The construction and analysis of competitive endogenous RNA (ceRNA) networks in metastatic renal cell carcinoma: a study based on The Cancer Genome Atlas

Abstract

BackgroundThe pathogenesis of metastatic renal cell carcinoma (mRCC), one of the most common malignant neoplasms, remains unknown. Studies on competitive endogenous RNAs (ceRNAs) have uncovered new interactions between RNAs, which suggest their roles in cancer pathogenesis. However, the role of ceRNA networks in mRCC has not yet been studied. Thus, this study aims to explore the role of ceRNA networks in mRCC development and identify potential prognostic indicators.MethodsWe analyzed RNA sequencing data of mRCC patients, which had been obtained from The Cancer Genome Atlas (TCGA) database. Next, differentially expressed long-noncoding RNAs (DElncRNAs), differentially expressed micro RNAs (DEmiRNAs), and differentially expressed messenger RNAs (DEmRNAs) in mRCC and clear cell RCC (ccRCC) samples were identified using the edgeR package that is available in R software. Moreover, based on the Database for Annotation, Visualization, and Integrated Discovery (DAVID), enrichment analyses for biological processes and pathways functional were performed. As such, we built a ceRNA network and performed a survival analysis using the survival package in R.ResultsA total of 369 DElncRNAs, 12 DEmiRNAs, and 728 DEmRNAs were identified for further analysis. Of these, 11 lncRNAs, 20 mRNAs, and 2 miRNAs were included in the ceRNA network. Moreover, 7 of the 11 lncRNAs and 3 of the 20 mRNAs were associated with the overall survival of mRCC patients (P<0.05).ConclusionsCollectively, our findings allow a deepened understanding of the molecular mechanism of the ceRNA network and its role in mRCC development, which can guide both mRCC therapy and related future research.