title: The gain and loss of long noncoding RNA associated-competing endogenous RNAs in prostate cancer.
abstract: 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.
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors.forename: Dianming
authors.initials: D
authors.lastname: Liu
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors.forename: Xuexin
authors.initials: X
authors.lastname: Yu
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors.forename: Shuyuan
authors.initials: S
authors.lastname: Wang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors.forename: Enyu
authors.initials: E
authors.lastname: Dai
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors.forename: Leiming
authors.initials: L
authors.lastname: Jiang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Yang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors.forename: Feng
authors.initials: F
authors.lastname: Yang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors.forename: Shunheng
authors.initials: S
authors.lastname: Zhou
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Jiang
mesh_terms: D051400:Aquaporin 3 / Q000378:metabolism; D051767:Early Growth Response Protein 2 / Q000378:metabolism; D005091:Exons; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006801:Humans; D047348:Hydrolyzable Tannins / Q000737:chemistry; D008297:Male; D035683:MicroRNAs / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D011379:Prognosis; D011471:Prostatic Neoplasms / Q000235:genetics* / Q000378:metabolism*; D062085:RNA, Long Noncoding / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics; D049490:Systems Biology
chemical_list: C586612:1,2,6-tri-O-galloyl-beta-D-glucopyranose; C496027:AQP3 protein, human; C497326:EGR2 protein, human; D051767:Early Growth Response Protein 2; D047348:Hydrolyzable Tannins; C557041:MALAT1 long non-coding RNA, human; C498907:MEG3 non-coding RNA, human; D035683:MicroRNAs; D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D051400:Aquaporin 3
keywords: ceRNA; lncRNA; miRNA; miRNA sponge; prostate cancer