Th17 cells have critical roles in mucosal defense and are major contributors to inflammatory disease. Their differentiation requires the nuclear hormone receptor RORγt working with multiple other essential transcription factors (TFs). We have used an iterative systems approach, combining genome-wide TF occupancy, expression profiling of TF mutants, and expression time series to delineate the Th17 global transcriptional regulatory network. We find that cooperatively-bound BATF and IRF4 contribute to initial chromatin accessibility, and with STAT3 initiate a transcriptional program that is then globally tuned by the lineage-specifying TF RORγt, which plays a focal deterministic role at key loci. Integration of multiple datasets allowed inference of an accurate predictive model that we computationally and experimentally validated, identifying multiple new Th17 regulators, including Fosl2, a key determinant of cellular plasticity. This interconnected network can be used to investigate new therapeutic approaches to manipulate Th17 functions in the setting of inflammatory disease.

Both microbial and host genetic factors contribute to the pathogenesis of autoimmune disease1–4. Accumulating evidence suggests that microbial species that potentiate chronic inflammation, as in inflammatory bowel disease (IBD), often also colonize healthy individuals. These microbes, including the Helicobacter species, have the propensity to induce pathogenic T cells and are collectively referred to as pathobionts4–6. However, an understanding of how such T cells are constrained in healthy individuals is lacking. Here we report that host tolerance to a potentially pathogenic bacterium, Helicobacter hepaticus (H. hepaticus), is mediated by induction of RORγt+Foxp3+ regulatory T cells (iTreg) that selectively restrain pro-inflammatory TH17 cells and whose function is dependent on the transcription factor c-Maf. Whereas H. hepaticus colonization of wild-type mice promoted differentiation of RORγt-expressing microbe-specific iTreg in the large intestine, in disease-susceptible IL-10-deficient animals there was instead expansion of colitogenic TH17 cells. Inactivation of c-Maf in the Treg compartment likewise impaired differentiation and function, including IL-10 production, of bacteria-specific iTreg, resulting in accumulation of H. hepaticus-specific inflammatory TH17 cells and spontaneous colitis. In contrast, RORγt inactivation in Treg only had a minor effect on bacterial-specific Treg-TH17 balance, and did not result in inflammation. Our results suggest that pathobiont-dependent IBD is driven by microbiota-reactive T cells that have escaped this c-Maf-dependent mechanism of iTreg-TH17 homeostasis.

The intestinal microbiota have critical roles in immune system and metabolic homeostasis, but they must be tolerated by the host to avoid inflammatory responses that can damage the epithelial barrier separating the host from the luminal contents1-6. Breakdown of this regulation and the resulting inappropriate immune response to commensals are thought to lead to the development of inflammatory bowel diseases (IBDs) such as Crohn's disease and ulcerative colitis7. We hypothesized that the intestinal immune system is instructed by the microbiota to limit responses to luminal antigens. We demonstrate that, at steady state, the microbiota inhibit the transport of both commensal and pathogenic bacteria from the lumen to a key immune inductive site, the mesenteric lymph node (MLN). However, in the absence of Myd88 or under conditions of antibiotic-induced dysbiosis, non-invasive bacteria trafficked to the MLN in a CCR7-dependent manner and induced both T cell responses and IgA production. Trafficking was carried out by CX3CR1hi mononuclear phagocytes, an intestinal cell population previously reported to be non-migratory8. These findings define a central role for commensals in regulating the migration to the MLN of CX3CR1hi mononuclear phagocytes endowed with the ability to capture luminal bacteria, thereby compartmentalizing the intestinal immune response to avoid inflammation.

Intestinal CX3CR1+ mononuclear phagocytes regulate ILC3 in vivo in response to colitis associated microbial signals.