The single-cell landscape of kidney immune cells reveals transcriptional heterogeneity in early diabetic kidney disease

The pathogenesis of diabetic kidney disease (DKD) involves multifactorial processes that converge to initiate and advance the disease. Although DKD is not typically classified as an inflammatory glomerular disease, mounting evidence supports the involvement of kidney inflammation as a key contributor in DKD pathogenesis, particularly through macrophages. However, detailed identification and corresponding phenotypic changes of macrophages in DKD remain poorly understood. To capture the gene expression changes in specific macrophage cell subsets in early DKD, we performed single-cell transcriptomic analysis of CD45-enriched kidney immune cells from type 1 diabetic OVE26 mice at two time points during the disease development. We also undertook a focused analysis of mononuclear phagocytes (macrophages and dendritic cells). Our results show increased resident and infiltrating macrophage subsets in the kidneys of mice with diabetes over time, with heightened expression of pro-inflammatory or anti-inflammatory genes in a subset-specific manner. Further analysis of macrophage polarization states in each subset in the kidneys showed changes consistent with the continuum of activation and differentiation states, with gene expression tending to shift toward undifferentiated phenotypes but with increased M1-like inflammatory phenotypes over time. By deconvolution analysis of RNAseq samples and by immunostaining of biopsies from patients with DKD, we further confirmed a differential expression of select genes in specific macrophage subsets essentially recapitulating the studies in mice. Thus, our study provides a comprehensive analysis of macrophage transcriptomic profiles in early DKD that underscores the dynamic macrophage phenotypes in disease progression. The pathogenesis of diabetic kidney disease (DKD) involves multifactorial processes that converge to initiate and advance the disease. Although DKD is not typically classified as an inflammatory glomerular disease, mounting evidence supports the involvement of kidney inflammation as a key contributor in DKD pathogenesis, particularly through macrophages. However, detailed identification and corresponding phenotypic changes of macrophages in DKD remain poorly understood. To capture the gene expression changes in specific macrophage cell subsets in early DKD, we performed single-cell transcriptomic analysis of CD45-enriched kidney immune cells from type 1 diabetic OVE26 mice at two time points during the disease development. We also undertook a focused analysis of mononuclear phagocytes (macrophages and dendritic cells). Our results show increased resident and infiltrating macrophage subsets in the kidneys of mice with diabetes over time, with heightened expression of pro-inflammatory or anti-inflammatory genes in a subset-specific manner. Further analysis of macrophage polarization states in each subset in the kidneys showed changes consistent with the continuum of activation and differentiation states, with gene expression tending to shift toward undifferentiated phenotypes but with increased M1-like inflammatory phenotypes over time. By deconvolution analysis of RNAseq samples and by immunostaining of biopsies from patients with DKD, we further confirmed a differential expression of select genes in specific macrophage subsets essentially recapitulating the studies in mice. Thus, our study provides a comprehensive analysis of macrophage transcriptomic profiles in early DKD that underscores the dynamic macrophage phenotypes in disease progression. Immune cell heterogeneity in a mouse model of diabetic kidney diseaseKidney InternationalVol. 102Issue 6PreviewTypical kidney single-cell RNA-sequencing contains relatively few leukocytes, complicating efforts to understand how immune cells impact kidney disease progression. In this issue, Fu et al. use a flow sorting strategy to generate a very large immune cell single-cell RNA-sequencing atlas in a mouse model of diabetic kidney disease. These findings highlight the importance of leukocyte cell subtypes in diabetic kidney disease. Full-Text PDF in this issueKidney InternationalVol. 102Issue 6PreviewAlthough diabetic kidney disease (DKD) is generally considered noninflammatory, there is abundant evidence for a role of tissue leukocytes in the progression of DKD. Fu et al. used single-cell RNA sequencing to evaluate gene expression changes of macrophage subsets in a mouse model of DKD over time. Compared with control kidneys, early DKD kidneys did not show a large shift in the proportion of intrarenal immune cells, but there were increases in specific subsets of macrophages. These included infiltrating, inflammatory, and high interferon-signature macrophages, along with macrophages that are involved in attenuation of inflammatory activity. Full-Text PDF