肉芽肿是结核病 (TB) 的一个关键病理特征，其特点是细胞异质性、空间组成和细胞相互作用，在肉芽肿进展和宿主预后中发挥着至关重要的作用。本研究旨在根据细胞群的空间位置分析其转录组谱，并了解肉芽肿形成和发展的核心转录组特征。方法在本研究中，我们收集了四份临床活检样本，包括结核分枝杆菌（Mtb）感染的肺（MTB-L）和大网膜组织（MTB-O），以及来自非结核病患者的两份肺和大网膜活检样本。通过空间转录组学分析组织以创建空间图谱。利用细胞富集评分和细胞间通讯分析，我们研究了不同空间区域细胞群的转录组特征，并鉴定了可能在肺和网膜结核肉芽肿形成中起决定性作用的基因。为了验证我们的主要发现，建立了基于类器官-巨噬细胞共培养的体外结核病模型。结果 空间转录组学绘制了感染 Mtb 的肺和网膜组织中结核肉芽肿的细胞组成和空间分布特征。肉芽肿中主要细胞群的特征和进化关系揭示了免疫微环境的转变：从肺肉芽肿中以 B 细胞和成纤维细胞为主转变为网膜肉芽肿中以骨髓细胞和成纤维细胞为主。此外，我们的数据确定了跨细胞簇和区域的关键差异表达基因，表明胶原蛋白基因的上调是肉芽肿的共同特征。使用类器官-巨噬细胞共培养模型，我们证明了 Thrombospondin-1 (THBS1) 在降低与细胞外基质重塑相关的蛋白质表达水平方面的显着功效。结论 这些结果为深入了解结核病的发病机制和发展提供了新的见解，增强了我们从空间角度对结核肉芽肿细胞的组成和相互作用的理解，并为结核病的新型辅助治疗铺平了道路。©作者。

Granulomas are a key pathological feature of tuberculosis (TB), characterized by cell heterogeneity, spatial composition, and cellular interactions, which play crucial roles in granuloma progression and host prognosis. This study aims to analyze the transcriptome profiles of cell populations based on their spatial location and to understand the core transcriptome characteristics of granuloma formation and development. Methods In this study, we collected four clinical biopsy samples including Mycobacterium tuberculosis (Mtb) infected lung (MTB-L) and omentum tissues (MTB-O), as well as two lung and omentum biopsies from non-TB patients. The tissues were analyzed by spatial transcriptomics to create a spatial atlas. Utilizing cell enrichment scores and intercellular communication analysis, we investigated the transcriptome signatures of cell populations in various spatial regions and identified genes that may play a decisive role in the formation of pulmonary and omental tuberculosis granulomas. To validate our major findings, an in vitro TB model based on organoid-macrophage co-culture was established. Results Spatial transcriptomics mapped the cell composition and spatial distribution characteristics of tuberculosis granulomas in lung and omental tissues infected with Mtb. The characteristics and evolutionary relationships of major cell populations in granulomas reveal a shift in the immune microenvironment: from a predominance of B cells and fibroblasts in pulmonary granulomas to a predominance of myeloid cells and fibroblasts in omental granulomas. Furthermore, our data identified key differentially expressed genes across cell clusters and regions, showing that upregulation of collagen genes is a common feature of granulomas. Using an organoid-macrophage co-culture model, we demonstrated the notable efficacy of Thrombospondin-1 (THBS1) in reducing protein expression levels related to extracellular matrix remodeling. Conclusion These results provide insights into the pathogenesis and development of tuberculosis, enhancing our understanding of the composition and interactions of tuberculosis granuloma cells from a spatial perspective, and pave the way for novel adjuvant treatments for tuberculosis.© The author(s).