Systematic identification of genes with a cancer-testis expression pattern in 19 cancer types

Cheng Wang; Yayun Gu; Kai Zhang; Kaipeng Xie; Meng Zhu; Ningbin Dai; Yue Jiang; Xuejiang Guo; Mingxi Liu; Juncheng Dai; Linxiang Wu; Guangfu Jin; Hongxia Ma; Tao Jiang; Rong Yin; Yankai Xia; Li Liu; Shouyu Wang; Bin Shen; Ran Huo; Qianghu Wang; Lin Xu; Liuqing Yang; Xingxu Huang; Hongbing Shen; Jiahao Sha; Zhibin Hu

doi:10.1038/ncomms10499

Systematic identification of genes with a cancer-testis expression pattern in 19 cancer types

Cheng Wang, Yayun Gu, Kai Zhang, Kaipeng Xie, Meng Zhu, Ningbin Dai, Yue Jiang, Xuejiang Guo, Mingxi Liu, Juncheng Dai, Linxiang Wu, Guangfu Jin, Hongxia Ma, Tao Jiang, Rong Yin, Yankai Xia, Li Liu, Shouyu Wang, Bin Shen, Ran HuoQianghu Wang, Lin Xu, Liuqing Yang, Xingxu Huang, Hongbing Shen, Jiahao Sha, Zhibin Hu

Bioinformatics & Computational Biology

Research output: Contribution to journal › Article › peer-review

108 Scopus citations

Abstract

Cancer-testis (CT) genes represent the similarity between the processes of spermatogenesis and tumorigenesis. It is possible that their selective expression pattern can help identify driver genes in cancer. In this study, we integrate transcriptomics data from multiple databases and systematically identify 876 new CT genes in 19 cancer types. We explore their relationship with testis-specific regulatory elements. We propose that extremely highly expressed CT genes (EECTGs) are potential drivers activated through epigenetic mechanisms. We find mutually exclusive associations between EECTGs and somatic mutations in mutated genes, such as PIK3CA in breast cancer. We also provide evidence that promoter demethylation and close non-coding RNAs (namely, CT-ncRNAs) may be two mechanisms to reactivate EECTG gene expression. We show that the meiosis-related EECTG (MEIOB) and its nearby CT-ncRNA have a role in tumorigenesis in lung adenocarcinoma. Our findings provide methods for identifying epigenetic-driver genes of cancer, which could serve as targets of future cancer therapies.

Original language	English (US)
Article number	10499
Journal	Nature communications
Volume	7
DOIs	https://doi.org/10.1038/ncomms10499
State	Published - Jan 27 2016

ASJC Scopus subject areas

General Chemistry
General Biochemistry, Genetics and Molecular Biology
General Physics and Astronomy

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10.1038/ncomms10499

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Wang, C, Gu, Y, Zhang, K, Xie, K, Zhu, M, Dai, N, Jiang, Y, Guo, X, Liu, M, Dai, J, Wu, L, Jin, G, Ma, H, Jiang, T, Yin, R, Xia, Y, Liu, L, Wang, S, Shen, B, Huo, R, Wang, Q, Xu, L, Yang, L, Huang, X, Shen, H, Sha, J & Hu, Z 2016, 'Systematic identification of genes with a cancer-testis expression pattern in 19 cancer types', Nature communications, vol. 7, 10499. https://doi.org/10.1038/ncomms10499

@article{837f625a06bb433d835f1556886fffe9,

title = "Systematic identification of genes with a cancer-testis expression pattern in 19 cancer types",

abstract = "Cancer-testis (CT) genes represent the similarity between the processes of spermatogenesis and tumorigenesis. It is possible that their selective expression pattern can help identify driver genes in cancer. In this study, we integrate transcriptomics data from multiple databases and systematically identify 876 new CT genes in 19 cancer types. We explore their relationship with testis-specific regulatory elements. We propose that extremely highly expressed CT genes (EECTGs) are potential drivers activated through epigenetic mechanisms. We find mutually exclusive associations between EECTGs and somatic mutations in mutated genes, such as PIK3CA in breast cancer. We also provide evidence that promoter demethylation and close non-coding RNAs (namely, CT-ncRNAs) may be two mechanisms to reactivate EECTG gene expression. We show that the meiosis-related EECTG (MEIOB) and its nearby CT-ncRNA have a role in tumorigenesis in lung adenocarcinoma. Our findings provide methods for identifying epigenetic-driver genes of cancer, which could serve as targets of future cancer therapies.",

author = "Cheng Wang and Yayun Gu and Kai Zhang and Kaipeng Xie and Meng Zhu and Ningbin Dai and Yue Jiang and Xuejiang Guo and Mingxi Liu and Juncheng Dai and Linxiang Wu and Guangfu Jin and Hongxia Ma and Tao Jiang and Rong Yin and Yankai Xia and Li Liu and Shouyu Wang and Bin Shen and Ran Huo and Qianghu Wang and Lin Xu and Liuqing Yang and Xingxu Huang and Hongbing Shen and Jiahao Sha and Zhibin Hu",

