Whole-genome sequencing of multiple myeloma reveals oncogenic pathways are targeted somatically through multiple mechanisms

Abstract

Multiple myeloma (MM) is a biologically heterogeneous malignancy, however, the mechanisms underlying this complexity are incompletely understood. We report an analysis of the whole-genome sequencing of 765 MM patients from CoMMpass. By employing promoter capture Hi-C in naïve B-cells, we identify cis-regulatory elements (CREs) that represent a highly enriched subset of the non-coding genome in which to search for driver mutations. We identify regulatory regions whose mutation significantly alters the expression of genes as candidate non-coding drivers, including copy number variation (CNV) at CREs of MYC and single-nucleotide variants (SNVs) in a PAX5 enhancer. To better inform the interplay between non-coding driver mutations with other driver mechanisms, and their respective roles in oncogenic pathways, we extended our analysis identifying coding drivers in 40 genes, including 11 novel candidates. We demonstrate the same pathways can be targeted by coding and non-coding mutations; exemplified by IRF4 and PRDM1, along with BCL6 and PAX5, genes that are central to plasma cell differentiation. This study reveals new insights into the complex genetic alterations driving MM development and an enhanced understanding of oncogenic pathways.

Fig. 1

Schematic analysis of the workflow. WES whole-exome sequencing, WGS whole-genome sequencing, SNV single-nucleotide variant, TSS transcription start site, CNV copy number variant, CRE cis-regulatory element

Fig. 2

SNVs at cis-regulatory elements affect gene expression in multiple myeloma. Mutations in the CRE significantly alter a PAX5 (n = 197 versus n = 13) and b ST6GAL1 (n = 315 versus n = 15) expression. Difference in expression was assessed pairwise by negative binomial test. *Q < 0.1, **Q < 0.05. The hinges of the boxplot indicate the first and third quartile range. c Chromatin looping interactions between PAX5 promoter and differentially expressed CRE. Also shown are the ChIP-seq signals and relative positions of SNVs

Fig. 3

Copy number variations at cis-regulatory elements affect MYC gene expression in multiple myeloma. a Upper panel shows MYC gene expression may be regulated by CREs; CNVs at either the upstream putative silencers or downstream putative enhancers causing upregulation of MYC. Middle panel shows chromatin looping interactions between MYC promoter and CREs. Lower panel details ChIP-seq signals and relative positions of CNVs at these CREs in naïve B-cells. b CNV status at CREs and MYC expression. Difference in expression was assessed pairwise between samples with different CNVs status and the same translocation status by negative binomial test. ***P < 0.01. Trans translocation, Del deletion. From left to right, n = 345, n = 9, respectively. The hinges of the boxplot indicate the first and third quartile range

Fig. 4

Several key pathways in multiple myeloma are disrupted by a range of mechanisms. Adapted from Manier et al. [1] and Kumar et al. [60]

Fig. 5

Mutational signatures in multiple myeloma. Mutational patterns of somatic mutations in CREs interacting with PAX5 promoters display both canonical (C > T/G in WRCY motifs with R = purine, Y = pyrimidine) and non-canonical (A > C/G in WA motifs) activation-induced cytidine deaminase (AID) signatures