = {cellenONE,full-length,RNAseq,single-cell,total RNA}, |
|
| 3679 | + file = {/Users/rmorin/Zotero/storage/YWSALRIT/Haile et al. - 2021 - A Scalable Strand-Specific Protocol Enabling Full-.pdf} |
|
| 3680 | +} |
|
| 3681 | + |
|
| 3682 | +@article{haileSourcesErroneousSequences2019, |
|
| 3683 | + title = {Sources of Erroneous Sequences and Artifact Chimeric Reads in next Generation Sequencing of Genomic {{DNA}} from Formalin-Fixed Paraffin-Embedded Samples}, |
|
| 3684 | + author = {Haile, Simon and Corbett, Richard D. and Bilobram, Steve and Bye, Morgan H. and Kirk, Heather and Pandoh, Pawan and Trinh, Eva and MacLeod, Tina and McDonald, Helen and Bala, Miruna and Miller, Diane and Novik, Karen and Coope, Robin J. and Moore, Richard A. and Zhao, Yongjun and Mungall, Andrew J. and Ma, Yussanne and Holt, Rob A. and Jones, Steven J. and Marra, Marco A.}, |
|
| 3685 | + date = {2019-01-25}, |
|
| 3686 | + journaltitle = {Nucleic Acids Research}, |
|
| 3687 | + shortjournal = {Nucleic Acids Res}, |
|
| 3688 | + volume = {47}, |
|
| 3689 | + number = {2}, |
|
| 3690 | + eprint = {30418619}, |
|
| 3691 | + eprinttype = {pmid}, |
|
| 3692 | + pages = {e12}, |
|
| 3693 | + issn = {1362-4962}, |
|
| 3694 | + doi = {10.1093/nar/gky1142}, |
|
| 3695 | + abstract = {Tissues used in pathology laboratories are typically stored in the form of formalin-fixed, paraffin-embedded (FFPE) samples. One important consideration in repurposing FFPE material for next generation sequencing (NGS) analysis is the sequencing artifacts that can arise from the significant damage to nucleic acids due to treatment with formalin, storage at room temperature and extraction. One such class of artifacts consists of chimeric reads that appear to be derived from non-contiguous portions of the genome. Here, we show that a major proportion of such chimeric reads align to both the 'Watson' and 'Crick' strands of the reference genome. We refer to these as strand-split artifact reads (SSARs). This study provides a conceptual framework for the mechanistic basis of the genesis of SSARs and other chimeric artifacts along with supporting experimental evidence, which have led to approaches to reduce the levels of such artifacts. We demonstrate that one of these approaches, involving S1 nuclease-mediated removal of single-stranded fragments and overhangs, also reduces sequence bias, base error rates, and false positive detection of copy number and single nucleotide variants. Finally, we describe an analytical approach for quantifying SSARs from NGS data.}, |
|
| 3696 | + langid = {english}, |
|
| 3697 | + pmcid = {PMC6344851}, |
|
| 3698 | + keywords = {Animals,Artifacts,Fixatives,Formaldehyde,Genomic Library,Genomics,High-Throughput Nucleotide Sequencing,Hot Temperature,Mice Inbred C57BL,Paraffin Embedding,Sequence Analysis DNA}, |
|
| 3699 | + file = {/Users/rmorin/Zotero/storage/M3LGUNET/Haile et al. - 2019 - Sources of erroneous sequences and artifact chimer.pdf} |
|
| 3700 | +} |
|
| 3701 | + |
|
| 3702 | +@article{halldorsdottirImpactTP53Mutation2011, |
|
| 3703 | + title = {Impact of {{TP53}} Mutation and 17p Deletion in Mantle Cell Lymphoma}, |
|
| 3704 | + author = {Halldórsdóttir, A. M. and Lundin, A. and Murray, F. and Mansouri, L. and Knuutila, S. and Sundström, C. and Laurell, A. and Ehrencrona, H. and Sander, B. and Rosenquist, R.}, |
|
| 3705 | + date = {2011-12}, |
|
| 3706 | + journaltitle = {Leukemia}, |
|
| 3707 | + volume = {25}, |
|
| 3708 | + number = {12}, |
|
| 3709 | + pages = {1904--1908}, |
|
| 3710 | + issn = {1476-5551}, |
|
| 3711 | + doi = {10.1038/leu.2011.162}, |
|
| 3712 | + url = {https://www.nature.com/articles/leu2011162}, |
|
| 3713 | + urldate = {2019-12-21}, |
|
| 3714 | + langid = {english}, |
|
| 3715 | + file = {/Users/rmorin/Zotero/storage/Z22YMEJQ/leu2011162.html} |
|
| 3716 | +} |
|
| 3717 | + |
|
| 3718 | +@article{hanahanHallmarksCancerNext2011, |
|
| 3719 | + title = {Hallmarks of {{Cancer}}: {{The Next Generation}}}, |
|
| 3720 | + shorttitle = {Hallmarks of {{Cancer}}}, |
|
| 3721 | + author = {Hanahan, Douglas and Weinberg, Robert A.}, |
|
| 3722 | + date = {2011-03-04}, |
|
| 3723 | + journaltitle = {Cell}, |
|
| 3724 | + shortjournal = {Cell}, |
|
| 3725 | + volume = {144}, |
|
| 3726 | + number = {5}, |
|
| 3727 | + eprint = {21376230}, |
|
| 3728 | + eprinttype = {pmid}, |
|
| 3729 | + pages = {646--674}, |
|
| 3730 | + publisher = {Elsevier}, |
|
| 3731 | + issn = {0092-8674, 1097-4172}, |
|
| 3732 | + doi = {10.1016/j.cell.2011.02.013}, |
|
| 3733 | + url = {https://www.cell.com/cell/abstract/S0092-8674(11)00127-9}, |
|
| 3734 | + urldate = {2022-10-25}, |
|
| 3735 | + langid = {english}, |
|
| 3736 | + file = {/Users/rmorin/Zotero/storage/3W8E7ZUH/Hanahan and Weinberg - 2011 - Hallmarks of Cancer The Next Generation.pdf;/Users/rmorin/Zotero/storage/6WDATB3Q/S0092-8674(11)00127-9.html} |
|
| 3737 | +} |
|
| 3738 | + |
|
| 3739 | +@article{hansConfirmationMolecularClassification2004, |
|
| 3740 | + title = {Confirmation of the Molecular Classification of Diffuse Large {{B-cell}} Lymphoma by Immunohistochemistry Using a Tissue Microarray}, |
|
| 3741 | + author = {Hans, Christine P. and Weisenburger, Dennis D. and Greiner, Timothy C. and Gascoyne, Randy D. and Delabie, Jan and Ott, German and Müller-Hermelink, H. Konrad and Campo, Elias and Braziel, Rita M. and Jaffe, Elaine S. and Pan, Zenggang and Farinha, Pedro and Smith, Lynette M. and Falini, Brunangelo and Banham, Alison H. and Rosenwald, Andreas and Staudt, Louis M. and Connors, Joseph M. and Armitage, James O. and Chan, Wing C.}, |
|
| 3742 | + date = {2004-04}, |
|
| 3743 | + journaltitle = {Blood}, |
|
| 3744 | + volume = {103}, |
|
| 3745 | + number = {1}, |
|
| 3746 | + eprint = {14504078}, |
|
| 3747 | + eprinttype = {pmid}, |
|
| 3748 | + pages = {275--282}, |
|
| 3749 | + issn = {0006-4971}, |
|
| 3750 | + doi = {10.1182/blood-2003-05-1545}, |
|
| 3751 | + url = {http://dx.doi.org/10.1182/blood-2003-05-1545}, |
|
| 3752 | + abstract = {Diffuse large B-cell lymphoma (DLBCL) can be divided into prognostically important subgroups with germinal center B-cell–like (GCB), activated B-cell–like (ABC), and type 3 gene expression profiles using a cDNA microarray. Tissue microarray (TMA) blocks were created from 152 cases of DLBCL, 142 of which had been successfully evaluated by cDNA microarray (75 GCB, 41 ABC, and 26 type 3). Sections were stained with antibodies to CD10, bcl-6, MUM1, FOXP1, cyclin D2, and bcl-2. Expression of bcl-6 (P {$<$} .001) or CD10 (P = .019) was associated with better overall survival (OS), whereas expression of MUM1 (P = .009) or cyclin D2 (P {$<$} .001) was associated with worse OS. Cases were subclassified using CD10, bcl-6, and MUM1 expression, and 64 cases (42\%) were considered GCB and 88 cases (58\%) non-GCB. The 5-year OS for the GCB group was 76\% compared with only 34\% for the non-GCB group (P {$<$} .001), which is similar to that reported using the cDNA microarray. Bcl-2 and cyclin D2 were adverse predictors in the non-GCB group. In multivariate analysis, a high International Prognostic Index score (3-5) and the non-GCB phenotype were independent adverse predictors (P {$<$} .0001). In summary, immunostains can be used to determine the GCB and non-GCB subtypes of DLBCL and predict survival similar to the cDNA microarray.}, |
|
| 3753 | + keywords = {nosource} |
|
| 3754 | +} |
|
| 3755 | + |
|
| 3756 | +@article{hansenSpontaneousGeneticallyEngineered2004, |
|
| 3757 | + title = {Spontaneous and Genetically Engineered Animal Models; Use in Preclinical Cancer Drug Development}, |
|
| 3758 | + author = {Hansen, K. and Khanna, C.}, |
|
| 3759 | + date = {2004-04}, |
|
| 3760 | + journaltitle = {European Journal of Cancer (Oxford, England: 1990)}, |
|
| 3761 | + shortjournal = {Eur J Cancer}, |
|
| 3762 | + volume = {40}, |
|
| 3763 | + number = {6}, |
|
| 3764 | + eprint = {15120042}, |
|
| 3765 | + eprinttype = {pmid}, |
|
| 3766 | + pages = {858--880}, |
|
| 3767 | + issn = {0959-8049}, |
|
| 3768 | + doi = {10.1016/j.ejca.2003.11.031}, |
|
| 3769 | + abstract = {The preclinical development of anticancer drugs has been based primarily on the transplantation of murine or human cancers into mice. Alternatives to these transplantation models are animals that naturally develop cancers with features relevant to the human disease. The first group of these models arises in mice that are genetically engineered to develop cancer. The second group includes pet dogs and cats that naturally develop cancer. This review will discuss the use and integration of these spontaneous cancer models into a comprehensive and comparative approach to preclinical drug development. Examples of their successful use and an outline of their relative strengths and weaknesses will be provided.}, |
|
| 3770 | + langid = {english}, |
|
| 3771 | + keywords = {Animals,Animals Domestic,Animals Genetically Modified,Antineoplastic Agents,Dogs,Drug Design,Drug Evaluation,Drug Screening Assays Antitumor,Genetic Engineering,Humans,Mice,Mice Transgenic,Models Animal,Neoplasms} |
|
| 3772 | +} |
|
| 3773 | + |
|
| 3774 | +@article{haoDictionaryLearningIntegrative2023, |
|
| 3775 | + title = {Dictionary Learning for Integrative, Multimodal and Scalable Single-Cell Analysis}, |
|
| 3776 | + author = {Hao, Yuhan and Stuart, Tim and Kowalski, Madeline H. and Choudhary, Saket and Hoffman, Paul and Hartman, Austin and Srivastava, Avi and Molla, Gesmira and Madad, Shaista and Fernandez-Granda, Carlos and Satija, Rahul}, |
|
| 3777 | + date = {2023-05-25}, |
|
| 3778 | + journaltitle = {Nature Biotechnology}, |
|
| 3779 | + shortjournal = {Nat Biotechnol}, |
|
| 3780 | + eprint = {37231261}, |
|
| 3781 | + eprinttype = {pmid}, |
|
| 3782 | + issn = {1546-1696}, |
|
| 3783 | + doi = {10.1038/s41587-023-01767-y}, |
|
| 3784 | + abstract = {Mapping single-cell sequencing profiles to comprehensive reference datasets provides a powerful alternative to unsupervised analysis. However, most reference datasets are constructed from single-cell RNA-sequencing data and cannot be used to annotate datasets that do not measure gene expression. Here we introduce 'bridge integration', a method to integrate single-cell datasets across modalities using a multiomic dataset as a molecular bridge. Each cell in the multiomic dataset constitutes an element in a 'dictionary', which is used to reconstruct unimodal datasets and transform them into a shared space. Our procedure accurately integrates transcriptomic data with independent single-cell measurements of chromatin accessibility, histone modifications, DNA methylation and protein levels. Moreover, we demonstrate how dictionary learning can be combined with sketching techniques to improve computational scalability and harmonize 8.6 million human immune cell profiles from sequencing and mass cytometry experiments. Our approach, implemented in version 5 of our Seurat toolkit ( http://www.satijalab.org/seurat ), broadens the utility of single-cell reference datasets and facilitates comparisons across diverse molecular modalities.}, |
|
| 3785 | + langid = {english}, |
|
| 3786 | + file = {/Users/rmorin/Zotero/storage/QUPJ4MLY/Hao et al. - 2023 - Dictionary learning for integrative, multimodal an.pdf} |
|
| 3787 | +} |
|
| 3788 | + |
|
| 3789 | +@article{haoIntegratedAnalysisMultimodal2021, |
|
| 3790 | + title = {Integrated Analysis of Multimodal Single-Cell Data}, |
|
| 3791 | + author = {Hao, Yuhan and Hao, Stephanie and Andersen-Nissen, Erica and Mauck, William M. and Zheng, Shiwei and Butler, Andrew and Lee, Maddie J. and Wilk, Aaron J. and Darby, Charlotte and Zager, Michael and Hoffman, Paul and Stoeckius, Marlon and Papalexi, Efthymia and Mimitou, Eleni P. and Jain, Jaison and Srivastava, Avi and Stuart, Tim and Fleming, Lamar M. and Yeung, Bertrand and Rogers, Angela J. and McElrath, Juliana M. and Blish, Catherine A. and Gottardo, Raphael and Smibert, Peter and Satija, Rahul}, |
|
| 3792 | + date = {2021-06-24}, |
|
| 3793 | + journaltitle = {Cell}, |
|
| 3794 | + shortjournal = {Cell}, |
|
| 3795 | + volume = {184}, |
|
| 3796 | + number = {13}, |
|
| 3797 | + eprint = {34062119}, |
|
| 3798 | + eprinttype = {pmid}, |
|
| 3799 | + pages = {3573-3587.e29}, |
|
| 3800 | + issn = {0092-8674}, |
|
| 3801 | + doi = {10.1016/j.cell.2021.04.048}, |
|
| 3802 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8238499/}, |
|
| 3803 | + urldate = {2022-02-01}, |
|
| 3804 | + abstract = {The simultaneous measurement of multiple modalities represents an exciting frontier for single-cell genomics and necessitates computational methods that can define cellular states based on multimodal data. Here, we introduce “weighted-nearest neighbor” analysis, an unsupervised framework to learn the relative utility of each data type in each cell, enabling an integrative analysis of multiple modalities. We apply our procedure to a CITE-seq dataset of 211,000 human peripheral blood mononuclear cells (PBMCs) with panels extending to 228 antibodies to construct a multimodal reference atlas of the circulating immune system. Multimodal analysis substantially improves our ability to resolve cell states, allowing us to identify and validate previously unreported lymphoid subpopulations. Moreover, we demonstrate how to leverage this reference to rapidly map new datasets and to interpret immune responses to vaccination and coronavirus disease 2019 (COVID-19). Our approach represents a broadly applicable strategy to analyze single-cell multimodal datasets and to look beyond the transcriptome toward a unified and multimodal definition of cellular identity., • “Weighted nearest neighbor” analysis integrates multimodal single-cell data • A multimodal reference “atlas” of the circulating human immune system • Identification and validation of novel sources of lymphoid heterogeneity • “Reference-based” mapping of query datasets onto a multimodal atlas , A framework that allows for the integration of multiple data types using single cells is applied to understand distinct immune cell states, previously unidentified immune populations, and to interpret immune responses to vaccinations.}, |
|
| 3805 | + pmcid = {PMC8238499}, |
|
| 3806 | + file = {/Users/rmorin/Zotero/storage/25ZZWT82/Hao et al. - 2021 - Integrated analysis of multimodal single-cell data.pdf} |
|
| 3807 | +} |
|
| 3808 | + |
|
| 3809 | +@article{hargreavesEvaluationHighThroughputGenomic2015, |
|
| 3810 | + title = {Evaluation of {{High-Throughput Genomic Assays}} for the {{Fc Gamma Receptor Locus}}}, |
|
| 3811 | + author = {Hargreaves, Chantal E. and Iriyama, Chisako and Rose-Zerilli, Matthew and Nagelkerke, Sietse Q. and Hussain, Khiyam and Ganderton, Rosalind and Lee, Charlotte and Machado, Lee R. and Hollox, Edward J. and Parker, Helen and Latham, Kate V. and Kuijpers, Taco W. and Potter, Kathleen N. and Coupland, Sarah E. and Davies, Andrew and Stackpole, Michael and Oates, Melanie and Pettitt, Andrew R. and Glennie, Martin J. and Cragg, Mark S. and Strefford, Jonathan C.}, |
|
| 3812 | + date = {2015}, |
|
| 3813 | + journaltitle = {PLOS ONE}, |
|
| 3814 | + volume = {10}, |
|
| 3815 | + number = {11}, |
|
| 3816 | + eprint = {26545243}, |
|
| 3817 | + eprinttype = {pmid}, |
|
| 3818 | + pages = {e0142379}, |
|
| 3819 | + issn = {1932-6203}, |
|
| 3820 | + doi = {10.1371/journal.pone.0142379}, |
|
| 3821 | + url = {http://dx.doi.org/10.1371/journal.pone.0142379}, |
|
| 3822 | + abstract = {Cancer immunotherapy has been revolutionised by the use monoclonal antibodies (mAb) that function through their interaction with Fc gamma receptors (FcγRs). The low-affinity FcγR genes are highly homologous, map to a complex locus at 1p23 and harbour single nucleotide polymorphisms (SNPs) and copy number variation (CNV) that can impact on receptor function and response to therapeutic mAbs. This complexity can hinder accurate characterisation of the locus. We therefore evaluated and optimised a suite of assays for the genomic analysis of the FcγR locus amenable to peripheral blood mononuclear cells and formalin-fixed paraffin-embedded (FFPE) material that can be employed in a high-throughput manner. Assessment of TaqMan genotyping for FCGR2A-131H/R, FCGR3A-158F/V and FCGR2B-232I/T SNPs demonstrated the need for additional methods to discriminate genotypes for the FCGR3A-158F/V and FCGR2B-232I/T SNPs due to sequence homology and CNV in the region. A multiplex ligation-dependent probe amplification assay provided high quality SNP and CNV data in PBMC cases, but there was greater data variability in FFPE material in a manner that was predicted by the BIOMED-2 multiplex PCR protocol. In conclusion, we have evaluated a suite of assays for the genomic analysis of the FcγR locus that are scalable for application in large clinical trials of mAb therapy. These assays will ultimately help establish the importance of FcγR genetics in predicting response to antibody therapeutics.}, |
|
| 3823 | + keywords = {nosource} |
|
| 3824 | +} |
|
| 3825 | + |
|
| 3826 | +@article{hargreavesFcgReceptorsGenetic2015, |
|
| 3827 | + title = {Fcγ Receptors: Genetic Variation, Function, and Disease}, |
|
| 3828 | + author = {Hargreaves, Chantal E. and Rose‐Zerilli, Matthew and Machado, Lee R. and Iriyama, Chisako and Hollox, Edward J. and Cragg, Mark S. and Strefford, Jonathan C.}, |
|
| 3829 | + date = {2015}, |
|
| 3830 | + journaltitle = {Immunological Reviews}, |
|
| 3831 | + volume = {268}, |
|
| 3832 | + number = {1}, |
|
| 3833 | + eprint = {26497510}, |
|
| 3834 | + eprinttype = {pmid}, |
|
| 3835 | + pages = {6--24}, |
|
| 3836 | + issn = {1600-065X}, |
|
| 3837 | + doi = {10.1111/imr.12341}, |
|
| 3838 | + url = {http://dx.doi.org/10.1111/imr.12341}, |
|
| 3839 | + abstract = {Fcγ receptors (FcγRs) are key immune receptors responsible for the effective control of both humoral and innate immunity and are central to maintaining the balance between generating appropriate responses to infection and preventing autoimmunity. When this balance is lost, pathology results in increased susceptibility to cancer, autoimmunity, and infection. In contrast, optimal FcγR engagement facilitates effective disease resolution and response to monoclonal antibody immunotherapy. The underlying genetics of the FcγR gene family are a central component of this careful balance. Complex in humans and generated through ancestral duplication events, here we review the evolution of the gene family in mammals, the potential importance of copy number, and functionally relevant single nucleotide polymorphisms, as well as discussing current approaches and limitations when exploring genetic variation in this region.}, |
|
| 3840 | + keywords = {nosource} |
|
| 3841 | +} |
|
| 3842 | + |
|
| 3843 | +@article{harringtonPreclinicalEvaluationNovel2016, |
|
| 3844 | + title = {Preclinical {{Evaluation}} of the {{Novel BTK Inhibitor Acalabrutinib}} in {{Canine Models}} of {{B-Cell Non-Hodgkin Lymphoma}}}, |
|
| 3845 | + author = {Harrington, Bonnie K. and Gardner, Heather L. and Izumi, Raquel and Hamdy, Ahmed and Rothbaum, Wayne and Coombes, Kevin R. and Covey, Todd and Kaptein, Allard and Gulrajani, Michael and Lith, Bart Van and Krejsa, Cecile and Coss, Christopher C. and Russell, Duncan S. and Zhang, Xiaoli and Urie, Bridget K. and London, Cheryl A. and Byrd, John C. and Johnson, Amy J. and Kisseberth, William C.}, |
|
| 3846 | + date = {2016-07-19}, |
|
| 3847 | + journaltitle = {PLOS ONE}, |
|
| 3848 | + shortjournal = {PLOS ONE}, |
|
| 3849 | + volume = {11}, |
|
| 3850 | + number = {7}, |
|
| 3851 | + pages = {e0159607}, |
|
| 3852 | + publisher = {Public Library of Science}, |
|
| 3853 | + issn = {1932-6203}, |
|
| 3854 | + doi = {10.1371/journal.pone.0159607}, |
|
| 3855 | + url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0159607}, |
|
| 3856 | + urldate = {2022-01-07}, |
|
| 3857 | + abstract = {Acalabrutinib (ACP-196) is a second-generation inhibitor of Bruton agammaglobulinemia tyrosine kinase (BTK) with increased target selectivity and potency compared to ibrutinib. In this study, we evaluated acalabrutinib in spontaneously occurring canine lymphoma, a model of B-cell malignancy similar to human diffuse large B-cell lymphoma (DLBCL). First, we demonstrated that acalabrutinib potently inhibited BTK activity and downstream effectors in CLBL1, a canine B-cell lymphoma cell line, and primary canine lymphoma cells. Acalabrutinib also inhibited proliferation in CLBL1 cells. Twenty dogs were enrolled in the clinical trial and treated with acalabrutinib at dosages of 2.5 to 20mg/kg every 12 or 24 hours. Acalabrutinib was generally well tolerated, with adverse events consisting primarily of grade 1 or 2 anorexia, weight loss, vomiting, diarrhea and lethargy. Overall response rate (ORR) was 25\% (5/20) with a median progression free survival (PFS) of 22.5 days. Clinical benefit was observed in 30\% (6/20) of dogs. These findings suggest that acalabrutinib is safe and exhibits activity in canine B-cell lymphoma patients and support the use of canine lymphoma as a relevant model for human non-Hodgkin lymphoma (NHL).}, |
|
| 3858 | + langid = {english}, |
|
| 3859 | + keywords = {B cells,Cancers and neoplasms,CAT assay,Dogs,Lymph nodes,Lymphoma,Lymphoma cells,Toxicity}, |
|
| 3860 | + file = {/Users/rmorin/Zotero/storage/JXBMQEUU/Harrington et al. - 2016 - Preclinical Evaluation of the Novel BTK Inhibitor .pdf;/Users/rmorin/Zotero/storage/XL9ADXRX/article.html} |
|
| 3861 | +} |
|
| 3862 | + |
|
| 3863 | +@article{hasselblomNumberTumourinfiltratingTIA1, |
|
| 3864 | + title = {The Number of Tumour-Infiltrating {{TIA-1}}+ Cytotoxic {{T}} Cells but Not {{FOXP3}}+ Regulatory {{T}} Cells Predicts Outcome in Diffuse Large {{B-cell}} Lymphoma.}, |
|
| 3865 | + author = {Hasselblom, Sverker and Sigurdadottir, Margret and Hansson, Ulrika and Nilsson-Ehle, Herman and Ridell, Börje and Andersson, Per-Ola}, |
|
| 3866 | + journaltitle = {Br J Haematol}, |
|
| 3867 | + volume = {137}, |
|
| 3868 | + number = {4}, |
|
| 3869 | + pages = {364--373}, |
|
| 3870 | + keywords = {nosource} |
|
| 3871 | +} |
|
| 3872 | + |
|
| 3873 | +@article{havensSpliceswitchingAntisenseOligonucleotides2016, |
|
| 3874 | + title = {Splice-Switching Antisense Oligonucleotides as Therapeutic Drugs}, |
|
| 3875 | + author = {Havens, Mallory A. and Hastings, Michelle L.}, |
|
| 3876 | + date = {2016-08-08}, |
|
| 3877 | + journaltitle = {Nucleic Acids Research}, |
|
| 3878 | + volume = {44}, |
|
| 3879 | + number = {14}, |
|
| 3880 | + eprint = {27288447}, |
|
| 3881 | + eprinttype = {pmid}, |
|
| 3882 | + pages = {6549}, |
|
| 3883 | + publisher = {Oxford University Press}, |
|
| 3884 | + doi = {10.1093/nar/gkw533}, |
|
| 3885 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5001604/}, |
|
| 3886 | + urldate = {2022-10-05}, |
|
| 3887 | + abstract = {Splice-switching oligonucleotides (SSOs) are short, synthetic, antisense, modified nucleic acids that base-pair with a pre-mRNA and disrupt the normal splicing repertoire of the transcript by blocking the RNA–RNA base-pairing or protein–RNA ...}, |
|
| 3888 | + langid = {english}, |
|
| 3889 | + file = {/Users/rmorin/Zotero/storage/4AKSZZRL/PMC5001604.html} |
|
| 3890 | +} |
|
| 3891 | + |
|
| 3892 | +@article{headleyNeorickettsiaHelminthoecaSalmon2011, |
|
| 3893 | + title = {Neorickettsia Helminthoeca and Salmon Poisoning Disease: A Review}, |
|
| 3894 | + shorttitle = {Neorickettsia Helminthoeca and Salmon Poisoning Disease}, |
|
| 3895 | + author = {Headley, Selwyn Arlington and Scorpio, Diana G. and Vidotto, Odilon and Dumler, J. Stephen}, |
|
| 3896 | + date = {2011-02}, |
|
| 3897 | + journaltitle = {Veterinary Journal (London, England: 1997)}, |
|
| 3898 | + shortjournal = {Vet. J.}, |
|
| 3899 | + volume = {187}, |
|
| 3900 | + number = {2}, |
|
| 3901 | + eprint = {20044285}, |
|
| 3902 | + eprinttype = {pmid}, |
|
| 3903 | + pages = {165--173}, |
|
| 3904 | + issn = {1532-2971}, |
|
| 3905 | + doi = {10.1016/j.tvjl.2009.11.019}, |
|
| 3906 | + abstract = {Neorickettsia helminthoeca is an obligate intra-cytoplasmic bacterium that causes salmon poisoning disease (SPD), an acute, febrile, fatal disease of dogs. The complex life-cycle of this pathogen involves stages in an intestinal fluke (Nanophyetus salmincola), a river snail (Oxytrema silicula), in fish, and in fish-eating mammals. This complexity has created confusion with respect to the various bacterial and parasitic infections associated with the disease and its significance in dogs in specific geographical locations has likely to have previously been under-estimated. This paper addresses the history, taxonomy, microbiology of N. helminthoeca and summarises the pathogenesis, clinical signs and pathological features associated with infection. Furthermore, the biological cycles, treatment, control, and both public and veterinary health impacts associated with this pathogen and the intestinal fluke N. salmincola are discussed.}, |
|
| 3907 | + langid = {english}, |
|
| 3908 | + keywords = {Anaplasmataceae Infections,Animals,Dog Diseases,Dogs,Food Parasitology,Foodborne Diseases,Neorickettsia,Salmon,Trematoda,Trematode Infections} |
|
| 3909 | +} |
|
| 3910 | + |
|
| 3911 | +@article{heAptamerBasedTargetedDrug2020, |
|
| 3912 | + title = {Aptamer-{{Based Targeted Drug Delivery Systems}}: {{Current Potential}} and {{Challenges}}}, |
|
| 3913 | + shorttitle = {Aptamer-{{Based Targeted Drug Delivery Systems}}}, |
|
| 3914 | + author = {He, Fen and Wen, Nachuan and Xiao, Daipeng and Yan, Jianhua and Xiong, Hongjie and Cai, Shundong and Liu, Zhenbao and Liu, Yanfei}, |
|
| 3915 | + date = {2020}, |
|
| 3916 | + journaltitle = {Current Medicinal Chemistry}, |
|
| 3917 | + shortjournal = {Curr Med Chem}, |
|
| 3918 | + volume = {27}, |
|
| 3919 | + number = {13}, |
|
| 3920 | + eprint = {30295183}, |
|
| 3921 | + eprinttype = {pmid}, |
|
| 3922 | + pages = {2189--2219}, |
|
| 3923 | + issn = {1875-533X}, |
|
| 3924 | + doi = {10.2174/0929867325666181008142831}, |
|
| 3925 | + abstract = {Aptamers are single-stranded DNA or RNA with 20-100 nucleotides in length that can specifically bind to target molecules via formed three-dimensional structures. These innovative targeting molecules have attracted an increasing interest in the biomedical field. Compared to traditional protein antibodies, aptamers have several advantages, such as small size, high binding affinity, specificity, good biocompatibility, high stability and low immunogenicity, which all contribute to their wide application in the biomedical field. Aptamers can bind to the receptors on the cell membrane and mediate themselves or conjugated nanoparticles to enter into cells. Therefore, aptamers can be served as ideal targeting ligands for drug delivery. Since their excellent properties, different aptamer-mediated drug delivery systems had been developed for cancer therapy. This review provides a brief overview of recent advances in drug delivery systems based on aptamers. The advantages, challenges and future prospectives are also discussed.}, |
|
| 3926 | + langid = {english}, |
|
| 3927 | + keywords = {Aptamer,Aptamers Nucleotide,cancer target therapy,drug carrier,drug delivery system,Drug Delivery Systems,Ligands,nano-medicine,nanomaterials.,Nanoparticles,RNA} |
|
| 3928 | +} |
|
| 3929 | + |
|
| 3930 | +@article{heinzSimpleCombinationsLineagedetermining2010, |
|
| 3931 | + title = {Simple Combinations of Lineage-Determining Transcription Factors Prime Cis-Regulatory Elements Required for Macrophage and {{B}} Cell Identities.}, |
|
| 3932 | + author = {Heinz, Sven and Benner, Christopher and Spann, Nathanael and Bertolino, Eric and Lin, Yin C and Laslo, Peter and Cheng, Jason X and Murre, Cornelis and Singh, Harinder and Glass, Christopher K}, |
|
| 3933 | + date = {2010-05}, |
|
| 3934 | + journaltitle = {Mol Cell}, |
|
| 3935 | + volume = {38}, |
|
| 3936 | + number = {4}, |
|
| 3937 | + pages = {576--589}, |
|
| 3938 | + keywords = {nosource} |
|
| 3939 | +} |
|
| 3940 | + |
|
| 3941 | +@article{heoReproductionMolecularSubtypes2019, |
|
| 3942 | + title = {Reproduction of Molecular Subtypes of Gastric Adenocarcinoma by Transcriptome Sequencing of Archival Tissue}, |
|
| 3943 | + author = {Heo, You Jeong and Park, Charny and Yu, Doyeong and Lee, Jeeyun and Kim, Kyoung-Mee}, |
|
| 3944 | + date = {2019-07-04}, |
|
| 3945 | + journaltitle = {Scientific Reports}, |
|
| 3946 | + shortjournal = {Sci Rep}, |
|
| 3947 | + volume = {9}, |
|
| 3948 | + number = {1}, |
|
| 3949 | + pages = {1--8}, |
|
| 3950 | + issn = {2045-2322}, |
|
| 3951 | + doi = {10.1038/s41598-019-46216-6}, |
|
| 3952 | + url = {https://www.nature.com/articles/s41598-019-46216-6}, |
|
| 3953 | + urldate = {2020-02-04}, |
|
| 3954 | + abstract = {Gastric cancer (GC) is a heterogeneous disease, so molecular classification is important for selecting the most appropriate treatment strategies for GC patients. To be applicable in the clinic, there is an urgent need for a platform that will allow screening real-life archival tissue specimens. For this purpose, we performed RNA sequencing of 50 samples from our Asian Cancer Research Group (ACRG) GC cohort to reproduce the molecular subtypes of GC using archival tissues with different platforms. We filtered out genes from the epithelial-to-mesenchymal transition (EMT) and microsatellite instability-high (MSI) signatures (coefficient\,≤\,0.4) followed by the ACRG molecular subtype strategy. Overall accuracy of reproduction of ACRG subtype was 66\% (33/50). Given the importance of EMT subtype in future clinical trials, we further developed the minimum number of genes (10 genes) for EMT signatures correlating highly with the original EMT signatures (correlation\,≥\,0.65). Using our 10-gene model, we could classify EMT subtypes with high sensitivity (0.9576) and specificity (0.811). In conclusion, we reproduced ACRG GC subtypes using different platforms and could predict EMT subtypes with 10 genes and are now planning to use them in our prospective clinical study of precision oncology in GC.}, |
|
| 3955 | + langid = {english}, |
|
| 3956 | + file = {/Users/rmorin/Zotero/storage/JLMV9J44/s41598-019-46216-6.html} |
|
| 3957 | +} |
|
| 3958 | + |
|
| 3959 | +@article{hernandez-ilizaliturriHigherResponseLenalidomide, |
|
| 3960 | + title = {Higher Response to Lenalidomide in Relapsed/Refractory Diffuse Large {{B-cell}} Lymphoma in Nongerminal Center {{B-cell-like}} than in Germinal Center {{B-cell-like}} Phenotype.}, |
|
| 3961 | + author = {Hernandez-Ilizaliturri, Francisco J and Deeb, George and Zinzani, Pier L and Pileri, Stefano A and Malik, Farhana and Macon, William R and Goy, Andre and Witzig, Thomas E and Czuczman, Myron S}, |
|
| 3962 | + journaltitle = {Cancer}, |
|
| 3963 | + volume = {117}, |
|
| 3964 | + number = {22}, |
|
| 3965 | + pages = {5058--5066}, |
|
| 3966 | + keywords = {nosource} |
|
| 3967 | +} |
|
| 3968 | + |
|
| 3969 | +@article{heroldAdultsPhiladelphiaChromosome2017, |
|
| 3970 | + title = {Adults with {{Philadelphia}} Chromosome–like Acute Lymphoblastic Leukemia Frequently Have {{IGH-CRLF2}} and {{JAK2}} Mutations, Persistence of Minimal Residual Disease and Poor Prognosis}, |
|
| 3971 | + author = {Herold, Tobias and Schneider, Stephanie and Metzeler, Klaus H. and Neumann, Martin and Hartmann, Luise and Roberts, Kathryn G. and Konstandin, Nikola P. and Greif, Philipp A. and Bräundl, Kathrin and Ksienzyk, Bianka and Huk, Natalia and Schneider, Irene and Zellmeier, Evelyn and Jurinovic, Vindi and Mansmann, Ulrich and Hiddemann, Wolfgang and Mullighan, Charles G. and Bohlander, Stefan K. and Spiekermann, Karsten and Hoelzer, Dieter and Brüggemann, Monika and Baldus, Claudia D. and Dreyling, Martin and Gökbuget, Nicola}, |
|
| 3972 | + date = {2017-01}, |
|
| 3973 | + journaltitle = {Haematologica}, |
|
| 3974 | + shortjournal = {Haematologica}, |
|
| 3975 | + volume = {102}, |
|
| 3976 | + number = {1}, |
|
| 3977 | + eprint = {27561722}, |
|
| 3978 | + eprinttype = {pmid}, |
|
| 3979 | + pages = {130--138}, |
|
| 3980 | + issn = {0390-6078}, |
|
| 3981 | + doi = {10.3324/haematol.2015.136366}, |
|
| 3982 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210243/}, |
|
| 3983 | + urldate = {2020-07-16}, |
|
| 3984 | + abstract = {Philadelphia-like B-cell precursor acute lymphoblastic leukemia (Ph-like ALL) is characterized by distinct genetic alterations and inferior prognosis in children and younger adults. The purpose of this study was a genetic and clinical characterization of Ph-like ALL in adults. Twenty-six (13\%) of 207 adult patients (median age: 42 years) with B-cell precursor ALL (BCP-ALL) were classified as having Ph-like ALL using gene expression profiling. The frequency of Ph-like ALL was 27\% among 95 BCP-ALL patients negative for BCR-ABL1 and KMT2A-rearrangements. IGH-CRLF2 rearrangements (6/16; P=0.002) and mutations in JAK2 (7/16; P{$<$}0.001) were found exclusively in the Ph-like ALL subgroup. Clinical and outcome analyses were restricted to patients treated in German Multicenter Study Group for Adult ALL (GMALL) trials 06/99 and 07/03 (n=107). The complete remission rate was 100\% among both Ph-like ALL patients (n=19) and the “remaining BCP-ALL” cases (n=40), i.e. patients negative for BCR-ABL1 and KMT2A-rearrangements and the Ph-like subtype. Significantly fewer Ph-like ALL patients reached molecular complete remission (33\% versus 79\%; P=0.02) and had a lower probability of continuous complete remission (26\% versus 60\%; P=0.03) and overall survival (22\% versus 64\%; P=0.006) at 5 years compared to the remaining BCP-ALL patients. The profile of genetic lesions in adults with Ph-like ALL, including older adults, resembles that of pediatric Ph-like ALL and differs from the profile in the remaining BCP-ALL. Our study is the first to demonstrate that Ph-like ALL is associated with inferior outcomes in intensively treated older adult patients. Ph-like adult ALL should be recognized as a distinct, high-risk entity and further research on improved diagnostic and therapeutic approaches is needed. (NCT00199056, NCT00198991)}, |
|
| 3985 | + pmcid = {PMC5210243}, |
|
| 3986 | + file = {/Users/rmorin/Zotero/storage/4HNWKW3Z/herold2016.pdf;/Users/rmorin/Zotero/storage/WBNMJU5W/Herold et al. - 2017 - Adults with Philadelphia chromosome–like acute lym.pdf} |
|
| 3987 | +} |
|
| 3988 | + |
|
| 3989 | +@article{herviouHnRNPDriveRNA2020, |
|
| 3990 | + title = {{{hnRNP H}}/{{F}} Drive {{RNA G-quadruplex-mediated}} Translation Linked to Genomic Instability and Therapy Resistance in Glioblastoma}, |
|
| 3991 | + author = {Herviou, Pauline and Le Bras, Morgane and Dumas, Leïla and Hieblot, Corinne and Gilhodes, Julia and Cioci, Gianluca and Hugnot, Jean-Philippe and Ameadan, Alfred and Guillonneau, François and Dassi, Erik and Cammas, Anne and Millevoi, Stefania}, |
|
| 3992 | + date = {2020-05-27}, |
|
| 3993 | + journaltitle = {Nature Communications}, |
|
| 3994 | + shortjournal = {Nat Commun}, |
|
| 3995 | + volume = {11}, |
|
| 3996 | + number = {1}, |
|
| 3997 | + pages = {2661}, |
|
| 3998 | + publisher = {Nature Publishing Group}, |
|
| 3999 | + issn = {2041-1723}, |
|
| 4000 | + doi = {10.1038/s41467-020-16168-x}, |
|
| 4001 | + url = {https://www.nature.com/articles/s41467-020-16168-x}, |
|
| 4002 | + urldate = {2022-10-15}, |
|
| 4003 | + abstract = {RNA G-quadruplexes (RG4s) are four-stranded structures known to control mRNA translation of cancer relevant genes. RG4 formation is pervasive in vitro but not in cellulo, indicating the existence of poorly characterized molecular machinery that remodels RG4s and maintains them unfolded. Here, we performed a quantitative proteomic screen to identify cytosolic proteins that interact with a canonical RG4 in its folded and unfolded conformation. Our results identified hnRNP H/F as important components of the cytoplasmic machinery modulating the~structural integrity~of RG4s, revealed their function in RG4-mediated translation and uncovered the underlying molecular mechanism impacting the~cellular stress response linked to the outcome of glioblastoma.}, |
|
| 4004 | + issue = {1}, |
|
| 4005 | + langid = {english}, |
|
| 4006 | + keywords = {RNA,RNA-binding proteins}, |
|
| 4007 | + file = {/Users/rmorin/Zotero/storage/97BQBNFC/Herviou et al. - 2020 - hnRNP HF drive RNA G-quadruplex-mediated translat.pdf;/Users/rmorin/Zotero/storage/FHP727DS/s41467-020-16168-x.html} |
|
| 4008 | +} |
|
| 4009 | + |
|
| 4010 | +@article{hicksFusDeficiencyMice2000, |
|
| 4011 | + title = {Fus Deficiency in Mice Results in Defective {{B-lymphocyte}} Development and Activation, High Levels of Chromosomal Instability and Perinatal Death}, |
|
| 4012 | + author = {Hicks, Geoffrey G. and Singh, Nagendra and Nashabi, Abudi and Mai, Sabine and Bozek, Gracjan and Klewes, Ludger and Arapovic, Djula and White, Erica K. and Koury, Mark J. and Oltz, Eugene M. and Van Kaer, Luc and Ruley, H. E.}, |
|
| 4013 | + date = {2000-02}, |
|
| 4014 | + journaltitle = {Nature Genetics}, |
|
| 4015 | + shortjournal = {Nat Genet}, |
|
| 4016 | + volume = {24}, |
|
| 4017 | + number = {2}, |
|
| 4018 | + pages = {175--179}, |
|
| 4019 | + publisher = {Nature Publishing Group}, |
|
| 4020 | + issn = {1546-1718}, |
|
| 4021 | + doi = {10.1038/72842}, |
|
| 4022 | + url = {https://www.nature.com/articles/ng0200_175}, |
|
| 4023 | + urldate = {2022-10-03}, |
|
| 4024 | + abstract = {The gene FUS (also known as TLS (for translocated in liposarcoma) and hnRNP P2) is translocated with the gene encoding the transcription factor ERG-1 in human myeloid leukaemias1,2,3. Although the functions of wild-type FUS are unknown, the protein contains an RNA-recognition motif and is a component of nuclear riboprotein complexes4,5. FUS resembles a transcription factor in that it binds DNA, contributes a transcriptional activation domain to the FUS–ERG oncoprotein and interacts with several transcription factors in vitro6,7,8. To better understand FUS function in vivo, we examined the consequences of disrupting Fus in mice. Our results indicate that Fus is essential for viability of neonatal animals, influences lymphocyte development in a non-cell-intrinsic manner, has an intrinsic role in the proliferative responses of B cells to specific mitogenic stimuli and is required for the maintenance of genomic stability. The involvement of a nuclear riboprotein in these processes in vivo indicates that Fus is important in genome maintenance.}, |
|
| 4025 | + issue = {2}, |
|
| 4026 | + langid = {english}, |
|
| 4027 | + keywords = {Agriculture,Animal Genetics and Genomics,Biomedicine,Cancer Research,Gene Function,general,Human Genetics}, |
|
| 4028 | + file = {/Users/rmorin/Zotero/storage/4ZRL2MVF/Hicks et al. - 2000 - Fus deficiency in mice results in defective B-lymp.pdf;/Users/rmorin/Zotero/storage/FRIZDJV4/ng0200_175.html} |
|
| 4029 | +} |
|
| 4030 | + |
|
| 4031 | +@article{hiltonRelapseTimingAssociated2023, |
|
| 4032 | + title = {Relapse {{Timing Is Associated With Distinct Evolutionary Dynamics}} in {{Diffuse Large B-Cell Lymphoma}}}, |
|
| 4033 | + author = {Hilton, Laura K. and Ngu, Henry S. and Collinge, Brett and Dreval, Kostiantyn and Ben-Neriah, Susana and Rushton, Christopher K. and Wong, Jasper C.H. and Cruz, Manuela and Roth, Andrew and Boyle, Merrill and Meissner, Barbara and Slack, Graham W. and Farinha, Pedro and Craig, Jeffrey W. and Gerrie, Alina S. and Freeman, Ciara L. and Villa, Diego and Rodrigo, Judith A. and Song, Kevin and Crump, Michael and Shepherd, Lois and Hay, Annette E. and Kuruvilla, John and Savage, Kerry J. and Kridel, Robert and Karsan, Aly and Marra, Marco A. and Sehn, Laurie H. and Steidl, Christian and Morin, Ryan D. and Scott, David W.}, |
|
| 4034 | + date = {2023-09}, |
|
| 4035 | + journaltitle = {Journal of Clinical Oncology}, |
|
| 4036 | + shortjournal = {JCO}, |
|
| 4037 | + volume = {41}, |
|
| 4038 | + number = {25}, |
|
| 4039 | + pages = {4164--4177}, |
|
| 4040 | + publisher = {Wolters Kluwer}, |
|
| 4041 | + issn = {0732-183X}, |
|
| 4042 | + doi = {10.1200/JCO.23.00570}, |
|
| 4043 | + url = {https://ascopubs.org/doi/full/10.1200/JCO.23.00570}, |
|
| 4044 | + urldate = {2023-10-21}, |
|
| 4045 | + abstract = {PURPOSE Diffuse large B-cell lymphoma (DLBCL) is cured in more than 60\% of patients, but outcomes remain poor for patients experiencing disease progression or relapse (refractory or relapsed DLBCL [rrDLBCL]), particularly if these events occur early. Although previous studies examining cohorts of rrDLBCL have identified features that are enriched at relapse, few have directly compared serial biopsies to uncover biological and evolutionary dynamics driving rrDLBCL. Here, we sought to confirm the relationship between relapse timing and outcomes after second-line (immuno)chemotherapy and determine the evolutionary dynamics that underpin that relationship. PATIENTS AND METHODS Outcomes were examined in a population-based cohort of 221 patients with DLBCL who experienced progression/relapse after frontline treatment and were treated with second-line (immuno)chemotherapy with an intention-to-treat with autologous stem-cell transplantation (ASCT). Serial DLBCL biopsies from a partially overlapping cohort of 129 patients underwent molecular characterization, including whole-genome or whole-exome sequencing in 73 patients. RESULTS Outcomes to second-line therapy and ASCT are superior for late relapse ({$>$}2 years postdiagnosis) versus primary refractory ({$<$}9 months) or early relapse (9-24 months). Diagnostic and relapse biopsies were mostly concordant for cell-of-origin classification and genetics-based subgroup. Despite this concordance, the number of mutations exclusive to each biopsy increased with time since diagnosis, and late relapses shared few mutations with their diagnostic counterpart, demonstrating a branching evolution pattern. In patients with highly divergent tumors, many of the same genes acquired new mutations independently in each tumor, suggesting that the earliest mutations in a shared precursor cell constrain tumor evolution toward the same genetics-based subgroups at both diagnosis and relapse. CONCLUSION These results suggest that late relapses commonly represent genetically distinct and chemotherapy-naïve disease and have implications for optimal patient management.}, |
|
| 4046 | + keywords = {Morinlab} |
|
| 4047 | +} |
|
| 4048 | + |
|
| 4049 | +@article{hinzpeterAlternativeSplicingNAGNAG2010, |
|
| 4050 | + title = {Alternative {{Splicing}} at a {{NAGNAG Acceptor Site}} as a {{Novel Phenotype Modifier}}}, |
|
| 4051 | + author = {Hinzpeter, Alexandre and Aissat, Abdel and Sondo, Elvira and Costa, Catherine and Arous, Nicole and Gameiro, Christine and Martin, Natacha and Tarze, Agathe and Weiss, Laurence and family=Becdelièvre, given=Alix, prefix=de, useprefix=false and Costes, Bruno and Goossens, Michel and Galietta, Luis J. and Girodon, Emmanuelle and Fanen, Pascale}, |
|
| 4052 | + date = {2010-10-07}, |
|
| 4053 | + journaltitle = {PLOS Genetics}, |
|
| 4054 | + shortjournal = {PLOS Genetics}, |
|
| 4055 | + volume = {6}, |
|
| 4056 | + number = {10}, |
|
| 4057 | + pages = {e1001153}, |
|
| 4058 | + publisher = {Public Library of Science}, |
|
| 4059 | + issn = {1553-7404}, |
|
| 4060 | + doi = {10.1371/journal.pgen.1001153}, |
|
| 4061 | + url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1001153}, |
|
| 4062 | + urldate = {2022-10-25}, |
|
| 4063 | + abstract = {Approximately 30\% of alleles causing genetic disorders generate premature termination codons (PTCs), which are usually associated with severe phenotypes. However, bypassing the deleterious stop codon can lead to a mild disease outcome. Splicing at NAGNAG tandem splice sites has been reported to result in insertion or deletion (indel) of three nucleotides. We identified such a mechanism as the origin of the mild to asymptomatic phenotype observed in cystic fibrosis patients homozygous for the E831X mutation (2623G{$>$}T) in the CFTR gene. Analyses performed on nasal epithelial cell mRNA detected three distinct isoforms, a considerably more complex situation than expected for a single nucleotide substitution. Structure-function studies and in silico analyses provided the first experimental evidence of an indel of a stop codon by alternative splicing at a NAGNAG acceptor site. In addition to contributing to proteome plasticity, alternative splicing at a NAGNAG tandem site can thus remove a disease-causing UAG stop codon. This molecular study reveals a naturally occurring mechanism where the effect of either modifier genes or epigenetic factors could be suspected. This finding is of importance for genetic counseling as well as for deciding appropriate therapeutic strategies.}, |
|
| 4064 | + langid = {english}, |
|
| 4065 | + keywords = {Alternative splicing,Epithelial cells,Messenger RNA,Nonsense mutation,Nucleotides,Polymerase chain reaction,Reverse transcriptase-polymerase chain reaction,Transfection}, |
|
| 4066 | + file = {/Users/rmorin/Zotero/storage/8FYCG565/Hinzpeter et al. - 2010 - Alternative Splicing at a NAGNAG Acceptor Site as .pdf;/Users/rmorin/Zotero/storage/PMNX6RMQ/article.html} |
|
| 4067 | +} |
|
| 4068 | + |
|
| 4069 | +@article{hirtRiskFollicularLymphoma2015, |
|
| 4070 | + title = {Risk of Follicular Lymphoma Associated with {{BCL2}} Translocations in Peripheral Blood}, |
|
| 4071 | + author = {Hirt, Carsten and Camargo, M. Constanza and Yu, Kelly J. and Hewitt, Stephen M. and Dölken, Gottfried and Rabkin, Charles S.}, |
|
| 4072 | + date = {2015}, |
|
| 4073 | + journaltitle = {Leukemia \& Lymphoma}, |
|
| 4074 | + shortjournal = {Leuk Lymphoma}, |
|
| 4075 | + volume = {56}, |
|
| 4076 | + number = {9}, |
|
| 4077 | + eprint = {25549806}, |
|
| 4078 | + eprinttype = {pmid}, |
|
| 4079 | + pages = {2625--2629}, |
|
| 4080 | + issn = {1029-2403}, |
|
| 4081 | + doi = {10.3109/10428194.2014.999324}, |
|
| 4082 | + abstract = {Many adults have circulating lymphocytes with the BCL2 gene translocation characteristic of follicular lymphoma. We therefore conducted a nested case-control study of incident lymphomas with peripheral blood obtained a median 4.9 years pre-diagnosis from the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial. Overall, 13 of 26 cases of lymphoma and 14 of 47 controls had BCL2 major breakpoint region (MBR) translocations in pre-diagnosis blood (odds ratio [OR] = 2.8). Nine cases had BCL2-MBR-positive tumors; eight of these nine had BCL2-MBR translocations in paired blood versus five of the 17 with BCL2-MBR-negative tumors (p = 0.01). Comparing both tumor types to controls, blood BCL2-MBR translocations had a strong, statistically significant association with BCL2-MBR-positive tumors (OR = 26), but not with BCL2-MBR-negative tumors (OR = 0.9). All eight BCL2-MBR-positive tumors with pre-diagnosis BCL2 translocations were clonally related to these circulating cells, based on similarity of recombination sequences. These data indicate that blood BCL2-MBR translocations represent lymphoma precursor clones with malignant potential.}, |
|
| 4083 | + langid = {english}, |
|
| 4084 | + pmcid = {PMC5819878}, |
|
| 4085 | + keywords = {Aged,Aged 80 and over,Blood Cells,Case-Control Studies,Chromosome Breakpoints,Chromosomes Human Pair 14,Chromosomes Human Pair 18,Female,Gene Dosage,Genes Immunoglobulin,Genetic Association Studies,Genetic Predisposition to Disease,Humans,Lymphoma and Hodgkin disease,Lymphoma Follicular,Male,Middle Aged,molecular genetics,Odds Ratio,Population Surveillance,prognostication,Proto-Oncogene Proteins c-bcl-2,Risk,Translocation Genetic,United States}, |
|
| 4086 | + file = {/Users/rmorin/Zotero/storage/X5JKIDSA/Hirt et al. - 2015 - Risk of follicular lymphoma associated with BCL2 t.pdf} |
|
| 4087 | +} |
|
| 4088 | + |
|
| 4089 | +@article{hirtRiskFollicularLymphoma2015a, |
|
| 4090 | + title = {Risk of Follicular Lymphoma Associated with {{BCL2}} Translocations in Peripheral Blood}, |
|
| 4091 | + author = {Hirt, Carsten and Camargo, M. Constanza and Yu, Kelly J. and Hewitt, Stephen M. and Dölken, Gottfried and Rabkin, Charles S.}, |
|
| 4092 | + date = {2015}, |
|
| 4093 | + journaltitle = {Leukemia \& Lymphoma}, |
|
| 4094 | + shortjournal = {Leuk Lymphoma}, |
|
| 4095 | + volume = {56}, |
|
| 4096 | + number = {9}, |
|
| 4097 | + eprint = {25549806}, |
|
| 4098 | + eprinttype = {pmid}, |
|
| 4099 | + pages = {2625--2629}, |
|
| 4100 | + issn = {1029-2403}, |
|
| 4101 | + doi = {10.3109/10428194.2014.999324}, |
|
| 4102 | + abstract = {Many adults have circulating lymphocytes with the BCL2 gene translocation characteristic of follicular lymphoma. We therefore conducted a nested case-control study of incident lymphomas with peripheral blood obtained a median 4.9 years pre-diagnosis from the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial. Overall, 13 of 26 cases of lymphoma and 14 of 47 controls had BCL2 major breakpoint region (MBR) translocations in pre-diagnosis blood (odds ratio [OR] = 2.8). Nine cases had BCL2-MBR-positive tumors; eight of these nine had BCL2-MBR translocations in paired blood versus five of the 17 with BCL2-MBR-negative tumors (p = 0.01). Comparing both tumor types to controls, blood BCL2-MBR translocations had a strong, statistically significant association with BCL2-MBR-positive tumors (OR = 26), but not with BCL2-MBR-negative tumors (OR = 0.9). All eight BCL2-MBR-positive tumors with pre-diagnosis BCL2 translocations were clonally related to these circulating cells, based on similarity of recombination sequences. These data indicate that blood BCL2-MBR translocations represent lymphoma precursor clones with malignant potential.}, |
|
| 4103 | + langid = {english}, |
|
| 4104 | + pmcid = {PMC5819878}, |
|
| 4105 | + keywords = {Aged,Aged 80 and over,Blood Cells,Case-Control Studies,Chromosome Breakpoints,Chromosomes Human Pair 14,Chromosomes Human Pair 18,Female,Gene Dosage,Genes Immunoglobulin,Genetic Association Studies,Genetic Predisposition to Disease,Humans,Lymphoma and Hodgkin disease,Lymphoma Follicular,Male,Middle Aged,molecular genetics,Odds Ratio,Population Surveillance,prognostication,Proto-Oncogene Proteins c-bcl-2,Risk,Translocation Genetic,United States}, |
|
| 4106 | + file = {/Users/rmorin/Zotero/storage/XBIUDU7M/Hirt et al. - 2015 - Risk of follicular lymphoma associated with BCL2 t.pdf} |
|
| 4107 | +} |
|
| 4108 | + |
|
| 4109 | +@article{hitzOutcomePatientsPrimary2015, |
|
| 4110 | + title = {Outcome of Patients with Primary Refractory Diffuse Large {{B}} Cell Lymphoma after {{R-CHOP}} Treatment}, |
|
| 4111 | + author = {Hitz, Felicitas and Connors, J. M. and Gascoyne, R. D. and Hoskins, P. and Moccia, A. and Savage, K. J. and Sehn, L. H. and Shenkier, T. and Villa, D. and Klasa, R.}, |
|
| 4112 | + date = {2015}, |
|
| 4113 | + journaltitle = {Annals of Hematology}, |
|
| 4114 | + volume = {94}, |
|
| 4115 | + number = {11}, |
|
| 4116 | + eprint = {26246466}, |
|
| 4117 | + eprinttype = {pmid}, |
|
| 4118 | + pages = {1839--1843}, |
|
| 4119 | + issn = {0939-5555}, |
|
| 4120 | + doi = {10.1007/s00277-015-2467-z}, |
|
| 4121 | + url = {http://dx.doi.org/10.1007/s00277-015-2467-z}, |
|
| 4122 | + abstract = {Primary refractory diffuse large B cell lymphoma (DLBCL) following R-CHOP chemotherapy is a major concern. We identified 1126 patients with DLBCL treated with R-CHOP from 2000 to 2009, of whom 166 (15 \%) had primary refractory disease. Of the 75/166 (45 \%) who were age {$<$}70 years and had been planned for stage-directed curative therapy, 43 (57 \%) were primary nonresponders and 32 (43 \%) relapsed within 3 months of completing R-CHOP. Thirty of 75 (40 \%) patients had serious comorbidity and organ dysfunction precluding intensive treatment and had palliative treatment only. Twelve of 45 (27 \%) patients responded to second-line treatment and underwent ASCT. The median overall survival for the 75 patients was 10 months with only seven patients alive without evidence of disease at follow-up ranging from 14 to 106 months. Primary refractory DLBCL after R-CHOP has a very poor outcome with only anecdotal survivors independent of the intended treatment approach.}, |
|
| 4123 | + keywords = {nosource} |
|
| 4124 | +} |
|
| 4125 | + |
|
| 4126 | +@online{HnRNPDriveRNA, |
|
| 4127 | + title = {{{hnRNP H}}/{{F}} Drive {{RNA G-quadruplex-mediated}} Translation Linked to Genomic Instability and Therapy Resistance in Glioblastoma | {{Nature Communications}}}, |
|
| 4128 | + url = {https://www.nature.com/articles/s41467-020-16168-x}, |
|
| 4129 | + urldate = {2022-10-15}, |
|
| 4130 | + file = {/Users/rmorin/Zotero/storage/4MS5D8XF/s41467-020-16168-x.html} |
|
| 4131 | +} |
|
| 4132 | + |
|
| 4133 | +@article{hodsonRNAbindingProteinsHematopoiesis2019, |
|
| 4134 | + title = {{{RNA-binding}} Proteins in Hematopoiesis and Hematological Malignancy}, |
|
| 4135 | + author = {Hodson, Daniel J. and Screen, Michael and Turner, Martin}, |
|
| 4136 | + date = {2019-05-30}, |
|
| 4137 | + journaltitle = {Blood}, |
|
| 4138 | + shortjournal = {Blood}, |
|
| 4139 | + volume = {133}, |
|
| 4140 | + number = {22}, |
|
| 4141 | + pages = {2365--2373}, |
|
| 4142 | + issn = {0006-4971}, |
|
| 4143 | + doi = {10.1182/blood-2018-10-839985}, |
|
| 4144 | + url = {https://doi.org/10.1182/blood-2018-10-839985}, |
|
| 4145 | + urldate = {2022-09-19}, |
|
| 4146 | + abstract = {RNA-binding proteins (RBPs) regulate fundamental processes, such as differentiation and self-renewal, by enabling the dynamic control of protein abundance or isoforms or through the regulation of noncoding RNA. RBPs are increasingly appreciated as being essential for normal hematopoiesis, and they are understood to play fundamental roles in hematological malignancies by acting as oncogenes or tumor suppressors. Alternative splicing has been shown to play roles in the development of specific hematopoietic lineages, and sequence-specific mutations in RBPs lead to dysregulated splicing in myeloid and lymphoid leukemias. RBPs that regulate translation contribute to the development and function of hematological lineages, act as nodes for the action of multiple signaling pathways, and contribute to hematological malignancies. These insights broaden our mechanistic understanding of the molecular regulation of hematopoiesis and offer opportunities to develop disease biomarkers and new therapeutic modalities.}, |
|
| 4147 | + file = {/Users/rmorin/Zotero/storage/KN37RDIF/Hodson et al. - 2019 - RNA-binding proteins in hematopoiesis and hematolo.html} |
|
| 4148 | +} |
|
| 4149 | + |
|
| 4150 | +@article{holdhoffAnalysisCirculatingTumor2009, |
|
| 4151 | + title = {Analysis of {{Circulating Tumor DNA}} to {{Confirm Somatic KRAS Mutations}}}, |
|
| 4152 | + author = {Holdhoff, M and Schmidt, K and Donehower, R and Diaz, L A}, |
|
| 4153 | + date = {2009-09}, |
|
| 4154 | + journaltitle = {JNCI Journal of the National Cancer Institute}, |
|
| 4155 | + volume = {101}, |
|
| 4156 | + number = {18}, |
|
| 4157 | + pages = {1284--1285}, |
|
| 4158 | + keywords = {nosource} |
|
| 4159 | +} |
|
| 4160 | + |
|
| 4161 | +@article{holienMYCAmplificationsMyeloma2015, |
|
| 4162 | + title = {{{MYC}} Amplifications in Myeloma Cell Lines: Correlation with {{MYC-inhibitor}} Efficacy}, |
|
| 4163 | + shorttitle = {{{MYC}} Amplifications in Myeloma Cell Lines}, |
|
| 4164 | + author = {Holien, Toril and Misund, Kristine and Olsen, Oddrun Elise and Baranowska, Katarzyna Anna and Buene, Glenn and Børset, Magne and Waage, Anders and Sundan, Anders}, |
|
| 4165 | + date = {2015-06-02}, |
|
| 4166 | + journaltitle = {Oncotarget}, |
|
| 4167 | + shortjournal = {Oncotarget}, |
|
| 4168 | + volume = {6}, |
|
| 4169 | + number = {26}, |
|
| 4170 | + eprint = {26087190}, |
|
| 4171 | + eprinttype = {pmid}, |
|
| 4172 | + pages = {22698--22705}, |
|
| 4173 | + issn = {1949-2553}, |
|
| 4174 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4673192/}, |
|
| 4175 | + urldate = {2022-10-05}, |
|
| 4176 | + abstract = {In multiple myeloma, elevated MYC expression is related to disease initiation and progression. We found that in myeloma cell lines, MYC gene amplifications were common and correlated with MYC mRNA and protein. In primary cell samples MYC mRNA levels were also relatively high; however gene copy number alterations were uncommon. Elevated levels of MYC in primary myeloma cells have been reported to arise from complex genetic aberrations and are more common than previously thought. Thus, elevated MYC expression is achieved differently in myeloma cell lines and primary cells. Sensitivity of myeloma cell lines to the MYC inhibitor 10058-F4 correlated with MYC expression, supporting that the activity of 10058-F4 was through specific inhibition of MYC.}, |
|
| 4177 | + pmcid = {PMC4673192}, |
|
| 4178 | + file = {/Users/rmorin/Zotero/storage/KUYJITZX/Holien et al. - 2015 - MYC amplifications in myeloma cell lines correlat.pdf} |
|
| 4179 | +} |
|
| 4180 | + |
|
| 4181 | +@article{hongRNABindingProtein2017, |
|
| 4182 | + title = {{{RNA Binding Protein}} as an {{Emerging Therapeutic Target}} for {{Cancer Prevention}} and {{Treatment}}}, |
|
| 4183 | + author = {Hong, Suntaek}, |
|
| 4184 | + date = {2017-12}, |
|
| 4185 | + journaltitle = {Journal of Cancer Prevention}, |
|
| 4186 | + shortjournal = {J Cancer Prev}, |
|
| 4187 | + volume = {22}, |
|
| 4188 | + number = {4}, |
|
| 4189 | + eprint = {29302577}, |
|
| 4190 | + eprinttype = {pmid}, |
|
| 4191 | + pages = {203--210}, |
|
| 4192 | + issn = {2288-3649}, |
|
| 4193 | + doi = {10.15430/JCP.2017.22.4.203}, |
|
| 4194 | + abstract = {After transcription, RNAs are always associated with RNA binding proteins (RBPs) to perform biological activities. RBPs can interact with target RNAs in sequence- and structure-dependent manner through their unique RNA binding domains. In development and progression of carcinogenesis, RBPs are aberrantly dysregulated in many human cancers with various mechanisms, such as genetic alteration, epigenetic change, noncoding RNA-mediated regulation, and post-translational modifications. Upon deregulation in cancers, RBPs influence every step in the development and progression of cancer, including sustained cell proliferation, evasion of apoptosis, avoiding immune surveillance, inducing angiogenesis, and activating metastasis. To develop therapeutic strategies targeting RBPs, RNA interference-based oligonucleotides or small molecule inhibitors have been screened based on reduced RBP-RNA interaction and changed level of target RNAs. Identification of binding RNAs with high-throughput techniques and integral analysis of multiple datasets will help us develop new therapeutic drugs or prognostic biomarkers for human cancers.}, |
|
| 4195 | + langid = {english}, |
|
| 4196 | + pmcid = {PMC5751837}, |
|
| 4197 | + keywords = {Cancer,Chemoprevention,RNA-binding proteins,Therapeutics} |
|
| 4198 | +} |
|
| 4199 | + |
|
| 4200 | +@article{honigbergBrutonTyrosineKinase2010, |
|
| 4201 | + title = {The {{Bruton}} Tyrosine Kinase Inhibitor {{PCI-32765}} Blocks {{B-cell}} Activation and Is Efficacious in Models of Autoimmune Disease and {{B-cell}} Malignancy}, |
|
| 4202 | + author = {Honigberg, Lee A. and Smith, Ashley M. and Sirisawad, Mint and Verner, Erik and Loury, David and Chang, Betty and Li, Shyr and Pan, Zhengying and Thamm, Douglas H. and Miller, Richard A. and Buggy, Joseph J.}, |
|
| 4203 | + date = {2010-07-20}, |
|
| 4204 | + journaltitle = {Proceedings of the National Academy of Sciences of the United States of America}, |
|
| 4205 | + shortjournal = {Proc Natl Acad Sci U S A}, |
|
| 4206 | + volume = {107}, |
|
| 4207 | + number = {29}, |
|
| 4208 | + eprint = {20615965}, |
|
| 4209 | + eprinttype = {pmid}, |
|
| 4210 | + pages = {13075--13080}, |
|
| 4211 | + issn = {1091-6490}, |
|
| 4212 | + doi = {10.1073/pnas.1004594107}, |
|
| 4213 | + abstract = {Activation of the B-cell antigen receptor (BCR) signaling pathway contributes to the initiation and maintenance of B-cell malignancies and autoimmune diseases. The Bruton tyrosine kinase (Btk) is specifically required for BCR signaling as demonstrated by human and mouse mutations that disrupt Btk function and prevent B-cell maturation at steps that require a functional BCR pathway. Herein we describe a selective and irreversible Btk inhibitor, PCI-32765, that is currently under clinical development in patients with B-cell non-Hodgkin lymphoma. We have used this inhibitor to investigate the biologic effects of Btk inhibition on mature B-cell function and the progression of B cell-associated diseases in vivo. PCI-32765 blocked BCR signaling in human peripheral B cells at concentrations that did not affect T cell receptor signaling. In mice with collagen-induced arthritis, orally administered PCI-32765 reduced the level of circulating autoantibodies and completely suppressed disease. PCI-32765 also inhibited autoantibody production and the development of kidney disease in the MRL-Fas(lpr) lupus model. Occupancy of the Btk active site by PCI-32765 was monitored in vitro and in vivo using a fluorescent affinity probe for Btk. Active site occupancy of Btk was tightly correlated with the blockade of BCR signaling and in vivo efficacy. Finally, PCI-32765 induced objective clinical responses in dogs with spontaneous B-cell non-Hodgkin lymphoma. These findings support Btk inhibition as a therapeutic approach for the treatment of human diseases associated with activation of the BCR pathway.}, |
|
| 4214 | + langid = {english}, |
|
| 4215 | + pmcid = {PMC2919935}, |
|
| 4216 | + keywords = {Administration Oral,Agammaglobulinaemia Tyrosine Kinase,Animals,Arthritis Experimental,Autoantibodies,Autoimmune Diseases,B-Lymphocytes,Benzofurans,Disease Models Animal,Dogs,Humans,Lymphocyte Activation,lymphoma,Lymphoma B-Cell,Mice,Protein Kinase Inhibitors,Protein-Tyrosine Kinases,Pyrazoles,Pyrimidines,Receptors Antigen B-Cell,Signal Transduction,Treatment Outcome,X-linked agammaglobulinemia}, |
|
| 4217 | + file = {/Users/rmorin/Zotero/storage/HN7VDJFA/Honigberg et al. - 2010 - The Bruton tyrosine kinase inhibitor PCI-32765 blo.pdf;/Users/rmorin/Zotero/storage/HZM4ZP35/13075.html} |
|
| 4218 | +} |
|
| 4219 | + |
|
| 4220 | +@article{honoreHeterogeneousNuclearRibonucleoproteins1995, |
|
| 4221 | + title = {Heterogeneous Nuclear Ribonucleoproteins {{H}}, {{H}}', and {{F}} Are Members of a Ubiquitously Expressed Subfamily of Related but Distinct Proteins Encoded by Genes Mapping to Different Chromosomes}, |
|
| 4222 | + author = {Honoré, B. and Rasmussen, H. H. and Vorum, H. and Dejgaard, K. and Liu, X. and Gromov, P. and Madsen, P. and Gesser, B. and Tommerup, N. and Celis, J. E.}, |
|
| 4223 | + date = {1995-12-01}, |
|
| 4224 | + journaltitle = {The Journal of Biological Chemistry}, |
|
| 4225 | + shortjournal = {J Biol Chem}, |
|
| 4226 | + volume = {270}, |
|
| 4227 | + number = {48}, |
|
| 4228 | + eprint = {7499401}, |
|
| 4229 | + eprinttype = {pmid}, |
|
| 4230 | + pages = {28780--28789}, |
|
| 4231 | + issn = {0021-9258}, |
|
| 4232 | + doi = {10.1074/jbc.270.48.28780}, |
|
| 4233 | + abstract = {Molecular cDNA cloning, two-dimensional gel immunoblotting, and amino acid microsequencing identified three sequence-unique and distinct proteins that constitute a subfamily of ubiquitously expressed heterogeneous nuclear ribonucleoproteins corresponding to hnRNPs H, H', and F. These proteins share epitopes and sequence identity with two other proteins, isoelectric focusing sample spot numbers 2222 (37.6 kDa; pI 6.5) and 2326 (39.5 kDa; pI 6.6), indicating that the subfamily may contain additional members. The identity between hnRNPs H and H' is 96\%, between H and F 78\%, and between H' and F 75\%, respectively. The three proteins contain three repeats, which we denote quasi-RRMs (qRRMs) since they have a remote similarity to the RNA recognition motif (RRM). The three qRRMs of hnRNP H, with a few additional NH2-terminal amino acids, were constructed by polymerase chain reaction amplification and used for ribohomopolymer binding studies. Each qRRM repeat bound poly(rG), while only the NH2-terminal qRRM bound poly(rC) and poly(rU). None of the repeats bound detectable amounts of poly(rA). The expression levels of hnRNPs H and F were differentially regulated in pairs of normal and transformed fibroblasts and keratinocytes. In normal human keratinocytes, the expression level of H was unaffected by treatment with several substances tested including two second messengers and seven cytokines. Likewise the expression level of F was independent of these substances, although it was strikingly down-regulated by long term treatment with 4 beta-phorbol 12-myristate 13-acetate, indicating that the protein kinase C signaling pathway regulates its expression. No effect of 4 beta-phorbol 12-myristate 13-acetate was observed on the expression of hnRNP H. The genes coding for hnRNPs H, H', and F were chromosome-mapped to 5q35.3 (HNRPH1), 6q25.3-q26, and/or Xq22 (HNRPH2) and 10q11.21-q11.22 (HNRPF), respectively.}, |
|
| 4234 | + langid = {english}, |
|
| 4235 | + keywords = {Amino Acid Sequence,Animals,Base Sequence,Cell Line,Cells Cultured,Chromosome Mapping,Chromosomes Human Pair 5,Chromosomes Human Pair 6,DNA Complementary,DNA Primers,Epitopes,Heterogeneous-Nuclear Ribonucleoprotein Group F-H,Heterogeneous-Nuclear Ribonucleoproteins,Humans,Molecular Sequence Data,Ribonucleoproteins,RNA Heterogeneous Nuclear,RNA-Binding Proteins,Sequence Homology Amino Acid,X Chromosome}, |
|
| 4236 | + file = {/Users/rmorin/Zotero/storage/YMIJ96HZ/Honoré et al. - 1995 - Heterogeneous nuclear ribonucleoproteins H, H', an.pdf} |
|
| 4237 | +} |
|
| 4238 | + |
|
| 4239 | +@article{honoreHeterogeneousNuclearRibonucleoproteins2004, |
|
| 4240 | + title = {Heterogeneous Nuclear Ribonucleoproteins {{F}} and {{H}}/{{H}}' Show Differential Expression in Normal and Selected Cancer Tissues}, |
|
| 4241 | + author = {Honoré, Bent and Baandrup, Ulrik and Vorum, Henrik}, |
|
| 4242 | + date = {2004-03-10}, |
|
| 4243 | + journaltitle = {Experimental Cell Research}, |
|
| 4244 | + shortjournal = {Exp. Cell Res.}, |
|
| 4245 | + volume = {294}, |
|
| 4246 | + number = {1}, |
|
| 4247 | + eprint = {14980514}, |
|
| 4248 | + eprinttype = {pmid}, |
|
| 4249 | + pages = {199--209}, |
|
| 4250 | + issn = {0014-4827}, |
|
| 4251 | + doi = {10.1016/j.yexcr.2003.11.011}, |
|
| 4252 | + abstract = {The heterogeneous nuclear ribonucleoproteins (hnRNPs) F and H/H', containing the quasi-RNA recognition motif (qRRM) domains, are implicated in several steps of pre-mRNA processing and in cellular differentiation. We have compared a set of tissues and found striking differences in their levels of expression as well as in the nuclear versus the cytoplasmic distribution. Generally, hnRNP F is broadly expressed in many tissues with extremely strong expression in the prostate gland while hnRNP H/H' shows a more restricted degree of expression with low expression in some tissues, for example, liver, exocrine acini of the pancreas, thyroid gland and heart. At the cellular level, hnRNP F is, with few exceptions, predominantly expressed in the cytoplasm while hnRNP H/H' is more abundant in the nuclei. A quite pronounced heterogeneous expression pattern is seen in the proximal tubules of the kidney where hnRNP F is present at moderate cytoplasmic levels while hnRNP H/H' is undetectable, whereas both proteins are more evenly expressed in distal tubules and collecting ducts. Generally, tumor tissues reveal a broad expression of hnRNP F in the nuclei as well as in the cytoplasm while hnRNP H/H' is expressed at higher levels in the nuclei than in the cytoplasm. Up-regulation of hnRNP H/H' is found in a few tissues that normally express low cytoplasmic levels of hnRNP H/H', for example, adenocarcinoma of the pancreas, hepatocellular carcinoma and gastric carcinoma. hnRNP F is down-regulated in hepatocellular carcinoma and up-regulated in gastric carcinoma. The present study indicates the important potential role of this subset of hnRNPs on the gene expression in many tissues.}, |
|
| 4253 | + langid = {english}, |
|
| 4254 | + keywords = {Adenocarcinoma,Carcinoma Hepatocellular,Heterogeneous-Nuclear Ribonucleoprotein Group F-H,Humans,Immunohistochemistry,Liver Neoplasms,Neoplasms,Pancreatic Neoplasms,Tissue Distribution,Tumor Cells Cultured} |
|
| 4255 | +} |
|
| 4256 | + |
|
| 4257 | +@article{huang1418Defines2002, |
|
| 4258 | + title = {The t(14;18) Defines a Unique Subset of Diffuse Large {{B-cell}} Lymphoma with a Germinal Center {{B-cell}} Gene Expression Profile}, |
|
| 4259 | + author = {Huang, James Z and Sanger, Warren G and Greiner, Timothy C and Staudt, Louis M and Weisenburger, Dennis D and Pickering, Diane L and Lynch, James C and Armitage, James O and Warnke, Roger A and Alizadeh, Ash A and Lossos, Izidore S and Levy, Ronald and Chan, Wing C}, |
|
| 4260 | + date = {2002-04}, |
|
| 4261 | + journaltitle = {Blood}, |
|
| 4262 | + volume = {99}, |
|
| 4263 | + number = {7}, |
|
| 4264 | + pages = {2285--2290}, |
|
| 4265 | + keywords = {nosource} |
|
| 4266 | +} |
|
| 4267 | + |
|
| 4268 | +@article{huangApplicationsSupportVector2018, |
|
| 4269 | + title = {Applications of {{Support Vector Machine}} ({{SVM}}) {{Learning}} in {{Cancer Genomics}}}, |
|
| 4270 | + author = {Huang, Shujun and Cai, Nianguang and Pacheco, Pedro Penzuti and Narrandes, Shavira and Wang, Yang and Xu, Wayne}, |
|
| 4271 | + date = {2018-01-01}, |
|
| 4272 | + journaltitle = {Cancer Genomics - Proteomics}, |
|
| 4273 | + shortjournal = {Cancer Genomics Proteomics}, |
|
| 4274 | + volume = {15}, |
|
| 4275 | + number = {1}, |
|
| 4276 | + eprint = {29275361}, |
|
| 4277 | + eprinttype = {pmid}, |
|
| 4278 | + pages = {41--51}, |
|
| 4279 | + issn = {1109-6535, 1790-6245}, |
|
| 4280 | + url = {http://cgp.iiarjournals.org/content/15/1/41}, |
|
| 4281 | + urldate = {2020-02-06}, |
|
| 4282 | + abstract = {Machine learning with maximization (support) of separating margin (vector), called support vector machine (SVM) learning, is a powerful classification tool that has been used for cancer genomic classification or subtyping. Today, as advancements in high-throughput technologies lead to production of large amounts of genomic and epigenomic data, the classification feature of SVMs is expanding its use in cancer genomics, leading to the discovery of new biomarkers, new drug targets, and a better understanding of cancer driver genes. Herein we reviewed the recent progress of SVMs in cancer genomic studies. We intend to comprehend the strength of the SVM learning and its future perspective in cancer genomic applications.}, |
|
| 4283 | + langid = {english}, |
|
| 4284 | + keywords = {biomarker discovery,cancer classification,classifier,driver gene,drug discovery,gene expression,gene selection,gene-gene interaction,genomics,kernel function,Machine learning (ML),review,support vector machine (SVM)}, |
|
| 4285 | + file = {/Users/rmorin/Zotero/storage/EKJQSGB7/41.html} |
|
| 4286 | +} |
|
| 4287 | + |
|
| 4288 | +@article{huangHighlyRecurrentTERT, |
|
| 4289 | + title = {Highly Recurrent {{TERT}} Promoter Mutations in Human Melanoma.}, |
|
| 4290 | + author = {Huang, Franklin W and Hodis, Eran and Xu, Mary Jue and Kryukov, Gregory V and Chin, Lynda and Garraway, Levi A}, |
|
| 4291 | + journaltitle = {Science}, |
|
| 4292 | + volume = {339}, |
|
| 4293 | + number = {6122}, |
|
| 4294 | + pages = {957--959}, |
|
| 4295 | + keywords = {nosource} |
|
| 4296 | +} |
|
| 4297 | + |
|
| 4298 | +@article{huangPCBP1RegulatesTranscription2021, |
|
| 4299 | + title = {{{PCBP1}} Regulates the Transcription and Alternative Splicing of Metastasis‑related Genes and Pathways in Hepatocellular Carcinoma}, |
|
| 4300 | + author = {Huang, Shuai and Luo, Kai and Jiang, Li and Zhang, Xu-Dong and Lv, Ying-Hao and Li, Ren-Feng}, |
|
| 4301 | + date = {2021-12-02}, |
|
| 4302 | + journaltitle = {Scientific Reports}, |
|
| 4303 | + shortjournal = {Sci Rep}, |
|
| 4304 | + volume = {11}, |
|
| 4305 | + number = {1}, |
|
| 4306 | + eprint = {34857818}, |
|
| 4307 | + eprinttype = {pmid}, |
|
| 4308 | + pages = {23356}, |
|
| 4309 | + issn = {2045-2322}, |
|
| 4310 | + doi = {10.1038/s41598-021-02642-z}, |
|
| 4311 | + abstract = {PCBP1 is a multifunctional RNA-binding protein (RBP) expressed in most human cells and is involved in posttranscriptional gene regulation. PCBP1 regulates the alternative splicing, translation and RNA stability of many cancer-related genes and has been identified as a potential tumour suppressor gene. PCBP1 inhibits the invasion of hepatocellular carcinoma (HCC) cells, but there are few studies on the specific regulatory target and mechanism of RBPs in HCC, and it is unclear whether PCBP1 plays a role in tumour metastasis as a splicing factor. We analysed the regulation of gene expression by PCBP1 at the transcriptional level. We obtained and analysed PCBP1-knockdown RNA-seq data and eCLIP-seq data of PCBP1 in HepG2 cells and found that PCBP1 widely regulates the alternative splicing and expression of genes enriched in cancer-related pathways, including extracellular matrix, cell adhesion, small molecule metabolic process and apoptosis. We validated five regulated alternative splicing events affected by PCBP1 using RT-qPCR and found that there was a significant difference in the expression of APOC1 and SPHK1 between tumour and normal tissues. In this study, we provided convincing evidence that human PCBP1 profoundly regulates the splicing of genes associated with tumour metastasis. These findings provide new insight into potential markers or therapeutic targets for HCC treatment.}, |
|
| 4312 | + langid = {english}, |
|
| 4313 | + pmcid = {PMC8640068}, |
|
| 4314 | + keywords = {Alternative Splicing,Biomarkers Tumor,Carcinoma Hepatocellular,DNA-Binding Proteins,Gene Expression Profiling,Gene Expression Regulation Neoplastic,Humans,Liver Neoplasms,Neoplasm Metastasis,Prognosis,RNA Splicing Factors,RNA-Binding Proteins,Tumor Cells Cultured}, |
|
| 4315 | + file = {/Users/rmorin/Zotero/storage/FYJ3YU6D/Huang et al. - 2021 - PCBP1 regulates the transcription and alternative .pdf} |
|
| 4316 | +} |
|
| 4317 | + |
|
| 4318 | +@article{hubschmannMutationalMechanismsShaping2021b, |
|
| 4319 | + title = {Mutational Mechanisms Shaping the Coding and Noncoding Genome of Germinal Center Derived {{B-cell}} Lymphomas}, |
|
| 4320 | + author = {Hübschmann, Daniel and Kleinheinz, Kortine and Wagener, Rabea and Bernhart, Stephan H. and López, Cristina and Toprak, Umut H. and Sungalee, Stephanie and Ishaque, Naveed and Kretzmer, Helene and Kreuz, Markus and Waszak, Sebastian M. and Paramasivam, Nagarajan and Ammerpohl, Ole and Aukema, Sietse M. and Beekman, Renée and Bergmann, Anke K. and Bieg, Matthias and Binder, Hans and Borkhardt, Arndt and Borst, Christoph and Brors, Benedikt and Bruns, Philipp and Carrillo de Santa Pau, Enrique and Claviez, Alexander and Doose, Gero and Haake, Andrea and Karsch, Dennis and Haas, Siegfried and Hansmann, Martin-Leo and Hoell, Jessica I. and Hovestadt, Volker and Huang, Bingding and Hummel, Michael and Jäger-Schmidt, Christina and Kerssemakers, Jules N. A. and Korbel, Jan O. and Kube, Dieter and Lawerenz, Chris and Lenze, Dido and Martens, Joost H. A. and Ott, German and Radlwimmer, Bernhard and Reisinger, Eva and Richter, Julia and Rico, Daniel and Rosenstiel, Philip and Rosenwald, Andreas and Schillhabel, Markus and Stilgenbauer, Stephan and Stadler, Peter F. and Martín-Subero, José I. and Szczepanowski, Monika and Warsow, Gregor and Weniger, Marc A. and Zapatka, Marc and Valencia, Alfonso and Stunnenberg, Hendrik G. and Lichter, Peter and Möller, Peter and Loeffler, Markus and Eils, Roland and Klapper, Wolfram and Hoffmann, Steve and Trümper, Lorenz and {ICGC MMML-Seq consortium} and {ICGC DE-Mining consortium} and {BLUEPRINT consortium} and Küppers, Ralf and Schlesner, Matthias and Siebert, Reiner}, |
|
| 4321 | + date = {2021-07}, |
|
| 4322 | + journaltitle = {Leukemia}, |
|
| 4323 | + shortjournal = {Leukemia}, |
|
| 4324 | + volume = {35}, |
|
| 4325 | + number = {7}, |
|
| 4326 | + eprint = {33953289}, |
|
| 4327 | + eprinttype = {pmid}, |
|
| 4328 | + pages = {2002--2016}, |
|
| 4329 | + issn = {1476-5551}, |
|
| 4330 | + doi = {10.1038/s41375-021-01251-z}, |
|
| 4331 | + abstract = {B cells have the unique property to somatically alter their immunoglobulin (IG) genes by V(D)J recombination, somatic hypermutation (SHM) and class-switch recombination (CSR). Aberrant targeting of these mechanisms is implicated in lymphomagenesis, but the mutational processes are poorly understood. By performing whole genome and transcriptome sequencing of 181 germinal center derived B-cell lymphomas (gcBCL) we identified distinct mutational signatures linked to SHM and CSR. We show that not only SHM, but presumably also CSR causes off-target mutations in non-IG genes. Kataegis clusters with high mutational density mainly affected early replicating regions and were enriched for SHM- and CSR-mediated off-target mutations. Moreover, they often co-occurred in loci physically interacting in the nucleus, suggesting that mutation hotspots promote increased mutation targeting of spatially co-localized loci (termed hypermutation by proxy). Only around 1\% of somatic small variants were in protein coding sequences, but in about half of the driver genes, a contribution of B-cell specific mutational processes to their mutations was found. The B-cell-specific mutational processes contribute to both lymphoma initiation and intratumoral heterogeneity. Overall, we demonstrate that mutational processes involved in the development of gcBCL are more complex than previously appreciated, and that B cell-specific mutational processes contribute via diverse mechanisms to lymphomagenesis.}, |
|
| 4332 | + langid = {english}, |
|
| 4333 | + pmcid = {PMC8257491}, |
|
| 4334 | + keywords = {Adult,B-Lymphocytes,Cell Line,Cell Line Tumor,Genes Immunoglobulin,Genome,Germinal Center,HeLa Cells,Hep G2 Cells,Human Umbilical Vein Endothelial Cells,Humans,Immunoglobulin Class Switching,K562 Cells,Lymphoma B-Cell,MCF-7 Cells,Mutation,Somatic Hypermutation Immunoglobulin,V(D)J Recombination}, |
|
| 4335 | + file = {/Users/rmorin/Zotero/storage/AVNGPBTQ/Hübschmann et al. - 2021 - Mutational mechanisms shaping the coding and nonco.pdf} |
|
| 4336 | +} |
|
| 4337 | + |
|
| 4338 | +@article{huIdentificationDNACleavage2015, |
|
| 4339 | + title = {Identification of {{DNA}} Cleavage- and Recombination-Specific {{hnRNP}} Cofactors for Activation-Induced Cytidine Deaminase}, |
|
| 4340 | + author = {Hu, Wenjun and Begum, Nasim A. and Mondal, Samiran and Stanlie, Andre and Honjo, Tasuku}, |
|
| 4341 | + date = {2015-05-05}, |
|
| 4342 | + journaltitle = {Proceedings of the National Academy of Sciences}, |
|
| 4343 | + volume = {112}, |
|
| 4344 | + number = {18}, |
|
| 4345 | + pages = {5791--5796}, |
|
| 4346 | + publisher = {Proceedings of the National Academy of Sciences}, |
|
| 4347 | + doi = {10.1073/pnas.1506167112}, |
|
| 4348 | + url = {https://www.pnas.org/doi/full/10.1073/pnas.1506167112}, |
|
| 4349 | + urldate = {2022-10-04}, |
|
| 4350 | + file = {/Users/rmorin/Zotero/storage/4YGZX3RU/Hu et al. - 2015 - Identification of DNA cleavage- and recombination-.pdf} |
|
| 4351 | +} |
|
| 4352 | + |
|
| 4353 | +@article{huiNovelFunctionalRole2003, |
|
| 4354 | + title = {Novel Functional Role of {{CA}} Repeats and {{hnRNP L}} in {{RNA}} Stability}, |
|
| 4355 | + author = {Hui, Jingyi and Reither, Gregor and Bindereif, Albrecht}, |
|
| 4356 | + date = {2003-01-08}, |
|
| 4357 | + journaltitle = {RNA}, |
|
| 4358 | + shortjournal = {RNA}, |
|
| 4359 | + volume = {9}, |
|
| 4360 | + number = {8}, |
|
| 4361 | + eprint = {12869704}, |
|
| 4362 | + eprinttype = {pmid}, |
|
| 4363 | + pages = {931--936}, |
|
| 4364 | + publisher = {Cold Spring Harbor Lab}, |
|
| 4365 | + issn = {1355-8382, 1469-9001}, |
|
| 4366 | + doi = {10.1261/rna.5660803}, |
|
| 4367 | + url = {http://rnajournal.cshlp.org/content/9/8/931}, |
|
| 4368 | + urldate = {2022-09-28}, |
|
| 4369 | + abstract = {CA dinucleotide repeat sequences are very common in the human genome. We have recently demonstrated that the polymorphic CA repeats in intron 13 of the human endothelial nitric oxide synthase (eNOS) gene function as an unusual, length-dependent splicing enhancer. The CA repeat enhancer requires for its activity specific binding of hnRNP L. Here we show that in the absence of bound hnRNP L, the pre-mRNA is cleaved directly upstream of the CA repeats. The addition of recombinant hnRNP L restores RNA stability. CA repeats are both necessary and sufficient for this specific cleavage in the 5′ adjacent RNA sequence. We conclude that—in addition to its role as a splicing activator—hnRNP L can act in vitro as a sequence-specific RNA protection factor. Based on the wide abundance of CA repetitive sequences in the human genome, this may represent a novel, generally important role of this abundant hnRNP protein.}, |
|
| 4370 | + langid = {english}, |
|
| 4371 | + keywords = {hnRNP L,Repetitive sequence,RNA stability,splicing}, |
|
| 4372 | + file = {/Users/rmorin/Zotero/storage/QVI8JQ9N/Hui et al. - 2003 - Novel functional role of CA repeats and hnRNP L in.pdf;/Users/rmorin/Zotero/storage/T5CXTGHJ/931.html} |
|
| 4373 | +} |
|
| 4374 | + |
|
| 4375 | +@article{hungDiverseRolesHnRNP2008, |
|
| 4376 | + title = {Diverse Roles of {{hnRNP L}} in Mammalian {{mRNA}} Processing: {{A}} Combined Microarray and {{RNAi}} Analysis}, |
|
| 4377 | + shorttitle = {Diverse Roles of {{hnRNP L}} in Mammalian {{mRNA}} Processing}, |
|
| 4378 | + author = {Hung, Lee-Hsueh and Heiner, Monika and Hui, Jingyi and Schreiner, Silke and Benes, Vladimir and Bindereif, Albrecht}, |
|
| 4379 | + date = {2008-01-02}, |
|
| 4380 | + journaltitle = {RNA}, |
|
| 4381 | + shortjournal = {RNA}, |
|
| 4382 | + volume = {14}, |
|
| 4383 | + number = {2}, |
|
| 4384 | + eprint = {18073345}, |
|
| 4385 | + eprinttype = {pmid}, |
|
| 4386 | + pages = {284--296}, |
|
| 4387 | + publisher = {Cold Spring Harbor Lab}, |
|
| 4388 | + issn = {1355-8382, 1469-9001}, |
|
| 4389 | + doi = {10.1261/rna.725208}, |
|
| 4390 | + url = {http://rnajournal.cshlp.org/content/14/2/284}, |
|
| 4391 | + urldate = {2022-10-04}, |
|
| 4392 | + abstract = {Alternative mRNA splicing patterns are determined by the combinatorial control of regulator proteins and their target RNA sequences. We have recently characterized human hnRNP L as a global regulator of alternative splicing, binding to diverse C/A-rich elements. To systematically identify hnRNP L target genes on a genome-wide level, we have combined splice-sensitive microarray analysis and an RNAi-knockdown approach. As a result, we describe 11 target genes of hnRNP L that were validated by RT-PCR and that represent several new modes of hnRNP L-dependent splicing regulation, involving both activator and repressor functions: first, intron retention; second, inclusion or skipping of cassette-type exons; third, suppression of multiple exons; and fourth, alternative poly(A) site selection. In sum, this approach revealed a surprising diversity of splicing-regulatory processes as well as poly(A) site selection in which hnRNP L is involved.}, |
|
| 4393 | + langid = {english}, |
|
| 4394 | + keywords = {alternative splicing hnRNP,microarray,polyadenylation,splicing}, |
|
| 4395 | + file = {/Users/rmorin/Zotero/storage/LSJIF3WS/Hung et al. - 2008 - Diverse roles of hnRNP L in mammalian mRNA process.pdf;/Users/rmorin/Zotero/storage/2PE5ILEM/284.html} |
|
| 4396 | +} |
|
| 4397 | + |
|
| 4398 | +@article{hunterOPTIMALOPTimizedImaging2023, |
|
| 4399 | + title = {{{OPTIMAL}}: {{An OPTimized Imaging Mass}} Cytometry {{AnaLysis}} Framework for Benchmarking Segmentation and Data Exploration}, |
|
| 4400 | + shorttitle = {{{OPTIMAL}}}, |
|
| 4401 | + author = {Hunter, Bethany and Nicorescu, Ioana and Foster, Emma and McDonald, David and Hulme, Gillian and Fuller, Andrew and Thomson, Amanda and Goldsborough, Thibaut and Hilkens, Catharien M. U. and Majo, Joaquim and Milross, Luke and Fisher, Andrew and Bankhead, Peter and Wills, John and Rees, Paul and Filby, Andrew and Merces, George}, |
|
| 4402 | + date = {2023-09-26}, |
|
| 4403 | + journaltitle = {Cytometry. Part A: The Journal of the International Society for Analytical Cytology}, |
|
| 4404 | + shortjournal = {Cytometry A}, |
|
| 4405 | + eprint = {37750225}, |
|
| 4406 | + eprinttype = {pmid}, |
|
| 4407 | + issn = {1552-4930}, |
|
| 4408 | + doi = {10.1002/cyto.a.24803}, |
|
| 4409 | + abstract = {Analysis of imaging mass cytometry (IMC) data and other low-resolution multiplexed tissue imaging technologies is often confounded by poor single-cell segmentation and suboptimal approaches for data visualization and exploration. This can lead to inaccurate identification of cell phenotypes, states, or spatial relationships compared to reference data from single-cell suspension technologies. To this end we have developed the "OPTimized Imaging Mass cytometry AnaLysis (OPTIMAL)" framework to benchmark any approaches for cell segmentation, parameter transformation, batch effect correction, data visualization/clustering, and spatial neighborhood analysis. Using a panel of 27 metal-tagged antibodies recognizing well-characterized phenotypic and functional markers to stain the same Formalin-Fixed Paraffin Embedded (FFPE) human tonsil sample tissue microarray over 12 temporally distinct batches we tested several cell segmentation models, a range of different arcsinh cofactor parameter transformation values, 5 different dimensionality reduction algorithms, and 2 clustering methods. Finally, we assessed the optimal approach for performing neighborhood analysis. We found that single-cell segmentation was improved by the use of an Ilastik-derived probability map but that issues with poor segmentation were only really evident after clustering and cell type/state identification and not always evident when using "classical" bivariate data display techniques. The optimal arcsinh cofactor for parameter transformation was 1 as it maximized the statistical separation between negative and positive signal distributions and a simple Z-score normalization step after arcsinh transformation eliminated batch effects. Of the five different dimensionality reduction approaches tested, PacMap gave the best data structure with FLOWSOM clustering out-performing phenograph in terms of cell type identification. We also found that neighborhood analysis was influenced by the method used for finding neighboring cells with a "disc" pixel expansion outperforming a "bounding box" approach combined with the need for filtering objects based on size and image-edge location. Importantly, OPTIMAL can be used to assess and integrate with any existing approach to IMC data analysis and, as it creates .FCS files from the segmentation output and allows for single-cell exploration to be conducted using a wide variety of accessible software and algorithms familiar to conventional flow cytometrists.}, |
|
| 4410 | + langid = {english}, |
|
| 4411 | + keywords = {image analysis,image cytometry,imaging mass cytometry,tissue segmentation}, |
|
| 4412 | + file = {/Users/rmorin/Zotero/storage/GFWUPGKR/Hunter et al. - 2023 - OPTIMAL An OPTimized Imaging Mass cytometry AnaLy.pdf} |
|
| 4413 | +} |
|
| 4414 | + |
|
| 4415 | +@article{huSplicingFactorHnRNPA2B12017, |
|
| 4416 | + title = {Splicing Factor {{hnRNPA2B1}} Contributes to Tumorigenic Potential of Breast Cancer Cells through {{STAT3}} and {{ERK1}}/2 Signaling Pathway}, |
|
| 4417 | + author = {Hu, Ying and Sun, Zihan and Deng, Jinmu and Hu, Baoquan and Yan, Wenting and Wei, Hongyi and Jiang, Jun}, |
|
| 4418 | + date = {2017-03-01}, |
|
| 4419 | + journaltitle = {Tumor Biology}, |
|
| 4420 | + shortjournal = {Tumour Biol.}, |
|
| 4421 | + volume = {39}, |
|
| 4422 | + number = {3}, |
|
| 4423 | + pages = {1010428317694318}, |
|
| 4424 | + publisher = {SAGE Publications Ltd STM}, |
|
| 4425 | + issn = {1010-4283}, |
|
| 4426 | + doi = {10.1177/1010428317694318}, |
|
| 4427 | + url = {https://doi.org/10.1177/1010428317694318}, |
|
| 4428 | + urldate = {2022-10-04}, |
|
| 4429 | + abstract = {Increasing evidence has indicated that the splicing factor hnRNPA2B1 plays a direct role in cancer development, progression, gene expression, and signal transduction. Previous studies have shown that knocking down hnRNPA2B1 in breast cancer cells induces apoptosis, but the mechanism and other functions of hnRNPA2B1 in breast cancer are unknown. The goal of this study was to investigate the biological function, clinical significance, and mechanism of hnRNPA2B1 in breast cancer. The expression of hnRNPA2B1 in 92 breast cancer and adjacent normal tissue pairs was analyzed by immunohistochemical staining. Stable clones exhibiting knockdown of hnRNPA2B1 via small hairpin RNA expression were generated using RNA interference technology in breast cancer cell lines. The effects of hnRNPA2B1 on cell proliferation were examined by MTT and EdU assay, and cellular apoptosis and the cell cycle were examined by flow cytometry. A nude mouse xenograft model was established to elucidate the function of hnRNPA2B1 in tumorigenesis in vivo. The role of hnRNPA2B1 in signaling pathways was investigated in vitro. Our data revealed that hnRNPA2B1 was overexpressed in breast cancer tissue specimens and cell lines. Knockdown of hnRNPA2B1 reduced breast cancer cell proliferation, induced apoptosis, and prolonged the S phase of the cell cycle in vitro. In addition, hnRNPA2B1 knockdown suppressed subcutaneous tumorigenicity in vivo. On a molecular level, hnRNPA2B1 knockdown decreased signal transducer and activator of transcription 3 and extracellular-signal-regulated kinase 1/2 phosphorylation. We concluded that hnRNPA2B1 promotes the tumorigenic potential of breast cancer cells, MCF-7 and MDA-MB-231, through the extracellular-signal-regulated kinase 1/2 or signal transducer and activator of transcription 3 pathway, which may serve as a target for future therapies.}, |
|
| 4430 | + langid = {english}, |
|
| 4431 | + file = {/Users/rmorin/Zotero/storage/WFSEA4LP/Hu et al. - 2017 - Splicing factor hnRNPA2B1 contributes to tumorigen.pdf} |
|
| 4432 | +} |
|
| 4433 | + |
|
| 4434 | +@article{husseyIdentificationMRNPComplex2011, |
|
| 4435 | + title = {Identification of an {{mRNP}} Complex Regulating Tumorigenesis at the Translational Elongation Step}, |
|
| 4436 | + author = {Hussey, George S. and Chaudhury, Arindam and Dawson, Andrea E. and Lindner, Daniel J. and Knudsen, Charlotte R. and Wilce, Matthew C. J. and Merrick, William C. and Howe, Philip H.}, |
|
| 4437 | + date = {2011-02-18}, |
|
| 4438 | + journaltitle = {Molecular cell}, |
|
| 4439 | + shortjournal = {Mol Cell}, |
|
| 4440 | + volume = {41}, |
|
| 4441 | + number = {4}, |
|
| 4442 | + eprint = {21329880}, |
|
| 4443 | + eprinttype = {pmid}, |
|
| 4444 | + pages = {419--431}, |
|
| 4445 | + issn = {1097-2765}, |
|
| 4446 | + doi = {10.1016/j.molcel.2011.02.003}, |
|
| 4447 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061437/}, |
|
| 4448 | + urldate = {2022-09-28}, |
|
| 4449 | + abstract = {Transcript-selective translational regulation of epithelial-mesenchymal transition (EMT) by transforming growth factor-β (TGFβ) is directed by the hnRNP E1-containing TGFβ-activated-translational (BAT) mRNP complex. Herein, eukaryotic elongation factor-1 A1 (eEF1A1) is identified as an integral component of the BAT complex. Translational silencing of Dab2 and ILEI, two EMT-transcripts, is mediated by binding of hnRNP E1 and eEF1A1 to their 3′-UTR BAT element, whereby hnRNP E1 stalls translational elongation by inhibiting the release of eEF1A1 from the ribosomal A site. TGFβ-mediated hnRNP E1 phosphorylation, through Akt2, disrupts the BAT complex, thereby restoring translation of target EMT-transcripts. Attenuation of hnRNP E1 expression in two non-invasive breast epithelial cells (NMuMG and MCF-7) induced not only EMT, but also enabled cells to form metastatic lesions in vivo. Thus, translational regulation by TGFβ, at the elongation stage, represents a critical checkpoint coordinating the expression of EMT-transcripts required during development and in tumorigenesis and metastatic progression.}, |
|
| 4450 | + pmcid = {PMC3061437}, |
|
| 4451 | + file = {/Users/rmorin/Zotero/storage/N7HSIS85/Hussey et al. - 2011 - Identification of an mRNP complex regulating tumor.pdf;/Users/rmorin/Zotero/storage/P8J7SNQ2/Hussey et al. - 2011 - Identification of an mRNP complex regulating tumor.pdf} |
|
| 4452 | +} |
|
| 4453 | + |
|
| 4454 | +@article{huTherapeuticSiRNAState2020, |
|
| 4455 | + title = {Therapeutic {{siRNA}}: State of the Art}, |
|
| 4456 | + shorttitle = {Therapeutic {{siRNA}}}, |
|
| 4457 | + author = {Hu, Bo and Zhong, Liping and Weng, Yuhua and Peng, Ling and Huang, Yuanyu and Zhao, Yongxiang and Liang, Xing-Jie}, |
|
| 4458 | + date = {2020-06-19}, |
|
| 4459 | + journaltitle = {Signal Transduction and Targeted Therapy}, |
|
| 4460 | + shortjournal = {Sig Transduct Target Ther}, |
|
| 4461 | + volume = {5}, |
|
| 4462 | + number = {1}, |
|
| 4463 | + pages = {1--25}, |
|
| 4464 | + publisher = {Nature Publishing Group}, |
|
| 4465 | + issn = {2059-3635}, |
|
| 4466 | + doi = {10.1038/s41392-020-0207-x}, |
|
| 4467 | + url = {https://www.nature.com/articles/s41392-020-0207-x}, |
|
| 4468 | + urldate = {2022-10-05}, |
|
| 4469 | + abstract = {RNA interference (RNAi) is an ancient biological mechanism used to defend against external invasion. It theoretically can silence any disease-related genes in a sequence-specific manner, making small interfering RNA (siRNA) a promising therapeutic modality. After a two-decade journey from its discovery, two approvals of siRNA therapeutics, ONPATTRO® (patisiran) and GIVLAARI™ (givosiran), have been achieved by Alnylam Pharmaceuticals. Reviewing the long-term pharmaceutical history of human beings, siRNA therapy currently has set up an extraordinary milestone, as it has already changed and will continue to change the treatment and management of human diseases. It can be administered quarterly, even twice-yearly, to achieve therapeutic effects, which is not the case for small molecules and antibodies. The drug development process was extremely hard, aiming to surmount complex obstacles, such as how to efficiently and safely deliver siRNAs to desired tissues and cells and how to enhance the performance of siRNAs with respect to their activity, stability, specificity and potential off-target effects. In this review, the evolution of siRNA chemical modifications and their biomedical performance are comprehensively reviewed. All clinically explored and commercialized siRNA delivery platforms, including the GalNAc (N-acetylgalactosamine)–siRNA conjugate, and their fundamental design principles are thoroughly discussed. The latest progress in siRNA therapeutic development is also summarized. This review provides a comprehensive view and roadmap for general readers working in the field.}, |
|
| 4470 | + issue = {1}, |
|
| 4471 | + langid = {english}, |
|
| 4472 | + keywords = {Drug delivery,Gene therapy,Nucleic-acid therapeutics,Oligo delivery}, |
|
| 4473 | + file = {/Users/rmorin/Zotero/storage/7I3ABA35/Hu et al. - 2020 - Therapeutic siRNA state of the art.pdf;/Users/rmorin/Zotero/storage/BIZZ6RZL/s41392-020-0207-x.html} |
|
| 4474 | +} |
|
| 4475 | + |
|
| 4476 | +@article{hwangPhosphorylationPolyRC2017, |
|
| 4477 | + title = {Phosphorylation of Poly({{rC}}) Binding Protein 1 ({{PCBP1}}) Contributes to Stabilization of Mu Opioid Receptor ({{MOR}}) {{mRNA}} via Interaction with {{AU-rich}} Element {{RNA-binding}} Protein 1 ({{AUF1}}) and Poly {{A}} Binding Protein ({{PABP}})}, |
|
| 4478 | + author = {Hwang, Cheol Kyu and Wagley, Yadav and Law, Ping-Yee and Wei, Li-Na and Loh, Horace H.}, |
|
| 4479 | + date = {2017-01-20}, |
|
| 4480 | + journaltitle = {Gene}, |
|
| 4481 | + shortjournal = {Gene}, |
|
| 4482 | + volume = {598}, |
|
| 4483 | + eprint = {27836661}, |
|
| 4484 | + eprinttype = {pmid}, |
|
| 4485 | + pages = {113--130}, |
|
| 4486 | + issn = {1879-0038}, |
|
| 4487 | + doi = {10.1016/j.gene.2016.11.003}, |
|
| 4488 | + abstract = {Gene regulation at the post-transcriptional level is frequently based on cis- and trans-acting factors on target mRNAs. We found a C-rich element (CRE) in mu-opioid receptor (MOR) 3'-untranslated region (UTR) to which poly (rC) binding protein 1 (PCBP1) binds, resulting in MOR mRNA stabilization. RNA immunoprecipitation and RNA EMSA revealed the formation of PCBP1-RNA complexes at the element. Knockdown of PCBP1 decreased MOR mRNA half-life and protein expression. Stimulation by forskolin increased cytoplasmic localization of PCBP1 and PCBP1/MOR 3'-UTR interactions via increased serine phosphorylation that was blocked by protein kinase A (PKA) or (phosphatidyl inositol-3) PI3-kinase inhibitors. The forskolin treatment also enhanced serine- and tyrosine-phosphorylation of AU-rich element binding protein (AUF1), concurrent with its increased binding to the CRE, and led to an increased interaction of poly A binding protein (PABP) with the CRE and poly(A) sites. AUF1 phosphorylation also led to an increased interaction with PCBP1. These findings suggest that a single co-regulator, PCBP1, plays a crucial role in stabilizing MOR mRNA, and is induced by PKA signaling by conforming to AUF1 and PABP.}, |
|
| 4489 | + langid = {english}, |
|
| 4490 | + pmcid = {PMC5214663}, |
|
| 4491 | + keywords = {3' Untranslated Regions,3′-Untranslated region,Binding Sites,Cell Line Tumor,Colforsin,DNA-Binding Proteins,Gene Knockdown Techniques,Heterogeneous Nuclear Ribonucleoprotein D0,Heterogeneous-Nuclear Ribonucleoprotein D,Heterogeneous-Nuclear Ribonucleoproteins,Humans,Models Biological,Mu opioid receptor,Phosphorylation,Poly(A)-Binding Proteins,Protein kinase A signaling,Receptors Opioid mu,RNA binding protein,RNA Messenger,RNA Processing Post-Transcriptional,RNA stability,RNA Stability,RNA-Binding Proteins,Up-Regulation}, |
|
| 4492 | + file = {/Users/rmorin/Zotero/storage/HDL3JHI2/Hwang et al. - 2017 - Phosphorylation of poly(rC) binding protein 1 (PCB.pdf;/Users/rmorin/Zotero/storage/T7EUFQRA/Hwang et al. - 2017 - Phosphorylation of poly(rC) binding protein 1 (PCB.pdf} |
|
| 4493 | +} |
|
| 4494 | + |
|
| 4495 | +@article{irishBcellSignalingNetworks2010, |
|
| 4496 | + title = {B-Cell Signaling Networks Reveal a Negative Prognostic Human Lymphoma Cell Subset That Emerges during Tumor Progression}, |
|
| 4497 | + author = {Irish, Jonathan M and Myklebust, June H and Alizadeh, Ash A and Houot, Roch and Sharman, Jeff P and Czerwinski, Debra K and Nolan, Garry P and Levy, Ronald}, |
|
| 4498 | + date = {2010-07}, |
|
| 4499 | + volume = {107}, |
|
| 4500 | + number = {29}, |
|
| 4501 | + pages = {12747--12754}, |
|
| 4502 | + keywords = {nosource} |
|
| 4503 | +} |
|
| 4504 | + |
|
| 4505 | +@article{irizarrySummariesAffymetrixGeneChip2003, |
|
| 4506 | + title = {Summaries of {{Affymetrix GeneChip}} Probe Level Data}, |
|
| 4507 | + author = {Irizarry, Rafael A. and Bolstad, Benjamin M. and Collin, Francois and Cope, Leslie M. and Hobbs, Bridget and Speed, Terence P.}, |
|
| 4508 | + date = {2003-02-15}, |
|
| 4509 | + journaltitle = {Nucleic Acids Research}, |
|
| 4510 | + shortjournal = {Nucleic Acids Res.}, |
|
| 4511 | + volume = {31}, |
|
| 4512 | + number = {4}, |
|
| 4513 | + eprint = {12582260}, |
|
| 4514 | + eprinttype = {pmid}, |
|
| 4515 | + pages = {e15}, |
|
| 4516 | + issn = {1362-4962}, |
|
| 4517 | + doi = {10.1093/nar/gng015}, |
|
| 4518 | + abstract = {High density oligonucleotide array technology is widely used in many areas of biomedical research for quantitative and highly parallel measurements of gene expression. Affymetrix GeneChip arrays are the most popular. In this technology each gene is typically represented by a set of 11-20 pairs of probes. In order to obtain expression measures it is necessary to summarize the probe level data. Using two extensive spike-in studies and a dilution study, we developed a set of tools for assessing the effectiveness of expression measures. We found that the performance of the current version of the default expression measure provided by Affymetrix Microarray Suite can be significantly improved by the use of probe level summaries derived from empirically motivated statistical models. In particular, improvements in the ability to detect differentially expressed genes are demonstrated.}, |
|
| 4519 | + langid = {english}, |
|
| 4520 | + pmcid = {PMC150247}, |
|
| 4521 | + keywords = {Central Nervous System,DNA Probes,Gene Expression Profiling,Humans,Liver,Oligonucleotide Array Sequence Analysis,Reproducibility of Results,RNA Messenger,Software}, |
|
| 4522 | + file = {/Users/rmorin/Zotero/storage/CSDBWGEC/irizarry2003.pdf;/Users/rmorin/Zotero/storage/TC9ZSC29/irizarry2003.pdf} |
|
| 4523 | +} |
|
| 4524 | + |
|
| 4525 | +@article{ishiiRoleAuf1Elimination2015, |
|
| 4526 | + title = {Role of {{Auf1}} in Elimination of Oxidatively Damaged Messenger {{RNA}} in Human Cells}, |
|
| 4527 | + author = {Ishii, Takashi and Hayakawa, Hiroshi and Sekiguchi, Takeshi and Adachi, Noritaka and Sekiguchi, Mutsuo}, |
|
| 4528 | + date = {2015-02}, |
|
| 4529 | + journaltitle = {Free Radical Biology \& Medicine}, |
|
| 4530 | + shortjournal = {Free Radic Biol Med}, |
|
| 4531 | + volume = {79}, |
|
| 4532 | + eprint = {25486179}, |
|
| 4533 | + eprinttype = {pmid}, |
|
| 4534 | + pages = {109--116}, |
|
| 4535 | + issn = {1873-4596}, |
|
| 4536 | + doi = {10.1016/j.freeradbiomed.2014.11.018}, |
|
| 4537 | + abstract = {In aerobically growing cells, in which reactive oxygen species are produced, the guanine base of RNA is oxidized to 8-oxo-7,8-dihydroguanine, which induces alterations in gene expression. Here we show that the human Auf1 protein, also called HNRNPD, binds specifically to RNA containing this oxidized base and may be involved in cellular processes associated with managing the problems caused by RNA oxidation. Auf1-deficient cells were constructed from human HeLa and Nalm-6 lines using two different targeting procedures. Both types of Auf1-deficient cells are viable, but exhibit growth retardation. The stability of messenger RNA for four different housekeeping genes was determined in Auf1-deficient and -proficient cells, treated with or without hydrogen peroxide. The level of oxidized messenger RNA was considerably higher in Auf1-deficient cells than in Auf1-proficient cells. Auf1 may play a role in the elimination of oxidized RNA, which is required for the maintenance of proper gene expression under conditions of oxidative stress.}, |
|
| 4538 | + langid = {english}, |
|
| 4539 | + keywords = {8-Oxo-78-dihydroguanine,Auf1 protein,Cell Line,Free radicals,Heterogeneous Nuclear Ribonucleoprotein D0,Heterogeneous-Nuclear Ribonucleoprotein D,Humans,Oxidative stress,Oxidative Stress,Oxidized RNA,RNA degradation,RNA Messenger} |
|
| 4540 | +} |
|
| 4541 | + |
|
| 4542 | +@article{ishiiSpecificBindingPCBP12018, |
|
| 4543 | + title = {Specific Binding of {{PCBP1}} to Heavily Oxidized {{RNA}} to Induce Cell Death}, |
|
| 4544 | + author = {Ishii, Takashi and Hayakawa, Hiroshi and Igawa, Tatsuhiro and Sekiguchi, Takeshi and Sekiguchi, Mutsuo}, |
|
| 4545 | + date = {2018-06-26}, |
|
| 4546 | + journaltitle = {Proceedings of the National Academy of Sciences of the United States of America}, |
|
| 4547 | + shortjournal = {Proc Natl Acad Sci U S A}, |
|
| 4548 | + volume = {115}, |
|
| 4549 | + number = {26}, |
|
| 4550 | + eprint = {29891675}, |
|
| 4551 | + eprinttype = {pmid}, |
|
| 4552 | + pages = {6715--6720}, |
|
| 4553 | + issn = {0027-8424}, |
|
| 4554 | + doi = {10.1073/pnas.1806912115}, |
|
| 4555 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6042155/}, |
|
| 4556 | + urldate = {2022-09-28}, |
|
| 4557 | + abstract = {The binding of human PCBP1 protein to heavily oxidized RNA triggers the induction of apoptosis-related reactions, including the activation of caspase-3 and the cleavage of PARP-1. The introduction of amino acid substitutions in the PCBP1 abolishes this, resulting in the failure of PARP-1 cleavage. Human cells appear to possess a mechanism to induce cell death when their messenger RNAs are severely damaged. This mechanism might be related to the accumulation of abnormal proteins in long-lived cells, such as those in the nervous system., In aerobically growing cells, the guanine base of RNA is oxidized to 8-oxo-7,8-dihydroguanine (8-oxoG), which induces alteration in their gene expression. We previously demonstrated that the human AUF1 protein binds to 8-oxoG in RNA to induce the selective degradation of oxidized messenger RNA. We herein report that the poly(C)-binding protein PCBP1 binds to more severely oxidized RNA to activate apoptosis-related reactions. While AUF1 binds to oligoribonucleotides carrying a single 8-oxoG, PCBP1 does not bind to such oligoribonucleotides but instead binds firmly to oligoribonucleotides in which two 8-oxoG residues are located nearby. PCBP1-deficient cells, constructed from the human HeLa S3 line using the CRISPR-Cas9 system, exhibited higher survival rates than HeLa S3 cells when small doses of hydrogen peroxide were applied. The levels of caspase-3 activation and PARP-1 cleavage in the PCBP1-deficient cells were significantly lower than those in wild-type cells. The structure–function relationship of PCBP1 was established with the use of PCBP1 mutant proteins in which the conserved KH domains were defective. Human cells appear to possess two distinct mechanisms, one controlled by AUF1 and the other by PCBP1, with the former functioning when messenger RNA is moderately oxidized and the latter operating when the RNA is more severely damaged.}, |
|
| 4558 | + pmcid = {PMC6042155}, |
|
| 4559 | + file = {/Users/rmorin/Zotero/storage/JHDYM53D/Ishii et al. - 2018 - Specific binding of PCBP1 to heavily oxidized RNA .pdf} |
|
| 4560 | +} |
|
| 4561 | + |
|
| 4562 | +@article{islamUncoveringNovelMutational2022, |
|
| 4563 | + title = {Uncovering Novel Mutational Signatures by de Novo Extraction with {{SigProfilerExtractor}}}, |
|
| 4564 | + author = {Islam, S. M. Ashiqul and Díaz-Gay, Marcos and Wu, Yang and Barnes, Mark and Vangara, Raviteja and Bergstrom, Erik N. and He, Yudou and Vella, Mike and Wang, Jingwei and Teague, Jon W. and Clapham, Peter and Moody, Sarah and Senkin, Sergey and Li, Yun Rose and Riva, Laura and Zhang, Tongwu and Gruber, Andreas J. and Steele, Christopher D. and Otlu, Burçak and Khandekar, Azhar and Abbasi, Ammal and Humphreys, Laura and Syulyukina, Natalia and Brady, Samuel W. and Alexandrov, Boian S. and Pillay, Nischalan and Zhang, Jinghui and Adams, David J. and Martincorena, Iñigo and Wedge, David C. and Landi, Maria Teresa and Brennan, Paul and Stratton, Michael R. and Rozen, Steven G. and Alexandrov, Ludmil B.}, |
|
| 4565 | + date = {2022-11-09}, |
|
| 4566 | + journaltitle = {Cell Genomics}, |
|
| 4567 | + shortjournal = {Cell Genomics}, |
|
| 4568 | + volume = {2}, |
|
| 4569 | + number = {11}, |
|
| 4570 | + pages = {100179}, |
|
| 4571 | + issn = {2666-979X}, |
|
| 4572 | + doi = {10.1016/j.xgen.2022.100179}, |
|
| 4573 | + url = {https://www.sciencedirect.com/science/article/pii/S2666979X22001240}, |
|
| 4574 | + urldate = {2023-12-18}, |
|
| 4575 | + abstract = {Mutational signature analysis is commonly performed in cancer genomic studies. Here, we present SigProfilerExtractor, an automated tool for de novo extraction of mutational signatures, and benchmark it against another 13 bioinformatics tools by using 34 scenarios encompassing 2,500 simulated signatures found in 60,000 synthetic genomes and 20,000 synthetic exomes. For simulations with 5\% noise, reflecting high-quality datasets, SigProfilerExtractor outperforms other approaches by elucidating between 20\% and~50\% more true-positive signatures while yielding 5-fold less false-positive signatures. Applying SigProfilerExtractor to 4,643 whole-genome- and 19,184 whole-exome-sequenced cancers reveals four novel signatures. Two of the signatures are confirmed in independent cohorts, and one of these signatures is associated with tobacco smoking. In summary, this report provides a reference tool for analysis of mutational signatures, a comprehensive benchmarking of bioinformatics tools for extracting signatures, and several novel mutational signatures, including one putatively attributed to direct tobacco smoking mutagenesis in bladder tissues.}, |
|
| 4576 | + keywords = {cancer genomics,genomics,mutagenesis,mutational signatures}, |
|
| 4577 | + file = {/Users/rmorin/Zotero/storage/M53JAH76/Islam et al. - 2022 - Uncovering novel mutational signatures by de novo .pdf;/Users/rmorin/Zotero/storage/K4442PTY/S2666979X22001240.html} |
|
| 4578 | +} |
|
| 4579 | + |
|
| 4580 | +@article{itoCanineLymphomaComparative2014, |
|
| 4581 | + title = {Canine Lymphoma as a Comparative Model for Human Non-{{Hodgkin}} Lymphoma: Recent Progress and Applications}, |
|
| 4582 | + shorttitle = {Canine Lymphoma as a Comparative Model for Human Non-{{Hodgkin}} Lymphoma}, |
|
| 4583 | + author = {Ito, Daisuke and Frantz, Aric M. and Modiano, Jaime F.}, |
|
| 4584 | + date = {2014-06-15}, |
|
| 4585 | + journaltitle = {Veterinary Immunology and Immunopathology}, |
|
| 4586 | + shortjournal = {Veterinary Immunology and Immunopathology}, |
|
| 4587 | + series = {Special {{Issue}}: {{Dual Purpose}} with {{Dual Benefit Research Models}} in {{Veterinary}} and {{Biomedical Research}}}, |
|
| 4588 | + volume = {159}, |
|
| 4589 | + number = {3}, |
|
| 4590 | + pages = {192--201}, |
|
| 4591 | + issn = {0165-2427}, |
|
| 4592 | + doi = {10.1016/j.vetimm.2014.02.016}, |
|
| 4593 | + url = {https://www.sciencedirect.com/science/article/pii/S016524271400052X}, |
|
| 4594 | + urldate = {2021-05-13}, |
|
| 4595 | + abstract = {The term “lymphoma” describes a heterogeneous group of disorders involving monoclonal proliferation of malignant lymphocytes. As a group, lymphomas are among the most common tumors of dogs. Yet our enumeration and understanding of the many subtypes of lymphoma have been relatively slow, perhaps in part because for many years lymphoma was treated as a singular entity rather than a group of distinct diseases. The recognition that the full spectrum of lymphoid malignancies seen in humans also occurs in dogs, and that these tumors retain not only morphologic similarities and biological behavior but also synonymous driver molecular abnormalities, sets an ideal stage for dual-purpose research that can accelerate progress for these diseases in both species. Specifically, dogs represent exceptional models for defining causality, understanding progression, and developing new treatments for lymphoma in comparatively brief windows of time. Unique advantages of canine models include (1) spontaneous disease occurring without an isogenic background or genetic engineering; (2) chronology of disease adapted to lifespan, (3) shared environment and societal status that allows dogs to be treated as “patients,” while at the same time being able to ethically explore translational innovations that are not possible in human subjects; and (4) organization of dogs into breeds with relatively homogeneous genetic backgrounds and distinct predisposition for lymphomas. Here, we will review recent studies describing intrinsic and extrinsic factors that contribute to the pathogenesis of canine and human lymphomas, as well as newly developed tools that will enhance the fidelity of these models to improve diagnosis and develop new treatments.}, |
|
| 4596 | + langid = {english}, |
|
| 4597 | + file = {/Users/rmorin/Zotero/storage/T8LYHYXM/Ito et al. - 2014 - Canine lymphoma as a comparative model for human n.pdf;/Users/rmorin/Zotero/storage/SMPHXZGJ/S016524271400052X.html} |
|
| 4598 | +} |
|
| 4599 | + |
|
| 4600 | +@article{iwanagaHeterogeneousNuclearRibonucleoprotein2005, |
|
| 4601 | + title = {Heterogeneous Nuclear Ribonucleoprotein {{B1}} Protein Impairs {{DNA}} Repair Mediated through the Inhibition of {{DNA-dependent}} Protein Kinase Activity}, |
|
| 4602 | + author = {Iwanaga, Kentaro and Sueoka, Naoko and Sato, Akemi and Hayashi, Shinichiro and Sueoka, Eisaburo}, |
|
| 4603 | + date = {2005-08-05}, |
|
| 4604 | + journaltitle = {Biochemical and Biophysical Research Communications}, |
|
| 4605 | + shortjournal = {Biochemical and Biophysical Research Communications}, |
|
| 4606 | + volume = {333}, |
|
| 4607 | + number = {3}, |
|
| 4608 | + pages = {888--895}, |
|
| 4609 | + issn = {0006-291X}, |
|
| 4610 | + doi = {10.1016/j.bbrc.2005.05.180}, |
|
| 4611 | + url = {https://www.sciencedirect.com/science/article/pii/S0006291X05011897}, |
|
| 4612 | + urldate = {2022-10-04}, |
|
| 4613 | + abstract = {Heterogeneous nuclear ribonucleoprotein B1, an RNA binding protein, is overexpressed from the early stage of lung cancers; it is evident even in bronchial dysplasia, a premalignant lesion. We evaluated the proteins bound with hnRNP B1 and found that hnRNP B1 interacted with DNA-dependent protein kinase (DNA-PK) complex, and recombinant hnRNP B1 protein dose-dependently inhibited DNA-PK activity in vitro. To test the effect of hnRNP B1 on DNA repair, we performed comet assay after irradiation, using normal human bronchial epithelial (HBE) cells treated with siRNA for hnRNP A2/B1: reduction of hnRNP B1 treated with siRNA for hnRNP A2/B1 induced faster DNA repair in normal HBE cells. Considering these results, we assume that overexpression of hnRNP B1 occurring in the early stage of carcinogenesis inhibits DNA-PK activity, resulting in subsequent accumulation of erroneous rejoining of DNA double-strand breaks, causing tumor progression.}, |
|
| 4614 | + langid = {english}, |
|
| 4615 | + keywords = {DNA double-strand break repair,DNA-dependent protein kinase,hnRNP B1,Lung cancer,RNA binding protein,RNA splicing}, |
|
| 4616 | + file = {/Users/rmorin/Zotero/storage/CLFH5SF4/Iwanaga et al. - 2005 - Heterogeneous nuclear ribonucleoprotein B1 protein.pdf;/Users/rmorin/Zotero/storage/PIRU9TKP/S0006291X05011897.html} |
|
| 4617 | +} |
|
| 4618 | + |
|
| 4619 | +@article{jacksonSinglecellPathologyLandscape2020, |
|
| 4620 | + title = {The Single-Cell Pathology Landscape of Breast Cancer}, |
|
| 4621 | + author = {Jackson, Hartland W. and Fischer, Jana R. and Zanotelli, Vito R. T. and Ali, H. Raza and Mechera, Robert and Soysal, Savas D. and Moch, Holger and Muenst, Simone and Varga, Zsuzsanna and Weber, Walter P. and Bodenmiller, Bernd}, |
|
| 4622 | + date = {2020-02}, |
|
| 4623 | + journaltitle = {Nature}, |
|
| 4624 | + volume = {578}, |
|
| 4625 | + number = {7796}, |
|
| 4626 | + pages = {615--620}, |
|
| 4627 | + publisher = {Nature Publishing Group}, |
|
| 4628 | + issn = {1476-4687}, |
|
| 4629 | + doi = {10.1038/s41586-019-1876-x}, |
|
| 4630 | + url = {https://www.nature.com/articles/s41586-019-1876-x}, |
|
| 4631 | + urldate = {2022-02-03}, |
|
| 4632 | + abstract = {Single-cell analyses have revealed extensive heterogeneity between and within human tumours1–4, but complex single-cell phenotypes and their spatial context are not at present reflected in the histological stratification that is the foundation of many clinical decisions. Here we use imaging mass cytometry5 to simultaneously quantify 35 biomarkers, resulting in 720 high-dimensional pathology images of tumour tissue from 352 patients with breast cancer, with long-term survival data available~for 281 patients. Spatially resolved, single-cell analysis identified the phenotypes of tumour and stromal single cells, their organization and their heterogeneity, and enabled the cellular architecture of breast cancer tissue to be characterized on the basis of cellular composition and tissue organization. Our analysis reveals multicellular features of the tumour microenvironment and novel subgroups of breast cancer that are associated with distinct clinical outcomes. Thus, spatially resolved, single-cell analysis can characterize intratumour phenotypic heterogeneity in a disease-relevant manner, with the potential to inform patient-specific diagnosis.}, |
|
| 4633 | + issue = {7796}, |
|
| 4634 | + langid = {english}, |
|
| 4635 | + keywords = {Breast cancer,Imaging,Systems biology,Tumour heterogeneity}, |
|
| 4636 | + file = {/Users/rmorin/Zotero/storage/RHEXB6QR/Jackson et al. - 2020 - The single-cell pathology landscape of breast canc.pdf;/Users/rmorin/Zotero/storage/9P3GC8X2/s41586-019-1876-x.html} |
|
| 4637 | +} |
|
| 4638 | + |
|
| 4639 | +@article{jainNanoporeSequencingAssembly2018, |
|
| 4640 | + title = {Nanopore Sequencing and Assembly of a Human Genome with Ultra-Long Reads}, |
|
| 4641 | + author = {Jain, Miten and Koren, Sergey and Miga, Karen H and Quick, Josh and Rand, Arthur C and Sasani, Thomas A and Tyson, John R and Beggs, Andrew D and Dilthey, Alexander T and Fiddes, Ian T and Malla, Sunir and Marriott, Hannah and Nieto, Tom and O'Grady, Justin and Olsen, Hugh E and Pedersen, Brent S and Rhie, Arang and Richardson, Hollian and Quinlan, Aaron R and Snutch, Terrance P and Tee, Louise and Paten, Benedict and Phillippy, Adam M and Simpson, Jared T and Loman, Nicholas J and Loose, Matthew}, |
|
| 4642 | + date = {2018}, |
|
| 4643 | + journaltitle = {Nature Biotechnology}, |
|
| 4644 | + volume = {36}, |
|
| 4645 | + number = {4}, |
|
| 4646 | + eprint = {29431738}, |
|
| 4647 | + eprinttype = {pmid}, |
|
| 4648 | + pages = {338}, |
|
| 4649 | + issn = {1546-1696}, |
|
| 4650 | + doi = {10.1038/nbt.4060}, |
|
| 4651 | + url = {http://dx.doi.org/10.1038/nbt.4060}, |
|
| 4652 | + abstract = {We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, representing ∼30× theoretical coverage, were produced. Reference-based alignment enabled detection of large structural variants and epigenetic modifications. De novo assembly of nanopore reads alone yielded a contiguous assembly (NG50 ∼3 Mb). We developed a protocol to generate ultra-long reads (N50 {$>$} 100 kb, read lengths up to 882 kb). Incorporating an additional 5× coverage of these ultra-long reads more than doubled the assembly contiguity (NG50 ∼6.4 Mb). The final assembled genome was 2,867 million bases in size, covering 85.8\% of the reference. Assembly accuracy, after incorporating complementary short-read sequencing data, exceeded 99.8\%. Ultra-long reads enabled assembly and phasing of the 4-Mb major histocompatibility complex (MHC) locus in its entirety, measurement of telomere repeat length, and closure of gaps in the reference human genome assembly GRCh38.}, |
|
| 4653 | + keywords = {nosource} |
|
| 4654 | +} |
|
| 4655 | + |
|
| 4656 | +@article{jainRulesRNASpecificity2017, |
|
| 4657 | + title = {Rules of {{RNA}} Specificity of {{hnRNP A1}} Revealed by Global and Quantitative Analysis of Its Affinity Distribution}, |
|
| 4658 | + author = {Jain, Niyati and Lin, Hsuan-Chun and Morgan, Christopher E. and Harris, Michael E. and Tolbert, Blanton S.}, |
|
| 4659 | + date = {2017-02-28}, |
|
| 4660 | + journaltitle = {Proceedings of the National Academy of Sciences}, |
|
| 4661 | + volume = {114}, |
|
| 4662 | + number = {9}, |
|
| 4663 | + pages = {2206--2211}, |
|
| 4664 | + publisher = {Proceedings of the National Academy of Sciences}, |
|
| 4665 | + doi = {10.1073/pnas.1616371114}, |
|
| 4666 | + url = {https://www.pnas.org/doi/10.1073/pnas.1616371114}, |
|
| 4667 | + urldate = {2022-09-26}, |
|
| 4668 | + file = {/Users/rmorin/Zotero/storage/U2J2F5K5/Jain et al. - 2017 - Rules of RNA specificity of hnRNP A1 revealed by g.pdf} |
|
| 4669 | +} |
|
| 4670 | + |
|
| 4671 | +@article{jalladesExomeSequencingIdentifies2017, |
|
| 4672 | + title = {Exome Sequencing Identifies Recurrent {{BCOR}} Alterations and the Absence of {{KLF2}}, {{TNFAIP3}} and {{MYD88}} Mutations in Splenic Diffuse Red Pulp Small {{B-cell}} Lymphoma}, |
|
| 4673 | + author = {Jallades, Laurent and Baseggio, Lucile and Sujobert, Pierre and Huet, Sarah and Chabane, Kaddour and Callet-Bauchu, Evelyne and Verney, Aurélie and Hayette, Sandrine and Desvignes, Jean-Pierre and Salgado, David and Levy, Nicolas and Béroud, Christophe and Felman, Pascale and Berger, Françoise and Magaud, Jean-Pierre and Genestier, Laurent and Salles, Gilles and Traverse-Glehen, Alexandra}, |
|
| 4674 | + date = {2017-10}, |
|
| 4675 | + journaltitle = {Haematologica}, |
|
| 4676 | + shortjournal = {Haematologica}, |
|
| 4677 | + volume = {102}, |
|
| 4678 | + number = {10}, |
|
| 4679 | + eprint = {28751561}, |
|
| 4680 | + eprinttype = {pmid}, |
|
| 4681 | + pages = {1758--1766}, |
|
| 4682 | + issn = {1592-8721}, |
|
| 4683 | + doi = {10.3324/haematol.2016.160192}, |
|
| 4684 | + abstract = {Splenic diffuse red pulp lymphoma is an indolent small B-cell lymphoma recognized as a provisional entity in the World Health Organization 2008 classification. Its precise relationship to other related splenic B-cell lymphomas with frequent leukemic involvement or other lymphoproliferative disorders remains undetermined. We performed whole-exome sequencing to explore the genetic landscape of ten cases of splenic diffuse red pulp lymphoma using paired tumor and normal samples. A selection of 109 somatic mutations was then evaluated in a cohort including 42 samples of splenic diffuse red pulp lymphoma and compared to those identified in 46 samples of splenic marginal zone lymphoma and eight samples of hairy-cell leukemia. Recurrent mutations or losses in BCOR (the gene encoding the BCL6 corepressor) - frameshift (n=3), nonsense (n=2), splicing site (n=1), and copy number loss (n=4) - were identified in 10/42 samples of splenic diffuse red pulp lymphoma (24\%), whereas only one frameshift mutation was identified in 46 cases of splenic marginal zone lymphoma (2\%). Inversely, KLF2, TNFAIP3 and MYD88, common mutations in splenic marginal zone lymphoma, were rare (one KLF2 mutant in 42 samples; 2\%) or absent (TNFAIP3 and MYD88) in splenic diffuse red pulp lymphoma. These findings define an original genetic profile of splenic diffuse red pulp lymphoma and suggest that the mechanisms of pathogenesis of this lymphoma are distinct from those of splenic marginal zone lymphoma and hairy-cell leukemia.}, |
|
| 4685 | + langid = {english}, |
|
| 4686 | + pmcid = {PMC5622860}, |
|
| 4687 | + keywords = {Aged,Aged 80 and over,Biomarkers Tumor,Chromosome Aberrations,DNA Copy Number Variations,Exome Sequencing,Female,Genetic Variation,Humans,Kruppel-Like Transcription Factors,Leukemia Hairy Cell,Lymphoma B-Cell,Lymphoma B-Cell Marginal Zone,Middle Aged,Mutation,Myeloid Differentiation Factor 88,Proto-Oncogene Proteins,Repressor Proteins,Splenic Neoplasms,Tumor Necrosis Factor alpha-Induced Protein 3}, |
|
| 4688 | + file = {/Users/rmorin/Zotero/storage/7Z4ZI44H/Jallades et al. - 2017 - Exome sequencing identifies recurrent BCOR alterat.pdf} |
|
| 4689 | +} |
|
| 4690 | + |
|
| 4691 | +@article{jangSIRT1ExpressionAssociated, |
|
| 4692 | + title = {{{SIRT1}} Expression Is Associated with Poor Prognosis of Diffuse Large {{B-cell}} Lymphoma.}, |
|
| 4693 | + author = {Jang, Kyu Yun and Hwang, Sung Ho and Kwon, Keun Sang and Kim, Kyung Ryoul and Choi, Ha Na and Lee, Na-Ri and Kwak, Jae-Yong and Park, Byung-Hyun and Park, Ho Sung and Chung, Myoung Ja and Kang, Myoung Jae and Lee, Dong Geun and Kim, Hun Soo and Shim, Hyeok and Moon, Woo Sung}, |
|
| 4694 | + journaltitle = {The American journal of surgical pathology}, |
|
| 4695 | + volume = {32}, |
|
| 4696 | + number = {10}, |
|
| 4697 | + pages = {1523--1531}, |
|
| 4698 | + keywords = {nosource} |
|
| 4699 | +} |
|
| 4700 | + |
|
| 4701 | +@article{jardinRecurrentMutationsExportin2016a, |
|
| 4702 | + title = {Recurrent Mutations of the Exportin 1 Gene ({{XPO1}}) and Their Impact on Selective Inhibitor of Nuclear Export Compounds Sensitivity in Primary Mediastinal {{B-cell}} Lymphoma}, |
|
| 4703 | + author = {Jardin, Fabrice and Pujals, Anais and Pelletier, Laura and Bohers, Elodie and Camus, Vincent and Mareschal, Sylvain and Dubois, Sydney and Sola, Brigitte and Ochmann, Marlène and Lemonnier, François and Viailly, Pierre-Julien and Bertrand, Philippe and Maingonnat, Catherine and Traverse-Glehen, Alexandra and Gaulard, Philippe and Damotte, Diane and Delarue, Richard and Haioun, Corinne and Argueta, Christian and Landesman, Yosef and Salles, Gilles and Jais, Jean-Philippe and Figeac, Martin and Copie-Bergman, Christiane and Molina, Thierry Jo and Picquenot, Jean Michel and Cornic, Marie and Fest, Thierry and Milpied, Noel and Lemasle, Emilie and Stamatoullas, Aspasia and Moeller, Peter and Dyer, Martin J. S. and Sundstrom, Christer and Bastard, Christian and Tilly, Hervé and Leroy, Karen}, |
|
| 4704 | + date = {2016-09}, |
|
| 4705 | + journaltitle = {American Journal of Hematology}, |
|
| 4706 | + shortjournal = {Am J Hematol}, |
|
| 4707 | + volume = {91}, |
|
| 4708 | + number = {9}, |
|
| 4709 | + eprint = {27312795}, |
|
| 4710 | + eprinttype = {pmid}, |
|
| 4711 | + pages = {923--930}, |
|
| 4712 | + issn = {1096-8652}, |
|
| 4713 | + doi = {10.1002/ajh.24451}, |
|
| 4714 | + abstract = {Primary mediastinal B-cell lymphoma (PMBL) is an entity of B-cell lymphoma distinct from the other molecular subtypes of diffuse large B-cell lymphoma (DLBCL). We investigated the prevalence, specificity, and clinical relevance of mutations of XPO1, which encodes a member of the karyopherin-β nuclear transporters, in a large cohort of PMBL. PMBL cases defined histologically or by gene expression profiling (GEP) were sequenced and the XPO1 mutational status was correlated to genetic and clinical characteristics. The XPO1 mutational status was also assessed in DLBCL, Hodgkin lymphoma (HL) and mediastinal gray-zone lymphoma (MGZL).The biological impact of the mutation on Selective Inhibitor of Nuclear Export (SINE) compounds (KPT-185/330) sensitivity was investigated in vitro. XPO1 mutations were present in 28/117 (24\%) PMBL cases and in 5/19 (26\%) HL cases but absent/rare in MGZL (0/20) or DLBCL (3/197). A higher prevalence (50\%) of the recurrent codon 571 variant (p.E571K) was observed in GEP-defined PMBL and was associated with shorter PFS. Age, International Prognostic Index and bulky mass were similar in XPO1 mutant and wild-type cases. KPT-185 induced a dose-dependent decrease in cell proliferation and increased cell-death in PMBL cell lines harboring wild type or XPO1 E571K mutant alleles. Experiments in transfected U2OS cells further confirmed that the XPO1 E571K mutation does not have a drastic impact on KPT-330 binding. To conclude the XPO1 E571K mutation represents a genetic hallmark of the PMBL subtype and serves as a new relevant PMBL biomarker. SINE compounds appear active for both mutated and wild-type protein. Am. J. Hematol. 91:923-930, 2016. © 2016 Wiley Periodicals, Inc.}, |
|
| 4715 | + langid = {english}, |
|
| 4716 | + keywords = {Acrylates,Active Transport Cell Nucleus,Adolescent,Adult,Aged,Biomarkers,Cell Line Tumor,Exportin 1 Protein,Female,Gene Expression Profiling,Hodgkin Disease,Humans,Hydrazines,Karyopherins,Lymphoma B-Cell,Male,Mediastinal Neoplasms,Middle Aged,Mutation,Receptors Cytoplasmic and Nuclear,Sequence Analysis DNA,Triazoles,Young Adult}, |
|
| 4717 | + file = {/Users/rmorin/Zotero/storage/RYZUYQXP/Jardin et al. - 2016 - Recurrent mutations of the exportin 1 gene (XPO1) .pdf} |
|
| 4718 | +} |
|
| 4719 | + |
|
| 4720 | +@article{jean-philippeHnRNPA1Swiss2013, |
|
| 4721 | + title = {{{hnRNP A1}}: {{The Swiss Army Knife}} of {{Gene Expression}}}, |
|
| 4722 | + shorttitle = {{{hnRNP A1}}}, |
|
| 4723 | + author = {Jean-Philippe, Jacques and Paz, Sean and Caputi, Massimo}, |
|
| 4724 | + date = {2013-09}, |
|
| 4725 | + journaltitle = {International Journal of Molecular Sciences}, |
|
| 4726 | + volume = {14}, |
|
| 4727 | + number = {9}, |
|
| 4728 | + pages = {18999--19024}, |
|
| 4729 | + publisher = {Multidisciplinary Digital Publishing Institute}, |
|
| 4730 | + issn = {1422-0067}, |
|
| 4731 | + doi = {10.3390/ijms140918999}, |
|
| 4732 | + url = {https://www.mdpi.com/1422-0067/14/9/18999}, |
|
| 4733 | + urldate = {2022-10-05}, |
|
| 4734 | + abstract = {Eukaryotic cells express a large variety of RNA binding proteins (RBPs), with diverse affinities and specificities towards target RNAs. These proteins play a crucial role in almost every aspect of RNA biogenesis, expression and function. The heterogeneous nuclear ribonucleoproteins (hnRNPs) are a complex and diverse family of RNA binding proteins. hnRNPs display multiple functions in the processing of heterogeneous nuclear RNAs into mature messenger RNAs. hnRNP A1 is one of the most abundant and ubiquitously expressed members of this protein family. hnRNP A1 plays multiple roles in gene expression by regulating major steps in the processing of nascent RNA transcripts. The transcription, splicing, stability, export through nuclear pores and translation of cellular and viral transcripts are all mechanisms modulated by this protein. The diverse functions played by hnRNP A1 are not limited to mRNA biogenesis, but extend to the processing of microRNAs, telomere maintenance and the regulation of transcription factor activity. Genomic approaches have recently uncovered the extent of hnRNP A1 roles in the development and differentiation of living organisms. The aim of this review is to highlight recent developments in the study of this protein and to describe its functions in cellular and viral gene expression and its role in human pathologies.}, |
|
| 4735 | + issue = {9}, |
|
| 4736 | + langid = {english}, |
|
| 4737 | + keywords = {hnRNP,miRNA,mRNA,splicing,telomere,transcription,translation}, |
|
| 4738 | + file = {/Users/rmorin/Zotero/storage/3NMJ4YQQ/Jean-Philippe et al. - 2013 - hnRNP A1 The Swiss Army Knife of Gene Expression.pdf;/Users/rmorin/Zotero/storage/BWY8AFQT/18999.html} |
|
| 4739 | +} |
|
| 4740 | + |
|
| 4741 | +@article{jeltschCleavageRoquinRegnase12014, |
|
| 4742 | + title = {Cleavage of Roquin and Regnase-1 by the Paracaspase {{MALT1}} Releases Their Cooperatively Repressed Targets to Promote {{TH17}} Differentiation}, |
|
| 4743 | + author = {Jeltsch, Katharina M and Hu, Desheng and Brenner, Sven and Zöller, Jessica and Heinz, Gitta A and Nagel, Daniel and Vogel, Katharina U and Rehage, Nina and Warth, Sebastian C and Edelmann, Stephanie L and Gloury, Renee and Martin, Nina and Lohs, Claudia and Lech, Maciej and Stehklein, Jenny E and Geerlof, Arie and Kremmer, Elisabeth and Weber, Achim and Anders, Hans-Joachim and Schmitz, Ingo and Schmidt-Supprian, Marc and Fu, Mingui and Holtmann, Helmut and Krappmann, Daniel and Ruland, Jürgen and Kallies, Axel and Heikenwalder, Mathias and Heissmeyer, Vigo}, |
|
| 4744 | + date = {2014-10}, |
|
| 4745 | + journaltitle = {Nat Immunol}, |
|
| 4746 | + volume = {15}, |
|
| 4747 | + number = {11}, |
|
| 4748 | + pages = {1079--1089}, |
|
| 4749 | + keywords = {nosource} |
|
| 4750 | +} |
