Background GI stromal tumours (GISTs) are clinically heterogenous exhibiting varying degrees of disease aggressiveness in individual patients.
Objectives We sought to identify genetic alterations associated with high-risk GIST, explore their molecular consequences, and test their utility as prognostic markers.
Designs Exome sequencing of 18 GISTs was performed (9 patients with high-risk/metastatic and 5 patients with low/intermediate-risk), corresponding to 11 primary and 7 metastatic tumours. Candidate alterations were validated by prevalence screening in an independent patient cohort (n=120). Functional consequences of SETD2 mutations were investigated in primary tissues and cell lines. Transcriptomic profiles for 8 GISTs (4 SETD2 mutated, 4 SETD2 wild type) and DNA methylation profiles for 22 GISTs (10 SETD2 mutated, 12 SETD2 wild type) were analysed. Statistical associations between molecular, clinicopathological factors, and relapse-free survival were determined.
Results High-risk GISTs harboured increased numbers of somatic mutations compared with low-risk GISTs (25.2 mutations/high-risk cases vs 6.8 mutations/low-risk cases; two sample t test p=3.1×10−5). Somatic alterations in the SETD2 histone modifier gene occurred in 3 out of 9 high-risk/metastatic cases but no low/intermediate-risk cases. Prevalence screening identified additional SETD2 mutations in 7 out of 80 high-risk/metastatic cases but no low/intermediate-risk cases (n=29). Combined, the frequency of SETD2 mutations was 11.2% (10/89) and 0% (0/34) in high-risk and low-risk GISTs respectively. SETD2 mutant GISTs exhibited decreased H3K36me3 expression while SETD2 silencing promoted DNA damage in GIST-T1 cells. In gastric GISTs, SETD2 mutations were associated with overexpression of HOXC cluster genes and a DNA methylation signature of hypomethylated heterochromatin. Gastric GISTs with SETD2 mutations, or GISTs with hypomethylated heterochromatin, showed significantly shorter relapse-free survival on univariate analysis (log rank p=4.1×10−5).
Conclusions Our data suggest that SETD2 is a novel GIST tumour suppressor gene associated with disease progression. Assessing SETD2 genetic status and SETD2-associated epigenomic phenotypes may guide risk stratification and provide insights into mechanisms of GIST clinical aggressiveness.
- GENE MUTATION
- GASTROINTESTINAL CANCER
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SR, BTT, RQ and PT contributed equally.
Contributors KKH, IBT, SR, BTT, RQ, PT: conception and design of the study; drafting and revision of the manuscript; approval of the final version of the manuscript. KKH, JRM, STT, KD, CCYN, N-YC, SLZ, SSM, LH, VR, DH, JLL, AG, ANHS, XXS, LTD, ML, KCS, LLPJO, HSO, AC, PK-HC, WKW, SS, CKO, KHL, TN: generation, collection, assembly of data. KKH, JRM, IBT, SR, BTT, RQ, PT: analysis and interpretation of data.
Funding This work was supported by grants from National Medical Research Council (NMRC/TCR/009-NUHS/2013 and NMRC/STAR/0006/2009), National Cancer Centre Research Fund (NCCRF-Y2011-T2-101), National University Health System Center Grant (NMRC/CG/012/2013), Duke-NUS Graduate Medical School Singapore, Cancer Science Institute of Singapore, the Lee Foundation, the Verdant Foundation, Hong Kong and Tanoto Foundation, Indonesia. A portion of this research was supported by the National Research Foundation Singapore and the Singapore Ministry of Education under its Research Centres of Excellence initiative. These sponsors played no role in the study design or the collection, analysis, and interpretation of data.
Competing interests These authors disclose the following. RQ has received honoraria from Novartis. PK-HC has received travel and accommodation expenses from Novartis. The remaining authors disclose no conflicts.
Patient consent Obtained.
Ethics approval Singapore Health Services (SingHealth) Institutional Review Board (application 2010/347/B).
Provenance and peer review Not commissioned; externally peer reviewed.