The transcription factor IRF4 regulates the homeostasis and function of intestinal ILC3s

Group 3 innate lymphoid cells (ILC3s) serve as critical guardians of mucosal immunity. However, the transcriptional networks governing their function remain incompletely characterized. Here, we demonstrate that interferon regulatory factor 4 (IRF4) is essential for maintaining intestinal ILC3 homeostasis and function. IRF4-deficient mice exhibit reduced NKp46+ ILC3s, expanded precursor-like NKp46-CCR6- ILC3s, and impaired interleukin-22 (IL-22)/IL-17A production, increasing susceptibility to infections. Furthermore, IRF4 loss disrupted major histocompatibility complex (MHC)-class II-associated transcriptional signatures in ILC3s, particularly in CCR6+ ILC3s, accompanied by downregulation of MHC class II protein expression. This perturbation consequently diminished ILC-mediated apoptosis of effector CD4+ T cells. Sequencing and trajectory analysis link IRF4 to NKp46+ ILC3 maintenance and Tbx21 regulation. ATAC-seq/CUT&Tag reveal direct IRF4 binding to Batf, Tbx21, Il22, Il17a, and MHC II loci. Overexpression of T-bet partially rescued the differentiation defects in intestinal ILC3s, whereas Batf overexpression partially restored functional impairments and significantly enhanced MHC class II expression in ILC3s.