|
| 4751 | + |
|
| 4752 | +@article{jinInferenceAnalysisCellcell2021, |
|
| 4753 | + title = {Inference and Analysis of Cell-Cell Communication Using {{CellChat}}}, |
|
| 4754 | + author = {Jin, Suoqin and Guerrero-Juarez, Christian F. and Zhang, Lihua and Chang, Ivan and Ramos, Raul and Kuan, Chen-Hsiang and Myung, Peggy and Plikus, Maksim V. and Nie, Qing}, |
|
| 4755 | + date = {2021-02-17}, |
|
| 4756 | + journaltitle = {Nature Communications}, |
|
| 4757 | + shortjournal = {Nat Commun}, |
|
| 4758 | + volume = {12}, |
|
| 4759 | + number = {1}, |
|
| 4760 | + eprint = {33597522}, |
|
| 4761 | + eprinttype = {pmid}, |
|
| 4762 | + pages = {1088}, |
|
| 4763 | + issn = {2041-1723}, |
|
| 4764 | + doi = {10.1038/s41467-021-21246-9}, |
|
| 4765 | + abstract = {Understanding global communications among cells requires accurate representation of cell-cell signaling links and effective systems-level analyses of those links. We construct a database of interactions among ligands, receptors and their cofactors that accurately represent known heteromeric molecular complexes. We then develop CellChat, a tool that is able to quantitatively infer and analyze intercellular communication networks from single-cell RNA-sequencing (scRNA-seq) data. CellChat predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Through manifold learning and quantitative contrasts, CellChat classifies signaling pathways and delineates conserved and context-specific pathways across different datasets. Applying CellChat to mouse and human skin datasets shows its ability to extract complex signaling patterns. Our versatile and easy-to-use toolkit CellChat and a web-based Explorer ( http://www.cellchat.org/ ) will help discover novel intercellular communications and build cell-cell communication atlases in diverse tissues.}, |
|
| 4766 | + langid = {english}, |
|
| 4767 | + pmcid = {PMC7889871}, |
|
| 4768 | + keywords = {Algorithms,Animals,Cell Communication,Computational Biology,Gene Expression Profiling,Humans,Internet,Mice,Models Theoretical,Sequence Analysis RNA,Signal Transduction,Single-Cell Analysis,Skin,Software}, |
|
| 4769 | + file = {/Users/rmorin/Zotero/storage/7HW8BB8B/Jin et al. - 2021 - Inference and analysis of cell-cell communication .pdf} |
|
| 4770 | +} |
|
| 4771 | + |
|
| 4772 | +@article{johnsonDiffuseLargeBcell2009, |
|
| 4773 | + title = {Diffuse Large {{B-cell}} Lymphoma: Reduced {{CD20}} Expression Is Associated with an Inferior Survival}, |
|
| 4774 | + author = {Johnson, N A and Boyle, M and Bashashati, A and Leach, S and Brooks-Wilson, A and Sehn, L H and Chhanabhai, M and Brinkman, R R and Connors, J M and Weng, A P and Gascoyne, R D}, |
|
| 4775 | + date = {2009-04}, |
|
| 4776 | + journaltitle = {Blood}, |
|
| 4777 | + volume = {113}, |
|
| 4778 | + number = {16}, |
|
| 4779 | + pages = {3773--3780}, |
|
| 4780 | + keywords = {nosource} |
|
| 4781 | +} |
|
| 4782 | + |
|
| 4783 | +@article{johnstonCmycHypermutationBurkitt1992, |
|
| 4784 | + title = {C-Myc Hypermutation in {{Burkitt}}'s Lymphoma}, |
|
| 4785 | + author = {Johnston, J. M. and Carroll, W. L.}, |
|
| 4786 | + date = {1992-12}, |
|
| 4787 | + journaltitle = {Leukemia \& Lymphoma}, |
|
| 4788 | + shortjournal = {Leuk Lymphoma}, |
|
| 4789 | + volume = {8}, |
|
| 4790 | + number = {6}, |
|
| 4791 | + eprint = {1297477}, |
|
| 4792 | + eprinttype = {pmid}, |
|
| 4793 | + pages = {431--439}, |
|
| 4794 | + issn = {1042-8194}, |
|
| 4795 | + doi = {10.3109/10428199209051025}, |
|
| 4796 | + abstract = {Translocation between the c-myc protooncogene and one of the three immunoglobulin loci is a cytogenetic hallmark of the B cell tumor, Burkitt's lymphoma. The resulting deregulation of c-myc expression is a critical step in tumorigenesis. The translocation breakpoint may lie within c-myc proper, in which case deregulation is due, in part, to dissociation of key 5' regulatory sequences from the protein-coding portions of the gene. Alternatively, the breakpoint may flank c-myc, leaving the gene grossly intact. In these latter cases, mutation, which may be extensive, is usually seen within c-myc, specifically at or near the same key regulatory sequences. The precise contribution of these mutations to c-myc deregulation is gradually being clarified. The mechanisms underlying c-myc mutations are not known. Hypermutation in c-myc may reflect the influence of the juxtaposed immunoglobulin gene, which is subject to hypermutation during an intermediate stage of normal B lymphoid development. This relationship, however, has not been firmly established.}, |
|
| 4797 | + langid = {english}, |
|
| 4798 | + keywords = {B-Lymphocytes,Burkitt Lymphoma,Gene Expression Regulation Neoplastic,Genes Immunoglobulin,Genes myc,Humans,Mutation,Transcription Genetic} |
|
| 4799 | +} |
|
| 4800 | + |
|
| 4801 | +@article{jumaaSplicingFactorSRp201997, |
|
| 4802 | + title = {The Splicing Factor {{SRp20}} Modifies Splicing of Its Own {{mRNA}} and {{ASF}}/{{SF2}} Antagonizes This Regulation}, |
|
| 4803 | + author = {Jumaa, H. and Nielsen, P. J.}, |
|
| 4804 | + date = {1997-08-15}, |
|
| 4805 | + journaltitle = {The EMBO journal}, |
|
| 4806 | + shortjournal = {EMBO J.}, |
|
| 4807 | + volume = {16}, |
|
| 4808 | + number = {16}, |
|
| 4809 | + eprint = {9305649}, |
|
| 4810 | + eprinttype = {pmid}, |
|
| 4811 | + pages = {5077--5085}, |
|
| 4812 | + issn = {0261-4189}, |
|
| 4813 | + doi = {10.1093/emboj/16.16.5077}, |
|
| 4814 | + abstract = {SRp20 is a member of the highly conserved SR family of splicing regulators. Using a variety of reporter gene constructs, we show that SRp20 regulates alternative splicing of its own mRNA. Overexpression of SRp20 results in a reduction in the level of exon 4-skipped SRp20 transcripts and activates the production of transcripts containing exon 4. These exon 4-included transcripts encode a truncated protein lacking the C-terminal RS domain. We provide evidence that SRp20 probably enhances the recognition of the otherwise unused, weak splice acceptor of exon 4. The recognition of exons with weak splice acceptor sites may be a general activity of SRp20. Unexpectedly, ASF/SF2, another member of the SR family, antagonizes the effect of SRp20 on SRp20 pre-mRNA splicing and suppresses the production of the exon 4-included form. Our results indicate that ASF/SF2 suppresses the use of the alternative exon 4, most likely by inhibiting the recognition of the splice donor of exon 4. These results demonstrate, for the first time, an auto-regulatory activity of an SR protein which is antagonized by a second SR protein.}, |
|
| 4815 | + langid = {english}, |
|
| 4816 | + pmcid = {PMC1170142}, |
|
| 4817 | + keywords = {Alternative Splicing,Animals,Base Sequence,Blotting Northern,Blotting Western,Cloning Molecular,Exons,Gene Expression Regulation,Genes Reporter,Genetic Vectors,Mice,Molecular Sequence Data,Mutagenesis Site-Directed,Nuclear Proteins,Promoter Regions Genetic,RNA Messenger,RNA Precursors,RNA-Binding Proteins,Sequence Analysis DNA,Serine-Arginine Splicing Factors,Spliceosomes,Transfection,Tumor Cells Cultured} |
|
| 4818 | +} |
|
| 4819 | + |
|
| 4820 | +@article{junEfficientScalableAnalysis2015, |
|
| 4821 | + title = {An Efficient and Scalable Analysis Framework for Variant Extraction and Refinement from Population-Scale {{DNA}} Sequence Data}, |
|
| 4822 | + author = {Jun, Goo and Wing, Mary Kate and Abecasis, Gonçalo R. and Kang, Hyun Min}, |
|
| 4823 | + date = {2015-06}, |
|
| 4824 | + journaltitle = {Genome Research}, |
|
| 4825 | + shortjournal = {Genome Res.}, |
|
| 4826 | + volume = {25}, |
|
| 4827 | + number = {6}, |
|
| 4828 | + eprint = {25883319}, |
|
| 4829 | + eprinttype = {pmid}, |
|
| 4830 | + pages = {918--925}, |
|
| 4831 | + issn = {1549-5469}, |
|
| 4832 | + doi = {10.1101/gr.176552.114}, |
|
| 4833 | + abstract = {The analysis of next-generation sequencing data is computationally and statistically challenging because of the massive volume of data and imperfect data quality. We present GotCloud, a pipeline for efficiently detecting and genotyping high-quality variants from large-scale sequencing data. GotCloud automates sequence alignment, sample-level quality control, variant calling, filtering of likely artifacts using machine-learning techniques, and genotype refinement using haplotype information. The pipeline can process thousands of samples in parallel and requires less computational resources than current alternatives. Experiments with whole-genome and exome-targeted sequence data generated by the 1000 Genomes Project show that the pipeline provides effective filtering against false positive variants and high power to detect true variants. Our pipeline has already contributed to variant detection and genotyping in several large-scale sequencing projects, including the 1000 Genomes Project and the NHLBI Exome Sequencing Project. We hope it will now prove useful to many medical sequencing studies.}, |
|
| 4834 | + langid = {english}, |
|
| 4835 | + pmcid = {PMC4448687}, |
|
| 4836 | + keywords = {Computational Biology,Databases Genetic,Exome,Genetics Population,Genome Human,Haplotypes,High-Throughput Nucleotide Sequencing,Humans,Polymorphism Single Nucleotide,Sequence Alignment,Sequence Analysis DNA,Software} |
|
| 4837 | +} |
|
| 4838 | + |
|
| 4839 | +@article{juszczynskiBCL6ModulatesTonic2009, |
|
| 4840 | + title = {{{BCL6}} Modulates Tonic {{BCR}} Signaling in Diffuse Large {{B-cell}} Lymphomas by Repressing the {{SYK}} Phosphatase, {{PTPROt}}.}, |
|
| 4841 | + author = {Juszczynski, Przemyslaw and Chen, Linfeng and O'Donnell, Evan and Polo, Jose M and Ranuncolo, Stella M and Dalla-Favera, Riccardo and Melnick, Ari and Shipp, Margaret A}, |
|
| 4842 | + date = {2009-12}, |
|
| 4843 | + journaltitle = {Blood}, |
|
| 4844 | + volume = {114}, |
|
| 4845 | + number = {26}, |
|
| 4846 | + pages = {5315--5321}, |
|
| 4847 | + keywords = {nosource} |
|
| 4848 | +} |
|
| 4849 | + |
|
| 4850 | +@article{kachaevInterplayMRNACapping2020, |
|
| 4851 | + title = {Interplay of {{mRNA}} Capping and Transcription Machineries}, |
|
| 4852 | + author = {Kachaev, Zaur M. and Lebedeva, Lyubov A. and Kozlov, Eugene N. and Shidlovskii, Yulii V.}, |
|
| 4853 | + date = {2020-01-24}, |
|
| 4854 | + journaltitle = {Bioscience Reports}, |
|
| 4855 | + shortjournal = {Biosci Rep}, |
|
| 4856 | + volume = {40}, |
|
| 4857 | + number = {1}, |
|
| 4858 | + eprint = {31904821}, |
|
| 4859 | + eprinttype = {pmid}, |
|
| 4860 | + pages = {BSR20192825}, |
|
| 4861 | + issn = {0144-8463}, |
|
| 4862 | + doi = {10.1042/BSR20192825}, |
|
| 4863 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6981093/}, |
|
| 4864 | + urldate = {2022-10-06}, |
|
| 4865 | + abstract = {Early stages of transcription from eukaryotic promoters include two principal events: the capping of newly synthesized mRNA and the transition of RNA polymerase II from the preinitiation complex to the productive elongation state. The capping checkpoint model implies that these events are tightly coupled, which is necessary for ensuring the proper capping of newly synthesized mRNA. Recent findings also show that the capping machinery has a wider effect on transcription and the entire gene expression process. The molecular basis of these phenomena is discussed.}, |
|
| 4866 | + pmcid = {PMC6981093}, |
|
| 4867 | + file = {/Users/rmorin/Zotero/storage/ER899FZJ/Kachaev et al. - 2020 - Interplay of mRNA capping and transcription machin.pdf} |
|
| 4868 | +} |
|
| 4869 | + |
|
| 4870 | +@article{kalmbachNovelInsightsPathogenesis2023, |
|
| 4871 | + title = {Novel Insights into the Pathogenesis of Follicular Lymphoma by Molecular Profiling of Localized and Systemic Disease Forms}, |
|
| 4872 | + author = {Kalmbach, Sabrina and Grau, Michael and Zapukhlyak, Myroslav and Leich, Ellen and Jurinovic, Vindi and Hoster, Eva and Staiger, Annette M. and Kurz, Katrin S. and Weigert, Oliver and Gaitzsch, Erik and Passerini, Verena and Engelhard, Marianne and Herfarth, Klaus and Beiske, Klaus and Micci, Francesca and Möller, Peter and Bernd, Heinz-Wolfram and Feller, Alfred C. and Klapper, Wolfram and Stein, Harald and Hansmann, Martin-Leo and Hartmann, Sylvia and Dreyling, Martin and Holte, Harald and Lenz, Georg and Rosenwald, Andreas and Ott, German and Horn, Heike and {German Lymphoma Alliance (GLA)}}, |
|
| 4873 | + date = {2023-10}, |
|
| 4874 | + journaltitle = {Leukemia}, |
|
| 4875 | + shortjournal = {Leukemia}, |
|
| 4876 | + volume = {37}, |
|
| 4877 | + number = {10}, |
|
| 4878 | + eprint = {37563306}, |
|
| 4879 | + eprinttype = {pmid}, |
|
| 4880 | + pages = {2058--2065}, |
|
| 4881 | + issn = {1476-5551}, |
|
| 4882 | + doi = {10.1038/s41375-023-01995-w}, |
|
| 4883 | + abstract = {Knowledge on the pathogenesis of FL is mainly based on data derived from advanced/systemic stages of FL (sFL) and only small cohorts of localized FL (lFL) have been characterized intensively so far. Comprehensive analysis with profiling of somatic copy number alterations (SCNA) and whole exome sequencing (WES) was performed in 147 lFL and 122 sFL. Putative targets were analyzed for gene and protein expression. Overall, lFL and sFL, as well as BCL2 translocation-positive (BCL2+) and -negative (BCL2-) FL showed overlapping features in SCNA and mutational profiles. Significant differences between lFL and sFL, however, were detected for SCNA frequencies, e.g., in 18q-gains (14\% lFL vs. 36\% sFL; p\,=\,0.0003). Although rare in lFL, gains in 18q21 were associated with inferior progression-free survival (PFS). The mutational landscape of lFL and sFL included typical genetic lesions. However, ARID1A mutations were significantly more often detected in sFL (29\%) compared to lFL (6\%, p\,=\,0.0001). In BCL2\,+\,FL mutations in KMT2D, BCL2, ABL2, IGLL5 and ARID1A were enriched, while STAT6 mutations more frequently occurred in BCL2- FL. Although the landscape of lFL and sFL showed overlapping features, molecular profiling revealed novel insights and identified gains in 18q21 as prognostic marker in lFL.}, |
|
| 4884 | + langid = {english}, |
|
| 4885 | + pmcid = {PMC10539171}, |
|
| 4886 | + keywords = {Humans,In Situ Hybridization Fluorescence,Lymphoma Follicular,Mutation,Proto-Oncogene Proteins c-bcl-2,Translocation Genetic}, |
|
| 4887 | + file = {/Users/rmorin/Zotero/storage/VFNRD566/Kalmbach et al. - 2023 - Novel insights into the pathogenesis of follicular.pdf} |
|
| 4888 | +} |
|
| 4889 | + |
|
| 4890 | +@article{kaneVelcadeFDAApproval2003, |
|
| 4891 | + title = {Velcade: {{U}}.{{S}}. {{FDA}} Approval for the Treatment of Multiple Myeloma Progressing on Prior Therapy}, |
|
| 4892 | + shorttitle = {Velcade}, |
|
| 4893 | + author = {Kane, Robert C. and Bross, Peter F. and Farrell, Ann T. and Pazdur, Richard}, |
|
| 4894 | + date = {2003}, |
|
| 4895 | + journaltitle = {The Oncologist}, |
|
| 4896 | + shortjournal = {Oncologist}, |
|
| 4897 | + volume = {8}, |
|
| 4898 | + number = {6}, |
|
| 4899 | + eprint = {14657528}, |
|
| 4900 | + eprinttype = {pmid}, |
|
| 4901 | + pages = {508--513}, |
|
| 4902 | + issn = {1083-7159}, |
|
| 4903 | + doi = {10.1634/theoncologist.8-6-508}, |
|
| 4904 | + abstract = {Bortezomib (formerly PS-341), a promising new drug for the treatment of multiple myeloma, recently received accelerated approval from the U.S. Food and Drug Administration (FDA) for the therapy of patients with progressive myeloma after previous treatment. Two phase II studies of bortezomib used the same schedule of twice-weekly i.v. dosing for the first 2 weeks of each 3-week cycle. In a randomized study of 54 patients, two doses were compared (1.0 and 1.3 mg/m2) and objective responses occurred at both dose levels (23\% versus 35\%), including one complete response in each arm. In the other phase II study, 202 heavily pretreated patients (median of six prior therapies) all received the same schedule at 1.3 mg/m2. Of 188 evaluable patients, complete responses occurred in five (3\%) and partial responses occurred in 47 (25\%). The median duration of response was 365 days. The most clinically relevant adverse events were asthenic conditions, nausea, vomiting, diarrhea, thrombocytopenia, and a peripheral neuropathy that often was painful. This report highlights the FDA analysis supporting the accelerated approval.}, |
|
| 4905 | + langid = {english}, |
|
| 4906 | + keywords = {Antineoplastic Agents,Boronic Acids,Bortezomib,Drug Approval,Humans,Multiple Myeloma,Pyrazines,Randomized Controlled Trials as Topic,United States,United States Food and Drug Administration} |
|
| 4907 | +} |
|
| 4908 | + |
|
| 4909 | +@article{karczewskiMutationalConstraintSpectrum2020, |
|
| 4910 | + title = {The Mutational Constraint Spectrum Quantified from Variation in 141,456 Humans}, |
|
| 4911 | + author = {Karczewski, Konrad J. and Francioli, Laurent C. and Tiao, Grace and Cummings, Beryl B. and Alföldi, Jessica and Wang, Qingbo and Collins, Ryan L. and Laricchia, Kristen M. and Ganna, Andrea and Birnbaum, Daniel P. and Gauthier, Laura D. and Brand, Harrison and Solomonson, Matthew and Watts, Nicholas A. and Rhodes, Daniel and Singer-Berk, Moriel and England, Eleina M. and Seaby, Eleanor G. and Kosmicki, Jack A. and Walters, Raymond K. and Tashman, Katherine and Farjoun, Yossi and Banks, Eric and Poterba, Timothy and Wang, Arcturus and Seed, Cotton and Whiffin, Nicola and Chong, Jessica X. and Samocha, Kaitlin E. and Pierce-Hoffman, Emma and Zappala, Zachary and O’Donnell-Luria, Anne H. and Minikel, Eric Vallabh and Weisburd, Ben and Lek, Monkol and Ware, James S. and Vittal, Christopher and Armean, Irina M. and Bergelson, Louis and Cibulskis, Kristian and Connolly, Kristen M. and Covarrubias, Miguel and Donnelly, Stacey and Ferriera, Steven and Gabriel, Stacey and Gentry, Jeff and Gupta, Namrata and Jeandet, Thibault and Kaplan, Diane and Llanwarne, Christopher and Munshi, Ruchi and Novod, Sam and Petrillo, Nikelle and Roazen, David and Ruano-Rubio, Valentin and Saltzman, Andrea and Schleicher, Molly and Soto, Jose and Tibbetts, Kathleen and Tolonen, Charlotte and Wade, Gordon and Talkowski, Michael E. and Consortium, Genome Aggregation Database (gnomAD) and Neale, Benjamin M. and Daly, Mark J. and MacArthur, Daniel G.}, |
|
| 4912 | + date = {2020-04-08}, |
|
| 4913 | + journaltitle = {bioRxiv}, |
|
| 4914 | + pages = {531210}, |
|
| 4915 | + publisher = {Cold Spring Harbor Laboratory}, |
|
| 4916 | + doi = {10.1101/531210}, |
|
| 4917 | + url = {https://www.biorxiv.org/content/10.1101/531210v4}, |
|
| 4918 | + urldate = {2020-04-27}, |
|
| 4919 | + abstract = {{$<$}p{$>$}Genetic variants that inactivate protein-coding genes are a powerful source of information about the phenotypic consequences of gene disruption: genes critical for an organism9s function will be depleted for such variants in natural populations, while non-essential genes will tolerate their accumulation. However, predicted loss-of-function (pLoF) variants are enriched for annotation errors, and tend to be found at extremely low frequencies, so their analysis requires careful variant annotation and very large sample sizes. Here, we describe the aggregation of 125,748 exomes and 15,708 genomes from human sequencing studies into the Genome Aggregation Database (gnomAD). We identify 443,769 high-confidence pLoF variants in this cohort after filtering for sequencing and annotation artifacts. Using an improved human mutation rate model, we classify human protein-coding genes along a spectrum representing tolerance to inactivation, validate this classification using data from model organisms and engineered human cells, and show that it can be used to improve gene discovery power for both common and rare diseases.{$<$}/p{$>$}}, |
|
| 4920 | + langid = {english}, |
|
| 4921 | + file = {/Users/rmorin/Zotero/storage/SR2XI39R/Karczewski et al. - 2020 - The mutational constraint spectrum quantified from.pdf;/Users/rmorin/Zotero/storage/XH8YIQ72/531210v4.html} |
|
| 4922 | +} |
|
| 4923 | + |
|
| 4924 | +@article{kaufmannMEDICC2WholegenomeDoubling2021, |
|
| 4925 | + title = {{{MEDICC2}}: Whole-Genome Doubling Aware Copy-Number Phylogenies for Cancer Evolution}, |
|
| 4926 | + shorttitle = {{{MEDICC2}}}, |
|
| 4927 | + author = {Kaufmann, Tom L. and Petkovic, Marina and Watkins, Thomas BK and Colliver, Emma C. and Laskina, Sofya and Thapa, Nisha and Minussi, Darlan C. and Navin, Nicholas and Swanton, Charles and Loo, Peter Van and Haase, Kerstin and Tarabichi, Maxime and Schwarz, Roland F.}, |
|
| 4928 | + date = {2021-09-06}, |
|
| 4929 | + pages = {2021.02.28.433227}, |
|
| 4930 | + publisher = {bioRxiv}, |
|
| 4931 | + doi = {10.1101/2021.02.28.433227}, |
|
| 4932 | + url = {https://www.biorxiv.org/content/10.1101/2021.02.28.433227v2}, |
|
| 4933 | + urldate = {2022-02-01}, |
|
| 4934 | + abstract = {Chromosomal instability (CIN) and somatic copy-number alterations (SCNA) play a key role in the evolutionary process that shapes cancer genomes. SC-NAs comprise many classes of clinically relevant events, such as localised amplifications, gains, losses, loss-of-heterozygosity (LOH) events, and recently discovered parallel evolutionary events revealed by multi-sample phasing. These events frequently appear jointly with whole genome doubling (WGD), a transformative event in tumour evolution involving tetraploidization of genomes preceded or followed by individual chromosomal copy-number changes and associated with an overall increase in structural CIN. While SCNAs have been leveraged for phylogeny reconstruction in the past, existing methods do not take WGD events into account and cannot model parallel evolution. They frequently make use of the infinite sites assumption, do not model horizontal dependencies between adjacent genomic loci and can not infer ancestral genomes. Here we present MEDICC2, a new phylogeny inference algorithm for allele-specific SCNA data that addresses these shortcomings. MEDICC2 dispenses with the infinite sites assumption, models parallel evolution and accurately identifies clonal and subclonal WGD events. It times SCNAs relative to each other, quantifies SCNA burden in single-sample studies and infers phylogenetic trees and ancestral genomes in multi-sample or single-cell sequencing scenarios with thousands of cells. We demonstrate MEDICC2’s ability on simulated data, real-world data of 2,778 single sample tumours from the Pan-cancer analysis of whole genomes (PCAWG), 10 bulk multi-region prostate cancer patients and two recent single-cell datasets of triple-negative breast cancer comprising several thousands of single cells.}, |
|
| 4935 | + langid = {english}, |
|
| 4936 | + file = {/Users/rmorin/Zotero/storage/Q6PF2XKC/Kaufmann et al. - 2021 - MEDICC2 whole-genome doubling aware copy-number p.pdf;/Users/rmorin/Zotero/storage/3PQWJ2P3/2021.02.28.html} |
|
| 4937 | +} |
|
| 4938 | + |
|
| 4939 | +@article{kaymazComprehensiveTranscriptomeMutational2017, |
|
| 4940 | + title = {Comprehensive {{Transcriptome}} and {{Mutational Profiling}} of {{Endemic Burkitt Lymphoma Reveals EBV Type}}–{{Specific Differences}}}, |
|
| 4941 | + author = {Kaymaz, Yasin and Oduor, Cliff I. and Yu, Hongbo and Otieno, Juliana A. and Ong'echa, John Michael and Moormann, Ann M. and Bailey, Jeffrey A.}, |
|
| 4942 | + date = {2017-05-01}, |
|
| 4943 | + journaltitle = {Molecular Cancer Research}, |
|
| 4944 | + shortjournal = {Molecular Cancer Research}, |
|
| 4945 | + volume = {15}, |
|
| 4946 | + number = {5}, |
|
| 4947 | + pages = {563--576}, |
|
| 4948 | + issn = {1541-7786}, |
|
| 4949 | + doi = {10.1158/1541-7786.MCR-16-0305}, |
|
| 4950 | + url = {https://doi.org/10.1158/1541-7786.MCR-16-0305}, |
|
| 4951 | + urldate = {2022-05-29}, |
|
| 4952 | + abstract = {Endemic Burkitt lymphoma (eBL) is the most common pediatric cancer in malaria-endemic equatorial Africa and nearly always contains Epstein–Barr virus (EBV), unlike sporadic Burkitt lymphoma (sBL) that occurs with a lower incidence in developed countries. Given these differences and the variable clinical presentation and outcomes, we sought to further understand pathogenesis by investigating transcriptomes using RNA sequencing (RNAseq) from multiple primary eBL tumors compared with sBL tumors. Within eBL tumors, minimal expression differences were found based on: anatomical presentation site, in-hospital survival rates, and EBV genome type, suggesting that eBL tumors are homogeneous without marked subtypes. The outstanding difference detected using surrogate variable analysis was the significantly decreased expression of key genes in the immunoproteasome complex (PSMB9/β1i, PSMB10/β2i, PSMB8/β5i, and PSME2/PA28β) in eBL tumors carrying type 2 EBV compared with type 1 EBV. Second, in comparison with previously published pediatric sBL specimens, the majority of the expression and pathway differences was related to the PTEN/PI3K/mTOR signaling pathway and was correlated most strongly with EBV status rather than geographic designation. Third, common mutations were observed significantly less frequently in eBL tumors harboring EBV type 1, with mutation frequencies similar between tumors with EBV type 2 and without EBV. In addition to the previously reported genes, a set of new genes mutated in BL, including TFAP4, MSH6, PRRC2C, BCL7A, FOXO1, PLCG2, PRKDC, RAD50, and RPRD2, were identified. Overall, these data establish that EBV, particularly EBV type 1, supports BL oncogenesis, alleviating the need for certain driver mutations in the human genome.Implications: Genomic and mutational analyses of Burkitt lymphoma tumors identify key differences based on viral content and clinical outcomes suggesting new avenues for the development of prognostic molecular biomarkers and therapeutic interventions. Mol Cancer Res; 15(5); 563–76. ©2017 AACR.}, |
|
| 4953 | + file = {/Users/rmorin/Zotero/storage/W6QWHA5F/Kaymaz et al. - 2017 - Comprehensive Transcriptome and Mutational Profili.pdf;/Users/rmorin/Zotero/storage/UGK4XMGZ/Comprehensive-Transcriptome-and-Mutational.html} |
|
| 4954 | +} |
|
| 4955 | + |
|
| 4956 | +@article{kendrickDiffuseLargeBcell2016, |
|
| 4957 | + title = {Diffuse Large {{B-cell}} Lymphoma Cell-of-Origin Classification Using the {{Lymph2Cx}} Assay in the Context of {{BCL2}} and {{MYC}} Expression Status.}, |
|
| 4958 | + author = {Kendrick, Samantha and Tus, Katalin and Wright, George and Jaffe, Elaine S and Rosenwald, Andreas and Campo, Elias and Chan, Wing-Chung and Connors, Joseph M and Braziel, Rita M and Ott, German and Delabie, Jan and Cook, James R and Weisenburger, Dennis D and Greiner, Timothy C and Fu, Kai and Staudt, Louis M and Gascoyne, Randy D and Scott, David W and Rimsza, Lisa M}, |
|
| 4959 | + date = {2016}, |
|
| 4960 | + journaltitle = {Leuk lymphoma}, |
|
| 4961 | + volume = {57}, |
|
| 4962 | + number = {3}, |
|
| 4963 | + pages = {717--720}, |
|
| 4964 | + keywords = {nosource} |
|
| 4965 | +} |
|
| 4966 | + |
|
| 4967 | +@article{khanHnRNPHnRNPH12021, |
|
| 4968 | + title = {{{HnRNP F}} and {{hnRNP H1}} Regulate {{mRNA}} Stability of Amyloid Precursor Protein}, |
|
| 4969 | + author = {Khan, Muhammad I. and Zhang, Juan and Liu, Qiang}, |
|
| 4970 | + date = {2021-06-09}, |
|
| 4971 | + journaltitle = {Neuroreport}, |
|
| 4972 | + shortjournal = {Neuroreport}, |
|
| 4973 | + volume = {32}, |
|
| 4974 | + number = {9}, |
|
| 4975 | + eprint = {33994531}, |
|
| 4976 | + eprinttype = {pmid}, |
|
| 4977 | + pages = {824--832}, |
|
| 4978 | + issn = {1473-558X}, |
|
| 4979 | + doi = {10.1097/WNR.0000000000001662}, |
|
| 4980 | + abstract = {Amyloid precursor protein (APP) is a transmembrane protein that plays a crucial role in the production of amyloid-β peptides. Any disruption in APP protein production, its mRNA decay rate or processing may result in abnormal production of amyloid-β peptides and subsequent development of protein aggregation diseases. Therefore, the equilibrium is crucial for neuronal function. An association study of heterogeneous nuclear ribonucleoprotein (hnRNP)-F and hnRNP H1 with APP was carried out in Neuro-2a (N2a) cells. In the present study, we found that hnRNP F and hnRNP H1 were significantly upregulated in the hippocampus of APP/PS1 mice. The changes in APP expression were positively associated with hnRNP F and hnRNP H1 when hnRNP F and hnRNP H1 were depleted or increased in N2a cells. Importantly, cross-linked RNA immunoprecipitation demonstrated binding affinities of hnRNP F and hnRNP H1 for App mRNA. Mechanistically, mRNA stability assay revealed that overexpression of hnRNP F or hnRNP H1 increases the APP level by stabilizing App mRNA half-life, implying that levels of hnRNP F and hnRNP H1 can change the production of APP. Further understanding of the regulatory mechanism of APP expression in association with hnRNP F and hnRNP H1 would provide insights into the mechanism underlying the maintenance of brain health and cognition. This study provides a theoretical basis for the development of hnRNP-stabilizing compounds to regulate APP.}, |
|
| 4981 | + langid = {english}, |
|
| 4982 | + keywords = {Alzheimer Disease,Amyloid beta-Protein Precursor,Animals,Cell Line Tumor,Gene Expression Regulation,Heterogeneous-Nuclear Ribonucleoprotein Group F-H,Hippocampus,Mice,Mice Transgenic,RNA Messenger,RNA Stability} |
|
| 4983 | +} |
|
| 4984 | + |
|
| 4985 | +@article{kharelPropertiesBiologicalImpact2020, |
|
| 4986 | + title = {Properties and Biological Impact of {{RNA G-quadruplexes}}: From Order to Turmoil and Back}, |
|
| 4987 | + shorttitle = {Properties and Biological Impact of {{RNA G-quadruplexes}}}, |
|
| 4988 | + author = {Kharel, Prakash and Becker, Gertraud and Tsvetkov, Vladimir and Ivanov, Pavel}, |
|
| 4989 | + date = {2020-12-16}, |
|
| 4990 | + journaltitle = {Nucleic Acids Research}, |
|
| 4991 | + shortjournal = {Nucleic Acids Research}, |
|
| 4992 | + volume = {48}, |
|
| 4993 | + number = {22}, |
|
| 4994 | + pages = {12534--12555}, |
|
| 4995 | + issn = {0305-1048}, |
|
| 4996 | + doi = {10.1093/nar/gkaa1126}, |
|
| 4997 | + url = {https://doi.org/10.1093/nar/gkaa1126}, |
|
| 4998 | + urldate = {2022-10-15}, |
|
| 4999 | + abstract = {Guanine-quadruplexes (G4s) are non-canonical four-stranded structures that can be formed in guanine (G) rich nucleic acid sequences. A great number of G-rich sequences capable of forming G4 structures have been described based on in vitro analysis, and evidence supporting their formation in live cells continues to accumulate. While formation of DNA G4s (dG4s) within chromatin in vivo has been supported by different chemical, imaging and genomic approaches, formation of RNA G4s (rG4s) in vivo remains a matter of discussion. Recent data support the dynamic nature of G4 formation in the transcriptome. Such dynamic fluctuation of rG4 folding-unfolding underpins the biological significance of these structures in the regulation of RNA metabolism. Moreover, rG4-mediated functions may ultimately be connected to mechanisms underlying disease pathologies and, potentially, provide novel options for therapeutics. In this framework, we will review the landscape of rG4s within the transcriptome, focus on their potential impact on biological processes, and consider an emerging connection of these functions in human health and disease.}, |
|
| 5000 | + file = {/Users/rmorin/Zotero/storage/QDQTZYMS/Kharel et al. - 2020 - Properties and biological impact of RNA G-quadrupl.pdf;/Users/rmorin/Zotero/storage/BKM8S2AC/6017353.html} |
|
| 5001 | +} |
|
| 5002 | + |
|
| 5003 | +@article{khodabakhshiRecurrentTargetsAberrant2012, |
|
| 5004 | + title = {Recurrent Targets of Aberrant Somatic Hypermutation in Lymphoma}, |
|
| 5005 | + author = {Khodabakhshi, Alireza Hadj and Morin, Ryan D. and Fejes, Anthony P. and Mungall, Andrew J. and Mungall, Karen L. and Bolger-Munro, Madison and Johnson, Nathalie A. and Connors, Joseph M. and Gascoyne, Randy D. and Marra, Marco A. and Birol, Inanc and Jones, Steven J. M.}, |
|
| 5006 | + date = {2012-11-12}, |
|
| 5007 | + journaltitle = {Oncotarget}, |
|
| 5008 | + shortjournal = {Oncotarget}, |
|
| 5009 | + volume = {3}, |
|
| 5010 | + number = {11}, |
|
| 5011 | + eprint = {23131835}, |
|
| 5012 | + eprinttype = {pmid}, |
|
| 5013 | + pages = {1308--1319}, |
|
| 5014 | + issn = {1949-2553}, |
|
| 5015 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3717795/}, |
|
| 5016 | + urldate = {2021-08-25}, |
|
| 5017 | + abstract = {Somatic hypermutation (SHM) in the variable region of immunoglobulin genes (IGV) naturally occurs in a narrow window of B cell development to provide high-affinity antibodies. However, SHM can also aberrantly target proto-oncogenes and cause genome instability. The role of aberrant SHM (aSHM) has been widely studied in various non-Hodgkin's lymphoma particularly in diffuse large B-cell lymphoma (DLBCL). Although, it has been speculated that aSHM targets a wide range of genome loci so far only twelve genes have been identified as targets of aSHM through the targeted sequencing of selected genes. A genome-wide study aiming at identifying a comprehensive set of aSHM targets recurrently occurring in DLBCL has not been previously undertaken. Here, we present a comprehensive assessment of the somatic hypermutated genes in DLBCL identified through an analysis of genomic and transcriptome data derived from 40 DLBCL patients. Our analysis verifies that there are indeed many genes that are recurrently affected by aSHM. In particular, we have identified 32 novel targets that show same or higher level of aSHM activity than genes previously reported. Amongst these novel targets, 22 genes showed a significant correlation between mRNA abundance and aSHM.}, |
|
| 5018 | + pmcid = {PMC3717795}, |
|
| 5019 | + file = {/Users/rmorin/Zotero/storage/DTEEGUE6/Khodabakhshi et al. - 2012 - Recurrent targets of aberrant somatic hypermutatio.pdf} |
|
| 5020 | +} |
|
| 5021 | + |
|
| 5022 | +@article{khodadoustAntigenPresentationProfiling2017, |
|
| 5023 | + title = {Antigen Presentation Profiling Reveals Recognition of Lymphoma Immunoglobulin Neoantigens}, |
|
| 5024 | + author = {Khodadoust, Michael S. and Olsson, Niclas and Wagar, Lisa E. and Haabeth, Ole A. W. and Chen, Binbin and Swaminathan, Kavya and Rawson, Keith and Liu, Chih Long and Steiner, David and Lund, Peder and Rao, Samhita and Zhang, Lichao and Marceau, Caleb and Stehr, Henning and Newman, Aaron M. and Czerwinski, Debra K. and Carlton, Victoria E. H. and Moorhead, Martin and Faham, Malek and Kohrt, Holbrook E. and Carette, Jan and Green, Michael R. and Davis, Mark M. and Levy, Ronald and Elias, Joshua E. and Alizadeh, Ash A.}, |
|
| 5025 | + date = {2017-03}, |
|
| 5026 | + journaltitle = {Nature}, |
|
| 5027 | + volume = {543}, |
|
| 5028 | + number = {7647}, |
|
| 5029 | + pages = {723--727}, |
|
| 5030 | + issn = {1476-4687}, |
|
| 5031 | + doi = {10.1038/nature21433}, |
|
| 5032 | + url = {https://www.nature.com/articles/nature21433}, |
|
| 5033 | + urldate = {2019-12-21}, |
|
| 5034 | + abstract = {Evidence for the abundant presentation of class II neoantigens by a human B-cell lymphoma.}, |
|
| 5035 | + langid = {english}, |
|
| 5036 | + file = {/Users/rmorin/Zotero/storage/ESDZ8SMW/nature21433.html} |
|
| 5037 | +} |
|
| 5038 | + |
|
| 5039 | +@article{kimCD79BMYD88Mutations2014, |
|
| 5040 | + title = {{{CD79B}} and {{MYD88}} Mutations in Diffuse Large {{B-cell}} Lymphoma.}, |
|
| 5041 | + author = {Kim, Yuil and Ju, Hyunjeong and Kim, Dong Hoon and Yoo, Hae Yong and Kim, Suk Jin and Kim, Won Seog and Ko, Young-Hyeh}, |
|
| 5042 | + date = {2014-03}, |
|
| 5043 | + journaltitle = {Hum Pathol}, |
|
| 5044 | + volume = {45}, |
|
| 5045 | + number = {3}, |
|
| 5046 | + pages = {556--564}, |
|
| 5047 | + keywords = {nosource} |
|
| 5048 | +} |
|
| 5049 | + |
|
| 5050 | +@article{kimHnRNPMediatesPhasedependent2011, |
|
| 5051 | + title = {{{hnRNP Q}} Mediates a Phase-Dependent Translation-Coupled {{mRNA}} Decay of Mouse {{Period3}}}, |
|
| 5052 | + author = {Kim, Do-Yeon and Kwak, Eunyee and Kim, Sung-Hoon and Lee, Kyung-Ha and Woo, Kyung-Chul and Kim, Kyong-Tai}, |
|
| 5053 | + date = {2011-11-01}, |
|
| 5054 | + journaltitle = {Nucleic Acids Research}, |
|
| 5055 | + shortjournal = {Nucleic Acids Research}, |
|
| 5056 | + volume = {39}, |
|
| 5057 | + number = {20}, |
|
| 5058 | + pages = {8901--8914}, |
|
| 5059 | + issn = {0305-1048}, |
|
| 5060 | + doi = {10.1093/nar/gkr605}, |
|
| 5061 | + url = {https://doi.org/10.1093/nar/gkr605}, |
|
| 5062 | + urldate = {2022-09-28}, |
|
| 5063 | + abstract = {Daily mRNA oscillations of circadian clock genes largely depend on transcriptional regulation. However, several lines of evidence highlight the critical role of post-transcriptional regulation in the oscillations of circadian mRNA oscillations. Clearly, variations in the mRNA decay rate lead to changes in the cycling profiles. However, the mechanisms controlling the mRNA stability of clock genes are not fully understood. Here we demonstrate that the turnover rate of mouse Period3 (m Per3 ) mRNA is dramatically changed in a circadian phase-dependent manner. Furthermore, the circadian regulation of m Per3 mRNA stability requires the cooperative function of 5′- and 3′-untranslated regions (UTRs). Heterogeneous nuclear ribonucleoprotein Q (hnRNP Q) binds to both 5′- and 3′-UTR and triggers enhancement of translation and acceleration of mRNA decay. We propose the phase-dependent translation coupled mRNA decay mediated by hnRNP Q as a new regulatory mechanism of the rhythmically regulated decay of m Per3 mRNA.}, |
|
| 5064 | + file = {/Users/rmorin/Zotero/storage/7IIWIKRX/Kim et al. - 2011 - hnRNP Q mediates a phase-dependent translation-cou.pdf;/Users/rmorin/Zotero/storage/BG7M24JY/2409628.html} |
|
| 5065 | +} |
|
| 5066 | + |
|
| 5067 | +@article{kimmelmanFaithfulCompanionsProposal2007, |
|
| 5068 | + title = {Faithful Companions: A Proposal for Neurooncology Trials in Pet Dogs}, |
|
| 5069 | + shorttitle = {Faithful Companions}, |
|
| 5070 | + author = {Kimmelman, Jonathan and Nalbantoglu, Josephine}, |
|
| 5071 | + date = {2007-05-15}, |
|
| 5072 | + journaltitle = {Cancer Research}, |
|
| 5073 | + shortjournal = {Cancer Res}, |
|
| 5074 | + volume = {67}, |
|
| 5075 | + number = {10}, |
|
| 5076 | + eprint = {17510377}, |
|
| 5077 | + eprinttype = {pmid}, |
|
| 5078 | + pages = {4541--4544}, |
|
| 5079 | + issn = {0008-5472}, |
|
| 5080 | + doi = {10.1158/0008-5472.CAN-06-3792}, |
|
| 5081 | + abstract = {Although relatively rare, malignant glioma (MG) is frequently used for testing novel cancer treatments. However, human MG trials have often been initiated on the basis of preclinical models that involve numerous discontinuities with the human disease. Below, we discuss various limitations of the mainstay model used in MG preclinical research, the murine orthotopic xenograft. After discussing alternative model systems like transgenic mouse models and canine xenografts, we argue that companion animals with spontaneous brain cancers offer a scientifically and ethically attractive system for preclinical testing of novel MG interventions. Ethical advantages and practical challenges of companion animal brain cancer trials are briefly discussed.}, |
|
| 5082 | + langid = {english}, |
|
| 5083 | + keywords = {Animal Welfare,Animals,Animals Domestic,Brain Neoplasms,Clinical Trials as Topic,Disease Models Animal,Dogs,Glioma,Humans,Mice,Mice Transgenic,Xenograft Model Antitumor Assays} |
|
| 5084 | +} |
|
| 5085 | + |
|
| 5086 | +@report{kimStrelka2FastAccurate2017, |
|
| 5087 | + type = {preprint}, |
|
| 5088 | + title = {Strelka2: {{Fast}} and Accurate Variant Calling for Clinical Sequencing Applications}, |
|
| 5089 | + shorttitle = {Strelka2}, |
|
| 5090 | + author = {Kim, Sangtae and Scheffler, Konrad and Halpern, Aaron L and Bekritsky, Mitchell A and Noh, Eunho and Källberg, Morten and Chen, Xiaoyu and Beyter, Doruk and Krusche, Peter and Saunders, Christopher T}, |
|
| 5091 | + date = {2017-09-23}, |
|
| 5092 | + institution = {Bioinformatics}, |
|
| 5093 | + doi = {10.1101/192872}, |
|
| 5094 | + url = {http://biorxiv.org/lookup/doi/10.1101/192872}, |
|
| 5095 | + urldate = {2020-06-01}, |
|
| 5096 | + abstract = {We describe Strelka2 ( https://github.com/Illumina/strelka ), an open-source small variant calling method for clinical germline and somatic sequencing applications. Strelka2 introduces a novel mixture-model based estimation of indel error parameters from each sample, an efficient tiered haplotype modeling strategy and a normal sample contamination model to improve liquid tumor analysis. For both germline and somatic calling, Strelka2 substantially outperforms current leading tools on both variant calling accuracy and compute cost.}, |
|
| 5097 | + langid = {english}, |
|
| 5098 | + file = {/Users/rmorin/Zotero/storage/A4V9LSBH/Kim et al. - 2017 - Strelka2 Fast and accurate variant calling for cl.pdf} |
|
| 5099 | +} |
|
| 5100 | + |
|
| 5101 | +@article{kimStrelka2FastAccurate2018, |
|
| 5102 | + title = {Strelka2: Fast and Accurate Calling of Germline and Somatic Variants}, |
|
| 5103 | + shorttitle = {Strelka2}, |
|
| 5104 | + author = {Kim, Sangtae and Scheffler, Konrad and Halpern, Aaron L. and Bekritsky, Mitchell A. and Noh, Eunho and Källberg, Morten and Chen, Xiaoyu and Kim, Yeonbin and Beyter, Doruk and Krusche, Peter and Saunders, Christopher T.}, |
|
| 5105 | + date = {2018-08}, |
|
| 5106 | + journaltitle = {Nature Methods}, |
|
| 5107 | + shortjournal = {Nat. Methods}, |
|
| 5108 | + volume = {15}, |
|
| 5109 | + number = {8}, |
|
| 5110 | + eprint = {30013048}, |
|
| 5111 | + eprinttype = {pmid}, |
|
| 5112 | + pages = {591--594}, |
|
| 5113 | + issn = {1548-7105}, |
|
| 5114 | + doi = {10.1038/s41592-018-0051-x}, |
|
| 5115 | + abstract = {We describe Strelka2 ( https://github.com/Illumina/strelka ), an open-source small-variant-calling method for research and clinical germline and somatic sequencing applications. Strelka2 introduces a novel mixture-model-based estimation of insertion/deletion error parameters from each sample, an efficient tiered haplotype-modeling strategy, and a normal sample contamination model to improve liquid tumor analysis. For both germline and somatic calling, Strelka2 substantially outperformed the current leading tools in terms of both variant-calling accuracy and computing cost.}, |
|
| 5116 | + langid = {english}, |
|
| 5117 | + keywords = {Databases Genetic,Genetic Variation,Germ-Line Mutation,Haplotypes,High-Throughput Nucleotide Sequencing,Humans,INDEL Mutation,Models Genetic,Neoplasms,Software,Whole Genome Sequencing} |
|
| 5118 | +} |
|
| 5119 | + |
|
| 5120 | +@article{kingFalsenegativeRatesMYC2019, |
|
| 5121 | + title = {False-Negative Rates for {{MYC}} Fluorescence in Situ Hybridization Probes in {{B-cell}} Neoplasms}, |
|
| 5122 | + author = {King, Rebecca L. and McPhail, Ellen D. and Meyer, Reid G. and Vasmatzis, George and Pearce, Kathryn and Smadbeck, James B. and Ketterling, Rhett P. and Smoley, Stephanie A. and Greipp, Patricia T. and Hoppman, Nicole L. and Peterson, Jess F. and Baughn, Linda B.}, |
|
| 5123 | + date = {2019-06}, |
|
| 5124 | + journaltitle = {Haematologica}, |
|
| 5125 | + shortjournal = {Haematologica}, |
|
| 5126 | + volume = {104}, |
|
| 5127 | + number = {6}, |
|
| 5128 | + eprint = {30523057}, |
|
| 5129 | + eprinttype = {pmid}, |
|
| 5130 | + pages = {e248-e251}, |
|
| 5131 | + issn = {1592-8721}, |
|
| 5132 | + doi = {10.3324/haematol.2018.207290}, |
|
| 5133 | + langid = {english}, |
|
| 5134 | + pmcid = {PMC6545835} |
|
| 5135 | +} |
|
| 5136 | + |
|
| 5137 | +@article{kishorHnRNPLdependentProtection2019, |
|
| 5138 | + title = {{{hnRNP L-dependent}} Protection of Normal {{mRNAs}} from {{NMD}} Subverts Quality Control in {{B}} Cell Lymphoma}, |
|
| 5139 | + author = {Kishor, Aparna and Ge, Zhiyun and Hogg, J Robert}, |
|
| 5140 | + date = {2019-02-01}, |
|
| 5141 | + journaltitle = {The EMBO Journal}, |
|
| 5142 | + shortjournal = {The EMBO Journal}, |
|
| 5143 | + volume = {38}, |
|
| 5144 | + number = {3}, |
|
| 5145 | + pages = {e99128}, |
|
| 5146 | + issn = {0261-4189}, |
|
| 5147 | + doi = {10.15252/embj.201899128}, |
|
| 5148 | + url = {https://www.embopress.org/doi/abs/10.15252/embj.201899128}, |
|
| 5149 | + urldate = {2019-12-23}, |
|
| 5150 | + abstract = {Abstract The human nonsense-mediated mRNA decay pathway (NMD) performs quality control and regulatory functions within complex post-transcriptional regulatory networks. In addition to degradation-promoting factors, efficient and accurate detection of NMD substrates involves proteins that safeguard normal mRNAs. Here, we identify hnRNP L as a factor that protects mRNAs with NMD-inducing features including long 3?UTRs. Using biochemical and transcriptome-wide approaches, we provide evidence that the susceptibility of a given transcript to NMD can be modulated by its 3?UTR length and ability to recruit hnRNP L. Integrating these findings with the previously defined role of polypyrimidine tract binding protein 1 in NMD evasion enables enhanced prediction of transcript susceptibility to NMD. Unexpectedly, this system is subverted in B cell lymphomas harboring translocations that produce BCL2:IGH fusion mRNAs. CRISPR/Cas9 deletion of hnRNP L binding sites near the BCL2 stop codon reduces expression of the fusion mRNAs and induces apoptosis. Together, our data indicate that protection by hnRNP L overrides the presence of multiple 3?UTR introns, allowing these aberrant mRNAs to evade NMD and promoting BCL2 overexpression and neoplasia.}, |
|
| 5151 | + keywords = {B cell lymphoma,BCL2,hnRNP L,nonsense-mediated mRNA decay,UPF1}, |
|
| 5152 | + file = {/Users/rmorin/Zotero/storage/ZZQNYXXW/Kishor et al. - 2019 - hnRNP L‐dependent protection of normal mRNAs from .pdf;/Users/rmorin/Zotero/storage/MWSFXKP8/embj.html} |
|
| 5153 | +} |
|
| 5154 | + |
|
| 5155 | +@article{klapperPatientAgeDiagnosis2012, |
|
| 5156 | + title = {Patient Age at Diagnosis Is Associated with the Molecular Characteristics of Diffuse Large {{B-cell}} Lymphoma.}, |
|
| 5157 | + author = {Klapper, Wolfram and Kreuz, Markus and Kohler, Christian W and Burkhardt, Birgit and Szczepanowski, Monika and Salaverria, Itziar and Hummel, Michael and Loeffler, Markus and Pellissery, Shoji and Woessmann, Wilhelm and Schwänen, Carsten and Trümper, Lorenz and Wessendorf, Swen and Spang, Rainer and Hasenclever, Dirk and Siebert, Reiner and Krebshilfe, Molecular Mechanisms in Malignant Lymphomas Network Project of the Deutsche}, |
|
| 5158 | + date = {2012-02}, |
|
| 5159 | + journaltitle = {Blood}, |
|
| 5160 | + volume = {119}, |
|
| 5161 | + number = {8}, |
|
| 5162 | + pages = {1882--1887}, |
|
| 5163 | + keywords = {nosource} |
|
| 5164 | +} |
|
| 5165 | + |
|
| 5166 | +@article{knutsonSelectiveInhibitionEZH22014, |
|
| 5167 | + title = {Selective {{Inhibition}} of {{EZH2}} by {{EPZ-6438 Leads}} to {{Potent Antitumor Activity}} in {{EZH2-Mutant Non-Hodgkin Lymphoma}}}, |
|
| 5168 | + author = {Knutson, Sarah K. and Kawano, Satoshi and Minoshima, Yukinori and Warholic, Natalie M. and Huang, Kuan-Chun and Xiao, Yonghong and Kadowaki, Tadashi and Uesugi, Mai and Kuznetsov, Galina and Kumar, Namita and Wigle, Tim J. and Klaus, Christine R. and Allain, Christina J. and Raimondi, Alejandra and Waters, Nigel J. and Smith, Jesse J. and Porter-Scott, Margaret and Chesworth, Richard and Moyer, Mikel P. and Copeland, Robert A. and Richon, Victoria M. and Uenaka, Toshimitsu and Pollock, Roy M. and Kuntz, Kevin W. and Yokoi, Akira and Keilhack, Heike}, |
|
| 5169 | + date = {2014}, |
|
| 5170 | + journaltitle = {Molecular Cancer Therapeutics}, |
|
| 5171 | + volume = {13}, |
|
| 5172 | + number = {4}, |
|
| 5173 | + eprint = {24563539}, |
|
| 5174 | + eprinttype = {pmid}, |
|
| 5175 | + pages = {842--854}, |
|
| 5176 | + issn = {1535-7163}, |
|
| 5177 | + doi = {10.1158/1535-7163.mct-13-0773}, |
|
| 5178 | + url = {http://dx.doi.org/10.1158/1535-7163.mct-13-0773}, |
|
| 5179 | + abstract = {Mutations within the catalytic domain of the histone methyltransferase EZH2 have been identified in subsets of patients with non-Hodgkin lymphoma (NHL). These genetic alterations are hypothesized to confer an oncogenic dependency on EZH2 enzymatic activity in these cancers. We have previously reported the discovery of EPZ005678 and EPZ-6438, potent and selective S-adenosyl-methionine-competitive small molecule inhibitors of EZH2. Although both compounds are similar with respect to their mechanism of action and selectivity, EPZ-6438 possesses superior potency and drug-like properties, including good oral bioavailability in animals. Here, we characterize the activity of EPZ-6438 in preclinical models of NHL. EPZ-6438 selectively inhibits intracellular lysine 27 of histone H3 (H3K27) methylation in a concentration- and time-dependent manner in both EZH2 wild-type and mutant lymphoma cells. Inhibition of H3K27 trimethylation (H3K27Me3) leads to selective cell killing of human lymphoma cell lines bearing EZH2 catalytic domain point mutations. Treatment of EZH2-mutant NHL xenograft-bearing mice with EPZ-6438 causes dose-dependent tumor growth inhibition, including complete and sustained tumor regressions with correlative diminution of H3K27Me3 levels in tumors and selected normal tissues. Mice dosed orally with EPZ-6438 for 28 days remained tumor free for up to 63 days after stopping compound treatment in two EZH2-mutant xenograft models. These data confirm the dependency of EZH2-mutant NHL on EZH2 activity and portend the utility of EPZ-6438 as a potential treatment for these genetically defined cancers. Mol Cancer Ther; 13(4); 842–54. ©2014 AACR.}, |
|
| 5180 | + keywords = {nosource} |
|
| 5181 | +} |
|
| 5182 | + |
|
| 5183 | +@article{kochanIFcombinedSmRNAFISH2016, |
|
| 5184 | + title = {{{IF-combined smRNA FISH}} Reveals Interaction of {{MCPIP1}} Protein with {{IER3 mRNA}}.}, |
|
| 5185 | + author = {Kochan, Jakub and Wawro, Mateusz and Kasza, Aneta}, |
|
| 5186 | + date = {2016}, |
|
| 5187 | + journaltitle = {Biology Open}, |
|
| 5188 | + volume = {5}, |
|
| 5189 | + number = {7}, |
|
| 5190 | + pages = {889--898}, |
|
| 5191 | + keywords = {nosource} |
|
| 5192 | +} |
|
| 5193 | + |
|
| 5194 | +@article{koenigDistinctPhenotypePolarized2023, |
|
| 5195 | + title = {A {{Distinct Phenotype}} of {{Polarized Memory B}} Cell Holds {{IgE Memory}}}, |
|
| 5196 | + author = {Koenig, Joshua F. E. and Knudsen, Niels Peter H. and Phelps, Allyssa and Bruton, Kelly and Hoof, Ilka and Lund, Gitte and Libera, Danielle Della and Lund, Anders and Christensen, Lars Harder and Glass, David R. and Walker, Tina and Fang, Allison and Waserman, Susan and Jordana, Manel and Andersen, Peter S.}, |
|
| 5197 | + date = {2023-01-25}, |
|
| 5198 | + journaltitle = {bioRxiv}, |
|
| 5199 | + pages = {2023.01.25.525495}, |
|
| 5200 | + doi = {10.1101/2023.01.25.525495}, |
|
| 5201 | + url = {https://www.biorxiv.org/content/10.1101/2023.01.25.525495v1}, |
|
| 5202 | + urldate = {2023-12-16}, |
|
| 5203 | + abstract = {Allergen-specific IgE antibodies mediate allergic pathology in diseases such as allergic rhinitis and food allergy. Memory B cells (MBCs) contribute to circulating IgE by regenerating IgE-producing plasma cells upon allergen encounter. We report a population of type 2 polarized MBCs defined as CD23hi, IL-4Rαhi, CD32low at the transcriptional and surface protein levels. These “MBC2s” are enriched in IgG1 and IgG4-expressing cells, while constitutively expressing germline transcripts for IgE. Allergen-specific B cells from patients with allergic rhinitis and food allergy were enriched in MBC2s. MBC2s generated allergen specific-IgE during sublingual immunotherapy, thereby identifying these cells as the primary reservoir of IgE. The identification of MBC2s provides insights into the maintenance of IgE memory, which is detrimental in allergic diseases, but which could be beneficial in protection against venoms and helminths. One-Sentence Summary Identification of a novel memory B cell subset which holds allergen specific IgE memory.}, |
|
| 5204 | + langid = {english}, |
|
| 5205 | + file = {/Users/rmorin/Zotero/storage/Q5GMRSC9/Koenig et al. - 2023 - A Distinct Phenotype of Polarized Memory B cell ho.pdf} |
|
| 5206 | +} |
|
| 5207 | + |
|
| 5208 | +@article{kogureWholegenomeLandscapeAdult2022, |
|
| 5209 | + title = {Whole-Genome Landscape of Adult {{T-cell}} Leukemia/Lymphoma}, |
|
| 5210 | + author = {Kogure, Yasunori and Kameda, Takuro and Koya, Junji and Yoshimitsu, Makoto and Nosaka, Kisato and Yasunaga, Jun-Ichirou and Imaizumi, Yoshitaka and Watanabe, Mizuki and Saito, Yuki and Ito, Yuta and McClure, Marni B. and Tabata, Mariko and Shingaki, Sumito and Yoshifuji, Kota and Chiba, Kenichi and Okada, Ai and Kakiuchi, Nobuyuki and Nannya, Yasuhito and Kamiunten, Ayako and Tahira, Yuki and Akizuki, Keiichi and Sekine, Masaaki and Shide, Kotaro and Hidaka, Tomonori and Kubuki, Yoko and Kitanaka, Akira and Hidaka, Michihiro and Nakano, Nobuaki and Utsunomiya, Atae and Sica, R. Alejandro and Acuna-Villaorduna, Ana and Janakiram, Murali and Shah, Urvi and Ramos, Juan Carlos and Shibata, Tatsuhiro and Takeuchi, Kengo and Takaori-Kondo, Akifumi and Miyazaki, Yasushi and Matsuoka, Masao and Ishitsuka, Kenji and Shiraishi, Yuichi and Miyano, Satoru and Ogawa, Seishi and Ye, B. Hilda and Shimoda, Kazuya and Kataoka, Keisuke}, |
|
| 5211 | + date = {2022-02-17}, |
|
| 5212 | + journaltitle = {Blood}, |
|
| 5213 | + shortjournal = {Blood}, |
|
| 5214 | + volume = {139}, |
|
| 5215 | + number = {7}, |
|
| 5216 | + eprint = {34695199}, |
|
| 5217 | + eprinttype = {pmid}, |
|
| 5218 | + pages = {967--982}, |
|
| 5219 | + issn = {1528-0020}, |
|
| 5220 | + doi = {10.1182/blood.2021013568}, |
|
| 5221 | + abstract = {Adult T-cell leukemia/lymphoma (ATL) is an aggressive neoplasm immunophenotypically resembling regulatory T cells, associated with human T-cell leukemia virus type-1. Here, we performed whole-genome sequencing (WGS) of 150 ATL cases to reveal the overarching landscape of genetic alterations in ATL. We discovered frequent (33\%) loss-of-function alterations preferentially targeting the CIC long isoform, which were overlooked by previous exome-centric studies of various cancer types. Long but not short isoform-specific inactivation of Cic selectively increased CD4+CD25+Foxp3+ T cells in~vivo. We also found recurrent (13\%) 3'-truncations of REL, which induce transcriptional upregulation and generate gain-of-function proteins. More importantly, REL truncations are also common in diffuse large B-cell lymphoma, especially in germinal center B-cell-like subtype (12\%). In the non-coding genome, we identified recurrent mutations in regulatory elements, particularly splice sites, of several driver genes. In addition, we characterized the different mutational processes operative in clustered hypermutation sites within and outside immunoglobulin/T-cell receptor genes and identified the mutational enrichment at the binding sites of host and viral transcription factors, suggesting their activities in ATL. By combining the analyses for coding and noncoding mutations, structural variations, and copy number alterations, we discovered 56 recurrently altered driver genes, including 11 novel ones. Finally, ATL cases were classified into 2 molecular groups with distinct clinical and genetic characteristics based on the driver alteration profile. Our findings not only help to improve diagnostic and therapeutic strategies in ATL, but also provide insights into T-cell biology and have implications for genome-wide cancer driver discovery.}, |
|
| 5222 | + langid = {english}, |
|
| 5223 | + pmcid = {PMC8854674}, |
|
| 5224 | + keywords = {Animals,Ataxin-1,Biomarkers Tumor,DNA Copy Number Variations,Female,Gene Expression Regulation Neoplastic,Genome Human,Humans,Leukemia-Lymphoma Adult T-Cell,Mice,Mice Inbred C57BL,Mutation,Prognosis,Proto-Oncogene Proteins c-rel,Repressor Proteins,Survival Rate,Whole Exome Sequencing} |
|
| 5225 | +} |
|
| 5226 | + |
|
| 5227 | +@article{kopetzGenomicClassifierColoPrint2015, |
|
| 5228 | + title = {Genomic Classifier {{ColoPrint}} Predicts Recurrence in Stage {{II}} Colorectal Cancer Patients More Accurately than Clinical Factors}, |
|
| 5229 | + author = {Kopetz, Scott and Tabernero, Josep and Rosenberg, Robert and Jiang, Zhi-Qin and Moreno, Víctor and Bachleitner-Hofmann, Thomas and Lanza, Giovanni and Stork-Sloots, Lisette and Maru, Dipen and Simon, Iris and Capellà, Gabriel and Salazar, Ramon}, |
|
| 5230 | + date = {2015-02}, |
|
| 5231 | + journaltitle = {The Oncologist}, |
|
| 5232 | + shortjournal = {Oncologist}, |
|
| 5233 | + volume = {20}, |
|
| 5234 | + number = {2}, |
|
| 5235 | + eprint = {25561511}, |
|
| 5236 | + eprinttype = {pmid}, |
|
| 5237 | + pages = {127--133}, |
|
| 5238 | + issn = {1549-490X}, |
|
| 5239 | + doi = {10.1634/theoncologist.2014-0325}, |
|
| 5240 | + abstract = {BACKGROUND: Approximately 20\% of patients with stage II colorectal cancer will experience a relapse. Current clinical-pathologic stratification factors do not allow clear identification of these high-risk patients. ColoPrint (Agendia, Amsterdam, The Netherlands, http://www.agendia.com) is a gene expression classifier that distinguishes patients with low or high risk of disease relapse. METHODS: ColoPrint was developed using whole-genome expression data and validated in several independent validation cohorts. Stage II patients from these studies were pooled (n = 416), and ColoPrint was compared with clinical risk factors described in the National Comprehensive Cancer Network (NCCN) 2013 Guidelines for Colon Cancer. Median follow-up was 81 months. Most patients (70\%) did not receive adjuvant chemotherapy. Risk of relapse (ROR) was defined as survival until first event of recurrence or death from cancer. RESULTS: In the pooled stage II data set, ColoPrint identified 63\% of patients as low risk with a 5-year ROR of 10\%, whereas high-risk patients (37\%) had a 5-year ROR of 21\%, with a hazard ratio (HR) of 2.16 (p = .004). This remained significant in a multivariate model that included number of lymph nodes retrieved and microsatellite instability. In the T3 microsatellite-stable subgroup (n = 301), ColoPrint classified 59\% of patients as low risk with a 5-year ROR of 9.9\%. High-risk patients (31\%) had a 22.4\% ROR (HR: 2.41; p = .005). In contrast, the NCCN clinical high-risk factors were unable to distinguish high- and low-risk patients (15\% vs. 13\% ROR; p = .55). CONCLUSION: ColoPrint significantly improved prognostic accuracy independent of microsatellite status or clinical variables, facilitating the identification of patients at higher risk who might be considered for additional treatment.}, |
|
| 5241 | + langid = {english}, |
|
| 5242 | + pmcid = {PMC4319631}, |
|
| 5243 | + keywords = {Adult,Aged,Aged 80 and over,Colorectal Neoplasms,Female,Gene Expression Profiling,Gene Expression Regulation Neoplastic,Gene expression signature,Genomics,Humans,Male,Middle Aged,Neoplasm Recurrence Local,Neoplasm Staging,Netherlands,Prognosis,Risk Assessment,Risk classification,Risk prediction,Stage II colon cancer} |
|
| 5244 | +} |
|
| 5245 | + |
|
| 5246 | +@article{kridelHistologicalTransformationProgression2016, |
|
| 5247 | + title = {Histological {{Transformation}} and {{Progression}} in {{Follicular Lymphoma}}: {{A Clonal Evolution Study}}}, |
|
| 5248 | + shorttitle = {Histological {{Transformation}} and {{Progression}} in {{Follicular Lymphoma}}}, |
|
| 5249 | + author = {Kridel, Robert and Chan, Fong Chun and Mottok, Anja and Boyle, Merrill and Farinha, Pedro and Tan, King and Meissner, Barbara and Bashashati, Ali and McPherson, Andrew and Roth, Andrew and Shumansky, Karey and Yap, Damian and Ben-Neriah, Susana and Rosner, Jamie and Smith, Maia A. and Nielsen, Cydney and Giné, Eva and Telenius, Adele and Ennishi, Daisuke and Mungall, Andrew and Moore, Richard and Morin, Ryan D. and Johnson, Nathalie A. and Sehn, Laurie H. and Tousseyn, Thomas and Dogan, Ahmet and Connors, Joseph M. and Scott, David W. and Steidl, Christian and Marra, Marco A. and Gascoyne, Randy D. and Shah, Sohrab P.}, |
|
| 5250 | + date = {2016-12}, |
|
| 5251 | + journaltitle = {PLoS medicine}, |
|
| 5252 | + shortjournal = {PLoS Med}, |
|
| 5253 | + volume = {13}, |
|
| 5254 | + number = {12}, |
|
| 5255 | + eprint = {27959929}, |
|
| 5256 | + eprinttype = {pmid}, |
|
| 5257 | + pages = {e1002197}, |
|
| 5258 | + issn = {1549-1676}, |
|
| 5259 | + doi = {10.1371/journal.pmed.1002197}, |
|
| 5260 | + abstract = {BACKGROUND: Follicular lymphoma (FL) is an indolent, yet incurable B cell malignancy. A subset of patients experience an increased mortality rate driven by two distinct clinical end points: histological transformation and early progression after immunochemotherapy. The nature of tumor clonal dynamics leading to these clinical end points is poorly understood, and previously determined genetic alterations do not explain the majority of transformed cases or accurately predict early progressive disease. We contend that detailed knowledge of the expansion patterns of specific cell populations plus their associated mutations would provide insight into therapeutic strategies and disease biology over the time course of FL clinical histories. METHODS AND FINDINGS: Using a combination of whole genome sequencing, targeted deep sequencing, and digital droplet PCR on matched diagnostic and relapse specimens, we deciphered the constituent clonal populations in 15 transformation cases and 6 progression cases, and measured the change in clonal population abundance over time. We observed widely divergent patterns of clonal dynamics in transformed cases relative to progressed cases. Transformation specimens were generally composed of clones that were rare or absent in diagnostic specimens, consistent with dramatic clonal expansions that came to dominate the transformation specimens. This pattern was independent of time to transformation and treatment modality. By contrast, early progression specimens were composed of clones that were already present in the diagnostic specimens and exhibited only moderate clonal dynamics, even in the presence of immunochemotherapy. Analysis of somatic mutations impacting 94 genes was undertaken in an extension cohort consisting of 395 samples from 277 patients in order to decipher disrupted biology in the two clinical end points. We found 12 genes that were more commonly mutated in transformed samples than in the preceding FL tumors, including TP53, B2M, CCND3, GNA13, S1PR2, and P2RY8. Moreover, ten genes were more commonly mutated in diagnostic specimens of patients with early progression, including TP53, BTG1, MKI67, and XBP1. CONCLUSIONS: Our results illuminate contrasting modes of evolution shaping the clinical histories of transformation and progression. They have implications for interpretation of evolutionary dynamics in the context of treatment-induced selective pressures, and indicate that transformation and progression will require different clinical management strategies.}, |
|
| 5261 | + langid = {english}, |
|
| 5262 | + pmcid = {PMC5154502}, |
|
| 5263 | + keywords = {Clonal Evolution,Clone Cells,Disease Progression,Humans,Lymphoma Follicular,Mutation} |
|
| 5264 | +} |
|
| 5265 | + |
|
| 5266 | +@article{kridelWholeTranscriptomeSequencing2012, |
|
| 5267 | + title = {Whole Transcriptome Sequencing Reveals Recurrent {{NOTCH1}} Mutations in Mantle Cell Lymphoma}, |
|
| 5268 | + author = {Kridel, Robert and Meissner, Barbara and Rogic, Sanja and Boyle, Merrill and Telenius, Adele and Woolcock, Bruce and Gunawardana, Jay and Jenkins, Christopher and Cochrane, Chris and Ben-Neriah, Susana and Tan, King and Morin, Ryan D. and Opat, Stephen and Sehn, Laurie H. and Connors, Joseph M. and Marra, Marco A. and Weng, Andrew P. and Steidl, Christian and Gascoyne, Randy D.}, |
|
| 5269 | + date = {2012-03-01}, |
|
| 5270 | + journaltitle = {Blood}, |
|
| 5271 | + shortjournal = {Blood}, |
|
| 5272 | + volume = {119}, |
|
| 5273 | + number = {9}, |
|
| 5274 | + eprint = {22210878}, |
|
| 5275 | + eprinttype = {pmid}, |
|
| 5276 | + pages = {1963--1971}, |
|
| 5277 | + issn = {1528-0020}, |
|
| 5278 | + doi = {10.1182/blood-2011-11-391474}, |
|
| 5279 | + abstract = {Mantle cell lymphoma (MCL), an aggressive subtype of non-Hodgkin lymphoma, is characterized by the hallmark translocation t(11;14)(q13;q32) and the resulting overexpression of cyclin D1 (CCND1). Our current knowledge of this disease encompasses frequent secondary cytogenetic aberrations and the recurrent mutation of a handful of genes, such as TP53, ATM, and CCND1. However, these findings insufficiently explain the biologic underpinnings of MCL. Here, we performed whole transcriptome sequencing on a discovery cohort of 18 primary tissue MCL samples and 2 cell lines. We found recurrent mutations in NOTCH1, a finding that we confirmed in an extension cohort of 108 clinical samples and 8 cell lines. In total, 12\% of clinical samples and 20\% of cell lines harbored somatic NOTCH1 coding sequence mutations that clustered in the PEST domain and predominantly consisted of truncating mutations or small frame-shifting indels. NOTCH1 mutations were associated with poor overall survival (P = .003). Furthermore, we showed that inhibition of the NOTCH pathway reduced proliferation and induced apoptosis in 2 MCL cell lines. In summary, we have identified recurrent NOTCH1 mutations that provide the preclinical rationale for therapeutic inhibition of the NOTCH pathway in a subset of patients with MCL.}, |
|
| 5280 | + langid = {english}, |
|
| 5281 | + keywords = {Adult,Aged,Aged 80 and over,Amyloid Precursor Protein Secretases,Apoptosis,Base Sequence,Benzodiazepinones,Cell Line Tumor,Cell Proliferation,Cyclin D1,Exons,Female,Gene Expression Profiling,Humans,Lymphoma Mantle-Cell,Male,Middle Aged,Mutation,Prognosis,Receptor Notch1,Sequence Analysis RNA,Signal Transduction,Survival Analysis,Transcriptome} |
|
| 5282 | +} |
|
| 5283 | + |
|
| 5284 | +@article{krysiakRecurrentSomaticMutations2017b, |
|
| 5285 | + title = {Recurrent Somatic Mutations Affecting {{B-cell}} Receptor Signaling Pathway Genes in Follicular Lymphoma}, |
|
| 5286 | + author = {Krysiak, Kilannin and Gomez, Felicia and White, Brian S. and Matlock, Matthew and Miller, Christopher A. and Trani, Lee and Fronick, Catrina C. and Fulton, Robert S. and Kreisel, Friederike and Cashen, Amanda F. and Carson, Kenneth R. and Berrien-Elliott, Melissa M. and Bartlett, Nancy L. and Griffith, Malachi and Griffith, Obi L. and Fehniger, Todd A.}, |
|
| 5287 | + date = {2017-01-26}, |
|
| 5288 | + journaltitle = {Blood}, |
|
| 5289 | + shortjournal = {Blood}, |
|
| 5290 | + volume = {129}, |
|
| 5291 | + number = {4}, |
|
| 5292 | + eprint = {28064239}, |
|
| 5293 | + eprinttype = {pmid}, |
|
| 5294 | + pages = {473--483}, |
|
| 5295 | + issn = {1528-0020}, |
|
| 5296 | + doi = {10.1182/blood-2016-07-729954}, |
|
| 5297 | + abstract = {Follicular lymphoma (FL) is the most common form of indolent non-Hodgkin lymphoma, yet it remains only partially characterized at the genomic level. To improve our understanding of the genetic underpinnings of this incurable and clinically heterogeneous disease, whole-exome sequencing was performed on tumor/normal pairs from a discovery cohort of 24 patients with FL. Using these data and mutations identified in other B-cell malignancies, 1716 genes were sequenced in 113 FL tumor samples from 105 primarily treatment-naive individuals. We identified 39 genes that were mutated significantly above background mutation rates. CREBBP mutations were associated with inferior PFS. In contrast, mutations in previously unreported HVCN1, a voltage-gated proton channel-encoding gene and B-cell receptor signaling modulator, were associated with improved PFS. In total, 47 (44.8\%) patients harbor mutations in the interconnected B-cell receptor (BCR) and CXCR4 signaling pathways. Histone gene mutations were more frequent than previously reported (identified in 43.8\% of patients) and often co-occurred (17.1\% of patients). A novel, recurrent hotspot was identified at a posttranslationally modified residue in the histone H2B family. This study expands the number of mutated genes described in several known signaling pathways and complexes involved in lymphoma pathogenesis (BCR, Notch, SWitch/sucrose nonfermentable (SWI/SNF), vacuolar ATPases) and identified novel recurrent mutations (EGR1/2, POU2AF1, BTK, ZNF608, HVCN1) that require further investigation in the context of FL biology, prognosis, and treatment.}, |
|
| 5298 | + langid = {english}, |
|
| 5299 | + pmcid = {PMC5270390}, |
|
| 5300 | + keywords = {Adult,Agammaglobulinaemia Tyrosine Kinase,Aged,Aged 80 and over,CREB-Binding Protein,Disease-Free Survival,Early Growth Response Protein 1,Female,Gene Expression Profiling,Gene Expression Regulation Neoplastic,Histones,Humans,Ion Channels,Lymphoma Follicular,Male,Middle Aged,Mutation,Protein-Tyrosine Kinases,Receptors Antigen B-Cell,Receptors CXCR4,Receptors Notch,Repressor Proteins,Signal Transduction,Trans-Activators,Vacuolar Proton-Translocating ATPases}, |
|
| 5301 | + file = {/Users/rmorin/Zotero/storage/6KQ6DZ4I/Krysiak et al. - 2017 - Recurrent somatic mutations affecting B-cell recep.pdf} |
|
| 5302 | +} |
|
| 5303 | + |
|
| 5304 | +@article{kubuschokLearningFailuresDrug2017, |
|
| 5305 | + title = {Learning from the Failures of Drug Discovery in {{B-cell}} Non-{{Hodgkin}} Lymphomas and Perspectives for the Future: Chronic Lymphocytic Leukemia and Diffuse Large {{B-cell}} Lymphoma as Two Ends of a Spectrum in Drug Development}, |
|
| 5306 | + author = {Kubuschok, Boris and Trepel, Martin}, |
|
| 5307 | + date = {2017}, |
|
| 5308 | + journaltitle = {Expert Opinion on Drug Discovery}, |
|
| 5309 | + volume = {12}, |
|
| 5310 | + number = {7}, |
|
| 5311 | + eprint = {28494631}, |
|
| 5312 | + eprinttype = {pmid}, |
|
| 5313 | + pages = {733--745}, |
|
| 5314 | + issn = {1746-0441}, |
|
| 5315 | + doi = {10.1080/17460441.2017.1329293}, |
|
| 5316 | + url = {http://dx.doi.org/10.1080/17460441.2017.1329293}, |
|
| 5317 | + abstract = {Introduction: Despite substantial recent advances, there is still an unmet need for better therapies in B-cell non Hodgkin lymphomas (B-NHL), especially in relapsed or refractory disease. Many novel targeted drugs have been developed based on a better molecular understanding of B-NHL. Areas covered: This article focuses on chronic lymphocytic leukemia (CLL) as a representative for indolent lymphomas and paradigmatic for the tremendous progress in treating B-NHL on the one hand and diffuse large B-cell lymphoma (DLBCL) as a representative for aggressive lymphomas and paradigmatic for many unsolved problems in lymphoma treatment or the other hand. We highlight salient points in current therapies targeting genetic, epigenetic, immunological and microenvironmental alterations. Possible reasons for drug failure in clinical trials like tumor heterogeneity, clonal evolution and drug resistance mechanisms are discussed. Based thereon, some perspectives for further drug discovery are given. Expert opinion: In view of the pathogenetic complexity of lymphomas, therapies targeting exclusively a single alteration may fail because resistance mechanisms are present either initially or evolve during treatment. Therefore, future therapies in B-NHL may have to target the greatest possible number of genetic, immunological or epigenetic alterations still allowing tolerability and to monitor these alterations during therapy.}, |
|
| 5318 | + keywords = {nosource} |
|
| 5319 | +} |
|
| 5320 | + |
|
| 5321 | +@article{kukalevActinHnRNPCooperate2005, |
|
| 5322 | + title = {Actin and {{hnRNP U}} Cooperate for Productive Transcription by {{RNA}} Polymerase {{II}}}, |
|
| 5323 | + author = {Kukalev, Alexander and Nord, Ylva and Palmberg, Carina and Bergman, Tomas and Percipalle, Piergiorgio}, |
|
| 5324 | + date = {2005-03}, |
|
| 5325 | + journaltitle = {Nature Structural \& Molecular Biology}, |
|
| 5326 | + shortjournal = {Nat Struct Mol Biol}, |
|
| 5327 | + volume = {12}, |
|
| 5328 | + number = {3}, |
|
| 5329 | + pages = {238--244}, |
|
| 5330 | + publisher = {Nature Publishing Group}, |
|
| 5331 | + issn = {1545-9985}, |
|
| 5332 | + doi = {10.1038/nsmb904}, |
|
| 5333 | + url = {https://www.nature.com/articles/nsmb904}, |
|
| 5334 | + urldate = {2022-09-27}, |
|
| 5335 | + abstract = {To determine the role of actin–ribonucleoprotein complexes in transcription, we set out to identify novel actin-binding proteins associated with RNA polymerase II (Pol II). Using affinity chromatography on fractionated HeLa cells, we found that hnRNP U binds actin through a short amino acid sequence in its C-terminal domain. Post-transcriptional gene silencing of hnRNP U and nuclear microinjections of a short peptide encompassing the hnRNP U actin-binding sequence inhibited BrUTP incorporation in vivo. In living cells, we found that both actin and hnRNP U are associated with the phosphorylated C-terminal domain of Pol II, and antibodies to actin and hnRNP U blocked Pol II–mediated transcription. Taken together, our results indicate that a general actin-based mechanism is implicated in the transcription of most Pol II genes. Actin in complex with hnRNP U may carry out its regulatory role during the initial phases of transcription activation.}, |
|
| 5336 | + issue = {3}, |
|
| 5337 | + langid = {english}, |
|
| 5338 | + keywords = {Biochemistry,Biological Microscopy,general,Life Sciences,Membrane Biology,Protein Structure}, |
|
| 5339 | + file = {/Users/rmorin/Zotero/storage/TJWI5HS3/Kukalev et al. - 2005 - Actin and hnRNP U cooperate for productive transcr.pdf;/Users/rmorin/Zotero/storage/MGEPJTBE/nsmb904.html} |
|
| 5340 | +} |
|
| 5341 | + |
|
| 5342 | +@article{kulkarniPosttranscriptionalRegulationHLAA2017, |
|
| 5343 | + title = {Posttranscriptional {{Regulation}} of {{HLA-A Protein Expression}} by {{Alternative Polyadenylation Signals Involving}} the {{RNA-Binding Protein Syncrip}}}, |
|
| 5344 | + author = {Kulkarni, Smita and Ramsuran, Veron and Rucevic, Marijana and Singh, Sukhvinder and Lied, Alexandra and Kulkarni, Viraj and O'hUigin, Colm and Le Gall, Sylvie and Carrington, Mary}, |
|
| 5345 | + date = {2017-12-01}, |
|
| 5346 | + journaltitle = {Journal of Immunology (Baltimore, Md.: 1950)}, |
|
| 5347 | + shortjournal = {J Immunol}, |
|
| 5348 | + volume = {199}, |
|
| 5349 | + number = {11}, |
|
| 5350 | + eprint = {29055006}, |
|
| 5351 | + eprinttype = {pmid}, |
|
| 5352 | + pages = {3892--3899}, |
|
| 5353 | + issn = {1550-6606}, |
|
| 5354 | + doi = {10.4049/jimmunol.1700697}, |
|
| 5355 | + abstract = {Genomic variation in the untranslated region (UTR) has been shown to influence HLA class I expression level and associate with disease outcomes. Sequencing of the 3'UTR of common HLA-A alleles indicated the presence of two polyadenylation signals (PAS). The proximal PAS is conserved, whereas the distal PAS is disrupted within certain alleles by sequence variants. Using 3'RACE, we confirmed expression of two distinct forms of the HLA-A 3'UTR based on use of either the proximal or the distal PAS, which differ in length by 100 bp. Specific HLA-A alleles varied in the usage of the proximal versus distal PAS, with some alleles using only the proximal PAS, and others using both the proximal and distal PAS to differing degrees. We show that the short and the long 3'UTR produced similar mRNA expression levels. However, the long 3'UTR conferred lower luciferase activity as compared with the short form, indicating translation inhibition of the long 3'UTR. RNA affinity pull-down followed by mass spectrometry analysis as well as RNA coimmunoprecipitation indicated differential binding of Syncrip to the long versus short 3'UTR. Depletion of Syncrip by small interfering RNA increased surface expression of an HLA-A allotype that uses primarily the long 3'UTR, whereas an allotype expressing only the short form was unaffected. Furthermore, specific blocking of the proximal 3'UTR reduced surface expression without decreasing mRNA expression. These data demonstrate HLA-A allele-specific variation in PAS usage, which modulates their cell surface expression posttranscriptionally.}, |
|
| 5356 | + langid = {english}, |
|
| 5357 | + pmcid = {PMC5812486}, |
|
| 5358 | + keywords = {3' Untranslated Regions,Gene Expression Regulation,Genotype,Heterogeneous-Nuclear Ribonucleoproteins,HLA-A Antigens,Humans,Jurkat Cells,Polyadenylation,Polymorphism Genetic,Protein Binding,Protein Isoforms,RNA Processing Post-Transcriptional,RNA Small Interfering,RNA Splice Sites,RNA-Binding Motifs}, |
|
| 5359 | + file = {/Users/rmorin/Zotero/storage/AXYPCNJM/Kulkarni et al. - 2017 - Posttranscriptional Regulation of HLA-A Protein Ex.pdf} |
|
| 5360 | +} |
|
| 5361 | + |
|
| 5362 | +@article{kumanovicsDiffuseLargeCell2010, |
|
| 5363 | + title = {Diffuse Large {{B}} Cell Lymphoma in Hyper-{{IgE}} Syndrome Due to {{STAT3}} Mutation.}, |
|
| 5364 | + author = {Kumánovics, Attila and Perkins, Sherrie L and Gilbert, Heather and Cessna, Melissa H and Augustine, Nancy H and Hill, Harry R}, |
|
| 5365 | + date = {2010-11}, |
|
| 5366 | + journaltitle = {Journal of clinical immunology}, |
|
| 5367 | + volume = {30}, |
|
| 5368 | + number = {6}, |
|
| 5369 | + pages = {886--893}, |
|
| 5370 | + keywords = {nosource} |
|
| 5371 | +} |
|
| 5372 | + |
|
| 5373 | +@article{kumarMultipleMyeloma2017, |
|
| 5374 | + title = {Multiple Myeloma}, |
|
| 5375 | + author = {Kumar, Shaji K. and Rajkumar, Vincent and Kyle, Robert A. and family=Duin, given=Mark, prefix=van, useprefix=true and Sonneveld, Pieter and Mateos, María-Victoria and Gay, Francesca and Anderson, Kenneth C.}, |
|
| 5376 | + date = {2017-07-20}, |
|
| 5377 | + journaltitle = {Nature Reviews Disease Primers}, |
|
| 5378 | + shortjournal = {Nat Rev Dis Primers}, |
|
| 5379 | + volume = {3}, |
|
| 5380 | + number = {1}, |
|
| 5381 | + pages = {1--20}, |
|
| 5382 | + publisher = {Nature Publishing Group}, |
|
| 5383 | + issn = {2056-676X}, |
|
| 5384 | + doi = {10.1038/nrdp.2017.46}, |
|
| 5385 | + url = {https://www.nature.com/articles/nrdp201746}, |
|
| 5386 | + urldate = {2022-10-05}, |
|
| 5387 | + abstract = {Multiple myeloma is a malignancy of terminally differentiated plasma cells, and patients typically present with bone marrow infiltration of clonal plasma cells and monoclonal protein in the serum and/or urine. The diagnosis of multiple myeloma is made when clear end-organ damage attributable to the plasma cell proliferative disorder or when findings that suggest a high likelihood of their development are present. Distinguishing symptomatic multiple myeloma that requires treatment from the precursor stages of monoclonal gammopathy of undetermined significance and smouldering multiple myeloma is important, as observation is the standard for those conditions. Much progress has been made over the past decade in the understanding of disease biology and individualized treatment approaches. Several new classes of drugs, such as proteasome inhibitors and immunomodulatory drugs, have joined the traditional armamentarium (corticosteroids, alkylating agents and anthracyclines) and, along with high-dose therapy and autologous haemopoietic stem cell transplantation, have led to deeper and durable clinical responses. Indeed, an increasing proportion of patients are achieving lasting remissions, raising the possibility of cure for this disease. Success will probably depend on using combinations of effective agents and treating patients in the early stages of disease, such as patients with smouldering multiple myeloma.}, |
|
| 5388 | + issue = {1}, |
|
| 5389 | + langid = {english}, |
|
| 5390 | + keywords = {Cancer genetics,Cancer microenvironment,Cancer therapy,Myeloma}, |
|
| 5391 | + file = {/Users/rmorin/Zotero/storage/3CIDUHDH/nrdp201746.html} |
|
| 5392 | +} |
|
| 5393 | + |
|
| 5394 | +@article{kurtzNoninvasiveMonitoringDiffuse2015, |
|
| 5395 | + title = {Noninvasive Monitoring of Diffuse Large {{B-cell}} Lymphoma by Immunoglobulin High-Throughput Sequencing.}, |
|
| 5396 | + author = {Kurtz, David M and Green, Michael R and Bratman, Scott V and Scherer, Florian and Liu, Chih Long and Kunder, Christian A and Takahashi, Kazuhiro and Glover, Cynthia and Keane, Colm and Kihira, Shingo and Visser, Brendan and Callahan, Jason and Kong, Katherine A and Faham, Malek and Corbelli, Karen S and Miklos, David and Advani, Ranjana H and Levy, Ronald and Hicks, Rodney J and Hertzberg, Mark and Ohgami, Robert S and Gandhi, Maher K and Diehn, Maximilian and Alizadeh, Ash A}, |
|
| 5397 | + date = {2015-06}, |
|
| 5398 | + journaltitle = {Blood}, |
|
| 5399 | + volume = {125}, |
|
| 5400 | + number = {24}, |
|
| 5401 | + pages = {3679--3687}, |
|
| 5402 | + keywords = {nosource} |
|
| 5403 | +} |
|
| 5404 | + |
|
| 5405 | +@article{kwanGenomeStellerSea2019, |
|
| 5406 | + title = {The {{Genome}} of the {{Steller Sea Lion}} ({{Eumetopias}} Jubatus)}, |
|
| 5407 | + author = {Kwan, Harwood H. and Culibrk, Luka and Taylor, Gregory A. and Leelakumari, Sreeja and Tan, Ryan and Jackman, Shaun D. and Tse, Kane and MacLeod, Tina and Cheng, Dean and Chuah, Eric and Kirk, Heather and Pandoh, Pawan and Carlsen, Rebecca and Zhao, Yongjun and Mungall, Andrew J. and Moore, Richard and Birol, Inanc and Marra, Marco A. and Rosen, David A.S. and Haulena, Martin and Jones, Steven J. M.}, |
|
| 5408 | + date = {2019-06-26}, |
|
| 5409 | + journaltitle = {Genes}, |
|
| 5410 | + shortjournal = {Genes (Basel)}, |
|
| 5411 | + volume = {10}, |
|
| 5412 | + number = {7}, |
|
| 5413 | + eprint = {31248052}, |
|
| 5414 | + eprinttype = {pmid}, |
|
| 5415 | + pages = {486}, |
|
| 5416 | + issn = {2073-4425}, |
|
| 5417 | + doi = {10.3390/genes10070486}, |
|
| 5418 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6678222/}, |
|
| 5419 | + urldate = {2022-02-01}, |
|
| 5420 | + abstract = {The Steller sea lion is the largest member of the Otariidae family and is found in the coastal waters of the northern Pacific Rim. Here, we present the Steller sea lion genome, determined through DNA sequencing approaches that utilized microfluidic partitioning library construction, as well as nanopore technologies. These methods constructed a highly contiguous assembly with a scaffold N50 length of over 14 megabases, a contig N50 length of over 242 kilobases and a total length of 2.404 gigabases. As a measure of completeness, 95.1\% of 4104 highly conserved mammalian genes were found to be complete within the assembly. Further annotation identified 19,668 protein coding genes. The assembled genome sequence and underlying sequence data can be found at the National Center for Biotechnology Information (NCBI) under the BioProject accession number PRJNA475770.}, |
|
| 5421 | + pmcid = {PMC6678222}, |
|
| 5422 | + file = {/Users/rmorin/Zotero/storage/DQ4D7KUE/Kwan et al. - 2019 - The Genome of the Steller Sea Lion (Eumetopias jub.pdf} |
|
| 5423 | +} |
|
| 5424 | + |
|
| 5425 | +@article{kwanhianMicroRNA142Mutated202012b, |
|
| 5426 | + title = {{{MicroRNA-142}} Is Mutated in about 20\% of Diffuse Large {{B-cell}} Lymphoma}, |
|
| 5427 | + author = {Kwanhian, Wiyada and Lenze, Dido and Alles, Julia and Motsch, Natalie and Barth, Stephanie and Döll, Celina and Imig, Jochen and Hummel, Michael and Tinguely, Marianne and Trivedi, Pankaj and Lulitanond, Viraphong and Meister, Gunter and Renner, Christoph and Grässer, Friedrich A.}, |
|
| 5428 | + date = {2012-10}, |
|
| 5429 | + journaltitle = {Cancer Medicine}, |
|
| 5430 | + shortjournal = {Cancer Med}, |
|
| 5431 | + volume = {1}, |
|
| 5432 | + number = {2}, |
|
| 5433 | + eprint = {23342264}, |
|
| 5434 | + eprinttype = {pmid}, |
|
| 5435 | + pages = {141--155}, |
|
| 5436 | + issn = {2045-7634}, |
|
| 5437 | + doi = {10.1002/cam4.29}, |
|
| 5438 | + abstract = {MicroRNAs (miRNAs) are short 18-23 nucleotide long noncoding RNAs that posttranscriptionally regulate gene expression by binding to mRNA. Our previous miRNA profiling of diffuse large B-cell lymphoma (DLBCL) revealed a mutation in the seed sequence of miR-142-3p. Further analysis now showed that miR-142 was mutated in 11 (19.64\%) of the 56 DLBCL cases. Of these, one case had a mutation in both alleles, with the remainder being heterozygous. Four mutations were found in the mature miR-142-5p, four in the mature miR-142-3p, and three mutations affected the miR-142 precursor. Two mutations in the seed sequence redirected miR-142-3p to the mRNA of the transcriptional repressor ZEB2 and one of them also targeted the ZEB1 mRNA. However, the other mutations in the mature miR-142-3p did not influence either the ZEB1 or ZEB2 3' untranslated region (3' UTR). On the other hand, the mutations affecting the seed sequence of miR-142-3p resulted in a loss of responsiveness in the 3' UTR of the known miR-142-3p targets RAC1 and ADCY9. In contrast to the mouse p300 gene, the human p300 gene was not found to be a target for miR-142-5p. In one case with a mutation of the precursor, we observed aberrant processing of the miR-142-5p. Our data suggest that the mutations in miR-142 probably lead to a loss rather than a gain of function. This is the first report describing mutations of a miRNA gene in a large percentage of a distinct lymphoma subtype.}, |
|
| 5439 | + langid = {english}, |
|
| 5440 | + pmcid = {PMC3544448}, |
|
| 5441 | + keywords = {Animals,Base Sequence,Carcinogenesis,Cell Line,cellular biology,E1A-Associated p300 Protein,genomics,HEK293 Cells,Homeodomain Proteins,Humans,In Situ Hybridization Fluorescence,Lymphoma Large B-Cell Diffuse,Mice,MicroRNAs,molecular genetics,Mutation,rac1 GTP-Binding Protein,Repressor Proteins,RNA Messenger,Sequence Analysis DNA,Transcription Factors,Zinc Finger E-box Binding Homeobox 2,Zinc Finger E-box-Binding Homeobox 1}, |
|
| 5442 | + file = {/Users/rmorin/Zotero/storage/3ADD99BS/Kwanhian et al. - 2012 - MicroRNA-142 is mutated in about 20% of diffuse la.pdf} |
|
| 5443 | +} |
|
| 5444 | + |
|
| 5445 | +@article{kwonOPOSSUM3AdvancedAnalysis2012, |
|
| 5446 | + title = {{{oPOSSUM-3}}: Advanced Analysis of Regulatory Motif over-Representation across Genes or {{ChIP-Seq}} Datasets.}, |
|
| 5447 | + author = {Kwon, Andrew T and Arenillas, David J and Worsley Hunt, Rebecca and Wasserman, Wyeth W}, |
|
| 5448 | + date = {2012-09}, |
|
| 5449 | + journaltitle = {G3 (Bethesda, Md.)}, |
|
| 5450 | + volume = {2}, |
|
| 5451 | + number = {9}, |
|
| 5452 | + pages = {987--1002}, |
|
| 5453 | + keywords = {nosource} |
|
| 5454 | +} |
|
| 5455 | + |
|
| 5456 | +@article{lahtveeAbsoluteQuantificationProtein2017, |
|
| 5457 | + title = {Absolute {{Quantification}} of {{Protein}} and {{mRNA Abundances Demonstrate Variability}} in {{Gene-Specific Translation Efficiency}} in {{Yeast}}}, |
|
| 5458 | + author = {Lahtvee, Petri-Jaan and Sánchez, Benjamín J. and Smialowska, Agata and Kasvandik, Sergo and Elsemman, Ibrahim E. and Gatto, Francesco and Nielsen, Jens}, |
|
| 5459 | + date = {2017-05-24}, |
|
| 5460 | + journaltitle = {Cell Systems}, |
|
| 5461 | + shortjournal = {Cell Syst}, |
|
| 5462 | + volume = {4}, |
|
| 5463 | + number = {5}, |
|
| 5464 | + eprint = {28365149}, |
|
| 5465 | + eprinttype = {pmid}, |
|
| 5466 | + pages = {495-504.e5}, |
|
| 5467 | + issn = {2405-4712}, |
|
| 5468 | + doi = {10.1016/j.cels.2017.03.003}, |
|
| 5469 | + abstract = {Protein synthesis is the most energy-consuming process in a proliferating cell, and understanding what controls protein abundances represents a key question in biology and biotechnology. We quantified absolute abundances of 5,354 mRNAs and 2,198 proteins in Saccharomyces cerevisiae under ten environmental conditions and protein turnover for 1,384 proteins under a reference condition. The overall correlation between mRNA and protein abundances across all conditions was low (0.46), but for differentially expressed proteins (n~= 202), the median mRNA-protein correlation was 0.88. We used these data to model translation efficiencies and found that they vary more than 400-fold between genes. Non-linear regression analysis detected that mRNA abundance and translation elongation were the dominant factors controlling protein synthesis, explaining 61\% and 15\% of its variance. Metabolic flux balance analysis further showed that only mitochondrial fluxes were positively associated with changes at the transcript level. The present dataset represents a crucial expansion to the current resources for future studies on yeast physiology.}, |
|
| 5470 | + langid = {english}, |
|
| 5471 | + keywords = {absolute proteome,absolute transcriptome,genome-scale metabolic modeling,integrative data analysis,protein degradation rates,protein turnover,translation efficiency,translational control} |
|
| 5472 | +} |
|
| 5473 | + |
|
| 5474 | +@article{lakeMutationsNFKBIAEncoding2009, |
|
| 5475 | + title = {Mutations of {{NFKBIA}}, Encoding {{IkappaB}} Alpha, Are a Recurrent Finding in Classical {{Hodgkin}} Lymphoma but Are Not a Unifying Feature of Non-{{EBV-associated}} Cases}, |
|
| 5476 | + author = {Lake, Annette and Shield, Lesley A. and Cordano, Pablo and Chui, Daniel T. Y. and Osborne, Julie and Crae, Shauna and Wilson, Katherine S. and Tosi, Sabrina and Knight, Samantha J. L. and Gesk, Stefan and Siebert, Reiner and Hay, Ron T. and Jarrett, Ruth F.}, |
|
| 5477 | + date = {2009-09-15}, |
|
| 5478 | + journaltitle = {International Journal of Cancer}, |
|
| 5479 | + shortjournal = {Int J Cancer}, |
|
| 5480 | + volume = {125}, |
|
| 5481 | + number = {6}, |
|
| 5482 | + eprint = {19507254}, |
|
| 5483 | + eprinttype = {pmid}, |
|
| 5484 | + pages = {1334--1342}, |
|
| 5485 | + issn = {1097-0215}, |
|
| 5486 | + doi = {10.1002/ijc.24502}, |
|
| 5487 | + abstract = {A consistent feature of the Hodgkin and Reed-Sternberg (HRS) cells in classical Hodgkin lymphoma (cHL) is the constitutive activation of NF-kappaB transcription factors. In Epstein-Barr virus (EBV)-associated cases of cHL, expression of viral antigens most probably leads to NF-kappaB activation but for non-EBV-associated cases, the mechanism is not clear. Previous small studies have demonstrated deleterious mutations of NFKBIA, the gene encoding IkappaB alpha, in HRS cells. In the present study, we aimed to establish the frequency of NFKBIA mutation in cHL by investigating a larger series of cases and to determine whether these mutations are a characteristic feature of non-EBV-associated cHL. Single HRS cells from 20 cases of cHL were analysed by PCRs covering all 6 exons of the gene. Clonal deleterious mutations were detected in 3 cases and in 1 case both alleles of the gene were shown to harbour mutations. NFKBIA mutations were detected only in non-EBV-associated cases but the majority of these cases had wild-type NFKBIA. It remains possible that defects in genes encoding other inhibitors of NF-kappaB, such as TNFAIP3 (A20) and CYLD, are involved in the latter cases, as described for one case in this series.}, |
|
| 5488 | + langid = {english}, |
|
| 5489 | + keywords = {Adolescent,Adult,Aged,Child,Comparative Genomic Hybridization,DNA-Binding Proteins,Epstein-Barr Virus Infections,Female,Gene Expression Profiling,Herpesvirus 4 Human,Hodgkin Disease,Humans,I-kappa B Proteins,Male,Middle Aged,Mutation,NF-KappaB Inhibitor alpha,Oligonucleotide Array Sequence Analysis,Polymorphism Single Nucleotide,Young Adult}, |
|
| 5490 | + file = {/Users/rmorin/Zotero/storage/VSJ3LDSQ/Lake et al. - 2009 - Mutations of NFKBIA, encoding IkappaB alpha, are a.pdf} |
|
| 5491 | +} |
|
| 5492 | + |
|
| 5493 | +@article{laksClonalDecompositionDNA2019, |
|
| 5494 | + title = {Clonal {{Decomposition}} and {{DNA Replication States Defined}} by {{Scaled Single-Cell Genome Sequencing}}}, |
|
| 5495 | + author = {Laks, Emma and McPherson, Andrew and Zahn, Hans and Lai, Daniel and Steif, Adi and Brimhall, Jazmine and Biele, Justina and Wang, Beixi and Masud, Tehmina and Ting, Jerome and Grewal, Diljot and Nielsen, Cydney and Leung, Samantha and Bojilova, Viktoria and Smith, Maia and Golovko, Oleg and Poon, Steven and Eirew, Peter and Kabeer, Farhia and Ruiz de Algara, Teresa and Lee, So Ra and Taghiyar, M. Jafar and Huebner, Curtis and Ngo, Jessica and Chan, Tim and Vatrt-Watts, Spencer and Walters, Pascale and Abrar, Nafis and Chan, Sophia and Wiens, Matt and Martin, Lauren and Scott, R. Wilder and Underhill, T. Michael and Chavez, Elizabeth and Steidl, Christian and Da Costa, Daniel and Ma, Yussanne and Coope, Robin J. N. and Corbett, Richard and Pleasance, Stephen and Moore, Richard and Mungall, Andrew J. and Mar, Colin and Cafferty, Fergus and Gelmon, Karen and Chia, Stephen and {CRUK IMAXT Grand Challenge Team} and Marra, Marco A. and Hansen, Carl and Shah, Sohrab P. and Aparicio, Samuel}, |
|
| 5496 | + date = {2019-11-14}, |
|
| 5497 | + journaltitle = {Cell}, |
|
| 5498 | + shortjournal = {Cell}, |
|
| 5499 | + volume = {179}, |
|
| 5500 | + number = {5}, |
|
| 5501 | + eprint = {31730858}, |
|
| 5502 | + eprinttype = {pmid}, |
|
| 5503 | + pages = {1207-1221.e22}, |
|
| 5504 | + issn = {1097-4172}, |
|
| 5505 | + doi = {10.1016/j.cell.2019.10.026}, |
|
| 5506 | + abstract = {Accurate measurement of clonal genotypes, mutational processes, and replication states from individual tumor-cell genomes will facilitate improved understanding of tumor evolution. We have developed DLP+, a scalable single-cell whole-genome sequencing platform implemented using commodity instruments, image-based object recognition, and open source computational methods. Using DLP+, we have generated a resource of 51,926 single-cell genomes and matched cell images from diverse cell types including cell lines, xenografts, and diagnostic samples with limited material. From this resource we have defined variation in mitotic mis-segregation rates across tissue types and genotypes. Analysis of matched genomic and image measurements revealed correlations between cellular morphology and genome ploidy states. Aggregation of cells sharing copy number profiles allowed for calculation of single-nucleotide resolution clonal genotypes and inference of clonal phylogenies and avoided the limitations of bulk deconvolution. Finally, joint analysis over the above features defined clone-specific chromosomal aneuploidy in polyclonal populations.}, |
|
| 5507 | + langid = {english}, |
|
| 5508 | + pmcid = {PMC6912164}, |
|
| 5509 | + keywords = {aneuploidy,Aneuploidy,Animals,cancer genomics,cell cycle,Cell Cycle,Cell Line Tumor,Cell Shape,Cell Survival,Chromosomes Human,Clone Cells,copy number,Diploidy,DNA Replication,DNA sequencing,DNA Transposable Elements,Female,Genome Human,genomic instability,Genotype,High-Throughput Nucleotide Sequencing,Humans,Male,Mice,Mutation,Phylogeny,Polymorphism Single Nucleotide,single cell,Single-Cell Analysis,tumor evolution,tumor heterogeneity}, |
|
| 5510 | + file = {/Users/rmorin/Zotero/storage/BUGBY4R7/Laks et al. - 2019 - Clonal Decomposition and DNA Replication States De.pdf} |
|
| 5511 | +} |
|
| 5512 | + |
|
| 5513 | +@article{lambertYinYangRNA2019, |
|
| 5514 | + title = {The {{Yin}} and {{Yang}} of {{RNA}} Surveillance in {{B}} Lymphocytes and Antibody-Secreting Plasma Cells}, |
|
| 5515 | + author = {Lambert, Jean-Marie and Srour, Nivine and Delpy, Laurent}, |
|
| 5516 | + date = {2019-12}, |
|
| 5517 | + journaltitle = {BMB Reports}, |
|
| 5518 | + shortjournal = {BMB Rep}, |
|
| 5519 | + volume = {52}, |
|
| 5520 | + number = {12}, |
|
| 5521 | + eprint = {31619318}, |
|
| 5522 | + eprinttype = {pmid}, |
|
| 5523 | + pages = {671--678}, |
|
| 5524 | + issn = {1976-6696}, |
|
| 5525 | + doi = {10.5483/BMBRep.2019.52.12.232}, |
|
| 5526 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6941761/}, |
|
| 5527 | + urldate = {2022-10-25}, |
|
| 5528 | + abstract = {The random V(D)J recombination process ensures the diversity of the primary immunoglobulin (Ig) repertoire. In two thirds of cases, imprecise recombination between variable (V), diversity (D), and joining (J) segments induces a frameshift in the open reading frame that leads to the appearance of premature termination codons (PTCs). Thus, many B lineage cells harbour biallelic V(D)J-rearrangements of Ig heavy or light chain genes, with a productively-recombined allele encoding the functional Ig chain and a nonproductive allele potentially encoding truncated Ig polypeptides. Since the pattern of Ig gene expression is mostly biallelic, transcription initiated from nonproductive Ig alleles generates considerable amounts of primary transcripts with out-of-frame V(D)J junctions. How RNA surveillance pathways cooperate to control the noise from nonproductive Ig genes will be discussed in this review, focusing on the benefits of nonsense-mediated mRNA decay (NMD) activation during B-cell development and detrimental effects of nonsense-associated altered splicing (NAS) in terminally differentiated plasma cells.}, |
|
| 5529 | + pmcid = {PMC6941761}, |
|
| 5530 | + file = {/Users/rmorin/Zotero/storage/IS2C8IMG/Lambert et al. - 2019 - The Yin and Yang of RNA surveillance in B lymphocy.pdf} |
|
| 5531 | +} |
|
| 5532 | + |
|
| 5533 | +@article{lamSmallMoleculeInhibitors, |
|
| 5534 | + title = {Small Molecule Inhibitors of {{IkappaB}} Kinase Are Selectively Toxic for Subgroups of Diffuse Large {{B-cell}} Lymphoma Defined by Gene Expression Profiling.}, |
|
| 5535 | + author = {Lam, Lloyd T and Davis, R Eric and Pierce, Jackie and Hepperle, Michael and Xu, Yajun and Hottelet, Maria and Nong, Yuhua and Wen, Danyi and Adams, Julian and Dang, Lenny and Staudt, Louis M}, |
|
| 5536 | + journaltitle = {Clin Cancer Res}, |
|
| 5537 | + volume = {11}, |
|
| 5538 | + number = {1}, |
|
| 5539 | + pages = {28--40}, |
|
| 5540 | + keywords = {nosource} |
|
| 5541 | +} |
|
| 5542 | + |
|
| 5543 | +@article{lawrenceDiscoverySaturationAnalysis2014, |
|
| 5544 | + title = {Discovery and Saturation Analysis of Cancer Genes across 21 Tumour Types}, |
|
| 5545 | + author = {Lawrence, Michael S. and Stojanov, Petar and Mermel, Craig H. and Robinson, James T. and Garraway, Levi A. and Golub, Todd R. and Meyerson, Matthew and Gabriel, Stacey B. and Lander, Eric S. and Getz, Gad}, |
|
| 5546 | + date = {2014-01-23}, |
|
| 5547 | + journaltitle = {Nature}, |
|
| 5548 | + shortjournal = {Nature}, |
|
| 5549 | + volume = {505}, |
|
| 5550 | + number = {7484}, |
|
| 5551 | + eprint = {24390350}, |
|
| 5552 | + eprinttype = {pmid}, |
|
| 5553 | + pages = {495--501}, |
|
| 5554 | + issn = {1476-4687}, |
|
| 5555 | + doi = {10.1038/nature12912}, |
|
| 5556 | + abstract = {Although a few cancer genes are mutated in a high proportion of tumours of a given type ({$>$}20\%), most are mutated at intermediate frequencies (2-20\%). To explore the feasibility of creating a comprehensive catalogue of cancer genes, we analysed somatic point mutations in exome sequences from 4,742 human cancers and their matched normal-tissue samples across 21 cancer types. We found that large-scale genomic analysis can identify nearly all known cancer genes in these tumour types. Our analysis also identified 33 genes that were not previously known to be significantly mutated in cancer, including genes related to proliferation, apoptosis, genome stability, chromatin regulation, immune evasion, RNA processing and protein homeostasis. Down-sampling analysis indicates that larger sample sizes will reveal many more genes mutated at clinically important frequencies. We estimate that near-saturation may be achieved with 600-5,000 samples per tumour type, depending on background mutation frequency. The results may help to guide the next stage of cancer genomics.}, |
|
| 5557 | + langid = {english}, |
|
| 5558 | + pmcid = {PMC4048962}, |
|
| 5559 | + keywords = {Apoptosis,Case-Control Studies,Cell Proliferation,Chromatin,DNA Mutational Analysis,Exome,Genes Neoplasm,Genome Human,Genomic Instability,Genomics,Humans,Immune Evasion,Mutation Rate,Neoplasms,Point Mutation,RNA Processing Post-Transcriptional,Sample Size}, |
|
| 5560 | + file = {/Users/rmorin/Zotero/storage/EPQ45MDH/Lawrence et al. - 2014 - Discovery and saturation analysis of cancer genes .pdf} |
|
| 5561 | +} |
|
| 5562 | + |
|
| 5563 | +@article{lawrenceMutationalHeterogeneityCancer2013, |
|
| 5564 | + title = {Mutational Heterogeneity in Cancer and the Search for New Cancer-Associated Genes}, |
|
| 5565 | + author = {Lawrence, Michael S. and Stojanov, Petar and Polak, Paz and Kryukov, Gregory V. and Cibulskis, Kristian and Sivachenko, Andrey and Carter, Scott L. and Stewart, Chip and Mermel, Craig H. and Roberts, Steven A. and Kiezun, Adam and Hammerman, Peter S. and McKenna, Aaron and Drier, Yotam and Zou, Lihua and Ramos, Alex H. and Pugh, Trevor J. and Stransky, Nicolas and Helman, Elena and Kim, Jaegil and Sougnez, Carrie and Ambrogio, Lauren and Nickerson, Elizabeth and Shefler, Erica and Cortés, Maria L. and Auclair, Daniel and Saksena, Gordon and Voet, Douglas and Noble, Michael and DiCara, Daniel and Lin, Pei and Lichtenstein, Lee and Heiman, David I. and Fennell, Timothy and Imielinski, Marcin and Hernandez, Bryan and Hodis, Eran and Baca, Sylvan and Dulak, Austin M. and Lohr, Jens and Landau, Dan-Avi and Wu, Catherine J. and Melendez-Zajgla, Jorge and Hidalgo-Miranda, Alfredo and Koren, Amnon and McCarroll, Steven A. and Mora, Jaume and Lee, Ryan S. and Crompton, Brian and Onofrio, Robert and Parkin, Melissa and Winckler, Wendy and Ardlie, Kristin and Gabriel, Stacey B. and Roberts, Charles W. M. and Biegel, Jaclyn A. and Stegmaier, Kimberly and Bass, Adam J. and Garraway, Levi A. and Meyerson, Matthew and Golub, Todd R. and Gordenin, Dmitry A. and Sunyaev, Shamil and Lander, Eric S. and Getz, Gad}, |
|
| 5566 | + date = {2013-07}, |
|
| 5567 | + journaltitle = {Nature}, |
|
| 5568 | + volume = {499}, |
|
| 5569 | + number = {7457}, |
|
| 5570 | + pages = {214--218}, |
|
| 5571 | + issn = {1476-4687}, |
|
| 5572 | + doi = {10.1038/nature12213}, |
|
| 5573 | + url = {https://www.nature.com/articles/nature12213}, |
|
| 5574 | + urldate = {2019-12-21}, |
|
| 5575 | + abstract = {As the sample size in cancer genome studies increases, the list of genes identified as significantly mutated is likely to include more false positives; here, this problem is identified as stemming largely from mutation heterogeneity, and a new analytical methodology designed to overcome this problem is described.}, |
|
| 5576 | + langid = {english}, |
|
| 5577 | + file = {/Users/rmorin/Zotero/storage/SWDMW46Q/nature12213.html} |
|
| 5578 | +} |
|
| 5579 | + |
|
| 5580 | +@article{lawrieDetectionElevatedLevels2008, |
|
| 5581 | + title = {Detection of Elevated Levels of Tumour-Associated {{microRNAs}} in Serum of Patients with Diffuse Large {{B-cell}} Lymphoma}, |
|
| 5582 | + author = {Lawrie, Charles and Gal, Shira and Dunlop, Heather and Pushkaran, Beena and Liggins, Amanda and Pulford, Karen and Banham, Alison and Pezzella, Francesco and Boultwood, Jacqueline and Wainscoat, James and Hatton, Christian and Harris, Adrian}, |
|
| 5583 | + date = {2008}, |
|
| 5584 | + journaltitle = {Br J Haematol}, |
|
| 5585 | + volume = {141}, |
|
| 5586 | + number = {5}, |
|
| 5587 | + pages = {672--675}, |
|
| 5588 | + keywords = {nosource} |
|
| 5589 | +} |
|
| 5590 | + |
|
| 5591 | +@article{leeExpressionInhibitoryFc2015, |
|
| 5592 | + title = {Expression of the Inhibitory {{Fc}} Gamma Receptor {{IIB}} ({{FCGR2B}}, {{CD32B}}) on Follicular Lymphoma Cells Lowers the Response Rate to Rituximab Monotherapy ({{SAKK}} 35/98).}, |
|
| 5593 | + author = {Lee, Chern Siang and Ashton-Key, Margaret and Cogliatti, Sergio and Rondeau, Stephanie and Schmitz, Shu-Fang Hsu and Ghielmini, Michele and Cragg, Mark S and Johnson, Peter}, |
|
| 5594 | + date = {2015-01}, |
|
| 5595 | + journaltitle = {Br J Haematol}, |
|
| 5596 | + volume = {168}, |
|
| 5597 | + number = {1}, |
|
| 5598 | + pages = {145--148}, |
|
| 5599 | + keywords = {nosource} |
|
| 5600 | +} |
|
| 5601 | + |
|
| 5602 | +@article{leeGainoffunctionMutationsCopy2009, |
|
| 5603 | + title = {Gain-of-Function Mutations and Copy Number Increases of {{Notch2}} in Diffuse Large {{B-cell}} Lymphoma.}, |
|
| 5604 | + author = {Lee, Suk-Young and Kumano, Keiki and Nakazaki, Kumi and Sanada, Masashi and Matsumoto, Akihiko and Yamamoto, Go and Nannya, Yasuhito and Suzuki, Ritsuro and Ota, Satoshi and Ota, Yasunori and Izutsu, Koji and Sakata-Yanagimoto, Mamiko and Hangaishi, Akira and Yagita, Hideo and Fukayama, Masashi and Seto, Masao and Kurokawa, Mineo and Ogawa, Seishi and Chiba, Shigeru}, |
|
| 5605 | + date = {2009-05}, |
|
| 5606 | + journaltitle = {Cancer Sci}, |
|
| 5607 | + volume = {100}, |
|
| 5608 | + number = {5}, |
|
| 5609 | + pages = {920--926}, |
|
| 5610 | + keywords = {nosource} |
|
| 5611 | +} |
|
| 5612 | + |
|
| 5613 | +@article{leeGenomedefinedAfricanAncestry2020, |
|
| 5614 | + title = {Genome-Defined {{African}} Ancestry Is Associated with Distinct Mutations and Worse Survival in Patients with Diffuse Large {{B-cell}} Lymphoma}, |
|
| 5615 | + author = {Lee, Michelle J. and Koff, Jean L. and Switchenko, Jeffrey M. and Jhaney, C. Ileen and Harkins, R. Andrew and Patel, Sharvil P. and Dave, Sandeep S. and Flowers, Christopher R.}, |
|
| 5616 | + date = {2020-08-01}, |
|
| 5617 | + journaltitle = {Cancer}, |
|
| 5618 | + shortjournal = {Cancer}, |
|
| 5619 | + volume = {126}, |
|
| 5620 | + number = {15}, |
|
| 5621 | + eprint = {32469082}, |
|
| 5622 | + eprinttype = {pmid}, |
|
| 5623 | + pages = {3493--3503}, |
|
| 5624 | + issn = {1097-0142}, |
|
| 5625 | + doi = {10.1002/cncr.32866}, |
|
| 5626 | + abstract = {BACKGROUND: Significant racial differences have been observed in the incidence and clinical outcomes of diffuse large B-cell lymphoma (DLBCL) in the United States, but to the authors' knowledge it remains unclear whether genomic differences contribute to these disparities. METHODS: To understand the influences of genetic ancestry on tumor genomic alterations, the authors estimated the genetic ancestry of 1001 previously described patients with DLBCL using unsupervised model-based Admixture global ancestry analysis applied to exome sequencing data and examined the mutational profile of 150 DLBCL driver genes in tumors obtained from this cohort. RESULTS: Global ancestry prediction identified 619 patients with {$>$}90\% European ancestry, 81 patients with {$>$}90\% African ancestry, and 50 patients with {$>$}90\% Asian ancestry. Compared with patients with DLBCL with European ancestry, patients with African ancestry were aged {$>$}10~years younger at the time of diagnosis and were more likely to present with B symptoms, elevated serum lactate dehydrogenase, extranodal disease, and advanced stage disease. Patients with African ancestry demonstrated worse overall survival compared with patients with European ancestry (median, 4.9~years vs 8.8~years; P~=~.04). Recurrent mutations of MLL2 (KMT2D), HIST1H1E, MYD88, BCL2, and PIM1 were found across all ancestry groups, suggesting shared mechanisms underlying tumor biology. The authors also identified 6 DLBCL driver genes that were more commonly mutated in patients with African ancestry compared with patients with European ancestry: ATM (21.0\% vs 7.75\%; P~{$<~$}.001), MGA (19.7\% vs 5.33\%; P~{$<~$}.001), SETD2 (17.3\% vs 5.17\%; P~{$<~$}.001), TET2 (12.3\% vs 5.82\%; P~=~.029), MLL3 (KMT2C) (11.1\% vs 4.36\%; P~=~.013), and DNMT3A (11.1\% vs 4.52\%; P~=~.016). CONCLUSIONS: Distinct prevalence and patterns of mutation highlight an important difference in the mutational landscapes of DLBCL arising in different ancestry groups. To the authors' knowledge, the results of the current study provide the first-ever characterization of genetic alterations among patients with African descent who are diagnosed with DLBCL.}, |
|
| 5627 | + langid = {english}, |
|
| 5628 | + pmcid = {PMC7494053}, |
|
| 5629 | + keywords = {Adult,African continental ancestry group,Aged,Asians,Blacks,Cohort Studies,diffuse large B-cell lymphoma,Disease-Free Survival,DNA-Binding Proteins,Exome,Female,Genome Human,Histones,Humans,Lymphoma Large B-Cell Diffuse,Male,Middle Aged,mutation,Mutation,Myeloid Differentiation Factor 88,Neoplasm Proteins,Prognosis,Proto-Oncogene Proteins c-bcl-2,racial factors,Whites,Whole Exome Sequencing,Young Adult}, |
|
| 5630 | + file = {/Users/rmorin/Zotero/storage/59EWS5GS/Lee et al. - 2020 - Genome-defined African ancestry is associated with.pdf} |
|
| 5631 | +} |
|
| 5632 | + |
|
| 5633 | +@article{lefaveSplicingFactorHnRNPH2011, |
|
| 5634 | + title = {Splicing Factor {{hnRNPH}} Drives an Oncogenic Splicing Switch in Gliomas}, |
|
| 5635 | + author = {LeFave, Clare V and Squatrito, Massimo and Vorlova, Sandra and Rocco, Gina L and Brennan, Cameron W and Holland, Eric C and Pan, Ying-Xian and Cartegni, Luca}, |
|
| 5636 | + date = {2011-10-05}, |
|
| 5637 | + journaltitle = {The EMBO Journal}, |
|
| 5638 | + shortjournal = {The EMBO Journal}, |
|
| 5639 | + volume = {30}, |
|
| 5640 | + number = {19}, |
|
| 5641 | + pages = {4084--4097}, |
|
| 5642 | + issn = {0261-4189}, |
|
| 5643 | + doi = {10.1038/emboj.2011.259}, |
|
| 5644 | + url = {https://www.embopress.org/doi/10.1038/emboj.2011.259}, |
|
| 5645 | + urldate = {2019-12-21}, |
|
| 5646 | + abstract = {In tumours, aberrant splicing generates variants that contribute to multiple aspects of tumour establishment, progression and maintenance. We show that in glioblastoma multiforme (GBM) specimens, death-domain adaptor protein Insuloma-Glucagonoma protein 20 (IG20) is consistently aberrantly spliced to generate an antagonist, anti-apoptotic isoform (MAP-kinase activating death domain protein, MADD), which effectively redirects TNF-α/TRAIL-induced death signalling to promote survival and proliferation instead of triggering apoptosis. Splicing factor hnRNPH, which is upregulated in gliomas, controls this splicing event and similarly mediates switching to a ligand-independent, constitutively active Recepteur d?Origine Nantais (RON) tyrosine kinase receptor variant that promotes migration and invasion. The increased cell death and the reduced invasiveness caused by hnRNPH ablation can be rescued by the targeted downregulation of IG20/MADD exon 16- or RON exon 11-containing variants, respectively, using isoform-specific knockdown or splicing redirection approaches. Thus, hnRNPH activity appears to be involved in the pathogenesis and progression of malignant gliomas as the centre of a splicing oncogenic switch, which might reflect reactivation of stem cell patterns and mediates multiple key aspects of aggressive tumour behaviour, including evasion from apoptosis and invasiveness.}, |
|
| 5647 | + keywords = {antisense,cancer,FSD-NMD,hnRNPH,MADD,RON,splicing}, |
|
| 5648 | + file = {/Users/rmorin/Zotero/storage/GNAHQRIC/emboj.2011.html} |
|
| 5649 | +} |
|
| 5650 | + |
|
| 5651 | +@article{lefrancIMGTInternationalImMunoGeneTics2015, |
|
| 5652 | + title = {{{IMGT}}®, the International {{ImMunoGeneTics}} Information System® 25 Years On}, |
|
| 5653 | + author = {Lefranc, Marie-Paule and Giudicelli, Véronique and Duroux, Patrice and Jabado-Michaloud, Joumana and Folch, Géraldine and Aouinti, Safa and Carillon, Emilie and Duvergey, Hugo and Houles, Amélie and Paysan-Lafosse, Typhaine and Hadi-Saljoqi, Saida and Sasorith, Souphatta and Lefranc, Gérard and Kossida, Sofia}, |
|
| 5654 | + date = {2015-01}, |
|
| 5655 | + journaltitle = {Nucleic Acids Research}, |
|
| 5656 | + shortjournal = {Nucleic Acids Res}, |
|
| 5657 | + volume = {43}, |
|
| 5658 | + eprint = {25378316}, |
|
| 5659 | + eprinttype = {pmid}, |
|
| 5660 | + pages = {D413-422}, |
|
| 5661 | + issn = {1362-4962}, |
|
| 5662 | + doi = {10.1093/nar/gku1056}, |
|
| 5663 | + abstract = {IMGT(®), the international ImMunoGeneTics information system(®)(http://www.imgt.org) is the global reference in immunogenetics and immunoinformatics. By its creation in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS), IMGT(®) marked the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. IMGT(®) is specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) and proteins of the IgSF and MhSF superfamilies. IMGT(®) is built on the IMGT-ONTOLOGY axioms and concepts, which bridged the gap between genes, sequences and 3D structures. The concepts include the IMGT(®) standardized keywords (identification), IMGT(®) standardized labels (description), IMGT(®) standardized nomenclature (classification), IMGT unique numbering and IMGT Colliers de Perles (numerotation). IMGT(®) comprises 7 databases, 17 online tools and 15,000 pages of web resources, and provides a high-quality and integrated system for analysis of the genomic and expressed IG and TR repertoire of the adaptive immune responses, including NGS high-throughput data. Tools and databases are used in basic, veterinary and medical research, in clinical applications (mutation analysis in leukemia and lymphoma) and in antibody engineering and humanization. The IMGT/mAb-DB interface was developed for therapeutic antibodies and fusion proteins for immunological applications (FPIA). IMGT(®) is freely available at http://www.imgt.org.}, |
|
| 5664 | + issue = {Database issue}, |
|
| 5665 | + langid = {english}, |
|
| 5666 | + pmcid = {PMC4383898}, |
|
| 5667 | + keywords = {Alleles,Animals,Biological Ontologies,Computational Biology,Databases Genetic,Genes Immunoglobulin,Genes T-Cell Receptor,Histocompatibility Antigens,Humans,Immunogenetics,Immunoglobulins,Internet,Major Histocompatibility Complex,Receptors Antigen T-Cell,Software}, |
|
| 5668 | + file = {/Users/rmorin/Zotero/storage/H9GXVXH6/Lefranc et al. - 2015 - IMGT®, the international ImMunoGeneTics informatio.pdf} |
|
| 5669 | +} |
|
| 5670 | + |
|
| 5671 | +@article{leiCancerMutationD83V2018, |
|
| 5672 | + title = {The {{Cancer Mutation D83V Induces}} an α-{{Helix}} to β-{{Strand Conformation Switch}} in {{MEF2B}}}, |
|
| 5673 | + author = {Lei, Xiao and Kou, Yi and Fu, Yang and Rajashekar, Niroop and Shi, Haoran and Wu, Fang and Xu, Jiang and Luo, Yibing and Chen, Lin}, |
|
| 5674 | + date = {2018-04-13}, |
|
| 5675 | + journaltitle = {Journal of Molecular Biology}, |
|
| 5676 | + shortjournal = {J. Mol. Biol.}, |
|
| 5677 | + volume = {430}, |
|
| 5678 | + number = {8}, |
|
| 5679 | + eprint = {29477338}, |
|
| 5680 | + eprinttype = {pmid}, |
|
| 5681 | + pages = {1157--1172}, |
|
| 5682 | + issn = {1089-8638}, |
|
| 5683 | + doi = {10.1016/j.jmb.2018.02.012}, |
|
| 5684 | + abstract = {MEF2B is a major target of somatic mutations in non-Hodgkin lymphoma. Most of these mutations are non-synonymous substitutions of surface residues in the MADS-box/MEF2 domain. Among them, D83V is the most frequent mutation found in tumor cells. The link between this hotspot mutation and cancer is not well understood. Here we show that the D83V mutation induces a dramatic α-helix to β-strand switch in the MEF2 domain. Located in an α-helix region rich in β-branched residues, the D83V mutation not only removes the extensive helix stabilization interactions but also introduces an additional β-branched residue that further shifts the conformation equilibrium from α-helix to β-strand. Cross-database analyses of cancer mutations and chameleon sequences revealed a number of well-known cancer targets harboring β-strand favoring mutations in chameleon α-helices, suggesting a commonality of such conformational switch in certain cancers and a new factor to consider when stratifying the rapidly expanding cancer mutation data.}, |
|
| 5685 | + langid = {english}, |
|
| 5686 | + keywords = {Amino Acid Substitution,cancer mutation,Crystallography X-Ray,Humans,lymphoma,Lymphoma Non-Hodgkin,MEF2 Transcription Factors,MEF2B,metamorphic protein structure,Models Molecular,Protein Conformation alpha-Helical,Protein Conformation beta-Strand,protein conformation change,Protein Domains} |
|
| 5687 | +} |
|
| 5688 | + |
|
| 5689 | +@article{lenzAberrantImmunoglobulinClass2007, |
|
| 5690 | + title = {Aberrant Immunoglobulin Class Switch Recombination and Switch Translocations in Activated {{B}} Cell-like Diffuse Large {{B}} Cell Lymphoma}, |
|
| 5691 | + author = {Lenz, G and Nagel, I and Siebert, R and Roschke, A and Sanger, W and Wright, G and Dave, S and Tan, B and Zhao, H and Rosenwald, A and Muller-Hermelink, H and Gascoyne, R and Campo, E and Jaffe, E and Smeland, E and Fisher, R and Kuehl, W and Chan, W and Staudt, L}, |
|
| 5692 | + date = {2007}, |
|
| 5693 | + journaltitle = {J Exp Med}, |
|
| 5694 | + volume = {204}, |
|
| 5695 | + number = {3}, |
|
| 5696 | + pages = {633--643}, |
|
| 5697 | + keywords = {nosource} |
|
| 5698 | +} |
|
| 5699 | + |
|
| 5700 | +@article{lenzMolecularSubtypesDiffuse2008, |
|
| 5701 | + title = {Molecular Subtypes of Diffuse Large {{B-cell}} Lymphoma Arise by Distinct Genetic Pathways}, |
|
| 5702 | + author = {Lenz, Georg and Wright, George W. and Emre, N. C. Tolga and Kohlhammer, Holger and Dave, Sandeep S. and Davis, R. Eric and Carty, Shannon and Lam, Lloyd T. and Shaffer, A. L. and Xiao, Wenming and Powell, John and Rosenwald, Andreas and Ott, German and Muller-Hermelink, Hans Konrad and Gascoyne, Randy D. and Connors, Joseph M. and Campo, Elias and Jaffe, Elaine S. and Delabie, Jan and Smeland, Erlend B. and Rimsza, Lisa M. and Fisher, Richard I. and Weisenburger, Dennis D. and Chan, Wing C. and Staudt, Louis M.}, |
|
| 5703 | + date = {2008-09-09}, |
|
| 5704 | + journaltitle = {Proceedings of the National Academy of Sciences}, |
|
| 5705 | + shortjournal = {Proc Natl Acad Sci}, |
|
| 5706 | + volume = {105}, |
|
| 5707 | + number = {36}, |
|
| 5708 | + eprint = {18765795}, |
|
| 5709 | + eprinttype = {pmid}, |
|
| 5710 | + pages = {13520--13525}, |
|
| 5711 | + issn = {1091-6490}, |
|
| 5712 | + doi = {10.1073/pnas.0804295105}, |
|
| 5713 | + abstract = {Gene-expression profiling has been used to define 3 molecular subtypes of diffuse large B-cell lymphoma (DLBCL), termed germinal center B-cell-like (GCB) DLBCL, activated B-cell-like (ABC) DLBCL, and primary mediastinal B-cell lymphoma (PMBL). To investigate whether these DLBCL subtypes arise by distinct pathogenetic mechanisms, we analyzed 203 DLBCL biopsy samples by high-resolution, genome-wide copy number analysis coupled with gene-expression profiling. Of 272 recurrent chromosomal aberrations that were associated with gene-expression alterations, 30 were used differentially by the DLBCL subtypes (P {$<$} 0.006). An amplicon on chromosome 19 was detected in 26\% of ABC DLBCLs but in only 3\% of GCB DLBCLs and PMBLs. A highly up-regulated gene in this amplicon was SPIB, which encodes an ETS family transcription factor. Knockdown of SPIB by RNA interference was toxic to ABC DLBCL cell lines but not to GCB DLBCL, PMBL, or myeloma cell lines, strongly implicating SPIB as an oncogene involved in the pathogenesis of ABC DLBCL. Deletion of the INK4a/ARF tumor suppressor locus and trisomy 3 also occurred almost exclusively in ABC DLBCLs and was associated with inferior outcome within this subtype. FOXP1 emerged as a potential oncogene in ABC DLBCL that was up-regulated by trisomy 3 and by more focal high-level amplifications. In GCB DLBCL, amplification of the oncogenic mir-17-92 microRNA cluster and deletion of the tumor suppressor PTEN were recurrent, but these events did not occur in ABC DLBCL. Together, these data provide genetic evidence that the DLBCL subtypes are distinct diseases that use different oncogenic pathways.}, |
|
| 5714 | + langid = {english}, |
|
| 5715 | + pmcid = {PMC2533222}, |
|
| 5716 | + keywords = {Biopsy,Cell Survival,Chromosome Aberrations,Gene Expression Profiling,Gene Expression Regulation Neoplastic,Genome Human,Humans,Lymphoma Large B-Cell Diffuse,Oncogene Proteins,Prognosis,Tumor Suppressor Proteins}, |
|
| 5717 | + file = {/Users/rmorin/Zotero/storage/8JSCAVNK/Lenz et al. - 2008 - Molecular subtypes of diffuse large B-cell lymphom.pdf} |
|
| 5718 | +} |
|
| 5719 | + |
|
| 5720 | +@article{lenzOncogenicCARD11Mutations2008, |
|
| 5721 | + title = {Oncogenic {{CARD11}} Mutations in Human Diffuse Large {{B}} Cell Lymphoma.}, |
|
| 5722 | + author = {Lenz, Georg and Davis, R Eric and Ngo, Vu N and Lam, Lloyd and George, Thaddeus C and Wright, George W and Dave, Sandeep S and Zhao, Hong and Xu, Weihong and Rosenwald, Andreas and Ott, German and Müller-Hermelink, Hans-Konrad and Gascoyne, Randy D and Connors, Joseph M and Rimsza, Lisa M and Campo, Elias and Jaffe, Elaine S and Delabie, Jan and Smeland, Erlend B and Fisher, Richard I and Chan, Wing C and Staudt, Louis M}, |
|
| 5723 | + date = {2008-03}, |
|
| 5724 | + journaltitle = {Science}, |
|
| 5725 | + volume = {319}, |
|
| 5726 | + number = {5870}, |
|
| 5727 | + pages = {1676--1679}, |
|
| 5728 | + keywords = {nosource} |
|
| 5729 | +} |
|
| 5730 | + |
|
| 5731 | +@article{lenzStromalGeneSignatures2008, |
|
| 5732 | + title = {Stromal Gene Signatures in Large-{{B-cell}} Lymphomas}, |
|
| 5733 | + author = {Lenz, G. and Wright, G. and Dave, S. S. and Xiao, W. and Powell, J. and Zhao, H. and Xu, W. and Tan, B. and Goldschmidt, N. and Iqbal, J. and Vose, J. and Bast, M. and Fu, K. and Weisenburger, D. D. and Greiner, T. C. and Armitage, J. O. and Kyle, A. and May, L. and Gascoyne, R. D. and Connors, J. M. and Troen, G. and Holte, H. and Kvaloy, S. and Dierickx, D. and Verhoef, G. and Delabie, J. and Smeland, E. B. and Jares, P. and Martinez, A. and Lopez-Guillermo, A. and Montserrat, E. and Campo, E. and Braziel, R. M. and Miller, T. P. and Rimsza, L. M. and Cook, J. R. and Pohlman, B. and Sweetenham, J. and Tubbs, R. R. and Fisher, R. I. and Hartmann, E. and Rosenwald, A. and Ott, G. and Muller-Hermelink, H.-K. and Wrench, D. and Lister, T. A. and Jaffe, E. S. and Wilson, W. H. and Chan, W. C. and Staudt, L. M. and {Lymphoma/Leukemia Molecular Profiling Project}}, |
|
| 5734 | + date = {2008-11-27}, |
|
| 5735 | + journaltitle = {The New England Journal of Medicine}, |
|
| 5736 | + shortjournal = {N. Engl. J. Med.}, |
|
| 5737 | + volume = {359}, |
|
| 5738 | + number = {22}, |
|
| 5739 | + eprint = {19038878}, |
|
| 5740 | + eprinttype = {pmid}, |
|
| 5741 | + pages = {2313--2323}, |
|
| 5742 | + issn = {1533-4406}, |
|
| 5743 | + doi = {10.1056/NEJMoa0802885}, |
|
| 5744 | + abstract = {BACKGROUND: The addition of rituximab to combination chemotherapy with cyclophosphamide, doxorubicin, vincristine, and prednisone (CHOP), or R-CHOP, has significantly improved the survival of patients with diffuse large-B-cell lymphoma. Whether gene-expression signatures correlate with survival after treatment of diffuse large-B-cell lymphoma is unclear. METHODS: We profiled gene expression in pretreatment biopsy specimens from 181 patients with diffuse large-B-cell lymphoma who received CHOP and 233 patients with this disease who received R-CHOP. A multivariate gene-expression-based survival-predictor model derived from a training group was tested in a validation group. RESULTS: A multivariate model created from three gene-expression signatures--termed "germinal-center B-cell," "stromal-1," and "stromal-2"--predicted survival both in patients who received CHOP and patients who received R-CHOP. The prognostically favorable stromal-1 signature reflected extracellular-matrix deposition and histiocytic infiltration. By contrast, the prognostically unfavorable stromal-2 signature reflected tumor blood-vessel density. CONCLUSIONS: Survival after treatment of diffuse large-B-cell lymphoma is influenced by differences in immune cells, fibrosis, and angiogenesis in the tumor microenvironment.}, |
|
| 5745 | + langid = {english}, |
|
| 5746 | + keywords = {Antibodies Monoclonal,Antibodies Monoclonal Murine-Derived,Antineoplastic Combined Chemotherapy Protocols,Cyclophosphamide,Disease Progression,Doxorubicin,Extracellular Matrix,Gene Expression,Gene Expression Profiling,Gene Expression Regulation Neoplastic,Genes MHC Class II,Germinal Center,Humans,Immunologic Factors,Kaplan-Meier Estimate,Lymphoma Large B-Cell Diffuse,Middle Aged,Multivariate Analysis,Neovascularization Pathologic,Prednisone,Prognosis,Rituximab,Stromal Cells,Vincristine} |
|
| 5747 | +} |
|
| 5748 | + |
|
| 5749 | +@article{leonardTargetedTreatmentNew2008, |
|
| 5750 | + title = {Targeted Treatment and New Agents in Diffuse Large {{B-cell}} Lymphoma}, |
|
| 5751 | + author = {Leonard, John P and Martin, Peter and Barrientos, Jacqueline and Elstrom, Rebecca}, |
|
| 5752 | + date = {2008-07}, |
|
| 5753 | + journaltitle = {Seminars in hematology}, |
|
| 5754 | + volume = {45}, |
|
| 5755 | + pages = {S11--6}, |
|
| 5756 | + issue = {3 Suppl 2}, |
|
| 5757 | + keywords = {nosource} |
|
| 5758 | +} |
|
| 5759 | + |
|
| 5760 | +@article{liAligningSequenceReads2013, |
|
| 5761 | + title = {Aligning Sequence Reads, Clone Sequences and Assembly Contigs with {{BWA-MEM}}}, |
|
| 5762 | + author = {Li, Heng}, |
|
| 5763 | + date = {2013-03-16}, |
|
| 5764 | + journaltitle = {arXiv}, |
|
| 5765 | + volume = {arXiv:1303.3997}, |
|
| 5766 | + eprint = {1303.3997}, |
|
| 5767 | + eprinttype = {arxiv}, |
|
| 5768 | + url = {http://arxiv.org/abs/1303.3997}, |
|
| 5769 | + urldate = {2019-07-08}, |
|
| 5770 | + abstract = {Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads and performs chimeric alignment. The algorithm is robust to sequencing errors and applicable to a wide range of sequence lengths from 70bp to a few megabases. For mapping 100bp sequences, BWA-MEM shows better performance than several state-of-art read aligners to date. Availability and implementation: BWA-MEM is implemented as a component of BWA, which is available at http://github.com/lh3/bwa. Contact: hengli@broadinstitute.org}, |
|
| 5771 | + keywords = {Quantitative Biology - Genomics}, |
|
| 5772 | + file = {/Users/rmorin/Zotero/storage/IA9ACMDB/1303.html} |
|
| 5773 | +} |
|
| 5774 | + |
|
| 5775 | +@article{liaoFeatureCountsEfficientGeneral2014, |
|
| 5776 | + title = {{{featureCounts}}: An Efficient General Purpose Program for Assigning Sequence Reads to Genomic Features}, |
|
| 5777 | + shorttitle = {{{featureCounts}}}, |
|
| 5778 | + author = {Liao, Yang and Smyth, Gordon K. and Shi, Wei}, |
|
| 5779 | + date = {2014-04-01}, |
|
| 5780 | + journaltitle = {Bioinformatics (Oxford, England)}, |
|
| 5781 | + shortjournal = {Bioinformatics}, |
|
| 5782 | + volume = {30}, |
|
| 5783 | + number = {7}, |
|
| 5784 | + eprint = {24227677}, |
|
| 5785 | + eprinttype = {pmid}, |
|
| 5786 | + pages = {923--930}, |
|
| 5787 | + issn = {1367-4811}, |
|
| 5788 | + doi = {10.1093/bioinformatics/btt656}, |
|
| 5789 | + abstract = {MOTIVATION: Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to each genomic feature, for example to each exon or each gene. The process of counting reads is called read summarization. Read summarization is required for a great variety of genomic analyses but has so far received relatively little attention in the literature. RESULTS: We present featureCounts, a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments. featureCounts implements highly efficient chromosome hashing and feature blocking techniques. It is considerably faster than existing methods (by an order of magnitude for gene-level summarization) and requires far less computer memory. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications. AVAILABILITY AND IMPLEMENTATION: featureCounts is available under GNU General Public License as part of the Subread (http://subread.sourceforge.net) or Rsubread (http://www.bioconductor.org) software packages.}, |
|
| 5790 | + langid = {english}, |
|
| 5791 | + keywords = {Algorithms,Genome,Genomics,High-Throughput Nucleotide Sequencing,Histones,Sequence Analysis RNA,Software} |
|
| 5792 | +} |
|
| 5793 | + |
|
| 5794 | +@article{liAptamerBC15Heterogeneous2012, |
|
| 5795 | + title = {Aptamer {{BC15}} against Heterogeneous Nuclear Ribonucleoprotein {{A1}} Has Potential Value in Diagnosis and Therapy of Hepatocarcinoma}, |
|
| 5796 | + author = {Li, Shaohua and Wang, Wei and Ding, Hongmei and Xu, Hua and Zhao, Qiang and Li, Jie and Li, Hui and Xia, Wei and Su, Xueting and Chen, Ying and Fang, Tao and Shao, Ningsheng and Zhang, Hongwen}, |
|
| 5797 | + date = {2012-12}, |
|
| 5798 | + journaltitle = {Nucleic Acid Therapeutics}, |
|
| 5799 | + shortjournal = {Nucleic Acid Ther}, |
|
| 5800 | + volume = {22}, |
|
| 5801 | + number = {6}, |
|
| 5802 | + eprint = {23062008}, |
|
| 5803 | + eprinttype = {pmid}, |
|
| 5804 | + pages = {391--398}, |
|
| 5805 | + issn = {2159-3345}, |
|
| 5806 | + doi = {10.1089/nat.2012.0363}, |
|
| 5807 | + abstract = {The heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) was reported to be participated in tumor development. The association between hnRNP A1 and liver cancer and the functional role of hnRNP A1 in liver cancer have never been reported. Herein, hnRNP A1-specific single-stranded DNA aptamer, BC15, was used to (a) evaluate hnRNP A1 expression in liver cancer, and (b) treat hepatocarcinoma by acting as an inhibitor of hnRNP A1. Results showed that there is high hnRNP A1 expression in liver cancer including serum α-fetoprotein-negative liver cancer tissues compared with either para-cancer or benign controls. Down regulation of hnRNP A1 expression by RNA interference inhibits the proliferation and migration of cancerous HepG2 cells, while overexpression of hnRNP A1 in normal HL-7702 cells increased the proliferation and migration of the cells. Importantly, BC15 showed a stronger inhibiting effect on the proliferation of cultured hepatoma cells than hnRNP A1 small interfering RNA, strongly suggesting that BC15 could also be a potential drug candidate for an hnRNP A1 inhibitor besides its prospect utility in in situ histological examination.}, |
|
| 5808 | + langid = {english}, |
|
| 5809 | + keywords = {Animals,Antineoplastic Agents,Aptamers Nucleotide,Carcinoma Hepatocellular,Cell Line Tumor,Cell Movement,Cell Proliferation,Gene Knockdown Techniques,Hep G2 Cells,Heterogeneous Nuclear Ribonucleoprotein A1,Heterogeneous-Nuclear Ribonucleoprotein Group A-B,Humans,Liver Neoplasms,Mice,Mice Nude,Neoplasm Invasiveness,RNA Small Interfering,Xenograft Model Antitumor Assays} |
|
| 5810 | +} |
|
| 5811 | + |
|
| 5812 | +@article{liEffectsLongNoncoding2017, |
|
| 5813 | + title = {The Effects of the Long Non-Coding {{RNA MALAT-1}} Regulated Autophagy-Related Signaling Pathway on Chemotherapy Resistance in Diffuse Large {{B-cell}} Lymphoma}, |
|
| 5814 | + author = {Li, Li-Juan and Chai, Ye and Guo, Xiao-Jia and Chu, Song-Lin and Zhang, Lian-Sheng}, |
|
| 5815 | + date = {2017-05}, |
|
| 5816 | + journaltitle = {Biomedicine \& Pharmacotherapy}, |
|
| 5817 | + volume = {89}, |
|
| 5818 | + pages = {939--948}, |
|
| 5819 | + keywords = {nosource} |
|
| 5820 | +} |
|
| 5821 | + |
|
| 5822 | +@article{lienAtlanticSalmonGenome2016, |
|
| 5823 | + title = {The {{Atlantic}} Salmon Genome Provides Insights into Rediploidization}, |
|
