The single-cell revolution in transplantation: high-resolution mapping of graft rejection, tolerance, and injury

Single-cell sequencing technologies are fundamentally revolutionizing our understanding of transplantation biology by providing high-resolution cellular and molecular maps of graft rejection, immune tolerance, and injury. This review systematically summarizes the application of technologies such as single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics in solid organ and islet transplantation, aiming to elucidate the mechanisms that determine graft fate. Single-cell analyses have revealed profound insights unattainable by traditional methods, such as identifying key effector cell subpopulations-clonally expanded CD8+ tissue-resident memory T cells (TRM) - in acute rejection, and discovering new pathogenic pathways in chronic dysfunction, like antibody production driven by innate-like B cells. In parallel, these atlases have also uncovered the complex regulatory networks that mediate immune tolerance, composed of regulatory T cells and specific macrophage subpopulations. Furthermore, this technology has pioneered new clinical applications, including non-invasive monitoring through urinary single-cell sequencing and pre-transplant quality assessment of donor organs. By transitioning transplantation medicine from a morphology-based diagnostic model to a new era of molecular endophenotyping based on precise molecular signatures, single-cell technologies offer unprecedented opportunities for developing personalized immunosuppressive regimens, finding new therapeutic targets, and achieving non-invasive diagnostic monitoring. Although clinical translation still faces challenges, it has the potential to become a key tool for improving transplant outcomes in the future.