Developmental features and unique characteristics of peptide-specific PLZF+ innate-like T cells

Innate-like T cells are considered a family of T lymphocytes capable of mounting quick responses, yet restricted to conserved antigens of non-peptide nature. Here, we performed single-cell transcriptomic analyses of peptide-specific PLZF+ innate-like T (PILT) cells and compared them to other members of the innate-like T cell family. Our data revealed that PILT cells share similar transcriptional profiles and overlapping developmental trajectories with invariant Natural Killer T (iNKT) cells as well as mucosal-associated invariant T (MAIT) cells. Yet, in contrast to iNKT and MAIT cells, PILT cells displayed a polyclonal T cell receptor (TCR) repertoire closely resembling the one of conventional CD8 T cells, inferring MHC I restriction and a broader range of antigen specificity. We further show that artificial thymic organoid cultures (ATOC) support selection and development of PILT cells in vitro exhibiting similar transcriptional profiles to their counterparts maturing in the thymus. Lastly, using an “on-time” T-cell receptor retrogenic ATOC system, we demonstrate that PILT1 derived TCR clonotypes favour acquisition of PILT1 innate-like phenotype during T cell development in vitro suggesting an instructive role of TCR specificity in PILT cell lineage commitment and functional differentiation.