| 5824 | + author = {Lien, Sigbjørn and Koop, Ben F. and Sandve, Simen R. and Miller, Jason R. and Kent, Matthew P. and Nome, Torfinn and Hvidsten, Torgeir R. and Leong, Jong S. and Minkley, David R. and Zimin, Aleksey and Grammes, Fabian and Grove, Harald and Gjuvsland, Arne and Walenz, Brian and Hermansen, Russell A. and family=Schalburg, given=Kris, prefix=von, useprefix=true and Rondeau, Eric B. and Di Genova, Alex and Samy, Jeevan K. A. and Olav Vik, Jon and Vigeland, Magnus D. and Caler, Lis and Grimholt, Unni and Jentoft, Sissel and Våge, Dag Inge and family=Jong, given=Pieter, prefix=de, useprefix=true and Moen, Thomas and Baranski, Matthew and Palti, Yniv and Smith, Douglas R. and Yorke, James A. and Nederbragt, Alexander J. and Tooming-Klunderud, Ave and Jakobsen, Kjetill S. and Jiang, Xuanting and Fan, Dingding and Hu, Yan and Liberles, David A. and Vidal, Rodrigo and Iturra, Patricia and Jones, Steven J. M. and Jonassen, Inge and Maass, Alejandro and Omholt, Stig W. and Davidson, William S.}, |
|
| 5825 | + date = {2016-12-05}, |
|
| 5826 | + journaltitle = {Nature}, |
|
| 5827 | + shortjournal = {Nature}, |
|
| 5828 | + volume = {533}, |
|
| 5829 | + number = {7602}, |
|
| 5830 | + eprint = {27088604}, |
|
| 5831 | + eprinttype = {pmid}, |
|
| 5832 | + pages = {200--205}, |
|
| 5833 | + issn = {1476-4687}, |
|
| 5834 | + doi = {10.1038/nature17164}, |
|
| 5835 | + abstract = {The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.}, |
|
| 5836 | + langid = {english}, |
|
| 5837 | + keywords = {Animals,Diploidy,DNA Transposable Elements,Evolution Molecular,Female,Gene Duplication,Genes Duplicate,Genome,Genomics,Male,Models Genetic,Mutagenesis,Phylogeny,Reference Standards,Salmo salar,Sequence Homology} |
|
| 5838 | +} |
|
| 5839 | + |
|
| 5840 | +@article{liFastAccurateLongread2010, |
|
| 5841 | + title = {Fast and Accurate Long-Read Alignment with {{Burrows}}–{{Wheeler}} Transform}, |
|
| 5842 | + author = {Li, Heng and Durbin, Richard}, |
|
| 5843 | + date = {2010-03-01}, |
|
| 5844 | + journaltitle = {Bioinformatics}, |
|
| 5845 | + shortjournal = {Bioinformatics}, |
|
| 5846 | + volume = {26}, |
|
| 5847 | + number = {5}, |
|
| 5848 | + pages = {589--595}, |
|
| 5849 | + issn = {1367-4803}, |
|
| 5850 | + doi = {10.1093/bioinformatics/btp698}, |
|
| 5851 | + url = {https://academic.oup.com/bioinformatics/article/26/5/589/211735}, |
|
| 5852 | + urldate = {2019-07-02}, |
|
| 5853 | + abstract = {Abstract. Motivation: Many programs for aligning short sequencing reads to a reference genome have been developed in the last 2 years. Most of them are very ef}, |
|
| 5854 | + langid = {english}, |
|
| 5855 | + file = {/Users/rmorin/Zotero/storage/VTMEF9LQ/211735.html} |
|
| 5856 | +} |
|
| 5857 | + |
|
| 5858 | +@article{liHNRNPH1RequiredRhabdomyosarcoma2018, |
|
| 5859 | + title = {{{HNRNPH1}} Is Required for Rhabdomyosarcoma Cell Growth and Survival}, |
|
| 5860 | + author = {Li, Yanfeng and Bakke, Jesse and Finkelstein, David and Zeng, Hu and Wu, Jing and Chen, Taosheng}, |
|
| 5861 | + date = {2018-01-24}, |
|
| 5862 | + journaltitle = {Oncogenesis}, |
|
| 5863 | + volume = {7}, |
|
| 5864 | + number = {1}, |
|
| 5865 | + pages = {1--13}, |
|
| 5866 | + publisher = {Nature Publishing Group}, |
|
| 5867 | + issn = {2157-9024}, |
|
| 5868 | + doi = {10.1038/s41389-017-0024-4}, |
|
| 5869 | + url = {https://www.nature.com/articles/s41389-017-0024-4}, |
|
| 5870 | + urldate = {2022-09-28}, |
|
| 5871 | + abstract = {Rhabdomyosarcoma (RMS) is an aggressive and difficult to treat cancer characterized by a muscle-like phenotype. Although the average 5-y survival rate is 65\% for newly diagnosed RMS, the treatment options for metastatic disease are limited in efficacy, with the 5-y survival rate plummeting to 30\%. Heterogenous nuclear ribonucleoprotein H1 (HNRNPH1) is an RNA-binding protein that is highly expressed in many cancers, including RMS. To determine the role HNRNPH1 plays in RMS tumorigenesis, we investigated its expression and effect on growth in three cellular models of RMS: RD, RH30, and RH41 cells. Upon knockdown of HNRNPH1, growth of all cell lines was reduced, most likely through a combination of apoptosis and cell cycle arrest. We then recapitulated this finding by performing in vivo xenograft studies, in which knockdown of HNRNPH1 resulted in a reduction of tumor formation and growth. We used RNA sequencing to identify changes in gene expression after HNRNPH1 knockdown and found altered splicing of some oncogenes. Our data contribute to understanding the role of HNRNPH1 in RMS development.}, |
|
| 5872 | + issue = {1}, |
|
| 5873 | + langid = {english}, |
|
| 5874 | + keywords = {Cell growth,Sarcoma}, |
|
| 5875 | + file = {/Users/rmorin/Zotero/storage/Z3H5Z4JW/Li et al. - 2018 - HNRNPH1 is required for rhabdomyosarcoma cell grow.pdf;/Users/rmorin/Zotero/storage/LRFWP6DH/s41389-017-0024-4.html} |
|
| 5876 | +} |
|
| 5877 | + |
|
| 5878 | +@article{limEffectModulationHnRNP2010, |
|
| 5879 | + title = {Effect of {{Modulation}} of {{hnRNP L Levels}} on the {{Decay}} of Bcl-2 {{mRNA}} in {{MCF-7 Cells}}}, |
|
| 5880 | + author = {Lim, Mi-Hyun and Lee, Dong-Hyoung and Jung, Seung Eun and Youn, Dong-Ye and Park, Chan Sun and Lee, Jeong-Hwa}, |
|
| 5881 | + date = {2010-02}, |
|
| 5882 | + journaltitle = {The Korean Journal of Physiology \& Pharmacology: Official Journal of the Korean Physiological Society and the Korean Society of Pharmacology}, |
|
| 5883 | + shortjournal = {Korean J Physiol Pharmacol}, |
|
| 5884 | + volume = {14}, |
|
| 5885 | + number = {1}, |
|
| 5886 | + eprint = {20221275}, |
|
| 5887 | + eprinttype = {pmid}, |
|
| 5888 | + pages = {15--20}, |
|
| 5889 | + issn = {2093-3827}, |
|
| 5890 | + doi = {10.4196/kjpp.2010.14.1.15}, |
|
| 5891 | + abstract = {It has been shown that CA repeats in the 3'-untranslated region (UTR) of bcl-2 mRNA contribute the constitutive decay of bcl-2 mRNA and that hnRNP L (heterogenous nuclear ribonucleoprotein L) interacts with CA repeats in the 3'-UTR of bcl-2 mRNA, both in vitro and in vivo. The aim of this study was to determine whether the alteration of hnRNP L affects the stability of bcl-2 mRNA in vivo. Human breast carcinoma MCF-7 cells were transfected with hnRNP L-specific shRNA or hnRNP L-expressing vector to decrease or increase hnRNP L levels, respectively, followed by an actinomycin D chase. An RT-PCR analysis showed that the rate of degradation of endogenous bcl-2 mRNA was not affected by the decrease or increase in the hnRNP L levels. Furthermore, during apoptosis or autophagy, in which bcl-2 expression has been reported to decrease, no difference in the degradation of bcl-2 mRNA was observed between control and hnRNP L-knock down MCF-7 Cells. On the other hand, the levels of AUF-1 and nucleolin, transacting factors for ARE in the 3'UTR of bcl-2 mRNA, were not significantly affected by the decrease in hnRNP L, suggesting that a disturbance in the quantitative balance between these transacting factors is not likely to interfere with the effect of hnRNP L. Collectively, the findings indicate that the decay of bcl-2 mRNA does not appear to be directly controlled by hnRNP L in vivo.}, |
|
| 5892 | + langid = {english}, |
|
| 5893 | + pmcid = {PMC2835978}, |
|
| 5894 | + keywords = {bcl-2 mRNA stability,hnRNP L}, |
|
| 5895 | + file = {/Users/rmorin/Zotero/storage/PKQG7PVX/Lim et al. - 2010 - Effect of Modulation of hnRNP L Levels on the Deca.pdf} |
|
| 5896 | +} |
|
| 5897 | + |
|
| 5898 | +@article{limFcGammaReceptor2011, |
|
| 5899 | + title = {Fc Gamma Receptor {{IIb}} on Target {{B}} Cells Promotes Rituximab Internalization and Reduces Clinical Efficacy}, |
|
| 5900 | + author = {Lim, S H and Vaughan, A T and Ashton-Key, M and Williams, E L and Dixon, S V and Chan, H T C and Beers, S A and French, R R and Cox, K L and Davies, A J and Potter, K N and Mockridge, C I and Oscier, D G and Johnson, P W M and Cragg, M S and Glennie, M J}, |
|
| 5901 | + date = {2011-08}, |
|
| 5902 | + journaltitle = {Blood}, |
|
| 5903 | + volume = {118}, |
|
| 5904 | + number = {9}, |
|
| 5905 | + pages = {1--12}, |
|
| 5906 | + keywords = {nosource} |
|
| 5907 | +} |
|
| 5908 | + |
|
| 5909 | +@article{limMantleCellLymphoma2010, |
|
| 5910 | + title = {The {{Mantle Cell Lymphoma International Prognostic Index}}: {{Does}} It Work in Routine Practice?}, |
|
| 5911 | + shorttitle = {The {{Mantle Cell Lymphoma International Prognostic Index}}}, |
|
| 5912 | + author = {Lim, S. Y. and Horsman, J. M. and Hancock, B. W.}, |
|
| 5913 | + date = {2010-01}, |
|
| 5914 | + journaltitle = {Oncology Letters}, |
|
| 5915 | + shortjournal = {Oncol Lett}, |
|
| 5916 | + volume = {1}, |
|
| 5917 | + number = {1}, |
|
| 5918 | + eprint = {22966280}, |
|
| 5919 | + eprinttype = {pmid}, |
|
| 5920 | + pages = {187--188}, |
|
| 5921 | + issn = {1792-1074}, |
|
| 5922 | + doi = {10.3892/ol_00000034}, |
|
| 5923 | + abstract = {The Mantle Cell Lymphoma International Prognostic Index (MIPI) combines four factors to differentiate low-, intermediate- and high-risk prognostic groups in advanced mantle cell lymphoma using data from patients treated in clinical trials. To evaluate its use in routine practice, we applied the simplified index retrospectively to 50 consecutive new patients attending our lymphoma service. In the log-rank and multiple comparison statistical tests there was favorable differentiation between survival curves, and particularly between the high- and low-risk groups. We concluded that the MIPI is of value in routine lymphoma practice.}, |
|
| 5924 | + langid = {english}, |
|
| 5925 | + pmcid = {PMC3436357} |
|
| 5926 | +} |
|
| 5927 | + |
|
| 5928 | +@article{limMisalignedSequencingReads2022, |
|
| 5929 | + title = {Misaligned Sequencing Reads from the {{GNAQ-pseudogene}} Locus May Yield {{GNAQ}} Artefact Variants}, |
|
| 5930 | + author = {Lim, Jing Quan and Lim, Soon Thye and Ong, Choon Kiat}, |
|
| 5931 | + date = {2022-01-24}, |
|
| 5932 | + journaltitle = {Nature Communications}, |
|
| 5933 | + shortjournal = {Nat Commun}, |
|
| 5934 | + volume = {13}, |
|
| 5935 | + number = {1}, |
|
| 5936 | + pages = {458}, |
|
| 5937 | + publisher = {Nature Publishing Group}, |
|
| 5938 | + issn = {2041-1723}, |
|
| 5939 | + doi = {10.1038/s41467-022-28115-z}, |
|
| 5940 | + url = {https://www.nature.com/articles/s41467-022-28115-z}, |
|
| 5941 | + urldate = {2022-05-20}, |
|
| 5942 | + issue = {1}, |
|
| 5943 | + langid = {english}, |
|
| 5944 | + keywords = {Cancer,Computational biology and bioinformatics,Genetics}, |
|
| 5945 | + file = {/Users/rmorin/Zotero/storage/CXIQ5CW9/Lim et al. - 2022 - Misaligned sequencing reads from the GNAQ-pseudoge.pdf;/Users/rmorin/Zotero/storage/NX9VEW3W/s41467-022-28115-z.html} |
|
| 5946 | +} |
|
| 5947 | + |
|
| 5948 | +@article{liNanoparticleconjugatedAptamerTargeting2015, |
|
| 5949 | + title = {Nanoparticle-Conjugated Aptamer Targeting {{hnRNP A2}}/{{B1}} Can Recognize Multiple Tumor Cells and Inhibit Their Proliferation}, |
|
| 5950 | + author = {Li, Hui and Guo, Lei and Huang, Aixue and Xu, Hua and Liu, Xuemei and Ding, Hongmei and Dong, Jie and Li, Jie and Wang, Chaonan and Su, Xueting and Ge, Xingfeng and Sun, Leqiao and Bai, Chenjun and Shen, Xuelian and Fang, Tao and Li, Zhanghua and Zhou, Yong and Zhan, Linsheng and Li, Shaohua and Xie, Jianwei and Shao, Ningsheng}, |
|
| 5951 | + date = {2015-09-01}, |
|
| 5952 | + journaltitle = {Biomaterials}, |
|
| 5953 | + shortjournal = {Biomaterials}, |
|
| 5954 | + volume = {63}, |
|
| 5955 | + pages = {168--176}, |
|
| 5956 | + issn = {0142-9612}, |
|
| 5957 | + doi = {10.1016/j.biomaterials.2015.06.013}, |
|
| 5958 | + url = {https://www.sciencedirect.com/science/article/pii/S014296121500527X}, |
|
| 5959 | + urldate = {2022-10-14}, |
|
| 5960 | + abstract = {In this study, we further investigated a previously developed aptamer targeting ROS 17/2.8 (rat osteosarcoma) cells. We found that this C6-8 aptamer specifically binds to heterogeneous nuclear ribonucleoprotein (hnRNP) A2/B1 and that it specifically labeled multiple tumor-cell lines as effectively as hnRNP A2/B1 monoclonal antibodies. When conjugated with fluorescent carbon nanodots (CDots) it could freely enter multiple living tumor cell lines (HepG2, MCF-7, H1299, and HeLa), whose growth it inhibited by targeting hnRNP A2/B1. Similar inhibitory effects were observed when the GFP-HepG2 hepatocarcinoma cells treated with C6-8-conjugated CDots were implanted in nude mice. Our work provides a new aptamer for targeting/labeling multiple tumor cell types, and its nanoparticle conjugates bring further advantages that increase its potential for use in cancer diagnosis and therapy.}, |
|
| 5961 | + langid = {english}, |
|
| 5962 | + keywords = {Aptamer,Heterogeneous nuclear ribonucleoprotein A2/B1,Nanoparticles,SELEX,Tumor cells}, |
|
| 5963 | + file = {/Users/rmorin/Zotero/storage/RP7HL4CD/S014296121500527X.html} |
|
| 5964 | +} |
|
| 5965 | + |
|
| 5966 | +@article{lindenblattIkBzExpressionRegulated2014, |
|
| 5967 | + title = {{{IκBζ}} Expression Is Regulated by {{miR-124a}}}, |
|
| 5968 | + author = {Lindenblatt, Charlotte and Schulze-Osthoff, Klaus and Totzke, Gudrun}, |
|
| 5969 | + date = {2014-10}, |
|
| 5970 | + journaltitle = {Cell Cycle (Georgetown, Tex.)}, |
|
| 5971 | + volume = {8}, |
|
| 5972 | + number = {13}, |
|
| 5973 | + pages = {2019--2023}, |
|
| 5974 | + keywords = {nosource} |
|
| 5975 | +} |
|
| 5976 | + |
|
| 5977 | +@article{linGenomeDynamicsHuman2014, |
|
| 5978 | + title = {Genome Dynamics of the Human Embryonic Kidney 293 Lineage in Response to Cell Biology Manipulations}, |
|
| 5979 | + author = {Lin, Yao-Cheng and Boone, Morgane and Meuris, Leander and Lemmens, Irma and Roy, Nadine Van and Soete, Arne and Reumers, Joke and Moisse, Matthieu and Plaisance, Stéphane and Drmanac, Radoje and Chen, Jason and Speleman, Frank and Lambrechts, Diether and family=Peer, given=Yves Van, prefix=de, useprefix=false and Tavernier, Jan and Callewaert, Nico}, |
|
| 5980 | + date = {2014-09-03}, |
|
| 5981 | + journaltitle = {Nature Communications}, |
|
| 5982 | + shortjournal = {Nat Commun}, |
|
| 5983 | + volume = {5}, |
|
| 5984 | + number = {1}, |
|
| 5985 | + pages = {1--12}, |
|
| 5986 | + issn = {2041-1723}, |
|
| 5987 | + doi = {10.1038/ncomms5767}, |
|
| 5988 | + url = {https://www.nature.com/articles/ncomms5767}, |
|
| 5989 | + urldate = {2019-12-24}, |
|
| 5990 | + abstract = {The human embryonic kidney 293 (HEK293) cell lineage is widely used in cell biology and biotechnology. Here, the authors apply whole genome resequencing methods to characterise genomic variation in six HEK293 cell lines and suggest that this variation could affect experiments using these cell lines.}, |
|
| 5991 | + langid = {english}, |
|
| 5992 | + file = {/Users/rmorin/Zotero/storage/IBYGIW6U/ncomms5767.html} |
|
| 5993 | +} |
|
| 5994 | + |
|
| 5995 | +@article{linNovelNucleocytoplasmicShuttling2006, |
|
| 5996 | + title = {A Novel Nucleocytoplasmic Shuttling Sequence of {{DAZAP1}}, a Testis-Abundant {{RNA-binding}} Protein}, |
|
| 5997 | + author = {Lin, Yi-Tzu and Yen, Pauline H.}, |
|
| 5998 | + date = {2006-08}, |
|
| 5999 | + journaltitle = {RNA (New York, N.Y.)}, |
|
| 6000 | + shortjournal = {RNA}, |
|
| 6001 | + volume = {12}, |
|
| 6002 | + number = {8}, |
|
| 6003 | + eprint = {16772659}, |
|
| 6004 | + eprinttype = {pmid}, |
|
| 6005 | + pages = {1486--1493}, |
|
| 6006 | + issn = {1355-8382}, |
|
| 6007 | + doi = {10.1261/rna.42206}, |
|
| 6008 | + abstract = {Deleted in Azoospermia Associated Protein 1 (DAZAP1) is a ubiquitous RNA-binding protein highly expressed in the human and the mouse testes. It shows a dynamic subcellular localization during spermatogenesis, present predominantly in the nuclei of late-stage spermatocytes and round spermatids and translocated to the cytoplasm during spermatid elongation. To test the hypothesis that DAZAP1 shuttles between the nucleus and the cytoplasm, we studied the nuclear transport of DAZAP1 in somatic cells using immunostaining, heterokaryon formation, and mutagenesis. DAZAP1 is detected exclusively in the nucleus and has the ability to shuttle between the nucleus and the cytoplasm using a highly conserved 25 amino acid segment, designated ZNS, at its C terminus. ZNS shares no sequence homology with other known nuclear localization or export signals. Attachment of ZNS to a red fluorescent protein DsRed2 confers the nucleocytoplasmic shuttling ability to that protein. The nuclear localization of DAZAP1 depends on active transcription. In the presence of an RNA polymerase II inhibitor, DAZAP1 is retained in the cytoplasm. DAZAP1 colocalizes with hnRNP A1 and hnRNP C1 in the nucleus and is a component of the heterogeneous nuclear ribonucleoprotein particles. Our results suggest that DAZAP1 plays a key role in mRNA transport during spermatogenesis.}, |
|
| 6009 | + langid = {english}, |
|
| 6010 | + pmcid = {PMC1524892}, |
|
| 6011 | + keywords = {3T3 Cells,Active Transport Cell Nucleus,Amino Acid Sequence,Animals,Cell Line,Cell Nucleus,Cercopithecus aethiops,Conserved Sequence,COS Cells,Cytoplasm,Dactinomycin,HeLa Cells,Heterogeneous Nuclear Ribonucleoprotein A1,Heterogeneous-Nuclear Ribonucleoprotein Group A-B,Heterogeneous-Nuclear Ribonucleoprotein Group C,Humans,Male,Mice,Molecular Sequence Data,Mutagenesis Site-Directed,Mutation,Nuclear Localization Signals,Recombinant Fusion Proteins,RNA-Binding Proteins,Testis,Transcription Genetic} |
|
| 6012 | +} |
|
| 6013 | + |
|
| 6014 | +@article{liPolyRCBinding, |
|
| 6015 | + title = {Poly({{rC}}) {{Binding Protein}} 1 {{Represses}} the {{Translation}} of {{STAT3}} through 5' {{UTR}}}, |
|
| 6016 | + author = {Li, Ziwei and Wang, Xiaole and Jia, Rong}, |
|
| 6017 | + journaltitle = {Current Gene Therapy}, |
|
| 6018 | + volume = {22}, |
|
| 6019 | + number = {5}, |
|
| 6020 | + pages = {397--405}, |
|
| 6021 | + url = {https://benthamscience.com/article/123400}, |
|
| 6022 | + urldate = {2022-09-28}, |
|
| 6023 | + abstract = {Background: Signal transducer and activator of transcription 3 (STAT3) is an oncogene and frequently overexpressed in cancers. However, the regulatory mechanisms of STAT3 expression are not fully understood. Poly(rC)-binding protein1 (PCBP1) is an RNA-binding protein that regulates mRNA stability, splicing, and translation. PCBP1 is a tumor suppressor and can inhibit the translation of several oncogenic genes. Objective: We aimed to understand the regulatory mechanisms of STAT3 expression. Methods: The 5' UTR or 3’ UTR regions of the human STAT3 gene were inserted upstream or downstream of the green fluorescent gene (GFP), respectively, which were used as reporter systems to analyze the inhibitory effects of PCBP1 on the STAT3 gene expression. The deletion and point mutation in 5' UTR were used to search the essential regulatory sequences of the translation inhibition. The mutations of PCBP1 protein were analyzed in the cBioPortal online service. The effects of mutated PCBP1 proteins on STAT3 expression, cancer cell proliferation, and colony formation were analyzed in oral squamous cell carcinoma (OSCC) cell lines. Results: PCBP1 inhibits mRNA translation through a motif in the 5' UTR of STAT3. Moreover, we found two leucine residues (Leu100 and Leu102) of PCBP1 protein frequently mutated in cancers. These mutations abolished the inhibition function of PCBP1 on STAT3 translation. Surprisingly, in contrast to wild-type PCBP1 protein, these mutations can promote the growth and colony formation of cancer cells. Conclusion: Overall, we demonstrate that PCBP1 can inhibit the expression of STAT3 through its 5' UTR, and two leucine residues of PCBP1 protein are essential for its functions.}, |
|
| 6024 | + langid = {english}, |
|
| 6025 | + file = {/Users/rmorin/Zotero/storage/H3PCG7BC/123400.html} |
|
| 6026 | +} |
|
| 6027 | + |
|
| 6028 | +@article{liQuantitativeNuclearHistomorphometric2019, |
|
| 6029 | + title = {Quantitative Nuclear Histomorphometric Features Are Predictive of {{Oncotype DX}} Risk Categories in Ductal Carcinoma in Situ: Preliminary Findings}, |
|
| 6030 | + shorttitle = {Quantitative Nuclear Histomorphometric Features Are Predictive of {{Oncotype DX}} Risk Categories in Ductal Carcinoma in Situ}, |
|
| 6031 | + author = {Li, Haojia and Whitney, Jon and Bera, Kaustav and Gilmore, Hannah and Thorat, Mangesh A. and Badve, Sunil and Madabhushi, Anant}, |
|
| 6032 | + date = {2019-10-17}, |
|
| 6033 | + journaltitle = {Breast Cancer Research}, |
|
| 6034 | + shortjournal = {Breast Cancer Research}, |
|
| 6035 | + volume = {21}, |
|
| 6036 | + number = {1}, |
|
| 6037 | + pages = {114}, |
|
| 6038 | + issn = {1465-542X}, |
|
| 6039 | + doi = {10.1186/s13058-019-1200-6}, |
|
| 6040 | + url = {https://doi.org/10.1186/s13058-019-1200-6}, |
|
| 6041 | + urldate = {2020-02-04}, |
|
| 6042 | + abstract = {Oncotype DX (ODx) is a 12-gene assay assessing the recurrence risk (high, intermediate, and low) of ductal carcinoma in situ (pre-invasive breast cancer), which guides clinicians regarding prescription of radiotherapy. However, ODx is expensive, time-consuming, and tissue-destructive. In addition, the actual prognostic meaning for the intermediate ODx risk category remains unclear.}, |
|
| 6043 | + file = {/Users/rmorin/Zotero/storage/4572EHCJ/s13058-019-1200-6.html} |
|
| 6044 | +} |
|
| 6045 | + |
|
| 6046 | +@article{liuGerminalCenterCells1991, |
|
| 6047 | + title = {Germinal Center Cells Express Bcl-2 Protein after Activation by Signals Which Prevent Their Entry into Apoptosis}, |
|
| 6048 | + author = {Liu, Y. J. and Mason, D. Y. and Johnson, G. D. and Abbot, S. and Gregory, C. D. and Hardie, D. L. and Gordon, J. and MacLennan, I. C.}, |
|
| 6049 | + date = {1991-08}, |
|
| 6050 | + journaltitle = {European Journal of Immunology}, |
|
| 6051 | + shortjournal = {Eur J Immunol}, |
|
| 6052 | + volume = {21}, |
|
| 6053 | + number = {8}, |
|
| 6054 | + eprint = {1868875}, |
|
| 6055 | + eprinttype = {pmid}, |
|
| 6056 | + pages = {1905--1910}, |
|
| 6057 | + issn = {0014-2980}, |
|
| 6058 | + doi = {10.1002/eji.1830210819}, |
|
| 6059 | + abstract = {B cells undergo selection within germinal centers on the basis of their capacity to be activated by antigen held on follicular dendritic cells. Isolated germinal center B cells in culture kill themselves by apoptosis but this is prevented if their receptors for antigen are cross-linked. In this study it is confirmed that almost all germinal center B cells, unlike other B cells, do not express the 25-kDa protein encoded by the bcl-2 oncogene. Cross-linking the surface Ig of isolated germinal center cells causes them to express bcl-2 protein. Two other stimuli which inhibit the entry of germinal center cells to apoptosis result in the expression of bcl-2 protein. These stimuli are: (a) CD40 antibody and (b) recombinant 25-kDa fragment of the CD23 protein plus recombinant interleukin 1 alpha. Respectively, these induce germinal center cells to differentiate to resting B cells or plasmablasts. Dual-fluorescence studies on small lymphocytes confirm the presence of bcl-2 protein in mitochondria but show that this is also present in other extra-nuclear areas. Burkitt lymphoma cells have a phenotype which indicates that they are neoplastic cells of germinal center origin. The expression of bcl-2 protein by Burkitt lymphoma lines was also studied. Burkitt lines which retain the phenotype of fresh Burkitt lymphoma cells can be induced to enter apoptosis on culture with the Ca2+ ionophore ionomycin. These cells were found not to express bcl-2 protein. By contrast, Burkitt lines which have drifted towards a lymphoblastoid cell line phenotype and are resistant to the induction of apoptosis express high levels of the bcl-2 protein. The findings support the concept that the susceptibility of germinal center cells to entering apoptosis is associated with their lack of expression of bcl-2 protein. Aberrant expression of bcl-2 protein by some neoplastic germinal center cells may allow survival in situations where their normal counterparts die.}, |
|
| 6060 | + langid = {english}, |
|
| 6061 | + keywords = {Antibodies Monoclonal,B-Lymphocytes,Burkitt Lymphoma,Cell Survival,Cells Cultured,Humans,Mitochondria,Proto-Oncogene Proteins,Proto-Oncogene Proteins c-bcl-2} |
|
| 6062 | +} |
|
| 6063 | + |
|
| 6064 | +@article{liuHnRNPA1SpecificallyRecognizes2018, |
|
| 6065 | + title = {{{HnRNPA1 Specifically Recognizes}} the {{Base}} of {{Nucleotide}} at the {{Loop}} of {{RNA G-Quadruplex}}}, |
|
| 6066 | + author = {Liu, Xiao and Xu, Yan}, |
|
| 6067 | + date = {2018-01-22}, |
|
| 6068 | + journaltitle = {Molecules (Basel, Switzerland)}, |
|
| 6069 | + shortjournal = {Molecules}, |
|
| 6070 | + volume = {23}, |
|
| 6071 | + eprint = {29361764}, |
|
| 6072 | + eprinttype = {pmid}, |
|
| 6073 | + pages = {E237}, |
|
| 6074 | + issn = {1420-3049}, |
|
| 6075 | + doi = {10.3390/molecules23010237}, |
|
| 6076 | + abstract = {Human telomere RNA performs various cellular functions, such as telomere length regulation, heterochromatin formation, and end protection. We recently demonstrated that the loops in the RNA G-quadruplex are important in the interaction of telomere RNA with heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1). Here, we report on a detailed analysis of hnRNPA1 binding to telomere RNA G-quadruplexes with a group of loop variants using an electrophoretic mobility shift assay (EMSA) and circular dichroism (CD) spectroscopy. We found that the hnRNPA1 binds to RNA G-quadruplexes with the 2'-O-methyl and DNA loops, but fails to bind with the abasic RNA and DNA loops. These results suggested that hnRNPA1 binds to the loop of the RNA G-quadruplex by recognizing the base of the loop's nucleotides. The observation provides the first evidence that the base of the loop's nucleotides is a key factor for hnRNPA1 specifically recognizing the RNA G-quadruplex.}, |
|
| 6077 | + langid = {english}, |
|
| 6078 | + pmcid = {PMC6017123}, |
|
| 6079 | + keywords = {base,Circular Dichroism,Electrophoretic Mobility Shift Assay,G-Quadruplexes,Heterogeneous Nuclear Ribonucleoprotein A1,hnRNPA1,Humans,loop of RNA G-quadruplex,Nucleotides,Protein Binding,RNA,RNA G-quadruplex,Telomere,telomere RNA}, |
|
| 6080 | + file = {/Users/rmorin/Zotero/storage/2T4SP6N2/Liu and Xu - 2018 - HnRNPA1 Specifically Recognizes the Base of Nucleo.pdf} |
|
| 6081 | +} |
|
| 6082 | + |
|
| 6083 | +@article{liuHNRNPH1NovelRegulator2021, |
|
| 6084 | + title = {{{HNRNPH1 Is}} a {{Novel Regulator Of Cellular Proliferation}} and {{Disease Progression}} in {{Chronic Myeloid Leukemia}}}, |
|
| 6085 | + author = {Liu, Menghan and Yang, Lin and Liu, Xiaojun and Nie, Ziyuan and Zhang, Xiaoyan and Lu, Yaqiong and Pan, Yuxia and Wang, Xingzhe and Luo, Jianmin}, |
|
| 6086 | + date = {2021-07-06}, |
|
| 6087 | + journaltitle = {Frontiers in Oncology}, |
|
| 6088 | + shortjournal = {Front Oncol}, |
|
| 6089 | + volume = {11}, |
|
| 6090 | + eprint = {34295818}, |
|
| 6091 | + eprinttype = {pmid}, |
|
| 6092 | + pages = {682859}, |
|
| 6093 | + issn = {2234-943X}, |
|
| 6094 | + doi = {10.3389/fonc.2021.682859}, |
|
| 6095 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8290130/}, |
|
| 6096 | + urldate = {2023-01-10}, |
|
| 6097 | + abstract = {RNA binding proteins act as essential modulators in cancers by regulating biological cellular processes. Heterogeneous nuclear ribonucleoprotein H1 (HNRNPH1), as a key member of the heterogeneous nuclear ribonucleoproteins family, is frequently upregulated in multiple cancer cells and involved in tumorigenesis. However, the function of HNRNPH1 in chronic myeloid leukemia (CML) remains unclear. In the present study, we revealed that HNRNPH1 expression level was upregulated in CML patients and cell lines. Moreover, the higher level of HNRNPH1 was correlated with disease progression of CML. In vivo and in vitro experiments showed that knockdown of HNRNPH1 inhibited cell proliferation and promoted cell apoptosis in CML cells. Importantly, knockdown of HNRNPH1 in CML cells enhanced sensitivity to imatinib. Mechanically, HNRNPH1 could bind to the mRNA of PTPN6 and negatively regulated its expression. PTPN6 mediated the regulation between HNRNPH1 and PI3K/AKT activation. Furthermore, the HNRNPH1–PTPN6–PI3K/AKT axis played a critical role in CML tumorigenesis and development. The present study first investigated the deregulated HNRNPH1–PTPN6–PI3K/AKT axis moderated cell growth and apoptosis in CML cells, whereby targeting this pathway may be a therapeutic CML treatment.}, |
|
| 6098 | + pmcid = {PMC8290130}, |
|
| 6099 | + file = {/Users/rmorin/Zotero/storage/6LB7QGTS/Liu et al. - 2021 - HNRNPH1 Is a Novel Regulator Of Cellular Prolifera.pdf} |
|
| 6100 | +} |
|
| 6101 | + |
|
| 6102 | +@article{liuMethyladenosinedependentRNAStructural2015, |
|
| 6103 | + title = {N(6)-Methyladenosine-Dependent {{RNA}} Structural Switches Regulate {{RNA-protein}} Interactions}, |
|
| 6104 | + author = {Liu, Nian and Dai, Qing and Zheng, Guanqun and He, Chuan and Parisien, Marc and Pan, Tao}, |
|
| 6105 | + date = {2015-02-26}, |
|
| 6106 | + journaltitle = {Nature}, |
|
| 6107 | + shortjournal = {Nature}, |
|
| 6108 | + volume = {518}, |
|
| 6109 | + number = {7540}, |
|
| 6110 | + eprint = {25719671}, |
|
| 6111 | + eprinttype = {pmid}, |
|
| 6112 | + pages = {560--564}, |
|
| 6113 | + issn = {1476-4687}, |
|
| 6114 | + doi = {10.1038/nature14234}, |
|
| 6115 | + abstract = {RNA-binding proteins control many aspects of cellular biology through binding single-stranded RNA binding motifs (RBMs). However, RBMs can be buried within their local RNA structures, thus inhibiting RNA-protein interactions. N(6)-methyladenosine (m(6)A), the most abundant and dynamic internal modification in eukaryotic messenger RNA, can be selectively recognized by the YTHDF2 protein to affect the stability of cytoplasmic mRNAs, but how m(6)A achieves its wide-ranging physiological role needs further exploration. Here we show in human cells that m(6)A controls the RNA-structure-dependent accessibility of RBMs to affect RNA-protein interactions for biological regulation; we term this mechanism 'the m(6)A-switch'. We found that m(6)A alters the local structure in mRNA and long non-coding RNA (lncRNA) to facilitate binding of heterogeneous nuclear ribonucleoprotein C (HNRNPC), an abundant nuclear RNA-binding protein responsible for pre-mRNA processing. Combining photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) and anti-m(6)A immunoprecipitation (MeRIP) approaches enabled us to identify 39,060 m(6)A-switches among HNRNPC-binding sites; and global m(6)A reduction decreased HNRNPC binding at 2,798 high-confidence m(6)A-switches. We determined that these m(6)A-switch-regulated HNRNPC-binding activities affect the abundance as well as alternative splicing of target mRNAs, demonstrating the regulatory role of m(6)A-switches on gene expression and RNA maturation. Our results illustrate how RNA-binding proteins gain regulated access to their RBMs through m(6)A-dependent RNA structural remodelling, and provide a new direction for investigating RNA-modification-coded cellular biology.}, |
|
| 6116 | + langid = {english}, |
|
| 6117 | + pmcid = {PMC4355918}, |
|
| 6118 | + keywords = {Adenosine,Alternative Splicing,Base Sequence,Cross-Linking Reagents,HEK293 Cells,HeLa Cells,Heterogeneous-Nuclear Ribonucleoprotein Group C,Humans,Immunoprecipitation,Nucleic Acid Conformation,Nucleotide Motifs,Protein Binding,RNA Messenger,Transcriptome}, |
|
| 6119 | + file = {/Users/rmorin/Zotero/storage/HP4XTS5C/Liu et al. - 2015 - N(6)-methyladenosine-dependent RNA structural swit.pdf} |
|
| 6120 | +} |
|
| 6121 | + |
|
| 6122 | +@article{liuMuscleDevelopmentalDefects2017, |
|
| 6123 | + title = {Muscle Developmental Defects in Heterogeneous Nuclear {{Ribonucleoprotein A1}} Knockout Mice}, |
|
| 6124 | + author = {Liu, Ting-Yuan and Chen, Yu-Chia and Jong, Yuh-Jyh and Tsai, Huai-Jen and Lee, Chien-Chin and Chang, Ya-Sian and Chang, Jan-Gowth and Chang, Yung-Fu}, |
|
| 6125 | + date = {2017-01-11}, |
|
| 6126 | + journaltitle = {Open Biology}, |
|
| 6127 | + shortjournal = {Open Biol}, |
|
| 6128 | + volume = {7}, |
|
| 6129 | + number = {1}, |
|
| 6130 | + eprint = {28077597}, |
|
| 6131 | + eprinttype = {pmid}, |
|
| 6132 | + pages = {160303}, |
|
| 6133 | + issn = {2046-2441}, |
|
| 6134 | + doi = {10.1098/rsob.160303}, |
|
| 6135 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5303281/}, |
|
| 6136 | + urldate = {2023-01-09}, |
|
| 6137 | + abstract = {Heterogeneous ribonucleoprotein A1 (hnRNP A1) is crucial for regulating alternative splicing. Its integrated function within an organism has not, however, been identified. We generated hnRNP A1 knockout mice to study the role of hnRNP A1 in vivo. The knockout mice, hnRNP A1−/−, showed embryonic lethality because of muscle developmental defects. The blood pressure and heart rate of the heterozygous mice were higher than those of the wild-type mice, indicating heart function defects. We performed mouse exon arrays to study the muscle development mechanism. The processes regulated by hnRNP A1 included cell adhesion and muscle contraction. The expression levels of muscle development-related genes in hnRNP A1+/− mice were significantly different from those in wild-type mice, as detected using qRT-PCR. We further confirmed the alternative splicing patterns of muscle development-related genes including mef2c, lrrfip1, usp28 and abcc9. Alternative mRNA isoforms of these genes were increased in hnRNP A1+/− mice compared with wild-type mice. Furthermore, we revealed that the functionally similar hnRNP A2/B1 did not compensate for the expression of hnRNP A1 in organisms. In summary, our study demonstrated that hnRNP A1 plays a critical and irreplaceable role in embryonic muscle development by regulating the expression and alternative splicing of muscle-related genes.}, |
|
| 6138 | + pmcid = {PMC5303281}, |
|
| 6139 | + file = {/Users/rmorin/Zotero/storage/HGP55Q95/Liu et al. - 2017 - Muscle developmental defects in heterogeneous nucl.pdf} |
|
| 6140 | +} |
|
| 6141 | + |
|
| 6142 | +@article{liuN6methyladenosineAltersRNA2017, |
|
| 6143 | + title = {N6-Methyladenosine Alters {{RNA}} Structure to Regulate Binding of a Low-Complexity Protein}, |
|
| 6144 | + author = {Liu, Nian and Zhou, Katherine I. and Parisien, Marc and Dai, Qing and Diatchenko, Luda and Pan, Tao}, |
|
| 6145 | + date = {2017-06-02}, |
|
| 6146 | + journaltitle = {Nucleic Acids Research}, |
|
| 6147 | + shortjournal = {Nucleic Acids Res}, |
|
| 6148 | + volume = {45}, |
|
| 6149 | + number = {10}, |
|
| 6150 | + eprint = {28334903}, |
|
| 6151 | + eprinttype = {pmid}, |
|
| 6152 | + pages = {6051--6063}, |
|
| 6153 | + issn = {1362-4962}, |
|
| 6154 | + doi = {10.1093/nar/gkx141}, |
|
| 6155 | + abstract = {N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic messenger RNA (mRNA), and affects almost every stage of the mRNA life cycle. The YTH-domain proteins can specifically recognize m6A modification to control mRNA maturation, translation and decay. m6A can also alter RNA structures to affect RNA-protein interactions in cells. Here, we show that m6A increases the accessibility of its surrounding RNA sequence to bind heterogeneous nuclear ribonucleoprotein G (HNRNPG). Furthermore, HNRNPG binds m6A-methylated RNAs through its C-terminal low-complexity region, which self-assembles into large particles in vitro. The Arg-Gly-Gly repeats within the low-complexity region are required for binding to the RNA motif exposed by m6A methylation. We identified 13,191 m6A sites in the transcriptome that regulate RNA-HNRNPG interaction and thereby alter the expression and alternative splicing pattern of target mRNAs. Low-complexity regions are pervasive among mRNA binding proteins. Our results show that m6A-dependent RNA structural alterations can promote direct binding of m6A-modified RNAs to low-complexity regions in RNA binding proteins.}, |
|
| 6156 | + langid = {english}, |
|
| 6157 | + pmcid = {PMC5449601}, |
|
| 6158 | + keywords = {Adenosine,Alternative Splicing,Conserved Sequence,Gene Knockdown Techniques,HEK293 Cells,HeLa Cells,Heterogeneous-Nuclear Ribonucleoproteins,Humans,Methyltransferases,Nucleic Acid Conformation,Oligoribonucleotides,Phylogeny,Protein Binding,RNA,RNA Interference,RNA Long Noncoding,RNA Small Interfering,Sequence Analysis RNA,Transcriptome}, |
|
| 6159 | + file = {/Users/rmorin/Zotero/storage/DWCHGYG7/Liu et al. - 2017 - N6-methyladenosine alters RNA structure to regulat.pdf} |
|
| 6160 | +} |
|
| 6161 | + |
|
| 6162 | +@article{liuS1PR1EffectiveTarget2012, |
|
| 6163 | + title = {{{S1PR1}} Is an Effective Target to Block {{STAT3}} Signaling in Activated {{B}} Cell-like Diffuse Large {{B-cell}} Lymphoma.}, |
|
| 6164 | + author = {Liu, Yong and Deng, Jiehui and Wang, Lin and Lee, Heehyoung and Armstrong, Brian and Scuto, Anna and Kowolik, Claudia and Weiss, Lawrence M and Forman, Stephen and Yu, Hua}, |
|
| 6165 | + date = {2012-08}, |
|
| 6166 | + journaltitle = {Blood}, |
|
| 6167 | + volume = {120}, |
|
| 6168 | + number = {7}, |
|
| 6169 | + pages = {1458--1465}, |
|
| 6170 | + keywords = {nosource} |
|
| 6171 | +} |
|
| 6172 | + |
|
| 6173 | +@article{lohrDiscoveryPrioritizationSomatic2012a, |
|
| 6174 | + title = {Discovery and Prioritization of Somatic Mutations in Diffuse Large {{B-cell}} Lymphoma ({{DLBCL}}) by Whole-Exome Sequencing}, |
|
| 6175 | + author = {Lohr, Jens G. and Stojanov, Petar and Lawrence, Michael S. and Auclair, Daniel and Chapuy, Bjoern and Sougnez, Carrie and Cruz-Gordillo, Peter and Knoechel, Birgit and Asmann, Yan W. and Slager, Susan L. and Novak, Anne J. and Dogan, Ahmet and Ansell, Stephen M. and Link, Brian K. and Zou, Lihua and Gould, Joshua and Saksena, Gordon and Stransky, Nicolas and Rangel-Escareño, Claudia and Fernandez-Lopez, Juan Carlos and Hidalgo-Miranda, Alfredo and Melendez-Zajgla, Jorge and Hernández-Lemus, Enrique and Schwarz-Cruz y Celis, Angela and Imaz-Rosshandler, Ivan and Ojesina, Akinyemi I. and Jung, Joonil and Pedamallu, Chandra S. and Lander, Eric S. and Habermann, Thomas M. and Cerhan, James R. and Shipp, Margaret A. and Getz, Gad and Golub, Todd R.}, |
|
| 6176 | + date = {2012-03-06}, |
|
| 6177 | + journaltitle = {Proceedings of the National Academy of Sciences of the United States of America}, |
|
| 6178 | + shortjournal = {Proc Natl Acad Sci U S A}, |
|
| 6179 | + volume = {109}, |
|
| 6180 | + number = {10}, |
|
| 6181 | + eprint = {22343534}, |
|
| 6182 | + eprinttype = {pmid}, |
|
| 6183 | + pages = {3879--3884}, |
|
| 6184 | + issn = {1091-6490}, |
|
| 6185 | + doi = {10.1073/pnas.1121343109}, |
|
| 6186 | + abstract = {To gain insight into the genomic basis of diffuse large B-cell lymphoma (DLBCL), we performed massively parallel whole-exome sequencing of 55 primary tumor samples from patients with DLBCL and matched normal tissue. We identified recurrent mutations in genes that are well known to be functionally relevant in DLBCL, including MYD88, CARD11, EZH2, and CREBBP. We also identified somatic mutations in genes for which a functional role in DLBCL has not been previously suspected. These genes include MEF2B, MLL2, BTG1, GNA13, ACTB, P2RY8, PCLO, and TNFRSF14. Further, we show that BCL2 mutations commonly occur in patients with BCL2/IgH rearrangements as a result of somatic hypermutation normally occurring at the IgH locus. The BCL2 point mutations are primarily synonymous, and likely caused by activation-induced cytidine deaminase-mediated somatic hypermutation, as shown by comprehensive analysis of enrichment of mutations in WRCY target motifs. Those nonsynonymous mutations that are observed tend to be found outside of the functionally important BH domains of the protein, suggesting that strong negative selection against BCL2 loss-of-function mutations is at play. Last, by using an algorithm designed to identify likely functionally relevant but infrequent mutations, we identify KRAS, BRAF, and NOTCH1 as likely drivers of DLBCL pathogenesis in some patients. Our data provide an unbiased view of the landscape of mutations in DLBCL, and this in turn may point toward new therapeutic strategies for the disease.}, |
|
| 6187 | + langid = {english}, |
|
| 6188 | + pmcid = {PMC3309757}, |
|
| 6189 | + keywords = {Amino Acid Motifs,Cluster Analysis,DNA Mutational Analysis,Exome,Exons,Gene Expression Regulation Neoplastic,Humans,Lymphoma Large B-Cell Diffuse,Models Genetic,Mutation,Polymerase Chain Reaction,Sequence Analysis DNA,Translocation Genetic}, |
|
| 6190 | + file = {/Users/rmorin/Zotero/storage/RD6D94NK/Lohr et al. - 2012 - Discovery and prioritization of somatic mutations .pdf} |
|
| 6191 | +} |
|
| 6192 | + |
|
| 6193 | +@article{lopezGenomicTranscriptomicChanges2019, |
|
| 6194 | + title = {Genomic and Transcriptomic Changes Complement Each Other in the Pathogenesis of Sporadic {{Burkitt}} Lymphoma}, |
|
| 6195 | + author = {López, Cristina and Kleinheinz, Kortine and Aukema, Sietse M. and Rohde, Marius and Bernhart, Stephan H. and Hübschmann, Daniel and Wagener, Rabea and Toprak, Umut H. and Raimondi, Francesco and Kreuz, Markus and Waszak, Sebastian M. and Huang, Zhiqin and Sieverling, Lina and Paramasivam, Nagarajan and Seufert, Julian and Sungalee, Stephanie and Russell, Robert B. and Bausinger, Julia and Kretzmer, Helene and Ammerpohl, Ole and Bergmann, Anke K. and Binder, Hans and Borkhardt, Arndt and Brors, Benedikt and Claviez, Alexander and Doose, Gero and Feuerbach, Lars and Haake, Andrea and Hansmann, Martin-Leo and Hoell, Jessica and Hummel, Michael and Korbel, Jan O. and Lawerenz, Chris and Lenze, Dido and Radlwimmer, Bernhard and Richter, Julia and Rosenstiel, Philip and Rosenwald, Andreas and Schilhabel, Markus B. and Stein, Harald and Stilgenbauer, Stephan and Stadler, Peter F. and Szczepanowski, Monika and Weniger, Marc A. and Zapatka, Marc and Eils, Roland and Lichter, Peter and Loeffler, Markus and Möller, Peter and Trümper, Lorenz and Klapper, Wolfram and Hoffmann, Steve and Küppers, Ralf and Burkhardt, Birgit and Schlesner, Matthias and Siebert, Reiner}, |
|
| 6196 | + date = {2019-03-29}, |
|
| 6197 | + journaltitle = {Nature Communications}, |
|
| 6198 | + shortjournal = {Nat Commun}, |
|
| 6199 | + volume = {10}, |
|
| 6200 | + number = {1}, |
|
| 6201 | + pages = {1459}, |
|
| 6202 | + publisher = {Nature Publishing Group}, |
|
| 6203 | + issn = {2041-1723}, |
|
| 6204 | + doi = {10.1038/s41467-019-08578-3}, |
|
| 6205 | + url = {https://www.nature.com/articles/s41467-019-08578-3}, |
|
| 6206 | + urldate = {2021-11-30}, |
|
| 6207 | + abstract = {Burkitt lymphoma (BL) is the most common B-cell lymphoma in children. Within the International Cancer Genome Consortium (ICGC), we performed whole genome and transcriptome sequencing of 39 sporadic BL. Here, we unravel~interaction of structural, mutational, and transcriptional changes, which contribute to MYC oncogene dysregulation together with the pathognomonic IG-MYC translocation. Moreover, by mapping IGH translocation breakpoints, we provide evidence that the precursor of at least a subset of BL is a B-cell poised to express IGHA. We describe the landscape of mutations, structural variants, and mutational processes, and identified a series of driver genes in the pathogenesis of BL, which can be targeted by various mechanisms, including IG-non MYC translocations, germline and somatic mutations, fusion transcripts, and alternative splicing.}, |
|
| 6208 | + issue = {1}, |
|
| 6209 | + langid = {english}, |
|
| 6210 | + keywords = {Cancer genomics,Lymphocytes,Lymphoid tissues,Oncology}, |
|
| 6211 | + annotation = {Bandiera\_abtest: a\\ |
|
| 6212 | +Cc\_license\_type: cc\_by\\ |
|
| 6213 | +Cg\_type: Nature Research Journals\\ |
|
| 6214 | +Primary\_atype: Research\\ |
|
| 6215 | +Subject\_term: Cancer genomics;Lymphocytes;Lymphoid tissues;Oncology\\ |
|
| 6216 | +Subject\_term\_id: cancer-genomics;lymphocytes;lymphoid-tissues;oncology}, |
|
| 6217 | + file = {/Users/rmorin/Zotero/storage/YFWS8UMA/López et al. - 2019 - Genomic and transcriptomic changes complement each.pdf;/Users/rmorin/Zotero/storage/J2E27QWW/s41467-019-08578-3.html} |
|
| 6218 | +} |
|
| 6219 | + |
|
| 6220 | +@article{lossosAIDExpressedGerminal2004, |
|
| 6221 | + title = {{{AID}} Is Expressed in Germinal Center {{B-cell-like}} and Activated {{B-cell-like}} Diffuse Large-Cell Lymphomas and Is Not Correlated with Intraclonal Heterogeneity}, |
|
| 6222 | + author = {Lossos, I S and Levy, R and Alizadeh, A A}, |
|
| 6223 | + date = {2004-09}, |
|
| 6224 | + journaltitle = {Leukemia}, |
|
| 6225 | + volume = {18}, |
|
| 6226 | + number = {11}, |
|
| 6227 | + pages = {1775--1779}, |
|
| 6228 | + keywords = {nosource} |
|
| 6229 | +} |
|
| 6230 | + |
|
| 6231 | +@article{lossosHGALNovelInterleukin4inducible2003, |
|
| 6232 | + title = {{{HGAL}} Is a Novel Interleukin-4-Inducible Gene That Strongly Predicts Survival in Diffuse Large {{B-cell}} Lymphoma}, |
|
| 6233 | + author = {Lossos, I S}, |
|
| 6234 | + date = {2003-01}, |
|
| 6235 | + journaltitle = {Blood}, |
|
| 6236 | + volume = {101}, |
|
| 6237 | + number = {2}, |
|
| 6238 | + pages = {433--440}, |
|
| 6239 | + keywords = {nosource} |
|
| 6240 | +} |
|
| 6241 | + |
|
| 6242 | +@article{lossosMolecularPathogenesisDiffuse2005, |
|
| 6243 | + title = {Molecular {{Pathogenesis}} of {{Diffuse Large B-Cell Lymphoma}}}, |
|
| 6244 | + author = {Lossos, I S}, |
|
| 6245 | + date = {2005-09}, |
|
| 6246 | + journaltitle = {J Clin Oncol}, |
|
| 6247 | + volume = {23}, |
|
| 6248 | + number = {26}, |
|
| 6249 | + pages = {6351--6357}, |
|
| 6250 | + keywords = {nosource} |
|
| 6251 | +} |
|
| 6252 | + |
|
| 6253 | +@article{lossosOngoingImmunoglobulinSomatic2000, |
|
| 6254 | + title = {Ongoing Immunoglobulin Somatic Mutation in Germinal Center {{B}} Cell-like but Not in Activated {{B}} Cell-like Diffuse Large Cell Lymphomas}, |
|
| 6255 | + author = {Lossos, I S and Alizadeh, A A and Eisen, M B and Chan, W C and Brown, P O and Botstein, D and Staudt, L M and Levy, R}, |
|
| 6256 | + date = {2000-08}, |
|
| 6257 | + volume = {97}, |
|
| 6258 | + number = {18}, |
|
| 6259 | + pages = {10209--10213}, |
|
| 6260 | + keywords = {nosource} |
|
| 6261 | +} |
|
| 6262 | + |
|
| 6263 | +@article{lossosPredictionSurvivalDiffuse2004, |
|
| 6264 | + title = {Prediction of {{Survival}} in {{Diffuse Large-B-Cell Lymphoma Based}} on the {{Expression}} of {{Six Genes}}}, |
|
| 6265 | + author = {Lossos, Izidore S and Czerwinski, Debra K and Alizadeh, Ash A and Wechser, Mark A and Tibshirani, Rob and Botstein, David and Levy, Ronald}, |
|
| 6266 | + date = {2004-04}, |
|
| 6267 | + journaltitle = {N Engl J Med}, |
|
| 6268 | + volume = {350}, |
|
| 6269 | + number = {18}, |
|
| 6270 | + pages = {1828--1837}, |
|
| 6271 | + keywords = {nosource} |
|
| 6272 | +} |
|
| 6273 | + |
|
| 6274 | +@article{louissaintPediatrictypeNodalFollicular2016a, |
|
| 6275 | + title = {Pediatric-Type Nodal Follicular Lymphoma: A Biologically Distinct Lymphoma with Frequent {{MAPK}} Pathway Mutations}, |
|
| 6276 | + shorttitle = {Pediatric-Type Nodal Follicular Lymphoma}, |
|
| 6277 | + author = {Louissaint, Abner and Schafernak, Kristian T. and Geyer, Julia T. and Kovach, Alexandra E. and Ghandi, Mahmoud and Gratzinger, Dita and Roth, Christine G. and Paxton, Christian N. and Kim, Sunhee and Namgyal, Chungdak and Morin, Ryan and Morgan, Elizabeth A. and Neuberg, Donna S. and South, Sarah T. and Harris, Marian H. and Hasserjian, Robert P. and Hochberg, Ephraim P. and Garraway, Levi A. and Harris, Nancy Lee and Weinstock, David M.}, |
|
| 6278 | + date = {2016-08-25}, |
|
| 6279 | + journaltitle = {Blood}, |
|
| 6280 | + shortjournal = {Blood}, |
|
| 6281 | + volume = {128}, |
|
| 6282 | + number = {8}, |
|
| 6283 | + eprint = {27325104}, |
|
| 6284 | + eprinttype = {pmid}, |
|
| 6285 | + pages = {1093--1100}, |
|
| 6286 | + issn = {1528-0020}, |
|
| 6287 | + doi = {10.1182/blood-2015-12-682591}, |
|
| 6288 | + abstract = {Pediatric-type nodal follicular lymphoma (PTNFL) is a variant of follicular lymphoma (FL) characterized by limited-stage presentation and invariably benign behavior despite often high-grade histological appearance. It is important to distinguish PTNFL from typical FL in order to avoid unnecessary treatment; however, this distinction relies solely on clinical and pathological criteria, which may be variably applied. To define the genetic landscape of PTNFL, we performed copy number analysis and exome and/or targeted sequencing of 26 PTNFLs (16 pediatric and 10 adult). The most commonly mutated gene in PTNFL was MAP2K1, encoding MEK1, with a mutation frequency of 43\%. All MAP2K1 mutations were activating missense mutations localized to exons 2 and 3, which encode negative regulatory and catalytic domains, respectively. Missense mutations in MAPK1 (2/22) and RRAS (1/22) were identified in cases that lacked MAP2K1 mutations. The second most commonly mutated gene in PTNFL was TNFRSF14, with a mutation frequency of 29\%, similar to that seen in limited-stage typical FL (P = .35). PTNFL was otherwise genomically bland and specifically lacked recurrent mutations in epigenetic modifiers (eg, CREBBP, KMT2D). Copy number aberrations affected a mean of only 0.5\% of PTNFL genomes, compared with 10\% of limited-stage typical FL genomes (P {$<$} .02). Importantly, the mutational profiles of PTNFLs in children and adults were highly similar. Together, these findings define PTNFL as a biologically and clinically distinct indolent lymphoma of children and adults characterized by a high prevalence of MAPK pathway mutations and a near absence of mutations in epigenetic modifiers.}, |
|
| 6289 | + langid = {english}, |
|
| 6290 | + pmcid = {PMC5000844}, |
|
| 6291 | + keywords = {Adolescent,Age Factors,Cell Shape,Child,Child Preschool,DNA Copy Number Variations,Epigenesis Genetic,Female,Humans,Immunophenotyping,Infant,Lymphoma Follicular,Male,MAP Kinase Signaling System,Mutation}, |
|
| 6292 | + file = {/Users/rmorin/Zotero/storage/JZ459PU3/Louissaint et al. - 2016 - Pediatric-type nodal follicular lymphoma a biolog.pdf} |
|
| 6293 | +} |
|
| 6294 | + |
|
| 6295 | +@article{loveGeneticLandscapeMutations2012, |
|
| 6296 | + title = {The Genetic Landscape of Mutations in {{Burkitt}} Lymphoma}, |
|
| 6297 | + author = {Love, Cassandra and Sun, Zhen and Jima, Dereje and Li, Guojie and Zhang, Jenny and Miles, Rodney and Richards, Kristy L. and Dunphy, Cherie H. and Choi, William W. L. and Srivastava, Gopesh and Lugar, Patricia L. and Rizzieri, David A. and Lagoo, Anand S. and Bernal-Mizrachi, Leon and Mann, Karen P. and Flowers, Christopher R. and Naresh, Kikkeri N. and Evens, Andrew M. and Chadburn, Amy and Gordon, Leo I. and Czader, Magdalena B. and Gill, Javed I. and Hsi, Eric D. and Greenough, Adrienne and Moffitt, Andrea B. and McKinney, Matthew and Banerjee, Anjishnu and Grubor, Vladimir and Levy, Shawn and Dunson, David B. and Dave, Sandeep S.}, |
|
| 6298 | + date = {2012-12}, |
|
| 6299 | + journaltitle = {Nature Genetics}, |
|
| 6300 | + shortjournal = {Nat Genet}, |
|
| 6301 | + volume = {44}, |
|
| 6302 | + number = {12}, |
|
| 6303 | + eprint = {23143597}, |
|
| 6304 | + eprinttype = {pmid}, |
|
| 6305 | + pages = {1321--1325}, |
|
| 6306 | + issn = {1546-1718}, |
|
| 6307 | + doi = {10.1038/ng.2468}, |
|
| 6308 | + abstract = {Burkitt lymphoma is characterized by deregulation of MYC, but the contribution of other genetic mutations to the disease is largely unknown. Here, we describe the first completely sequenced genome from a Burkitt lymphoma tumor and germline DNA from the same affected individual. We further sequenced the exomes of 59 Burkitt lymphoma tumors and compared them to sequenced exomes from 94 diffuse large B-cell lymphoma (DLBCL) tumors. We identified 70 genes that were recurrently mutated in Burkitt lymphomas, including ID3, GNA13, RET, PIK3R1 and the SWI/SNF genes ARID1A and SMARCA4. Our data implicate a number of genes in cancer for the first time, including CCT6B, SALL3, FTCD and PC. ID3 mutations occurred in 34\% of Burkitt lymphomas and not in DLBCLs. We show experimentally that ID3 mutations promote cell cycle progression and proliferation. Our work thus elucidates commonly occurring gene-coding mutations in Burkitt lymphoma and implicates ID3 as a new tumor suppressor gene.}, |
|
| 6309 | + langid = {english}, |
|
| 6310 | + pmcid = {PMC3674561}, |
|
| 6311 | + keywords = {Ammonia-Lyases,Base Sequence,Burkitt Lymphoma,Cell Line Tumor,Chaperonin Containing TCP-1,DNA Helicases,DNA-Binding Proteins,Genes myc,Genome Human,Glutamate Formimidoyltransferase,GTP-Binding Protein alpha Subunits G12-G13,Homeodomain Proteins,Humans,Inhibitor of Differentiation Proteins,Intracellular Signaling Peptides and Proteins,Lymphoma Large B-Cell Diffuse,Membrane Proteins,Molecular Sequence Data,Multifunctional Enzymes,Mutation,Neoplasm Proteins,Nuclear Proteins,Proto-Oncogene Proteins c-ret,Sequence Analysis DNA,Transcription Factors,Translocation Genetic}, |
|
| 6312 | + file = {/Users/rmorin/Zotero/storage/T6RYPBYW/Love et al. - 2012 - The genetic landscape of mutations in Burkitt lymp.pdf} |
|
| 6313 | +} |
|
| 6314 | + |
|
| 6315 | +@article{loveModeratedEstimationFold2014, |
|
| 6316 | + title = {Moderated Estimation of Fold Change and Dispersion for {{RNA-seq}} Data with {{DESeq2}}}, |
|
| 6317 | + author = {Love, Michael I. and Huber, Wolfgang and Anders, Simon}, |
|
| 6318 | + date = {2014}, |
|
| 6319 | + journaltitle = {Genome Biology}, |
|
| 6320 | + shortjournal = {Genome Biol.}, |
|
| 6321 | + volume = {15}, |
|
| 6322 | + number = {12}, |
|
| 6323 | + eprint = {25516281}, |
|
| 6324 | + eprinttype = {pmid}, |
|
| 6325 | + pages = {550}, |
|
| 6326 | + issn = {1474-760X}, |
|
| 6327 | + doi = {10.1186/s13059-014-0550-8}, |
|
| 6328 | + abstract = {In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html webcite.}, |
|
| 6329 | + langid = {english}, |
|
| 6330 | + pmcid = {PMC4302049}, |
|
| 6331 | + keywords = {Algorithms,Computational Biology,High-Throughput Nucleotide Sequencing,Models Genetic,RNA,Sequence Analysis RNA,Software} |
|
| 6332 | +} |
|
| 6333 | + |
|
| 6334 | +@article{luMCPIP1SelectivelyDestabilizes2016, |
|
| 6335 | + title = {{{MCPIP1 Selectively Destabilizes Transcripts Associated}} with an {{Antiapoptotic Gene Expression Program}} in {{Breast Cancer Cells That Can Elicit Complete Tumor Regression}}}, |
|
| 6336 | + author = {Lu, W and Ning, H and Gu, L and Peng, H and Wang, Q and Hou, R and Fu, M and Hoft, D F and Liu, J}, |
|
| 6337 | + date = {2016-03}, |
|
| 6338 | + journaltitle = {Cancer Res}, |
|
| 6339 | + volume = {76}, |
|
| 6340 | + number = {6}, |
|
| 6341 | + pages = {1429--1440}, |
|
| 6342 | + keywords = {nosource} |
|
| 6343 | +} |
|
| 6344 | + |
|
| 6345 | +@article{luoMultitaskConvolutionalDeep2019, |
|
| 6346 | + title = {A Multi-Task Convolutional Deep Neural Network for Variant Calling in Single Molecule Sequencing}, |
|
| 6347 | + author = {Luo, Ruibang and Sedlazeck, Fritz J. and Lam, Tak-Wah and Schatz, Michael C.}, |
|
| 6348 | + date = {2019-03-01}, |
|
| 6349 | + journaltitle = {Nature Communications}, |
|
| 6350 | + shortjournal = {Nat Commun}, |
|
| 6351 | + volume = {10}, |
|
| 6352 | + number = {1}, |
|
| 6353 | + eprint = {30824707}, |
|
| 6354 | + eprinttype = {pmid}, |
|
| 6355 | + pages = {998}, |
|
| 6356 | + issn = {2041-1723}, |
|
| 6357 | + doi = {10.1038/s41467-019-09025-z}, |
|
| 6358 | + abstract = {The accurate identification of DNA sequence variants is an important, but challenging task in genomics. It is particularly difficult for single molecule sequencing, which has a per-nucleotide error rate of \textasciitilde 5-15\%. Meeting this demand, we developed Clairvoyante, a multi-task five-layer convolutional neural network model for predicting variant type (SNP or indel), zygosity, alternative allele and indel length from aligned reads. For the well-characterized NA12878 human sample, Clairvoyante achieves 99.67, 95.78, 90.53\% F1-score on 1KP common variants, and 98.65, 92.57, 87.26\% F1-score for whole-genome analysis, using Illumina, PacBio, and Oxford Nanopore data, respectively. Training on a second human sample shows Clairvoyante is sample agnostic and finds variants in less than 2\,h on a standard server. Furthermore, we present 3,135 variants that are missed using Illumina but supported independently by both PacBio and Oxford Nanopore reads. Clairvoyante is available open-source ( https://github.com/aquaskyline/Clairvoyante ), with modules to train, utilize and visualize the model.}, |
|
| 6359 | + langid = {english}, |
|
| 6360 | + pmcid = {PMC6397153}, |
|
| 6361 | + keywords = {Base Sequence,Computational Biology,DNA Mutational Analysis,Genome Human,Genome-Wide Association Study,Genomics,Genotype,Genotyping Techniques,Humans,INDEL Mutation,Nanopores,Neural Networks Computer,Polymorphism Single Nucleotide,Sequence Analysis DNA,Software}, |
|
| 6362 | + file = {/Users/rmorin/Zotero/storage/8IXFMWMU/Luo et al. - 2019 - A multi-task convolutional deep neural network for.pdf} |
|
| 6363 | +} |
|
| 6364 | + |
|
| 6365 | +@article{luPatternsFunctionalImplications2015, |
|
| 6366 | + title = {Patterns and Functional Implications of Rare Germline Variants across 12 Cancer Types}, |
|
| 6367 | + author = {Lu, Charles and Xie, Mingchao and Wendl, Michael C. and Wang, Jiayin and McLellan, Michael D. and Leiserson, Mark D. M. and Huang, Kuan-lin and Wyczalkowski, Matthew A. and Jayasinghe, Reyka and Banerjee, Tapahsama and Ning, Jie and Tripathi, Piyush and Zhang, Qunyuan and Niu, Beifang and Ye, Kai and Schmidt, Heather K. and Fulton, Robert S. and McMichael, Joshua F. and Batra, Prag and Kandoth, Cyriac and Bharadwaj, Maheetha and Koboldt, Daniel C. and Miller, Christopher A. and Kanchi, Krishna L. and Eldred, James M. and Larson, David E. and Welch, John S. and You, Ming and Ozenberger, Bradley A. and Govindan, Ramaswamy and Walter, Matthew J. and Ellis, Matthew J. and Mardis, Elaine R. and Graubert, Timothy A. and Dipersio, John F. and Ley, Timothy J. and Wilson, Richard K. and Goodfellow, Paul J. and Raphael, Benjamin J. and Chen, Feng and Johnson, Kimberly J. and Parvin, Jeffrey D. and Ding, Li}, |
|
| 6368 | + date = {2015-12-22}, |
|
| 6369 | + journaltitle = {Nature Communications}, |
|
| 6370 | + shortjournal = {Nat Commun}, |
|
| 6371 | + volume = {6}, |
|
| 6372 | + number = {1}, |
|
| 6373 | + pages = {10086}, |
|
| 6374 | + publisher = {Nature Publishing Group}, |
|
| 6375 | + issn = {2041-1723}, |
|
| 6376 | + doi = {10.1038/ncomms10086}, |
|
| 6377 | + url = {https://www.nature.com/articles/ncomms10086}, |
|
| 6378 | + urldate = {2022-05-19}, |
|
| 6379 | + abstract = {Large-scale cancer sequencing data enable discovery of rare germline cancer susceptibility variants. Here we systematically analyse 4,034 cases from The Cancer Genome Atlas cancer cases representing 12 cancer types. We find that the frequency of rare germline truncations in 114 cancer-susceptibility-associated genes varies widely, from 4\% (acute myeloid leukaemia (AML)) to 19\% (ovarian cancer), with a notably high frequency of 11\% in stomach cancer. Burden testing identifies 13 cancer genes with significant enrichment of rare truncations, some associated with specific cancers (for example, RAD51C, PALB2 and MSH6 in AML, stomach and endometrial cancers, respectively). Significant, tumour-specific loss of heterozygosity occurs in nine genes (ATM, BAP1, BRCA1/2, BRIP1, FANCM, PALB2 and RAD51C/D). Moreover, our homology-directed repair assay of 68 BRCA1 rare missense variants supports the utility of allelic enrichment analysis for characterizing variants of unknown significance. The scale of this analysis and the somatic-germline integration enable the detection of rare variants that may affect individual susceptibility to tumour development, a critical step toward precision medicine.}, |
|
| 6380 | + issue = {1}, |
|
| 6381 | + langid = {english}, |
|
| 6382 | + keywords = {Cancer genetics,Genetic variation}, |
|
| 6383 | + file = {/Users/rmorin/Zotero/storage/A49Y9IHF/Lu et al. - 2015 - Patterns and functional implications of rare germl.pdf;/Users/rmorin/Zotero/storage/3QK745ZB/ncomms10086.html} |
|
| 6384 | +} |
|
| 6385 | + |
|
| 6386 | +@article{lyuRGelBLySFusion, |
|
| 6387 | + title = {The {{rGel}}/{{BLyS}} Fusion Toxin Inhibits {{STAT3}} Signaling via down-Regulation of Interleukin-6 Receptor in Diffuse Large {{B-cell}} Lymphoma}, |
|
| 6388 | + author = {Lyu, Mi-Ae and Sung, Bokyung and Cheung, Lawrence H and Marks, John W and Aggarwal, Bharat B and Aguiar, Ricardo C T and Rosenblum, Michael G}, |
|
| 6389 | + journaltitle = {Biochemical Pharmacology}, |
|
| 6390 | + volume = {80}, |
|
| 6391 | + number = {9}, |
|
| 6392 | + pages = {1335--1342}, |
|
| 6393 | + keywords = {nosource} |
|
| 6394 | +} |
|
| 6395 | + |
|
| 6396 | +@article{machadoDiverseMutationalLandscapes2022, |
|
| 6397 | + title = {Diverse Mutational Landscapes in Human Lymphocytes}, |
|
| 6398 | + author = {Machado, Heather E. and Mitchell, Emily and Øbro, Nina F. and Kübler, Kirsten and Davies, Megan and Leongamornlert, Daniel and Cull, Alyssa and Maura, Francesco and Sanders, Mathijs A. and Cagan, Alex T. J. and McDonald, Craig and Belmonte, Miriam and Shepherd, Mairi S. and Vieira Braga, Felipe A. and Osborne, Robert J. and Mahbubani, Krishnaa and Martincorena, Iñigo and Laurenti, Elisa and Green, Anthony R. and Getz, Gad and Polak, Paz and Saeb-Parsy, Kourosh and Hodson, Daniel J. and Kent, David G. and Campbell, Peter J.}, |
|
| 6399 | + date = {2022-08}, |
|
| 6400 | + journaltitle = {Nature}, |
|
| 6401 | + shortjournal = {Nature}, |
|
| 6402 | + volume = {608}, |
|
| 6403 | + number = {7924}, |
|
| 6404 | + eprint = {35948631}, |
|
| 6405 | + eprinttype = {pmid}, |
|
| 6406 | + pages = {724--732}, |
|
| 6407 | + issn = {1476-4687}, |
|
| 6408 | + doi = {10.1038/s41586-022-05072-7}, |
|
| 6409 | + abstract = {The lymphocyte genome is prone to many threats, including programmed mutation during differentiation1, antigen-driven proliferation and residency in diverse microenvironments. Here, after developing protocols for expansion of single-cell lymphocyte cultures, we sequenced whole genomes from 717 normal naive and memory B and T cells and haematopoietic stem cells. All lymphocyte subsets carried more point mutations and structural variants than haematopoietic stem cells, with higher burdens in memory cells than in naive cells, and with T cells accumulating mutations at a higher rate throughout life. Off-target effects of immunological diversification accounted for approximately half of the additional differentiation-associated mutations in lymphocytes. Memory B cells acquired, on average, 18 off-target mutations genome-wide for every on-target IGHV mutation during the germinal centre reaction. Structural variation was 16-fold higher in lymphocytes than in stem cells, with around 15\% of deletions being attributable to off-target recombinase-activating gene activity. DNA damage from ultraviolet light exposure and other sporadic mutational processes generated hundreds to thousands of mutations in some memory cells. The mutation burden and signatures of normal B cells were broadly similar to those seen in many B-cell cancers, suggesting that malignant transformation of lymphocytes arises from the same mutational processes that are active across normal ontogeny. The mutational landscape of normal lymphocytes chronicles the off-target effects of programmed genome engineering during immunological diversification and the consequences of differentiation, proliferation and residency in diverse microenvironments.}, |
|
| 6410 | + langid = {english}, |
|
| 6411 | + pmcid = {PMC9402440}, |
|
| 6412 | + keywords = {B-Lymphocytes,Cell Differentiation,Cell Proliferation,Cellular Microenvironment,DNA Damage,Germinal Center,Humans,Immunologic Memory,Lymphocytes,Mutation,Neoplasms}, |
|
| 6413 | + file = {/Users/rmorin/Zotero/storage/N6KFJQ6M/Machado et al. - 2022 - Diverse mutational landscapes in human lymphocytes.pdf} |
|
| 6414 | +} |
|
| 6415 | + |
|
| 6416 | +@article{machadoEvolutionaryHistoryCopyNumberVariable2012, |
|
| 6417 | + title = {Evolutionary {{History}} of {{Copy-Number-Variable Locus}} for the {{Low-Affinity Fcγ Receptor}}: {{Mutation Rate}}, {{Autoimmune Disease}}, and the {{Legacy}} of {{Helminth Infection}}}, |
|
| 6418 | + author = {Machado, Lee R. and Hardwick, Robert J. and Bowdrey, Jennifer and Bogle, Helen and Knowles, Timothy J. and Sironi, Manuela and Hollox, Edward J.}, |
|
| 6419 | + date = {2012-12}, |
|
| 6420 | + journaltitle = {The American Journal of Human Genetics}, |
|
| 6421 | + volume = {90}, |
|
| 6422 | + number = {6}, |
|
| 6423 | + eprint = {22608500}, |
|
| 6424 | + eprinttype = {pmid}, |
|
| 6425 | + pages = {973--985}, |
|
| 6426 | + issn = {0002-9297}, |
|
| 6427 | + doi = {10.1016/j.ajhg.2012.04.018}, |
|
| 6428 | + url = {http://dx.doi.org/10.1016/j.ajhg.2012.04.018}, |
|
| 6429 | + abstract = {Both sequence variation and copy-number variation (CNV) of the genes encoding receptors for immunoglobulin G (Fcγ receptors) have been genetically and functionally associated with a number of autoimmune diseases. However, the molecular nature and evolutionary context of this variation is unknown. Here, we describe the structure of the CNV, estimate its mutation rate and diversity, and place it in the context of the known functional alloantigen variation of these genes. Deletion of Fcγ receptor IIIB, associated with systemic lupus erythematosus, is a result of independent nonallelic homologous recombination events with a frequency of approximately 0.1\%. We also show that pathogen diversity, in particular helminth diversity, has played a critical role in shaping the functional variation at these genes both between mammalian species and between human populations. Positively selected amino acids are involved in the interaction with IgG and include some amino acids that are known polymorphic alloantigens in humans. This supports a genetic contribution to the hygiene hypothesis, which states that past evolution in the context of helminth diversity has left humans with an array of susceptibility alleles for autoimmune disease in the context of a helminth-free environment. This approach shows the link between pathogens and autoimmune disease at the genetic level and provides a strategy for interrogating the genetic variation underlying autoimmune-disease risk and infectious-disease susceptibility.}, |
|
| 6430 | + keywords = {nosource} |
|
| 6431 | +} |
|
| 6432 | + |
|
| 6433 | +@article{maddocksIbrutinibBcellLymphomas2014, |
|
| 6434 | + title = {Ibrutinib in {{B-cell Lymphomas}}.}, |
|
| 6435 | + author = {Maddocks, Kami and Blum, Kristie A}, |
|
| 6436 | + date = {2014-06}, |
|
| 6437 | + journaltitle = {Current treatment options in oncology}, |
|
| 6438 | + volume = {15}, |
|
| 6439 | + number = {2}, |
|
| 6440 | + pages = {226--237}, |
|
| 6441 | + keywords = {nosource} |
|
| 6442 | +} |
|
| 6443 | + |
|
| 6444 | +@article{maddocksUpdateMantleCell2018, |
|
| 6445 | + title = {Update on Mantle Cell Lymphoma}, |
|
| 6446 | + author = {Maddocks, Kami}, |
|
| 6447 | + date = {2018-10-18}, |
|
| 6448 | + journaltitle = {Blood}, |
|
| 6449 | + shortjournal = {Blood}, |
|
| 6450 | + volume = {132}, |
|
| 6451 | + number = {16}, |
|
| 6452 | + eprint = {30154113}, |
|
| 6453 | + eprinttype = {pmid}, |
|
| 6454 | + pages = {1647--1656}, |
|
| 6455 | + issn = {1528-0020}, |
|
| 6456 | + doi = {10.1182/blood-2018-03-791392}, |
|
| 6457 | + abstract = {Mantle cell lymphoma (MCL) is a rare subtype of non-Hodgkin lymphoma that is most commonly treated with combination chemo-immunotherapy at diagnosis because of the poor prognosis. More indolent presentations have been described including patients who can defer initial therapy without adverse impact on survival. The 2016 World Health Organization updated classification describes 2 major subtypes, classical and leukemic nonnodal MCL, each with unique molecular features and clinical presentations. Although there is no standard of care for MCL, aggressive chemo-immunotherapy regimens containing rituximab and cytarabine, followed by consolidation with autologous stem cell transplantation and maintenance rituximab, are the most used approach in young fit patients, and chemo-immunotherapy, followed by rituximab maintenance, is most commonly used in older patients. Despite the improvement in response durations with currently available therapies, patients will inevitably relapse. A number of targeted therapies are approved in the relapsed setting and are now under evaluation in combination with standard frontline therapy. Although the approval of ibrutinib changed the landscape of therapy for relapsed MCL, prognosis remains poor after progression on ibrutinib supporting the development of ibrutinib combinations to prolong response duration as well as the development of other novel agents for ibrutinib refractory disease. With ibrutinib being incorporated into initial therapy regimens, new options will be needed at relapse. Prognostic markers, such as minimal residual disease, have been shown to correlate independently with outcomes along with predicting relapse, with the potential to guide therapeutic decisions. The future treatment of MCL therapy will need to incorporate therapy based on risk-stratification and nonchemotherapeutic approaches.}, |
|
| 6458 | + langid = {english}, |
|
| 6459 | + keywords = {Animals,Humans,Lymphoma Mantle-Cell,Prognosis} |
|
| 6460 | +} |
|
| 6461 | + |
|
| 6462 | +@article{mahmoudSignificanceBcl2Bcl62011, |
|
| 6463 | + title = {Significance of {{Bcl-2}} and {{Bcl-6}} Immunostaining in {{B-Non Hodgkin}}'s Lymphoma}, |
|
| 6464 | + author = {Mahmoud, Hanan Mohamed and El-Sakhawy, Yasmin Nabil}, |
|
| 6465 | + date = {2011-11-16}, |
|
| 6466 | + journaltitle = {Hematology Reports}, |
|
| 6467 | + shortjournal = {Hematol Rep}, |
|
| 6468 | + volume = {3}, |
|
| 6469 | + number = {3}, |
|
| 6470 | + eprint = {22593817}, |
|
| 6471 | + eprinttype = {pmid}, |
|
| 6472 | + pages = {e26}, |
|
| 6473 | + issn = {2038-8322}, |
|
| 6474 | + doi = {10.4081/hr.2011.e26}, |
|
| 6475 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3269794/}, |
|
| 6476 | + urldate = {2022-10-04}, |
|
| 6477 | + abstract = {The determination of prognosis for B-Non-Hodgkin's lymphoma (NHL) is known to be related to the multiple differences in tumor cell biology. Bcl-2 and Bcl-6 are two markers linked to germinal center B cells. Both markers are thought to have an effect on prognosis of mature B-cell neoplasms. Forty-four patients with chronic B-cell neoplasm were included; Bcl-2 and Bcl-6 expression by immunohistochemistry was examined. Bcl-2 protein was positive in 36.4\% (16 of 44) of cases (62.5\% of follicular lymphoma, 16.7\% of mantle cell lymphoma and 30\% of diffuse large B-cell lymphoma); the positive group implying a bad prognostic effect of the marker in NHL. Bcl-6 was positive in 13.6\% (6 of 44) of cases (11.1\% of mantle cell lymphoma and 40\% of diffuse large B-cell lymphoma) and its positivity implies a better disease course. Bcl-2 and Bcl-6 can be used as prognostic marker in NHL.}, |
|
| 6478 | + pmcid = {PMC3269794}, |
|
| 6479 | + file = {/Users/rmorin/Zotero/storage/3KPEBK57/Mahmoud and El-Sakhawy - 2011 - Significance of Bcl-2 and Bcl-6 immunostaining in .pdf} |
|
| 6480 | +} |
|
| 6481 | + |
|
| 6482 | +@article{makhafolaApoptosisCancerCells2020, |
|
| 6483 | + title = {Apoptosis in {{Cancer Cells Is Induced}} by {{Alternative Splicing}} of {{hnRNPA2}}/{{B1 Through Splicing}} of {{Bcl-x}}, a {{Mechanism}} That {{Can Be Stimulated}} by an {{Extract}} of the {{South African Medicinal Plant}}, {{Cotyledon}} Orbiculata}, |
|
| 6484 | + author = {Makhafola, Tshepiso Jan and Mbele, Mzwandile and Yacqub-Usman, Kiren and Hendren, Amy and Haigh, Daisy Belle and Blackley, Zoe and Meyer, Mervin and Mongan, Nigel Patrick and Bates, David Owen and Dlamini, Zodwa}, |
|
| 6485 | + date = {2020-10-08}, |
|
| 6486 | + journaltitle = {Frontiers in Oncology}, |
|
| 6487 | + shortjournal = {Front. Oncol.}, |
|
| 6488 | + volume = {10}, |
|
| 6489 | + pages = {547392}, |
|
| 6490 | + issn = {2234-943X}, |
|
| 6491 | + doi = {10.3389/fonc.2020.547392}, |
|
| 6492 | + url = {https://www.frontiersin.org/article/10.3389/fonc.2020.547392/full}, |
|
| 6493 | + urldate = {2022-10-04}, |
|
| 6494 | + langid = {english}, |
|
| 6495 | + file = {/Users/rmorin/Zotero/storage/T2BQMQZ2/Makhafola et al. - 2020 - Apoptosis in Cancer Cells Is Induced by Alternativ.pdf} |
|
| 6496 | +} |
|
| 6497 | + |
|
| 6498 | +@article{makkiHistoneDeacetylaseInhibitor2016, |
|
| 6499 | + title = {Histone {{Deacetylase Inhibitor Vorinostat}} ({{SAHA}}, {{MK0683}}) {{Perturb miR-9-MCPIP1 Axis To Block IL-1β-induced IL-6 Expression}} in {{Human OA Chondrocytes}}}, |
|
| 6500 | + author = {Makki, Mohammad S and Haqqi, Tariq M}, |
|
| 6501 | + date = {2016-07}, |
|
| 6502 | + journaltitle = {Connective Tissue Research}, |
|
| 6503 | + pages = {03008207.2016.1211113--37}, |
|
| 6504 | + keywords = {nosource} |
|
| 6505 | +} |
|
| 6506 | + |
|
| 6507 | +@article{mandelbaumBLIMP1TumorSuppressor2010, |
|
| 6508 | + title = {{{BLIMP1}} Is a Tumor Suppressor Gene Frequently Disrupted in Activated {{B}} Cell-like Diffuse Large {{B}} Cell Lymphoma.}, |
|
| 6509 | + author = {Mandelbaum, Jonathan and Bhagat, Govind and Tang, Hongyan and Mo, Tongwei and Brahmachary, Manisha and Shen, Qiong and Chadburn, Amy and Rajewsky, Klaus and Tarakhovsky, Alexander and Pasqualucci, Laura and Dalla-Favera, Riccardo}, |
|
| 6510 | + date = {2010-12}, |
|
| 6511 | + journaltitle = {Cancer Cell}, |
|
| 6512 | + volume = {18}, |
|
| 6513 | + number = {6}, |
|
| 6514 | + pages = {568--579}, |
|
| 6515 | + keywords = {nosource} |
|
| 6516 | +} |
|
| 6517 | + |
|
| 6518 | +@article{mangLongNoncodingRNA2017, |
|
| 6519 | + title = {Long Noncoding {{RNA NEAT1}} Promotes Cell Proliferation and Invasion by Regulating {{hnRNP A2}} Expression in Hepatocellular Carcinoma Cells}, |
|
| 6520 | + author = {Mang, Yuanyi and Li, Li and Ran, Jianghua and Zhang, Shengning and Liu, Jing and Li, Laibang and Chen, Yiming and Liu, Jian and Gao, Yang and Ren, Gang}, |
|
| 6521 | + date = {2017-02-20}, |
|
| 6522 | + journaltitle = {OncoTargets and Therapy}, |
|
| 6523 | + shortjournal = {OTT}, |
|
| 6524 | + volume = {10}, |
|
| 6525 | + pages = {1003--1016}, |
|
| 6526 | + publisher = {Dove Press}, |
|
| 6527 | + doi = {10.2147/OTT.S116319}, |
|
| 6528 | + url = {https://www.dovepress.com/long-noncoding-rna-neat1-promotes-cell-proliferation-and-invasion-by-r-peer-reviewed-fulltext-article-OTT}, |
|
| 6529 | + urldate = {2022-09-28}, |
|
| 6530 | + abstract = {Long noncoding RNA NEAT1 promotes cell proliferation and invasion by regulating hnRNP A2 expression in hepatocellular carcinoma cells Yuanyi Mang, Li Li, Jianghua Ran, Shengning Zhang, Jing Liu, Laibang Li, Yiming Chen, Jian Liu, Yang Gao, Gang Ren Department of Hepato-Biliary-Pancreatic Surgery, The Calmette Affiliated Hospital of Kunming Medical University, The First Hospital of Kunming, Kunming, Yunnan, People\’s Republic of China Abstract: Growing evidence demonstrates that long noncoding RNAs (lncRNAs) are involved in the progression of various cancers, including hepatocellular carcinoma (HCC). The role of nuclear-enriched abundant transcript 1 (NEAT1), an essential lncRNA for the formation of nuclear body paraspeckles, has not been fully explored in HCC. We aimed to determine the expression, roles and functional mechanisms of NEAT1 in the proliferation and invasion of HCC. Based on real-time polymerase chain reaction data, we suggest that NEAT1 is upregulated in HCC tissues compared with noncancerous liver tissues. The knockdown of NEAT1 altered global gene expression patterns and reduced HCC cell proliferation, invasion and migration. RNA immunoprecipitation and RNA pull-down assays confirmed that U2AF65 binds to NEAT1. Furthermore, the study indicated that NEAT1 regulated hnRNP A2 expression and that this regulation may be associated with the NEAT1\–U2AF65 protein complex. Thus, the NEAT1-hnRNP A2 regulation mechanism promotes HCC pathogenesis and may provide a potential target for the prognosis and treatment of HCC. Keywords: long noncoding RNA, NEAT1, RNA-binding protein, HCC}, |
|
| 6531 | + langid = {english}, |
|
| 6532 | + file = {/Users/rmorin/Zotero/storage/D4SH4KBY/Mang et al. - 2017 - Long noncoding RNA NEAT1 promotes cell proliferati.pdf;/Users/rmorin/Zotero/storage/R2ESTMYV/long-noncoding-rna-neat1-promotes-cell-proliferation-and-invasion-by-r-peer-reviewed-fulltext-a.html} |
|
| 6533 | +} |
|
| 6534 | + |
|
| 6535 | +@article{mannenSam68NuclearBody2016, |
|
| 6536 | + title = {The {{Sam68}} Nuclear Body Is Composed of Two {{RNase-sensitive}} Substructures Joined by the Adaptor {{HNRNPL}}}, |
|
| 6537 | + author = {Mannen, Taro and Yamashita, Seisuke and Tomita, Kozo and Goshima, Naoki and Hirose, Tetsuro}, |
|
| 6538 | + date = {2016-07-04}, |
|
| 6539 | + journaltitle = {Journal of Cell Biology}, |
|
| 6540 | + shortjournal = {Journal of Cell Biology}, |
|
| 6541 | + volume = {214}, |
|
| 6542 | + number = {1}, |
|
| 6543 | + pages = {45--59}, |
|
| 6544 | + issn = {0021-9525}, |
|
| 6545 | + doi = {10.1083/jcb.201601024}, |
|
| 6546 | + url = {https://doi.org/10.1083/jcb.201601024}, |
|
| 6547 | + urldate = {2023-01-09}, |
|
| 6548 | + abstract = {The mammalian cell nucleus contains membraneless suborganelles referred to as nuclear bodies (NBs). Some NBs are formed with an architectural RNA (arcRNA) as the structural core. Here, we searched for new NBs that are built on unidentified arcRNAs by screening for ribonuclease (RNase)-sensitive NBs using 32,651 fluorescently tagged human cDNA clones. We identified 32 tagged proteins that required RNA for their localization in distinct nuclear foci. Among them, seven RNA-binding proteins commonly localized in the Sam68 nuclear body (SNB), which was disrupted by RNase treatment. Knockdown of each SNB protein revealed that SNBs are composed of two distinct RNase-sensitive substructures. One substructure is present as a distinct NB, termed the DBC1 body, in certain conditions, and the more dynamic substructure including Sam68 joins to form the intact SNB. HNRNPL acts as the adaptor to combine the two substructures and form the intact SNB through the interaction of two sets of RNA recognition motifs with the putative arcRNAs in the respective substructures.}, |
|
| 6549 | + file = {/Users/rmorin/Zotero/storage/4DKGASEA/Mannen et al. - 2016 - The Sam68 nuclear body is composed of two RNase-se.pdf} |
|
| 6550 | +} |
|
| 6551 | + |
|
| 6552 | +@article{mansouriFrequentNFKBIEDeletions2016, |
|
| 6553 | + title = {Frequent {{NFKBIE}} Deletions Are Associated with Poor Outcome in Primary Mediastinal {{B-cell}} Lymphoma}, |
|
| 6554 | + author = {Mansouri, Larry and Noerenberg, Daniel and Young, Emma and Mylonas, Elena and Abdulla, Maysaa and Frick, Mareike and Asmar, Fazila and Ljungström, Viktor and Schneider, Markus and Yoshida, Kenichi and Skaftason, Aron and Pandzic, Tatjana and Gonzalez, Blanca and Tasidou, Anna and Waldhueter, Nils and Rivas-Delgado, Alfredo and Angelopoulou, Maria and Ziepert, Marita and Arends, Christopher Maximilian and Couronné, Lucile and Lenze, Dido and Baldus, Claudia D. and Bastard, Christian and Okosun, Jessica and Fitzgibbon, Jude and Dörken, Bernd and Drexler, Hans G. and Roos-Weil, Damien and Schmitt, Clemens A. and Munch-Petersen, Helga D. and Zenz, Thorsten and Hansmann, Martin-Leo and Strefford, Jonathan C. and Enblad, Gunilla and Bernard, Olivier A. and Ralfkiaer, Elisabeth and Erlanson, Martin and Korkolopoulou, Penelope and Hultdin, Magnus and Papadaki, Theodora and Grønbæk, Kirsten and Lopez-Guillermo, Armando and Ogawa, Seishi and Küppers, Ralf and Stamatopoulos, Kostas and Stavroyianni, Niki and Kanellis, George and Rosenwald, Andreas and Campo, Elias and Amini, Rose-Marie and Ott, German and Vassilakopoulos, Theodoros P. and Hummel, Michael and Rosenquist, Richard and Damm, Frederik}, |
|
| 6555 | + date = {2016-12-08}, |
|
| 6556 | + journaltitle = {Blood}, |
|
| 6557 | + shortjournal = {Blood}, |
|
| 6558 | + volume = {128}, |
|
| 6559 | + number = {23}, |
|
| 6560 | + pages = {2666--2670}, |
|
| 6561 | + issn = {0006-4971}, |
|
| 6562 | + doi = {10.1182/blood-2016-03-704528}, |
|
| 6563 | + url = {https://ashpublications.org/blood/article/128/23/2666/35651/Frequent-NFKBIE-deletions-are-associated-with-poor}, |
|
| 6564 | + urldate = {2019-12-21}, |
|
| 6565 | + langid = {english}, |
|
| 6566 | + file = {/Users/rmorin/Zotero/storage/Y7UJZ5JW/blood-2016-03-704528.html} |
|
| 6567 | +} |
|
| 6568 | + |
|
| 6569 | +@article{mareschalWholeExomeSequencing2016, |
|
| 6570 | + title = {Whole Exome Sequencing of Relapsed/Refractory Patients Expands the Repertoire of Somatic Mutations in Diffuse Large {{B-cell}} Lymphoma}, |
|
| 6571 | + author = {Mareschal, Sylvain and Dubois, Sydney and Viailly, Pierre-Julien and Bertrand, Philippe and Bohers, Elodie and Maingonnat, Catherine and Jaïs, Jean-Philippe and Tesson, Bruno and Ruminy, Philippe and Peyrouze, Pauline and Copie-Bergman, Christiane and Fest, Thierry and Jo Molina, Thierry and Haioun, Corinne and Salles, Gilles and Tilly, Hervé and Lecroq, Thierry and Leroy, Karen and Jardin, Fabrice}, |
|
| 6572 | + date = {2016-03}, |
|
| 6573 | + journaltitle = {Genes, Chromosomes \& Cancer}, |
|
| 6574 | + shortjournal = {Genes Chromosomes Cancer}, |
|
| 6575 | + volume = {55}, |
|
| 6576 | + number = {3}, |
|
| 6577 | + eprint = {26608593}, |
|
| 6578 | + eprinttype = {pmid}, |
|
| 6579 | + pages = {251--267}, |
|
| 6580 | + issn = {1098-2264}, |
|
| 6581 | + doi = {10.1002/gcc.22328}, |
|
| 6582 | + abstract = {Despite the many efforts already spent to enumerate somatic mutations in diffuse large B-cell lymphoma (DLBCL), previous whole-genome and whole-exome studies conducted on patients of mixed outcomes failed at characterizing the 30\% of patients who will relapse or resist current immunochemotherapies. To address this issue, we performed whole-exome sequencing of normal/tumoral DNA pairs in 14 relapsed/refractory (R/R) patients subclassified by full-transcriptome arrays (six activated B-cell like, three germinal center B-cell like, and five primary mediastinal B-cell lymphomas), from the LNH-03 LYSA clinical trial program. Aside from well-known DLBCL features, gene and pathway level recurrence analyses proposed several interesting leads including TBL1XR1 and activating mutations in IRF4 or in the insulin regulation pathway. Sequencing-based copy number analysis defined 23 short recurrently altered regions involving genes such as REL, CDKN2A, HYAL2, and TP53. Moreover, it highlighted mutations in genes such as GNA13, CARD11, MFHAS1, and PCLO as associated with secondary variant allele amplification events. The five primary mediastinal B-cell lymphomas (PMBL), while unexpected in a R/R cohort, showed a significantly higher mutation rate (P = 0.003) and provided many insights on this classical Hodgkin lymphoma related subtype. Novel genes such as XPO1, MFHAS1, and ITPKB were found particularly mutated, along with various cytokine-based signaling pathways. Among these analyses, somatic events in the NF-κB pathway were found preponderant in the three DLBCL subtypes, confirming its major implication in DLBCL aggressiveness and pinpointing several new candidate genes.}, |
|
| 6583 | + langid = {english}, |
|
| 6584 | + keywords = {Adult,Aged,Aged 80 and over,DNA Neoplasm,Exome,Female,High-Throughput Nucleotide Sequencing,Humans,Interferon Regulatory Factors,Lymphoma Large B-Cell Diffuse,Male,Middle Aged,Mutation,Neoplasm Recurrence Local,NF-kappa B,Signal Transduction} |
|
| 6585 | +} |
|
| 6586 | + |
|
| 6587 | +@article{martinez-climentTransformationFollicularLymphoma2003, |
|
| 6588 | + title = {Transformation of Follicular Lymphoma to Diffuse Large Cell Lymphoma Is Associated with a Heterogeneous Set of {{DNA}} Copy Number and Gene Expression Alterations.}, |
|
| 6589 | + author = {Martinez-Climent, Jose A and Alizadeh, Ash A and Segraves, Richard and Blesa, David and Rubio-Moscardo, Fanny and Albertson, Donna G and Garcia-Conde, Javier and Dyer, Martin J S and Levy, Ronald and Pinkel, Daniel and Lossos, Izidore S}, |
|
| 6590 | + date = {2003-04}, |
|
| 6591 | + journaltitle = {Blood}, |
|
| 6592 | + volume = {101}, |
|
| 6593 | + number = {8}, |
|
| 6594 | + pages = {3109--3117}, |
|
| 6595 | + keywords = {nosource} |
|
| 6596 | +} |
|
| 6597 | + |
|
| 6598 | +@article{martinezProteinRNANetworksRegulated2016, |
|
| 6599 | + title = {Protein-{{RNA Networks Regulated}} by {{Normal}} and {{ALS-Associated Mutant HNRNPA2B1}} in the {{Nervous System}}}, |
|
| 6600 | + author = {Martinez, Fernando J. and Pratt, Gabriel A. and Van Nostrand, Eric L. and Batra, Ranjan and Huelga, Stephanie C. and Kapeli, Katannya and Freese, Peter and Chun, Seung J. and Ling, Karen and Gelboin-Burkhart, Chelsea and Fijany, Layla and Wang, Harrison C. and Nussbacher, Julia K. and Broski, Sara M. and Kim, Hong Joo and Lardelli, Rea and Sundararaman, Balaji and Donohue, John P. and Javaherian, Ashkan and Lykke-Andersen, Jens and Finkbeiner, Steven and Bennett, C. Frank and Ares, Manuel and Burge, Christopher B. and Taylor, J. Paul and Rigo, Frank and Yeo, Gene W.}, |
|
| 6601 | + date = {2016-11-23}, |
|
| 6602 | + journaltitle = {Neuron}, |
|
| 6603 | + shortjournal = {Neuron}, |
|
| 6604 | + volume = {92}, |
|
| 6605 | + number = {4}, |
|
| 6606 | + pages = {780--795}, |
|
| 6607 | + issn = {0896-6273}, |
|
| 6608 | + doi = {10.1016/j.neuron.2016.09.050}, |
|
| 6609 | + url = {http://www.sciencedirect.com/science/article/pii/S0896627316306559}, |
|
| 6610 | + urldate = {2019-12-21}, |
|
| 6611 | + abstract = {HnRNPA2B1 encodes an RNA binding protein associated with neurodegeneration. However, its function in the nervous system is unclear. Transcriptome-wide crosslinking and immunoprecipitation in mouse spinal cord discover UAGG motifs enriched within ∼2,500 hnRNP A2/B1 binding sites and an unexpected role for hnRNP A2/B1 in alternative polyadenylation. HnRNP A2/B1 loss results in alternative splicing (AS), including skipping of an exon in amyotrophic lateral sclerosis (ALS)-associated D-amino acid oxidase (DAO) that reduces D-serine metabolism. ALS-associated hnRNP A2/B1 D290V mutant patient fibroblasts and motor neurons differentiated from induced pluripotent stem cells (iPSC-MNs) demonstrate abnormal splicing changes, likely due to increased nuclear-insoluble hnRNP A2/B1. Mutant iPSC-MNs display decreased survival in long-term culture and exhibit hnRNP A2/B1 localization to cytoplasmic granules as well as exacerbated changes in gene expression and splicing upon cellular stress. Our findings provide a cellular resource and reveal RNA networks relevant to neurodegeneration, regulated by normal and mutant hnRNP A2/B1. Video Abstract}, |
|
| 6612 | + langid = {english}, |
|
| 6613 | + file = {/Users/rmorin/Zotero/storage/FFPNYITZ/S0896627316306559.html} |
|
| 6614 | +} |
|
| 6615 | + |
|
| 6616 | +@article{maruyamaScreeningPosttranscriptionalRegulatory2016, |
|
| 6617 | + title = {Screening of Posttranscriptional Regulatory Molecules of {{I}}\κ{{B-}}\ζ}, |
|
| 6618 | + author = {MaruYama, Takashi and Sayama, Aoi and Ishii, Ken J and Muta, Tatsushi}, |
|
| 6619 | + date = {2016-01}, |
|
| 6620 | + journaltitle = {Biochemical and biophysical research communications}, |
|
| 6621 | + volume = {469}, |
|
| 6622 | + number = {3}, |
|
| 6623 | + pages = {711--715}, |
|
| 6624 | + keywords = {nosource} |
|
| 6625 | +} |
|
| 6626 | + |
|
| 6627 | +@article{marxTargetedProteomics2012, |
|
| 6628 | + title = {Targeted Proteomics}, |
|
| 6629 | + author = {Marx, Vivien}, |
|
| 6630 | + date = {2012-12}, |
|
| 6631 | + journaltitle = {Nature Methods}, |
|
| 6632 | + volume = {10}, |
|
| 6633 | + number = {1}, |
|
| 6634 | + eprint = {23547293}, |
|
| 6635 | + eprinttype = {pmid}, |
|
| 6636 | + pages = {nmeth.2285}, |
|
| 6637 | + issn = {1548-7105}, |
|
| 6638 | + doi = {10.1038/nmeth.2285}, |
|
| 6639 | + url = {http://dx.doi.org/10.1038/nmeth.2285}, |
|
| 6640 | + abstract = {{$<$}p{$>$}Analysis of a preselected group of proteins delivers more precise, quantitative, sensitive data to more biologists. Vivien Marx reports.{$<$}/p{$>$}}, |
|
| 6641 | + keywords = {nosource} |
|
| 6642 | +} |
|
| 6643 | + |
|
| 6644 | +@article{matthewsRegulationImmunoglobulinClassSwitch2014, |
|
| 6645 | + title = {Regulation of {{Immunoglobulin Class-Switch Recombination}}: {{Choreography}} of {{Noncoding Transcription}}, {{Targeted DNA Deamination}}, and {{Long-Range DNA Repair}}}, |
|
| 6646 | + shorttitle = {Regulation of {{Immunoglobulin Class-Switch Recombination}}}, |
|
| 6647 | + author = {Matthews, Allysia J. and Zheng, Simin and DiMenna, Lauren J. and Chaudhuri, Jayanta}, |
|
| 6648 | + date = {2014}, |
|
| 6649 | + journaltitle = {Advances in immunology}, |
|
| 6650 | + shortjournal = {Adv Immunol}, |
|
| 6651 | + volume = {122}, |
|
| 6652 | + eprint = {24507154}, |
|
| 6653 | + eprinttype = {pmid}, |
|
| 6654 | + pages = {1--57}, |
|
| 6655 | + issn = {0065-2776}, |
|
| 6656 | + doi = {10.1016/B978-0-12-800267-4.00001-8}, |
|
| 6657 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4150736/}, |
|
| 6658 | + urldate = {2023-12-18}, |
|
| 6659 | + abstract = {Upon encountering antigens, mature IgM-positive B lymphocytes undergo class-switch recombination (CSR) wherein exons encoding the default Cμ constant coding gene segment of the immunoglobulin (Ig) heavy-chain (Igh) locus are excised and replaced with a new constant gene segment (referred to as “Ch genes”, e.g., Cγ, Cε, or Cα). The B cell thereby changes from expressing IgM to one producing IgG, IgE, or IgA, with each antibody isotype having a different effector function during an immune reaction. CSR is a DNA deletional-recombination reaction that proceeds through the generation of DNA double-strand breaks (DSBs) in repetitive switch (S) sequences preceding each Ch gene and is completed by end-joining between donor Sμ and acceptor S regions. CSR is a multistep reaction requiring transcription through S regions, the DNA cytidine deaminase AID, and the participation of several general DNA repair pathways including base excision repair, mismatch repair, and classical nonhomologous end-joining. In this review, we discuss our current understanding of how transcription through S regions generates substrates for AID-mediated deamination and how AID participates not only in the initiation of CSR but also in the conversion of deaminated residues into DSBs. Additionally, we review the multiple processes that regulate AID expression and facilitate its recruitment specifically to the Ig loci, and how deregulation of AID specificity leads to oncogenic translocations. Finally, we summarize recent data on the potential role of AID in the maintenance of the pluripotent stem cell state during epigenetic reprogramming.}, |
|
| 6660 | + pmcid = {PMC4150736}, |
|
| 6661 | + file = {/Users/rmorin/Zotero/storage/8PH3SNTP/Matthews et al. - 2014 - Regulation of Immunoglobulin Class-Switch Recombin.pdf} |
|
| 6662 | +} |
|
| 6663 | + |
|
| 6664 | +@article{maurerEventfreeSurvival242014, |
|
| 6665 | + title = {Event-Free Survival at 24 Months Is a Robust End Point for Disease-Related Outcome in Diffuse Large {{B-cell}} Lymphoma Treated with Immunochemotherapy}, |
|
| 6666 | + author = {Maurer, Matthew J. and Ghesquières, Hervé and Jais, Jean-Philippe and Witzig, Thomas E. and Haioun, Corinne and Thompson, Carrie A. and Delarue, Richard and Micallef, Ivana N. and Peyrade, Frédéric and Macon, William R. and Jo Molina, Thierry and Ketterer, Nicolas and Syrbu, Sergei I. and Fitoussi, Olivier and Kurtin, Paul J. and Allmer, Cristine and Nicolas-Virelizier, Emmanuelle and Slager, Susan L. and Habermann, Thomas M. and Link, Brian K. and Salles, Gilles and Tilly, Hervé and Cerhan, James R.}, |
|
| 6667 | + date = {2014-04-01}, |
|
| 6668 | + journaltitle = {Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology}, |
|
| 6669 | + shortjournal = {J Clin Oncol}, |
|
| 6670 | + volume = {32}, |
|
| 6671 | + number = {10}, |
|
| 6672 | + eprint = {24550425}, |
|
| 6673 | + eprinttype = {pmid}, |
|
| 6674 | + pages = {1066--1073}, |
|
| 6675 | + issn = {1527-7755}, |
|
| 6676 | + doi = {10.1200/JCO.2013.51.5866}, |
|
| 6677 | + abstract = {PURPOSE: Studies of diffuse large B-cell lymphoma (DLBCL) are typically evaluated by using a time-to-event approach with relapse, re-treatment, and death commonly used as the events. We evaluated the timing and type of events in newly diagnosed DLBCL and compared patient outcome with reference population data. PATIENTS AND METHODS: Patients with newly diagnosed DLBCL treated with immunochemotherapy were prospectively enrolled onto the University of Iowa/Mayo Clinic Specialized Program of Research Excellence Molecular Epidemiology Resource (MER) and the North Central Cancer Treatment Group NCCTG-N0489 clinical trial from 2002 to 2009. Patient outcomes were evaluated at diagnosis and in the subsets of patients achieving event-free status at 12 months (EFS12) and 24 months (EFS24) from diagnosis. Overall survival was compared with age- and sex-matched population data. Results were replicated in an external validation cohort from the Groupe d'Etude des Lymphomes de l'Adulte (GELA) Lymphome Non Hodgkinien 2003 (LNH2003) program and a registry based in Lyon, France. RESULTS: In all, 767 patients with newly diagnosed DLBCL who had a median age of 63 years were enrolled onto the MER and NCCTG studies. At a median follow-up of 60 months (range, 8 to 116 months), 299 patients had an event and 210 patients had died. Patients achieving EFS24 had an overall survival equivalent to that of the age- and sex-matched general population (standardized mortality ratio [SMR], 1.18; P = .25). This result was confirmed in 820 patients from the GELA study and registry in Lyon (SMR, 1.09; P = .71). Simulation studies showed that EFS24 has comparable power to continuous EFS when evaluating clinical trials in DLBCL. CONCLUSION: Patients with DLBCL who achieve EFS24 have a subsequent overall survival equivalent to that of the age- and sex-matched general population. EFS24 will be useful in patient counseling and should be considered as an end point for future studies of newly diagnosed DLBCL.}, |
|
| 6678 | + langid = {english}, |
|
| 6679 | + pmcid = {PMC3965261}, |
|
| 6680 | + keywords = {Adolescent,Adult,Aged,Aged 80 and over,Antibodies Monoclonal Murine-Derived,Antineoplastic Combined Chemotherapy Protocols,Case-Control Studies,Clinical Trials as Topic,Disease-Free Survival,Female,Humans,Kaplan-Meier Estimate,Lymphoma Large B-Cell Diffuse,Male,Middle Aged,Recurrence,Rituximab,Time Factors,Young Adult}, |
|
| 6681 | + file = {/Users/rmorin/Zotero/storage/44F7FPZ8/Maurer et al. - 2014 - Event-free survival at 24 months is a robust end p.pdf} |
|
| 6682 | +} |
|
| 6683 | + |
|
| 6684 | +@article{mcglincyExpressionProteomicsUPF12010, |
|
| 6685 | + title = {Expression Proteomics of {{UPF1}} Knockdown in {{HeLa}} Cells Reveals Autoregulation of {{hnRNP A2}}/{{B1}} Mediated by Alternative Splicing Resulting in Nonsense-Mediated {{mRNA}} Decay}, |
|
| 6686 | + author = {McGlincy, Nicholas J. and Tan, Lit-Yeen and Paul, Nicodeme and Zavolan, Mihaela and Lilley, Kathryn S. and Smith, Christopher WJ}, |
|
| 6687 | + date = {2010-10-14}, |
|
| 6688 | + journaltitle = {BMC Genomics}, |
|
| 6689 | + shortjournal = {BMC Genomics}, |
|
| 6690 | + volume = {11}, |
|
| 6691 | + number = {1}, |
|
| 6692 | + pages = {565}, |
|
| 6693 | + issn = {1471-2164}, |
|
| 6694 | + doi = {10.1186/1471-2164-11-565}, |
|
| 6695 | + url = {https://doi.org/10.1186/1471-2164-11-565}, |
|
| 6696 | + urldate = {2022-09-28}, |
|
| 6697 | + abstract = {In addition to acting as an RNA quality control pathway, nonsense-mediated mRNA decay (NMD) plays roles in regulating normal gene expression. In particular, the extent to which alternative splicing is coupled to NMD and the roles of NMD in regulating uORF containing transcripts have been a matter of debate.}, |
|
| 6698 | + langid = {english}, |
|
| 6699 | + keywords = {Exon Junction Complex,HeLa Cell,Napa,Protein Spot,Upstream Open Reading Frame}, |
|
| 6700 | + file = {/Users/rmorin/Zotero/storage/CWMMQNTT/McGlincy et al. - 2010 - Expression proteomics of UPF1 knockdown in HeLa ce.pdf} |
|
| 6701 | +} |
|
| 6702 | + |
|
| 6703 | +@article{mckennaGenomeAnalysisToolkit2010, |
|
| 6704 | + title = {The {{Genome Analysis Toolkit}}: A {{MapReduce}} Framework for Analyzing next-Generation {{DNA}} Sequencing Data}, |
|
| 6705 | + shorttitle = {The {{Genome Analysis Toolkit}}}, |
|
| 6706 | + author = {McKenna, Aaron and Hanna, Matthew and Banks, Eric and Sivachenko, Andrey and Cibulskis, Kristian and Kernytsky, Andrew and Garimella, Kiran and Altshuler, David and Gabriel, Stacey and Daly, Mark and DePristo, Mark A.}, |
|
| 6707 | + date = {2010-09}, |
|
| 6708 | + journaltitle = {Genome Research}, |
|
| 6709 | + shortjournal = {Genome Res.}, |
|
| 6710 | + volume = {20}, |
|
| 6711 | + number = {9}, |
|
| 6712 | + eprint = {20644199}, |
|
| 6713 | + eprinttype = {pmid}, |
|
| 6714 | + pages = {1297--1303}, |
|
| 6715 | + issn = {1549-5469}, |
|
| 6716 | + doi = {10.1101/gr.107524.110}, |
|
| 6717 | + abstract = {Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding of genetic variation among individuals. However, the massive data sets generated by NGS--the 1000 Genome pilot alone includes nearly five terabases--make writing feature-rich, efficient, and robust analysis tools difficult for even computationally sophisticated individuals. Indeed, many professionals are limited in the scope and the ease with which they can answer scientific questions by the complexity of accessing and manipulating the data produced by these machines. Here, we discuss our Genome Analysis Toolkit (GATK), a structured programming framework designed to ease the development of efficient and robust analysis tools for next-generation DNA sequencers using the functional programming philosophy of MapReduce. The GATK provides a small but rich set of data access patterns that encompass the majority of analysis tool needs. Separating specific analysis calculations from common data management infrastructure enables us to optimize the GATK framework for correctness, stability, and CPU and memory efficiency and to enable distributed and shared memory parallelization. We highlight the capabilities of the GATK by describing the implementation and application of robust, scale-tolerant tools like coverage calculators and single nucleotide polymorphism (SNP) calling. We conclude that the GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.}, |
|
| 6718 | + langid = {english}, |
|
| 6719 | + pmcid = {PMC2928508}, |
|
| 6720 | + keywords = {Base Sequence,Genome,Genomics,Sequence Analysis DNA,Software} |
|
| 6721 | +} |
|
| 6722 | + |
|
| 6723 | +@article{mclarenEnsemblVariantEffect2016, |
|
| 6724 | + title = {The {{Ensembl Variant Effect Predictor}}}, |
|
| 6725 | + author = {McLaren, William and Gil, Laurent and Hunt, Sarah E. and Riat, Harpreet Singh and Ritchie, Graham R. S. and Thormann, Anja and Flicek, Paul and Cunningham, Fiona}, |
|
| 6726 | + date = {2016-06-06}, |
|
| 6727 | + journaltitle = {Genome Biology}, |
|
| 6728 | + shortjournal = {Genome Biol.}, |
|
| 6729 | + volume = {17}, |
|
| 6730 | + number = {1}, |
|
| 6731 | + eprint = {27268795}, |
|
| 6732 | + eprinttype = {pmid}, |
|
| 6733 | + pages = {122}, |
|
| 6734 | + issn = {1474-760X}, |
|
| 6735 | + doi = {10.1186/s13059-016-0974-4}, |
|
| 6736 | + abstract = {The Ensembl Variant Effect Predictor is a powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions. It provides access to an extensive collection of genomic annotation, with a variety of interfaces to suit different requirements, and simple options for configuring and extending analysis. It is open source, free to use, and supports full reproducibility of results. The Ensembl Variant Effect Predictor can simplify and accelerate variant interpretation in a wide range of study designs.}, |
|
| 6737 | + langid = {english}, |
|
| 6738 | + pmcid = {PMC4893825}, |
|
| 6739 | + keywords = {Computational Biology,Databases Nucleic Acid,Genetic Variation,Genome,Genomics,Humans,Internet,Molecular Sequence Annotation,NGS,SNP,Software,Variant annotation} |
|
| 6740 | +} |
|
| 6741 | + |
|
| 6742 | +@online{MechanismsBcellLymphoma, |
|
| 6743 | + title = {Mechanisms of {{B-cell}} Lymphoma Pathogenesis - {{PubMed}}}, |
|
| 6744 | + url = {https://pubmed.ncbi.nlm.nih.gov/15803153/}, |
|
| 6745 | + urldate = {2024-03-25}, |
|
| 6746 | + file = {/Users/rmorin/Zotero/storage/U35T36VC/15803153.html} |
|
| 6747 | +} |
|
| 6748 | + |
|
| 6749 | +@article{meissnerE3UbiquitinLigase2013, |
|
| 6750 | + title = {The {{E3}} Ubiquitin Ligase {{UBR5}} Is Recurrently Mutated in Mantle Cell Lymphoma}, |
|
| 6751 | + author = {Meissner, Barbara and Kridel, Robert and Lim, Raymond S. and Rogic, Sanja and Tse, Kane and Scott, David W. and Moore, Richard and Mungall, Andy J. and Marra, Marco A. and Connors, Joseph M. and Steidl, Christian and Gascoyne, Randy D.}, |
|
| 6752 | + date = {2013-04-18}, |
|
| 6753 | + journaltitle = {Blood}, |
|
| 6754 | + shortjournal = {Blood}, |
|
| 6755 | + volume = {121}, |
|
| 6756 | + number = {16}, |
|
| 6757 | + pages = {3161--3164}, |
|
| 6758 | + issn = {0006-4971}, |
|
| 6759 | + doi = {10.1182/blood-2013-01-478834}, |
|
| 6760 | + url = {https://ashpublications.org/blood/article/121/16/3161/31598/The-E3-ubiquitin-ligase-UBR5-is-recurrently}, |
|
| 6761 | + urldate = {2019-12-21}, |
|
| 6762 | + langid = {english}, |
|
| 6763 | + file = {/Users/rmorin/Zotero/storage/DVQGH7VS/blood-2013-01-478834.html} |
|
| 6764 | +} |
|
| 6765 | + |
|
| 6766 | +@article{mellorCriticalReviewRole2013, |
|
| 6767 | + title = {A Critical Review of the Role of {{Fc}} Gamma Receptor Polymorphisms in the Response to Monoclonal Antibodies in Cancer.}, |
|
| 6768 | + author = {Mellor, James D and Brown, Michael P and Irving, Helen R and Zalcberg, John R and Dobrovic, Alexander}, |
|
| 6769 | + date = {2013}, |
|
| 6770 | + journaltitle = {Journal of hematology \& oncology}, |
|
| 6771 | + volume = {6}, |
|
| 6772 | + eprint = {23286345}, |
|
| 6773 | + eprinttype = {pmid}, |
|
| 6774 | + pages = {1}, |
|
| 6775 | + issn = {1756-8722}, |
|
| 6776 | + doi = {10.1186/1756-8722-6-1}, |
|
| 6777 | + url = {http://dx.doi.org/10.1186/1756-8722-6-1}, |
|
| 6778 | + abstract = {Antibody-dependent cellular cytotoxicity (ADCC) is a major mechanism of action of therapeutic monoclonal antibodies (mAbs) such as cetuximab, rituximab and trastuzumab. Fc gamma receptors (FcgR) on human white blood cells are an integral part of the ADCC pathway. Differential response to therapeutic mAbs has been reported to correlate with specific polymorphisms in two of these genes: FCGR2A (H131R) and FCGR3A (V158F). These polymorphisms are associated with differential affinity of the receptors for mAbs. This review critically examines the current evidence for genotyping the corresponding single nucleotide polymorphisms (SNPs) to predict response to mAbs in patients with cancer.}, |
|
| 6779 | + keywords = {nosource} |
|
| 6780 | +} |
|
| 6781 | + |
|
| 6782 | +@article{mendez-lagoMutationsMLL2MEF2B2010, |
|
| 6783 | + title = {Mutations {{In MLL2}} and {{MEF2B Genes In Follicular Lymphoma}} and {{Diffuse Large B-Cell Lymphoma}}}, |
|
| 6784 | + author = {Mendez-Lago, M and Morin, R D and Mungall, A J}, |
|
| 6785 | + date = {2010}, |
|
| 6786 | + journaltitle = {Blood}, |
|
| 6787 | + volume = {116}, |
|
| 6788 | + pages = {473}, |
|
| 6789 | + keywords = {nosource} |
|
| 6790 | +} |
|
| 6791 | + |
|
| 6792 | +@article{mengSignalingdependentCoordinatedRegulation2007, |
|
| 6793 | + title = {Signaling-Dependent and Coordinated Regulation of Transcription, Splicing, and Translation Resides in a Single Coregulator, {{PCBP1}}}, |
|
| 6794 | + author = {Meng, Qingchang and Rayala, Suresh K. and Gururaj, Anupama E. and Talukder, Amjad H. and O'Malley, Bert W. and Kumar, Rakesh}, |
|
| 6795 | + date = {2007-04-03}, |
|
| 6796 | + journaltitle = {Proceedings of the National Academy of Sciences of the United States of America}, |
|
| 6797 | + shortjournal = {Proc Natl Acad Sci U S A}, |
|
| 6798 | + volume = {104}, |
|
| 6799 | + number = {14}, |
|
| 6800 | + eprint = {17389360}, |
|
| 6801 | + eprinttype = {pmid}, |
|
| 6802 | + pages = {5866--5871}, |
|
| 6803 | + issn = {0027-8424}, |
|
| 6804 | + doi = {10.1073/pnas.0701065104}, |
|
| 6805 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851583/}, |
|
| 6806 | + urldate = {2022-09-28}, |
|
| 6807 | + abstract = {Transcription, splicing, and translation are potentially coordinately regulatable in a temporospatial-dependent manner, although supporting experimental evidence for this notion is scarce. Yeast two-hybrid screening of a mammary gland cDNA library with human p21-activated kinase 1 (Pak1) as bait identified polyC-RNA-binding protein 1 (PCBP1), which controls translation from mRNAs containing the DICE (differentiation control element). Mitogenic stimulation of human cells phosphorylated PCBP1 on threonines 60 and 127 in a Pak1-sensitive manner. Pak1-dependent phosphorylation of PCBP1 released its binding and translational inhibition from a DICE-minigene. Overexpression of PCBP1 also inhibited the translation of the endogenous L1 cell adhesion molecule mRNA, which contains two DICE motifs in the 3′ untranslated region. We also found that Pak1 activation led to an increased nuclear retention of PCBP1, recruitment to the eukaryotic translation initiation factor 4E (eIF4E) promoter, and stimulation of eIF4E expression in a Pak1-sensitive manner. Moreover, mitogenic stimulation promoted Pak1- and PCBP1-dependent alternative splicing and exon inclusion from a CD44 minigene. The alternative splicing functions of PCBP1 were in turn mediated by its intrinsic interaction with Caper α, a U2 snRNP auxiliary factor-related protein previously implicated in RNA splicing. These findings establish the principle that a single coregulator can function as a signal-dependent and coordinated regulator of transcription, splicing, and translation.}, |
|
| 6808 | + pmcid = {PMC1851583}, |
|
| 6809 | + file = {/Users/rmorin/Zotero/storage/966TSWJR/Meng et al. - 2007 - Signaling-dependent and coordinated regulation of .pdf} |
|
| 6810 | +} |
|
| 6811 | + |
|
| 6812 | +@article{meyerReflecting25Years2008, |
|
| 6813 | + title = {Reflecting on 25 Years with {{MYC}}}, |
|
| 6814 | + author = {Meyer, Natalie and Penn, Linda Z.}, |
|
| 6815 | + date = {2008-12}, |
|
| 6816 | + journaltitle = {Nature Reviews Cancer}, |
|
| 6817 | + shortjournal = {Nat Rev Cancer}, |
|
| 6818 | + volume = {8}, |
|
| 6819 | + number = {12}, |
|
| 6820 | + pages = {976--990}, |
|
| 6821 | + publisher = {Nature Publishing Group}, |
|
| 6822 | + issn = {1474-1768}, |
|
| 6823 | + doi = {10.1038/nrc2231}, |
|
| 6824 | + url = {https://www.nature.com/articles/nrc2231}, |
|
| 6825 | + urldate = {2022-10-06}, |
|
| 6826 | + abstract = {MYC is an iconic oncogene that has been at the forefront of cancer research since its discovery. Looking back over the history of MYC research provides us with a framework with which to progress in the next 25 years, as outlined in this Timeline.}, |
|
| 6827 | + issue = {12}, |
|
| 6828 | + langid = {english}, |
|
| 6829 | + keywords = {Biomedicine,Cancer Research,general}, |
|
| 6830 | + file = {/Users/rmorin/Zotero/storage/EL4NQLYZ/Meyer and Penn - 2008 - Reflecting on 25 years with MYC.pdf;/Users/rmorin/Zotero/storage/4YUSLWZQ/nrc2231.html} |
|
| 6831 | +} |
|
| 6832 | + |
|
| 6833 | +@article{miaoTargetedDisruptionMCPIP12013, |
|
| 6834 | + title = {Targeted Disruption of {{MCPIP1}}\/{{Zc3h12a}} Results in Fatal Inflammatory Disease}, |
|
| 6835 | + author = {Miao, Ruidong and Huang, Shengping and Zhou, Zhou and Quinn, Tim and Van Treeck, Benjamin and Nayyar, Tehreem and Dim, Daniel and Jiang, Zhisheng and Papasian, Christopher J and Chen, Y Eugene and Liu, Gang and Fu, Mingui}, |
|
| 6836 | + date = {2013-04}, |
|
| 6837 | + journaltitle = {Immunology and cell biology}, |
|
| 6838 | + volume = {91}, |
|
| 6839 | + number = {5}, |
|
| 6840 | + pages = {368--376}, |
|
| 6841 | + keywords = {nosource} |
|
| 6842 | +} |
|
| 6843 | + |
|
| 6844 | +@article{michaelNuclearExportSignal1995, |
|
| 6845 | + title = {A Nuclear Export Signal in {{hnRNP A1}}: A Signal-Mediated, Temperature-Dependent Nuclear Protein Export Pathway}, |
|
| 6846 | + shorttitle = {A Nuclear Export Signal in {{hnRNP A1}}}, |
|
| 6847 | + author = {Michael, W. M. and Choi, M. and Dreyfuss, G.}, |
|
| 6848 | + date = {1995-11-03}, |
|
| 6849 | + journaltitle = {Cell}, |
|
| 6850 | + shortjournal = {Cell}, |
|
| 6851 | + volume = {83}, |
|
| 6852 | + number = {3}, |
|
| 6853 | + eprint = {8521471}, |
|
| 6854 | + eprinttype = {pmid}, |
|
| 6855 | + pages = {415--422}, |
|
| 6856 | + issn = {0092-8674}, |
|
| 6857 | + doi = {10.1016/0092-8674(95)90119-1}, |
|
| 6858 | + abstract = {Pre-mRNAs are associated with hnRNPs, and these proteins play important roles in the biogenesis of mRNAs. The hnRNP A1 is one of the most abundant hnRNPs, and although localized primarily in the nucleoplasm, shuttles continuously between the nucleus and the cytoplasm. A 38 amino acid domain within A1, termed M9, which bears no resemblance to classical nuclear localization signal (NLS) sequences, localizes A1 to the nucleus. Here we show that M9 is also a nuclear export signal; placing M9 on a protein that is otherwise restricted to the nucleus, the nucleoplasmin core domain (NPc), efficiently exports it to the cytoplasm in a temperature-dependent manner. In contrast, classical NLSs cannot promote the export of NPc. These findings demonstrate that there is a signal-dependent, temperature-sensitive nuclear export pathway and strengthen the suggestion that A1 and other shuttling hnRNPs function as carriers for RNA during export to the cytoplasm.}, |
|
| 6859 | + langid = {english}, |
|
| 6860 | + keywords = {Amino Acid Sequence,Biological Transport,Cell Nucleus,HeLa Cells,Heterogeneous Nuclear Ribonucleoprotein A1,Heterogeneous-Nuclear Ribonucleoprotein Group A-B,Heterogeneous-Nuclear Ribonucleoproteins,Humans,Molecular Sequence Data,Nuclear Proteins,Protein Sorting Signals,Recombinant Proteins,Ribonucleoproteins,RNA Messenger,RNA-Binding Proteins,Temperature}, |
|
| 6861 | + file = {/Users/rmorin/Zotero/storage/ZDVBDEQS/Michael et al. - 1995 - A nuclear export signal in hnRNP A1 a signal-medi.pdf} |
|
| 6862 | +} |
|
| 6863 | + |
|
| 6864 | +@article{michaelNuclearShuttlingDomain1997, |
|
| 6865 | + title = {The {{K}} Nuclear Shuttling Domain: A Novel Signal for Nuclear Import and Nuclear Export in the {{hnRNP K}} Protein.}, |
|
| 6866 | + shorttitle = {The {{K}} Nuclear Shuttling Domain}, |
|
| 6867 | + author = {Michael, W M and Eder, P S and Dreyfuss, G}, |
|
| 6868 | + date = {1997-06-15}, |
|
| 6869 | + journaltitle = {The EMBO Journal}, |
|
| 6870 | + shortjournal = {EMBO J}, |
|
| 6871 | + volume = {16}, |
|
| 6872 | + number = {12}, |
|
| 6873 | + eprint = {9218800}, |
|
| 6874 | + eprinttype = {pmid}, |
|
| 6875 | + pages = {3587--3598}, |
|
| 6876 | + issn = {0261-4189}, |
|
| 6877 | + doi = {10.1093/emboj/16.12.3587}, |
|
| 6878 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1169983/}, |
|
| 6879 | + urldate = {2022-09-28}, |
|
| 6880 | + abstract = {Protein import into the nucleus and export from the nucleus are signal-mediated processes that require energy. The nuclear transport process about which the most information is currently available is classical nuclear localization signal (NLS)-mediated nuclear import. However, details concerning the signal-mediated export of proteins and RNAs as well as alternative nuclear import pathways are beginning to emerge. An example of this is the heterogeneous nuclear ribonucleoprotein (hnRNP) A1 protein which, by virtue of its M9 domain, is actively exported from the nucleus and imported into the nucleus via a novel pathway mediated by the recently characterized transportin protein. Here we report that the shuttling hnRNP K protein contains a novel shuttling domain (termed KNS) which has many of the characteristics of M9, in that it confers bi-directional transport across the nuclear envelope. KNS-mediated nuclear import is dependent on RNA polymerase II transcription, and we show that a classical NLS can override this effect. Furthermore, KNS accesses a separate import pathway from either classical NLSs or M9. This demonstrates the existence of a third protein import pathway into the nucleus and thereby defines a new type of nuclear import/export signal.}, |
|
| 6881 | + pmcid = {PMC1169983}, |
|
| 6882 | + file = {/Users/rmorin/Zotero/storage/IIQQLBD9/Michael et al. - 1997 - The K nuclear shuttling domain a novel signal for.pdf} |
|
| 6883 | +} |
|
| 6884 | + |
|
| 6885 | +@article{michaelSignalSequencesThat1995, |
|
| 6886 | + title = {Signal Sequences That Target Nuclear Import and Nuclear Export of Pre-{{mRNA-binding}} Proteins}, |
|
| 6887 | + author = {Michael, W. M. and Siomi, H. and Choi, M. and Piñol-Roma, S. and Nakielny, S. and Liu, Q. and Dreyfuss, G.}, |
|
| 6888 | + date = {1995}, |
|
| 6889 | + journaltitle = {Cold Spring Harbor Symposia on Quantitative Biology}, |
|
| 6890 | + shortjournal = {Cold Spring Harb Symp Quant Biol}, |
|
| 6891 | + volume = {60}, |
|
| 6892 | + eprint = {8824440}, |
|
| 6893 | + eprinttype = {pmid}, |
|
| 6894 | + pages = {663--668}, |
|
| 6895 | + issn = {0091-7451}, |
|
| 6896 | + doi = {10.1101/sqb.1995.060.01.071}, |
|
| 6897 | + langid = {english}, |
|
| 6898 | + keywords = {Amino Acid Sequence,Animals,Biological Transport Active,Cell Nucleus,Cytoplasm,Fungal Proteins,HeLa Cells,Heterogeneous-Nuclear Ribonucleoproteins,Humans,Molecular Sequence Data,Protein Sorting Signals,Ribonucleoproteins,RNA Precursors,RNA-Binding Proteins,Saccharomyces cerevisiae,Sequence Homology Amino Acid,Signal Transduction} |
|
| 6899 | +} |
|
| 6900 | + |
|
| 6901 | +@article{michelottiHeterogeneousNuclearRibonucleoprotein1996, |
|
| 6902 | + title = {Heterogeneous Nuclear Ribonucleoprotein {{K}} Is a Transcription Factor}, |
|
| 6903 | + author = {Michelotti, E.F. and Michelotti, G.A. and Aronsohn, A.I. and Levens, D.}, |
|
| 6904 | + date = {1996}, |
|
| 6905 | + journaltitle = {Molecular and Cellular Biology}, |
|
| 6906 | + volume = {16}, |
|
| 6907 | + number = {5}, |
|
| 6908 | + pages = {2350--2360}, |
|
| 6909 | + issn = {0270-7306}, |
|
| 6910 | + doi = {10.1128/MCB.16.5.2350}, |
|
| 6911 | + abstract = {The CT element is a positively acting homopyrimidine tract upstream of the c-myc gene to which the well-characterized transcription factor Sp1 and heterogeneous nuclear ribonucleoprotein (hnRNP) K, a less well-characterized protein associated with hnRNP complexes, have previously been shown to bind. The present work demonstrates that both of these molecules contribute to CT element-activated transcription in vitro. The pyrimidine-rich strand of the CT element both bound to hnRNP K and competitively inhibited transcription in vitro, suggesting a role for hnRNP K in activating transcription through this single-stranded sequence. Direct addition of recombinant hnRNP K to reaction mixtures programmed with templates bearing single-stranded CT elements increased specific RNA synthesis. If hnRNP K is a transcription factor, then interactions with the RNA polymerase II transcription apparatus are predicted. Affinity columns charged with recombinant hnRNP K specifically bind a component(s) necessary for transcription activation. The depleted factors were biochemically complemented by a crude TFIID phosphocellulose fraction, indicating that hnRNP K might interact with the TATA-binding protein (TBP)-TBP-associated factor complex. Coimmunoprecipitation of a complex formed in vivo between hnRNP K and epitope-tagged TBP as well as binding in vitro between recombinant proteins demonstrated a protein-protein interaction between TBP and hnRNP K. Furthermore, when the two proteins were overexpressed in vivo, transcription from a CT element-dependent reporter was synergistically activated. These data indicate that hnRNP K binds to a specific cis element, interacts with the RNA polymerase II transcription machinery, and stimulates transcription and thus has all of the properties of a transcription factor.}, |
|
| 6912 | + langid = {english}, |
|
| 6913 | + file = {/Users/rmorin/Zotero/storage/P5G86I4T/Michelotti et al. - 1996 - Heterogeneous nuclear ribonucleoprotein K is a tra.pdf;/Users/rmorin/Zotero/storage/LZF2LXBM/display.html} |
|
| 6914 | +} |
|
| 6915 | + |
|
| 6916 | +@article{mihailovichMiR1792FinetunesMYC2015, |
|
| 6917 | + title = {{{miR-17-92}} Fine-Tunes {{MYC}} Expression and Function to Ensure Optimal {{B}} Cell Lymphoma Growth}, |
|
| 6918 | + author = {Mihailovich, Marija and Bremang, Michael and Spadotto, Valeria and Musiani, Daniele and Vitale, Elena and Varano, Gabriele and Zambelli, Federico and Mancuso, Francesco M. and Cairns, David A. and Pavesi, Giulio and Casola, Stefano and Bonaldi, Tiziana}, |
|
| 6919 | + date = {2015-11-10}, |
|
| 6920 | + journaltitle = {Nature Communications}, |
|
| 6921 | + shortjournal = {Nat Commun}, |
|
| 6922 | + volume = {6}, |
|
| 6923 | + eprint = {26555894}, |
|
| 6924 | + eprinttype = {pmid}, |
|
| 6925 | + pages = {8725}, |
|
| 6926 | + issn = {2041-1723}, |
|
| 6927 | + doi = {10.1038/ncomms9725}, |
|
| 6928 | + abstract = {The synergism between c-MYC and miR-17-19b, a truncated version of the miR-17-92 cluster, is well-documented during tumor initiation. However, little is known about miR-17-19b function in established cancers. Here we investigate the role of miR-17-19b in c-MYC-driven lymphomas by integrating SILAC-based quantitative proteomics, transcriptomics and 3' untranslated region (UTR) analysis upon miR-17-19b overexpression. We identify over one hundred miR-17-19b targets, of which 40\% are co-regulated by c-MYC. Downregulation of a new miR-17/20 target, checkpoint kinase 2 (Chek2), increases the recruitment of HuR to c-MYC transcripts, resulting in the inhibition of c-MYC translation and thus interfering with in vivo tumor growth. Hence, in established lymphomas, miR-17-19b fine-tunes c-MYC activity through a tight control of its function and expression, ultimately ensuring cancer cell homeostasis. Our data highlight the plasticity of miRNA function, reflecting changes in the mRNA landscape and 3' UTR shortening at different stages of tumorigenesis.}, |
|
| 6929 | + langid = {english}, |
|
| 6930 | + pmcid = {PMC4667639}, |
|
| 6931 | + keywords = {Animals,Cell Line Tumor,Checkpoint Kinase 2,Cloning Molecular,ELAV-Like Protein 1,Gene Expression Regulation Neoplastic,Lymphoma B-Cell,Mice,Mice Transgenic,MicroRNAs,Proteome,Proto-Oncogene Proteins c-myc} |
|
| 6932 | +} |
|
| 6933 | + |
|
| 6934 | +@article{milosevicSubcellularFractionationTGFbeta1stimulated2009, |
|
| 6935 | + title = {Subcellular Fractionation of {{TGF-beta1-stimulated}} Lung Epithelial Cells: A Novel Proteomic Approach for Identifying Signaling Intermediates}, |
|
| 6936 | + shorttitle = {Subcellular Fractionation of {{TGF-beta1-stimulated}} Lung Epithelial Cells}, |
|
| 6937 | + author = {Milosevic, Jadranka and Bulau, Patrick and Mortz, Ejvind and Eickelberg, Oliver}, |
|
| 6938 | + date = {2009-03}, |
|
| 6939 | + journaltitle = {Proteomics}, |
|
| 6940 | + shortjournal = {Proteomics}, |
|
| 6941 | + volume = {9}, |
|
| 6942 | + number = {5}, |
|
| 6943 | + eprint = {19253281}, |
|
| 6944 | + eprinttype = {pmid}, |
|
| 6945 | + pages = {1230--1240}, |
|
| 6946 | + issn = {1615-9861}, |
|
| 6947 | + doi = {10.1002/pmic.200700604}, |
|
| 6948 | + abstract = {Members of the transforming growth factor (TGF)-beta superfamily are key regulators of lung development and homeostasis, in particular by controlling alveolar/bronchial epithelial cell function. TGF-beta signaling involves ligand-dependent activation of receptor serine/threonine kinases, activation and subsequent nuclear translocation of pathway-specific transcription factors (Smads), and ultimately, modulation of gene expression. While Smad-dependent responses represent the primary signaling components activated by TGF-beta receptors, their function is controlled by a variety of cofactors. In addition, alternative signaling systems mediating TGF-beta-induced effects have recently been described such as MAP kinase pathways. To uncover novel proteins that participate in TGF-beta signaling via nuclear/cytoplasmic shuttling in lung epithelial cells, we have analyzed A549 human lung epithelial cells, using subcellular fractionation combined with 2-D PAGE, tryptic digestion, and MS. We identified a rapid increase in the cytosolic localization of KH-type splicing regulatory protein (KHSRP), far upstream element-binding protein (FUBP1), hnRNP-L, and hnRNP-H1, concomitant with a decrease in their nuclear localization in response to TGF-beta1. Proteomic data were confirmed by immunofluorescence and immunoblot analyses. In summary, we represent a powerful novel technology for the identification of previously unknown signaling intermediates.}, |
|
| 6949 | + langid = {english}, |
|
| 6950 | + keywords = {Cell Differentiation,Cell Line,Cell Nucleus,Cytosol,Electrophoresis Gel Two-Dimensional,Epithelial Cells,Humans,Lung,Proteome,Spectrometry Mass Matrix-Assisted Laser Desorption-Ionization,Subcellular Fractions,Transforming Growth Factor beta1} |
|
| 6951 | +} |
|
| 6952 | + |
|
| 6953 | +@article{milpiedHumanGerminalCenter2018, |
|
| 6954 | + title = {Human Germinal Center Transcriptional Programs Are De-Synchronized in {{B}} Cell Lymphoma}, |
|
| 6955 | + author = {Milpied, Pierre and Cervera-Marzal, Iñaki and Mollichella, Marie-Laure and Tesson, Bruno and Brisou, Gabriel and Traverse-Glehen, Alexandra and Salles, Gilles and Spinelli, Lionel and Nadel, Bertrand}, |
|
| 6956 | + date = {2018-09}, |
|
| 6957 | + journaltitle = {Nature Immunology}, |
|
| 6958 | + volume = {19}, |
|
| 6959 | + number = {9}, |
|
| 6960 | + pages = {1013}, |
|
| 6961 | + issn = {1529-2916}, |
|
| 6962 | + doi = {10.1038/s41590-018-0181-4}, |
|
| 6963 | + url = {https://www.nature.com/articles/s41590-018-0181-4}, |
|
| 6964 | + urldate = {2019-07-08}, |
|
| 6965 | + abstract = {Human follicular lymphomas arise from germinal center B cells. Milpied and colleagues use single-cell transcriptomic analysis to show that follicular lymphoma cells lose synchronized gene-expression patterns that characterize normal germinal center B cells.}, |
|
| 6966 | + langid = {english}, |
|
| 6967 | + file = {/Users/rmorin/Zotero/storage/4WYBMXRT/s41590-018-0181-4.html} |
|
| 6968 | +} |
|
| 6969 | + |
|
| 6970 | +@article{minoRegnase1RoquinRegulate2015, |
|
| 6971 | + title = {Regnase-1 and {{Roquin}} Regulate Inflammatory {{mRNAs}}.}, |
|
| 6972 | + author = {Mino, Takashi and Takeuchi, Osamu}, |
|
| 6973 | + date = {2015-07}, |
|
| 6974 | + journaltitle = {Oncotarget}, |
|
| 6975 | + volume = {6}, |
|
| 6976 | + number = {20}, |
|
| 6977 | + pages = {17869--17870}, |
|
| 6978 | + keywords = {nosource} |
|
| 6979 | +} |
|
| 6980 | + |
|
| 6981 | +@article{minoRegnase1RoquinRegulate2015a, |
|
| 6982 | + title = {Regnase-1 and {{Roquin Regulate}} a {{Common Element}} in {{Inflammatory mRNAs}} by {{Spatiotemporally Distinct Mechanisms}}.}, |
|
| 6983 | + author = {Mino, Takashi and Murakawa, Yasuhiro and Fukao, Akira and Vandenbon, Alexis and Wessels, Hans-Hermann and Ori, Daisuke and Uehata, Takuya and Tartey, Sarang and Akira, Shizuo and Suzuki, Yutaka and Vinuesa, Carola G and Ohler, Uwe and Standley, Daron M and Landthaler, Markus and Fujiwara, Toshinobu and Takeuchi, Osamu}, |
|
| 6984 | + date = {2015-05}, |
|
| 6985 | + journaltitle = {Cell}, |
|
| 6986 | + volume = {161}, |
|
| 6987 | + number = {5}, |
|
| 6988 | + pages = {1058--1073}, |
|
| 6989 | + keywords = {nosource} |
|
| 6990 | +} |
|
| 6991 | + |
|
| 6992 | +@article{modianoDistinctBCellTCell2005, |
|
| 6993 | + title = {Distinct {{B-Cell}} and {{T-Cell Lymphoproliferative Disease Prevalence}} among {{Dog Breeds Indicates Heritable Risk}}}, |
|
| 6994 | + author = {Modiano, Jaime F. and Breen, Matthew and Burnett, Robert C. and Parker, Heidi G. and Inusah, Seidu and Thomas, Rachael and Avery, Paul R. and Lindblad-Toh, Kerstin and Ostrander, Elaine A. and Cutter, Gary C. and Avery, Anne C.}, |
|
| 6995 | + date = {2005-07-01}, |
|
| 6996 | + journaltitle = {Cancer Research}, |
|
| 6997 | + shortjournal = {Cancer Res}, |
|
| 6998 | + volume = {65}, |
|
| 6999 | + number = {13}, |
|
| 7000 | + eprint = {15994938}, |
|
| 7001 | + eprinttype = {pmid}, |
|
| 7002 | + pages = {5654--5661}, |
|
| 7003 | + publisher = {American Association for Cancer Research}, |
|
| 7004 | + issn = {0008-5472, 1538-7445}, |
|
| 7005 | + doi = {10.1158/0008-5472.CAN-04-4613}, |
|
| 7006 | + url = {https://cancerres.aacrjournals.org/content/65/13/5654}, |
|
| 7007 | + urldate = {2021-05-13}, |
|
| 7008 | + abstract = {Immunophenotypes in lymphoproliferative diseases (LPD) are prognostically significant, yet causative factors for these conditions, and specifically those associated with heritable risk, remain elusive. The full spectrum of LPD seen in humans occurs in dogs, but the incidence and lifetime risk of naturally occurring LPD differs among dog breeds. Taking advantage of the limited genetic heterogeneity that exists within dog breeds, we tested the hypothesis that the prevalence of LPD immunophenotypes would differ among different breeds. The sample population included 1,263 dogs representing 87 breeds. Immunophenotype was determined by the presence of clonal rearrangements of immunoglobulin heavy chain or T-cell receptor γ chain. The probability of observing the number of B-cell or T-cell tumors in a particular breed or breed group was compared with three reference populations. Significance was computed using χ2 test, and logistic regression was used to confirm binomial predictions. The data show that, among 87 breeds tested, 15 showed significant differences from the prevalence of LPD immunophenotypes seen across the dog population as a whole. More significantly, elevated risk for T-cell LPD seems to have arisen ancestrally and is retained in related breed groups, whereas increased risk for B-cell disease may stem from different risk factors, or combinations of risk factors, arising during the process of breed derivation and selection. The data show that domestic dogs provide a unique and valuable resource to define factors that mediate risk as well as genes involved in the initiation of B-cell and T-cell LPD.}, |
|
| 7009 | + langid = {english}, |
|
| 7010 | + file = {/Users/rmorin/Zotero/storage/DIXCHXCU/Modiano et al. - 2005 - Distinct B-Cell and T-Cell Lymphoproliferative Dis.pdf;/Users/rmorin/Zotero/storage/XG7YAQNM/5654.html} |
|
| 7011 | +} |
|
| 7012 | + |
|
| 7013 | +@article{mohantyCCND1MutationsIncrease2016, |
|
| 7014 | + title = {{{CCND1}} Mutations Increase Protein Stability and Promote Ibrutinib Resistance in Mantle Cell Lymphoma}, |
|
| 7015 | + author = {Mohanty, Atish and Sandoval, Natalie and Das, Manasi and Pillai, Raju and Chen, Lu and Chen, Robert W. and Amin, Hesham M. and Wang, Michael and Marcucci, Guido and Weisenburger, Dennis D. and Rosen, Steven T. and Pham, Lan V. and Ngo, Vu N.}, |
|
| 7016 | + date = {2016-10-04}, |
|
| 7017 | + journaltitle = {Oncotarget}, |
|
| 7018 | + volume = {7}, |
|
| 7019 | + number = {45}, |
|
| 7020 | + pages = {73558--73572}, |
|
| 7021 | + issn = {1949-2553}, |
|
| 7022 | + doi = {10.18632/oncotarget.12434}, |
|
| 7023 | + url = {http://www.oncotarget.com/index.php?journal=oncotarget&page=article&op=view&path[]=12434&pubmed-linkout=1}, |
|
| 7024 | + urldate = {2019-12-21}, |
|
| 7025 | + abstract = {Oncotarget | https://doi.org/10.18632/oncotarget.12434 Atish Mohanty, Natalie Sandoval, Manasi Das, Raju Pillai, Lu Chen, Robert W. Chen, Hesham M. Amin, Michael Wang, Guido Marcucci, Dennis D. Weisenburger,...}, |
|
| 7026 | + file = {/Users/rmorin/Zotero/storage/RVFI7VRP/index.html} |
|
| 7027 | +} |
|
| 7028 | + |
|
| 7029 | +@article{mondalFunctionalRequirementsAID2016, |
|
| 7030 | + title = {Functional Requirements of {{AID}}’s Higher Order Structures and Their Interaction with {{RNA-binding}} Proteins}, |
|
| 7031 | + author = {Mondal, Samiran and Begum, Nasim A. and Hu, Wenjun and Honjo, Tasuku}, |
|
| 7032 | + date = {2016-03-15}, |
|
| 7033 | + journaltitle = {Proceedings of the National Academy of Sciences}, |
|
| 7034 | + volume = {113}, |
|
| 7035 | + number = {11}, |
|
| 7036 | + pages = {E1545-E1554}, |
|
| 7037 | + publisher = {Proceedings of the National Academy of Sciences}, |
|
| 7038 | + doi = {10.1073/pnas.1601678113}, |
|
| 7039 | + url = {https://www.pnas.org/doi/full/10.1073/pnas.1601678113}, |
|
| 7040 | + urldate = {2022-10-04}, |
|
| 7041 | + file = {/Users/rmorin/Zotero/storage/LJD54XKN/Mondal et al. - 2016 - Functional requirements of AID’s higher order stru.pdf} |
|
| 7042 | +} |
|
| 7043 | + |
|
| 7044 | +@article{montiIntegrativeAnalysisReveals2012, |
|
| 7045 | + title = {Integrative {{Analysis Reveals}} an {{Outcome-Associated}} and {{Targetable Pattern}} of P53 and {{Cell Cycle Deregulation}} in {{Diffuse Large B Cell Lymphoma}}}, |
|
| 7046 | + author = {Monti, Stefano and Chapuy, Bjoern and Takeyama, Kunihiko and Rodig, Scott~J. and Hao, Yansheng and Yeda, Kelly~T. and Inguilizian, Haig and Mermel, Craig and Currie, Treeve and Dogan, Ahmet and Kutok, Jeffery~L. and Beroukhim, Rameen and Neuberg, Donna and Habermann, Thomas~M. and Getz, Gad and Kung, Andrew~L. and Golub, Todd~R. and Shipp, Margaret~A.}, |
|
| 7047 | + date = {2012-09-11}, |
|
| 7048 | + journaltitle = {Cancer Cell}, |
|
| 7049 | + shortjournal = {Cancer Cell}, |
|
| 7050 | + volume = {22}, |
|
| 7051 | + number = {3}, |
|
| 7052 | + pages = {359--372}, |
|
| 7053 | + issn = {1535-6108}, |
|
| 7054 | + doi = {10.1016/j.ccr.2012.07.014}, |
|
| 7055 | + url = {http://www.sciencedirect.com/science/article/pii/S1535610812003066}, |
|
| 7056 | + urldate = {2019-07-08}, |
|
| 7057 | + abstract = {Summary Diffuse large B cell lymphoma (DLBCL) is a clinically and biologically heterogeneous disease with a high proliferation rate. By integrating copy number data with transcriptional profiles and performing pathway analysis in primary DLBCLs, we identified a comprehensive set of copy number alterations (CNAs) that decreased p53 activity and perturbed cell cycle regulation. Primary tumors either had multiple complementary alterations of p53 and cell cycle components or largely lacked these lesions. DLBCLs with p53 and cell cycle pathway CNAs had decreased abundance of p53 target transcripts and increased expression of E2F target genes and the Ki67 proliferation marker. CNAs of the CDKN2A-TP53-RB-E2F axis provide a structural basis for increased proliferation in DLBCL, predict outcome with current therapy, and suggest targeted treatment approaches.}, |
