Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers
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....
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Published in | Cancer cell Vol. 28; no. 4; pp. 529 - 540 |
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Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Format | Journal Article |
Language | English |
Published |
United States
Elsevier Inc
12.10.2015
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Subjects | |
Online Access | Get full text |
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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.
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•lncRNA dysregulation was characterized in 5,037 tumor samples across 13 cancer types•lncRNAs are altered in cancers at transcriptional, genomic, and epigenetic levels•The expression and dysregulation of lncRNAs are strikingly cancer-type specific•This study provides a resource to systematically identify cancer driver lncRNAs
Yan et al. analyze long non-coding RNA (lncRNA) alterations at transcriptional, genomic, and epigenetic levels across multiple cancer types from TCGA datasets and cancer cell lines. They also present a screening strategy and “co-expression” approach using the integrative data to identify cancer driver lncRNAs. |
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AbstractList | 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. 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 (TCGA). Our results suggest that the expression and dysregulation of lncRNAs are highly cancer-type specific compared to 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. 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. [Display omitted] •lncRNA dysregulation was characterized in 5,037 tumor samples across 13 cancer types•lncRNAs are altered in cancers at transcriptional, genomic, and epigenetic levels•The expression and dysregulation of lncRNAs are strikingly cancer-type specific•This study provides a resource to systematically identify cancer driver lncRNAs Yan et al. analyze long non-coding RNA (lncRNA) alterations at transcriptional, genomic, and epigenetic levels across multiple cancer types from TCGA datasets and cancer cell lines. They also present a screening strategy and “co-expression” approach using the integrative data to identify cancer driver lncRNAs. |
Author | Fan, Lingling Yang, Lu Rebbeck, Timothy Fan, Yi Li, Chunsheng Huang, Qihong Mills, Gordon B. Dang, Chi V. Yan, Xiaohui Feng, Yi Zhang, Dongmei Yuan, Jiao Montone, Kathleen Coukos, George Sood, Anil K. Hu, Xiaowen Zhang, Youyou Zhao, Sihai D. Hua, Keqin Lu, Yiling He, Qun Zhang, Lin Hu, Zhongyi Tanyi, Janos L. Yuan, Chao-Xing Yuan, Huiqing Boyd, Jeff Shan, Weiwei Kandalaft, Lana E. Katsaros, Dionyssios |
AuthorAffiliation | 11 Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan 250012, China 17 Department of Gynecologic Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77054 1 Center for Research on Reproduction & Women’s Health, University of Pennsylvania, Philadelphia, PA 19104 9 Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China 15 Ludwig Center for Cancer Research and Department of Oncology, University of Lausanne, Lausanne 1007, Switzerland 18 Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054 2 Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104 7 Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA 19104 13 Department of Surgical Sciences, Gynecologic Oncology, Azienda Ospedaliero - Universitaria Citta della Salute, Turin |
AuthorAffiliation_xml | – name: 8 Department of Medicine Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 – name: 15 Ludwig Center for Cancer Research and Department of Oncology, University of Lausanne, Lausanne 1007, Switzerland – name: 7 Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA 19104 – name: 13 Department of Surgical Sciences, Gynecologic Oncology, Azienda Ospedaliero - Universitaria Citta della Salute, Turin 10126, Italy – name: 18 Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054 – name: 10 Department of Statistics, University of Illinois at Urbana-Champaign, Champaign, IL 61820 – name: 16 Cancer Genome Institute, Fox Chase Cancer Center, Philadelphia, PA, 19111 – name: 9 Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China – name: 6 Department of Radiation Oncology, University of Pennsylvania, Philadelphia, PA 19104 – name: 12 West China Medical School, Sichuan University, Chengdu 610041, China – name: 17 Department of Gynecologic Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77054 – name: 1 Center for Research on Reproduction & Women’s Health, University of Pennsylvania, Philadelphia, PA 19104 – name: 11 Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan 250012, China – name: 4 Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104 – name: 3 Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA 19104 – name: 2 Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104 – name: 5 Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104 – name: 14 Wistar Institute, Philadelphia, PA 19104 |
