Identification of hsa-miR-4770 as characteristic microRNA of gallbladder carcinoma and exploration on the ceRNA regulation mechanism via integrated bioinformatics analysis

Abstract

Background and Aims: Gallbladder carcinoma (GBC) is a highly malignant tumor with a poor overall prognosis. This study aimed to identify the characteristic microRNAs (miRNAs) of GBC and the competing endogenous RNA (ceRNA) regulatory mechanisms. Methods GBC-related differentially expressed miRNAs (DE-miRNAs) were authenticated by differential expression analysis and weighted gene co-expression network analysis (WGCNA). The characteristic miRNA was extracted by least absolute shrinkage and selection operator (LASSO) and Support vector machine-recursive feature elimination (SVM-RFE). Targeting genes (mRNAs), upstream circularRNAs (circRNAs), and long noncoding RNAs (lncRNAs) prediction for the characteristic miRNAs was conducted by using the Starbase database. The lncRNA(circRNA)-miRNA-mRNA network was created by Cytoscape software. Gene Ontology (GO) and KEGG enrichment analysis was implemented by clusterProfiler R package. The varElect was applied to analyse the target genes, and search for functions and interactions by GeneMANIA. The expression of characteristic miRNA in clinical samples was verified by quantitative real-time polymerase chain reaction (RT-qPCR). Results A total of 131 GBC-related DE-miRNAs were obtained. The hsa-miR-4770 was defined as characteristic miRNA for GBC. The ceRNA network containing 211 mRNAs, 1 miRNA, 2 lncRNAs, and 48 circRNAs was created. The downstream genes were mainly involved in actin filament organization, cell-substrate adhesion, cell-matrix adhesion, reactive oxygen species metabolic process, glutamine metabolic process and extracellular matrix (ECM)-receptor interaction pathway. 10 key genes in the network, namely BRCA1, CHEK2, RB1, CASP8, PTGS2, CD44, KRT19, CDK1, PVT1, and MXRA5 were found to be most correlated with disease. Multiple genes involved in cell cycle-related processes, p53 related pathway, and extrinsic apoptotic signaling pathway. RT-qPCR result demonstrated that the expression trends of hsa-miR-4770 was consistent with the public database. Conclusion We identified hsa-miR-4770 as the characteristic miRNA for GBC. The ceRNA network of hsa-miR-4770 may play key roles in GBC. This study provided a little basis for potential pathogenesis of GBC.