Identification of pterygium-related conjunctival epithelium microRNA and mRNA expression profiles by high-throughput screening analysis

Abstract Purpose. To detect the hub mRNAs and construct a microRNA (miRNA)-mRNA regulatory network by comparing pterygium-related conjunctival epithelium (PCE) and normal conjunctival epithelium (NCE) patient samples by high-throughput sequencing.Methods. Bulbar conjunctival epithelium samples were obtained from patients with primary pterygium and from donated normal eyeballs. Bioinformatics analysis, which included differential gene expression, gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis, was applied for the functional enrichment analysis of differentially expressed mRNAs (DEmRNAs). Protein-protein interaction (PPI) analysis and gene set enrichment analysis (GSEA) were performed on DEmRNAs whose pathways were related to the development of pterygium. Potential miRNAs binding to these hub DEmRNAs were predicted using software, and a hub mRNA-miRNA regulatory network was constructed. MiRNAs were verified through RT-qPCR.Results. Overall, the results showed 280 upregulated and 256 downregulated DEmRNAs. To explore the potential functions of DEmRNAs, we performed bioinformatics analysis to detect the potential functions of DEmRNAs and the relevant pathways related to the pathogenesis of pterygium in PCE. In addition, we enriched six pathways that were involved in the development of pterygium using a heatmap. Then, the GSEA results showed that galactose metabolism, epithelial mesenchymal transition and so on were significantly enriched among upregulated mRNAs (P＜0.001, and NES ≥ 1). Cytokine-cytokine receptor interaction, primary immunodeficiency, MAPK signalling pathway and so on were significantly enriched among downregulated mRNAs (P＜0.001, and NES ≤ -1). Then, a miRNA/mRNA regulatory network was constructed with 20 miRNAs and 48 differentially expressed genes (DEGs). The RT-qPCR validation study confirmed nine downregulated miRNAs (miR-653-3p, miR-3617-5p, miR-4681, miR-4802-3p, miR-888-3p, miR-7106-3p, miR-543, miR-200b-3p and miR-203a-3p) and two upregulated miRNAs (miR-5579b-3p and miR-6844).Conclusion. Our study shows the mRNA expression profile and miRNA/mRNA regulatory network of the PCE and provides a new perspective on the pathogenesis of pterygium.