Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR.

CD4 T regulatory cells (T) are central to immune homeostasis, their phenotypic heterogeneity reflecting the diverse environments and target cells that they regulate. To understand this heterogeneity, we combined single-cell RNA-seq, activation reporter and T cell receptor (TCR) analysis to profile thousands of T or conventional CD4FoxP3 T cells (T) from mouse lymphoid organs and human blood. T and T pools showed areas of overlap, as resting 'furtive' T with overall similarity to T or as a convergence of activated states. All T expressed a small core of FoxP3-dependent transcripts, onto which additional programs were added less uniformly. Among suppressive functions, Il2ra and Ctla4 were quasiconstant, inhibitory cytokines being more sparsely distributed. TCR signal intensity did not affect resting/activated T proportions but molded activated T programs. The main lines of T heterogeneity in mice were strikingly conserved in human blood. These results reveal unexpected TCR-shaped states of activation, providing a framework to synthesize previous observations of T heterogeneity.