Single-cell and spatial transcriptomics reveal the pathogenesis of chronic granulomatous disease in a natural model

Genetic defects in NADPH oxidase 2 (NOX2) cause chronic granulomatous disease (CGD), which is characterized by increased susceptibility to infections and excessive inflammation leading to granuloma formation. We developed a CGD model using Ncf2^-/- mice through controlled environmental exposure. Unlike in specific-pathogen-free environments, these mice spontaneously developed pulmonary granulomas under clean-grade conditions. In the affected lung tissue, significant changes in microbial communities were observed, accompanied by the infiltration of neutrophils and monocyte-derived macrophages (MDMs). Specific nitric oxide synthase 2 (NOS2)^high neutrophils with a pro-inflammatory transcriptional profile localize at the granuloma core, while an MDM subpopulation marked by MMP12 at the periphery exhibits a pro-fibrotic signature. Pharmacological inhibition of macrophage migration inhibitory factor (MIF), deletion of the pro-survival gene myeloid RNA regulator of Bim-induced death (Morrbid), and knockout of Il1r1 all suppressed granuloma formation by mitigating inflammation. This study underscores the establishment of a natural CGD model through environmental control, elucidates the mechanisms of granuloma formation, and develops potent therapeutic interventions.