Cancer Specific Long Noncoding RNAs Show Differential Expression Patterns and Competing Endogenous RNA Potential in Hepatocellular Carcinoma

Long noncoding RNAs (lncRNAs) regulate gene expression by acting with microRNAs (miRNAs). However, the roles of cancer specific lncRNA and its related competitive endogenous RNAs (ceRNA) network in hepatocellular cell carcinoma (HCC) are not fully understood. The lncRNA profiles in 372 HCC patients,...

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Bibliographic Details
Published in:PloS one 2015-10, Vol.10 (10), p.e0141042-e0141042
Main Authors: Zhang, Jian, Fan, Dahua, Jian, Zhixiang, Chen, George G, Lai, Paul B S
Format: Article
Language:English
Subjects:
Analysis
Base Sequence
Bioinformatics
Cancer
Cancer genetics
Carcinoma
Carcinoma, Hepatocellular - genetics
Carcinoma, Hepatocellular - mortality
Datasets
Development and progression
Female
Gene expression
Gene Expression Regulation, Neoplastic - genetics
Genes
Genetic aspects
Genetic Predisposition to Disease
Genomes
Genomics
Hepatocellular carcinoma
Humans
Jian Zhang
Liver
Liver cancer
Liver Neoplasms - genetics
Liver Neoplasms - mortality
Male
Metastasis
MicroRNA
MicroRNAs
miRNA
Proteins
Ribonucleic acid
RNA
RNA, Long Noncoding - biosynthesis
RNA, Long Noncoding - genetics
Sequence Analysis, RNA
Surgery
Transfer RNA
Tumors
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Summary:Long noncoding RNAs (lncRNAs) regulate gene expression by acting with microRNAs (miRNAs). However, the roles of cancer specific lncRNA and its related competitive endogenous RNAs (ceRNA) network in hepatocellular cell carcinoma (HCC) are not fully understood. The lncRNA profiles in 372 HCC patients, including 372 tumor and 48 adjacent non-tumor liver tissues, from The Cancer Genome Atlas (TCGA) and NCBI GEO omnibus (GSE65485) were analyzed. Cancer specific lncRNAs (or HCC related lncRNAs) were identified and correlated with clinical features. Based on bioinformatics generated from miRcode, starBase, and miRTarBase, we constructed an lncRNA-miRNA-mRNA network (ceRNA network) in HCC. We found 177 cancer specific lncRNAs in HCC (fold change ≥ 1.5, P < 0.01), 41 of them were also discriminatively expressed with gender, race, tumor grade, AJCC tumor stage, and AJCC TNM staging system. Six lncRNAs (CECR7, LINC00346, MAPKAPK5-AS1, LOC338651, FLJ90757, and LOC283663) were found to be significantly associated with overall survival (OS, log-rank P < 0.05). Collectively, our results showed the lncRNA expression patterns and a complex ceRNA network in HCC, and identified a complex cancer specific ceRNA network, which includes 14 lncRNAs and 17 miRNAs in HCC.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0141042