Identification of RNA Transcript Makers Associated With Prognosis of Kidney Renal Clear Cell Carcinoma by a Competing Endogenous RNA Network Analysis

Objective: This study aims to identify several RNA transcripts associated with the prognosis of kidney renal clear cell carcinoma (KIRC). Methods: The differentially expressed mRNAs, lncRNAs and miRNAs (DEmRNAs, DElncRNAs and DEmiRNAs) between KIRC cases and controls were screened based on an RNA-seq dataset from The Cancer Genome Atlas (TCGA) database. Subsequently, miRcode, miRDB and TargetScan database were used to predict interactions between lncRNAs, miRNAs and target mRNAs. Then, a ceRNA network was built using miRNAs-mRNAs and lncRNAs-miRNAs pairs. Functional analysis of mRNAs in ceRNA was performed. Finally, the survival analysis of RNA transcripts in ceRNA network and correlation analysis for key RNA regulators were carried out. Results: There were 1527 DElncRNAs, 54 DEmiRNAs and 2321 DEmRNAs. A ceRNA network was constructed among 81 lncRNAs, 9 miRNAs and 197 mRNAs. Functional analysis showed that numerous mRNAs were significantly associated with regulation of cellular glucuronidation. In addition, 35 lncRNAs, 84 mRNAs and two miRNAs were significantly corelated to the survival of patients with KIRC (P < 0.05). Among them, miRNA-21 and miRNA-155 were negatively related to three lncRNAs (LINC00472, SLC25A5.AS1 and TCL6). Seven mRNA targets of miRNA-21 (FASLG, FGF1, TGFBI, ALX1, SLC30A10, ADCY2 and ABAT) and 12 mRNAs targets of miRNA-155 (STXBP5L, SCG2, SPI1, C12orf40, TYRP1, CTHRC1, TDO2, PTPRQ, TRPM8, ERMP1, CD36 and ST9SIA4) also acted as prognostic biomarkers for KIRC patients. Conclusion: We screened numerous novel prognosis-related RNA markers for KIRC patients by a ceRNA network analysis, providing deeper understandings of prognostic values of RNA transcripts for KIRC.