Antigen-specific type 1 regulatory T cells have a distinct molecular identity and suppress through CTLA-4 and PD-1

We report the bulk-cell-based TCR sequences profiling from high-throughput sequencing of human healthy T-allo10 cells. The T-allo10 cell product is consistently enriched for Tr1 cells, is specifically anergic, and suppresses alloantigen-responsive Teff cells. Analysis of Tr1 cells from the T-allo10 product showed that the both TCRa and TCRb repertoires are highly skewed towards dominant clones and has diverged from the parental CD4+ T cells used to generate the T-allo10 product, non-Tr1 cells from the same T-allo10 product, and Teff cells from the control T-allo product. The data indicate that T-allo10-derived Tr1 cells, but not non-Tr1 cells, undergo clonal expansion in response to the alloantigen stimulation, suggesting that the Tr1 cells are the antigen specific component of the T-allo10 cell product. T-allo10 cells are currently undergoing clinical evaluation for safety in a phase I clinical trial (ClinicalTrials.gov ID: NCT03198234). Overall design: To determine if CD49b+LAG3+ Tr1 or non-Tr1 cells from the total T-allo10 cell product undergo clonal expansion during co-culture with DC-10, we sequenced the TCR repertoires of total T-allo10, sorted Tr1 and non-Tr1 cells from the T-allo10 cells, parental CD4+ T and total control T-allo Teff cells by Illumina Miseq for pair-ended 2x250 or 2x300 sequencing runs.