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+@article{balSuperenhancerHypermutationAlters2022,
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+ title = {Super-Enhancer Hypermutation Alters Oncogene Expression in {{B}} Cell Lymphoma},
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+ 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},
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+ date = {2022-07},
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+ journaltitle = {Nature},
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+ shortjournal = {Nature},
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+ volume = {607},
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+ number = {7920},
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+ eprint = {35794478},
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+ eprinttype = {pmid},
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+ pages = {808--815},
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+ issn = {1476-4687},
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+ doi = {10.1038/s41586-022-04906-8},
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+ 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.},
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+ langid = {english},
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+ pmcid = {PMC9583699},
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+ keywords = {Down-Regulation,Enhancer Elements Genetic,Gene Expression Regulation Neoplastic,Humans,Lymphoma Large B-Cell Diffuse,mustread,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},
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+ file = {/Users/rmorin/Zotero/storage/AU9PZ65P/Bal et al. - 2022 - Super-enhancer hypermutation alters oncogene expre.pdf}
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+}
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@article{deschGenotypingCirculatingTumor2020,
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title = {Genotyping Circulating Tumor {{DNA}} of Pediatric {{Hodgkin}} Lymphoma},
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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},