Spatial Transcriptomics Uncovers Hybrid, Pro-Inflammatory and Pro-Fibrotic Cellular Niches in Pulmonary Granuloma of Patients with Chronic Sarcoidosis

Background Sarcoidosis is a disease of unknown etiology characterized by the formation of immune cell accumulation (granuloma) in the lung and other tissues. Chronic sarcoidosis may lead to pulmonary fibrosis. Aim To unravel cellular niches within pulmonary granuloma of chronic sarcoidosis patients using spatial transcriptomics. Methods Spatial transcriptomics using the Visium platform (10x Genomics) was performed on nine granuloma-containing lung explants from sarcoidosis patients. Validation of gene expression was performed through immunohistofluorescence protein staining and RNA in situ hybridization. Results Spatial gene expression covered 30,587 gene expression spots and 173 granulomas. A CD68+ macrophage niche was localized in the center of the granuloma, with a CD3+ T and CD20+ B cell niche in close proximity, surrounded by a COL3A1+ fibroblast niche. In the Central Granuloma Macrophage niche, expression of the pro-fibrotic macrophage genes SPP1, CHIT1 and CHI3L1 was observed, genes whose expression has recently been described for macrophages in idiopathic pulmonary fibrosis. Additionally, pro-inflammatory macrophage genes were expressed in the Central Granuloma Macrophage niche: macrophages appear armed for lysosomal degradation and ready for phagocytosis. Inner granuloma niches showed higher expression of interferon gamma (IFN-γ)-inducible genes. Higher collagen and CTHRC1 expression were observed in fibroblast-containing granuloma niches, characteristics of pro-fibrotic lung remodeling. Ligand-receptor analysis identified pro-inflammatory and pro-fibrotic interactions between granuloma niches. Conclusion Taken together, macrophages in the center of the sarcoidosis granuloma form an armed-and-ready, hybrid pro-inflammatory and pro-fibrotic niche, supporting granuloma persistence through continuous IFN-γ stimulation and collagen expression by fibroblasts localized in periphery of granuloma.