GSE121731
Treg cells adapting to Th2 environment maintain Treg signature despite destabilizing Foxp3
The emerging recognition of heterogeneity among T regulatory cells (Treg) in peripheral tissues raises renewed questions of how Treg cells adapt to changing environments and diverse inflammatory settings. Herein, we addressed the consequences of a T helper 2 (Th2) type environment on the phenotype and function of Foxp3-expressing Treg cells. In vivo, both Treg cells and conventional T cells exhibited discrete transcriptional states corresponding to naïve and activated conditions influenced by shared microenvironmental cues affecting both cell types. By inducing asthma, Treg cells in the lung exhibited loss of established Foxp3 expression. To model the state of Treg cells experiencing destabilized Foxp3 expression in a Th2 milieu, we generated exFoxp3+ cells from induced Treg (iTreg) cells by IL-4 signaling in vitro. ExFoxp3-iTreg cells provided protection against T cell-mediated colitis despite absence of Foxp3 while IL-10 producing Th2 cells failed to provide protection. Globally, exFoxp3-iTreg cells remodeled enhancers towards a Th2-like landscape, but still maintained key Treg-like enhancers including the Ctla4 super-enhancer region. These active Ctl4a enhancers were specifically accessible in Treg but not in T helper effector cells generated in vivo. Therefore, Treg specific enhancers can serve as a better correlate of regulatory capability of both ex vivo and in vitro T cells than Ctla4 expression itself. At the single cell level, we observed that the shared transcriptomic signature among tissue-Treg cells is not only enriched in activated Treg cells but also in a sub-fraction of effector cells devoid of Foxp3 expression, indicating the existence of effector cells with regulatory module in vivo. Our data collectively suggest that Treg cells adapting to Th2 inflammation can sustain regulatory function by maintaining the activated Treg transcriptome despite significant downregulation of Foxp3 protein. Overall design: Characterizing Treg cells that lose Foxp3 expression in an inflammatory environment using genome-wide measurements of gene expression (Bulk RNA-seq, nascent RNA-seq, single cell RNA-seq), histone modification (ChIP-seq), transcription factor binding (ChIP-seq), and accessible chromatin (ATAC-seq).