Single-cell multi-omics characterization of rejection in transplanted kidneys reveals key cell types and candidate regulators of chronic rejection

Chronic rejection is a major determinant of long-term kidney allograft survival, yet the immunological mechanisms underlying its initiation and progression remain incompletely understood. To elucidate the dynamic evolution and interaction networks of immune cells during chronic kidney transplant rejection, we established a mouse kidney transplantation model, performed single-cell RNA-seq and ATAC-seq on immune cells from allografts at different post-transplant stages, and constructed an immune multi-omic atlas spanning acute rejection to chronic fibrosis. Single-cell sequencing revealed that a late-stage, terminal-like SPP1 + macrophage state is enriched in chronic allografts and occupies a central position in a macrophage-centered interaction network. Chromatin accessibility and motif analyses further identified a CEBPβ-centered regulatory program that is associated with sustained activation of extracellular matrix remodeling genes in this subset. Integrative ligand–receptor and pathway analyses delineated a regulatory axis centered on the interaction between SPP1⁺ macrophages and CD8⁺ Trm cells, suggesting that this predicted interaction network is associated with fibrosis-related immune remodeling during chronic rejection. This study provides a high-resolution longitudinal immune atlas of kidney allograft rejection and identifies SPP1 + macrophages and a CEBPβ-associated regulatory program as candidate contributors to the fibrotic process during chronic rejection. These findings offer a framework for future mechanistic and therapeutic investigations, while functional validation and human translation remain necessary before clinical application.