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

Abstract

BackgroundLittle 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.MethodsIntegrated 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.ResultsA 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.ConclusionsComplementary technologies identified novel myeloid subtypes, based on transcriptomics in single cells, that represent therapeutic targets to inhibit progression or promote regression of kidney disease.

Infusion of Phagocytic Macrophages Overexpressing CPT1a Ameliorates Kidney Fibrosis in the UUO Model

“…Other studies [ 20 ] previously confirmed marked changes in the proportion and gene expression of at least 12 myeloid cell subsets involved in kidney injury and repair in a reversible UUO model. In addition, they described a novel Mmp121 macrophage subset that acts during repair.…”

Single-Cell RNA Sequencing Reveals the Immunological Profiles of Renal Allograft Rejection in Mice

“…In the present study, we developed further in-depth analysis of these immune cell types with comprehensive classification and description of cell subtypes including their specific marker genes, functional characteristics, transcriptional regulation, and the proportional dynamics from the renal allograft rejection peak on D7 to the regression phase on D15. In naïve mouse kidneys, monocytes/macrophages, neutrophils, DCs, B and T lymphocytes, NK cells could all be observed (16,41,42). Among macrophage subtypes, infiltrating Ly6C hi Chil3 + macrophage and Ly6C lo patrolling macrophages are commonly found in normal kidneys (16,42), whereas IFNIC and Mrc1 + macrophages are more common to disease models like unilateral ureteric obstruction model (42).…”

“…In naïve mouse kidneys, monocytes/macrophages, neutrophils, DCs, B and T lymphocytes, NK cells could all be observed (16,41,42). Among macrophage subtypes, infiltrating Ly6C hi Chil3 + macrophage and Ly6C lo patrolling macrophages are commonly found in normal kidneys (16,42), whereas IFNIC and Mrc1 + macrophages are more common to disease models like unilateral ureteric obstruction model (42). Study of kidney allograft biopsies from human recipients undergoing AR and CR also identified immune populations like those in mice, including monocytes, B cells, T cells, plasma cells (43)(44)(45), therefore independently supporting a role of these cells in kidney rejection in humans.…”

Chess Not Checkers: Complexities Within the Myeloid Response to the Acute Kidney Injury Syndrome

“…Recent work has shed light on more refined strategies for separating mononuclear phagocyte cell (MPC) populations within the kidney and shows promise for enhancing our sophistication and accuracy when investigating these cells in the context of AKI. In addition to F4/80, flow cytometry studies have shown that CD11b, CD11c, CX3CR1, Ly6C, CD64, CD14, CD16, MHC II, and CD103 are also useful markers for delineating myeloid populations within the mouse kidney ( Table 1 ) ( 21 , 69 – 80 ). A study from Lee et al used several of these markers to identify a novel MPC population in the kidney that is also CD45-intermediate (CD45 int CD11b int F4/80 + MHCII + CX3CR1 + Ly6C − ).…”