Single-Cell RNA Sequencing and Spatial Transcriptomics Reveal Unique Subpopulations of Infiltrating Macrophages and Dendritic Cells following AKI

Background: Kidney infiltrating macrophages (KIMs) and kidney dendritic cells (KDCs) have been strongly associated with inflammation and fibrosis in acute kidney injury (AKI). Contrary to kidney resident macrophages (KRMs), which are self-renewing and present in the kidney prior to injury, KIMs are bone-marrow derived F4/80int, CD11bhigh macrophages. Here, we combined single-cell RNA sequencing (scRNAseq) and spatial transcriptomics to elucidate temporal, spatial, and transcriptional characteristics of unique subpopulations of KIMs and KDCs in AKI. Methods: CD11bhigh KIMs and KDCs from C57BL/6J mice were sorted using fluorescence activated cell sorting (FACS). We collected macrophages before injury and at days 1, 6, and 28 following 19 minutes of bilateral ischemia reperfusion injury (BIRI). Cells were subjected to scRNAseq using the 10X Genomics Chromium platform. Gene ontology was conducted to elucidate the functional roles of differentially expressed genes. Spatial transcriptomics were evaluated using the 10X Visium Spatial Gene platform. Data from all timepoints were integrated and analyzed using Seurat 5.0. Results: scRNAseq results revealed 3 unique KIM and 2 KDC subpopulations. All 5 clusters were localized in unique microenvironments in untreated mice, and their locations were dynamically regulated following BIRI. We have shown that a specific KIM cluster, identified by its Arginase 1 expression, infiltrates the kidney medulla at day 1 and migrates to the cortex at day 6 post-injury. We have also identified a macrophage precursor cell population that expresses genes specific to cell proliferation and regeneration (e.g., Stmn1 and Top2a) that are predicted to reside in the medulla in uninjured states. Gene ontology analysis revealed distinctive functional characteristics that set apart each KIM and KDC population. Conclusion: We have identified distinct subpopulations of KIMs and KDCs within the kidney, each of which infiltrates at different times (i.e., 1 and 6 days) and occupies specific microenvironments after AKI. Because KIMs and KDCs are involved in inflammation and AKI, it is paramount we understand their dynamics—temporally and spatially—to develop macrophage-specific therapeutics aimed towards targeting kidney disease and promoting tissue repair. Funding: NIDDK Support