|
| 7058 | + file = {/Users/rmorin/Zotero/storage/2L4AAXXK/S1535610812003066.html} |
|
| 7059 | +} |
|
| 7060 | + |
|
| 7061 | +@article{montiMolecularProfilingDiffuse2005, |
|
| 7062 | + title = {Molecular Profiling of Diffuse Large {{B-cell}} Lymphoma Identifies Robust Subtypes Including One Characterized by Host Inflammatory Response}, |
|
| 7063 | + author = {Monti, S}, |
|
| 7064 | + date = {2005-03}, |
|
| 7065 | + journaltitle = {Blood}, |
|
| 7066 | + volume = {105}, |
|
| 7067 | + number = {5}, |
|
| 7068 | + pages = {1851--1861}, |
|
| 7069 | + keywords = {nosource} |
|
| 7070 | +} |
|
| 7071 | + |
|
| 7072 | +@article{monzon-casanovaRNABindingProtein2018, |
|
| 7073 | + title = {The {{RNA}} Binding Protein {{PTBP1}} Is Necessary for {{B}} Cell Selection in Germinal Centers}, |
|
| 7074 | + author = {Monzón-Casanova, Elisa and Screen, Michael and Díaz-Muñoz, Manuel D. and Coulson, Richard M. R. and Bell, Sarah E. and Lamers, Greta and Solimena, Michele and Smith, Christopher W.J. and Turner, Martin}, |
|
| 7075 | + date = {2018-03}, |
|
| 7076 | + journaltitle = {Nature immunology}, |
|
| 7077 | + shortjournal = {Nat Immunol}, |
|
| 7078 | + volume = {19}, |
|
| 7079 | + number = {3}, |
|
| 7080 | + eprint = {29358707}, |
|
| 7081 | + eprinttype = {pmid}, |
|
| 7082 | + pages = {267--278}, |
|
| 7083 | + issn = {1529-2908}, |
|
| 7084 | + doi = {10.1038/s41590-017-0035-5}, |
|
| 7085 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5842895/}, |
|
| 7086 | + urldate = {2022-10-06}, |
|
| 7087 | + abstract = {Antibody affinity maturation occurs in germinal centres (GC) where B cells cycle between the light zone (LZ) and the dark zone. In the LZ GC B cells bearing immunoglobulins with the highest affinity for antigen receive positive selection signals from T helper cells that promotes their rapid proliferation. Here we show that the RNA binding protein PTBP1 is necessary for the progression of GC B cells through late S-phase of the cell cycle and for affinity maturation. PTBP1 is required for the proper expression of the c-MYC-dependent gene program induced in GC B cells receiving T cell help and directly regulates the alternative splicing and abundance of transcripts increased during positive selection to promote proliferation.}, |
|
| 7088 | + pmcid = {PMC5842895}, |
|
| 7089 | + file = {/Users/rmorin/Zotero/storage/MRH3HVR2/Monzón-Casanova et al. - 2018 - The RNA binding protein PTBP1 is necessary for B c.pdf} |
|
| 7090 | +} |
|
| 7091 | + |
|
| 7092 | +@article{moreiraUpstreamSequenceElement1998, |
|
| 7093 | + title = {The Upstream Sequence Element of the {{C2}} Complement Poly({{A}}) Signal Activates {{mRNA}} 3′ End Formation by Two Distinct Mechanisms}, |
|
| 7094 | + author = {Moreira, Alexandra and Takagaki, Yoshio and Brackenridge, Simon and Wollerton, Matthew and Manley, James L. and Proudfoot, Nicholas J.}, |
|
| 7095 | + date = {1998-08-15}, |
|
| 7096 | + journaltitle = {Genes \& Development}, |
|
| 7097 | + shortjournal = {Genes Dev.}, |
|
| 7098 | + volume = {12}, |
|
| 7099 | + number = {16}, |
|
| 7100 | + pages = {2522--2534}, |
|
| 7101 | + publisher = {Cold Spring Harbor Lab}, |
|
| 7102 | + issn = {0890-9369, 1549-5477}, |
|
| 7103 | + doi = {10.1101/gad.12.16.2522}, |
|
| 7104 | + url = {http://genesdev.cshlp.org/content/12/16/2522}, |
|
| 7105 | + urldate = {2022-09-27}, |
|
| 7106 | + abstract = {The poly(A) signal of the C2 complement gene is unusual in that it possesses an upstream sequence element (USE) required for full activity in vivo. We describe here in vitro experiments demonstrating that this USE enhances both the cleavage and poly(A) addition reactions. We also show that the C2 USE can be cross-linked efficiently to a 55-kD protein that we identify as the polypyrimidine tract-binding protein (PTB), implicated previously in modulation of pre-mRNA splicing. Mutation of the PTB-binding site significantly reduces the efficiency of the C2 poly(A) site both in vivo and in vitro. Furthermore, addition of PTB to reconstituted processing reactions enhances cleavage at the C2 poly(A) site, indicating that PTB has a direct role in recognition of this signal. The C2 USE, however, also increases the affinity of general polyadenylation factors independently for the C2 poly(A) signal as detected by enhanced binding of cleavage-stimulaton factor (CstF). Strikingly, this leads to a novel CstF-dependant enhancement of the poly(A) synthesis phase of the reaction. These studies both emphasize the interconnection between splicing and polyadenylation and indicate an unexpected flexibility in the organization of mammalian poly(A) sites.}, |
|
| 7107 | + langid = {english}, |
|
| 7108 | + keywords = {C2 complement gene,cleavage and polyadenylation,poly(A) signal,PTB,upstream sequence element}, |
|
| 7109 | + file = {/Users/rmorin/Zotero/storage/FBXLWW9H/Moreira et al. - 1998 - The upstream sequence element of the C2 complement.pdf;/Users/rmorin/Zotero/storage/8FHCRV8G/2522.html} |
|
| 7110 | +} |
|
| 7111 | + |
|
| 7112 | +@article{morinFrequentMutationHistonemodifying2011, |
|
| 7113 | + title = {Frequent Mutation of Histone-Modifying Genes in Non-{{Hodgkin}} Lymphoma}, |
|
| 7114 | + author = {Morin, Ryan D. and Mendez-Lago, Maria and Mungall, Andrew J. and Goya, Rodrigo and Mungall, Karen L. and Corbett, Richard D. and Johnson, Nathalie A. and Severson, Tesa M. and Chiu, Readman and Field, Matthew and Jackman, Shaun and Krzywinski, Martin and Scott, David W. and Trinh, Diane L. and Tamura-Wells, Jessica and Li, Sa and Firme, Marlo R. and Rogic, Sanja and Griffith, Malachi and Chan, Susanna and Yakovenko, Oleksandr and Meyer, Irmtraud M. and Zhao, Eric Y. and Smailus, Duane and Moksa, Michelle and Chittaranjan, Suganthi and Rimsza, Lisa and Brooks-Wilson, Angela and Spinelli, John J. and Ben-Neriah, Susana and Meissner, Barbara and Woolcock, Bruce and Boyle, Merrill and McDonald, Helen and Tam, Angela and Zhao, Yongjun and Delaney, Allen and Zeng, Thomas and Tse, Kane and Butterfield, Yaron and Birol, Inanç and Holt, Rob and Schein, Jacqueline and Horsman, Douglas E. and Moore, Richard and Jones, Steven J. M. and Connors, Joseph M. and Hirst, Martin and Gascoyne, Randy D. and Marra, Marco A.}, |
|
| 7115 | + date = {2011-07-27}, |
|
| 7116 | + journaltitle = {Nature}, |
|
| 7117 | + shortjournal = {Nature}, |
|
| 7118 | + volume = {476}, |
|
| 7119 | + number = {7360}, |
|
| 7120 | + eprint = {21796119}, |
|
| 7121 | + eprinttype = {pmid}, |
|
| 7122 | + pages = {298--303}, |
|
| 7123 | + issn = {1476-4687}, |
|
| 7124 | + doi = {10.1038/nature10351}, |
|
| 7125 | + abstract = {Follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL) are the two most common non-Hodgkin lymphomas (NHLs). Here we sequenced tumour and matched normal DNA from 13 DLBCL cases and one FL case to identify genes with mutations in B-cell NHL. We analysed RNA-seq data from these and another 113 NHLs to identify genes with candidate mutations, and then re-sequenced tumour and matched normal DNA from these cases to confirm 109 genes with multiple somatic mutations. Genes with roles in histone modification were frequent targets of somatic mutation. For example, 32\% of DLBCL and 89\% of FL cases had somatic mutations in MLL2, which encodes a histone methyltransferase, and 11.4\% and 13.4\% of DLBCL and FL cases, respectively, had mutations in MEF2B, a calcium-regulated gene that cooperates with CREBBP and EP300 in acetylating histones. Our analysis suggests a previously unappreciated disruption of chromatin biology in lymphomagenesis.}, |
|
| 7126 | + langid = {english}, |
|
| 7127 | + pmcid = {PMC3210554}, |
|
| 7128 | + keywords = {Chromatin,DNA-Binding Proteins,Genome Human,Histone Acetyltransferases,Histone Methyltransferases,Histone-Lysine N-Methyltransferase,Histones,Humans,Loss of Heterozygosity,Lymphoma Follicular,Lymphoma Large B-Cell Diffuse,Lymphoma Non-Hodgkin,MADS Domain Proteins,MEF2 Transcription Factors,Mutation,Myogenic Regulatory Factors,Neoplasm Proteins}, |
|
| 7129 | + file = {/Users/rmorin/Zotero/storage/Y23YWY2C/Morin et al. - 2011 - Frequent mutation of histone-modifying genes in no.pdf} |
|
| 7130 | +} |
|
| 7131 | + |
|
| 7132 | +@article{morinGeneticLandscapesRelapsed2016, |
|
| 7133 | + title = {Genetic {{Landscapes}} of {{Relapsed}} and {{Refractory Diffuse Large B-Cell Lymphomas}}}, |
|
| 7134 | + author = {Morin, Ryan D. and Assouline, Sarit and Alcaide, Miguel and Mohajeri, Arezoo and Johnston, Rebecca L. and Chong, Lauren and Grewal, Jasleen and Yu, Stephen and Fornika, Daniel and Bushell, Kevin and Nielsen, Torsten Holm and Petrogiannis-Haliotis, Tina and Crump, Michael and Tosikyan, Axel and Grande, Bruno M. and MacDonald, David and Rousseau, Caroline and Bayat, Maryam and Sesques, Pierre and Froment, Remi and Albuquerque, Marco and Monczak, Yury and Oros, Kathleen Klein and Greenwood, Celia and Riazalhosseini, Yasser and Arseneault, Madeleine and Camlioglu, Errol and Constantin, André and Pan-Hammarstrom, Qiang and Peng, Roujun and Mann, Koren K. and Johnson, Nathalie A.}, |
|
| 7135 | + date = {2016-05-01}, |
|
| 7136 | + journaltitle = {Clinical Cancer Research: An Official Journal of the American Association for Cancer Research}, |
|
| 7137 | + shortjournal = {Clin Cancer Res}, |
|
| 7138 | + volume = {22}, |
|
| 7139 | + number = {9}, |
|
| 7140 | + eprint = {26647218}, |
|
| 7141 | + eprinttype = {pmid}, |
|
| 7142 | + pages = {2290--2300}, |
|
| 7143 | + issn = {1557-3265}, |
|
| 7144 | + doi = {10.1158/1078-0432.CCR-15-2123}, |
|
| 7145 | + abstract = {PURPOSE: Relapsed or refractory diffuse large B-cell lymphoma (rrDLBCL) is fatal in 90\% of patients, and yet little is known about its biology. EXPERIMENTAL DESIGN: Using exome sequencing, we characterized the mutation profiles of 38 rrDLBCL biopsies obtained at the time of progression after immunochemotherapy. To identify genes that may be associated with relapse, we compared the mutation frequency in samples obtained at relapse to an unrelated cohort of 138 diagnostic DLBCLs and separately amplified specific mutations in their matched diagnostic samples to identify clonal expansions. RESULTS: On the basis of a higher frequency at relapse and evidence for clonal selection, TP53, FOXO1, MLL3 (KMT2C), CCND3, NFKBIZ, and STAT6 emerged as top candidate genes implicated in therapeutic resistance. We observed individual examples of clonal expansions affecting genes whose mutations had not been previously associated with DLBCL including two regulators of NF-κB: NFKBIE and NFKBIZ We detected mutations that may be affect sensitivity to novel therapeutics, such as MYD88 and CD79B mutations, in 31\% and 23\% of patients with activated B-cell-type of rrDLBCL, respectively. We also identified recurrent STAT6 mutations affecting D419 in 36\% of patients with the germinal center B (GCB) cell rrDLBCL. These were associated with activated JAK/STAT signaling, increased phospho-STAT6 protein expression and increased expression of STAT6 target genes. CONCLUSIONS: This work improves our understanding of therapeutic resistance in rrDLBCL and has identified novel therapeutic opportunities especially for the high-risk patients with GCB-type rrDLBCL. Clin Cancer Res; 22(9); 2290-300. ©2015 AACR.}, |
|
| 7146 | + langid = {english}, |
|
| 7147 | + keywords = {Adult,Aged,B-Lymphocytes,CD79 Antigens,Cyclin D3,Female,Forkhead Box Protein O1,Gene Expression Regulation Neoplastic,Germinal Center,Humans,Janus Kinases,Lymphoma Large B-Cell Diffuse,Male,Middle Aged,Morinlab,Mutation,Myeloid Differentiation Factor 88,Myeloid-Lymphoid Leukemia Protein,Neoplasm Recurrence Local,NF-kappa B,Nuclear Proteins,Prospective Studies,Signal Transduction,STAT6 Transcription Factor,Tumor Suppressor Protein p53} |
|
| 7148 | +} |
|
| 7149 | + |
|
| 7150 | +@article{morinMolecularProfilingDiffuse2022, |
|
| 7151 | + title = {Molecular Profiling in Diffuse Large {{B-cell}} Lymphoma: Why so Many Types of Subtypes?}, |
|
| 7152 | + shorttitle = {Molecular Profiling in Diffuse Large {{B-cell}} Lymphoma}, |
|
| 7153 | + author = {Morin, Ryan D. and Arthur, Sarah E. and Hodson, Daniel J.}, |
|
| 7154 | + date = {2022-02}, |
|
| 7155 | + journaltitle = {British Journal of Haematology}, |
|
| 7156 | + shortjournal = {Br J Haematol}, |
|
| 7157 | + volume = {196}, |
|
| 7158 | + number = {4}, |
|
| 7159 | + eprint = {34467527}, |
|
| 7160 | + eprinttype = {pmid}, |
|
| 7161 | + pages = {814--829}, |
|
| 7162 | + issn = {1365-2141}, |
|
| 7163 | + doi = {10.1111/bjh.17811}, |
|
| 7164 | + abstract = {The term diffuse large B-cell lymphoma (DLBCL) includes a heterogeneous collection of biologically distinct tumours. This heterogeneity currently presents a barrier to the successful deployment of novel, biologically targeted therapies. Molecular profiling studies have recently proposed new molecular classification systems. These have the potential to resolve the biological heterogeneity of DLBCL into manageable subgroups of tumours that rely on shared oncogenic programmes. In many cases these biological programmes straddle the boundaries of our existing systems for classifying B-cell lymphomas. Here we review the findings from these major molecular profiling studies with a specific focus on those that propose new genetic subgroups of DLBCL. We highlight the areas of consensus and discordance between these studies and discuss the implications for current clinical practice and for clinical trials. Finally, we address the outstanding challenges and solutions to the introduction of genomic subtyping and precision medicine in DLBCL.}, |
|
| 7165 | + langid = {english}, |
|
| 7166 | + keywords = {cancer genetics,classifications,diffuse large B-cell lymphoma,Gene Expression Profiling,Genomics,Humans,Lymphoma Large B-Cell Diffuse,lymphomas,Morinlab,mutation analysis,Prognosis}, |
|
| 7167 | + file = {/Users/rmorin/Zotero/storage/QC2LGSN4/Morin et al. - 2022 - Molecular profiling in diffuse large B-cell lympho.pdf} |
|
| 7168 | +} |
|
| 7169 | + |
|
| 7170 | +@article{morinMutationalStructuralAnalysis2013, |
|
| 7171 | + title = {Mutational and Structural Analysis of Diffuse Large {{B-cell}} Lymphoma Using Whole-Genome Sequencing}, |
|
| 7172 | + author = {Morin, Ryan D. and Mungall, Karen and Pleasance, Erin and Mungall, Andrew J. and Goya, Rodrigo and Huff, Ryan D. and Scott, David W. and Ding, Jiarui and Roth, Andrew and Chiu, Readman and Corbett, Richard D. and Chan, Fong Chun and Mendez-Lago, Maria and Trinh, Diane L. and Bolger-Munro, Madison and Taylor, Greg and Hadj Khodabakhshi, Alireza and Ben-Neriah, Susana and Pon, Julia and Meissner, Barbara and Woolcock, Bruce and Farnoud, Noushin and Rogic, Sanja and Lim, Emilia L. and Johnson, Nathalie A. and Shah, Sohrab and Jones, Steven and Steidl, Christian and Holt, Robert and Birol, Inanc and Moore, Richard and Connors, Joseph M. and Gascoyne, Randy D. and Marra, Marco A.}, |
|
| 7173 | + date = {2013-08-15}, |
|
| 7174 | + journaltitle = {Blood}, |
|
| 7175 | + shortjournal = {Blood}, |
|
| 7176 | + volume = {122}, |
|
| 7177 | + number = {7}, |
|
| 7178 | + eprint = {23699601}, |
|
| 7179 | + eprinttype = {pmid}, |
|
| 7180 | + pages = {1256--1265}, |
|
| 7181 | + issn = {1528-0020}, |
|
| 7182 | + doi = {10.1182/blood-2013-02-483727}, |
|
| 7183 | + abstract = {Diffuse large B-cell lymphoma (DLBCL) is a genetically heterogeneous cancer composed of at least 2 molecular subtypes that differ in gene expression and distribution of mutations. Recently, application of genome/exome sequencing and RNA-seq to DLBCL has revealed numerous genes that are recurrent targets of somatic point mutation in this disease. Here we provide a whole-genome-sequencing-based perspective of DLBCL mutational complexity by characterizing 40 de novo DLBCL cases and 13 DLBCL cell lines and combining these data with DNA copy number analysis and RNA-seq from an extended cohort of 96 cases. Our analysis identified widespread genomic rearrangements including evidence for chromothripsis as well as the presence of known and novel fusion transcripts. We uncovered new gene targets of recurrent somatic point mutations and genes that are targeted by focal somatic deletions in this disease. We highlight the recurrence of germinal center B-cell-restricted mutations affecting genes that encode the S1P receptor and 2 small GTPases (GNA13 and GNAI2) that together converge on regulation of B-cell homing. We further analyzed our data to approximate the relative temporal order in which some recurrent mutations were acquired and demonstrate that ongoing acquisition of mutations and intratumoral clonal heterogeneity are common features of DLBCL. This study further improves our understanding of the processes and pathways involved in lymphomagenesis, and some of the pathways mutated here may indicate new avenues for therapeutic intervention.}, |
|
| 7184 | + langid = {english}, |
|
| 7185 | + pmcid = {PMC3744992}, |
|
| 7186 | + keywords = {Biomarkers Tumor,DNA Copy Number Variations,Gene Expression Profiling,Genome Human,GTP-Binding Protein alpha Subunits G12-G13,High-Throughput Nucleotide Sequencing,Humans,Lymphoma Large B-Cell Diffuse,Mutation,Oligonucleotide Array Sequence Analysis,Real-Time Polymerase Chain Reaction,Reverse Transcriptase Polymerase Chain Reaction,RNA Messenger,Tumor Cells Cultured}, |
|
| 7187 | + file = {/Users/rmorin/Zotero/storage/YQZALE78/Morin et al. - 2013 - Mutational and structural analysis of diffuse larg.pdf} |
|
| 7188 | +} |
|
| 7189 | + |
|
| 7190 | +@article{morinSomaticMutationsAltering2010a, |
|
| 7191 | + title = {Somatic Mutations Altering {{EZH2}} ({{Tyr641}}) in Follicular and Diffuse Large {{B-cell}} Lymphomas of Germinal-Center Origin}, |
|
| 7192 | + author = {Morin, Ryan D. and Johnson, Nathalie A. and Severson, Tesa M. and Mungall, Andrew J. and An, Jianghong and Goya, Rodrigo and Paul, Jessica E. and Boyle, Merrill and Woolcock, Bruce W. and Kuchenbauer, Florian and Yap, Damian and Humphries, R. Keith and Griffith, Obi L. and Shah, Sohrab and Zhu, Henry and Kimbara, Michelle and Shashkin, Pavel and Charlot, Jean F. and Tcherpakov, Marianna and Corbett, Richard and Tam, Angela and Varhol, Richard and Smailus, Duane and Moksa, Michelle and Zhao, Yongjun and Delaney, Allen and Qian, Hong and Birol, Inanc and Schein, Jacqueline and Moore, Richard and Holt, Robert and Horsman, Doug E. and Connors, Joseph M. and Jones, Steven and Aparicio, Samuel and Hirst, Martin and Gascoyne, Randy D. and Marra, Marco A.}, |
|
| 7193 | + date = {2010-02}, |
|
| 7194 | + journaltitle = {Nature Genetics}, |
|
| 7195 | + shortjournal = {Nat Genet}, |
|
| 7196 | + volume = {42}, |
|
| 7197 | + number = {2}, |
|
| 7198 | + eprint = {20081860}, |
|
| 7199 | + eprinttype = {pmid}, |
|
| 7200 | + pages = {181--185}, |
|
| 7201 | + issn = {1546-1718}, |
|
| 7202 | + doi = {10.1038/ng.518}, |
|
| 7203 | + abstract = {Follicular lymphoma (FL) and the GCB subtype of diffuse large B-cell lymphoma (DLBCL) derive from germinal center B cells. Targeted resequencing studies have revealed mutations in various genes encoding proteins in the NF-kappaB pathway that contribute to the activated B-cell (ABC) DLBCL subtype, but thus far few GCB-specific mutations have been identified. Here we report recurrent somatic mutations affecting the polycomb-group oncogene EZH2, which encodes a histone methyltransferase responsible for trimethylating Lys27 of histone H3 (H3K27). After the recent discovery of mutations in KDM6A (UTX), which encodes the histone H3K27me3 demethylase UTX, in several cancer types, EZH2 is the second histone methyltransferase gene found to be mutated in cancer. These mutations, which result in the replacement of a single tyrosine in the SET domain of the EZH2 protein (Tyr641), occur in 21.7\% of GCB DLBCLs and 7.2\% of FLs and are absent from ABC DLBCLs. Our data are consistent with the notion that EZH2 proteins with mutant Tyr641 have reduced enzymatic activity in vitro.}, |
|
| 7204 | + langid = {english}, |
|
| 7205 | + pmcid = {PMC2850970}, |
|
| 7206 | + keywords = {Adult,Aged,Amino Acid Sequence,Base Sequence,DNA Mutational Analysis,DNA-Binding Proteins,Enhancer of Zeste Homolog 2 Protein,Exons,Female,Gene Expression Profiling,Gene Expression Regulation Neoplastic,Genome Human,Germinal Center,Humans,Lymphoma Follicular,Lymphoma Large B-Cell Diffuse,Male,Middle Aged,Molecular Sequence Data,Mutant Proteins,Mutation,Polycomb Repressive Complex 2,Transcription Factors,Tyrosine}, |
|
| 7207 | + file = {/Users/rmorin/Zotero/storage/59YI29V2/Morin et al. - 2010 - Somatic mutations altering EZH2 (Tyr641) in follic.pdf} |
|
| 7208 | +} |
|
| 7209 | + |
|
| 7210 | +@article{morinTreatingLymphomaNow2021, |
|
| 7211 | + title = {Treating Lymphoma Is Now a Bit {{EZ-er}}}, |
|
| 7212 | + author = {Morin, Ryan D. and Arthur, Sarah E. and Assouline, Sarit}, |
|
| 7213 | + date = {2021-04-27}, |
|
| 7214 | + journaltitle = {Blood Advances}, |
|
| 7215 | + shortjournal = {Blood Adv}, |
|
| 7216 | + volume = {5}, |
|
| 7217 | + number = {8}, |
|
| 7218 | + eprint = {33904892}, |
|
| 7219 | + eprinttype = {pmid}, |
|
| 7220 | + pages = {2256--2263}, |
|
| 7221 | + issn = {2473-9537}, |
|
| 7222 | + doi = {10.1182/bloodadvances.2020002773}, |
|
| 7223 | + abstract = {Tazemetostat represents the first epigenetic therapy approved for the treatment of follicular lymphoma (FL). It inhibits the activity of the enhancer of zeste homolog 2 (EZH2) histone methyltransferase, the first of a multitude of epigenetic regulators that have been identified as recurrently mutated in FL and germinal center diffuse large B-cell lymphoma. In this review, we discuss the initial discovery and ongoing exploration of the functional role of EZH2 mutations in lymphomagenesis. We also explore the path from the preclinical development of tazemetostat to its approval for the treatment of relapsed FL, and potential future therapeutic applications. We discuss the clinical data that led to the approval of tazemetostat and ongoing research into the function of EZH2 and of tazemetostat in lymphomas that derive from the germinal center, which could increase the applicability of this drug in the future.}, |
|
| 7224 | + langid = {english}, |
|
| 7225 | + pmcid = {PMC8095133}, |
|
| 7226 | + keywords = {Germinal Center,Humans,Lymphoma Follicular,Lymphoma Large B-Cell Diffuse,Mutation}, |
|
| 7227 | + file = {/Users/rmorin/Zotero/storage/XK4T3XCB/Morin et al. - 2021 - Treating lymphoma is now a bit EZ-er.pdf} |
|
| 7228 | +} |
|
| 7229 | + |
|
| 7230 | +@article{moritaEfficacyAprepitantCHOP2017, |
|
| 7231 | + title = {Efficacy of Aprepitant for {{CHOP}} Chemotherapy-Induced Nausea, Vomiting, and Anorexia}, |
|
| 7232 | + author = {Morita, Mihoko and Kishi, Shinji and Ookura, Miyuki and Matsuda, Yasufumi and Tai, Katsunori and Yamauchi, Takahiro and Ueda, Takanori}, |
|
| 7233 | + date = {2017-11-01}, |
|
| 7234 | + journaltitle = {Current Problems in Cancer}, |
|
| 7235 | + shortjournal = {Current Problems in Cancer}, |
|
| 7236 | + volume = {41}, |
|
| 7237 | + number = {6}, |
|
| 7238 | + pages = {419--425}, |
|
| 7239 | + issn = {0147-0272}, |
|
| 7240 | + doi = {10.1016/j.currproblcancer.2017.09.001}, |
|
| 7241 | + url = {https://www.sciencedirect.com/science/article/pii/S014702721730140X}, |
|
| 7242 | + urldate = {2024-01-31}, |
|
| 7243 | + abstract = {The objective of this study was to evaluate whether aprepitant in addition to 5-HT3 receptor antagonist is useful for preventing chemotherapy-induced nausea and vomiting (CINV) and anorexia in patients receiving CHOP therapy, and to evaluate the relationship between in vivo kinetics of plasma substance P and these adverse events. Patients with malignant lymphoma who received CHOP chemotherapy or THP (THP-ADR)-COP therapy were investigated for CINV and anorexia for 5 days after the start of chemotherapy. With the first course of chemotherapy, all patients received only granisetron on day1 as an antiemetic. Patients who experienced nausea, vomiting, or anorexia exceeding grade 1 in the first course received aprepitant for 3 days in addition to granisetron with the second course of CHOP chemotherapy. Plasma substance P concentrations at 24 and 72 hours after chemotherapy were measured. Nineteen patients were evaluated. Nausea, vomiting, or anorexia was observed with the first course in 7 of 19 patients. During the second course with aprepitant, no patients experienced vomiting, and the toxicity grade of nausea, vomiting, or anorexia was decreased compared with those in the first course. Substance P concentrations showed no differences after chemotherapy, in patients with nausea, vomiting, or anorexia and in patients without. The addition of aprepitant to 5-HT3 receptor antagonist appears effective for CINV or anorexia for patients who received CHOP chemotherapy.}, |
|
| 7244 | + keywords = {Aprepitant,CHOP chemotherapy,CINV,Malignant lymphoma,Substance P}, |
|
| 7245 | + file = {/Users/rmorin/Zotero/storage/J2M83YK8/S014702721730140X.html} |
|
| 7246 | +} |
|
| 7247 | + |
|
| 7248 | +@article{moritaEfficacyAprepitantCHOP2017a, |
|
| 7249 | + title = {Efficacy of Aprepitant for {{CHOP}} Chemotherapy-Induced Nausea, Vomiting, and Anorexia}, |
|
| 7250 | + author = {Morita, Mihoko and Kishi, Shinji and Ookura, Miyuki and Matsuda, Yasufumi and Tai, Katsunori and Yamauchi, Takahiro and Ueda, Takanori}, |
|
| 7251 | + date = {2017}, |
|
| 7252 | + journaltitle = {Current Problems in Cancer}, |
|
| 7253 | + shortjournal = {Curr Probl Cancer}, |
|
| 7254 | + volume = {41}, |
|
| 7255 | + number = {6}, |
|
| 7256 | + eprint = {29061362}, |
|
| 7257 | + eprinttype = {pmid}, |
|
| 7258 | + pages = {419--425}, |
|
| 7259 | + issn = {1535-6345}, |
|
| 7260 | + doi = {10.1016/j.currproblcancer.2017.09.001}, |
|
| 7261 | + abstract = {The objective of this study was to evaluate whether aprepitant in addition to 5-HT3 receptor antagonist is useful for preventing chemotherapy-induced nausea and vomiting (CINV) and anorexia in patients receiving CHOP therapy, and to evaluate the relationship between in vivo kinetics of plasma substance P and these adverse events. Patients with malignant lymphoma who received CHOP chemotherapy or THP (THP-ADR)-COP therapy were investigated for CINV and anorexia for 5 days after the start of chemotherapy. With the first course of chemotherapy, all patients received only granisetron on day1 as an antiemetic. Patients who experienced nausea, vomiting, or anorexia exceeding grade 1 in the first course received aprepitant for 3 days in addition to granisetron with the second course of CHOP chemotherapy. Plasma substance P concentrations at 24 and 72 hours after chemotherapy were measured. Nineteen patients were evaluated. Nausea, vomiting, or anorexia was observed with the first course in 7 of 19 patients. During the second course with aprepitant, no patients experienced vomiting, and the toxicity grade of nausea, vomiting, or anorexia was decreased compared with those in the first course. Substance P concentrations showed no differences after chemotherapy, in patients with nausea, vomiting, or anorexia and in patients without. The addition of aprepitant to 5-HT3 receptor antagonist appears effective for CINV or anorexia for patients who received CHOP chemotherapy.}, |
|
| 7262 | + langid = {english}, |
|
| 7263 | + keywords = {Adult,Aged,Anorexia,Antiemetics,Antineoplastic Combined Chemotherapy Protocols,Aprepitant,CHOP chemotherapy,CINV,Cyclophosphamide,Doxorubicin,Female,Granisetron,Humans,Lymphoma,Male,Malignant lymphoma,Middle Aged,Morpholines,Nausea,Neurokinin-1 Receptor Antagonists,Prednisone,Receptors Neurokinin-1,Serotonin 5-HT3 Receptor Antagonists,Substance P,Vincristine,Vomiting} |
|
| 7264 | +} |
|
| 7265 | + |
|
| 7266 | +@article{motoyamaPositiveNegativeRegulation2005, |
|
| 7267 | + title = {Positive and {{Negative Regulation}} of {{Nuclear Factor- B-mediated Transcription}} by {{I B-}} , an {{Inducible Nuclear Protein}}}, |
|
| 7268 | + author = {Motoyama, M and Yamazaki, S and Eto-Kimura, A and Takeshige, K and Muta, T}, |
|
| 7269 | + date = {2005-02}, |
|
| 7270 | + journaltitle = {J Biol Chem}, |
|
| 7271 | + volume = {280}, |
|
| 7272 | + number = {9}, |
|
| 7273 | + pages = {7444--7451}, |
|
| 7274 | + keywords = {nosource} |
|
| 7275 | +} |
|
| 7276 | + |
|
| 7277 | +@article{mottokGenomicAlterationsCIITA2015b, |
|
| 7278 | + title = {Genomic {{Alterations}} in {{CIITA Are Frequent}} in {{Primary Mediastinal Large B Cell Lymphoma}} and {{Are Associated}} with {{Diminished MHC Class II Expression}}}, |
|
| 7279 | + author = {Mottok, Anja and Woolcock, Bruce and Chan, Fong Chun and Tong, King Mong and Chong, Lauren and Farinha, Pedro and Telenius, Adèle and Chavez, Elizabeth and Ramchandani, Suvan and Drake, Marie and Boyle, Merrill and Ben-Neriah, Susana and Scott, David W. and Rimsza, Lisa M. and Siebert, Reiner and Gascoyne, Randy D. and Steidl, Christian}, |
|
| 7280 | + date = {2015-11-17}, |
|
| 7281 | + journaltitle = {Cell Reports}, |
|
| 7282 | + shortjournal = {Cell Rep}, |
|
| 7283 | + volume = {13}, |
|
| 7284 | + number = {7}, |
|
| 7285 | + eprint = {26549456}, |
|
| 7286 | + eprinttype = {pmid}, |
|
| 7287 | + pages = {1418--1431}, |
|
| 7288 | + issn = {2211-1247}, |
|
| 7289 | + doi = {10.1016/j.celrep.2015.10.008}, |
|
| 7290 | + abstract = {Primary mediastinal large B cell lymphoma (PMBCL) is an aggressive non-Hodgkin's lymphoma, predominantly affecting young patients. We analyzed 45 primary PMBCL tumor biopsies and 3 PMBCL-derived cell lines for the presence of genetic alterations involving the major histocompatibility complex (MHC) class II transactivator CIITA and found frequent aberrations consisting of structural genomic rearrangements, missense, nonsense, and frame-shift mutations (53\% of primary tumor biopsies and all cell lines). We also detected intron 1 mutations in 47\% of the cases, and detailed sequence analysis strongly suggests AID-mediated aberrant somatic hypermutation as the mutational mechanism. Furthermore, we demonstrate that genomic lesions in CIITA result in decreased protein expression and reduction of MHC class II surface expression, creating an immune privilege phenotype in PMBCL. In summary, we establish CIITA alterations as a common mechanism of immune escape through reduction of MHC class II expression in PMBCL, with potential implications for future treatments targeting microenvironment-related biology.}, |
|
| 7291 | + langid = {english}, |
|
| 7292 | + keywords = {Cell Line,DNA Mutational Analysis,Gene Expression,Genetic Association Studies,Genetic Predisposition to Disease,Histocompatibility Antigens Class II,Humans,Introns,Lymphoma Large B-Cell Diffuse,Male,Mediastinal Neoplasms,Nuclear Proteins,Point Mutation,Sequence Deletion,Trans-Activators,Tumor Escape}, |
|
| 7293 | + file = {/Users/rmorin/Zotero/storage/DJ8D5CGX/Mottok et al. - 2015 - Genomic Alterations in CIITA Are Frequent in Prima.pdf} |
|
| 7294 | +} |
|
| 7295 | + |
|
| 7296 | +@article{mottokIntegrativeGenomicAnalysis2019b, |
|
| 7297 | + title = {Integrative Genomic Analysis Identifies Key Pathogenic Mechanisms in Primary Mediastinal Large {{B-cell}} Lymphoma}, |
|
| 7298 | + author = {Mottok, Anja and Hung, Stacy S. and Chavez, Elizabeth A. and Woolcock, Bruce and Telenius, Adèle and Chong, Lauren C. and Meissner, Barbara and Nakamura, Hisae and Rushton, Christopher and Viganò, Elena and Sarkozy, Clementine and Gascoyne, Randy D. and Connors, Joseph M. and Ben-Neriah, Susana and Mungall, Andrew and Marra, Marco A. and Siebert, Reiner and Scott, David W. and Savage, Kerry J. and Steidl, Christian}, |
|
| 7299 | + date = {2019-09-05}, |
|
| 7300 | + journaltitle = {Blood}, |
|
| 7301 | + shortjournal = {Blood}, |
|
| 7302 | + volume = {134}, |
|
| 7303 | + number = {10}, |
|
| 7304 | + eprint = {31292115}, |
|
| 7305 | + eprinttype = {pmid}, |
|
| 7306 | + pages = {802--813}, |
|
| 7307 | + issn = {1528-0020}, |
|
| 7308 | + doi = {10.1182/blood.2019001126}, |
|
| 7309 | + abstract = {Primary mediastinal large B-cell lymphoma (PMBL) represents a clinically and pathologically distinct subtype of large B-cell lymphomas. Furthermore, molecular studies, including global gene expression profiling, have provided evidence that PMBL is more closely related to classical Hodgkin lymphoma (cHL). Although targeted sequencing studies have revealed a number of mutations involved in PMBL pathogenesis, a comprehensive description of disease-associated genetic alterations and perturbed pathways is still lacking. Here, we performed whole-exome sequencing of 95 PMBL tumors to inform on oncogenic driver genes and recurrent copy number alterations. The integration of somatic gene mutations with gene expression signatures provides further insights into genotype-phenotype interrelation in PMBL. We identified highly recurrent oncogenic mutations in the Janus kinase-signal transducer and activator of transcription and nuclear factor κB pathways, and provide additional evidence of the importance of immune evasion in PMBL (CIITA, CD58, B2M, CD274, and PDCD1LG2). Our analyses highlight the interferon response factor (IRF) pathway as a putative novel hallmark with frequent alterations in multiple pathway members (IRF2BP2, IRF4, and IRF8). In addition, our integrative analysis illustrates the importance of JAK1, RELB, and EP300 mutations driving oncogenic signaling. The identified driver genes were significantly more frequently mutated in PMBL compared with diffuse large B-cell lymphoma, whereas only a limited number of genes were significantly different between PMBL and cHL, emphasizing the close relation between these entities. Our study, performed on a large cohort of PMBL, highlights the importance of distinctive genetic alterations for disease taxonomy with relevance for diagnostic evaluation and therapeutic decision-making.}, |
|
| 7310 | + langid = {english}, |
|
| 7311 | + keywords = {Adolescent,Adult,Aged,Cohort Studies,DNA Mutational Analysis,Female,Gene Expression Profiling,Gene Expression Regulation Neoplastic,Genomics,Humans,Lymphoma Large B-Cell Diffuse,Male,Mediastinal Neoplasms,Middle Aged,Mutation,Systems Integration,Young Adult}, |
|
| 7312 | + file = {/Users/rmorin/Zotero/storage/URERFTTM/Mottok et al. - 2019 - Integrative genomic analysis identifies key pathog.pdf} |
|
| 7313 | +} |
|
| 7314 | + |
|
| 7315 | +@article{mottokMolecularClassificationPrimary2018, |
|
| 7316 | + title = {Molecular Classification of Primary Mediastinal Large {{B-cell}} Lymphoma Using Routinely Available Tissue Specimens}, |
|
| 7317 | + author = {Mottok, Anja and Wright, George and Rosenwald, Andreas and Ott, German and Ramsower, Colleen and Campo, Elias and Braziel, Rita M. and Delabie, Jan and Weisenburger, Dennis D. and Song, Joo Y. and Chan, Wing C. and Cook, James R. and Fu, Kai and Greiner, Tim and Smeland, Erlend and Holte, Harald and Savage, Kerry J. and Glinsmann-Gibson, Betty J. and Gascoyne, Randy D. and Staudt, Louis M. and Jaffe, Elaine S. and Connors, Joseph M. and Scott, David W. and Steidl, Christian and Rimsza, Lisa M.}, |
|
| 7318 | + date = {2018-11-29}, |
|
| 7319 | + journaltitle = {Blood}, |
|
| 7320 | + shortjournal = {Blood}, |
|
| 7321 | + volume = {132}, |
|
| 7322 | + number = {22}, |
|
| 7323 | + eprint = {30257882}, |
|
| 7324 | + eprinttype = {pmid}, |
|
| 7325 | + pages = {2401--2405}, |
|
| 7326 | + issn = {0006-4971}, |
|
| 7327 | + doi = {10.1182/blood-2018-05-851154}, |
|
| 7328 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6265647/}, |
|
| 7329 | + urldate = {2020-03-09}, |
|
| 7330 | + abstract = {Publisher's Note: There is a Blood Commentary on this article in this issue., A 58-gene expression-based assay aids in the molecular distinction of PMBCL and DLBCL using archival tissue biopsy specimens. , Primary mediastinal large B-cell lymphoma (PMBCL) is recognized as a distinct entity in the World Health Organization classification. Currently, the diagnosis relies on consensus of histopathology, clinical variables, and presentation, giving rise to diagnostic inaccuracy in routine practice. Previous studies have demonstrated that PMBCL can be distinguished from subtypes of diffuse large B-cell lymphoma (DLBCL) based on gene expression signatures. However, requirement of fresh-frozen biopsy material has precluded the transfer of gene expression–based assays to the clinic. Here, we developed a robust and accurate molecular classification assay (Lymph3Cx) for the distinction of PMBCL from DLBCL subtypes based on gene expression measurements in formalin-fixed, paraffin-embedded tissue. A probabilistic model accounting for classification error, comprising 58 gene features, was trained on 68 cases of PMBCL and DLBCL. Performance of the model was subsequently evaluated in an independent validation cohort of 158 cases and showed high agreement of the Lymph3Cx molecular classification with the clinicopathological diagnosis of an expert panel (frank misclassification rate, 3.8\%). Furthermore, we demonstrate reproducibility of the assay with 100\% concordance of subtype assignments at 2 independent laboratories. Future studies will determine Lymph3Cx’s utility for routine diagnostic purposes and therapeutic decision making.,}, |
|
| 7331 | + pmcid = {PMC6265647} |
|
| 7332 | +} |
|
| 7333 | + |
|
| 7334 | +@article{moumenHnRNPHDM2Target2005, |
|
| 7335 | + title = {{{hnRNP K}}: {{An HDM2 Target}} and {{Transcriptional Coactivator}} of P53 in {{Response}} to {{DNA Damage}}}, |
|
| 7336 | + shorttitle = {{{hnRNP K}}}, |
|
| 7337 | + author = {Moumen, Abdeladim and Masterson, Philip and O'Connor, Mark J. and Jackson, Stephen P.}, |
|
| 7338 | + date = {2005-12-16}, |
|
| 7339 | + journaltitle = {Cell}, |
|
| 7340 | + shortjournal = {Cell}, |
|
| 7341 | + volume = {123}, |
|
| 7342 | + number = {6}, |
|
| 7343 | + eprint = {16360036}, |
|
| 7344 | + eprinttype = {pmid}, |
|
| 7345 | + pages = {1065--1078}, |
|
| 7346 | + publisher = {Elsevier}, |
|
| 7347 | + issn = {0092-8674, 1097-4172}, |
|
| 7348 | + doi = {10.1016/j.cell.2005.09.032}, |
|
| 7349 | + url = {https://www.cell.com/cell/abstract/S0092-8674(05)01038-X}, |
|
| 7350 | + urldate = {2022-09-25}, |
|
| 7351 | + langid = {english}, |
|
| 7352 | + file = {/Users/rmorin/Zotero/storage/EHEPFPEH/Moumen et al. - 2005 - hnRNP K An HDM2 Target and Transcriptional Coacti.pdf;/Users/rmorin/Zotero/storage/A72LH7F4/S0092-8674(05)01038-X.html} |
|
| 7353 | +} |
|
| 7354 | + |
|
| 7355 | +@online{MRNACappingBiological, |
|
| 7356 | + title = {{{mRNA}} Capping: Biological Functions and Applications | {{Nucleic Acids Research}} | {{Oxford Academic}}}, |
|
| 7357 | + url = {https://academic.oup.com/nar/article/44/16/7511/2460195}, |
|
| 7358 | + urldate = {2023-01-09}, |
|
| 7359 | + keywords = {nosource} |
|
| 7360 | +} |
|
| 7361 | + |
|
| 7362 | +@online{MRNACappingBiologicala, |
|
| 7363 | + title = {{{mRNA}} Capping: Biological Functions and Applications | {{Nucleic Acids Research}} | {{Oxford Academic}}}, |
|
| 7364 | + url = {https://academic.oup.com/nar/article/44/16/7511/2460195}, |
|
| 7365 | + urldate = {2022-10-06}, |
|
| 7366 | + keywords = {nosource} |
|
| 7367 | +} |
|
| 7368 | + |
|
| 7369 | +@article{muellerGenomicPathologySLEAssociated2013, |
|
| 7370 | + title = {Genomic {{Pathology}} of {{SLE-Associated Copy-Number Variation}} at the {{FCGR2C}}/{{FCGR3B}}/{{FCGR2B Locus}}}, |
|
| 7371 | + author = {Mueller, Michael and Barros, Paula and Witherden, Abigail S and Roberts, Amy L and Zhang, Zhou and Schaschl, Helmut and Yu, Chack-Yung and Hurles, Matthew E and Schaffner, Catherine and Floto, R Andres and Game, Laurence and Steinberg, Karyn Meltz and Wilson, Richard K and Graves, Tina A and Eichler, Evan E and Cook, H Terence and Vyse, Timothy J and Aitman, Timothy J}, |
|
| 7372 | + date = {2013}, |
|
| 7373 | + journaltitle = {Am J Hum Genet}, |
|
| 7374 | + volume = {92}, |
|
| 7375 | + number = {1}, |
|
| 7376 | + pages = {28--40}, |
|
| 7377 | + keywords = {nosource} |
|
| 7378 | +} |
|
| 7379 | + |
|
| 7380 | +@article{mularoniOncodriveFMLGeneralFramework2016, |
|
| 7381 | + title = {{{OncodriveFML}}: A General Framework to Identify Coding and Non-Coding Regions with Cancer Driver Mutations}, |
|
| 7382 | + shorttitle = {{{OncodriveFML}}}, |
|
| 7383 | + author = {Mularoni, Loris and Sabarinathan, Radhakrishnan and Deu-Pons, Jordi and Gonzalez-Perez, Abel and López-Bigas, Núria}, |
|
| 7384 | + date = {2016-06-16}, |
|
| 7385 | + journaltitle = {Genome Biology}, |
|
| 7386 | + shortjournal = {Genome Biol}, |
|
| 7387 | + volume = {17}, |
|
| 7388 | + number = {1}, |
|
| 7389 | + eprint = {27311963}, |
|
| 7390 | + eprinttype = {pmid}, |
|
| 7391 | + pages = {128}, |
|
| 7392 | + issn = {1474-760X}, |
|
| 7393 | + doi = {10.1186/s13059-016-0994-0}, |
|
| 7394 | + abstract = {Distinguishing the driver mutations from somatic mutations in a tumor genome is one of the major challenges of cancer research. This challenge is more acute and far from solved for non-coding mutations. Here we present OncodriveFML, a method designed to analyze the pattern of somatic mutations across tumors in both coding and non-coding genomic regions to identify signals of positive selection, and therefore, their involvement in tumorigenesis. We describe the method and illustrate its usefulness to identify protein-coding genes, promoters, untranslated regions, intronic splice regions, and lncRNAs-containing driver mutations in several malignancies.}, |
|
| 7395 | + langid = {english}, |
|
| 7396 | + pmcid = {PMC4910259}, |
|
| 7397 | + keywords = {Cancer drivers,Carcinogenesis,Computational Biology,Genome Human,Humans,Local functional mutations bias,Mutation,Neoplasms,Non-coding drivers,Non-coding regions,Open Reading Frames,Promoter Regions Genetic,RNA Long Noncoding,Software}, |
|
| 7398 | + file = {/Users/rmorin/Zotero/storage/WECR24US/Mularoni et al. - 2016 - OncodriveFML a general framework to identify codi.pdf} |
|
| 7399 | +} |
|
| 7400 | + |
|
| 7401 | +@article{muppidiLossSignalingGa132014b, |
|
| 7402 | + title = {Loss of Signaling via {{Gα13}} in Germinal Center {{B}} Cell-Derived Lymphoma}, |
|
| 7403 | + author = {Muppidi, J. and Schmitz, R. and Green, Jesse A. and Green, Jesse A. and Xiao, Wenming and Larsen, Adrien B. and Braun, S. and An, Jinping and Xu, Ying and Rosenwald, A. and Ott, G. and Gascoyne, R. and Rimsza, L. and Campo, E. and Jaffe, E. and Delabie, J. and Smeland, E. and Braziel, R. and Tubbs, R. and Cook, J. and Weisenburger, D. and Chan, W. and Vaidehi, N. and Staudt, L. and Cyster, J.}, |
|
| 7404 | + date = {2014}, |
|
| 7405 | + journaltitle = {Nature}, |
|
| 7406 | + shortjournal = {Nature}, |
|
| 7407 | + volume = {516}, |
|
| 7408 | + pages = {254--258}, |
|
| 7409 | + doi = {10.1038/nature13765}, |
|
| 7410 | + file = {/Users/rmorin/Zotero/storage/5FHQMRFB/Muppidi et al. - 2014 - Loss of signaling via Gα13 in germinal center B ce.pdf} |
|
| 7411 | +} |
|
| 7412 | + |
|
| 7413 | +@article{nadeuGenomicEpigenomicInsights2020b, |
|
| 7414 | + title = {Genomic and Epigenomic Insights into the Origin, Pathogenesis and Clinical Behavior of Mantle Cell Lymphoma Subtypes.}, |
|
| 7415 | + author = {Nadeu, F. and Martín-García, D. and Clot, G. and Díaz-Navarro, A. and Duran-Ferrer, M. and Navarro, A. and Vilarrasa-Blasi, Roser and Kulis, M. and Royo, R. and Gutiérrez-Abril, J. and Valdés-Mas, R. and López, C. and Chapaprieta, V. and Puiggrós, Montserrat and Castellano, G. and Costa, D. and Aymerich, M. and Jares, P. and Espinet, B. and Muntañola, A. and Ribera‐Cortada, Inmaculada and Siebert, R. and Colomer, D. and Torrents, D. and Giné, E. and López-Guillermo, A. and Küppers, R. and Martín-Subero, J. and Puente, X. and Beà, S. and Campo, E.}, |
|
| 7416 | + date = {2020}, |
|
| 7417 | + journaltitle = {Blood}, |
|
| 7418 | + shortjournal = {Blood}, |
|
| 7419 | + doi = {10.1182/blood.2020005289}, |
|
| 7420 | + file = {/Users/rmorin/Zotero/storage/464M2VUB/Nadeu et al. - 2020 - Genomic and epigenomic insights into the origin, p.pdf} |
|
| 7421 | +} |
|
| 7422 | + |
|
| 7423 | +@article{nadeuIgCallerReconstructingImmunoglobulin2020, |
|
| 7424 | + title = {{{IgCaller}} for Reconstructing Immunoglobulin Gene Rearrangements and Oncogenic Translocations from Whole-Genome Sequencing in Lymphoid Neoplasms}, |
|
| 7425 | + author = {Nadeu, Ferran and Mas-de-Les-Valls, Rut and Navarro, Alba and Royo, Romina and Martín, Silvia and Villamor, Neus and Suárez-Cisneros, Helena and Mares, Rosó and Lu, Junyan and Enjuanes, Anna and Rivas-Delgado, Alfredo and Aymerich, Marta and Baumann, Tycho and Colomer, Dolors and Delgado, Julio and Morin, Ryan D. and Zenz, Thorsten and Puente, Xose S. and Campbell, Peter J. and Beà, Sílvia and Maura, Francesco and Campo, Elías}, |
|
| 7426 | + date = {2020-07-07}, |
|
| 7427 | + journaltitle = {Nature Communications}, |
|
| 7428 | + shortjournal = {Nat Commun}, |
|
| 7429 | + volume = {11}, |
|
| 7430 | + number = {1}, |
|
| 7431 | + eprint = {32636395}, |
|
| 7432 | + eprinttype = {pmid}, |
|
| 7433 | + pages = {3390}, |
|
| 7434 | + issn = {2041-1723}, |
|
| 7435 | + doi = {10.1038/s41467-020-17095-7}, |
|
| 7436 | + abstract = {Immunoglobulin (Ig) gene rearrangements and oncogenic translocations are routinely assessed during the characterization of B cell neoplasms and stratification of patients with distinct clinical and biological features, with the assessment done using Sanger sequencing, targeted next-generation sequencing, or fluorescence in situ hybridization (FISH). Currently, a complete Ig characterization cannot be extracted from whole-genome sequencing (WGS) data due to the inherent complexity of the Ig loci. Here, we introduce IgCaller, an algorithm designed to fully characterize Ig gene rearrangements and oncogenic translocations from short-read WGS data. Using a cohort of 404 patients comprising different subtypes of B cell neoplasms, we demonstrate that IgCaller identifies both heavy and light chain rearrangements to provide additional information on their functionality, somatic mutational status, class switch recombination, and oncogenic Ig translocations. Our data thus support IgCaller to be a reliable alternative to Sanger sequencing and FISH for studying the genetic properties of the Ig loci.}, |
|
| 7437 | + langid = {english}, |
|
| 7438 | + pmcid = {PMC7341758}, |
|
| 7439 | + keywords = {Algorithms,Cohort Studies,Genes Immunoglobulin,Genome Human,Hematologic Neoplasms,High-Throughput Nucleotide Sequencing,Humans,Immunoglobulin Class Switching,In Situ Hybridization Fluorescence,Lymphoma B-Cell,Oncogenes,Software,Translocation Genetic,Whole Genome Sequencing}, |
|
| 7440 | + file = {/Users/rmorin/Zotero/storage/Q8DV2HMG/Nadeu et al. - 2020 - IgCaller for reconstructing immunoglobulin gene re.pdf} |
|
| 7441 | +} |
|
| 7442 | + |
|
| 7443 | +@article{nagarajDeepProteomeTranscriptome2011, |
|
| 7444 | + title = {Deep Proteome and Transcriptome Mapping of a Human Cancer Cell Line}, |
|
| 7445 | + author = {Nagaraj, Nagarjuna and Wisniewski, Jacek R. and Geiger, Tamar and Cox, Juergen and Kircher, Martin and Kelso, Janet and Pääbo, Svante and Mann, Matthias}, |
|
| 7446 | + date = {2011-01-01}, |
|
| 7447 | + journaltitle = {Molecular Systems Biology}, |
|
| 7448 | + volume = {7}, |
|
| 7449 | + number = {1}, |
|
| 7450 | + eprint = {22068331}, |
|
| 7451 | + eprinttype = {pmid}, |
|
| 7452 | + pages = {548}, |
|
| 7453 | + issn = {1744-4292, 1744-4292}, |
|
| 7454 | + doi = {10.1038/msb.2011.81}, |
|
| 7455 | + url = {http://msb.embopress.org/content/7/1/548}, |
|
| 7456 | + urldate = {2018-08-30}, |
|
| 7457 | + abstract = {While the number and identity of proteins expressed in a single human cell type is currently unknown, this fundamental question can be addressed by advanced mass spectrometry (MS)‐based proteomics. Online liquid chromatography coupled to high‐resolution MS and MS/MS yielded 166 420 peptides with unique amino‐acid sequence from HeLa cells. These peptides identified 10 255 different human proteins encoded by 9207 human genes, providing a lower limit on the proteome in this cancer cell line. Deep transcriptome sequencing revealed transcripts for nearly all detected proteins. We calculate copy numbers for the expressed proteins and show that the abundances of {$>$}90\% of them are within a factor 60 of the median protein expression level. Comparisons of the proteome and the transcriptome, and analysis of protein complex databases and GO categories, suggest that we achieved deep coverage of the functional transcriptome and the proteome of a single cell type.}, |
|
| 7458 | + langid = {english}, |
|
| 7459 | + keywords = {mass spectrometry,proteomics,RNA‐Seq,systems biology,transcriptomics}, |
|
| 7460 | + file = {/Users/rmorin/Zotero/storage/IY6UNMRS/548.html} |
|
| 7461 | +} |
|
| 7462 | + |
|
| 7463 | +@article{nagelkerkeImmunomodulationIVIgRole2014, |
|
| 7464 | + title = {Immunomodulation by {{IVIg}} and the {{Role}} of {{Fc-Gamma Receptors}}: {{Classic Mechanisms}} of {{Action}} after All?}, |
|
| 7465 | + author = {Nagelkerke, Sietse Q and Kuijpers, Taco W}, |
|
| 7466 | + date = {2014}, |
|
| 7467 | + journaltitle = {Frontiers in Immunology}, |
|
| 7468 | + volume = {5}, |
|
| 7469 | + number = {8232}, |
|
| 7470 | + pages = {674}, |
|
| 7471 | + keywords = {nosource} |
|
| 7472 | +} |
|
| 7473 | + |
|
| 7474 | +@article{nagelkerkeNonallelicHomologousRecombination2015, |
|
| 7475 | + title = {Nonallelic Homologous Recombination of the {{FCGR2}}/3 Locus Results in Copy Number Variation and Novel Chimeric {{FCGR2}} Genes with Aberrant Functional Expression}, |
|
| 7476 | + author = {Nagelkerke, S Q and Tacke, C E and Breunis, W B and Geissler, J and Sins, J and Appelhof, B and Berg, T and family=Boer, given=M, prefix=de, useprefix=false and Kuijpers, T W}, |
|
| 7477 | + date = {2015}, |
|
| 7478 | + journaltitle = {Genes and Immunity}, |
|
| 7479 | + volume = {16}, |
|
| 7480 | + number = {6}, |
|
| 7481 | + eprint = {26133275}, |
|
| 7482 | + eprinttype = {pmid}, |
|
| 7483 | + pages = {422--429}, |
|
| 7484 | + issn = {1466-4879}, |
|
| 7485 | + doi = {10.1038/gene.2015.25}, |
|
| 7486 | + url = {http://dx.doi.org/10.1038/gene.2015.25}, |
|
| 7487 | + abstract = {The human FCGR2/3 locus, containing five highly homologous genes encoding the major IgG receptors, shows extensive copy number variation (CNV) associated with susceptibility to autoimmune diseases. Having genotyped {$>$}4000 individuals, we show that all CNV at this locus can be explained by nonallelic homologous recombination (NAHR) of the two paralogous repeats that constitute the majority of the locus, and describe four distinct CNV regions (CNRs) with a highly variable prevalence in the population. Apart from CNV, NAHR events also created several hitherto unidentified chimeric FCGR2 genes. These include an FCGR2A/2C chimeric gene that causes a decreased expression of FcγRIIa on phagocytes, resulting in a decreased production of reactive oxygen species in response to immune complexes, compared with wild-type FCGR2A. Conversely, FCGR2C/2A chimeric genes were identified to lead to an increased expression of FCGR2C. Finally, a rare FCGR2B null-variant allele was found, in which a polymorphic stop codon of FCGR2C is introduced into one FCGR2B gene, resulting in a 50\% reduction in protein expression. Our study on CNRs and the chimeric genes is essential for the correct interpretation of association studies on FCGR genes as a determinant for disease susceptibility, and may explain some as yet unidentified extreme phenotypes of immune-mediated disease.}, |
|
| 7488 | + keywords = {nosource} |
|
| 7489 | +} |
|
| 7490 | + |
|
| 7491 | +@article{nakamuraTranslocationsInvolvingImmunoglobulin2008, |
|
| 7492 | + title = {Translocations Involving the Immunoglobulin Heavy Chain Gene Locus Predict Better Survival in Gastric Diffuse Large {{B-cell}} Lymphoma}, |
|
| 7493 | + author = {Nakamura, S and Ye, H and Bacon, C and Goatly, A and Liu, H and Kerr, L and Banham, A and Streubel, B and Yao, T and Tsuneyoshi, M and Savio, A and Takeshita, M and Dartigues, P and Ruskone-Fourmestraux, A and Matsumoto, T and Iida, M and Du, M}, |
|
| 7494 | + date = {2008}, |
|
| 7495 | + journaltitle = {Clin Cancer Res}, |
|
| 7496 | + volume = {14}, |
|
| 7497 | + number = {10}, |
|
| 7498 | + pages = {3002--3010}, |
|
| 7499 | + keywords = {nosource} |
|
| 7500 | +} |
|
| 7501 | + |
|
| 7502 | +@article{natarajanHnRNPKLysineSpecific2022, |
|
| 7503 | + title = {{{HnRNPK}} and Lysine Specific Histone Demethylase-1 Regulates {{IP-10 mRNA}} Stability in Monocytes}, |
|
| 7504 | + author = {Natarajan, Kartiga and Sundaramoorthy, Arun and Shanmugam, Narkunaraja}, |
|
| 7505 | + date = {2022-04-05}, |
|
| 7506 | + journaltitle = {European Journal of Pharmacology}, |
|
| 7507 | + shortjournal = {European Journal of Pharmacology}, |
|
| 7508 | + volume = {920}, |
|
| 7509 | + pages = {174683}, |
|
| 7510 | + issn = {0014-2999}, |
|
| 7511 | + doi = {10.1016/j.ejphar.2021.174683}, |
|
| 7512 | + url = {https://www.sciencedirect.com/science/article/pii/S0014299921008396}, |
|
| 7513 | + urldate = {2022-09-22}, |
|
| 7514 | + abstract = {Altered mRNA metabolism is a feature of many inflammatory diseases. Post transcriptional regulation of interferon-γ-inducible protein (IP)-10 has been uncharacterized in diabetes conditions. RNA-affinity capture method and RNA immuno-precipitation revealed S100b treatment increased the binding of heterogeneous nuclear ribonucleoprotein (hnRNP)K to the IP-10 3′UTR and increased IP-10 mRNA accumulation. Luciferase activity assay using reporter plasmids showed involvement of IP-10 3′UTR. Knocking down of hnRNPK destabilized S100b induced IP-10 mRNA accumulation. S100b promoted the translocation of hnRNPK from nucleus to the cytoplasm and this was confirmed by phosphomimetic S284/353D mutant and non-phosphatable S284/353A hnRNPK mutant. S100b treatment demethylates hnRNPK at Lys219 by Lysine Specific Demethylase (LSD)-1. HnRNPKK219I, a demethylation defective mutant increased IP-10 mRNA stability. Apparently, triple mutant hnRNPKK219I/S284D/353D promoted IP-10 mRNA stability. Interestingly, knocking down LSD-1 abolished S100b induced IP-10 mRNA accumulation. These observations show for the first time that IP-10 mRNA stability is dynamically regulated by Lysine demethylation of hnRNPK by LSD-1. These results indicate that hnRNPK plays an important role in IP-10 mRNA stability induced by S100b which could exacerbate monocyte activation, relevant to the pathogenesis of diabetic complications like atherosclerosis.}, |
|
| 7515 | + langid = {english}, |
|
| 7516 | + keywords = {hnRNPK,IP-10,LSD-1,mRNA stability,Non-histone demethylation,RAGE}, |
|
| 7517 | + file = {/Users/rmorin/Zotero/storage/YULE2B65/Natarajan et al. - 2022 - HnRNPK and lysine specific histone demethylase-1 r.pdf;/Users/rmorin/Zotero/storage/GKENEA5D/S0014299921008396.html} |
|
| 7518 | +} |
|
| 7519 | + |
|
| 7520 | +@article{nazarovKHDomainPolyBinding2019, |
|
| 7521 | + title = {{{KH-Domain Poly}}({{C}})-{{Binding Proteins}} as {{Versatile Regulators}} of {{Multiple Biological Processes}}}, |
|
| 7522 | + author = {Nazarov, I. B. and Bakhmet, E. I. and Tomilin, A. N.}, |
|
| 7523 | + date = {2019-03}, |
|
| 7524 | + journaltitle = {Biochemistry. Biokhimiia}, |
|
| 7525 | + shortjournal = {Biochemistry (Mosc)}, |
|
| 7526 | + volume = {84}, |
|
| 7527 | + number = {3}, |
|
| 7528 | + eprint = {31221059}, |
|
| 7529 | + eprinttype = {pmid}, |
|
| 7530 | + pages = {205--219}, |
|
| 7531 | + issn = {1608-3040}, |
|
| 7532 | + doi = {10.1134/S0006297919030039}, |
|
| 7533 | + abstract = {Five known members of the family of KH-domain poly(C)-binding proteins (Pcbp1-4, hnRNP-K) have an unusually broad spectrum of cellular functions that include regulation of gene transcription, regulation of pre-mRNA processing, splicing, mRNA stability, translational silencing and enhancement, the control of iron turnover, and many others. Mechanistically, these proteins act via nucleic acid binding and protein-protein interactions. Through performing these multiple tasks, the KH-domain poly(C)-binding family members are involved in a wide variety of biological processes such as embryonic development, cell differentiation, and cancer. Deregulation of KH-domain protein expression is frequently associated with severe developmental defects and neoplasia. This review summarizes progress in studies of the KH-domain proteins made over past two decades. The review also reports our recent finding implying an involvement of the KH-factor Pcbp1 into control of transition from naïve to primed pluripotency cell state.}, |
|
| 7534 | + langid = {english}, |
|
| 7535 | + keywords = {Animals,Heterogeneous-Nuclear Ribonucleoprotein K,Humans,Pluripotent Stem Cells} |
|
| 7536 | +} |
|
| 7537 | + |
|
| 7538 | +@article{nazimCompetitiveRegulationAlternative2017, |
|
| 7539 | + title = {Competitive Regulation of Alternative Splicing and Alternative Polyadenylation by {{hnRNP H}} and {{CstF64}} Determines Acetylcholinesterase Isoforms}, |
|
| 7540 | + author = {Nazim, Mohammad and Masuda, Akio and Rahman, Mohammad Alinoor and Nasrin, Farhana and Takeda, Jun-ichi and Ohe, Kenji and Ohkawara, Bisei and Ito, Mikako and Ohno, Kinji}, |
|
| 7541 | + date = {2017-02-17}, |
|
| 7542 | + journaltitle = {Nucleic Acids Research}, |
|
| 7543 | + shortjournal = {Nucleic Acids Research}, |
|
| 7544 | + volume = {45}, |
|
| 7545 | + number = {3}, |
|
| 7546 | + pages = {1455--1468}, |
|
| 7547 | + issn = {0305-1048}, |
|
| 7548 | + doi = {10.1093/nar/gkw823}, |
|
| 7549 | + url = {https://doi.org/10.1093/nar/gkw823}, |
|
| 7550 | + urldate = {2022-09-27}, |
|
| 7551 | + abstract = {Acetylcholinesterase (AChE), encoded by the ACHE gene, hydrolyzes the neurotransmitter acetylcholine to terminate synaptic transmission. Alternative splicing close to the 3΄ end generates three distinct isoforms of AChET, AChEH and AChER. We found that hnRNP H binds to two specific G-runs in exon 5a of human ACHE and activates the distal alternative 3΄ splice site (ss) between exons 5a and 5b to generate AChET. Specific effect of hnRNP H was corroborated by siRNA-mediated knockdown and artificial tethering of hnRNP H. Furthermore, hnRNP H competes for binding of CstF64 to the overlapping binding sites in exon 5a, and suppresses the selection of a cryptic polyadenylation site (PAS), which additionally ensures transcription of the distal 3΄ ss required for the generation of AChET. Expression levels of hnRNP H were positively correlated with the proportions of the AChET isoform in three different cell lines. HnRNP H thus critically generates AChET by enhancing the distal 3΄ ss and by suppressing the cryptic PAS. Global analysis of CLIP-seq and RNA-seq also revealed that hnRNP H competitively regulates alternative 3΄ ss and alternative PAS in other genes. We propose that hnRNP H is an essential factor that competitively regulates alternative splicing and alternative polyadenylation.}, |
|
| 7552 | + file = {/Users/rmorin/Zotero/storage/TKN45SWU/Nazim et al. - 2017 - Competitive regulation of alternative splicing and.pdf;/Users/rmorin/Zotero/storage/MCPCZF3K/2972192.html} |
|
| 7553 | +} |
|
| 7554 | + |
|
| 7555 | +@article{necklesHNRNPH1dependentSplicingFusion2019, |
|
| 7556 | + title = {{{HNRNPH1-dependent}} Splicing of a Fusion Oncogene Reveals a Targetable {{RNA G-quadruplex}} Interaction}, |
|
| 7557 | + author = {Neckles, Carla and Boer, Robert E. and Aboreden, Nicholas and Cross, Allison M. and Walker, Robert L. and Kim, Bong-Hyun and Kim, Suntae and John S. Schneekloth, Jr and Caplen, Natasha J.}, |
|
| 7558 | + date = {2019-12}, |
|
| 7559 | + journaltitle = {RNA}, |
|
| 7560 | + volume = {25}, |
|
| 7561 | + number = {12}, |
|
| 7562 | + eprint = {31511320}, |
|
| 7563 | + eprinttype = {pmid}, |
|
| 7564 | + pages = {1731}, |
|
| 7565 | + publisher = {Cold Spring Harbor Laboratory Press}, |
|
| 7566 | + doi = {10.1261/rna.072454.119}, |
|
| 7567 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6859848/}, |
|
| 7568 | + urldate = {2022-10-15}, |
|
| 7569 | + abstract = {The primary oncogenic event in ∼85\% of Ewing sarcomas is a chromosomal translocation that generates a fusion oncogene encoding an aberrant transcription factor. The exact genomic breakpoints within the translocated genes, EWSR1 and FLI1, vary; ...}, |
|
| 7570 | + langid = {english}, |
|
| 7571 | + file = {/Users/rmorin/Zotero/storage/JZCMHZVS/Neckles et al. - 2019 - HNRNPH1-dependent splicing of a fusion oncogene re.pdf;/Users/rmorin/Zotero/storage/U4W6HVVI/PMC6859848.html} |
|
| 7572 | +} |
|
| 7573 | + |
|
| 7574 | +@article{newmanIntegratedDigitalError2016, |
|
| 7575 | + title = {Integrated Digital Error Suppression for Improved Detection of Circulating Tumor {{DNA}}}, |
|
| 7576 | + author = {Newman, Aaron M and Lovejoy, Alexander F and Klass, Daniel M and Kurtz, David M and Chabon, Jacob J and Scherer, Florian and Stehr, Henning and Liu, Chih Long and Bratman, Scott V and Say, Carmen and Zhou, Li and Carter, Justin N and West, Robert B and Sledge Jr, George W and Shrager, Joseph B and Loo, Billy W and Neal, Joel W and Wakelee, Heather A and Diehn, Maximilian and Alizadeh, Ash A}, |
|
| 7577 | + date = {2016-03}, |
|
| 7578 | + journaltitle = {Nat Biotechnol}, |
|
| 7579 | + pages = {1--14}, |
|
| 7580 | + keywords = {nosource} |
|
| 7581 | +} |
|
| 7582 | + |
|
| 7583 | +@article{newmanUltrasensitiveMethodQuantitating, |
|
| 7584 | + title = {An Ultrasensitive Method for Quantitating Circulating Tumor {{DNA}} with Broad Patient Coverage.}, |
|
| 7585 | + author = {Newman, Aaron M and Bratman, Scott V and To, Jacqueline and Wynne, Jacob F and Eclov, Neville C W and Modlin, Leslie A and Liu, Chih Long and Neal, Joel W and Wakelee, Heather A and Merritt, Robert E and Shrager, Joseph B and Loo, Billy W and Alizadeh, Ash A and Diehn, Maximilian}, |
|
| 7586 | + journaltitle = {Nature Medicine}, |
|
| 7587 | + keywords = {nosource} |
|
| 7588 | +} |
|
| 7589 | + |
|
| 7590 | +@article{ngoOncogenicallyActiveMYD882011a, |
|
| 7591 | + title = {Oncogenically Active {{MYD88}} Mutations in Human Lymphoma}, |
|
| 7592 | + author = {Ngo, Vu N. and Young, Ryan M. and Schmitz, Roland and Jhavar, Sameer and Xiao, Wenming and Lim, Kian-Huat and Kohlhammer, Holger and Xu, Weihong and Yang, Yandan and Zhao, Hong and Shaffer, Arthur L. and Romesser, Paul and Wright, George and Powell, John and Rosenwald, Andreas and Muller-Hermelink, Hans Konrad and Ott, German and Gascoyne, Randy D. and Connors, Joseph M. and Rimsza, Lisa M. and Campo, Elias and Jaffe, Elaine S. and Delabie, Jan and Smeland, Erlend B. and Fisher, Richard I. and Braziel, Rita M. and Tubbs, Raymond R. and Cook, J. R. and Weisenburger, Denny D. and Chan, Wing C. and Staudt, Louis M.}, |
|
| 7593 | + date = {2011-02-03}, |
|
| 7594 | + journaltitle = {Nature}, |
|
| 7595 | + shortjournal = {Nature}, |
|
| 7596 | + volume = {470}, |
|
| 7597 | + number = {7332}, |
|
| 7598 | + eprint = {21179087}, |
|
| 7599 | + eprinttype = {pmid}, |
|
| 7600 | + pages = {115--119}, |
|
| 7601 | + issn = {1476-4687}, |
|
| 7602 | + doi = {10.1038/nature09671}, |
|
| 7603 | + abstract = {The activated B-cell-like (ABC) subtype of diffuse large B-cell lymphoma (DLBCL) remains the least curable form of this malignancy despite recent advances in therapy. Constitutive nuclear factor (NF)-κB and JAK kinase signalling promotes malignant cell survival in these lymphomas, but the genetic basis for this signalling is incompletely understood. Here we describe the dependence of ABC DLBCLs on MYD88, an adaptor protein that mediates toll and interleukin (IL)-1 receptor signalling, and the discovery of highly recurrent oncogenic mutations affecting MYD88 in ABC DLBCL tumours. RNA interference screening revealed that MYD88 and the associated kinases IRAK1 and IRAK4 are essential for ABC DLBCL survival. High-throughput RNA resequencing uncovered MYD88 mutations in ABC DLBCL lines. Notably, 29\% of ABC DLBCL tumours harboured the same amino acid substitution, L265P, in the MYD88 Toll/IL-1 receptor (TIR) domain at an evolutionarily invariant residue in its hydrophobic core. This mutation was rare or absent in other DLBCL subtypes and Burkitt's lymphoma, but was observed in 9\% of mucosa-associated lymphoid tissue lymphomas. At a lower frequency, additional mutations were observed in the MYD88 TIR domain, occurring in both the ABC and germinal centre B-cell-like (GCB) DLBCL subtypes. Survival of ABC DLBCL cells bearing the L265P mutation was sustained by the mutant but not the wild-type MYD88 isoform, demonstrating that L265P is a gain-of-function driver mutation. The L265P mutant promoted cell survival by spontaneously assembling a protein complex containing IRAK1 and IRAK4, leading to IRAK4 kinase activity, IRAK1 phosphorylation, NF-κB signalling, JAK kinase activation of STAT3, and secretion of IL-6, IL-10 and interferon-β. Hence, the MYD88 signalling pathway is integral to the pathogenesis of ABC DLBCL, supporting the development of inhibitors of IRAK4 kinase and other components of this pathway for the treatment of tumours bearing oncogenic MYD88 mutations.}, |
|
| 7604 | + langid = {english}, |
|
| 7605 | + pmcid = {PMC5024568}, |
|
| 7606 | + keywords = {Amino Acid Sequence,Amino Acid Substitution,Burkitt Lymphoma,Cell Line Tumor,Cell Survival,Cytokines,High-Throughput Nucleotide Sequencing,Humans,Hydrophobic and Hydrophilic Interactions,Interleukin-1 Receptor-Associated Kinases,Janus Kinases,Lymphoma B-Cell Marginal Zone,Lymphoma Large B-Cell Diffuse,Molecular Sequence Data,Mutant Proteins,Mutation,Myeloid Differentiation Factor 88,NF-kappa B,Oncogenes,Phosphorylation,Protein Structure Tertiary,Receptors Interleukin-1,RNA Interference,Sequence Analysis RNA,Signal Transduction,STAT3 Transcription Factor,Toll-Like Receptors}, |
|
| 7607 | + file = {/Users/rmorin/Zotero/storage/MTJVNXFT/Ngo et al. - 2011 - Oncogenically active MYD88 mutations in human lymp.pdf} |
|
| 7608 | +} |
|
| 7609 | + |
|
| 7610 | +@article{nicholsLossHeterozygosityEssential2020, |
|
| 7611 | + title = {Loss of Heterozygosity of Essential Genes Represents a Widespread Class of Potential Cancer Vulnerabilities}, |
|
| 7612 | + author = {Nichols, Caitlin A. and Gibson, William J. and Brown, Meredith S. and Kosmicki, Jack A. and Busanovich, John P. and Wei, Hope and Urbanski, Laura M. and Curimjee, Naomi and Berger, Ashton C. and Gao, Galen F. and Cherniack, Andrew D. and Dhe-Paganon, Sirano and Paolella, Brenton R. and Beroukhim, Rameen}, |
|
| 7613 | + date = {2020-05-20}, |
|
| 7614 | + journaltitle = {Nature Communications}, |
|
| 7615 | + shortjournal = {Nat Commun}, |
|
| 7616 | + volume = {11}, |
|
| 7617 | + number = {1}, |
|
| 7618 | + pages = {2517}, |
|
| 7619 | + publisher = {Nature Publishing Group}, |
|
| 7620 | + issn = {2041-1723}, |
|
| 7621 | + doi = {10.1038/s41467-020-16399-y}, |
|
| 7622 | + url = {https://www.nature.com/articles/s41467-020-16399-y}, |
|
| 7623 | + urldate = {2023-01-10}, |
|
| 7624 | + abstract = {Alterations in non-driver genes represent an emerging class of potential therapeutic targets in cancer. Hundreds to thousands of non-driver genes undergo loss of heterozygosity (LOH) events per tumor, generating discrete differences between tumor and normal cells. Here we interrogate LOH of polymorphisms in essential genes as a novel class of therapeutic targets. We hypothesized that monoallelic inactivation of the allele retained in tumors can selectively kill cancer cells but not somatic cells, which retain both alleles. We identified 5664 variants in 1278 essential genes that undergo LOH in cancer and evaluated the potential for each to be targeted using allele-specific gene-editing, RNAi, or small-molecule approaches. We further show that allele-specific inactivation of either of two essential genes (PRIM1 and EXOSC8) reduces growth of cells harboring that allele, while cells harboring the non-targeted allele remain intact. We conclude that LOH of essential genes represents a rich class of non-driver cancer vulnerabilities.}, |
|
| 7625 | + issue = {1}, |
|
| 7626 | + langid = {english}, |
|
| 7627 | + keywords = {Cancer,Cancer genomics,Molecular biology}, |
|
| 7628 | + file = {/Users/rmorin/Zotero/storage/SA9C5458/Nichols et al. - 2020 - Loss of heterozygosity of essential genes represen.pdf} |
|
| 7629 | +} |
|
| 7630 | + |
|
| 7631 | +@article{nieIntegrativeAnalysisTranscriptomic2007, |
|
| 7632 | + title = {Integrative {{Analysis}} of {{Transcriptomic}} and {{Proteomic Data}}: {{Challenges}}, {{Solutions}} and {{Applications}}}, |
|
| 7633 | + shorttitle = {Integrative {{Analysis}} of {{Transcriptomic}} and {{Proteomic Data}}}, |
|
| 7634 | + author = {Nie, Lei and Wu, Gang and Culley, David E. and Scholten, Johannes C. M. and Zhang, Weiwen}, |
|
| 7635 | + date = {2007-01-01}, |
|
| 7636 | + journaltitle = {Critical Reviews in Biotechnology}, |
|
| 7637 | + volume = {27}, |
|
| 7638 | + number = {2}, |
|
| 7639 | + eprint = {17578703}, |
|
| 7640 | + eprinttype = {pmid}, |
|
| 7641 | + pages = {63--75}, |
|
| 7642 | + issn = {0738-8551}, |
|
| 7643 | + doi = {10.1080/07388550701334212}, |
|
| 7644 | + url = {https://doi.org/10.1080/07388550701334212}, |
|
| 7645 | + urldate = {2018-08-30}, |
|
| 7646 | + abstract = {Recent advances in high-throughput technologies enable quantitative monitoring of the abundance of various biological molecules and allow determination of their variation between biological states on a genomic scale. Two popular platforms are DNA microarrays that measure messenger RNA transcript levels, and gel-free proteomic analyses that quantify protein abundance. Obviously, no single approach can fully unravel the complexities of fundamental biology and it is equally clear that integrative analysis of multiple levels of gene expression would be valuable in this endeavor. However, most integrative transcriptomic and proteomic studies have thus far either failed to find a correlation or only observed a weak correlation. In addition to various biological factors, it is suggested that the poor correlation could be quite possibly due to the inadequacy of available statistical tools to compensate for biases in the data collection methodologies. To address this issue, attempts have recently been made to systematically investigate the correlation patterns between transcriptomic and proteomic datasets, and to develop sophisticated statistical tools to improve the chances of capturing a relationship. The goal of these efforts is to enhance understanding of the relationship between transcriptomes and proteomes so that integrative analyses may be utilized to reveal new biological insights that are not accessible through one-dimensional datasets. In this review, we outline some of the challenges associated with integrative analyses and present some preliminary statistical solutions. In addition, some new applications of integrated transcriptomic and proteomic analysis to the investigation of post-transcriptional regulation are also discussed.}, |
|
| 7647 | + keywords = {integration,proteomics,statistical,transcriptomics}, |
|
| 7648 | + file = {/Users/rmorin/Zotero/storage/A9LHY882/07388550701334212.html} |
|
| 7649 | +} |
|
| 7650 | + |
|
| 7651 | +@article{nielsenMethodsSampleAcquisition2014, |
|
| 7652 | + title = {Methods for Sample Acquisition and Processing of Serial Blood and Tumor Biopsies for Multicenter Diffuse Large {{B-cell}} Lymphoma Clinical Trials.}, |
|
| 7653 | + author = {Nielsen, Torsten Holm and Diaz, Zuanel and Christodoulopoulos, Rosa and Charbonneau, Fredrick and Qureshi, Samia and Rousseau, Caroline and Benlimame, Naciba and Camlioglu, Errol and Constantin, André Marc and Oros, Kathleen Klein and Krumsiek, Jan and Crump, Michael and Morin, Ryan D and Cerchietti, Leandro and Johnson, Nathalie A and Petrogiannis-Haliotis, Tina and Miller, Wilson H and Assouline, Sarit E and Mann, Koren K}, |
|
| 7654 | + date = {2014-12}, |
|
| 7655 | + journaltitle = {Cancer epidemiology, biomarkers \& prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology}, |
|
| 7656 | + volume = {23}, |
|
| 7657 | + number = {12}, |
|
| 7658 | + pages = {2688--2693}, |
|
| 7659 | + keywords = {nosource} |
|
| 7660 | +} |
|
| 7661 | + |
|
| 7662 | +@article{nik-zainalLifeHistory212012, |
|
| 7663 | + title = {The Life History of 21 Breast Cancers}, |
|
| 7664 | + author = {Nik-Zainal, Serena and Van Loo, Peter and Wedge, David C. and Alexandrov, Ludmil B. and Greenman, Christopher D. and Lau, King Wai and Raine, Keiran and Jones, David and Marshall, John and Ramakrishna, Manasa and Shlien, Adam and Cooke, Susanna L. and Hinton, Jonathan and Menzies, Andrew and Stebbings, Lucy A. and Leroy, Catherine and Jia, Mingming and Rance, Richard and Mudie, Laura J. and Gamble, Stephen J. and Stephens, Philip J. and McLaren, Stuart and Tarpey, Patrick S. and Papaemmanuil, Elli and Davies, Helen R. and Varela, Ignacio and McBride, David J. and Bignell, Graham R. and Leung, Kenric and Butler, Adam P. and Teague, Jon W. and Martin, Sancha and Jönsson, Goran and Mariani, Odette and Boyault, Sandrine and Miron, Penelope and Fatima, Aquila and Langerød, Anita and Aparicio, Samuel A. J. R. and Tutt, Andrew and Sieuwerts, Anieta M. and Borg, Åke and Thomas, Gilles and Salomon, Anne Vincent and Richardson, Andrea L. and Børresen-Dale, Anne-Lise and Futreal, P. Andrew and Stratton, Michael R. and Campbell, Peter J. and {Breast Cancer Working Group of the International Cancer Genome Consortium}}, |
|
| 7665 | + date = {2012-05-25}, |
|
| 7666 | + journaltitle = {Cell}, |
|
| 7667 | + shortjournal = {Cell}, |
|
| 7668 | + volume = {149}, |
|
| 7669 | + number = {5}, |
|
| 7670 | + eprint = {22608083}, |
|
| 7671 | + eprinttype = {pmid}, |
|
| 7672 | + pages = {994--1007}, |
|
| 7673 | + issn = {1097-4172}, |
|
| 7674 | + doi = {10.1016/j.cell.2012.04.023}, |
|
| 7675 | + abstract = {Cancer evolves dynamically as clonal expansions supersede one another driven by shifting selective pressures, mutational processes, and disrupted cancer genes. These processes mark the genome, such that a cancer's life history is encrypted in the somatic mutations present. We developed algorithms to decipher this narrative and applied them to 21 breast cancers. Mutational processes evolve across a cancer's lifespan, with many emerging late but contributing extensive genetic variation. Subclonal diversification is prominent, and most mutations are found in just a fraction of tumor cells. Every tumor has a dominant subclonal lineage, representing more than 50\% of tumor cells. Minimal expansion of these subclones occurs until many hundreds to thousands of mutations have accumulated, implying the existence of long-lived, quiescent cell lineages capable of substantial proliferation upon acquisition of enabling genomic changes. Expansion of the dominant subclone to an appreciable mass may therefore represent the final rate-limiting step in a breast cancer's development, triggering diagnosis.}, |
|
| 7676 | + langid = {english}, |
|
| 7677 | + pmcid = {PMC3428864}, |
|
| 7678 | + keywords = {Algorithms,Breast Neoplasms,Cell Transformation Neoplastic,Chromosome Aberrations,Clonal Evolution,Female,Humans,Mutation,Point Mutation}, |
|
| 7679 | + file = {/Users/rmorin/Zotero/storage/RGYJEQNE/Nik-Zainal et al. - 2012 - The life history of 21 breast cancers.pdf} |
|
| 7680 | +} |
|
| 7681 | + |
|
| 7682 | +@article{nileathlobhairEvolutionaryHistoryDogs2018, |
|
| 7683 | + title = {The Evolutionary History of Dogs in the {{Americas}}}, |
|
| 7684 | + author = {Ní Leathlobhair, Máire and Perri, Angela R. and Irving-Pease, Evan K. and Witt, Kelsey E. and Linderholm, Anna and Haile, James and Lebrasseur, Ophelie and Ameen, Carly and Blick, Jeffrey and Boyko, Adam R. and Brace, Selina and Cortes, Yahaira Nunes and Crockford, Susan J. and Devault, Alison and Dimopoulos, Evangelos A. and Eldridge, Morley and Enk, Jacob and Gopalakrishnan, Shyam and Gori, Kevin and Grimes, Vaughan and Guiry, Eric and Hansen, Anders J. and Hulme-Beaman, Ardern and Johnson, John and Kitchen, Andrew and Kasparov, Aleksei K. and Kwon, Young-Mi and Nikolskiy, Pavel A. and Lope, Carlos Peraza and Manin, Aurélie and Martin, Terrance and Meyer, Michael and Myers, Kelsey Noack and Omura, Mark and Rouillard, Jean-Marie and Pavlova, Elena Y. and Sciulli, Paul and Sinding, Mikkel-Holger S. and Strakova, Andrea and Ivanova, Varvara V. and Widga, Christopher and Willerslev, Eske and Pitulko, Vladimir V. and Barnes, Ian and Gilbert, M. Thomas P. and Dobney, Keith M. and Malhi, Ripan S. and Murchison, Elizabeth P. and Larson, Greger and Frantz, Laurent A. F.}, |
|
| 7685 | + date = {2018-07-06}, |
|
| 7686 | + journaltitle = {Science (New York, N.Y.)}, |
|
| 7687 | + shortjournal = {Science}, |
|
| 7688 | + volume = {361}, |
|
| 7689 | + number = {6397}, |
|
| 7690 | + eprint = {29976825}, |
|
| 7691 | + eprinttype = {pmid}, |
|
| 7692 | + pages = {81--85}, |
|
| 7693 | + issn = {1095-9203}, |
|
| 7694 | + doi = {10.1126/science.aao4776}, |
|
| 7695 | + abstract = {Dogs were present in the Americas before the arrival of European colonists, but the origin and fate of these precontact dogs are largely unknown. We sequenced 71 mitochondrial and 7 nuclear genomes from ancient North American and Siberian dogs from time frames spanning \textasciitilde 9000 years. Our analysis indicates that American dogs were not derived from North American wolves. Instead, American dogs form a monophyletic lineage that likely originated in Siberia and dispersed into the Americas alongside people. After the arrival of Europeans, native American dogs almost completely disappeared, leaving a minimal genetic legacy in modern dog populations. The closest detectable extant lineage to precontact American dogs is the canine transmissible venereal tumor, a contagious cancer clone derived from an individual dog that lived up to 8000 years ago.}, |
|
| 7696 | + langid = {english}, |
|
| 7697 | + keywords = {Americas,Animals,Biological Evolution,Cell Nucleus,Dog Diseases,Dogs,Domestication,Genome Mitochondrial,Human Migration,Humans,Neoplasms,Phylogeny,Sexually Transmitted Diseases,Siberia,Wolves} |
|
| 7698 | +} |
|
| 7699 | + |
|
| 7700 | +@article{niuUSP10InhibitsGenotoxic2013, |
|
| 7701 | + title = {{{USP10}} Inhibits Genotoxic {{NF-κB}} Activation by {{MCPIP1-facilitated}} Deubiquitination of {{NEMO}}.}, |
|
| 7702 | + author = {Niu, Jixiao and Shi, Yuling and Xue, Jingyan and Miao, Ruidong and Huang, Shengping and Wang, Tianyi and Wu, Jiong and Fu, Mingui and Wu, Zhao-Hui}, |
|
| 7703 | + date = {2013-12}, |
|
| 7704 | + journaltitle = {The EMBO Journal}, |
|
| 7705 | + volume = {32}, |
|
| 7706 | + number = {24}, |
|
| 7707 | + pages = {3206--3219}, |
|
| 7708 | + keywords = {nosource} |
|
| 7709 | +} |
|
| 7710 | + |
|
| 7711 | +@article{nobleDevelopmentSignificanceMouse2019, |
|
| 7712 | + title = {Development and {{Significance}} of {{Mouse Models}} in {{Lymphoma Research}}}, |
|
| 7713 | + author = {Noble, Jordan N. and Mishra, Anjali}, |
|
| 7714 | + date = {2019-04-01}, |
|
| 7715 | + journaltitle = {Current Hematologic Malignancy Reports}, |
|
| 7716 | + shortjournal = {Curr Hematol Malig Rep}, |
|
| 7717 | + volume = {14}, |
|
| 7718 | + number = {2}, |
|
| 7719 | + pages = {119--126}, |
|
| 7720 | + issn = {1558-822X}, |
|
| 7721 | + doi = {10.1007/s11899-019-00504-0}, |
|
| 7722 | + url = {https://doi.org/10.1007/s11899-019-00504-0}, |
|
| 7723 | + urldate = {2021-11-30}, |
|
| 7724 | + abstract = {Animal models have played an indispensable role in interpreting cancer gene functions, pathogenesis of disease, and in the development of innovative therapeutic approaches targeting aberrant biological pathways in human cancers.}, |
|
| 7725 | + langid = {english}, |
|
| 7726 | + keywords = {nosource} |
|
| 7727 | +} |
|
| 7728 | + |
|
| 7729 | +@article{noensieStrategyDiseaseGene2001, |
|
| 7730 | + title = {A Strategy for Disease Gene Identification through Nonsense-Mediated {{mRNA}} Decay Inhibition}, |
|
| 7731 | + author = {Noensie, E. N. and Dietz, H. C.}, |
|
| 7732 | + date = {2001-05}, |
|
| 7733 | + journaltitle = {Nature Biotechnology}, |
|
| 7734 | + shortjournal = {Nat. Biotechnol.}, |
|
| 7735 | + volume = {19}, |
|
| 7736 | + number = {5}, |
|
| 7737 | + eprint = {11329012}, |
|
| 7738 | + eprinttype = {pmid}, |
|
| 7739 | + pages = {434--439}, |
|
| 7740 | + issn = {1087-0156}, |
|
| 7741 | + doi = {10.1038/88099}, |
|
| 7742 | + abstract = {Premature termination codons (PTCs) have been shown to initiate degradation of mutant transcripts through the nonsense-mediated messenger RNA (mRNA) decay (NMD) pathway. We report a strategy, termed gene identification by NMD inhibition (GINI), to identify genes harboring nonsense codons that underlie human diseases. In this strategy, the NMD pathway is pharmacologically inhibited in cultured patient cells, resulting in stabilization of nonsense transcripts. To distinguish stabilized nonsense transcripts from background transcripts upregulated by drug treatment, drug-induced expression changes are measured in control and disease cell lines with complementary DNA (cDNA) microarrays. Transcripts are ranked by a nonsense enrichment index (NEI), which relates expression changes for a given transcript in NMD-inhibited control and patient cell lines. The most promising candidates can be selected using information such as map location or biological function; however, an important advantage of the GINI strategy is that a priori information is not essential for disease gene identification. GINI was tested on colon cancer and Sandhoff disease cell lines, which contained previously characterized nonsense mutations in the MutL homolog 1 (MLH1) and hexosaminidase B (HEXB) genes, respectively. A list of genes was produced in which the MLH1 and HEXB genes were among the top 1\% of candidates, thus validating the strategy.}, |
|
| 7743 | + langid = {english}, |
|
| 7744 | + keywords = {Adaptor Proteins Signal Transducing,Bacterial Proteins,beta-Hexosaminidase beta Chain,beta-N-Acetylhexosaminidases,Carrier Proteins,Cell Line,Codon Nonsense,Codon Terminator,Colonic Neoplasms,DNA-Binding Proteins,Hexosaminidase B,Humans,Male,MutL Protein Homolog 1,Neoplasm Proteins,Nuclear Proteins,Oligonucleotide Array Sequence Analysis,Peptide Chain Termination Translational,RNA Messenger,Sandhoff Disease,Tumor Cells Cultured,Tumor Suppressor Protein p53} |
|
| 7745 | +} |
|
| 7746 | + |
|
| 7747 | +@article{nogaiControlsConstitutiveNF2013, |
|
| 7748 | + title = {I {{B-}} Controls the Constitutive {{NF- B}} Target Gene Network and Survival of {{ABC DLBCL}}}, |
|
| 7749 | + author = {Nogai, H and Wenzel, S S and Hailfinger, S and Grau, M and Kaergel, E and Seitz, V and Wollert-Wulf, B and Pfeifer, M and Wolf, A and Frick, M and Dietze, K and Madle, H and Tzankov, A and Hummel, M and Dörken, B and Scheidereit, C and Janz, M and Lenz, P and Thome, M and Lenz, G}, |
|
| 7750 | + date = {2013-09}, |
|
| 7751 | + journaltitle = {Blood}, |
|
| 7752 | + volume = {122}, |
|
| 7753 | + number = {13}, |
|
| 7754 | + pages = {2242--2250}, |
|
| 7755 | + keywords = {nosource} |
|
| 7756 | +} |
|
| 7757 | + |
|
| 7758 | +@article{nouriSpectralClusteringbasedMethod2018, |
|
| 7759 | + title = {A Spectral Clustering-Based Method for Identifying Clones from High-Throughput {{B}} Cell Repertoire Sequencing Data}, |
|
| 7760 | + author = {Nouri, Nima and Kleinstein, Steven H.}, |
|
| 7761 | + date = {2018-07-01}, |
|
| 7762 | + journaltitle = {Bioinformatics (Oxford, England)}, |
|
| 7763 | + shortjournal = {Bioinformatics}, |
|
| 7764 | + volume = {34}, |
|
| 7765 | + number = {13}, |
|
| 7766 | + eprint = {29949968}, |
|
| 7767 | + eprinttype = {pmid}, |
|
| 7768 | + pages = {i341-i349}, |
|
| 7769 | + issn = {1367-4811}, |
|
| 7770 | + doi = {10.1093/bioinformatics/bty235}, |
|
| 7771 | + abstract = {Motivation: B cells derive their antigen-specificity through the expression of Immunoglobulin (Ig) receptors on their surface. These receptors are initially generated stochastically by somatic re-arrangement of the DNA and further diversified following antigen-activation by a process of somatic hypermutation, which introduces mainly point substitutions into the receptor DNA at a high rate. Recent advances in next-generation sequencing have enabled large-scale profiling of the B cell Ig repertoire from blood and tissue samples. A key computational challenge in the analysis of these data is partitioning the sequences to identify descendants of a common B cell (i.e. a clone). Current methods group sequences using a fixed distance threshold, or a likelihood calculation that is computationally-intensive. Here, we propose a new method based on spectral clustering with an adaptive threshold to determine the local sequence neighborhood. Validation using simulated and experimental datasets demonstrates that this method has high sensitivity and specificity compared to a fixed threshold that is optimized for these measures. In addition, this method works on datasets where choosing an optimal fixed threshold is difficult and is more computationally efficient in all cases. The ability to quickly and accurately identify members of a clone from repertoire sequencing data will greatly improve downstream analyses. Clonally-related sequences cannot be treated independently in statistical models, and clonal partitions are used as the basis for the calculation of diversity metrics, lineage reconstruction and selection analysis. Thus, the spectral clustering-based method here represents an important contribution to repertoire analysis. Availability and implementation: Source code for this method is freely available in the SCOPe (Spectral Clustering for clOne Partitioning) R package in the Immcantation framework: www.immcantation.org under the CC BY-SA 4.0 license. Supplementary information: Supplementary data are available at Bioinformatics online.}, |
|
| 7772 | + langid = {english}, |
|
| 7773 | + pmcid = {PMC6022594}, |
|
| 7774 | + keywords = {B-Lymphocytes,Clone Cells,Cluster Analysis,High-Throughput Nucleotide Sequencing,Models Statistical,Sequence Analysis DNA,Software}, |
|
| 7775 | + file = {/Users/rmorin/Zotero/storage/RYUWS7RW/Nouri and Kleinstein - 2018 - A spectral clustering-based method for identifying.pdf} |
|
| 7776 | +} |
|
| 7777 | + |
|
| 7778 | +@article{nowickaPrognosticSignificanceFCGR2B2021, |
|
| 7779 | + title = {Prognostic Significance of {{FCGR2B}} Expression for the Response of {{DLBCL}} Patients to Rituximab or Obinutuzumab Treatment}, |
|
| 7780 | + author = {Nowicka, Malgorzata and Hilton, Laura K. and Ashton-Key, Margaret and Hargreaves, Chantal E. and Lee, Chern and Foxall, Russell and Carter, Matthew J. and Beers, Stephen A. and Potter, Kathleen N. and Bolen, Christopher R. and Klein, Christian and Knapp, Andrea and Mir, Farheen and Rose-Zerilli, Matthew and Burton, Cathy and Klapper, Wolfram and Scott, David W. and Sehn, Laurie H. and Vitolo, Umberto and Martelli, Maurizio and Trneny, Marek and Rushton, Christopher K. and Slack, Graham W. and Farinha, Pedro and Strefford, Jonathan C. and Oestergaard, Mikkel Z. and Morin, Ryan D. and Cragg, Mark S.}, |
|
| 7781 | + date = {2021-08-10}, |
|
| 7782 | + journaltitle = {Blood Advances}, |
|
| 7783 | + shortjournal = {Blood Adv}, |
|
| 7784 | + volume = {5}, |
|
| 7785 | + number = {15}, |
|
| 7786 | + eprint = {34323958}, |
|
| 7787 | + eprinttype = {pmid}, |
|
| 7788 | + pages = {2945--2957}, |
|
| 7789 | + issn = {2473-9537}, |
|
| 7790 | + doi = {10.1182/bloodadvances.2021004770}, |
|
| 7791 | + abstract = {Fc γ receptor IIB (FcγRIIB) is an inhibitory molecule capable of reducing antibody immunotherapy efficacy. We hypothesized its expression could confer resistance in patients with diffuse large B-cell lymphoma (DLBCL) treated with anti-CD20 monoclonal antibody (mAb) chemoimmunotherapy, with outcomes varying depending on mAb (rituximab [R]/obinutuzumab [G]) because of different mechanisms of action. We evaluated correlates between FCGR2B messenger RNA and/or FcγRIIB protein expression and outcomes in 3 de novo DLBCL discovery cohorts treated with R plus cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) reported by Arthur, Schmitz, and Reddy, and R-CHOP/G-CHOP-treated patients in the GOYA trial (NCT01287741). In the discovery cohorts, higher FCGR2B expression was associated with significantly shorter progression-free survival (PFS; Arthur: hazard ratio [HR], 1.09; 95\% confidence interval [CI], 1.01-1.19; P = .0360; Schmitz: HR, 1.13; 95\% CI, 1.02-1.26; P = .0243). Similar results were observed in GOYA with R-CHOP (HR, 1.26; 95\% CI, 1.00-1.58; P = .0455), but not G-CHOP (HR, 0.91; 95\% CI, 0.69-1.20; P = .50). A nonsignificant trend that high FCGR2B expression favored G-CHOP over R-CHOP was observed (HR, 0.67; 95\% CI, 0.44-1.02; P = .0622); however, low FCGR2B expression favored R-CHOP (HR, 1.58; 95\% CI, 1.00-2.50; P = .0503). In Arthur and GOYA, FCGR2B expression was associated with tumor FcγRIIB expression; correlating with shorter PFS for R-CHOP (HR, 2.17; 95\% CI, 1.04-4.50; P = .0378), but not G-CHOP (HR, 1.37; 95\% CI, 0.66-2.87; P = .3997). This effect was independent of established prognostic biomarkers. High FcγRIIB/FCGR2B expression has prognostic value in R-treated patients with DLBCL and may confer differential responsiveness to R-CHOP/G-CHOP.}, |
|
| 7792 | + langid = {english}, |
|
| 7793 | + pmcid = {PMC8361458}, |
|
| 7794 | + keywords = {Antibodies Monoclonal Humanized,Antineoplastic Combined Chemotherapy Protocols,Cyclophosphamide,Humans,Lymphoma Large B-Cell Diffuse,Morinlab,Prognosis,Receptors IgG,Rituximab,Vincristine}, |
|
| 7795 | + file = {/Users/rmorin/Zotero/storage/95RTJJ57/Nowicka et al. - 2021 - Prognostic significance of FCGR2B expression for t.pdf} |
|
| 7796 | +} |
|
| 7797 | + |
|
| 7798 | +@article{ognibeneHighFrequencyDevelopment, |
|
| 7799 | + title = {High Frequency of Development of {{B}} Cell Lymphoproliferation and Diffuse Large {{B}} Cell Lymphoma in {{Dbl}} Knock-in Mice.}, |
|
| 7800 | + author = {Ognibene, Marzia and Barbieri, Ottavia and Vanni, Cristina and Mastracci, Luca and Astigiano, Simonetta and Emionite, Laura and Salani, Barbara and Fedele, Manuela and Resaz, Roberta and Tenca, Claudya and Fais, Franco and Sabatini, Federica and De Santanna, Amleto and Altruda, Fiorella and Varesio, Luigi and Hirsch, Emilio and Eva, Alessandra}, |
|
| 7801 | + journaltitle = {Journal of Molecular Medicine (Berlin, Germany)}, |
|
| 7802 | + volume = {89}, |
|
| 7803 | + number = {5}, |
|
| 7804 | + pages = {493--504}, |
|
| 7805 | + keywords = {nosource} |
|
| 7806 | +} |
|
| 7807 | + |
|
| 7808 | +@article{ohgamiSTAT3MutationsAre2014, |
|
| 7809 | + title = {{{STAT3}} Mutations Are Present in Aggressive {{B-cell}} Lymphomas Including a Subset of Diffuse Large {{B-cell}} Lymphomas with {{CD30}} Expression}, |
|
| 7810 | + author = {Ohgami, Robert S. and Ma, Lisa and Monabati, Ahmad and Zehnder, James L. and Arber, Daniel A.}, |
|
| 7811 | + date = {2014-07}, |
|
| 7812 | + journaltitle = {Haematologica}, |
|
| 7813 | + shortjournal = {Haematologica}, |
|
| 7814 | + volume = {99}, |
|
| 7815 | + number = {7}, |
|
| 7816 | + eprint = {24837465}, |
|
| 7817 | + eprinttype = {pmid}, |
|
| 7818 | + pages = {e105-107}, |
|
| 7819 | + issn = {1592-8721}, |
|
| 7820 | + doi = {10.3324/haematol.2013.101543}, |
|
| 7821 | + langid = {english}, |
|
| 7822 | + pmcid = {PMC4077094}, |
|
| 7823 | + keywords = {anaplastic large cell lymphoma,Animals,B-cell lymphoma unclassifiable with features intermediate between DLBCL and Burkitt lymphoma,Bone Marrow Transplantation,CD30,diffuse large B-cell lymphoma,Disease Models Animal,Hematologic Neoplasms,Humans,Mutation,Myeloproliferative Disorders,STAT3,STAT3 Transcription Factor}, |
|
| 7824 | + file = {/Users/rmorin/Zotero/storage/SNEBHUB4/Ohgami et al. - 2014 - STAT3 mutations are present in aggressive B-cell l.pdf} |
|
| 7825 | +} |
|
| 7826 | + |
|
| 7827 | +@article{okamotoIkappaBzetaRegulates172010, |
|
| 7828 | + title = {{{IkappaBzeta}} Regulates {{T}}({{H}})17 Development by Cooperating with {{ROR}} Nuclear Receptors.}, |
|
| 7829 | + author = {Okamoto, Kazuo and Iwai, Yoshiko and Oh-hora, Masatsugu and Yamamoto, Masahiro and Morio, Tomohiro and Aoki, Kazuhiro and Ohya, Keiichi and Jetten, Anton M and Akira, Shizuo and Muta, Tatsushi and Takayanagi, Hiroshi}, |
|
| 7830 | + date = {2010-04}, |
|
| 7831 | + journaltitle = {Nature}, |
|
| 7832 | + volume = {464}, |
|
| 7833 | + number = {7293}, |
|
| 7834 | + pages = {1381--1385}, |
|
| 7835 | + keywords = {nosource} |
|
| 7836 | +} |
|
| 7837 | + |
|
| 7838 | +@article{okosunRecurrentMTORC1activatingRRAGC2016a, |
|
| 7839 | + title = {Recurrent {{mTORC1-activating RRAGC}} Mutations in Follicular Lymphoma}, |
|
| 7840 | + author = {Okosun, Jessica and Wolfson, Rachel L. and Wang, Jun and Araf, Shamzah and Wilkins, Lucy and Castellano, Brian M. and Escudero-Ibarz, Leire and Al Seraihi, Ahad Fahad and Richter, Julia and Bernhart, Stephan H. and Efeyan, Alejo and Iqbal, Sameena and Matthews, Janet and Clear, Andrew and Guerra-Assunção, José Afonso and Bödör, Csaba and Quentmeier, Hilmar and Mansbridge, Christopher and Johnson, Peter and Davies, Andrew and Strefford, Jonathan C. and Packham, Graham and Barrans, Sharon and Jack, Andrew and Du, Ming-Qing and Calaminici, Maria and Lister, T. Andrew and Auer, Rebecca and Montoto, Silvia and Gribben, John G. and Siebert, Reiner and Chelala, Claude and Zoncu, Roberto and Sabatini, David M. and Fitzgibbon, Jude}, |
|
| 7841 | + date = {2016-02}, |
|
| 7842 | + journaltitle = {Nature Genetics}, |
|
| 7843 | + shortjournal = {Nat Genet}, |
|
| 7844 | + volume = {48}, |
|
| 7845 | + number = {2}, |
|
| 7846 | + eprint = {26691987}, |
|
| 7847 | + eprinttype = {pmid}, |
|
| 7848 | + pages = {183--188}, |
|
| 7849 | + issn = {1546-1718}, |
|
| 7850 | + doi = {10.1038/ng.3473}, |
|
| 7851 | + abstract = {Follicular lymphoma is an incurable B cell malignancy characterized by the t(14;18) translocation and mutations affecting the epigenome. Although frequent gene mutations in key signaling pathways, including JAK-STAT, NOTCH and NF-κB, have also been defined, the spectrum of these mutations typically overlaps with that in the closely related diffuse large B cell lymphoma (DLBCL). Using a combination of discovery exome and extended targeted sequencing, we identified recurrent somatic mutations in RRAGC uniquely enriched in patients with follicular lymphoma (17\%). More than half of the mutations preferentially co-occurred with mutations in ATP6V1B2 and ATP6AP1, which encode components of the vacuolar H(+)-ATP ATPase (V-ATPase) known to be necessary for amino acid-induced activation of mTORC1. The RagC variants increased raptor binding while rendering mTORC1 signaling resistant to amino acid deprivation. The activating nature of the RRAGC mutations, their existence in the dominant clone and their stability during disease progression support their potential as an excellent candidate for therapeutic targeting.}, |
|
| 7852 | + langid = {english}, |
|
| 7853 | + pmcid = {PMC4731318}, |
|
| 7854 | + keywords = {Amino Acid Sequence,Animals,Humans,Lymphoma Follicular,Mechanistic Target of Rapamycin Complex 1,Molecular Sequence Data,Monomeric GTP-Binding Proteins,Multiprotein Complexes,Mutation,Sequence Homology Amino Acid,TOR Serine-Threonine Kinases}, |
|
| 7855 | + file = {/Users/rmorin/Zotero/storage/4AZZXLUH/Okosun et al. - 2016 - Recurrent mTORC1-activating RRAGC mutations in fol.pdf} |
|
| 7856 | +} |
|
| 7857 | + |
|
| 7858 | +@article{omerVDJbaseAdaptiveImmune2020, |
|
| 7859 | + title = {{{VDJbase}}: An Adaptive Immune Receptor Genotype and Haplotype Database}, |
|
| 7860 | + shorttitle = {{{VDJbase}}}, |
|
| 7861 | + author = {Omer, Aviv and Shemesh, Or and Peres, Ayelet and Polak, Pazit and Shepherd, Adrian J. and Watson, Corey T. and Boyd, Scott D. and Collins, Andrew M. and Lees, William and Yaari, Gur}, |
|
| 7862 | + date = {2020-08-01}, |
|
| 7863 | + journaltitle = {Nucleic Acids Research}, |
|
| 7864 | + shortjournal = {Nucleic Acids Res.}, |
|
| 7865 | + volume = {48}, |
|
| 7866 | + number = {D1}, |
|
| 7867 | + eprint = {31602484}, |
|
| 7868 | + eprinttype = {pmid}, |
|
| 7869 | + pages = {D1051-D1056}, |
|
| 7870 | + issn = {1362-4962}, |
|
| 7871 | + doi = {10.1093/nar/gkz872}, |
|
| 7872 | + abstract = {VDJbase is a publicly available database that offers easy searching of data describing the complete sets of gene sequences (genotypes and haplotypes) inferred from adaptive immune receptor repertoire sequencing datasets. VDJbase is designed to act as a resource that will allow the scientific community to explore the genetic variability of the immunoglobulin (Ig) and T cell receptor (TR) gene loci. It can also assist in the investigation of Ig- and TR-related genetic predispositions to diseases. Our database includes web-based query and online tools to assist in visualization and analysis of the genotype and haplotype data. It enables users to detect those alleles and genes that are significantly over-represented in a particular population, in terms of genotype, haplotype and gene expression. The database website can be freely accessed at https://www.vdjbase.org/, and no login is required. The data and code use creative common licenses and are freely downloadable from https://bitbucket.org/account/user/yaarilab/projects/GPHP.}, |
|
| 7873 | + langid = {english}, |
|
| 7874 | + pmcid = {PMC6943044}, |
|
| 7875 | + keywords = {Computational Biology,Databases Genetic,Genotype,Haplotypes,Humans,Molecular Sequence Annotation,Receptors Antigen B-Cell,Receptors Antigen T-Cell,Receptors Immunologic,Software,Software Design,V(D)J Recombination,Web Browser,Workflow}, |
|
| 7876 | + file = {/Users/rmorin/Zotero/storage/UFDT9B96/Omer et al. - 2020 - VDJbase an adaptive immune receptor genotype and .pdf} |
|
| 7877 | +} |
|
| 7878 | + |
|
| 7879 | +@article{oricchioGeneticEpigeneticInactivation2017b, |
|
| 7880 | + title = {Genetic and Epigenetic Inactivation of {{SESTRIN1}} Controls {{mTORC1}} and Response to {{EZH2}} Inhibition in Follicular Lymphoma}, |
|
| 7881 | + author = {Oricchio, Elisa and Katanayeva, Natalya and Donaldson, Maria Christine and Sungalee, Stephanie and Pasion, Joyce P. and Béguelin, Wendy and Battistello, Elena and Sanghvi, Viraj R. and Jiang, Man and Jiang, Yanwen and Teater, Matt and Parmigiani, Anita and Budanov, Andrei V. and Chan, Fong Chun and Shah, Sohrab P. and Kridel, Robert and Melnick, Ari M. and Ciriello, Giovanni and Wendel, Hans-Guido}, |
|
| 7882 | + date = {2017-06-28}, |
|
| 7883 | + journaltitle = {Science Translational Medicine}, |
|
| 7884 | + shortjournal = {Sci Transl Med}, |
|
| 7885 | + volume = {9}, |
|
| 7886 | + number = {396}, |
|
| 7887 | + eprint = {28659443}, |
|
| 7888 | + eprinttype = {pmid}, |
|
| 7889 | + pages = {eaak9969}, |
|
| 7890 | + issn = {1946-6242}, |
|
| 7891 | + doi = {10.1126/scitranslmed.aak9969}, |
|
| 7892 | + abstract = {Follicular lymphoma (FL) is an incurable form of B cell lymphoma. Genomic studies have cataloged common genetic lesions in FL such as translocation t(14;18), frequent losses of chromosome 6q, and mutations in epigenetic regulators such as EZH2 Using a focused genetic screen, we identified SESTRIN1 as a relevant target of the 6q deletion and demonstrate tumor suppression by SESTRIN1 in vivo. Moreover, SESTRIN1 is a direct target of the lymphoma-specific EZH2 gain-of-function mutation (EZH2Y641X ). SESTRIN1 inactivation disrupts p53-mediated control of mammalian target of rapamycin complex 1 (mTORC1) and enables mRNA translation under genotoxic stress. SESTRIN1 loss represents an alternative to RRAGC mutations that maintain mTORC1 activity under nutrient starvation. The antitumor efficacy of pharmacological EZH2 inhibition depends on SESTRIN1, indicating that mTORC1 control is a critical function of EZH2 in lymphoma. Conversely, EZH2Y641X mutant lymphomas show increased sensitivity to RapaLink-1, a bifunctional mTOR inhibitor. Hence, SESTRIN1 contributes to the genetic and epigenetic control of mTORC1 in lymphoma and influences responses to targeted therapies.}, |
|
| 7893 | + langid = {english}, |
|
| 7894 | + pmcid = {PMC5559734}, |
|
| 7895 | + keywords = {Animals,Chromosome Deletion,Chromosomes Human Pair 6,Enhancer of Zeste Homolog 2 Protein,Epigenesis Genetic,Gene Silencing,Genetic Testing,Genome Human,Heat-Shock Proteins,Humans,Lymphoma Follicular,Mechanistic Target of Rapamycin Complex 1,Mice,Mutation,Protein Biosynthesis,RNA Messenger}, |
|
| 7896 | + file = {/Users/rmorin/Zotero/storage/YI8W64IF/Oricchio et al. - 2017 - Genetic and epigenetic inactivation of SESTRIN1 co.pdf} |
|
| 7897 | +} |
|
| 7898 | + |
|
| 7899 | +@article{oskarsdottirBamHashChecksumProgram2016, |
|
| 7900 | + title = {{{BamHash}}: A Checksum Program for Verifying the Integrity of Sequence Data}, |
|
| 7901 | + shorttitle = {{{BamHash}}}, |
|
| 7902 | + author = {Óskarsdóttir, Arna and Másson, Gísli and Melsted, Páll}, |
|
| 7903 | + date = {2016-01-01}, |
|
| 7904 | + journaltitle = {Bioinformatics}, |
|
| 7905 | + shortjournal = {Bioinformatics}, |
|
| 7906 | + volume = {32}, |
|
| 7907 | + number = {1}, |
|
| 7908 | + pages = {140--141}, |
|
| 7909 | + issn = {1367-4803}, |
|
| 7910 | + doi = {10.1093/bioinformatics/btv539}, |
|
| 7911 | + url = {https://academic.oup.com/bioinformatics/article/32/1/140/1743564}, |
|
| 7912 | + urldate = {2019-12-21}, |
|
| 7913 | + abstract = {Abstract. Summary : Large resequencing projects require a significant amount of storage for raw sequences, as well as alignment files. Because the raw sequence}, |
|
| 7914 | + langid = {english}, |
|
| 7915 | + file = {/Users/rmorin/Zotero/storage/MZIYA8QV/1743564.html} |
|
| 7916 | +} |
|
| 7917 | + |
|
| 7918 | +@article{ostareck-ledererCSrcmediatedPhosphorylationHnRNP2002, |
|
| 7919 | + title = {C-{{Src-mediated}} Phosphorylation of {{hnRNP K}} Drives Translational Activation of Specifically Silenced {{mRNAs}}}, |
|
| 7920 | + author = {Ostareck-Lederer, Antje and Ostareck, Dirk H. and Cans, Christophe and Neubauer, Gitte and Bomsztyk, Karol and Superti-Furga, Giulio and Hentze, Matthias W.}, |
|
| 7921 | + date = {2002-07}, |
|
| 7922 | + journaltitle = {Molecular and Cellular Biology}, |
|
| 7923 | + shortjournal = {Mol Cell Biol}, |
|
| 7924 | + volume = {22}, |
|
| 7925 | + number = {13}, |
|
| 7926 | + eprint = {12052863}, |
|
| 7927 | + eprinttype = {pmid}, |
|
| 7928 | + pages = {4535--4543}, |
|
| 7929 | + issn = {0270-7306}, |
|
| 7930 | + doi = {10.1128/MCB.22.13.4535-4543.2002}, |
|
| 7931 | + abstract = {hnRNPK and hnRNP E1/E2 mediate translational silencing of cellular and viral mRNAs in a differentiation-dependent way by binding to specific regulatory sequences. The translation of 15-lipoxygenase (LOX) mRNA in erythroid precursor cells and of the L2 mRNA of human papilloma virus type 16 (HPV-16) in squamous epithelial cells is silenced when either of these cells is immature and is activated in maturing cells by unknown mechanisms. Here we address the question of how the silenced mRNA can be translationally activated. We show that hnRNP K and the c-Src kinase specifically interact with each other, leading to c-Src activation and tyrosine phosphorylation of hnRNP K in vivo and in vitro. c-Src-mediated phosphorylation reversibly inhibits the binding of hnRNP K to the differentiation control element (DICE) of the LOX mRNA 3' untranslated region in vitro and specifically derepresses the translation of DICE-bearing mRNAs in vivo. Our results establish a novel role of c-Src kinase in translational gene regulation and reveal a mechanism by which silenced mRNAs can be translationally activated.}, |
|
| 7932 | + langid = {english}, |
|
| 7933 | + pmcid = {PMC133888}, |
|
| 7934 | + keywords = {3' Untranslated Regions,Amino Acid Sequence,Arachidonate 15-Lipoxygenase,CSK Tyrosine-Protein Kinase,Gene Silencing,HeLa Cells,Heterogeneous-Nuclear Ribonucleoprotein K,Heterogeneous-Nuclear Ribonucleoproteins,Humans,Molecular Sequence Data,Mutation,Phosphopyruvate Hydratase,Phosphorylation,Protein Biosynthesis,Protein-Tyrosine Kinases,Ribonucleoproteins,RNA Messenger,src Homology Domains,src-Family Kinases,Tyrosine}, |
|
| 7935 | + file = {/Users/rmorin/Zotero/storage/Q5QLBRDZ/Ostareck-Lederer et al. - 2002 - c-Src-mediated phosphorylation of hnRNP K drives t.pdf} |
|
| 7936 | +} |
|
| 7937 | + |
|
| 7938 | +@article{otaMemoryPathogenicIgE2023, |
|
| 7939 | + title = {The Memory of Pathogenic {{IgE}} Is Contained within {{CD23}}+{{IgG1}}+ Memory {{B}} Cells Poised to Switch to {{IgE}} in Food Allergy}, |
|
| 7940 | + author = {Ota, Miyo and Hoehn, Kenneth B. and Ota, Takayuki and Aranda, Carlos J. and Friedman, Sara and Braga, Weslley F. and Malbari, Alefiyah and Kleinstein, Steven H. and Sicherer, Scott H. and family=Lafaille, given=Maria A. Curotto, prefix=de, useprefix=false}, |
|
| 7941 | + date = {2023-01-25}, |
|
| 7942 | + journaltitle = {bioRxiv}, |
|
| 7943 | + pages = {2023.01.25.525506}, |
|
| 7944 | + doi = {10.1101/2023.01.25.525506}, |
|
| 7945 | + url = {https://www.biorxiv.org/content/10.1101/2023.01.25.525506v1}, |
|
| 7946 | + urldate = {2023-12-16}, |
|
| 7947 | + abstract = {Food allergy is caused by allergen-specific IgE antibodies but little is known about the B cell memory of persistent IgE responses. Here we describe in human pediatric peanut allergy CD23+IgG1+ memory B cells arising in type 2 responses that contain peanut specific clones and generate IgE cells on activation. These ‘type2-marked’ IgG1+ memory B cells differentially express IL-4/IL-13 regulated genes FCER2/CD23, IL4R, and germline IGHE and carry highly mutated B cell receptors (BCRs). Further, high affinity memory B cells specific for the main peanut allergen Ara h 2 mapped to the population of ‘type2-marked’ IgG1+ memory B cells and included convergent BCRs across different individuals. Our findings indicate that CD23+IgG1+ memory B cells transcribing germline IGHE are a unique memory population containing precursors of pathogenic IgE. One-Sentence Summary We describe a unique population of IgG+ memory B cells poised to switch to IgE that contains high affinity allergen-specific clones in peanut allergy.}, |
|
| 7948 | + langid = {english}, |
|
| 7949 | + file = {/Users/rmorin/Zotero/storage/CEMS8KQ7/Ota et al. - 2023 - The memory of pathogenic IgE is contained within C.pdf} |
|
| 7950 | +} |
|
| 7951 | + |
|
| 7952 | +@article{otoshiCytoplasmicAccumulationHeterogeneous2015, |
|
| 7953 | + title = {Cytoplasmic {{Accumulation}} of {{Heterogeneous Nuclear Ribonucleoprotein K Strongly Promotes Tumor Invasion}} in {{Renal Cell Carcinoma Cells}}}, |
|
| 7954 | + author = {Otoshi, Taiyo and Tanaka, Tomoaki and Morimoto, Kazuya and Nakatani, Tatsuya}, |
|
| 7955 | + date = {2015-12-29}, |
|
| 7956 | + journaltitle = {PLOS ONE}, |
|
| 7957 | + shortjournal = {PLOS ONE}, |
|
| 7958 | + volume = {10}, |
|
| 7959 | + number = {12}, |
|
| 7960 | + pages = {e0145769}, |
|
| 7961 | + publisher = {Public Library of Science}, |
|
| 7962 | + issn = {1932-6203}, |
|
| 7963 | + doi = {10.1371/journal.pone.0145769}, |
|
| 7964 | + url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0145769}, |
|
| 7965 | + urldate = {2023-01-09}, |
|
| 7966 | + abstract = {Heterogeneous nuclear ribonucleoprotein (hnRNP) K is a part of the ribonucleoprotein complex which regulates diverse biological events. While overexpression of hnRNP K has been shown to be related to tumorigenesis in several cancers, both the expression patterns and biological mechanisms of hnRNP K in renal cell carcinoma (RCC) cells remain unclear. In this study, we showed that hnRNP K protein was strongly expressed in selected RCC cell lines (ACHN, A498, Caki-1, 786–0), and knock-down of hnRNP K expression by siRNA induced cell growth inhibition and apoptosis. Based on immunohistochemical (IHC) analysis of hnRNP K expression in human clear cell RCC specimens, we demonstrated that there was a significant positive correlation between hnRNP K staining score and tumor aggressiveness (e.g., Fuhrman grade, metastasis). Particularly, the rate of cytoplasmic localization of hnRNP K in primary RCC with distant metastasis was significantly higher than that in RCC without metastasis. Additionally, our results indicated that the cytoplasmic distribution of hnRNP K induced by TGF-β stimulus mainly contributed to TGF-β-triggered tumor cell invasion in RCC cells. Dominant cytoplasmic expression of ectopic hnRNP K markedly suppressed the inhibition of invasion by knock-down of endogenous hnRNP K. The expression level of matrix metalloproteinase protein-2 was decreased by endogenous hnRNP K knock-down, and restored by ectopic hnRNP K. Therefore, hnRNP K may be a key molecule involved in cell motility in RCC cells, and molecular mechanism associated with the subcellular localization of hnRNP K may be a novel target in the treatment of metastatic RCC.}, |
|
| 7967 | + langid = {english}, |
|
| 7968 | + keywords = {Cell staining,Cytoplasm,Cytoplasmic staining,Metastasis,Renal cancer,Renal cell carcinoma,Small interfering RNA,Transfection}, |
|
| 7969 | + file = {/Users/rmorin/Zotero/storage/TPAXKYQE/Otoshi et al. - 2015 - Cytoplasmic Accumulation of Heterogeneous Nuclear .pdf} |
|
| 7970 | +} |
|
| 7971 | + |
|
| 7972 | +@article{ottoGeneticLesionsTRAF32012a, |
|
| 7973 | + title = {Genetic Lesions of the {{TRAF3}} and {{MAP3K14}} Genes in Classical {{Hodgkin}} Lymphoma}, |
|
| 7974 | + author = {Otto, Claudia and Giefing, Maciej and Massow, Anne and Vater, Inga and Gesk, Stefan and Schlesner, Matthias and Richter, Julia and Klapper, Wolfram and Hansmann, Martin-Leo and Siebert, Reiner and Küppers, Ralf}, |
|
| 7975 | + date = {2012-06}, |
|
| 7976 | + journaltitle = {British Journal of Haematology}, |
|
| 7977 | + shortjournal = {Br J Haematol}, |
|
| 7978 | + volume = {157}, |
|
| 7979 | + number = {6}, |
|
| 7980 | + eprint = {22469134}, |
|
| 7981 | + eprinttype = {pmid}, |
|
| 7982 | + pages = {702--708}, |
|
| 7983 | + issn = {1365-2141}, |
|
| 7984 | + doi = {10.1111/j.1365-2141.2012.09113.x}, |
|
| 7985 | + abstract = {Hodgkin and Reed/Sternberg (HRS) cells in classical Hodgkin lymphoma (cHL) show constitutive activation of nuclear factor (NF)-κB. Several genetic lesions contribute to this deregulated NF-κB activity. Here, we analysed two further NF-κB regulators for genetic lesions, the inhibitory factor TRAF3 and the key signalling component of the alternative NF-κB pathway, MAP3K14 (NIK). Single nucleotide polymorphism (SNP) array analysis of cHL cell lines revealed a uniparental disomy of the long arm of chromosome 14 associated with a biallelic deletion of TRAF3 located on this chromosome in cell line U-HO1. Cloning of the deletion breakpoint showed a 123~371 bp deletion. No inactivating mutations of TRAF3 were found in six other cHL cell lines or in microdissected HRS cells from seven cHL. However, in primary cHL samples interphase cytogenetic analyses revealed signal patterns indicating monoallelic deletion of TRAF3 in 3/20 other cases. SNP array analysis revealed a gain of copy number for MAP3K14 in three cHL cell lines. Gains of MAP3K14 were detected in 5/16 cases of primary cHL. In conclusion, in rare instances, HRS cells harbour inactivating mutations of the TRAF3 gene and recurrently show gains of MAP3K14, indicating that more components of NF-κB signalling show genetic lesions in HRS cells than previously known.}, |
|
| 7986 | + langid = {english}, |
|
| 7987 | + keywords = {Adolescent,Adult,Aged,Cell Line Tumor,Child,Cytogenetic Analysis,Female,Gene Deletion,Gene Dosage,Hodgkin Disease,Humans,Male,Middle Aged,NF-kappaB-Inducing Kinase,Polymorphism Single Nucleotide,Protein Serine-Threonine Kinases,Proto-Oncogene Proteins,Signal Transduction,TNF Receptor-Associated Factor 3,Trans-Activators} |
|
| 7988 | +} |
|
| 7989 | + |
|
| 7990 | +@article{painterCelloforiginDiffuseLarge2019, |
|
| 7991 | + title = {Cell-of-Origin in Diffuse Large {{B-cell}} Lymphoma: Findings from the {{UK}}'s Population-Based {{Haematological Malignancy Research Network}}}, |
|
| 7992 | + shorttitle = {Cell-of-Origin in Diffuse Large {{B-cell}} Lymphoma}, |
|
| 7993 | + author = {Painter, Daniel and Barrans, Sharon and Lacy, Stuart and Smith, Alexandra and Crouch, Simon and Westhead, David and Sha, Chulin and Patmore, Russell and Tooze, Reuben and Burton, Cathy and Roman, Eve}, |
|
| 7994 | + date = {2019}, |
|
| 7995 | + journaltitle = {British Journal of Haematology}, |
|
| 7996 | + volume = {185}, |
|
| 7997 | + number = {4}, |
|
| 7998 | + pages = {781--784}, |
|
| 7999 | + issn = {1365-2141}, |
|
| 8000 | + doi = {10.1111/bjh.15619}, |
|
| 8001 | + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/bjh.15619}, |
|
| 8002 | + urldate = {2023-01-16}, |
|
| 8003 | + langid = {english}, |
|
| 8004 | + keywords = {epidemiology,gene-expression,prognostic factors,survival}, |
|
| 8005 | + file = {/Users/rmorin/Zotero/storage/P852EJWR/Painter et al. - 2019 - Cell-of-origin in diffuse large B-cell lymphoma f.pdf;/Users/rmorin/Zotero/storage/BYGY9HI7/bjh.html} |
|
| 8006 | +} |
|
| 8007 | + |
|
| 8008 | +@article{paneaWholeGenomeLandscape2019, |
|
| 8009 | + title = {The Whole Genome Landscape of {{Burkitt}} Lymphoma Subtypes.}, |
|
| 8010 | + author = {Panea, R. and Love, C. and Shingleton, Jennifer R. and Reddy, Anupama and Bailey, J. and Moormann, A. and Otieno, J. and Ong'echa, J. and Oduor, C. and Schroêder, K. and Masalu, N. and Chao, N. and Agajanian, M. and Major, M. and Fedoriw, Y. and Richards, K. and Rymkiewicz, G. and Miles, R. and Alobeid, B. and Bhagat, G. and Flowers, C. and Ondrejka, S. and Hsi, E. and Choi, W. and Au-Yeung, R. and Hartmann, W. and Lenz, G. and Meyerson, H. and Lin, Yen-Yu and Zhuang, Y. and Luftig, M. and Waldrop, A. and Dave, Tushar and Thakkar, D. and Sahay, Harshit and Li, Guojie and Palus, B. and Seshadri, V. and Kim, S. and Gascoyne, R. and Levy, S. and Mukhopadhyay, Minerva and Dunson, D. and Dave, S.}, |
|
| 8011 | + date = {2019}, |
|
| 8012 | + journaltitle = {Blood}, |
|
| 8013 | + shortjournal = {Blood}, |
|
| 8014 | + doi = {10.1182/blood.2019001880}, |
|
| 8015 | + file = {/Users/rmorin/Zotero/storage/IXPD2JLE/Panea et al. - 2019 - The whole genome landscape of Burkitt lymphoma sub.pdf} |
|
| 8016 | +} |
|
| 8017 | + |
|
| 8018 | +@article{pararajalingamCodingNoncodingDrivers2020, |
|
| 8019 | + title = {Coding and Noncoding Drivers of Mantle Cell Lymphoma Identified through Exome and Genome Sequencing}, |
|
| 8020 | + author = {Pararajalingam, Prasath and Coyle, Krysta M. and Arthur, Sarah E. and Thomas, Nicole and Alcaide, Miguel and Meissner, Barbara and Boyle, Merrill and Qureshi, Quratulain and Grande, Bruno M. and Rushton, Christopher and Slack, Graham W. and Mungall, Andrew J. and Tam, Constantine S. and Agarwal, Rishu and Dawson, Sarah-Jane and Lenz, Georg and Balasubramanian, Sriram and Gascoyne, Randy D. and Steidl, Christian and Connors, Joseph and Villa, Diego and Audas, Timothy E. and Marra, Marco A. and Johnson, Nathalie A. and Scott, David W. and Morin, Ryan D.}, |
|
| 8021 | + date = {2020-07-30}, |
|
| 8022 | + journaltitle = {Blood}, |
|
| 8023 | + shortjournal = {Blood}, |
|
| 8024 | + volume = {136}, |
|
| 8025 | + number = {5}, |
|
| 8026 | + eprint = {32160292}, |
|
| 8027 | + eprinttype = {pmid}, |
|
| 8028 | + pages = {572--584}, |
|
| 8029 | + issn = {1528-0020}, |
|
| 8030 | + doi = {10.1182/blood.2019002385}, |
|
| 8031 | + abstract = {Mantle cell lymphoma (MCL) is an uncommon B-cell non-Hodgkin lymphoma (NHL) that is incurable with standard therapies. The genetic drivers of this cancer have not been firmly established, and the features that contribute to differences in clinical course remain limited. To extend our understanding of the biological pathways involved in this malignancy, we performed a large-scale genomic analysis of MCL using data from 51 exomes and 34 genomes alongside previously published exome cohorts. To confirm our findings, we resequenced the genes identified in the exome cohort in 191 MCL tumors, each having clinical follow-up data. We confirmed the prognostic association of TP53 and NOTCH1 mutations. Our sequencing revealed novel recurrent noncoding mutations surrounding a single exon of the HNRNPH1gene. In RNA-seq data from 103 of these cases, MCL tumors with these mutations had a distinct imbalance of HNRNPH1 isoforms. This altered splicing of HNRNPH1 was associated with inferior outcomes in MCL and showed a significant increase in protein expression by immunohistochemistry. We describe a functional role for these recurrent noncoding mutations in disrupting an autoregulatory feedback mechanism, thereby deregulating HNRNPH1 protein expression. Taken together, these data strongly imply a role for aberrant regulation of messenger RNA processing in MCL pathobiology.}, |
|
| 8032 | + langid = {english}, |
|
| 8033 | + pmcid = {PMC7440974}, |
|
| 8034 | + keywords = {Adult,Aged,Aged 80 and over,Female,Genetic Predisposition to Disease,Genotype,Heterogeneous-Nuclear Ribonucleoproteins,Humans,Lymphoma Mantle-Cell,Male,Middle Aged,Morinlab,Mutation,Whole Genome Sequencing}, |
|
| 8035 | + file = {/Users/rmorin/Zotero/storage/4LTEMRUG/Pararajalingam et al. - 2020 - Coding and noncoding drivers of mantle cell lympho.pdf} |
|
| 8036 | +} |
|
| 8037 | + |
|
| 8038 | +@article{parekhTherapeuticTargetingBCL6, |
|
| 8039 | + title = {Therapeutic Targeting of the {{BCL6}} Oncogene for Diffuse Large {{B-cell}} Lymphomas}, |
|
| 8040 | + author = {Parekh, Samir and Privé, Gilbert and Melnick, Ari}, |
|
| 8041 | + journaltitle = {Leuk lymphoma}, |
|
| 8042 | + volume = {49}, |
|
| 8043 | + number = {5}, |
|
| 8044 | + pages = {874--882}, |
|
| 8045 | + keywords = {nosource} |
|
| 8046 | +} |
|
| 8047 | + |
|
| 8048 | +@article{parkHeterogeneousNuclearRibonucleoprotein2017, |
|
| 8049 | + title = {Heterogeneous {{Nuclear Ribonucleoprotein A2B1 Exerts}} a {{Regulatory Role}} in {{Lipopolysaccharide-stimulated 38B9 B Cell Activation}}}, |
|
| 8050 | + author = {Park, Jisang and Choe, Chung-Hyeon and Kim, Ju and Yang, Jing Shian and Kim, Jin Hyun and Jang, Hyonseok and Jang, Yong-Suk}, |
|
| 8051 | + date = {2017-12}, |
|
| 8052 | + journaltitle = {Immune Network}, |
|
| 8053 | + shortjournal = {Immune Netw}, |
|
| 8054 | + volume = {17}, |
|
| 8055 | + number = {6}, |
|
| 8056 | + eprint = {29302256}, |
|
| 8057 | + eprinttype = {pmid}, |
|
| 8058 | + pages = {437--450}, |
|
| 8059 | + issn = {1598-2629}, |
|
| 8060 | + doi = {10.4110/in.2017.17.6.437}, |
|
| 8061 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5746613/}, |
|
| 8062 | + urldate = {2022-10-06}, |
|
| 8063 | + abstract = {Major histocompatibility complex (MHC) class II molecules, which are recognized for their primary function of presenting an antigen to the T cell receptor, are involved in various signaling pathways in B cell activation. We identified heterogeneous nuclear ribonucleoprotein (hnRNP) A2B1 as an MHC class II molecule-associated protein involved in MHC class II-mediated signal transduction in lipopolysaccharide (LPS)-stimulated 38B9 B cells. Although the function of hnRNP A2B1 in the nucleus is primarily known, the level of hnRNP A2B1 in the cytoplasm was increased in LPS-stimulated 38B9 cells, while it was not detected in the cytoplasm of non-treated 38B9 cells. The silencing of hnRNP A2B1 expression using siRNA disturbed B cell maturation by regulation of mitogen-activated protein kinase signaling, NF-κB activation, and protein kinase B activation. These results suggest that hnRNP A2B1 is associated with MHC class II molecules and is involved in B cell activation signaling pathways in LPS-stimulated 38B9 cells.}, |
|
| 8064 | + pmcid = {PMC5746613}, |
|
| 8065 | + file = {/Users/rmorin/Zotero/storage/D2XFT4HY/Park et al. - 2017 - Heterogeneous Nuclear Ribonucleoprotein A2B1 Exert.pdf} |
|
| 8066 | +} |
|
| 8067 | + |
|
| 8068 | +@article{parkInteractionBCL2Interleukin102009, |
|
| 8069 | + title = {Interaction between {{BCL2}} and {{Interleukin-10 Gene Polymorphisms Alter Outcomes}} of {{Diffuse Large B-Cell Lymphoma}} Following {{Rituximab Plus CHOP Chemotherapy}}}, |
|
| 8070 | + author = {Park, Y H and Sohn, S K and Kim, J G and Lee, M-H and Song, H S and Kim, M K and Jung, J S and Lee, J-J and Kim, H J and Kim, D H}, |
|
| 8071 | + date = {2009-03}, |
|
| 8072 | + journaltitle = {Clin Cancer Res}, |
|
| 8073 | + volume = {15}, |
|
| 8074 | + number = {6}, |
|
| 8075 | + pages = {2107--2115}, |
|
| 8076 | + keywords = {nosource} |
|
| 8077 | +} |
|
| 8078 | + |
|
| 8079 | +@article{paronettoEwingSarcomaProtein2011, |
|
| 8080 | + title = {The {{Ewing Sarcoma Protein Regulates DNA Damage-Induced Alternative Splicing}}}, |
|
| 8081 | + author = {Paronetto, Maria Paola and Miñana, Belén and Valcárcel, Juan}, |
|
| 8082 | + date = {2011-08-05}, |
|
| 8083 | + journaltitle = {Molecular Cell}, |
|
| 8084 | + shortjournal = {Molecular Cell}, |
|
| 8085 | + volume = {43}, |
|
| 8086 | + number = {3}, |
|
| 8087 | + eprint = {21816343}, |
|
| 8088 | + eprinttype = {pmid}, |
|
| 8089 | + pages = {353--368}, |
|
| 8090 | + issn = {1097-2765}, |
|
| 8091 | + doi = {10.1016/j.molcel.2011.05.035}, |
|
| 8092 | + url = {https://www.cell.com/molecular-cell/abstract/S1097-2765(11)00462-X}, |
|
| 8093 | + urldate = {2019-12-21}, |
|
| 8094 | + langid = {english}, |
|
| 8095 | + file = {/Users/rmorin/Zotero/storage/R8UDTW6U/S1097-2765(11)00462-X.html} |
|
| 8096 | +} |
|
| 8097 | + |
|
| 8098 | +@article{parryWholeExomeSequencing2013, |
|
| 8099 | + title = {Whole Exome Sequencing Identifies Novel Recurrently Mutated Genes in Patients with Splenic Marginal Zone Lymphoma}, |
|
| 8100 | + author = {Parry, Marina and Rose-Zerilli, Matthew J. J. and Gibson, Jane and Ennis, Sarah and Walewska, Renata and Forster, Jade and Parker, Helen and Davis, Zadie and Gardiner, Anne and Collins, Andrew and Oscier, David G. and Strefford, Jonathan C.}, |
|
| 8101 | + date = {2013}, |
|
| 8102 | + journaltitle = {PloS One}, |
|
| 8103 | + shortjournal = {PLoS One}, |
|
| 8104 | + volume = {8}, |
|
| 8105 | + number = {12}, |
|
| 8106 | + eprint = {24349473}, |
|
| 8107 | + eprinttype = {pmid}, |
|
| 8108 | + pages = {e83244}, |
|
| 8109 | + issn = {1932-6203}, |
|
| 8110 | + doi = {10.1371/journal.pone.0083244}, |
|
| 8111 | + abstract = {The pathogenesis of splenic marginal zone lymphoma (SMZL) remains largely unknown. Recent high-throughput sequencing studies have identified recurrent mutations in key pathways, most notably NOTCH2 mutations in {$>$}25\% of patients. These studies are based on small, heterogeneous discovery cohorts, and therefore only captured a fraction of the lesions present in the SMZL genome. To identify further novel pathogenic mutations within related biochemical pathways, we applied whole exome sequencing (WES) and copy number (CN) analysis to a biologically and clinically homogeneous cohort of seven SMZL patients with 7q abnormalities and IGHV1-2*04 gene usage. We identified 173 somatic non-silent variants, affecting 160 distinct genes. In additional to providing independent validation of the presence of mutation in several previously reported genes (NOTCH2, TNFAIP3, MAP3K14, MLL2 and SPEN), our study defined eight additional recurrently mutated genes in SMZL; these genes are CREBBP, CBFA2T3, AMOTL1, FAT4, FBXO11, PLA2G4D, TRRAP and USH2A. By integrating our WES and CN data we identified three mutated putative candidate genes targeted by 7q deletions (CUL1, EZH2 and FLNC), with FLNC positioned within the well-characterized 7q minimally deleted region. Taken together, this work expands the reported directory of recurrently mutated cancer genes in this disease, thereby expanding our understanding of SMZL pathogenesis. Ultimately, this work will help to establish a stratified approach to care including the possibility of targeted therapy.}, |
|
| 8112 | + langid = {english}, |
|
| 8113 | + pmcid = {PMC3862727}, |
|
| 8114 | + keywords = {Chromosomes Human Pair 7,DNA Mutational Analysis,Exome,Female,Humans,Lymphoma B-Cell Marginal Zone,Male,Mutation,Neoplasm Proteins,Splenic Neoplasms}, |
|
| 8115 | + file = {/Users/rmorin/Zotero/storage/B2MPJG8V/Parry et al. - 2013 - Whole exome sequencing identifies novel recurrentl.pdf} |
|
| 8116 | +} |
|
| 8117 | + |
|
| 8118 | +@article{pasqualucciAnalysisCodingGenome2011, |
|
| 8119 | + title = {Analysis of the Coding Genome of Diffuse Large {{B-cell}} Lymphoma}, |
|
| 8120 | + author = {Pasqualucci, Laura and Trifonov, Vladimir and Fabbri, Giulia and Ma, Jing and Rossi, Davide and Chiarenza, Annalisa and Wells, Victoria A. and Grunn, Adina and Messina, Monica and Elliot, Oliver and Chan, Joseph and Bhagat, Govind and Chadburn, Amy and Gaidano, Gianluca and Mullighan, Charles G. and Rabadan, Raul and Dalla-Favera, Riccardo}, |
|
| 8121 | + date = {2011-07-31}, |
|
| 8122 | + journaltitle = {Nature Genetics}, |
|
| 8123 | + shortjournal = {Nat Genet}, |
|
| 8124 | + volume = {43}, |
|
| 8125 | + number = {9}, |
|
| 8126 | + eprint = {21804550}, |
|
| 8127 | + eprinttype = {pmid}, |
|
| 8128 | + pages = {830--837}, |
|
| 8129 | + issn = {1546-1718}, |
|
| 8130 | + doi = {10.1038/ng.892}, |
|
| 8131 | + abstract = {Diffuse large B-cell lymphoma (DLBCL) is the most common form of human lymphoma. Although a number of structural alterations have been associated with the pathogenesis of this malignancy, the full spectrum of genetic lesions that are present in the DLBCL genome, and therefore the identity of dysregulated cellular pathways, remains unknown. By combining next-generation sequencing and copy number analysis, we show that the DLBCL coding genome contains, on average, more than 30 clonally represented gene alterations per case. This analysis also revealed mutations in genes not previously implicated in DLBCL pathogenesis, including those regulating chromatin methylation (MLL2; 24\% of samples) and immune recognition by T cells. These results provide initial data on the complexity of the DLBCL coding genome and identify novel dysregulated pathways underlying its pathogenesis.}, |
|
| 8132 | + langid = {english}, |
|
| 8133 | + pmcid = {PMC3297422}, |
|
| 8134 | + keywords = {Chromatin,Diploidy,DNA Mutational Analysis,Gene Dosage,Gene Expression Regulation Leukemic,Genome Human,Germinal Center,Humans,Lymphoma Large B-Cell Diffuse,Methylation,Neoplasm Recurrence Local,Point Mutation,Polymorphism Single Nucleotide,T-Lymphocytes}, |
|
| 8135 | + file = {/Users/rmorin/Zotero/storage/LWVP97BH/Pasqualucci et al. - 2011 - Analysis of the coding genome of diffuse large B-c.pdf} |
|
| 8136 | +} |
|
| 8137 | + |
|
| 8138 | +@article{pasqualucciGeneticLandscapeDiffuse, |
|
| 8139 | + title = {The {{Genetic Landscape}} of {{Diffuse Large B-Cell Lymphoma}}}, |
|
| 8140 | + author = {Pasqualucci, Laura and Dalla-Favera, Riccardo}, |
|
| 8141 | + journaltitle = {Seminars in Hematology}, |
|
| 8142 | + volume = {52}, |
|
| 8143 | + number = {2}, |
|
| 8144 | + pages = {67--76}, |
|
| 8145 | + keywords = {nosource} |
|
| 8146 | +} |
|
| 8147 | + |
|
| 8148 | +@article{pasqualucciHypermutationMultipleProtooncogenes, |
|
| 8149 | + title = {Hypermutation of Multiple Proto-Oncogenes in {{B-cell}} Diffuse Large-Cell Lymphomas}, |
|
| 8150 | + author = {Pasqualucci, L and Neumeister, P and Stoorvogel, W and Nanjangud, G and Chaganti, R and Kuppers, R and Dalla-Favera, R}, |
|
| 8151 | + journaltitle = {Nature}, |
|
| 8152 | + volume = {412}, |
|
| 8153 | + number = {6844}, |
|
| 8154 | + pages = {341--346}, |
|
| 8155 | + keywords = {nosource} |
|
| 8156 | +} |
|
| 8157 | + |
|
| 8158 | +@article{pasqualucciHypermutationMultipleProtooncogenes2001a, |
|
| 8159 | + title = {Hypermutation of Multiple Proto-Oncogenes in {{B-cell}} Diffuse Large-Cell Lymphomas}, |
|
| 8160 | + author = {Pasqualucci, L. and Neumeister, P. and Goossens, T. and Nanjangud, G. and Chaganti, R. S. and Küppers, R. and Dalla-Favera, R.}, |
|
| 8161 | + date = {2001-07-19}, |
|
| 8162 | + journaltitle = {Nature}, |
|
| 8163 | + shortjournal = {Nature}, |
|
| 8164 | + volume = {412}, |
|
| 8165 | + number = {6844}, |
|
| 8166 | + eprint = {11460166}, |
|
| 8167 | + eprinttype = {pmid}, |
|
| 8168 | + pages = {341--346}, |
|
| 8169 | + issn = {0028-0836}, |
|
| 8170 | + doi = {10.1038/35085588}, |
|
| 8171 | + abstract = {Genomic instability promotes tumorigenesis and can occur through various mechanisms, including defective segregation of chromosomes or inactivation of DNA mismatch repair. Although B-cell lymphomas are associated with chromosomal translocations that deregulate oncogene expression, a mechanism for genome-wide instability during lymphomagenesis has not been described. During B-cell development, the immunoglobulin variable (V) region genes are subject to somatic hypermutation in germinal-centre B cells. Here we report that an aberrant hypermutation activity targets multiple loci, including the proto-oncogenes PIM1, MYC, RhoH/TTF (ARHH) and PAX5, in more than 50\% of diffuse large-cell lymphomas (DLCLs), which are tumours derived from germinal centres. Mutations are distributed in the 5' untranslated or coding sequences, are independent of chromosomal translocations, and share features typical of V-region-associated somatic hypermutation. In contrast to mutations in V regions, however, these mutations are not detectable in normal germinal-centre B cells or in other germinal-centre-derived lymphomas, suggesting a DLCL-associated malfunction of somatic hypermutation. Intriguingly, the four hypermutable genes are susceptible to chromosomal translocations in the same region, consistent with a role for hypermutation in generating translocations by DNA double-strand breaks. By mutating multiple genes, and possibly by favouring chromosomal translocations, aberrant hypermutation may represent the major contributor to lymphomagenesis.}, |
|
| 8172 | + langid = {english}, |
|
| 8173 | + keywords = {B-Lymphocytes,DNA Mutational Analysis,DNA-Binding Proteins,Genes myc,Germinal Center,Humans,Lymphoma B-Cell,Lymphoma Large B-Cell Diffuse,Molecular Sequence Data,Mutation,PAX5 Transcription Factor,Proteins,Proto-Oncogenes,Transcription Factors} |
|
| 8174 | +} |
|
| 8175 | + |
|
| 8176 | +@article{pasqualucciInactivatingMutationsAcetyltransferase2011a, |
|
| 8177 | + title = {Inactivating Mutations of Acetyltransferase Genes in {{B-cell}} Lymphoma}, |
|
| 8178 | + author = {Pasqualucci, Laura and Dominguez-Sola, David and Chiarenza, Annalisa and Fabbri, Giulia and Grunn, Adina and Trifonov, Vladimir and Kasper, Lawryn H. and Lerach, Stephanie and Tang, Hongyan and Ma, Jing and Rossi, Davide and Chadburn, Amy and Murty, Vundavalli V. and Mullighan, Charles G. and Gaidano, Gianluca and Rabadan, Raul and Brindle, Paul K. and Dalla-Favera, Riccardo}, |
