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.

Coding and non-coding drivers of mantle cell lymphoma identified through exome and genome sequencing

“…DNA extracted from 212 formalin-fixed paraffin-embedded (FFPE) diagnostic MCL tumor biopsies were used to generate libraries that were enriched for exons corresponding to a set of putative MCL-related genes using a hybridization-based capture approach involving complementary DNA oligonucleotides 30 . These were pooled and sequenced using a MiSeq (Illumina).…”

“…Variants from targeted sequencing cases that did not overlap with exome or genome cases were included in the final variant set. We compared the mutation patterns to diffuse large B-cell lymphoma (DLBCL) using targeted and exome sequencing data from 1616 unique patients 30,33,34 and removed variants with minor allele frequencies greater than 0.0001 in any gnomAD population 31 .…”

Molecular pathogenesis of germinal center‐derived B cell lymphomas

“…92,95,134,[156][157][158] Of over 700 genes that have been found mutated in these tumors, ~150 have been catalogued as significant genetic drivers of the disease based on recurrence and mutation features, with a median of 17 drivers/case in the coding genome. 102,103,159 Further genetic diversity is conferred by the significant intratumor heterogeneity, which has only been marginally addressed but may play important roles particularly in the context of chemorefractoriness and relapsed disease, as it could facilitate the emergence of minor clones with improved fitness and acquired resistance to therapy. This includes sequences potentially affected by ASHM, long non-coding RNAs, microRNAs, and other putative cis-regulatory regions.…”

“…Supporting this view, initial sequencing studies have uncovered the presence of mutational hotspots in several non-coding regions of the DLBCL genome, with some preference for putative enhancers. 102,103,159 Further genetic diversity is conferred by the significant intratumor heterogeneity, which has only been marginally addressed but may play important roles particularly in the context of chemorefractoriness and relapsed disease, as it could facilitate the emergence of minor clones with improved fitness and acquired resistance to therapy. 160 While some of the identified hits can be found in both transcriptional subtypes of DLBCL, likely reflecting more general mechanisms of malignant transformation, a variety of recurrent oncogenic lesions show preferential distribution in GCB-and ABC-DLBCL (next sections, and recent review).…”

Robust gene expression-based classification of cancers without normalization

“…Mutations from a targeted sequencing a panel of lymphoma-related genes [31] were reduced to a mutation matrix where known targets of non-synonymous or hotspot mutations were binary coded as mutated or unmutated. Known targets of aberrant somatic hypermutation (aSHM) were coded according to the number of mutations within the typical target region for aSHM, defined for each gene as the region proximal to the transcription start site containing high frequency of either coding and non-coding mutations.…”