The expression profiling and ontology analysis of noncoding RNAs in peritoneal fibrosis induced by peritoneal dialysis fluid.

Increasing amounts of evidence have indicated that noncoding RNAs (ncRNAs) have important regulatory potential in various biological processes. However, the contributions of ncRNAs, especially long noncoding RNAs (lncRNAs), to peritoneal fibrosis remain largely unknown. The aim of this study was to investigate miRNA, lncRNA and mRNA expression profiles and their potential roles in the process of peritoneal fibrosis. Microarray expression profiles of the miRNAs, lncRNAs and mRNAs were determined in normal control peritoneum and in a mouse model of peritoneal dialysis fluid (PDF)-induced fibrotic peritoneum. Differential expression, pathway and gene network analyses were developed to identify possible functional RNA molecules in peritoneal fibrosis. Compared to the normal control, 232 lncRNAs (127 up-regulated and 105 down-regulated), 154 mRNAs (87 up-regulated and 67 down-regulated) and 15 miRNAs (14 miRNAs up-regulated and 1 down-regulated) were differentially expressed in the fibrotic peritoneum. Among the differentially expressed ncRNAs, 9 lncRNAs and 5 miRNAs were validated by real-time RT-PCR. Pathway analysis showed that the Jak-STAT, TGF-beta and MAPK signaling pathways had a close relationship with peritoneal fibrosis. Gene co-expression network analysis identified many genes, including JunB, HSP72, and Nedd9. It also identified lncRNAs AK089579, AK080622, and ENSMUST00000053838 and miRNAs miR-182 and miR-488. All of these species potentially play a key role in peritoneal fibrosis. Our results provide a foundation and an expansive view of the roles and mechanisms of ncRNAs in PDF-induced peritoneal fibrosis.