|
| 8179 | + date = {2011-03-10}, |
|
| 8180 | + journaltitle = {Nature}, |
|
| 8181 | + shortjournal = {Nature}, |
|
| 8182 | + volume = {471}, |
|
| 8183 | + number = {7337}, |
|
| 8184 | + eprint = {21390126}, |
|
| 8185 | + eprinttype = {pmid}, |
|
| 8186 | + pages = {189--195}, |
|
| 8187 | + issn = {1476-4687}, |
|
| 8188 | + doi = {10.1038/nature09730}, |
|
| 8189 | + abstract = {B-cell non-Hodgkin's lymphoma comprises biologically and clinically distinct diseases the pathogenesis of which is associated with genetic lesions affecting oncogenes and tumour-suppressor genes. We report here that the two most common types--follicular lymphoma and diffuse large B-cell lymphoma--harbour frequent structural alterations inactivating CREBBP and, more rarely, EP300, two highly related histone and non-histone acetyltransferases (HATs) that act as transcriptional co-activators in multiple signalling pathways. Overall, about 39\% of diffuse large B-cell lymphoma and 41\% of follicular lymphoma cases display genomic deletions and/or somatic mutations that remove or inactivate the HAT coding domain of these two genes. These lesions usually affect one allele, suggesting that reduction in HAT dosage is important for lymphomagenesis. We demonstrate specific defects in acetylation-mediated inactivation of the BCL6 oncoprotein and activation of the p53 tumour suppressor. These results identify CREBBP/EP300 mutations as a major pathogenetic mechanism shared by common forms of B-cell non-Hodgkin's lymphoma, with direct implications for the use of drugs targeting acetylation/deacetylation mechanisms.}, |
|
| 8190 | + langid = {english}, |
|
| 8191 | + pmcid = {PMC3271441}, |
|
| 8192 | + keywords = {Acetyl Coenzyme A,Acetylation,Acetyltransferases,Animals,Base Sequence,Cells Cultured,CREB-Binding Protein,DNA-Binding Proteins,E1A-Associated p300 Protein,Gene Expression Regulation Neoplastic,HEK293 Cells,Histone Acetyltransferases,Humans,Lymphoma B-Cell,Lymphoma Follicular,Lymphoma Large B-Cell Diffuse,Mice,Mutation,Mutation Missense,Polymorphism Single Nucleotide,Protein Binding,Protein Structure Tertiary,Proto-Oncogene Proteins c-bcl-6,Recurrence,Sequence Deletion,Tumor Suppressor Protein p53}, |
|
| 8193 | + file = {/Users/rmorin/Zotero/storage/QXY7P37X/Pasqualucci et al. - 2011 - Inactivating mutations of acetyltransferase genes .pdf} |
|
| 8194 | +} |
|
| 8195 | + |
|
| 8196 | +@article{pasqualucciInactivationPRDM1BLIMP12006a, |
|
| 8197 | + title = {Inactivation of the {{PRDM1}}/{{BLIMP1}} Gene in Diffuse Large {{B}} Cell Lymphoma.}, |
|
| 8198 | + author = {Pasqualucci, Laura and Compagno, Mara and Houldsworth, Jane and Monti, Stefano and Grunn, Adina and Nandula, Subhadra V and Aster, Jon C and Murty, Vundavally V and Shipp, Margaret A and Dalla-Favera, Riccardo}, |
|
| 8199 | + date = {2006-02}, |
|
| 8200 | + journaltitle = {J Exp Med}, |
|
| 8201 | + volume = {203}, |
|
| 8202 | + number = {2}, |
|
| 8203 | + pages = {311--317}, |
|
| 8204 | + keywords = {nosource} |
|
| 8205 | +} |
|
| 8206 | + |
|
| 8207 | +@article{pasqualucciMutationsBCL6Protooncogene2003, |
|
| 8208 | + title = {Mutations of the {{BCL6}} Proto-Oncogene Disrupt Its Negative Autoregulation in Diffuse Large {{B-cell}} Lymphoma}, |
|
| 8209 | + author = {Pasqualucci, Laura and Migliazza, Anna and Basso, Katia and Houldsworth, Jane and Chaganti, R S K and Dalla-Favera, Riccardo}, |
|
| 8210 | + date = {2003-04}, |
|
| 8211 | + journaltitle = {Blood}, |
|
| 8212 | + volume = {101}, |
|
| 8213 | + number = {8}, |
|
| 8214 | + pages = {2914--2923}, |
|
| 8215 | + keywords = {nosource} |
|
| 8216 | +} |
|
| 8217 | + |
|
| 8218 | +@article{patroSalmonProvidesFast2017, |
|
| 8219 | + title = {Salmon Provides Fast and Bias-Aware Quantification of Transcript Expression}, |
|
| 8220 | + author = {Patro, Rob and Duggal, Geet and Love, Michael I. and Irizarry, Rafael A. and Kingsford, Carl}, |
|
| 8221 | + date = {2017-04}, |
|
| 8222 | + journaltitle = {Nature Methods}, |
|
| 8223 | + shortjournal = {Nat. Methods}, |
|
| 8224 | + volume = {14}, |
|
| 8225 | + number = {4}, |
|
| 8226 | + eprint = {28263959}, |
|
| 8227 | + eprinttype = {pmid}, |
|
| 8228 | + pages = {417--419}, |
|
| 8229 | + issn = {1548-7105}, |
|
| 8230 | + doi = {10.1038/nmeth.4197}, |
|
| 8231 | + abstract = {We introduce Salmon, a lightweight method for quantifying transcript abundance from RNA-seq reads. Salmon combines a new dual-phase parallel inference algorithm and feature-rich bias models with an ultra-fast read mapping procedure. It is the first transcriptome-wide quantifier to correct for fragment GC-content bias, which, as we demonstrate here, substantially improves the accuracy of abundance estimates and the sensitivity of subsequent differential expression analysis.}, |
|
| 8232 | + langid = {english}, |
|
| 8233 | + pmcid = {PMC5600148}, |
|
| 8234 | + keywords = {Algorithms,Base Composition,Bayes Theorem,Gene Expression Profiling,Sequence Analysis RNA} |
|
| 8235 | +} |
|
| 8236 | + |
|
| 8237 | +@article{pengHnRNPKPromotesGastric2019, |
|
| 8238 | + title = {{{hnRNPK}} Promotes Gastric Tumorigenesis through Regulating {{CD44E}} Alternative Splicing}, |
|
| 8239 | + author = {Peng, Wei-zhao and Liu, Ji-xi and Li, Chao-feng and Ma, Ren and Jie, Jian-zheng}, |
|
| 8240 | + date = {2019-12-12}, |
|
| 8241 | + journaltitle = {Cancer Cell International}, |
|
| 8242 | + shortjournal = {Cancer Cell International}, |
|
| 8243 | + volume = {19}, |
|
| 8244 | + number = {1}, |
|
| 8245 | + pages = {335}, |
|
| 8246 | + issn = {1475-2867}, |
|
| 8247 | + doi = {10.1186/s12935-019-1020-x}, |
|
| 8248 | + url = {https://doi.org/10.1186/s12935-019-1020-x}, |
|
| 8249 | + urldate = {2022-09-22}, |
|
| 8250 | + abstract = {The high prevalence of alternative splicing among genes implies the importance of genomic complexity in regulating normal physiological processes and diseases such as gastric cancer (GC). The standard form of stem cell marker CD44 (CD44S) and its alternatives with additional exons are reported to play important roles in multiple types of tumors, but the regulation mechanism of CD44 alternative splicing is not fully understood.}, |
|
| 8251 | + keywords = {Alternative splicing,CD44E,Gastric cancer,hnRNPK,SRSF1}, |
|
| 8252 | + file = {/Users/rmorin/Zotero/storage/MERVLKMZ/Peng et al. - 2019 - hnRNPK promotes gastric tumorigenesis through regu.pdf;/Users/rmorin/Zotero/storage/GE7CRTI5/s12935-019-1020-x.html} |
|
| 8253 | +} |
|
| 8254 | + |
|
| 8255 | +@article{peperzakFunctionalDisparitiesBCL22017, |
|
| 8256 | + title = {Functional Disparities among {{BCL-2}} Members in Tonsillar and Leukemic {{B-cell}} Subsets Assessed by {{BH3-mimetic}} Profiling}, |
|
| 8257 | + author = {Peperzak, Victor and Slinger, Erik and Ter Burg, Johanna and Eldering, Eric}, |
|
| 8258 | + date = {2017-01}, |
|
| 8259 | + journaltitle = {Cell Death \& Differentiation}, |
|
| 8260 | + shortjournal = {Cell Death Differ}, |
|
| 8261 | + volume = {24}, |
|
| 8262 | + number = {1}, |
|
| 8263 | + pages = {111--119}, |
|
| 8264 | + publisher = {Nature Publishing Group}, |
|
| 8265 | + issn = {1476-5403}, |
|
| 8266 | + doi = {10.1038/cdd.2016.105}, |
|
| 8267 | + url = {https://www.nature.com/articles/cdd2016105}, |
|
| 8268 | + urldate = {2022-10-06}, |
|
| 8269 | + abstract = {For successful treatment of malignant B-cells it is crucial to understand intrinsic survival requirements in relation to their normal progenitors. Long-lived humoral immunity as well as most B-cell malignancies, originate in the germinal center (GC). Murine GC B-cells depend on pro-survival protein MCL-1, but not BCL-XL. In contrast, naive and memory B-cells depend on BCL-2, but not BCL-XL or MCL-1. For human B-cell subsets, the functional relationships among BCL-2 members are unclear, and also if and how they shift after malignant transformation. We here dissect these aspects in human tonsil and primary leukemia (CLL) cells by single and combined treatment with novel, highly specific BH3-mimetics. We found that MCL-1 expression in GC B-cells is regulated post-translationally and its importance is highlighted by preferential binding to pro-apoptotic BIM. In contrast, BCL-XL is transcriptionally induced and binds solely to weak sensitizer BIK, potentially explaining why BCL-XL is not required for GC B-cell survival. Using novel BH3-mimetics, we found that naive and memory B-cells depend on BCL-2, GC cells predominantly on MCL-1, whereas plasma cells need both BCL-XL and MCL-1 for survival. CLL cells switch from highly sensitive for BCL-2 inhibition to resistant after CD40-stimulation. However, combined inhibition of BCL-2, plus BCL-XL or MCL-1 effectively kills these cells, thus exposing a weakness that may be therapeutically useful. These general principles offer important clues for designing treatment strategies for B-cell malignancies.}, |
|
| 8270 | + issue = {1}, |
|
| 8271 | + langid = {english}, |
|
| 8272 | + keywords = {Cell death and immune response,Oncogenes}, |
|
| 8273 | + file = {/Users/rmorin/Zotero/storage/T8UECTYL/Peperzak et al. - 2017 - Functional disparities among BCL-2 members in tons.pdf;/Users/rmorin/Zotero/storage/5LB6TUHC/cdd2016105.html} |
|
| 8274 | +} |
|
| 8275 | + |
|
| 8276 | +@article{pereiraRNABindingProteinsCancer2017, |
|
| 8277 | + title = {{{RNA-Binding Proteins}} in {{Cancer}}: {{Old Players}} and {{New Actors}}}, |
|
| 8278 | + shorttitle = {{{RNA-Binding Proteins}} in {{Cancer}}}, |
|
| 8279 | + author = {Pereira, Bruno and Billaud, Marc and Almeida, Raquel}, |
|
| 8280 | + date = {2017-07}, |
|
| 8281 | + journaltitle = {Trends in Cancer}, |
|
| 8282 | + shortjournal = {Trends Cancer}, |
|
| 8283 | + volume = {3}, |
|
| 8284 | + number = {7}, |
|
| 8285 | + eprint = {28718405}, |
|
| 8286 | + eprinttype = {pmid}, |
|
| 8287 | + pages = {506--528}, |
|
| 8288 | + issn = {2405-8025}, |
|
| 8289 | + doi = {10.1016/j.trecan.2017.05.003}, |
|
| 8290 | + abstract = {RNA-binding proteins (RBPs) are key players in post-transcriptional events. The combination of versatility of their RNA-binding domains with structural flexibility enables RBPs to control the metabolism of a large array of transcripts. Perturbations in RBP-RNA networks activity have been causally associated with cancer development, but the rational framework describing these contributions remains fragmented. We review here the evidence that RBPs modulate multiple cancer traits, emphasize their functional diversity, and assess future trends in the study of RBPs in cancer.}, |
|
| 8291 | + langid = {english}, |
|
| 8292 | + keywords = {Alternative Splicing,Animals,Antineoplastic Agents,Biomarkers Tumor,cancer,Carcinogenesis,Disease Progression,Gene Regulatory Networks,Humans,Molecular Targeted Therapy,Neoplasm Invasiveness,Neoplasms,post-transcriptional regulation,ribonucleoprotein complex,RNA,RNA Processing Post-Transcriptional,RNA-Binding Motifs,RNA-binding protein,RNA-Binding Proteins} |
|
| 8293 | +} |
|
| 8294 | + |
|
| 8295 | +@article{pereverzevMethodQuantitativeAnalysis2015, |
|
| 8296 | + title = {Method for Quantitative Analysis of Nonsense-Mediated {{mRNA}} Decay at the Single Cell Level}, |
|
| 8297 | + author = {Pereverzev, Anton P. and Gurskaya, Nadya G. and Ermakova, Galina V. and Kudryavtseva, Elena I. and Markina, Nadezhda M. and Kotlobay, Alexey A. and Lukyanov, Sergey A. and Zaraisky, Andrey G. and Lukyanov, Konstantin A.}, |
|
| 8298 | + date = {2015-01-12}, |
|
| 8299 | + journaltitle = {Scientific Reports}, |
|
| 8300 | + volume = {5}, |
|
| 8301 | + number = {1}, |
|
| 8302 | + pages = {1--10}, |
|
| 8303 | + issn = {2045-2322}, |
|
| 8304 | + doi = {10.1038/srep07729}, |
|
| 8305 | + url = {https://www.nature.com/articles/srep07729}, |
|
| 8306 | + urldate = {2019-12-21}, |
|
| 8307 | + abstract = {Nonsense-mediated mRNA decay (NMD) is a ubiquitous mechanism of degradation of transcripts with a premature termination codon. NMD eliminates aberrant mRNA species derived from sources of genetic variation such as gene mutations, alternative splicing and DNA rearrangements in immune cells. In addition, recent data suggest that NMD is an important mechanism of global gene expression regulation. Here, we describe new reporters to quantify NMD activity at the single cell level using fluorescent proteins of two colors: green TagGFP2 and far-red Katushka. TagGFP2 was encoded by mRNA targeted to either the splicing-dependent or the long 3'UTR-dependent NMD pathway. Katushka was used as an expression level control. Comparison of the fluorescence intensities of cells expressing these reporters and cells expressing TagGFP2 and Katushka from corresponding control NMD-independent vectors allowed for the assessment of NMD activity at the single cell level using fluorescence microscopy and flow cytometry. The proposed reporter system was successfully tested in several mammalian cell lines and in transgenic Xenopus embryos.}, |
|
| 8308 | + langid = {english}, |
|
| 8309 | + file = {/Users/rmorin/Zotero/storage/N66DDKMD/srep07729.html} |
|
| 8310 | +} |
|
| 8311 | + |
|
| 8312 | +@article{perez-bozaHnRNPA2B1InhibitsExosomal2020, |
|
| 8313 | + title = {{{hnRNPA2B1}} Inhibits the Exosomal Export of {{miR-503}} in Endothelial Cells}, |
|
| 8314 | + author = {Pérez-Boza, Jennifer and Boeckx, Amandine and Lion, Michele and Dequiedt, Franck and Struman, Ingrid}, |
|
| 8315 | + date = {2020-11-01}, |
|
| 8316 | + journaltitle = {Cellular and Molecular Life Sciences}, |
|
| 8317 | + shortjournal = {Cell. Mol. Life Sci.}, |
|
| 8318 | + volume = {77}, |
|
| 8319 | + number = {21}, |
|
| 8320 | + pages = {4413--4428}, |
|
| 8321 | + issn = {1420-9071}, |
|
| 8322 | + doi = {10.1007/s00018-019-03425-6}, |
|
| 8323 | + url = {https://doi.org/10.1007/s00018-019-03425-6}, |
|
| 8324 | + urldate = {2022-10-04}, |
|
| 8325 | + abstract = {The chemotherapeutic drug epirubicin increases the exosomal export of miR-503 in endothelial cells. To understand the mechanisms behind this process, we transfected endothelial cells with miR-503 carrying a biotin tag. Then, we pulled-down the proteins interacting with miR-503 and studied their role in microRNA exosomal export. A total of four different binding partners were identified by mass spectrometry and validated by western blotting and negative controls, among them ANXA2 and hnRNPA2B1. Using knock-down systems combined with pull-down analysis, we determined that epirubicin mediates the export of miR-503 by disrupting the interaction between hnRNPA2B1 and miR-503. Then, both ANXA2 and miR-503 are sorted into exosomes while hnRNPA2B1 is relocated into the nucleus. The combination of these processes culminates in the increased export of miR-503. These results suggest, for the first time, that RNA-binding proteins can negatively regulate the exosomal sorting of microRNAs.}, |
|
| 8326 | + langid = {english}, |
|
| 8327 | + keywords = {EVs,Exosomal export,Exosomes,MicroRNAs,RNA-binding proteins}, |
|
| 8328 | + file = {/Users/rmorin/Zotero/storage/G2QHD9YT/Pérez-Boza et al. - 2020 - hnRNPA2B1 inhibits the exosomal export of miR-503 .pdf} |
|
| 8329 | +} |
|
| 8330 | + |
|
| 8331 | +@article{perteaStringTieEnablesImproved2015, |
|
| 8332 | + title = {{{StringTie}} Enables Improved Reconstruction of a Transcriptome from {{RNA-seq}} Reads}, |
|
| 8333 | + author = {Pertea, Mihaela and Pertea, Geo M. and Antonescu, Corina M. and Chang, Tsung-Cheng and Mendell, Joshua T. and Salzberg, Steven L.}, |
|
| 8334 | + date = {2015-03}, |
|
| 8335 | + journaltitle = {Nature Biotechnology}, |
|
| 8336 | + shortjournal = {Nat Biotechnol}, |
|
| 8337 | + volume = {33}, |
|
| 8338 | + number = {3}, |
|
| 8339 | + pages = {290--295}, |
|
| 8340 | + publisher = {Nature Publishing Group}, |
|
| 8341 | + issn = {1546-1696}, |
|
| 8342 | + doi = {10.1038/nbt.3122}, |
|
| 8343 | + url = {https://www.nature.com/articles/nbt.3122}, |
|
| 8344 | + urldate = {2021-11-30}, |
|
| 8345 | + abstract = {Using a network flow algorithm from optimization theory enables improved assembly of transcriptomes from RNA-seq reads.}, |
|
| 8346 | + issue = {3}, |
|
| 8347 | + langid = {english}, |
|
| 8348 | + keywords = {Genome assembly algorithms,Transcriptomics}, |
|
| 8349 | + annotation = {Bandiera\_abtest: a\\ |
|
| 8350 | +Cg\_type: Nature Research Journals\\ |
|
| 8351 | +Primary\_atype: Research\\ |
|
| 8352 | +Subject\_term: Genome assembly algorithms;Transcriptomics\\ |
|
| 8353 | +Subject\_term\_id: genome-assembly-algorithms;transcriptomics}, |
|
| 8354 | + file = {/Users/rmorin/Zotero/storage/TLEH2R6W/Pertea et al. - 2015 - StringTie enables improved reconstruction of a tra.pdf;/Users/rmorin/Zotero/storage/38G82X5U/nbt.html} |
|
| 8355 | +} |
|
| 8356 | + |
|
| 8357 | +@article{pervouchineIntegrativeTranscriptomicAnalysis2019, |
|
| 8358 | + title = {Integrative Transcriptomic Analysis Suggests New Autoregulatory Splicing Events Coupled with Nonsense-Mediated {{mRNA}} Decay}, |
|
| 8359 | + author = {Pervouchine, Dmitri and Popov, Yaroslav and Berry, Andy and Borsari, Beatrice and Frankish, Adam and Guigó, Roderic}, |
|
| 8360 | + date = {2019-04-06}, |
|
| 8361 | + journaltitle = {Nucleic Acids Research}, |
|
| 8362 | + shortjournal = {Nucleic Acids Res.}, |
|
| 8363 | + volume = {47}, |
|
| 8364 | + number = {10}, |
|
| 8365 | + eprint = {30916337}, |
|
| 8366 | + eprinttype = {pmid}, |
|
| 8367 | + pages = {5293--5306}, |
|
| 8368 | + issn = {1362-4962}, |
|
| 8369 | + doi = {10.1093/nar/gkz193}, |
|
| 8370 | + abstract = {Nonsense-mediated decay (NMD) is a eukaryotic mRNA surveillance system that selectively degrades transcripts with premature termination codons (PTC). Many RNA-binding proteins (RBP) regulate their expression levels by a negative feedback loop, in which RBP binds its own pre-mRNA and causes alternative splicing to introduce a PTC. We present a bioinformatic analysis integrating three data sources, eCLIP assays for a large RBP panel, shRNA inactivation of NMD pathway, and shRNA-depletion of RBPs followed by RNA-seq, to identify novel such autoregulatory feedback loops. We show that RBPs frequently bind their own pre-mRNAs, their exons respond prominently to NMD pathway disruption, and that the responding exons are enriched with nearby eCLIP peaks. We confirm previously proposed models of autoregulation in SRSF7 and U2AF1 genes and present two novel models, in which (i) SFPQ binds its mRNA and promotes switching to an alternative distal 3'-UTR that is targeted by NMD, and (ii) RPS3 binding activates a poison 5'-splice site in its pre-mRNA that leads to a frame shift and degradation by NMD. We also suggest specific splicing events that could be implicated in autoregulatory feedback loops in RBM39, HNRNPM, and U2AF2 genes. The results are available through a UCSC Genome Browser track hub.}, |
|
| 8371 | + langid = {english}, |
|
| 8372 | + pmcid = {PMC6547761}, |
|
| 8373 | + keywords = {3' Untranslated Regions,Alternative Splicing,Codon Nonsense,Computational Biology,Exons,Frameshift Mutation,Heterogeneous-Nuclear Ribonucleoprotein Group M,Humans,Nonsense Mediated mRNA Decay,Nuclear Proteins,RNA Messenger,RNA Precursors,RNA Small Interfering,RNA Splicing,RNA-Binding Proteins,Serine-Arginine Splicing Factors,Spliceosomes,Splicing Factor U2AF,Transcriptome} |
|
| 8374 | +} |
|
| 8375 | + |
|
| 8376 | +@article{petereitPipelineAutomationSnakemake2022, |
|
| 8377 | + title = {Pipeline {{Automation}} via {{Snakemake}}}, |
|
| 8378 | + author = {Petereit, Jakob}, |
|
| 8379 | + date = {2022}, |
|
| 8380 | + journaltitle = {Methods in Molecular Biology (Clifton, N.J.)}, |
|
| 8381 | + shortjournal = {Methods Mol Biol}, |
|
| 8382 | + volume = {2443}, |
|
| 8383 | + eprint = {35037206}, |
|
| 8384 | + eprinttype = {pmid}, |
|
| 8385 | + pages = {181--196}, |
|
| 8386 | + issn = {1940-6029}, |
|
| 8387 | + doi = {10.1007/978-1-0716-2067-0_9}, |
|
| 8388 | + abstract = {With third generation DNA sequencing and a general reduction of sequencing costs, the production of bioinformatic data has become easier than ever. Several pipeline automation tools have emerged to ease data processing through a multitude of steps. Here, we describe the setup and use of Snakemake, a pipeline automation tool derived from GNU MAKE.}, |
|
| 8389 | + langid = {english}, |
|
| 8390 | + keywords = {Bioinformatics,Bowtie2 alignments,fastQC,Pipeline,Snakemake,Trimming} |
|
| 8391 | +} |
|
| 8392 | + |
|
| 8393 | +@article{petersonElucidatingFalsenegativeMYC2019, |
|
| 8394 | + title = {Elucidating a False-Negative {{MYC}} Break-Apart Fluorescence in Situ Hybridization Probe Study by next-Generation Sequencing in a Patient with High-Grade {{B-cell}} Lymphoma with {{IGH}}/{{MYC}} and {{IGH}}/{{BCL2}} Rearrangements}, |
|
| 8395 | + author = {Peterson, Jess F. and Pitel, Beth A. and Smoley, Stephanie A. and Vasmatzis, George and Smadbeck, James B. and Greipp, Patricia T. and Ketterling, Rhett P. and Macon, William R. and Baughn, Linda B.}, |
|
| 8396 | + date = {2019-06}, |
|
| 8397 | + journaltitle = {Cold Spring Harbor Molecular Case Studies}, |
|
| 8398 | + shortjournal = {Cold Spring Harb Mol Case Stud}, |
|
| 8399 | + volume = {5}, |
|
| 8400 | + number = {3}, |
|
| 8401 | + eprint = {31160360}, |
|
| 8402 | + eprinttype = {pmid}, |
|
| 8403 | + pages = {a004077}, |
|
| 8404 | + issn = {2373-2873}, |
|
| 8405 | + doi = {10.1101/mcs.a004077}, |
|
| 8406 | + abstract = {The identification of MYC rearrangements in several mature B-cell neoplasms is critical for diagnostic and prognostic purposes. Commercially available fluorescence in situ hybridization (FISH) probe sets, including IGH/MYC dual-color dual-fusion (D-FISH) and MYC break-apart probes (BAPs), serve as the primary methodology utilized to detect MYC rearrangements. However, performing either IGH/MYC D-FISH or MYC BAP FISH studies in isolation has been reported to result in false-negative results because of the complex nature of 8q24 rearrangements involving the MYC gene region. We report a 60-yr-old male with newly diagnosed high-grade B-cell lymphoma with a negative MYC BAP study, but with positive BCL2 and BCL6 BAP studies. Per our current laboratory algorithm to concurrently interrogate the MYC gene region with both MYC BAP and IGH/MYC D-FISH probe sets, we performed IGH/MYC D-FISH studies and detected an IGH/MYC fusion. To further characterize the discrepant MYC results obtained by FISH, a next-generation sequencing strategy, mate-pair sequencing (MPseq), was performed and revealed a small insertion (∼200 kb) of the IGH locus downstream from the MYC gene that was undetectable by MYC BAP studies. This case highlights the importance of utilizing both IGH/MYC D-FISH and MYC BAP sets to detect potential cryptic MYC rearrangements and also demonstrates the power of MPseq to characterize complex structural rearrangements and copy-number abnormalities unappreciable by FISH.}, |
|
| 8407 | + langid = {english}, |
|
| 8408 | + pmcid = {PMC6549546}, |
|
| 8409 | + keywords = {B-cell lymphoma} |
|
| 8410 | +} |
|
| 8411 | + |
|
| 8412 | +@article{pham-ledardHighFrequencyClinical, |
|
| 8413 | + title = {High Frequency and Clinical Prognostic Value of {{MYD88 L265P}} Mutation in Primary Cutaneous Diffuse Large {{B-cell}} Lymphoma, Leg-Type.}, |
|
| 8414 | + author = {Pham-Ledard, Anne and Beylot-Barry, Marie and Barbe, Coralie and Leduc, Marion and Petrella, Tony and Vergier, Béatrice and Martinez, Fabian and Cappellen, David and Merlio, Jean-Philippe and Grange, Florent}, |
|
| 8415 | + journaltitle = {JAMA dermatology}, |
|
| 8416 | + volume = {150}, |
|
| 8417 | + number = {11}, |
|
| 8418 | + pages = {1173--1179}, |
|
| 8419 | + keywords = {nosource} |
|
| 8420 | +} |
|
| 8421 | + |
|
| 8422 | +@article{pinol-romaShuttlingPremRNABinding1992, |
|
| 8423 | + title = {Shuttling of Pre-{{mRNA}} Binding Proteins between Nucleus and Cytoplasm}, |
|
| 8424 | + author = {Piñol-Roma, S. and Dreyfuss, G.}, |
|
| 8425 | + date = {1992-02-20}, |
|
| 8426 | + journaltitle = {Nature}, |
|
| 8427 | + shortjournal = {Nature}, |
|
| 8428 | + volume = {355}, |
|
| 8429 | + number = {6362}, |
|
| 8430 | + eprint = {1371331}, |
|
| 8431 | + eprinttype = {pmid}, |
|
| 8432 | + pages = {730--732}, |
|
| 8433 | + issn = {0028-0836}, |
|
| 8434 | + doi = {10.1038/355730a0}, |
|
| 8435 | + abstract = {RNA polymerase II transcripts, heterogeneous nuclear RNAs (hnRNAs), associate in the nucleus with specific proteins that bind premessenger RNA (hnRNP proteins) and with small nuclear ribonucleoprotein particles (snRNPs). These hnRNA-hnRNP-snRNP complexes assemble on nascent transcripts and hnRNA is processed to mRNA in them. HnRNP proteins have been localized to the nucleoplasm and their functions were presumed to be limited to nuclear events in mRNA biogenesis. It was proposed that an exchange of hnRNP for mRNA-binding proteins accompanies transport of mRNA from the nucleus to the cytoplasm. We show here that several of the abundant hnRNP proteins, including A1, shuttle between the nucleus and the cytoplasm. HnRNP proteins may thus also have cytoplasmic functions. Furthermore, when in the cytoplasm, A1 is bound to mRNA and RNA polymerase II transcription is necessary before it can return to the nucleus. We propose that the cytoplasmic ribonucleoprotein complex of mRNA with hnRNP proteins is the substrate of nuclear-cytoplasmic transport of mRNA.}, |
|
| 8436 | + langid = {english}, |
|
| 8437 | + keywords = {Animals,Cell Nucleus,Cytoplasm,Dactinomycin,DNA Polymerase II,Fluorescent Antibody Technique,HeLa Cells,Heterogeneous Nuclear Ribonucleoprotein A1,Heterogeneous-Nuclear Ribonucleoprotein Group A-B,Heterogeneous-Nuclear Ribonucleoproteins,Humanities and Social Sciences,Humans,multidisciplinary,Poly A,Ribonucleoproteins,RNA,RNA Messenger,RNA Splicing,Science,Ultraviolet Rays,Xenopus laevis}, |
|
| 8438 | + file = {/Users/rmorin/Zotero/storage/TTLEN8WL/Piñol-Roma and Dreyfuss - 1992 - Shuttling of pre-mRNA binding proteins between nuc.pdf;/Users/rmorin/Zotero/storage/3NN594FP/355730a0.html} |
|
| 8439 | +} |
|
| 8440 | + |
|
| 8441 | +@article{plinerCiceroPredictsCisRegulatory2018, |
|
| 8442 | + title = {Cicero {{Predicts}} Cis-{{Regulatory DNA Interactions}} from {{Single-Cell Chromatin Accessibility Data}}}, |
|
| 8443 | + author = {Pliner, Hannah A. and Packer, Jonathan S. and McFaline-Figueroa, José L. and Cusanovich, Darren A. and Daza, Riza M. and Aghamirzaie, Delasa and Srivatsan, Sanjay and Qiu, Xiaojie and Jackson, Dana and Minkina, Anna and Adey, Andrew C. and Steemers, Frank J. and Shendure, Jay and Trapnell, Cole}, |
|
| 8444 | + date = {2018-09-06}, |
|
| 8445 | + journaltitle = {Molecular Cell}, |
|
| 8446 | + shortjournal = {Mol Cell}, |
|
| 8447 | + volume = {71}, |
|
| 8448 | + number = {5}, |
|
| 8449 | + eprint = {30078726}, |
|
| 8450 | + eprinttype = {pmid}, |
|
| 8451 | + pages = {858-871.e8}, |
|
| 8452 | + issn = {1097-4164}, |
|
| 8453 | + doi = {10.1016/j.molcel.2018.06.044}, |
|
| 8454 | + abstract = {Linking regulatory DNA elements to their target genes, which may be located hundreds of kilobases away, remains challenging. Here, we introduce Cicero, an algorithm that identifies co-accessible pairs of DNA elements using single-cell chromatin accessibility data and so connects regulatory elements to their putative target genes. We apply Cicero to investigate how dynamically accessible elements orchestrate gene regulation in differentiating myoblasts. Groups of Cicero-linked regulatory elements meet criteria of "chromatin hubs"-they are enriched for physical proximity, interact with a common set of transcription factors, and undergo coordinated changes in histone marks that are predictive of changes in gene expression. Pseudotemporal analysis revealed that most DNA elements remain in chromatin hubs throughout differentiation. A subset of elements bound by MYOD1 in myoblasts exhibit early opening in a PBX1- and MEIS1-dependent manner. Our strategy can be applied to dissect the architecture, sequence determinants, and mechanisms of cis-regulation on a genome-wide scale.}, |
|
| 8455 | + langid = {english}, |
|
| 8456 | + pmcid = {PMC6582963}, |
|
| 8457 | + keywords = {Adolescent,ATAC-seq,Cell Differentiation,Chromatin,chromatin accessibility,Chromatin Assembly and Disassembly,co-accessibility,DNA,Enhancer Elements Genetic,Female,Gene Expression Regulation,gene regulation,Genes Homeobox,Histones,Humans,machine learning,myoblast differentiation,Myoblasts,single-cell,Transcription Factors}, |
|
| 8458 | + file = {/Users/rmorin/Zotero/storage/BZQNU4XJ/Pliner et al. - 2018 - Cicero Predicts cis-Regulatory DNA Interactions fr.pdf} |
|
| 8459 | +} |
|
| 8460 | + |
|
| 8461 | +@article{podolskyEvaluationMachineLearning2016, |
|
| 8462 | + title = {Evaluation of {{Machine Learning Algorithm Utilization}} for {{Lung Cancer Classification Based}} on {{Gene Expression Levels}}}, |
|
| 8463 | + author = {Podolsky, Maxim D. and Barchuk, Anton A. and Kuznetcov, Vladimir I. and Gusarova, Natalia F. and Gaidukov, Vadim S. and Tarakanov, Segrey A.}, |
|
| 8464 | + date = {2016}, |
|
| 8465 | + journaltitle = {Asian Pacific journal of cancer prevention: APJCP}, |
|
| 8466 | + shortjournal = {Asian Pac. J. Cancer Prev.}, |
|
| 8467 | + volume = {17}, |
|
| 8468 | + number = {2}, |
|
| 8469 | + eprint = {26925688}, |
|
| 8470 | + eprinttype = {pmid}, |
|
| 8471 | + pages = {835--838}, |
|
| 8472 | + issn = {2476-762X}, |
|
| 8473 | + doi = {10.7314/apjcp.2016.17.2.835}, |
|
| 8474 | + abstract = {BACKGROUND: Lung cancer remains one of the most common cancers in the world, both in terms of new cases (about 13\% of total per year) and deaths (nearly one cancer death in five), because of the high case fatality. Errors in lung cancer type or malignant growth determination lead to degraded treatment efficacy, because anticancer strategy depends on tumor morphology. MATERIALS AND METHODS: We have made an attempt to evaluate effectiveness of machine learning algorithms in the task of lung cancer classification based on gene expression levels. We processed four publicly available data sets. The Dana-Farber Cancer Institute data set contains 203 samples and the task was to classify four cancer types and sound tissue samples. With the University of Michigan data set of 96 samples, the task was to execute a binary classification of adenocarcinoma and non-neoplastic tissues. The University of Toronto data set contains 39 samples and the task was to detect recurrence, while with the Brigham and Women's Hospital data set of 181 samples it was to make a binary classification of malignant pleural mesothelioma and adenocarcinoma. We used the k-nearest neighbor algorithm (k=1, k=5, k=10), naive Bayes classifier with assumption of both a normal distribution of attributes and a distribution through histograms, support vector machine and C4.5 decision tree. Effectiveness of machine learning algorithms was evaluated with the Matthews correlation coefficient. RESULTS: The support vector machine method showed best results among data sets from the Dana-Farber Cancer Institute and Brigham and Women's Hospital. All algorithms with the exception of the C4.5 decision tree showed maximum potential effectiveness in the University of Michigan data set. However, the C4.5 decision tree showed best results for the University of Toronto data set. CONCLUSIONS: Machine learning algorithms can be used for lung cancer morphology classification and similar tasks based on gene expression level evaluation.}, |
|
| 8475 | + langid = {english}, |
|
| 8476 | + keywords = {Adenocarcinoma,Algorithms,Biomarkers Tumor,Carcinoma Squamous Cell,Case-Control Studies,Databases Factual,Decision Trees,Gene Expression Profiling,Humans,Lung Neoplasms,Machine Learning,nosource,Small Cell Lung Carcinoma,Support Vector Machine} |
|
| 8477 | +} |
|
| 8478 | + |
|
| 8479 | +@article{ponMEF2BMutationsNonHodgkin2015, |
|
| 8480 | + title = {{{MEF2B}} Mutations in Non-{{Hodgkin}} Lymphoma Dysregulate Cell Migration by Decreasing {{MEF2B}} Target Gene Activation}, |
|
| 8481 | + author = {Pon, Julia R. and Wong, Jackson and Saberi, Saeed and Alder, Olivia and Moksa, Michelle and Grace Cheng, S.-W. and Morin, Gregg B. and Hoodless, Pamela A. and Hirst, Martin and Marra, Marco A.}, |
|
| 8482 | + date = {2015-08-06}, |
|
| 8483 | + journaltitle = {Nature Communications}, |
|
| 8484 | + volume = {6}, |
|
| 8485 | + number = {1}, |
|
| 8486 | + pages = {1--15}, |
|
| 8487 | + issn = {2041-1723}, |
|
| 8488 | + doi = {10.1038/ncomms8953}, |
|
| 8489 | + url = {https://www.nature.com/articles/ncomms8953}, |
|
| 8490 | + urldate = {2019-12-21}, |
|
| 8491 | + abstract = {Mutations in the transcription factor MEF2B are found in diffuse large B-cell lymphoma. In this study, the authors map the DNA-binding sites of the transcription factor in cells in vitroand find that the mutations decrease the ability of MEF2B to activate transcription.}, |
|
| 8492 | + langid = {english}, |
|
| 8493 | + file = {/Users/rmorin/Zotero/storage/Q24PTBH5/ncomms8953.html} |
|
| 8494 | +} |
|
| 8495 | + |
|
| 8496 | +@article{pontMRNADecayFactor2012, |
|
| 8497 | + title = {{{mRNA Decay Factor AUF1 Maintains Normal Aging}}, {{Telomere Maintenance}}, and {{Suppression}} of {{Senescence}} by {{Activation}} of {{Telomerase Transcription}}}, |
|
| 8498 | + author = {Pont, Adam R. and Sadri, Navid and Hsiao, Susan J. and Smith, Susan and Schneider, Robert J.}, |
|
| 8499 | + date = {2012-07-13}, |
|
| 8500 | + journaltitle = {Molecular Cell}, |
|
| 8501 | + shortjournal = {Molecular Cell}, |
|
| 8502 | + volume = {47}, |
|
| 8503 | + number = {1}, |
|
| 8504 | + eprint = {22633954}, |
|
| 8505 | + eprinttype = {pmid}, |
|
| 8506 | + pages = {5--15}, |
|
| 8507 | + publisher = {Elsevier}, |
|
| 8508 | + issn = {1097-2765}, |
|
| 8509 | + doi = {10.1016/j.molcel.2012.04.019}, |
|
| 8510 | + url = {https://www.cell.com/molecular-cell/abstract/S1097-2765(12)00341-3}, |
|
| 8511 | + urldate = {2022-09-27}, |
|
| 8512 | + langid = {english}, |
|
| 8513 | + file = {/Users/rmorin/Zotero/storage/MAXUCVCV/Pont et al. - 2012 - mRNA Decay Factor AUF1 Maintains Normal Aging, Tel.pdf;/Users/rmorin/Zotero/storage/2JSKNTBU/S1097-2765(12)00341-3.html} |
|
| 8514 | +} |
|
| 8515 | + |
|
| 8516 | +@article{prietoRNARegulatorsLeukemia2020, |
|
| 8517 | + title = {{{RNA Regulators}} in {{Leukemia}} and {{Lymphoma}}}, |
|
| 8518 | + author = {Prieto, Camila and Kharas, Michael G.}, |
|
| 8519 | + date = {2020-05}, |
|
| 8520 | + journaltitle = {Cold Spring Harbor Perspectives in Medicine}, |
|
| 8521 | + shortjournal = {Cold Spring Harb Perspect Med}, |
|
| 8522 | + volume = {10}, |
|
| 8523 | + number = {5}, |
|
| 8524 | + eprint = {31615866}, |
|
| 8525 | + eprinttype = {pmid}, |
|
| 8526 | + pages = {a034967}, |
|
| 8527 | + issn = {2157-1422}, |
|
| 8528 | + doi = {10.1101/cshperspect.a034967}, |
|
| 8529 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7197419/}, |
|
| 8530 | + urldate = {2022-09-25}, |
|
| 8531 | + abstract = {Posttranscriptional regulation of mRNA is a powerful and tightly controlled process in which cells command the integrity, diversity, and abundance of their protein products. RNA-binding proteins (RBPs) are the principal players that control many intermediary steps of posttranscriptional regulation. Recent advances in this field have discovered the importance of RBPs in hematological diseases. Herein we will review a number of RBPs that have been determined to play critical functions in leukemia and lymphoma. Furthermore, we will discuss the potential therapeutic strategies that are currently being studied to specifically target RBPs in these diseases.}, |
|
| 8532 | + pmcid = {PMC7197419}, |
|
| 8533 | + file = {/Users/rmorin/Zotero/storage/T8ANLPTE/Prieto and Kharas - 2020 - RNA Regulators in Leukemia and Lymphoma.pdf} |
|
| 8534 | +} |
|
| 8535 | + |
|
| 8536 | +@article{quesadaExomeSequencingIdentifies2011, |
|
| 8537 | + title = {Exome Sequencing Identifies Recurrent Mutations of the Splicing Factor {{SF3B1}} Gene in Chronic Lymphocytic Leukemia}, |
|
| 8538 | + author = {Quesada, Víctor and Conde, Laura and Villamor, Neus and Ordóñez, Gonzalo R. and Jares, Pedro and Bassaganyas, Laia and Ramsay, Andrew J. and Beà, Sílvia and Pinyol, Magda and Martínez-Trillos, Alejandra and López-Guerra, Mónica and Colomer, Dolors and Navarro, Alba and Baumann, Tycho and Aymerich, Marta and Rozman, María and Delgado, Julio and Giné, Eva and Hernández, Jesús M. and González-Díaz, Marcos and Puente, Diana A. and Velasco, Gloria and Freije, José M. P. and Tubío, José M. C. and Royo, Romina and Gelpí, Josep L. and Orozco, Modesto and Pisano, David G. and Zamora, Jorge and Vázquez, Miguel and Valencia, Alfonso and Himmelbauer, Heinz and Bayés, Mónica and Heath, Simon and Gut, Marta and Gut, Ivo and Estivill, Xavier and López-Guillermo, Armando and Puente, Xose S. and Campo, Elías and López-Otín, Carlos}, |
|
| 8539 | + date = {2011-12-11}, |
|
| 8540 | + journaltitle = {Nature Genetics}, |
|
| 8541 | + shortjournal = {Nat. Genet.}, |
|
| 8542 | + volume = {44}, |
|
| 8543 | + number = {1}, |
|
| 8544 | + eprint = {22158541}, |
|
| 8545 | + eprinttype = {pmid}, |
|
| 8546 | + pages = {47--52}, |
|
| 8547 | + issn = {1546-1718}, |
|
| 8548 | + doi = {10.1038/ng.1032}, |
|
| 8549 | + abstract = {Here we perform whole-exome sequencing of samples from 105 individuals with chronic lymphocytic leukemia (CLL), the most frequent leukemia in adults in Western countries. We found 1,246 somatic mutations potentially affecting gene function and identified 78 genes with predicted functional alterations in more than one tumor sample. Among these genes, SF3B1, encoding a subunit of the spliceosomal U2 small nuclear ribonucleoprotein (snRNP), is somatically mutated in 9.7\% of affected individuals. Further analysis in 279 individuals with CLL showed that SF3B1 mutations were associated with faster disease progression and poor overall survival. This work provides the first comprehensive catalog of somatic mutations in CLL with relevant clinical correlates and defines a large set of new genes that may drive the development of this common form of leukemia. The results reinforce the idea that targeting several well-known genetic pathways, including mRNA splicing, could be useful in the treatment of CLL and other malignancies.}, |
|
| 8550 | + langid = {english}, |
|
| 8551 | + keywords = {Amino Acid Sequence,Disease Progression,Exome,Humans,Leukemia Lymphocytic Chronic B-Cell,Mutation,Phosphoproteins,Ribonucleoprotein U2 Small Nuclear,RNA Splicing Factors,Sequence Alignment} |
|
| 8552 | +} |
|
| 8553 | + |
|
| 8554 | +@article{rahbariUnderstandingGenomicStructure2017, |
|
| 8555 | + title = {Understanding the {{Genomic Structure}} of {{Copy}}‐{{Number Variation}} of the {{Low}}‐{{Affinity Fcγ Receptor Region Allows Confirmation}} of the {{Association}} of {{FCGR3B Deletion}} with {{Rheumatoid Arthritis}}}, |
|
| 8556 | + author = {Rahbari, Raheleh and Zuccherato, Luciana W and Tischler, German and Chihota, Belinda and Ozturk, Hasret and Saleem, Sara and Tarazona‐Santos, Eduardo and Machado, Lee R and Hollox, Edward J}, |
|
| 8557 | + date = {2017}, |
|
| 8558 | + journaltitle = {Human Mutation}, |
|
| 8559 | + volume = {38}, |
|
| 8560 | + number = {4}, |
|
| 8561 | + eprint = {27995740}, |
|
| 8562 | + eprinttype = {pmid}, |
|
| 8563 | + pages = {390--399}, |
|
| 8564 | + issn = {1098-1004}, |
|
| 8565 | + doi = {10.1002/humu.23159}, |
|
| 8566 | + url = {http://dx.doi.org/10.1002/humu.23159}, |
|
| 8567 | + abstract = {Fcγ receptors are a family of cell–surface receptors that are expressed by a host of different innate and adaptive immune cells, and mediate inflammatory responses by binding the Fc portion of immunoglobulin G. In humans, five low-affinity receptors are encoded by the genes FCGR2A, FCGR2B, FCGR2C, FCGR3A, and FCGR3B, which are located in an 82.5-kb segmental tandem duplication on chromosome 1q23.3, which shows extensive copy-number variation (CNV). Deletions of FCGR3B have been suggested to increase the risk of inflammatory diseases such as systemic lupus erythematosus and rheumatoid arthritis (RA). In this study, we identify the deletion breakpoints of FCGR3B deletion alleles in the UK population and endogamous native American population, and show that some but not all alleles are likely to be identical-by-descent. We also localize a duplication breakpoint, confirming that the mechanism of CNV generation is nonallelic homologous recombination, and identify several alleles with gene conversion events using fosmid sequencing data. We use information on the structure of the deletion alleles to distinguish FCGR3B deletions from FCGR3A deletions in whole-genome array comparative genomic hybridization (aCGH) data. Reanalysis of published aCGH data using this approach supports association of FCGR3B deletion with increased risk of RA in a large cohort of 1,982 cases and 3,271 controls (odds ratio 1.61, P = 2.9×10−3).}, |
|
| 8568 | + keywords = {nosource} |
|
| 8569 | +} |
|
| 8570 | + |
|
| 8571 | +@article{raiCoordinatedExpressionMicroRNA1552008, |
|
| 8572 | + title = {Coordinated Expression of {{microRNA-155}} and Predicted Target Genes in Diffuse Large {{B-cell}} Lymphoma.}, |
|
| 8573 | + author = {Rai, Deepak and Karanti, Shailaja and Jung, Inkyung and Dahia, Patricia L M and Aguiar, Ricardo C T}, |
|
| 8574 | + date = {2008-02}, |
|
| 8575 | + journaltitle = {Cancer genetics and cytogenetics}, |
|
| 8576 | + volume = {181}, |
|
| 8577 | + number = {1}, |
|
| 8578 | + pages = {8--15}, |
|
| 8579 | + keywords = {nosource} |
|
| 8580 | +} |
|
| 8581 | + |
|
| 8582 | +@article{ramanathanMRNACappingBiological2016, |
|
| 8583 | + title = {{{mRNA}} Capping: Biological Functions and Applications}, |
|
| 8584 | + shorttitle = {{{mRNA}} Capping}, |
|
| 8585 | + author = {Ramanathan, Anand and Robb, G. Brett and Chan, Siu-Hong}, |
|
| 8586 | + date = {2016-09-19}, |
|
| 8587 | + journaltitle = {Nucleic Acids Research}, |
|
| 8588 | + shortjournal = {Nucleic Acids Res}, |
|
| 8589 | + volume = {44}, |
|
| 8590 | + number = {16}, |
|
| 8591 | + eprint = {27317694}, |
|
| 8592 | + eprinttype = {pmid}, |
|
| 8593 | + pages = {7511--7526}, |
|
| 8594 | + issn = {1362-4962}, |
|
| 8595 | + doi = {10.1093/nar/gkw551}, |
|
| 8596 | + abstract = {The 5' m7G cap is an evolutionarily conserved modification of eukaryotic mRNA. Decades of research have established that the m7G cap serves as a unique molecular module that recruits cellular proteins and mediates cap-related biological functions such as pre-mRNA processing, nuclear export and cap-dependent protein synthesis. Only recently has the role of the cap 2'O methylation as an identifier of self RNA in the innate immune system against foreign RNA has become clear. The discovery of the cytoplasmic capping machinery suggests a novel level of control network. These new findings underscore the importance of a proper cap structure in the synthesis of functional messenger RNA. In this review, we will summarize the current knowledge of the biological roles of mRNA caps in eukaryotic cells. We will also discuss different means that viruses and their host cells use to cap their RNA and the application of these capping machineries to synthesize functional mRNA. Novel applications of RNA capping enzymes in the discovery of new RNA species and sequencing the microbiome transcriptome will also be discussed. We will end with a summary of novel findings in RNA capping and the questions these findings pose.}, |
|
| 8597 | + langid = {english}, |
|
| 8598 | + pmcid = {PMC5027499}, |
|
| 8599 | + keywords = {Animals,Eukaryotic Cells,Humans,Models Molecular,Nucleotidyltransferases,RNA Caps,RNA Viral}, |
|
| 8600 | + file = {/Users/rmorin/Zotero/storage/IRKHRHBY/Ramanathan et al. - 2016 - mRNA capping biological functions and application.pdf} |
|
| 8601 | +} |
|
| 8602 | + |
|
| 8603 | +@article{rauchHeterogeneousNuclearRibonucleoprotein2010, |
|
| 8604 | + title = {Heterogeneous Nuclear Ribonucleoprotein {{H}} Blocks {{MST2-mediated}} Apoptosis in Cancer Cells by Regulating {{A-Raf}} Transcription}, |
|
| 8605 | + author = {Rauch, Jens and O'Neill, Eric and Mack, Brigitte and Matthias, Christoph and Munz, Markus and Kolch, Walter and Gires, Olivier}, |
|
| 8606 | + date = {2010-02-15}, |
|
| 8607 | + journaltitle = {Cancer Research}, |
|
| 8608 | + shortjournal = {Cancer Res.}, |
|
| 8609 | + volume = {70}, |
|
| 8610 | + number = {4}, |
|
| 8611 | + eprint = {20145135}, |
|
| 8612 | + eprinttype = {pmid}, |
|
| 8613 | + pages = {1679--1688}, |
|
| 8614 | + issn = {1538-7445}, |
|
| 8615 | + doi = {10.1158/0008-5472.CAN-09-2740}, |
|
| 8616 | + abstract = {A-Raf belongs to the family of oncogenic Raf kinases that are involved in mitogenic signaling by activating the mitogen-activated protein (MAP)/extracellular signal-regulated kinase (ERK) kinase (MEK)-ERK pathway. Low kinase activity of A-Raf toward MEK suggested that A-Raf might have alternative functions. Here, we show that A-Raf prevents cancer cell apoptosis contingent on the expression of the heterogeneous nuclear ribonucleoprotein H (hnRNP H) splice factor, which is required for the correct transcription and expression of a-raf. Apoptosis was prevented by A-Raf through sequestration and inactivation of the proapoptotic MST2 kinase. Small interfering RNA-mediated knockdown of hnRNP H or A-Raf resulted in MST2-dependent apoptosis. In contrast, enforced expression of either hnRNP H or A-Raf partially counteracted apoptosis induced by etoposide. In vivo expression studies of colon specimens corroborated the overexpression of hnRNP H in malignant tissues and its correlation with A-Raf levels. Our findings define a novel mechanism that is usurped in tumor cells to escape naturally imposed apoptotic signals.}, |
|
| 8617 | + langid = {english}, |
|
| 8618 | + pmcid = {PMC2880479}, |
|
| 8619 | + keywords = {Apoptosis,Cells Cultured,Gene Expression Regulation Neoplastic,HCT116 Cells,HeLa Cells,Heterogeneous-Nuclear Ribonucleoprotein Group F-H,Humans,Models Biological,Neoplasms,Protein Binding,Protein-Serine-Threonine Kinases,Proto-Oncogene Proteins A-raf,RNA Small Interfering,Signal Transduction,Transcription Genetic} |
|
| 8620 | +} |
|
| 8621 | + |
|
| 8622 | +@article{rauchInterferonRegulatoryFactor2020, |
|
| 8623 | + title = {Interferon Regulatory Factor 4 as a Therapeutic Target in Adult {{T-cell}} Leukemia Lymphoma}, |
|
| 8624 | + author = {Rauch, Daniel A. and Olson, Sydney L. and Harding, John C. and Sundaramoorthi, Hemalatha and Kim, Youngsoo and Zhou, Tianyuan and MacLeod, A. Robert and Challen, Grant and Ratner, Lee}, |
|
| 8625 | + date = {2020-08-28}, |
|
| 8626 | + journaltitle = {Retrovirology}, |
|
| 8627 | + shortjournal = {Retrovirology}, |
|
| 8628 | + volume = {17}, |
|
| 8629 | + eprint = {32859220}, |
|
| 8630 | + eprinttype = {pmid}, |
|
| 8631 | + pages = {27}, |
|
| 8632 | + issn = {1742-4690}, |
|
| 8633 | + doi = {10.1186/s12977-020-00535-z}, |
|
| 8634 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7456374/}, |
|
| 8635 | + urldate = {2021-11-30}, |
|
| 8636 | + abstract = {Background Adult T-cell leukemia lymphoma (ATLL) is a chemotherapy-resistant malignancy with a median survival of less than one year that will afflict between one hundred thousand and one million individuals worldwide who are currently infected with human T-cell leukemia virus type 1. Recurrent somatic mutations in host genes have exposed the T-cell receptor pathway through nuclear factor κB to interferon regulatory factor 4 (IRF4) as an essential driver for this malignancy. We sought to determine if IRF4 represents a therapeutic target for ATLL and to identify downstream effectors and biomarkers of IRF4 signaling in vivo. Results ATLL cell lines, particularly Tax viral oncoprotein-negative cell lines, that most closely resemble ATLL in humans, were sensitive to dose- and time-dependent inhibition by a next-generation class of IRF4 antisense oligonucleotides (ASOs) that employ constrained ethyl residues that mediate RNase H-dependent RNA degradation. ATLL cell lines were also sensitive to lenalidomide, which repressed IRF4 expression. Both ASOs and lenalidomide inhibited ATLL proliferation in vitro and in vivo. To identify biomarkers of IRF4-mediated CD4\,+\,T-cell expansion in vivo, transcriptomic analysis identified several genes that encode key regulators of ATLL, including interleukin 2 receptor subunits α and β, KIT ligand, cytotoxic T-lymphocyte-associated protein 4, and thymocyte selection-associated high mobility group protein TOX 2. Conclusions These data support the pursuit of IRF4 as a therapeutic target in ATLL with the use of either ASOs or lenalidomide.}, |
|
| 8637 | + pmcid = {PMC7456374}, |
|
| 8638 | + file = {/Users/rmorin/Zotero/storage/7RAE8HEU/Rauch et al. - 2020 - Interferon regulatory factor 4 as a therapeutic ta.pdf} |
|
| 8639 | +} |
|
| 8640 | + |
|
| 8641 | +@online{Rbfox1LymphomaGoogle, |
|
| 8642 | + title = {Rbfox1 Lymphoma - {{Google Search}}}, |
|
| 8643 | + url = {https://www.google.com/search?q=rbfox1+lymphoma&rlz=1C5CHFA_enCA1020CA1020&oq=rbfox1+lymphoma&aqs=chrome..69i57j33i160l2.2521j0j4&sourceid=chrome&ie=UTF-8}, |
|
| 8644 | + urldate = {2022-10-27}, |
|
| 8645 | + file = {/Users/rmorin/Zotero/storage/5S5KPWS8/search.html} |
|
| 8646 | +} |
|
| 8647 | + |
|
| 8648 | +@article{reddyGeneticFunctionalDrivers2017, |
|
| 8649 | + title = {Genetic and {{Functional Drivers}} of {{Diffuse Large B Cell Lymphoma}}.}, |
|
| 8650 | + author = {Reddy, Anupama and Zhang, Jenny and Davis, Nicholas S and Moffitt, Andrea B and Love, Cassandra L and Waldrop, Alexander and Leppa, Sirpa and Pasanen, Annika and Meriranta, Leo and Karjalainen-Lindsberg, Marja-Liisa and Nørgaard, Peter and Pedersen, Mette and Gang, Anne O and Høgdall, Estrid and Heavican, Tayla B and Lone, Waseem and Iqbal, Javeed and Qin, Qiu and Li, Guojie and Kim, So Young and Healy, Jane and Richards, Kristy L and Fedoriw, Yuri and Bernal-Mizrachi, Leon and Koff, Jean L and Staton, Ashley D and Flowers, Christopher R and Paltiel, Ora and Goldschmidt, Neta and Calaminici, Maria and Clear, Andrew and Gribben, John and Nguyen, Evelyn and Czader, Magdalena B and Ondrejka, Sarah L and Collie, Angela and Hsi, Eric D and Tse, Eric and Au-Yeung, Rex K H and Kwong, Yok Lam and Srivastava, Gopesh and Choi, William W L and Evens, Andrew M and Pilichowska, Monika and Sengar, Manju and Reddy, Nishitha and Li, Shaoying and Chadburn, Amy and Gordon, Leo I and Jaffe, Elaine S and Levy, Shawn and Rempel, Rachel and Tzeng, Tiffany and Happ, Lanie E and Dave, Tushar and Rajagopalan, Deepthi and Datta, Jyotishka and Dunson, David B and Dave, Sandeep S}, |
|
| 8651 | + date = {2017-10}, |
|
| 8652 | + journaltitle = {Cell}, |
|
| 8653 | + volume = {171}, |
|
| 8654 | + number = {2}, |
|
| 8655 | + pages = {481--494.e15}, |
|
| 8656 | + keywords = {nosource} |
|
| 8657 | +} |
|
| 8658 | + |
|
| 8659 | +@article{reddyInternalizationRituximabEfficiency2015, |
|
| 8660 | + title = {Internalization of {{Rituximab}} and the {{Efficiency}} of {{B Cell Depletion}} in {{Rheumatoid Arthritis}} and {{Systemic Lupus Erythematosus}}}, |
|
| 8661 | + author = {Reddy, Venkat and Cambridge, Geraldine and Isenberg, David A and Glennie, Martin J and Cragg, Mark S and Leandro, Maria}, |
|
| 8662 | + date = {2015}, |
|
| 8663 | + journaltitle = {Arthritis \& Rheumatology}, |
|
| 8664 | + volume = {67}, |
|
| 8665 | + number = {8}, |
|
| 8666 | + eprint = {25916583}, |
|
| 8667 | + eprinttype = {pmid}, |
|
| 8668 | + pages = {2046--2055}, |
|
| 8669 | + issn = {2326-5205}, |
|
| 8670 | + doi = {10.1002/art.39167}, |
|
| 8671 | + url = {http://dx.doi.org/10.1002/art.39167}, |
|
| 8672 | + abstract = {Rituximab, a type I anti-CD20 monoclonal antibody (mAb), induces incomplete B cell depletion in some patients with rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), thus contributing to a poor clinical response. The mechanisms of this resistance remain elusive. The purpose of this study was to determine whether type II mAb are more efficient than type I mAb at depleting B cells from RA and SLE patients, whether internalization influences the efficiency of depletion, and whether Fcγ receptor type IIb (FcγRIIb) and the B cell receptor regulate this internalization process. We used an in vitro whole blood B cell–depletion assay to assess the efficiency of depletion, flow cytometry to study cell surface protein expression, and surface fluorescence–quenching assays to assess rituximab internalization, in samples from patients with RA and patients with SLE. Paired t-test or Mann-Whitney U test was used to compare groups, and Spearman's rank correlation test was used to assess correlation. We found that type II mAb internalized significantly less rituximab than type I mAb and depleted B cells from patients with RA and SLE at least 2-fold more efficiently than type I mAb. Internalization of rituximab was highly variable between patients, was regulated by FcγRIIb, and inversely correlated with cytotoxicity in whole blood B cell–depletion assays. The lowest levels of internalization were seen in IgD– B cells, including postswitched (IgD–CD27+) memory cells. Internalization of type I anti-CD20 mAb was also partially inhibited by anti-IgM stimulation. Variability in internalization of rituximab was observed and was correlated with impaired B cell depletion. Therefore, slower-internalizing type II mAb should be considered as alternative B cell–depleting agents for the treatment of RA and SLE.}, |
|
| 8673 | + keywords = {nosource} |
|
| 8674 | +} |
|
| 8675 | + |
|
| 8676 | +@article{reichelFlowSortingExome2015a, |
|
| 8677 | + title = {Flow Sorting and Exome Sequencing Reveal the Oncogenome of Primary {{Hodgkin}} and {{Reed-Sternberg}} Cells}, |
|
| 8678 | + author = {Reichel, Jonathan and Chadburn, Amy and Rubinstein, Paul G. and Giulino-Roth, Lisa and Tam, Wayne and Liu, Yifang and Gaiolla, Rafael and Eng, Kenneth and Brody, Joshua and Inghirami, Giorgio and Carlo-Stella, Carmelo and Santoro, Armando and Rahal, Daoud and Totonchy, Jennifer and Elemento, Olivier and Cesarman, Ethel and Roshal, Mikhail}, |
|
| 8679 | + date = {2015-02-12}, |
|
| 8680 | + journaltitle = {Blood}, |
|
| 8681 | + shortjournal = {Blood}, |
|
| 8682 | + volume = {125}, |
|
| 8683 | + number = {7}, |
|
| 8684 | + eprint = {25488972}, |
|
| 8685 | + eprinttype = {pmid}, |
|
| 8686 | + pages = {1061--1072}, |
|
| 8687 | + issn = {1528-0020}, |
|
| 8688 | + doi = {10.1182/blood-2014-11-610436}, |
|
| 8689 | + abstract = {Classical Hodgkin lymphoma (cHL) is characterized by sparsely distributed Hodgkin and Reed-Sternberg (HRS) cells amid reactive host background, complicating the acquisition of neoplastic DNA without extensive background contamination. We overcame this limitation by using flow-sorted HRS and intratumor T cells and optimized low-input exome sequencing of 10 patient samples to reveal alterations in genes involved in antigen presentation, chromosome integrity, transcriptional regulation, and ubiquitination. β-2-microglobulin (B2M) is the most commonly altered gene in HRS cells, with 7 of 10 cases having inactivating mutations that lead to loss of major histocompatibility complex class I (MHC-I) expression. Enforced wild-type B2M expression in a cHL cell line restored MHC-I expression. In an extended cohort of 145 patients, the absence of B2M protein in the HRS cells was associated with lower stage of disease, younger age at diagnosis, and better overall and progression-free survival. B2M-deficient cases encompassed most of the nodular sclerosis subtype cases and only a minority of mixed cellularity cases, suggesting that B2M deficiency determines the tumor microenvironment and may define a major subset of cHL that has more uniform clinical and morphologic features. In addition, we report previously unknown genetic alterations that may render selected patients sensitive to specific targeted therapies.}, |
|
| 8690 | + langid = {english}, |
|
| 8691 | + keywords = {Adolescent,Adult,Aged,Aged 80 and over,Cell Line Tumor,Cell Separation,Child,Cohort Studies,Exome,Female,Flow Cytometry,Genes Neoplasm,Genome Human,High-Throughput Nucleotide Sequencing,Hodgkin Disease,Humans,Male,Middle Aged,Reed-Sternberg Cells,Young Adult}, |
|
| 8692 | + file = {/Users/rmorin/Zotero/storage/6YLBC6JE/Reichel et al. - 2015 - Flow sorting and exome sequencing reveal the oncog.pdf} |
|
| 8693 | +} |
|
| 8694 | + |
|
| 8695 | +@article{rheinbayRecurrentFunctionalRegulatory2017, |
|
| 8696 | + title = {Recurrent and Functional Regulatory Mutations in Breast Cancer}, |
|
| 8697 | + author = {Rheinbay, Esther and Parasuraman, Prasanna and Grimsby, Jonna and Tiao, Grace and Engreitz, Jesse M and Kim, Jaegil and Lawrence, Michael S and Taylor-Weiner, Amaro and Rodriguez-Cuevas, Sergio and Rosenberg, Mara and Hess, Julian and Stewart, Chip and Maruvka, Yosef E and Stojanov, Petar and Cortés, Maria L and Seepo, Sara and Cibulskis, Carrie and Tracy, Adam and Pugh, Trevor J and Lee, Jesse and Zheng, Zongli and Ellisen, Leif W and Iafrate, A John and Boehm, Jesse S and Gabriel, Stacey B and Meyerson, Matthew and Golub, Todd R and Baselga, José and Hidalgo-Miranda, Alfredo and Shioda, Toshi and Bernards, Andre and Lander, Eric S and Getz, Gad}, |
|
| 8698 | + date = {2017-07}, |
|
| 8699 | + journaltitle = {Nature}, |
|
| 8700 | + volume = {547}, |
|
| 8701 | + number = {7661}, |
|
| 8702 | + pages = {55--60}, |
|
| 8703 | + keywords = {nosource} |
|
| 8704 | +} |
|
| 8705 | + |
|
| 8706 | +@article{richterRecurrentMutationID32012a, |
|
| 8707 | + title = {Recurrent Mutation of the {{ID3}} Gene in {{Burkitt}} Lymphoma Identified by Integrated Genome, Exome and Transcriptome Sequencing}, |
|
| 8708 | + author = {Richter, Julia and Schlesner, Matthias and Hoffmann, Steve and Kreuz, Markus and Leich, Ellen and Burkhardt, Birgit and Rosolowski, Maciej and Ammerpohl, Ole and Wagener, Rabea and Bernhart, Stephan H. and Lenze, Dido and Szczepanowski, Monika and Paulsen, Maren and Lipinski, Simone and Russell, Robert B. and Adam-Klages, Sabine and Apic, Gordana and Claviez, Alexander and Hasenclever, Dirk and Hovestadt, Volker and Hornig, Nadine and Korbel, Jan O. and Kube, Dieter and Langenberger, David and Lawerenz, Chris and Lisfeld, Jasmin and Meyer, Katharina and Picelli, Simone and Pischimarov, Jordan and Radlwimmer, Bernhard and Rausch, Tobias and Rohde, Marius and Schilhabel, Markus and Scholtysik, René and Spang, Rainer and Trautmann, Heiko and Zenz, Thorsten and Borkhardt, Arndt and Drexler, Hans G. and Möller, Peter and MacLeod, Roderick A. F. and Pott, Christiane and Schreiber, Stefan and Trümper, Lorenz and Loeffler, Markus and Stadler, Peter F. and Lichter, Peter and Eils, Roland and Küppers, Ralf and Hummel, Michael and Klapper, Wolfram and Rosenstiel, Philip and Rosenwald, Andreas and Brors, Benedikt and Siebert, Reiner and {ICGC MMML-Seq Project}}, |
|
| 8709 | + date = {2012-12}, |
|
| 8710 | + journaltitle = {Nature Genetics}, |
|
| 8711 | + shortjournal = {Nat Genet}, |
|
| 8712 | + volume = {44}, |
|
| 8713 | + number = {12}, |
|
| 8714 | + eprint = {23143595}, |
|
| 8715 | + eprinttype = {pmid}, |
|
| 8716 | + pages = {1316--1320}, |
|
| 8717 | + issn = {1546-1718}, |
|
| 8718 | + doi = {10.1038/ng.2469}, |
|
| 8719 | + abstract = {Burkitt lymphoma is a mature aggressive B-cell lymphoma derived from germinal center B cells. Its cytogenetic hallmark is the Burkitt translocation t(8;14)(q24;q32) and its variants, which juxtapose the MYC oncogene with one of the three immunoglobulin loci. Consequently, MYC is deregulated, resulting in massive perturbation of gene expression. Nevertheless, MYC deregulation alone seems not to be sufficient to drive Burkitt lymphomagenesis. By whole-genome, whole-exome and transcriptome sequencing of four prototypical Burkitt lymphomas with immunoglobulin gene (IG)-MYC translocation, we identified seven recurrently mutated genes. One of these genes, ID3, mapped to a region of focal homozygous loss in Burkitt lymphoma. In an extended cohort, 36 of 53 molecularly defined Burkitt lymphomas (68\%) carried potentially damaging mutations of ID3. These were strongly enriched at somatic hypermutation motifs. Only 6 of 47 other B-cell lymphomas with the IG-MYC translocation (13\%) carried ID3 mutations. These findings suggest that cooperation between ID3 inactivation and IG-MYC translocation is a hallmark of Burkitt lymphomagenesis.}, |
|
| 8720 | + langid = {english}, |
|
| 8721 | + keywords = {Base Sequence,Burkitt Lymphoma,Chromosome Mapping,Chromosomes Human Pair 14,Chromosomes Human Pair 8,Cohort Studies,Female,Genes Immunoglobulin,Genes myc,Genome Human,Humans,Inhibitor of Differentiation Proteins,Male,Molecular Sequence Data,Mutation,Neoplasm Proteins,Sequence Analysis DNA,Somatic Hypermutation Immunoglobulin,Transcriptome,Translocation Genetic}, |
|
| 8722 | + file = {/Users/rmorin/Zotero/storage/Z3LR9H6S/Richter et al. - 2012 - Recurrent mutation of the ID3 gene in Burkitt lymp.pdf} |
|
| 8723 | +} |
|
| 8724 | + |
|
| 8725 | +@article{rimszaAccurateClassificationDiffuse2011, |
|
| 8726 | + title = {Accurate Classification of Diffuse Large {{B-cell}} Lymphoma into Germinal Center and Activated {{B-cell}} Subtypes Using a Nuclease Protection Assay on Formalin-Fixed, Paraffin-Embedded Tissues}, |
|
| 8727 | + author = {Rimsza, Lisa M. and Wright, George and Schwartz, Mark and Chan, Wing C. and Jaffe, Elaine S. and Gascoyne, Randy D. and Campo, Elias and Rosenwald, Andreas and Ott, German and Cook, James R. and Tubbs, Raymond R. and Braziel, Rita M. and Delabie, Jan and Miller, Tom P. and Staudt, Louis M.}, |
|
| 8728 | + date = {2011-06-01}, |
|
| 8729 | + journaltitle = {Clinical Cancer Research: An Official Journal of the American Association for Cancer Research}, |
|
| 8730 | + shortjournal = {Clin Cancer Res}, |
|
| 8731 | + volume = {17}, |
|
| 8732 | + number = {11}, |
|
| 8733 | + eprint = {21364035}, |
|
| 8734 | + eprinttype = {pmid}, |
|
| 8735 | + pages = {3727--3732}, |
|
| 8736 | + issn = {1557-3265}, |
|
| 8737 | + doi = {10.1158/1078-0432.CCR-10-2573}, |
|
| 8738 | + abstract = {Classification of diffuse large B-cell lymphoma (DLBCL) into cell-of-origin (COO) subtypes based on gene expression profiles has well-established prognostic value. These subtypes, termed germinal center B cell (GCB) and activated B cell (ABC) also have different genetic alterations and overexpression of different pathways that may serve as therapeutic targets. Thus, accurate classification is essential for analysis of clinical trial results and planning new trials by using targeted agents. The current standard for COO classification uses gene expression profiling (GEP) of snap frozen tissues, and a Bayesian predictor algorithm. However, this is generally not feasible. In this study, we investigated whether the qNPA technique could be used for accurate classification of COO by using formalin-fixed, paraffin-embedded (FFPE) tissues. We analyzed expression levels of 14 genes in 121 cases of R-CHOP-treated DLBCL that had previously undergone GEP by using the Affymetrix U133 Plus 2.0 microarray and had matching FFPE blocks. Results were evaluated by using the previously published algorithm with a leave-one-out cross-validation approach. These results were compared with COO classification based on frozen tissue GEP profiles. For each case, a probability statistic was generated indicating the likelihood that the classification by using qNPA was accurate. When data were dichotomized into GCB or non-GCB, overall accuracy was 92\%. The qNPA technique accurately categorized DLBCL into GCB and ABC subtypes, as defined by GEP. This approach is quantifiable, applicable to FFPE tissues with no technical failures, and has potential for significant impact on DLBCL research and clinical trial development.}, |
|
| 8739 | + langid = {english}, |
|
| 8740 | + pmcid = {PMC3107869}, |
|
| 8741 | + keywords = {B-Lymphocyte Subsets,Gene Expression Profiling,Gene Expression Regulation Neoplastic,Germinal Center,Humans,Lymphocyte Activation,Lymphoma Large B-Cell Diffuse,Nuclease Protection Assays,Oligonucleotide Array Sequence Analysis,Paraffin Embedding,Prognosis}, |
|
| 8742 | + file = {/Users/rmorin/Zotero/storage/I9XIPAXN/Rimsza et al. - 2011 - Accurate classification of diffuse large B-cell ly.pdf} |
|
| 8743 | +} |
|
| 8744 | + |
|
| 8745 | +@article{rimszaClassificationDiffuseLarge, |
|
| 8746 | + title = {Classification of {{Diffuse Large B}} Cell {{Lymphoma}} into {{Germinal Center}} and {{Activated B}} Cell {{Subtypes Using}} a {{Nuclease Protection Assay}} on {{Paraffin Embedded Tissues}}.}, |
|
| 8747 | + author = {Rimsza, Lisa M and Wright, George W and Schwartz, Mark and Chan, Wing and Jaffe, Elaine and Gascoyne, Randy D and Campo, Elias and Rosenwald, Andreas and Ott, German and Cook, James and Tubbs, Raymond R and Braziel, Rita M and Delabie, Jan and Miller, Thomas P and Staudt, Louis M}, |
|
| 8748 | + journaltitle = {Clin Cancer Res}, |
|
| 8749 | + keywords = {nosource} |
|
| 8750 | +} |
|
| 8751 | + |
|
| 8752 | +@article{rimszaLossMHCClass2004, |
|
| 8753 | + title = {Loss of {{MHC}} Class {{II}} Gene and Protein Expression in Diffuse Large {{B-cell}} Lymphoma Is Related to Decreased Tumor Immunosurveillance and Poor Patient Survival Regardless of Other Prognostic Factors: A Follow-up Study from the {{Leukemia}} and {{Lymphoma Molecular Profiling Project}}}, |
|
| 8754 | + author = {Rimsza, L M}, |
|
| 8755 | + date = {2004-06}, |
|
| 8756 | + journaltitle = {Blood}, |
|
| 8757 | + volume = {103}, |
|
| 8758 | + number = {11}, |
|
| 8759 | + pages = {4251--4258}, |
|
| 8760 | + keywords = {nosource} |
|
| 8761 | +} |
|
| 8762 | + |
|
| 8763 | +@article{ritchieLimmaPowersDifferential2015, |
|
| 8764 | + title = {Limma Powers Differential Expression Analyses for {{RNA-sequencing}} and Microarray Studies}, |
|
| 8765 | + author = {Ritchie, Matthew E. and Phipson, Belinda and Wu, Di and Hu, Yifang and Law, Charity W. and Shi, Wei and Smyth, Gordon K.}, |
|
| 8766 | + date = {2015-04-20}, |
|
| 8767 | + journaltitle = {Nucleic Acids Research}, |
|
| 8768 | + shortjournal = {Nucleic Acids Research}, |
|
| 8769 | + volume = {43}, |
|
| 8770 | + number = {7}, |
|
| 8771 | + pages = {e47}, |
|
| 8772 | + issn = {0305-1048}, |
|
| 8773 | + doi = {10.1093/nar/gkv007}, |
|
| 8774 | + url = {https://doi.org/10.1093/nar/gkv007}, |
|
| 8775 | + urldate = {2024-03-19}, |
|
| 8776 | + abstract = {limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. Over the past decade, limma has been a popular choice for gene discovery through differential expression analyses of microarray and high-throughput PCR data. The package contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions. First, the package can now perform both differential expression and differential splicing analyses of RNA sequencing (RNA-seq) data. All the downstream analysis tools previously restricted to microarray data are now available for RNA-seq as well. These capabilities allow users to analyse both RNA-seq and microarray data with very similar pipelines. Second, the package is now able to go past the traditional gene-wise expression analyses in a variety of ways, analysing expression profiles in terms of co-regulated sets of genes or in terms of higher-order expression signatures. This provides enhanced possibilities for biological interpretation of gene expression differences. This article reviews the philosophy and design of the limma package, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.}, |
|
| 8777 | + file = {/Users/rmorin/Zotero/storage/BVLTWVYL/Ritchie et al. - 2015 - limma powers differential expression analyses for .pdf;/Users/rmorin/Zotero/storage/RG92Q5W3/2414268.html} |
|
| 8778 | +} |
|
| 8779 | + |
|
| 8780 | +@article{ritzRecurrentMutationsSTAT62009a, |
|
| 8781 | + title = {Recurrent Mutations of the {{STAT6 DNA}} Binding Domain in Primary Mediastinal {{B-cell}} Lymphoma}, |
|
| 8782 | + author = {Ritz, Olga and Guiter, Chrystelle and Castellano, Flavia and Dorsch, Karola and Melzner, Julia and Jais, Jean-Philippe and Dubois, Gwendoline and Gaulard, Philippe and Möller, Peter and Leroy, Karen}, |
|
| 8783 | + date = {2009-08-06}, |
|
| 8784 | + journaltitle = {Blood}, |
|
| 8785 | + shortjournal = {Blood}, |
|
| 8786 | + volume = {114}, |
|
| 8787 | + number = {6}, |
|
| 8788 | + eprint = {19423726}, |
|
| 8789 | + eprinttype = {pmid}, |
|
| 8790 | + pages = {1236--1242}, |
|
| 8791 | + issn = {1528-0020}, |
|
| 8792 | + doi = {10.1182/blood-2009-03-209759}, |
|
| 8793 | + abstract = {Primary mediastinal B-cell lymphoma (PMBL) is a separate entity of aggressive B-cell lymphoma, characterized by a constitutive activation of janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling pathway, also observed in Hodgkin lymphoma. Although many cancers exhibit constitutive JAK-STAT pathway activation, mutations of STAT genes have not been reported in neoplasms. Here, we show that MedB-1 PMBL-derived and L1236 Hodgkin-derived cell lines and 20 of 55 (36\%) PMBL cases harbor heterozygous missense mutations in STAT6 DNA binding domain, whereas no mutation was found in 25 diffuse large B-cell lymphoma samples. In 3 cases, somatic origin was indicated by the absence of the mutations in the nontumoral tissue. The pattern of STAT6 mutations was different from the classical features of somatic hypermutations. The mutant STAT6 proteins showed a decreased DNA binding ability in transfected HEK cells, but no decrease in expression of STAT6 canonical target genes was observed in PMBL cases with a mutated STAT6 gene. Although the oncogenic properties of STAT6 mutant proteins remain to be determined, their recurrent selection in PMBL strongly argues for their involvement in the pathogenesis of this aggressive B-cell lymphoma.}, |
|
| 8794 | + langid = {english}, |
|
| 8795 | + pmcid = {PMC2824656}, |
|
| 8796 | + keywords = {Cell Line Tumor,Female,Gene Expression Regulation Neoplastic,Humans,Lymphoma Large B-Cell Diffuse,Male,Mediastinal Neoplasms,Mutation,Neoplasm Proteins,Protein Structure Tertiary,Signal Transduction,STAT6 Transcription Factor}, |
|
| 8797 | + file = {/Users/rmorin/Zotero/storage/S3FFXJVP/Ritz et al. - 2009 - Recurrent mutations of the STAT6 DNA binding domai.pdf} |
|
| 8798 | +} |
|
| 8799 | + |
|
| 8800 | +@article{robertsGeneticAlterationsActivating2012, |
|
| 8801 | + title = {Genetic Alterations Activating Kinase and Cytokine Receptor Signaling in High-Risk Acute Lymphoblastic Leukemia}, |
|
| 8802 | + author = {Roberts, Kathryn G. and Morin, Ryan D. and Zhang, Jinghui and Hirst, Martin and Zhao, Yongjun and Su, Xiaoping and Chen, Shann-Ching and Payne-Turner, Debbie and Churchman, Michelle and Harvey, Richard C. and Chen, Xiang and Kasap, Corynn and Yan, Chunhua and Becksfort, Jared and Finney, Richard P. and Teachey, David T. and Maude, Shannon L. and Tse, Kane and Moore, Richard and Jones, Steven and Mungall, Karen and Birol, Inanc and Edmonson, Michael N. and Hu, Ying and Buetow, Kenneth E. and Chen, I-Ming and Carroll, William L. and Wei, Lei and Ma, Jing and Kleppe, Maria and Levine, Ross L. and Garcia-Manero, Guillermo and Larsen, Eric and Shah, Neil P. and Devidas, Meenakshi and Reaman, Gregory and Smith, Malcolm and Paugh, Steven W. and Evans, William E. and Grupp, Stephan A. and Jeha, Sima and Pui, Ching-Hon and Gerhard, Daniela S. and Downing, James R. and Willman, Cheryl L. and Loh, Mignon and Hunger, Stephen P. and Marra, Marco and Mullighan, Charles G.}, |
|
| 8803 | + date = {2012-08-14}, |
|
| 8804 | + journaltitle = {Cancer cell}, |
|
| 8805 | + shortjournal = {Cancer Cell}, |
|
| 8806 | + volume = {22}, |
|
| 8807 | + number = {2}, |
|
| 8808 | + eprint = {22897847}, |
|
| 8809 | + eprinttype = {pmid}, |
|
| 8810 | + pages = {153--166}, |
|
| 8811 | + issn = {1535-6108}, |
|
| 8812 | + doi = {10.1016/j.ccr.2012.06.005}, |
|
| 8813 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3422513/}, |
|
| 8814 | + urldate = {2020-07-16}, |
|
| 8815 | + abstract = {Genomic profiling has identified a subtype of high-risk B-progenitor acute lymphoblastic leukemia (B-ALL) with alteration of IKZF1, a gene expression profile similar to BCR-ABL1-positive ALL and poor outcome (Ph-like ALL). The genetic alterations that activate kinase signaling in Ph-like ALL are poorly understood. We performed transcriptome and whole genome sequencing on 15 cases of Ph-like ALL, and identified rearrangements involving ABL1, JAK2, PDGFRB, CRLF2 and EPOR, activating mutations of IL7R and FLT3, and deletion of SH2B3, which encodes the JAK2 negative regulator LNK. Importantly, several of these alterations induce transformation that is attenuated with tyrosine kinase inhibitors, suggesting the treatment outcome of these patients may be improved with targeted therapy.}, |
|
| 8816 | + pmcid = {PMC3422513}, |
|
| 8817 | + file = {/Users/rmorin/Zotero/storage/22I5L3JJ/roberts2012.pdf;/Users/rmorin/Zotero/storage/H549YKYV/Roberts et al. - 2012 - Genetic alterations activating kinase and cytokine.pdf} |
|
| 8818 | +} |
|
| 8819 | + |
|
| 8820 | +@article{rocoClassSwitchRecombinationOccurs2019, |
|
| 8821 | + title = {Class-{{Switch Recombination Occurs Infrequently}} in {{Germinal Centers}}}, |
|
| 8822 | + author = {Roco, Jonathan A. and Mesin, Luka and Binder, Sebastian C. and Nefzger, Christian and Gonzalez-Figueroa, Paula and Canete, Pablo F. and Ellyard, Julia and Shen, Qian and Robert, Philippe A. and Cappello, Jean and Vohra, Harpreet and Zhang, Yang and Nowosad, Carla R. and Schiepers, Arien and Corcoran, Lynn M. and Toellner, Kai-Michael and Polo, Jose M. and Meyer-Hermann, Michael and Victora, Gabriel D. and Vinuesa, Carola G.}, |
|
| 8823 | + date = {2019-08-20}, |
|
| 8824 | + journaltitle = {Immunity}, |
|
| 8825 | + shortjournal = {Immunity}, |
|
| 8826 | + volume = {51}, |
|
| 8827 | + number = {2}, |
|
| 8828 | + eprint = {31375460}, |
|
| 8829 | + eprinttype = {pmid}, |
|
| 8830 | + pages = {337-350.e7}, |
|
| 8831 | + publisher = {Elsevier}, |
|
| 8832 | + issn = {1074-7613}, |
|
| 8833 | + doi = {10.1016/j.immuni.2019.07.001}, |
|
| 8834 | + url = {https://www.cell.com/immunity/abstract/S1074-7613(19)30317-6}, |
|
| 8835 | + urldate = {2020-05-25}, |
|
| 8836 | + langid = {english}, |
|
| 8837 | + file = {/Users/rmorin/Zotero/storage/QWI39AZC/roco2019.pdf;/Users/rmorin/Zotero/storage/UB44LPCJ/S1074-7613(19)30317-6.html} |
|
| 8838 | +} |
|
| 8839 | + |
|
| 8840 | +@article{roghanianAntagonisticHumanFcgRIIB2015, |
|
| 8841 | + title = {Antagonistic {{Human FcγRIIB}} ({{CD32B}}) {{Antibodies Have Anti-Tumor Activity}} and {{Overcome Resistance}} to {{Antibody Therapy In Vivo}}}, |
|
| 8842 | + author = {Roghanian, Ali and Teige, Ingrid and Mårtensson, Linda and Cox, Kerry L. and Kovacek, Mathilda and Ljungars, Anne and Mattson, Jenny and Sundberg, Annika and Vaughan, Andrew T. and Shah, Vallari and Smyth, Neil R. and Sheth, Bhavwanti and Chan, H.T. Claude and Li, Zhan-Chun and Williams, Emily L. and Manfredi, Giusi and Oldham, Robert J. and Mockridge, C. Ian and James, Sonya A. and Dahal, Lekh N. and Hussain, Khiyam and Nilsson, Björn and Verbeek, J. Sjef and Juliusson, Gunnar and Hansson, Markus and Jerkeman, Mats and Johnson, Peter W.M. and Davies, Andrew and Beers, Stephen A. and Glennie, Martin J. and Frendéus, Björn and Cragg, Mark S.}, |
|
| 8843 | + date = {2015}, |
|
| 8844 | + journaltitle = {Cancer Cell}, |
|
| 8845 | + volume = {27}, |
|
| 8846 | + number = {4}, |
|
| 8847 | + eprint = {25873171}, |
|
| 8848 | + eprinttype = {pmid}, |
|
| 8849 | + pages = {473--488}, |
|
| 8850 | + issn = {1535-6108}, |
|
| 8851 | + doi = {10.1016/j.ccell.2015.03.005}, |
|
| 8852 | + url = {http://dx.doi.org/10.1016/j.ccell.2015.03.005}, |
|
| 8853 | + abstract = {Therapeutic antibodies have transformed cancer therapy, unlocking mechanisms of action by engaging the immune system. Unfortunately, cures rarely occur and patients display intrinsic or acquired resistance. Here, we demonstrate the therapeutic potential of targeting human (h) FcγRIIB (CD32B), a receptor implicated in immune cell desensitization and tumor cell resistance. FcγRIIB-blocking antibodies prevented internalization of the CD20-specific antibody rituximab, thereby maximizing cell surface accessibility and immune effector cell mediated antitumor activity. In hFcγRIIB-transgenic (Tg) mice, FcγRIIB-blocking antibodies effectively deleted target cells in combination with rituximab, and other therapeutic antibodies, from resistance-prone stromal compartments. Similar efficacy was seen in primary human tumor xenografts, including with cells from patients with relapsed/refractory disease. These data support the further development of hFcγRIIB antibodies for clinical assessment.}, |
|
| 8854 | + keywords = {nosource} |
|
| 8855 | +} |
|
| 8856 | + |
|
| 8857 | +@article{roghanianResistanceFutileTargeting2016, |
|
| 8858 | + title = {Resistance Is Futile: {{Targeting}} the Inhibitory {{FcγRIIB}} ({{CD32B}}) to Maximize Immunotherapy.}, |
|
| 8859 | + author = {Roghanian, Ali and Cragg, Mark S and Frendéus, Bjorn}, |
|
| 8860 | + date = {2016-02}, |
|
| 8861 | + journaltitle = {OncoImmunology}, |
|
| 8862 | + volume = {5}, |
|
| 8863 | + number = {2}, |
|
| 8864 | + pages = {e1069939}, |
|
| 8865 | + keywords = {nosource} |
|
| 8866 | +} |
|
| 8867 | + |
|
| 8868 | +@article{romero-camareroGerminalCentreProtein2013, |
|
| 8869 | + title = {Germinal Centre Protein {{HGAL}} Promotes Lymphoid Hyperplasia and Amyloidosis via {{BCR-mediated Syk}} Activation.}, |
|
| 8870 | + author = {Romero-Camarero, Isabel and Jiang, Xiaoyu and Natkunam, Yasodha and Lu, Xiaoqing and Vicente-Dueñas, Carolina and Gonzalez-Herrero, Ines and Flores, Teresa and Garcia, Juan Luis and McNamara, George and Kunder, Christian and Zhao, Shuchun and Segura, Victor and Fontan, Lorena and Martinez-Climent, Jose A and García-Criado, Francisco Javier and Theis, Jason D and Dogan, Ahmet and Campos-Sánchez, Elena and Green, Michael R and Alizadeh, Ash A and Cobaleda, Cesar and Sánchez-García, Isidro and Lossos, Izidore S}, |
|
| 8871 | + date = {2013}, |
|
| 8872 | + journaltitle = {Nature communications}, |
|
| 8873 | + volume = {4}, |
|
| 8874 | + pages = {1338}, |
|
| 8875 | + keywords = {nosource} |
|
| 8876 | +} |
|
| 8877 | + |
|
| 8878 | +@article{roschewskiCirculatingTumourDNA, |
|
| 8879 | + title = {Circulating Tumour {{DNA}} and {{CT}} Monitoring in Patients with Untreated Diffuse Large {{B-cell}} Lymphoma: A Correlative Biomarker Study.}, |
|
| 8880 | + author = {Roschewski, Mark and Dunleavy, Kieron and Pittaluga, Stefania and Moorhead, Martin and Pepin, Francois and Kong, Katherine and Shovlin, Margaret and Jaffe, Elaine S and Staudt, Louis M and Lai, Catherine and Steinberg, Seth M and Chen, Clara C and Zheng, Jianbiao and Willis, Thomas D and Faham, Malek and Wilson, Wyndham H}, |
|
| 8881 | + journaltitle = {Lancet Oncol}, |
|
| 8882 | + keywords = {nosource} |
|
| 8883 | +} |
|
| 8884 | + |
|
| 8885 | +@article{rosenwaldGeneExpressionProfiling, |
|
| 8886 | + title = {Gene Expression Profiling of Diffuse Large {{B-cell}} Lymphoma}, |
|
| 8887 | + author = {Rosenwald, A and Staudt, L}, |
|
| 8888 | + journaltitle = {Leuk lymphoma}, |
|
| 8889 | + volume = {44 Suppl 3}, |
|
| 8890 | + pages = {S41--7--S41--7}, |
|
| 8891 | + keywords = {nosource} |
|
| 8892 | +} |
|
| 8893 | + |
|
| 8894 | +@article{rosenwaldMolecularDiagnosisPrimary2003, |
|
| 8895 | + title = {Molecular Diagnosis of Primary Mediastinal {{B}} Cell Lymphoma Identifies a Clinically Favorable Subgroup of Diffuse Large {{B}} Cell Lymphoma Related to {{Hodgkin}} Lymphoma}, |
|
| 8896 | + author = {Rosenwald, Andreas and Wright, George and Leroy, Karen and Yu, Xin and Gaulard, Philippe and Gascoyne, Randy D. and Chan, Wing C. and Zhao, Tong and Haioun, Corinne and Greiner, Timothy C. and Weisenburger, Dennis D. and Lynch, James C. and Vose, Julie and Armitage, James O. and Smeland, Erlend B. and Kvaloy, Stein and Holte, Harald and Delabie, Jan and Campo, Elias and Montserrat, Emili and Lopez-Guillermo, Armando and Ott, German and Muller-Hermelink, H. Konrad and Connors, Joseph M. and Braziel, Rita and Grogan, Thomas M. and Fisher, Richard I. and Miller, Thomas P. and LeBlanc, Michael and Chiorazzi, Michael and Zhao, Hong and Yang, Liming and Powell, John and Wilson, Wyndham H. and Jaffe, Elaine S. and Simon, Richard and Klausner, Richard D. and Staudt, Louis M.}, |
|
| 8897 | + date = {2003-09-15}, |
|
| 8898 | + journaltitle = {The Journal of Experimental Medicine}, |
|
| 8899 | + shortjournal = {J Exp Med}, |
|
| 8900 | + volume = {198}, |
|
| 8901 | + number = {6}, |
|
| 8902 | + eprint = {12975453}, |
|
| 8903 | + eprinttype = {pmid}, |
|
| 8904 | + pages = {851--862}, |
|
| 8905 | + issn = {0022-1007}, |
|
| 8906 | + doi = {10.1084/jem.20031074}, |
|
| 8907 | + abstract = {Using current diagnostic criteria, primary mediastinal B cell lymphoma (PMBL) cannot be distinguished from other types of diffuse large B cell lymphoma (DLBCL) reliably. We used gene expression profiling to develop a more precise molecular diagnosis of PMBL. PMBL patients were considerably younger than other DLBCL patients, and their lymphomas frequently involved other thoracic structures but not extrathoracic sites typical of other DLBCLs. PMBL patients had a relatively favorable clinical outcome, with a 5-yr survival rate of 64\% compared with 46\% for other DLBCL patients. Gene expression profiling strongly supported a relationship between PMBL and Hodgkin lymphoma: over one third of the genes that were more highly expressed in PMBL than in other DLBCLs were also characteristically expressed in Hodgkin lymphoma cells. PDL2, which encodes a regulator of T cell activation, was the gene that best discriminated PMBL from other DLBCLs and was also highly expressed in Hodgkin lymphoma cells. The genomic loci for PDL2 and several neighboring genes were amplified in over half of the PMBLs and in Hodgkin lymphoma cell lines. The molecular diagnosis of PMBL should significantly aid in the development of therapies tailored to this clinically and pathogenetically distinctive subgroup of DLBCL.}, |
|
| 8908 | + langid = {english}, |
|
| 8909 | + pmcid = {PMC2194208}, |
|
| 8910 | + keywords = {Adult,Chromosomes Human Pair 19,Diagnosis Differential,Gene Expression Profiling,Hodgkin Disease,Humans,Lymphoma B-Cell,Lymphoma Large B-Cell Diffuse,Mediastinal Neoplasms,Middle Aged,Molecular Diagnostic Techniques,Oligonucleotide Array Sequence Analysis,Survival Rate,Treatment Outcome,Tumor Cells Cultured}, |
|
| 8911 | + file = {/Users/rmorin/Zotero/storage/6CGRL8K8/Rosenwald et al. - 2003 - Molecular diagnosis of primary mediastinal B cell .pdf} |
|
| 8912 | +} |
|
| 8913 | + |
|
| 8914 | +@article{rosenwaldProliferationGeneExpression2003, |
|
| 8915 | + title = {The Proliferation Gene Expression Signature Is a Quantitative Integrator of Oncogenic Events That Predicts Survival in Mantle Cell Lymphoma}, |
|
| 8916 | + author = {Rosenwald, Andreas and Wright, George and Wiestner, Adrian and Chan, Wing C. and Connors, Joseph M. and Campo, Elias and Gascoyne, Randy D. and Grogan, Thomas M. and Muller-Hermelink, H. Konrad and Smeland, Erlend B. and Chiorazzi, Michael and Giltnane, Jena M. and Hurt, Elaine M. and Zhao, Hong and Averett, Lauren and Henrickson, Sarah and Yang, Liming and Powell, John and Wilson, Wyndham H. and Jaffe, Elaine S. and Simon, Richard and Klausner, Richard D. and Montserrat, Emilio and Bosch, Francesc and Greiner, Timothy C. and Weisenburger, Dennis D. and Sanger, Warren G. and Dave, Bhavana J. and Lynch, James C. and Vose, Julie and Armitage, James O. and Fisher, Richard I. and Miller, Thomas P. and LeBlanc, Michael and Ott, German and Kvaloy, Stein and Holte, Harald and Delabie, Jan and Staudt, Louis M.}, |
|
| 8917 | + date = {2003-02-01}, |
|
| 8918 | + journaltitle = {Cancer Cell}, |
|
| 8919 | + shortjournal = {Cancer Cell}, |
|
| 8920 | + volume = {3}, |
|
| 8921 | + number = {2}, |
|
| 8922 | + eprint = {12620412}, |
|
| 8923 | + eprinttype = {pmid}, |
|
| 8924 | + pages = {185--197}, |
|
| 8925 | + issn = {1535-6108, 1878-3686}, |
|
| 8926 | + doi = {10.1016/S1535-6108(03)00028-X}, |
|
| 8927 | + url = {https://www.cell.com/cancer-cell/abstract/S1535-6108(03)00028-X}, |
|
| 8928 | + urldate = {2019-12-21}, |
|
| 8929 | + langid = {english}, |
|
| 8930 | + file = {/Users/rmorin/Zotero/storage/W3RE3HLZ/S1535-6108(03)00028-X.html} |
|
| 8931 | +} |
|
| 8932 | + |
|
| 8933 | +@article{rosenwaldUseMolecularProfiling2002, |
|
| 8934 | + title = {The {{Use}} of {{Molecular Profiling}} to {{Predict Survival}} after {{Chemotherapy}} for {{Diffuse Large-B-Cell Lymphoma}}}, |
|
| 8935 | + author = {Rosenwald, Andreas and Wright, George and Chan, Wing C and Connors, Joseph M and Campo, Elias and Fisher, Richard I and Gascoyne, Randy D and Muller-Hermelink, H Konrad and Smeland, Erlend B and Giltnane, Jena M and Hurt, Elaine M and Zhao, Hong and Averett, Lauren and Yang, Liming and Wilson, Wyndham H and Jaffe, Elaine S and Simon, Richard and Klausner, Richard D and Powell, John and Duffey, Patricia L and Longo, Dan L and Greiner, Timothy C and Weisenburger, Dennis D and Sanger, Warren G and Dave, Bhavana J and Lynch, James C and Vose, Julie and Armitage, James O and Montserrat, Emilio and López-Guillermo, Armando and Grogan, Thomas M and Miller, Thomas P and LeBlanc, Michel and Ott, German and Kvaloy, Stein and Delabie, Jan and Holte, Harald and Krajci, Peter and Stokke, Trond and Staudt, Louis M}, |
|
| 8936 | + date = {2002-06}, |
|
| 8937 | + journaltitle = {N Engl J Med}, |
|
| 8938 | + volume = {346}, |
|
| 8939 | + number = {25}, |
|
| 8940 | + pages = {1937--1947}, |
|
| 8941 | + keywords = {nosource} |
|
| 8942 | +} |
|
| 8943 | + |
|
| 8944 | +@article{rossbachAutoCrossRegulationHnRNP2009, |
|
| 8945 | + title = {Auto- and {{Cross-Regulation}} of the {{hnRNP L Proteins}} by {{Alternative Splicing}}}, |
|
| 8946 | + author = {Rossbach, Oliver and Hung, Lee-Hsueh and Schreiner, Silke and Grishina, Inna and Heiner, Monika and Hui, Jingyi and Bindereif, Albrecht}, |
|
| 8947 | + date = {2009-03-15}, |
|
| 8948 | + journaltitle = {Molecular and Cellular Biology}, |
|
| 8949 | + volume = {29}, |
|
| 8950 | + number = {6}, |
|
| 8951 | + eprint = {19124611}, |
|
| 8952 | + eprinttype = {pmid}, |
|
| 8953 | + pages = {1442--1451}, |
|
| 8954 | + issn = {0270-7306, 1098-5549}, |
|
| 8955 | + doi = {10.1128/MCB.01689-08}, |
|
| 8956 | + url = {https://mcb.asm.org/content/29/6/1442}, |
|
| 8957 | + urldate = {2019-12-21}, |
|
| 8958 | + abstract = {We recently characterized human hnRNP L as a global regulator of alternative splicing, binding to CA-repeat and CA-rich elements. Here we report that hnRNP L autoregulates its own expression on the level of alternative splicing. Intron 6 of the human hnRNP L gene contains a short exon that, if used, introduces a premature termination codon, resulting in nonsense-mediated decay (NMD). This “poison exon” is preceded by a highly conserved CA-rich cluster extending over 800 nucleotides that binds hnRNP L and functions as an unusually extended, intronic enhancer, promoting inclusion of the poison exon. As a result, excess hnRNP L activates NMD of its own mRNA, thereby creating a negative autoregulatory feedback loop and contributing to homeostasis of hnRNP L levels. We present experimental evidence for this mechanism, based on NMD inactivation, hnRNP L binding assays, and hnRNP L-dependent alternative splicing of heterologous constructs. In addition, we demonstrate that hnRNP L cross-regulates inclusion of an analogous poison exon in the hnRNP L-like pre-mRNA, which explains the reciprocal expression of the two closely related hnRNP L proteins.}, |
|
| 8959 | + langid = {english}, |
|
| 8960 | + file = {/Users/rmorin/Zotero/storage/C4T8HNRB/1442.html} |
|
| 8961 | +} |
|
| 8962 | + |
|
| 8963 | +@article{rossi2006, |
|
| 8964 | + title = {1}, |
|
| 8965 | + author = {Rossi, D and Berra, E and Cerri, M and Deambrogi, C and Barbieri, C and Franceschetti, S and Lunghi, M and Conconi, A and Paulli, M and Matolcsy, A and Pasqualucci, L and Capello, D and Gaidano, G}, |
|
| 8966 | + date = {2006-10}, |
|
| 8967 | + journaltitle = {Haematologica}, |
|
| 8968 | + volume = {91}, |
|
| 8969 | + number = {10}, |
|
| 8970 | + pages = {1405--1409}, |
|
| 8971 | + keywords = {nosource} |
|
| 8972 | +} |
|
| 8973 | + |
|
| 8974 | +@article{rossiAlterationBIRC3Multiple2011a, |
|
| 8975 | + title = {Alteration of {{BIRC3}} and Multiple Other {{NF-κB}} Pathway Genes in Splenic Marginal Zone Lymphoma}, |
|
| 8976 | + author = {Rossi, Davide and Deaglio, Silvia and Dominguez-Sola, David and Rasi, Silvia and Vaisitti, Tiziana and Agostinelli, Claudio and Spina, Valeria and Bruscaggin, Alessio and Monti, Sara and Cerri, Michaela and Cresta, Stefania and Fangazio, Marco and Arcaini, Luca and Lucioni, Marco and Marasca, Roberto and Thieblemont, Catherine and Capello, Daniela and Facchetti, Fabio and Kwee, Ivo and Pileri, Stefano A. and Foà, Robin and Bertoni, Francesco and Dalla-Favera, Riccardo and Pasqualucci, Laura and Gaidano, Gianluca}, |
|
| 8977 | + date = {2011-11-03}, |
|
| 8978 | + journaltitle = {Blood}, |
|
| 8979 | + shortjournal = {Blood}, |
|
| 8980 | + volume = {118}, |
|
| 8981 | + number = {18}, |
|
| 8982 | + eprint = {21881048}, |
|
| 8983 | + eprinttype = {pmid}, |
|
| 8984 | + pages = {4930--4934}, |
|
| 8985 | + issn = {1528-0020}, |
|
| 8986 | + doi = {10.1182/blood-2011-06-359166}, |
|
| 8987 | + abstract = {Splenic marginal zone lymphoma (SMZL) is one of the few B-cell lymphoma types that remain orphan of molecular lesions in cancer-related genes. Detection of active NF-κB signaling in 14 (58\%) of 24 SMZLs prompted the investigation of NF-κB molecular alterations in 101 SMZLs. Mutations and copy number abnormalities of NF-κB genes occurred in 36 (36\%) of 101 SMZLs and targeted both canonical (TNFAIP3 and IKBKB) and noncanonical (BIRC3, TRAF3, MAP3K14) NF-κB pathways. Most alterations were mutually exclusive, documenting the existence of multiple independent mechanisms affecting NF-κB in SMZL. BIRC3 inactivation in SMZL recurred because of somatic mutations that disrupted the same RING domain that in extranodal marginal zone lymphoma is removed by the t(11;18) translocation, which points to BIRC3 disruption as a common mechanism across marginal zone B-cell lymphomagenesis. Genetic lesions of NF-κB provide a molecular basis for the pathogenesis of more than 30\% of SMZLs and offer a suitable target for NF-κB therapeutic approaches in this lymphoma.}, |
|
| 8988 | + langid = {english}, |
|
| 8989 | + keywords = {Baculoviral IAP Repeat-Containing 3 Protein,Case-Control Studies,Cluster Analysis,DNA Mutational Analysis,Gene Expression Profiling,Gene Expression Regulation Neoplastic,Humans,Inhibitor of Apoptosis Proteins,Lymphoma B-Cell Marginal Zone,Microarray Analysis,Models Biological,NF-kappa B,Signal Transduction,Splenic Neoplasms,Ubiquitin-Protein Ligases}, |
|
| 8990 | + file = {/Users/rmorin/Zotero/storage/BPUGBZHC/Rossi et al. - 2011 - Alteration of BIRC3 and multiple other NF-κB pathw.pdf} |
|
| 8991 | +} |
|
| 8992 | + |
|
| 8993 | +@article{rossiCodingGenomeSplenic2012c, |
|
| 8994 | + title = {The Coding Genome of Splenic Marginal Zone Lymphoma: Activation of {{NOTCH2}} and Other Pathways Regulating Marginal Zone Development}, |
|
| 8995 | + shorttitle = {The Coding Genome of Splenic Marginal Zone Lymphoma}, |
|
| 8996 | + author = {Rossi, Davide and Trifonov, Vladimir and Fangazio, Marco and Bruscaggin, Alessio and Rasi, Silvia and Spina, Valeria and Monti, Sara and Vaisitti, Tiziana and Arruga, Francesca and Famà, Rosella and Ciardullo, Carmela and Greco, Mariangela and Cresta, Stefania and Piranda, Daniela and Holmes, Antony and Fabbri, Giulia and Messina, Monica and Rinaldi, Andrea and Wang, Jiguang and Agostinelli, Claudio and Piccaluga, Pier Paolo and Lucioni, Marco and Tabbò, Fabrizio and Serra, Roberto and Franceschetti, Silvia and Deambrogi, Clara and Daniele, Giulia and Gattei, Valter and Marasca, Roberto and Facchetti, Fabio and Arcaini, Luca and Inghirami, Giorgio and Bertoni, Francesco and Pileri, Stefano A. and Deaglio, Silvia and Foà, Robin and Dalla-Favera, Riccardo and Pasqualucci, Laura and Rabadan, Raul and Gaidano, Gianluca}, |
|
| 8997 | + date = {2012-08-27}, |
|
| 8998 | + journaltitle = {The Journal of Experimental Medicine}, |
|
| 8999 | + shortjournal = {J Exp Med}, |
|
| 9000 | + volume = {209}, |
|
| 9001 | + number = {9}, |
|
| 9002 | + eprint = {22891273}, |
|
| 9003 | + eprinttype = {pmid}, |
|
| 9004 | + pages = {1537--1551}, |
|
| 9005 | + issn = {1540-9538}, |
|
| 9006 | + doi = {10.1084/jem.20120904}, |
|
| 9007 | + abstract = {Splenic marginal zone lymphoma (SMZL) is a B cell malignancy of unknown pathogenesis, and thus an orphan of targeted therapies. By integrating whole-exome sequencing and copy-number analysis, we show that the SMZL exome carries at least 30 nonsilent gene alterations. Mutations in NOTCH2, a gene required for marginal-zone (MZ) B cell development, represent the most frequent lesion in SMZL, accounting for ∼20\% of cases. All NOTCH2 mutations are predicted to cause impaired degradation of the NOTCH2 protein by eliminating the C-terminal PEST domain, which is required for proteasomal recruitment. Among indolent B cell lymphoproliferative disorders, NOTCH2 mutations are restricted to SMZL, thus representing a potential diagnostic marker for this lymphoma type. In addition to NOTCH2, other modulators or members of the NOTCH pathway are recurrently targeted by genetic lesions in SMZL; these include NOTCH1, SPEN, and DTX1. We also noted mutations in other signaling pathways normally involved in MZ B cell development, suggesting that deregulation of MZ B cell development pathways plays a role in the pathogenesis of ∼60\% SMZL. These findings have direct implications for the treatment of SMZL patients, given the availability of drugs that can target NOTCH, NF-κB, and other pathways deregulated in this disease.}, |
|
| 9008 | + langid = {english}, |
|
| 9009 | + pmcid = {PMC3428941}, |
|
| 9010 | + keywords = {B-Lymphocytes,Chromatin Assembly and Disassembly,DNA-Binding Proteins,Exome,Gene Expression Regulation Neoplastic,Homeodomain Proteins,Humans,Lymphoma B-Cell,Mutation,NF-kappa B,Nuclear Proteins,Polymorphism Single Nucleotide,Receptor Notch1,Receptor Notch2,RNA-Binding Proteins,Signal Transduction,Splenic Neoplasms}, |
|
| 9011 | + file = {/Users/rmorin/Zotero/storage/X9MCVVRL/Rossi et al. - 2012 - The coding genome of splenic marginal zone lymphom.pdf} |
|
| 9012 | +} |
|
| 9013 | + |
|
| 9014 | +@article{rossiMutationsSF3B1Splicing2011, |
|
| 9015 | + title = {Mutations of the {{SF3B1}} Splicing Factor in Chronic Lymphocytic Leukemia: Association with Progression and Fludarabine-Refractoriness}, |
|
| 9016 | + shorttitle = {Mutations of the {{SF3B1}} Splicing Factor in Chronic Lymphocytic Leukemia}, |
|
| 9017 | + author = {Rossi, Davide and Bruscaggin, Alessio and Spina, Valeria and Rasi, Silvia and Khiabanian, Hossein and Messina, Monica and Fangazio, Marco and Vaisitti, Tiziana and Monti, Sara and Chiaretti, Sabina and Guarini, Anna and Del Giudice, Ilaria and Cerri, Michaela and Cresta, Stefania and Deambrogi, Clara and Gargiulo, Ernesto and Gattei, Valter and Forconi, Francesco and Bertoni, Francesco and Deaglio, Silvia and Rabadan, Raul and Pasqualucci, Laura and Foà, Robin and Dalla-Favera, Riccardo and Gaidano, Gianluca}, |
|
| 9018 | + date = {2011-12-22}, |
|
| 9019 | + journaltitle = {Blood}, |
|
| 9020 | + shortjournal = {Blood}, |
|
| 9021 | + volume = {118}, |
|
| 9022 | + number = {26}, |
|
| 9023 | + eprint = {22039264}, |
|
| 9024 | + eprinttype = {pmid}, |
|
| 9025 | + pages = {6904--6908}, |
|
| 9026 | + issn = {1528-0020}, |
|
| 9027 | + doi = {10.1182/blood-2011-08-373159}, |
|
| 9028 | + abstract = {The genetic lesions identified in chronic lymphocytic leukemia (CLL) do not entirely recapitulate the disease pathogenesis and the development of serious complications, such as chemorefractoriness. While investigating the coding genome of fludarabine-refractory CLL, we observed that mutations of SF3B1, encoding a splicing factor and representing a critical component of the cell spliceosome, were recurrent in 10 of 59 (17\%) fludarabine-refractory cases, with a frequency significantly greater than that observed in a consecutive CLL cohort sampled at diagnosis (17/301, 5\%; P = .002). Mutations were somatically acquired, were generally represented by missense nucleotide changes, clustered in selected HEAT repeats of the SF3B1 protein, recurrently targeted 3 hotspots (codons 662, 666, and 700), and were predictive of a poor prognosis. In fludarabine-refractory CLL, SF3B1 mutations and TP53 disruption distributed in a mutually exclusive fashion (P = .046). The identification of SF3B1 mutations points to splicing regulation as a novel pathogenetic mechanism of potential clinical relevance in CLL.}, |
|
| 9029 | + langid = {english}, |
|
| 9030 | + pmcid = {PMC3245210}, |
|
| 9031 | + keywords = {Amino Acid Sequence,Antineoplastic Agents,Disease Progression,DNA Mutational Analysis,Drug Resistance Neoplasm,Gene Expression Profiling,Gene Expression Regulation Leukemic,Humans,In Situ Hybridization Fluorescence,Karyotyping,Leukemia Lymphocytic Chronic B-Cell,Molecular Sequence Data,Mutation,Oligonucleotide Array Sequence Analysis,Phosphoproteins,Polymorphism Single Nucleotide,Ribonucleoprotein U2 Small Nuclear,RNA Splicing Factors,Sequence Homology Amino Acid,Spliceosomes,Tumor Suppressor Protein p53,Vidarabine} |
|
| 9032 | +} |
|
| 9033 | + |
|
| 9034 | +@article{rothrockHnRNPRepressesExon2005, |
|
| 9035 | + title = {{{HnRNP L}} Represses Exon Splicing via a Regulated Exonic Splicing Silencer}, |
|
| 9036 | + author = {Rothrock, Caryn R and House, Amy E and Lynch, Kristen W}, |
|
| 9037 | + date = {2005-08-03}, |
|
| 9038 | + journaltitle = {The EMBO Journal}, |
|
| 9039 | + volume = {24}, |
|
| 9040 | + number = {15}, |
|
| 9041 | + pages = {2792--2802}, |
|
| 9042 | + publisher = {John Wiley \& Sons, Ltd}, |
|
| 9043 | + issn = {0261-4189}, |
|
| 9044 | + doi = {10.1038/sj.emboj.7600745}, |
|
| 9045 | + url = {https://www.embopress.org/doi/full/10.1038/sj.emboj.7600745}, |
|
| 9046 | + urldate = {2022-09-27}, |
|
| 9047 | + abstract = {Skipping of mammalian exons during pre-mRNA splicing is commonly mediated by the activity of exonic splicing silencers (ESSs). We have recently identified a regulated ESS within variable exon 4 of the CD45 gene, named ESS1, that is necessary and sufficient for partial exon repression in resting T cells and has additional silencing activity upon T-cell activation. In this study, we identify three heterogeneous nuclear ribonucleoproteins (hnRNPs) that bind specifically to ESS1. The binding of one of these proteins, hnRNP-L, is significantly decreased by mutations that disrupt both the basal and induced activities of ESS1. Recombinant hnRNP-L functions to repress exon inclusion in vitro in an ESS1-dependent manner. Moreover, depletion of hnRNP-L, either in vitro or in vivo, leads to increased exon inclusion. In contrast, the other ESS1-binding proteins, PTB and hnRNP E2, do not discriminate between wild-type and mutant ESS1 in binding studies, and do not specifically alter ESS1-dependent splicing in vitro. Together, these studies demonstrate that hnRNP-L is the primary protein through which CD45 exon 4 silencing is mediated by the regulatory sequence ESS1.}, |
|
| 9048 | + keywords = {alternative splicing,CD45,ESS,hnRNP}, |
|
| 9049 | + file = {/Users/rmorin/Zotero/storage/I37LXP7P/Rothrock et al. - 2005 - HnRNP L represses exon splicing via a regulated ex.pdf} |
|
| 9050 | +} |
|
| 9051 | + |
|
| 9052 | +@article{roulland1418Translocation2014, |
|
| 9053 | + title = {T(14;18) {{Translocation}}: {{A}} Predictive Blood Biomarker for Follicular Lymphoma}, |
|
| 9054 | + shorttitle = {T(14;18) {{Translocation}}}, |
|
| 9055 | + author = {Roulland, Sandrine and Kelly, Rachel S. and Morgado, Ester and Sungalee, Stéphanie and Solal-Celigny, Philippe and Colombat, Philippe and Jouve, Nathalie and Palli, Domenico and Pala, Valeria and Tumino, Rosario and Panico, Salvatore and Sacerdote, Carlotta and Quirós, José R. and Gonzáles, Carlos A. and Sánchez, Maria-José and Dorronsoro, Miren and Navarro, Carmen and Barricarte, Aurelio and Tjønneland, Anne and Olsen, Anja and Overvad, Kim and Canzian, Federico and Kaaks, Rudolf and Boeing, Heiner and Drogan, Dagmar and Nieters, Alexandra and Clavel-Chapelon, Françoise and Trichopoulou, Antonia and Trichopoulos, Dimitrios and Lagiou, Pagona and Bueno-de-Mesquita, H. Bas and Peeters, Petra H. M. and Vermeulen, Roel and Hallmans, Göran and Melin, Beatrice and Borgquist, Signe and Carlson, Joyce and Lund, Eiliv and Weiderpass, Elisabete and Khaw, Kay-Tee and Wareham, Nick and Key, Timothy J. and Travis, Ruth C. and Ferrari, Pietro and Romieu, Isabelle and Riboli, Elio and Salles, Gilles and Vineis, Paolo and Nadel, Bertrand}, |
|
| 9056 | + date = {2014-05-01}, |
|
| 9057 | + journaltitle = {Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology}, |
|
| 9058 | + shortjournal = {J Clin Oncol}, |
|
| 9059 | + volume = {32}, |
|
| 9060 | + number = {13}, |
|
| 9061 | + eprint = {24687831}, |
|
| 9062 | + eprinttype = {pmid}, |
|
| 9063 | + pages = {1347--1355}, |
|
| 9064 | + issn = {1527-7755}, |
|
| 9065 | + doi = {10.1200/JCO.2013.52.8190}, |
|
| 9066 | + abstract = {PURPOSE: The (14;18) translocation constitutes both a genetic hallmark and critical early event in the natural history of follicular lymphoma (FL). However, t(14;18) is also detectable in the blood of otherwise healthy persons, and its relationship with progression to disease remains unclear. Here we sought to determine whether t(14;18)-positive cells in healthy individuals represent tumor precursors and whether their detection could be used as an early predictor for FL. PARTICIPANTS AND METHODS: Among 520,000 healthy participants enrolled onto the EPIC (European Prospective Investigation Into Cancer and Nutrition) cohort, we identified 100 who developed FL 2 to 161 months after enrollment. Prediagnostic blood from these and 218 controls were screened for t(14;18) using sensitive polymerase chain reaction-based assays. Results were subsequently validated in an independent cohort (65 case participants; 128 controls). Clonal relationships between t(14;18) cells and FL were also assessed by molecular backtracking of paired prediagnostic blood and tumor samples. RESULTS: Clonal analysis of t(14;18) junctions in paired prediagnostic blood versus tumor samples demonstrated that progression to FL occurred from t(14;18)-positive committed precursors. Furthermore, healthy participants at enrollment who developed FL up to 15 years later showed a markedly higher t(14;18) prevalence and frequency than controls (P {$<$} .001). Altogether, we estimated a 23-fold higher risk of subsequent FL in blood samples associated with a frequency {$>$} 10(-4) (odds ratio, 23.17; 95\% CI, 9.98 to 67.31; P {$<$} .001). Remarkably, risk estimates remained high and significant up to 15 years before diagnosis. CONCLUSION: High t(14;18) frequency in blood from healthy individuals defines the first predictive biomarker for FL, effective years before diagnosis.}, |
|
| 9067 | + langid = {english}, |
|
| 9068 | + keywords = {Adult,Aged,Biomarkers Tumor,Case-Control Studies,Chromosomes Human Pair 14,Chromosomes Human Pair 18,Cohort Studies,Europe,Female,Humans,Lymphoma Follicular,Male,Middle Aged,Molecular Epidemiology,Polymerase Chain Reaction,Prevalence,Translocation Genetic}, |
|
| 9069 | + file = {/Users/rmorin/Zotero/storage/ZWISR2XZ/Roulland et al. - 2014 - t(14;18) Translocation A predictive blood biomark.pdf} |
|
| 9070 | +} |
|
| 9071 | + |
|
| 9072 | +@article{rungeApplicationLymphGenClassification2021, |
|
| 9073 | + title = {Application of the {{LymphGen}} Classification Tool to 928 Clinically and Genetically-Characterised Cases of Diffuse Large {{B}} Cell Lymphoma ({{DLBCL}})}, |
|
| 9074 | + author = {Runge, Hendrik F. P. and Lacy, Stuart and Barrans, Sharon and Beer, Philip A and Painter, Daniel and Smith, Alexandra and Roman, Eve and Burton, Cathy and Crouch, Simon and Tooze, Reuben and Hodson, Daniel J.}, |
|
| 9075 | + date = {2021}, |
|
| 9076 | + journaltitle = {British Journal of Haematology}, |
|
| 9077 | + volume = {192}, |
|
| 9078 | + number = {1}, |
|
| 9079 | + pages = {216--220}, |
|
| 9080 | + issn = {1365-2141}, |
|
| 9081 | + doi = {10.1111/bjh.17132}, |
|
| 9082 | + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/bjh.17132}, |
|
| 9083 | + urldate = {2023-01-16}, |
|
| 9084 | + langid = {english}, |
|
| 9085 | + file = {/Users/rmorin/Zotero/storage/VT3HQ35D/Runge et al. - 2021 - Application of the LymphGen classification tool to.pdf;/Users/rmorin/Zotero/storage/GNLJVPZ6/bjh.html} |
|
| 9086 | +} |
|
| 9087 | + |
|
| 9088 | +@article{rushtonGeneticEvolutionaryPatterns2020, |
|
| 9089 | + title = {Genetic and Evolutionary Patterns of Treatment Resistance in Relapsed {{B-cell}} Lymphoma}, |
|
| 9090 | + author = {Rushton, Christopher K. and Arthur, Sarah E. and Alcaide, Miguel and Cheung, Matthew and Jiang, Aixiang and Coyle, Krysta M. and Cleary, Kirstie L. S. and Thomas, Nicole and Hilton, Laura K. and Michaud, Neil and Daigle, Scott and Davidson, Jordan and Bushell, Kevin and Yu, Stephen and Rys, Ryan N. and Jain, Michael and Shepherd, Lois and Marra, Marco A. and Kuruvilla, John and Crump, Michael and Mann, Koren and Assouline, Sarit and Connors, Joseph M. and Steidl, Christian and Cragg, Mark S. and Scott, David W. and Johnson, Nathalie A. and Morin, Ryan D.}, |
|
| 9091 | + date = {2020-07-14}, |
|
| 9092 | + journaltitle = {Blood Advances}, |
|
| 9093 | + shortjournal = {Blood Adv}, |
|
| 9094 | + volume = {4}, |
|
| 9095 | + number = {13}, |
|
| 9096 | + eprint = {32589730}, |
|
| 9097 | + eprinttype = {pmid}, |
|
| 9098 | + pages = {2886--2898}, |
|
| 9099 | + issn = {2473-9537}, |
|
| 9100 | + doi = {10.1182/bloodadvances.2020001696}, |
|
| 9101 | + abstract = {Diffuse large B-cell lymphoma (DLBCL) patients are typically treated with immunochemotherapy containing rituximab (rituximab, cyclophosphamide, hydroxydaunorubicin-vincristine (Oncovin), and prednisone [R-CHOP]); however, prognosis is extremely poor if R-CHOP fails. To identify genetic mechanisms contributing to primary or acquired R-CHOP resistance, we performed target-panel sequencing of 135 relapsed/refractory DLBCLs (rrDLBCLs), primarily comprising circulating tumor DNA from patients on clinical trials. Comparison with a metacohort of 1670 diagnostic DLBCLs identified 6 genes significantly enriched for mutations upon relapse. TP53 and KMT2D were mutated in the majority of rrDLBCLs, and these mutations remained clonally persistent throughout treatment in paired diagnostic-relapse samples, suggesting a role in primary treatment resistance. Nonsense and missense mutations affecting MS4A1, which encodes CD20, are exceedingly rare in diagnostic samples but show recurrent patterns of clonal expansion following rituximab-based therapy. MS4A1 missense mutations within the transmembrane domains lead to loss of CD20 in vitro, and patient tumors harboring these mutations lacked CD20 protein expression. In a time series from a patient treated with multiple rounds of therapy, tumor heterogeneity and minor MS4A1-harboring subclones contributed to rapid disease recurrence, with MS4A1 mutations as founding events for these subclones. TP53 and KMT2D mutation status, in combination with other prognostic factors, may be used to identify high-risk patients prior to R-CHOP for posttreatment monitoring. Using liquid biopsies, we show the potential to identify tumors with loss of CD20 surface expression stemming from MS4A1 mutations. Implementation of noninvasive assays to detect such features of acquired treatment resistance may allow timely transition to more effective treatment regimens.}, |
|
| 9102 | + langid = {english}, |
|
| 9103 | + pmcid = {PMC7362366}, |
|
| 9104 | + keywords = {Antibodies Monoclonal Murine-Derived,Antineoplastic Combined Chemotherapy Protocols,Humans,Lymphoma Large B-Cell Diffuse,Morinlab,Neoplasm Recurrence Local,Rituximab}, |
|
| 9105 | + file = {/Users/rmorin/Zotero/storage/IDL2CAUC/Rushton et al. - 2020 - Genetic and evolutionary patterns of treatment res.pdf} |
|
| 9106 | +} |
|
| 9107 | + |
|
| 9108 | +@article{russler-germainMutationsAssociatedProgression2023b, |
|
| 9109 | + title = {Mutations Associated with Progression in Follicular Lymphoma Predict Inferior Outcomes at Diagnosis: {{Alliance A151303}}}, |
|
| 9110 | + author = {Russler-Germain, David A. and Krysiak, Kilannin and Ramirez, Cody A. and Mosior, Matthew and Watkins, Marcus P. and Gomez, Felicia and Skidmore, Zachary L. and Trani, L. and Gao, F. and Geyer, Susan and Cashen, A. and Mehta-Shah, N. and Kahl, B. and Bartlett, N. and Alderuccio, J. and Lossos, I. and Ondrejka, S. and Hsi, E. and Martin, P. and Leonard, J. and Griffith, M. and Griffith, O. and Fehniger, T.}, |
|
| 9111 | + date = {2023}, |
|
| 9112 | + journaltitle = {Blood Advances}, |
|
| 9113 | + shortjournal = {Blood Advances}, |
|
| 9114 | + volume = {7}, |
|
| 9115 | + pages = {5524--5539}, |
|
| 9116 | + doi = {10.1182/bloodadvances.2023010779}, |
|
| 9117 | + file = {/Users/rmorin/Zotero/storage/73R8F2F8/Russler-Germain et al. - 2023 - Mutations associated with progression in follicula.pdf} |
|
| 9118 | +} |
|
| 9119 | + |
|
| 9120 | +@article{russoHnRNPH1Intronic2010, |
|
| 9121 | + title = {{{hnRNP H1}} and Intronic {{G}} Runs in the Splicing Control of the Human {{rpL3}} Gene}, |
|
| 9122 | + author = {Russo, Annapina and Siciliano, Gabriella and Catillo, Morena and Giangrande, Chiara and Amoresano, Angela and Pucci, Pietro and Pietropaolo, Concetta and Russo, Giulia}, |
|
| 9123 | + date = {2010-05-01}, |
|
| 9124 | + journaltitle = {Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms}, |
|
| 9125 | + shortjournal = {Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms}, |
|
| 9126 | + volume = {1799}, |
|
| 9127 | + number = {5}, |
|
| 9128 | + pages = {419--428}, |
|
| 9129 | + issn = {1874-9399}, |
|
| 9130 | + doi = {10.1016/j.bbagrm.2010.01.008}, |
|
| 9131 | + url = {https://www.sciencedirect.com/science/article/pii/S1874939910000192}, |
|
| 9132 | + urldate = {2022-09-28}, |
|
| 9133 | + abstract = {By generating mRNA containing a premature termination codon (PTC), alternative splicing (AS) can quantitatively regulate the expression of genes that are degraded by nonsense-mediated mRNA decay (NMD). We previously demonstrated that AS-induced retention of part of intron 3 of rpL3 pre-mRNA produces an mRNA isoform that contains a PTC and is targeted for decay by NMD. We also demonstrated that overexpression of rpL3 downregulates canonical splicing and upregulates the alternative splicing of its pre-mRNA. We are currently investigating the molecular mechanism underlying rpL3 autoregulation. Here we report that the heterogeneous nuclear ribonucleoprotein (hnRNP) H1 is a transacting factor able to interact in vitro and in vivo with rpL3 and with intron 3 of the rpL3 gene. We investigated the role played by hnRNP H1 in the regulation of splicing of rpL3 pre-mRNA by manipulating its expression level. Depletion of hnRNP H1 reduced the level of the PTC-containing mRNA isoform, whereas its overexpression favored the selection of the cryptic 3′ splice site of intron 3. We also identified and characterized the cis-acting regulatory elements involved in hnRNP H1-mediated regulation of splicing. RNA electromobility shift assay demonstrated that hnRNP H1 specifically recognizes and binds directly to the intron 3 region that contains seven copies of G-rich elements. Site-directed mutagenesis analysis and in vivo studies showed that the G3 and G6 elements are required for hnRNP H1-mediated regulation of rpL3 pre-mRNA splicing. We propose a working model in which rpL3 recruits hnRNP H1 and, through cooperation with other splicing factors, promotes selection of the alternative splice site.}, |
|
| 9134 | + langid = {english}, |
|
| 9135 | + keywords = {Alternative splicing,hnRNP H1,NMD,Ribosomal protein,Splicing regulation}, |
|
| 9136 | + file = {/Users/rmorin/Zotero/storage/S2HK77Q6/Russo et al. - 2010 - hnRNP H1 and intronic G runs in the splicing contr.pdf;/Users/rmorin/Zotero/storage/Z7RW4U7C/S1874939910000192.html} |
|
| 9137 | +} |
|
| 9138 | + |
|
| 9139 | +@article{sadriAUF1InvolvedSplenic2010, |
|
| 9140 | + title = {{{AUF1}} Is Involved in Splenic Follicular {{B}} Cell Maintenance}, |
|
| 9141 | + author = {Sadri, Navid and Lu, Jin-Yu and Badura, Michelle L. and Schneider, Robert J.}, |
|
| 9142 | + date = {2010-01-11}, |
|
| 9143 | + journaltitle = {BMC Immunology}, |
|
| 9144 | + shortjournal = {BMC Immunology}, |
|
| 9145 | + volume = {11}, |
|
| 9146 | + number = {1}, |
|
| 9147 | + pages = {1}, |
|
| 9148 | + issn = {1471-2172}, |
|
| 9149 | + doi = {10.1186/1471-2172-11-1}, |
|
| 9150 | + url = {https://doi.org/10.1186/1471-2172-11-1}, |
|
| 9151 | + urldate = {2022-10-04}, |
|
| 9152 | + abstract = {The adenosine/uridine-rich element (ARE)-binding protein AUF1 functions to regulate the inflammatory response through the targeted degradation of cytokine and other mRNAs that contain specific AREs in their 3' noncoding region (3' NCR). To investigate the role of AUF1 in the immune system, we characterized the lymphoid compartments of AUF1-deficient mice.}, |
|
| 9153 | + keywords = {CD40 Engagement,Class Switch Recombination,Germinal Center,Marginal Zone,Splenic Lymphocyte}, |
|
| 9154 | + file = {/Users/rmorin/Zotero/storage/ANBREMX4/Sadri et al. - 2010 - AUF1 is involved in splenic follicular B cell main.pdf;/Users/rmorin/Zotero/storage/U7MNGGBX/1471-2172-11-1.html} |
|
| 9155 | +} |
|
| 9156 | + |
|
| 9157 | +@article{sahaTranscriptomicAnalysisIdentifies2019, |
|
| 9158 | + title = {Transcriptomic {{Analysis Identifies RNA Binding Proteins}} as {{Putative Regulators}} of {{Myelopoiesis}} and {{Leukemia}}}, |
|
| 9159 | + author = {Saha, Subha and Murmu, Krushna Chandra and Biswas, Mayukh and Chakraborty, Sohini and Basu, Jhinuk and Madhulika, Swati and Kolapalli, Srinivasa Prasad and Chauhan, Santosh and Sengupta, Amitava and Prasad, Punit}, |
|
| 9160 | + date = {2019}, |
|
| 9161 | + journaltitle = {Frontiers in Oncology}, |
|
| 9162 | + shortjournal = {Front. Oncol.}, |
|
| 9163 | + volume = {9}, |
|
| 9164 | + issn = {2234-943X}, |
|
| 9165 | + doi = {10.3389/fonc.2019.00692}, |
|
| 9166 | + url = {https://www.frontiersin.org/articles/10.3389/fonc.2019.00692/full}, |
|
| 9167 | + urldate = {2019-12-21}, |
|
| 9168 | + abstract = {Acute myeloid leukemia (AML) is a common and aggressive hematological malignancy. Acquisition of heterogeneous genetic aberrations and epigenetic dysregulation lead to the transformation of hematopoietic stem cells (HSC) into leukemic stem cells (LSC), which subsequently gives rise to immature blast cells and a leukemic phenotype. LSCs are responsible for disease relapse as current chemotherapeutic regimens are not able to completely eradicate these cellular sub-populations. Therefore, it is critical to improve upon the existing knowledge of LSC specific markers, which would allow for specific targeting of these cells more effectively. Although significant milestones in decoding the aberrant transcriptional network of various cancers, including leukemia, have been achieved, studies on the involvement of post-transcriptional gene regulation (PTGR) in disease progression are beginning to unfold. RNA binding proteins (RBPs), are key players in mediating PTGR and they regulate the intracellular fate of individual transcripts, from their biogenesis to RNA metabolism. In this study, we have used an integrative approach to systematically profile RBP expression and identify key regulatory RBPs involved in normal myeloid development and AML. We have analyzed RNA-seq datasets (GSE74246) of HSCs, common myeloid progenitors (CMPs), granulocyte-macrophage progenitors (GMPs), monocytes, LSCs, and blasts. We observed that normal and leukemic cells can be distinguished on the basis of RBP expression, which is indicative of cell type specific expression. We identified that distinctly co-expressing modules of RBPs and their subclasses were enriched in hematopoietic stem/progenitor (HSCP) and differentiated monocytes. We detected expression of DZIP3, an E3 ubiquitin ligase, in HSCP, knockdown of which promotes monocytic differentiation in cell line model. We identified co-expression modules of RBP genes in LSCs and among these, distinct modules of RBP genes with high and low expression. The expression of several AML-specific RBPs were validated byqRT-PCR. Network analysis identified densely connected hubs of ribosomal RBP genes (rRBPs) with low expression in LSCs, suggesting the dependency of LSCs on altered ribosome dynamics. In conclusion, our systematic analysis elucidates the RBP transcriptomic landscape in normal and malignant myelopoiesis, and highlights the functional consequences that may result from perturbation of RBP gene expression in these cellular landscapes.}, |
|
| 9169 | + langid = {english}, |
|
| 9170 | + keywords = {acute myeloid leukemia (AML),Hematopoietic stem cells (HSC),leukemic stem cells (LSCs),myeloid development,nosource,RNA binding proteins (RBP)} |
|
| 9171 | +} |
|
| 9172 | + |
|
| 9173 | +@article{sakrIdentificationDoubleHit2019, |
|
| 9174 | + title = {Identification of "{{Double Hit}}" {{Lymphomas Using Updated WHO Criteria}}: {{Insights From Routine MYC Immunohistochemistry}} in 272 {{Consecutive Cases}} of {{Aggressive B-Cell Lymphomas}}}, |
|
| 9175 | + shorttitle = {Identification of "{{Double Hit}}" {{Lymphomas Using Updated WHO Criteria}}}, |
|
| 9176 | + author = {Sakr, Hany and Cook, James R.}, |
|
| 9177 | + date = {2019-07}, |
|
| 9178 | + journaltitle = {Applied immunohistochemistry \& molecular morphology: AIMM}, |
|
| 9179 | + shortjournal = {Appl. Immunohistochem. Mol. Morphol.}, |
|
| 9180 | + volume = {27}, |
|
| 9181 | + number = {6}, |
|
| 9182 | + eprint = {29629947}, |
|
| 9183 | + eprinttype = {pmid}, |
|
| 9184 | + pages = {410--415}, |
|
| 9185 | + issn = {1533-4058}, |
|
| 9186 | + doi = {10.1097/PAI.0000000000000657}, |
|
| 9187 | + abstract = {Aggressive lymphomas with MYC and BCL2 and/or BCL6 translocations ("double hit" lymphomas, DHL) represent a distinct diagnostic category in the updated World Health Organization (WHO) classification. The diagnostic yield of MYC immunohistochemistry (IHC) for the identification of DHL is currently uncertain. MYC IHC was performed in 272 consecutive cases of aggressive B-cell lymphoma, and results correlated with fluorescence in situ hybridization (FISH) for MYC translocations. Among 156 patients with IHC and FISH data, MYC IHC identified MYC translocations with 89\% sensitivity, 38\% specificity, 92\% negative predictive value, and 29\% positive predictive value. Three of 15 (20\%) of DHL were MYC IHC negative. One case contained a MYC translocation detectable IGH/MYC fusion probes but not MYC break-apart probes. A subset of DHL lack MYC protein expression, and recognition of this subset of cases requires FISH testing. These results provide an appropriate diagnostic algorithm for implementation of 2016 WHO diagnostic criteria.}, |
|
| 9188 | + langid = {english} |
|
| 9189 | +} |
|
| 9190 | + |
|
| 9191 | +@article{salaverriaRecurrent11qAberration2014, |
|
| 9192 | + title = {A Recurrent 11q Aberration Pattern Characterizes a Subset of {{MYC-negative}} High-Grade {{B-cell}} Lymphomas Resembling {{Burkitt}} Lymphoma}, |
|
| 9193 | + author = {Salaverria, Itziar and Martin-Guerrero, Idoia and Wagener, Rabea and Kreuz, Markus and Kohler, Christian W. and Richter, Julia and Pienkowska-Grela, Barbara and Adam, Patrick and Burkhardt, Birgit and Claviez, Alexander and Damm-Welk, Christine and Drexler, Hans G. and Hummel, Michael and Jaffe, Elaine S. and Küppers, Ralf and Lefebvre, Christine and Lisfeld, Jasmin and Löffler, Markus and Macleod, Roderick A. F. and Nagel, Inga and Oschlies, Ilske and Rosolowski, Maciej and Russell, Robert B. and Rymkiewicz, Grzegorz and Schindler, Detlev and Schlesner, Matthias and Scholtysik, René and Schwaenen, Carsten and Spang, Rainer and Szczepanowski, Monika and Trümper, Lorenz and Vater, Inga and Wessendorf, Swen and Klapper, Wolfram and Siebert, Reiner and {Molecular Mechanisms in Malignant Lymphoma Network Project} and {Berlin-Frankfurt-Münster Non-Hodgkin Lymphoma Group}}, |
|
| 9194 | + date = {2014-02-20}, |
|
| 9195 | + journaltitle = {Blood}, |
|
| 9196 | + shortjournal = {Blood}, |
|
| 9197 | + volume = {123}, |
|
| 9198 | + number = {8}, |
|
| 9199 | + eprint = {24398325}, |
|
| 9200 | + eprinttype = {pmid}, |
|
| 9201 | + pages = {1187--1198}, |
|
| 9202 | + issn = {1528-0020}, |
|
| 9203 | + doi = {10.1182/blood-2013-06-507996}, |
|
| 9204 | + abstract = {The genetic hallmark of Burkitt lymphoma (BL) is the t(8;14)(q24;q32) and its variants leading to activation of the MYC oncogene. It is a matter of debate whether true BL without MYC translocation exists. Here, we identified 59 lymphomas concordantly called BL by 2 gene expression classifiers among 753 B-cell lymphomas. Only 2 (3\%) of these 59 molecular BL lacked a MYC translocation, which both shared a peculiar pattern of chromosome 11q aberration characterized by interstitial gains including 11q23.2-q23.3 and telomeric losses of 11q24.1-qter. We extended our analysis to 17 MYC-negative high-grade B-cell lymphomas with a similar 11q aberration and showed this aberration to be recurrently associated with morphologic and clinical features of BL. The minimal region of gain was defined by high-level amplifications in 11q23.3 and associated with overexpression of genes including PAFAH1B2 on a transcriptional and protein level. The recurrent region of loss contained a focal homozygous deletion in 11q24.2-q24.3 including the ETS1 gene, which was shown to be mutated in 4 of 16 investigated cases. These findings indicate the existence of a molecularly distinct subset of B-cell lymphomas reminiscent of BL, which is characterized by deregulation of genes in 11q.}, |
|
| 9205 | + langid = {english}, |
|
| 9206 | + pmcid = {PMC3931189}, |
|
| 9207 | + keywords = {Adolescent,Adult,Aged,B-Lymphocytes,Burkitt Lymphoma,Cell Line,Child,Chromosomes Human Pair 11,Chromosomes Human Pair 14,Chromosomes Human Pair 8,Female,Gene Expression Regulation Neoplastic,Genes myc,Humans,Male,Neoplasm Grading,Recurrence,Translocation Genetic,Young Adult} |
|
| 9208 | +} |
|
| 9209 | + |
|
| 9210 | +@article{salehiCancerPhylogeneticTree2021, |
|
| 9211 | + title = {Cancer Phylogenetic Tree Inference at Scale from 1000s of Single Cell Genomes}, |
|
| 9212 | + author = {Salehi, Sohrab and Dorri, Fatemeh and Chern, Kevin and Kabeer, Farhia and Rusk, Nicole and Funnell, Tyler and Williams, Marc J. and Lai, Daniel and Andronescu, Mirela and Campbell, Kieran R. and McPherson, Andrew and Aparicio, Samuel and Roth, Andrew and Shah, Sohrab and Bouchard-Côté, Alexandre}, |
|
| 9213 | + date = {2021-09-04}, |
|
| 9214 | + pages = {2020.05.06.058180}, |
|
| 9215 | + publisher = {bioRxiv}, |
|
| 9216 | + doi = {10.1101/2020.05.06.058180}, |
|
| 9217 | + url = {https://www.biorxiv.org/content/10.1101/2020.05.06.058180v2}, |
|
| 9218 | + urldate = {2022-02-01}, |
|
| 9219 | + abstract = {A new generation of scalable single cell whole genome sequencing (scWGS) methods allows unprecedented high resolution measurement of the evolutionary dynamics of cancer cell populations. Phylogenetic reconstruction is central to identifying sub-populations and distinguishing the mutational processes that gave rise to them. Existing phylogenetic tree building models do not scale to the tens of thousands of high resolution genomes achievable with current scWGS methods. We constructed a phylogenetic model and associated Bayesian inference procedure, sitka, specifically for scWGS data. The method is based on a novel phylogenetic encoding of copy number (CN) data, the sitka transformation, that simplifies the site dependencies induced by rearrangements while still forming a sound foundation to phylogenetic inference. The sitka transformation allows us to design novel scalable Markov chain Monte Carlo (MCMC) algorithms. Moreover, we introduce a novel point mutation calling method that incorporates the CN data and the underlying phylogenetic tree to overcome the low per-cell coverage of scWGS. We demonstrate our method on three single cell datasets, including a novel PDX series, and analyse the topological properties of the inferred trees. Sitka is freely available at https://github.com/UBC-Stat-ML/sitkatree.git.}, |
|
| 9220 | + langid = {english}, |
|
| 9221 | + file = {/Users/rmorin/Zotero/storage/B9GLXYUB/Salehi et al. - 2021 - Cancer phylogenetic tree inference at scale from 1.pdf;/Users/rmorin/Zotero/storage/K929KX24/2020.05.06.html} |
|
| 9222 | +} |
|
| 9223 | + |
|
| 9224 | +@article{salehiClonalFitnessInferred2021, |
|
| 9225 | + title = {Clonal Fitness Inferred from Time-Series Modelling of Single-Cell Cancer Genomes}, |
|
| 9226 | + author = {Salehi, Sohrab and Kabeer, Farhia and Ceglia, Nicholas and Andronescu, Mirela and Williams, Marc J. and Campbell, Kieran R. and Masud, Tehmina and Wang, Beixi and Biele, Justina and Brimhall, Jazmine and Gee, David and Lee, Hakwoo and Ting, Jerome and Zhang, Allen W. and Tran, Hoa and O'Flanagan, Ciara and Dorri, Fatemeh and Rusk, Nicole and family=Algara, given=Teresa Ruiz, prefix=de, useprefix=true and Lee, So Ra and Cheng, Brian Yu Chieh and Eirew, Peter and Kono, Takako and Pham, Jenifer and Grewal, Diljot and Lai, Daniel and Moore, Richard and Mungall, Andrew J. and Marra, Marco A. and {IMAXT Consortium} and McPherson, Andrew and Bouchard-Côté, Alexandre and Aparicio, Samuel and Shah, Sohrab P.}, |
|
| 9227 | + date = {2021-07}, |
|
| 9228 | + journaltitle = {Nature}, |
|
| 9229 | + shortjournal = {Nature}, |
|
| 9230 | + volume = {595}, |
|
| 9231 | + number = {7868}, |
|
| 9232 | + eprint = {34163070}, |
|
| 9233 | + eprinttype = {pmid}, |
|
| 9234 | + pages = {585--590}, |
|
| 9235 | + issn = {1476-4687}, |
|
| 9236 | + doi = {10.1038/s41586-021-03648-3}, |
|
| 9237 | + abstract = {Progress in defining genomic fitness landscapes in cancer, especially those defined by copy number alterations (CNAs), has been impeded by lack of time-series single-cell sampling of polyclonal populations and temporal statistical models1-7. Here we generated 42,000 genomes from multi-year time-series single-cell whole-genome sequencing of breast epithelium and primary triple-negative breast cancer (TNBC) patient-derived xenografts (PDXs), revealing the nature of CNA-defined clonal fitness dynamics induced by TP53 mutation and cisplatin chemotherapy. Using a new Wright-Fisher population genetics model8,9 to infer clonal fitness, we found that TP53 mutation alters the fitness landscape, reproducibly distributing fitness over a larger number of clones associated with distinct CNAs. Furthermore, in TNBC PDX models with mutated TP53, inferred fitness coefficients from CNA-based genotypes accurately forecast experimentally enforced clonal competition dynamics. Drug treatment in three long-term serially passaged TNBC PDXs resulted in cisplatin-resistant clones emerging from low-fitness phylogenetic lineages in the untreated setting. Conversely, high-fitness clones from treatment-naive controls were eradicated, signalling an inversion of the fitness landscape. Finally, upon release of drug, selection pressure dynamics were reversed, indicating a fitness cost of treatment resistance. Together, our findings define clonal fitness linked to both CNA and therapeutic resistance in polyclonal tumours.}, |
|
| 9238 | + langid = {english}, |
|
| 9239 | + pmcid = {PMC8396073}, |
|
| 9240 | + keywords = {Animals,Cell Line Tumor,Cisplatin,Clone Cells,DNA Copy Number Variations,Drug Resistance Neoplasm,Female,Genetic Fitness,Humans,Mice,Models Statistical,Neoplasm Transplantation,Triple Negative Breast Neoplasms,Tumor Suppressor Protein p53,Whole Genome Sequencing}, |
|
| 9241 | + file = {/Users/rmorin/Zotero/storage/C3YYYA42/Salehi et al. - 2021 - Clonal fitness inferred from time-series modelling.pdf} |
|
| 9242 | +} |
|
| 9243 | + |
|
| 9244 | +@article{salghettiDestructionMycUbiquitinmediated1999, |
|
| 9245 | + title = {Destruction of {{Myc}} by Ubiquitin-Mediated Proteolysis: Cancer-Associated and Transforming Mutations Stabilize {{Myc}}}, |
|
| 9246 | + shorttitle = {Destruction of {{Myc}} by Ubiquitin-Mediated Proteolysis}, |
|
| 9247 | + author = {Salghetti, Simone E. and Young Kim, So and Tansey, William P.}, |
|
| 9248 | + date = {1999-02-01}, |
|
| 9249 | + journaltitle = {The EMBO Journal}, |
|
| 9250 | + shortjournal = {The EMBO Journal}, |
|
| 9251 | + volume = {18}, |
|
| 9252 | + number = {3}, |
|
| 9253 | + pages = {717--726}, |
|
| 9254 | + publisher = {John Wiley \& Sons, Ltd}, |
|
| 9255 | + issn = {0261-4189}, |
|
| 9256 | + doi = {10.1093/emboj/18.3.717}, |
|
| 9257 | + url = {https://www.embopress.org/doi/full/10.1093/emboj/18.3.717}, |
|
| 9258 | + urldate = {2021-04-29}, |
|
| 9259 | + abstract = {The human proto-oncogene c-myc encodes a highly unstable transcription factor that promotes cell proliferation. Although the extreme instability of Myc plays an important role in preventing its accumulation in normal cells, little is known about how Myc is targeted for rapid destruction. Here, we have investigated mechanisms regulating the stability of Myc. We show that Myc is destroyed by ubiquitin-mediated proteolysis, and define two elements in Myc that oppositely regulate its stability: a transcriptional activation domain that promotes Myc destruction, and a region required for association with the POZ domain protein Miz-1 that stabilizes Myc. We also show that Myc is stabilized by cancer-associated and transforming mutations within its transcriptional activation domain. Our data reveal a complex network of interactions regulating Myc destruction, and imply that enhanced protein stability contributes to oncogenic transformation by mutant Myc proteins.}, |
|
| 9260 | + keywords = {Miz-1,Myc,transcription,ubiquitin-mediated proteolysis}, |
|
| 9261 | + file = {/Users/rmorin/Zotero/storage/SVDK29I6/Salghetti et al. - 1999 - Destruction of Myc by ubiquitin-mediated proteolys.pdf;/Users/rmorin/Zotero/storage/HDBBGX9H/18.3.html} |
|
| 9262 | +} |
|
| 9263 | + |
|
| 9264 | +@article{sallesPrognosticSignificanceImmunohistochemical2011, |
