Single-cell chimerism and transcriptional profiling identify long-term human skin-resident host T cells after stem cell transplantation

Tissue-resident memory T cells (TRM) have recently emerged as crucial cellular players for host defense in a wide variety of tissues and barrier sites. Insights into the maintenance and regulatory checkpoints of human TRM cells remain scarce, especially due to the difficulties associated with tracking T cells over time and spatially in humans. We therefore aimed to identify and characterize skin resident T cells in humans defined by their long-term in situ lodgement. Allogeneic hematopoietic stem cell transplantation paired with myeloablative chemotherapy unmasked long-term sequestration of host T cell subsets in the human skin despite complete donor T cell chimerism in the blood. Single-cell chimerism analysis paired with single-cell transcriptional profiling comprehensively characterized these bona fide long-term skin resident T cells and revealed differential tissue maintenance for distinct T cell subsets, specific TRM cell markers such as galectin-3, but also tissue exit potential with retention of the transcriptomic TRM cell identity. Analysis of 26 patients revealed profound interindividual variation in the tissue maintenance of host skin T cells and excluded a role for host T cells for the pathogenesis of chronic GvHD. Our data exemplify the power of exploiting a clinical situation as a proof-of-concept for the existence of bona fide human skin TRM cells and reveal long-term persistence of host immunity in the peripheral tissue but not in the circulation or bone marrow for a subset of patients. Overall design: Comparison of skin versus blood CD4 and CD8 T cell bulk transcriptomes and lymphocytes from blood versus skin of a healthy donor and a HSCT patient **Samples GSM5776288-GSM5776291 do not have raw data due to patient privacy concerns**