Introduction: Kidney xenotransplantation is emerging as a promising solution to the organ shortage crisis. However, the molecular mechanisms underlying xenograft failure remain poorly understood. To realize the clinical potential of kidney xenotransplantation, it is critical to elucidate the molecular and cellular characteristics that drive xenograft failure.
Methods: Life-supporting renal xenotransplantations were performed using genetically engineered pigs with targeted coagulation modifications (GE6 to GE8) into cynomolgus monkeys. The immunosuppressive regimen comprised multiple agents, including anti-CD154 monoclonal antibody, abatacept, tocilizumab, crovalimab, corticosteroids, tacrolimus, mycophenolate mofetil, and etanercept. Renal biopsies were obtained at predefined intervals and at euthanasia. Integrative molecular profiling was conducted using bulk RNA sequencing (n=14), single-nucleus RNA sequencing (snRNA-seq, n=15), and spatial transcriptomics (Visium, n=12). Single-cell resolution cell type expression profiles derived from snRNA-seq were mapped onto spatial transcriptomics data using cell2location. Intercellular communication analysis was performed using LIANA and NicheNet to delineate molecular interactions and signaling events.
Results: Histopathological analysis showed that chronic injuries were exclusively identified after week 4 (Table), which was accompanied by a transcriptional transition identified through integrative analysis of bulk and single-nucleus RNA sequencing datasets.


snRNA-seq data identified two noticeable degenerative stromal populations—dFIB and dVSMC/P—marked by high FN1, ACTA2, COL3A1 and COL1A1 expression. Enrichment analysis identified extracellular matrix organization and collagen biosynthesis as the predominant pathways in these stromal populations, reflecting active and pathological extracellular matrix remodeling driven by excessive collagen production and assembly by degenerative stromal cells. Intercellular-communication modeling revealed a directional axis from nonclassical monocytes (ncMonocyte) and M2 macrophages to these stromal cells, with TGF-β1 and SPP1 as principal ligands. Spatial transcriptomics showed TGF-β target genes concentrated around glomeruli (median distance < 500 µm), indicating a periglomerular fibrotic niche driven by innate immune–mediated signaling (Figure).


Conclusions: Our findings reveal that innate immune cell–mediated fibrotic remodeling underlies chronic injury in kidney xenografts, with the periglomerular region serving as a focal site of pathological extracellular matrix activation. These results highlight TGF-β1–driven signaling as a pivotal mechanism of chronic graft failure and suggest that targeting innate immune–fibrotic interactions may enhance long-term xenograft survival.