Kidney resident macrophages have distinct subsets and multifunctional roles

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) and chronic kidney disease (CKD). 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 ischemia-induced AKI. scRNAseq revealed three KIM, two KDC, and one proliferative macrophage subpopulation. All six clusters were localized in unique, spatially constrained microenvironments and their locations were dynamically regulated following bilateral ischemia reperfusion injury. We showed that a specific Arginase 1-expressing KIM cluster infiltrates the kidney cortex at day 1 after 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 after ischemia, the transcriptional profiles of KIMs upregulate C1q, Cd81, and Cd74, markers normally limited to KRMs in quiescence and early AKI. Since KIMs and KDCs are profoundly involved in AKI, it is paramount that we understand their dynamics-temporally and spatially-and identify their key genes and surface protein markers to develop macrophage-specific therapeutics aimed toward targeting kidney disease.NEW & NOTEWORTHY In this work, we fully characterized both single cell and spatial transcriptomes of kidney infiltrating macrophages (KIMs) and kidney dendritic cells (KDCs) following bilateral ischemia reperfusion injury. We also discovered distinct markers that differentiate KIMs from one another and kidney resident macrophages (KRMs). Finally, we show evidence suggesting that KIMs may reprogram and express genes previously limited to KRMs by day 28 following injury resolution.

Tissue-resident macrophages and renal diseases: landscapes and treatment directions

Tissue-resident macrophage (TRM) is a specialized subset of macrophage that resides within specific tissues and organs. TRMs play crucial roles in resisting pathogen invasion, maintaining the homeostasis of the immune microenvironment, and promoting tissue repair and regeneration. The development and function of TRMs exhibit significant heterogeneity across different tissues. Kidney TRMs (KTRMs) originate from both embryonic yolk sac erythro-myeloid progenitors and the fetal liver, demonstrating the capacity for self-renewal independent of bone marrow hematopoiesis. KTRMs are not only essential for the maintenance of renal homeostasis and the monitoring of microvascular environment, but contribute to renal injury due to inflammation, fibrosis and immune dysfunction in kidneys. In this review, we summarize currently available studies on the regulatory role of KTRMs in processes of renal injury and repair. The altering effects and underlying mechanisms of KTRMs in regulating local tissue cells and immune cells in different renal diseases are reviewed, primarily including lupus nephritis, diabetic nephropathy, renal fibrosis, and renal carcinoma. Understanding the plasticity and immune regulatory functions of KTRMs may offer new insights into the pathogenesis and the exploration of therapeutic strategies of kidney diseases.