ScRNA-seq Data Reveal Gene Upregulation and Downregulation in Oxygen-Induced Retinopathy

BACKGROUND Retinopathy of prematurity is characterized by retinal vascular ischemia and hypoxia that lead to neovascularization, potentially causing retinal detachment and blindness. This study aimed to explore target genes involved in oxygen-induced retinopathy (OIR) through comprehensive single-cell RNA sequencing (scRNA-seq) data analysis. MATERIAL AND METHODS ScRNA-seq data of retinal tissues obtained from mice under normoxic and OIR conditions were retrieved from the Gene Expression Omnibus (GEO; accession number GSE150703). A suite of bioinformatics tools was used for data processing, cell clustering, cell type annotation, differential gene expression analysis, gene set enrichment analysis, and protein-protein interaction network prediction to identify key hub genes associated with OIR. RESULTS Analysis of GSE150703 OIR mouse data identified 10 retinal cell types. These findings were supported by pathway enrichment analyses, including Gene Ontology and Kyoto Encyclopedia of Genes and Genomes, which indicated significant upregulation of Hnrnpu, Vamp2, Ybx1, Ywhab, and Csnk1a1, and downregulation of Xist and mt-Co1, among others. Interacting proteins from protein-protein interaction network studies identified major hub genes involving Srsf1, Srsf11, Sf3b1, and Hnrnpu, among others. Moreover, the research explored how mutations of Chchd10 and Sf3b1 influence the development of the disease and downregulation of mitochondrial-associated genes, such as lncRNA-Xist, Ndufs5, and mt-Co1, which may provide further insight into their roles in the pathogenesis of OIR. CONCLUSIONS The single-cell data analysis suggests that Hnrnpu, Vamp2, Ybx1, Ywhab, Csnk1a1, Pfkp, Rho, Srsf1, Srsf11, Mt1, Tpr, Hnrnpc, Chchd10, Sf3b1, Xist, Ndufs5, and mt-Co1 may be potential target genes in OIR in retinopathy of prematurity.