Spatial transcriptomics analysis on post- and current TB lung resections. (A) Heatmap showing the expression of human TB-myofibroblast gene signature and SPP1⁺CHI3L1⁺ macrophage markers on selective tissue slides from patients who are post-TB (top) or current TB (bottom), alongside paired H&E staining (these H&E stains are also shown in Fig. S1 A together with those other samples used for spatial transcriptomics not shown here). (B) Distribution of human TB-myofibroblast signature expression on the spatial cohort. HIV statuses are shown in different shades of blue for positive or negative. Two-sided Mann–Whitney U test without correction was used for statistical testing. Statistical annotation: P value < 0.0001 (****). (C) Distribution of SPP1⁺CHI3L1⁺ macrophage markers and human TB-myofibroblast signature on the spatial data across all Visium spots. Left two panels: Manual segmentation of the granuloma structure was done to allow separation of the Visium slide into three different regions: in granuloma, on granuloma border (cuff), and outside of granuloma (Materials and methods). Right two panels: The same as left panels with the exception that “on border” = True means on granuloma cuff and False means the rest. Two-sided Mann–Whitney U test without correction was used for statistical testing. Statistical annotation: P value < 0.0001 (****). (D) Correlation between human TB-myofibroblast signature and all macrophage subpopulations’ markers. Each circle represents a Visium sample. Boxplot of the Pearson’s r distribution is shown for each macrophage subtype. Mann–Whitney U test without correction were used for statistical testing. Statistical annotation: P value < 0.0001 (****). (E) Spatially informed ligand–receptor (L–R) analysis using LIANA+ on Visium samples. Examples are shown where SPP1(L)–CD44(R) interactions are being nominated as top L–R pairs. H&E overlaid with pathology annotation for granuloma structures are shown next to heatmap of L–R interaction scores, which are calculated at each Visium spot using spatially weighted Cosine similarity (Materials and methods).