Single-Cell RNA Sequencing Profiles Identify Important Pathophysiologic Factors in the Progression of Diabetic Nephropathy

Xi Lu; Li Li; Luolan Suo; Ping Huang; Hongjie Wang; Su Han; Mingming Cao

doi:10.3389/fcell.2022.798316

Single-Cell RNA Sequencing Profiles Identify Important Pathophysiologic Factors in the Progression of Diabetic Nephropathy

Front Cell Dev Biol. 2022 May 10:10:798316. doi: 10.3389/fcell.2022.798316. eCollection 2022.

Authors

Xi Lu¹, Li Li², Luolan Suo², Ping Huang², Hongjie Wang³, Su Han⁴, Mingming Cao²

Affiliations

¹ Department of Gastroenterology, The First Affiliated Hospital of Harbin Medical University, Harbin, China.
² Department of Endocrinology, The First Affiliated Hospital of Harbin Medical University, Harbin, China.
³ Department of Endocrinology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China.
⁴ Department of Parasitology, Harbin Medical University, Harbin, China.

Abstract

Objective: Single-cell RNA sequencing (scRNA-seq) analyses have provided a novel insight into cell-specific gene expression changes in diseases. Here, this study was conducted to identify cell types and pathophysiologic factors in diabetic nephropathy. Methods: Single-cell RNA sequencing data of three human diabetic kidney specimens and three controls were retrieved from the GSE131882 dataset. Following preprocessing and normalization, cell clustering was presented and cell types were identified. Marker genes of each cell type were identified by comparing with other cell types. A ligand-receptor network analysis of immune cells was then conducted. Differentially expressed marker genes of immune cells were screened between diabetic nephropathy tissues and controls and their biological functions were analyzed. Diabetic nephropathy rat models were established and key marker genes were validated by RT-qPCR and Western blot. Results: Here, 10 cell types were clustered, including tubular cells, endothelium, parietal epithelial cells, podocytes, collecting duct, mesangial cells, immune cells, distal convoluted tubule, the thick ascending limb, and proximal tubule in the diabetic kidney specimens and controls. Among them, immune cells had the highest proportion in diabetic nephropathy. Immune cells had close interactions with other cells by receptor-ligand interactions. Differentially expressed marker genes of immune cells EIF4B, RICTOR, and PRKCB were significantly enriched in the mTOR pathway, which were confirmed to be up-regulated in diabetic nephropathy. Conclusion: Our findings identified immune cells and their marker genes (EIF4B, RICTOR, and PRKCB) as key pathophysiologic factors that might contribute to diabetic nephropathy progression.

Keywords: diabetic nephropathy; immune cells; mTOR pathway; marker genes; single-cell RNA sequencing.