Single-cell transcriptomic landscape of metabolic reprogramming in kidney allograft rejection

Abstract

Introduction Chronic rejection remains a major barrier to long-term survival after renal transplantation. However, our understanding of the transcriptional programs and metabolic alterations that shape the functions of human kidney cell populations during rejection is still limited. Objectives To generate a comprehensive, cell type–specific transcriptomic map of metabolic states in healthy and transplanted human kidney samples. Methods We performed single-cell RNA sequencing on 33 kidney samples, constructing an atlas comprising 82,661 cells. Results Analysis of average metabolic pathway activity across cell subpopulations revealed distinct metabolic profiles. These differences provided insights into both unique abnormalities and shared features underlying various rejection states. We identified downregulation of mitochondrial programs in multiple non-proximal tubular cell populations compared with their counterparts in healthy kidneys. In contrast, both proximal tubular (PT) cells and T cells exhibited relatively elevated oxidative phosphorylation-related transcriptional scores, though the mechanisms driving this shift were specific to cell type and rejection status. Additionally, rejection-associated macrophages demonstrated altered amino acid metabolism, accompanied by enhanced IL-1 signaling. Conclusion This single-cell atlas, together with a metabolically based stratification of chronic kidney transplant rejection, offers novel insights into the heterogeneous nature of rejection and provides valuable guidance for the development of targeted therapies.