Spatial single-cell profiling reveals macrophage niches in severe COVID-19 lungs
Abstract
Aims: Severe coronavirus disease 2019 (COVID-19) is characterized by marked heterogeneity in lung pathology, including diffuse alveolar damage, inflammation, and fibrosis. However, how spatially organized cellular interactions contribute to these divergent pathological outcomes remains incompletely understood. We aimed to define the spatial organization of cellular microenvironments in severe COVID-19 lungs and identify niche-specific cellular interactions associated with distinct histopathological states. Methods: We applied imaging-based single-cell spatial transcriptomics to post-mortem lung tissues from patients with severe COVID-19 and control subjects, enabling high-resolution mapping of cellular composition, spatial neighborhoods, and predicted ligand-receptor interactions within intact tissue architecture. Results: Analysis of 76,973 cells identified 20 distinct cell populations and revealed marked heterogeneity between COVID-19 samples, corresponding to different histopathological states. Spatial niche analysis identified discrete macrophage-associated microenvironments. Fibrotic niches were enriched in chitinase 3-like 1 (CHI3L1)/matrix metalloproteinase 9 (MMP9hi) macrophages spatially associated with collagen type I alpha 1 chain (COL1A1+) fibroblasts and basal cells. Ligand-receptor inference predicted macrophage-derived transforming growth factor beta (TGF-β) and galectin-3 signaling as drivers of pathogenic fibroblast activation and extracellular matrix remodeling. In contrast, alveolar niches contained secreted phosphoprotein 1 (SPP1hi) macrophages exposed to epithelial-derived cues, including WNT ligands and granulocyte-macrophage colony-stimulating factor (GM-CSF), consistent with differentiation toward an alveolar macrophage-like state. Conclusion: Severe COVID-19 lungs are organized into distinct spatial niches associated with divergent immunopathological trajectories. Imaging-based spatial transcriptomics provides a platform to link histopathological states with localized cellular interactions and macrophage-driven tissue remodeling programs.