Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data

BMC Genomics

Research

Junfeng Jiang¹  Bairong Shen¹  Yuxin Lin¹  Weirong Cui¹  Xiaoke Zhou¹  Yulan Qian²  Zhongming Zhao³  Jiajia Chen⁴ 

[1] Center for Systems Biology, Soochow University, 215006, Suzhou, China;Clinical Pharmacology Laboratory, the First Affiliated Hospital of Soochow University, 215006, Suzhou, China;Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA;Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA;School of Chemistry, Biology and Material Engineering, Suzhou University of Science and Technology, 215009, Suzhou, China;

关键词: Prostate Cancer;    Androgen Receptor;    Serum Response Factor;    Module Eigengenes;    Intergenic Noncoding RNAs;   

DOI  :  10.1186/1471-2164-16-S7-S3

来源: Springer

【 摘 要 】

BackgroundProstate cancer (PCa) is a leading cause of cancer-related death of men worldwide. There is an urgent need to develop novel biomarkers for PCa prognosis and diagnosis in the post prostate specific antigen era. Long intergenic noncoding RNAs (lincRNAs) play essential roles in many physiological processes and can serve as alternative biomarkers for prostate cancer, but there has been no systematic investigation of lincRNAs in PCa yet.ResultsNine lincRNA co-expression modules were identified from PCa RNA-Seq data. The association between the principle component of each module and the PCa phenotype was examined by calculating the Pearson's correlation coefficients. Three modules (M1, M3, and M5) were found associated with PCa. Two modules (M3 and M5) were significantly enriched with lincRNAs, and one of them, M3, may be used as a lincRNA module-biomarker for PCa diagnosis. This module includes seven essential lincRNAs: TCONS_l2_00001418, TCONS_l2_00008237, TCONS_l2_00011130, TCONS_l2_00013175, TCONS_l2_00022611, TCONS_l2_00022670 and linc-PXN-1. The clustering analysis and microRNA enrichment analysis further confirmed our findings.ConclusionThe correlation between lincRNAs and protein-coding genes is helpful for further exploration of functional mechanisms of lincRNAs in PCa. This study provides some important insights into the roles of lincRNAs in PCa and suggests a few lincRNAs as candidate biomarkers for PCa diagnosis and prognosis.

【 授权许可】

Unknown   
© Cui et al.; licensee BioMed Central Ltd. 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 cited. 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.