Deciphering multicellular microenvironment of tuberculosis lung granulomas associated with bacterial control using high-throughput single-cell mRNA sequencing

Abstract Infection with Mycobacterium tuberculosis results in the formation of tuberculosis (TB) lung granulomas, which are complex structures with a network of multiple immune cells closely intertwined and function together. Within a given host, granulomas have unique trajectories and outcomes. Some granulomas are able to control bacterial replication, while others fail resulting in persistent bacterial replication. The molecular features associated with these outcomes are not well understood. Using high-throughput single-cell mRNA sequencing on individual TB lung granulomas and computational algorithms, we are generating models to understand infection dynamics that incorporate immune cell composition, its function and interaction; bacterial burden and trajectories of the granulomas to identify robust drivers of bacterial control. We evaluated 28 granulomas from 4 cynomolgus macaques, that were infected for 10 weeks with the Erdman strain of M. tuberculosis. We identified over 30 functional clusters of cells spanning multiple immune and non-immune cells types including T cells, B cells, plasma cells, dendritic cells, mast cells, macrophages, neutrophils, type 2 pneumocytes, fibroblasts and endothelial cells. We observe differential cellular composition and host-cell intercellular communication constituting granulomas that are associated with bacterial burden, that may inform systems level properties across granulomas and animals. By understanding features of the cellular microenvironment that limit bacterial replication, we hope to identify novel targets for host-directed immune therapies and prophylactics in M. tuberculosis infection and other granulomatous disease.