Donor and recipient immune programs underlying delayed graft function in kidney transplantation revealed by temporal single-cell profiling

Delayed graft function after kidney transplant is associated with increased acute rejection rates and poorer long-term outcomes. It is significantly more prevalent in recipients of deceased than living donor kidneys due to increased ischemia-reperfusion injury associated with prolonged warm and cold ischemic times. Although specific immune populations are associated with ischemia-reperfusion injury and delayed graft function, the precise cellular circuits distinguishing deceased from living donor transplants, as well as the donor and recipient-derived immune programs involved in early immunological responses, have not been defined at cellular resolution.

Using single-cell RNA-sequencing to examine this, we compared the pre-transplant immune landscape in 20 living and six deceased donor kidneys, with two additional deceased donor samples assessed by spatial transcriptomics. We then examined temporal immune changes using fixed single-cell RNA-profiling across eight matched pre- and post-transplant allograft pairs (16 samples total) from recipients of deceased kidney transplants who developed delayed graft function.

Deceased donor allografts had donor-derived resident macrophages with reduced expression of chemokines, cytokines, and antigen presentation genes but increased autophagy and ubiquitination related transcripts. These macrophages persisted following transplantation and were spatially positioned to interact with multiple parenchymal populations. A loss of amphiregulin-expressing NK cells and CD8⁺ T cells expressing TIGIT and KLRC1 (NKG2A), accompanied by an enrichment of CD8⁺ T cells expressing KLRK1 (NKG2D) and a pro inflammatory signature were observed in both pre- and early post-transplant kidneys from deceased donors. Notably, a transcriptionally distinct, interferon-stimulated, recipient-derived macrophage population emerged early post-transplant, defined by expression of CXCL10, TNFSF10, TNFSF13B, CCL8 and ICAM1, consistent with a role in recruiting and activating recipient-derived B and T cells.

Collectively, our findings define donor- and recipient-derived immune programs that distinguish living from deceased donor allografts, and shape early post-transplant immune responses in delayed graft function.