Fig 2: Cx3cr1 is required for accumulation of Ccr2+ KRM in the kidney cortex. (A) UMAP of cell clusters in control (N=2 mice; both female) and Cx3cr1 gfp/gfp knockout (N=2 mice; both female) mice. The control group shown in this figure is the same as the data shown in Figure 1 . (B) Composite UMAP of cells from control and Cx3cr1 gfp/gfp mice. (C) Quantification of cluster composition. T-test. (D) Quantification of flow cytometry data analyzing KRM subsets as a percentage of CD11b and F4/80 positive cells or as a percentage of live single cells in the kidney. Two-way ANOVA. (E) Representative confocal microscopy images of kidney sections isolated from the cortex of Cx3cr1 gfp/wt Ccr2 rfp/wt (top) or Cx3cr1 gfp/gfp Ccr2 rfp/wt (bottom) stained with the pan macrophage marker F4/80. Mice were 6-8 weeks of age at harvest. N=2-4 mice per group. (F) Quantification of RFP+ F4/80+ area normalized to total nuclear area in Cx3cr1 control or knockout mice. Each dot represents an individual image that was quantified from a combined 2-4 mice per group. T-test. (G) Representative confocal microscopy images of kidney sections isolated from the cortex (left) or medulla (right) of Cx3cr1 gfp/wt (top) or Cx3cr1 gfp/gfp (bottom) mice stained with the pan macrophage marker F4/80 and CD206. Mice were 6-8 weeks of age at the time of harvest. N=3-4 mice per group. (H) Quantification of F4/80+ CD206+ area normalized to total nuclear area in the cortex or medulla of Cx3cr1 control or knockout mice. Each dot represents an individual image that was quantified from a combined 3-4 mice per group. Two-way ANOVA. (I) Volcano plot showing genes that were enriched in Cd63+ KRM isolated from control or Cx3cr1 gfp/gfp kidneys. (J) Metascape pathway analysis of genes that were significantly enriched (adjusted p value < 0.05) in Cd63+ KRM isolated from control or Cx3cr1 gfp/gfp kidneys. (K) Metascape pathway analysis of genes that were significantly enriched (adjusted p value < 0.05) in Mrc1+ KRM compared to Cd63+ KRM. #P <0.1, *P< 0.05, **P< 0.01, ***P< 0.001, ****P< 0.0001.

Fig 3: Loss of Cx3cr1 reduces injury accelerated cystic disease. (A) UMAP showing clusters of macrophages and dendritic cells in cystic (CM IR) and control mice (CM sham, cont IR) mice 56 days post IR injury or sham surgery. (B) Quantification of cluster composition in biological duplicates. (C, D) Pathway analysis of genes that were enriched (adjusted P value < 0.05) in (C) Ccr2+ KRM or (D) Cd63+ KRM from cystic mice compared to control mice (CM sham and cont IR). (E) Representative H&E images and quantification of cystic index in CM IR mice on the Cx3cr1 gfp/wt or Cx3cr1 gfp/gfp background 56 days post injury. **P< 0.01.