Whole-genome sequencing of chronic lymphocytic leukaemia reveals distinct differences in the mutational landscape between IgHVmut and IgHVunmut subgroups

Abstract

Chronic lymphocytic leukaemia (CLL) consists of two biologically and clinically distinct subtypes defined by the abundance of somatic hypermutation (SHM) affecting the Ig variable heavy-chain locus (IgHV). The molecular mechanisms underlying these subtypes are incompletely understood. Here, we present a comprehensive whole-genome sequencing analysis of somatically acquired genetic events from 46 CLL patients, including a systematic comparison of coding and non-coding single-nucleotide variants, copy number variants and structural variants, regions of kataegis and mutation signatures between IgHVmut and IgHVunmut subtypes. We demonstrate that one-quarter of non-coding mutations in regions of kataegis outside the Ig loci are located in genes relevant to CLL. We show that non-coding mutations in ATM may negatively impact on ATM expression and find non-coding and regulatory region mutations in TCL1A, and in IgHVunmut CLL in IKZF3, SAMHD1,PAX5 and BIRC3. Finally, we show that IgHVunmut CLL is dominated by coding mutations in driver genes and an aging signature, whereas IgHVmut CLL has a high incidence of promoter and enhancer mutations caused by aberrant activation-induced cytidine deaminase activity. Taken together, our data support the hypothesis that differences in clinical outcome and biological characteristics between the two subgroups might reflect differences in mutation distribution, incidence and distinct underlying mutagenic mechanisms.

Single-cell whole-genome sequencing reveals the functional landscape of somatic mutations in B lymphocytes across the human lifespan

“…While not significant (P=0.134, one tailed Fisher's exact test) this finding contributes to the notion that the hotspots we found are AID off-targets. Indeed, this conclusion is strengthened by the fact that about half of the 24 hotspots have been reported in other studies as associated with human lymphoma, leukemia, or AID off-target loci in mouse B cells 24,25,[27][28][29][30][31] (Supplementary Table 4). Moreover, the hotspots significantly overlap with or are close to open chromatin regions, transcription start sites (TSS), and transcription factor (TF) binding sites associated with AID binding (Supplementary Table 4; Methods).…”

Second primary cancers in patients with acute lymphoblastic, chronic lymphocytic and hairy cell leukaemia

“…CLL can be divided into two main subtypes, according to whether CLL cells express an unmutated or mutated immunoglobulin heavy‐chain variable region gene (Kipps et al , ). Numerous genetic changes take place during the evolution of CLL, including somatic mutations and chromosomal aberrations (Kipps et al , ; Burns et al , ). Many patients are diagnosed at an asymptomatic stage with monoclonal B‐cell lymphocytosis and may not initially require treatment, but once entering the symptomatic stage management strategies include chemotherapy with alkylating agents and purine analogues, combination of chemotherapy and immunotherapy, and recently, drugs that target key signalling pathways (Kristinsson et al , ; Nabhan & Rosen, ; Kipps et al , ).…”

The diagnostic chronic lymphocytic leukaemia genome by nanopore sequencing

“…Our study cohort was recruited from our own CLL database, and was selected by the presence of TP53 mutations and del17p13.1. The 11 samples included both mutated (n=5) and unmutated (n=6) IgHV genes (including three cases with two rearrangements each), seven mutations in TP53 (five missense, one stop gain and one frameshift deletion) and four del17p13.1events (table 1), previously identified through at least one of either short-read whole genome sequencing 23 (WGS), whole transcriptome sequencing 23,24 (WTS), targeted deep-sequencing 25 or Sanger sequencing 24 . Genomic DNA was extracted from peripheral blood samples of the 12 untreated CLL patients using a Qiagen DNA Blood mini kit (Qiagen, Hilden, Germany).…”