Abstract / Summary
Abstract Granulomas are a defining feature of Crohn’s disease associated with a more severe disease course, yet their developmental origins and cellular organization remain poorly understood. Here, we integrate single-cell and spatial transcriptomics of human intestinal tissues with in situ validation and functional macrophage assays to investigate granuloma formation. Crohn’s disease granulomas share cellular, transcriptional and spatial features with isolated lymphoid follicles, suggesting that chronic inflammation may repurpose pre-existing lymphoid structures. We identify a previously uncharacterized population of PLA2G2D-expressing macrophages enriched in isolated lymphoid follicles and at granuloma peripheries. Lymphotoxin-α1β2, LIGHT and TNF induce this macrophage programme in vitro , while TNF and low-dose lipopolysaccharide promote CXCL9 production together with PLA2G2D expression, potentially supporting effector T-cell recruitment in the granuloma environment. Conversely, SPP1-expressing macrophages preferentially occupy granuloma cores, are induced by IL-1β or hypoxia, and interact with inflammatory fibroblasts through profibrotic signalling networks. These findings define spatially and functionally distinct macrophage niches within Crohn’s disease granulomas and support a model in which inflammatory signals transform homeostatic lymphoid macrophage programmes to promote granuloma organization and fibrotic remodelling.