Fig. 3: The transcriptional response to M.tb infection by 28 HAMs.

A Venn diagram of differentially expressed (DE) genes between M.tb-infected and uninfected controls at three time points. Total number of genes with detectable expression (≥1RPM) was ~12,000. DE genes were detected with DESeq2 (adjusted p values < 0.05): 62 at 2 h, 2177 at 24 h, and 3662 at 72 h, with overlaps displayed in the Venn diagram. Log₂ fold change and log₂ average expression for DE genes at 2 h (B), 24 h (C) and 72 h (D). M1 and M2 genes are shown in blue and red, respectively. E The number of DE genes with >2-fold upregulation defined as ‘M1-like’ or ‘M2-like’. This uses an independent definition of ‘M1-like’ and ‘M2-like’ genes to (F). F Gene set enrichment analysis of DE genes from 72 h using 48 gene expression modules previously determined as operational in macrophage differentiation. Modules annotated as ‘M1-like’ or ‘M2-like’ are shown in blue and red, another major grouping of modules was related to ex vivo TPP (TNF, PGE2 and P3C) stimulation in macrophages⁴⁰ and are highlighted by a line.