Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma

Granulomas are the pathological hallmark of Tuberculosis (TB), and the niche in which bacilli can either grow and disseminate or the immunological microenvironment in which host cells interact to prevent bacterial dissemination. Here, after in situ sequencing, thirty-four immune transcripts in lung sections from Mycobacterium tuberculosis -infected mice were aligned to the tissue morphology at cellular resolution, allowing the analysis of local immune interactions in the granuloma. Co-localizing transcript networks at <10 μm in C57BL/6 mouse granulomas increased in complexity with time after infection. B-cell clusters developed late after infection. Transcripts from activated macrophages were enriched at subcellular distances from M. tuberculosis . Encapsulated C3HeB/FeJ granulomas showed necrotic centers with transcripts associated with immunosuppression ( foxp3, il10 ), while those in the granuloma rims associated with activated T cells and macrophages. Highly diverse networks with common interactors were observed in similar lesions. Thus, different immune landscapes of M. tuberculosis granulomas depending on the time after infection, the histopathological features of the lesion and the proximity to bacteria were here defined.