Engineered probiotics limit T-cell driven CNS autoimmunity by activating AHR-KLF4-FADS3 signaling in intestinal dendritic cells 2235071

Introduction Dendritic cells (DCs) control effector immune responses and tolerance. Their function is regulated by transcriptional, epigenetic and metabolic programs, but the mechanisms controlling DC metabolism and its impact on autoimmune diseases remain poorly defined. Methods We used single-cell and bulk RNA-sequencing of multiple sclerosis patients and preclinical models in combination with in vivo DC-specific gene perturbations and in vitro human systems. Results We identified an aryl hydrocarbon receptor (AHR) - Krüppel-like factor 4 (KLF4) - fatty acid desaturase enzyme 3 (FADS3) axis that drives docosahexaenoic acid (DHA) production in DCs, limiting pathogenic T-cell responses and experimental autoimmune encephalomyelitis (EAE) development. Specifically, AHR drives KLF4 expression in conventional DCs (cDCs); AHR and KLF4 cooperate to induce FADS3 expression, promoting DHA synthesis. AHR, KLF4 or FADS3 inactivation in cDCs decreases DHA production, resulting in increased encephalitogenic T-cell responses and EAE worsening. To evaluate therapeutic potential, we engineered a probiotic (EcNIAA) that produces the AHR agonist indole-3-acetic acid (IAA). Oral EcNIAA activates AHR-KLF4-FADS3 signaling in intestinal cDCs, boosted DHA production, and suppressed encephalitogenic T-cells migrating from the gut to the central nervous system. Conclusion Briefly, we identified a novel immunometabolic axis in DCs to limit effector T-cell responses and can be targeted with engineered probiotics to treat autoimmunity.