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

Kidney infiltrating macrophages (KIMs) and kidney dendritic cells (KDCs) are 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 that infiltrate the kidney during AKI. Here, we combined single-cell RNA sequencing (scRNAseq), spatial transcriptomics, and cellular indexing of transcriptomes and epitopes (CITE)-sequencing to elucidate temporal, spatial, and transcriptional characteristics of unique subpopulations of KIMs and KDCs in AKI. scRNAseq revealed three KIM, two KDC, and one proliferative macrophage subpopulation. All 6 clusters were localized in unique, spatially constrained microenvironments and their locations were dynamically regulated following bilateral ischemic reperfusion injury. We showed that a specific Arginase 1-specific KIM cluster infiltrates the kidney cortex at day 1 post-ischemia. We also identified a macrophage subpopulation that expresses genes specific to cell proliferation that resides in the cortex in uninjured states and in the medulla at day 6 during the reparative phase of AKI. Gene ontology analysis revealed functional characteristics that distinguish each KIM and KDC population. By day 28 post-ischemia, the transcriptional profiles of KIMs significantly upregulate C1q, Cd81, and Cd74, markers normally limited to KRMs in quiescence and early AKI. Because KIMs and KDCs are profoundly involved in AKI, it is paramount we understand their dynamics—temporally and spatially— and identify their key genes and surface protein markers to develop macrophage-specific therapeutics aimed towards targeting kidney disease.