Paired single-cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation

ABSTRACT Granulomas are classic manifestations of tuberculosis pathogenesis. They result from an ensemble of immune responses to Mycobacterium tuberculosis infection, but the identities, arrangement, cellular interactions, and regulation of the cells that comprise them have thus far been incompletely understood. To better understand the composition of granulomas, we conducted spatial and single-cell RNA sequencing of granulomas in biopsy specimens from patients with tuberculosis. We found that granulomas consist of concentric transcriptional laminae surrounding areas of central necrosis. We identified distinct populations of granuloma-associated stromal cells, fibroblasts, lymphocytes, mast cells, dendritic cells, neutrophils, and macrophages. Furthermore, gene expression among these cell populations differed by location within granulomas. We used inferential analysis to predict dominant granuloma cell-cell interactions, the activity of major signaling pathways, and transcription factor activities. Using spatial deconvolution, we mapped a conserved pattern of cellular organization dominated by macrophages rich in SPP1 /osteopontin expression. Trajectory analysis of macrophage subtypes mapped their differentiation and supported the importance of SPP1 to granuloma macrophage polarization. Using the Mycobacterium marinum -zebrafish model, we found that mycobacterial infection induces spp1 expression in macrophages and that spp1 ablation results in granuloma formation defects and reduced survival in adult animals. Cumulatively, we have identified a dominant macrophage granuloma population as well as its central regulatory gene in human samples and confirmed the importance of spp1 to granuloma biology in vivo . IMPORTANCE Tuberculosis is the world’s most deadly single-pathogen infection. Its causative bacterium, Mycobacterium tuberculosis , sickens over 10 million people annually. Mycobacterial granulomas are the pathological hallmark of the infection and are critical determinants of disease trajectory. Granulomas form as a physiological barrier to contain infected macrophages and reduce bacterial dissemination. However, that barrier also reduces access of antibiotics and mycobactericidal immune cells to the pathogen, thereby promoting chronic infection and end-organ damage. This work supplies the field with a map of the conserved features of human tuberculosis granulomas and provides a valuable resource for future exploration of critical factors in tuberculosis pathogenesis, exemplified here by functional findings around the roles of spp1 /osteopontin-expressing macrophages in mycobacterial granulomas.