Fig. 3: Granuloma myeloid cells express a spatially coordinated immunoregulatory program.

a, UMAP visualization of all myeloid populations across all TB FOVs colored by subset (left) and normalized expression of phenotypic markers used to delineate subsets. b, IDO1 and PD-L1 normalized expression overlaid on the UMAP. c, Representative images of TB granulomas showing expression of IDO1 (magenta) and PD-L1 (cyan). d, PD-L1 and IDO1 expression values across all myeloid cells as a biaxial scatter plot. Plot displays Pearson’s r and P value calculated by a t test (two tailed). e, Giant cells identified from a MIBI-scanned TB sample (CD45, green; Vimentin, blue; CD31, red). Representative giant cells displayed in zoomed insets (lower left) with H&E staining or IDO1 (magenta) and PD-L1 (cyan) expression. Bar plot displays the percentage of IDO1⁺ and PD-L1⁺ giant cells (n = 34, normalized expression >0). f, The frequency of IDO1⁺ and PD-L1⁺ nongranulocytic myeloid cells in aggregate and broken down by ME. Bars represent mean ± s.e.m. (n = 30). g, ME_Mcore1 and ME_IntMono maximum probability maps and representative images of a pulmonary (top) and pleural (bottom) TB sample showing expression of IDO1 (magenta) and PD-L1 (cyan). h, Frequency of PD-L1⁺ CD163⁺ macrophages (left) across MEs with a representative MaxPM. Insets are colored by ME (top), cell type (blue, middle) and CD163 (yellow) and PD-L1 (cyan), with the segmentation boundaries overlaid (white). The frequency of IDO1⁺ CD11c⁺ DCs (right) across MEs with a representative MaxPM. Insets are colored by ME (top), cell type (green, middle) and IDO1 (magenta), with the segmentation boundaries overlaid (white). Dashed lines represent the total frequency of positive cells (PD-L1 or IDO1) for the indicated cell subset. HLA, human leukocyte antigen; HLA-DR-DQ-DP, HLA-DR/HLA-DQ/HLA-DP.