GM-CSF regulates ILC states and myeloid cell signaling during ulceration in Crohn’s disease

Abstract Macrophage (M-), granulocyte (G-), and granulocyte–macrophage (GM-) colony-stimulating factors (CSFs) regulate myeloid cell function, yet their relative roles during inflammation remain poorly defined. To uncover how CSFs shape spatial immune niches in Crohn’s disease, we performed Xenium single-cell spatial transcriptomics on ileal tissues, revealing cell-type–specific expression and source–target interactions for each CSF. GM-CSF, unlike M-CSF or G-CSF, was locally enriched in ulcerated regions where lymphocytes adjacent to macrophage aggregates signaled through STAT5 phosphorylation. To study functional consequences, we developed a csf2rb⁻/⁻ zebrafish model of intestinal injury. Using this model, we found that loss of GM-CSF signaling exacerbated epithelial damage and inflammation, whereas recombinant human GM-CSF limited injury by restraining ILC1 expansion, sustaining ILC3 maintenance, and promoting IL-22 production. Cross-species single-cell analysis revealed conserved ILC gene modules and GM-CSF–dependent transcriptional networks linking lymphoid and myeloid populations. These findings establish GM-CSF as a critical spatial regulator of myeloid–lymphoid crosstalk and intestinal immune homeostasis in Crohn’s disease. Competing Interest Statement The authors have declared no competing interest. Footnotes This version of the manuscript has been revised to include additional supplementary materials and to improve clarity, transparency, and reproducibility of the study. Specifically, we have added new supplementary figures and tables that provide expanded methodological details, additional validation analyses, and extended data supporting the main findings.