Single-Cell RNA Sequencing Identifies a Unique Population of Macrophages in the Aristolochic Acid-Induced AKI-to-CKD Transition Murine Model

Background: The transition from acute kidney injury (AKI) to chronic kidney disease (CKD) is a significant contributor to kidney injury progression, and effective treatments to prevent or slow this transition are lacking. Macrophages are known to play a pivotal role in this process, but the specific subtypes involved and their interactions with other cell types remain unclear. Methods: We induced AKI in mice via intraperitoneal injections of Aristolochic Acid I (AAI) every 3 days for 2 weeks, followed by a 2 week remodeling phase without injections. Single-cell RNA sequencing (scRNA-seq) was then performed on kidney samples from control, AKI, and CKD phases using 10x Genomics. Following stringent quality control and feature selection using Scanpy, SoupX, and scDblFinder, we harmonized gene symbols and integrated the data using deep generative modeling (scVI). We identified cell subclusters, cell-to-cell communication, and cellular trajectories using Scanpy, LIANA, and scVelo. Differentially expressed genes (DEGs) and enriched pathways were determined using edgeR. Immunofluorescence of the unique population of macrophages was confirmed in both human CKD kidney samples and the murine AAI-induced AKI to CKD model. Results: We profiled 56,325 single cells representing 30 major cell types across three time points. Significant changes in immune cell clusters, particularly macrophages, were observed during the AKI to CKD transition. Enriched pathways in the CKD phase included mitochondrial ATP synthesis and electron transport, while the AKI phase was characterized by inflammatory and innate immune responses. A unique population of Ctsk+ and Mmp9+ macrophages was identified in the CKD phase. These macrophages interacted with T cells (via Lgals1/Ptprc and Calr/Itgav), injured proximal tubules and fibroblasts (via Apoe/Lrp2), and dendritic cells and basophils (via Vim/Cd44). Increased expression of CTSK and MMP9-positive macrophages was confirmed by immunofluorescence staining in both the CKD phase of the murine model and human CKD samples. Conclusion: ScRNA-seq of the murine AAI model identified a unique population of CTSK and MMP9-positive macrophages as critical responders in the AKI to CKD transition. Targeting these macrophages may present a valuable therapeutic strategy for preventing the progression from AKI to CKD. Funding: Government Support – Non-U.S.