Fig. 5: Single-cell RNA sequencing reveals type-I interferon and anti-viral gene expression in antigen presenting cells. | Nature Communications

Fig. 5: Single-cell RNA sequencing reveals type-I interferon and anti-viral gene expression in antigen presenting cells.

From: Antiviral responses induced by Tdap-IPV vaccination are associated with persistent humoral immunity to Bordetella pertussis

Fig. 5

A UMAP visualization of all single-cells (N = 6348 cell across 14 blood samples representing two timepoints (D1 and D0) from N = 7 participants of the Netherlands cohort) colored according to subpopulation with (B) dot plots of protein markers (left panel) and RNA expression profiles of top discriminating genes (right panel). C Upregulated differentially expressed genes (DEGs) 1 day after vaccination are marked with a black border. Expression of DEGs is also shown for other subpopulations if the nominal p < 0.05. Right margin: the number of upregulated DEGs for each subpopulation. Statistical significance was calculated with a negative binomial linear model and false-discovery rate (FDR) adjusted two-sided p values were calculated. Upregulated DEGs were defined as log2 fold change (D1/D0) > 0, FDR < 0.1. D Gene set enrichment analysis (GSEA) was used to calculate the normalized enrichment score (NES) of GO terms for each subpopulation using a list of all genes ranked by the log2-fold change over baseline (D1/D0). Statistical significance and p-values were calculated against an empirical null distribution and reflect two-sided tests. FDR adjusted p values were calculated. Selected GO terms are shown (nominal p < 0.05) and those with FDR < 0.05 are highlighted with a black border. E Correlations of whole blood BTM gene expression (y-axis) with gene expression of each APC subpopulation (x-axis). BTMs that are enriched at D1 in whole blood of the Netherlands cohort are shown on the y-axis (related to Fig. 2B) and are colored according to whether those BTMs are correlated with antibody responses (related to Fig. 3). Heatmap color indicates Pearson’s correlation coefficient. The degree of statistical significance (nominal two-sided p value) is also shown * p < 0.05; ** p < 0.01; *** p < 0.001. BTMs are grouped based on their biological function on the right margin. F Correlations between log2 fold change (D1/D0) of gene expression in whole blood vs classical monocytes for the M75_antiviral IFN signature BTM (N = 22 genes), and (G) correlations between gene expression in whole blood vs classical DC2 for the M150_antiviral IFN signature BTM (N = 12 genes). Genes in each module are labeled with Pearson’s correlation coefficient and nominal two-sided p value. Source data are provided in the Source Data file.

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