Follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL) are the two most common non-Hodgkin lymphomas (NHLs). To identify genes with mutations in B-cell NHL we sequenced tumour and matched normal DNA from 13 DLBCL cases and one FL case. 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. 11.4% of DLBCL and 13.4% of FL cases had somatic mutations in MEF2B, a calcium-regulated gene that cooperates with CREBBP and EP300 in acetylating histones. Our analysis thus suggests a previously unappreciated disruption of chromatin biology in lymphomagenesis.

A B S T R A C T PurposeDiffuse large B-cell lymphoma (DLBCL) is curable in 60% of patients treated with rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP). MYC translocations, with or without BCL2 translocations, have been associated with inferior survival in DLBCL. We investigated whether expression of MYC protein, with or without BCL2 protein expression, could risk-stratify patients at diagnosis. Patients and MethodsWe determined the correlation between presence of MYC and BCL2 proteins by immunohistochemistry (IHC) with survival in two independent cohorts of patients with DLBCL treated with R-CHOP. We further determined if MYC protein expression correlated with high MYC mRNA and/or presence of MYC translocation. ResultsIn the training cohort (n ϭ 167), MYC and BCL2 proteins were detected in 29% and 44% of patients, respectively. Concurrent expression (MYC positive/BCL2 positive) was present in 21% of patients. MYC protein correlated with presence of high MYC mRNA and MYC translocation (both P Ͻ .001), but the latter was less frequent (both 11%). MYC protein expression was only associated with inferior overall and progression-free survival when BCL2 protein was coexpressed (P Ͻ .001). Importantly, the poor prognostic effect of MYC positive/BCL2 positive was validated in an independent cohort of 140 patients with DLBCL and remained significant (P Ͻ .05) after adjusting for presence of high-risk features in a multivariable model that included elevated international prognostic index score, activated B-cell molecular subtype, and presence of concurrent MYC and BCL2 translocations. ConclusionAssessment of MYC and BCL2 expression by IHC represents a robust, rapid, and inexpensive approach to risk-stratify patients with DLBCL at diagnosis.

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Approximately 5% to 10% of diffuse large B-cell lymphomas (DLBCLs) harbor an MYC oncogene rearrangement (MYC ؉ ). The prognostic significance of MYC ؉ DLBCL was determined in an unselected population of patients with newly diagnosed DLBCL treated with rituximab in combination with cyclophosphamide, doxorubicin, vincristine, and prednisone chemotherapy (R-CHOP). Using a Vysis break-apart fluorescence in situ hybridization probe, 12 of 135 (8.8%) cases of MYC ؉ DLBCL were identified that had no defining high-risk features. MYC ؉ DLBCL was associated with an inferior 5-year progression-free survival (66% vs 31%, P ‫؍‬ .006) and overall survival (72% vs 33%, P ‫؍‬ .016). Multivariate analysis confirmed the prognostic importance of MYC for both progression-free survival (hazard ratio ‫؍‬ 3.28; 95% confidence interval, 1.49-7.21, P ‫؍‬ .003) and overall survival (hazard ratio ‫؍‬ 2.98; 95% confidence interval, 1.28-6.95, P ‫؍‬ .011). Cases of MYC ؉ DLBCL also had a higher risk of central nervous system relapse (P ‫؍‬ . IntroductionDiffuse large B-cell lymphomas (DLBCLs) are recognized to be a heterogeneous group of diseases with clinical, morphologic, immunohistochemical, and molecular subtypes defined in the updated World Health Organization (WHO) classification. 1 Further, a new category has been created defined as "borderline cases," which are considered B-cell lymphomas, unclassifiable, with features intermediate between DLBCL and Burkitt lymphoma. 2 Morphologically, these tumors typically have a mixture of medium-to large-sized cells, a high proliferation rate, and 35% to 50% of cases have an 8q24/MYC translocation. 2 However, approximately 5% to 10% of DLBCLs with typical morphology also harbor an MYC rearrangement (herein after referred to as MYC ϩ ), and these cases are considered in the category of DLBCL, not otherwise specified, in the updated WHO classification. 3 There is very little information regarding the prognostic importance of an isolated MYC rearrangement in DLBCL using modern diagnostic criteria. A recent study suggested that MYC gene rearrangements identified by fluorescence in situ hybridization (FISH) in pathologically defined DLBCL patients treated with cyclophosphamide, doxorubicin, vincristine, prednisone (CHOP)-like chemotherapy are associated with an inferior prognosis. 4 However, it is unclear whether there are identifiable clinical or pathologic characteristics that suggest that a case may harbor an MYC rearrangement to prompt evaluation. Further, prior studies evaluating the prognostic implications of MYC in DLBCL have been performed before the use of rituximab. With studies showing improved outcome using rituximab in combination with CHOP (R-CHOP) or CHOP-like therapies in the treatment of DLBCL, 5-8 the importance of MYC rearrangement status in this population must be reestablished.The purpose of this study was 2-fold: (1) to screen an unselected series of patients with DLBCL for MYC rearrangements to determine the frequency of this occurrence and whether there were any pathologic or ...

Key Points• Complete genome sequence analysis of 40 DLBCL tumors and 13 cell lines reveals novel somatic point mutations, rearrangements, and fusions. • Recurrence of mutations in genes involved in B-cell homing were identified in germinal center B-cell DLBCLs.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 RNAseq 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. (Blood. 2013;122(7):1256-1265 Introduction Diffuse large B-cell lymphoma (DLBCL) is an aggressive nonHodgkin lymphoma (NHL) with at least 2 molecular subtypes that demonstrate distinct clinical outcomes and gene expression profiles. Because these cancers derive from mature B cells, the mutations that arise in DLBCLs can result from somatic hypermutation that targets a small number of genes, 1 as well as structural rearrangements that arise from double-strand breaks that can be initiated by the B-cell recombination apparatus. In recent years, multiple groups have used massively parallel sequencing (genome/ exome sequencing and RNA-seq) to ascertain the full set of genes targeted by somatic single-nucleotide variants (SNVs) in this disease.2-5 On the basis of these and earlier studies, 6 it is now known that the 2 molecular subtypes also harbor distinct repertoires of somatic copy number alterations (CNAs) and SNVs. In particular, mutations affecting genes involved in B-cell receptor signaling and nuclear factor kB are common in the activated B-cell variety, 7 whereas those affecting certain genes with roles in histone modification may be more common in the germinal center B-cell (GCB) subtype. 2,8,9 These studies have confirmed t...