Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas

De Chen Lin*, Huy Q. Dinh, Jian Jun Xie, Anand Mayakonda, Tiago Chedraoui Silva, Yan Yi Jiang, Ling Wen Ding, Jian Zhong He, Xiu E. Xu, Jia Jie Hao, Ming Rong Wang, Chunquan Li, Li Yan Xu, En Min Li, Benjamin P. Berman, H. Phillip Koeffler

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

90 Scopus citations

Abstract

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.

Original languageAmerican English
Pages (from-to)1769-1779
Number of pages11
JournalGut
Volume67
Issue number10
DOIs
StatePublished - 2018
Externally publishedYes

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© 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.

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