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

Abstract

Genetic defects in NOX2 can cause chronic granulomatous disease (CGD), characterized by increased susceptibility to infections and pronounced inflammatory responses that lead to granuloma formation. We developed a CGD model using Ncf2-/- mice through controlled environmental exposure. Unlike in specific pathogen-free environment, these mice spontaneously developed pulmonary granulomas under clean-grade conditions. Employing single-cell RNA sequencing, we observed an expansion of neutrophils and monocyte-derived macrophages (MDMs) within the lung tissue, identifying pro-inflammatory NOS2high-neutrophils and a distinct MDMs subset marked by NOS2 and ARG1. Spatial transcriptomics demonstrated that NOS2high-neutrophils were located at the core area, while the MDMs subset was positioned at the periphery, facilitating extracellular matrix remodeling. Pharmacological targeting of MIF, deletion of the pro-survival gene Morrbid, and elimination of Il1r1 all suppressed granuloma formation by mitigating inflammation. This study underscores how environmental control can establish a natural CGD model, elucidates the mechanisms of granuloma formation, and develops potent therapeutic interventions. HighlightsO_LIThrough installing a mutation in a NOX2 subunit gene Ncf2 and changing the husbandry environment, we generated a natural CGD mouse model with progressive pulmonary granuloma formation. C_LIO_LINOS2high neutrophils located in the core region of CGD lung granulomas, exhibit a pro-inflammatory transcriptional profile. C_LIO_LIMonocyte-derived macrophages marked by Nos2 and Arg1 are located at the periphery of granulomas and exhibit a profibrotic transcriptional profile. C_LIO_LIThe transcriptomic studies assist the development of three effective perturbations for treating the rare disease CGD via targeting Il1r1, Morrbid, and Mif respectively. C_LI