Single-Cell RNA-Seq Mapping of Human Thymopoiesis Reveals Lineage Specification Trajectories and a Commitment Spectrum in T Cell Development

The challenges in recapitulating in vivo human T cell development in laboratory models have posed a barrier to understanding human thymopoiesis. Here, we used single-cell RNA sequencing (sRNA-seq) to interrogate the rare CD34+ progenitor and the more differentiated CD34– fractions in the human postnatal thymus. CD34+ thymic progenitors were comprised of a spectrum of specification and commitment states characterized by multilineage priming followed by gradual T cell commitment. The earliest progenitors in the differentiation trajectory were CD7– and expressed a stem-cell-like transcriptional profile, but had also initiated T cell priming. Clustering analysis identified a CD34+ subpopulation primed for the plasmacytoid dendritic lineage, suggesting an intrathymic dendritic specification pathway. CD2 expression defined T cell commitment stages where loss of B cell potential preceded that of myeloid potential. These datasets delineate gene expression profiles spanning key differentiation events in human thymopoiesis and provide a resource for the further study of human T cell development. [Display omitted] •CD34+ human thymic progenitors present a spectrum of specification and commitment states•Earliest progenitors are CD7– and exhibit stem-cell-like and T-primed transcriptomes•Loss of B-potential precedes that of myeloid and NK potentials during T-commitment•A CD34+ subpopulation of cells is primed for the plasmacytoid dendritic lineage Le et al. use single-cell RNA-seq to interrogate the rare CD34+ progenitor and the more differentiated CD34– fractions in the human postnatal thymus, identifying a CD34+ subpopulation primed for the plasmacytoid dendritic lineage and revealing multilineage priming followed by gradual commitment to the T cell lineage during the initial stages of thymopoiesis.