Single-cell atlas of pig-to-monkey kidney xenotransplantation reveals macrophage chimerism and an IFN-ε orchestrated graft protective immune niche

The clinical translation of xenotransplantation is constrained by an incomplete understanding of the cellular circuitry governing graft rejection versus adaptation under current immunosuppressive regimens. Here, we present a high-resolution single-cell atlas of pig-to-monkey kidney xenotransplantation in a preclinical model, capturing the early immune dynamics preceding graft loss. Our analysis reveals a landscape dominated by innate immunity, characterized by species-specific distribution of macrophages. We identify recipient-derived macrophage subsets (ACKR1 + , FN1 + , MARCO + , IDO1 + ) enriched for multiple immune checkpoint molecules, alongside donor-resident subpopulations (APOE + , CCL2 + , IL-1A + ) exhibiting pro-inflammatory pathogenic signatures, and leverage their transcriptional profiles to computationally predict candidate therapies (belatacept, abatacept, pexidartinib). Further analysis demonstrates that despite divergent differentiation trajectories, both recipient-derived and donor-resident macrophages converge toward hybrid M1/M2 states at their terminal stages. Notably, we uncover a graft-protective circuit orchestrated by epithelial-derived interferon-epsilon (IFN-ε), which specifically engages multiple subsets including IDO1 + macrophages to establish a localized immune-tolerant niche. This study establishes the xenograft epithelium as an active participant in immune modulation via the IFN-ε axis and reveals macrophage functional chimerism as a key actionable feature of cross-species immune responses.