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

Weirong Cui,Junfeng Jiang,Yuxin Lin,Zhongming Zhao,Xiaoke Zhou,Bairong Shen,Yulan Qian,Jiajia Chen

doi:10.1186/1471-2164-16-s7-s3

Abstract

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.

Highlights

Prostate cancer (PCa) is a leading cause of cancer-related death of men worldwide
From the genetic point of view, long non-coding RNAs (lncRNAs) can be classified into five broad categories [11]: (i) sense - when a lncRNA overlaps one or more exons of another transcript on the same strand, (ii) antisense - when a lncRNA overlaps one or more exons of another transcript on the opposite strand, (iii) bidirectional - when the expression of the lncRNA and a neighboring coding transcript on the opposite strand is initiated in close genomic proximity, (iv) intronic - when a lncRNA is derived from an intron of a second transcript, and (v) intergenic - when a lncRNA lies as an independent unit within the genomic interval between two genes
We focused on the co-expression between coding genes and lincRNAs to investigate the role of lincRNAs and to identify the putative lincRNA module biomarkers in prostate cancer, the PCa biomarker identification is becoming very essential in the era of post prostate specific antigen [12,13]

Summary

Introduction

Prostate 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. Researchers have primarily focused on investigating the roles of protein-coding genes in cancer development. It has been recognized that lncRNAs are a new class of ncRNAs for its essential roles in controlling every level of gene expression in various physiological processes, including development, differentiation and other biological mechanisms [9]. We focused on the co-expression between coding genes and lincRNAs to investigate the role of lincRNAs and to identify the putative lincRNA module biomarkers in prostate cancer, the PCa biomarker identification is becoming very essential in the era of post prostate specific antigen [12,13]

Methods

Results

Conclusion