A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples
Chen, Han; Li, Chunyan; Peng, Xinxin; Zhou, Zhicheng; Weinstein, John N; Liang, Han; Cancer Genome Atlas Research Network
(2018) Cell, volume 173, issue 2, pp. 386 - 399.e12
(Article)
Abstract
The role of enhancers, a key class of non-coding regulatory DNA elements, in cancer development has increasingly been appreciated. Here, we present the detection and characterization of a large number of expressed enhancers in a genome-wide analysis of 8928 tumor samples across 33 cancer types using TCGA RNA-seq data. Compared
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with matched normal tissues, global enhancer activation was observed in most cancers. Across cancer types, global enhancer activity was positively associated with aneuploidy, but not mutation load, suggesting a hypothesis centered on “chromatin-state” to explain their interplay. Integrating eQTL, mRNA co-expression, and Hi-C data analysis, we developed a computational method to infer causal enhancer-gene interactions, revealing enhancers of clinically actionable genes. Having identified an enhancer ∼140 kb downstream of PD-L1, a major immunotherapy target, we validated it experimentally. This study provides a systematic view of enhancer activity in diverse tumor contexts and suggests the clinical implications of enhancers. Causal enhancer-target-gene relationships are inferred from a systematic analysis of 33 cancer types.
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Keywords: aneuploidy, chromatin state, enhancer expression, mutation burden, pan-cancer analysis, PD-L1 expression, prognostic markers, The Cancer Genome Atlas, General Biochemistry,Genetics and Molecular Biology
ISSN: 0092-8674
Publisher: Cell Press
Note: Funding Information: This study was supported by grants from the U.S. National Institutes of Health ( CA175486 and CA209851 to H.L., and CCSG grant CA016672 ); a grant from the Cancer Prevention and Research Institute of Texas ( RP140462 to H.L.); a University of Texas System STARS award (to H.L.), and a training fellowship from the Gulf Coast Consortia on the NLM Training Program in Biomedical Informatics and Data Science ( T15 LM007093 to H.C.), CAS-Sponsored Scholarship Program for Visiting Scholars ( 2015-40 to C.L.). We thank the MD Anderson high-performance computing core facility for computing, Feng Yue for comments, and LeeAnn Chastain for editorial assistance. Funding Information: Michael Seiler, Peter G. Smith, Ping Zhu, Silvia Buonamici, and Lihua Yu are employees of H3 Biomedicine, Inc. Parts of this work are the subject of a patent application: WO2017040526 titled “Splice variants associated with neomorphic sf3b1 mutants.” Shouyoung Peng, Anant A. Agrawal, James Palacino, and Teng Teng are employees of H3 Biomedicine, Inc. Andrew D. Cherniack, Ashton C. Berger, and Galen F. Gao receive research support from Bayer Pharmaceuticals. Gordon B. Mills serves on the External Scientific Review Board of Astrazeneca. Anil Sood is on the Scientific Advisory Board for Kiyatec and is a shareholder in BioPath. Jonathan S. Serody receives funding from Merck, Inc. Kyle R. Covington is an employee of Castle Biosciences, Inc. Preethi H. Gunaratne is founder, CSO, and shareholder of NextmiRNA Therapeutics. Christina Yau is a part-time employee/consultant at NantOmics. Franz X. Schaub is an employee and shareholder of SEngine Precision Medicine, Inc. Carla Grandori is an employee, founder, and shareholder of SEngine Precision Medicine, Inc. Robert N. Eisenman is a member of the Scientific Advisory Boards and shareholder of Shenogen Pharma and Kronos Bio. Daniel J. Weisenberger is a consultant for Zymo Research Corporation. Joshua M. Stuart is the founder of Five3 Genomics and shareholder of NantOmics. Marc T. Goodman receives research support from Merck, Inc. Andrew J. Gentles is a consultant for Cibermed. Charles M. Perou is an equity stock holder, consultant, and Board of Directors member of BioClassifier and GeneCentric Diagnostics and is also listed as an inventor on patent applications on the Breast PAM50 and Lung Cancer Subtyping assays. Matthew Meyerson receives research support from Bayer Pharmaceuticals; is an equity holder in, consultant for, and Scientific Advisory Board chair for OrigiMed; and is an inventor of a patent for EGFR mutation diagnosis in lung cancer, licensed to LabCorp. Eduard Porta-Pardo is an inventor of a patent for domainXplorer. Han Liang is a shareholder and scientific advisor of Precision Scientific and Eagle Nebula. Da Yang is an inventor on a pending patent application describing the use of antisense oligonucleotides against specific lncRNA sequence as diagnostic and therapeutic tools. Yonghong Xiao was an employee and shareholder of TESARO, Inc. Bin Feng is an employee and shareholder of TESARO, Inc. Carter Van Waes received research funding for the study of IAP inhibitor ASTX660 through a Cooperative Agreement between NIDCD, NIH, and Astex Pharmaceuticals. Raunaq Malhotra is an employee and shareholder of Seven Bridges, Inc. Peter W. Laird serves on the Scientific Advisory Board for AnchorDx. Joel Tepper is a consultant at EMD Serono. Kenneth Wang serves on the Advisory Board for Boston Scientific, Microtech, and Olympus. Andrea Califano is a founder, shareholder, and advisory board member of DarwinHealth, Inc. and a shareholder and advisory board member of Tempus, Inc. Toni K. Choueiri serves as needed on advisory boards for Bristol-Myers Squibb, Merck, and Roche. Lawrence Kwong receives research support from Array BioPharma. Sharon E. Plon is a member of the Scientific Advisory Board for Baylor Genetics Laboratory. Beth Y. Karlan serves on the Advisory Board of Invitae. Funding Information: This study was supported by grants from the U.S. National Institutes of Health (CA175486 and CA209851 to H.L., and CCSG grant CA016672); a grant from the Cancer Prevention and Research Institute of Texas (RP140462 to H.L.); a University of Texas System STARS award (to H.L.), and a training fellowship from the Gulf Coast Consortia on the NLM Training Program in Biomedical Informatics and Data Science (T15 LM007093 to H.C.), CAS-Sponsored Scholarship Program for Visiting Scholars (2015-40 to C.L.). We thank the MD Anderson high-performance computing core facility for computing, Feng Yue for comments, and LeeAnn Chastain for editorial assistance. Publisher Copyright: © 2018 The Authors
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