The impact of alloreactivity on the turnover rate, phenotype and repertoire of gut-resident lymphoid cells populating human intestinal allografts is unknown. We prospectively analyzed the phenotype, origin and alloreactivity of graft-resident T cells in human intestinal allografts using multicolor flow cytometry and high-throughput TCR sequencing. Intra-epithelial lymphocytes (IEL) and lamina propria lymphocytes (LPL) obtained from graft biopsies were studied longitudinally in 9 consecutive intestinal transplant recipients (median follow-up: 375; range 197-1055 days).

Complete T-cell turnover was seen in 5 patients after a median time of 370 (range: 197-1055) days. Strikingly, the replacement rate of CD4+ αβ+ IEL and LPL was significantly (p<0.01) faster over the first 200 days in the patients who experienced early (<90 days) moderate to severe rejection episodes. In the remaining 4 patients, donor cells still accounted for 97.3, 94.2, 40.8, and 61.4% of CD3+ IEL at last follow-up (ranging from 303 to 895 days post-transplant). Donor-derived IEL and LPL T cells exhibited a gut-resident phenotype (CD103+, CD69+, CD28low) in all biopsies and were progressively replaced by gut-imprinted recipient cells. Notably, the emergence of recipient-derived blood-like CD28+ CD8+ αβ T cells in the IEL compartment was strongly associated with rejection (p=0.001).

We next investigated the presence of alloreactive T cell clones in human intestinal allografts. Donor-specific and non-donor-specific recipient T cell clones were identified via pre-transplant CFSE-MLR (recipient anti-donor) sorted into CFSElow or high populations followed by high-throughput sequencing of TCRβ CDR3 regions. We subsequently tracked these clones in 3 patients. In all biopsies with rejection, we found a significant enrichment in donor-specific relative to non-donor specific clones in the CD4 T cell compartment (p<0.0001). We are currently addressing whether or not alloreactive clones persist in late biopsies free of acute rejection and might thus contribute to the development of chronic rejection.

This study provides new insights into the two processes driving human intestinal graft repopulation by host cells (physiologic turnover and alloreactivity), as well as important new tools to differentiate these two processes.

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