Abstract
In T cells, T cell receptor (TCR) signalling initiates downstream transcriptional mechanisms for T cell activation and differentiation. Foxp3-expressing regulatory T cells (Treg) require TCR signals for their suppressive function and maintenance in the periphery. It is, however, unclear how TCR signalling controls the transcriptional programme of Treg. Since most of studies identified the transcriptional features of Treg in comparison to naïve T cells, the relationship between Treg and non-naïve T cells including memory-phenotype T cells (Tmem) and effector T cells (Teff) is not well understood. Here we dissect the transcriptomes of various T cell subsets from independent datasets using the multidimensional analysis method Canonical Correspondence Analysis (CCA). We show that resting Treg share gene modules for activation with Tmem and Teff. Importantly, Tmem activate the distinct transcriptional modules for T cell activation, which are uniquely repressed in Treg. The activation signature of Treg is dependent on TCR signals, and is more actively operating in activated Treg. Furthermore, by analysing single cell RNA-seq data from tumour-infiltrating T cells, we identified the common shared transcriptional modules for T cell activation, including CTLA-4, in activated Treg and activated Teff. Moreover, we identified distinct FOXP3-driven and T follicular helper-like transcriptional modules in activated FOXP3+ Treg and FOXP3-Teff, respectively. Collectively, we reveal the multidimensional identities and single cell-level heterogeneity of Treg, identifying the differential regulation of the activation and differentiation gene modules in Treg, Tmem and Teff during homeostasis and in the tumour microenvironment.