ABSTRACT: Background: Acute T cell-mediated rejection (TCMR) is a common immunological feature in renal transplantation and is associated with reduced graft survival. However, the full immunological profiling of acute TCMR remains unknown. Methods: A fully mismatched acute TCMR model was induced by transplanting the left kidneys from BALB/c mice into C56BL/6J mice. Allografted kidneys were harvested on day 7 (D7) and sorted for CD45+ leukocytes for single cell RNA sequencing (scRNA-seq) . In addition, scRNA-seq data of CD45+ immune cells on day 15 (D15) containing GSE157292 dataset (samples GSM4761000 and GSM4761003) were downloaded from Gene Expression Omnibus. All data obtained from D7 and D15 were integrated and analyzed. Results: We identified 20 major immune cell types among 10921 immune cells, including macrophages, B cells, T cells, dendritic cells, natural killer cells, neutrophils, and basophils in kidney allografts. Macrophages and CD8 T cells constituted the main immune cell populations on both D7 and D15. In the process towards immune regression, the proportion of CD8 T cells dropped significantly by about 25%, mainly due to decreased proliferation and naïve CD8 T cell infiltration. The proportion of both B cells and neutrophils also decreased by about 3 folds. On the contrary, the relative proportion of macrophages and DCs increased significantly, especially by a 4 fold increase in Ly6cloMrc1+ resident macrophages A group of Ly6cloEar2+ macrophages also increased by about 3 folds. Moreover, myeloid cells harbored the richest ligand and receptor (LR) pairs with other cell types, particularly for chemokine ligands such as Cxcl9, Cxcl10, Cxcl16 and Yars. However, macrophages with weak response to interferon gamma (IFNg) contributed to rejection regression. Conclusions: There is a comprehensive single-cell landscape of the kidney allograft immune cells from rejection progression to regression in acute TCMR. Reduction in CD8 T cells, B cells, and neutrophils while increasing in Ly6clo macrophages, including Ly6cloMrc1+ resident macrophages and Ly6cloEar2+ macrophages, may contribute significantly to immune rejection regression during acute TCMR.
