8dc46ef3feba5d121df036f5090b8d27d2f62b5f
DLBCL_genes.md
| ... | ... | @@ -11,7 +11,7 @@ link-citations: true |
| 11 | 11 | |
| 12 | 12 | ## Tier 1 DLBCL genes |
| 13 | 13 | |
| 14 | -### *125 total* |
|
| 14 | +### *126 total* |
|
| 15 | 15 | |
| 16 | 16 | |Gene|Summary| First DLBCL study | Other entities | QC result | |
| 17 | 17 | |:-:|:-:|:-:|:-|:-| |
| ... | ... | @@ -91,6 +91,7 @@ link-citations: true |
| 91 | 91 | |[MEF2B](MEF2B)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@yingMEF2BMutationsLead]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@beaLandscapeSomaticMutations2013]|| |
| 92 | 92 | |[MEF2C](MEF2C)|Tier 1 GE[@arthurGenomewideDiscoverySomatic2018], FE[@jingjingNovelMEF2CMutation2020]|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)||| |
| 93 | 93 | |[MGA](MGA)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017], CE[@guoSGK1MutationStatus2022b]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@jalladesExomeSequencingIdentifies2017]|| |
| 94 | +|[MIR142](MIR142)|Tier 1 GE[@kwanhianMicroRNA142Mutated202012b]|[Kwanhian et al](papers/kwanhianMicroRNA142Mutated202012b)|[@grandeGenomewideDiscoverySomatic2019]|| |
|
| 94 | 95 | |[MPEG1](MPEG1)|Tier 1 GE[@morinMutationalStructuralAnalysis2013], CE[@guoSGK1MutationStatus2022b]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)||| |
| 95 | 96 | |[MS4A1](MS4A1)|Tier 1 GE[@rushtonGeneticEvolutionaryPatterns2020], FE[@rushtonGeneticEvolutionaryPatterns2020], CE[@rushtonGeneticEvolutionaryPatterns2020]|[Rushton et al](papers/rushtonGeneticEvolutionaryPatterns2020)|[@mottokIntegrativeGenomicAnalysis2019b]|| |
| 96 | 97 | |[MTOR](MTOR)|Tier 1 GE[@zhangGeneticHeterogeneityDiffuse2013]|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)|[@paneaWholeGenomeLandscape2019]|| |
| ... | ... | @@ -120,7 +121,7 @@ link-citations: true |
| 120 | 121 | |[SGK1](SGK1)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@hartmannHighlyRecurrentMutations2016b], CE[@guoSGK1MutationStatus2022b]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@dunsCharacterizationDLBCLPMBL2021b]|| |
| 121 | 122 | |[SIN3A](SIN3A)|Tier 1 GE[@chapuyMolecularSubtypesDiffuse2018b]|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)|[@grandeGenomewideDiscoverySomatic2019; @rossiCodingGenomeSplenic2012c]|| |
| 122 | 123 | |[SMARCA4](SMARCA4)|Tier 1 GE[@reddyGeneticFunctionalDrivers2017], FE[@dengSMARCA4HaploinsufficientCell2024]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@krysiakRecurrentSomaticMutations2017b; @nadeuGenomicEpigenomicInsights2020b; @richterRecurrentMutationID32012a]|| |
| 123 | -|[SOCS1](SOCS1)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@wenigerMutationsTumorSuppressor2006a]|| |
|
| 124 | +|[SOCS1](SOCS1)|Tier 1 GE[@morinFrequentMutationHistonemodifying2011], FE[@melznerBiallelicMutationSOCS12005a]|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)|[@wenigerMutationsTumorSuppressor2006a]|| |
|
| 124 | 125 | |[SPEN](SPEN)|Tier 1 GE[@albuquerqueEnhancingKnowledgeDiscovery2017a], CE[@guoSGK1MutationStatus2022b]|[Albuquerque et al](papers/albuquerqueEnhancingKnowledgeDiscovery2017a)|[@rossiCodingGenomeSplenic2012c; @sarkozyMutationalLandscapeGray2021a]|| |
| 125 | 126 | |[STAT3](STAT3)|Tier 1 GE[@lohrDiscoveryPrioritizationSomatic2012a], FE[@huNovelMissenseM206K2013b]|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)||| |
| 126 | 127 | |[STAT6](STAT6)|Tier 1 GE[@yildizActivatingSTAT6Mutations2015c], FE[@yildizActivatingSTAT6Mutations2015c]|[Yildiz et al](papers/yildizActivatingSTAT6Mutations2015c)|[@ritzRecurrentMutationsSTAT62009a]|| |
| ... | ... | @@ -143,7 +144,7 @@ link-citations: true |
| 143 | 144 | |
| 144 | 145 | ## Tier 2 DLBCL genes |
| 145 | 146 | |
| 146 | -### *180 total* |
|
| 147 | +### *179 total* |
|
| 147 | 148 | |
| 148 | 149 | |Gene|Summary| First DLBCL study | Other entities | QC result | |
| 149 | 150 | |:-:|:-:|:-:|:-|:-| |
| ... | ... | @@ -235,7 +236,6 @@ link-citations: true |
| 235 | 236 | |[MCL1](MCL1)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)|[@dunsCharacterizationDLBCLPMBL2021b; @paneaWholeGenomeLandscape2019]|PASS| |
