Extended Data Fig. 4: Immunoregulatory protein expression in TB granulomas.

a, Frequency of cells positive for IDO1 (top) or PD-L1 (bottom) broken down by FOV and cell phenotype. b, Normalized expression of IDO1 (top) and PD-L1 (bottom) for major myeloid subsets ordered by decreasing median expression value. Dashed line indicates the cutoff for positivity for IDO1 (cutoff = 0.26) and PD-L1 (cutoff = 0.25). c, Frequency of IDO1⁺ or PD-L1⁺ cells (of total cells) across specimen type (postmortem specimen = green, biopsy = red, therapeutic resection = blue) with dot shape representing organ site (lung = triangle, extrapulmonary = circle). d, Pearson correlation coefficient and p-value determined by t-test (two-tailed) broken down by specimen type. e, Frequency of neutrophils (left) and epithelial cells (right) positive for PD-L1 or IDO1 across all FOVs. f, The count of giant cells across all regions, colored by specimen origin as in c. g, The frequency of IDO1⁺ and PD-L1⁺ myeloid cells for all non-granulocytic myeloid cell subsets across ME. Any ME with fewer than 1% of the total cell subset is shaded gray. h, Linear relationship between count of Tregs in Mcore1 with count of IDO1⁺ (left) and PD-L1⁺ (right) cells in Mcore1. Linear regression (black solid line) with 95% confidence interval (grey silhouette) displayed. Significance was established with a two-tailed t-test. i, Count of PD-1⁺ cells across all MEs with >0 positive cells. j The count of IFNγ⁺ cells in all FOVs with > 0 positive cells, colored by cell type. Unless otherwise specified all p values were determined with a Wilcoxon Rank Sum Test (two-tailed) where: * p < 0.05, ** p < 0.01, **** p < 0.0001.