Fig. 4: Granuloma lymphocytes display a paradoxical absence of exhaustion markers.

a, Frequency of lymphocyte subsets in all TB FOVs pooled together (left) and representative images of each subset (right). b, Frequency of CD4⁺ and CD8⁺ T cells relative to the frequency of total immune cells in four MEs of interest (top). The frequency of T_reg cells relative to the frequency of total CD4⁺ T cells (lower left) (n = 30). c, Frequency of Ki-67⁺ cells broken down by lymphocyte subset (n = 30). d, Representative image of a TB granuloma, colored by ME assignment (left). Zoomed inset displays T_reg cell assignment (upper right: purple, T_reg cell; gray, non-T_reg cell) and expression of Ki-67 (magenta), CD3 (cyan) and Foxp3 (white) (lower right). e, Percentage of lymphocytes positive for PD-1 (left) and Lag3 (right) in all TB FOVs and TNBC. Bars represent mean ± s.e.m. (TB n = 30, TNBC n = 43). f, The ratio of PD-1⁺ to PD-L1⁺ immune cells represented as a log₂ fold change in all TB FOVs and TNBC (TB n = 30, TNBC n = 43). Boxplots display the median and interquartile range (IQR; 25–75%) with whiskers representing the upper- and lower-quartile ±1.5× IQR. All P values were calculated with a Wilcoxon rank-sum test (two tailed) (**P < 0.01; ***P < 0.001; ****P < 0.0001).