Dynamic establishment of recipient resident memory T cell repertoire after human intestinal transplantation

Background Understanding formation of the human tissue resident memory T cell (TRM) repertoire requires longitudinal access to human non -lymphoid tissues. Methods By applying flow cytometry and next generation sequencing to serial blood, lymphoid tissue, and gut samples from 16 intestinal transplantation (ITx) patients, we assessed the origin, distribution, and specificity of human TRMs at phenotypic and clonal levels. Findings Donor age >= 1 year and blood T cell macrochimerism (peak level >= 4%) were associated with delayed establishment of stable recipient TRM repertoires in the transplanted ileum. T cell receptor (TCR) overlap between paired gut and blood repertoires from ITx patients was significantly greater than that in healthy controls, demonstrating increased gut -blood crosstalk after ITx. Crosstalk with the circulating pool remained high for years of followup. TCR sequences identifiable in pre -Tx recipient gut but not those in lymphoid tissues alone were more likely to populate post -Tx ileal allografts. Clones detected in both pre -Tx gut and lymphoid tissue had distinct transcriptional profiles from those identifiable in only one tissue. Recipient T cells were distributed widely throughout the gut, including allograft and native colon, which had substantial repertoire overlap. Both alloreactive and microbereactive recipient T cells persisted in transplanted ileum, contributing to the TRM repertoire. Interpretation Our studies reveal human intestinal TRM repertoire establishment from the circulation, preferentially involving lymphoid tissue counterparts of recipient intestinal T cell clones, including TRMs. We have described the temporal and spatial dynamics of this active crosstalk between the circulating pool and the intestinal TRM pool.