title: Integrative analyses of transcriptome sequencing identify novel functional lncRNAs in esophageal squamous cell carcinoma.
abstract: Long non-coding RNAs (lncRNAs) have a critical role in cancer initiation and progression, and thus may mediate oncogenic or tumor suppressing effects, as well as be a new class of cancer therapeutic targets. We performed high-throughput sequencing of RNA (RNA-seq) to investigate the expression level of lncRNAs and protein-coding genes in 30 esophageal samples, comprised of 15 esophageal squamous cell carcinoma (ESCC) samples and their 15 paired non-tumor tissues. We further developed an integrative bioinformatics method, denoted URW-LPE, to identify key functional lncRNAs that regulate expression of downstream protein-coding genes in ESCC. A number of known onco-lncRNA and many putative novel ones were effectively identified by URW-LPE. Importantly, we identified lncRNA625 as a novel regulator of ESCC cell proliferation, invasion and migration. ESCC patients with high lncRNA625 expression had significantly shorter survival time than those with low expression. LncRNA625 also showed specific prognostic value for patients with metastatic ESCC. Finally, we identified E1A-binding protein p300 (EP300) as a downstream executor of lncRNA625-induced transcriptional responses. These findings establish a catalog of novel cancer-associated functional lncRNAs, which will promote our understanding of lncRNA-mediated regulation in this malignancy.
authors.affiliation: The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.|School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China.
authors.forename: C-Q
authors.initials: CQ
authors.lastname: Li
authors.affiliation: The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
authors.forename: G-W
authors.initials: GW
authors.lastname: Huang
authors.affiliation: Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou, China.
authors.forename: Z-Y
authors.initials: ZY
authors.lastname: Wu
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: Y-J
authors.initials: YJ
authors.lastname: Xu
authors.affiliation: School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China.
authors.forename: X-C
authors.initials: XC
authors.lastname: Li
authors.affiliation: The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
authors.forename: Y-J
authors.initials: YJ
authors.lastname: Xue
authors.affiliation: The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
authors.forename: Y
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.|School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China.
authors.forename: J-M
authors.initials: JM
authors.lastname: Zhao
authors.affiliation: School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China.
authors.forename: M
authors.initials: M
authors.lastname: Li
authors.affiliation: School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China.
authors.forename: J
authors.initials: J
authors.lastname: Zhang
authors.affiliation: The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
authors.forename: J-Y
authors.initials: JY
authors.lastname: Wu
authors.affiliation: The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
authors.forename: F
authors.initials: F
authors.lastname: Lei
authors.affiliation: The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.|School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China.
authors.forename: Q-Y
authors.initials: QY
authors.lastname: Wang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: S
authors.initials: S
authors.lastname: Li
authors.affiliation: Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou, China.
authors.forename: C-P
authors.initials: CP
authors.lastname: Zheng
authors.affiliation: School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China.
authors.forename: B
authors.initials: B
authors.lastname: Ai
authors.affiliation: School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China.
authors.forename: Z-D
authors.initials: ZD
authors.lastname: Tang
authors.affiliation: School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China.
authors.forename: C-C
authors.initials: CC
authors.lastname: Feng
authors.affiliation: The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
authors.forename: L-D
authors.initials: LD
authors.lastname: Liao
authors.affiliation: Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou, China.
authors.forename: S-H
authors.initials: SH
authors.lastname: Wang
authors.affiliation: Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou, China.
authors.forename: J-H
authors.initials: JH
authors.lastname: Shen
authors.affiliation: School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China.
authors.forename: Y-J
authors.initials: YJ
authors.lastname: Liu
authors.affiliation: School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China.
authors.forename: X-F
authors.initials: XF
authors.lastname: Bai
authors.affiliation: The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
authors.forename: J-Z
authors.initials: JZ
authors.lastname: He
authors.affiliation: The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
authors.forename: H-H
authors.initials: HH
authors.lastname: Cao
authors.affiliation: The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
authors.forename: B-L
authors.initials: BL
authors.lastname: Wu
authors.affiliation: Cancer Institute/Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.
authors.forename: M-R
authors.initials: MR
authors.lastname: Wang
authors.affiliation: Division of Hematology/Oncology, Cedars-Sinai Medical Center, University of California, Los Angeles School of Medicine, Los Angeles, CA, USA.
authors.forename: D-C
authors.initials: DC
authors.lastname: Lin
authors.affiliation: Division of Hematology/Oncology, Cedars-Sinai Medical Center, University of California, Los Angeles School of Medicine, Los Angeles, CA, USA.|Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.|National University Cancer Institute of Singapore, National University Health System and National University Hospital, Singapore, Singapore.
authors.forename: H P
authors.initials: HP
authors.lastname: Koeffler
authors.affiliation: Henan Key Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China.
authors.forename: L-D
authors.initials: LD
authors.lastname: Wang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: X
authors.initials: X
authors.lastname: Li
authors.affiliation: The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
authors.forename: E-M
authors.initials: EM
authors.lastname: Li
authors.affiliation: The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
authors.forename: L-Y
authors.initials: LY
authors.lastname: Xu