Fig. 1: Differential infection efficiency and host cell transcriptome between primary and secondary infections. | Nature Communications

Fig. 1: Differential infection efficiency and host cell transcriptome between primary and secondary infections.

From: Epithelial cells maintain memory of prior infection with Streptococcus pneumoniae through di-methylation of histone H3

Fig. 1

A Experimental scheme, showing A549 or RPMI cells infected with S. pneumoniae, pink for uninfected cells (UI), green for primary infection (1°), blue for cells maintained post first infection (PI), purple for secondary infection (2°). Addition of an antibiotics cocktail (Ab) 1 or 3 hours after infection is indicated below the scheme and correlates with the rapid decrease in colony forming units (CFUs) after infection. Sample collection times are indicated by: α = 1 h or 3 h (for 1° and 2°) and 7d for (PI), β = 24 h (for 1° and 2°) and 8d (for PI), γ = 48 h (for 1° and 2°) and 9d (for PI). B Principal component analysis of gene expression A549 cells of the UI, PI, 1° and 2° infection at time α (3 h). Principal components calculated on count data after removal of replicate batch effect with ComBat. Samples are colored according to the time point, all replicates (Rep) are shown. C Differential expression analysis. Number of genes significantly (adjusted p value < 0.05) up or downregulated in the 1° or 2° infection in comparison, respectively, to UI and PI cells. Column height indicates the number of genes defined as differentially expressed (DEG) in one or more of the above comparisons. Column color specifies whether the subset of genes is differentially expressed only in the 1° (green) or 2° (purple) infection or in both (green/purple gradient). D Functional scoring analysis. Reactome categories, selected among those significantly enriched (False discovery rate, FDR < 0.05) in the 1° and/or 2° infection in comparison to, respectively, UI and PI cells are indicated by star. Heatmaps represent the intensity of the Normalized Enrichment Score (NES) obtained by the Gene Set Enrichment Analysis (GSEA) for each pathway. Pathways are separated depending on whether they are enriched specifically in the 1° or 2° infection, or in both. Categories of genes with differential gene expression between 1° and 2° infection are in bold. Complete list of pathways corresponding to each category in supplementary table S1. Source Data were deposited into the Gene Expression Omnibus (GEO) repository of the National Center for Biotechnology Information under accession number GSE230142.

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