Identification of distinct functional thymic programming of fetal and pediatric human gamma delta thymocytes via single-cell analysis

Developmental thymic waves of innate-like and adaptive-like gamma delta T cells have been described, but the current understanding of gamma delta T cell development is mainly limited to mouse models. Here, we combine single cell (sc) RNA gene expression and sc gamma delta T cell receptor (TCR) sequencing on fetal and pediatric gamma delta thymocytes in order to understand the ontogeny of human gamma delta T cells. Mature fetal gamma delta thymocytes (both the V gamma 9V delta 2 and nonV gamma 9V delta 2 subsets) are committed to either a type 1, a type 3 or a type 2-like effector fate displaying a wave-like pattern depending on gestation age, and are enriched for public CDR3 features upon maturation. Strikingly, these effector modules express different CDR3 sequences and follow distinct developmental trajectories. In contrast, the pediatric thymus generates only a small effector subset that is highly biased towards V gamma 9V delta 2 TCR usage and shows a mixed type 1/type 3 effector profile. Thus, our combined dataset of gene expression and detailed TCR information at the single-cell level identifies distinct functional thymic programming of gamma delta T cell immunity in human.