The gain and loss of long noncoding RNA associated-competing endogenous RNAs in prostate cancer
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Dianming Liu1,*, Xuexin Yu1,*, Shuyuan Wang1, Enyu Dai1, Leiming Jiang1, Jing Wang1, Qian Yang1, Feng Yang1, Shunheng Zhou1, Wei Jiang1
1College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
*These authors have contributed equally to the work
Wei Jiang, email: firstname.lastname@example.org
Keywords: lncRNA, miRNA, ceRNA, prostate cancer, miRNA sponge
Received: March 03, 2016 Accepted: July 27, 2016 Published: August 09, 2016
Prostate cancer (PC) is one of the most common solid tumors in men. However, the molecular mechanism of PC remains unclear. Numerous studies have demonstrated that long noncoding RNA (lncRNA) can act as microRNA (miRNA) sponge, one type of competing endogenous RNAs (ceRNAs), which offers a novel viewpoint to elucidate the mechanisms of PC. Here, we proposed an integrative systems biology approach to infer the gain and loss of ceRNAs in PC. First, we re-annotated exon microarray data to obtain lncRNA expression profiles of PC. Second, by integrating mRNA and miRNA expression, as well as miRNA targets, we constructed lncRNA-miRNA-mRNA ceRNA networks in cancer and normal samples. The lncRNAs in these two ceRNA networks tended to have a longer transcript length and cover more exons than the lncRNAs not involved in ceRNA networks. Next, we further extracted the gain and loss ceRNA networks in PC. We found that the gain ceRNAs in PC participated in cell cycle, and the loss ceRNAs in PC were associated with metabolism. We also identified potential prognostic ceRNA pairs such as MALAT1-EGR2 and MEG3-AQP3. Finally, we inferred a novel mechanism of known drugs, such as cisplatin, for the treatment of PC through gain and loss ceRNA networks. The potential drugs such as 1,2,6-tri-O-galloyl-beta-D-glucopyranose (TGGP) could modulate lncRNA-mRNA competing relationships, which may uncover new strategy for treating PC. In summary, we systematically investigated the gain and loss of ceRNAs in PC, which may prove useful for identifying potential biomarkers and therapeutics for PC.
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