Extended Data Fig. 2: Transcriptional signatures of memory alveolar macrophages induced by s.c. BCG vaccination and respiratory mucosal viral-vectored vaccine.
(a) Heatmap of genes differentially expressed in airway AM by at least one of the comparisons. The difference was called when an absolute fold change was at least 1.5. Data are average levels of expression for each gene in each group. (b) Volcano plot for the comparison of airway AM from BCG-vaccinated vs. PBS animals without stimulation (US), with a threshold of absolute fold change set at 1.5. (c) Volcano plot for the comparison of airway AM from BCG-vaccinated vs. PBS animals with M.tb WCL stimulation (S), with a threshold of absolute fold change set at 1.5. (d) Pathways of the genes significantly up-regulated in un-stimulated (US) airway AM from BCG-vaccinated animals compared to those from PBS-treated animals. (e & f) Comparison of signature scores of the genes involved in glycolysis (e) and mTOR (f) in airway AM of BCG-vaccinated animals with those from control PBS animals, with (S) or without (US) stimulation. (g) Volcano plot for the comparison of airway AM from intranasal adenoviral-vectored vaccine (Ad)-immunized vs. PBS control animals without stimulation (US) with a threshold of absolute fold change set at 1.5. (h) Comparison of signature scores of the genes involved in Ag processing/presentation (****p = 6.15×10-7), fatty acid oxidation (*p = 1.6×10−2), glycolysis and mTOR pathway in airway AM of intranasal adenoviral-vectored vaccine (Ad)- immunized animals with those from PBS control animals without (US) stimulation. Horizontal lines in violin plots denote medians and dotted lines denote lower and upper quartiles. Data in a-g are from experiments with 3 samples/group/condition. Vertical lines in volcano plots (b, c & g) denote the threshold of absolute fold change 1.5 and the horizontal line denotes adjusted p value set at 0.05. Significant genes are marked in colors with up-regulated ones in red and down-regulated ones in blue. Adjusted p values are presented for violin plots (h) and obtained using limma package and BH correction (see Methods).
