Molecular diversification of regulatory T cells in nonlymphoid tissues

Different tissue microenvironments differentially refine Treg cell transcriptional regulatory modules already primed in lymphoid organs. Mapping Treg regulomes Technological advances are allowing immunologists to study rare populations of immune cells that take residence in various tissues including adipose tissue, skin, and the lung. Here, DiSpirito et al. have generated transcriptomes and chromatin accessibility maps of mouse regulatory T cells (Tregs) that reside in visceral adipose tissue, muscle, and the colon and compared them with the profiles generated from splenic Tregs. They have used these data sets to define transcriptional networks that are shared by all these populations and to identify networks that are unique to one or more tissue-resident Treg populations. Foxp3+CD4+ regulatory T cells (Tregs) accumulate in certain nonlymphoid tissues, where they control diverse aspects of organ homeostasis. Populations of tissue Tregs, as they have been termed, have transcriptomes distinct from those of their counterparts in lymphoid organs and other nonlymphoid tissues. We examined the diversification of Tregs in visceral adipose tissue, skeletal muscle, and the colon vis-à-vis lymphoid organs from the same individuals. The unique transcriptomes of the various tissue Treg populations resulted from layering of tissue-restricted open chromatin regions over regions already open in the spleen, the latter tagged by super-enhancers and particular histone marks. The binding motifs for a small number of transcription factor (TF) families were repeatedly enriched within the accessible chromatin stretches of Tregs in the three nonlymphoid tissues. However, a bioinformatically and experimentally validated transcriptional network, constructed by integrating chromatin accessibility and single-cell transcriptomic data, predicted reliance on different TF family members in the different tissues. The network analysis also revealed that tissue-restricted and broadly acting TFs were integrated into feed-forward loops to enforce tissue-specific gene expression in nonlymphoid-tissue Tregs. Overall, this study provides a framework for understanding the epigenetic dynamics of T cells operating in nonlymphoid tissues, which should inform strategies for specifically targeting them.

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