Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers

Xiaohui Yan; Zhongyi Hu; Yi Feng; Xiaowen Hu; Jiao Yuan; Sihai D. Zhao; Youyou Zhang; Lu Yang; Weiwei Shan; Qun He; Lingling Fan; Lana E. Kandalaft; Janos L. Tanyi; Chunsheng Li; Chao Xing Yuan; Dongmei Zhang; Huiqing Yuan; Keqin Hua; Yiling Lu; Dionyssios Katsaros; Qihong Huang; Kathleen Montone; Yi Fan; George Coukos; Jeff Boyd; Anil K. Sood; Timothy Rebbeck; Gordon B. Mills; Chi V. Dang; Lin Zhang

doi:10.1016/j.ccell.2015.09.006

Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers

Xiaohui Yan, Zhongyi Hu, Yi Feng, Xiaowen Hu, Jiao Yuan, Sihai D. Zhao, Youyou Zhang, Lu Yang, Weiwei Shan, Qun He, Lingling Fan, Lana E. Kandalaft, Janos L. Tanyi, Chunsheng Li, Chao Xing Yuan, Dongmei Zhang, Huiqing Yuan, Keqin Hua, Yiling Lu, Dionyssios KatsarosQihong Huang, Kathleen Montone, Yi Fan, George Coukos, Jeff Boyd, Anil K. Sood, Timothy Rebbeck, Gordon B. Mills, Chi V. Dang, Lin Zhang

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

545 Scopus citations

Abstract

The discovery of long non-coding RNA (lncRNA) has dramatically altered our understanding of cancer. Here, we describe a comprehensive analysis of lncRNA alterations at transcriptional, genomic, and epigenetic levels in 5,037 human tumor specimens across 13 cancer types from The Cancer Genome Atlas. Our results suggest that the expression and dysregulation of lncRNAs are highly cancer type specific compared with protein-coding genes. Using the integrative data generated by this analysis, we present a clinically guided small interfering RNA screening strategy and a co-expression analysis approach to identify cancer driver lncRNAs and predict their functions. This provides a resource for investigating lncRNAs in cancer and lays the groundwork for the development of new diagnostics and treatments.

Original language	English (US)
Article number	2143
Pages (from-to)	529-540
Number of pages	12
Journal	Cancer cell
Volume	28
Issue number	4
DOIs	https://doi.org/10.1016/j.ccell.2015.09.006
State	Published - Oct 12 2015

ASJC Scopus subject areas

Oncology
Cell Biology
Cancer Research

MD Anderson CCSG core facilities

Advanced Technology Genomics Core
Bioinformatics Shared Resource
Functional Proteomics Reverse Phase Protein Array Core
Cytogenetics and Cell Authentication Core

Access to Document

10.1016/j.ccell.2015.09.006

Cite this

Yan, X., Hu, Z., Feng, Y., Hu, X., Yuan, J., Zhao, S. D., Zhang, Y., Yang, L., Shan, W., He, Q., Fan, L., Kandalaft, L. E., Tanyi, J. L., Li, C., Yuan, C. X., Zhang, D., Yuan, H., Hua, K., Lu, Y., ... Zhang, L. (2015). Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers. Cancer cell, 28(4), 529-540. Article 2143. https://doi.org/10.1016/j.ccell.2015.09.006

Yan, X, Hu, Z, Feng, Y, Hu, X, Yuan, J, Zhao, SD, Zhang, Y, Yang, L, Shan, W, He, Q, Fan, L, Kandalaft, LE, Tanyi, JL, Li, C, Yuan, CX, Zhang, D, Yuan, H, Hua, K, Lu, Y, Katsaros, D, Huang, Q, Montone, K, Fan, Y, Coukos, G, Boyd, J, Sood, AK, Rebbeck, T, Mills, GB, Dang, CV & Zhang, L 2015, 'Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers', Cancer cell, vol. 28, no. 4, 2143, pp. 529-540. https://doi.org/10.1016/j.ccell.2015.09.006

