Prediction of long noncoding RNA functions with co-expression network in esophageal squamous cell carcinoma

BMC Cancer

Research Article

Rodrigo JS Dalmolin¹  Ming Yan²  Fachun Shi³  Fu Tian⁴  Xiaobing Chen⁴  Wei Cao⁴  Yibin Hao⁴  Guoyong Chen⁴  Wei Wu⁵ 

[1] Department of Biochemistry, Bioscience Center and Institute of Tropical Medicine of Rio Grande do Norte, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil;Medical School, Zhengzhou University, Zhengzhou, Henan, China;Science and Education Department, Health Bureau of ZhengZhou, Zhengzhou, China;Zhengzhou Central Hospital, Affiliated to Zhengzhou University, China, 195 Tongbai Road, 450007, Zhengzhou, PR, China;Zhengzhou Central Hospital, Affiliated to Zhengzhou University, China, 195 Tongbai Road, 450007, Zhengzhou, PR, China;Department of Pathology and Experimental Medicine, University of Calgary, Calgary, AB, Canada;

关键词: Long noncoding RNA;    lncRNA;    Co-expression network;    Esophageal cancer;    ESCC;    ESCCAL-1;    Cancer initiatome;   

DOI  :  10.1186/s12885-015-1179-z

 received in 2014-08-25, accepted in 2015-03-09,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundLong non-coding RNAs (lncRNAs) are pervasively transcribed in the genome. They have important regulatory functions in chromatin remodeling and gene expression. Dysregulated lncRNAs have been studied in cancers, but their role in esophageal squamous cell carcinoma (ESCC) remains largely unknown. We have conducted lncRNA expression screening and a genome-wide analysis of lncRNA and coding gene expression on primary tumor and adjacent normal tissue from four ESCC patients, tend to understand the functionality of lncRNAs in carcinogenesis of esopheagus in combination with experimental and bioinformatics approach.MethodsLncRNA array was used for coding and non-coding RNA expression. R program and Bioconductor packages (limma and RedeR) were used for differential expression and co-expression network analysis, followed by independent confirmation and functional studies of inferred onco-lncRNA ESCCAL-1 using quantitative real time polymerase chain reaction, small interfering RNA-mediated knockdown, apoptosis and invasion assays in vitro.ResultsThe global coding and lncRNA gene expression pattern is able to distinguish ESCC from adjacent normal tissue. The co-expression network from differentially expressed coding and lncRNA genes in ESCC was constructed, and the lncRNA function may be inferred from the co-expression network. LncRNA ESCCAL-1 is such an example as a predicted novel onco-lncRNA, and it is overexpressed in 65% of an independent ESCC patient cohort (n = 26). More over, knockdown of ESCCAL-1 expression increases esophageal cancer cell apoptosis and reduces the invasion in vitro.ConclusionOur study uncovered the landscape of ESCC-associated lncRNAs. The systematic analysis of coding and lncRNAs co-expression network increases our understanding of lncRNAs in biological network. ESCCAL-1 is a novel putative onco-lncRNA in esophageal cancer development.

【 授权许可】

Unknown   
© Hao et al.; licensee BioMed Central. 2015. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.