Extended Data Fig. 2: Transcriptional signatures of macrophages and T cells adjacent to the TLSs in human TB granulomas.
a, Representative images showing the distribution of TLSs in human TB granulomas. White and yellow dashed lines respectively indicate the non-necrotic and necrotic centers of granulomas from independent lung specimens. Arrows indicate the TLSs. Scale bars, 500 μm. b,c, Heatmap of differentially expressed genes (DEGs) (left) and enrichment of their biological functions (right) in CD68+ macrophages (b) or CD3+ T cells (c) in the regions adjacent to TLSs (MacL and TL, respectively) compared to those in the non-TLS normal control regions, respectively. Top 20 upregulated and downregulated DEGs are listed, in which the genes encoding ligands and receptors are highlighted in blue and purple, respectively. n = 4 ROIs for each group. One-sided tests were performed, and P values were corrected for multiple testing using FDR adjustment. d, Representative images showing IDO1 expression in CD68+ macrophages and LTF expression in CD3+ T cells in the TLS-adjacent regions. The boxed areas enlarged on the right represent the CD68+IDO1+ macrophages (field 1) or CD3+LTF+ T cells (field 2) adjacent to TLSs. The yellow dashed line indicates the necrotic center of a granuloma. Arrows indicate the TLSs. Scale bars, 50 μm. e,f, Quantification of IDO1 expression (e) in CD68+ macrophages or LTF expression (f) in CD3+ T cells in the TLS-adjacent regions or non-TLS control regions. Data are shown as mean ± SEM of n = 5 lung samples (unpaired two-tailed Student’s t test for e,f).
