Oncotarget

Research Papers:

Integrative analysis reveals clinical phenotypes and oncogenic potentials of long non-coding RNAs across 15 cancer types

Ze-Lin Wang, Bin Li, Stephen R. Piccolo, Xiao-Qin Zhang, Jun-Hao Li, Hui Zhou, Jian-Hua Yang _ and Liang-Hu Qu

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Oncotarget. 2016; 7:35044-35055. https://doi.org/10.18632/oncotarget.9037

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Abstract

Ze-Lin Wang1,2,*, Bin Li1,2,*, Stephen R. Piccolo3,4, Xiao-Qin Zhang5, Jun-Hao Li1,2, Hui Zhou1,2, Jian-Hua Yang1,2, Liang-Hu Qu1,2

1Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou, China

2State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, China

3Department of Biology, Brigham Young University, Provo, Utah, USA

4Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah, USA

5Department of Surgery, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong

*These authors have contributed equally to this work

Correspondence to:

Jian-Hua Yang, e-mail: yangjh7@mail.sysu.edu.cn

Liang-Hu Qu, e-mail: lssqlh@mail.sysu.edu.cn

Keywords: lncRNA, expression profile, prognostification, somatic copy number alteration

Received: October 22, 2015     Accepted: April 11, 2016     Published: April 27, 2016

ABSTRACT

Long non-coding RNAs (lncRNAs) have been shown to contribute to tumorigenesis. However, surprisingly little is known about the comprehensive clinical and genomic characterization of lncRNAs across human cancer. In this study, we conducted comprehensive analyses for the expression profile, clinical outcomes, somatic copy number alterations (SCNAs) profile of lncRNAs in ~7000 clinical samples from 15 different cancer types. We identified significantly differentially expressed lncRNAs between tumor and normal tissues from each cancer. Notably, we characterized 47 lncRNAs which were extensively dysregulated in at least 10 cancer types, suggesting a conserved function in cancer development. We also analyzed the associations between lncRNA expressions and patient survival, and identified sets of lncRNAs that possessed significant prognostic values in specific cancer types. Our combined analysis of SCNA data and expression data uncovered 116 dysregulated lncRNAs are strikingly genomic altered across 15 cancer types, indicating their oncogenic potentials. Our study may lay the groundwork for future functional studies of lncRNAs and help facilitate the discovery of novel clinical biomarkers.


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