Multi-faceted epigenetic dysregulation of gene expression promotes esophageal squamous cell carcinoma

Wei Cao (), Hayan Lee, Wei Wu (), Aubhishek Zaman, Sean McCorkle, Ming Yan, Justin Chen, Qinghe Xing, Nasa Sinnott-Armstrong, Hongen Xu, M. Reza Sailani, Wenxue Tang, Yuanbo Cui, Jia Liu, Hongyan Guan, Pengju Lv, Xiaoyan Sun, Lei Sun, Pengli Han, Yanan Lou, Jing Chang, Jinwu Wang, Yuchi Gao, Jiancheng Guo, Gundolf Schenk, Alan Hunter Shain, Fred G. Biddle, Eric Collisson, Michael Snyder () and Trever G. Bivona ()
Additional contact information
Wei Cao: Zhengzhou Central Hospital Affiliated Zhengzhou University
Hayan Lee: School of Medicine
Wei Wu: University of California San Francisco
Aubhishek Zaman: University of California San Francisco
Sean McCorkle: Brookhaven National Laboratory
Ming Yan: Zhengzhou University
Justin Chen: School of Medicine
Qinghe Xing: Fudan University
Nasa Sinnott-Armstrong: School of Medicine
Hongen Xu: Zhengzhou University
M. Reza Sailani: School of Medicine
Wenxue Tang: Zhengzhou University
Yuanbo Cui: Zhengzhou Central Hospital Affiliated Zhengzhou University
Jia Liu: Zhengzhou Central Hospital Affiliated Zhengzhou University
Hongyan Guan: Zhengzhou Central Hospital Affiliated Zhengzhou University
Pengju Lv: Zhengzhou Central Hospital Affiliated Zhengzhou University
Xiaoyan Sun: Zhengzhou Central Hospital Affiliated Zhengzhou University
Lei Sun: Zhengzhou Central Hospital Affiliated Zhengzhou University
Pengli Han: Zhengzhou Central Hospital Affiliated Zhengzhou University
Yanan Lou: Zhengzhou Central Hospital Affiliated Zhengzhou University
Jing Chang: Jiangsu Mai Jian Biotechnology Development Company
Jinwu Wang: Linzhou Cancer Hospital
Yuchi Gao: Annoroad Gene Company
Jiancheng Guo: Zhengzhou University
Gundolf Schenk: University of California San Francisco
Alan Hunter Shain: University of California San Francisco
Fred G. Biddle: University of Calgary
Eric Collisson: University of California San Francisco
Michael Snyder: School of Medicine
Trever G. Bivona: University of California San Francisco

Nature Communications, 2020, vol. 11, issue 1, 1-19

Abstract: Abstract Epigenetic landscapes can shape physiologic and disease phenotypes. We used integrative, high resolution multi-omics methods to delineate the methylome landscape and characterize the oncogenic drivers of esophageal squamous cell carcinoma (ESCC). We found 98% of CpGs are hypomethylated across the ESCC genome. Hypo-methylated regions are enriched in areas with heterochromatin binding markers (H3K9me3, H3K27me3), while hyper-methylated regions are enriched in polycomb repressive complex (EZH2/SUZ12) recognizing regions. Altered methylation in promoters, enhancers, and gene bodies, as well as in polycomb repressive complex occupancy and CTCF binding sites are associated with cancer-specific gene dysregulation. Epigenetic-mediated activation of non-canonical WNT/β-catenin/MMP signaling and a YY1/lncRNA ESCCAL-1/ribosomal protein network are uncovered and validated as potential novel ESCC driver alterations. This study advances our understanding of how epigenetic landscapes shape cancer pathogenesis and provides a resource for biomarker and target discovery.

Date: 2020
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DOI: 10.1038/s41467-020-17227-z

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