TY - JOUR
T1 - Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas
AU - Lin, De Chen
AU - Dinh, Huy Q.
AU - Xie, Jian Jun
AU - Mayakonda, Anand
AU - Silva, Tiago Chedraoui
AU - Jiang, Yan Yi
AU - Ding, Ling Wen
AU - He, Jian Zhong
AU - Xu, Xiu E.
AU - Hao, Jia Jie
AU - Wang, Ming Rong
AU - Li, Chunquan
AU - Xu, Li Yan
AU - Li, En Min
AU - Berman, Benjamin P.
AU - Phillip Koeffler, H.
N1 - Publisher Copyright:
© Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.
PY - 2018
Y1 - 2018
N2 - Objectives Oesophageal squamous cell carcinoma (OScc) and adenocarcinoma (OAC) are distinct cancers in terms of a number of clinical and epidemiological characteristics, complicating the design of clinical trials and biomarker developments. We analysed 1048 oesophageal tumour-germline pairs from both subtypes, to characterise their genomic features, and biological and clinical significance. Design Previously exome-sequenced samples were re-analysed to identify significantly mutated genes (SMGs) and mutational signatures. The biological functions of novel SMGs were investigated using cell line and xenograft models. We further performed whole-genome bisulfite sequencing and chromatin immunoprecipitation (chiP)-seq to characterise epigenetic alterations. results OScc and OAc displayed nearly mutually exclusive sets of driver genes, indicating that they follow independent developmental paths. The combined sample size allowed the statistical identification of a number of novel subtype-specific SMGs, mutational signatures and prognostic biomarkers. Particularly, we identified a novel mutational signature similar to catalogue Of Somatic Mutations In cancer (cOSMic)signature 16, which has prognostic value in OScc. Two newly discovered SMGs, CUL3 and ZFP36L2, were validated as important tumour-suppressors specific to the OScc subtype. We further identified their additional loss-of-function mechanisms. CUL3 was homozygously deleted specifically in OScc and other squamous cell cancers (Sccs). Notably, ZFP36L2 is associated with super-enhancer in healthy oesophageal mucosa; DNA hypermethylation in its super-enhancer reduced active histone markers in squamous cancer cells, suggesting an epigenetic inactivation of a super-enhancer-associated Scc suppressor. Conclusions These data comprehensively contrast differences between OScc and OAc at both genomic and epigenomic levels, and reveal novel molecular features for further delineating the pathophysiological mechanisms and treatment strategies for these cancers.
AB - Objectives Oesophageal squamous cell carcinoma (OScc) and adenocarcinoma (OAC) are distinct cancers in terms of a number of clinical and epidemiological characteristics, complicating the design of clinical trials and biomarker developments. We analysed 1048 oesophageal tumour-germline pairs from both subtypes, to characterise their genomic features, and biological and clinical significance. Design Previously exome-sequenced samples were re-analysed to identify significantly mutated genes (SMGs) and mutational signatures. The biological functions of novel SMGs were investigated using cell line and xenograft models. We further performed whole-genome bisulfite sequencing and chromatin immunoprecipitation (chiP)-seq to characterise epigenetic alterations. results OScc and OAc displayed nearly mutually exclusive sets of driver genes, indicating that they follow independent developmental paths. The combined sample size allowed the statistical identification of a number of novel subtype-specific SMGs, mutational signatures and prognostic biomarkers. Particularly, we identified a novel mutational signature similar to catalogue Of Somatic Mutations In cancer (cOSMic)signature 16, which has prognostic value in OScc. Two newly discovered SMGs, CUL3 and ZFP36L2, were validated as important tumour-suppressors specific to the OScc subtype. We further identified their additional loss-of-function mechanisms. CUL3 was homozygously deleted specifically in OScc and other squamous cell cancers (Sccs). Notably, ZFP36L2 is associated with super-enhancer in healthy oesophageal mucosa; DNA hypermethylation in its super-enhancer reduced active histone markers in squamous cancer cells, suggesting an epigenetic inactivation of a super-enhancer-associated Scc suppressor. Conclusions These data comprehensively contrast differences between OScc and OAc at both genomic and epigenomic levels, and reveal novel molecular features for further delineating the pathophysiological mechanisms and treatment strategies for these cancers.
UR - http://www.scopus.com/inward/record.url?scp=85048629888&partnerID=8YFLogxK
U2 - 10.1136/gutjnl-2017-314607
DO - 10.1136/gutjnl-2017-314607
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C2 - 28860350
AN - SCOPUS:85048629888
SN - 0017-5749
VL - 67
SP - 1769
EP - 1779
JO - Gut
JF - Gut
IS - 10
ER -