|
| 9265 | + title = {Prognostic Significance of Immunohistochemical Biomarkers in Diffuse Large {{B-cell}} Lymphoma: A Study from the {{Lunenburg Lymphoma Biomarker Consortium}}.}, |
|
| 9266 | + author = {Salles, Gilles and family=Jong, given=Daphne, prefix=de, useprefix=true and Xie, Wanling and Rosenwald, Andreas and Chhanabhai, Mukesh and Gaulard, Philippe and Klapper, Wolfram and Calaminici, Maria and Sander, Birgitta and Thorns, Christoph and Campo, Elias and Molina, Thierry and Lee, Abigail and Pfreundschuh, Michael and Horning, Sandra and Lister, Andrew and Sehn, Laurie H and Raemaekers, John and Hagenbeek, Anton and Gascoyne, Randy D and Weller, Edie}, |
|
| 9267 | + date = {2011-05}, |
|
| 9268 | + journaltitle = {Blood}, |
|
| 9269 | + keywords = {nosource} |
|
| 9270 | +} |
|
| 9271 | + |
|
| 9272 | +@article{saltzmanRegulationAlternativeSplicing2011, |
|
| 9273 | + title = {Regulation of Alternative Splicing by the Core Spliceosomal Machinery}, |
|
| 9274 | + author = {Saltzman, Arneet L. and Pan, Qun and Blencowe, Benjamin J.}, |
|
| 9275 | + date = {2011-02-15}, |
|
| 9276 | + journaltitle = {Genes \& Development}, |
|
| 9277 | + shortjournal = {Genes Dev.}, |
|
| 9278 | + volume = {25}, |
|
| 9279 | + number = {4}, |
|
| 9280 | + eprint = {21325135}, |
|
| 9281 | + eprinttype = {pmid}, |
|
| 9282 | + pages = {373--384}, |
|
| 9283 | + issn = {0890-9369, 1549-5477}, |
|
| 9284 | + doi = {10.1101/gad.2004811}, |
|
| 9285 | + url = {http://genesdev.cshlp.org/content/25/4/373}, |
|
| 9286 | + urldate = {2019-12-21}, |
|
| 9287 | + abstract = {Alternative splicing (AS) plays a major role in the generation of proteomic diversity and in gene regulation. However, the role of the basal splicing machinery in regulating AS remains poorly understood. Here we show that the core snRNP (small nuclear ribonucleoprotein) protein SmB/B′ self-regulates its expression by promoting the inclusion of a highly conserved alternative exon in its own pre-mRNA that targets the spliced transcript for nonsense-mediated mRNA decay (NMD). Depletion of SmB/B′ in human cells results in reduced levels of snRNPs and a striking reduction in the inclusion levels of hundreds of additional alternative exons, with comparatively few effects on constitutive exon splicing levels. The affected alternative exons are enriched in genes encoding RNA processing and other RNA-binding factors, and a subset of these exons also regulate gene expression by activating NMD. Our results thus demonstrate a role for the core spliceosomal machinery in controlling an exon network that appears to modulate the levels of many RNA processing factors.}, |
|
| 9288 | + langid = {english}, |
|
| 9289 | + keywords = {alternative splicing,autoregulation,exon network,NMD,Sm proteins,snRNP}, |
|
| 9290 | + file = {/Users/rmorin/Zotero/storage/RPSUI7TL/373.html} |
|
| 9291 | +} |
|
| 9292 | + |
|
| 9293 | +@article{sanchez-martinQuadruplexLigandsCancer2021, |
|
| 9294 | + title = {Quadruplex {{Ligands}} in {{Cancer Therapy}}}, |
|
| 9295 | + author = {Sanchez-Martin, Victoria and Soriano, Miguel and Garcia-Salcedo, Jose Antonio}, |
|
| 9296 | + date = {2021-06-24}, |
|
| 9297 | + journaltitle = {Cancers}, |
|
| 9298 | + shortjournal = {Cancers (Basel)}, |
|
| 9299 | + volume = {13}, |
|
| 9300 | + number = {13}, |
|
| 9301 | + eprint = {34202648}, |
|
| 9302 | + eprinttype = {pmid}, |
|
| 9303 | + pages = {3156}, |
|
| 9304 | + issn = {2072-6694}, |
|
| 9305 | + doi = {10.3390/cancers13133156}, |
|
| 9306 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8267697/}, |
|
| 9307 | + urldate = {2022-10-15}, |
|
| 9308 | + abstract = {Simple Summary Four-stranded nucleic acid secondary structures (quadruplexes) including DNA G-quadruplexes, RNA G-quadruplexes and i-Motifs display key regulatory functions in the human genome. Quadruplexes play an important role in telomere lengthening and the expression control of several cancer-related genes. In this context, quadruplex ligands are considered as potential strategies for anticancer drug discovery. Previous reviews are mainly focused on ligands targeting DNA G-quadruplexes, RNA G-quadruplexes and i-Motifs in a separate way, hindering a holistic study. The present review overcomes this limitation by providing a general overview of the recent research on ligands targeting the three different quadruplex structures in cancer. Abstract Nucleic acids can adopt alternative secondary conformations including four-stranded structures known as quadruplexes. To date, quadruplexes have been demonstrated to exist both in human chromatin DNA and RNA. In particular, quadruplexes are found in guanine-rich sequences constituting G-quadruplexes, and in cytosine-rich sequences forming i-Motifs as a counterpart. Quadruplexes are associated with key biological processes ranging from transcription and translation of several oncogenes and tumor suppressors to telomeres maintenance and genome instability. In this context, quadruplexes have prompted investigations on their possible role in cancer biology and the evaluation of small-molecule ligands as potential therapeutic agents. This review aims to provide an updated close-up view of the literature on quadruplex ligands in cancer therapy, by grouping together ligands for DNA and RNA G-quadruplexes and DNA i-Motifs.}, |
|
| 9309 | + pmcid = {PMC8267697}, |
|
| 9310 | + file = {/Users/rmorin/Zotero/storage/EZPQEGDJ/Sanchez-Martin et al. - 2021 - Quadruplex Ligands in Cancer Therapy.pdf} |
|
| 9311 | +} |
|
| 9312 | + |
|
| 9313 | +@article{sanchezCoupledAlterationTranscription2008, |
|
| 9314 | + title = {Coupled Alteration of Transcription and Splicing by a Single Oncogene: {{Boosting}} the Effect on Cyclin {{D1}} Activity}, |
|
| 9315 | + shorttitle = {Coupled Alteration of Transcription and Splicing by a Single Oncogene}, |
|
| 9316 | + author = {Sanchez, Gabriel and Delattre, Olivier and Auboeuf, Didier and Dutertre, Martin}, |
|
| 9317 | + date = {2008-08-01}, |
|
| 9318 | + journaltitle = {Cell Cycle}, |
|
| 9319 | + volume = {7}, |
|
| 9320 | + number = {15}, |
|
| 9321 | + eprint = {18677114}, |
|
| 9322 | + eprinttype = {pmid}, |
|
| 9323 | + pages = {2299--2305}, |
|
| 9324 | + issn = {1538-4101}, |
|
| 9325 | + doi = {10.4161/cc.6445}, |
|
| 9326 | + url = {https://doi.org/10.4161/cc.6445}, |
|
| 9327 | + urldate = {2019-12-21}, |
|
| 9328 | + abstract = {In cancer cells, gene expression is altered at the levels of transcription and mRNA maturation, with many splice variants being associated with cancer. Splicing is tightly connected to transcription and can be affected by transcription elongation dynamics. Moreover, various transcriptional coregulators that are altered in cancer, such as the proto-oncogene EWS, are thought to play a role in splicing. A recent study shows that an alteration of EWS in Ewing sarcoma alters the dynamics of RNA polymerase II over the CCND1 proto-oncogene encoding cyclin D1, leading to an increase in its transcription and to an alteration of splicing that results in high levels of the oncogenic cyclin D1b splice isoform. The cyclin D1b isoform is highly expressed in Ewing sarcoma cells and tumors and stimulates Ewing sarcoma cell growth. Thus, alterations of transcriptional regulators in disease may lead to splicing alterations. We review these data and discuss how this concept may apply to various factors that are altered in cancer.}, |
|
| 9329 | + file = {/Users/rmorin/Zotero/storage/WNTJ6ZL2/cc.html} |
|
| 9330 | +} |
|
| 9331 | + |
|
| 9332 | +@article{sapirHeterogeneousNuclearRibonucleoprotein, |
|
| 9333 | + title = {Heterogeneous Nuclear Ribonucleoprotein {{U}} ({{HNRNPU}}) Safeguards the Developing Mouse Cortex - {{PMC}}}, |
|
| 9334 | + author = {Sapir, Tamar and Kshirsagar, Aditya and Gorelik, Anna}, |
|
| 9335 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9304408/}, |
|
| 9336 | + urldate = {2023-01-09}, |
|
| 9337 | + file = {/Users/rmorin/Zotero/storage/R6GNLZLP/PMC9304408.html} |
|
| 9338 | +} |
|
| 9339 | + |
|
| 9340 | +@article{sapirHeterogeneousNuclearRibonucleoprotein2022, |
|
| 9341 | + title = {Heterogeneous Nuclear Ribonucleoprotein {{U}} ({{HNRNPU}}) Safeguards the Developing Mouse Cortex}, |
|
| 9342 | + author = {Sapir, Tamar and Kshirsagar, Aditya and Gorelik, Anna and Olender, Tsviya and Porat, Ziv and Scheffer, Ingrid E. and Goldstein, David B. and Devinsky, Orrin and Reiner, Orly}, |
|
| 9343 | + date = {2022-07-21}, |
|
| 9344 | + journaltitle = {Nature Communications}, |
|
| 9345 | + shortjournal = {Nat Commun}, |
|
| 9346 | + volume = {13}, |
|
| 9347 | + eprint = {35864088}, |
|
| 9348 | + eprinttype = {pmid}, |
|
| 9349 | + pages = {4209}, |
|
| 9350 | + issn = {2041-1723}, |
|
| 9351 | + doi = {10.1038/s41467-022-31752-z}, |
|
| 9352 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9304408/}, |
|
| 9353 | + urldate = {2023-01-09}, |
|
| 9354 | + abstract = {HNRNPU encodes the heterogeneous nuclear ribonucleoprotein U, which participates in RNA splicing and chromatin organization. Microdeletions in the 1q44 locus encompassing HNRNPU and other genes and point mutations in HNRNPU cause brain disorders, including early-onset seizures and severe intellectual disability. We aimed to understand HNRNPU’s roles in the developing brain. Our work revealed that HNRNPU loss of function leads to rapid cell death of both postmitotic neurons and neural progenitors, with an apparent higher sensitivity of the latter. Further, expression and alternative splicing of multiple genes involved in cell survival, cell motility, and synapse formation are affected following Hnrnpu’s conditional truncation. Finally, we identified pharmaceutical and genetic agents that can partially reverse the loss of cortical structures in Hnrnpu mutated embryonic brains, ameliorate radial neuronal migration defects and rescue cultured neural progenitors’ cell death., HNRNPU is an RNA splicing protein associated with brain disorders such as early onset seizures. Here they show that HNRNPU functions to maintain neural progenitors and their progeny by regulating splicing of key neuronal genes.}, |
|
| 9355 | + pmcid = {PMC9304408}, |
|
| 9356 | + file = {/Users/rmorin/Zotero/storage/7V69HLX7/Sapir et al. - 2022 - Heterogeneous nuclear ribonucleoprotein U (HNRNPU).pdf} |
|
| 9357 | +} |
|
| 9358 | + |
|
| 9359 | +@article{sardoneAntisenseOligonucleotideBasedTherapy2017, |
|
| 9360 | + title = {Antisense {{Oligonucleotide-Based Therapy}} for {{Neuromuscular Disease}}}, |
|
| 9361 | + author = {Sardone, Valentina and Zhou, Haiyan and Muntoni, Francesco and Ferlini, Alessandra and Falzarano, Maria Sofia}, |
|
| 9362 | + date = {2017-04-05}, |
|
| 9363 | + journaltitle = {Molecules : A Journal of Synthetic Chemistry and Natural Product Chemistry}, |
|
| 9364 | + shortjournal = {Molecules}, |
|
| 9365 | + volume = {22}, |
|
| 9366 | + number = {4}, |
|
| 9367 | + eprint = {28379182}, |
|
| 9368 | + eprinttype = {pmid}, |
|
| 9369 | + pages = {563}, |
|
| 9370 | + issn = {1420-3049}, |
|
| 9371 | + doi = {10.3390/molecules22040563}, |
|
| 9372 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6154734/}, |
|
| 9373 | + urldate = {2021-11-30}, |
|
| 9374 | + abstract = {Neuromuscular disorders such as Duchenne Muscular Dystrophy and Spinal Muscular Atrophy are neurodegenerative genetic diseases characterized primarily by muscle weakness and wasting. Until recently there were no effective therapies for these conditions, but antisense oligonucleotides, a new class of synthetic single stranded molecules of nucleic acids, have demonstrated promising experimental results and are at different stages of regulatory approval. The antisense oligonucleotides can modulate the protein expression via targeting hnRNAs or mRNAs and inducing interference with splicing, mRNA degradation, or arrest of translation, finally, resulting in rescue or reduction of the target protein expression. Different classes of antisense oligonucleotides are being tested in several clinical trials, and limitations of their clinical efficacy and toxicity have been reported for some of these compounds, while more encouraging results have supported the development of others. New generation antisense oligonucleotides are also being tested in preclinical models together with specific delivery systems that could allow some of the limitations of current antisense oligonucleotides to be overcome, to improve the cell penetration, to achieve more robust target engagement, and hopefully also be associated with acceptable toxicity. This review article describes the chemical properties and molecular mechanisms of action of the antisense oligonucleotides and the therapeutic implications these compounds have in neuromuscular diseases. Current strategies and carrier systems available for the oligonucleotides delivery will be also described to provide an overview on the past, present and future of these appealing molecules.}, |
|
| 9375 | + pmcid = {PMC6154734}, |
|
| 9376 | + file = {/Users/rmorin/Zotero/storage/IGDH7CSX/Sardone et al. - 2017 - Antisense Oligonucleotide-Based Therapy for Neurom.pdf} |
|
| 9377 | +} |
|
| 9378 | + |
|
| 9379 | +@article{sarkozyMutationalLandscapeGray2021a, |
|
| 9380 | + title = {Mutational Landscape of Gray Zone Lymphoma}, |
|
| 9381 | + author = {Sarkozy, Clémentine and Hung, Stacy S. and Chavez, Elizabeth A. and Duns, Gerben and Takata, Katsuyoshi and Chong, Lauren C. and Aoki, Tomohiro and Jiang, Aixiang and Miyata-Takata, Tomoko and Telenius, Adèle and Slack, Graham W. and Molina, Thierry Jo and Ben-Neriah, Susana and Farinha, Pedro and Dartigues, Peggy and Damotte, Diane and Mottok, Anja and Salles, Gilles A. and Casasnovas, Rene-Olivier and Savage, Kerry J. and Laurent, Camille and Scott, David W. and Traverse-Glehen, Alexandra and Steidl, Christian}, |
|
| 9382 | + date = {2021-04-01}, |
|
| 9383 | + journaltitle = {Blood}, |
|
| 9384 | + shortjournal = {Blood}, |
|
| 9385 | + volume = {137}, |
|
| 9386 | + number = {13}, |
|
| 9387 | + eprint = {32961552}, |
|
| 9388 | + eprinttype = {pmid}, |
|
| 9389 | + pages = {1765--1776}, |
|
| 9390 | + issn = {1528-0020}, |
|
| 9391 | + doi = {10.1182/blood.2020007507}, |
|
| 9392 | + abstract = {The mutational landscape of gray zone lymphoma (GZL) has not yet been established, and differences from related entities are largely unknown. Here, we studied coding sequence mutations of 50 Epstein-Barr virus (EBV)-negative GZLs and 20 polymorphic EBV+ diffuse large B-cell lymphoma (DLBCL) not otherwise specified (poly-EBV-L) in comparison with classical Hodgkin lymphoma (cHL), primary mediastinal large B-cell lymphoma (PMBCL), and DLBCL. Exomes of 21 GZL and 7 poly-EBV-L cases, along with paired constitutional DNA, were analyzed as a discovery cohort, followed by targeted sequencing of 217 genes in an extension cohort of 29 GZL and 13 poly-EBV-L cases. GZL cases with thymic niche involvement (anterior mediastinal mass) exhibited a mutation profile closely resembling cHL and PMBCL, with SOCS1 (45\%), B2M (45\%), TNFAIP3 (35\%), GNA13 (35\%), LRRN3 (32\%), and NFKBIA (29\%) being the most recurrently mutated genes. In contrast, GZL cases without thymic niche involvement (n = 18) had a significantly distinct pattern that was enriched in mutations related to apoptosis defects (TP53 [39\%], BCL2 [28\%], BIRC6 [22\%]) and depleted in GNA13, XPO1, or NF-κB signaling pathway mutations (TNFAIP3, NFKBIE, IKBKB, NFKBIA). They also exhibited more BCL2/BCL6 rearrangements compared with thymic GZL. Poly-EBV-L cases presented a distinct mutational profile, including STAT3 mutations and a significantly lower coding mutation load in comparison with EBV- GZL. Our study highlights characteristic mutational patterns in GZL associated with presentation in the thymic niche, suggesting a common cell of origin and disease evolution overlapping with related anterior mediastinal lymphomas.}, |
|
| 9393 | + langid = {english}, |
|
| 9394 | + keywords = {Adolescent,Adult,Aged,Aged 80 and over,Epstein-Barr Virus Infections,Female,Hodgkin Disease,Humans,Lymphoma Large B-Cell Diffuse,Male,Mediastinal Neoplasms,Middle Aged,Mutation,Thymus Gland,Young Adult}, |
|
| 9395 | + file = {/Users/rmorin/Zotero/storage/DMQ5Z88E/Sarkozy et al. - 2021 - Mutational landscape of gray zone lymphoma.pdf} |
|
| 9396 | +} |
|
| 9397 | + |
|
| 9398 | +@article{satijaSpatialReconstructionSinglecell2015, |
|
| 9399 | + title = {Spatial Reconstruction of Single-Cell Gene Expression Data}, |
|
| 9400 | + author = {Satija, Rahul and Farrell, Jeffrey A. and Gennert, David and Schier, Alexander F. and Regev, Aviv}, |
|
| 9401 | + date = {2015-05}, |
|
| 9402 | + journaltitle = {Nature Biotechnology}, |
|
| 9403 | + shortjournal = {Nat Biotechnol}, |
|
| 9404 | + volume = {33}, |
|
| 9405 | + number = {5}, |
|
| 9406 | + pages = {495--502}, |
|
| 9407 | + publisher = {Nature Publishing Group}, |
|
| 9408 | + issn = {1546-1696}, |
|
| 9409 | + doi = {10.1038/nbt.3192}, |
|
| 9410 | + url = {https://www.nature.com/articles/nbt.3192}, |
|
| 9411 | + urldate = {2022-02-01}, |
|
| 9412 | + abstract = {RNA-seq data from single cells are mapped to their location in complex tissues using gene expression atlases based on in situ hybridization.}, |
|
| 9413 | + issue = {5}, |
|
| 9414 | + langid = {english}, |
|
| 9415 | + keywords = {Gastrulation,Machine learning,Statistical methods}, |
|
| 9416 | + file = {/Users/rmorin/Zotero/storage/TH6L8LQZ/Satija et al. - 2015 - Spatial reconstruction of single-cell gene express.pdf;/Users/rmorin/Zotero/storage/JX254NUC/nbt.html} |
|
| 9417 | +} |
|
| 9418 | + |
|
| 9419 | +@article{satouPrognosticImpactMUM12017, |
|
| 9420 | + title = {Prognostic {{Impact}} of {{MUM1}}/{{IRF4 Expression}} in {{Burkitt Lymphoma}} ({{BL}}): {{A Reappraisal}} of 88 {{BL Patients}} in {{Japan}}}, |
|
| 9421 | + shorttitle = {Prognostic {{Impact}} of {{MUM1}}/{{IRF4 Expression}} in {{Burkitt Lymphoma}} ({{BL}})}, |
|
| 9422 | + author = {Satou, Akira and Asano, Naoko and Kato, Seiichi and Elsayed, Ahmed A. and Nakamura, Naoya and Miyoshi, Hiroaki and Ohshima, Koichi and Nakamura, Shigeo}, |
|
| 9423 | + date = {2017-03}, |
|
| 9424 | + journaltitle = {The American Journal of Surgical Pathology}, |
|
| 9425 | + shortjournal = {Am J Surg Pathol}, |
|
| 9426 | + volume = {41}, |
|
| 9427 | + number = {3}, |
|
| 9428 | + eprint = {28079574}, |
|
| 9429 | + eprinttype = {pmid}, |
|
| 9430 | + pages = {389--395}, |
|
| 9431 | + issn = {1532-0979}, |
|
| 9432 | + doi = {10.1097/PAS.0000000000000804}, |
|
| 9433 | + abstract = {MUM1/IRF4 expression is detected in 18\% to 41\% of Burkitt lymphoma (BL). However, only a few studies of MUM1-positive (MUM1) BL have been reported, and its characteristics still remain controversial. To highlight the features of MUM1 BL, we compared the clinicopathologic characteristics of 37 cases of MUM1 and 51 cases of MUM1-negative (MUM1) BL in Japan. Compared with MUM1 BL, patients with MUM1 BL showed significantly younger onset (P=0.0062) and a higher ratio of females (P=0.013). We have also revealed the difference in the involved sites. The MUM1 group showed lower incidences of involvement of stomach (P=0.012) and tonsil (P=0.069). There was a more tendency in MUM1 group to involve colon (P=0.072), breast (P=0.073), and kidney (P=0.073). Regarding the prognosis, a trend toward a lower overall survival for MUM1 group was noted (P=0.089). Notably, comparing MUM1 and MUM1 BL cases of adults (age16 y old and above), the former showed significantly worse prognosis (P=0.041). Among the BL patients treated with the intensive chemotherapy, a standard therapy for BL, MUM1 cases showed worse prognosis (P=0.056). In conclusion, MUM1 BL showed worse prognosis, particularly in adult cases, compared with MUM1 BL. In addition, the difference of the onset age, sex ratio, and involved sites between the 2 groups was noted. Our results demonstrate that MUM1 expression might predict worse prognosis of BL, and MUM1 BL should be distinguished from MUM1 BL.}, |
|
| 9434 | + langid = {english}, |
|
| 9435 | + keywords = {Adolescent,Adult,Aged,Aged 80 and over,Biomarkers Tumor,Burkitt Lymphoma,Child,Child Preschool,Female,Follow-Up Studies,Humans,Immunohistochemistry,In Situ Hybridization Fluorescence,Interferon Regulatory Factors,Japan,Male,Middle Aged,Prognosis,Retrospective Studies,Survival Analysis,Young Adult} |
|
| 9436 | +} |
|
| 9437 | + |
|
| 9438 | +@article{satpathyMassivelyParallelSinglecell2019, |
|
| 9439 | + title = {Massively Parallel Single-Cell Chromatin Landscapes of Human Immune Cell Development and Intratumoral {{T}} Cell Exhaustion}, |
|
| 9440 | + author = {Satpathy, Ansuman T. and Granja, Jeffrey M. and Yost, Kathryn E. and Qi, Yanyan and Meschi, Francesca and McDermott, Geoffrey P. and Olsen, Brett N. and Mumbach, Maxwell R. and Pierce, Sarah E. and Corces, M. Ryan and Shah, Preyas and Bell, Jason C. and Jhutty, Darisha and Nemec, Corey M. and Wang, Jean and Wang, Li and Yin, Yifeng and Giresi, Paul G. and Chang, Anne Lynn S. and Zheng, Grace X. Y. and Greenleaf, William J. and Chang, Howard Y.}, |
|
| 9441 | + date = {2019-08}, |
|
| 9442 | + journaltitle = {Nature Biotechnology}, |
|
| 9443 | + shortjournal = {Nat Biotechnol}, |
|
| 9444 | + volume = {37}, |
|
| 9445 | + number = {8}, |
|
| 9446 | + eprint = {31375813}, |
|
| 9447 | + eprinttype = {pmid}, |
|
| 9448 | + pages = {925--936}, |
|
| 9449 | + issn = {1546-1696}, |
|
| 9450 | + doi = {10.1038/s41587-019-0206-z}, |
|
| 9451 | + abstract = {Understanding complex tissues requires single-cell deconstruction of gene regulation with precision and scale. Here, we assess the performance of a massively parallel droplet-based method for mapping transposase-accessible chromatin in single cells using sequencing (scATAC-seq). We apply scATAC-seq to obtain chromatin profiles of more than 200,000 single cells in human blood and basal cell carcinoma. In blood, application of scATAC-seq enables marker-free identification of cell type-specific cis- and trans-regulatory elements, mapping of disease-associated enhancer activity and reconstruction of trajectories of cellular differentiation. In basal cell carcinoma, application of scATAC-seq reveals regulatory networks in malignant, stromal and immune cells in the tumor microenvironment. Analysis of scATAC-seq profiles from serial tumor biopsies before and after programmed cell death protein 1 blockade identifies chromatin regulators of therapy-responsive T cell subsets and reveals a shared regulatory program that governs intratumoral CD8+ T cell exhaustion and CD4+ T follicular helper cell development. We anticipate that scATAC-seq will enable the unbiased discovery of gene regulatory factors across diverse biological systems.}, |
|
| 9452 | + langid = {english}, |
|
| 9453 | + pmcid = {PMC7299161}, |
|
| 9454 | + keywords = {Bone Marrow Cells,Cell Line,Chromatin,Computer Simulation,Gene Expression Regulation,Hematopoiesis,High-Throughput Nucleotide Sequencing,Humans,Leukocytes Mononuclear,Single-Cell Analysis,T-Lymphocytes,Transcription Factors}, |
|
| 9455 | + file = {/Users/rmorin/Zotero/storage/AF24WFDJ/Satpathy et al. - 2019 - Massively parallel single-cell chromatin landscape.pdf} |
|
| 9456 | +} |
|
| 9457 | + |
|
| 9458 | +@article{saundersStrelkaAccurateSomatic2012, |
|
| 9459 | + title = {Strelka: Accurate Somatic Small-Variant Calling from Sequenced Tumor-Normal Sample Pairs}, |
|
| 9460 | + shorttitle = {Strelka}, |
|
| 9461 | + author = {Saunders, Christopher T. and Wong, Wendy S. W. and Swamy, Sajani and Becq, Jennifer and Murray, Lisa J. and Cheetham, R. Keira}, |
|
| 9462 | + date = {2012-07-15}, |
|
| 9463 | + journaltitle = {Bioinformatics (Oxford, England)}, |
|
| 9464 | + shortjournal = {Bioinformatics}, |
|
| 9465 | + volume = {28}, |
|
| 9466 | + number = {14}, |
|
| 9467 | + eprint = {22581179}, |
|
| 9468 | + eprinttype = {pmid}, |
|
| 9469 | + pages = {1811--1817}, |
|
| 9470 | + issn = {1367-4811}, |
|
| 9471 | + doi = {10.1093/bioinformatics/bts271}, |
|
| 9472 | + abstract = {MOTIVATION: Whole genome and exome sequencing of matched tumor-normal sample pairs is becoming routine in cancer research. The consequent increased demand for somatic variant analysis of paired samples requires methods specialized to model this problem so as to sensitively call variants at any practical level of tumor impurity. RESULTS: We describe Strelka, a method for somatic SNV and small indel detection from sequencing data of matched tumor-normal samples. The method uses a novel Bayesian approach which represents continuous allele frequencies for both tumor and normal samples, while leveraging the expected genotype structure of the normal. This is achieved by representing the normal sample as a mixture of germline variation with noise, and representing the tumor sample as a mixture of the normal sample with somatic variation. A natural consequence of the model structure is that sensitivity can be maintained at high tumor impurity without requiring purity estimates. We demonstrate that the method has superior accuracy and sensitivity on impure samples compared with approaches based on either diploid genotype likelihoods or general allele-frequency tests. AVAILABILITY: The Strelka workflow source code is available at ftp://strelka@ftp.illumina.com/. CONTACT: csaunders@illumina.com}, |
|
| 9473 | + langid = {english}, |
|
| 9474 | + keywords = {Bayes Theorem,Computational Biology,Exome,Gene Frequency,Genetic Variation,Genome,Humans,INDEL Mutation,Models Genetic,Neoplasms,Sequence Alignment} |
|
| 9475 | +} |
|
| 9476 | + |
|
| 9477 | +@article{savageMolecularSignatureMediastinal2003, |
|
| 9478 | + title = {The Molecular Signature of Mediastinal Large {{B-cell}} Lymphoma Differs from That of Other Diffuse Large {{B-cell}} Lymphomas and Shares Features with Classical {{Hodgkin}} Lymphoma.}, |
|
| 9479 | + author = {Savage, Kerry J and Monti, Stefano and Kutok, Jeffery L and Cattoretti, Giorgio and Neuberg, Donna and family=Leval, given=Laurence, prefix=de, useprefix=true and Kurtin, Paul and Dal Cin, Paola and Ladd, Christine and Feuerhake, Friedrich and Aguiar, Ricardo C T and Li, Sigui and Salles, Gilles and Berger, Francoise and Jing, Wen and Pinkus, Geraldine S and Habermann, Thomas and Dalla-Favera, Riccardo and Harris, Nancy Lee and Aster, Jon C and Golub, Todd R and Shipp, Margaret A}, |
|
| 9480 | + date = {2003-12}, |
|
| 9481 | + journaltitle = {Blood}, |
|
| 9482 | + volume = {102}, |
|
| 9483 | + number = {12}, |
|
| 9484 | + pages = {3871--3879}, |
|
| 9485 | + keywords = {nosource} |
|
| 9486 | +} |
|
| 9487 | + |
|
| 9488 | +@article{schapiroHistoCATAnalysisCell2017, |
|
| 9489 | + title = {{{histoCAT}}: Analysis of Cell Phenotypes and Interactions in Multiplex Image Cytometry Data}, |
|
| 9490 | + shorttitle = {{{histoCAT}}}, |
|
| 9491 | + author = {Schapiro, Denis and Jackson, Hartland W. and Raghuraman, Swetha and Fischer, Jana R. and Zanotelli, Vito R. T. and Schulz, Daniel and Giesen, Charlotte and Catena, Raúl and Varga, Zsuzsanna and Bodenmiller, Bernd}, |
|
| 9492 | + date = {2017-09}, |
|
| 9493 | + journaltitle = {Nature Methods}, |
|
| 9494 | + shortjournal = {Nat Methods}, |
|
| 9495 | + volume = {14}, |
|
| 9496 | + number = {9}, |
|
| 9497 | + pages = {873--876}, |
|
| 9498 | + publisher = {Nature Publishing Group}, |
|
| 9499 | + issn = {1548-7105}, |
|
| 9500 | + doi = {10.1038/nmeth.4391}, |
|
| 9501 | + url = {https://www.nature.com/articles/nmeth.4391}, |
|
| 9502 | + urldate = {2022-02-03}, |
|
| 9503 | + abstract = {The histology topography cytometry analysis toolbox (histoCAT) enables quantitative analysis and exploration of highly multiplexed imaging data for better understanding of individual cells in the context of tissue architecture.}, |
|
| 9504 | + issue = {9}, |
|
| 9505 | + langid = {english}, |
|
| 9506 | + keywords = {Imaging,Software}, |
|
| 9507 | + file = {/Users/rmorin/Zotero/storage/FR6CHYWL/Schapiro et al. - 2017 - histoCAT analysis of cell phenotypes and interact.pdf} |
|
| 9508 | +} |
|
| 9509 | + |
|
| 9510 | +@article{schererDistinctBiologicalSubtypes2016, |
|
| 9511 | + title = {Distinct Biological Subtypes and Patterns of Genome Evolution in Lymphoma Revealed by Circulating Tumor {{DNA}}.}, |
|
| 9512 | + author = {Scherer, Florian and Kurtz, David M and Newman, Aaron M and Stehr, Henning and Craig, Alexander F M and Esfahani, Mohammad Shahrokh and Lovejoy, Alexander F and Chabon, Jacob J and Klass, Daniel M and Liu, Chih Long and Zhou, Li and Glover, Cynthia and Visser, Brendan C and Poultsides, George A and Advani, Ranjana H and Maeda, Lauren S and Gupta, Neel K and Levy, Ronald and Ohgami, Robert S and Kunder, Christian A and Diehn, Maximilian and Alizadeh, Ash A}, |
|
| 9513 | + date = {2016-11}, |
|
| 9514 | + journaltitle = {Science translational medicine}, |
|
| 9515 | + volume = {8}, |
|
| 9516 | + number = {364}, |
|
| 9517 | + pages = {364ra155}, |
|
| 9518 | + keywords = {nosource} |
|
| 9519 | +} |
|
| 9520 | + |
|
| 9521 | +@article{schifSOCS1MutationSubtypes, |
|
| 9522 | + title = {{{SOCS1 Mutation Subtypes Predict Divergent Outcomes}} in {{Diffuse Large B-Cell Lymphoma}} ({{DLBCL}}) {{Patients}}.}, |
|
| 9523 | + author = {Schif, Birgit and Lennerz, Jochen K and Kohler, Christian W and Bentink, Stefan and Kreuz, Markus and Melzner, Ingo and Ritz, Olga and Trümper, Lorenz and Loeffler, Markus and Spang, Rainer and Möller, Peter}, |
|
| 9524 | + journaltitle = {Oncotarget}, |
|
| 9525 | + keywords = {nosource} |
|
| 9526 | +} |
|
| 9527 | + |
|
| 9528 | +@article{schmidlinNewInsightsRegulation2009, |
|
| 9529 | + title = {New Insights into the Regulation of Human {{B-cell}} Differentiation}, |
|
| 9530 | + author = {Schmidlin, Heike and Diehl, Sean A. and Blom, Bianca}, |
|
| 9531 | + date = {2009-06-01}, |
|
| 9532 | + journaltitle = {Trends in Immunology}, |
|
| 9533 | + shortjournal = {Trends in Immunology}, |
|
| 9534 | + volume = {30}, |
|
| 9535 | + number = {6}, |
|
| 9536 | + pages = {277--285}, |
|
| 9537 | + issn = {1471-4906}, |
|
| 9538 | + doi = {10.1016/j.it.2009.03.008}, |
|
| 9539 | + url = {https://www.sciencedirect.com/science/article/pii/S1471490609000787}, |
|
| 9540 | + urldate = {2022-10-06}, |
|
| 9541 | + abstract = {B lymphocytes provide the cellular basis of the humoral immune response. All stages of this process, from B-cell activation to formation of germinal centers and differentiation into memory B cells or plasma cells, are influenced by extrinsic signals and controlled by transcriptional regulation. Compared to naïve B cells, memory B cells display a distinct expression profile, which allows for their rapid secondary responses. Indisputably, many B-cell malignancies result from aberrations in the circuitry controlling B-cell function, particularly during the germinal centre (GC) reaction. Here, we review new insights into memory B-cell subtypes, recent literature on transcription factors regulating human B-cell differentiation and further evidence for B-cell lymphomagenesis emanating from errors during GC cell reactions.}, |
|
| 9542 | + langid = {english}, |
|
| 9543 | + file = {/Users/rmorin/Zotero/storage/TN3QDTGH/Schmidlin et al. - 2009 - New insights into the regulation of human B-cell d.pdf} |
|
| 9544 | +} |
|
| 9545 | + |
|
| 9546 | +@article{schmidtCirculatingTumorDNA, |
|
| 9547 | + title = {Circulating Tumor {{DNA}} Reflects Therapy Response in Colorectal Cancer}, |
|
| 9548 | + author = {Schmidt, Kerstin and Diehl, Frank and Choti, Michael and Romans, Kathy and Kinzler, Kenneth and Diaz, Luis and Vogelstein, Bert}, |
|
| 9549 | + journaltitle = {AACR Meeting Abstracts}, |
|
| 9550 | + volume = {2008}, |
|
| 9551 | + pages = {40}, |
|
| 9552 | + issue = {3\_Molecular\_Diagnostics\_Meeting}, |
|
| 9553 | + keywords = {nosource} |
|
| 9554 | +} |
|
| 9555 | + |
|
| 9556 | +@article{schmitzBurkittLymphomaPathogenesis2012, |
|
| 9557 | + title = {Burkitt Lymphoma Pathogenesis and Therapeutic Targets from Structural and Functional Genomics}, |
|
| 9558 | + author = {Schmitz, Roland and Young, Ryan M. and Ceribelli, Michele and Jhavar, Sameer and Xiao, Wenming and Zhang, Meili and Wright, George and Shaffer, Arthur L. and Hodson, Daniel J. and Buras, Eric and Liu, Xuelu and Powell, John and Yang, Yandan and Xu, Weihong and Zhao, Hong and Kohlhammer, Holger and Rosenwald, Andreas and Kluin, Philip and Müller-Hermelink, Hans Konrad and Ott, German and Gascoyne, Randy D. and Connors, Joseph M. and Rimsza, Lisa M. and Campo, Elias and Jaffe, Elaine S. and Delabie, Jan and Smeland, Erlend B. and Ogwang, Martin D. and Reynolds, Steven J. and Fisher, Richard I. and Braziel, Rita M. and Tubbs, Raymond R. and Cook, James R. and Weisenburger, Dennis D. and Chan, Wing C. and Pittaluga, Stefania and Wilson, Wyndham and Waldmann, Thomas A. and Rowe, Martin and Mbulaiteye, Sam M. and Rickinson, Alan B. and Staudt, Louis M.}, |
|
| 9559 | + date = {2012-10-04}, |
|
| 9560 | + journaltitle = {Nature}, |
|
| 9561 | + shortjournal = {Nature}, |
|
| 9562 | + volume = {490}, |
|
| 9563 | + number = {7418}, |
|
| 9564 | + eprint = {22885699}, |
|
| 9565 | + eprinttype = {pmid}, |
|
| 9566 | + pages = {116--120}, |
|
| 9567 | + issn = {1476-4687}, |
|
| 9568 | + doi = {10.1038/nature11378}, |
|
| 9569 | + abstract = {Burkitt's lymphoma (BL) can often be cured by intensive chemotherapy, but the toxicity of such therapy precludes its use in the elderly and in patients with endemic BL in developing countries, necessitating new strategies. The normal germinal centre B cell is the presumed cell of origin for both BL and diffuse large B-cell lymphoma (DLBCL), yet gene expression analysis suggests that these malignancies may use different oncogenic pathways. BL is subdivided into a sporadic subtype that is diagnosed in developed countries, the Epstein-Barr-virus-associated endemic subtype, and an HIV-associated subtype, but it is unclear whether these subtypes use similar or divergent oncogenic mechanisms. Here we used high-throughput RNA sequencing and RNA interference screening to discover essential regulatory pathways in BL that cooperate with MYC, the defining oncogene of this cancer. In 70\% of sporadic BL cases, mutations affecting the transcription factor TCF3 (E2A) or its negative regulator ID3 fostered TCF3 dependency. TCF3 activated the pro-survival phosphatidylinositol-3-OH kinase pathway in BL, in part by augmenting tonic B-cell receptor signalling. In 38\% of sporadic BL cases, oncogenic CCND3 mutations produced highly stable cyclin D3 isoforms that drive cell cycle progression. These findings suggest opportunities to improve therapy for patients with BL.}, |
|
| 9570 | + langid = {english}, |
|
| 9571 | + pmcid = {PMC3609867}, |
|
| 9572 | + keywords = {Basic Helix-Loop-Helix Transcription Factors,Burkitt Lymphoma,Cell Cycle,Cyclin D3,Cyclin-Dependent Kinase 6,Genes myc,Genomics,High-Throughput Nucleotide Sequencing,Humans,Inhibitor of Differentiation Proteins,Molecular Targeted Therapy,Neoplasm Proteins,Phosphatidylinositol 3-Kinases,Receptors Antigen B-Cell,RNA Interference,Signal Transduction}, |
|
| 9573 | + file = {/Users/rmorin/Zotero/storage/3ICCJF6Q/Schmitz et al. - 2012 - Burkitt lymphoma pathogenesis and therapeutic targ.pdf} |
|
| 9574 | +} |
|
| 9575 | + |
|
| 9576 | +@article{schmitzGeneticsPathogenesisDiffuse2018a, |
|
| 9577 | + title = {Genetics and {{Pathogenesis}} of {{Diffuse Large B-Cell Lymphoma}}}, |
|
| 9578 | + author = {Schmitz, Roland and Wright, George W. and Huang, Da Wei and Johnson, Calvin A. and Phelan, James D. and Wang, James Q. and Roulland, Sandrine and Kasbekar, Monica and Young, Ryan M. and Shaffer, Arthur L. and Hodson, Daniel J. and Xiao, Wenming and Yu, Xin and Yang, Yandan and Zhao, Hong and Xu, Weihong and Liu, Xuelu and Zhou, Bin and Du, Wei and Chan, Wing C. and Jaffe, Elaine S. and Gascoyne, Randy D. and Connors, Joseph M. and Campo, Elias and Lopez-Guillermo, Armando and Rosenwald, Andreas and Ott, German and Delabie, Jan and Rimsza, Lisa M. and Tay Kuang Wei, Kevin and Zelenetz, Andrew D. and Leonard, John P. and Bartlett, Nancy L. and Tran, Bao and Shetty, Jyoti and Zhao, Yongmei and Soppet, Dan R. and Pittaluga, Stefania and Wilson, Wyndham H. and Staudt, Louis M.}, |
|
| 9579 | + date = {2018-04-12}, |
|
| 9580 | + journaltitle = {The New England Journal of Medicine}, |
|
| 9581 | + shortjournal = {N Engl J Med}, |
|
| 9582 | + volume = {378}, |
|
| 9583 | + number = {15}, |
|
| 9584 | + eprint = {29641966}, |
|
| 9585 | + eprinttype = {pmid}, |
|
| 9586 | + pages = {1396--1407}, |
|
| 9587 | + issn = {1533-4406}, |
|
| 9588 | + doi = {10.1056/NEJMoa1801445}, |
|
| 9589 | + abstract = {BACKGROUND: Diffuse large B-cell lymphomas (DLBCLs) are phenotypically and genetically heterogeneous. Gene-expression profiling has identified subgroups of DLBCL (activated B-cell-like [ABC], germinal-center B-cell-like [GCB], and unclassified) according to cell of origin that are associated with a differential response to chemotherapy and targeted agents. We sought to extend these findings by identifying genetic subtypes of DLBCL based on shared genomic abnormalities and to uncover therapeutic vulnerabilities based on tumor genetics. METHODS: We studied 574 DLBCL biopsy samples using exome and transcriptome sequencing, array-based DNA copy-number analysis, and targeted amplicon resequencing of 372 genes to identify genes with recurrent aberrations. We developed and implemented an algorithm to discover genetic subtypes based on the co-occurrence of genetic alterations. RESULTS: We identified four prominent genetic subtypes in DLBCL, termed MCD (based on the co-occurrence of MYD88L265P and CD79B mutations), BN2 (based on BCL6 fusions and NOTCH2 mutations), N1 (based on NOTCH1 mutations), and EZB (based on EZH2 mutations and BCL2 translocations). Genetic aberrations in multiple genes distinguished each genetic subtype from other DLBCLs. These subtypes differed phenotypically, as judged by differences in gene-expression signatures and responses to immunochemotherapy, with favorable survival in the BN2 and EZB subtypes and inferior outcomes in the MCD and N1 subtypes. Analysis of genetic pathways suggested that MCD and BN2 DLBCLs rely on "chronic active" B-cell receptor signaling that is amenable to therapeutic inhibition. CONCLUSIONS: We uncovered genetic subtypes of DLBCL with distinct genotypic, epigenetic, and clinical characteristics, providing a potential nosology for precision-medicine strategies in DLBCL. (Funded by the Intramural Research Program of the National Institutes of Health and others.).}, |
|
| 9590 | + langid = {english}, |
|
| 9591 | + pmcid = {PMC6010183}, |
|
| 9592 | + keywords = {Antineoplastic Combined Chemotherapy Protocols,Biopsy,Epigenesis Genetic,Exome,Gene Expression Profiling,Genetic Heterogeneity,Genotype,Humans,Kaplan-Meier Estimate,Lymphoma Large B-Cell Diffuse,Mutation,Prognosis,Sequence Analysis DNA,Transcriptome}, |
|
| 9593 | + file = {/Users/rmorin/Zotero/storage/9TLCAPX5/Schmitz et al. - 2018 - Genetics and Pathogenesis of Diffuse Large B-Cell .pdf} |
|
| 9594 | +} |
|
| 9595 | + |
|
| 9596 | +@article{schmitzTNFAIP3A20Tumor2009a, |
|
| 9597 | + title = {{{TNFAIP3}} ({{A20}}) Is a Tumor Suppressor Gene in {{Hodgkin}} Lymphoma and Primary Mediastinal {{B}} Cell Lymphoma}, |
|
| 9598 | + author = {Schmitz, Roland and Hansmann, Martin-Leo and Bohle, Verena and Martin-Subero, Jose Ignacio and Hartmann, Sylvia and Mechtersheimer, Gunhild and Klapper, Wolfram and Vater, Inga and Giefing, Maciej and Gesk, Stefan and Stanelle, Jens and Siebert, Reiner and Küppers, Ralf}, |
|
| 9599 | + date = {2009-05-11}, |
|
| 9600 | + journaltitle = {The Journal of Experimental Medicine}, |
|
| 9601 | + shortjournal = {J Exp Med}, |
|
| 9602 | + volume = {206}, |
|
| 9603 | + number = {5}, |
|
| 9604 | + eprint = {19380639}, |
|
| 9605 | + eprinttype = {pmid}, |
|
| 9606 | + pages = {981--989}, |
|
| 9607 | + issn = {1540-9538}, |
|
| 9608 | + doi = {10.1084/jem.20090528}, |
|
| 9609 | + abstract = {Proliferation and survival of Hodgkin and Reed/Sternberg (HRS) cells, the malignant cells of classical Hodgkin lymphoma (cHL), are dependent on constitutive activation of nuclear factor kappaB (NF-kappaB). NF-kappaB activation through various stimuli is negatively regulated by the zinc finger protein A20. To determine whether A20 contributes to the pathogenesis of cHL, we sequenced TNFAIP3, encoding A20, in HL cell lines and laser-microdissected HRS cells from cHL biopsies. We detected somatic mutations in 16 out of 36 cHLs (44\%), including missense mutations in 2 out of 16 Epstein-Barr virus-positive (EBV(+)) cHLs and a missense mutation, nonsense mutations, and frameshift-causing insertions or deletions in 14 out of 20 EBV(-) cHLs. In most mutated cases, both TNFAIP3 alleles were inactivated, including frequent chromosomal deletions of TNFAIP3. Reconstitution of wild-type TNFAIP3 in A20-deficient cHL cell lines revealed a significant decrease in transcripts of selected NF-kappaB target genes and caused cytotoxicity. Extending the mutation analysis to primary mediastinal B cell lymphoma (PMBL), another lymphoma with constitutive NF-kappaB activity, revealed destructive mutations in 5 out of 14 PMBLs (36\%). This report identifies TNFAIP3 (A20), a key regulator of NF-kappaB activity, as a novel tumor suppressor gene in cHL and PMBL. The significantly higher frequency of TNFAIP3 mutations in EBV(-) than EBV(+) cHL suggests complementing functions of TNFAIP3 inactivation and EBV infection in cHL pathogenesis.}, |
|
| 9610 | + langid = {english}, |
|
| 9611 | + pmcid = {PMC2715030}, |
|
| 9612 | + keywords = {Cell Line Tumor,Chromosome Deletion,DNA Transposable Elements,DNA-Binding Proteins,Epstein-Barr Virus Infections,Frameshift Mutation,Genes Tumor Suppressor,Hodgkin Disease,Humans,Intracellular Signaling Peptides and Proteins,Lymphoma B-Cell,Mutation,Mutation Missense,Nuclear Proteins,Polymorphism Single Nucleotide,Transcription Genetic,Tumor Necrosis Factor alpha-Induced Protein 3}, |
|
| 9613 | + file = {/Users/rmorin/Zotero/storage/689R2CV6/Schmitz et al. - 2009 - TNFAIP3 (A20) is a tumor suppressor gene in Hodgki.pdf} |
|
| 9614 | +} |
|
| 9615 | + |
|
| 9616 | +@article{schneiderAlterationsCD58Gene2015a, |
|
| 9617 | + title = {Alterations of the {{CD58}} Gene in Classical {{Hodgkin}} Lymphoma}, |
|
| 9618 | + author = {Schneider, Markus and Schneider, Stefanie and Zühlke-Jenisch, Reina and Klapper, Wolfram and Sundström, Christer and Hartmann, Sylvia and Hansmann, Martin-Leo and Siebert, Reiner and Küppers, Ralf and Giefing, Maciej}, |
|
| 9619 | + date = {2015-10}, |
|
| 9620 | + journaltitle = {Genes, Chromosomes \& Cancer}, |
|
| 9621 | + shortjournal = {Genes Chromosomes Cancer}, |
|
| 9622 | + volume = {54}, |
|
| 9623 | + number = {10}, |
|
| 9624 | + eprint = {26194173}, |
|
| 9625 | + eprinttype = {pmid}, |
|
| 9626 | + pages = {638--645}, |
|
| 9627 | + issn = {1098-2264}, |
|
| 9628 | + doi = {10.1002/gcc.22276}, |
|
| 9629 | + abstract = {Immune evasion plays a central role in the pathophysiology of classical Hodgkin lymphoma (cHL). As mutations of the CD58 gene contribute to immune evasion of diffuse large B cell lymphoma tumor cells, we studied whether alterations of the CD58 gene also occur in Hodgkin and Reed/Sternberg (HRS) cells of cHL. Single nucleotide polymorphism chip analysis revealed homozygous deletions within the CD58 gene in two cHL cell lines (SUP-HD1 and U-HO1). Sequencing of the CD58 gene in seven cHL cell lines disclosed in addition a homozygous splice site mutation in cell line KM-H2. None of the three mutated lines expressed CD58 protein on their surface. Thus, three of seven cHL cell lines analyzed harbor destructive CD58 mutations. Molecular analysis of isolated HRS cells from 10 primary cases of cHL; however, did not reveal any case with a CD58 mutation. A FICTION study indicated heterozygous deletions of CD58 in 3 of 13 cHL analyzed. Overall, we report frequent inactivating mutations of CD58 in cHL cell lines, but their rare occurrence in primary HRS cells. As the three cHL cell lines with CD58 mutations were all established from HRS cells located in pleural effusions, i.e., outside the normal lymph node microenvironment, in end-stages of the disease, CD58 inactivation in cHL might be predominantly prevalent to such situations.}, |
|
| 9630 | + langid = {english}, |
|
| 9631 | + keywords = {CD58 Antigens,Cell Line Tumor,Cells Cultured,Hodgkin Disease,Humans,Mutation,Tumor Escape} |
|
| 9632 | +} |
|
| 9633 | + |
|
| 9634 | +@article{schollMutationsRegionFAS2007, |
|
| 9635 | + title = {Mutations within the 5' Region of {{FAS}}/{{CD95}} Gene in Nodal Diffuse Large {{B-cell}} Lymphoma}, |
|
| 9636 | + author = {Scholl, Vanesa and Stefanoff, Claudio Gustavo and Hassan, Rocio and Spector, Nelson and Renault, Ilana Zalcberg}, |
|
| 9637 | + date = {2007-05}, |
|
| 9638 | + journaltitle = {Leukemia \& Lymphoma}, |
|
| 9639 | + shortjournal = {Leuk Lymphoma}, |
|
| 9640 | + volume = {48}, |
|
| 9641 | + number = {5}, |
|
| 9642 | + eprint = {17487740}, |
|
| 9643 | + eprinttype = {pmid}, |
|
| 9644 | + pages = {957--963}, |
|
| 9645 | + issn = {1042-8194}, |
|
| 9646 | + doi = {10.1080/10428190701230858}, |
|
| 9647 | + abstract = {CD95 is a cell-surface receptor that mediates apoptosis. A possible association between CD95 mutations and extranodal diffuse large B-cell lymphomas (DLBCL) has been reported. To further elucidate this question, a mutation analysis within the 5' region and exon 9 of CD95 was performed in a series of 66 DLBCL patients, by polymerase chain reaction, single-strand conformational polymorphism, and sequencing in all cases. Four mutations, all within the 5' region, were detected in three cases of primary nodal DLBCL (6.3\% of primary DLBCL), probably originated as by-products of the somatic hypermutation process. No CD95 mutations in the two analyzed regions were detected in primary extranodal DLBCL, mediastinal large B-cell lymphoma (MLBCL), and DLBCL arising from indolent low-grade lymphomas. Because of our results, a review of published data with respect to the site of mutations was performed, which suggested a different distribution of mutations in nodal and extranodal DLBCL.}, |
|
| 9648 | + langid = {english}, |
|
| 9649 | + keywords = {Apoptosis,Base Sequence,Disease Progression,DNA Mutational Analysis,fas Receptor,Gene Expression Regulation Neoplastic,Humans,Lymphatic Metastasis,Lymphoma B-Cell,Lymphoma Large B-Cell Diffuse,Models Genetic,Molecular Sequence Data,Mutation,Polymerase Chain Reaction,Polymorphism Single-Stranded Conformational} |
|
| 9650 | +} |
|
| 9651 | + |
|
| 9652 | +@article{scolesAntisenseOligonucleotidesPrimer2019, |
|
| 9653 | + title = {Antisense Oligonucleotides: {{A}} Primer}, |
|
| 9654 | + shorttitle = {Antisense Oligonucleotides}, |
|
| 9655 | + author = {Scoles, Daniel R. and Minikel, Eric V. and Pulst, Stefan M.}, |
|
| 9656 | + date = {2019-04-01}, |
|
| 9657 | + journaltitle = {Neurology Genetics}, |
|
| 9658 | + volume = {5}, |
|
| 9659 | + number = {2}, |
|
| 9660 | + publisher = {Wolters Kluwer Health, Inc. on behalf of the American Academy of Neurology}, |
|
| 9661 | + issn = {2376-7839}, |
|
| 9662 | + doi = {10.1212/NXG.0000000000000323}, |
|
| 9663 | + url = {https://ng.neurology.org/content/5/2/e323}, |
|
| 9664 | + urldate = {2022-10-05}, |
|
| 9665 | + abstract = {There are few disease-modifying therapeutics for neurodegenerative diseases, but successes on the development of antisense oligonucleotide (ASO) therapeutics for spinal muscular atrophy and Duchenne muscular dystrophy predict a robust future for ASOs in medicine. Indeed, existing pipelines for the development of ASO therapies for spinocerebellar ataxias, Huntington disease, Alzheimer disease, amyotrophic lateral sclerosis, Parkinson disease, and others, and increased focus by the pharmaceutical industry on ASO development, strengthen the outlook for using ASOs for neurodegenerative diseases. Perhaps the most significant advantage to ASO therapeutics over other small molecule approaches is that acquisition of the target sequence provides immediate knowledge of putative complementary oligonucleotide therapeutics. In this review, we describe the various types of ASOs, how they are used therapeutically, and the present efforts to develop new ASO therapies that will contribute to a forthcoming toolkit for treating multiple neurodegenerative diseases.}, |
|
| 9666 | + langid = {english}, |
|
| 9667 | + file = {/Users/rmorin/Zotero/storage/KALZMKXI/Scoles et al. - 2019 - Antisense oligonucleotides A primer.pdf;/Users/rmorin/Zotero/storage/77D2B664/e323.html} |
|
| 9668 | +} |
|
| 9669 | + |
|
| 9670 | +@article{scottDeterminingCelloforiginSubtypes2014, |
|
| 9671 | + title = {Determining Cell-of-Origin Subtypes of Diffuse Large {{B-cell}} Lymphoma Using Gene Expression in Formalin-Fixed Paraffin-Embedded Tissue.}, |
|
| 9672 | + author = {Scott, David W and Wright, George W and Williams, P Mickey and Lih, Chih-Jian and Walsh, William and Jaffe, Elaine S and Rosenwald, Andreas and Campo, Elias and Chan, Wing C and Connors, Joseph M and Smeland, Erlend B and Mottok, Anja and Braziel, Rita M and Ott, German and Delabie, Jan and Tubbs, Raymond R and Cook, James R and Weisenburger, Dennis D and Greiner, Timothy C and Glinsmann-Gibson, Betty J and Fu, Kai and Staudt, Louis M and Gascoyne, Randy D and Rimsza, Lisa M}, |
|
| 9673 | + date = {2014-02}, |
|
| 9674 | + journaltitle = {Blood}, |
|
| 9675 | + volume = {123}, |
|
| 9676 | + number = {8}, |
|
| 9677 | + pages = {1214--1217}, |
|
| 9678 | + keywords = {nosource} |
|
| 9679 | +} |
|
| 9680 | + |
|
| 9681 | +@article{scottHighgradeBcellLymphoma2018, |
|
| 9682 | + title = {High-Grade {{B-cell}} Lymphoma with {{MYC}} and {{BCL2}} and/or {{BCL6}} Rearrangements with Diffuse Large {{B-cell}} Lymphoma Morphology}, |
|
| 9683 | + author = {Scott, David W. and King, Rebecca L. and Staiger, Annette M. and Ben-Neriah, Susana and Jiang, Aixiang and Horn, Heike and Mottok, Anja and Farinha, Pedro and Slack, Graham W. and Ennishi, Daisuke and Schmitz, Norbert and Pfreundschuh, Michael and Nowakowski, Grzegorz S. and Kahl, Brad S. and Connors, Joseph M. and Gascoyne, Randy D. and Ott, German and Macon, William R. and Rosenwald, Andreas}, |
|
| 9684 | + date = {2018-05-03}, |
|
| 9685 | + journaltitle = {Blood}, |
|
| 9686 | + volume = {131}, |
|
| 9687 | + number = {18}, |
|
| 9688 | + eprint = {29475959}, |
|
| 9689 | + eprinttype = {pmid}, |
|
| 9690 | + pages = {2060--2064}, |
|
| 9691 | + issn = {0006-4971, 1528-0020}, |
|
| 9692 | + doi = {10.1182/blood-2017-12-820605}, |
|
| 9693 | + url = {http://www.bloodjournal.org/content/131/18/2060}, |
|
| 9694 | + urldate = {2019-07-08}, |
|
| 9695 | + abstract = {Visual Abstract {$<$}img class="highwire-fragment fragment-image" alt="Figure1" src="http://www.bloodjournal.org/content/bloodjournal/131/18/2060/F1.medium.gif" width="440" height="394"/{$>$}Download figureOpen in new tabDownload powerpoint High-grade B-cell lymphoma with MYC and BCL2 and/or BCL6 rearrangements (HGBL-DH/TH) is a newly defined entity in the latest World Health Organization Classification. Accurate diagnosis would appear to mandate fluorescence in situ hybridization (FISH) for all tumors with diffuse large B-cell lymphoma (DLBCL) morphology. We present the results of FISH, cell-of-origin, and immunohistochemistry (IHC) testing from 1228 DLBCL biopsies from 3 clinical trials and a population-based registry. HGBL-DH/TH made up 7.9\% of the DLBCL, confined primarily to the germinal center B-cell–like (GCB; 13.3\%) compared with activated B-cell-like (ABC; 1.7\%) subtype (P {$<$} .001). HGBL-DH/TH with BCL2 rearrangement is a GCB phenomenon with no cases observed in 415 ABC DLBCL. A screening strategy restricting FISH testing to tumors of GCB subtype (by Lymph2Cx or Hans IHC) plus dual protein expression of MYC and BCL2 by IHC could limit testing to 11\% to 14\% of tumors, with a positive predictive value of 30\% to 37\%; however, this strategy would miss approximately one-quarter of tumors with HBGL-DH/TH with BCL2 rearrangement and one-third of all HGBL-DH/TH. These results provide accurate estimation of the proportion of HGBL-DH/TH among tumors with DLBCL morphology and allow determination of the impact of various methods available to screen DLBCL tumors for FISH testing.}, |
|
| 9696 | + langid = {english}, |
|
| 9697 | + file = {/Users/rmorin/Zotero/storage/W9LKADMI/2060.html} |
|
| 9698 | +} |
|
| 9699 | + |
|
| 9700 | +@article{scottNewMolecularAssay2017, |
|
| 9701 | + title = {New {{Molecular Assay}} for the {{Proliferation Signature}} in {{Mantle Cell Lymphoma Applicable}} to {{Formalin-Fixed Paraffin-Embedded Biopsies}}}, |
|
| 9702 | + author = {Scott, David W. and Abrisqueta, Pau and Wright, George W. and Slack, Graham W. and Mottok, Anja and Villa, Diego and Jares, Pedro and Rauert-Wunderlich, Hilka and Royo, Cristina and Clot, Guillem and Pinyol, Magda and Boyle, Merrill and Chan, Fong Chun and Braziel, Rita M. and Chan, Wing C. and Weisenburger, Dennis D. and Cook, James R. and Greiner, Timothy C. and Fu, Kai and Ott, German and Delabie, Jan and Smeland, Erlend B. and Holte, Harald and Jaffe, Elaine S. and Steidl, Christian and Connors, Joseph M. and Gascoyne, Randy D. and Rosenwald, Andreas and Staudt, Louis M. and Campo, Elias and Rimsza, Lisa M.}, |
|
| 9703 | + date = {2017-03-14}, |
|
| 9704 | + journaltitle = {Journal of Clinical Oncology}, |
|
| 9705 | + shortjournal = {JCO}, |
|
| 9706 | + volume = {35}, |
|
| 9707 | + number = {15}, |
|
| 9708 | + pages = {1668--1677}, |
|
| 9709 | + issn = {0732-183X}, |
|
| 9710 | + doi = {10.1200/JCO.2016.70.7901}, |
|
| 9711 | + url = {https://ascopubs.org/doi/full/10.1200/JCO.2016.70.7901}, |
|
| 9712 | + urldate = {2019-12-21}, |
|
| 9713 | + abstract = {PurposeMantle cell lymphoma is an aggressive B-cell neoplasm that displays heterogeneous outcomes after treatment. In 2003, the Lymphoma/Leukemia Molecular Profiling Project described a powerful biomarker—the proliferation signature—using gene expression in fresh frozen material. Herein, we describe the training and validation of a new assay that measures the proliferation signature in RNA derived from routinely available formalin-fixed paraffin-embedded (FFPE) biopsies.MethodsForty-seven FFPE biopsies were used to train an assay on the NanoString platform, using microarray gene expression data of matched fresh frozen biopsies as a gold standard. The locked assay was applied to pretreatment FFPE lymph node biopsies from an independent cohort of 110 patients uniformly treated with rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone. Seventeen biopsies were tested across three laboratories to assess assay reproducibility.ResultsThe MCL35 assay, which contained a 17-gene proliferation signature, yielded gene expression of sufficient quality to assign an assay score and risk group in 108 (98\%) of 110 archival FFPE biopsies. The MCL35 assay assigned patients to high-risk (26\%), standard-risk (29\%), and low-risk (45\%) groups, with different lengths of overall survival (OS): a median of 1.1, 2.6, and 8.6 years, respectively (log-rank for trend, P {$<$} .001). In multivariable analysis, these risk groups and the Mantle Cell Lymphoma International Prognostic Index were independently associated with OS (P {$<$} .001 for both variables). Concordance of risk assignment across the three independent laboratories was 100\%.ConclusionThe newly developed and validated MCL35 assay for FFPE biopsies uses the proliferation signature to define groups of patients with significantly different OS independent of the Mantle Cell Lymphoma International Prognostic Index. Importantly, the analytic and clinical validity of this assay defines it as a reliable biomarker to support risk-adapted clinical trials.}, |
|
| 9714 | + file = {/Users/rmorin/Zotero/storage/4HKTDFE4/JCO.2016.70.html} |
|
| 9715 | +} |
|
| 9716 | + |
|
| 9717 | +@article{scruccaMclustClusteringClassification2016, |
|
| 9718 | + title = {Mclust 5: {{Clustering}}, {{Classification}} and {{Density Estimation Using Gaussian Finite Mixture Models}}}, |
|
| 9719 | + shorttitle = {Mclust 5}, |
|
| 9720 | + author = {Scrucca, Luca and Fop, Michael and Murphy, T. Brendan and Raftery, Adrian E.}, |
|
| 9721 | + date = {2016-08}, |
|
| 9722 | + journaltitle = {The R Journal}, |
|
| 9723 | + shortjournal = {R J}, |
|
| 9724 | + volume = {8}, |
|
| 9725 | + number = {1}, |
|
| 9726 | + eprint = {27818791}, |
|
| 9727 | + eprinttype = {pmid}, |
|
| 9728 | + pages = {289--317}, |
|
| 9729 | + issn = {2073-4859}, |
|
| 9730 | + abstract = {Finite mixture models are being used increasingly to model a wide variety of random phenomena for clustering, classification and density estimation. mclust is a powerful and popular package which allows modelling of data as a Gaussian finite mixture with different covariance structures and different numbers of mixture components, for a variety of purposes of analysis. Recently, version 5 of the package has been made available on CRAN. This updated version adds new covariance structures, dimension reduction capabilities for visualisation, model selection criteria, initialisation strategies for the EM algorithm, and bootstrap-based inference, making it a full-featured R package for data analysis via finite mixture modelling.}, |
|
| 9731 | + langid = {english}, |
|
| 9732 | + pmcid = {PMC5096736} |
|
| 9733 | +} |
|
| 9734 | + |
|
| 9735 | +@article{sedlazeckAccurateDetectionComplex2018, |
|
| 9736 | + title = {Accurate Detection of Complex Structural Variations Using Single Molecule Sequencing}, |
|
| 9737 | + author = {Sedlazeck, Fritz J. and Rescheneder, Philipp and Smolka, Moritz and Fang, Han and Nattestad, Maria and family=Haeseler, given=Arndt, prefix=von, useprefix=true and Schatz, Michael C.}, |
|
| 9738 | + date = {2018-06}, |
|
| 9739 | + journaltitle = {Nature methods}, |
|
| 9740 | + shortjournal = {Nat Methods}, |
|
| 9741 | + volume = {15}, |
|
| 9742 | + number = {6}, |
|
| 9743 | + eprint = {29713083}, |
|
| 9744 | + eprinttype = {pmid}, |
|
| 9745 | + pages = {461--468}, |
|
| 9746 | + issn = {1548-7091}, |
|
| 9747 | + doi = {10.1038/s41592-018-0001-7}, |
|
| 9748 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5990442/}, |
|
| 9749 | + urldate = {2022-02-07}, |
|
| 9750 | + abstract = {Structural variations (SVs) are the largest source of genetic variation, but remain poorly understood because of limited genomics technology. Single molecule long-read sequencing from Pacific Biosciences and Oxford Nanopore has the potential to dramatically advance the field, although their high error rates challenge existing methods. Addressing this need, we introduce open-source methods for long-read alignment (NGMLR, https://github.com/philres/ngmlr) and SV identification (Sniffles, https://github.com/fritzsedlazeck/Sniffles) that enable unprecedented SV sensitivity and precision, including within repeat-rich regions and of complex nested events that can have significant impact on human disorders. Examining several datasets, including healthy and cancerous human genomes, we discover thousands of novel variants using long-reads and categorize systematic errors in short-read approaches. NGMLR and Sniffles are further able to automatically filter false events and operate on low amounts of coverage to address the cost factor that has hindered the application of long-reads in clinical and research settings.}, |
|
| 9751 | + pmcid = {PMC5990442}, |
|
| 9752 | + file = {/Users/rmorin/Zotero/storage/U8W6K3EX/Sedlazeck et al. - 2018 - Accurate detection of complex structural variation.pdf} |
|
| 9753 | +} |
|
| 9754 | + |
|
| 9755 | +@article{sehnRevisedInternationalPrognostic, |
|
| 9756 | + title = {The Revised {{International Prognostic Index}} ({{R-IPI}}) Is a Better Predictor of Outcome than the Standard {{IPI}} for Patients with Diffuse Large {{B-cell}} Lymphoma Treated with {{R-CHOP}}.}, |
|
| 9757 | + author = {Sehn, Laurie H and Berry, Brian and Chhanabhai, Mukesh and Fitzgerald, Catherine and Gill, Karamjit and Hoskins, Paul and Klasa, Richard and Savage, Kerry J and Shenkier, Tamara and Sutherland, Judy and Gascoyne, Randy D and Connors, Joseph M}, |
|
| 9758 | + journaltitle = {Blood}, |
|
| 9759 | + volume = {109}, |
|
| 9760 | + number = {5}, |
|
| 9761 | + pages = {1857--1861}, |
|
| 9762 | + keywords = {nosource} |
|
| 9763 | +} |
|
| 9764 | + |
|
| 9765 | +@article{seifertOriginPathogenesisCell2013, |
|
| 9766 | + title = {Origin and Pathogenesis of {{B}} Cell Lymphomas.}, |
|
| 9767 | + author = {Seifert, M. and Scholtysik, R. and Küppers, R.}, |
|
| 9768 | + date = {2013}, |
|
| 9769 | + journaltitle = {Methods in molecular biology}, |
|
| 9770 | + volume = {971}, |
|
| 9771 | + pages = {1--25} |
|
| 9772 | +} |
|
| 9773 | + |
|
| 9774 | +@article{shaMolecularHighGradeBCell2018, |
|
| 9775 | + title = {Molecular {{High-Grade B-Cell Lymphoma}}: {{Defining}} a {{Poor-Risk Group That Requires Different Approaches}} to {{Therapy}}}, |
|
| 9776 | + shorttitle = {Molecular {{High-Grade B-Cell Lymphoma}}}, |
|
| 9777 | + author = {Sha, Chulin and Barrans, Sharon and Cucco, Francesco and Bentley, Michael A. and Care, Matthew A. and Cummin, Thomas and Kennedy, Hannah and Thompson, Joe S. and Uddin, Rahman and Worrillow, Lisa and Chalkley, Rebecca and family=Hoppe, given=Moniek, prefix=van, useprefix=true and Ahmed, Sophia and Maishman, Tom and Caddy, Josh and Schuh, Anna and Mamot, Christoph and Burton, Catherine and Tooze, Reuben and Davies, Andrew and Du, Ming-Qing and Johnson, Peter W.M. and Westhead, David R.}, |
|
| 9778 | + date = {2018-12-03}, |
|
| 9779 | + journaltitle = {Journal of Clinical Oncology}, |
|
| 9780 | + shortjournal = {J Clin Oncol}, |
|
| 9781 | + volume = {37}, |
|
| 9782 | + number = {3}, |
|
| 9783 | + pages = {202--212}, |
|
| 9784 | + issn = {0732-183X}, |
|
| 9785 | + doi = {10.1200/JCO.18.01314}, |
|
| 9786 | + url = {https://ascopubs.org/doi/full/10.1200/JCO.18.01314}, |
|
| 9787 | + urldate = {2019-07-08}, |
|
| 9788 | + abstract = {PurposeBiologic heterogeneity is a feature of diffuse large B-cell lymphoma (DLBCL), and the existence of a subgroup with poor prognosis and phenotypic proximity to Burkitt lymphoma is well known. Conventional cytogenetics identifies some patients with rearrangements of MYC and BCL2 and/or BCL6 (double-hit lymphomas) who are increasingly treated with more intensive chemotherapy, but a more biologically coherent and clinically useful definition of this group is required.Patients and MethodsWe defined a molecular high-grade (MHG) group by applying a gene expression–based classifier to 928 patients with DLBCL from a clinical trial that investigated the addition of bortezomib to standard rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) therapy. The prognostic significance of MHG was compared with existing biomarkers. We performed targeted sequencing of 70 genes in 400 patients and explored molecular pathology using gene expression signature databases. Findings were validated in an independent data set.ResultsThe MHG group comprised 83 patients (9\%), with 75 in the cell-of-origin germinal center B-cell-like group. MYC rearranged and double-hit groups were strongly over-represented in MHG but comprised only one half of the total. Gene expression analysis revealed a proliferative phenotype with a relationship to centroblasts. Progression-free survival rate at 36 months after R-CHOP in the MHG group was 37\% (95\% CI, 24\% to 55\%) compared with 72\% (95\% CI, 68\% to 77\%) for others, and an analysis of treatment effects suggested a possible positive effect of bortezomib. Double-hit lymphomas lacking the MHG signature showed no evidence of worse outcome than other germinal center B-cell-like cases.ConclusionMHG defines a biologically coherent high-grade B-cell lymphoma group with distinct molecular features and clinical outcomes that effectively doubles the size of the poor-prognosis, double-hit group. Patients with MHG may benefit from intensified chemotherapy or novel targeted therapies.}, |
|
| 9789 | + file = {/Users/rmorin/Zotero/storage/M6AL4F6C/JCO.18.html} |
|
| 9790 | +} |
|
| 9791 | + |
|
| 9792 | +@article{shannonGeneticStructureVillage2015, |
|
| 9793 | + title = {Genetic Structure in Village Dogs Reveals a {{Central Asian}} Domestication Origin}, |
|
| 9794 | + author = {Shannon, Laura M. and Boyko, Ryan H. and Castelhano, Marta and Corey, Elizabeth and Hayward, Jessica J. and McLean, Corin and White, Michelle E. and Said, Mounir Abi and Anita, Baddley A. and Bondjengo, Nono Ikombe and Calero, Jorge and Galov, Ana and Hedimbi, Marius and Imam, Bulu and Khalap, Rajashree and Lally, Douglas and Masta, Andrew and Oliveira, Kyle C. and Pérez, Lucía and Randall, Julia and Tam, Nguyen Minh and Trujillo-Cornejo, Francisco J. and Valeriano, Carlos and Sutter, Nathan B. and Todhunter, Rory J. and Bustamante, Carlos D. and Boyko, Adam R.}, |
|
| 9795 | + date = {2015-11-03}, |
|
| 9796 | + journaltitle = {Proceedings of the National Academy of Sciences}, |
|
| 9797 | + shortjournal = {PNAS}, |
|
| 9798 | + volume = {112}, |
|
| 9799 | + number = {44}, |
|
| 9800 | + eprint = {26483491}, |
|
| 9801 | + eprinttype = {pmid}, |
|
| 9802 | + pages = {13639--13644}, |
|
| 9803 | + issn = {0027-8424, 1091-6490}, |
|
| 9804 | + doi = {10.1073/pnas.1516215112}, |
|
| 9805 | + url = {http://www.pnas.org/content/112/44/13639}, |
|
| 9806 | + urldate = {2018-10-29}, |
|
| 9807 | + abstract = {Dogs were the first domesticated species, originating at least 15,000 y ago from Eurasian gray wolves. Dogs today consist primarily of two specialized groups—a diverse set of nearly 400 pure breeds and a far more populous group of free-ranging animals adapted to a human commensal lifestyle (village dogs). Village dogs are more genetically diverse and geographically widespread than purebred dogs making them vital for unraveling dog population history. Using a semicustom 185,805-marker genotyping array, we conducted a large-scale survey of autosomal, mitochondrial, and Y chromosome diversity in 4,676 purebred dogs from 161 breeds and 549 village dogs from 38 countries. Geographic structure shows both isolation and gene flow have shaped genetic diversity in village dog populations. Some populations (notably those in the Neotropics and the South Pacific) are almost completely derived from European stock, whereas others are clearly admixed between indigenous and European dogs. Importantly, many populations—including those of Vietnam, India, and Egypt—show minimal evidence of European admixture. These populations exhibit a clear gradient of short-range linkage disequilibrium consistent with a Central Asian domestication origin.}, |
|
| 9808 | + langid = {english}, |
|
| 9809 | + keywords = {admixture,domestication,haplotype diversity,introgression,linkage disequilibrium}, |
|
| 9810 | + file = {/Users/rmorin/Zotero/storage/UL54QM9I/13639.html} |
|
| 9811 | +} |
|
| 9812 | + |
|
| 9813 | +@article{shatkinEndsAffairCapping2000, |
|
| 9814 | + title = {The Ends of the Affair: {{Capping}} and Polyadenylation}, |
|
| 9815 | + shorttitle = {The Ends of the Affair}, |
|
| 9816 | + author = {Shatkin, Aaron J. and Manley, James L.}, |
|
| 9817 | + date = {2000-10}, |
|
| 9818 | + journaltitle = {Nature Structural Biology}, |
|
| 9819 | + shortjournal = {Nat Struct Mol Biol}, |
|
| 9820 | + volume = {7}, |
|
| 9821 | + number = {10}, |
|
| 9822 | + pages = {838--842}, |
|
| 9823 | + publisher = {Nature Publishing Group}, |
|
| 9824 | + issn = {1545-9985}, |
|
| 9825 | + doi = {10.1038/79583}, |
|
| 9826 | + url = {https://www.nature.com/articles/nsb1000_838}, |
|
| 9827 | + urldate = {2022-10-06}, |
|
| 9828 | + abstract = {Nearly all mRNAs are post-transcriptionally modified at their 5′ and 3′ ends, by capping and polyadenylation, respectively. These essential modifications are of course chemically quite distinct, as are the enzymatic complexes responsible for their synthesis. But recent studies have uncovered some similarities as well. For example, both involve entirely protein machinery, which is now the exception rather than the rule in RNA processing and modification reactions, and the two reactions share one important factor, namely RNA polymerase II. In this brief review, we describe progress in understanding the enzymes and factors that participate in these two processes, highlighting the evolutionary conservation, from yeast to humans, that has become apparent.}, |
|
| 9829 | + issue = {10}, |
|
| 9830 | + langid = {english}, |
|
| 9831 | + keywords = {Biochemistry,Biological Microscopy,general,Life Sciences,Membrane Biology,Protein Structure}, |
|
| 9832 | + file = {/Users/rmorin/Zotero/storage/5HNWKWVN/Shatkin and Manley - 2000 - The ends of the affair Capping and polyadenylatio.pdf} |
|
| 9833 | +} |
|
| 9834 | + |
|
| 9835 | +@article{shaTransferringGenomicsClinic2015, |
|
| 9836 | + title = {Transferring Genomics to the Clinic: Distinguishing {{Burkitt}} and Diffuse Large {{B}} Cell Lymphomas}, |
|
| 9837 | + shorttitle = {Transferring Genomics to the Clinic}, |
|
| 9838 | + author = {Sha, Chulin and Barrans, Sharon and Care, Matthew A. and Cunningham, David and Tooze, Reuben M. and Jack, Andrew and Westhead, David R.}, |
|
| 9839 | + date = {2015-07-01}, |
|
| 9840 | + journaltitle = {Genome Medicine}, |
|
| 9841 | + shortjournal = {Genome Med}, |
|
| 9842 | + volume = {7}, |
|
| 9843 | + number = {1}, |
|
| 9844 | + eprint = {26207141}, |
|
| 9845 | + eprinttype = {pmid}, |
|
| 9846 | + issn = {1756-994X}, |
|
| 9847 | + doi = {10.1186/s13073-015-0187-6}, |
|
| 9848 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4512160/}, |
|
| 9849 | + urldate = {2020-02-05}, |
|
| 9850 | + abstract = {Background Classifiers based on molecular criteria such as gene expression signatures have been developed to distinguish Burkitt lymphoma and diffuse large B cell lymphoma, which help to explore the intermediate cases where traditional diagnosis is difficult. Transfer of these research classifiers into a clinical setting is challenging because there are competing classifiers in the literature based on different methodology and gene sets with no clear best choice; classifiers based on one expression measurement platform may not transfer effectively to another; and, classifiers developed using fresh frozen samples may not work effectively with the commonly used and more convenient formalin fixed paraffin-embedded samples used in routine diagnosis. Methods Here we thoroughly compared two published high profile classifiers developed on data from different Affymetrix array platforms and fresh-frozen tissue, examining their transferability and concordance. Based on this analysis, a new Burkitt and diffuse large B cell lymphoma classifier (BDC) was developed and employed on Illumina DASL data from our own paraffin-embedded samples, allowing comparison with the diagnosis made in a central haematopathology laboratory and evaluation of clinical relevance. Results We show that both previous classifiers can be recapitulated using very much smaller gene sets than originally employed, and that the classification result is closely dependent on the Burkitt lymphoma criteria applied in the training set. The BDC classification on our data exhibits high agreement (\textasciitilde 95 \%) with the original diagnosis. A simple outcome comparison in the patients presenting intermediate features on conventional criteria suggests that the cases classified as Burkitt lymphoma by BDC have worse response to standard diffuse large B cell lymphoma treatment than those classified as diffuse large B cell lymphoma. Conclusions In this study, we comprehensively investigate two previous Burkitt lymphoma molecular classifiers, and implement a new gene expression classifier, BDC, that works effectively on paraffin-embedded samples and provides useful information for treatment decisions. The classifier is available as a free software package under the GNU public licence within the R statistical software environment through the link http://www.bioinformatics.leeds.ac.uk/labpages/softwares/ or on github https://github.com/Sharlene/BDC. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0187-6) contains supplementary material, which is available to authorized users.}, |
|
| 9851 | + pmcid = {PMC4512160} |
|
| 9852 | +} |
|
| 9853 | + |
|
| 9854 | +@article{shenBCL2ProteinExpression2004, |
|
| 9855 | + title = {{{BCL2}} Protein Expression Parallels Its {{mRNA}} Level in Normal and Malignant {{B}} Cells}, |
|
| 9856 | + author = {Shen, Yulei and Iqbal, Javeed and Huang, James Z. and Zhou, Guimei and Chan, Wing C.}, |
|
| 9857 | + date = {2004-11-01}, |
|
| 9858 | + journaltitle = {Blood}, |
|
| 9859 | + shortjournal = {Blood}, |
|
| 9860 | + volume = {104}, |
|
| 9861 | + number = {9}, |
|
| 9862 | + pages = {2936--2939}, |
|
| 9863 | + issn = {0006-4971}, |
|
| 9864 | + doi = {10.1182/blood-2004-01-0243}, |
|
| 9865 | + url = {https://doi.org/10.1182/blood-2004-01-0243}, |
|
| 9866 | + urldate = {2022-10-06}, |
|
| 9867 | + abstract = {The regulation of B-cell lymphoma 2 (BCL2) protein expression in germinal center (GC) B cells has been controversial. Previous reports have indicated posttranscriptional regulation plays a dominant role. However, a number of recent studies contradicted these reports. Using real-time polymerase chain reaction (PCR) and Standardized Reverse Transcriptase-PCR (StaRT-PCR), we measured the level of mRNA expression in GC, mantle zone (MNZ), and marginal zone (MGZ) cells from laser capture microdissection. Both quantitative RT-PCR measurements of microdissected GC cells from tonsils showed that GC cells had low expression of BCL2 transcripts commensurate with the low protein expression level. These results are in agreement with microarray studies on fluorescence-activated cell sorter (FACS)-sorted cells and microdissected GC cells. We also examined BCL2 mRNA and protein expression on a series of 30 cases of diffuse large B-cell lymphoma (DLBCL) and found, in general, a good correlation. The results suggested that BCL2 protein expression is regulated at the transcriptional level in normal B cells and in the neoplastic cells in most B-cell lymphoproliferative disorders.}, |
|
| 9868 | + file = {/Users/rmorin/Zotero/storage/4W7VWCHE/Shen et al. - 2004 - BCL2 protein expression parallels its mRNA level i.pdf;/Users/rmorin/Zotero/storage/LGSD3IL9/BCL2-protein-expression-parallels-its-mRNA-level.html} |
|
| 9869 | +} |
|
| 9870 | + |
|
| 9871 | +@article{shenSensitiveTumourDetection2018, |
|
| 9872 | + title = {Sensitive Tumour Detection and Classification Using Plasma Cell-Free {{DNA}} Methylomes}, |
|
| 9873 | + author = {Shen, Shu Yi and Singhania, Rajat and Fehringer, Gordon and Chakravarthy, Ankur and Roehrl, Michael H. A. and Chadwick, Dianne and Zuzarte, Philip C. and Borgida, Ayelet and Wang, Ting Ting and Li, Tiantian and Kis, Olena and Zhao, Zhen and Spreafico, Anna and Medina, Tiago da Silva and Wang, Yadon and Roulois, David and Ettayebi, Ilias and Chen, Zhuo and Chow, Signy and Murphy, Tracy and Arruda, Andrea and O'Kane, Grainne M. and Liu, Jessica and Mansour, Mark and McPherson, John D. and O'Brien, Catherine and Leighl, Natasha and Bedard, Philippe L. and Fleshner, Neil and Liu, Geoffrey and Minden, Mark D. and Gallinger, Steven and Goldenberg, Anna and Pugh, Trevor J. and Hoffman, Michael M. and Bratman, Scott V. and Hung, Rayjean J. and De Carvalho, Daniel D.}, |
|
| 9874 | + date = {2018-11}, |
|
| 9875 | + journaltitle = {Nature}, |
|
| 9876 | + shortjournal = {Nature}, |
|
| 9877 | + volume = {563}, |
|
| 9878 | + number = {7732}, |
|
| 9879 | + eprint = {30429608}, |
|
| 9880 | + eprinttype = {pmid}, |
|
| 9881 | + pages = {579--583}, |
|
| 9882 | + issn = {1476-4687}, |
|
| 9883 | + doi = {10.1038/s41586-018-0703-0}, |
|
| 9884 | + abstract = {The use of liquid biopsies for cancer detection and management is rapidly gaining prominence1. Current methods for the detection of circulating tumour DNA involve sequencing somatic mutations using cell-free DNA, but the sensitivity of these methods may be low among patients with early-stage cancer given the limited number of recurrent mutations2-5. By contrast, large-scale epigenetic alterations-which are tissue- and cancer-type specific-are not similarly constrained6 and therefore potentially have greater ability to detect and classify cancers in patients with early-stage disease. Here we develop a sensitive, immunoprecipitation-based protocol to analyse the methylome of small quantities of circulating cell-free DNA, and demonstrate the ability to detect large-scale DNA methylation changes that are enriched for tumour-specific patterns. We also demonstrate robust performance in cancer detection and classification across an extensive collection of plasma samples from several tumour types. This work sets the stage to establish biomarkers for the minimally invasive detection, interception and classification of early-stage cancers based on plasma cell-free DNA methylation patterns.}, |
|
| 9885 | + langid = {english}, |
|
| 9886 | + keywords = {Adenocarcinoma,Animals,Biomarkers Tumor,Cell Line Tumor,Cell-Free Nucleic Acids,Colorectal Neoplasms,DNA Methylation,DNA Mutational Analysis,DNA Neoplasm,Early Detection of Cancer,Epigenesis Genetic,Female,Heterografts,Humans,Liquid Biopsy,Male,Mice,Mice Inbred NOD,Mice SCID,Neoplasm Transplantation,Neoplasms,Organ Specificity,Pancreatic Neoplasms}, |
|
| 9887 | + file = {/Users/rmorin/Zotero/storage/3F9ZJB79/Shen et al. - 2018 - Sensitive tumour detection and classification usin.pdf;/Users/rmorin/Zotero/storage/4UNK76K5/shen2018.pdf} |
|
| 9888 | +} |
|
| 9889 | + |
|
| 9890 | +@article{shenTATABindingProtein2000, |
|
| 9891 | + title = {The {{TATA}} Binding Protein, c-{{Myc}} and Survivin Genes Are Not Somatically Hypermutated, While {{Ig}} and {{BCL6}} Genes Are Hypermutated in Human Memory {{B}} Cells}, |
|
| 9892 | + author = {Shen, Hong Ming and Michael, Nancy and Kim, Nayun and Storb, Ursula}, |
|
| 9893 | + date = {2000-07-01}, |
|
| 9894 | + journaltitle = {International Immunology}, |
|
| 9895 | + shortjournal = {International Immunology}, |
|
| 9896 | + volume = {12}, |
|
| 9897 | + number = {7}, |
|
| 9898 | + pages = {1085--1093}, |
|
| 9899 | + issn = {0953-8178}, |
|
| 9900 | + doi = {10.1093/intimm/12.7.1085}, |
|
| 9901 | + url = {https://doi.org/10.1093/intimm/12.7.1085}, |
|
| 9902 | + urldate = {2024-03-25}, |
|
| 9903 | + abstract = {Immunoglobulin (Ig) genes are hypermutated in mature B cells after interaction with antigen and T cells in a germinal center reaction. We and others have recently shown that the human BCL6 gene is also hypermutated in human peripheral blood memory B cells and tonsils. A preliminary analysis of other non-Ig genes (c-Myc, S14 and AFP) suggested that they were not mutated in memory B cells. We have now performed an in-depth analysis of three non-Ig genes that are expressed in germinal center B cells in two human donors in whom BCL6 is highly mutated. It was found that the TATA binding protein (TBP), c-Myc and survivin genes are not hypermutated. This lack of targeting by the Ig hypermutation mechanism must be due to the lack of regulatory DNA elements, since the primary sequences of the three tested genes have at least as high intrinsic mutability indices as the BCL6 gene.}, |
|
| 9904 | + file = {/Users/rmorin/Zotero/storage/4UBFN2EH/Shen et al. - 2000 - The TATA binding protein, c-Myc and survivin genes.pdf;/Users/rmorin/Zotero/storage/IPAJBLME/661503.html} |
|
| 9905 | +} |
|
| 9906 | + |
|
| 9907 | +@article{sherryDbSNPNCBIDatabase2001, |
|
| 9908 | + title = {{{dbSNP}}: The {{NCBI}} Database of Genetic Variation}, |
|
| 9909 | + shorttitle = {{{dbSNP}}}, |
|
| 9910 | + author = {Sherry, S. T. and Ward, M.-H. and Kholodov, M. and Baker, J. and Phan, L. and Smigielski, E. M. and Sirotkin, K.}, |
|
| 9911 | + date = {2001-01-01}, |
|
| 9912 | + journaltitle = {Nucleic Acids Research}, |
|
| 9913 | + shortjournal = {Nucleic Acids Research}, |
|
| 9914 | + volume = {29}, |
|
| 9915 | + number = {1}, |
|
| 9916 | + pages = {308--311}, |
|
| 9917 | + issn = {0305-1048}, |
|
| 9918 | + doi = {10.1093/nar/29.1.308}, |
|
| 9919 | + url = {https://doi.org/10.1093/nar/29.1.308}, |
|
| 9920 | + urldate = {2021-05-13}, |
|
| 9921 | + abstract = {In response to a need for a general catalog of genome variation to address the large-scale sampling designs required by association studies, gene mapping and evolutionary biology, the National Center for Biotechnology Information (NCBI) has established the dbSNP database [S.T.Sherry, M.Ward and K.Sirotkin (1999) Genome Res., 9, 677–679]. Submissions to dbSNP will be integrated with other sources of information at NCBI such as GenBank, PubMed, LocusLink and the Human Genome Project data. The complete contents of dbSNP are available to the public at website: http://www.ncbi.nlm.nih.gov/SNP. The complete contents of dbSNP can also be downloaded in multiple formats via anonymous FTP at ftp://ncbi.nlm.nih.gov/snp/.}, |
|
| 9922 | + file = {/Users/rmorin/Zotero/storage/JVY2RHA7/Sherry et al. - 2001 - dbSNP the NCBI database of genetic variation.pdf;/Users/rmorin/Zotero/storage/7M9DH8I6/1116004.html} |
|
| 9923 | +} |
|
| 9924 | + |
|
| 9925 | +@article{shiIL6inducedEnhancementCMyc2011, |
|
| 9926 | + title = {{{IL-6-induced Enhancement}} of c-{{Myc Translation}} in {{Multiple Myeloma Cells}}: {{CRITICAL ROLE OF CYTOPLASMIC LOCALIZATION OF THE RNA-BINDING PROTEIN hnRNP A1}} *}, |
|
| 9927 | + shorttitle = {{{IL-6-induced Enhancement}} of c-{{Myc Translation}} in {{Multiple Myeloma Cells}}}, |
|
| 9928 | + author = {Shi, Yijiang and Frost, Patrick and Hoang, Bao and Benavides, Angelica and Gera, Joseph and Lichtenstein, Alan}, |
|
| 9929 | + date = {2011-01-07}, |
|
| 9930 | + journaltitle = {Journal of Biological Chemistry}, |
|
| 9931 | + shortjournal = {Journal of Biological Chemistry}, |
|
| 9932 | + volume = {286}, |
|
| 9933 | + number = {1}, |
|
| 9934 | + eprint = {20974848}, |
|
| 9935 | + eprinttype = {pmid}, |
|
| 9936 | + pages = {67--78}, |
|
| 9937 | + publisher = {Elsevier}, |
|
| 9938 | + issn = {0021-9258, 1083-351X}, |
|
| 9939 | + doi = {10.1074/jbc.M110.153221}, |
|
| 9940 | + url = {https://www.jbc.org/article/S0021-9258(20)54197-5/abstract}, |
|
| 9941 | + urldate = {2022-10-05}, |
|
| 9942 | + abstract = {{$<$}p{$>$}Prior work indicates that IL-6 can stimulate c-Myc expression in multiple myeloma (MM) cells, which is independent of effects on transcription and due to enhanced translation mediated by an internal ribosome entry site in the 5′-UTR of the c-Myc RNA. The RNA-binding protein hnRNP A1 (A1) was also critical to IL-6-stimulated translation. Because A1 shuttles between nucleus and cytoplasm, we investigated whether the ability of IL-6 to enhance Myc translation was mediated by stimulation of A1 shuttling. In MM cell lines and primary specimens, IL-6 increased A1 cytoplasmic localization. In contrast, there was no effect on the total cellular levels of A1. Use of a dominant negative A1 construct, which prevents endogenous A1 from nucleus-to-cytoplasm transit, prevented the ability of IL-6 to enhance Myc internal ribosome entry site activity, Myc protein expression, and MM cell growth. IL-6-stimulated cytoplasmic localization was mediated by alterations in the C-terminal M9 peptide of A1, and this correlated with the ability of IL-6 to induce serine phosphorylation of this domain. A p38 kinase inhibitor prevented IL-6-induced A1 phosphorylation. Thus, IL-6 activates c-Myc translation in MM cells by inducing A1 phosphorylation and cytoplasmic localization in a p38-dependent fashion. These data suggest A1 as a potential therapeutic target in MM.{$<$}/p{$>$}}, |
|
| 9943 | + langid = {english}, |
|
| 9944 | + file = {/Users/rmorin/Zotero/storage/82IXXMH4/Shi et al. - 2011 - IL-6-induced Enhancement of c-Myc Translation in M.pdf;/Users/rmorin/Zotero/storage/BT4PDAYY/fulltext.html} |
|
| 9945 | +} |
|
| 9946 | + |
|
| 9947 | +@article{shiIL6InducedStimulation2008, |
|
| 9948 | + title = {{{IL-6}}–{{Induced Stimulation}} of c-{{Myc Translation}} in {{Multiple Myeloma Cells Is Mediated}} by {{Myc Internal Ribosome Entry Site Function}} and the {{RNA-Binding Protein}}, {{hnRNP A1}}}, |
|
| 9949 | + author = {Shi, Yijiang and Frost, Patrick J. and Hoang, Bao Q. and Benavides, Angelica and Sharma, Sanjai and Gera, Joseph F. and Lichtenstein, Alan K.}, |
|
| 9950 | + date = {2008-12-15}, |
|
| 9951 | + journaltitle = {Cancer Research}, |
|
| 9952 | + shortjournal = {Cancer Research}, |
|
| 9953 | + volume = {68}, |
|
| 9954 | + number = {24}, |
|
| 9955 | + pages = {10215--10222}, |
|
| 9956 | + issn = {0008-5472}, |
|
| 9957 | + doi = {10.1158/0008-5472.CAN-08-1066}, |
|
| 9958 | + url = {https://doi.org/10.1158/0008-5472.CAN-08-1066}, |
|
| 9959 | + urldate = {2022-10-05}, |
|
| 9960 | + abstract = {Prior work indicates that c-myc translation is up-regulated in multiple myeloma cells. To test a role for interleukin (IL)-6 in myc translation, we studied the IL-6–responsive ANBL-6 and IL-6–autocrine U266 cell lines as well as primary patient samples. IL-6 increased c-myc translation, which was resistant to rapamycin, indicating a mechanism independent of mammalian target of rapamycin (mTOR) and cap-dependent translation. In contrast, the cytokine enhanced cap-independent translation via a stimulatory effect on the myc internal ribosome entry site (IRES). As known IRES-trans–activating factors (ITAF) were unaffected by IL-6, we used a yeast-three-hybrid screen to identify novel ITAFs and identified hnRNP A1 (A1) as a mediator of the IL-6 effect. A1 specifically interacted with the myc IRES in filter binding assays as well as EMSAs. Treatment of myeloma cells with IL-6 induced serine phosphorylation of A1 and increased its binding to the myc IRES in vivo in myeloma cells. Primary patient samples also showed binding between A1 and the IRES. RNA interference to knock down hnRNP A1 prevented an IL-6 increase in myc protein expression, myc IRES activity, and cell growth. These data point to hnRNP A1 as a critical regulator of c-myc translation and a potential therapeutic target in multiple myeloma. [Cancer Res 2008;68(24):10215–22]}, |
|
| 9961 | + file = {/Users/rmorin/Zotero/storage/ZEKZBBKR/Shi et al. - 2008 - IL-6–Induced Stimulation of c-Myc Translation in M.pdf;/Users/rmorin/Zotero/storage/VRX4483I/IL-6-Induced-Stimulation-of-c-Myc-Translation-in.html} |
|
| 9962 | +} |
|
| 9963 | + |
|
| 9964 | +@article{shinBRAFV600EMAP2K12015, |
|
| 9965 | + title = {{{BRAF V600E}} and {{MAP2K1}} Mutations in Hairy Cell Leukemia and Splenic Marginal Zone Lymphoma Cases}, |
|
| 9966 | + author = {Shin, Sang-Yong and Lee, Seung-Tae and Kim, Hee-Jin and Ki, Chang-Seok and Jung, Chul Won and Kim, Jong-Won and Kim, Sun-Hee}, |
|
| 9967 | + date = {2015-03}, |
|
| 9968 | + journaltitle = {Annals of Laboratory Medicine}, |
|
| 9969 | + shortjournal = {Ann Lab Med}, |
|
| 9970 | + volume = {35}, |
|
| 9971 | + number = {2}, |
|
| 9972 | + eprint = {25729732}, |
|
| 9973 | + eprinttype = {pmid}, |
|
| 9974 | + pages = {257--259}, |
|
| 9975 | + issn = {2234-3814}, |
|
| 9976 | + doi = {10.3343/alm.2015.35.2.257}, |
|
| 9977 | + langid = {english}, |
|
| 9978 | + pmcid = {PMC4330180}, |
|
| 9979 | + keywords = {Adult,Aged,Antineoplastic Combined Chemotherapy Protocols,Cyclophosphamide,Doxorubicin,Female,Humans,Immunoglobulin Variable Region,Leukemia Hairy Cell,Lymphoma Non-Hodgkin,Male,MAP Kinase Kinase 1,Middle Aged,Mutation,Polymorphism Single Nucleotide,Prednisone,Pregnancy,Proto-Oncogene Proteins B-raf,Real-Time Polymerase Chain Reaction,Vincristine}, |
|
| 9980 | + file = {/Users/rmorin/Zotero/storage/VNU92JZK/Shin et al. - 2015 - BRAF V600E and MAP2K1 mutations in hairy cell leuk.pdf} |
|
| 9981 | +} |
|
| 9982 | + |
|
| 9983 | +@article{shiPCBP1DepletionPromotes2018, |
|
| 9984 | + title = {{{PCBP1}} Depletion Promotes Tumorigenesis through Attenuation of {{p27Kip1 mRNA}} Stability and Translation}, |
|
| 9985 | + author = {Shi, Hongshun and Li, Hui and Yuan, Ronghua and Guan, Wen and Zhang, Xiaomei and Zhang, Shaoyang and Zhang, Wenliang and Tong, Fang and Li, Li and Song, Zhihong and Wang, Changwei and Yang, Shulan and Wang, Haihe}, |
|
| 9986 | + date = {2018-08-07}, |
|
| 9987 | + journaltitle = {Journal of experimental \& clinical cancer research: CR}, |
|
| 9988 | + shortjournal = {J Exp Clin Cancer Res}, |
|
| 9989 | + volume = {37}, |
|
| 9990 | + number = {1}, |
|
| 9991 | + eprint = {30086790}, |
|
| 9992 | + eprinttype = {pmid}, |
|
| 9993 | + pages = {187}, |
|
| 9994 | + issn = {1756-9966}, |
|
| 9995 | + doi = {10.1186/s13046-018-0840-1}, |
|
| 9996 | + abstract = {BACKGROUND: Poly C Binding Protein 1 (PCBP1) is an RNA-binding protein that binds and regulates translational activity of subsets of cellular mRNAs. Depletion of PCBP1 is implicated in various carcinomas, but the underlying mechanism in tumorigenesis remains elusive. METHODS: We performed a transcriptome-wide screen to identify novel bounding mRNA of PCBP1. The bind regions between PCBP1 with target mRNA were investigated by using point mutation and luciferase assay. Cell proliferation, cell cycle, tumorigenesis and cell apoptosis were also evaluated in ovary and colon cancer cell lines. The mechanism that PCBP1 affects p27 was analyzed by mRNA stability and ribosome profiling assays. We analyzed PCBP1 and p27 expression in ovary, colon and renal tumor samples and adjacent non-tumor tissues using RT-PCR, Western Blotting and immunohistochemistry. The prognostic significance of PCBP1 and p27 also analyzed using online databases. RESULTS: We identified cell cycle inhibitor p27Kip1 (p27) as a novel PCBP1-bound transcript. We then demonstrated that binding of PCBP1 to p27 3'UTR via its KH1 domain mainly stabilizes p27 mRNA, while enhances its translation to fuel p27 expression, prior to p27 protein degradation. The upregulated p27 consequently inhibits cell proliferation, cell cycle progression and tumorigenesis, whereas promotes cell apoptosis under paclitaxel treatment. Conversely, knockdown of PCBP1 in turn compromises p27 mRNA stability, leading to lower p27 level and tumorigenesis in vivo. Moreover, forced depletion of p27 counteracts the tumor suppressive ability of PCBP1 in the same PCBP1 over-expressing cells. Physiologically, we showed that decreases of both p27 mRNA and its protein expressions are well correlated to PCBP1 depletion in ovary, colon and renal tumor samples, independent of the p27 ubiquitin ligase Skp2 level. Correlation of PCBP1 with p27 is also found in the tamoxifen, doxorubincin and lapatinib resistant breast cancer cells of GEO database. CONCLUSION: Our results thereby indicate that loss of PCBP1 expression firstly attenuates p27 expression at post-transcriptional level, and subsequently promotes carcinogenesis. PCBP1 could be used as a diagnostic marker to cancer patients.}, |
|
| 9997 | + langid = {english}, |
|
| 9998 | + pmcid = {PMC6081911}, |
|
| 9999 | + keywords = {3' Untranslated Regions,Animals,Apoptosis,Breast Neoplasms,Carcinogenesis,Cell Cycle,Cell Line Tumor,Cyclin-Dependent Kinase Inhibitor p27,DNA-Binding Proteins,Female,Heterogeneous-Nuclear Ribonucleoproteins,Heterografts,Humans,Mice,Mice Inbred BALB C,mRNA stability,Ovarian Neoplasms,p27,PCBP1,Phosphorylation,Protein Biosynthesis,RNA Messenger,RNA Stability,RNA-Binding Proteins,Up-Regulation}, |
|
| 10000 | + file = {/Users/rmorin/Zotero/storage/SG4JGSBG/Shi et al. - 2018 - PCBP1 depletion promotes tumorigenesis through att.pdf} |
|
| 10001 | +} |
|
| 10002 | + |
|
| 10003 | +@article{shlienCopyNumberVariations2009, |
|
| 10004 | + title = {Copy Number Variations and Cancer}, |
|
| 10005 | + author = {Shlien, Adam and Malkin, David}, |
|
| 10006 | + date = {2009-06-16}, |
|
| 10007 | + journaltitle = {Genome Medicine}, |
|
| 10008 | + shortjournal = {Genome Medicine}, |
|
| 10009 | + volume = {1}, |
|
| 10010 | + number = {6}, |
|
| 10011 | + pages = {62}, |
|
| 10012 | + issn = {1756-994X}, |
|
| 10013 | + doi = {10.1186/gm62}, |
|
| 10014 | + url = {https://doi.org/10.1186/gm62}, |
|
| 10015 | + urldate = {2020-05-25}, |
|
| 10016 | + abstract = {DNA copy number variations (CNVs) are an important component of genetic variation, affecting a greater fraction of the genome than single nucleotide polymorphisms (SNPs). The advent of high-resolution SNP arrays has made it possible to identify CNVs. Characterization of widespread constitutional (germline) CNVs has provided insight into their role in susceptibility to a wide spectrum of diseases, and somatic CNVs can be used to identify regions of the genome involved in disease phenotypes. The role of CNVs as risk factors for cancer is currently underappreciated. However, the genomic instability and structural dynamism that characterize cancer cells would seem to make this form of genetic variation particularly intriguing to study in cancer. Here, we provide a detailed overview of the current understanding of the CNVs that arise in the human genome and explore the emerging literature that reveals associations of both constitutional and somatic CNVs with a wide variety of human cancers.}, |
|
| 10017 | + file = {/Users/rmorin/Zotero/storage/LYNNM3AJ/Shlien and Malkin - 2009 - Copy number variations and cancer.pdf;/Users/rmorin/Zotero/storage/6FSA2DIK/gm62.html} |
|
| 10018 | +} |
|
| 10019 | + |
|
| 10020 | +@article{shustikCorrelationsBCL6Rearrangement2010, |
|
| 10021 | + title = {Correlations between {{BCL6}} Rearrangement and Outcome in Patients with Diffuse Large {{B-cell}} Lymphoma Treated with {{CHOP}} or {{R-CHOP}}.}, |
|
| 10022 | + author = {Shustik, Jesse and Han, Guangming and Farinha, Pedro and Johnson, Nathalie A and Ben-Neriah, Susana and Connors, Joseph M and Sehn, Laurie H and Horsman, Douglas E and Gascoyne, Randy D and Steidl, Christian}, |
|
| 10023 | + date = {2010-01}, |
|
| 10024 | + journaltitle = {Haematologica}, |
|
| 10025 | + volume = {95}, |
|
| 10026 | + number = {1}, |
|
| 10027 | + pages = {96--101}, |
|
| 10028 | + keywords = {nosource} |
|
| 10029 | +} |
|
| 10030 | + |
|
| 10031 | +@article{simpsonDetectingDNACytosine2017, |
|
| 10032 | + title = {Detecting {{DNA}} Cytosine Methylation Using Nanopore Sequencing}, |
|
| 10033 | + author = {Simpson, Jared T and Workman, Rachael E and family=Zuzarte, given=PC, given-i=PC and David, Matei and family=Dursi, given=LJ, given-i=LJ and Timp, Winston}, |
|
| 10034 | + date = {2017}, |
|
| 10035 | + journaltitle = {Nature Methods}, |
|
| 10036 | + volume = {14}, |
|
| 10037 | + number = {4}, |
|
| 10038 | + eprint = {28218898}, |
|
| 10039 | + eprinttype = {pmid}, |
|
| 10040 | + pages = {407--410}, |
|
| 10041 | + issn = {1548-7091}, |
|
| 10042 | + doi = {10.1038/nmeth.4184}, |
|
| 10043 | + url = {http://dx.doi.org/10.1038/nmeth.4184}, |
|
| 10044 | + abstract = {In nanopore sequencing devices, electrolytic current signals are sensitive to base modifications, such as 5-methylcytosine (5-mC). Here we quantified the strength of this effect for the Oxford Nanopore Technologies MinION sequencer. By using synthetically methylated DNA, we were able to train a hidden Markov model to distinguish 5-mC from unmethylated cytosine. We applied our method to sequence the methylome of human DNA, without requiring special steps for library preparation.}, |
|
| 10045 | + file = {/Users/rmorin/Zotero/storage/UIACPCMU/Simpson et al. - 2017 - Detecting DNA cytosine methylation using nanopore .pdf;/Users/rmorin/Zotero/storage/UTJCMGRV/nmeth.html} |
|
| 10046 | +} |
|
| 10047 | + |
|
| 10048 | +@article{sipahimalaniSystematicEvaluationAtaxia2007, |
|
| 10049 | + title = {A Systematic Evaluation of the Ataxia Telangiectasia Mutated Gene Does Not Show an Association with non‐{{Hodgkin}} Lymphoma}, |
|
| 10050 | + author = {Sipahimalani, Payal and Spinelli, John J. and MacArthur, Amy C. and Lai, Agnes and Leach, Stephen R. and Janoo‐Gilani, Rozmin T. and Palmquist, Diana L. and Connors, Joseph M. and Gascoyne, Randy D. and Gallagher, Richard P. and Brooks‐Wilson, Angela R.}, |
|
| 10051 | + date = {2007-07}, |
|
| 10052 | + journaltitle = {International Journal of Cancer}, |
|
| 10053 | + volume = {121}, |
|
| 10054 | + number = {9}, |
|
| 10055 | + eprint = {17640065}, |
|
| 10056 | + eprinttype = {pmid}, |
|
| 10057 | + pages = {1967--1975}, |
|
| 10058 | + issn = {1097-0215}, |
|
| 10059 | + doi = {10.1002/ijc.22888}, |
|
| 10060 | + url = {http://dx.doi.org/10.1002/ijc.22888}, |
|
| 10061 | + abstract = {The ataxia telangiectasia mutated (ATM) gene is critical for the detection and repair of DNA double-stranded breaks. Mutations in this gene cause the autosomal recessive syndrome ataxia telangiectasia (AT), an attribute of which is an increased risk of cancer, particularly lymphoma. We have undertaken a population-based case/control study to assess the influence of genetic variation in ATM on the risk of non-Hodgkin lymphoma (NHL). A number of the subtypes that constitute NHL have in common the occurrence of specific somatic translocations that contribute to lymphomagenesis. We hypothesize that ATM function is slightly attenuated by some variants, which could reduce double-stranded break repair capacity, contributing to the occurrence of translocations and subsequent lymphomas. We sequenced the promoter and all exons of ATM in the germline DNA of 86 NHL patients and identified 79 variants. Eighteen of these variants correspond to nonsynonymous amino acid differences, 6 of which were predicted to be deleterious to protein function; these variants were all rare. Eleven common variants make up 10 haplotypes that are specified by 7 tagSNPs. Linkage disequilibrium across the ATM gene is high but incomplete. TagSNPs and the 6 putatively deleterious variants were genotyped in 798 NHL cases and 793 controls. Our results indicate that common variants of ATM do not significantly contribute to the risk of NHL in the general population. However, some rare, functionally deleterious variants may contribute to an increased risk of development of rare subtypes of the disease. © 2007 Wiley-Liss, Inc.}, |
|
| 10062 | + keywords = {nosource} |
|
| 10063 | +} |
|
| 10064 | + |
|
| 10065 | +@article{skalniakMCPIP1ContributesToxicity2014, |
|
| 10066 | + title = {{{MCPIP1}} Contributes to the Toxicity of Proteasome Inhibitor {{MG-132}} in {{HeLa}} Cells by the Inhibition of {{NF-κB}}}, |
|
| 10067 | + author = {Skalniak, Lukasz and Dziendziel, Monika and Jura, Jolanta}, |
|
| 10068 | + date = {2014-07}, |
|
| 10069 | + journaltitle = {Molecular and cellular biochemistry}, |
|
| 10070 | + volume = {395}, |
|
| 10071 | + number = {1-2}, |
|
| 10072 | + pages = {253--263}, |
|
| 10073 | + keywords = {nosource} |
|
| 10074 | +} |
|
| 10075 | + |
|
| 10076 | +@article{skinniderBcl6Bcl2Protein, |
|
| 10077 | + title = {Bcl-6 and {{Bcl-2}} Protein Expression in Diffuse Large {{B-cell}} Lymphoma and Follicular Lymphoma: Correlation with 3q27 and 18q21 Chromosomal Abnormalities}, |
|
| 10078 | + author = {Skinnider, B and Horsman, D and Dupuis, B and Gascoyne, R}, |
|
| 10079 | + journaltitle = {Hum Pathol}, |
|
| 10080 | + volume = {30}, |
|
| 10081 | + number = {7}, |
|
| 10082 | + pages = {803--808}, |
|
| 10083 | + keywords = {nosource} |
|
| 10084 | +} |
|
| 10085 | + |
|
| 10086 | +@article{smithDAZAP1RNAbindingProtein2011, |
|
| 10087 | + title = {{{DAZAP1}}, an {{RNA-binding}} Protein Required for Development and Spermatogenesis, Can Regulate {{mRNA}} Translation}, |
|
| 10088 | + author = {Smith, Richard W. P. and Anderson, Ross C. and Smith, Joel W. S. and Brook, Matthew and Richardson, William A. and Gray, Nicola K.}, |
|
| 10089 | + date = {2011-07}, |
|
| 10090 | + journaltitle = {RNA (New York, N.Y.)}, |
|
| 10091 | + shortjournal = {RNA}, |
|
| 10092 | + volume = {17}, |
|
| 10093 | + number = {7}, |
|
| 10094 | + eprint = {21576381}, |
|
| 10095 | + eprinttype = {pmid}, |
|
| 10096 | + pages = {1282--1295}, |
|
| 10097 | + issn = {1469-9001}, |
|
| 10098 | + doi = {10.1261/rna.2717711}, |
|
| 10099 | + abstract = {DAZ-associated protein 1 (DAZAP1) is an RNA-binding protein required for normal growth, development, and fertility in mice. However, its molecular functions have not been elucidated. Here we find that Xenopus laevis and human DAZAP1, which are each expressed as short and long forms, act as mRNA-specific activators of translation in a manner that is sensitive to the number of binding sites present within the 3' UTR. Domain mapping suggests that this conserved function is mainly associated with C-terminal regions of DAZAP1. Interestingly, we find that the expression of xDAZAP1 and its polysome association are developmentally controlled, the latter suggesting that the translational activator function of DAZAP1 is regulated. However, ERK phosphorylation of DAZAP1, which can alter protein interactions with its C terminus, does not play a role in regulating its ability to participate in translational complexes. Since relatively few mRNA-specific activators have been identified, we explored the mechanism by which DAZAP1 activates translation. By utilizing reporter mRNAs with internal ribosome entry sites, we establish that DAZAP1 stimulates translation initiation. Importantly, this activity is not dependent on the recognition of the 5' cap by initiation factors, showing that it functions downstream from this frequently regulated event, but is modulated by changes in the adenylation status of mRNAs. This suggests a function in the formation of "end-to-end" complexes, which are important for efficient initiation, which we show to be independent of a direct interaction with the bridging protein eIF4G.}, |
|
| 10100 | + langid = {english}, |
|
| 10101 | + pmcid = {PMC3138565}, |
|
| 10102 | + keywords = {Amino Acid Sequence,Animals,Embryo Nonmammalian,Extracellular Signal-Regulated MAP Kinases,Gene Expression Regulation Developmental,Growth and Development,Humans,Male,Models Biological,Molecular Sequence Data,Oocytes,Phosphorylation,Protein Biosynthesis,RNA Messenger,RNA-Binding Proteins,Sequence Homology Amino Acid,Spermatogenesis,Xenopus laevis} |
|
| 10103 | +} |
|
| 10104 | + |
|
| 10105 | +@article{smithPhosphodiesterasePDE4BLimits, |
|
| 10106 | + title = {The Phosphodiesterase {{PDE4B}} Limits {{cAMP-associated PI3K}}/{{AKT-dependent}} Apoptosis in Diffuse Large {{B-cell}} Lymphoma}, |
|
| 10107 | + author = {Smith, P G}, |
|
| 10108 | + journaltitle = {Blood}, |
|
| 10109 | + volume = {105}, |
|
| 10110 | + number = {1}, |
|
| 10111 | + pages = {308--316}, |
|
| 10112 | + keywords = {nosource} |
|
| 10113 | +} |
|
| 10114 | + |
|
| 10115 | +@article{smithPrevalenceCharacterisationTRAF32020, |
|
| 10116 | + title = {The Prevalence and Characterisation of {{TRAF3}} and {{POT1}} Mutations in Canine {{B-cell}} Lymphoma}, |
|
| 10117 | + author = {Smith, P. A. D. and Waugh, E. M. and Crichton, C. and Jarrett, R. F. and Morris, J. S.}, |
|
| 10118 | + date = {2020-12-01}, |
|
| 10119 | + journaltitle = {The Veterinary Journal}, |
|
| 10120 | + shortjournal = {The Veterinary Journal}, |
|
| 10121 | + volume = {266}, |
|
| 10122 | + pages = {105575}, |
|
| 10123 | + issn = {1090-0233}, |
|
| 10124 | + doi = {10.1016/j.tvjl.2020.105575}, |
|
| 10125 | + url = {https://www.sciencedirect.com/science/article/pii/S1090023320301520}, |
|
| 10126 | + urldate = {2021-04-29}, |
|
| 10127 | + abstract = {The genetic and mutational basis of canine lymphoma remains poorly understood. Several genes, including TRAF3 and POT1, are mutated in canine B-cell lymphoma (cBCL), and are likely involved in the pathogenesis of this disease. The purpose of this study was to assess the prevalence of TRAF3 and POT1 mutations in a cohort of dogs with cBCL, compared to dogs with non-cBCL diseases (including four dogs with T-cell lymphoma [cTCL]). Forty-nine dogs were included (n = 24 cBCL; n = 25 non-cBCL). Eleven dogs had matched non-tumour DNA assessed to determine if mutations were germline or somatic. All dogs had TRAF3 and POT1 assessed by Sanger sequencing. The prevalence of deleterious TRAF3 and POT1 mutations in cBCL was 36\% and 17\%, respectively. A deleterious TRAF3 mutation was suspected to be germline in 1/5 cases with matched non-tumour DNA available for comparison. Deleterious mutations were not found in specimens from the non-cBCL group. Several synonymous variants were identified in both genes in cBCL and non-cBCL samples, which likely represent polymorphisms. These results indicate TRAF3 and POT1 mutations are common in cBCL. Deleterious TRAF3 and POT1 mutations were only identified in dogs with cBCL, and not in dogs with non-cBCL diseases, suggesting they are important in the pathogenesis of cBCL. Future studies to investigate the prognostic and therapeutic implications of these mutations are required.}, |
|
| 10128 | + langid = {english}, |
|
| 10129 | + keywords = {Canine lymphoma,Genetics}, |
|
| 10130 | + file = {/Users/rmorin/Zotero/storage/M4SC2WJH/S1090023320301520.html} |
|
| 10131 | +} |
|
| 10132 | + |
|
| 10133 | +@article{soDiagnosticChallengesCase2013, |
|
| 10134 | + title = {Diagnostic Challenges in a Case of {{B}} Cell Lymphoma Unclassifiable with Features Intermediate between Diffuse Large {{B-cell}} Lymphoma and {{Burkitt}} Lymphoma.}, |
|
| 10135 | + author = {So, Chi-Chiu and Yung, Ka-Hung and Chu, Man-Leng and Wan, Thomas S K}, |
|
| 10136 | + date = {2013-10}, |
|
| 10137 | + journaltitle = {International journal of hematology}, |
|
| 10138 | + volume = {98}, |
|
| 10139 | + number = {4}, |
|
| 10140 | + pages = {478--482}, |
|
| 10141 | + keywords = {nosource} |
|
| 10142 | +} |
|
| 10143 | + |
|
| 10144 | +@inproceedings{soldiniNewlyDiscoveredMutations2013, |
|
| 10145 | + title = {The Newly Discovered Mutations in {{Burkitt}} ’ s Lymphoma May Constitute New Markers for Diagnosis , Prognosis and Predictive Value for Novel Therapeutic Targets ”}, |
|
| 10146 | + author = {Soldini, D. and Campo, E.}, |
|
| 10147 | + date = {2013} |
|
| 10148 | +} |
|
| 10149 | + |
|
| 10150 | +@article{solinMultigeneExpressionAssay2013, |
|
| 10151 | + title = {A Multigene Expression Assay to Predict Local Recurrence Risk for Ductal Carcinoma in Situ of the Breast}, |
|
| 10152 | + author = {Solin, Lawrence J. and Gray, Robert and Baehner, Frederick L. and Butler, Steven M. and Hughes, Lorie L. and Yoshizawa, Carl and Cherbavaz, Diana B. and Shak, Steven and Page, David L. and Sledge, George W. and Davidson, Nancy E. and Ingle, James N. and Perez, Edith A. and Wood, William C. and Sparano, Joseph A. and Badve, Sunil}, |
|
| 10153 | + date = {2013-05-15}, |
|
| 10154 | + journaltitle = {Journal of the National Cancer Institute}, |
|
| 10155 | + shortjournal = {J. Natl. Cancer Inst.}, |
|
| 10156 | + volume = {105}, |
|
| 10157 | + number = {10}, |
|
| 10158 | + eprint = {23641039}, |
|
| 10159 | + eprinttype = {pmid}, |
|
| 10160 | + pages = {701--710}, |
|
| 10161 | + issn = {1460-2105}, |
|
| 10162 | + doi = {10.1093/jnci/djt067}, |
|
| 10163 | + abstract = {BACKGROUND: For women with ductal carcinoma in situ (DCIS) of the breast, the risk of developing an ipsilateral breast event (IBE; defined as local recurrence of DCIS or invasive carcinoma) after surgical excision without radiation is not well defined by clinical and pathologic characteristics. METHODS: The Oncotype DX breast cancer assay was performed for patients with DCIS treated with surgical excision without radiation in the Eastern Cooperative Oncology Group (ECOG) E5194 study. The association of the prospectively defined DCIS Score (calculated from seven cancer-related genes and five reference genes) with the risk of developing an IBE was analyzed using Cox regression. All statistical tests were two-sided. RESULTS: There were 327 patients with adequate tissue for analysis. The continuous DCIS Score was statistically significantly associated with the risk of developing an IBE (hazard ratio [HR] = 2.31, 95\% confidence interval [CI] = 1.15 to 4.49; P = .02) when adjusted for tamoxifen use (prespecified primary analysis) and with invasive IBE (unadjusted HR = 3.68, 95\% CI = 1.34 to 9.62; P = .01). For the prespecified DCIS risk groups of low, intermediate, and high, the 10-year risks of developing an IBE were 10.6\%, 26.7\%, and 25.9\%, respectively, and for an invasive IBE, 3.7\%, 12.3\%, and 19.2\%, respectively (both log rank P ≤ .006). In multivariable analyses, factors associated with IBE risk were DCIS Score, tumor size, and menopausal status (all P ≤ .02). CONCLUSIONS: The DCIS Score quantifies IBE risk and invasive IBE risk, complements traditional clinical and pathologic factors, and provides a new clinical tool to improve selecting individualized treatment for women with DCIS who meet the ECOG E5194 criteria.}, |
|
| 10164 | + langid = {english}, |
|
| 10165 | + pmcid = {PMC3653823}, |
|
| 10166 | + keywords = {Adult,Aged,Biomarkers Tumor,Breast Neoplasms,Carcinoma Ductal Breast,Carcinoma Intraductal Noninfiltrating,Female,Gene Expression Profiling,Gene Expression Regulation Neoplastic,Humans,Kaplan-Meier Estimate,Mastectomy Segmental,Middle Aged,Neoplasm Grading,Neoplasm Recurrence Local,Neoplasm Staging,Predictive Value of Tests,Prognosis,Risk Assessment,Risk Factors} |
|
| 10167 | +} |
|
| 10168 | + |
|
| 10169 | +@article{songBlimp1ProteinHans, |
|
| 10170 | + title = {Blimp-1 Protein and {{Hans}} Classification on Prognosis of Diffuse Large {{B-cell}} Lymphoma and Their Interrelation.}, |
|
| 10171 | + author = {Song, Yan and Cao, Zhi and Li, Ling and Zhang, Hong-Tu and Zhang, Xun}, |
|
| 10172 | + journaltitle = {Chinese journal of cancer}, |
|
| 10173 | + volume = {29}, |
|
| 10174 | + number = {9}, |
|
| 10175 | + pages = {781--786}, |
|
| 10176 | + keywords = {nosource} |
|
| 10177 | +} |
|
| 10178 | + |
|
| 10179 | +@article{spinaGeneticsNodalMarginal2016b, |
|
| 10180 | + title = {The Genetics of Nodal Marginal Zone Lymphoma}, |
|
| 10181 | + author = {Spina, Valeria and Khiabanian, Hossein and Messina, Monica and Monti, Sara and Cascione, Luciano and Bruscaggin, Alessio and Spaccarotella, Elisa and Holmes, Antony B. and Arcaini, Luca and Lucioni, Marco and Tabbò, Fabrizio and Zairis, Sakellarios and Diop, Fary and Cerri, Michaela and Chiaretti, Sabina and Marasca, Roberto and Ponzoni, Maurilio and Deaglio, Silvia and Ramponi, Antonio and Tiacci, Enrico and Pasqualucci, Laura and Paulli, Marco and Falini, Brunangelo and Inghirami, Giorgio and Bertoni, Francesco and Foà, Robin and Rabadan, Raul and Gaidano, Gianluca and Rossi, Davide}, |
|
| 10182 | + date = {2016-09-08}, |
|
| 10183 | + journaltitle = {Blood}, |
|
| 10184 | + shortjournal = {Blood}, |
|
| 10185 | + volume = {128}, |
|
| 10186 | + number = {10}, |
|
| 10187 | + pages = {1362--1373}, |
|
| 10188 | + issn = {0006-4971}, |
|
| 10189 | + doi = {10.1182/blood-2016-02-696757}, |
|
| 10190 | + url = {https://doi.org/10.1182/blood-2016-02-696757}, |
|
| 10191 | + urldate = {2024-05-25}, |
|
| 10192 | + abstract = {Nodal marginal zone lymphoma (NMZL) is a rare, indolent B-cell tumor that is distinguished from splenic marginal zone lymphoma (SMZL) by the different pattern of dissemination. NMZL still lacks distinct markers and remains orphan of specific cancer gene lesions. By combining whole-exome sequencing, targeted sequencing of tumor-related genes, whole-transcriptome sequencing, and high-resolution single nucleotide polymorphism array analysis, we aimed at disclosing the pathways that are molecularly deregulated in NMZL and we compare the molecular profile of NMZL with that of SMZL. These analyses identified a distinctive pattern of nonsilent somatic lesions in NMZL. In 35 NMZL patients, 41 genes were found recurrently affected in ≥3 (9\%) cases, including highly prevalent molecular lesions of MLL2 (also known as KMT2D; 34\%), PTPRD (20\%), NOTCH2 (20\%), and KLF2 (17\%). Mutations of PTPRD, a receptor-type protein tyrosine phosphatase regulating cell growth, were enriched in NMZL across mature B-cell tumors, functionally caused the loss of the phosphatase activity of PTPRD, and were associated with cell-cycle transcriptional program deregulation and increased proliferation index in NMZL. Although NMZL shared with SMZL a common mutation profile, NMZL harbored PTPRD lesions that were otherwise absent in SMZL. Collectively, these findings provide new insights into the genetics of NMZL, identify PTPRD lesions as a novel marker for this lymphoma across mature B-cell tumors, and support the distinction of NMZL as an independent clinicopathologic entity within the current lymphoma classification.}, |
|
| 10193 | + file = {/Users/rmorin/Zotero/storage/7DAPGDTD/Spina et al. - 2016 - The genetics of nodal marginal zone lymphoma.pdf;/Users/rmorin/Zotero/storage/BMYIIXJH/The-genetics-of-nodal-marginal-zone-lymphoma.html} |
|
| 10194 | +} |
|
| 10195 | + |
|
| 10196 | +@article{stansfeldUpdatedKielClassification1988, |
|
| 10197 | + title = {Updated {{Kiel}} Classification for Lymphomas}, |
|
| 10198 | + author = {Stansfeld, A. G. and Diebold, J. and Noel, H. and Kapanci, Y. and Rilke, F. and Kelényi, G. and Sundstrom, C. and Lennert, K. and family=Unnik, given=J. A., prefix=van, useprefix=true and Mioduszewska, O.}, |
|
| 10199 | + date = {1988-02-06}, |
|
| 10200 | + journaltitle = {Lancet (London, England)}, |
|
| 10201 | + shortjournal = {Lancet}, |
|
| 10202 | + volume = {1}, |
|
| 10203 | + number = {8580}, |
|
| 10204 | + eprint = {2893097}, |
|
| 10205 | + eprinttype = {pmid}, |
|
| 10206 | + pages = {292--293}, |
|
| 10207 | + issn = {0140-6736}, |
|
| 10208 | + doi = {10.1016/s0140-6736(88)90367-4}, |
|
| 10209 | + langid = {english}, |
|
| 10210 | + keywords = {B-Lymphocytes,Humans,Lymphoma,Lymphoma Non-Hodgkin,T-Lymphocytes} |
|
| 10211 | +} |
|
| 10212 | + |
|
| 10213 | +@article{steenLandscapeTumorCell2021, |
|
| 10214 | + title = {The Landscape of Tumor Cell States and Ecosystems in Diffuse Large {{B}} Cell Lymphoma}, |
|
| 10215 | + author = {Steen, Chloé B. and Luca, Bogdan A. and Esfahani, Mohammad S. and Azizi, Armon and Sworder, Brian J. and Nabet, Barzin Y. and Kurtz, David M. and Liu, Chih Long and Khameneh, Farnaz and Advani, Ranjana H. and Natkunam, Yasodha and Myklebust, June H. and Diehn, Maximilian and Gentles, Andrew J. and Newman, Aaron M. and Alizadeh, Ash A.}, |
|
| 10216 | + date = {2021-10-11}, |
|
| 10217 | + journaltitle = {Cancer Cell}, |
|
| 10218 | + shortjournal = {Cancer Cell}, |
|
| 10219 | + volume = {39}, |
|
| 10220 | + number = {10}, |
|
| 10221 | + eprint = {34597589}, |
|
| 10222 | + eprinttype = {pmid}, |
|
| 10223 | + pages = {1422-1437.e10}, |
|
| 10224 | + issn = {1878-3686}, |
|
| 10225 | + doi = {10.1016/j.ccell.2021.08.011}, |
|
| 10226 | + abstract = {Biological heterogeneity in diffuse large B cell lymphoma (DLBCL) is partly driven by cell-of-origin subtypes and associated genomic lesions, but also by diverse cell types and cell states in the tumor microenvironment (TME). However, dissecting these cell states and their clinical relevance at scale remains challenging. Here, we implemented EcoTyper, a machine-learning framework integrating transcriptome deconvolution and single-cell RNA sequencing, to characterize clinically relevant DLBCL cell states and ecosystems. Using this approach, we identified five cell states of malignant B cells that vary in prognostic associations and differentiation status. We also identified striking variation in cell states for 12 other lineages comprising the TME and forming cell state interactions in stereotyped ecosystems. While cell-of-origin subtypes have distinct TME composition, DLBCL ecosystems capture clinical heterogeneity within existing subtypes and extend beyond cell-of-origin and genotypic classes. These results resolve the DLBCL microenvironment at systems-level resolution and identify opportunities for therapeutic targeting (https://ecotyper.stanford.edu/lymphoma).}, |
|
| 10227 | + langid = {english}, |
|
| 10228 | + pmcid = {PMC9205168}, |
|
| 10229 | + keywords = {CIBERSORTx,diffuse large B cell lymphoma,digital cytometry,DLBCL,Ecosystem,EcoTyper,expression deconvolution,Humans,lymphoma,Lymphoma Large B-Cell Diffuse,Prognosis,tumor ecosystems,tumor immunology,tumor microenvironment,Tumor Microenvironment}, |
|
| 10230 | + file = {/Users/rmorin/Zotero/storage/NRQMMRJE/Steen et al. - 2021 - The landscape of tumor cell states and ecosystems .pdf} |
|
| 10231 | +} |
|
| 10232 | + |
|
| 10233 | +@article{steenProfilingCellType2020, |
|
| 10234 | + title = {Profiling {{Cell Type Abundance}} and {{Expression}} in {{Bulk Tissues}} with {{CIBERSORTx}}}, |
|
| 10235 | + author = {Steen, Chloé B. and Liu, Chih Long and Alizadeh, Ash A. and Newman, Aaron M.}, |
|
| 10236 | + date = {2020}, |
|
| 10237 | + journaltitle = {Methods in Molecular Biology (Clifton, N.J.)}, |
|
| 10238 | + shortjournal = {Methods Mol Biol}, |
|
| 10239 | + volume = {2117}, |
|
| 10240 | + eprint = {31960376}, |
|
| 10241 | + eprinttype = {pmid}, |
|
| 10242 | + pages = {135--157}, |
|
| 10243 | + issn = {1940-6029}, |
|
| 10244 | + doi = {10.1007/978-1-0716-0301-7_7}, |
|
| 10245 | + abstract = {CIBERSORTx is a suite of machine learning tools for the assessment of cellular abundance and cell type-specific gene expression patterns from bulk tissue transcriptome profiles. With this framework, single-cell or bulk-sorted RNA sequencing data can be used to learn molecular signatures of distinct cell types from a small collection of biospecimens. These signatures can then be repeatedly applied to characterize cellular heterogeneity from bulk tissue transcriptomes without physical cell isolation. In this chapter, we provide a detailed primer on CIBERSORTx and demonstrate its capabilities for high-throughput profiling of cell types and cellular states in normal and neoplastic tissues.}, |
|
| 10246 | + langid = {english}, |
|
| 10247 | + pmcid = {PMC7695353}, |
|
| 10248 | + keywords = {Case-Control Studies,Cell Line Tumor,Cell Separation,Cellular heterogeneity,Computational Biology,Deconvolution,Digital cytometry,Gene expression,Gene Expression Profiling,Gene Expression Regulation Neoplastic,High-Throughput Nucleotide Sequencing,Humans,Machine Learning,Neoplasms,Organ Specificity,scRNA-seq,Single-Cell Analysis,Tumor microenvironment}, |
|
| 10249 | + file = {/Users/rmorin/Zotero/storage/ZWBKNI2P/Steen et al. - 2020 - Profiling Cell Type Abundance and Expression in Bu.pdf} |
|
| 10250 | +} |
|
| 10251 | + |
|
| 10252 | +@article{steinhartPromisingPersonalizedTherapeutic, |
|
| 10253 | + title = {Promising Personalized Therapeutic Options for Diffuse Large {{B-cell}} Lymphoma Subtypes with Oncogene Addictions}, |
|
| 10254 | + author = {Steinhart, J and Gartenhaus, R B}, |
|
| 10255 | + journaltitle = {Clin Cancer Res}, |
|
| 10256 | + keywords = {nosource} |
|
| 10257 | +} |
|
| 10258 | + |
|
| 10259 | +@incollection{storeySAMThresholdingFalse2003, |
|
| 10260 | + title = {{{SAM Thresholding}} and {{False Discovery Rates}} for {{Detecting Differential Gene Expression}} in {{DNA Microarrays}}}, |
|
| 10261 | + booktitle = {The {{Analysis}} of {{Gene Expression Data}}: {{Methods}} and {{Software}}}, |
|
| 10262 | + author = {Storey, John D. and Tibshirani, Robert}, |
|
| 10263 | + editor = {Parmigiani, Giovanni and Garrett, Elizabeth S. and Irizarry, Rafael A. and Zeger, Scott L.}, |
|
| 10264 | + date = {2003}, |
|
| 10265 | + series = {Statistics for {{Biology}} and {{Health}}}, |
|
| 10266 | + pages = {272--290}, |
|
| 10267 | + publisher = {Springer}, |
|
| 10268 | + location = {New York, NY}, |
|
| 10269 | + doi = {10.1007/0-387-21679-0_12}, |
|
| 10270 | + url = {https://doi.org/10.1007/0-387-21679-0_12}, |
|
| 10271 | + urldate = {2020-07-20}, |
|
| 10272 | + abstract = {SAM is a computer package for correlating gene expression with an outcome parameter such as treatment, survival time, or diagnostic class. It thresholds an appropriate test statistic and reports the q-value of each test based on a set of sample permutations. SAM works as a Microsoft Excel add-in and has additional features for fold-change thresholding and block permutations. Here, we explain how the SAM methodology works in the context of a general approach to detecting differential gene expression in DNA microarrays. Some recently developed methodology for estimating false discovery rates and q-values has been included in the SAM software, which we summarize here.}, |
|
| 10273 | + isbn = {978-0-387-21679-9}, |
|
| 10274 | + langid = {english}, |
|
| 10275 | + keywords = {False Discovery Rate,Multiple Hypothesis Testing,nosource,Null Distribution,Null Statistic,Rejection Region} |
|
| 10276 | +} |
|
| 10277 | + |
|
| 10278 | +@article{StrongExpressionFOXP12004, |
|
| 10279 | + title = {Strong Expression of {{FOXP1}} Identifies a Distinct Subset of Diffuse Large {{B-cell}} Lymphoma ({{DLBCL}}) Patients with Poor Outcome}, |
|
| 10280 | + date = {2004-10}, |
|
| 10281 | + pages = {1--4}, |
|
| 10282 | + keywords = {nosource} |
|
| 10283 | +} |
|
| 10284 | + |
|
| 10285 | +@article{stuartSinglecellChromatinState2021, |
|
| 10286 | + title = {Single-Cell Chromatin State Analysis with {{Signac}}}, |
|
| 10287 | + author = {Stuart, Tim and Srivastava, Avi and Madad, Shaista and Lareau, Caleb A. and Satija, Rahul}, |
|
| 10288 | + date = {2021-11}, |
|
| 10289 | + journaltitle = {Nature Methods}, |
|
| 10290 | + shortjournal = {Nat Methods}, |
|
| 10291 | + volume = {18}, |
|
| 10292 | + number = {11}, |
|
| 10293 | + eprint = {34725479}, |
|
| 10294 | + eprinttype = {pmid}, |
|
| 10295 | + pages = {1333--1341}, |
|
| 10296 | + issn = {1548-7105}, |
|
| 10297 | + doi = {10.1038/s41592-021-01282-5}, |
|
| 10298 | + abstract = {The recent development of experimental methods for measuring chromatin state at single-cell resolution has created a need for computational tools capable of analyzing these datasets. Here we developed Signac, a comprehensive toolkit for the analysis of single-cell chromatin data. Signac enables an end-to-end analysis of single-cell chromatin data, including peak calling, quantification, quality control, dimension reduction, clustering, integration with single-cell gene expression datasets, DNA motif analysis and interactive visualization. Through its seamless compatibility with the Seurat package, Signac facilitates the analysis of diverse multimodal single-cell chromatin data, including datasets that co-assay DNA accessibility with gene expression, protein abundance and mitochondrial genotype. We demonstrate scaling of the Signac framework to analyze datasets containing over 700,000 cells.}, |
|
| 10299 | + langid = {english}, |
|
| 10300 | + keywords = {Bone Marrow Cells,Chromatin,Computational Biology,Gene Expression Profiling,Humans,Leukocytes Mononuclear,Mitochondria,Sequence Analysis DNA,Single-Cell Analysis,Software} |
|
| 10301 | +} |
|
| 10302 | + |
|
| 10303 | +@article{sukBortezomibInhibitsBurkitt2015, |
|
| 10304 | + title = {Bortezomib Inhibits {{Burkitt}}'s Lymphoma Cell Proliferation by Downregulating Sumoylated {{hnRNP K}} and c-{{Myc}} Expression}, |
|
| 10305 | + author = {Suk, Fat-Moon and Lin, Shyr-Yi and Lin, Ren-Jye and Hsine, Yung-Hsin and Liao, Yen-Ju and Fang, Sheng-Uei and Liang, Yu-Chih}, |
|
| 10306 | + date = {2015-09-22}, |
|
| 10307 | + journaltitle = {Oncotarget}, |
|
| 10308 | + shortjournal = {Oncotarget}, |
|
| 10309 | + volume = {6}, |
|
| 10310 | + number = {28}, |
|
| 10311 | + eprint = {26317903}, |
|
| 10312 | + eprinttype = {pmid}, |
|
| 10313 | + pages = {25988--26001}, |
|
| 10314 | + issn = {1949-2553}, |
|
| 10315 | + doi = {10.18632/oncotarget.4620}, |
|
| 10316 | + abstract = {Bortezomib (Velcal) was the first proteasome inhibitor to be approved by the US Food and Drug Administration to treat patients with relapsed/refractory multiple myelomas. Previous studies have demonstrated that bortezomib inhibits tumor cell proliferation and induces apoptosis by blocking the nuclear factor (NF)-κB pathway. However, the exact mechanism by which bortezomib induces cancer cell apoptosis is still not well understood. In this study, we found that bortezomib significantly inhibited cell proliferation in both human Burkitt's lymphoma CA46 and Daudi cells. Through proteomic analysis, we found that bortezomib treatment changed the expression of various proteins in distinct functional categories including unfolding protein response (UPS), RNA processing, protein targeting and biosynthesis, apoptosis, and signal transduction. Among the proteins with altered expression, hnRNP K, hnRNP H, Hsp90α, Grp78, and Hsp7C were common to both Daudi and CA46 cells. Interestingly, bortezomib treatment downregulated the expression of high-molecular-weight (HMw) hnRNP K and c-Myc but upregulated the expression of low-molecular-weight (LMw) hnRNP K. Moreover, cell proliferation was significantly correlated with high expression of HMw hnRNP K and c-Myc. HMw and LMw hnRNP K were identified as sumoylated and desumoylated hnRNP K, respectively. Using transient transfection, we found that sumoylated hnRNP K increased c-Myc expression at the translational level and contributed to cell proliferation, and that Lys422 of hnRNP K is the candidate sumoylated residue. Our results suggest that besides inhibiting the ubiquitin-proteasome pathway, bortezomib may inhibit cell proliferation by downregulating sumoylated hnRNP K and c-Myc expression in Burkitt's lymphoma cells.}, |
|
| 10317 | + langid = {english}, |
|
| 10318 | + pmcid = {PMC4694880}, |
|
| 10319 | + keywords = {Antineoplastic Agents,Bortezomib,Burkitt Lymphoma,Burkitt’s lymphoma,c-Myc,Cell Line Tumor,Cell Proliferation,Electrophoresis Gel Two-Dimensional,Endoplasmic Reticulum Chaperone BiP,Gene Expression Regulation Neoplastic,Heterogeneous-Nuclear Ribonucleoprotein K,hnRNP K,Humans,Immunoblotting,Lysine,Mutation,Proteomics,Proto-Oncogene Proteins c-myc,Spectrometry Mass Matrix-Assisted Laser Desorption-Ionization,sumoylation,Sumoylation}, |
|
| 10320 | + file = {/Users/rmorin/Zotero/storage/BD5T4C7K/Suk et al. - 2015 - Bortezomib inhibits Burkitt's lymphoma cell prolif.pdf} |
|
| 10321 | +} |
|
| 10322 | + |
|
| 10323 | +@article{summersFrequencyBcl2IgH2001, |
|
| 10324 | + title = {Frequency of the {{Bcl-2}}/{{IgH}} Rearrangement in Normal Individuals: Implications for the Monitoring of Disease in Patients with Follicular Lymphoma}, |
|
| 10325 | + shorttitle = {Frequency of the {{Bcl-2}}/{{IgH}} Rearrangement in Normal Individuals}, |
|
| 10326 | + author = {Summers, K. E. and Goff, L. K. and Wilson, A. G. and Gupta, R. K. and Lister, T. A. and Fitzgibbon, J.}, |
|
| 10327 | + date = {2001-01-15}, |
|
| 10328 | + journaltitle = {Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology}, |
|
| 10329 | + shortjournal = {J Clin Oncol}, |
|
| 10330 | + volume = {19}, |
|
| 10331 | + number = {2}, |
|
| 10332 | + eprint = {11208834}, |
|
| 10333 | + eprinttype = {pmid}, |
|
| 10334 | + pages = {420--424}, |
|
| 10335 | + issn = {0732-183X}, |
|
| 10336 | + doi = {10.1200/JCO.2001.19.2.420}, |
|
| 10337 | + abstract = {PURPOSE: To determine the incidence and frequency of the Bcl-2/IgH rearrangement in the peripheral blood of normal individuals to define the potential complication this may pose for the molecular monitoring of disease in patients with follicular lymphoma (FL). MATERIALS AND METHODS: The incidence and frequency of the major breakpoint cluster region rearrangement in DNA extracted from peripheral blood or lymphoblastoid cell lines from 481 normal individuals was determined using a TaqMan real-time polymerase chain reaction assay (PE Applied Biosystems, Foster City, CA). RESULTS: Twenty three percent of samples were positive for the Bcl-2/IgH rearrangement, with approximately 3\% of these at levels of more than 1 in 10(4) cells. CONCLUSION: The presence of circulating Bcl-2/IgH+ cells, other than those derived from the malignant clone, could confound the detection and quantitation of minimal residual disease in patients with FL, particularly at low levels of tumor burden.}, |
|
| 10338 | + langid = {english}, |
|
| 10339 | + keywords = {Adult,DNA,Gene Frequency,Gene Rearrangement,Genes bcl-2,Humans,Immunoglobulins,Lymphoma Follicular,Middle Aged,Neoplasm Residual,Oncogene Proteins Fusion,Polymerase Chain Reaction,Reference Values,Sequence Analysis DNA,Tumor Cells Cultured} |
|
| 10340 | +} |
|
| 10341 | + |
|
| 10342 | +@article{sunCirculatingTumorCells2011, |
|
| 10343 | + title = {Circulating Tumor Cells: Advances in Detection Methods, Biological Issues, and Clinical Relevance.}, |
|
| 10344 | + author = {Sun, Yun-Fan and Yang, Xin-Rong and Zhou, Jian and Qiu, Shuang-Jian and Fan, Jia and Xu, Yang}, |
|
| 10345 | + date = {2011-08}, |
|
| 10346 | + journaltitle = {Journal of cancer research and clinical oncology}, |
|
| 10347 | + volume = {137}, |
|
| 10348 | + number = {8}, |
|
| 10349 | + pages = {1151--1173}, |
|
| 10350 | + keywords = {nosource} |
|
| 10351 | +} |
|
| 10352 | + |
|
| 10353 | +@article{sunProteinGeneExpression2016, |
|
| 10354 | + title = {Protein and Gene Expression Characteristics of Heterogeneous Nuclear Ribonucleoprotein {{H1}} in Esophageal Squamous Cell Carcinoma}, |
|
| 10355 | + author = {Sun, Yu-Lin and Liu, Fei and Liu, Fang and Zhao, Xiao-Hang}, |
|
| 10356 | + date = {2016-08-28}, |
|
| 10357 | + journaltitle = {World Journal of Gastroenterology}, |
|
| 10358 | + shortjournal = {World J Gastroenterol}, |
|
| 10359 | + volume = {22}, |
|
| 10360 | + number = {32}, |
|
| 10361 | + eprint = {27621578}, |
|
| 10362 | + eprinttype = {pmid}, |
|
| 10363 | + pages = {7322--7331}, |
|
| 10364 | + issn = {1007-9327}, |
|
| 10365 | + doi = {10.3748/wjg.v22.i32.7322}, |
|
| 10366 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4997634/}, |
|
| 10367 | + urldate = {2019-12-21}, |
|
