Kidney Single-Cell Atlas Reveals Myeloid Heterogeneity in Progression and Regression of Kidney Disease

Significance Statement The innate immune system is central to injury and repair in the kidney, but the heterogeneity of myeloid cell subsets behind these processes is unknown. Complementary technologies—including bulk tissue transcriptomics, integrated droplet– and plate-based single-cell RNA sequencing, and paired blood exchange—resolved myeloid cell heterogeneity in a murine model of reversible unilateral ureteric obstruction, creating a single-cell atlas. The identified novel myeloid subsets could be targeted to ameliorate injury or enhance repair, including an Arg1+ monocyte subset present during injury and Mmp12+ macrophages present during repair. Standard flow cytometry to detect cell surface markers would have missed these subsets. Complementary techniques capture the complexity and dynamics of monocyte, dendritic cell, and macrophage phenotypes in the injured and repairing kidney. Background Little is known about the roles of myeloid cell subsets in kidney injury and in the limited ability of the organ to repair itself. Characterizing these cells based only on surface markers using flow cytometry might not provide a full phenotypic picture. Defining these cells at the single-cell, transcriptomic level could reveal myeloid heterogeneity in the progression and regression of kidney disease. Methods Integrated droplet– and plate-based single-cell RNA sequencing were used in the murine, reversible, unilateral ureteric obstruction model to dissect the transcriptomic landscape at the single-cell level during renal injury and the resolution of fibrosis. Paired blood exchange tracked the fate of monocytes recruited to the injured kidney. Results A single-cell atlas of the kidney generated using transcriptomics revealed marked changes in the proportion and gene expression of renal cell types during injury and repair. Conventional flow cytometry markers would not have identified the 12 myeloid cell subsets. Monocytes recruited to the kidney early after injury rapidly adopt a proinflammatory, profibrotic phenotype that expresses Arg1 , before transitioning to become Ccr2 + macrophages that accumulate in late injury. Conversely, a novel Mmp12 + macrophage subset acts during repair. Conclusions Complementary technologies identified novel myeloid subtypes, based on transcriptomics in single cells, that represent therapeutic targets to inhibit progression or promote regression of kidney disease.