Figure 3.
Analysis of the pro-inflammatory AM subsets. The AM subsets also include host cell populations that have an inflammatory phenotype and appear capable of inducing stress in Mtb. (a) Umap plot showing the clustering of the myeloid cell populations in the integrated dataset. The AM_Pro-Infl population, a subset of the AM_1 cluster, is highlighted. (b) Dot plot showing scaled expression values for the pro-inflammatory gene signature related to infected AMs. Higher expression levels are represented in yellow/green, while lower expression levels are shown in blue. The size of the dot corresponds to the percentage of cells that express each gene in each cluster. (c) Violin plot showing ADT staining levels (in log-normalized counts) for the SiglecF surface marker among the different subpopulations of infected macrophages. (d) Scatter plots (split-view) showing coexpression levels (in log-normalized counts) for Zeb2 and Cxcl2 marker genes in AM_2, IM_1, and AM_Pro-Infl subpopulations across different infection states. (e) Stacked violin plots showing staining levels (in log-normalized values) for the ADT antibodies CD63, CD11b, and CD38 in different clusters of macrophages and across the different infection conditions. As evidenced in the text, the infected and bystander AM_Pro-Infl populations show higher expression levels for these surface markers. (f) Umap plots (split view) showing expression values (in log-normalized counts) for the Cxcl2 and Malt1 genes (part of the AM_2 NF-κB signature) across the different infection conditions. Higher expression values are displayed in yellow, while low expression values are shown in blue. (g) Umap plots showing expression values (in log-normalized counts) for the Spag9 and Slc15a3 genes in the integrated dataset. Higher expression values are displayed in yellow, while low expression values are shown in blue. (h) Dot plot showing scaled expression values among subsets of AMs for genes whose expression is associated with the AM_1 and AM_3 clusters in the integrated dataset. Higher expression levels are represented in yellow/green, while lower expression levels are shown in blue. The size of the dot corresponds to the percentage of cells that express each gene in each cluster. n = 5 for the infected population, n = 2 for the uninfected population. All the genes highlighted in the different figures show statistically significant greater expression in their clusters compared with cells in different clusters (FDR < 0.05; Wilcoxon rank-sum test; see Materials and methods).

Analysis of the pro-inflammatory AM subsets. The AM subsets also include host cell populations that have an inflammatory phenotype and appear capable of inducing stress in Mtb. (a) Umap plot showing the clustering of the myeloid cell populations in the integrated dataset. The AM_Pro-Infl population, a subset of the AM_1 cluster, is highlighted. (b) Dot plot showing scaled expression values for the pro-inflammatory gene signature related to infected AMs. Higher expression levels are represented in yellow/green, while lower expression levels are shown in blue. The size of the dot corresponds to the percentage of cells that express each gene in each cluster. (c) Violin plot showing ADT staining levels (in log-normalized counts) for the SiglecF surface marker among the different subpopulations of infected macrophages. (d) Scatter plots (split-view) showing coexpression levels (in log-normalized counts) for Zeb2 and Cxcl2 marker genes in AM_2, IM_1, and AM_Pro-Infl subpopulations across different infection states. (e) Stacked violin plots showing staining levels (in log-normalized values) for the ADT antibodies CD63, CD11b, and CD38 in different clusters of macrophages and across the different infection conditions. As evidenced in the text, the infected and bystander AM_Pro-Infl populations show higher expression levels for these surface markers. (f) Umap plots (split view) showing expression values (in log-normalized counts) for the Cxcl2 and Malt1 genes (part of the AM_2 NF-κB signature) across the different infection conditions. Higher expression values are displayed in yellow, while low expression values are shown in blue. (g) Umap plots showing expression values (in log-normalized counts) for the Spag9 and Slc15a3 genes in the integrated dataset. Higher expression values are displayed in yellow, while low expression values are shown in blue. (h) Dot plot showing scaled expression values among subsets of AMs for genes whose expression is associated with the AM_1 and AM_3 clusters in the integrated dataset. Higher expression levels are represented in yellow/green, while lower expression levels are shown in blue. The size of the dot corresponds to the percentage of cells that express each gene in each cluster. n = 5 for the infected population, n = 2 for the uninfected population. All the genes highlighted in the different figures show statistically significant greater expression in their clusters compared with cells in different clusters (FDR < 0.05; Wilcoxon rank-sum test; see Materials and methods).

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