Identification of Key ncRNAs and ceRNA Network in DR via Bioinformation Analysis

This study aimed to find potential diagnostic biomarkers for diabetic retinopathy (DR) , explore its ceRNA mechanism and analyze the role of immune cell infiltration in DR. Method.Three microarray datasets for human retina tissues and aqueous humor in DR were downloaded from the Gene Expression Omnibus (GEO) database. First, differentially expressed miRNAs (DE-miRNAs) and differentially expressed mRNAs (DE-mRNAs) were identified by R software. Then xCell and ImmuCellAI were used to evaluate the infiltration of immune cells in DR retina tissues. BioGPS was used to identify tissue/organ-specific genes; DE-mRNA was enriched, and a protein-protein interaction (PPI) network was constructed to understand its functions and enrichment pathways and identify hub genes. Finally, we used target gene prediction software to construct competing endogenous RNA (ceRNA) networks for hub genes and visualized them with Cytoscape.Result.A total of 90 DE-miRNAs were identified in the GSE140959 datasets. Among these DE-miRNAs, the top 3 upregulated miRNAs, hsa-miR-3960, -548y and -7, may be potential biomarkers for diagnosis of DR. In the GSE160306 datasets, we recognized 147 DE-mRNAs. The xCell analysis identified immune cells that are significantly changed after DR, such as memory B-cells, eosinophils and M2 macrophages. Immune cell infiltration analysis found that natural killer T (NKT) cells, mucosal-associated invariant T (MAIT) cells, exhausted T cells and macrophages may be involved in the DR process. Comprehensive analysis showed that the negative regulation of cellular defense response and adaptive immune response was the main process of significant enrichment of DE-mRNAs. Among these DE-mRNAs, we identified 91 tissue/organ-specific expressed genes and intersected with 10 cytoHubba genes to finally obtain three central hub genes: IL6, SLAMF1 and CCL8. And finally constructed PP12613/hsa-miR-2114-3p/IL6, LINC00960/has-miR-6891-5p/SLAMF1 and KCNQ1OT1/hsa-miR-7151-3p/CCL8 network with potential regulatory effect on DR progression. Conclusions.In conclusion, we believe that hsa-miR-3960, -548y and -7 can be used as diagnostic markers for DR, and PP12613/hsa-miR-2114-3p/IL6, LINC00960/has-miR-6891-5p/SLAMF1 and KCNQ1OT1/hsa-miR-7151-3p/CCL8 regulatory networks play important roles in the occurrence and progression of DR. At the same time, the infiltration of immune cells is also an important part of DR pathology, regulating the severity of DR. Our data provide compelling insights into the pathogenesis and potential therapeutic targets of DR.