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

TL;DR

The study shows that IRF4 is crucial for the function and balance of intestinal ILC3s, which are important for gut immunity.

Contribution

The study identifies IRF4 as a key regulator of ILC3 homeostasis and function through multi-omics analysis and functional rescue experiments.

Findings

IRF4-deficient mice show reduced NKp46+ ILC3s and impaired IL-22/IL-17A production.

IRF4 directly binds to Batf, Tbx21, Il22, and MHC II loci, influencing ILC3 function.

Overexpression of T-bet or BATF can partially restore ILC3 differentiation and function.

Abstract

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.

•IRF4 is a master regulator of intestinal NKp46⁺ ILC3 homeostasis and function•Revealing IRF4’s dual role in sustaining MHC-II⁺ ILC3s-mediated T-cell tolerance via BATF•Integrating multi-omics to map IRF4’s direct binding to Batf, Tbx21, Il22, and MHC-II loci•Demonstrating functional rescue of IRF4-deficient ILC3s by T-bet/BATF overexpression

IRF4 is a master regulator of intestinal NKp46⁺ ILC3 homeostasis and function

Revealing IRF4’s dual role in sustaining MHC-II⁺ ILC3s-mediated T-cell tolerance via BATF

Integrating multi-omics to map IRF4’s direct binding to Batf, Tbx21, Il22, and MHC-II loci

Demonstrating functional rescue of IRF4-deficient ILC3s by T-bet/BATF overexpression

Health sciences; Biological sciences; Molecular biology; Molecular biology experimental approach

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