| 10368 | + abstract = {AIM To investigate the expression characteristics of heterogeneous nuclear ribonucleoprotein H1 (HNRNPH1) mRNA and protein in cell lines and tissues of esophageal squamous cell carcinoma (ESCC). METHODS Western blotting was used to assess the expression of HNRNPH1 protein in seven ESCC cell lines and 30 paired fresh tissue specimens. The subcellular localization of HNRNPH1 was determined by immunofluorescence in ESCC cells. The RNA sequencing data from 87 patients with ESCC were obtained from the cancer genome atlas (TCGA), and the expression and clinical characteristics analysis of different transcript variants of HNRNPH1 were evaluated in this dataset. In addition, immunohistochemistry was carried out to detect the expression of HNRNPH1 protein in 125 patients. RESULTS The expression of HNRNPH1 protein varied across different ESCC cell lines. It was exclusively restricted to the nucleus of the ESCC cells. There are two transcript variants of the HNRNPH1 gene. Variant 1 was constitutively expressed, and its expression did not change during tumorigenesis. In contrast, levels of variant 2 were low in non-tumorous tissues and were dramatically increased in ESCC (P = 0.0026). The high levels of variant 2 were associated with poorer differentiated tumors (P = 0.0287). Furthermore, in paired fresh tissue specimens, HNRNPH1 protein was overexpressed in 73.3\% (22/30) of neoplastic tissues. HNRNPH1 was significantly upregulated in ESCC, with strong staining in 43.2\% (54/125) of tumor tissues and 22.4\% (28/125) of matched non-cancerous tissues (P = 0.0005). Positive HNRNPH1 expression was significantly associated with poor tumor differentiation degree (P = 0.0337). CONCLUSION The different alternative transcript variants of HNRNPH1 exhibited different expression changes during tumorigenesis. Its mRNA and protein were overexpressed in ESCC and associated with poorer differentiation of tumor cells. These findings highlight the potential of HNRNPH1 in the therapy and diagnosis of ESCC.}, |
|
| 10369 | + pmcid = {PMC4997634} |
|
| 10370 | +} |
|
| 10371 | + |
|
| 10372 | +@article{svitkinControlTranslationMiRNADependent2013, |
|
| 10373 | + title = {Control of {{Translation}} and {{miRNA-Dependent Repression}} by a {{Novel Poly}}({{A}}) {{Binding Protein}}, {{hnRNP-Q}}}, |
|
| 10374 | + author = {Svitkin, Yuri V. and Yanagiya, Akiko and Karetnikov, Alexey E. and Alain, Tommy and Fabian, Marc R. and Khoutorsky, Arkady and Perreault, Sandra and Topisirovic, Ivan and Sonenberg, Nahum}, |
|
| 10375 | + date = {2013-05-21}, |
|
| 10376 | + journaltitle = {PLOS Biology}, |
|
| 10377 | + shortjournal = {PLOS Biology}, |
|
| 10378 | + volume = {11}, |
|
| 10379 | + number = {5}, |
|
| 10380 | + pages = {e1001564}, |
|
| 10381 | + publisher = {Public Library of Science}, |
|
| 10382 | + issn = {1545-7885}, |
|
| 10383 | + doi = {10.1371/journal.pbio.1001564}, |
|
| 10384 | + url = {https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001564}, |
|
| 10385 | + urldate = {2022-09-27}, |
|
| 10386 | + abstract = {The heterogeneous nuclear ribonucleoprotein Q2 competitively binds mRNA poly(A) tails to regulate translational and miRNA-related functions of PABP.}, |
|
| 10387 | + langid = {english}, |
|
| 10388 | + keywords = {Cross-linking,Immunoprecipitation,Messenger RNA,Protein synthesis,Protein translation,Ribosomes,RNA extraction,Translation initiation}, |
|
| 10389 | + file = {/Users/rmorin/Zotero/storage/3HH95KPS/Svitkin et al. - 2013 - Control of Translation and miRNA-Dependent Repress.pdf;/Users/rmorin/Zotero/storage/6BNN6FT6/Svitkin et al. - 2013 - Control of Translation and miRNA-Dependent Repress.pdf;/Users/rmorin/Zotero/storage/CRALEFCR/article.html} |
|
| 10390 | +} |
|
| 10391 | + |
|
| 10392 | +@article{svitkinGeneralRNABinding1996, |
|
| 10393 | + title = {General {{RNA}} Binding Proteins Render Translation Cap Dependent}, |
|
| 10394 | + author = {Svitkin, Y. V. and Ovchinnikov, L. P. and Dreyfuss, G. and Sonenberg, N.}, |
|
| 10395 | + date = {1996-12-16}, |
|
| 10396 | + journaltitle = {The EMBO journal}, |
|
| 10397 | + shortjournal = {EMBO J}, |
|
| 10398 | + volume = {15}, |
|
| 10399 | + number = {24}, |
|
| 10400 | + eprint = {9003790}, |
|
| 10401 | + eprinttype = {pmid}, |
|
| 10402 | + pages = {7147--7155}, |
|
| 10403 | + issn = {0261-4189}, |
|
| 10404 | + abstract = {Translation in rabbit reticulocyte lysate is relatively independent of the presence of the mRNA m7G cap structure and the cap binding protein, eIF-4E. In addition, initiation occurs frequently at spurious internal sites. Here we show that a critical parameter which contributes to cap-dependent translation is the amount of general RNA binding proteins in the extract. Addition of several general RNA binding proteins, such as hnRNP A1, La autoantigen, pyrimidine tract binding protein (hnRNP I/PTB) and the major core protein of cytoplasmic mRNP (p50), rendered translation in a rabbit reticulocyte lysate cap dependent. These proteins drastically inhibited the translation of an uncapped mRNA, but had no effect on translation of a capped mRNA. Based on these and other results, we suggest that one function of general mRNA binding proteins in the cytoplasm is to promote ribosome binding by a 5' end, cap-mediated mechanism, and prevent spurious initiations at aberrant translation start sites.}, |
|
| 10405 | + langid = {english}, |
|
| 10406 | + pmcid = {PMC452541}, |
|
| 10407 | + keywords = {Animals,Eukaryotic Initiation Factor-4E,Peptide Initiation Factors,Protein Biosynthesis,Rabbits,Repressor Proteins,RNA Messenger,RNA-Binding Proteins} |
|
| 10408 | +} |
|
| 10409 | + |
|
| 10410 | +@article{swerdlowWorldTurnsEvolving2020, |
|
| 10411 | + title = {As the World Turns, Evolving Lymphoma Classifications-Past, Present and Future}, |
|
| 10412 | + author = {Swerdlow, Steven H. and Cook, James R.}, |
|
| 10413 | + date = {2020-01}, |
|
| 10414 | + journaltitle = {Human Pathology}, |
|
| 10415 | + shortjournal = {Hum Pathol}, |
|
| 10416 | + volume = {95}, |
|
| 10417 | + eprint = {31493426}, |
|
| 10418 | + eprinttype = {pmid}, |
|
| 10419 | + pages = {55--77}, |
|
| 10420 | + issn = {1532-8392}, |
|
| 10421 | + doi = {10.1016/j.humpath.2019.08.019}, |
|
| 10422 | + abstract = {The last century and a half has seen first the recognition of lymphomas, and then the publication of one lymphoma classification after another often together with highly critical comments about preceding classifications or a welcome that was less than warm. The introduction of HUMAN PATHOLOGY in 1970 came just before one of the very acrimonious periods in lymphoma classification, as we were learning more about the normal immune system and with the proposed functional lymphoma classifications of Lukes/Collins and Kiel in 1974 relating the lymphomas to their normal B-cell or T-cell 'counterparts'. Those difficult times were followed by the regressive strictly morphologic NCI Working Formulation in 1982, with the REAL classification in 1994 putting us back on a rational path, once again grouping the lymphoid neoplasms first into those of B-cell and T- and putative NK-cell origin, and then using multiple parameters to define specific entities. Planning for the first modern WHO lymphoma classification began soon afterward, with concordance and collegiality leading to the 2001 WHO classification, which then evolved with publication of the 2008 and 2016 WHO classifications. While this review looks at these important past developments which have gotten us to where we are today, it also concentrates on where we are now, what has been learned since the most recent WHO classification and 'Blue Book' were published and on some of the unanswered questions that remain as we look to the future.}, |
|
| 10423 | + langid = {english}, |
|
| 10424 | + keywords = {Biomarkers Tumor,Classification,Diffusion of Innovation,History 20th Century,History 21st Century,Humans,Kiel,Lukes/Collins,Lymphoma,Pathology,Rappaport,REAL,Terminology as Topic,WHO} |
|
| 10425 | +} |
|
| 10426 | + |
|
| 10427 | +@article{takimotoSpecificBindingHeterogeneous1993, |
|
| 10428 | + title = {Specific Binding of Heterogeneous Ribonucleoprotein Particle Protein {{K}} to the Human C-Myc Promoter, in Vitro}, |
|
| 10429 | + author = {Takimoto, M. and Tomonaga, T. and Matunis, M. and Avigan, M. and Krutzsch, H. and Dreyfuss, G. and Levens, D.}, |
|
| 10430 | + date = {1993-08-25}, |
|
| 10431 | + journaltitle = {The Journal of Biological Chemistry}, |
|
| 10432 | + shortjournal = {J Biol Chem}, |
|
| 10433 | + volume = {268}, |
|
| 10434 | + number = {24}, |
|
| 10435 | + eprint = {8349701}, |
|
| 10436 | + eprinttype = {pmid}, |
|
| 10437 | + pages = {18249--18258}, |
|
| 10438 | + issn = {0021-9258}, |
|
| 10439 | + abstract = {A homopurine/homopyrimidine-like sequence is found 100-150 base pairs upstream of the human c-myc promoter P1. This element, termed the CT-element, has been shown to augment expression from P1, and it serves as a positive transcriptional element when coupled to a heterologous promoter in vivo and in vitro. Synthetic oligonucleotides comprising this element were used to form DNA-protein complexes in electrophoretic mobility shift assays. By using conventional and affinity methods, 61- and 34-kDa proteins were shown to be associated with these complexes. Amino acid sequence analysis and immunological methods have identified these proteins as heterogeneous ribonucleoprotein particle (hnRNP) proteins K and A1. Surprisingly, hnRNP protein K binds to the pyrimidine-rich strand of the CT-element in a sequence-specific manner as well as to the double-stranded molecule. Cotransfection of vectors encoding hnRNP protein K in the sense or anti-sense orientations with reporter plasmids driven by wild-type or mutant CT-elements demonstrates that hnRNP protein K augments gene expression in a cis-element-dependent manner. Taken together, these results suggest that hnRNP protein K may play a role in the transcriptional regulation of the human c-myc gene.}, |
|
| 10440 | + langid = {english}, |
|
| 10441 | + keywords = {Amino Acid Sequence,Base Sequence,Cell Nucleus,Electrophoresis Polyacrylamide Gel,Genes myc,Genetic Vectors,HeLa Cells,Heterogeneous Nuclear Ribonucleoprotein A1,Heterogeneous-Nuclear Ribonucleoprotein Group A-B,Heterogeneous-Nuclear Ribonucleoproteins,Humans,Immunoblotting,Molecular Sequence Data,Molecular Weight,Oligodeoxyribonucleotides,Oligonucleotides Antisense,Peptide Fragments,Promoter Regions Genetic,Protein Binding,Ribonucleoproteins,RNA-Binding Proteins,Transfection} |
|
| 10442 | +} |
|
| 10443 | + |
|
| 10444 | +@article{tamboreroOncodriveCISMethodReveal2013, |
|
| 10445 | + title = {Oncodrive-{{CIS}}: {{A Method}} to {{Reveal Likely Driver Genes Based}} on the {{Impact}} of {{Their Copy Number Changes}} on {{Expression}}}, |
|
| 10446 | + author = {Tamborero, David and López-Bigas, Nuria and Gonzalez-Perez, Abel}, |
|
| 10447 | + date = {2013-02}, |
|
| 10448 | + journaltitle = {PloS one}, |
|
| 10449 | + volume = {8}, |
|
| 10450 | + number = {2}, |
|
| 10451 | + pages = {e55489}, |
|
| 10452 | + keywords = {nosource} |
|
| 10453 | +} |
|
| 10454 | + |
|
| 10455 | +@article{tamboreroOncodriveCLUSTExploitingPositional2013, |
|
| 10456 | + title = {{{OncodriveCLUST}}: Exploiting the Positional Clustering of Somatic Mutations to Identify Cancer Genes}, |
|
| 10457 | + shorttitle = {{{OncodriveCLUST}}}, |
|
| 10458 | + author = {Tamborero, David and Gonzalez-Perez, Abel and Lopez-Bigas, Nuria}, |
|
| 10459 | + date = {2013-09-15}, |
|
| 10460 | + journaltitle = {Bioinformatics (Oxford, England)}, |
|
| 10461 | + shortjournal = {Bioinformatics}, |
|
| 10462 | + volume = {29}, |
|
| 10463 | + number = {18}, |
|
| 10464 | + eprint = {23884480}, |
|
| 10465 | + eprinttype = {pmid}, |
|
| 10466 | + pages = {2238--2244}, |
|
| 10467 | + issn = {1367-4811}, |
|
| 10468 | + doi = {10.1093/bioinformatics/btt395}, |
|
| 10469 | + abstract = {MOTIVATION: Gain-of-function mutations often cluster in specific protein regions, a signal that those mutations provide an adaptive advantage to cancer cells and consequently are positively selected during clonal evolution of tumours. We sought to determine the overall extent of this feature in cancer and the possibility to use this feature to identify drivers. RESULTS: We have developed OncodriveCLUST, a method to identify genes with a significant bias towards mutation clustering within the protein sequence. This method constructs the background model by assessing coding-silent mutations, which are assumed not to be under positive selection and thus may reflect the baseline tendency of somatic mutations to be clustered. OncodriveCLUST analysis of the Catalogue of Somatic Mutations in Cancer retrieved a list of genes enriched by the Cancer Gene Census, prioritizing those with dominant phenotypes but also highlighting some recessive cancer genes, which showed wider but still delimited mutation clusters. Assessment of datasets from The Cancer Genome Atlas demonstrated that OncodriveCLUST selected cancer genes that were nevertheless missed by methods based on frequency and functional impact criteria. This stressed the benefit of combining approaches based on complementary principles to identify driver mutations. We propose OncodriveCLUST as an effective tool for that purpose. AVAILABILITY: OncodriveCLUST has been implemented as a Python script and is freely available from http://bg.upf.edu/oncodriveclust CONTACT: nuria.lopez@upf.edu or abel.gonzalez@upf.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, |
|
| 10470 | + langid = {english}, |
|
| 10471 | + keywords = {Cluster Analysis,Genes Neoplasm,Genomics,Humans,Mutation,Neoplasm Proteins,Sequence Analysis Protein,Software} |
|
| 10472 | +} |
|
| 10473 | + |
|
| 10474 | +@article{tamIbrutinibVenetoclaxTreatment2018, |
|
| 10475 | + title = {Ibrutinib plus {{Venetoclax}} for the {{Treatment}} of {{Mantle-Cell Lymphoma}}}, |
|
| 10476 | + author = {Tam, Constantine S. and Anderson, Mary Ann and Pott, Christiane and Agarwal, Rishu and Handunnetti, Sasanka and Hicks, Rodney J. and Burbury, Kate and Turner, Gillian and Di Iulio, Juliana and Bressel, Mathias and Westerman, David and Lade, Stephen and Dreyling, Martin and Dawson, Sarah-Jane and Dawson, Mark A. and Seymour, John F. and Roberts, Andrew W.}, |
|
| 10477 | + date = {2018-03-29}, |
|
| 10478 | + journaltitle = {The New England Journal of Medicine}, |
|
| 10479 | + shortjournal = {N. Engl. J. Med.}, |
|
| 10480 | + volume = {378}, |
|
| 10481 | + number = {13}, |
|
| 10482 | + eprint = {29590547}, |
|
| 10483 | + eprinttype = {pmid}, |
|
| 10484 | + pages = {1211--1223}, |
|
| 10485 | + issn = {1533-4406}, |
|
| 10486 | + doi = {10.1056/NEJMoa1715519}, |
|
| 10487 | + abstract = {BACKGROUND: Both the BTK inhibitor ibrutinib and the BCL2 inhibitor venetoclax are active as monotherapy in the treatment of mantle-cell lymphoma. Complete response rates of 21\% have been observed for each agent when administered as long-term continuous therapy. Preclinical models predict synergy in combination. METHODS: We conducted a single-group, phase 2 study of daily oral ibrutinib and venetoclax in patients, as compared with historical controls. Patients commenced ibrutinib monotherapy at a dose of 560 mg per day. After 4 weeks, venetoclax was added in stepwise, weekly increasing doses to 400 mg per day. Both drugs were continued until progression or an unacceptable level of adverse events. The primary end point was the rate of complete response at week 16. Minimal residual disease (MRD) was assessed by flow cytometry in bone marrow and by allele-specific oligonucleotide-polymerase chain reaction (ASO-PCR) in blood. RESULTS: The study included 24 patients with relapsed or refractory mantle-cell lymphoma (23 patients) or previously untreated mantle-cell lymphoma (1 patient). Patients were 47 to 81 years of age, and the number of previous treatments ranged from none to six. Half the patients had aberrations of TP53, and 75\% had a high-risk prognostic score. The complete response rate according to computed tomography at week 16 was 42\%, which was higher than the historical result of 9\% at this time point with ibrutinib monotherapy (P{$<$}0.001). The rate of complete response as assessed by positron-emission tomography was 62\% at week 16 and 71\% overall. MRD clearance was confirmed by flow cytometry in 67\% of the patients and by ASO-PCR in 38\%. In a time-to-event analysis, 78\% of the patients with a response were estimated to have an ongoing response at 15 months. The tumor lysis syndrome occurred in 2 patients. Common side effects were generally low grade and included diarrhea (in 83\% of the patients), fatigue (in 75\%), and nausea or vomiting (in 71\%). CONCLUSIONS: In this study involving historical controls, dual targeting of BTK and BCL2 with ibrutinib and venetoclax was consistent with improved outcomes in patients with mantle-cell lymphoma who had been predicted to have poor outcomes with current therapy. (Funded by Janssen and others; AIM ClinicalTrials.gov number, NCT02471391 .).}, |
|
| 10488 | + langid = {english}, |
|
| 10489 | + keywords = {Administration Oral,Agammaglobulinaemia Tyrosine Kinase,Aged,Aged 80 and over,Antineoplastic Combined Chemotherapy Protocols,Bone Marrow Examination,Bridged Bicyclo Compounds Heterocyclic,Disease-Free Survival,Female,Historically Controlled Study,Humans,Intention to Treat Analysis,Lymph Nodes,Lymphoma Mantle-Cell,Male,Middle Aged,Mutation,Neoplasm Residual,Prognosis,Protein Kinase Inhibitors,Protein-Tyrosine Kinases,Proto-Oncogene Proteins c-bcl-2,Pyrazoles,Pyrimidines,Sulfonamides,Survival Rate} |
|
| 10490 | +} |
|
| 10491 | + |
|
| 10492 | +@article{tamMutationalAnalysisPRDM12006, |
|
| 10493 | + title = {Mutational Analysis of {{PRDM1}} Indicates a Tumor-Suppressor Role in Diffuse Large {{B-cell}} Lymphomas}, |
|
| 10494 | + author = {Tam, W}, |
|
| 10495 | + date = {2006-05}, |
|
| 10496 | + journaltitle = {Blood}, |
|
| 10497 | + volume = {107}, |
|
| 10498 | + number = {10}, |
|
| 10499 | + pages = {4090--4100}, |
|
| 10500 | + keywords = {nosource} |
|
| 10501 | +} |
|
| 10502 | + |
|
| 10503 | +@article{tanakaFrequentIncidenceSomatic1992, |
|
| 10504 | + title = {Frequent Incidence of Somatic Mutations in Translocated {{BCL2}} Oncogenes of Non-{{Hodgkin}}'s Lymphomas}, |
|
| 10505 | + author = {Tanaka, S. and Louie, D. C. and Kant, J. A. and Reed, J. C.}, |
|
| 10506 | + date = {1992-01-01}, |
|
| 10507 | + journaltitle = {Blood}, |
|
| 10508 | + shortjournal = {Blood}, |
|
| 10509 | + volume = {79}, |
|
| 10510 | + number = {1}, |
|
| 10511 | + eprint = {1339299}, |
|
| 10512 | + eprinttype = {pmid}, |
|
| 10513 | + pages = {229--237}, |
|
| 10514 | + issn = {0006-4971}, |
|
| 10515 | + abstract = {The majority of non-Hodgkin's B-cell lymphomas contain a t(14;18) translocation that places the bc12 gene into juxtaposition with the transcriptically active Ig heavy-chain locus, thus deregulating the expression of this proto-oncogene. The bc12 gene product is a membrane-associated mitochondrial protein that regulates cell survival through unknown mechanisms. Although overproduction of the normal protein appears sufficient for conferring a selective growth or survival advantage to B cells, point mutations that alter the coding region of translocated bc12 genes have been described previously by others in a lymphoma cell line. However, it is not known whether somatic mutations that alter BCL2 proteins occur in vivo or whether they result from chemotherapy or arise through other mechanisms. For these reasons, we obtained DNA from the t(14;18)-containing tumors of five patients who had not undergone treatment for their disease, and used a polymerase chain reaction (PCR)-mismatch technique for rapid identification of point mutations in a portion of the bc12 open reading frame (ORF) corresponding to the first 131 aminoacids (aa) of the 239 aa p26 BCL2 protein. DNAs from two t(14;18)-containing cell lines were also analyzed. Point mutations in this region of the bc12 gene ORF were detected in three of five patients' tumors and in both cell lines. PCR-mismatch analysis of bc12 in cell lines and non-Hodgkin's lymphoma cases that lacked the t(14;18) translocation was negative, thus establishing the specificity of these results. DNA sequencing determined that these mutations are predicted to produce aa substitutions in the BCL2 proteins of two of the primary tumors and one of the cell lines. Interestingly, two of the patients contained an identical C----T transition that resulted in a nonconservative aa substitution (proline----serine) at position 59 of the BCL2 protein. Further analysis excluded the possibility that these mutations represented hereditary polymorphisms or PCR artifacts. A cluster of four point mutations within the translocation + bc12 allele of one patient had hallmarks of the somatic hypermutation mechanism that is associated with Ig genes and that contributes to antibody diversity. Because of the region of the bcl2 gene analyzed in these t(14;18) translocations is located nearly 300 kbp from the Ig heavy-chain locus, our data suggest that the Ig gene somatic hypermutation mechanism can act over extreme distances of DNA. It remains to be established whether these somatic mutations that alter BCL2 proteins influence the pathobiology of nonHodgkin's lymphomas.}, |
|
| 10516 | + langid = {english}, |
|
| 10517 | + keywords = {Base Sequence,Chromosomes Human Pair 14,Chromosomes Human Pair 18,DNA Neoplasm,Humans,Lymphoma Non-Hodgkin,Molecular Sequence Data,Mutation,Polymerase Chain Reaction,Proto-Oncogene Mas,Proto-Oncogene Proteins,Proto-Oncogene Proteins c-bcl-2,Translocation Genetic,Tumor Cells Cultured} |
|
| 10518 | +} |
|
| 10519 | + |
|
| 10520 | +@article{tangHnRNPA2B1PromotesColon2021, |
|
| 10521 | + title = {{{hnRNPA2B1 Promotes Colon Cancer Progression}} via the {{MAPK Pathway}}}, |
|
| 10522 | + author = {Tang, Jingzhi and Chen, Zhimin and Wang, Qi and Hao, Weijie and Gao, Wei-Qiang and Xu, Huiming}, |
|
| 10523 | + date = {2021}, |
|
| 10524 | + journaltitle = {Frontiers in Genetics}, |
|
| 10525 | + volume = {12}, |
|
| 10526 | + issn = {1664-8021}, |
|
| 10527 | + url = {https://www.frontiersin.org/articles/10.3389/fgene.2021.666451}, |
|
| 10528 | + urldate = {2022-10-04}, |
|
| 10529 | + abstract = {HNRNPA2B1, an RNA-binding protein, plays a key role in primary microRNA processing, alternative splicing, mRNA metabolism and transport. Interestingly, hnRNPA2B1 also works as an N6-methyladenosine (m6A) reader and is critical during tumorigenesis of various tissue types. However, its role in colon cancer is still unclear. In this study, we aimed to elucidate the biological functions of hnRNPA2B1 and to explore its underlying mechanisms in colon cancer. We examined the expression of hnRNPA2B1 in Oncomine and TCGA databases. Then verified the findings in colon cancer cells and clinical samples with western blotting and immunohistochemistry (IHC). We used CRISPR/Cas9 directed gene editing to knockout hnRNPA2B1 expression in human colon cancer cell line SW480 and HCT-116 and carried out both in vivo and in vitro experiments. The results were further confirmed by RNA-seq analyses. We found that hnRNPA2B1 significantly promoted colon cancer cell proliferation both in vitro and in vivo, while knockout of hnRNPA2B1 induced apoptosis and cell cycle arrest in SW480. RNA-seq analyses revealed that the ERK/MAPK pathway was activated by hnRNPA2B1 upregulation. In addition, both hnRNPA2B1 and MAPK pathway were activated in clinical colon cancer specimens and positively correlated. Mechanistically, hnRNPA2B1 appeared to be an upstream regulator of the ERK/MAPK pathway and inhibition of MAPK signaling blocked the effects of hnRNPA2B1. Taken together, our data demonstrated that the RNA-binding protein hnRNPA2B1 promotes cell proliferation and regulates cell cycle and apoptosis of human colon cancer by activating the ERK/MAPK signaling, which may provide a new insight into the development of hnRNPA2B1 as a potential therapeutic target for treatment of colon cancer.}, |
|
| 10530 | + file = {/Users/rmorin/Zotero/storage/6PRATNCU/Tang et al. - 2021 - hnRNPA2B1 Promotes Colon Cancer Progression via th.pdf} |
|
| 10531 | +} |
|
| 10532 | + |
|
| 10533 | +@article{tangIDogIntegratedResource2019, |
|
| 10534 | + title = {{{iDog}}: An Integrated Resource for Domestic Dogs and Wild Canids}, |
|
| 10535 | + shorttitle = {{{iDog}}}, |
|
| 10536 | + author = {Tang, Bixia and Zhou, Qing and Dong, Lili and Li, Wulue and Zhang, Xiangquan and Lan, Li and Zhai, Shuang and Xiao, Jingfa and Zhang, Zhang and Bao, Yiming and Zhang, Ya-Ping and Wang, Guo-Dong and Zhao, Wenming}, |
|
| 10537 | + date = {2019-01-08}, |
|
| 10538 | + journaltitle = {Nucleic Acids Research}, |
|
| 10539 | + shortjournal = {Nucleic Acids Research}, |
|
| 10540 | + volume = {47}, |
|
| 10541 | + number = {D1}, |
|
| 10542 | + pages = {D793-D800}, |
|
| 10543 | + issn = {0305-1048}, |
|
| 10544 | + doi = {10.1093/nar/gky1041}, |
|
| 10545 | + url = {https://doi.org/10.1093/nar/gky1041}, |
|
| 10546 | + urldate = {2021-05-13}, |
|
| 10547 | + abstract = {The domestic dog (Canis lupus familiaris) is indisputably one of man's best friends. It is also a fundamental model for many heritable human diseases. Here, we present iDog (http://bigd.big.ac.cn/idog), the first integrated resource dedicated to domestic dogs and wild canids. It incorporates a variety of omics data, including genome sequences assemblies for dhole and wolf, genomic variations extracted from hundreds of dog/wolf whole genomes, phenotype/disease traits curated from dog research communities and public resources, gene expression profiles derived from published RNA-Seq data, gene ontology for functional annotation, homolog gene information for multiple organisms and disease-related literature. Additionally, iDog integrates sequence alignment tools for data analyses and a genome browser for data visualization. iDog will not only benefit the global dog research community, but also provide access to a user-friendly consolidation of dog information to a large number of dog enthusiasts.}, |
|
| 10548 | + file = {/Users/rmorin/Zotero/storage/MIKPATST/Tang et al. - 2019 - iDog an integrated resource for domestic dogs and.pdf;/Users/rmorin/Zotero/storage/57FRG3VV/5146205.html} |
|
| 10549 | +} |
|
| 10550 | + |
|
| 10551 | +@article{taniOverexpressionHeterogeneousNuclear2002, |
|
| 10552 | + title = {Overexpression of Heterogeneous Nuclear Ribonucleoprotein {{B1}} in Lymphoproliferative Disorders: {{High}} Expression in Cells of Follicular Center Origin}, |
|
| 10553 | + shorttitle = {Overexpression of Heterogeneous Nuclear Ribonucleoprotein {{B1}} in Lymphoproliferative Disorders}, |
|
| 10554 | + author = {Tani, Hiroki and Ohshima, Koichi and Haraoka, Seiji and Hamasaki, Makoto and Kamma, Hiroshi and Ikeda, Seiyo and Kikuchi, Masahiro}, |
|
| 10555 | + date = {2002-11-01}, |
|
| 10556 | + journaltitle = {International Journal of Oncology}, |
|
| 10557 | + volume = {21}, |
|
| 10558 | + number = {5}, |
|
| 10559 | + pages = {957--963}, |
|
| 10560 | + publisher = {Spandidos Publications}, |
|
| 10561 | + issn = {1019-6439}, |
|
| 10562 | + doi = {10.3892/ijo.21.5.957}, |
|
| 10563 | + url = {https://www.spandidos-publications.com/10.3892/ijo.21.5.957}, |
|
| 10564 | + urldate = {2022-10-04}, |
|
| 10565 | + abstract = {It is reported that overexpression of hnRNP A2 and B1 proteins is useful for detecting early cancers, and that B1, a splicing minor isoform of A2, is more specific than A2. The B1 expression is still undetermined in human lymphoid tissues. We quantitatively studied the B1 expression in 85 lymph node specimens, comprising reactive lymphoid hyperplasia (RLH; n=8), B-cell lymphoma (n=23), T-cell lymphoma (n=22), and metastatic carcinoma (n=32). Immunostaining and immunoblotting analyses with an anti-B1 monoclonal antibody, 2B2 were performed, and the two sets of results correlated with each other (p{$<$}0.05). In RLH specimens, B1 expression rate was significantly higher in follicular centers (FC; 44\%) than in mantle zone (MZ; 15\%) and paracortex (16\%) (p{$<$}0.01). B1 expression was statistically higher in B-cell lymphoma than in T-cell lymphoma (p{$<$}0.01). In B-cell lymphomas, B1 expression rates were 51\% in diffuse large B-cell lymphoma (DLBL; n=5) and 45\% in follicular lymphoma (FL; n=16), and they were almost the same as that of the FC. Especially in DLBLs, CD10+ FC-origin lymphomas expressed greater amount of B1 than CD10- non-FC-origin lymphomas. B1 expression rate was low in mantle cell lymphoma (MCL; n=2) and similar to that of MZ in RLH. These results suggest that B1 expression is associated with differentiation in lymphoid tissue rather than transformation. B1 expression increases during the process of B-cell differentiation in the FC, and that high B1 expression is maintained in B-cell lymphomagenesis, especially in cells of FC-origin DLBL.}, |
|
| 10566 | + file = {/Users/rmorin/Zotero/storage/UW57LJ47/957.html} |
|
| 10567 | +} |
|
| 10568 | + |
|
| 10569 | +@article{taniReducedExpressionHeterogeneous2003, |
|
| 10570 | + title = {Reduced Expression of Heterogeneous Nuclear Ribonucleoprotein {{B1}} in Adult {{T-cell}} Lymphoma/Leukemia}, |
|
| 10571 | + author = {Tani, Hiroki and Ohshima, Koichi and Haraoka, Seiji and Hamasaki, Makoto and Kamma, Hiroshi and Ikeda, Seiyo and Kikuchi, Masahiro}, |
|
| 10572 | + date = {2003-03-01}, |
|
| 10573 | + journaltitle = {International Journal of Oncology}, |
|
| 10574 | + volume = {22}, |
|
| 10575 | + number = {3}, |
|
| 10576 | + pages = {529--534}, |
|
| 10577 | + publisher = {Spandidos Publications}, |
|
| 10578 | + issn = {1019-6439}, |
|
| 10579 | + doi = {10.3892/ijo.22.3.529}, |
|
| 10580 | + url = {https://www.spandidos-publications.com/10.3892/ijo.22.3.529}, |
|
| 10581 | + urldate = {2022-10-04}, |
|
| 10582 | + abstract = {It is considered that hnRNP B1 expresses similarly in the various types of tumor cells. Recently, we demonstrated high B1 expression in B-cell lymphoma and carcinoma. To evaluate the difference of B1 expression between B and T-cell lymphoma, we immunologically studied the B1 expression in 22 cases with nodal T-cell lymphoma, comprising adult T-cell leukemia/lymphoma (ATLL; n=15) and angioimmunoblastic T-cell lymphoma (AILD; n=7), using an anti-hnRNP B1 monoclonal antibody, 2B2. In ATLL cases, scattered large transformed lymphoma cells demonstrated strong B1 expression, while the medium-sized lymphoma cells were negative. On the one hand, lymphoma cells in AILD diffusely expressed B1. The mean B1 expression rate in ATLL was 22\%, which was significantly lower than that in AILDs (45\%), B-cell lymphomas (44\%), and metastatic carcinomas (53\%) (p{$<$}0.01). Our result might suggest that process of hnRNP B1 expression in ATLL differs from those in other lymphoid neoplasms and carcinoma.}, |
|
| 10583 | + file = {/Users/rmorin/Zotero/storage/EKVICZRF/529.html} |
|
| 10584 | +} |
|
| 10585 | + |
|
| 10586 | +@article{tarabichiPracticalGuideCancer2021, |
|
| 10587 | + title = {A Practical Guide to Cancer Subclonal Reconstruction from {{DNA}} Sequencing}, |
|
| 10588 | + author = {Tarabichi, Maxime and Salcedo, Adriana and Deshwar, Amit G. and Ni Leathlobhair, Máire and Wintersinger, Jeff and Wedge, David C. and Van Loo, Peter and Morris, Quaid D. and Boutros, Paul C.}, |
|
| 10589 | + date = {2021-02}, |
|
| 10590 | + journaltitle = {Nature Methods}, |
|
| 10591 | + shortjournal = {Nat Methods}, |
|
| 10592 | + volume = {18}, |
|
| 10593 | + number = {2}, |
|
| 10594 | + eprint = {33398189}, |
|
| 10595 | + eprinttype = {pmid}, |
|
| 10596 | + pages = {144--155}, |
|
| 10597 | + issn = {1548-7105}, |
|
| 10598 | + doi = {10.1038/s41592-020-01013-2}, |
|
| 10599 | + abstract = {Subclonal reconstruction from bulk tumor DNA sequencing has become a pillar of cancer evolution studies, providing insight into the clonality and relative ordering of mutations and mutational processes. We provide an outline of the complex computational approaches used for subclonal reconstruction from single and multiple tumor samples. We identify the underlying assumptions and uncertainties in each step and suggest best practices for analysis and quality assessment. This guide provides a pragmatic resource for the growing user community of subclonal reconstruction methods.}, |
|
| 10600 | + langid = {english}, |
|
| 10601 | + pmcid = {PMC7867630}, |
|
| 10602 | + keywords = {Algorithms,DNA Neoplasm,Humans,Neoplasms,Polymorphism Single Nucleotide,Sequence Analysis DNA}, |
|
| 10603 | + file = {/Users/rmorin/Zotero/storage/PHPF5EIL/Tarabichi et al. - 2021 - A practical guide to cancer subclonal reconstructi.pdf;/Users/rmorin/Zotero/storage/TGAEU3B9/Tarabichi et al. - 2021 - A practical guide to cancer subclonal reconstructi.pdf} |
|
| 10604 | +} |
|
| 10605 | + |
|
| 10606 | +@article{tarellaProlongedSurvivalPoorrisk2007, |
|
| 10607 | + title = {Prolonged Survival in Poor-Risk Diffuse Large {{B-cell}} Lymphoma Following Front-Line Treatment with Rituximab-Supplemented, Early-Intensified Chemotherapy with Multiple Autologous Hematopoietic Stem Cell Support: A Multicenter Study by {{GITIL}} ({{Gruppo Italiano Terapie Innovative}} Nei {{Linfomi}})}, |
|
| 10608 | + author = {Tarella, C and Zanni, M and Di Nicola, M and Patti, C and Calvi, R and Pescarollo, A and Zoli, V and Fornari, A and Novero, D and Cabras, A and Stella, M and Comino, A and Remotti, D and Ponzoni, M and Caracciolo, D and Ladetto, M and Magni, M and Devizzi, L and Rosato, R and Boccadoro, M and Bregni, M and Corradini, P and Gallamini, A and Majolino, I and Mirto, S and Gianni, A M and family=Linfomi, given=Gruppo Italiano Terapie Innovative, prefix=nei, useprefix=false}, |
|
| 10609 | + date = {2007-08}, |
|
| 10610 | + journaltitle = {Leukemia}, |
|
| 10611 | + volume = {21}, |
|
| 10612 | + number = {8}, |
|
| 10613 | + pages = {1802--1811}, |
|
| 10614 | + keywords = {nosource} |
|
| 10615 | +} |
|
| 10616 | + |
|
| 10617 | +@article{taylorGenomeNorthAmerican2018, |
|
| 10618 | + title = {The {{Genome}} of the {{North American Brown Bear}} or {{Grizzly}}: {{Ursus}} Arctos Ssp. Horribilis}, |
|
| 10619 | + shorttitle = {The {{Genome}} of the {{North American Brown Bear}} or {{Grizzly}}}, |
|
| 10620 | + author = {Taylor, Gregory A. and Kirk, Heather and Coombe, Lauren and Jackman, Shaun D. and Chu, Justin and Tse, Kane and Cheng, Dean and Chuah, Eric and Pandoh, Pawan and Carlsen, Rebecca and Zhao, Yongjun and Mungall, Andrew J. and Moore, Richard and Birol, Inanc and Franke, Maria and Marra, Marco A. and Dutton, Christopher and Jones, Steven J. M.}, |
|
| 10621 | + date = {2018-11-30}, |
|
| 10622 | + journaltitle = {Genes}, |
|
| 10623 | + shortjournal = {Genes (Basel)}, |
|
| 10624 | + volume = {9}, |
|
| 10625 | + number = {12}, |
|
| 10626 | + eprint = {30513700}, |
|
| 10627 | + eprinttype = {pmid}, |
|
| 10628 | + pages = {E598}, |
|
| 10629 | + issn = {2073-4425}, |
|
| 10630 | + doi = {10.3390/genes9120598}, |
|
| 10631 | + abstract = {The grizzly bear (Ursus arctos ssp. horribilis) represents the largest population of brown bears in North America. Its genome was sequenced using a microfluidic partitioning library construction technique, and these data were supplemented with sequencing from a nanopore-based long read platform. The final assembly was 2.33 Gb with a scaffold N50 of 36.7 Mb, and the genome is of comparable size to that of its close relative the polar bear (2.30 Gb). An analysis using 4104 highly conserved mammalian genes indicated that 96.1\% were found to be complete within the assembly. An automated annotation of the genome identified 19,848 protein coding genes. Our study shows that the combination of the two sequencing modalities that we used is sufficient for the construction of highly contiguous reference quality mammalian genomes. The assembled genome sequence and the supporting raw sequence reads are available from the NCBI (National Center for Biotechnology Information) under the bioproject identifier PRJNA493656, and the assembly described in this paper is version QXTK01000000.}, |
|
| 10632 | + langid = {english}, |
|
| 10633 | + pmcid = {PMC6315469}, |
|
| 10634 | + keywords = {genome,grizzly bear,microfluidic partitioning,nanopore,Ursus arctos ssp. Horribilis}, |
|
| 10635 | + file = {/Users/rmorin/Zotero/storage/WJTMZQCX/Taylor et al. - 2018 - The Genome of the North American Brown Bear or Gri.pdf} |
|
| 10636 | +} |
|
| 10637 | + |
|
| 10638 | +@article{taylorPromotingCoherentMinimum2008, |
|
| 10639 | + title = {Promoting Coherent Minimum Reporting Guidelines for Biological and Biomedical Investigations: The {{MIBBI}} Project}, |
|
| 10640 | + shorttitle = {Promoting Coherent Minimum Reporting Guidelines for Biological and Biomedical Investigations}, |
|
| 10641 | + author = {Taylor, Chris F. and Field, Dawn and Sansone, Susanna-Assunta and Aerts, Jan and Apweiler, Rolf and Ashburner, Michael and Ball, Catherine A. and Binz, Pierre-Alain and Bogue, Molly and Booth, Tim and Brazma, Alvis and Brinkman, Ryan R. and Michael Clark, Adam and Deutsch, Eric W. and Fiehn, Oliver and Fostel, Jennifer and Ghazal, Peter and Gibson, Frank and Gray, Tanya and Grimes, Graeme and Hancock, John M. and Hardy, Nigel W. and Hermjakob, Henning and Julian, Randall K. and Kane, Matthew and Kettner, Carsten and Kinsinger, Christopher and Kolker, Eugene and Kuiper, Martin and Novère, Nicolas Le and Leebens-Mack, Jim and Lewis, Suzanna E. and Lord, Phillip and Mallon, Ann-Marie and Marthandan, Nishanth and Masuya, Hiroshi and McNally, Ruth and Mehrle, Alexander and Morrison, Norman and Orchard, Sandra and Quackenbush, John and Reecy, James M. and Robertson, Donald G. and Rocca-Serra, Philippe and Rodriguez, Henry and Rosenfelder, Heiko and Santoyo-Lopez, Javier and Scheuermann, Richard H. and Schober, Daniel and Smith, Barry and Snape, Jason and Stoeckert, Christian J. and Tipton, Keith and Sterk, Peter and Untergasser, Andreas and Vandesompele, Jo and Wiemann, Stefan}, |
|
| 10642 | + date = {2008-08}, |
|
| 10643 | + journaltitle = {Nature Biotechnology}, |
|
| 10644 | + shortjournal = {Nat Biotechnol}, |
|
| 10645 | + volume = {26}, |
|
| 10646 | + number = {8}, |
|
| 10647 | + pages = {889--896}, |
|
| 10648 | + publisher = {Nature Publishing Group}, |
|
| 10649 | + issn = {1546-1696}, |
|
| 10650 | + doi = {10.1038/nbt.1411}, |
|
| 10651 | + url = {https://www.nature.com/articles/nbt.1411}, |
|
| 10652 | + urldate = {2022-05-19}, |
|
| 10653 | + abstract = {The Minimum Information for Biological and Biomedical Investigations (MIBBI) project aims to foster the coordinated development of minimum-information checklists and provide a resource for those exploring the range of extant checklists.}, |
|
| 10654 | + issue = {8}, |
|
| 10655 | + langid = {english}, |
|
| 10656 | + keywords = {Agriculture,Bioinformatics,Biomedical Engineering/Biotechnology,Biomedicine,Biotechnology,general,Life Sciences}, |
|
| 10657 | + file = {/Users/rmorin/Zotero/storage/2HECFVTG/Taylor et al. - 2008 - Promoting coherent minimum reporting guidelines fo.pdf;/Users/rmorin/Zotero/storage/NGEMHFYA/nbt.html} |
|
| 10658 | +} |
|
| 10659 | + |
|
| 10660 | +@article{teraaImpactSF3B1Mutations2015, |
|
| 10661 | + title = {The Impact of {{SF3B1}} Mutations in {{CLL}} on the {{DNA-damage}} Response}, |
|
| 10662 | + author = {Te Raa, G. D. and Derks, I. a. M. and Navrkalova, V. and Skowronska, A. and Moerland, P. D. and family=Laar, given=J., prefix=van, useprefix=true and Oldreive, C. and Monsuur, H. and Trbusek, M. and Malcikova, J. and Lodén, M. and Geisler, C. H. and Hüllein, J. and Jethwa, A. and Zenz, T. and Pospisilova, S. and Stankovic, T. and family=Oers, given=M. H. J., prefix=van, useprefix=true and Kater, A. P. and Eldering, E.}, |
|
| 10663 | + date = {2015-05}, |
|
| 10664 | + journaltitle = {Leukemia}, |
|
| 10665 | + shortjournal = {Leukemia}, |
|
| 10666 | + volume = {29}, |
|
| 10667 | + number = {5}, |
|
| 10668 | + eprint = {25371178}, |
|
| 10669 | + eprinttype = {pmid}, |
|
| 10670 | + pages = {1133--1142}, |
|
| 10671 | + issn = {1476-5551}, |
|
| 10672 | + doi = {10.1038/leu.2014.318}, |
|
| 10673 | + abstract = {Mutations or deletions in TP53 or ATM are well-known determinants of poor prognosis in chronic lymphocytic leukemia (CLL), but only account for approximately 40\% of chemo-resistant patients. Genome-wide sequencing has uncovered novel mutations in the splicing factor sf3b1, that were in part associated with ATM aberrations, suggesting functional synergy. We first performed detailed genetic analyses in a CLL cohort (n=110) containing ATM, SF3B1 and TP53 gene defects. Next, we applied a newly developed multiplex assay for p53/ATM target gene induction and measured apoptotic responses to DNA damage. Interestingly, SF3B1 mutated samples without concurrent ATM and TP53 aberrations (sole SF3B1) displayed partially defective ATM/p53 transcriptional and apoptotic responses to various DNA-damaging regimens. In contrast, NOTCH1 or K/N-RAS mutated CLL displayed normal responses in p53/ATM target gene induction and apoptosis. In sole SF3B1 mutated cases, ATM kinase function remained intact, and γH2AX formation, a marker for DNA damage, was increased at baseline and upon irradiation. Our data demonstrate that single mutations in sf3b1 are associated with increased DNA damage and/or an aberrant response to DNA damage. Together, our observations may offer an explanation for the poor prognosis associated with SF3B1 mutations.}, |
|
| 10674 | + langid = {english}, |
|
| 10675 | + keywords = {Apoptosis,Ataxia Telangiectasia Mutated Proteins,Cohort Studies,DNA Damage,DNA Mutational Analysis,Doxorubicin,Flow Cytometry,Gene Deletion,Gene Expression Regulation Leukemic,Genome Human,Histones,Humans,Imidazoles,Leukemia Lymphocytic Chronic B-Cell,Mutation,Phosphoproteins,Piperazines,Prognosis,Receptor Notch1,Ribonucleoprotein U2 Small Nuclear,RNA Splicing Factors,Tumor Suppressor Protein p53,Vidarabine} |
|
| 10676 | +} |
|
| 10677 | + |
|
| 10678 | +@article{teschendorffConsensusPrognosticGene2006, |
|
| 10679 | + title = {A Consensus Prognostic Gene Expression Classifier for {{ER}} Positive Breast Cancer}, |
|
| 10680 | + author = {Teschendorff, Andrew E. and Naderi, Ali and Barbosa-Morais, Nuno L. and Pinder, Sarah E. and Ellis, Ian O. and Aparicio, Sam and Brenton, James D. and Caldas, Carlos}, |
|
| 10681 | + date = {2006}, |
|
| 10682 | + journaltitle = {Genome Biology}, |
|
| 10683 | + shortjournal = {Genome Biol.}, |
|
| 10684 | + volume = {7}, |
|
| 10685 | + number = {10}, |
|
| 10686 | + eprint = {17076897}, |
|
| 10687 | + eprinttype = {pmid}, |
|
| 10688 | + pages = {R101}, |
|
| 10689 | + issn = {1474-760X}, |
|
| 10690 | + doi = {10.1186/gb-2006-7-10-r101}, |
|
| 10691 | + abstract = {BACKGROUND: A consensus prognostic gene expression classifier is still elusive in heterogeneous diseases such as breast cancer. RESULTS: Here we perform a combined analysis of three major breast cancer microarray data sets to hone in on a universally valid prognostic molecular classifier in estrogen receptor (ER) positive tumors. Using a recently developed robust measure of prognostic separation, we further validate the prognostic classifier in three external independent cohorts, confirming the validity of our molecular classifier in a total of 877 ER positive samples. Furthermore, we find that molecular classifiers may not outperform classical prognostic indices but that they can be used in hybrid molecular-pathological classification schemes to improve prognostic separation. CONCLUSION: The prognostic molecular classifier presented here is the first to be valid in over 877 ER positive breast cancer samples and across three different microarray platforms. Larger multi-institutional studies will be needed to fully determine the added prognostic value of molecular classifiers when combined with standard prognostic factors.}, |
|
| 10692 | + langid = {english}, |
|
| 10693 | + pmcid = {PMC1794561}, |
|
| 10694 | + keywords = {Breast Neoplasms,Cohort Studies,Female,Gene Expression Profiling,Genetic Markers,Humans,Oligonucleotide Array Sequence Analysis,Prognosis,Receptors Estrogen,Reproducibility of Results} |
|
| 10695 | +} |
|
| 10696 | + |
|
| 10697 | +@article{testoniGainsMYCLocus, |
|
| 10698 | + title = {Gains of {{MYC}} Locus and Outcome in Patients with Diffuse Large {{B-cell}} Lymphoma Treated with {{R-CHOP}}.}, |
|
| 10699 | + author = {Testoni, Monica and Kwee, Ivo and Greiner, Timothy C and Montes-Moreno, Santiago and Vose, Julie and Chan, Wing C and Chiappella, Annalisa and Baldini, Luca and Ferreri, Andrés J M and Gaidano, Gianluca and Mian, Michael and Zucca, Emanuele and Bertoni, Francesco}, |
|
| 10700 | + journaltitle = {Br J Haematol}, |
|
| 10701 | + volume = {155}, |
|
| 10702 | + number = {2}, |
|
| 10703 | + pages = {274--277}, |
|
| 10704 | + keywords = {nosource} |
|
| 10705 | +} |
|
| 10706 | + |
|
| 10707 | +@article{thierryClinicalValidationDetection, |
|
| 10708 | + title = {Clinical Validation of the Detection of {{KRAS}} and {{BRAF}} Mutations from Circulating Tumor {{DNA}}}, |
|
| 10709 | + author = {Thierry, Alain R and Mouliere, Florent and El Messaoudi, Safia and Mollevi, Caroline and Lopez-Crapez, Evelyne and Rolet, Fanny and Gillet, Brigitte and Gongora, Celine and Dechelotte, Pierre and Robert, Bruno and Del Rio, Maguy and Lamy, Pierre-Jean and Bibeau, Frederic and Nouaille, Michelle and Loriot, Virginie and Jarrousse, Anne-Sophie and Molina, Franck and Mathonnet, Muriel and Pezet, Denis and Ychou, Marc}, |
|
| 10710 | + journaltitle = {Nature Medicine}, |
|
| 10711 | + pages = {1--7}, |
|
| 10712 | + keywords = {nosource} |
|
| 10713 | +} |
|
| 10714 | + |
|
| 10715 | +@article{thomasGENETICSUBGROUPSINFORM, |
|
| 10716 | + title = {{{GENETIC SUBGROUPS INFORM ON PATHOBIOLOGY IN ADULT AND PEDIATRIC BURKITT LYMPHOMA}}}, |
|
| 10717 | + author = {Thomas, Nicole and Gerhard, Daniela}, |
|
| 10718 | + pages = {40}, |
|
| 10719 | + abstract = {Burkitt lymphoma (BL) accounts for the majority of pediatric non-Hodgkin lymphomas being less common but significantly more lethal when diagnosed in adults. Much of our knowledge of the genetics of BL thus far has originated from the study of pediatric BL (pBL), leaving its relationship to adult (aBL) and other adult lymphomas not fully explored. We sought to more thoroughly identify the somatic changes that underlie lymphomagenesis in aBL and any molecular features that associate with clinical disparities within and between pBL and aBL. Through comprehensive whole-genome sequencing of 230 BL and 295 diffuse large B-cell lymphoma (DLBCL) tumors, we identified additional significantly mutated genes (SMGs) including more genetic features that associate with tumor EBV status, and unraveled new distinct subgroupings within BL and DLBCL with three predominantly comprising BLs: DGG-BL (DDX3X, GNA13 and GNAI2), IC-BL (ID3, CCND3), and Q53-BL (quiet TP53). Each BL subgroup is characterized by combinations of common driver and noncoding mutations caused by aberrant somatic hypermutation (aSHM). The largest subgroups of BL cases, IC-BL and DGG-BL are further characterized by distinct biological and gene expression differences. IC-BL and DGG-BL and their prototypical genetic features (ID3 and TP53) had significant associations with patient outcomes that were different among aBL and pBL cohorts. These findings highlight shared pathogenesis between aBL and pBL, and establish genetic subtypes within BL that serve to delineate tumors with distinct molecular features, providing a new framework for epidemiological, diagnostic, and therapeutic strategies.}, |
|
| 10720 | + langid = {english}, |
|
| 10721 | + file = {/Users/rmorin/Zotero/storage/844ZGGUA/Thomas and Gerhard - GENETIC SUBGROUPS INFORM ON PATHOBIOLOGY IN ADULT .pdf} |
|
| 10722 | +} |
|
| 10723 | + |
|
| 10724 | +@article{thomasGeneticSubgroupsInform2023, |
|
| 10725 | + title = {Genetic Subgroups Inform on Pathobiology in Adult and Pediatric {{Burkitt}} Lymphoma}, |
|
| 10726 | + author = {Thomas, Nicole and Dreval, Kostiantyn and Gerhard, Daniela S. and Hilton, Laura K. and Abramson, Jeremy S. and Ambinder, Richard F. and Barta, Stefan and Bartlett, Nancy L. and Bethony, Jeffrey and Bhatia, Kishor and Bowen, Jay and Bryan, Anthony C. and Cesarman, Ethel and Casper, Corey and Chadburn, Amy and Cruz, Manuela and Dittmer, Dirk P. and Dyer, Maureen A. and Farinha, Pedro and Gastier-Foster, Julie M. and Gerrie, Alina S. and Grande, Bruno M. and Greiner, Timothy and Griner, Nicholas B. and Gross, Thomas G. and Harris, Nancy L. and Irvin, John D. and Jaffe, Elaine S. and Henry, David and Huppi, Rebecca and Leal, Fabio E. and Lee, Michael S. and Martin, Jean Paul and Martin, Marie-Reine and Mbulaiteye, Sam M. and Mitsuyasu, Ronald and Morris, Vivian and Mullighan, Charles G. and Mungall, Andrew J. and Mungall, Karen and Mutyaba, Innocent and Nokta, Mostafa and Namirembe, Constance and Noy, Ariela and Ogwang, Martin D. and Omoding, Abraham and Orem, Jackson and Ott, German and Petrello, Hilary and Pittaluga, Stefania and Phelan, James D. and Ramos, Juan Carlos and Ratner, Lee and Reynolds, Steven J. and Rubinstein, Paul G. and Sissolak, Gerhard and Slack, Graham and Soudi, Shaghayegh and Swerdlow, Steven H. and Traverse-Glehen, Alexandra and Wilson, Wyndham H. and Wong, Jasper and Yarchoan, Robert and ZenKlusen, Jean C. and Marra, Marco A. and Staudt, Louis M. and Scott, David W. and Morin, Ryan D.}, |
|
| 10727 | + date = {2023-02-23}, |
|
| 10728 | + journaltitle = {Blood}, |
|
| 10729 | + shortjournal = {Blood}, |
|
| 10730 | + volume = {141}, |
|
| 10731 | + number = {8}, |
|
| 10732 | + pages = {904--916}, |
|
| 10733 | + issn = {0006-4971}, |
|
| 10734 | + doi = {10.1182/blood.2022016534}, |
|
| 10735 | + url = {https://doi.org/10.1182/blood.2022016534}, |
|
| 10736 | + urldate = {2024-01-19}, |
|
| 10737 | + abstract = {Burkitt lymphoma (BL) accounts for most pediatric non-Hodgkin lymphomas, being less common but significantly more lethal when diagnosed in adults. Much of the knowledge of the genetics of BL thus far has originated from the study of pediatric BL (pBL), leaving its relationship to adult BL (aBL) and other adult lymphomas not fully explored. We sought to more thoroughly identify the somatic changes that underlie lymphomagenesis in aBL and any molecular features that associate with clinical disparities within and between pBL and aBL. Through comprehensive whole-genome sequencing of 230 BL and 295 diffuse large B-cell lymphoma (DLBCL) tumors, we identified additional significantly mutated genes, including more genetic features that associate with tumor Epstein-Barr virus status, and unraveled new distinct subgroupings within BL and DLBCL with 3 predominantly comprising BLs: DGG-BL (DDX3X, GNA13, and GNAI2), IC-BL (ID3 and CCND3), and Q53-BL (quiet TP53). Each BL subgroup is characterized by combinations of common driver and noncoding mutations caused by aberrant somatic hypermutation. The largest subgroups of BL cases, IC-BL and DGG-BL, are further characterized by distinct biological and gene expression differences. IC-BL and DGG-BL and their prototypical genetic features (ID3 and TP53) had significant associations with patient outcomes that were different among aBL and pBL cohorts. These findings highlight shared pathogenesis between aBL and pBL, and establish genetic subtypes within BL that serve to delineate tumors with distinct molecular features, providing a new framework for epidemiologic, diagnostic, and therapeutic strategies.}, |
|
| 10738 | + keywords = {Morinlab}, |
|
| 10739 | + file = {/Users/rmorin/Zotero/storage/NTCK8RLE/Thomas et al. - 2023 - Genetic subgroups inform on pathobiology in adult .pdf;/Users/rmorin/Zotero/storage/9Z8QM8ZX/Genetic-subgroups-inform-on-pathobiology-in-adult.html} |
|
| 10740 | +} |
|
| 10741 | + |
|
| 10742 | +@article{tiacciAnalyzingPrimaryHodgkin2012a, |
|
| 10743 | + title = {Analyzing Primary {{Hodgkin}} and {{Reed-Sternberg}} Cells to Capture the Molecular and Cellular Pathogenesis of Classical {{Hodgkin}} Lymphoma}, |
|
| 10744 | + author = {Tiacci, Enrico and Döring, Claudia and Brune, Verena and family=Noesel, given=Carel J. M., prefix=van, useprefix=true and Klapper, Wolfram and Mechtersheimer, Gunhild and Falini, Brunangelo and Küppers, Ralf and Hansmann, Martin-Leo}, |
|
| 10745 | + date = {2012-11-29}, |
|
| 10746 | + journaltitle = {Blood}, |
|
| 10747 | + shortjournal = {Blood}, |
|
| 10748 | + volume = {120}, |
|
| 10749 | + number = {23}, |
|
| 10750 | + eprint = {22955914}, |
|
| 10751 | + eprinttype = {pmid}, |
|
| 10752 | + pages = {4609--4620}, |
|
| 10753 | + issn = {1528-0020}, |
|
| 10754 | + doi = {10.1182/blood-2012-05-428896}, |
|
| 10755 | + abstract = {The pathogenesis of classical Hodgkin lymphoma (cHL), the most common lymphoma in the young, is still enigmatic, largely because its Hodgkin and Reed-Sternberg (HRS) tumor cells are rare in the involved lymph node and therefore difficult to analyze. Here, by overcoming this technical challenge and performing, for the first time, a genome-wide transcriptional analysis of microdissected HRS cells compared with other B-cell lymphomas, cHL lines, and normal B-cell subsets, we show that they differ extensively from the usually studied cHL cell lines, that the lost B-cell identity of cHLs is not linked to the acquisition of a plasma cell-like gene expression program, and that Epstein-Barr virus infection of HRS cells has a minor transcriptional influence on the established cHL clone. Moreover, although cHL appears a distinct lymphoma entity overall, HRS cells of its histologic subtypes diverged in their similarity to other related lymphomas. Unexpectedly, we identified 2 molecular subgroups of cHL associated with differential strengths of the transcription factor activity of the NOTCH1, MYC, and IRF4 proto-oncogenes. Finally, HRS cells display deregulated expression of several genes potentially highly relevant to lymphoma pathogenesis, including silencing of the apoptosis-inducer BIK and of INPP5D, an inhibitor of the PI3K-driven oncogenic pathway.}, |
|
| 10756 | + langid = {english}, |
|
| 10757 | + keywords = {Adult,Apoptosis Regulatory Proteins,B-Lymphocytes,Cell Line Tumor,Cells Cultured,Cluster Analysis,Gene Expression Profiling,Gene Expression Regulation Neoplastic,Hodgkin Disease,Humans,Immunohistochemistry,Inositol Polyphosphate 5-Phosphatases,Lymphoma B-Cell,Membrane Proteins,Mitochondrial Proteins,Oligonucleotide Array Sequence Analysis,Phosphatidylinositol-345-Trisphosphate 5-Phosphatases,Phosphoric Monoester Hydrolases,Reed-Sternberg Cells,Tumor Cells Cultured,Tumor Microenvironment} |
|
| 10758 | +} |
|
| 10759 | + |
|
| 10760 | +@article{tiacciBRAFMutationsHairycell2011a, |
|
| 10761 | + title = {{{BRAF}} Mutations in Hairy-Cell Leukemia}, |
|
| 10762 | + author = {Tiacci, Enrico and Trifonov, Vladimir and Schiavoni, Gianluca and Holmes, Antony and Kern, Wolfgang and Martelli, Maria Paola and Pucciarini, Alessandra and Bigerna, Barbara and Pacini, Roberta and Wells, Victoria A. and Sportoletti, Paolo and Pettirossi, Valentina and Mannucci, Roberta and Elliott, Oliver and Liso, Arcangelo and Ambrosetti, Achille and Pulsoni, Alessandro and Forconi, Francesco and Trentin, Livio and Semenzato, Gianpietro and Inghirami, Giorgio and Capponi, Monia and Di Raimondo, Francesco and Patti, Caterina and Arcaini, Luca and Musto, Pellegrino and Pileri, Stefano and Haferlach, Claudia and Schnittger, Susanne and Pizzolo, Giovanni and Foà, Robin and Farinelli, Laurent and Haferlach, Torsten and Pasqualucci, Laura and Rabadan, Raul and Falini, Brunangelo}, |
|
| 10763 | + date = {2011-06-16}, |
|
| 10764 | + journaltitle = {The New England Journal of Medicine}, |
|
| 10765 | + shortjournal = {N Engl J Med}, |
|
| 10766 | + volume = {364}, |
|
| 10767 | + number = {24}, |
|
| 10768 | + eprint = {21663470}, |
|
| 10769 | + eprinttype = {pmid}, |
|
| 10770 | + pages = {2305--2315}, |
|
| 10771 | + issn = {1533-4406}, |
|
| 10772 | + doi = {10.1056/NEJMoa1014209}, |
|
| 10773 | + abstract = {BACKGROUND: Hairy-cell leukemia (HCL) is a well-defined clinicopathological entity whose underlying genetic lesion is still obscure. METHODS: We searched for HCL-associated mutations by performing massively parallel sequencing of the whole exome of leukemic and matched normal cells purified from the peripheral blood of an index patient with HCL. Findings were validated by Sanger sequencing in 47 additional patients with HCL. RESULTS: Whole-exome sequencing identified five missense somatic clonal mutations that were confirmed on Sanger sequencing, including a heterozygous mutation in BRAF that results in the BRAF V600E variant protein. Since BRAF V600E is oncogenic in other tumors, further analyses were focused on this genetic lesion. The same BRAF mutation was noted in all the other 47 patients with HCL who were evaluated by means of Sanger sequencing. None of the 195 patients with other peripheral B-cell lymphomas or leukemias who were evaluated carried the BRAF V600E variant, including 38 patients with splenic marginal-zone lymphomas or unclassifiable splenic lymphomas or leukemias. In immunohistologic and Western blot studies, HCL cells expressed phosphorylated MEK and ERK (the downstream targets of the BRAF kinase), indicating a constitutive activation of the RAF-MEK-ERK mitogen-activated protein kinase pathway in HCL. In vitro incubation of BRAF-mutated primary leukemic hairy cells from 5 patients with PLX-4720, a specific inhibitor of active BRAF, led to a marked decrease in phosphorylated ERK and MEK. CONCLUSIONS; The BRAF V600E mutation was present in all patients with HCL who were evaluated. This finding may have implications for the pathogenesis, diagnosis, and targeted therapy of HCL. (Funded by Associazione Italiana per la Ricerca sul Cancro and others.).}, |
|
| 10774 | + langid = {english}, |
|
| 10775 | + pmcid = {PMC3689585}, |
|
| 10776 | + keywords = {Adult,Aged,Extracellular Signal-Regulated MAP Kinases,Female,Humans,Leukemia Hairy Cell,Lymphoma B-Cell,Male,MAP Kinase Kinase Kinases,Middle Aged,Mutation,Proto-Oncogene Proteins B-raf,Sequence Analysis DNA}, |
|
| 10777 | + file = {/Users/rmorin/Zotero/storage/T4FCXCLK/Tiacci et al. - 2011 - BRAF mutations in hairy-cell leukemia.pdf} |
|
| 10778 | +} |
|
| 10779 | + |
|
| 10780 | +@article{tiacciPervasiveMutationsJAKSTAT2018b, |
|
| 10781 | + title = {Pervasive Mutations of {{JAK-STAT}} Pathway Genes in Classical {{Hodgkin}} Lymphoma}, |
|
| 10782 | + author = {Tiacci, Enrico and Ladewig, Erik and Schiavoni, Gianluca and Penson, Alex and Fortini, Elisabetta and Pettirossi, Valentina and Wang, Yuchun and Rosseto, Ariele and Venanzi, Alessandra and Vlasevska, Sofija and Pacini, Roberta and Piattoni, Simonetta and Tabarrini, Alessia and Pucciarini, Alessandra and Bigerna, Barbara and Santi, Alessia and Gianni, Alessandro M. and Viviani, Simonetta and Cabras, Antonello and Ascani, Stefano and Crescenzi, Barbara and Mecucci, Cristina and Pasqualucci, Laura and Rabadan, Raul and Falini, Brunangelo}, |
|
| 10783 | + date = {2018-05-31}, |
|
| 10784 | + journaltitle = {Blood}, |
|
| 10785 | + shortjournal = {Blood}, |
|
| 10786 | + volume = {131}, |
|
| 10787 | + number = {22}, |
|
| 10788 | + eprint = {29650799}, |
|
| 10789 | + eprinttype = {pmid}, |
|
| 10790 | + pages = {2454--2465}, |
|
| 10791 | + issn = {1528-0020}, |
|
| 10792 | + doi = {10.1182/blood-2017-11-814913}, |
|
| 10793 | + abstract = {Dissecting the pathogenesis of classical Hodgkin lymphoma (cHL), a common cancer in young adults, remains challenging because of the rarity of tumor cells in involved tissues (usually {$<$}5\%). Here, we analyzed the coding genome of cHL by microdissecting tumor and normal cells from 34 patient biopsies for a total of ∼50\,000 singly isolated lymphoma cells. We uncovered several recurrently mutated genes, namely, STAT6 (32\% of cases), GNA13 (24\%), XPO1 (18\%), and ITPKB (16\%), and document the functional role of mutant STAT6 in sustaining tumor cell viability. Mutations of STAT6 genetically and functionally cooperated with disruption of SOCS1, a JAK-STAT pathway inhibitor, to promote cHL growth. Overall, 87\% of cases showed dysregulation of the JAK-STAT pathway by genetic alterations in multiple genes (also including STAT3, STAT5B, JAK1, JAK2, and PTPN1), attesting to the pivotal role of this pathway in cHL pathogenesis and highlighting its potential as a new therapeutic target in this disease.}, |
|
| 10794 | + langid = {english}, |
|
| 10795 | + pmcid = {PMC6634958}, |
|
| 10796 | + keywords = {Cell Line Tumor,DNA Mutational Analysis,Gene Expression Regulation Neoplastic,Hodgkin Disease,Humans,Janus Kinases,Mutation,Signal Transduction,STAT Transcription Factors}, |
|
| 10797 | + file = {/Users/rmorin/Zotero/storage/MCDNUTRM/Tiacci et al. - 2018 - Pervasive mutations of JAK-STAT pathway genes in c.pdf} |
|
| 10798 | +} |
|
| 10799 | + |
|
| 10800 | +@article{tillyPolatuzumabVedotinPreviously2022, |
|
| 10801 | + title = {Polatuzumab {{Vedotin}} in {{Previously Untreated Diffuse Large B-Cell Lymphoma}}}, |
|
| 10802 | + author = {Tilly, Hervé and Morschhauser, Franck and Sehn, Laurie H. and Friedberg, Jonathan W. and Trněný, Marek and Sharman, Jeff P. and Herbaux, Charles and Burke, John M. and Matasar, Matthew and Rai, Shinya and Izutsu, Koji and Mehta-Shah, Neha and Oberic, Lucie and Chauchet, Adrien and Jurczak, Wojciech and Song, Yuqin and Greil, Richard and Mykhalska, Larysa and Bergua-Burgués, Juan M. and Cheung, Matthew C. and Pinto, Antonio and Shin, Ho-Jin and Hapgood, Greg and Munhoz, Eduardo and Abrisqueta, Pau and Gau, Jyh-Pyng and Hirata, Jamie and Jiang, Yanwen and Yan, Mark and Lee, Calvin and Flowers, Christopher R. and Salles, Gilles}, |
|
| 10803 | + date = {2022-01-27}, |
|
| 10804 | + journaltitle = {The New England Journal of Medicine}, |
|
| 10805 | + shortjournal = {N Engl J Med}, |
|
| 10806 | + volume = {386}, |
|
| 10807 | + number = {4}, |
|
| 10808 | + eprint = {34904799}, |
|
| 10809 | + eprinttype = {pmid}, |
|
| 10810 | + pages = {351--363}, |
|
| 10811 | + issn = {1533-4406}, |
|
| 10812 | + doi = {10.1056/NEJMoa2115304}, |
|
| 10813 | + abstract = {BACKGROUND: Diffuse large B-cell lymphoma (DLBCL) is typically treated with rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP). However, only 60\% of patients are cured with R-CHOP. Polatuzumab vedotin is an antibody-drug conjugate targeting CD79b, which is ubiquitously expressed on the surface of malignant B cells. METHODS: We conducted a double-blind, placebo-controlled, international phase 3 trial to evaluate a modified regimen of R-CHOP (pola-R-CHP), in which vincristine was replaced with polatuzumab vedotin, as compared with standard R-CHOP, in patients with previously untreated intermediate-risk or high-risk DLBCL. Patients 18 to 80 years of age were randomly assigned in a 1:1 ratio to receive six cycles of either pola-R-CHP or R-CHOP, plus two cycles of rituximab alone. The primary end point was investigator-assessed progression-free survival. Secondary end points included overall survival and safety. RESULTS: Overall, 879 patients underwent randomization: 440 were assigned to the pola-R-CHP group and 439 to the R-CHOP group. After a median follow-up of 28.2 months, the percentage of patients surviving without progression was significantly higher in the pola-R-CHP group than in the R-CHOP group (76.7\% [95\% confidence interval (CI), 72.7 to 80.8] vs. 70.2\% [95\% CI, 65.8 to 74.6] at 2 years; stratified hazard ratio for progression, relapse, or death, 0.73 by Cox regression; 95\% CI, 0.57 to 0.95; P\,=\,0.02). Overall survival at 2 years did not differ significantly between the groups (88.7\% [95\% CI, 85.7 to 91.6] in the pola-R-CHP group and 88.6\% [95\% CI, 85.6 to 91.6] in the R-CHOP group; hazard ratio for death, 0.94; 95\% CI, 0.65 to 1.37; P\,=\,0.75). The safety profile was similar in the two groups. CONCLUSIONS: Among patients with previously untreated intermediate-risk or high-risk DLBCL, the risk of disease progression, relapse, or death was lower among those who received pola-R-CHP than among those who received R-CHOP. (Funded by F. Hoffmann-La Roche/Genentech; POLARIX ClinicalTrials.gov number, NCT03274492.).}, |
|
| 10814 | + langid = {english}, |
|
| 10815 | + keywords = {Adult,Aged,Antibodies Monoclonal,Antineoplastic Combined Chemotherapy Protocols,Cyclophosphamide,Double-Blind Method,Doxorubicin,Female,Humans,Immunoconjugates,Lymphoma Large B-Cell Diffuse,Male,Middle Aged,Prednisone,Progression-Free Survival,Rituximab,Vincristine} |
|
| 10816 | +} |
|
| 10817 | + |
|
| 10818 | +@article{tohStretchyBinaryClassification2018, |
|
| 10819 | + title = {Stretchy Binary Classification}, |
|
| 10820 | + author = {Toh, Kar-Ann and Lin, Zhiping and Sun, Lei and Li, Zhengguo}, |
|
| 10821 | + date = {2018-01}, |
|
| 10822 | + journaltitle = {Neural Networks: The Official Journal of the International Neural Network Society}, |
|
| 10823 | + shortjournal = {Neural Netw}, |
|
| 10824 | + volume = {97}, |
|
| 10825 | + eprint = {29096204}, |
|
| 10826 | + eprinttype = {pmid}, |
|
| 10827 | + pages = {74--91}, |
|
| 10828 | + issn = {1879-2782}, |
|
| 10829 | + doi = {10.1016/j.neunet.2017.09.015}, |
|
| 10830 | + abstract = {In this article, we introduce an analytic formulation for compressive binary classification. The formulation seeks to solve the least ℓp-norm of the parameter vector subject to a classification error constraint. An analytic and stretchable estimation is conjectured where the estimation can be viewed as an extension of the pseudoinverse with left and right constructions. Our variance analysis indicates that the estimation based on the left pseudoinverse is unbiased and the estimation based on the right pseudoinverse is biased. Sparseness can be obtained for the biased estimation under certain mild conditions. The proposed estimation is investigated numerically using both synthetic and real-world data.}, |
|
| 10831 | + langid = {english}, |
|
| 10832 | + keywords = {Algorithms,Arabidopsis,Benchmarking,Breast Neoplasms,Classification,Computer Simulation,Data Compression,Databases Genetic,Female,Fuzzy Logic,Gene Expression,Humans,Leukemia,Linear Models,Parameter learning,Pattern classification,Pattern Recognition Automated,Reproducibility of Results,Sparse estimation,User-Computer Interface} |
|
| 10833 | +} |
|
| 10834 | + |
|
| 10835 | +@article{totzkeNovelMemberIkappaB2006, |
|
| 10836 | + title = {A Novel Member of the {{IkappaB}} Family, Human {{IkappaB-zeta}}, Inhibits Transactivation of P65 and Its {{DNA}} Binding.}, |
|
| 10837 | + author = {Totzke, Gudrun and Essmann, Frank and Pohlmann, Stephan and Lindenblatt, Charlotte and Jänicke, Reiner U and Schulze-Osthoff, Klaus}, |
|
| 10838 | + date = {2006-05}, |
|
| 10839 | + journaltitle = {J Biol Chem}, |
|
| 10840 | + volume = {281}, |
|
| 10841 | + number = {18}, |
|
| 10842 | + pages = {12645--12654}, |
|
| 10843 | + keywords = {nosource} |
|
| 10844 | +} |
|
| 10845 | + |
|
| 10846 | +@article{trinhAnalysisFOXO1Mutations, |
|
| 10847 | + title = {Analysis of {{FOXO1}} Mutations in Diffuse Large {{B-cell}} Lymphoma.}, |
|
| 10848 | + author = {Trinh, Diane L and Scott, David W and Morin, Ryan D and Mendez-Lago, Maria and An, Jianghong and Jones, Steven J M and Mungall, Andrew J and Zhao, Yongjun and Schein, Jacqueline and Steidl, Christian and Connors, Joseph M and Gascoyne, Randy D and Marra, Marco A}, |
|
| 10849 | + journaltitle = {Blood}, |
|
| 10850 | + keywords = {nosource} |
|
| 10851 | +} |
|
| 10852 | + |
|
| 10853 | +@article{troenNOTCH2MutationsMarginal2008, |
|
| 10854 | + title = {{{NOTCH2}} Mutations in Marginal Zone Lymphoma}, |
|
| 10855 | + author = {Trøen, Gunhild and Wlodarska, Iwona and Warsame, Abdirashid and Hernández Llodrà, Silvia and De Wolf-Peeters, Christiane and Delabie, Jan}, |
|
| 10856 | + date = {2008-07}, |
|
| 10857 | + journaltitle = {Haematologica}, |
|
| 10858 | + shortjournal = {Haematologica}, |
|
| 10859 | + volume = {93}, |
|
| 10860 | + number = {7}, |
|
| 10861 | + eprint = {18508802}, |
|
| 10862 | + eprinttype = {pmid}, |
|
| 10863 | + pages = {1107--1109}, |
|
| 10864 | + issn = {1592-8721}, |
|
| 10865 | + doi = {10.3324/haematol.11635}, |
|
| 10866 | + langid = {english}, |
|
| 10867 | + keywords = {B-Lymphocytes,Base Sequence,Dimerization,DNA Complementary,Gene Deletion,Gene Expression Regulation Neoplastic,Humans,In Situ Hybridization Fluorescence,Ligands,Lymphoma B-Cell Marginal Zone,Molecular Sequence Data,Mutation,Protein Structure Tertiary,Receptor Notch2,Sequence Analysis DNA}, |
|
| 10868 | + file = {/Users/rmorin/Zotero/storage/RDA593FF/Trøen et al. - 2008 - NOTCH2 mutations in marginal zone lymphoma.pdf} |
|
| 10869 | +} |
|
| 10870 | + |
|
| 10871 | +@article{turunenHnRNPH1H2U12013, |
|
| 10872 | + title = {{{HnRNPH1}}/{{H2}}, {{U1 snRNP}}, and {{U11 snRNP}} Cooperate to Regulate the Stability of the {{U11-48K}} Pre-{{mRNA}}}, |
|
| 10873 | + author = {Turunen, Janne J. and Verma, Bhupendra and Nyman, Tuula A. and Frilander, Mikko J.}, |
|
| 10874 | + date = {2013-03}, |
|
| 10875 | + journaltitle = {RNA (New York, N.Y.)}, |
|
| 10876 | + shortjournal = {RNA}, |
|
| 10877 | + volume = {19}, |
|
| 10878 | + number = {3}, |
|
| 10879 | + eprint = {23335637}, |
|
| 10880 | + eprinttype = {pmid}, |
|
| 10881 | + pages = {380--389}, |
|
| 10882 | + issn = {1469-9001}, |
|
| 10883 | + doi = {10.1261/rna.036715.112}, |
|
| 10884 | + abstract = {Alternative splicing (AS) is a major contributor to proteome diversity, but it also regulates gene expression by introducing premature termination codons (PTCs) that destabilize transcripts, typically via the nonsense-mediated decay (NMD) pathway. Such AS events often take place within long, conserved sequence elements, particularly in genes encoding various RNA binding proteins. AS-NMD is often activated by the protein encoded by the same gene, leading to a self-regulating feedback loop that maintains constant protein levels. However, cross-regulation between different RNA binding proteins is also common, giving rise to finely tuned regulatory networks. Recently, we described a feedback mechanism regulating two protein components of the U12-dependent spliceosome (U11-48K and U11/U12-65K) through a highly conserved sequence element. These elements contain a U11 snRNP-binding splicing enhancer (USSE), which, through the U11 snRNP, activates an upstream U2-type 3'ss, resulting in the degradation of the U11-48K mRNA by AS-NMD. Through phylogenetic analysis, we now identify a G-rich sequence element that is conserved in fishes as well as mammals. We show that this element binds hnRNPF/H proteins in vitro. Knockdown of hnRNPH1/H2 or mutations in the G-run both lead to enhanced activation of the 3'ss in vivo, suggesting that hnRNPH1/H2 proteins counteract the 3'ss activation. Furthermore, we provide evidence that U1 binding immediately downstream from the G-run similarly counteracts the U11-mediated activation of the alternative 3'ss. Thus, our results elucidate the mechanism in which snRNPs from both spliceosomes together with hnRNPH1/H2 proteins regulate the recognition and activation of the highly conserved alternative splice sites within the U11-48K pre-mRNA.}, |
|
| 10885 | + langid = {english}, |
|
| 10886 | + pmcid = {PMC3677248}, |
|
| 10887 | + keywords = {Amino Acid Sequence,Animals,Binding Sites,HEK293 Cells,HeLa Cells,Humans,Ribonucleoprotein U1 Small Nuclear,Ribonucleoproteins Small Nuclear,RNA Heterogeneous Nuclear,RNA Precursors,RNA Splicing,RNA Stability,Spliceosomes} |
|
| 10888 | +} |
|
| 10889 | + |
|
| 10890 | +@article{tzankovPrognosticImmunophenotypicBiomarker2010, |
|
| 10891 | + title = {Prognostic Immunophenotypic Biomarker Studies in Diffuse Large {{B}} Cell Lymphoma with Special Emphasis on Rational Determination of Cut-off Scores.}, |
|
| 10892 | + author = {Tzankov, Alexandar and Zlobec, Inti and Went, Philip and Robl, Hannes and Hoeller, Sylvia and Dirnhofer, Stephan}, |
|
| 10893 | + date = {2010-02}, |
|
| 10894 | + journaltitle = {Leuk lymphoma}, |
|
| 10895 | + volume = {51}, |
|
| 10896 | + number = {2}, |
|
| 10897 | + pages = {199--212}, |
|
| 10898 | + keywords = {nosource} |
|
| 10899 | +} |
|
| 10900 | + |
|
| 10901 | +@article{ullrichDynamicChangesIntron2020, |
|
| 10902 | + title = {Dynamic Changes in Intron Retention Are Tightly Associated with Regulation of Splicing Factors and Proliferative Activity during {{B-cell}} Development}, |
|
| 10903 | + author = {Ullrich, Sebastian and Guigó, Roderic}, |
|
| 10904 | + date = {2020-02-20}, |
|
| 10905 | + journaltitle = {Nucleic Acids Research}, |
|
| 10906 | + shortjournal = {Nucleic Acids Research}, |
|
| 10907 | + volume = {48}, |
|
| 10908 | + number = {3}, |
|
| 10909 | + pages = {1327--1340}, |
|
| 10910 | + issn = {0305-1048}, |
|
| 10911 | + doi = {10.1093/nar/gkz1180}, |
|
| 10912 | + url = {https://doi.org/10.1093/nar/gkz1180}, |
|
| 10913 | + urldate = {2022-10-03}, |
|
| 10914 | + abstract = {Intron retention (IR) has been proposed to modulate the delay between transcription and translation. Here, we provide an exhaustive characterization of IR in differentiated white blood cells from both the myeloid and lymphoid lineage where we observed highest levels of IR in monocytes and B-cells, in addition to previously reported granulocytes. During B-cell differentiation, we found an increase in IR from the bone marrow precursors to cells residing in secondary lymphoid organs. B-cells that undergo affinity maturation to become antibody producing plasma cells steadily decrease retention. In general, we found an inverse relationship between global IR levels and both the proliferative state of cells, and the global levels of expression of splicing factors. IR dynamics during B-cell differentiation appear to be conserved between human and mouse, suggesting that IR plays an important biological role, evolutionary conserved, during blood cell differentiation. By correlating the expression of non-core splicing factors with global IR levels, and analyzing RNA binding protein knockdown and eCLIP data, we identify a few splicing factors likely playing an evolutionary conserved role in IR regulation. Our work provides new insights into the role of IR during hematopoiesis, and on the main factors involved in regulating IR.}, |
|
| 10915 | + file = {/Users/rmorin/Zotero/storage/SNY2EIGS/Ullrich and Guigó - 2020 - Dynamic changes in intron retention are tightly as.pdf;/Users/rmorin/Zotero/storage/UMZLJELK/5687827.html} |
|
| 10916 | +} |
|
| 10917 | + |
|
| 10918 | +@article{urenHighthroughputAnalysesHnRNP2016, |
|
| 10919 | + title = {High-Throughput Analyses of {{hnRNP H1}} Dissects Its Multi-Functional Aspect}, |
|
| 10920 | + author = {Uren, Philip J. and Bahrami-Samani, Emad and family=Araujo, given=Patricia Rosa, prefix=de, useprefix=true and Vogel, Christine and Qiao, Mei and Burns, Suzanne C. and Smith, Andrew D. and Penalva, Luiz O. F.}, |
|
| 10921 | + date = {2016}, |
|
| 10922 | + journaltitle = {RNA biology}, |
|
| 10923 | + shortjournal = {RNA Biol}, |
|
| 10924 | + volume = {13}, |
|
| 10925 | + number = {4}, |
|
| 10926 | + eprint = {26760575}, |
|
| 10927 | + eprinttype = {pmid}, |
|
| 10928 | + pages = {400--411}, |
|
| 10929 | + issn = {1555-8584}, |
|
| 10930 | + doi = {10.1080/15476286.2015.1138030}, |
|
| 10931 | + abstract = {hnRNPs are polyvalent RNA binding proteins that have been implicated in a range of regulatory roles including splicing, mRNA decay, translation, and miRNA metabolism. A variety of genome wide studies have taken advantage of methods like CLIP and RIP to identify the targets and binding sites of RNA binding proteins. However, due to the complex nature of RNA-binding proteins, these studies are incomplete without assays that characterize the impact of RBP binding on mRNA target expression. Here we used a suite of high-throughput approaches (RIP-Seq, iCLIP, RNA-Seq and shotgun proteomics) to provide a comprehensive view of hnRNP H1s ensemble of targets and its role in splicing, mRNA decay, and translation. The combination of RIP-Seq and iCLIP allowed us to identify a set of 1,086 high confidence target transcripts. Binding site motif analysis of these targets suggests the TGGG tetramer as a prevalent component of hnRNP H1 binding motif, with particular enrichment around intronic hnRNP H1 sites. Our analysis of the target transcripts and binding sites indicates that hnRNP H1s involvement in splicing is 2-fold: it directly affects a substantial number of splicing events, but also regulates the expression of major components of the splicing machinery and other RBPs with known roles in splicing regulation. The identified mRNA targets displayed function enrichment in MAPK signaling and ubiquitin mediated proteolysis, which might be main routes by which hnRNP H1 promotes tumorigenesis.}, |
|
| 10932 | + langid = {english}, |
|
| 10933 | + pmcid = {PMC4841607}, |
|
| 10934 | + keywords = {Binding Sites,HeLa Cells,Heterogeneous-Nuclear Ribonucleoprotein Group F-H,High-Throughput Nucleotide Sequencing,hnRNP H1,Humans,iCLIP,Integrated analysis,Proteomics,RIP-seq,RNA Splicing,RNA-binding proteins,RNA-seq} |
|
| 10935 | +} |
|
| 10936 | + |
|
| 10937 | +@article{urenSiteIdentificationHighthroughput2012, |
|
| 10938 | + title = {Site Identification in High-Throughput {{RNA-protein}} Interaction Data}, |
|
| 10939 | + author = {Uren, Philip J. and Bahrami-Samani, Emad and Burns, Suzanne C. and Qiao, Mei and Karginov, Fedor V. and Hodges, Emily and Hannon, Gregory J. and Sanford, Jeremy R. and Penalva, Luiz O. F. and Smith, Andrew D.}, |
|
| 10940 | + date = {2012-12-01}, |
|
| 10941 | + journaltitle = {Bioinformatics (Oxford, England)}, |
|
| 10942 | + shortjournal = {Bioinformatics}, |
|
| 10943 | + volume = {28}, |
|
| 10944 | + number = {23}, |
|
| 10945 | + eprint = {23024010}, |
|
| 10946 | + eprinttype = {pmid}, |
|
| 10947 | + pages = {3013--3020}, |
|
| 10948 | + issn = {1367-4811}, |
|
| 10949 | + doi = {10.1093/bioinformatics/bts569}, |
|
| 10950 | + abstract = {MOTIVATION: Post-transcriptional and co-transcriptional regulation is a crucial link between genotype and phenotype. The central players are the RNA-binding proteins, and experimental technologies [such as cross-linking with immunoprecipitation- (CLIP-) and RIP-seq] for probing their activities have advanced rapidly over the course of the past decade. Statistically robust, flexible computational methods for binding site identification from high-throughput immunoprecipitation assays are largely lacking however. RESULTS: We introduce a method for site identification which provides four key advantages over previous methods: (i) it can be applied on all variations of CLIP and RIP-seq technologies, (ii) it accurately models the underlying read-count distributions, (iii) it allows external covariates, such as transcript abundance (which we demonstrate is highly correlated with read count) to inform the site identification process and (iv) it allows for direct comparison of site usage across cell types or conditions. AVAILABILITY AND IMPLEMENTATION: We have implemented our method in a software tool called Piranha. Source code and binaries, licensed under the GNU General Public License (version 3) are freely available for download from http://smithlab.usc.edu. CONTACT: andrewds@usc.edu SUPPLEMENTARY INFORMATION: Supplementary data available at Bioinformatics online.}, |
|
| 10951 | + langid = {english}, |
|
| 10952 | + pmcid = {PMC3509493}, |
|
| 10953 | + keywords = {Base Sequence,Binding Sites,Computational Biology,HEK293 Cells,HeLa Cells,High-Throughput Nucleotide Sequencing,Humans,RNA,RNA-Binding Proteins,Sequence Analysis RNA,Software} |
|
| 10954 | +} |
|
| 10955 | + |
|
| 10956 | +@article{vaandragerRecombinasemediatedTranspositionBCL2gene2000, |
|
| 10957 | + title = {V({{D}}){{J}} Recombinase-Mediated Transposition of the {{BCL2gene}} to the {{IGH}} Locus in Follicular Lymphoma}, |
|
| 10958 | + author = {Vaandrager, Jan-Willem and Schuuring, Ed and Philippo, Katja and Kluin, Philip M.}, |
|
| 10959 | + date = {2000-09-01}, |
|
| 10960 | + journaltitle = {Blood}, |
|
| 10961 | + shortjournal = {Blood}, |
|
| 10962 | + volume = {96}, |
|
| 10963 | + number = {5}, |
|
| 10964 | + pages = {1947--1952}, |
|
| 10965 | + issn = {0006-4971}, |
|
| 10966 | + doi = {10.1182/blood.V96.5.1947}, |
|
| 10967 | + url = {https://www.sciencedirect.com/science/article/pii/S0006497120544753}, |
|
| 10968 | + urldate = {2023-10-17}, |
|
| 10969 | + abstract = {Using DNA fiber fluorescence in-situ hybridization (FISH) and 3-color interphase FISH, 2 cases of follicular lymphoma were identified in which the BCL2 gene was excised from 18q21 and inserted into the immunoglobulin heavy chain (IGH) locus at 14q32. Both the insertion breakpoint at 14q32 and the deletion breakpoint at 18q21 were cloned using inverse polymerase chain reaction. Sequence analysis showed that the JH sequences were juxtaposed to the 5′-side of BCL2, and the DH sequences were juxtaposed to the 3′-side of BCL2. There were breakpoints at both the JH and DH recombination signal sequences, and N-nucleotides were present at all breakpoint junctions. At theBCL2 locus, the 3′-breakpoints in both cases were localized at exactly the same nucleotide position, 6.2 kilobase downstream of the major breakpoint region, directly adjacent to a complete cryptic recombination signal sequence (RSS) consisting of a heptamer, a nonamer, and a 23–base pair (bp) spacer. The BCL25′-breakpoints were approximately 600 bp upstream of the gene, within the CA repeats. Although less evident than for the BCL23′-breakpoints, cryptic RSSs were also identified at these breakpoints, with a 12-bp spacer. On the basis of structural characteristics of these rearrangements, a model is proposed in which the BCL2 gene is deleted from its locus by recombination activation gene-1/-2 (RAG-1/-2)–mediated excision. The gene is subsequently inserted into the recombiningIGH locus, a process involving the formation of hybrid joints between the IGH coding ends and theBCL2 signal ends.}, |
|
| 10970 | + file = {/Users/rmorin/Zotero/storage/D845B4ND/Vaandrager et al. - 2000 - V(D)J recombinase-mediated transposition of the BC.pdf;/Users/rmorin/Zotero/storage/CIQPESJ2/S0006497120544753.html} |
|
| 10971 | +} |
|
| 10972 | + |
|
| 10973 | +@article{valliClassificationCanineMalignant2011, |
|
| 10974 | + title = {Classification of {{Canine Malignant Lymphomas According}} to the {{World Health Organization Criteria}}}, |
|
| 10975 | + author = {Valli, V. E. and Myint, M. San and Barthel, A. and Bienzle, D. and Caswell, J. and Colbatzky, F. and Durham, A. and Ehrhart, E. J. and Johnson, Y. and Jones, C. and Kiupel, M. and Labelle, P. and Lester, S. and Miller, M. and Moore, P. and Moroff, S. and Roccabianca, P. and Ramos-Vara, J. and Ross, A. and Scase, T. and Tvedten, H. and Vernau, W.}, |
|
| 10976 | + date = {2011-01-01}, |
|
| 10977 | + journaltitle = {Veterinary Pathology}, |
|
| 10978 | + shortjournal = {Vet Pathol}, |
|
| 10979 | + volume = {48}, |
|
| 10980 | + number = {1}, |
|
| 10981 | + pages = {198--211}, |
|
| 10982 | + publisher = {SAGE Publications Inc}, |
|
| 10983 | + issn = {0300-9858}, |
|
| 10984 | + doi = {10.1177/0300985810379428}, |
|
| 10985 | + url = {https://doi.org/10.1177/0300985810379428}, |
|
| 10986 | + urldate = {2021-05-13}, |
|
| 10987 | + abstract = {A study was carried out to test the accuracy and consistency of veterinary pathologists, not specialists in hematopathology, in applying the World Health Organization (WHO) system of classification of canine lymphomas. This study represents an initiative of the ACVP Oncology Committee, and the classification has been endorsed by the World Small Animal Veterinary Association (WASVA). Tissue biopsies from cases of canine lymphoma were received from veterinary oncologists, and a study by pathologists given only signalment was carried out on 300 cases. Twenty pathologists reviewed these 300 cases with each required to choose a diagnosis from a list of 43 B and T cell lymphomas. Three of the 20 were hematopathologists who determined the consensus diagnosis for each case. The 17 who formed the test group were experienced but not specialists in hematopathology, and most were diplomates of the American or European Colleges of Veterinary Pathology. The overall accuracy of the 17 pathologists on the 300 cases was 83\%. When the analysis was limited to the 6 most common diagnoses, containing 80\% of all cases, accuracy rose to 87\%. In a test of reproducibility enabled by reintroducing 5\% of cases entered under a different identity, the overall agreement between the first and second diagnosis ranged from 40 to 87\%. The statistical review included 43,000 data points for each of the 20 pathologists.}, |
|
| 10988 | + langid = {english}, |
|
| 10989 | + keywords = {Animals,dog,Dog Diseases,Dogs,Lymph Nodes,Lymphoma,Observer Variation,oncology,Pathology Veterinary,Veterinarians,World Health Organization}, |
|
| 10990 | + file = {/Users/rmorin/Zotero/storage/JA8SHQIH/Valli et al. - 2011 - Classification of canine malignant lymphomas accor.pdf;/Users/rmorin/Zotero/storage/ZK2RIIA3/Valli et al. - 2011 - Classification of Canine Malignant Lymphomas Accor.pdf} |
|
| 10991 | +} |
|
| 10992 | + |
|
| 10993 | +@article{valloisActivatingMutationsGenes2016, |
|
| 10994 | + title = {Activating Mutations in Genes Related to {{TCR}} Signaling in Angioimmunoblastic and Other Follicular Helper {{T-cell}}–Derived Lymphomas}, |
|
| 10995 | + author = {Vallois, David and Dobay, Maria Pamela D. and Morin, Ryan D. and Lemonnier, François and Missiaglia, Edoardo and Juilland, Mélanie and Iwaszkiewicz, Justyna and Fataccioli, Virginie and Bisig, Bettina and Roberti, Annalisa and Grewal, Jasleen and Bruneau, Julie and Fabiani, Bettina and Martin, Antoine and Bonnet, Christophe and Michielin, Olivier and Jais, Jean-Philippe and Figeac, Martin and Bernard, Olivier A. and Delorenzi, Mauro and Haioun, Corinne and Tournilhac, Olivier and Thome, Margot and Gascoyne, Randy D. and Gaulard, Philippe and De Leval, Laurence}, |
|
| 10996 | + date = {2016-09-15}, |
|
| 10997 | + journaltitle = {Blood}, |
|
| 10998 | + volume = {128}, |
|
| 10999 | + number = {11}, |
|
| 11000 | + pages = {1490--1502}, |
|
| 11001 | + issn = {0006-4971, 1528-0020}, |
|
| 11002 | + doi = {10.1182/blood-2016-02-698977}, |
|
| 11003 | + url = {https://ashpublications.org/blood/article/128/11/1490/35240/Activating-mutations-in-genes-related-to-TCR}, |
|
| 11004 | + urldate = {2023-10-26}, |
|
| 11005 | + abstract = {Key Points A high frequency of diverse activating mutations in costimulatory/TCR-related signaling genes occurs in AITL and other TFH-derived PTCL. Deregulated TCR activation may play a role in the pathogenesis of TFH-derived PTCL, paving the way for developing novel targeted therapies.}, |
|
| 11006 | + langid = {english}, |
|
| 11007 | + file = {/Users/rmorin/Zotero/storage/9D7MDZNV/Vallois et al. - 2016 - Activating mutations in genes related to TCR signa.pdf} |
|
| 11008 | +} |
|
| 11009 | + |
|
| 11010 | +@article{vandenbrandRecurrentMutationsGenes2017, |
|
| 11011 | + title = {Recurrent Mutations in Genes Involved in Nuclear Factor-{{κB}} Signalling in Nodal Marginal Zone Lymphoma-Diagnostic and Therapeutic Implications}, |
|
| 11012 | + author = {family=Brand, given=Michiel, prefix=van den, useprefix=true and Rijntjes, Jos and Hebeda, Konnie M. and Menting, Laura and Bregitha, Carolyn V. and Stevens, Wendy B. C. and family=Velden, given=Walter J. F. M., prefix=van der, useprefix=true and Tops, Bastiaan B. J. and family=Krieken, given=J. Han J. M., prefix=van, useprefix=true and Groenen, Patricia J. T. A.}, |
|
| 11013 | + date = {2017-01}, |
|
| 11014 | + journaltitle = {Histopathology}, |
|
| 11015 | + shortjournal = {Histopathology}, |
|
| 11016 | + volume = {70}, |
|
| 11017 | + number = {2}, |
|
| 11018 | + eprint = {27297871}, |
|
| 11019 | + eprinttype = {pmid}, |
|
| 11020 | + pages = {174--184}, |
|
| 11021 | + issn = {1365-2559}, |
|
| 11022 | + doi = {10.1111/his.13015}, |
|
| 11023 | + abstract = {AIMS: To investigate the spectrum of mutations in 20 genes involved in B-cell receptor and/or Toll-like receptor signalling resulting in activation of nuclear factor-κB (NF-κB) in 20 nodal marginal zone lymphomas (NMZLs), 20 follicular lymphomas (FLs), and 11 cases of B-cell lymphoma, unclassifiable (BCL-u). METHODS AND RESULTS: Nodal marginal zone lymphomas were diagnosed according to strict criteria, including the expression of at least one putative marginal zone marker (MNDA and/or IRTA1). Cases that showed features of NMZL but did not fulfil all criteria were included as BCL-u. All FLs were required to have a BCL2 rearrangement. Mutations were found in: nine NMZLs, with recurrent mutations in TNFAIP3 and CD79B; 12 FLs, with recurrent mutations in TNFRSF14, TNFAIP3, and CARD11; and five cases of BCL-u, with recurrent mutations in TNFRSF14. TNFRSF14 mutations were present in FL and BCL-u, but not in any of the NMZLs. In the BCL-u group, TNFRSF14 mutations clustered with a FL immunophenotype. CONCLUSIONS: These results suggest that TNFRSF14 mutations point towards a diagnosis of FL, and can be used in the sometimes difficult distinction between NMZL and FL, but to apply this in diagnostics would require confirmation in an independent cohort. In addition, the presence or absence of specific mutations in pathways converging on NF-κB could be important for decisions regarding targeted treatment.}, |
|
| 11024 | + langid = {english}, |
|
| 11025 | + keywords = {Aged,Biomarkers Tumor,diagnosis,Diagnosis Differential,Disease-Free Survival,Female,follicular lymphoma,High-Throughput Nucleotide Sequencing,Humans,Immunohistochemistry,Kaplan-Meier Estimate,Lymphoma B-Cell Marginal Zone,Lymphoma Follicular,Male,Middle Aged,Mutation,NF-kappa B,nodal marginal zone lymphoma,non-Hodgkin lymphoma,nuclear factor-κB,Receptors Tumor Necrosis Factor Member 14,Signal Transduction,TNFAIP3,TNFRSF14}, |
|
| 11026 | + file = {/Users/rmorin/Zotero/storage/JPDFW4JN/van den Brand et al. - 2017 - Recurrent mutations in genes involved in nuclear f.pdf} |
|
| 11027 | +} |
|
| 11028 | + |
|
| 11029 | +@article{vaughanInhibitoryFcgRIIbCD32b2014, |
|
| 11030 | + title = {Inhibitory {{FcγRIIb}} ({{CD32b}}) Becomes Activated by Therapeutic {{mAb}} in Both Cis and Trans and Drives Internalization According to Antibody Specificity}, |
|
| 11031 | + author = {Vaughan, Andrew T and Iriyama, Chisako and Beers, Stephen A and Chan, Claude H T and Lim, Sean H and Williams, Emily L and Shah, Vallari and Roghanian, Ali and Frendéus, Bjorn and Glennie, Martin J and Cragg, Mark S}, |
|
| 11032 | + date = {2014-01}, |
|
| 11033 | + journaltitle = {Blood}, |
|
| 11034 | + volume = {123}, |
|
| 11035 | + number = {5}, |
|
| 11036 | + pages = {669--677}, |
|
| 11037 | + keywords = {nosource} |
|
| 11038 | +} |
|
| 11039 | + |
|
| 11040 | +@article{veisBcl2deficientMiceDemonstrate1993, |
|
| 11041 | + title = {Bcl-2-Deficient Mice Demonstrate Fulminant Lymphoid Apoptosis, Polycystic Kidneys, and Hypopigmented Hair}, |
|
| 11042 | + author = {Veis, Deborah J. and Sorenson, Christine M. and Shutter, John R. and Korsmeyer, Stanley J.}, |
|
| 11043 | + date = {1993-10-22}, |
|
| 11044 | + journaltitle = {Cell}, |
|
| 11045 | + shortjournal = {Cell}, |
|
| 11046 | + volume = {75}, |
|
| 11047 | + number = {2}, |
|
| 11048 | + pages = {229--240}, |
|
| 11049 | + issn = {0092-8674}, |
|
| 11050 | + doi = {10.1016/0092-8674(93)80065-M}, |
|
| 11051 | + url = {https://www.sciencedirect.com/science/article/pii/009286749380065M}, |
|
| 11052 | + urldate = {2022-10-06}, |
|
| 11053 | + abstract = {bcl-2 —/— mice complete embryonic development, but display growth retardation and early mortality postnatally. Hematopoiesis including lymphocyte differentiation is initially normal, but thymus and spleen undergo massive apoptotic involution. Thymocytes require an apoptotic signal to manifest accelerated cell death. Renal failure results from severe polycystic kidney disease characterized by dilated proximal and distal tubular segments and hyperproliferation of epithelium and interstitium. bcl-2 —/— mice turn gray with the second hair follicle cycle, implicating a defect in redox-regulated melanin synthesis. The abnormalities in these loss of function mice argue that Bcl-2 is a death repressor molecule functioning in an antioxidant pathway.}, |
|
| 11054 | + langid = {english}, |
|
| 11055 | + file = {/Users/rmorin/Zotero/storage/73DDCIQI/Veis et al. - 1993 - Bcl-2-deficient mice demonstrate fulminant lymphoi.pdf;/Users/rmorin/Zotero/storage/W3RMTU4N/009286749380065M.html} |
|
| 11056 | +} |
|
| 11057 | + |
|
| 11058 | +@article{vela-chavezCyclinD1Positive2011, |
|
| 11059 | + title = {Cyclin {{D1}} Positive Diffuse Large {{B-cell}} Lymphoma Is a Post-Germinal Center-Type Lymphoma without Alterations in the {{CCND1}} Gene Locus.}, |
|
| 11060 | + author = {Vela-Chávez, Teresa and Adam, Patrick and Kremer, Marcus and Bink, Karin and Bacon, Christopher M and Menon, Geetha and Ferry, Judith A and Fend, Falko and Jaffe, Elaine S and Quintanilla-Martínez, Leticia}, |
|
| 11061 | + date = {2011-03}, |
|
| 11062 | + journaltitle = {Leuk lymphoma}, |
|
| 11063 | + volume = {52}, |
|
| 11064 | + number = {3}, |
|
| 11065 | + pages = {458--466}, |
|
| 11066 | + keywords = {nosource} |
|
| 11067 | +} |
|
| 11068 | + |
|
| 11069 | +@article{venablesMultipleSpecificMRNA2008, |
|
| 11070 | + title = {Multiple and {{Specific mRNA Processing Targets}} for the {{Major Human hnRNP Proteins}}}, |
|
| 11071 | + author = {Venables, Julian P. and Koh, Chu-Shin and Froehlich, Ulrike and Lapointe, Elvy and Couture, Sonia and Inkel, Lyna and Bramard, Anne and Paquet, Éric R. and Watier, Valérie and Durand, Mathieu and Lucier, Jean-François and Gervais-Bird, Julien and Tremblay, Karine and Prinos, Panagiotis and Klinck, Roscoe and Elela, Sherif Abou and Chabot, Benoit}, |
|
| 11072 | + date = {2008-10}, |
|
| 11073 | + journaltitle = {Molecular and Cellular Biology}, |
|
| 11074 | + volume = {28}, |
|
| 11075 | + number = {19}, |
|
| 11076 | + pages = {6033--6043}, |
|
| 11077 | + publisher = {American Society for Microbiology}, |
|
| 11078 | + doi = {10.1128/MCB.00726-08}, |
|
| 11079 | + url = {https://journals.asm.org/doi/full/10.1128/MCB.00726-08}, |
|
| 11080 | + urldate = {2022-09-27}, |
|
| 11081 | + file = {/Users/rmorin/Zotero/storage/3DTA8U93/Venables et al. - 2008 - Multiple and Specific mRNA Processing Targets for .pdf} |
|
| 11082 | +} |
|
| 11083 | + |
|
| 11084 | +@article{venkataramananDDX3XDDX3YAre2021, |
|
| 11085 | + title = {{{DDX3X}} and {{DDX3Y}} Are Redundant in Protein Synthesis}, |
|
| 11086 | + author = {Venkataramanan, Srivats and Gadek, Margaret and Calviello, Lorenzo and Wilkins, Kevin and Floor, Stephen}, |
|
| 11087 | + date = {2021-09-17}, |
|
| 11088 | + journaltitle = {RNA}, |
|
| 11089 | + shortjournal = {RNA}, |
|
| 11090 | + eprint = {34535544}, |
|
| 11091 | + eprinttype = {pmid}, |
|
| 11092 | + pages = {rna.078926.121}, |
|
| 11093 | + publisher = {Cold Spring Harbor Lab}, |
|
| 11094 | + issn = {1355-8382, 1469-9001}, |
|
| 11095 | + doi = {10.1261/rna.078926.121}, |
|
| 11096 | + url = {http://rnajournal.cshlp.org/content/early/2021/09/17/rna.078926.121}, |
|
| 11097 | + urldate = {2021-09-23}, |
|
| 11098 | + abstract = {DDX3 is a DEAD-box RNA helicase that regulates translation and is encoded by the X- and Y-linked paralogs DDX3X and DDX3Y. While DDX3X is ubiquitously expressed in human tissues and essential for viability, DDX3Y is male-specific and shows lower and more variable expression than DDX3X in somatic tissues. Heterozygous genetic lesions in DDX3X mediate a class of developmental disorders called DDX3X syndrome, while loss of DDX3Y is implicated in male infertility. One possible explanation for female-bias in DDX3X syndrome is that DDX3Y encodes a polypeptide with different biochemical activity. In this study, we use ribosome profiling and in vitro translation to demonstrate that the X- and Y-linked paralogs of DDX3 play functionally redundant roles in translation. We find that transcripts that are sensitive to DDX3X depletion or mutation are rescued by complementation with DDX3Y. Our data indicate that DDX3X and DDX3Y proteins can functionally complement each other in the context of mRNA translation in human cells. DDX3Y is not expressed in a large fraction of the central nervous system. These findings suggest that expression differences, not differences in paralog-dependent protein synthesis, underlie the sex-bias of DDX3X-associated diseases.}, |
|
| 11099 | + langid = {english}, |
|
| 11100 | + keywords = {DEAD-box proteins,RNA,sex differences,translational control}, |
|
| 11101 | + file = {/Users/rmorin/Zotero/storage/ATTED8P9/Venkataramanan et al. - 2021 - DDX3X and DDX3Y are redundant in protein synthesis.pdf;/Users/rmorin/Zotero/storage/XDKLBMP5/rna.078926.html} |
|
| 11102 | +} |
|
| 11103 | + |
|
| 11104 | +@article{veraldiHnRNPInfluencesBinding2001, |
|
| 11105 | + title = {{{hnRNP F Influences Binding}} of a 64-{{Kilodalton Subunit}} of {{Cleavage Stimulation Factor}} to {{mRNA Precursors}} in {{Mouse B Cells}}}, |
|
| 11106 | + author = {Veraldi, Kristen L. and Arhin, George K. and Martincic, Kathleen and Chung-Ganster, Ling-Hsiu and Wilusz, Jeffrey and Milcarek, Christine}, |
|
| 11107 | + date = {2001-02-15}, |
|
| 11108 | + journaltitle = {Molecular and Cellular Biology}, |
|
| 11109 | + volume = {21}, |
|
| 11110 | + number = {4}, |
|
| 11111 | + pages = {1228--1238}, |
|
| 11112 | + publisher = {American Society for Microbiology}, |
|
| 11113 | + doi = {10.1128/MCB.21.4.1228-1238.2001}, |
|
| 11114 | + url = {https://journals.asm.org/doi/full/10.1128/MCB.21.4.1228-1238.2001}, |
|
| 11115 | + urldate = {2022-10-03}, |
|
| 11116 | + file = {/Users/rmorin/Zotero/storage/Q6Y44KUA/Veraldi et al. - 2001 - hnRNP F Influences Binding of a 64-Kilodalton Subu.pdf} |
|
| 11117 | +} |
|
| 11118 | + |
|
| 11119 | +@article{viganoSomaticIL4RMutations2018b, |
|
| 11120 | + title = {Somatic {{IL4R}} Mutations in Primary Mediastinal Large {{B-cell}} Lymphoma Lead to Constitutive {{JAK-STAT}} Signaling Activation}, |
|
| 11121 | + author = {Viganò, Elena and Gunawardana, Jay and Mottok, Anja and Van Tol, Tessa and Mak, Katina and Chan, Fong Chun and Chong, Lauren and Chavez, Elizabeth and Woolcock, Bruce and Takata, Katsuyoshi and Twa, David and Shulha, Hennady P. and Telenius, Adèle and Kutovaya, Olga and Hung, Stacy S. and Healy, Shannon and Ben-Neriah, Susana and Leroy, Karen and Gaulard, Philippe and Diepstra, Arjan and Kridel, Robert and Savage, Kerry J. and Rimsza, Lisa and Gascoyne, Randy and Steidl, Christian}, |
|
| 11122 | + date = {2018-05-03}, |
|
| 11123 | + journaltitle = {Blood}, |
|
| 11124 | + shortjournal = {Blood}, |
|
| 11125 | + volume = {131}, |
|
| 11126 | + number = {18}, |
|
| 11127 | + eprint = {29467182}, |
|
| 11128 | + eprinttype = {pmid}, |
|
| 11129 | + pages = {2036--2046}, |
|
| 11130 | + issn = {1528-0020}, |
|
| 11131 | + doi = {10.1182/blood-2017-09-808907}, |
|
| 11132 | + abstract = {Primary mediastinal large B-cell lymphoma (PMBCL) is a distinct subtype of diffuse large B-cell lymphoma thought to arise from thymic medullary B cells. Gene mutations underlying the molecular pathogenesis of the disease are incompletely characterized. Here, we describe novel somatic IL4R mutations in 15 of 62 primary cases of PMBCL (24.2\%) and in all PMBCL-derived cell lines tested. The majority of mutations (11/21; 52\%) were hotspot single nucleotide variants in exon 8, leading to an I242N amino acid change in the transmembrane domain. Functional analyses establish this mutation as gain of function leading to constitutive activation of the JAK-STAT pathway and upregulation of downstream cytokine expression profiles and B cell-specific antigens. Moreover, expression of I242N mutant IL4R in a mouse xenotransplantation model conferred growth advantage in vivo. The pattern of concurrent mutations within the JAK-STAT signaling pathway suggests additive/synergistic effects of these gene mutations contributing to lymphomagenesis. Our data establish IL4R mutations as novel driver alterations and provide a strong preclinical rationale for therapeutic targeting of JAK-STAT signaling in PMBCL.}, |
|
| 11133 | + langid = {english}, |
|
| 11134 | + keywords = {Animals,Cell Line Tumor,Disease Models Animal,Female,Humans,Interleukin-4 Receptor alpha Subunit,Janus Kinases,Lymphoma Large B-Cell Diffuse,Mediastinal Neoplasms,Mice,Mutation,Phosphorylation,Signal Transduction,STAT Transcription Factors}, |
|
| 11135 | + file = {/Users/rmorin/Zotero/storage/NINPEDPI/Viganò et al. - 2018 - Somatic IL4R mutations in primary mediastinal larg.pdf} |
|
| 11136 | +} |
|
| 11137 | + |
|
| 11138 | +@article{vonhachtIdentificationCharacterizationRNA2014, |
|
| 11139 | + title = {Identification and Characterization of {{RNA}} Guanine-Quadruplex Binding Proteins}, |
|
| 11140 | + author = {family=Hacht, given=Annekathrin, prefix=von, useprefix=true and Seifert, Oliver and Menger, Marcus and Schütze, Tatjana and Arora, Amit and Konthur, Zoltán and Neubauer, Peter and Wagner, Anke and Weise, Christoph and Kurreck, Jens}, |
|
| 11141 | + date = {2014-06}, |
|
| 11142 | + journaltitle = {Nucleic Acids Research}, |
|
| 11143 | + shortjournal = {Nucleic Acids Res}, |
|
| 11144 | + volume = {42}, |
|
| 11145 | + number = {10}, |
|
| 11146 | + eprint = {24771345}, |
|
| 11147 | + eprinttype = {pmid}, |
|
| 11148 | + pages = {6630--6644}, |
|
| 11149 | + issn = {1362-4962}, |
|
| 11150 | + doi = {10.1093/nar/gku290}, |
|
| 11151 | + abstract = {Guanine quadruplex (G-quadruplex) motifs in the 5' untranslated region (5'-UTR) of mRNAs were recently shown to influence the efficiency of translation. In the present study, we investigate the interaction between cellular proteins and the G-quadruplexes located in two mRNAs (MMP16 and ARPC2). Formation of the G-quadruplexes was confirmed by biophysical characterization and the inhibitory activity on translation was shown by luciferase reporter assays. In experiments with whole cell extracts from different eukaryotic cell lines, G-quadruplex-binding proteins were isolated by pull-down assays and subsequently identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry. The binding partners of the RNA G-quadruplexes we discovered included several heterogeneous nuclear ribonucleoproteins, ribosomal proteins, and splicing factors, as well as other proteins that have previously not been described to interact with nucleic acids. While most of the proteins were specific for either of the investigated G-quadruplexes, some of them bound to both motifs. Selected candidate proteins were subsequently produced by recombinant expression and dissociation constants for the interaction between the proteins and RNA G-quadruplexes in the low nanomolar range were determined by surface plasmon resonance spectroscopy. The present study may thus help to increase our understanding of the mechanisms by which G-quadruplexes regulate translation.}, |
|
| 11152 | + langid = {english}, |
|
| 11153 | + pmcid = {PMC4041461}, |
|
| 11154 | + keywords = {5' Untranslated Regions,Actin-Related Protein 2,G-Quadruplexes,HEK293 Cells,HeLa Cells,Humans,Matrix Metalloproteinase 16,Protein Biosynthesis,RNA-Binding Proteins}, |
|
| 11155 | + file = {/Users/rmorin/Zotero/storage/C764KI4Q/von Hacht et al. - 2014 - Identification and characterization of RNA guanine.pdf} |
|
| 11156 | +} |
|
| 11157 | + |
|
| 11158 | +@article{voseMantleCellLymphoma2017, |
|
| 11159 | + title = {Mantle Cell Lymphoma: 2017 Update on Diagnosis, Risk-Stratification, and Clinical Management}, |
|
| 11160 | + shorttitle = {Mantle Cell Lymphoma}, |
|
| 11161 | + author = {Vose, Julie M.}, |
|
| 11162 | + date = {2017}, |
|
| 11163 | + journaltitle = {American Journal of Hematology}, |
|
| 11164 | + volume = {92}, |
|
| 11165 | + number = {8}, |
|
| 11166 | + pages = {806--813}, |
|
| 11167 | + issn = {1096-8652}, |
|
| 11168 | + doi = {10.1002/ajh.24797}, |
|
| 11169 | + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ajh.24797}, |
|
| 11170 | + urldate = {2019-12-21}, |
|
| 11171 | + abstract = {Disease Overview Mantle cell lymphoma (MCL) is a non-Hodgkin lymphoma characterized by involvement of the lymph nodes, spleen, blood and bone marrow with a short remission duration to standard therapies and a median overall survival (OS) of 4-5 years. Diagnosis Diagnosis is based on lymph node, bone marrow, or tissue morphology of centrocytic lymphocytes, small cell type, or blastoid variant cells. A chromosomal translocation t (11:14) is the molecular hallmark of MCL, resulting in the overexpression of cyclin D1. Cyclin D1 is detected by immunohistochemistry in 98\% of cases. The absence of SOX-11 or a low Ki-67 may correlate with a more indolent form of MCL. The differential diagnosis of MCL includes small lymphocytic lymphoma, marginal zone lymphoma, and follicular lymphoma. Risk Stratification The MCL International Prognostic Index (MIPI) is the prognostic model most often used and incorporates ECOG performance status, age, leukocyte count, and lactic dehydrogenase. A modification of the MIPI also adds the Ki-67 proliferative index if available. The median OS for the low-risk group was not reached (5-year OS of 60\%). The median OS for the intermediate risk group was 51 months and 29 months for the high risk group. Risk-Adapted Therapy For selected indolent, low MIPI MCL patients, initial observation may be appropriate therapy. For younger patients with intermediate or high risk MIPI MCL, aggressive therapy with a cytotoxic Regimen followed by autologous stem cell transplantation should be considered. Rituximab maintenance after autologous stem cell transplantation has also improved the progression-free and overall survival. For older symptomatic MCL patients with intermediate or high risk MIPI, combination chemotherapy with R-CHOP, R-Bendamustine, or a clinical trial should be considered. In addition, rituximab maintenance therapy may prolong the progression-free survival. At the time of relapse, agents directed at activated pathways in MCL cells such as bortezomib (NFkB inhibitor), lenalidamide (anti-angiogenesis) and Ibruitinib (Bruton's Tyrosine Kinase [BTK] inhibitor) have demonstrated excellent clinical activity in MCL patients. Autologous or allogeneic stem cell transplantation can also be considered in young patients. Clinical trials with novel agents are always a consideration for MCL patients.}, |
|
| 11172 | + langid = {english}, |
|
| 11173 | + file = {/Users/rmorin/Zotero/storage/7LI998DV/ajh.html} |
|
| 11174 | +} |
|
| 11175 | + |
|
| 11176 | +@article{wagenerCrypticInsertionMYC2019, |
|
| 11177 | + title = {Cryptic Insertion of {{MYC}} Exons 2 and 3 into the {{IGH}} Locus Detected by Whole Genome Sequencing in a Case of {{MYC-negative Burkitt}} Lymphoma [Published Online Ahead of Print {{May}} 2019]}, |
|
| 11178 | + author = {Wagener, Rabea and Bens, Susanne and Toprak, Umut H. and Seufert, Julian and López, Cristina and Scholz, Ingrid and Herbrueggen, Heidi and Oschlies, Ilske and Stilgenbauer, Stephan and Schlesner, Matthias and Klapper, Wolfram and Burkhardt, Birgit and Siebert, Reiner}, |
|
| 11179 | + date = {2019-05-09}, |
|
| 11180 | + journaltitle = {Haematologica}, |
|
| 11181 | + shortjournal = {Haematologica}, |
|
| 11182 | + volume = {10.3324/haematol.2018.208140}, |
|
| 11183 | + eprint = {31073073}, |
|
| 11184 | + eprinttype = {pmid}, |
|
| 11185 | + issn = {1592-8721}, |
|
| 11186 | + doi = {10.3324/haematol.2018.208140}, |
|
| 11187 | + langid = {english}, |
|
| 11188 | + keywords = {Aggressive Non-Hodgkin's Lymphoma,Cytogenetics and Molecular Genetics,IG-MYC translocation} |
|
| 11189 | +} |
|
| 11190 | + |
|
| 11191 | +@article{wagenerPCBP1GeneEncoding2015, |
|
| 11192 | + title = {The {{{\emph{PCBP1}}}} Gene Encoding Poly(Rc) Binding Protein i Is Recurrently Mutated in {{Burkitt}} Lymphoma: {{{\emph{PCBP1}}}} {{MUTATIONS IN BURKITT LYMPHOMA}}}, |
|
| 11193 | + shorttitle = {The {{{\emph{PCBP1}}}} Gene Encoding Poly(Rc) Binding Protein i Is Recurrently Mutated in {{Burkitt}} Lymphoma}, |
|
| 11194 | + author = {Wagener, Rabea and Aukema, Sietse M. and Schlesner, Matthias and Haake, Andrea and Burkhardt, Birgit and Claviez, Alexander and Drexler, Hans G. and Hummel, Michael and Kreuz, Markus and Loeffler, Markus and Rosolowski, Maciej and López, Cristina and Möller, Peter and Richter, Julia and Rohde, Marius and Betts, Matthew J. and Russell, Robert B. and Bernhart, Stephan H. and Hoffmann, Steve and Rosenstiel, Philip and Schilhabel, Markus and Szczepanowski, Monika and Trümper, Lorenz and Klapper, Wolfram and Siebert, Reiner and {on behalf of the ICGC MMML-Seq-Project and the “Molecular Mechanisms in Malignant Lymphomas” Network Project of the Deutsche Krebshilfe}}, |
|
| 11195 | + date = {2015-09}, |
|
| 11196 | + journaltitle = {Genes, Chromosomes and Cancer}, |
|
| 11197 | + shortjournal = {Genes Chromosomes Cancer}, |
|
| 11198 | + volume = {54}, |
|
| 11199 | + number = {9}, |
|
| 11200 | + pages = {555--564}, |
|
| 11201 | + issn = {10452257}, |
|
| 11202 | + doi = {10.1002/gcc.22268}, |
|
| 11203 | + url = {https://onlinelibrary.wiley.com/doi/10.1002/gcc.22268}, |
|
| 11204 | + urldate = {2022-09-25}, |
|
| 11205 | + langid = {english}, |
|
| 11206 | + file = {/Users/rmorin/Zotero/storage/KLIDY64Y/Wagener et al. - 2015 - The PCBP1 gene encoding poly(rc) binding pr.pdf} |
|
| 11207 | +} |
|
| 11208 | + |
|
| 11209 | +@article{wallaceDetectionBcl2142006, |
|
| 11210 | + title = {Detection of the Bcl-2 t(14;18) {{Translocation}} and {{Proto-Oncogene Expression}} in {{Primary Intraocular Lymphoma}}}, |
|
| 11211 | + author = {Wallace, Dana J. and Shen, DeFen and Reed, George F. and Miyanaga, Masaru and Mochizuki, Manabu and Sen, H. Nida and Dahr, Samuel S. and Buggage, Ronald R. and Nussenblatt, Robert B. and Chan, Chi-Chao}, |
|
| 11212 | + date = {2006-07-01}, |
|
| 11213 | + journaltitle = {Investigative Ophthalmology \& Visual Science}, |
|
| 11214 | + shortjournal = {Investigative Ophthalmology \& Visual Science}, |
|
| 11215 | + volume = {47}, |
|
| 11216 | + number = {7}, |
|
| 11217 | + pages = {2750--2756}, |
|
| 11218 | + issn = {1552-5783}, |
|
| 11219 | + doi = {10.1167/iovs.05-1312}, |
|
| 11220 | + url = {https://doi.org/10.1167/iovs.05-1312}, |
|
| 11221 | + urldate = {2022-10-04}, |
|
| 11222 | + abstract = {purpose. Primary intraocular lymphoma (PIOL) is a diffuse large B cell lymphoma that initially infiltrates the retina, vitreous, or optic nerve head, with or without central nervous system involvement. This study examined the expression of the bcl-2 t(14;18) translocation, the bcl-10 gene, and high expression of bcl-6 mRNA in PIOL cells. methods. Microdissection and PCR analysis were used to examine vitreous specimens in patients with PIOL for the presence of bcl-2 t(14;18) translocations, the bcl-10 gene, and expression of bcl-6 mRNA. A medical record review was also conducted to determine whether the bcl-2 t(14;18) translocation correlated with prognosis. results. Forty of 72 (55\%) PIOL patients expressed the bcl-2 t(14;18) translocation at the major breakpoint region. Fifteen of 68 (22\%) patients expressed the translocation at the minor cluster region. The bcl-10 gene was detected in 6 of 26 (23\%) patients, whereas 4 of 4 (100\%) PIOL patients expressed higher levels of bcl-6 mRNA compared with inflammatory lymphocytes. An analysis of clinical outcome in 23 PIOL patients revealed no significant association between bcl-2 t(14;18) translocations and survival or relapse. However, patients with the translocation were significantly younger. conclusions. PIOL has unique molecular patterns of bcl-2, bcl-10, and bcl-6 when compared with other systemic lymphomas. This study lays the foundation for future studies aimed at exploring the genotypic classification of PIOL based on the quantitative molecular framework of gene expression profiling, with the goal of providing useful adjuncts to the pathologic diagnosis of this complex disease.}, |
|
| 11223 | + file = {/Users/rmorin/Zotero/storage/YAUQ6DLN/Wallace et al. - 2006 - Detection of the bcl-2 t(14\;18) Translocation and .pdf;/Users/rmorin/Zotero/storage/RJHUFXT8/article.html} |
|
| 11224 | +} |
|
| 11225 | + |
|
| 11226 | +@article{wallCellularStressOrchestrates2020, |
|
| 11227 | + title = {Cellular Stress Orchestrates the Localization of {{hnRNP H}} to Stress Granules}, |
|
| 11228 | + author = {Wall, Michael L. and Bera, Amit and Wong, Florence K. and Lewis, Stephen M.}, |
|
| 11229 | + date = {2020-09-01}, |
|
| 11230 | + journaltitle = {Experimental Cell Research}, |
|
| 11231 | + shortjournal = {Experimental Cell Research}, |
|
| 11232 | + volume = {394}, |
|
| 11233 | + number = {1}, |
|
| 11234 | + pages = {112111}, |
|
| 11235 | + issn = {0014-4827}, |
|
| 11236 | + doi = {10.1016/j.yexcr.2020.112111}, |
|
| 11237 | + url = {https://www.sciencedirect.com/science/article/pii/S0014482720303578}, |
|
| 11238 | + urldate = {2023-01-09}, |
|
| 11239 | + abstract = {Heterogeneous nuclear ribonucleoprotein (hnRNP) H is a member of hnRNP H/F protein subfamily of hnRNPs that regulate the maturation and post-transcriptional processing of pre-mRNA. As a component of an mRNA export complex, hnRNP H shuttles mature mRNA from the nucleus to the cytoplasm. Although hnRNP H is primarily a nuclear protein, it can accumulate in the cytoplasm in certain tissues and cell types; however, the physiological relevance of hnRNP H cytoplasmic accumulation is unknown. Here we show that under cellular stress hnRNP H accumulates in the cytoplasm and is required for efficient recovery from cellular stress. Moreover, we find that cytoplasmic hnRNP H localizes to stress granules and that the RRM3 domain of hnRNP H is necessary for this localization. Together, our results demonstrate that hnRNP H accumulates in the cytoplasm under cellular stress and is recruited to stress granules.}, |
|
| 11240 | + langid = {english}, |
|
| 11241 | + keywords = {Cellular stress,hnRNP H,Osmotic stress,RNA-Binding protein,Stress granule}, |
|
| 11242 | + file = {/Users/rmorin/Zotero/storage/M7HWLYVZ/Wall et al. - 2020 - Cellular stress orchestrates the localization of h.pdf;/Users/rmorin/Zotero/storage/EFB5N6MB/S0014482720303578.html} |
|
| 11243 | +} |
|
| 11244 | + |
|
| 11245 | +@article{wangEmergingRolesHnRNPK2020, |
|
| 11246 | + title = {The Emerging Roles of {{hnRNPK}}}, |
|
| 11247 | + author = {Wang, Ziyi and Qiu, Heng and He, Jianbo and Liu, Langxia and Xue, Wei and Fox, Archa and Tickner, Jennifer and Xu, Jiake}, |
|
| 11248 | + date = {2020}, |
|
| 11249 | + journaltitle = {Journal of Cellular Physiology}, |
|
| 11250 | + volume = {235}, |
|
| 11251 | + number = {3}, |
|
| 11252 | + pages = {1995--2008}, |
|
| 11253 | + issn = {1097-4652}, |
|
| 11254 | + doi = {10.1002/jcp.29186}, |
|
| 11255 | + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jcp.29186}, |
|
| 11256 | + urldate = {2022-09-22}, |
|
| 11257 | + abstract = {Heterogeneous nuclear ribonucleoprotein K (hnRNPK) is an DNA/RNA-binding protein and regulates a wide range of biological processes and disease pathogenesis. It contains 3 K-homologous (KH) domains, which are conserved in other RNA-binding proteins, mediate nucleic acid binding activity, and function as an enhancer or repressor of gene transcription. Phosphorylation of the protein alters its regulatory function, which also enables the protein to serve as a docking platform for the signal transduction proteins. In terms of the function of hnRNPK, it is central to many cellular events, including long noncoding RNA (lncRNA) regulation, cancer development and bone homoeostasis. Many studies have identified hnRNPK as an oncogene, where it is overexpressed in cancer tissues compared with the nonneoplastic tissues and its expression level is related to the prognosis of different types of host malignancies. However, hnRNPK has also been identified as a tumour suppressor, as it is important for the activation of the p53/p21 pathway. Recently, the protein is also found to be exclusively related to the regulation of paraspeckles and lncRNAs such as Neat1, Lncenc1 and Xist. Interestingly, hnRNPK has been found to associate with the Kabuki-like syndrome and Au-Kline syndrome with prominent skeletal abnormalities. In vitro study revealed that the hnRNPK protein is essential for the formation of osteoclast, in line with its importance in the skeletal system.}, |
|
| 11258 | + langid = {english}, |
|
| 11259 | + keywords = {cancer,cell signal transduction,gene expression regulation,hnRNPK,lncRNA,skeletal remodelling}, |
|
| 11260 | + file = {/Users/rmorin/Zotero/storage/V66SVTKK/jcp.html} |
|
| 11261 | +} |
|
| 11262 | + |
|
| 11263 | +@article{wangGlobalProfilingAlternative2012, |
|
| 11264 | + title = {Global Profiling of Alternative Splicing Events and Gene Expression Regulated by {{hnRNPH}}/{{F}}}, |
|
| 11265 | + author = {Wang, Erming and Aslanzadeh, Vahid and Papa, Filomena and Zhu, Haiyan and family=Grange, given=Pierre, prefix=de la, useprefix=true and Cambi, Franca}, |
|
| 11266 | + date = {2012}, |
|
| 11267 | + journaltitle = {PloS One}, |
|
| 11268 | + shortjournal = {PLoS ONE}, |
|
| 11269 | + volume = {7}, |
|
| 11270 | + number = {12}, |
|
| 11271 | + eprint = {23284676}, |
|
| 11272 | + eprinttype = {pmid}, |
|
| 11273 | + pages = {e51266}, |
|
| 11274 | + issn = {1932-6203}, |
|
| 11275 | + doi = {10.1371/journal.pone.0051266}, |
|
| 11276 | + abstract = {In this study, we have investigated the global impact of heterogeneous nuclear Ribonuclear Protein (hnRNP) H/F-mediated regulation of splicing events and gene expression in oligodendrocytes. We have performed a genome-wide transcriptomic analysis at the gene and exon levels in Oli-neu cells treated with siRNA that targets hnRNPH/F compared to untreated cells using Affymetrix Exon Array. Gene expression levels and regulated exons were identified with the GenoSplice EASANA algorithm. Bioinformatics analyses were performed to determine the structural properties of G tracts that correlate with the function of hnRNPH/F as enhancers vs. repressors of exon inclusion. Different types of alternatively spliced events are regulated by hnRNPH/F. Intronic G tracts density, length and proximity to the 5' splice site correlate with the hnRNPH/F enhancer function. Additionally, 6\% of genes are differently expressed upon knock down of hnRNPH/F. Genes that regulate the transition of oligodendrocyte progenitor cells to oligodendrocytes are differentially expressed in hnRNPH/F depleted Oli-neu cells, resulting in a decrease of negative regulators and an increase of differentiation-inducing regulators. The changes were confirmed in developing oligodendrocytes in vivo. This is the first genome wide analysis of splicing events and gene expression regulated by hnRNPH/F in oligodendrocytes and the first report that hnRNPH/F regulate genes that are involved in the transition from oligodendrocyte progenitor cells to oligodendrocytes.}, |
|
| 11277 | + langid = {english}, |
|
| 11278 | + pmcid = {PMC3524136}, |
|
| 11279 | + keywords = {Alternative Splicing,Animals,Cell Differentiation,Exons,Gene Expression Profiling,Gene Expression Regulation,Genomics,Heterogeneous-Nuclear Ribonucleoprotein Group F-H,Mice,Oligodendroglia,Stem Cells} |
|
| 11280 | +} |
|
| 11281 | + |
|
| 11282 | +@article{wangLateRelapsesPatients2019, |
|
| 11283 | + title = {Late {{Relapses}} in {{Patients With Diffuse Large B-Cell Lymphoma Treated With Immunochemotherapy}}}, |
|
| 11284 | + author = {Wang, Yucai and Farooq, Umar and Link, Brian K. and Larson, Melissa C. and King, Rebecca L. and Maurer, Matthew J. and Allmer, Cristine and Hefazi, Mehrdad and Thompson, Carrie A. and Micallef, Ivana N. and Johnston, Patrick B. and Habermann, Thomas M. and Witzig, Thomas E. and Ansell, Stephen M. and Cerhan, James R. and Nowakowski, Grzegorz S.}, |
|
| 11285 | + date = {2019-07-20}, |
|
| 11286 | + journaltitle = {Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology}, |
|
| 11287 | + shortjournal = {J Clin Oncol}, |
|
| 11288 | + volume = {37}, |
|
| 11289 | + number = {21}, |
|
| 11290 | + eprint = {31170029}, |
|
| 11291 | + eprinttype = {pmid}, |
|
| 11292 | + pages = {1819--1827}, |
|
| 11293 | + issn = {1527-7755}, |
|
| 11294 | + doi = {10.1200/JCO.19.00014}, |
|
| 11295 | + abstract = {PURPOSE: In patients with diffuse large B-cell lymphoma (DLBCL), most relapses occur within the first 2 years of diagnosis. We sought to define the rate and outcome of late relapses that occurred after achieving event-free survival at 24 months (EFS24). METHODS: We prospectively followed 1,324 patients with newly diagnosed DLBCL from 2002 to 2015 and treated with immunochemotherapy. Cumulative incidences of late DLBCL and indolent lymphoma relapses were analyzed as competing events. Postrelapse survival was defined as time from first relapse to death from any cause. RESULTS: In 847 patients who achieved EFS24, the cumulative incidence of late relapse was 6.9\% at 3 years, 9.3\% at 5 years, and 10.3\% at 8 years after EFS24. The incidence of DLBCL relapse was similar in patients with DLBCL alone at diagnosis (6.3\% at 5 years), compared with patients with concurrent indolent lymphoma at diagnosis (5.2\%; P = .46). However, the rate of indolent lymphoma relapse was higher in patients with concurrent indolent lymphoma (7.4\% v 2.1\% at 5 years; P {$<$} .01). In patients with DLBCL alone, the rate of DLBCL relapse was similar in the germinal center B-cell-like (GCB) (4.1\% at 5 years) and non-GCB (4.0\%; P = .71) subtypes, whereas the rate of indolent lymphoma relapse was higher in patients with the GCB subtype (3.9\% v 0.0\% at 5 years; P = .02). Postrelapse survival was inferior for patients who relapsed with DLBCL than for those who relapsed with indolent lymphoma (median 29.9 months v unreached; P {$<$} .01). CONCLUSION: Patients with DLBCL with a concurrent indolent lymphoma and those with the GCB subtype had a higher rate of late relapse, owing to increased relapses with indolent lymphoma. Patients who relapsed with DLBCL had a worse prognosis than those who relapsed with indolent lymphoma.}, |
|
| 11296 | + langid = {english}, |
|
| 11297 | + pmcid = {PMC7001527}, |
|
| 11298 | + keywords = {Adult,Aged,Aged 80 and over,Female,Humans,Immunotherapy,Lymphoma Large B-Cell Diffuse,Male,Middle Aged,Neoplasm Recurrence Local,Progression-Free Survival,Prospective Studies}, |
|
| 11299 | + file = {/Users/rmorin/Zotero/storage/9MFFJJ5V/Wang et al. - 2019 - Late Relapses in Patients With Diffuse Large B-Cel.pdf} |
|
| 11300 | +} |
|
| 11301 | + |
|
| 11302 | +@article{wangNovelPreclinicalModel2019, |
|
| 11303 | + title = {A Novel Preclinical Model of Cholangiocarcinoma Based on Human Aberrant {{FBXW7}} Expression.}, |
|
| 11304 | + author = {Wang, Jingxiao and Wang, Haichuan and Peters, Michele and Ding, Ning and Ribback, Silvia and Utpatel, Kirsten and Evert, Matthias and Cigliano, Antonio and Dombrowski, Frank and Song, Xinhua and Cossu, Antonio and Xu, Meng and Che, Li and Gordan, John Dozier and Calvisi, Diego and Chen, Xin}, |
|
| 11305 | + date = {2019-05-20}, |
|
| 11306 | + journaltitle = {Journal of Clinical Oncology}, |
|
| 11307 | + shortjournal = {JCO}, |
|
| 11308 | + volume = {37}, |
|
| 11309 | + pages = {e15624-e15624}, |
|
| 11310 | + publisher = {Wolters Kluwer}, |
|
| 11311 | + issn = {0732-183X}, |
|
| 11312 | + doi = {10.1200/JCO.2019.37.15_suppl.e15624}, |
|
| 11313 | + url = {https://ascopubs.org/doi/abs/10.1200/JCO.2019.37.15_suppl.e15624}, |
|
| 11314 | + urldate = {2021-09-24}, |
|
| 11315 | + abstract = {e15624 Background: Pre-clinical models that mimic human genetic events occurring in intrahepatic cholangiocarcinoma (iCCA) are limited. The ubiquitin ligase F-box and WD repeat domain-containing 7 (FBXW7) is recognized as a tumor suppressor in many cancer types. Methods: Firstly, we determined the FBXW7 mutation frequency (n = 120) and mRNA expression (n = 87) in a collection of human iCCA. Based on the preliminary findings in human data, we generated a mouse model by hydrodynamic tail vein injection of activated/myristylated (myr-)AKT with Fbxw7ΔF, a dominant negative form of Fbxw7. Subsequently, we investigated the role of established targets of Fbxw7, namely Notch2, Yap, and c-Myc in this novel mouse model and in human CCA cell lines. Results: FBXW7 mRNA expression is almost ubiquitously downregulated (71/82; 86.6\%) in human iCCA specimens, while only 0.8\% of samples showed FBXW7 somatic mutations. In vivo, co-expression of AKT and Fbxw7ΔF triggered the development of iCCA lesions and mice were euthanized by 15 weeks post-injection due to high tumor burden. At the molecular level, a strong induction of FBXW7 canonical targets, including Yap, Notch2, and c-Myc oncoproteins, was detected. However, only c-Myc was consistently confirmed as a FBXW7 target in human CCA cell lines. Interestingly, selected ablation of c-Myc completely impaired iCCA formation in AKT/Fbxw7ΔF mice, whereas deletion of either Yap or Notch2 delayed cholangiocarcinogenesis in the same model. Furthermore, in human iCCA specimens, a strong, inverse correlation between the expression levels of FBXW7 and c-Myc was observed. Conclusions: Downregulation of FBXW7 is almost ubiquitous in human iCCA and cooperates with AKT to induce cholangiocarcinogenesis in mice. This pre-clinical mouse model could be used to test novel therapeutics targeting c-Myc, Notch2, and/or Yap.}, |
|
| 11316 | + issue = {15\_suppl}, |
|
| 11317 | + keywords = {1,11,2,283-237-2581-144-3866,3,3282-206-3220-2724,38092-17755,38092-22974,38092-23041,38092-32348,nosource} |
|
| 11318 | +} |
|
| 11319 | + |
|
| 11320 | +@article{wangOutSouthernEast2016, |
|
| 11321 | + title = {Out of Southern {{East Asia}}: The Natural History of Domestic Dogs across the World}, |
|
| 11322 | + shorttitle = {Out of Southern {{East Asia}}}, |
|
| 11323 | + author = {Wang, Guo-Dong and Zhai, Weiwei and Yang, He-Chuan and Wang, Lu and Zhong, Li and Liu, Yan-Hu and Fan, Ruo-Xi and Yin, Ting-Ting and Zhu, Chun-Ling and Poyarkov, Andrei D. and Irwin, David M. and Hytönen, Marjo K. and Lohi, Hannes and Wu, Chung-I. and Savolainen, Peter and Zhang, Ya-Ping}, |
|
| 11324 | + date = {2016-01}, |
|
| 11325 | + journaltitle = {Cell Research}, |
|
| 11326 | + volume = {26}, |
|
| 11327 | + number = {1}, |
|
| 11328 | + pages = {21--33}, |
|
| 11329 | + issn = {1748-7838}, |
|
| 11330 | + doi = {10.1038/cr.2015.147}, |
|
| 11331 | + url = {https://www.nature.com/articles/cr2015147}, |
|
| 11332 | + urldate = {2018-10-25}, |
|
| 11333 | + abstract = {The origin and evolution of the domestic dog remains a controversial question for the scientific community, with basic aspects such as the place and date of origin, and the number of times dogs were domesticated, open to dispute. Using whole genome sequences from a total of 58 canids (12 gray wolves, 27 primitive dogs from Asia and Africa, and a collection of 19 diverse breeds from across the world), we find that dogs from southern East Asia have significantly higher genetic diversity compared to other populations, and are the most basal group relating to gray wolves, indicating an ancient origin of domestic dogs in southern East Asia 33 000 years ago. Around 15 000 years ago, a subset of ancestral dogs started migrating to the Middle East, Africa and Europe, arriving in Europe at about 10 000 years ago. One of the out of Asia lineages also migrated back to the east, creating a series of admixed populations with the endemic Asian lineages in northern China before migrating to the New World. For the first time, our study unravels an extraordinary journey that the domestic dog has traveled on earth.}, |
|
| 11334 | + langid = {english}, |
|
| 11335 | + keywords = {nosource} |
|
| 11336 | +} |
|
| 11337 | + |
|
| 11338 | +@article{wangPCBP1SuppressesTranslation2010, |
|
| 11339 | + title = {{{PCBP1}} Suppresses the Translation of Metastasis-Associated {{PRL-3}} Phosphatase}, |
|
| 11340 | + author = {Wang, Haihe and Vardy, Leah A. and Tan, Cheng Peow and Loo, Jia Min and Guo, Ke and Li, Jie and Lim, Seng Gee and Zhou, Jianbiao and Chng, Wee Joo and Ng, Siok Bian and Li, Hui Xiang and Zeng, Qi}, |
|
| 11341 | + date = {2010-07-13}, |
|
| 11342 | + journaltitle = {Cancer Cell}, |
|
| 11343 | + shortjournal = {Cancer Cell}, |
|
| 11344 | + volume = {18}, |
|
| 11345 | + number = {1}, |
|
| 11346 | + eprint = {20609352}, |
|
| 11347 | + eprinttype = {pmid}, |
|
| 11348 | + pages = {52--62}, |
|
| 11349 | + issn = {1878-3686}, |
|
| 11350 | + doi = {10.1016/j.ccr.2010.04.028}, |
|
| 11351 | + abstract = {Overexpression of phosphatase of regenerating liver (PRL)-3 is associated with the progression of diverse human cancers. We show that the overexpression of PRL-3 protein is not directly associated with its transcript levels, indicating the existence of an underlying posttranscriptional regulation. The 5' untranslanted region (UTR) of PRL-3 mRNA possesses triple GCCCAG motifs capable of suppressing mRNA translation through interaction with PolyC-RNA-binding protein 1 (PCBP1), which retards PRL-3 mRNA transcript incorporation into polyribosomes. Overexpression of PCBP1 inhibits PRL-3 expression and inactivates AKT, whereas knockdown of PCBP1 causes upregulation of PRL-3 protein levels, activation of AKT, and promotion of tumorigenesis. An inverse correlation between protein levels of PRL-3 and PCBP1 in human primary cancers supports the clinical relevance.}, |
|
| 11352 | + langid = {english}, |
|
| 11353 | + keywords = {5' Untranslated Regions,Animals,Blotting Western,Cell Line Tumor,DNA-Binding Proteins,Electrophoretic Mobility Shift Assay,Gene Expression Regulation Neoplastic,Heterogeneous-Nuclear Ribonucleoproteins,Humans,Immunoenzyme Techniques,Luciferases,Lymphatic Metastasis,Mice,Mice Nude,Neoplasm Metastasis,Neoplasm Proteins,Neoplasms,Polyribosomes,Promoter Regions Genetic,Protein Biosynthesis,Protein Tyrosine Phosphatases,Proto-Oncogene Proteins c-akt,Reverse Transcriptase Polymerase Chain Reaction,RNA Messenger,RNA Small Interfering,RNA-Binding Proteins,Spectrometry Mass Matrix-Assisted Laser Desorption-Ionization,Tissue Array Analysis,Xenograft Model Antitumor Assays}, |
|
| 11354 | + file = {/Users/rmorin/Zotero/storage/QP3WGTIX/Wang et al. - 2010 - PCBP1 suppresses the translation of metastasis-ass.pdf} |
|
| 11355 | +} |
|
| 11356 | + |
|
| 11357 | +@article{wangSF3B1OtherNovel2011, |
|
| 11358 | + title = {{{SF3B1}} and Other Novel Cancer Genes in Chronic Lymphocytic Leukemia}, |
|
| 11359 | + author = {Wang, Lili and Lawrence, Michael S. and Wan, Youzhong and Stojanov, Petar and Sougnez, Carrie and Stevenson, Kristen and Werner, Lillian and Sivachenko, Andrey and DeLuca, David S. and Zhang, Li and Zhang, Wandi and Vartanov, Alexander R. and Fernandes, Stacey M. and Goldstein, Natalie R. and Folco, Eric G. and Cibulskis, Kristian and Tesar, Bethany and Sievers, Quinlan L. and Shefler, Erica and Gabriel, Stacey and Hacohen, Nir and Reed, Robin and Meyerson, Matthew and Golub, Todd R. and Lander, Eric S. and Neuberg, Donna and Brown, Jennifer R. and Getz, Gad and Wu, Catherine J.}, |
|
| 11360 | + date = {2011-12-29}, |
|
| 11361 | + journaltitle = {The New England Journal of Medicine}, |
|
| 11362 | + shortjournal = {N. Engl. J. Med.}, |
|
| 11363 | + volume = {365}, |
|
| 11364 | + number = {26}, |
|
| 11365 | + eprint = {22150006}, |
|
| 11366 | + eprinttype = {pmid}, |
|
