Extended Data Fig. 7: Comparative analysis of transcriptomes of inflammatory macrophages.
From: A druggable copper-signalling pathway that drives inflammation
a, Principal Component Analysis (PCA) of RNA-seq comparing naMDM (n = 10 donors) and aMDM (n = 10 donors) with MDM exposed to Salmonella typhimurium (n = 32 donors) vs control (n = 32 donors), macrophages from bronchoalveolar fluids of moderate (n = 3 donors) and severe COVID-19 individuals (sCOVID, n = 6 donors) vs control (n = 4 donors), MDM exposed to Leishmania major (n = 5 donors) vs control (n = 6 donors) and MDM exposed to Aspergillus fumigatus (n = 3 donors) vs control (n = 3 donors). b, GO term analyses of upregulated genes in MDM exposed to Salmonella typhimurium (n = 32 donors) vs control (n = 32 donors), sCOVID (n = 6 donors) vs control (n = 4 donors), Leishmania major (n = 5 donors) vs control (n = 6 donors) and Aspergillus fumigatus (n = 3 donors) vs control (n = 3 donors). c, RNA-seq analyses of gene expression in MDM exposed to Salmonella typhimurium (n = 32 donors) vs control (n = 32 donors), sCOVID (n = 6 donors) vs control (n = 4 donors), Leishmania major (n = 5 donors) vs control (n = 6 donors) and Aspergillus fumigatus (n = 3 donors) vs control (n = 3 donors). Inflammatory signature genes are highlighted. Dashed lines, adjusted P values = 0.05. d, RNA-seq analyses of gene expression in MDM exposed to Salmonella typhimurium (n = 32 donors) vs control (n = 32 donors), sCOVID (n = 6 donors) vs control (n = 4 donors), Leishmania major (n = 5 donors) vs control (n = 6 donors) and Aspergillus fumigatus (n = 3 donors) vs control (n = 3 donors). Genes encoding iron-dependent demethylases and acetyl-transferases are highlighted. Dashed lines, adjusted P values = 0.05. For b – d differential gene expression was assessed with the limma/voom framework. GO enrichment was assessed with the enrichGO method from clusterProfiler. P values were corrected for multiple testing with the Benjamini-Hochberg procedure.
