title: Expression profiling and functional prediction of long noncoding RNAs in nasopharyngeal nonkeratinizing carcinoma.
abstract: Rapidly growing evidence has shown that long noncoding RNAs (lncRNAs) are playing more and more important roles in a variety of biological processes and have been involved in various types of cancer. How to better decode these noncoding transcripts and how to predict their potential roles in tumorigenesis particularly in nasopharyngeal carcinoma (NPC) are still open questions. In this study, we applied our custom-designed lncRNA+mRNA gene expression microarray, which contains probes against 38,141 lncRNA transcripts, to assaying the expression profiling of flash-frozen tumorous and non-tumorous tissue samples from nonkeratinizing carcinoma (NKC), which is the major histologic type of NPC. As a result, 481 differentially expressed (DE) lncRNAs (231 up-regulated and 250 down-regulated) were identified. Moreover, integrated bioinformatics analyses including gene ontology, lncRNA functional prediction based on coding-noncoding gene co-expression network, interactive miRNAs, and transcription factor binding motifs were all carried out to decode the potential functional roles of these newly identified DE-lncRNAs. This work hence offers new resource and insight into lncRNAs for further understanding the molecular mechanisms of tumorigenesis of NKC, and may also define new biomarkers or therapy targets for the translational studies of NKC.
authors.affiliation: Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.|Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.|University of Chinese Academy of Sciences, Beijing 100049, China.|These authors contributed equally to this work.
authors.forename: Bao
authors.initials: B
authors.lastname: Zhang
authors.affiliation: Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.|Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.|University of Chinese Academy of Sciences, Beijing 100049, China.|These authors contributed equally to this work.
authors.forename: Dongpeng
authors.initials: D
authors.lastname: Wang
authors.affiliation: Cancer Center, First People's Hospital of Foshan, Foshan, Guangdong 528000, China.|These authors contributed equally to this work.
authors.forename: Jing
authors.initials: J
authors.lastname: Wu
authors.affiliation: Department of Otolaryngology, First People's Hospital of Foshan, Foshan, Guangdong 528000, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Tang
authors.affiliation: Department of Otolaryngology, First People's Hospital of Foshan, Foshan, Guangdong 528000, China.
authors.forename: Weixiong
authors.initials: W
authors.lastname: Chen
authors.affiliation: Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.|Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Xiaomin
authors.initials: X
authors.lastname: Chen
authors.affiliation: Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.|Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Dongdong
authors.initials: D
authors.lastname: Zhang
authors.affiliation: Cancer Center, First People's Hospital of Foshan, Foshan, Guangdong 528000, China.
authors.forename: Yanming
authors.initials: Y
authors.lastname: Deng
authors.affiliation: Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing 100853, China.
authors.forename: Mingzhou
authors.initials: M
authors.lastname: Guo
authors.affiliation: Department of Otolaryngology, First People's Hospital of Foshan, Foshan, Guangdong 528000, China.
authors.forename: Yuejian
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.|Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Jianjun
authors.initials: J
authors.lastname: Luo
authors.affiliation: Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.|Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
mesh_terms: D015415:Biomarkers; D063646:Carcinogenesis / Q000235:genetics; D002277:Carcinoma / Q000235:genetics*; D015536:Down-Regulation; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D035683:MicroRNAs / Q000235:genetics* / Q000302:isolation & purification; D000077274:Nasopharyngeal Carcinoma; D009303:Nasopharyngeal Neoplasms / Q000235:genetics*; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000302:isolation & purification; D012333:RNA, Messenger / Q000235:genetics* / Q000302:isolation & purification; D060888:Real-Time Polymerase Chain Reaction; D015854:Up-Regulation
chemical_list: D015415:Biomarkers; D035683:MicroRNAs; D062085:RNA, Long Noncoding; D012333:RNA, Messenger