4c3df70b90f6d190ecf893de69de39bf3cd1ac40
FOXO1.md
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| 1 | +--- |
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| 2 | +bibliography: 'morinlab.bib' |
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| 3 | +csl: 'NLM.csl' |
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| 4 | +link-citations: true |
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| 5 | +--- |
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| 1 | 6 | # FOXO1 |
| 2 | 7 | |
| 3 | 8 | ## Overview |
| 4 | 9 | Mutations in the FOXO1 gene, which encodes a member of the forkhead family of transcription factors, play a significant role in diffuse large B-cell lymphoma (DLBCL). Mutations primarily occur in the first exon, with significant portions affecting the N-terminal region and the Forkhead DNA binding domain.<sup>1</sup> These mutations are common in DLBCL, BL and, to a lesser extent, FL.<sup>2,3</sup> FOXO1 mutations can contribute to resistance to certain therapies, such as anti-CD20-based immunotherapies, by repressing MS4A1 (CD20) expression.<sup>4</sup> |
| 10 | + |
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| 5 | 11 | ## History |
| 6 | 12 | ```mermaid |
| 7 | 13 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -17,10 +23,10 @@ timeline |
| 17 | 23 | |Entity|Tier|Description | |
| 18 | 24 | |:------:|:----:|--------------------------| |
| 19 | 25 | ||1|high-confidence MZL gene| |
| 20 | -||2|relevance in PMBL/cHL/GZL not firmly established| |
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| 21 | -| |1 |high-confidence BL gene | |
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| 22 | -| |1 |high-confidence DLBCL gene| |
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| 23 | -| |1 |high-confidence FL gene | |
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| 26 | +||2|relevance in PMBL/cHL/GZL not firmly established[@dunsCharacterizationDLBCLPMBL2021b]| |
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| 27 | +| |1 |high-confidence BL gene [@schmitzBurkittLymphomaPathogenesis2012]| |
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| 28 | +| |1 |high-confidence DLBCL gene[@morinFrequentMutationHistonemodifying2011]| |
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| 29 | +| |1 |high-confidence FL gene [@morinFrequentMutationHistonemodifying2011]| |
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| 24 | 30 | |
| 25 | 31 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 26 | 32 |
GNA13.md
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| 1 | +--- |
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| 2 | +bibliography: 'morinlab.bib' |
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| 3 | +csl: 'NLM.csl' |
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| 4 | +link-citations: true |
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| 5 | +--- |
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| 1 | 6 | # GNA13 |
| 2 | 7 | |
| 3 | 8 | ## Overview |
| 4 | 9 | Mutations in GNA13, which encodes a G protein alpha subunit involved in multiple signaling pathways, have been identified as significant contributors to the pathogenesis of germinal centre-derived B-cell lymphomas, including diffuse large B-cell lymphoma (DLBCL) and Burkitt lymphoma (BL).<sup>1</sup> This gene has some recurrent sites of mutations (hot spots). Overall, mutations are often loss-of-function in nature, disrupting the normal activity of GNA13. GNA13 regulates B-cell homing and growth suppression within the germinal center niche and its loss of function promotes lymphoma development.<sup>2</sup> |
| 10 | + |
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| 5 | 11 | ## History |
| 6 | 12 | |
| 7 | 13 | ```mermaid |
| ... | ... | @@ -17,10 +23,10 @@ timeline |
| 17 | 23 | |
| 18 | 24 | |Entity|Tier|Description | |
| 19 | 25 | |:------:|:----:|--------------------------| |
| 20 | -||1|high-confidence PMBL/cHL/GZL gene| |
|
| 21 | -| |1 |high-confidence BL gene | |
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| 22 | -| |1 |high-confidence DLBCL gene| |
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| 23 | -| |1 |high-confidence FL gene | |
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| 26 | +||1|high-confidence PMBL/cHL/GZL gene[@reichelFlowSortingExome2015a]| |
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| 27 | +| |1 |high-confidence BL gene [@loveGeneticLandscapeMutations2012]| |
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| 28 | +| |1 |high-confidence DLBCL gene[@morinFrequentMutationHistonemodifying2011]| |
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| 29 | +| |1 |high-confidence FL gene [@morinFrequentMutationHistonemodifying2011]| |
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| 24 | 30 | |
| 25 | 31 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 26 | 32 |
ID3.md
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| 1 | +--- |
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| 2 | +bibliography: 'morinlab.bib' |
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| 3 | +csl: 'NLM.csl' |
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| 4 | +link-citations: true |
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| 5 | +--- |
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| 1 | 6 | # ID3 |
| 2 | 7 | |
| 3 | 8 | ## History |
| 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> |
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| 9 | +ID3 was first reported as mutated in BL in 2012 by Richter et al.[@richterRecurrentMutationID32012a] |
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| 10 | +The existence of mutations in DLBCL were described in 2012 by Schmitz et al[@schmitzBurkittLymphomaPathogenesis2] and later in MZL by Spina et al.[@spinaGeneticsNodalMarginal2016b] |
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| 5 | 11 | |
| 6 | 12 | ```mermaid |
| 7 | 13 | %%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% |
| ... | ... | @@ -16,9 +22,9 @@ ID3 was first reported as mutated in BL in 2012 by Richter et al.<sup>1</sup> Th |
| 16 | 22 | |
| 17 | 23 | |Entity|Tier|Description | |
| 18 | 24 | |:------:|:----:|-----------------------------------------| |
| 19 | -| |1 | high-confidence BL gene | |
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| 20 | -| |1 | high-confidence MZL gene | |
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| 21 | -| |2 | Although recurrent, the relevance of mutations in DLBCL is tenuous | |
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| 25 | +| |1 | high-confidence BL gene [@richterRecurrentMutationID32012a]| |
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| 26 | +| |1 | high-confidence MZL gene [@spinaGeneticsNodalMarginal2016b]| |
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| 27 | +| |2 | Although recurrent, the relevance of mutations in DLBCL is tenuous [@schmitzBurkittLymphomaPathogenesis2012]| |
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| 22 | 28 | |
| 23 | 29 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 24 | 30 | |
| ... | ... | @@ -59,9 +65,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I |
| 59 | 65 |  |
| 60 | 66 | |
| 61 | 67 | ## References |
| 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* |
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| 63 | -2. *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* |
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| 64 | -3. *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.* |
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| 65 | 68 | |
| 66 | 69 | <!-- ORIGIN: 22885699 --> |
| 67 | 70 | <!-- BL: richterRecurrentMutationID32012a --> |