Genomic disruption of the histone methyltransferase SETD2 in chronic lymphocytic leukaemia

Abstract

Histone methyltransferases (HMTs) are important epigenetic regulators of gene transcription and are disrupted at the genomic level in a spectrum of human tumours including haematological malignancies. Using high-resolution single nucleotide polymorphism (SNP) arrays, we identified recurrent deletions of the SETD2 locus in 3% (8/261) of chronic lymphocytic leukaemia (CLL) patients. Further validation in two independent cohorts showed that SETD2 deletions were associated with loss of TP53, genomic complexity and chromothripsis. With next-generation sequencing we detected mutations of SETD2 in an additional 3.8% of patients (23/602). In most cases, SETD2 deletions or mutations were often observed as a clonal event and always as a mono-allelic lesion, leading to reduced mRNA expression in SETD2-disrupted cases. Patients with SETD2 abnormalities and wild-type TP53 and ATM from five clinical trials employing chemotherapy or chemo-immunotherapy had reduced progression-free and overall survival compared with cases wild type for all three genes. Consistent with its postulated role as a tumour suppressor, our data highlight SETD2 aberration as a recurrent, early loss-of-function event in CLL pathobiology linked to aggressive disease.

Figure 1

SETD2 deletions in our discovery, extension and ultra-high-risk cohorts. (a) SNP6.0 data for the del(3p) cases. Genomic location is indicated by the ladder to the left. Each column represents one patient. Loss, gain and normal copy number are shown as blue, red and white, respectively. The black box indicates the MDR, and is displayed in greater detail for our discovery and extension cohorts. The genes in the MDR with their transcriptional direction are displayed in the middle, with the MDR from the discovery and extension cohorts shown by the red and purple bars, respectively. (b) Matrix displaying the biomarkers and genomic features associated with del(3p) cases with the discovery, extension and ultra-high-risk cases shown in red, purple and yellow, respectively. (c) Real-time PCR expression for the five genes localized in the discovery MDR in cases with or without del(3p). All the samples were negative for KIF9. 18 s was employed as housekeeping gene. Expression in normal B-cells was used as a normalization sample. Mean±s.d. is represented. (d) Scatterplots displaying the number of CNA observed in subgroups of our cohort (excluding ultra-high-risk cases). Cases were assigned to a subgroup using a hierarchical model; presence of del(17p) and/or TP53 mutation, then del(11q) and/or ATM mutation, then del(3p) cases with and without TP53 abnormalities and then wild-type (WT) cases containing no del(17p), del(11q), del(3p) or mutations in ATM and TP53. Mean±s.d. is represented.

Figure 2

SETD2 mutations in our discovery and extension cohorts. (a) Schematic diagram of the Setd2 protein with their key functional domains. Mutations are displayed in the diagram. The colour denotes the cohort, and the filled circles are mutations that have been confirmed as somatically acquired. (b) Matrix displaying the biomarkers and genomic features associated with SETD2-mutated cases in the discovery (red) and extension (purple) cases. (c) Analysis of the clonality for SETD2 and other recurrently mutated genes on CLL. For each case the cancer cell fraction (CCF) is derived manually or with the ABSOLUTE algorithm. Only somatically acquired validated mutations are displayed (cases 69, 100, S21 and 88). The number of mutations (n) for each gene in the analysis is shown (bottom). (d) Percentage of cases harbouring clonal or subclonal mutations for each of the genes displayed. (e) Kaplan–Meier and log-rank analysis for progression-free survival (PFS) in patients carrying SETD2 abnormalities (‘SETD2 ab') but wild type for TP53 or ATM deletion and/or mutation compared with those with TP53 abnormalities (‘TP53 ab') and those wild type for TP53, ATM and SETD2 (‘wild type'). (f) Kaplan–Meier and log-rank analysis for overall survival (OS) in the same categories described in (e).