Background Competing endogenous RNA (ceRNA) networks may be used to relate the functions of protein-coding mRNAs with those of the non-coding RNAs, such as microRNAs (miRNAs) and the long non-coding RNAs (lncRNAs). ceRNAs enable the post-transcriptional regulation of gene expression by competing for the shared miRNAs. However, the role and function of the lncRNA-miRNA-mRNA ceRNA network in thymic epithelial neoplasms (TEN) remains unknown.
Methods The miRNA, mRNA, and lncRNA expression profiles of 124 patients with TEN were downloaded from The Cancer Genome Atlas. We identified the differentially expressed (DE) miRNAs, mRNAs, and lncRNAs using the limma package in R software. The GDCRNATools package was used for the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotations. Cytoscape software was used to construct the lncRNA-miRNA-mRNA ceRNA network. The Gene Expression Profiling Interactive Analysis platform was used to estimate the overall survival (OS) rates of the patients. Survival curves were analyzed using the log-rank test. Finally, the mRNAs in the ceRNA network were analyzed using the GOplot package in R.
Results A total of 1513, 188, and 579 TEN-specific mRNAs, lncRNAs, and miRNAs, respectively, were identified. The lncRNA-miRNA-mRNA ceRNA network was constructed, and included 53 mRNAs, 4 lncRNAs, and 27 miRNAs. A total of 10 DEmRNAs (DLX2, C8orf88, CD38, GATA3, MAL, FOXQ1, FOLH1, NLRP12, HJURP, and ACSM1) and 1 lncRNA (SNHG3) were found to be significantly associated with OS ( P <0.05).
Conclusion In this study, we constructed a lncRNA-miRNA-mRNA ceRNA gene regulatory network for TEN, and identified potential prognostic and diagnostic biomarkers, as well as therapeutic targets, for the disease.