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

Understanding formation of the human tissue resident memory T cell (TRM) repertoire requires access to longitudinal human tissue samples. Following human intestinal transplantation (ITx), we longitudinally assessed the origin, distribution, and specificity of human TRMs at the phenotypic and clonal levels. Applying next generation sequencing to blood, lymphoid tissue, and gut samples from 16 ITx patients, we found that 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. Recipient T cells rapidly populated grafts from donors <1 year old and cross-talk with the circulating pool remained high for years of follow-up. TCR sequences identifiable from pre-Tx recipient gut but not lymphoid tissues were over-represented in post-Tx allograft ileum, demonstrating a circulating counterpart of pre-existing intestinal TRMs. Recipient T cells were distributed widely throughout the gut, including allograft and native colon, which had substantial repertoire overlap. Both alloreactive and microbe-reactive recipient T cells persisted in transplanted ileum, contributing to the TRM repertoire. Together, our study provides novel spatial, temporal, and functional insights into human TRM repertoire establishment.