Author_xml | – sequence: 1 givenname: Xiaohui surname: Yan fullname: Yan, Xiaohui organization: Center for Research on Reproduction & Women’s Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 2 givenname: Zhongyi surname: Hu fullname: Hu, Zhongyi organization: Center for Research on Reproduction & Women’s Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 3 givenname: Yi surname: Feng fullname: Feng, Yi organization: Center for Research on Reproduction & Women’s Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 4 givenname: Xiaowen surname: Hu fullname: Hu, Xiaowen organization: Center for Research on Reproduction & Women’s Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 5 givenname: Jiao surname: Yuan fullname: Yuan, Jiao organization: Center for Research on Reproduction & Women’s Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 6 givenname: Sihai D. surname: Zhao fullname: Zhao, Sihai D. organization: Department of Statistics, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA – sequence: 7 givenname: Youyou surname: Zhang fullname: Zhang, Youyou organization: Center for Research on Reproduction & Women’s Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 8 givenname: Lu surname: Yang fullname: Yang, Lu organization: Center for Research on Reproduction & Women’s Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 9 givenname: Weiwei surname: Shan fullname: Shan, Weiwei organization: Center for Research on Reproduction & Women’s Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 10 givenname: Qun surname: He fullname: He, Qun organization: Center for Research on Reproduction & Women’s Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 11 givenname: Lingling surname: Fan fullname: Fan, Lingling organization: Center for Research on Reproduction & Women’s Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 12 givenname: Lana E. surname: Kandalaft fullname: Kandalaft, Lana E. organization: Center for Research on Reproduction & Women’s Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 13 givenname: Janos L. surname: Tanyi fullname: Tanyi, Janos L. organization: Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 14 givenname: Chunsheng surname: Li fullname: Li, Chunsheng organization: Center for Research on Reproduction & Women’s Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 15 givenname: Chao-Xing surname: Yuan fullname: Yuan, Chao-Xing organization: Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 16 givenname: Dongmei surname: Zhang fullname: Zhang, Dongmei organization: Center for Research on Reproduction & Women’s Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 17 givenname: Huiqing surname: Yuan fullname: Yuan, Huiqing organization: Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan 250012, China – sequence: 18 givenname: Keqin surname: Hua fullname: Hua, Keqin organization: Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China – sequence: 19 givenname: Yiling surname: Lu fullname: Lu, Yiling organization: Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA – sequence: 20 givenname: Dionyssios surname: Katsaros fullname: Katsaros, Dionyssios organization: Department of Surgical Sciences, Gynecologic Oncology, Azienda Ospedaliero - Universitaria Citta della Salute, Turin 10126, Italy – sequence: 21 givenname: Qihong surname: Huang fullname: Huang, Qihong organization: Wistar Institute, Philadelphia, PA 19104, USA – sequence: 22 givenname: Kathleen surname: Montone fullname: Montone, Kathleen organization: Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 23 givenname: Yi surname: Fan fullname: Fan, Yi organization: Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 24 givenname: George surname: Coukos fullname: Coukos, George organization: Ludwig Center for Cancer Research and Department of Oncology, University of Lausanne, Lausanne 1007, Switzerland – sequence: 25 givenname: Jeff surname: Boyd fullname: Boyd, Jeff organization: Cancer Genome Institute, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA – sequence: 26 givenname: Anil K. surname: Sood fullname: Sood, Anil K. organization: Department of Gynecologic Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA – sequence: 27 givenname: Timothy surname: Rebbeck fullname: Rebbeck, Timothy organization: Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 28 givenname: Gordon B. surname: Mills fullname: Mills, Gordon B. organization: Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA – sequence: 29 givenname: Chi V. surname: Dang fullname: Dang, Chi V. email: dangvchi@exchange.upenn.edu organization: Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA – sequence: 30 givenname: Lin surname: Zhang fullname: Zhang, Lin email: linzhang@mail.med.upenn.edu organization: Center for Research on Reproduction & Women’s Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/26461095$$D View this record in MEDLINE/PubMed |
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Snippet | The discovery of long non-coding RNA (lncRNA) has dramatically altered our understanding of cancer. Here, we describe a comprehensive analysis of lncRNA... |
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SubjectTerms | Cell Line, Tumor Computational Biology - methods Epigenesis, Genetic Gene Expression Profiling Gene Expression Regulation, Neoplastic Genetic Variation Genome, Human Humans Neoplasms - genetics RNA, Long Noncoding - genetics Transcription, Genetic |
Title | Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers |
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