GSE201808
Single-cell transcriptional profiling identifies a spectrum of unconventional intraepithelial T lineage cells in human cord blood [bulk RNA-Seq]
Conventional CD4 and CD8 single positive T cell lineages constitute the main differentiation pathway in the thymus. In human thymus, a minor TCRaß differentiation pathway diverges from the early double positive stage, consisting of CD10+ PD-1+ cells. These cells are phenotypically and functionally similar to murine agonist-selected intraepithelial T lymphocyte precursors (IELps) which home to the small intestine. Here, the progeny of the human agonist-selected IEL lineage was identified in antigen-inexperienced cord blood (CB) with a polyclonal T cell receptor (TCR) repertoire exhibiting a bias towards early TCR alpha chain rearrangements and elevated autoreactive indices. Single-cell RNA sequencing allowed further delineation of this unconventional lineage in CB. Trajectory analysis, along with TCR repertoire analysis and transcriptomics, suggests a precursor-progeny relationship with the thymic IELps. The distinct, heterogeneous CB population can now be defined as CD3+ TCRaß+ CD4- CCR7- CD26-. Besides recent thymic emigrants, this population also consists of newly identified effector clusters and previously described populations: the suppressive NK receptor expressing CD8+ Treg population, the KIR/NKG2A+ EOMES+  virtual memory population and the CD8aa+ T cell populations. The population shows a discriminating stable Helios expression and is exclusively able to downregulate CD8ß expression, resulting in double negative T cells. The functional properties of this population suggest that the cells expand on inflammatory cues and exert cytotoxic and proinflammatory activity. Overall design: To identify additional marker genes in cord blood for unconventional intraepithelial T cells, 3 T cell populations were sorted from cord blood: I. TCR?d+, II. CD3+/low PD-1+ (unconventional intraepithelial T cells) and III. CD3+ PD-1- (conventional T cells). For each sort 3 replicates from 3 different donors wereused in a differential expression analysis with DeSeq2 to identify additional markers. The same populations were sorted from post natal thymus (also 3 replicates from 3 different donors per cell population) to use as a comparison.