@article{0d09762ddc494a92b2db7074ed8ff4f9,

title = "Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers",

abstract = "The discovery of long non-coding RNA (lncRNA) has dramatically altered our understanding of cancer. Here, we describe a comprehensive analysis of lncRNA alterations at transcriptional, genomic, and epigenetic levels in 5,037 human tumor specimens across 13 cancer types from The Cancer Genome Atlas. Our results suggest that the expression and dysregulation of lncRNAs are highly cancer type specific compared with protein-coding genes. Using the integrative data generated by this analysis, we present a clinically guided small interfering RNA screening strategy and a co-expression analysis approach to identify cancer driver lncRNAs and predict their functions. This provides a resource for investigating lncRNAs in cancer and lays the groundwork for the development of new diagnostics and treatments.",

author = "Xiaohui Yan and Zhongyi Hu and Yi Feng and Xiaowen Hu and Jiao Yuan and Zhao, {Sihai D.} and Youyou Zhang and Lu Yang and Weiwei Shan and Qun He and Lingling Fan and Kandalaft, {Lana E.} and Tanyi, {Janos L.} and Chunsheng Li and Yuan, {Chao Xing} and Dongmei Zhang and Huiqing Yuan and Keqin Hua and Yiling Lu and Dionyssios Katsaros and Qihong Huang and Kathleen Montone and Yi Fan and George Coukos and Jeff Boyd and Sood, {Anil K.} and Timothy Rebbeck and Mills, {Gordon B.} and Dang, {Chi V.} and Lin Zhang",

note = "Publisher Copyright: {\textcopyright} 2015 Elsevier Inc.",

year = "2015",

month = oct,

day = "12",

doi = "10.1016/j.ccell.2015.09.006",

language = "English (US)",

volume = "28",

pages = "529--540",

journal = "Cancer cell",

issn = "1535-6108",

publisher = "Cell Press",

number = "4",

}

TY - JOUR

T1 - Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers

AU - Yan, Xiaohui

AU - Hu, Zhongyi

AU - Feng, Yi

AU - Hu, Xiaowen

AU - Yuan, Jiao

AU - Zhao, Sihai D.

AU - Zhang, Youyou

AU - Yang, Lu

AU - Shan, Weiwei

AU - He, Qun

AU - Fan, Lingling

AU - Kandalaft, Lana E.

AU - Tanyi, Janos L.

AU - Li, Chunsheng

AU - Yuan, Chao Xing

AU - Zhang, Dongmei

AU - Yuan, Huiqing

AU - Hua, Keqin

AU - Lu, Yiling

AU - Katsaros, Dionyssios

AU - Huang, Qihong

AU - Montone, Kathleen

AU - Fan, Yi

AU - Coukos, George

AU - Boyd, Jeff

AU - Sood, Anil K.

AU - Rebbeck, Timothy

AU - Mills, Gordon B.

AU - Dang, Chi V.

AU - Zhang, Lin

PY - 2015/10/12

Y1 - 2015/10/12

N2 - The discovery of long non-coding RNA (lncRNA) has dramatically altered our understanding of cancer. Here, we describe a comprehensive analysis of lncRNA alterations at transcriptional, genomic, and epigenetic levels in 5,037 human tumor specimens across 13 cancer types from The Cancer Genome Atlas. Our results suggest that the expression and dysregulation of lncRNAs are highly cancer type specific compared with protein-coding genes. Using the integrative data generated by this analysis, we present a clinically guided small interfering RNA screening strategy and a co-expression analysis approach to identify cancer driver lncRNAs and predict their functions. This provides a resource for investigating lncRNAs in cancer and lays the groundwork for the development of new diagnostics and treatments.

AB - The discovery of long non-coding RNA (lncRNA) has dramatically altered our understanding of cancer. Here, we describe a comprehensive analysis of lncRNA alterations at transcriptional, genomic, and epigenetic levels in 5,037 human tumor specimens across 13 cancer types from The Cancer Genome Atlas. Our results suggest that the expression and dysregulation of lncRNAs are highly cancer type specific compared with protein-coding genes. Using the integrative data generated by this analysis, we present a clinically guided small interfering RNA screening strategy and a co-expression analysis approach to identify cancer driver lncRNAs and predict their functions. This provides a resource for investigating lncRNAs in cancer and lays the groundwork for the development of new diagnostics and treatments.

UR - http://www.scopus.com/inward/record.url?scp=84944077358&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84944077358&partnerID=8YFLogxK

U2 - 10.1016/j.ccell.2015.09.006

DO - 10.1016/j.ccell.2015.09.006

M3 - Article

C2 - 26461095

AN - SCOPUS:84944077358

SN - 1535-6108

VL - 28

SP - 529

EP - 540

JO - Cancer cell

JF - Cancer cell

IS - 4

M1 - 2143

ER -

Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers

Abstract

ASJC Scopus subject areas

MD Anderson CCSG core facilities

Access to Document

Other files and links

Fingerprint

Cite this