| 11367 | + pages = {2497--2506}, |
|
| 11368 | + issn = {1533-4406}, |
|
| 11369 | + doi = {10.1056/NEJMoa1109016}, |
|
| 11370 | + abstract = {BACKGROUND: The somatic genetic basis of chronic lymphocytic leukemia, a common and clinically heterogeneous leukemia occurring in adults, remains poorly understood. METHODS: We obtained DNA samples from leukemia cells in 91 patients with chronic lymphocytic leukemia and performed massively parallel sequencing of 88 whole exomes and whole genomes, together with sequencing of matched germline DNA, to characterize the spectrum of somatic mutations in this disease. RESULTS: Nine genes that are mutated at significant frequencies were identified, including four with established roles in chronic lymphocytic leukemia (TP53 in 15\% of patients, ATM in 9\%, MYD88 in 10\%, and NOTCH1 in 4\%) and five with unestablished roles (SF3B1, ZMYM3, MAPK1, FBXW7, and DDX3X). SF3B1, which functions at the catalytic core of the spliceosome, was the second most frequently mutated gene (with mutations occurring in 15\% of patients). SF3B1 mutations occurred primarily in tumors with deletions in chromosome 11q, which are associated with a poor prognosis in patients with chronic lymphocytic leukemia. We further discovered that tumor samples with mutations in SF3B1 had alterations in pre-messenger RNA (mRNA) splicing. CONCLUSIONS: Our study defines the landscape of somatic mutations in chronic lymphocytic leukemia and highlights pre-mRNA splicing as a critical cellular process contributing to chronic lymphocytic leukemia.}, |
|
| 11371 | + langid = {english}, |
|
| 11372 | + pmcid = {PMC3685413}, |
|
| 11373 | + keywords = {Adult,Chromosome Deletion,Chromosomes Human Pair 11,DNA Neoplasm,Exome,Gene Library,High-Throughput Nucleotide Sequencing,Humans,Leukemia Lymphocytic Chronic B-Cell,Mutation,Mutation Missense,RNA Splicing,Spliceosomes} |
|
| 11374 | +} |
|
| 11375 | + |
|
| 11376 | +@article{wangSinglecellProfilingReveals2022, |
|
| 11377 | + title = {Single-Cell Profiling Reveals a Memory {{B}} Cell-like Subtype of Follicular Lymphoma with Increased Transformation Risk}, |
|
| 11378 | + author = {Wang, Xuehai and Nissen, Michael and Gracias, Deanne and Kusakabe, Manabu and Simkin, Guillermo and Jiang, Aixiang and Duns, Gerben and Sarkozy, Clementine and Hilton, Laura and Chavez, Elizabeth A. and Segat, Gabriela C. and Wong, Rachel and Kim, Jubin and Aoki, Tomohiro and Islam, Rashedul and May, Christina and Hung, Stacy and Tyshchenko, Kate and Brinkman, Ryan R. and Hirst, Martin and Karsan, Aly and Freeman, Ciara and Sehn, Laurie H. and Morin, Ryan D. and Roth, Andrew J. and Savage, Kerry J. and Craig, Jeffrey W. and Shah, Sohrab P. and Steidl, Christian and Scott, David W. and Weng, Andrew P.}, |
|
| 11379 | + date = {2022-11-09}, |
|
| 11380 | + journaltitle = {Nature Communications}, |
|
| 11381 | + shortjournal = {Nat Commun}, |
|
| 11382 | + volume = {13}, |
|
| 11383 | + number = {1}, |
|
| 11384 | + eprint = {36351924}, |
|
| 11385 | + eprinttype = {pmid}, |
|
| 11386 | + pages = {6772}, |
|
| 11387 | + issn = {2041-1723}, |
|
| 11388 | + doi = {10.1038/s41467-022-34408-0}, |
|
| 11389 | + abstract = {Follicular lymphoma (FL) is an indolent cancer of mature B-cells but with ongoing risk of transformation to more aggressive histology over time. Recurrent mutations associated with transformation have been identified; however, prognostic features that can be discerned at diagnosis could be clinically useful. We present here comprehensive profiling of both tumor and immune compartments in 155 diagnostic FL biopsies at single-cell resolution by mass cytometry. This revealed a diversity of phenotypes but included two recurrent patterns, one which closely resembles germinal center B-cells (GCB) and another which appears more related to memory B-cells (MB). GCB-type tumors are enriched for EZH2, TNFRSF14, and MEF2B mutations, while MB-type tumors contain increased follicular helper T-cells. MB-type and intratumoral phenotypic diversity are independently associated with increased risk of transformation, supporting biological relevance of these features. Notably, a reduced 26-marker panel retains sufficient information to allow phenotypic profiling of future cohorts by conventional flow cytometry.}, |
|
| 11390 | + langid = {english}, |
|
| 11391 | + pmcid = {PMC9646774}, |
|
| 11392 | + keywords = {B-Lymphocytes,Germinal Center,Humans,Lymphoma Follicular,Memory B Cells,Mutation}, |
|
| 11393 | + file = {/Users/rmorin/Zotero/storage/WAWCXHX9/Wang et al. - 2022 - Single-cell profiling reveals a memory B cell-like.pdf} |
|
| 11394 | +} |
|
| 11395 | + |
|
| 11396 | +@article{wangTranscriptomicCharacterizationSF3B12016, |
|
| 11397 | + title = {Transcriptomic {{Characterization}} of {{SF3B1 Mutation Reveals Its Pleiotropic Effects}} in {{Chronic Lymphocytic Leukemia}}}, |
|
| 11398 | + author = {Wang, Lili and Brooks, Angela N. and Fan, Jean and Wan, Youzhong and Gambe, Rutendo and Li, Shuqiang and Hergert, Sarah and Yin, Shanye and Freeman, Samuel S. and Levin, Joshua Z. and Fan, Lin and Seiler, Michael and Buonamici, Silvia and Smith, Peter G. and Chau, Kevin F. and Cibulskis, Carrie L. and Zhang, Wandi and Rassenti, Laura Z. and Ghia, Emanuela M. and Kipps, Thomas J. and Fernandes, Stacey and Bloch, Donald B. and Kotliar, Dylan and Landau, Dan A. and Shukla, Sachet A. and Aster, Jon C. and Reed, Robin and DeLuca, David S. and Brown, Jennifer R. and Neuberg, Donna and Getz, Gad and Livak, Kenneth J. and Meyerson, Matthew M. and Kharchenko, Peter V. and Wu, Catherine J.}, |
|
| 11399 | + date = {2016-11-14}, |
|
| 11400 | + journaltitle = {Cancer Cell}, |
|
| 11401 | + shortjournal = {Cancer Cell}, |
|
| 11402 | + volume = {30}, |
|
| 11403 | + number = {5}, |
|
| 11404 | + eprint = {27818134}, |
|
| 11405 | + eprinttype = {pmid}, |
|
| 11406 | + pages = {750--763}, |
|
| 11407 | + issn = {1535-6108, 1878-3686}, |
|
| 11408 | + doi = {10.1016/j.ccell.2016.10.005}, |
|
| 11409 | + url = {https://www.cell.com/cancer-cell/abstract/S1535-6108(16)30492-5}, |
|
| 11410 | + urldate = {2019-12-21}, |
|
| 11411 | + langid = {english}, |
|
| 11412 | + keywords = {alternative splicing,CLL,Notch signaling,RNA sequencing,SF3B1}, |
|
| 11413 | + file = {/Users/rmorin/Zotero/storage/7VVFYYA3/S1535-6108(16)30492-5.html} |
|
| 11414 | +} |
|
| 11415 | + |
|
| 11416 | +@article{weighardtRolesHeterogeneousNuclear1996, |
|
| 11417 | + title = {The Roles of Heterogeneous Nuclear Ribonucleoproteins ({{hnRNP}}) in {{RNA}} Metabolism}, |
|
| 11418 | + author = {Weighardt, Florian and Biamonti, Giuseppe and Riva, Silvano}, |
|
| 11419 | + date = {1996}, |
|
| 11420 | + journaltitle = {BioEssays}, |
|
| 11421 | + volume = {18}, |
|
| 11422 | + number = {9}, |
|
| 11423 | + pages = {747--756}, |
|
| 11424 | + issn = {1521-1878}, |
|
| 11425 | + doi = {10.1002/bies.950180910}, |
|
| 11426 | + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/bies.950180910}, |
|
| 11427 | + urldate = {2022-09-26}, |
|
| 11428 | + abstract = {In eukaryotic cells, messenger RNAs are formed by extensive posttranscriptional processing of primary transcripts, assembled with a large number of proteins and processing factors in ribonucleoprotein complexes. The protein moiety of these complexes mainly constitutes a class of about 20 major polypeptides called heterogeneous nuclear ribonucleoproteins or hnRNPs. The function and the mechanism of action of hnRNPs is still not fully understood, but the identification of RNA binding domains and RNA binding specificities, and the development of new functional assays, has stimulated interest in them. In contrast to previous models that hypothesised a mere structural (histone-like) function, a more diversified and dynamic role for these proteins is now emerging. In fact, they can be viewed as a subset of the trans-acting pre-mRNA maturation factors. They might actively participate in post-transcriptional events such as regulated splicing and mRNA export. Moreover, recent data suggest an involvement of some of these proteins in molecular diseases. Here we present an overview of the most relevant properties of hnRNPs and discuss some emerging ideas on theiir roles.}, |
|
| 11429 | + langid = {english}, |
|
| 11430 | + file = {/Users/rmorin/Zotero/storage/XWSNID7E/bies.html} |
|
| 11431 | +} |
|
| 11432 | + |
|
| 11433 | +@article{weinsteinCancerGenomeAtlas2013, |
|
| 11434 | + title = {The {{Cancer Genome Atlas Pan-Cancer}} Analysis Project}, |
|
| 11435 | + author = {Weinstein, John N. and Collisson, Eric A. and Mills, Gordon B. and Shaw, Kenna R. Mills and Ozenberger, Brad A. and Ellrott, Kyle and Shmulevich, Ilya and Sander, Chris and Stuart, Joshua M.}, |
|
| 11436 | + date = {2013-10}, |
|
| 11437 | + journaltitle = {Nature Genetics}, |
|
| 11438 | + shortjournal = {Nat Genet}, |
|
| 11439 | + volume = {45}, |
|
| 11440 | + number = {10}, |
|
| 11441 | + pages = {1113--1120}, |
|
| 11442 | + publisher = {Nature Publishing Group}, |
|
| 11443 | + issn = {1546-1718}, |
|
| 11444 | + doi = {10.1038/ng.2764}, |
|
| 11445 | + url = {https://www.nature.com/articles/ng.2764}, |
|
| 11446 | + urldate = {2022-05-22}, |
|
| 11447 | + abstract = {Current clinical practice is organized according to tissue or organ of origin of tumors. Now, The Cancer Genome Atlas (TCGA) Research Network has started to identify genomic and other molecular commonalities among a dozen different types of cancer. Emerging similarities and contrasts will form the basis for targeted therapies of the future and for repurposing existing therapies by molecular rather than histological similarities of the diseases.}, |
|
| 11448 | + issue = {10}, |
|
| 11449 | + langid = {english}, |
|
| 11450 | + keywords = {Cancer,Genomics}, |
|
| 11451 | + file = {/Users/rmorin/Zotero/storage/LYRD765R/Weinstein et al. - 2013 - The Cancer Genome Atlas Pan-Cancer analysis projec.pdf;/Users/rmorin/Zotero/storage/2FHTLM8Q/ng.html} |
|
| 11452 | +} |
|
| 11453 | + |
|
| 11454 | +@article{weirauchDeterminationInferenceEukaryotic2014, |
|
| 11455 | + title = {Determination and {{Inference}} of {{Eukaryotic Transcription Factor Sequence Specificity}}}, |
|
| 11456 | + author = {Weirauch, Matthew T. and Yang, Ally and Albu, Mihai and Cote, Atina G. and Montenegro-Montero, Alejandro and Drewe, Philipp and Najafabadi, Hamed S. and Lambert, Samuel A. and Mann, Ishminder and Cook, Kate and Zheng, Hong and Goity, Alejandra and {van~Bakel}, Harm and Lozano, Jean-Claude and Galli, Mary and Lewsey, Mathew G. and Huang, Eryong and Mukherjee, Tuhin and Chen, Xiaoting and Reece-Hoyes, John S. and Govindarajan, Sridhar and Shaulsky, Gad and Walhout, Albertha J. M. and Bouget, François-Yves and Ratsch, Gunnar and Larrondo, Luis F. and Ecker, Joseph R. and Hughes, Timothy R.}, |
|
| 11457 | + date = {2014-09-11}, |
|
| 11458 | + journaltitle = {Cell}, |
|
| 11459 | + shortjournal = {Cell}, |
|
| 11460 | + volume = {158}, |
|
| 11461 | + number = {6}, |
|
| 11462 | + eprint = {25215497}, |
|
| 11463 | + eprinttype = {pmid}, |
|
| 11464 | + pages = {1431--1443}, |
|
| 11465 | + publisher = {Elsevier}, |
|
| 11466 | + issn = {0092-8674, 1097-4172}, |
|
| 11467 | + doi = {10.1016/j.cell.2014.08.009}, |
|
| 11468 | + url = {https://www.cell.com/cell/abstract/S0092-8674(14)01036-8}, |
|
| 11469 | + urldate = {2022-02-01}, |
|
| 11470 | + langid = {english}, |
|
| 11471 | + file = {/Users/rmorin/Zotero/storage/NVQ48RBP/Weirauch et al. - 2014 - Determination and Inference of Eukaryotic Transcri.pdf} |
|
| 11472 | +} |
|
| 11473 | + |
|
| 11474 | +@article{welckerFbw7TumorSuppressor2004, |
|
| 11475 | + title = {The {{Fbw7}} Tumor Suppressor Regulates Glycogen Synthase Kinase 3 Phosphorylation-Dependent c-{{Myc}} Protein Degradation}, |
|
| 11476 | + author = {Welcker, Markus and Orian, Amir and Jin, Jianping and Grim, Jonathan A. and Harper, J. Wade and Eisenman, Robert N. and Clurman, Bruce E.}, |
|
| 11477 | + date = {2004-06-15}, |
|
| 11478 | + journaltitle = {Proceedings of the National Academy of Sciences}, |
|
| 11479 | + shortjournal = {PNAS}, |
|
| 11480 | + volume = {101}, |
|
| 11481 | + number = {24}, |
|
| 11482 | + eprint = {15150404}, |
|
| 11483 | + eprinttype = {pmid}, |
|
| 11484 | + pages = {9085--9090}, |
|
| 11485 | + publisher = {National Academy of Sciences}, |
|
| 11486 | + issn = {0027-8424, 1091-6490}, |
|
| 11487 | + doi = {10.1073/pnas.0402770101}, |
|
| 11488 | + url = {https://www.pnas.org/content/101/24/9085}, |
|
| 11489 | + urldate = {2021-04-29}, |
|
| 11490 | + abstract = {Myc proteins regulate cell growth and division and are implicated in a wide range of human cancers. We show here that Fbw7, a component of the SCFFbw7 ubiquitin ligase and a tumor suppressor, promotes proteasome-dependent c-Myc turnover in vivo and c-Myc ubiquitination in vitro. Phosphorylation of c-Myc on threonine-58 (T58) by glycogen synthase kinase 3 regulates the binding of Fbw7 to c-Myc as well as Fbw7-mediated c-Myc degradation and ubiquitination. T58 is the most frequent site of c-myc mutations in lymphoma cells, and our findings suggest that c-Myc activation is one of the key oncogenic consequences of Fbw7 loss in cancer. Because Fbw7 mediates the degradation of cyclin E, Notch, and c-Jun, as well as c-Myc, the loss of Fbw7 is likely to elicit profound effects on cell proliferation during tumorigenesis.}, |
|
| 11491 | + langid = {english}, |
|
| 11492 | + file = {/Users/rmorin/Zotero/storage/KJDUS6BY/Welcker et al. - 2004 - The Fbw7 tumor suppressor regulates glycogen synth.pdf;/Users/rmorin/Zotero/storage/83V2FU86/9085.html} |
|
| 11493 | +} |
|
| 11494 | + |
|
| 11495 | +@article{wenigerMutationsTumorSuppressor2006a, |
|
| 11496 | + title = {Mutations of the Tumor Suppressor Gene {{SOCS-1}} in Classical {{Hodgkin}} Lymphoma Are Frequent and Associated with Nuclear Phospho-{{STAT5}} Accumulation}, |
|
| 11497 | + author = {Weniger, M. A. and Melzner, I. and Menz, C. K. and Wegener, S. and Bucur, A. J. and Dorsch, K. and Mattfeldt, T. and Barth, T. F. E. and Möller, P.}, |
|
| 11498 | + date = {2006-04-27}, |
|
| 11499 | + journaltitle = {Oncogene}, |
|
| 11500 | + shortjournal = {Oncogene}, |
|
| 11501 | + volume = {25}, |
|
| 11502 | + number = {18}, |
|
| 11503 | + eprint = {16532038}, |
|
| 11504 | + eprinttype = {pmid}, |
|
| 11505 | + pages = {2679--2684}, |
|
| 11506 | + issn = {0950-9232}, |
|
| 11507 | + doi = {10.1038/sj.onc.1209151}, |
|
| 11508 | + abstract = {The suppressors of cytokine signaling (SOCS) are critically involved in the regulation of cellular proliferation, survival, and apoptosis via cytokine-induced JAK/STAT signaling. SOCS-1 silencing by aberrant DNA methylation contributes to oncogenesis in various B-cell neoplasias and carcinomas. Recently, we showed an alternative loss of SOCS-1 function due to deleterious SOCS-1 mutations in a major subset of primary mediastinal B-cell lymphoma (PMBL) and in the PMBL line MedB-1, and a biallelic SOCS-1 deletion in PMBL line Karpas1106P. For both cell lines our previous data demonstrated retarded JAK2 degradation and sustained phospho-JAK2 action leading to enhanced DNA binding of phospho-STAT5. Here, we analysed SOCS-1 in laser-microdissected Hodgkin and Reed-Sternberg (HRS) cells of classical Hodgkin lymphoma (cHL). We detected SOCS-1 mutations in HRS cells of eight of 19 cHL samples and in three of five Hodgkin lymphoma (HL)-derived cell lines by sequencing analysis. Moreover, we found a significant association between mutated SOCS-1 of isolated HRS cells and nuclear phospho-STAT5 accumulation in HRS cells of cHL tumor tissue (P {$<$} 0.01). Collectively, these findings support the concept that PMBL and cHL share many overlapping features, and that defective tumor suppressor gene SOCS-1 triggers an oncogenic pathway operative in both lymphomas.}, |
|
| 11509 | + langid = {english}, |
|
| 11510 | + keywords = {Amino Acid Sequence,Base Sequence,Cell Nucleus,Gene Expression Regulation Neoplastic,Genes Tumor Suppressor,Hodgkin Disease,Humans,Intracellular Signaling Peptides and Proteins,Lasers,Molecular Sequence Data,Mutation,Phosphorylation,Reed-Sternberg Cells,Repressor Proteins,Sequence Homology Amino Acid,STAT5 Transcription Factor,Suppressor of Cytokine Signaling 1 Protein,Suppressor of Cytokine Signaling Proteins} |
|
| 11511 | +} |
|
| 11512 | + |
|
| 11513 | +@article{wesolowskiGeneExpressionProfiling2011, |
|
| 11514 | + title = {Gene Expression Profiling: Changing Face of Breast Cancer Classification and Management}, |
|
| 11515 | + shorttitle = {Gene Expression Profiling}, |
|
| 11516 | + author = {Wesolowski, Robert and Ramaswamy, Bhuvaneswari}, |
|
| 11517 | + date = {2011}, |
|
| 11518 | + journaltitle = {Gene Expression}, |
|
| 11519 | + shortjournal = {Gene Expr.}, |
|
| 11520 | + volume = {15}, |
|
| 11521 | + number = {3}, |
|
| 11522 | + eprint = {22268293}, |
|
| 11523 | + eprinttype = {pmid}, |
|
| 11524 | + pages = {105--115}, |
|
| 11525 | + issn = {1052-2166}, |
|
| 11526 | + doi = {10.3727/105221611x13176664479241}, |
|
| 11527 | + abstract = {Epithelial breast malignancies are a group of several disease entities that vary in their biology and response to specific therapies. Historically, classification of different molecular types of breast cancer was done through the use of conventional methods such as tumor morphology, grade, and immunophenotyping for estrogen, progesterone, and HER-2/neu receptor expression. Such techniques, although helpful, are not sufficient to accurately predict biologic behavior of breast cancers. Over the last several years, much progress has been made in more precise identification of molecular breast cancer subtypes. Such advances hold a great promise in improving estimation of prognosis and assigning most appropriate therapies. Thanks to use of cDNA microarrays expression technology and quantitative reverse transcriptase polymerase chain reaction (RT-PCR), tumors with specific gene expression patterns can now be identified. This process is presently reshaping perceptions of how breast cancer should be classified and treated. Categorization of breast cancers by gene expression is only beginning to make its way into the daily clinical practice and likely will complement, but not replace, the conventional methods of classification.}, |
|
| 11528 | + langid = {english}, |
|
| 11529 | + pmcid = {PMC3772713}, |
|
| 11530 | + keywords = {Antineoplastic Agents,Breast Neoplasms,Disease Management,Drug Resistance Neoplasm,Female,Gene Expression Profiling,Gene Expression Regulation Neoplastic,History 19th Century,History 20th Century,History 21st Century,Humans,Oligonucleotide Array Sequence Analysis,Receptor ErbB-2} |
|
| 11531 | +} |
|
| 11532 | + |
|
| 11533 | +@article{whalleyFrameworkQualityAssessment2020, |
|
| 11534 | + title = {Framework for Quality Assessment of Whole Genome Cancer Sequences}, |
|
| 11535 | + author = {Whalley, Justin P. and Buchhalter, Ivo and Rheinbay, Esther and Raine, Keiran M. and Stobbe, Miranda D. and Kleinheinz, Kortine and Werner, Johannes and Beltran, Sergi and Gut, Marta and Hübschmann, Daniel and Hutter, Barbara and Livitz, Dimitri and Perry, Marc D. and Rosenberg, Mara and Saksena, Gordon and Trotta, Jean-Rémi and Eils, Roland and Gerhard, Daniela S. and Campbell, Peter J. and Schlesner, Matthias and Gut, Ivo G.}, |
|
| 11536 | + date = {2020-10-07}, |
|
| 11537 | + journaltitle = {Nature Communications}, |
|
| 11538 | + shortjournal = {Nat Commun}, |
|
| 11539 | + volume = {11}, |
|
| 11540 | + number = {1}, |
|
| 11541 | + pages = {5040}, |
|
| 11542 | + publisher = {Nature Publishing Group}, |
|
| 11543 | + issn = {2041-1723}, |
|
| 11544 | + doi = {10.1038/s41467-020-18688-y}, |
|
| 11545 | + url = {https://www.nature.com/articles/s41467-020-18688-y}, |
|
| 11546 | + urldate = {2022-05-19}, |
|
| 11547 | + abstract = {Bringing together cancer genomes from different projects increases power and allows the investigation of pan-cancer, molecular mechanisms. However, working with whole genomes sequenced over several years in different sequencing centres requires a framework to compare the quality of these sequences. We used the Pan-Cancer Analysis of Whole Genomes cohort as a test case to construct such a framework. This cohort contains whole cancer genomes of 2832 donors from 18 sequencing centres. We developed a non-redundant set of five quality control (QC) measurements to establish a star rating system. These QC measures reflect known differences in sequencing protocol and provide a guide to downstream analyses and allow for exclusion of samples of poor quality. We have found that this is an effective framework of quality measures. The implementation of the framework is available at: https://dockstore.org/containers/quay.io/jwerner\_dkfz/pancanqc:1.2.2.}, |
|
| 11548 | + issue = {1}, |
|
| 11549 | + langid = {english}, |
|
| 11550 | + keywords = {Cancer genomics,DNA sequencing,Research data}, |
|
| 11551 | + file = {/Users/rmorin/Zotero/storage/SH7R8UQN/Whalley et al. - 2020 - Framework for quality assessment of whole genome c.pdf;/Users/rmorin/Zotero/storage/SY3IMK3U/s41467-020-18688-y.html} |
|
| 11552 | +} |
|
| 11553 | + |
|
| 11554 | +@article{wienandGenomicAnalysesFlowsorted2019b, |
|
| 11555 | + title = {Genomic Analyses of Flow-Sorted {{Hodgkin Reed-Sternberg}} Cells Reveal Complementary Mechanisms of Immune Evasion}, |
|
| 11556 | + author = {Wienand, Kirsty and Chapuy, Bjoern and Stewart, Chip and Dunford, Andrew J. and Wu, David and Kim, Jaegil and Kamburov, Atanas and Wood, Timothy R. and Cader, Fathima Zumla and Ducar, Matthew D. and Thorner, Aaron R. and Nag, Anwesha and Heubeck, Alexander T. and Buonopane, Michael J. and Redd, Robert A. and Bojarczuk, Kamil and Lawton, Lee N. and Armand, Philippe and Rodig, Scott J. and Fromm, Jonathan R. and Getz, Gad and Shipp, Margaret A.}, |
|
| 11557 | + date = {2019-12-10}, |
|
| 11558 | + journaltitle = {Blood Advances}, |
|
| 11559 | + shortjournal = {Blood Adv}, |
|
| 11560 | + volume = {3}, |
|
| 11561 | + number = {23}, |
|
| 11562 | + eprint = {31816062}, |
|
| 11563 | + eprinttype = {pmid}, |
|
| 11564 | + pages = {4065--4080}, |
|
| 11565 | + issn = {2473-9537}, |
|
| 11566 | + doi = {10.1182/bloodadvances.2019001012}, |
|
| 11567 | + abstract = {Classical Hodgkin lymphoma (cHL) is composed of rare malignant Hodgkin Reed-Sternberg (HRS) cells within an extensive, but ineffective, inflammatory/immune cell infiltrate. HRS cells exhibit near-universal somatic copy gains of chromosome 9p/9p24.1, which increase expression of the programmed cell death protein 1 (PD-1) ligands. To define genetic mechanisms of response and resistance to PD-1 blockade and identify complementary treatment targets, we performed whole-exome sequencing of flow cytometry-sorted HRS cells from 23 excisional biopsies of newly diagnosed cHLs, including 8 Epstein-Barr virus-positive (EBV+) tumors. We identified significantly mutated cancer candidate genes (CCGs) as well as somatic copy number alterations and structural variations and characterized their contribution to disease-defining immune evasion mechanisms and nuclear factor κB (NF-κB), JAK/STAT, and PI3K signaling pathways. EBV- cHLs had a higher prevalence of genetic alterations in the NF-κB and major histocompatibility complex class I antigen presentation pathways. In this young cHL cohort (median age, 26 years), we identified a predominant mutational signature of spontaneous deamination of cytosine- phosphate-guanines ("Aging"), in addition to apolipoprotein B mRNA editing catalytic polypeptide-like, activation-induced cytidine deaminase, and microsatellite instability (MSI)-associated hypermutation. In particular, the mutational burden in EBV- cHLs was among the highest reported, similar to that of carcinogen-induced tumors. Together, the overall high mutational burden, MSI-associated hypermutation, and newly identified genetic alterations represent additional potential bases for the efficacy of PD-1 blockade in cHL. Of note, recurrent cHL alterations, including B2M, TNFAIP3, STAT6, GNA13, and XPO1 mutations and 2p/2p15, 6p21.32, 6q23.3, and 9p/9p24.1 copy number alterations, were also identified in {$>$}20\% of primary mediastinal B-cell lymphomas, highlighting shared pathogenetic mechanisms in these diseases.}, |
|
| 11568 | + langid = {english}, |
|
| 11569 | + pmcid = {PMC6963251}, |
|
| 11570 | + keywords = {Adult,Genomics,Humans,Immune Evasion,Reed-Sternberg Cells}, |
|
| 11571 | + file = {/Users/rmorin/Zotero/storage/ZU75QHKF/Wienand et al. - 2019 - Genomic analyses of flow-sorted Hodgkin Reed-Stern.pdf} |
|
| 11572 | +} |
|
| 11573 | + |
|
| 11574 | +@article{wiestnerPointMutationsGenomic2007, |
|
| 11575 | + title = {Point Mutations and Genomic Deletions in {{CCND1}} Create Stable Truncated Cyclin {{D1 mRNAs}} That Are Associated with Increased Proliferation Rate and Shorter Survival}, |
|
| 11576 | + author = {Wiestner, Adrian and Tehrani, Mahsa and Chiorazzi, Michael and Wright, George and Gibellini, Federica and Nakayama, Kazutaka and Liu, Hui and Rosenwald, Andreas and Muller-Hermelink, H. Konrad and Ott, German and Chan, Wing C. and Greiner, Timothy C. and Weisenburger, Dennis D. and Vose, Julie and Armitage, James O. and Gascoyne, Randy D. and Connors, Joseph M. and Campo, Elias and Montserrat, Emilio and Bosch, Francesc and Smeland, Erlend B. and Kvaloy, Stein and Holte, Harald and Delabie, Jan and Fisher, Richard I. and Grogan, Thomas M. and Miller, Thomas P. and Wilson, Wyndham H. and Jaffe, Elaine S. and Staudt, Louis M.}, |
|
| 11577 | + date = {2007-06-01}, |
|
| 11578 | + journaltitle = {Blood}, |
|
| 11579 | + shortjournal = {Blood}, |
|
| 11580 | + volume = {109}, |
|
| 11581 | + number = {11}, |
|
| 11582 | + pages = {4599--4606}, |
|
| 11583 | + issn = {0006-4971}, |
|
| 11584 | + doi = {10.1182/blood-2006-08-039859}, |
|
| 11585 | + url = {https://ashpublications.org/blood/article/109/11/4599/23037/Point-mutations-and-genomic-deletions-in-CCND1}, |
|
| 11586 | + urldate = {2019-12-21}, |
|
| 11587 | + langid = {english}, |
|
| 11588 | + file = {/Users/rmorin/Zotero/storage/FX9B7WMC/blood-2006-08-039859.html} |
|
| 11589 | +} |
|
| 11590 | + |
|
| 11591 | +@article{wildaInactivationARFMDM2p53Pathway2004, |
|
| 11592 | + title = {Inactivation of the {{ARF-MDM-2-p53}} Pathway in Sporadic {{Burkitt}}'s Lymphoma in Children}, |
|
| 11593 | + author = {Wilda, M. and Bruch, J. and Harder, L. and Rawer, D. and Reiter, A. and Borkhardt, A. and Woessmann, W.}, |
|
| 11594 | + date = {2004-03}, |
|
| 11595 | + journaltitle = {Leukemia}, |
|
| 11596 | + shortjournal = {Leukemia}, |
|
| 11597 | + volume = {18}, |
|
| 11598 | + number = {3}, |
|
| 11599 | + eprint = {14712292}, |
|
| 11600 | + eprinttype = {pmid}, |
|
| 11601 | + pages = {584--588}, |
|
| 11602 | + issn = {0887-6924}, |
|
| 11603 | + doi = {10.1038/sj.leu.2403254}, |
|
| 11604 | + abstract = {Burkitt's lymphomas (BLs) are characterized by an activated MYC gene that provides a constitutive proliferative signal. However, activated myc can initiate ARF-dependent activation of p53 and apoptosis as well. Data derived from cell culture and animal models suggest that the inactivation of the ARF-MDM-2-p53 apoptotic signaling pathway may be a necessary secondary event for the development of BL. This has not been tested in freshly excised BL tissue. We investigated the ARF-MDM-2-p53 pathway in tumor specimen from 24 children with sporadic BL/B-ALL. Direct sequencing revealed a point mutation in the p53 gene in four BL. Overexpression of MDM-2 was evident in 10 of the BL samples analyzed by real-time quantitative PCR. Deletion of the CDKN2A locus that encodes ARF or reduced expression of ARF could not be detected in any BL by fluorescence in situ hybridization analysis or real-time quantitative PCR, respectively. Our results indicate that the ARF-MDM-2-p53 apoptotic pathway is disrupted in about 55\% of the cases of childhood sporadic BL. We suggest that in addition to the inactivation of the ARF-MDM-2-p53 protective checkpoint function other antiapoptotic mutations may occur in a substantial part of children with sporadic BL.}, |
|
| 11605 | + langid = {english}, |
|
| 11606 | + keywords = {Adolescent,Burkitt Lymphoma,Case-Control Studies,Child,Child Preschool,Cyclin-Dependent Kinase Inhibitor p16,Female,Gene Deletion,Gene Expression Regulation Neoplastic,Humans,Lymphocytes,Male,Nuclear Proteins,Proto-Oncogene Proteins,Proto-Oncogene Proteins c-mdm2,RNA Neoplasm,RNA-Directed DNA Polymerase,Signal Transduction,Tumor Suppressor Protein p14ARF,Tumor Suppressor Protein p53} |
|
| 11607 | +} |
|
| 11608 | + |
|
| 11609 | +@article{willisNewPlayersGene2019, |
|
| 11610 | + title = {New Players in the Gene Regulatory Network Controlling Late {{B}} Cell Differentiation}, |
|
| 11611 | + author = {Willis, Simon N and Nutt, Stephen L}, |
|
| 11612 | + date = {2019-06-01}, |
|
| 11613 | + journaltitle = {Current Opinion in Immunology}, |
|
| 11614 | + shortjournal = {Current Opinion in Immunology}, |
|
| 11615 | + series = {Antigen Processing • {{Special}} Section on Precommited Lymphocytes}, |
|
| 11616 | + volume = {58}, |
|
| 11617 | + pages = {68--74}, |
|
| 11618 | + issn = {0952-7915}, |
|
| 11619 | + doi = {10.1016/j.coi.2019.04.007}, |
|
| 11620 | + url = {https://www.sciencedirect.com/science/article/pii/S0952791518300827}, |
|
| 11621 | + urldate = {2022-10-06}, |
|
| 11622 | + abstract = {The differentiation of B cells into antibody-secreting plasma cells is associated with profound changes in morphology, lifespan, and cellular metabolism that are needed to support high rates of antibody production. These processes are driven by dramatic alterations to the transcriptional program and to the organization of the nucleus itself that in turn are regulated by the activity of a select group of transcription factors and epigenetic regulators. Although the core differentiation program is conserved in all mature B cells, subset-specific regulators, such as those found in B1 or memory B cells, provide additional complexity. Here, we review the key components of the gene regulatory network controlling B-cell terminal differentiation, with an emphasis on the new players and processes that have emerged in recent years.}, |
|
| 11623 | + langid = {english}, |
|
| 11624 | + file = {/Users/rmorin/Zotero/storage/UEGRHALC/Willis and Nutt - 2019 - New players in the gene regulatory network control.pdf} |
|
| 11625 | +} |
|
| 11626 | + |
|
| 11627 | +@article{wilsonPhaseIIStudy, |
|
| 11628 | + title = {Phase {{II}} Study of Dose-Adjusted {{EPOCH}} and Rituximab in Untreated Diffuse Large {{B-cell}} Lymphoma with Analysis of Germinal Center and Post-Germinal Center Biomarkers}, |
|
| 11629 | + author = {Wilson, W and Dunleavy, K and Pittaluga, S and Hegde, U and Grant, N and Steinberg, S and Raffeld, M and Gutierrez, M and Chabner, B and Staudt, L and Jaffe, E and Janik, J}, |
|
| 11630 | + journaltitle = {J Clin Oncol}, |
|
| 11631 | + volume = {26}, |
|
| 11632 | + number = {16}, |
|
| 11633 | + pages = {2717--2724}, |
|
| 11634 | + keywords = {nosource} |
|
| 11635 | +} |
|
| 11636 | + |
|
| 11637 | +@article{wilsonTargetingCellReceptor, |
|
| 11638 | + title = {Targeting {{B}} Cell Receptor Signaling with Ibrutinib in Diffuse Large {{B}} Cell Lymphoma.}, |
|
| 11639 | + author = {Wilson, Wyndham H and Young, Ryan M and Schmitz, Roland and Yang, Yandan and Pittaluga, Stefania and Wright, George and Lih, Chih-Jian and Williams, P Mickey and Shaffer, Arthur L and Gerecitano, John and family=Vos, given=Sven, prefix=de, useprefix=true and Goy, Andre and Kenkre, Vaishalee P and Barr, Paul M and Blum, Kristie A and Shustov, Andrei and Advani, Ranjana and Fowler, Nathan H and Vose, Julie M and Elstrom, Rebecca L and Habermann, Thomas M and Barrientos, Jacqueline C and McGreivy, Jesse and Fardis, Maria and Chang, Betty Y and Clow, Fong and Munneke, Brian and Moussa, Davina and Beaupre, Darrin M and Staudt, Louis M}, |
|
| 11640 | + journaltitle = {Nature Medicine}, |
|
| 11641 | + volume = {21}, |
|
| 11642 | + number = {8}, |
|
| 11643 | + pages = {922--926}, |
|
| 11644 | + keywords = {nosource} |
|
| 11645 | +} |
|
| 11646 | + |
|
| 11647 | +@article{wlodarskaFOXP1GeneHighly2005, |
|
| 11648 | + title = {{{FOXP1}}, a Gene Highly Expressed in a Subset of Diffuse Large {{B-cell}} Lymphoma, Is Recurrently Targeted by Genomic Aberrations.}, |
|
| 11649 | + author = {Wlodarska, I and Veyt, E and De Paepe, P and Vandenberghe, P and Nooijen, P and Theate, I and Michaux, L and Sagaert, X and Marynen, P and Hagemeijer, A and De Wolf-Peeters, C}, |
|
| 11650 | + date = {2005-08}, |
|
| 11651 | + journaltitle = {Leukemia}, |
|
| 11652 | + volume = {19}, |
|
| 11653 | + number = {8}, |
|
| 11654 | + pages = {1299--1305}, |
|
| 11655 | + keywords = {nosource} |
|
| 11656 | +} |
|
| 11657 | + |
|
| 11658 | +@article{woosleyTGFvPromotesBreast2019, |
|
| 11659 | + title = {{{TGFβ}} Promotes Breast Cancer Stem Cell Self-Renewal through an {{ILEI}}/{{LIFR}} Signaling Axis}, |
|
| 11660 | + author = {Woosley, Alec N. and Dalton, Annamarie C. and Hussey, George S. and Howley, Breege V. and Mohanty, Bidyut K. and Grelet, Simon and Dincman, Toros and Bloos, Sean and Olsen, Shaun K. and Howe, Philip H.}, |
|
| 11661 | + date = {2019-05}, |
|
| 11662 | + journaltitle = {Oncogene}, |
|
| 11663 | + shortjournal = {Oncogene}, |
|
| 11664 | + volume = {38}, |
|
| 11665 | + number = {20}, |
|
| 11666 | + eprint = {30692635}, |
|
| 11667 | + eprinttype = {pmid}, |
|
| 11668 | + pages = {3794--3811}, |
|
| 11669 | + issn = {0950-9232}, |
|
| 11670 | + doi = {10.1038/s41388-019-0703-z}, |
|
| 11671 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6525020/}, |
|
| 11672 | + urldate = {2022-09-25}, |
|
| 11673 | + abstract = {FAM3C/Interleukin-like EMT Inducer (ILEI) is an oncogenic member of the FAM3 cytokine family and serves essential roles in both epithelial-mesenchymal transition (EMT) and breast cancer metastasis. ILEI expression levels are regulated through a non-canonical TGFβ signaling pathway by 3’-UTR-mediated translational silencing at the mRNA level by hnRNP E1. TGFβ stimulation or silencing of hnRNP E1 increases ILEI translation and induces an EMT program that correlates to enhanced invasion and migration. Recently, EMT has been linked to the formation of breast cancer stem cells (BCSCs) that confer both tumor cell heterogeneity as well as chemoresistant properties. Herein, we demonstrate that hnRNP E1 knockdown significantly shifts normal mammary epithelial cells to mesenchymal BCSCs in vitro and in vivo. We further validate that modulating ILEI protein levels results in the abrogation of these phenotypes, promoting further investigation into the unknown mechanism of ILEI signaling that drives tumor progression. We identify LIFR as the receptor for ILEI, which mediates signaling through STAT3 to drive both EMT and BCSC formation. Reduction of either ILEI or LIFR protein levels results in reduced tumor growth, fewer tumor initiating cells and reduced metastasis within the hnRNP E1 knock-down cell populations in vivo. These results reveal a novel ligand-receptor complex that drives the formation of BCSCs and represents a unique target for the development of metastatic breast cancer therapies.}, |
|
| 11674 | + pmcid = {PMC6525020}, |
|
| 11675 | + file = {/Users/rmorin/Zotero/storage/D7NIHWYL/Woosley et al. - 2019 - TGFβ promotes breast cancer stem cell self-renewal.pdf} |
|
| 11676 | +} |
|
| 11677 | + |
|
| 11678 | +@article{wrightGeneExpressionbasedMethod2003, |
|
| 11679 | + title = {A Gene Expression-Based Method to Diagnose Clinically Distinct Subgroups of Diffuse Large {{B}} Cell Lymphoma}, |
|
| 11680 | + author = {Wright, George and Tan, Bruce and Rosenwald, Andreas and Hurt, Elaine H. and Wiestner, Adrian and Staudt, Louis M.}, |
|
| 11681 | + date = {2003-08-19}, |
|
| 11682 | + journaltitle = {Proceedings of the National Academy of Sciences}, |
|
| 11683 | + shortjournal = {Proc. Natl. Acad. Sci.}, |
|
| 11684 | + volume = {100}, |
|
| 11685 | + number = {17}, |
|
| 11686 | + eprint = {12900505}, |
|
| 11687 | + eprinttype = {pmid}, |
|
| 11688 | + pages = {9991--9996}, |
|
| 11689 | + issn = {0027-8424, 1091-6490}, |
|
| 11690 | + doi = {10.1073/pnas.1732008100}, |
|
| 11691 | + url = {https://www.pnas.org/content/100/17/9991}, |
|
| 11692 | + urldate = {2020-01-24}, |
|
| 11693 | + abstract = {To classify cancer specimens by their gene expression profiles, we created a statistical method based on Bayes' rule that estimates the probability of membership in one of two cancer subgroups. We used this method to classify diffuse large B cell lymphoma (DLBCL) biopsy samples into two gene expression subgroups based on data obtained from spotted cDNA microarrays. The germinal center B cell-like (GCB) DLBCL subgroup expressed genes characteristic of normal germinal center B cells whereas the activated B cell-like (ABC) DLBCL subgroup expressed a subset of the genes that are characteristic of plasma cells, particularly those encoding endoplasmic reticulum and golgi proteins involved in secretion. We next used this predictor to discover these subgroups within a second set of DLBCL biopsies that had been profiled by using oligonucleotide microarrays [Shipp, M. A., et al. (2002) Nat. Med. 8, 68–74]. The GCB and ABC DLBCL subgroups identified in this data set had significantly different 5-yr survival rates after multiagent chemotherapy (62\% vs. 26\%; P ≤ 0.0051), in accord with analyses of other DLBCL cohorts. These results demonstrate the ability of this gene expression-based predictor to classify DLBCLs into biologically and clinically distinct subgroups irrespective of the method used to measure gene expression.}, |
|
| 11694 | + langid = {english}, |
|
| 11695 | + keywords = {Bayesian predictor,gene expression profile,microarray}, |
|
| 11696 | + file = {/Users/rmorin/Zotero/storage/MDJTVHHH/wright2003.pdf;/Users/rmorin/Zotero/storage/6HDXKRLA/9991.html} |
|
| 11697 | +} |
|
| 11698 | + |
|
| 11699 | +@article{wrightProbabilisticClassificationTool2020, |
|
| 11700 | + title = {A {{Probabilistic Classification Tool}} for {{Genetic Subtypes}} of {{Diffuse Large B Cell Lymphoma}} with {{Therapeutic Implications}}}, |
|
| 11701 | + author = {Wright, George W. and Huang, Da Wei and Phelan, James D. and Coulibaly, Zana A. and Roulland, Sandrine and Young, Ryan M. and Wang, James Q. and Schmitz, Roland and Morin, Ryan D. and Tang, Jeffrey and Jiang, Aixiang and Bagaev, Aleksander and Plotnikova, Olga and Kotlov, Nikita and Johnson, Calvin A. and Wilson, Wyndham H. and Scott, David W. and Staudt, Louis M.}, |
|
| 11702 | + date = {2020-04-13}, |
|
| 11703 | + journaltitle = {Cancer Cell}, |
|
| 11704 | + shortjournal = {Cancer Cell}, |
|
| 11705 | + volume = {37}, |
|
| 11706 | + number = {4}, |
|
| 11707 | + eprint = {32289277}, |
|
| 11708 | + eprinttype = {pmid}, |
|
| 11709 | + pages = {551-568.e14}, |
|
| 11710 | + issn = {1878-3686}, |
|
| 11711 | + doi = {10.1016/j.ccell.2020.03.015}, |
|
| 11712 | + abstract = {The development of precision medicine approaches for diffuse large B cell lymphoma (DLBCL) is confounded by its pronounced genetic, phenotypic, and clinical heterogeneity. Recent multiplatform genomic studies revealed the existence of genetic subtypes of DLBCL using clustering methodologies. Here, we describe an algorithm that determines the probability that a patient's lymphoma belongs to one of seven genetic subtypes based on its genetic features. This classification reveals genetic similarities between these DLBCL subtypes and various indolent and extranodal lymphoma types, suggesting a shared pathogenesis. These genetic subtypes also have distinct gene expression profiles, immune microenvironments, and outcomes following immunochemotherapy. Functional analysis of genetic subtype models highlights distinct vulnerabilities to targeted therapy, supporting the use of this classification in precision medicine trials.}, |
|
| 11713 | + langid = {english}, |
|
| 11714 | + keywords = {A53,BN2,DLBCL,EZB,genomic classification,LymphGen,lymphoma,MCD,N1,naive Bayes,ST2}, |
|
| 11715 | + file = {/Users/rmorin/Zotero/storage/NPL4RCDS/10.1016@j.ccell.2020.03.015.pdf} |
|
| 11716 | +} |
|
| 11717 | + |
|
| 11718 | +@article{wuGeneticHeterogeneityPrimary2016, |
|
| 11719 | + title = {Genetic Heterogeneity in Primary and Relapsed Mantle Cell Lymphomas: {{Impact}} of Recurrent {{CARD11}} Mutations}, |
|
| 11720 | + shorttitle = {Genetic Heterogeneity in Primary and Relapsed Mantle Cell Lymphomas}, |
|
| 11721 | + author = {Wu, Chenglin and family=Miranda, given=Noel Fcc, prefix=de, useprefix=true and Chen, Longyun and Wasik, Agata M. and Mansouri, Larry and Jurczak, Wojciech and Galazka, Krystyna and Dlugosz-Danecka, Monika and Machaczka, Maciej and Zhang, Huilai and Peng, Roujun and Morin, Ryan D. and Rosenquist, Richard and Sander, Birgitta and Pan-Hammarström, Qiang}, |
|
| 11722 | + date = {2016-06-21}, |
|
| 11723 | + journaltitle = {Oncotarget}, |
|
| 11724 | + shortjournal = {Oncotarget}, |
|
| 11725 | + volume = {7}, |
|
| 11726 | + number = {25}, |
|
| 11727 | + eprint = {27224912}, |
|
| 11728 | + eprinttype = {pmid}, |
|
| 11729 | + pages = {38180--38190}, |
|
| 11730 | + issn = {1949-2553}, |
|
| 11731 | + doi = {10.18632/oncotarget.9500}, |
|
| 11732 | + abstract = {The genetic mechanisms underlying disease progression, relapse and therapy resistance in mantle cell lymphoma (MCL) remain largely unknown. Whole-exome sequencing was performed in 27 MCL samples from 13 patients, representing the largest analyzed series of consecutive biopsies obtained at diagnosis and/or relapse for this type of lymphoma. Eighteen genes were found to be recurrently mutated in these samples, including known (ATM, MEF2B and MLL2) and novel mutation targets (S1PR1 and CARD11). CARD11, a scaffold protein required for B-cell receptor (BCR)-induced NF-κB activation, was subsequently screened in an additional 173 MCL samples and mutations were observed in 5.5\% of cases. Based on in vitro cell line-based experiments, overexpression of CARD11 mutants were demonstrated to confer resistance to the BCR-inhibitor ibrutinib and NF-κB-inhibitor lenalidomide. Genetic alterations acquired in the relapse samples were found to be largely non-recurrent, in line with the branched evolutionary pattern of clonal evolution observed in most cases. In summary, this study highlights the genetic heterogeneity in MCL, in particular at relapse, and provides for the first time genetic evidence of BCR/NF-κB activation in a subset of MCL.}, |
|
| 11733 | + langid = {english}, |
|
| 11734 | + pmcid = {PMC5122381}, |
|
| 11735 | + keywords = {CARD Signaling Adaptor Proteins,CARD11,Drug Resistance Neoplasm,Genetic Heterogeneity,Guanylate Cyclase,Humans,Lenalidomide,Lymphoma Mantle-Cell,mantle cell lymphoma,Mutation,NF-kappa B,NF-κB inhibitor,Pyrazoles,Pyrimidines,Recurrence,relapse,Signal Transduction,Thalidomide,Transfection,whole-exome sequencing} |
|
| 11736 | +} |
|
| 11737 | + |
|
| 11738 | +@article{wuMolecularBasisSpecific2018, |
|
| 11739 | + title = {Molecular Basis for the Specific and Multivariant Recognitions of {{RNA}} Substrates by Human {{hnRNP A2}}/{{B1}}}, |
|
| 11740 | + author = {Wu, Baixing and Su, Shichen and Patil, Deepak P. and Liu, Hehua and Gan, Jianhua and Jaffrey, Samie R. and Ma, Jinbiao}, |
|
| 11741 | + date = {2018-01-29}, |
|
| 11742 | + journaltitle = {Nature Communications}, |
|
| 11743 | + shortjournal = {Nat Commun}, |
|
| 11744 | + volume = {9}, |
|
| 11745 | + number = {1}, |
|
| 11746 | + pages = {420}, |
|
| 11747 | + publisher = {Nature Publishing Group}, |
|
| 11748 | + issn = {2041-1723}, |
|
| 11749 | + doi = {10.1038/s41467-017-02770-z}, |
|
| 11750 | + url = {https://www.nature.com/articles/s41467-017-02770-z}, |
|
| 11751 | + urldate = {2022-10-04}, |
|
| 11752 | + abstract = {Human hnRNP A2/B1 is an RNA-binding protein that plays important roles in many biological processes, including maturation, transport, and metabolism of mRNA, and gene regulation of long noncoding RNAs. hnRNP A2/B1 was reported to control the microRNAs sorting to exosomes and promote primary microRNA processing as a potential m6A “reader.” hnRNP A2/B1 contains two RNA recognition motifs that provide sequence-specific recognition of RNA substrates. Here, we determine crystal structures of tandem RRM domains of hnRNP A2/B1 in complex with various RNA substrates, elucidating specific recognitions of AGG and UAG motifs by RRM1 and RRM2 domains, respectively. Further structural and biochemical results demonstrate multivariant binding modes for sequence-diversified RNA substrates, supporting a RNA matchmaker mechanism in hnRNP A2/B1 function. Moreover, our studies in combination with bioinformatic analysis suggest that hnRNP A2/B1 may mediate effects of m6A through a “m6A switch” mechanism, instead of acting as a direct “reader” of m6A modification.}, |
|
| 11753 | + issue = {1}, |
|
| 11754 | + langid = {english}, |
|
| 11755 | + keywords = {RNA modification,RNA-binding proteins,X-ray crystallography}, |
|
| 11756 | + file = {/Users/rmorin/Zotero/storage/QSLCY3QZ/Wu et al. - 2018 - Molecular basis for the specific and multivariant .pdf;/Users/rmorin/Zotero/storage/26E4PWTA/s41467-017-02770-z.html} |
|
| 11757 | +} |
|
| 11758 | + |
|
| 11759 | +@article{wursterNusinersenSpinalMuscular2018, |
|
| 11760 | + title = {Nusinersen for Spinal Muscular Atrophy}, |
|
| 11761 | + author = {Wurster, Claudia D. and Ludolph, Albert C.}, |
|
| 11762 | + date = {2018-03-13}, |
|
| 11763 | + journaltitle = {Therapeutic Advances in Neurological Disorders}, |
|
| 11764 | + shortjournal = {Ther Adv Neurol Disord}, |
|
| 11765 | + volume = {11}, |
|
| 11766 | + eprint = {29568328}, |
|
| 11767 | + eprinttype = {pmid}, |
|
| 11768 | + issn = {1756-2856}, |
|
| 11769 | + doi = {10.1177/1756285618754459}, |
|
| 11770 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5858681/}, |
|
| 11771 | + urldate = {2020-09-22}, |
|
| 11772 | + pmcid = {PMC5858681}, |
|
| 11773 | + file = {/Users/rmorin/Zotero/storage/XHWYKBPX/Wurster and Ludolph - 2018 - Nusinersen for spinal muscular atrophy.pdf} |
|
| 11774 | +} |
|
| 11775 | + |
|
| 11776 | +@article{xieIdentificationIndividualizedRNA2021, |
|
| 11777 | + title = {Identification of an Individualized {{RNA}} Binding Protein‐based Prognostic Signature for Diffuse Large {{B}}‐cell Lymphoma}, |
|
| 11778 | + author = {Xie, Yongzhi and Luo, Ximei and He, Haiqing and Pan, Tao and He, Yizi}, |
|
| 11779 | + date = {2021-03-21}, |
|
| 11780 | + journaltitle = {Cancer Medicine}, |
|
| 11781 | + shortjournal = {Cancer Med}, |
|
| 11782 | + volume = {10}, |
|
| 11783 | + number = {8}, |
|
| 11784 | + eprint = {33749163}, |
|
| 11785 | + eprinttype = {pmid}, |
|
| 11786 | + pages = {2703--2713}, |
|
| 11787 | + issn = {2045-7634}, |
|
| 11788 | + doi = {10.1002/cam4.3859}, |
|
| 11789 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8026940/}, |
|
| 11790 | + urldate = {2022-10-04}, |
|
| 11791 | + abstract = {RNA binding proteins (RBPs) are increasingly appreciated as being essential for normal hematopoiesis and have a critical role in the progression of hematological malignancies. However, their functional consequences and clinical significance in diffuse large B‐cell lymphoma (DLBCL) remain unknown. Here, we conducted a systematic analysis to identify RBP‐related genes affecting DLBCL prognosis based on the Gene Expression Omnibus database. By univariate and multivariate Cox proportional hazards regression (CPHR) methods, six RBPs‐related genes (CMSS1, MAEL, THOC5, PSIP1, SNIP1, and ZCCHC7) were identified closely related to the overall survival (OS) of DLBCL patients. The RBPs signature could efficiently distinguished low‐risk from high‐risk patients and could serve as an independent and reliable factor for predicting OS. Moreover, Gene Set Enrichment Analysis revealed 17 significantly enriched pathways between high‐ versus low‐risk group, including the regulation of autophagy, chronic myeloid leukemia, NOTCH signaling pathway, and B cell receptor signaling pathway. Then we developed an RBP‐based nomogram combining other clinical risk factors. The receiver operating characteristic curve analysis demonstrated high prognostic predictive efficiency of this model with the area under the curve values were 0.820 and 0.780, respectively, in the primary set and entire set. In summary, our RBP‐based model could be a novel prognostic predictor and had the potential for developing treatment targets for DLBCL., We found that six RNA binding proteins are significantly related to the overall survival of diffuse large B‐cell lymphoma (DLBCL) patients, which could potentially be served as prognostic biomarkers. Gene Set Enrichment Analysis provided insight into the underlying mechanisms in the occurrence and development of DLBCL, which laid the foundation for further basic studies.}, |
|
| 11792 | + pmcid = {PMC8026940}, |
|
| 11793 | + keywords = {diffuse large B-cell lymphoma,GEO,prognosis,prognostic model,RNA-binding proteins}, |
|
| 11794 | + file = {/Users/rmorin/Zotero/storage/KPYVTUPW/Xie et al. - 2021 - Identification of an individualized RNA binding pr.pdf;/Users/rmorin/Zotero/storage/VR37JA47/Xie et al. - 2021 - Identification of an individualized RNA binding pr.pdf} |
|
| 11795 | +} |
|
| 11796 | + |
|
| 11797 | +@article{xu-monetteP63ExpressionConfers2016, |
|
| 11798 | + title = {P63 Expression Confers Significantly Better Survival Outcomes in High-Risk Diffuse Large {{B-cell}} Lymphoma and Demonstrates P53-like and P53-Independent Tumor Suppressor Function.}, |
|
| 11799 | + author = {Xu-Monette, Zijun Y and Zhang, Shanxiang and Li, Xin and Manyam, Ganiraju C and Wang, Xiao-Xiao and Xia, Yi and Visco, Carlo and Tzankov, Alexandar and Zhang, Li and Montes-Moreno, Santiago and Dybkaer, Karen and Chiu, April and Orazi, Attilio and Zu, Youli and Bhagat, Govind and Richards, Kristy L and Hsi, Eric D and Choi, William W L and family=Krieken, given=J Han, prefix=van, useprefix=true and Huh, Jooryung and Ponzoni, Maurilio and Ferreri, Andrés J M and Zhao, Xiaoying and Møller, Michael B and Parsons, Ben M and Winter, Jane N and Piris, Miguel A and Medeiros, L Jeffrey and Young, Ken H}, |
|
| 11800 | + date = {2016-02}, |
|
| 11801 | + journaltitle = {Aging}, |
|
| 11802 | + volume = {8}, |
|
| 11803 | + number = {2}, |
|
| 11804 | + pages = {345--365}, |
|
| 11805 | + keywords = {nosource} |
|
| 11806 | +} |
|
| 11807 | + |
|
| 11808 | +@article{xuHnRNPAssociateHTERC2019, |
|
| 11809 | + title = {{{HnRNP F}}/{{H}} Associate with {{hTERC}} and Telomerase Holoenzyme to Modulate Telomerase Function and Promote Cell Proliferation}, |
|
| 11810 | + author = {Xu, Chenzhong and Xie, Nan and Su, Yuanyuan and Sun, Zhaomeng and Liang, Yao and Zhang, Na and Liu, Doudou and Jia, Shuqin and Xing, Xiaofang and Han, Limin and Li, Guodong and Tong, Tanjun and Chen, Jun}, |
|
| 11811 | + date = {2019-12-20}, |
|
| 11812 | + journaltitle = {Cell Death and Differentiation}, |
|
| 11813 | + shortjournal = {Cell Death Differ.}, |
|
| 11814 | + eprint = {31863069}, |
|
| 11815 | + eprinttype = {pmid}, |
|
| 11816 | + issn = {1476-5403}, |
|
| 11817 | + doi = {10.1038/s41418-019-0483-6}, |
|
| 11818 | + abstract = {Human telomerase RNA component hTERC comprises multiple motifs that contribute to hTERC biogenesis, holoenzyme activity, and enzyme recruitment to telomeres. hTERC contains several guanine tracts (G-tracts) at its 5'-end, but its associated proteins and potential roles in telomerase function are still poorly understood. The heterogeneous nuclear ribonucleoproteins F, H1, and H2 (hnRNP F/H) are splicing factors that preferentially bind to poly(G)-rich sequences RNA. Here, we demonstrate that hnRNP F/H associate with both hTERC and telomerase holoenzyme to regulate telomerase activity. We reveal hnRNP F/H bind to the 5'-end region of hTERC in vitro and in vivo, and identify the first three G-tracts of hTERC and qRRM1 domain of hnRNP F/H are required for their interaction. Furthermore, hnRNP F/H also directly interact with telomerase holoenzyme. Functionally, we show that hnRNP F/H plays important roles in modulating telomerase activity and telomere length. Moreover, hnRNP F/H deletion greatly impair cancer and stem cell proliferation, and induce stem cell senescence, while hnRNP F/H overexpression delay stem cell senescence. Collectively, our findings unveil a novel role of hnRNP F/H as the binding partners of hTERC and telomerase holoenzyme to regulate telomerase function.}, |
|
| 11819 | + langid = {english} |
|
| 11820 | +} |
|
| 11821 | + |
|
| 11822 | +@article{xuLossIRF8Inhibits2015, |
|
| 11823 | + title = {Loss of {{IRF8 Inhibits}} the {{Growth}} of {{Diffuse Large B-cell Lymphoma}}}, |
|
| 11824 | + author = {Xu, Yulian and Jiang, Lei and Fang, Jianchen and Fang, Rong and Morse, Herbert C and Ouyang, Guifang and Zhou, Jeff X}, |
|
| 11825 | + date = {2015-08}, |
|
| 11826 | + journaltitle = {Journal of Cancer}, |
|
| 11827 | + volume = {6}, |
|
| 11828 | + number = {10}, |
|
| 11829 | + pages = {953--961}, |
|
| 11830 | + keywords = {nosource} |
|
| 11831 | +} |
|
| 11832 | + |
|
| 11833 | +@article{xuParallelComparisonIllumina2013, |
|
| 11834 | + title = {Parallel Comparison of {{Illumina RNA-Seq}} and {{Affymetrix}} Microarray Platforms on Transcriptomic Profiles Generated from 5-Aza-Deoxy-Cytidine Treated {{HT-29}} Colon Cancer Cells and Simulated Datasets}, |
|
| 11835 | + author = {Xu, Xiao and Zhang, Yuanhao and Williams, Jennie and Antoniou, Eric and McCombie, W. Richard and Wu, Song and Zhu, Wei and Davidson, Nicholas O. and Denoya, Paula and Li, Ellen}, |
|
| 11836 | + date = {2013}, |
|
| 11837 | + journaltitle = {BMC bioinformatics}, |
|
| 11838 | + shortjournal = {BMC Bioinformatics}, |
|
| 11839 | + volume = {14 Suppl 9}, |
|
| 11840 | + eprint = {23902433}, |
|
| 11841 | + eprinttype = {pmid}, |
|
| 11842 | + pages = {S1}, |
|
| 11843 | + issn = {1471-2105}, |
|
| 11844 | + doi = {10.1186/1471-2105-14-S9-S1}, |
|
| 11845 | + abstract = {BACKGROUND: High throughput parallel sequencing, RNA-Seq, has recently emerged as an appealing alternative to microarray in identifying differentially expressed genes (DEG) between biological groups. However, there still exists considerable discrepancy on gene expression measurements and DEG results between the two platforms. The objective of this study was to compare parallel paired-end RNA-Seq and microarray data generated on 5-azadeoxy-cytidine (5-Aza) treated HT-29 colon cancer cells with an additional simulation study. METHODS: We first performed general correlation analysis comparing gene expression profiles on both platforms. An Errors-In-Variables (EIV) regression model was subsequently applied to assess proportional and fixed biases between the two technologies. Then several existing algorithms, designed for DEG identification in RNA-Seq and microarray data, were applied to compare the cross-platform overlaps with respect to DEG lists, which were further validated using qRT-PCR assays on selected genes. Functional analyses were subsequently conducted using Ingenuity Pathway Analysis (IPA). RESULTS: Pearson and Spearman correlation coefficients between the RNA-Seq and microarray data each exceeded 0.80, with 66\%\textasciitilde 68\% overlap of genes on both platforms. The EIV regression model indicated the existence of both fixed and proportional biases between the two platforms. The DESeq and baySeq algorithms (RNA-Seq) and the SAM and eBayes algorithms (microarray) achieved the highest cross-platform overlap rate in DEG results from both experimental and simulated datasets. DESeq method exhibited a better control on the false discovery rate than baySeq on the simulated dataset although it performed slightly inferior to baySeq in the sensitivity test. RNA-Seq and qRT-PCR, but not microarray data, confirmed the expected reversal of SPARC gene suppression after treating HT-29 cells with 5-Aza. Thirty-three IPA canonical pathways were identified by both microarray and RNA-Seq data, 152 pathways by RNA-Seq data only, and none by microarray data only. CONCLUSIONS: These results suggest that RNA-Seq has advantages over microarray in identification of DEGs with the most consistent results generated from DESeq and SAM methods. The EIV regression model reveals both fixed and proportional biases between RNA-Seq and microarray. This may explain in part the lower cross-platform overlap in DEG lists compared to those in detectable genes.}, |
|
| 11846 | + langid = {english}, |
|
| 11847 | + pmcid = {PMC3697991}, |
|
| 11848 | + keywords = {Algorithms,Azacitidine,Colonic Neoplasms,Gene Expression Profiling,HT29 Cells,Humans,Oligonucleotide Array Sequence Analysis,Regression Analysis,RNA Neoplasm,Sensitivity and Specificity,Sequence Analysis RNA}, |
|
| 11849 | + file = {/Users/rmorin/Zotero/storage/Y3IGAYB6/Xu et al. - 2013 - Parallel comparison of Illumina RNA-Seq and Affyme.pdf} |
|
| 11850 | +} |
|
| 11851 | + |
|
| 11852 | +@article{yadaPhosphorylationdependentDegradationCMyc2004, |
|
| 11853 | + title = {Phosphorylation-Dependent Degradation of c-{{Myc}} Is Mediated by the {{F-box}} Protein {{Fbw7}}}, |
|
| 11854 | + author = {Yada, Masayoshi and Hatakeyama, Shigetsugu and Kamura, Takumi and Nishiyama, Masaaki and Tsunematsu, Ryosuke and Imaki, Hiroyuki and Ishida, Noriko and Okumura, Fumihiko and Nakayama, Keiko and Nakayama, Keiichi I.}, |
|
| 11855 | + date = {2004-05-19}, |
|
| 11856 | + journaltitle = {The EMBO journal}, |
|
| 11857 | + shortjournal = {EMBO J}, |
|
| 11858 | + volume = {23}, |
|
| 11859 | + number = {10}, |
|
| 11860 | + eprint = {15103331}, |
|
| 11861 | + eprinttype = {pmid}, |
|
| 11862 | + pages = {2116--2125}, |
|
| 11863 | + issn = {0261-4189}, |
|
| 11864 | + doi = {10.1038/sj.emboj.7600217}, |
|
| 11865 | + abstract = {The F-box protein Skp2 mediates c-Myc ubiquitylation by binding to the MB2 domain. However, the turnover of c-Myc is largely dependent on phosphorylation of threonine-58 and serine-62 in MB1, residues that are often mutated in cancer. We now show that the F-box protein Fbw7 interacts with and thereby destabilizes c-Myc in a manner dependent on phosphorylation of MB1. Whereas wild-type Fbw7 promoted c-Myc turnover in cells, an Fbw7 mutant lacking the F-box domain delayed it. Furthermore, depletion of Fbw7 by RNA interference increased both the abundance and transactivation activity of c-Myc. Accumulation of c-Myc was also apparent in mouse Fbw7-/- embryonic stem cells. These observations suggest that two F-box proteins, Fbw7 and Skp2, differentially regulate c-Myc stability by targeting MB1 and MB2, respectively.}, |
|
| 11866 | + langid = {english}, |
|
| 11867 | + pmcid = {PMC424394}, |
|
| 11868 | + keywords = {Animals,Cell Cycle Proteins,Cells Cultured,Cyclin E,F-Box Proteins,F-Box-WD Repeat-Containing Protein 7,Humans,Ligases,Mice,Mice Knockout,Peptides,Phosphorylation,Proto-Oncogene Proteins c-myc,Recombinant Proteins,RNA Interference,S-Phase Kinase-Associated Proteins,Serine,Stem Cells,Threonine,Transcriptional Activation,Ubiquitin,Ubiquitin-Protein Ligases}, |
|
| 11869 | + file = {/Users/rmorin/Zotero/storage/HF8IR6FT/Yada et al. - 2004 - Phosphorylation-dependent degradation of c-Myc is .pdf} |
|
| 11870 | +} |
|
| 11871 | + |
|
| 11872 | +@article{yamamotoRegulationTollIL1receptormediated2004, |
|
| 11873 | + title = {Regulation of {{Toll}}/{{IL-1-receptor-mediated}} Gene Expression by the Inducible Nuclear Protein {{IkappaBzeta}}}, |
|
| 11874 | + author = {Yamamoto, Masahiro and Yamazaki, Soh and Uematsu, Satoshi and Sato, Shintaro and Hemmi, Hiroaki and Hoshino, Katsuaki and Kaisho, Tsuneyasu and Kuwata, Hirotaka and Takeuchi, Osamu and Takeshige, Koichiro and Saitoh, Tatsuya and Yamaoka, Shoji and Yamamoto, Naoki and Yamamoto, Shunsuke and Muta, Tatsushi and Takeda, Kiyoshi and Akira, Shizuo}, |
|
| 11875 | + date = {2004-07-08}, |
|
| 11876 | + journaltitle = {Nature}, |
|
| 11877 | + shortjournal = {Nature}, |
|
| 11878 | + volume = {430}, |
|
| 11879 | + number = {6996}, |
|
| 11880 | + eprint = {15241416}, |
|
| 11881 | + eprinttype = {pmid}, |
|
| 11882 | + pages = {218--222}, |
|
| 11883 | + issn = {1476-4687}, |
|
| 11884 | + doi = {10.1038/nature02738}, |
|
| 11885 | + abstract = {Toll-like receptors (TLRs) recognize microbial components and trigger the inflammatory and immune responses against pathogens. IkappaBzeta (also known as MAIL and INAP) is an ankyrin-repeat-containing nuclear protein that is highly homologous to the IkappaB family member Bcl-3 (refs 1-6). Transcription of IkappaBzeta is rapidly induced by stimulation with TLR ligands and interleukin-1 (IL-1). Here we show that IkappaBzeta is indispensable for the expression of a subset of genes activated in TLR/IL-1R signalling pathways. IkappaBzeta-deficient cells show severe impairment of IL-6 production in response to a variety of TLR ligands as well as IL-1, but not in response to tumour-necrosis factor-alpha. Endogenous IkappaBzeta specifically associates with the p50 subunit of NF-kappaB, and is recruited to the NF-kappaB binding site of the IL-6 promoter on stimulation. Moreover, NF-kappaB1/p50-deficient mice show responses to TLR/IL-1R ligands similar to those of IkappaBzeta-deficient mice. Endotoxin-induced expression of other genes such as Il12b and Csf2 is also abrogated in IkappaBzeta-deficient macrophages. Given that the lipopolysaccharide-induced transcription of IkappaBzeta occurs earlier than transcription of these genes, some TLR/IL-1R-mediated responses may be regulated in a gene expression process of at least two steps that requires inducible IkappaBzeta.}, |
|
| 11886 | + langid = {english}, |
|
| 11887 | + keywords = {Adaptor Proteins Signal Transducing,Animals,Gene Expression Regulation,Interleukin-12,Interleukin-6,Kinetics,Ligands,Lipopolysaccharides,Membrane Glycoproteins,Mice,Mice Knockout,NF-kappa B,NF-kappa B p50 Subunit,Nuclear Proteins,Promoter Regions Genetic,Receptors Cell Surface,Receptors Interleukin-1,Response Elements,Signal Transduction,Toll-Like Receptors,Tumor Necrosis Factor-alpha,Up-Regulation} |
|
| 11888 | +} |
|
| 11889 | + |
|
| 11890 | +@article{yamamotoRoleNuclearIkB2008, |
|
| 11891 | + title = {Role of Nuclear {{IκB}} Proteins in the Regulation of Host Immune Responses}, |
|
| 11892 | + author = {Yamamoto, Masahiro and Takeda, Kiyoshi}, |
|
| 11893 | + date = {2008}, |
|
| 11894 | + journaltitle = {Journal of Infection and Chemotherapy}, |
|
| 11895 | + volume = {14}, |
|
| 11896 | + number = {4}, |
|
| 11897 | + pages = {265--269}, |
|
| 11898 | + keywords = {nosource} |
|
| 11899 | +} |
|
| 11900 | + |
|
| 11901 | +@article{yamazakiNovelIkBProtein2001, |
|
| 11902 | + title = {A {{Novel IκB Protein}}, {{IκB-ζ}}, {{Induced}} by {{Proinflammatory Stimuli}}, {{Negatively Regulates Nuclear Factor-κB}} in the {{Nuclei}}}, |
|
| 11903 | + author = {Yamazaki, Soh and Muta, Tatsushi and Takeshige, Koichiro}, |
|
| 11904 | + date = {2001-07-20}, |
|
| 11905 | + journaltitle = {Journal of Biological Chemistry}, |
|
| 11906 | + shortjournal = {J. Biol. Chem.}, |
|
| 11907 | + volume = {276}, |
|
| 11908 | + number = {29}, |
|
| 11909 | + eprint = {11356851}, |
|
| 11910 | + eprinttype = {pmid}, |
|
| 11911 | + pages = {27657--27662}, |
|
| 11912 | + issn = {0021-9258, 1083-351X}, |
|
| 11913 | + doi = {10.1074/jbc.M103426200}, |
|
| 11914 | + url = {http://www.jbc.org/content/276/29/27657}, |
|
| 11915 | + urldate = {2018-09-02}, |
|
| 11916 | + abstract = {The transcription factor nuclear factor-κB (NF-κB) plays crucial roles in a wide variety of cellular functions and its activity is strictly regulated by cytosolic inhibitors known as IκBs. We here report a new member of the IκB protein family, IκB-ζ, harboring six ankyrin repeats at its carboxyl terminus. IκB-ζ mRNA is strongly induced after stimulation by lipopolysaccharide. The induction of IκB-ζ is also observed by stimulation with interleukin-1β but not by tumor necrosis factor-α. In contrast to cytosolic IκB-α, -β, and -ε, the induced IκB-ζ localizes in the nucleus via its amino-terminal region, which shows no homology with other proteins. Transiently expressed IκB-ζ inhibits the NF-κB activity without affecting the nuclear translocation of NF-κB upon stimulation. The expressed IκB-ζ preferentially associates with the NF-κB subunit p50 rather than p65 and recombinant IκB-ζ proteins inhibit the DNA binding of the p65/p50 heterodimer and the p50/p50 homodimer. Thus, IκB-ζ negatively regulates NF-κB activity in the nucleus, possibly in order to prevent excessive inflammation. Moreover, transfection of IκB-ζ renders cells more susceptible to apoptosis induced by tumor necrosis factor-α. The proapoptotic activity of IκB-ζ further suggests that it might be one of key regulators for inflammation and other biologically relevant processes.}, |
|
| 11917 | + langid = {english}, |
|
| 11918 | + file = {/Users/rmorin/Zotero/storage/23D9ZQUW/27657.html} |
|
| 11919 | +} |
|
| 11920 | + |
|
| 11921 | +@article{yamazakiStimulusspecificInductionNovel2005, |
|
| 11922 | + title = {Stimulus-Specific Induction of a Novel Nuclear Factor-{{kappaB}} Regulator, {{IkappaB-zeta}}, via {{Toll}}/{{Interleukin-1}} Receptor Is Mediated by {{mRNA}} Stabilization.}, |
|
| 11923 | + author = {Yamazaki, Soh and Muta, Tatsushi and Matsuo, Susumu and Takeshige, Koichiro}, |
|
| 11924 | + date = {2005-01}, |
|
| 11925 | + journaltitle = {J Biol Chem}, |
|
| 11926 | + volume = {280}, |
|
| 11927 | + number = {2}, |
|
| 11928 | + pages = {1678--1687}, |
|
| 11929 | + keywords = {nosource} |
|
| 11930 | +} |
|
| 11931 | + |
|
| 11932 | +@article{yanBCRTLRSignaling2012a, |
|
| 11933 | + title = {{{BCR}} and {{TLR}} Signaling Pathways Are Recurrently Targeted by Genetic Changes in Splenic Marginal Zone Lymphomas}, |
|
| 11934 | + author = {Yan, Qingguo and Huang, Yuanxue and Watkins, A. James and Kocialkowski, Sylvia and Zeng, Naiyan and Hamoudi, Rifat A. and Isaacson, Peter G. and family=Leval, given=Laurence, prefix=de, useprefix=true and Wotherspoon, Andrew and Du, Ming-Qing}, |
|
| 11935 | + date = {2012-04}, |
|
| 11936 | + journaltitle = {Haematologica}, |
|
| 11937 | + shortjournal = {Haematologica}, |
|
| 11938 | + volume = {97}, |
|
| 11939 | + number = {4}, |
|
| 11940 | + eprint = {22102703}, |
|
| 11941 | + eprinttype = {pmid}, |
|
| 11942 | + pages = {595--598}, |
|
| 11943 | + issn = {1592-8721}, |
|
| 11944 | + doi = {10.3324/haematol.2011.054080}, |
|
| 11945 | + abstract = {The genetics and pathogenesis of splenic marginal zone lymphoma are poorly understood. The lymphoma lacks chromosome translocation, and approximately 30\% of cases are featured by 7q deletion, but the gene targeted by the deletion is unknown. A recent study showed inactivation of A20, a "global" NF-κB negative regulator, in 1 of 12 splenic marginal zone lymphomas. To investigate further whether deregulation of the NF-κB pathway plays a role in the pathogenesis of splenic marginal zone lymphoma, we screened several NF-κB regulators for genetic changes by PCR and sequencing. Somatic mutations were found in A20 (6/46=13\%), MYD88 (6/46=13\%), CARD11 (3/34=8.8\%), but not in CD79A, CD79B and ABIN1. Interestingly, these genetic changes are largely mutually exclusive from each other and MYD88 mutation was also mutually exclusive from 7q deletion. These results strongly suggest that deregulation of the TLR (toll like receptor) and BCR (B-cell receptor) signaling pathway may play an important role in the pathogenesis of splenic marginal zone lymphoma.}, |
|
| 11946 | + langid = {english}, |
|
| 11947 | + pmcid = {PMC3347666}, |
|
| 11948 | + keywords = {CARD Signaling Adaptor Proteins,Chromosome Deletion,Chromosomes Human Pair 7,DNA-Binding Proteins,Guanylate Cyclase,Humans,Intracellular Signaling Peptides and Proteins,Lymphoma B-Cell Marginal Zone,Mutation,Myeloid Differentiation Factor 88,Nuclear Proteins,Receptors Antigen B-Cell,Signal Transduction,Splenic Neoplasms,Toll-Like Receptors,Tumor Necrosis Factor alpha-Induced Protein 3,Tumor Suppressor Protein p53}, |
|
| 11949 | + file = {/Users/rmorin/Zotero/storage/NGCZ9TAP/Yan et al. - 2012 - BCR and TLR signaling pathways are recurrently tar.pdf} |
|
| 11950 | +} |
|
| 11951 | + |
|
| 11952 | +@article{yangDysregulationMiR212Promotes2016, |
|
| 11953 | + title = {Dysregulation of {{miR-212 Promotes Castration Resistance}} through {{hnRNPH1-Mediated Regulation}} of {{AR}} and {{AR-V7}}: {{Implications}} for {{Racial Disparity}} of {{Prostate Cancer}}}, |
|
| 11954 | + shorttitle = {Dysregulation of {{miR-212 Promotes Castration Resistance}} through {{hnRNPH1-Mediated Regulation}} of {{AR}} and {{AR-V7}}}, |
|
| 11955 | + author = {Yang, Yijun and Jia, Dingwu and Kim, Hogyoung and Abd Elmageed, Zakaria Y. and Datta, Amrita and Davis, Rodney and Srivastav, Sudesh and Moroz, Krzysztof and Crawford, Byron E. and Moparty, Krishnarao and Thomas, Raju and Hudson, Robert S. and Ambs, Stefan and Abdel-Mageed, Asim B.}, |
|
| 11956 | + date = {2016-03-31}, |
|
| 11957 | + journaltitle = {Clinical Cancer Research}, |
|
| 11958 | + shortjournal = {Clinical Cancer Research}, |
|
| 11959 | + volume = {22}, |
|
| 11960 | + number = {7}, |
|
| 11961 | + pages = {1744--1756}, |
|
| 11962 | + issn = {1078-0432}, |
|
| 11963 | + doi = {10.1158/1078-0432.CCR-15-1606}, |
|
| 11964 | + url = {https://doi.org/10.1158/1078-0432.CCR-15-1606}, |
|
| 11965 | + urldate = {2022-09-28}, |
|
| 11966 | + abstract = {Purpose: The causes of disproportionate incidence and mortality of prostate cancer among African Americans (AA) remain elusive. The purpose of this study was to investigate the mechanistic role and assess clinical utility of the splicing factor heterogeneous nuclear ribonucleoprotein H1 (hnRNP H1) in prostate cancer progression among AA men.Experimental Design: We employed an unbiased functional genomics approach coupled with suppressive subtractive hybridization (SSH) and custom cDNA microarrays to identify differentially expressed genes in microdissected tumors procured from age- and tumor grade–matched AA and Caucasian American (CA) men. Validation analysis was performed in independent cohorts and tissue microarrays. The underlying mechanisms of hnRNPH1 regulation and its impact on androgen receptor (AR) expression and tumor progression were explored.Results: Aberrant coexpression of AR and hnRNPH1 and downregulation of miR-212 were detected in prostate tumors and correlate with disease progression in AA men compared with CA men. Ectopic expression of miR-212 mimics downregulated hnRNPH1 transcripts, which in turn reduced expression of AR and its splice variant AR-V7 (or AR3) in prostate cancer cells. hnRNPH1 physically interacts with AR and steroid receptor coactivator-3 (SRC-3) and primes activation of androgen-regulated genes in a ligand-dependent and independent manner. siRNA silencing of hnRNPH1 sensitized prostate cancer cells to bicalutamide and inhibited prostate tumorigenesis in vivo.Conclusions: Our findings define novel roles for hnRNPH1 as a putative oncogene, splicing factor, and an auxiliary AR coregulator. Targeted disruption of the hnRNPH1-AR axis may have therapeutic implications to improve clinical outcomes in patients with advanced prostate cancer, especially among AA men. Clin Cancer Res; 22(7); 1744–56. ©2015 AACR.}, |
|
| 11967 | + file = {/Users/rmorin/Zotero/storage/H247WZ5W/Yang et al. - 2016 - Dysregulation of miR-212 Promotes Castration Resis.pdf;/Users/rmorin/Zotero/storage/S579FCQD/Dysregulation-of-miR-212-Promotes-Castration.html} |
|
| 11968 | +} |
|
| 11969 | + |
|
| 11970 | +@article{yangGenomicLandscapePrognostic2018, |
|
| 11971 | + title = {Genomic Landscape and Prognostic Analysis of Mantle Cell Lymphoma}, |
|
| 11972 | + author = {Yang, Ping and Zhang, Weilong and Wang, Jing and Liu, Yuanyuan and An, Ran and Jing, Hongmei}, |
|
| 11973 | + date = {2018-06}, |
|
| 11974 | + journaltitle = {Cancer Gene Therapy}, |
|
| 11975 | + shortjournal = {Cancer Gene Ther.}, |
|
| 11976 | + volume = {25}, |
|
| 11977 | + number = {5-6}, |
|
| 11978 | + eprint = {29755111}, |
|
| 11979 | + eprinttype = {pmid}, |
|
| 11980 | + pages = {129--140}, |
|
| 11981 | + issn = {1476-5500}, |
|
| 11982 | + doi = {10.1038/s41417-018-0022-5}, |
|
| 11983 | + abstract = {To gain insight into the molecular pathogenesis of patients with mantle cell lymphoma (MCL), next-generation whole-exome sequencing of 16 MCL patients was performed. We identified recurrent mutations in genes that are well known to be functionally relevant in MCL, including ATM (37.5\%), TP53 (31.3\%), WHSC1 (31.3\%), CCND1 (18.8\%), NOTCH2 (6.3\%), and CDKN2A (6.3\%). We also identified somatic mutations in genes for which a functional role in MCL has not been previously suspected. These genes included CCDC15, APC, CDH1, S1PR1, ATRX, BRCA2, CASP8, and NOTCH3. Further, we investigated the prognostic factors associated with MCL from clinical, pathological, and genetic mutations. Mutations of TP53 (P\,=\,0.021) was a significant prognostic factor with shorter overall survival (OS). Although there was no statistical difference, the median survival time of patients with WHSC1 mutations was shorter than those without mutations (P\,=\,0.070). Mutations in ATM and CCND1 had no prognostic value (P\,=\,0.552, 0.566). When adjusted for MCL International Prognostic Index (MIPI) or combined MCL-International Prognostic Index (MIPI-c), TP53 and WHSC1 mutations were the most important prognostic factors in MCL (P\,{$<$}\,0.05). Our data provide an unbiased view of the landscape of mutations in MCL and commend that all patients benefit from mutations of TP53 and WHSC1 at diagnosis, in addition to MIPI and MIPI-c score.}, |
|
| 11984 | + langid = {english}, |
|
| 11985 | + keywords = {Adult,Aged,Aged 80 and over,Disease-Free Survival,Female,Genome Human,Genome-Wide Association Study,Humans,Lymphoma Mantle-Cell,Male,Middle Aged,Mutation,Neoplasm Proteins,Survival Rate} |
|
| 11986 | +} |
|
| 11987 | + |
|
| 11988 | +@article{yangTyrosineKinaseInhibition, |
|
| 11989 | + title = {Tyrosine Kinase Inhibition in Diffuse Large {{B-cell}} Lymphoma: Molecular Basis for Antitumor Activity and Drug Resistance of Dasatinib}, |
|
| 11990 | + author = {Yang, C and Lu, P and Lee, F Y and Chadburn, A and Barrientos, J C and Leonard, J P and Ye, F and Zhang, D and Knowles, D M and Wang, Y L}, |
|
| 11991 | + journaltitle = {Leukemia}, |
|
| 11992 | + volume = {22}, |
|
| 11993 | + number = {9}, |
|
| 11994 | + pages = {1755--1766}, |
|
| 11995 | + keywords = {nosource} |
|
| 11996 | +} |
|
| 11997 | + |
|
| 11998 | +@article{yaoTCP1RingComplex2019, |
|
| 11999 | + title = {The {{TCP1}} Ring Complex Is Associated with Malignancy and Poor Prognosis in Hepatocellular Carcinoma.}, |
|
| 12000 | + author = {Yao, Liheng and Zou, X. and Liu, Li}, |
|
| 12001 | + date = {2019}, |
|
| 12002 | + journaltitle = {International journal of clinical and experimental pathology}, |
|
| 12003 | + volume = {12 9}, |
|
| 12004 | + pages = {3329--3343} |
|
| 12005 | +} |
|
| 12006 | + |
|
| 12007 | +@article{yeGenomewideMutationalSignatures2021, |
|
| 12008 | + title = {Genome-Wide Mutational Signatures Revealed Distinct Developmental Paths for Human {{B}} Cell Lymphomas}, |
|
| 12009 | + author = {Ye, Xiaofei and Ren, Weicheng and Liu, Dongbing and Li, Xiaobo and Li, Wei and Wang, Xianhuo and Meng, Fei-Long and Yeap, Leng-Siew and Hou, Yong and Zhu, Shida and Casellas, Rafael and Zhang, Huilai and Wu, Kui and Pan-Hammarström, Qiang}, |
|
| 12010 | + date = {2021-02-01}, |
|
| 12011 | + journaltitle = {The Journal of Experimental Medicine}, |
|
| 12012 | + shortjournal = {J Exp Med}, |
|
| 12013 | + volume = {218}, |
|
| 12014 | + number = {2}, |
|
| 12015 | + eprint = {33136155}, |
|
| 12016 | + eprinttype = {pmid}, |
|
| 12017 | + pages = {e20200573}, |
|
| 12018 | + issn = {1540-9538}, |
|
| 12019 | + doi = {10.1084/jem.20200573}, |
|
| 12020 | + abstract = {Both somatic hypermutation (SHM) and class switch recombination (CSR) are initiated by activation-induced cytidine deaminase (AID). Dysregulation of these processes has been linked to B cell lymphomagenesis. Here we performed an in-depth analysis of diffuse large B cell lymphoma (DLBCL) and follicular lymphoma (FL) genomes. We characterized seven genomic mutational signatures, including two B cell tumor-specific signatures, one of which is novel and associated with aberrant SHM. We further identified two major mutational signatures (K1 and K2) of clustered mutations (kataegis) resulting from the activities of AID or error-prone DNA polymerase η, respectively. K1 was associated with the immunoglobulin (Ig) switch region mutations/translocations and the ABC subtype of DLBCL, whereas K2 was related to the Ig variable region mutations and the GCB subtype of DLBCL and FL. Similar patterns were also observed in chronic lymphocytic leukemia subtypes. Thus, alterations associated with aberrant CSR and SHM activities can be linked to distinct developmental paths for different subtypes of B cell lymphomas.}, |
|
| 12021 | + langid = {english}, |
|
| 12022 | + pmcid = {PMC7608067}, |
|
| 12023 | + keywords = {B-Lymphocytes,Cell Line Tumor,Cytidine Deaminase,Female,Genome,Humans,Immunoglobulin Class Switching,Immunoglobulin Heavy Chains,Immunoglobulin Variable Region,Leukemia Lymphocytic Chronic B-Cell,Lymphoma Follicular,Lymphoma Large B-Cell Diffuse,Male,Middle Aged,Mutation,Somatic Hypermutation Immunoglobulin,Translocation Genetic}, |
|
| 12024 | + file = {/Users/rmorin/Zotero/storage/RZZKPPH2/Ye et al. - 2021 - Genome-wide mutational signatures revealed distinc.pdf} |
|
| 12025 | +} |
|
| 12026 | + |
|
| 12027 | +@article{yehFBXW7CriticalTumor2018, |
|
| 12028 | + title = {{{FBXW7}}: A Critical Tumor Suppressor of Human Cancers}, |
|
| 12029 | + shorttitle = {{{FBXW7}}}, |
|
| 12030 | + author = {Yeh, Chien-Hung and Bellon, Marcia and Nicot, Christophe}, |
|
| 12031 | + date = {2018-08-07}, |
|
| 12032 | + journaltitle = {Molecular Cancer}, |
|
| 12033 | + shortjournal = {Molecular Cancer}, |
|
| 12034 | + volume = {17}, |
|
| 12035 | + number = {1}, |
|
| 12036 | + pages = {115}, |
|
| 12037 | + issn = {1476-4598}, |
|
| 12038 | + doi = {10.1186/s12943-018-0857-2}, |
|
| 12039 | + url = {https://doi.org/10.1186/s12943-018-0857-2}, |
|
| 12040 | + urldate = {2021-08-25}, |
|
| 12041 | + abstract = {The ubiquitin-proteasome system (UPS) is involved in multiple aspects of cellular processes, such as cell cycle progression, cellular differentiation, and survival (Davis RJ et al., Cancer Cell 26:455-64, 2014; Skaar JR et al., Nat Rev Drug Discov 13:889-903, 2014; Nakayama KI and Nakayama K, Nat Rev Cancer 6:369-81, 2006). F-box and WD repeat domain containing 7 (FBXW7), also known as Sel10, hCDC4 or hAgo, is a member of the F-box protein family, which functions as the substrate recognition component of the SCF E3 ubiquitin ligase. FBXW7 is a critical tumor suppressor and one of the most commonly deregulated ubiquitin-proteasome system proteins in human cancer. FBXW7 controls proteasome-mediated degradation of oncoproteins such as cyclin E, c-Myc, Mcl-1, mTOR, Jun, Notch and AURKA. Consistent with the tumor suppressor role of FBXW7, it is located at chromosome 4q32, a genomic region deleted in more than 30\% of all human cancers (Spruck CH et al., Cancer Res 62:4535-9, 2002). Genetic profiles of human cancers based on high-throughput sequencing have revealed that FBXW7 is frequently mutated in human cancers. In addition to genetic mutations, other mechanisms involving microRNA, long non-coding RNA, and specific oncogenic signaling pathways can inactivate FBXW7 functions in cancer cells. In the following sections, we will discuss the regulation of FBXW7, its role in oncogenesis, and the clinical implications and prognostic value of loss of function of FBXW7 in human cancers.}, |
|
| 12042 | + keywords = {C-myc,Cancer,CDC4,Cyclin E,FBXW7,HTLV,Jun,mcl-1,mTOR,Notch}, |
|
| 12043 | + file = {/Users/rmorin/Zotero/storage/87YGK85E/Yeh et al. - 2018 - FBXW7 a critical tumor suppressor of human cancer.pdf;/Users/rmorin/Zotero/storage/TIZS7SSW/s12943-018-0857-2.html} |
|
| 12044 | +} |
|
| 12045 | + |
|
| 12046 | +@article{yildizActivatingSTAT6Mutations2015c, |
|
| 12047 | + title = {Activating {{STAT6}} Mutations in Follicular Lymphoma}, |
|
| 12048 | + author = {Yildiz, Mehmet and Li, Hongxiu and Bernard, Denzil and Amin, Nisar A. and Ouillette, Peter and Jones, Siân and Saiya-Cork, Kamlai and Parkin, Brian and Jacobi, Kathryn and Shedden, Kerby and Wang, Shaomeng and Chang, Alfred E. and Kaminski, Mark S. and Malek, Sami N.}, |
|
| 12049 | + date = {2015-01-22}, |
|
| 12050 | + journaltitle = {Blood}, |
|
| 12051 | + shortjournal = {Blood}, |
|
| 12052 | + volume = {125}, |
|
| 12053 | + number = {4}, |
|
| 12054 | + eprint = {25428220}, |
|
| 12055 | + eprinttype = {pmid}, |
|
| 12056 | + pages = {668--679}, |
|
| 12057 | + issn = {1528-0020}, |
|
| 12058 | + doi = {10.1182/blood-2014-06-582650}, |
|
| 12059 | + abstract = {Follicular lymphoma (FL) is the second most common non-Hodgkin lymphoma in the Western world. FL cell-intrinsic and cell-extrinsic factors influence FL biology and clinical outcome. To further our understanding of the genetic basis of FL, we performed whole-exome sequencing of 23 highly purified FL cases and 1 transformed FL case and expanded findings to a combined total of 114 FLs. We report recurrent mutations in the transcription factor STAT6 in 11\% of FLs and identified the STAT6 amino acid residue 419 as a novel STAT6 mutation hotspot (p.419D/G, p.419D/A, and p.419D/H). FL-associated STAT6 mutations were activating, as evidenced by increased transactivation in HEK293T cell-based transfection/luciferase reporter assays, heightened interleukin-4 (IL-4) -induced activation of target genes in stable STAT6 transfected lymphoma cell lines, and elevated baseline expression levels of STAT6 target genes in primary FL B cells harboring mutant STAT6. Mechanistically, FL-associated STAT6 mutations facilitated nuclear residency of STAT6, independent of IL-4-induced STAT6-Y641 phosphorylation. Structural modeling of STAT6 based on the structure of the STAT1-DNA complex revealed that most FL-associated STAT6 mutants locate to the STAT6-DNA interface, potentially facilitating heightened interactions. The genetic and functional data combined strengthen the recognition of the IL-4/JAK/STAT6 axis as a driver of FL pathogenesis.}, |
|
| 12060 | + langid = {english}, |
|
| 12061 | + pmcid = {PMC4729538}, |
|
| 12062 | + keywords = {Active Transport Cell Nucleus,Cell Line Tumor,Cell Nucleus,Gene Expression Regulation Neoplastic,Genome-Wide Association Study,HEK293 Cells,Humans,Interleukin-4,Janus Kinases,Lymphoma Follicular,Mutation Missense,Neoplasm Proteins,Phosphorylation,STAT6 Transcription Factor,Transcriptional Activation}, |
|
| 12063 | + file = {/Users/rmorin/Zotero/storage/XPKG5NQR/Yildiz et al. - 2015 - Activating STAT6 mutations in follicular lymphoma.pdf} |
|
| 12064 | +} |
|
| 12065 | + |
|
| 12066 | +@article{yingMEF2BMutationsLead, |
|
| 12067 | + title = {{{MEF2B Mutations Lead}} to {{De-Regulated Expression}} of the {{BCL6 Oncogene}} in {{Diffuse Large B-Cell Lymphoma}} and {{Follicular Lymphoma}}}, |
|
| 12068 | + author = {Ying, Carol Y and Dominguez-Sola, David and Fabi, Melissa and Lorenz, Ivo C and Bansal, Mukesh and Califano, Andrea and Pasqualucci, Laura and Basso, Katia and Dalla-Favera, Riccardo}, |
|
| 12069 | + journaltitle = {Blood}, |
|
| 12070 | + volume = {120}, |
|
| 12071 | + issue = {21 SP -}, |
|
| 12072 | + keywords = {nosource} |
|
| 12073 | +} |
|
| 12074 | + |
|
| 12075 | +@article{yinRNAbindingMotifsHnRNP2020, |
|
| 12076 | + title = {{{RNA-binding}} Motifs of {{hnRNP K}} Are Critical for Induction of Antibody Diversification by Activation-Induced Cytidine Deaminase}, |
|
| 12077 | + author = {Yin, Ziwei and Kobayashi, Maki and Hu, Wenjun and Higashi, Koichi and Begum, Nasim A. and Kurokawa, Ken and Honjo, Tasuku}, |
|
| 12078 | + date = {2020-05-26}, |
|
| 12079 | + journaltitle = {Proceedings of the National Academy of Sciences}, |
|
| 12080 | + volume = {117}, |
|
| 12081 | + number = {21}, |
|
| 12082 | + pages = {11624--11635}, |
|
| 12083 | + publisher = {Proceedings of the National Academy of Sciences}, |
|
| 12084 | + doi = {10.1073/pnas.1921115117}, |
|
| 12085 | + url = {https://www.pnas.org/doi/10.1073/pnas.1921115117}, |
|
| 12086 | + urldate = {2022-09-27}, |
|
| 12087 | + file = {/Users/rmorin/Zotero/storage/865533ZH/Yin et al. - 2020 - RNA-binding motifs of hnRNP K are critical for ind.pdf} |
|
| 12088 | +} |
|
| 12089 | + |
|
| 12090 | +@article{youngMutationsDNAbindingCodons2007, |
|
| 12091 | + title = {Mutations in the {{DNA-binding}} Codons of {{TP53}}, Which Are Associated with Decreased Expression of {{TRAILreceptor-2}}, Predict for Poor Survival in Diffuse Large {{B-cell}} Lymphoma}, |
|
| 12092 | + author = {Young, K H and Weisenburger, D D and Dave, B J and Smith, L and Sanger, W and Iqbal, J and Campo, E and Delabie, J and Gascoyne, R D and Ott, G and Rimsza, L and Muller-Hermelink, H K and Jaffe, E S and Rosenwald, A and Staudt, L M and Chan, W C and Greiner, T C}, |
|
| 12093 | + date = {2007-12}, |
|
| 12094 | + journaltitle = {Blood}, |
|
| 12095 | + volume = {110}, |
|
| 12096 | + number = {13}, |
|
| 12097 | + pages = {4396--4405}, |
|
| 12098 | + keywords = {nosource} |
|
| 12099 | +} |
|
| 12100 | + |
|
| 12101 | +@article{youngStructuralProfilesTP532008, |
|
| 12102 | + title = {Structural Profiles of {{TP53}} Gene Mutations Predict Clinical Outcome in Diffuse Large {{B-cell}} Lymphoma: An International Collaborative Study.}, |
|
| 12103 | + author = {Young, Ken H and Leroy, Karen and Møller, Michael B and Colleoni, Gisele W B and Sánchez-Beato, Margarita and Kerbauy, Fábio R and Haioun, Corinne and Eickhoff, Jens C and Young, Allen H and Gaulard, Philippe and Piris, Miguel A and Oberley, Terry D and Rehrauer, William M and Kahl, Brad S and Malter, James S and Campo, Elias and Delabie, Jan and Gascoyne, Randy D and Rosenwald, Andreas and Rimsza, Lisa and Huang, James and Braziel, Rita M and Jaffe, Elaine S and Wilson, Wyndham H and Staudt, Louis M and Vose, Julie M and Chan, Wing C and Weisenburger, Dennis D and Greiner, Timothy C}, |
|
| 12104 | + date = {2008-10}, |
|
| 12105 | + journaltitle = {Blood}, |
|
| 12106 | + volume = {112}, |
|
| 12107 | + number = {8}, |
|
| 12108 | + pages = {3088--3098}, |
|
| 12109 | + keywords = {nosource} |
|
| 12110 | +} |
|
| 12111 | + |
|
| 12112 | +@article{yugamiHnRNPUEnhancesExpression2007, |
|
| 12113 | + title = {{{hnRNP-U}} Enhances the Expression of Specific Genes by Stabilizing {{mRNA}}}, |
|
| 12114 | + author = {Yugami, Masato and Kabe, Yasuaki and Yamaguchi, Yuki and Wada, Tadashi and Handa, Hiroshi}, |
|
| 12115 | + date = {2007-01-09}, |
|
| 12116 | + journaltitle = {FEBS Letters}, |
|
| 12117 | + shortjournal = {FEBS Letters}, |
|
| 12118 | + volume = {581}, |
|
| 12119 | + number = {1}, |
|
| 12120 | + pages = {1--7}, |
|
| 12121 | + issn = {0014-5793}, |
|
| 12122 | + doi = {10.1016/j.febslet.2006.11.062}, |
|
| 12123 | + url = {https://www.sciencedirect.com/science/article/pii/S0014579306014037}, |
|
| 12124 | + urldate = {2022-09-28}, |
|
| 12125 | + abstract = {Heterogeneous nuclear ribonucleoproteins (hnRNPs) are thought to be involved in pre-mRNA processing. hnRNP-U, also termed scaffold attachment factor A (SAF-A), binds to pre-mRNA and nuclear matrix/scaffold attachment region DNA elements. However, its role in the regulation of gene expression is as yet poorly understood. In the present study, we show that hnRNP-U specifically enhances the expression of tumor necrosis factor α mRNA by increasing its stability, possibly through binding to the 3′ untranslated region. We also show that hnRNP-U enhances the expression of several other genes as well, including GADD45A, HEXIM1, HOXA2, IER3, NHLH2, and ZFY, by binding to and stabilizing these mRNAs. These results suggest that hnRNP-U enhances the expression of specific genes by regulating mRNA stability.}, |
|
| 12126 | + langid = {english}, |
|
| 12127 | + keywords = {3′ Untranslated region,Gene expression,Heterogeneous ribonucleoprotein,Tumor necrosis factor}, |
|
| 12128 | + file = {/Users/rmorin/Zotero/storage/PVCM6SU6/Yugami et al. - 2007 - hnRNP-U enhances the expression of specific genes .pdf;/Users/rmorin/Zotero/storage/333LFMS9/S0014579306014037.html} |
|
| 12129 | +} |
|
| 12130 | + |
|
| 12131 | +@article{zahnScalableWholegenomeSinglecell2017, |
|
| 12132 | + title = {Scalable Whole-Genome Single-Cell Library Preparation without Preamplification}, |
|
| 12133 | + author = {Zahn, Hans and Steif, Adi and Laks, Emma and Eirew, Peter and VanInsberghe, Michael and Shah, Sohrab P. and Aparicio, Samuel and Hansen, Carl L.}, |
|
| 12134 | + date = {2017-02}, |
|
| 12135 | + journaltitle = {Nature Methods}, |
|
| 12136 | + shortjournal = {Nat Methods}, |
|
| 12137 | + volume = {14}, |
|
| 12138 | + number = {2}, |
|
| 12139 | + eprint = {28068316}, |
|
| 12140 | + eprinttype = {pmid}, |
|
| 12141 | + pages = {167--173}, |
|
| 12142 | + issn = {1548-7105}, |
|
| 12143 | + doi = {10.1038/nmeth.4140}, |
|
| 12144 | + abstract = {Single-cell genomics is critical for understanding cellular heterogeneity in cancer, but existing library preparation methods are expensive, require sample preamplification and introduce coverage bias. Here we describe direct library preparation (DLP), a robust, scalable, and high-fidelity method that uses nanoliter-volume transposition reactions for single-cell whole-genome library preparation without preamplification. We examined 782 cells from cell lines and triple-negative breast xenograft tumors. Low-depth sequencing, compared with existing methods, revealed greater coverage uniformity and more reliable detection of copy-number alterations. Using phylogenetic analysis, we found minor xenograft subpopulations that were undetectable by bulk sequencing, as well as dynamic clonal expansion and diversification between passages. Merging single-cell genomes in silico, we generated 'bulk-equivalent' genomes with high depth and uniform coverage. Thus, low-depth sequencing of DLP libraries may provide an attractive replacement for conventional bulk sequencing methods, permitting analysis of copy number at the cell level and of other genomic variants at the population level.}, |
|
| 12145 | + langid = {english}, |
|
| 12146 | + keywords = {Animals,Breast Neoplasms,Cell Line Tumor,Female,Gene Library,Genomics,Humans,Lab-On-A-Chip Devices,Mice SCID,Phylogeny,Single-Cell Analysis,Xenograft Model Antitumor Assays} |
|
| 12147 | +} |
|
| 12148 | + |
|
| 12149 | +@article{zandhuisRNABindingProteinExpression2021, |
|
| 12150 | + title = {{{RNA-Binding Protein Expression Alters Upon Differentiation}} of {{Human B Cells}} and {{T Cells}}}, |
|
| 12151 | + author = {Zandhuis, Nordin D. and Nicolet, Benoit P. and Wolkers, Monika C.}, |
|
| 12152 | + date = {2021}, |
|
| 12153 | + journaltitle = {Frontiers in Immunology}, |
|
| 12154 | + volume = {12}, |
|
| 12155 | + issn = {1664-3224}, |
|
| 12156 | + url = {https://www.frontiersin.org/articles/10.3389/fimmu.2021.717324}, |
|
| 12157 | + urldate = {2022-09-26}, |
|
| 12158 | + abstract = {B cells and T cells are key players in the defence against infections and malignancies. To exert their function, B cells and T cells differentiate into effector and memory cells. Tight regulation of these differentiation processes is key to prevent their malfunction, which can result in life-threatening disease. Lymphocyte differentiation relies on the appropriate timing and dosage of regulatory molecules, and post-transcriptional gene regulation (PTR) is a key player herein. PTR includes the regulation through RNA-binding proteins (RBPs), which control the fate of RNA and its translation into proteins. To date, a comprehensive overview of the RBP expression throughout lymphocyte differentiation is lacking. Using transcriptome and proteome analyses, we here catalogued the RBP expression for human B cells and T cells. We observed that even though the overall RBP expression is conserved, the relative RBP expression is distinct between B cells and T cells. Differentiation into effector and memory cells alters the RBP expression, resulting into preferential expression of different classes of RBPs. For instance, whereas naive T cells express high levels of translation-regulating RBPs, effector T cells preferentially express RBPs that modulate mRNA stability. Lastly, we found that cytotoxic CD8+ and CD4+ T cells express a common RBP repertoire. Combined, our study reveals a cell type-specific and differentiation-dependent RBP expression landscape in human lymphocytes, which will help unravel the role of RBPs in lymphocyte function.}, |
|
| 12159 | + file = {/Users/rmorin/Zotero/storage/RSD9EXWG/Zandhuis et al. - 2021 - RNA-Binding Protein Expression Alters Upon Differe.pdf} |
|
| 12160 | +} |
|
| 12161 | + |
|
| 12162 | +@article{zandvlietCanineLymphomaReview2016, |
|
| 12163 | + title = {Canine Lymphoma: A Review}, |
|
| 12164 | + shorttitle = {Canine Lymphoma}, |
|
| 12165 | + author = {Zandvliet, M.}, |
|
| 12166 | + date = {2016-04-02}, |
|
| 12167 | + journaltitle = {Veterinary Quarterly}, |
|
| 12168 | + volume = {36}, |
|
| 12169 | + number = {2}, |
|
| 12170 | + eprint = {26953614}, |
|
| 12171 | + eprinttype = {pmid}, |
|
| 12172 | + pages = {76--104}, |
|
| 12173 | + publisher = {Taylor \& Francis}, |
|
| 12174 | + issn = {0165-2176}, |
|
| 12175 | + doi = {10.1080/01652176.2016.1152633}, |
|
| 12176 | + url = {https://doi.org/10.1080/01652176.2016.1152633}, |
|
| 12177 | + urldate = {2021-05-13}, |
|
| 12178 | + abstract = {Canine lymphoma (cL) is a common type of neoplasia in dogs with an estimated incidence rate of 20–100 cases per 100,000 dogs and is in many respects comparable to non-Hodgkin lymphoma in humans. Although the exact cause is unknown, environmental factors and genetic susceptibility are thought to play an important role. cL is not a single disease, and a wide variation in clinical presentations and histological subtypes is recognized. Despite this potential variation, most dogs present with generalized lymphadenopathy (multicentric form) and intermediate to high-grade lymphoma, more commonly of B-cell origin. The most common paraneoplastic sign is hypercalcemia that is associated with the T-cell immunophenotype. Chemotherapy is the treatment of choice and a doxorubicin-based multidrug protocol is currently the standard of care. A complete remission is obtained for most dogs and lasts for a median period of 7–10 months, resulting in a median survival of 10–14 months. Many prognostic factors have been reported, but stage, immunophenotype, tumor grade, and response to chemotherapy appear of particular importance. Failure to respond to chemotherapy suggests drug resistance, which can be partly attributed to the expression of drug transporters of the ABC-transporter superfamily, including P-gp and BCRP. Ultimately, most lymphomas will become drug resistant and the development of treatments aimed at reversing drug resistance or alternative treatment modalities (e.g. immunotherapy and targeted therapy) are of major importance. This review aims to summarize the relevant data on cL, as well as to provide an update of the recent literature.}, |
|
| 12179 | + keywords = {canine,Dog,lymphoma,non-Hodgkin,review}, |
|
| 12180 | + file = {/Users/rmorin/Zotero/storage/9TT53KSY/Zandvliet - 2016 - Canine lymphoma a review.pdf} |
|
| 12181 | +} |
|
| 12182 | + |
|
| 12183 | +@article{zangInhibitionPanclassPI32013, |
|
| 12184 | + title = {Inhibition of Pan-Class {{I PI3}} Kinase by {{NVP-BKM120}} Effectively Blocks Proliferation and Induces Cell Death in Diffuse Large {{B}} Cell Lymphoma}, |
|
| 12185 | + author = {Zang, Chuanbing and Eucker, Jan and Liu, Hongyu and Coordes, Annekatrin and Lenarz, Minoo and Possinger, Kurt and Scholz, Christian Wilfried}, |
|
| 12186 | + date = {2013-05}, |
|
| 12187 | + journaltitle = {Leuk lymphoma}, |
|
| 12188 | + pages = {1--21}, |
|
| 12189 | + keywords = {nosource} |
|
| 12190 | +} |
|
| 12191 | + |
|
| 12192 | +@software{zanotelliImcSegmentationPipelinePixelclassificationBased2017, |
|
| 12193 | + title = {{{ImcSegmentationPipeline}}: {{A}} Pixelclassification Based Multiplexed Image Segmentation Pipeline}, |
|
| 12194 | + shorttitle = {{{ImcSegmentationPipeline}}}, |
|
| 12195 | + author = {Zanotelli, Vito Riccardo Tomaso and Bodenmiller, Bernd}, |
|
| 12196 | + date = {2017-09-14}, |
|
| 12197 | + doi = {10.5281/zenodo.3841961}, |
|
| 12198 | + url = {https://zenodo.org/record/3841961}, |
|
| 12199 | + urldate = {2022-02-03}, |
|
| 12200 | + abstract = {This repository demonstrate and documents how the packages imctools, CellProfiler and Ilastik can be combined to segment highly multiplexed imaging mass cytometry images into regions corresponding to single cell slices.}, |
|
| 12201 | + organization = {Zenodo}, |
|
| 12202 | + file = {/Users/rmorin/Zotero/storage/QHV5MY6G/3841961.html} |
|
| 12203 | +} |
|
| 12204 | + |
|
| 12205 | +@article{zhangCREBBPAcetyltransferaseHaploinsufficient2017, |
|
| 12206 | + title = {The {{CREBBP Acetyltransferase Is}} a {{Haploinsufficient Tumor Suppressor}} in {{B-cell Lymphoma}}}, |
|
| 12207 | + author = {Zhang, Jiyuan and Vlasevska, Sofija and Wells, Victoria A. and Nataraj, Sarah and Holmes, Antony B. and Duval, Romain and Meyer, Stefanie N. and Mo, Tongwei and Basso, Katia and Brindle, Paul K. and Hussein, Shafinaz and Dalla-Favera, Riccardo and Pasqualucci, Laura}, |
|
| 12208 | + date = {2017-03}, |
|
| 12209 | + journaltitle = {Cancer Discovery}, |
|
| 12210 | + shortjournal = {Cancer Discov}, |
|
| 12211 | + volume = {7}, |
|
| 12212 | + number = {3}, |
|
| 12213 | + eprint = {28069569}, |
|
| 12214 | + eprinttype = {pmid}, |
|
| 12215 | + pages = {322--337}, |
|
| 12216 | + issn = {2159-8290}, |
|
| 12217 | + doi = {10.1158/2159-8290.CD-16-1417}, |
|
| 12218 | + abstract = {Inactivating mutations of the CREBBP acetyltransferase are highly frequent in diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL), the two most common germinal center (GC)-derived cancers. However, the role of CREBBP inactivation in lymphomagenesis remains unclear. Here, we show that CREBBP regulates enhancer/super-enhancer networks with central roles in GC/post-GC cell fate decisions, including genes involved in signal transduction by the B-cell receptor and CD40 receptor, transcriptional control of GC and plasma cell development, and antigen presentation. Consistently, Crebbp-deficient B cells exhibit enhanced response to mitogenic stimuli and perturbed plasma cell differentiation. Although GC-specific loss of Crebbp was insufficient to initiate malignant transformation, compound Crebbp-haploinsufficient/BCL2-transgenic mice, mimicking the genetics of FL and DLBCL, develop clonal lymphomas recapitulating the features of the human diseases. These findings establish CREBBP as a haploinsufficient tumor-suppressor gene in GC B cells and provide insights into the mechanisms by which its loss contributes to lymphomagenesis.Significance: Loss-of-function mutations of CREBBP are common and early lesions in FL and DLBCL, suggesting a prominent role in lymphoma initiation. Our studies identify the cellular program by which reduced CREBBP dosage facilitates malignant transformation, and have direct implications for targeted lymphoma therapy based on drugs affecting CREBBP-mediated chromatin acetylation. Cancer Discov; 7(3); 322-37. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 235.}, |
|
| 12219 | + langid = {english}, |
|
| 12220 | + pmcid = {PMC5386396}, |
|
| 12221 | + keywords = {Animals,B-Lymphocytes,Cell Differentiation,Chromatin,CREB-Binding Protein,Enhancer Elements Genetic,Epigenesis Genetic,Gene Expression Regulation Neoplastic,Genes Tumor Suppressor,Germinal Center,Haploinsufficiency,Humans,Lymphoma Follicular,Lymphoma Large B-Cell Diffuse,Mice Inbred C57BL,Mice Knockout,Plasma Cells,Proto-Oncogene Proteins c-bcl-6}, |
|
| 12222 | + file = {/Users/rmorin/Zotero/storage/T7ZGJ8B8/Zhang et al. - 2017 - The CREBBP Acetyltransferase Is a Haploinsufficien.pdf} |
|
| 12223 | +} |
|
| 12224 | + |
|
| 12225 | +@article{zhangGeneticHeterogeneityDiffuse2013, |
|
| 12226 | + title = {Genetic Heterogeneity of Diffuse Large {{B-cell}} Lymphoma.}, |
|
| 12227 | + author = {Zhang, Jenny and Grubor, Vladimir and Love, Cassandra L and Banerjee, Anjishnu and Richards, Kristy L and Mieczkowski, Piotr A and Dunphy, Cherie and Choi, William and Au, Wing Yan and Srivastava, Gopesh and Lugar, Patricia L and Rizzieri, David A and Lagoo, Anand S and Bernal-Mizrachi, Leon and Mann, Karen P and Flowers, Christopher and Naresh, Kikkeri and Evens, Andrew and Gordon, Leo I and Czader, Magdalena and Gill, Javed I and Hsi, Eric D and Liu, Qingquan and Fan, Alice and Walsh, Katherine and Jima, Dereje and Smith, Lisa L and Johnson, Amy J and Byrd, John C and Luftig, Micah A and Ni, Ting and Zhu, Jun and Chadburn, Amy and Levy, Shawn and Dunson, David and Dave, Sandeep S}, |
|
| 12228 | + date = {2013-01}, |
|
| 12229 | + keywords = {nosource} |
|
| 12230 | +} |
|
| 12231 | + |
|
| 12232 | +@article{zhangGenomicLandscapeMantle2014, |
|
| 12233 | + title = {The Genomic Landscape of Mantle Cell Lymphoma Is Related to the Epigenetically Determined Chromatin State of Normal {{B}} Cells}, |
|
| 12234 | + author = {Zhang, Jenny and Jima, Dereje and Moffitt, Andrea B. and Liu, Qingquan and Czader, Magdalena and Hsi, Eric D. and Fedoriw, Yuri and Dunphy, Cherie H. and Richards, Kristy L. and Gill, Javed I. and Sun, Zhen and Love, Cassandra and Scotland, Paula and Lock, Eric and Levy, Shawn and Hsu, David S. and Dunson, David and Dave, Sandeep S.}, |
|
| 12235 | + date = {2014-05-08}, |
|
| 12236 | + journaltitle = {Blood}, |
|
| 12237 | + shortjournal = {Blood}, |
|
| 12238 | + volume = {123}, |
|
| 12239 | + number = {19}, |
|
| 12240 | + pages = {2988--2996}, |
|
| 12241 | + issn = {0006-4971}, |
|
| 12242 | + doi = {10.1182/blood-2013-07-517177}, |
|
| 12243 | + url = {https://ashpublications.org/blood/article/123/19/2988/32656/The-genomic-landscape-of-mantle-cell-lymphoma-is}, |
|
| 12244 | + urldate = {2019-12-21}, |
|
| 12245 | + langid = {english}, |
|
| 12246 | + file = {/Users/rmorin/Zotero/storage/U5FI7VCK/blood-2013-07-517177.html} |
|
| 12247 | +} |
|
| 12248 | + |
|
| 12249 | +@article{zhangGlobalTranscriptionalNetwork2018, |
|
| 12250 | + title = {A Global Transcriptional Network Connecting Noncoding Mutations to Changes in Tumor Gene Expression}, |
|
| 12251 | + author = {Zhang, Wei and Bojorquez-Gomez, Ana and Velez, Daniel Ortiz and Xu, Guorong and Sanchez, Kyle S. and Shen, John Paul and Chen, Kevin and Licon, Katherine and Melton, Collin and Olson, Katrina M. and Yu, Michael Ku and Huang, Justin K. and Carter, Hannah and Farley, Emma K. and Snyder, Michael and Fraley, Stephanie I. and Kreisberg, Jason F. and Ideker, Trey}, |
|
| 12252 | + date = {2018-04}, |
|
| 12253 | + journaltitle = {Nature Genetics}, |
|
| 12254 | + shortjournal = {Nat. Genet.}, |
|
| 12255 | + volume = {50}, |
|
| 12256 | + number = {4}, |
|
| 12257 | + eprint = {29610481}, |
|
| 12258 | + eprinttype = {pmid}, |
|
| 12259 | + pages = {613--620}, |
|
| 12260 | + issn = {1546-1718}, |
|
| 12261 | + doi = {10.1038/s41588-018-0091-2}, |
|
| 12262 | + abstract = {Although cancer genomes are replete with noncoding mutations, the effects of these mutations remain poorly characterized. Here we perform an integrative analysis of 930 tumor whole genomes and matched transcriptomes, identifying a network of 193 noncoding loci in which mutations disrupt target gene expression. These 'somatic eQTLs' (expression quantitative trait loci) are frequently mutated in specific cancer tissues, and the majority can be validated in an independent cohort of 3,382 tumors. Among these, we find that the effects of noncoding mutations on DAAM1, MTG2 and HYI transcription are recapitulated in multiple cancer cell lines and that increasing DAAM1 expression leads to invasive cell migration. Collectively, the noncoding loci converge on a set of core pathways, permitting a classification of tumors into pathway-based subtypes. The somatic eQTL network is disrupted in 88\% of tumors, suggesting widespread impact of noncoding mutations in cancer.}, |
|
| 12263 | + langid = {english}, |
|
| 12264 | + pmcid = {PMC5893414} |
|
| 12265 | +} |
|
| 12266 | + |
|
| 12267 | +@article{zhangHighthroughputScreenIdentifies2019, |
|
| 12268 | + title = {A High-Throughput Screen Identifies Small Molecule Modulators of Alternative Splicing by Targeting {{RNA G-quadruplexes}}}, |
|
| 12269 | + author = {Zhang, Jing and Harvey, Samuel E and Cheng, Chonghui}, |
|
| 12270 | + date = {2019-04-23}, |
|
| 12271 | + journaltitle = {Nucleic Acids Research}, |
|
| 12272 | + shortjournal = {Nucleic Acids Res}, |
|
| 12273 | + volume = {47}, |
|
| 12274 | + number = {7}, |
|
| 12275 | + eprint = {30698802}, |
|
| 12276 | + eprinttype = {pmid}, |
|
| 12277 | + pages = {3667--3679}, |
|
| 12278 | + issn = {0305-1048}, |
|
| 12279 | + doi = {10.1093/nar/gkz036}, |
|
| 12280 | + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6468248/}, |
|
| 12281 | + urldate = {2022-10-15}, |
|
| 12282 | + abstract = {RNA secondary structures have been increasingly recognized to play an important regulatory role in post-transcriptional gene regulation. We recently showed that RNA G-quadruplexes, which serve as cis-elements to recruit splicing factors, play a critical role in regulating alternative splicing during the epithelial-mesenchymal transition. In this study, we performed a high-throughput screen using a dual-color splicing reporter to identify chemical compounds capable of regulating G-quadruplex-dependent alternative splicing. We identify emetine and its analog cephaeline as small molecules that disrupt RNA G-quadruplexes, resulting in inhibition of G-quadruplex-dependent alternative splicing. Transcriptome analysis reveals that emetine globally regulates alternative splicing, including splicing of variable exons that contain splice site-proximal G-quadruplexes. Our data suggest the use of emetine and cephaeline for investigating mechanisms of G-quadruplex-associated alternative splicing.}, |
|
| 12283 | + pmcid = {PMC6468248}, |
|
| 12284 | + file = {/Users/rmorin/Zotero/storage/6V2VA3G8/Zhang et al. - 2019 - A high-throughput screen identifies small molecule.pdf} |
|
| 12285 | +} |
|
| 12286 | + |
|
| 12287 | +@article{zhangLenalidomideEfficacyActivated2013, |
|
| 12288 | + title = {Lenalidomide Efficacy in Activated {{B-cell-like}} Subtype Diffuse Large {{B-cell}} Lymphoma Is Dependent upon {{IRF4}} and Cereblon Expression.}, |
|
| 12289 | + author = {Zhang, Ling-Hua and Kosek, Jolanta and Wang, Maria and Heise, Carla and Schafer, Peter H and Chopra, Rajesh}, |
|
| 12290 | + date = {2013-02}, |
|
| 12291 | + journaltitle = {Br J Haematol}, |
|
| 12292 | + volume = {160}, |
|
| 12293 | + number = {4}, |
|
| 12294 | + pages = {487--502}, |
|
| 12295 | + keywords = {nosource} |
|
| 12296 | +} |
|
| 12297 | + |
|
| 12298 | +@article{zhangMatchMixeRCrossplatformNormalization2020, |
|
| 12299 | + title = {{{MatchMixeR}}: A Cross-Platform Normalization Method for Gene Expression Data Integration}, |
|
| 12300 | + author = {Zhang, Serin and Shao, Jiang and Yu, Disa and Qiu, Xing and Zhang, Jinfeng}, |
|
| 12301 | + date = {2020-01-06}, |
|
| 12302 | + journaltitle = {Bioinformatics}, |
|
| 12303 | + shortjournal = {Bioinformatics}, |
|
| 12304 | + pages = {2486--2491}, |
|
| 12305 | + issn = {1367-4803}, |
|
| 12306 | + doi = {10.1093/bioinformatics/btz974}, |
|
| 12307 | + abstract = {Combining gene expression (GE) profiles generated from different platforms enables previously infeasible studies due to sample size limitations. Several cross-platform normalization methods have been developed to remove the systematic differences between platforms, but they may also remove meaningful biological differences among datasets. In this work, we propose a novel approach that removes the platform, not the biological differences. Dubbed as ‘MatchMixeR’, we model platform differences by a linear mixed effects regression (LMER) model, and estimate them from matched GE profiles of the same cell line or tissue measured on different platforms. The resulting model can then be used to remove platform differences in other datasets. By using LMER, we achieve better bias-variance trade-off in parameter estimation. We also design a computationally efficient algorithm based on the moment method, which is ideal for ultra-high-dimensional LMER analysis.Compared with several prominent competing methods, MatchMixeR achieved the highest after-normalization concordance. Subsequent differential expression analyses based on datasets integrated from different platforms showed that using MatchMixeR achieved the best trade-off between true and false discoveries, and this advantage is more apparent in datasets with limited samples or unbalanced group proportions.Our method is implemented in a R-package, ‘MatchMixeR’, freely available at: https://github.com/dy16b/Cross-Platform-Normalization.Supplementary data are available at Bioinformatics online.}, |
|
| 12308 | + issue = {btz974}, |
|
| 12309 | + keywords = {nosource} |
|
| 12310 | +} |
|
| 12311 | + |
|
| 12312 | +@article{zhangModelbasedAnalysisChIPSeq2008, |
|
| 12313 | + title = {Model-Based Analysis of {{ChIP-Seq}} ({{MACS}})}, |
|
| 12314 | + author = {Zhang, Yong and Liu, Tao and Meyer, Clifford A. and Eeckhoute, Jérôme and Johnson, David S. and Bernstein, Bradley E. and Nusbaum, Chad and Myers, Richard M. and Brown, Myles and Li, Wei and Liu, X. Shirley}, |
|
| 12315 | + date = {2008}, |
|
| 12316 | + journaltitle = {Genome Biology}, |
|
| 12317 | + shortjournal = {Genome Biol}, |
|
| 12318 | + volume = {9}, |
|
| 12319 | + number = {9}, |
|
| 12320 | + eprint = {18798982}, |
|
| 12321 | + eprinttype = {pmid}, |
|
| 12322 | + pages = {R137}, |
|
| 12323 | + issn = {1474-760X}, |
|
| 12324 | + doi = {10.1186/gb-2008-9-9-r137}, |
|
| 12325 | + abstract = {We present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shift size of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, and is freely available.}, |
|
| 12326 | + langid = {english}, |
|
| 12327 | + pmcid = {PMC2592715}, |
|
| 12328 | + keywords = {Algorithms,Cell Line Tumor,Chromatin Immunoprecipitation,Hepatocyte Nuclear Factor 3-alpha,Humans,Models Genetic,Oligonucleotide Array Sequence Analysis}, |
|
| 12329 | + file = {/Users/rmorin/Zotero/storage/EF2N6FNJ/Zhang et al. - 2008 - Model-based analysis of ChIP-Seq (MACS).pdf} |
|
| 12330 | +} |
|
| 12331 | + |
|
| 12332 | +@article{zhangPCBP1ImportantMediator2014, |
|
| 12333 | + title = {{{PCBP1}} Is an Important Mediator of {{TGF-β-induced}} Epithelial to Mesenchymal Transition in Gall Bladder Cancer Cell Line {{GBC-SD}}}, |
|
| 12334 | + author = {Zhang, Hang-Yu and Dou, Ke-Feng}, |
|
| 12335 | + date = {2014-08-01}, |
|
| 12336 | + journaltitle = {Molecular Biology Reports}, |
|
| 12337 | + shortjournal = {Mol Biol Rep}, |
|
| 12338 | + volume = {41}, |
|
| 12339 | + number = {8}, |
|
| 12340 | + pages = {5519--5524}, |
|
| 12341 | + issn = {1573-4978}, |
|
| 12342 | + doi = {10.1007/s11033-014-3428-7}, |
|
| 12343 | + url = {https://doi.org/10.1007/s11033-014-3428-7}, |
|
| 12344 | + urldate = {2022-09-28}, |
|
| 12345 | + abstract = {Gall bladder carcinoma (GBC) is the seventh most common cancer across the globe and the most common malignancy of the biliary tract. Most GBC related deaths occur due to secondary progression and metastasis to distant organs. Epithelial–mesenchymal transition (EMT) is an important pre-requisite for tumor metastasis, however its mechanism in GBC has not yet been defined. Using the GBC-SD cell line, we have uncovered an important mediator, poly r(C) binding protein-1 (PCBP1), of transforming growth factor-beta (TGF-β)-induced EMT in GBC. Our results show that TGF-β treatment resulted in PCBP1 phosphorylation in accordance with similar observation in other model systems. We further showed through gain- and loss-of-function assays that PCBP1 expression levels regulate the capacity of GBC-SD cells to migrate and invade in vitro. Finally, our results showed that PCBP1 expression levels also regulate generation of CD44+CD24− progenitor cell population in GBC-SD cells after TGF-β treatment. Cumulatively, our results indicate, pending further validation, that PCBP1 might be a prognostic marker for GBC metastasis.}, |
|
| 12346 | + langid = {english}, |
|
| 12347 | + keywords = {EMT,Epithelial–mesenchymal transition,Gall bladder cancer,GBC-SD,nosource,PCBP1} |
|
| 12348 | +} |
|
| 12349 | + |
|
| 12350 | +@article{zhangPCBP1RegulatesAlternative2010, |
|
| 12351 | + title = {{{PCBP-1}} Regulates Alternative Splicing of the {{CD44}} Gene and Inhibits Invasion in Human Hepatoma Cell Line {{HepG2}} Cells}, |
|
| 12352 | + author = {Zhang, Tong and Huang, Xian-Hong and Dong, Lan and Hu, Deqing and Ge, Changhui and Zhan, Yi-Qun and Xu, Wang-Xiang and Yu, Miao and Li, Wei and Wang, Xiaohui and Tang, Liujun and Li, Chang-Yan and Yang, Xiao-Ming}, |
|
| 12353 | + date = {2010-04-02}, |
|
| 12354 | + journaltitle = {Molecular Cancer}, |
|
| 12355 | + shortjournal = {Molecular Cancer}, |
|
| 12356 | + volume = {9}, |
|
| 12357 | + number = {1}, |
|
| 12358 | + pages = {72}, |
|
| 12359 | + issn = {1476-4598}, |
|
| 12360 | + doi = {10.1186/1476-4598-9-72}, |
|
| 12361 | + url = {https://doi.org/10.1186/1476-4598-9-72}, |
|
| 12362 | + urldate = {2022-09-28}, |
|
| 12363 | + abstract = {PCBP1 (or alpha CP1 or hnRNP E1), a member of the PCBP family, is widely expressed in many human tissues and involved in regulation of transcription, transportation process, and function of RNA molecules. However, the role of PCBP1 in CD44 variants splicing still remains elusive.}, |
|
| 12364 | + keywords = {CD44 Variant,Hepatocyte Growth Factor,HepG2 Cell,hnRNP Protein,Human Hepatoma Cell Line HepG2}, |
|
| 12365 | + file = {/Users/rmorin/Zotero/storage/L7L7TQJS/Zhang et al. - 2010 - PCBP-1 regulates alternative splicing of the CD44 .pdf;/Users/rmorin/Zotero/storage/P8TNZD8Z/1476-4598-9-72.html} |
|
| 12366 | +} |
|
| 12367 | + |
|
| 12368 | +@article{zhangPolyBindingProtein2020, |
|
| 12369 | + title = {Poly {{C Binding Protein}} 1 {{Regulates}} P62/{{SQSTM1 mRNA Stability}} and {{Autophagic Degradation}} to {{Repress Tumor Progression}}}, |
|
| 12370 | + author = {Zhang, Wenliang and Zhang, Shaoyang and Guan, Wen and Huang, Zhicong and Kong, Jianqiu and Huang, Chunlong and Wang, Haihe and Yang, Shulan}, |
|
| 12371 | + date = {2020}, |
|
| 12372 | + journaltitle = {Frontiers in Genetics}, |
|
| 12373 | + volume = {11}, |
|
| 12374 | + issn = {1664-8021}, |
|
| 12375 | + url = {https://www.frontiersin.org/articles/10.3389/fgene.2020.00930}, |
|
| 12376 | + urldate = {2022-09-28}, |
|
| 12377 | + abstract = {Accumulating evidence show that Poly C Binding Protein 1 (PCBP1) is deleted in distinct types of tumors as a novel tumor suppressor, but its tumor suppression mechanism remains elusive. Here, we firstly describe that downregulation of PCBP1 is significantly associated with clinical ovarian tumor progression. Mechanistically, PCBP1 overexpression affects various autophagy-related genes expression at various expression levels to attenuate the intrinsic cell autophagy, including the autophagy-initiating ULK, ATG12, ATG7 as well as the bona fide marker of autophagosome, LC3B. Accordingly, knockdown of the endogenous PCBP1 in turn enhances autophagy and less cell death. Meanwhile, PCBP1 upregulates p62/SQSTM1 via inhibition p62/SQSTM1 autophagolysome and proteasome degradation as well as its mRNA stability, consequently accompanying with the caspase 3 or 8 activation for tumor cell apoptosis. Importantly, clinical ovary cancer sample analysis consistently validates the relevance of PCBP1 expression to both p62/SQSTM1 and caspase-8 to overall survival, and indicates PCBP1 may be a master player to repress tumor initiation. Taken together, our results uncover the tumorigenic mechanism of PCBP1 depletion and suggest that inhibition of tumor cell autophagy with autophagic inhibitors could be an effective therapeutical strategy for PCBP1-deficient tumor.}, |
|
| 12378 | + file = {/Users/rmorin/Zotero/storage/WW8FVW5W/Zhang et al. - 2020 - Poly C Binding Protein 1 Regulates p62SQSTM1 mRNA.pdf} |
|
| 12379 | +} |
|
| 12380 | + |
|
| 12381 | +@article{zhangRegulationGerminalCenter2016, |
|
| 12382 | + title = {Regulation of Germinal Center {{B-cell}} Differentiation}, |
|
| 12383 | + author = {Zhang, Yang and Garcia-Ibanez, Laura and Toellner, Kai-Michael}, |
|
| 12384 | + date = {2016}, |
|
| 12385 | + journaltitle = {Immunological Reviews}, |
|
| 12386 | + volume = {270}, |
|
| 12387 | + number = {1}, |
|
| 12388 | + pages = {8--19}, |
|
| 12389 | + issn = {1600-065X}, |
|
| 12390 | + doi = {10.1111/imr.12396}, |
|
| 12391 | + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/imr.12396}, |
|
| 12392 | + urldate = {2022-10-06}, |
|
| 12393 | + abstract = {Germinal centers (GC) are the main sites where antigen-activated B-cell clones expand and undergo immunoglobulin gene hypermutation and selection. Iterations of this process will lead to affinity maturation, replicating Darwinian evolution on the cellular level. GC B-cell selection can lead to four different outcomes: further expansion and evolution, apoptosis (non-selection), or output from the GC with differentiation into memory B cells or plasma cells. T-helper cells in GC have been shown to have a central role in regulating B-cell selection by sensing the density of major histocompatibility complex (MHC):peptide antigen complexes. Antigen is provided on follicular dendritic cells in the form of immune complex. Antibody on these immune complexes regulates antigen accessibility by shielding antigen from B-cell receptor access. Replacement of antibody on immune complexes by antibody generated from GC-derived plasma cell output will gradually reduce the availability of antigen. This antibody feedback can lead to a situation where a slow rise in selection stringency caused by a changing environment leads to directional evolution toward higher affinity antibody.}, |
|
| 12394 | + langid = {english}, |
|
| 12395 | + keywords = {affinity maturation,B-cell selection,cytokines,germinal center,immune complex,Tfh cells}, |
|
| 12396 | + file = {/Users/rmorin/Zotero/storage/3WW7UFC7/Zhang et al. - 2016 - Regulation of germinal center B-cell differentiati.pdf} |
|
| 12397 | +} |
|
| 12398 | + |
|
| 12399 | +@article{zhaoCrossMapVersatileTool2014, |
|
| 12400 | + title = {{{CrossMap}}: A Versatile Tool for Coordinate Conversion between Genome Assemblies}, |
|
| 12401 | + shorttitle = {{{CrossMap}}}, |
|
| 12402 | + author = {Zhao, Hao and Sun, Zhifu and Wang, Jing and Huang, Haojie and Kocher, Jean-Pierre and Wang, Liguo}, |
|
| 12403 | + date = {2014-04-01}, |
|
| 12404 | + journaltitle = {Bioinformatics}, |
|
| 12405 | + shortjournal = {Bioinformatics}, |
|
| 12406 | + volume = {30}, |
|
| 12407 | + number = {7}, |
|
| 12408 | + pages = {1006--1007}, |
|
| 12409 | + issn = {1367-4803}, |
|
| 12410 | + doi = {10.1093/bioinformatics/btt730}, |
|
| 12411 | + url = {https://academic.oup.com/bioinformatics/article/30/7/1006/234947}, |
|
| 12412 | + urldate = {2020-01-24}, |
|
| 12413 | + abstract = {Abstract. Motivation: Reference genome assemblies are subject to change and refinement from time to time. Generally, researchers need to convert the results th}, |
|
| 12414 | + langid = {english}, |
|
| 12415 | + file = {/Users/rmorin/Zotero/storage/J77RNWLY/234947.html} |
|
| 12416 | +} |
|
| 12417 | + |
|
| 12418 | +@article{zhengHaplotypingGermlineCancer2016, |
|
| 12419 | + title = {Haplotyping Germline and Cancer Genomes with High-Throughput Linked-Read Sequencing}, |
|
| 12420 | + author = {Zheng, Grace X Y and Lau, Billy T and Schnall-Levin, Michael and Jarosz, Mirna and Bell, John M and Hindson, Christopher M and Kyriazopoulou-Panagiotopoulou, Sofia and Masquelier, Donald A and Merrill, Landon and Terry, Jessica M and Mudivarti, Patrice A and Wyatt, Paul W and Bharadwaj, Rajiv and Makarewicz, Anthony J and Li, Yuan and Belgrader, Phillip and Price, Andrew D and Lowe, Adam J and Marks, Patrick and Vurens, Gerard M and Hardenbol, Paul and Montesclaros, Luz and Luo, Melissa and Greenfield, Lawrence and Wong, Alexander and Birch, David E and Short, Steven W and Bjornson, Keith P and Patel, Pranav and Hopmans, Erik S and Wood, Christina and Kaur, Sukhvinder and Lockwood, Glenn K and Stafford, David and Delaney, Joshua P and Wu, Indira and Ordonez, Heather S and Grimes, Susan M and Greer, Stephanie and Lee, Josephine Y and Belhocine, Kamila and Giorda, Kristina M and Heaton, William H and McDermott, Geoffrey P and Bent, Zachary W and Meschi, Francesca and Kondov, Nikola O and Wilson, Ryan and Bernate, Jorge A and Gauby, Shawn and Kindwall, Alex and Bermejo, Clara and Fehr, Adrian N and Chan, Adrian and Saxonov, Serge and Ness, Kevin D and Hindson, Benjamin J and Ji, Hanlee P}, |
|
| 12421 | + date = {2016}, |
|
| 12422 | + journaltitle = {Nature Biotechnology}, |
|
| 12423 | + volume = {34}, |
|
| 12424 | + number = {3}, |
|
| 12425 | + eprint = {26829319}, |
|
| 12426 | + eprinttype = {pmid}, |
|
| 12427 | + pages = {303--311}, |
|
| 12428 | + issn = {1087-0156}, |
|
| 12429 | + doi = {10.1038/nbt.3432}, |
|
| 12430 | + url = {http://dx.doi.org/10.1038/nbt.3432}, |
|
| 12431 | + abstract = {Haplotyping of human chromosomes is a prerequisite for cataloguing the full repertoire of genetic variation. We present a microfluidics-based, linked-read sequencing technology that can phase and haplotype germline and cancer genomes using nanograms of input DNA. This high-throughput platform prepares barcoded libraries for short-read sequencing and computationally reconstructs long-range haplotype and structural variant information. We generate haplotype blocks in a nuclear trio that are concordant with expected inheritance patterns and phase a set of structural variants. We also resolve the structure of the EML4-ALK gene fusion in the NCI-H2228 cancer cell line using phased exome sequencing. Finally, we assign genetic aberrations to specific megabase-scale haplotypes generated from whole-genome sequencing of a primary colorectal adenocarcinoma. This approach resolves haplotype information using up to 100 times less genomic DNA than some methods and enables the accurate detection of structural variants.}, |
|
| 12432 | + keywords = {nosource} |
|
| 12433 | +} |
|
| 12434 | + |
|
| 12435 | +@article{zhengMassivelyParallelDigital2017, |
|
| 12436 | + title = {Massively Parallel Digital Transcriptional Profiling of Single Cells}, |
|
| 12437 | + author = {Zheng, Grace X. Y. and Terry, Jessica M. and Belgrader, Phillip and Ryvkin, Paul and Bent, Zachary W. and Wilson, Ryan and Ziraldo, Solongo B. and Wheeler, Tobias D. and McDermott, Geoff P. and Zhu, Junjie and Gregory, Mark T. and Shuga, Joe and Montesclaros, Luz and Underwood, Jason G. and Masquelier, Donald A. and Nishimura, Stefanie Y. and Schnall-Levin, Michael and Wyatt, Paul W. and Hindson, Christopher M. and Bharadwaj, Rajiv and Wong, Alexander and Ness, Kevin D. and Beppu, Lan W. and Deeg, H. Joachim and McFarland, Christopher and Loeb, Keith R. and Valente, William J. and Ericson, Nolan G. and Stevens, Emily A. and Radich, Jerald P. and Mikkelsen, Tarjei S. and Hindson, Benjamin J. and Bielas, Jason H.}, |
|
| 12438 | + date = {2017-01-16}, |
|
| 12439 | + journaltitle = {Nature Communications}, |
|
| 12440 | + shortjournal = {Nat Commun}, |
|
| 12441 | + volume = {8}, |
|
| 12442 | + eprint = {28091601}, |
|
| 12443 | + eprinttype = {pmid}, |
|
| 12444 | + pages = {14049}, |
|
| 12445 | + issn = {2041-1723}, |
|
| 12446 | + doi = {10.1038/ncomms14049}, |
|
| 12447 | + abstract = {Characterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. We describe a droplet-based system that enables 3' mRNA counting of tens of thousands of single cells per sample. Cell encapsulation, of up to 8 samples at a time, takes place in ∼6\,min, with ∼50\% cell capture efficiency. To demonstrate the system's technical performance, we collected transcriptome data from ∼250k single cells across 29 samples. We validated the sensitivity of the system and its ability to detect rare populations using cell lines and synthetic RNAs. We profiled 68k peripheral blood mononuclear cells to demonstrate the system's ability to characterize large immune populations. Finally, we used sequence variation in the transcriptome data to determine host and donor chimerism at single-cell resolution from bone marrow mononuclear cells isolated from transplant patients.}, |
|
| 12448 | + langid = {english}, |
|
| 12449 | + pmcid = {PMC5241818}, |
|
| 12450 | + keywords = {Cell Line,Female,Humans,Leukocytes Mononuclear,Male,RNA Messenger,Single-Cell Analysis,Transcriptome}, |
|
| 12451 | + file = {/Users/rmorin/Zotero/storage/D9ZXFP9D/Zheng et al. - 2017 - Massively parallel digital transcriptional profili.pdf} |
|
| 12452 | +} |
|
| 12453 | + |
|
| 12454 | +@article{zhouSporadicEndemicBurkitt2019, |
|
| 12455 | + title = {Sporadic and Endemic {{Burkitt}} Lymphoma Have Frequent {{FOXO1}} Mutations but Distinct Hotspots in the {{AKT}} Recognition Motif}, |
|
| 12456 | + author = {Zhou, Peixun and Blain, Alex E. and Newman, Alexander M. and Zaka, Masood and Chagaluka, George and Adlar, Filbert R. and Offor, Ugonna T. and Broadbent, Casey and Chaytor, Lewis and Whitehead, Amber and Hall, Amy and O'Connor, Hettie and Van Noorden, Susan and Lampert, Irvin and Bailey, Simon and Molyneux, Elizabeth and Bacon, Chris M. and Bomken, Simon and Rand, Vikki}, |
|
| 12457 | + date = {2019-07-23}, |
|
| 12458 | + journaltitle = {Blood Advances}, |
|
| 12459 | + shortjournal = {Blood Adv}, |
|
| 12460 | + volume = {3}, |
|
| 12461 | + number = {14}, |
|
| 12462 | + eprint = {31300419}, |
|
| 12463 | + eprinttype = {pmid}, |
|
| 12464 | + pages = {2118--2127}, |
|
| 12465 | + issn = {2473-9537}, |
|
| 12466 | + doi = {10.1182/bloodadvances.2018029546}, |
|
| 12467 | + abstract = {FOXO1 has an oncogenic role in adult germinal center-derived lymphomas, in which mutations, predominately within the AKT recognition motif, cause nuclear retention of FOXO1, resulting in increased cell proliferation. To determine the prevalence and distribution of FOXO1 mutations in pediatric Burkitt lymphoma (BL), we sequenced a large number of sporadic and endemic BL patient samples. We report a high frequency of FOXO1 mutations in both sporadic and endemic BL at diagnosis, occurring in 23/78 (29\%) and 48/89 (54\%) samples, respectively, as well as 8/16 (50\%) cases at relapse. Mutations of T24 were the most common in sporadic BL but were rare in endemic cases, in which mutations of residue S22, also within the AKT recognition motif, were the most frequent. FOXO1 mutations were almost always present in the major tumor cell clone but were not associated with outcome. Analysis of other recurrent mutations reported in BL revealed that FOXO1 mutations were associated with mutations of DDX3X and ARID1A, but not MYC, TCF3/ID3, or members of the phosphatidylinositol 3-kinase signaling pathway. We further show common nuclear retention of the FOXO1 protein, irrespective of mutation status, suggesting alternative unknown mechanisms for maintaining FOXO1 transcriptional activity in BL. CRISPR/Cas9 knockout of FOXO1 in an endemic cell line produced a significant decrease in cell proliferation, supporting an oncogenic role for FOXO1 in endemic BL. Thus, FOXO1 is frequently mutated in both sporadic and endemic BL and may offer a potential therapeutic target for pediatric BL patients worldwide.}, |
|
| 12468 | + langid = {english}, |
|
| 12469 | + pmcid = {PMC6650741}, |
|
| 12470 | + keywords = {Adolescent,Binding Sites,Burkitt Lymphoma,Child,Child Preschool,DEAD-box RNA Helicases,DNA-Binding Proteins,Female,Forkhead Box Protein O1,Gene Frequency,Gene Knockout Techniques,High-Throughput Nucleotide Sequencing,Humans,Infant,Infant Newborn,Kaplan-Meier Estimate,Male,Mutation,Neoplasm Staging,Nucleotide Motifs,Protein Binding,Proto-Oncogene Proteins c-akt,Transcription Factors,Young Adult}, |
|
| 12471 | + file = {/Users/rmorin/Zotero/storage/X7679SD6/Zhou et al. - 2019 - Sporadic and endemic Burkitt lymphoma have frequen.pdf} |
|
| 12472 | +} |
|
| 12473 | + |
|
| 12474 | +@article{zhouStrongExpressionEZH2, |
|
| 12475 | + title = {Strong Expression of {{EZH2}} and Accumulation of Trimethylated {{H3K27}} in Diffuse Large {{B-cell}} Lymphoma Independent of Cell of Origin and {{EZH2}} Codon 641 Mutation.}, |
|
| 12476 | + author = {Zhou, Zheng and Gao, Juehua and Popovic, Relja and Wolniak, Kristy and Parimi, Vamsi and Winter, Jane N and Licht, Jonathan D and Chen, Yi-Hua}, |
|
| 12477 | + journaltitle = {Leuk lymphoma}, |
|
| 12478 | + volume = {56}, |
|
| 12479 | + number = {10}, |
|
| 12480 | + pages = {2895--2901}, |
|
| 12481 | + keywords = {nosource} |
|
| 12482 | +} |
|
| 12483 | + |
|
| 12484 | +@article{ziakasFcgRIIaH131RVariantAssociated2016, |
|
| 12485 | + title = {{{FcγRIIa-H131R}} Variant Is Associated with Inferior Response in Diffuse Large {{B}} Cell Lymphoma: {{A}} Meta-Analysis of Genetic Risk.}, |
|
| 12486 | + author = {Ziakas, Panayiotis D and Poulou, Loukia S and Zintzaras, Elias}, |
|
| 12487 | + date = {2016-11}, |
|
| 12488 | + journaltitle = {Journal of B.U.ON. : official journal of the Balkan Union of Oncology}, |
|
| 12489 | + volume = {21}, |
|
| 12490 | + number = {6}, |
|
| 12491 | + pages = {1454--1458}, |
|
| 12492 | + keywords = {nosource} |
|
| 12493 | +} |
reformat.pl
| ... | ... | @@ -0,0 +1,29 @@ |
| 1 | +#!/usr/bin/env perl |
|
| 2 | +use strict; |
|
| 3 | +chomp(my @md_files = `ls *md`); |
|
| 4 | +#my @md_files; |
|
| 5 | +for my $md_orig (@md_files){ |
|
| 6 | + open F, $md_orig; |
|
| 7 | + chomp(my @lines = <F>); |
|
| 8 | + close F; |
|
| 9 | + my $found = grep /Mutation\stier/, @lines; |
|
| 10 | + if($found){ |
|
| 11 | + print "$md_orig"; |
|
| 12 | + my $line_num = 1; |
|
| 13 | + system("cp $md_orig backup/$md_orig.save"); |
|
| 14 | + open F, ">$md_orig\n"; |
|
| 15 | + for(@lines){ |
|
| 16 | + if($line_num==1){ |
|
| 17 | + s/[\]\[]+//g; |
|
| 18 | + } |
|
| 19 | + $line_num++; |
|
| 20 | + s/Mutation\stier/Relevance tier by entity/; |
|
| 21 | + s/\#\#\sMutation\sincidence/\n## Mutation incidence in large patient cohorts (GAMBL reanalysis)/; |
|
| 22 | + s/Mutation\spattern/Mutation pattern and selective pressure estimates/; |
|
| 23 | + print F "$_\n"; |
|
| 24 | + } |
|
| 25 | + close F; |
|
| 26 | + #die; |
|
| 27 | + } |
|
| 28 | +} |
|
| 29 | + |