SETD2 histone modifier loss in aggressive GI stromal tumours.
GI stromal tumours (GISTs) are clinically heterogenous exhibiting varying degrees of disease aggressiveness in individual patients.



We sought to identify genetic alterations associated with high-risk GIST, explore their molecular consequences, and test their utility as prognostic markers.



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.



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).



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.
Cancer Science Institute of Singapore, National University of Singapore, Center for Translational Medicine, Singapore, Singapore.|Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore.
Kie Kyon
KK
Huang
Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore.
John R
JR
McPherson
Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore.
Su Ting
ST
Tay
Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore.
Kakoli
K
Das
Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore.|Genome Institute of Singapore, Singapore, Singapore.
Iain Beehuat
IB
Tan
Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore.
Cedric Chuan Young
CC
Ng
Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore.
Na-Yu
NY
Chia
Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore.
Shen Li
SL
Zhang
Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore.
Swe Swe
SS
Myint
Cancer Science Institute of Singapore, National University of Singapore, Center for Translational Medicine, Singapore, Singapore.|Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore.
Longyu
L
Hu
Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore.
Vikneswari
V
Rajasegaran
Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore.
Dachuan
D
Huang
Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore.
Jia Liang
JL
Loh
Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore.
Anna
A
Gan
Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore.
Alisa Noor Hidayah
AN
Sairi
Department of Pathology, Singapore General Hospital, 11 Hospital Drive, Singapore, Singapore.
Xin Xiu
XX
Sam
Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore.
Lourdes Trinidad
LT
Dominguez
Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore.
Minghui
M
Lee
Division of Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore.
Khee Chee
KC
Soo
Department of Hepatopancreaticobiliary & Transplant Surgery, Singapore General Hospital, Singapore, Singapore.
London Lucien Peng Jin
LL
Ooi
Department of Upper GI & Bariatric Surgery, Singapore General Hospital, Singapore, Singapore.
Hock Soo
HS
Ong
Department of Hepatopancreaticobiliary & Transplant Surgery, Singapore General Hospital, Singapore, Singapore.
Alexander
A
Chung
Division of Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore.|Office of Clinical Sciences, Duke-NUS Graduate Medical School, Singapore, Singapore.|Program in Translational and Clinical Liver Research, National Cancer Center Singapore, 11 Hospital Drive, Singapore, Singapore.
Pierce Kah-Hoe
PK
Chow
Department of Upper GI & Bariatric Surgery, Singapore General Hospital, Singapore, Singapore.
Wai Keong
WK
Wong
Department of Pathology, Singapore General Hospital, 11 Hospital Drive, Singapore, Singapore.
Sathiyamoorthy
S
Selvarajan
Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore.
Choon Kiat
CK
Ong
Department of Pathology, Singapore General Hospital, 11 Hospital Drive, Singapore, Singapore.
Kiat Hon
KH
Lim
Genome Institute of Singapore, Singapore, Singapore.
Tannistha
T
Nandi
Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore.
Steve
S
Rozen
Cancer Science Institute of Singapore, National University of Singapore, Center for Translational Medicine, Singapore, Singapore.|Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore.|Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore.
Bin Tean
BT
Teh
Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore.
Richard
R
Quek
Cancer Science Institute of Singapore, National University of Singapore, Center for Translational Medicine, Singapore, Singapore.|Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore.|Genome Institute of Singapore, Singapore, Singapore.
Patrick
P
Tan
D014408:Biomarkers, Tumor / Q000235:genetics*; D016022:Case-Control Studies; D018389:Codon, Nonsense / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics; D059472:Exome / Q000235:genetics; D046152:Gastrointestinal Stromal Tumors / Q000453:epidemiology / Q000235:genetics* / Q000473:pathology; D011495:Histone-Lysine N-Methyltransferase / Q000235:genetics*; D006657:Histones / Q000235:genetics; D006801:Humans; D020125:Mutation, Missense / Q000235:genetics; D009361:Neoplasm Invasiveness; D010641:Phenotype; D015995:Prevalence; D011379:Prognosis; D012720:Severity of Illness Index; D012846:Singapore / Q000453:epidemiology
D014408:Biomarkers, Tumor; D018389:Codon, Nonsense; D006657:Histones; D011495:Histone-Lysine N-Methyltransferase; C521636:SETD2 protein, human
GASTROINTESTINAL CANCER; GENE MUTATION