| 236 | 237 | |[MECOM](MECOM)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS| |
| 237 | 238 | |[MET](MET)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS| |
| 238 | -|[MIR142](MIR142)|Tier 2 GE[@kwanhianMicroRNA142Mutated202012b]|[Kwanhian et al](papers/kwanhianMicroRNA142Mutated202012b)|[@grandeGenomewideDiscoverySomatic2019]|| |
|
| 239 | 239 | |[MIR155HG](MIR155HG)|Tier 2 GE|||| |
| 240 | 240 | |[MPDZ](MPDZ)|Tier 2 GE[@morinMutationalStructuralAnalysis2013]|[Morin et al](papers/morinMutationalStructuralAnalysis2013)|[@reichelFlowSortingExome2015a]|PASS| |
| 241 | 241 | |[MSH6](MSH6)|Tier 2 GE[@reddyGeneticFunctionalDrivers2017]|[Reddy et al](papers/reddyGeneticFunctionalDrivers2017)||PASS| |
morinlab.bib
| ... | ... | @@ -1,3 +1,21 @@ |
| 1 | +@article{melznerBiallelicMutationSOCS12005a, |
|
| 2 | + title = {Biallelic Mutation of {{SOCS-1}} Impairs {{JAK2}} Degradation and Sustains Phospho-{{JAK2}} Action in the {{MedB-1}} Mediastinal Lymphoma Line}, |
|
| 3 | + author = {Melzner, Ingo and Bucur, Alexandra Juliana and Brüderlein, Silke and Dorsch, Karola and Hasel, Cornelia and Barth, Thomas F. E. and Leithäuser, Frank and Möller, Peter}, |
|
| 4 | + date = {2005-03-15}, |
|
| 5 | + journaltitle = {Blood}, |
|
| 6 | + shortjournal = {Blood}, |
|
| 7 | + volume = {105}, |
|
| 8 | + number = {6}, |
|
| 9 | + eprint = {15572583}, |
|
| 10 | + eprinttype = {pmid}, |
|
| 11 | + pages = {2535--2542}, |
|
| 12 | + issn = {0006-4971}, |
|
| 13 | + doi = {10.1182/blood-2004-09-3701}, |
|
| 14 | + abstract = {Primary mediastinal B-cell lymphoma (PMBL) is a well-defined subtype of diffuse large B-cell lymphoma. Molecular cytogenetics revealed frequent gains of 9p24. JAK2, mapping in this region, is presently regarded as a candidate oncogene because expression profiling showed high Janus kinase-2 (JAK2) transcript levels and JAK2 was found to be constitutively phosphorylated in mediastinal B-cell lymphomas. We confirm that in the MedB-1 mediastinal B-cell line, harboring a trisomy 9, JAK2 transcription is elevated and the product is highly phosphorylated. However, JAK2 is not overexpressed at the protein level. On top, JAK2 protein turnover is even delayed. This unexpected finding coincides with a biallelic mutation of the suppressor of cytokine signaling-1 (SOCS-1) gene in this cell, which abrogates SOCS box function of the protein. Ectopic expression of wild-type (wt) SOCS-1 in MedB-1 leads to growth arrest and dramatic reduction of phospho-JAK2 and its downstream partner phospho-signal transducer and activator of transcription-5 (phospho-STAT5). Ultimately, the target gene cyclin D1 is repressed in transfectants while RB1, which is silenced in MedB-1, is induced. We conclude that, in MedB-1, action of phospho-JAK2 is sustained due to defective SOCS-1. Hence, SOCS-1 qualifies as a novel tumor suppressor. Of note, SOCS-1 mutations are also present in the parental tumor of MedB-1 and were detected in 9 of 20 PMBLs.}, |
|
| 15 | + langid = {english}, |
|
| 16 | + keywords = {Alleles,Cell Line Tumor,Chromosomes Human Pair 9,Cyclin D1,Gene Expression Regulation Leukemic,Humans,Intracellular Signaling Peptides and Proteins,Janus Kinase 2,Lymphoma B-Cell,Mediastinal Neoplasms,Mutation,Phosphorylation,Protein Processing Post-Translational,Protein-Tyrosine Kinases,Proto-Oncogene Proteins,Repressor Proteins,Retinoblastoma Protein,Signal Transduction,STAT5 Transcription Factor,Suppressor of Cytokine Signaling 1 Protein,Suppressor of Cytokine Signaling Proteins,Trisomy,Tumor Suppressor Proteins} |
|
| 17 | +} |
|
| 18 | + |
|
| 1 | 19 | @article{hakemCaspase8EssentialMaintaining2012, |
| 2 | 20 | title = {Caspase-8 Is Essential for Maintaining Chromosomal Stability and Suppressing {{B-cell}} Lymphomagenesis}, |
| 3 | 21 | author = {Hakem, Anne and El Ghamrasni, Samah and Maire, Georges and Lemmers, Benedicte and Karaskova, Jana and Jurisicova, Andrea and Sanchez, Otto and Squire, Jeremy and Hakem, Razqallah}, |