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Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma.

ABSTRACT: Diffuse large B-cell lymphoma (DLBCL) is an aggressive cancer originating from mature B-cells. Prognosis is strongly associated with molecular subgroup, although the driver mutations that distinguish the two main subgroups remain poorly defined. Through an integrative analysis of whole genomes, exomes, and transcriptomes, we have uncovered genes and non-coding loci that are commonly mutated in DLBCL. Our analysis has identified novel cis-regulatory sites, and implicates recurrent mutations in the 3' UTR of NFKBIZ as a novel mechanism of oncogene deregulation and NF-κB pathway activation in the activated B-cell (ABC) subgroup. Small amplifications associated with over-expression of FCGR2B (the Fcγ receptor protein IIB), primarily in the germinal centre B-cell (GCB) subgroup, correlate with poor patient outcomes suggestive of a novel oncogene. These results expand the list of subgroup driver mutations that may facilitate implementation of improved diagnostic assays and could offer new avenues for the development of targeted therapeutics.

SUBMITTER: Arthur SE

PROVIDER: S-EPMC6167379 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma.

Arthur Sarah E SE Jiang Aixiang A Grande Bruno M BM Alcaide Miguel M Cojocaru Razvan R Rushton Christopher K CK Mottok Anja A Hilton Laura K LK Lat Prince Kumar PK Zhao Eric Y EY Culibrk Luka L Ennishi Daisuke D Jessa Selin S Chong Lauren L Thomas Nicole N Pararajalingam Prasath P Meissner Barbara B Boyle Merrill M Davidson Jordan J Bushell Kevin R KR Lai Daniel D Farinha Pedro P Slack Graham W GW Morin Gregg B GB Shah Sohrab S Sen Dipankar D Jones Steven J M SJM Mungall Andrew J AJ Gascoyne Randy D RD Audas Timothy E TE Unrau Peter P Marra Marco A MA Connors Joseph M JM Steidl Christian C Scott David W DW Morin Ryan D RD

Nature communications 20181001 1

Diffuse large B-cell lymphoma (DLBCL) is an aggressive cancer originating from mature B-cells. Prognosis is strongly associated with molecular subgroup, although the driver mutations that distinguish the two main subgroups remain poorly defined. Through an integrative analysis of whole genomes, exomes, and transcriptomes, we have uncovered genes and non-coding loci that are commonly mutated in DLBCL. Our analysis has identified novel cis-regulatory sites, and implicates recurrent mutations in th ...[more]

PMID: 30275490

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Project description:PurposeWe performed a multistage genome-wide association study to identify inherited genetic variants that predict outcome in diffuse large B-cell lymphoma patients treated with immunochemotherapy.MethodsWe conducted a meta-analysis of two genome-wide association study data sets, one from the LNH2003B trial (N = 540), a prospective clinical trial from the Lymphoma Study Association, and the other from the Molecular Epidemiology Resource study (N = 312), a prospective observational study from the University of Iowa-Mayo Clinic Lymphoma Specialized Program of Research Excellence. Top single nucleotide polymorphisms were then genotyped in independent cohorts of patients from the Specialized Program of Research Excellence (N = 391) and the Groupe Ouest-Est des Leucémies Aiguës et Maladies du Sang (GOELAMS) -075 randomized trial (N = 294). We calculated the hazard ratios (HRs) and 95% CIs for event-free survival (EFS) and overall survival (OS) using a log-additive genetic model with adjustment for age, sex, and age-adjusted International Prognostic Index.ResultsIn a meta-analysis of the four studies, the top loci for EFS were marked by rs7712513 at 5q23.2 (near SNX2 and SNCAIP; HR, 1.39; 95% CI, 1.23 to 1.57; P = 2.08 × 10(-7)), and rs7765004 at 6q21 (near MARCKS and HDAC2; HR, 1.38; 95% CI, 1.22 to 1.57; P = 7.09 × 10(-7)), although they did not reach conventional genome-wide significance (P = 5 × 10(-8)). Both rs7712513 (HR, 1.49; 95% CI, 1.29 to 1.72; P = 3.53 × 10(-8)) and rs7765004 (HR, 1.47; 95% CI, 1.27 to 1.71; P = 5.36 × 10(-7)) were also associated with OS. In exploratory analyses, a two-single nucleotide polymorphism risk score was highly predictive of EFS (P = 1.78 × 10(-12)) and was independent of treatment, IPI, and cell-of-origin classification.ConclusionOur study provides encouraging evidence for associations between loci at 5q23.2 and 6q21 with EFS and OS in patients with diffuse large B-cell lymphoma treated with immunochemotherapy, suggesting novel biology and the potential contribution of host genetics to the prognosis of this aggressive malignancy.

Dataset Information

Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma.

Publications

Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma.

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