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.
authors.affiliation: Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China.
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Yan
authors.affiliation: Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Zhongyi
authors.initials: Z
authors.lastname: Hu
authors.affiliation: Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Feng
authors.affiliation: Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Xiaowen
authors.initials: X
authors.lastname: Hu
authors.affiliation: Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Jiao
authors.initials: J
authors.lastname: Yuan
authors.affiliation: Department of Statistics, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA.
authors.forename: Sihai D
authors.initials: SD
authors.lastname: Zhao
authors.affiliation: Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Youyou
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; West China Medical School, Sichuan University, Chengdu 610041, China.
authors.forename: Lu
authors.initials: L
authors.lastname: Yang
authors.affiliation: Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China.
authors.forename: Weiwei
authors.initials: W
authors.lastname: Shan
authors.affiliation: Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Qun
authors.initials: Q
authors.lastname: He
authors.affiliation: Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China.
authors.forename: Lingling
authors.initials: L
authors.lastname: Fan
authors.affiliation: Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Ludwig Center for Cancer Research and Department of Oncology, University of Lausanne, Lausanne 1007, Switzerland.
authors.forename: Lana E
authors.initials: LE
authors.lastname: Kandalaft
authors.affiliation: Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Janos L
authors.initials: JL
authors.lastname: Tanyi
authors.affiliation: Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Chunsheng
authors.initials: C
authors.lastname: Li
authors.affiliation: Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Chao-Xing
authors.initials: CX
authors.lastname: Yuan
authors.affiliation: Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; West China Medical School, Sichuan University, Chengdu 610041, China.
authors.forename: Dongmei
authors.initials: D
authors.lastname: Zhang
authors.affiliation: Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan 250012, China.
authors.forename: Huiqing
authors.initials: H
authors.lastname: Yuan
authors.affiliation: Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China.
authors.forename: Keqin
authors.initials: K
authors.lastname: Hua
authors.affiliation: Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
authors.forename: Yiling
authors.initials: Y
authors.lastname: Lu
authors.affiliation: Department of Surgical Sciences, Gynecologic Oncology, Azienda Ospedaliero - Universitaria Citta della Salute, Turin 10126, Italy.
authors.forename: Dionyssios
authors.initials: D
authors.lastname: Katsaros
authors.affiliation: Wistar Institute, Philadelphia, PA 19104, USA.
authors.forename: Qihong
authors.initials: Q
authors.lastname: Huang
authors.affiliation: Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Kathleen
authors.initials: K
authors.lastname: Montone
authors.affiliation: Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Fan
authors.affiliation: Ludwig Center for Cancer Research and Department of Oncology, University of Lausanne, Lausanne 1007, Switzerland.
authors.forename: George
authors.initials: G
authors.lastname: Coukos
authors.affiliation: Cancer Genome Institute, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
authors.forename: Jeff
authors.initials: J
authors.lastname: Boyd
authors.affiliation: Department of Gynecologic Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Center for RNA Interference and Non-Coding RNA, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
authors.forename: Anil K
authors.initials: AK
authors.lastname: Sood
authors.affiliation: Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Timothy
authors.initials: T
authors.lastname: Rebbeck
authors.affiliation: Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
authors.forename: Gordon B
authors.initials: GB
authors.lastname: Mills
authors.affiliation: Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: dangvchi@exchange.upenn.edu.
authors.forename: Chi V
authors.initials: CV
authors.lastname: Dang
authors.affiliation: Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: linzhang@mail.med.upenn.edu.
authors.forename: Lin
authors.initials: L
authors.lastname: Zhang
mesh_terms: D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D014644:Genetic Variation; D015894:Genome, Human; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D062085:RNA, Long Noncoding / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D062085:RNA, Long Noncoding