The gut microbiota promotes distal tissue regeneration via RORγ+ regulatory T cell emissaries [scRNA-seq]

Specific microbial signals induce the differentiation of a distinct pool of RORγ+ regulatory T cells (Tregs) crucial for intestinal homeostasis. We discovered highly analogous populations of microbiota-dependent Tregs that promote tissue regeneration at extra-gut sites, notably acutely injured skeletal muscle and fatty liver. Tissue damage elicited the emigration of RORγ+ Tregs from the gut to compromised tissues, wherein they regulated the dynamics and tenor of early inflammation and helped balance the proliferation versus differentiation of local stem cells. Reining in IL-17A-producing T cells was a major mechanism underlying these rheostatic functions. Our findings highlight the importance of gut-trained Treg emissaries in controlling the response to sterile injury of non-mucosal tissues. We investigated the transcriptional heterogeneity of skeletal muscle regulatory T cells (Tregs) 3 days after cardiotoxin-induced injury via single-cell RNA and Tcr sequencing (scRNA-seq/ scTcr-seq). For standard genome-wide scRNA-seq analyses, Tregs from hindlimb muscles of Foxp3-Gfp, Foxp3-cre x Maffl/fl (MafΔTreg) and Foxp3-cre x Mafwt/wt (Maf-wt) were sorted by flow cytometry and encapsulated using the Chromium Single Cell 3′ v2 platform. For coupled scRNA-seq and scTcr-seq, Tregs or CD4+ T cells from muscles and colon of six individual Foxp3Gfp mice were sorted and encapsulated using the Chromium Single Cell 5′ v3 and V(D)J platform (10x Genomics).