BHLHE40 Orchestrates TL1A-Driven ILC3 Effector Programs and RORγt⁺ APC-Mediated Tolerance [ATAC-Seq]

A central feature of the intestinal immune system is the ability to protect against pathogens while maintaining antigen-specific tolerance to the gut bacteria that coat its surface. Here, we identified Bhlhe40 as a central regulator of both ILC3- and ROR t⁺ APC-dependent mucosal immunity. TL1A stimulation and inflammatory bowel disease both enhance Bhlhe40 expression in intestinal ILC3s. Basal Bhlhe40 expression in ILC3s is essential for efficient transcription of cytokine effectors and maintenance of mucosal immunity, whereas TL1A-induced upregulation of Bhlhe40 further amplifies these effects. Bhlhe40 is also highly expressed in ROR t⁺ APCs, where it is required for optimal generation of antigen-specific Tregs. Together with the colonic microbiota, Bhlhe40 regulates expression of the co-stimulatory molecule Tnfsf4 (OX40L), which is necessary for the induction of Helicobacter hepaticus-specific Tregs. These findings reveal a previously unrecognized role for Bhlhe40 in orchestrating intestinal ILC3 responses and promoting Bhlhe40-dependent co-stimulatory signals in ROR t⁺ APCs that coordinate antigen-specific tolerance.