Deciphering the Molecular and Cellular Landscape of Early Diabetic Nephropathy through Single-Cell RNA Sequencing and Protein-Protein Interaction Networks.

Abstract

Diabetic nephropathy (DN) arises through complex pathological mechanisms that remain incompletely understood. This study employs transcriptomic and single-cell RNA sequencing (scRNA-seq) approaches to systematically characterize gene expression patterns, cellular composition changes, and intercellular communication networks in early DN. Analysis of the GSE111154 transcriptome dataset identified 259 differentially expressed genes (DEGs), including 118 protein-coding genes (70 downregulated and 189 upregulated) in DN samples. Functional enrichment analysis revealed significant involvement of these DEGs in immune response pathways and extracellular matrix (ECM) organization. Single-cell analysis of the GSE131882 dataset resolved 12 distinct renal cell populations, demonstrating significant shifts in cellular proportions in DN, with notable expansions of endothelial cells (ENDO), fibroblasts (FIB), principal cells (PC), and parietal epithelial cells (PEC). Protein-protein interaction network analysis identified COL1A2, FLNA, A2M, and PLG as central hub genes in DN pathogenesis. Cell-cell communication analysis revealed enhanced interaction frequency and intensity in DN, particularly involving FIB cells through specific signaling pathways including CDH5, KIT, THBS, EGF, and FN1. In DN originated FIBs, the differential genes enriched transcription factor was NR2F2. Through immunohistochemical staining, NR2F2 was up-expressed in DN samples while CD31 was down-regulated. These findings collectively demonstrate profound dysregulation of immune responses, ECM remodeling, and cellular crosstalk during DN progression, highlighting key molecular and cellular drivers of disease pathogenesis.