Single-cell analysis of human fetal and post-natal ?d thymocytes reveals distinct functional programming.

Developmental thymic waves of innate-like and adaptive-like gd T cells have been described, but the current understanding of ?d T cell development is mainly limited to mouse models. Here, we combined single cell (sc) RNA gene expression and sc ?d T cell receptor (TCR) sequencing on fetal and pediatric ?d thymocytes in order to understand the ontogeny of human ?d T cells. Mature fetal ?d thymocytes were committed to either a type 1, a type 3 or type 2-like effector fate, independent from ?d T cell subset type (V?9Vd2 vs nonV?9Vd2), and were enriched for public CDR3 features upon maturation. Strikingly, type 1, type 3 and type 2 cells expressed different CDR3 sequences and followed distinct developmental trajectories. In contrast, the pediatric thymus generated only a small effector subset that was highly biased towards V?9Vd2 TCR usage and showed a mixed type 1/type 3 effector profile. Thus, our combined dataset of gene expression and detailed TCR information at the single-cell level defines ?d thymocyte development in human and provides a resource for further study. Overall design: ?dT cells were sorted from fetal and pedriatic thymuses, followed by 5'-RNA single cell transcriptome and TCR sequening (10x genomics). In parallel, V?9+Vd2+ and nonV?9Vd2 subsets were sorted from fetal and pediatric thymus samples followed by bulk RNA-seq and TCR-seq runs.