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Epigenomic profiling of primary gastric adenocarcinoma reveals super-enhancer heterogeneity.

Publication ,  Journal Article
Ooi, WF; Xing, M; Xu, C; Yao, X; Ramlee, MK; Lim, MC; Cao, F; Lim, K; Babu, D; Poon, L-F; Lin Suling, J; Qamra, A; Irwanto, A; Nandi, T ...
Published in: Nat Commun
September 28, 2016

Regulatory enhancer elements in solid tumours remain poorly characterized. Here we apply micro-scale chromatin profiling to survey the distal enhancer landscape of primary gastric adenocarcinoma (GC), a leading cause of global cancer mortality. Integrating 110 epigenomic profiles from primary GCs, normal gastric tissues and cell lines, we highlight 36,973 predicted enhancers and 3,759 predicted super-enhancers respectively. Cell-line-defined super-enhancers can be subclassified by their somatic alteration status into somatic gain, loss and unaltered categories, each displaying distinct epigenetic, transcriptional and pathway enrichments. Somatic gain super-enhancers are associated with complex chromatin interaction profiles, expression patterns correlated with patient outcome and dense co-occupancy of the transcription factors CDX2 and HNF4α. Somatic super-enhancers are also enriched in genetic risk SNPs associated with cancer predisposition. Our results reveal a genome-wide reprogramming of the GC enhancer and super-enhancer landscape during tumorigenesis, contributing to dysregulated local and regional cancer gene expression.

Duke Scholars

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Published In

Nat Commun

DOI

EISSN

2041-1723

Publication Date

September 28, 2016

Volume

7

Start / End Page

12983

Location

England
 

Citation

APA
Chicago
ICMJE
MLA
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Ooi, W. F., Xing, M., Xu, C., Yao, X., Ramlee, M. K., Lim, M. C., … Tan, P. (2016). Epigenomic profiling of primary gastric adenocarcinoma reveals super-enhancer heterogeneity. Nat Commun, 7, 12983. https://doi.org/10.1038/ncomms12983
Ooi, Wen Fong, Manjie Xing, Chang Xu, Xiaosai Yao, Muhammad Khairul Ramlee, Mei Chee Lim, Fan Cao, et al. “Epigenomic profiling of primary gastric adenocarcinoma reveals super-enhancer heterogeneity.Nat Commun 7 (September 28, 2016): 12983. https://doi.org/10.1038/ncomms12983.
Ooi WF, Xing M, Xu C, Yao X, Ramlee MK, Lim MC, et al. Epigenomic profiling of primary gastric adenocarcinoma reveals super-enhancer heterogeneity. Nat Commun. 2016 Sep 28;7:12983.
Ooi, Wen Fong, et al. “Epigenomic profiling of primary gastric adenocarcinoma reveals super-enhancer heterogeneity.Nat Commun, vol. 7, Sept. 2016, p. 12983. Pubmed, doi:10.1038/ncomms12983.
Ooi WF, Xing M, Xu C, Yao X, Ramlee MK, Lim MC, Cao F, Lim K, Babu D, Poon L-F, Lin Suling J, Qamra A, Irwanto A, Qu Zhengzhong J, Nandi T, Lee-Lim AP, Chan YS, Tay ST, Lee MH, Davies JOJ, Wong WK, Soo KC, Chan WH, Ong HS, Chow P, Wong CY, Rha SY, Liu J, Hillmer AM, Hughes JR, Rozen S, Teh BT, Fullwood MJ, Li S, Tan P. Epigenomic profiling of primary gastric adenocarcinoma reveals super-enhancer heterogeneity. Nat Commun. 2016 Sep 28;7:12983.

Published In

Nat Commun

DOI

EISSN

2041-1723

Publication Date

September 28, 2016

Volume

7

Start / End Page

12983

Location

England