Single-Cell RNA Profiling of Glomerular Cells Shows Dynamic ... : Journal of the American Society of Nephrology (original) (raw)

Basic Research

Single-Cell RNA Profiling of Glomerular Cells Shows Dynamic Changes in Experimental Diabetic Kidney Disease

Fu, Jia1,2; Akat, Kemal M.3; Sun, Zeguo1; Zhang, Weijia1; Schlondorff, Detlef1; Liu, Zhihong2; Tuschl, Thomas3; Lee, Kyung1; He, John Cijiang1,4

1Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York;

2National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China;

3Laboratory of RNA Molecular Biology, The Rockefeller University, New York, New York; and

4Renal Program, James J Peters VA Medical Center at Bronx, New York, New York

J.F., and K.M.A. contributed equally to this work.

Correspondence: Dr. John Cijiang He or Dr. Kyung Lee, Division of Nephrology, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York NY 10029. E-mail: [email protected] or [email protected]

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Abstract

Significance Statement

Although transcriptomic profiling of kidney tissues or isolated glomeruli has provided insights into broad changes in the pathogenesis of diabetic kidney disease, the presence of multiple cell types in kidney samples limits what can be discerned about changes in specific types of cells. To better elucidate the mechanisms of early diabetic kidney injury, the authors used single-cell RNA sequencing technology to perform a gene expression analysis of individual kidney glomerular cells of a diabetic mouse model. A comparison of gene expression in normal versus diabetic mouse kidney cells at a single-cell level showed dynamic changes in the pattern of expressed genes. This approach may help identify important factors underlying the pathophysiology of diabetic kidney disease progression and point to potential new therapeutic approaches.

Background

Recent single-cell RNA sequencing (scRNA-seq) analyses have offered much insight into cell-specific gene expression profiles in normal kidneys. However, in diseased kidneys, understanding of changes in specific cells, particularly glomerular cells, remains limited.

Methods

To elucidate the glomerular cell–specific gene expression changes in diabetic kidney disease, we performed scRNA-seq analysis of isolated glomerular cells from streptozotocin-induced diabetic endothelial nitric oxide synthase (eNOS)–deficient (eNOS−/−) mice and control eNOS−/− mice.

Results

We identified five distinct cell populations, including glomerular endothelial cells, mesangial cells, podocytes, immune cells, and tubular cells. Using scRNA-seq analysis, we confirmed the expression of glomerular cell–specific markers and also identified several new potential markers of glomerular cells. The number of immune cells was significantly higher in diabetic glomeruli compared with control glomeruli, and further cluster analysis showed that these immune cells were predominantly macrophages. Analysis of differential gene expression in endothelial and mesangial cells of diabetic and control mice showed dynamic changes in the pattern of expressed genes, many of which are known to be involved in diabetic kidney disease. Moreover, gene expression analysis showed variable responses of individual cells to diabetic injury.

Conclusions

Our findings demonstrate the ability of scRNA-seq analysis in isolated glomerular cells from diabetic and control mice to reveal dynamic changes in gene expression in diabetic kidneys, with variable responses of individual cells. Such changes, which might not be apparent in bulk transcriptomic analysis of glomerular cells, may help identify important pathophysiologic factors contributing to the progression of diabetic kidney disease.

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