# Genetic diversity of Collaborative Cross mice implicates FFAR3 as a target for ILC2 anti-inflammatory reprogramming

**Authors:** Mark Rusznak, Shinji Toki, Yajing Hao, Marc J. C. Todd, Liddy Malone, Julia F. Goodhead, Catherine DuPuy, Weisong Zhou, Dominique Babin, Christian M. Warren, Masako Abney, Matthew T. Stier, Christopher M. Thomas, Jing Li, Justin Jacobse, Andrew P. Pahnke, Mark I. Petrovic, Jacqueline-Yvonne Cephus, Shelby N. Kuehnle, M. Wade Calcutt, Allison E. Norlander, Fang Yan, Jeremy A. Goettel, Darla R. Miller, Rachel M. Lynch, Daniel P. Cook, Dawn C. Newcomb, Fei Zou, R. Stokes Peebles

PMC · DOI: 10.1038/s41467-025-67813-2 · Nature Communications · 2026-01-03

## TL;DR

This study shows that genetic diversity in mice affects ILC2 function, identifying FFAR3 as a key gene that reprograms these cells to reduce inflammation in the lungs.

## Contribution

The study identifies FFAR3 as a novel target for reprogramming ILC2s to an anti-inflammatory state during lung inflammation.

## Key findings

- Ffar3 is responsible for a QTL that reduces ILC2 activation and Type 2 effector function in the lung.
- FFAR3 signaling promotes ILC2 survival, reduces cytokine production, and increases IL-10 expression.
- FFAR3-dependent reprogramming involves EGFR upregulation and is partially conserved in human ILC2s.

## Abstract

Pulmonary group 2 innate lymphoid cells (ILC2s) are key drivers of Type 2 inflammation in diseases like asthma, yet the molecular mechanisms regulating their function are incompletely understood. Using the genetically diverse Collaborative Cross (CC) mouse panel, we mapped a quantitative trait locus (QTL) that governs ILC2 prevalence in the lung after aeroallergen exposure. This QTL induces a large population of ILC2s in the lung that are resistant to activation and have diminished Type 2 effector function. We identified free-fatty acid receptor 3 (Ffar3) as a gene responsible for this effect and demonstrated that FFAR3 signaling reprograms ILC2s to an anti-inflammatory state by promoting their survival, reducing Type 2 cytokine production, and enhancing IL-10 expression. This anti-inflammatory state is dependent on IL-2 signaling, is characterized by decreased ST2 expression, and is distinct from previously described IL-10-producing ILC2 phenotypes. FFAR3-dependent reprogramming is mediated by epidermal growth factor receptor (EGFR) upregulation, and FFAR3’s anti-inflammatory effect is partially conserved in human ILC2s.

Pulmonary type 2 inflammation is associated with type 2 innate lymphoid cells. Here the authors use the Collaborative Cross mouse panel to show that ILC2 abundance during type 2 lung inflammation is different across the panel and identify free-fatty acid receptor 3 (Ffar3) as a gene responsible and show cytokine and ILC2 functional changes.

## Linked entities

- **Genes:** FFAR3 (free fatty acid receptor 3) [NCBI Gene 2865], ST2 (suppression of tumorigenicity 2) [NCBI Gene 6761], EGFR (epidermal growth factor receptor) [NCBI Gene 1956]
- **Proteins:** FFAR3 (free fatty acid receptor 3), IL10 (interleukin 10), IL2 (interleukin 2), ST2 (suppression of tumorigenicity 2), EGFR (epidermal growth factor receptor)
- **Diseases:** asthma (MONDO:0004979)
- **Species:** Mus musculus (taxon 10090)

## Full-text entities

- **Genes:** Il10 (interleukin 10) [NCBI Gene 16153] {aka CSIF, If2a, Il-10}, Egfr (epidermal growth factor receptor) [NCBI Gene 13649] {aka 9030024J15Rik, Erbb, Errb1, Errp, Wa5, wa-2}, Ffar3 (free fatty acid receptor 3) [NCBI Gene 233080] {aka Gm478, Gpr41}, Il1rl1 (interleukin 1 receptor-like 1) [NCBI Gene 17082] {aka DER4, Fit-1, Ly84, ST2L, St2, St2-rs1}, Il2 (interleukin 2) [NCBI Gene 16183] {aka Il-2}
- **Diseases:** Type 2 inflammation (MESH:D007249), asthma (MESH:D001249)
- **Species:** Mus musculus (house mouse, species) [taxon 10090], Homo sapiens (human, species) [taxon 9606]

## Full text

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## Figures

8 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12847941/full.md

## References

7 references — full list in the complete paper: https://tomesphere.com/paper/PMC12847941/full.md

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Source: https://tomesphere.com/paper/PMC12847941