note = "Funding Information: We thank The Genotype-Tissue Expression (GTEx) project for the use of expression abundance data from multiple normal tissues, The Encyclopedia of DNA Elements (ENCODE) project for use of methylation level data from multiple normal tissues, The Functional Annotation of The Mammalian Genome (FANTOM) project for use of promoter and enhancer activity data from multiple normal tissues and The Cancer Genome Atlas (TCGA) project for use of multiomics data from a large number of cancer samples. This research was supported by the National Key Basic Research Program Grant (2013CB911400, 2015CB943003), National Natural Science Foundation of China (31530047, 81230067), Science Foundation for Distinguished Young Scholars of Jiangsu (BK2012042), the National Science Foundation for Distinguished Young Scholars of China (81225020), and the Ten Thousand Talent Program and Distinguished Professor at Jiangsu. The funder agencies had no role in the study design, data collection and analysis, decision to publish or the preparation of the manuscript.",

year = "2016",

month = jan,

day = "27",

doi = "10.1038/ncomms10499",

language = "English (US)",

volume = "7",

journal = "Nature communications",

issn = "2041-1723",

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TY - JOUR

T1 - Systematic identification of genes with a cancer-testis expression pattern in 19 cancer types

AU - Wang, Cheng

AU - Gu, Yayun

AU - Zhang, Kai

AU - Xie, Kaipeng

AU - Zhu, Meng

AU - Dai, Ningbin

AU - Jiang, Yue

AU - Guo, Xuejiang

AU - Liu, Mingxi

AU - Dai, Juncheng

AU - Wu, Linxiang

AU - Jin, Guangfu

AU - Ma, Hongxia

AU - Jiang, Tao

AU - Yin, Rong

AU - Xia, Yankai

AU - Liu, Li

AU - Wang, Shouyu

AU - Shen, Bin

AU - Huo, Ran

AU - Wang, Qianghu

AU - Xu, Lin

AU - Yang, Liuqing

AU - Huang, Xingxu

AU - Shen, Hongbing

AU - Sha, Jiahao

AU - Hu, Zhibin

N1 - Funding Information: We thank The Genotype-Tissue Expression (GTEx) project for the use of expression abundance data from multiple normal tissues, The Encyclopedia of DNA Elements (ENCODE) project for use of methylation level data from multiple normal tissues, The Functional Annotation of The Mammalian Genome (FANTOM) project for use of promoter and enhancer activity data from multiple normal tissues and The Cancer Genome Atlas (TCGA) project for use of multiomics data from a large number of cancer samples. This research was supported by the National Key Basic Research Program Grant (2013CB911400, 2015CB943003), National Natural Science Foundation of China (31530047, 81230067), Science Foundation for Distinguished Young Scholars of Jiangsu (BK2012042), the National Science Foundation for Distinguished Young Scholars of China (81225020), and the Ten Thousand Talent Program and Distinguished Professor at Jiangsu. The funder agencies had no role in the study design, data collection and analysis, decision to publish or the preparation of the manuscript.

PY - 2016/1/27

Y1 - 2016/1/27

N2 - Cancer-testis (CT) genes represent the similarity between the processes of spermatogenesis and tumorigenesis. It is possible that their selective expression pattern can help identify driver genes in cancer. In this study, we integrate transcriptomics data from multiple databases and systematically identify 876 new CT genes in 19 cancer types. We explore their relationship with testis-specific regulatory elements. We propose that extremely highly expressed CT genes (EECTGs) are potential drivers activated through epigenetic mechanisms. We find mutually exclusive associations between EECTGs and somatic mutations in mutated genes, such as PIK3CA in breast cancer. We also provide evidence that promoter demethylation and close non-coding RNAs (namely, CT-ncRNAs) may be two mechanisms to reactivate EECTG gene expression. We show that the meiosis-related EECTG (MEIOB) and its nearby CT-ncRNA have a role in tumorigenesis in lung adenocarcinoma. Our findings provide methods for identifying epigenetic-driver genes of cancer, which could serve as targets of future cancer therapies.

AB - Cancer-testis (CT) genes represent the similarity between the processes of spermatogenesis and tumorigenesis. It is possible that their selective expression pattern can help identify driver genes in cancer. In this study, we integrate transcriptomics data from multiple databases and systematically identify 876 new CT genes in 19 cancer types. We explore their relationship with testis-specific regulatory elements. We propose that extremely highly expressed CT genes (EECTGs) are potential drivers activated through epigenetic mechanisms. We find mutually exclusive associations between EECTGs and somatic mutations in mutated genes, such as PIK3CA in breast cancer. We also provide evidence that promoter demethylation and close non-coding RNAs (namely, CT-ncRNAs) may be two mechanisms to reactivate EECTG gene expression. We show that the meiosis-related EECTG (MEIOB) and its nearby CT-ncRNA have a role in tumorigenesis in lung adenocarcinoma. Our findings provide methods for identifying epigenetic-driver genes of cancer, which could serve as targets of future cancer therapies.

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DO - 10.1038/ncomms10499

M3 - Article

C2 - 26813108

AN - SCOPUS:84955438813

SN - 2041-1723

VL - 7

JO - Nature communications

JF - Nature communications

M1 - 10499

ER -

Systematic identification of genes with a cancer-testis expression pattern in 19 cancer types

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