Single-Cell and Spatial Transcriptomic Analyses Deciphering the Three-Layer Architecture of Human Tuberculosis Granulomas

Abstract

BackgroundGranulomas (defining tuberculosis histopathological feature) are central to the host’s defense againstMycobacterium tuberculosis, critically influencing patient outcomes. However, knowledge of human granulomas’ structure and function are incomplete. This study employs single-cell and spatial transcriptomics to dissect human granuloma’s cellular composition, structure, communication and function from 19 pulmonary, lymphatic and skeletal samples.ResultsOur study identified nine key immune-activated/signaling-active cell clusters. Notably, we delineated a three-layered granuloma structure: a core with macrophages (Macro-c09, Macro-c10) and occasional fibroblasts (Fib-c03); a fibroblast-rich (Fib-c01) periphery; and an immune-infiltrated intermediate layer comprising diverse immune-cells recruited by strong signaling-molecules (SPP1/MIF) from core/periphery cells. This study also shows granuloma heterogeneity across individuals and tissues.ConclusionsBy merging scRNA-seq with ST-seq, we offer an intricate single-cell perspective of granulomas’ spatial-structure and formation mechanisms, identify signaling-molecules and significantly changed genes as potential targets for host-directed tuberculosis immunotherapy, highlight fibroblasts’ crucial role in granuloma formation, and provide an important reference/improved understanding of TB.