Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing

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.next-generation sequencing | human genetics | activation-induced deaminase D iffuse large B-cell lymphoma (DLBCL) is an aggressive nonHodgkin lymphoma that affects 30,000 new patients in the United States every year (1, 2). The standard of care for the treatment of most cases of DLBCL is the R-CHOP regimen (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone) consisting of multiagent chemotherapy plus a therapeutic antibody directed against CD20, a marker of B lymphocytes. The 3-year event-free survival rate is approximately 60%, with the majority of the remaining 40% dying of their disease (3). To date, treatment strategies to improve outcome have largely included increased doses of standard agents in the context of autologous stem cell transplantation (4). Therefore, there is a great medical need to define the genetic abnormalities that are associated with DLBCL to define novel targets for therapy.Germinal centers (GCs) in lymphoid tissues are sites of clonal expansion and editing of the Ig receptor in B lymphocytes, and this GC reaction is a physiological component of the humoral immune response. Somatic hypermutation (SHM) is part of the GC reaction, and its dysregulation contributes to the accumulation of somatic mutations in oncogenes and tumor-suppressor genes in B lymphocytes.Traditionally, DLBCL has been classified by the morphology and immunophenotype of the malignant B-cells but more recently, molecular classifications have been reported. Specifically, gene expression-based classification o...

Baraitser–Winter cerebrofrontofacial syndrome: delineation of the spectrum in 42 cases

“…27 Recurrent somatic ACTB mutations were found in 5/55 diffuse large B-cell lymphomas. 28 This finding is compatible with previous observations, that the cytoskeleton has a pivotal role in regulating the early events of B-cell activation. 29 Actin and actin-related proteins are subunits of the BAF/PBAF (Polybromo-associated-BRG1-or HRBM-associated factors) chromatin remodeling complex (homolog to the SWI/SNF or SWItch/Sucrose Non-Fermentable complex of yeast), which regulates DNA transcription, synthesis and repair.…”

Benign and malignant tumors in Rubinstein–Taybi syndrome

“…Since somatic CREBBP mutation is a very frequent early event in follicular B‐cell lymphoma and diffuse large B‐cell lymphoma (Lohr et al, 2012; Morin et al, 2011; Pasqualucci et al, 2011; Zhang et al, 2011), this case was studied for somatic CREBBP alterations (Stevens et al, 2017). A somatic CREBBP mutation on one allele was found (His1438Asp, variant allele frequency [VAF] 25%), while the known germline mutation ( CREBBP c.4837delG) was found in only 6% of sequence reads.…”

“…Mutations in CREBBP and EP300 have been demonstrated in various benign and malignant tumors, including in up to 40% of diffuse large cell B‐cell lymphoma (DLBCL) and follicular lymphoma cases (Lohr et al, 2012; Morin et al, 2011; Pasqualucci et al, 2011; Zhang et al, 2011). A specific type of acute myeloid leukemia is associated with a chromosomal translocation involving CREBBP (Rozman et al, 2004).…”

A double blinded, placebo-controlled pilot study to examine reduction of CD34+/CD117+/CD133+ lymphoma progenitor cells and duration of remission induced by neoadjuvant valspodar in dogs with large B-cell lymphoma

“…The gene encoding the enhancer of zeste homolog 2 (EZH2) had gain of function mutations in 7/49 (14%) DLBCL patients sequenced 48 . EZH2 is a histone methyltransferase that functions as part of the polycomb group complex, which controls the balance between self-renewal and differentiation 49 .…”