COL1A1 and SERPINE1 as Potential Therapeutic Targets in Diabetic Retinopathy: A Study Incorporating RNA Transcriptomics, Single-Cell RNA Sequencing, and Proteomics.
Diabetic retinopathy is caused by chronic hyperglycemia, which damages the retina's blood vessels and neurons. This study is aimed at identifying potential therapeutic targets for DR.
Transcriptomic and proteomic data were obtained from the Gene Expression Omnibus (GEO) and ProteomeXchange databases, respectively. Differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) were intersected. An enrichment analysis of the overlapping genes was performed based on the DAVID database. A protein-protein interaction (PPI) network (STRING) was analyzed via Cytoscape/cytoHubba to identify key genes. Single-cell RNA-sequencing (scRNA-seq) data were processed using Seurat. Gene set enrichment analysis (GSEA) (clusterProfiler) and molecular docking (EnrichR) were performed. High glucose-induced retinal microvascular endothelial cells (RMECs) were used for functional assays.
The intersection of DEGs and DEPs yielded shared genes, enriched in the PI3K-Akt signaling pathway, AGE-RAGE signaling pathway in diabetic complications, complement and coagulation cascades, and ECM-receptor interaction; a PPI network incorporating these genes revealed two key DR-associated highly expressed genes, COL1A1 and SERPINE1. GSEA showed that samples with high expression of these key genes were enriched in pathways such as reactome signaling by TGFB family members, inflammatory response, TGF-β signaling, and reactome cell extracellular matrix interactions. Single-cell and molecular docking analyses revealed high expression of the two key genes in fibroblasts and binding between SERPINE1 and paricalcitol, and HG induction increased their levels in RMECs, whereas knockdown of SERPINE1 repressed RMEC proliferation, migration, and invasion in vitro.
This study identifies SERPINE1 and COL1A1 as possible DR therapeutic targets, providing new insights into relevant therapeutic development.
Transcriptomic and proteomic data were obtained from the Gene Expression Omnibus (GEO) and ProteomeXchange databases, respectively. Differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) were intersected. An enrichment analysis of the overlapping genes was performed based on the DAVID database. A protein-protein interaction (PPI) network (STRING) was analyzed via Cytoscape/cytoHubba to identify key genes. Single-cell RNA-sequencing (scRNA-seq) data were processed using Seurat. Gene set enrichment analysis (GSEA) (clusterProfiler) and molecular docking (EnrichR) were performed. High glucose-induced retinal microvascular endothelial cells (RMECs) were used for functional assays.
The intersection of DEGs and DEPs yielded shared genes, enriched in the PI3K-Akt signaling pathway, AGE-RAGE signaling pathway in diabetic complications, complement and coagulation cascades, and ECM-receptor interaction; a PPI network incorporating these genes revealed two key DR-associated highly expressed genes, COL1A1 and SERPINE1. GSEA showed that samples with high expression of these key genes were enriched in pathways such as reactome signaling by TGFB family members, inflammatory response, TGF-β signaling, and reactome cell extracellular matrix interactions. Single-cell and molecular docking analyses revealed high expression of the two key genes in fibroblasts and binding between SERPINE1 and paricalcitol, and HG induction increased their levels in RMECs, whereas knockdown of SERPINE1 repressed RMEC proliferation, migration, and invasion in vitro.
This study identifies SERPINE1 and COL1A1 as possible DR therapeutic targets, providing new insights into relevant therapeutic development.