Fig. 4
Dynamic deconvolution of immune cell states reveals differences between WT and TLR10 individuals. a Overview of the bulk RNA-seq experiment: isolated PBMCs from blood of eight healthy individuals: WT (green) and TLR10 (purple), were infected ex vivo with Salmonella and bulk RNA-seq was measured before infection (t = 0), 4 (t = 4), and 8 (t = 8) hours post-infection in triplicates. b Box-plots of the relative abundance or infection-induced state of each cell type before and 4 or 8 h post-infection in WT vs. TLR10 uncover significant difference in NKT infection-induced states following infection. The box represents the median and 25–75th percentile, whiskers encompass all data points. *p-value < 0.05, two sample t-test. Values are inferred from bulk measurements using our deconvolution algorithm; estimators of cell-type index are in arbitrary units (au). c Unique molecular identifier (UMI) counts of IFNγ from each cell by scRNA-seq data revealed production of IFNγ exclusively from NKT cells 4 h post-infection; color-coded cell types are indicated at the bottom. d Gene Set Enrichment Analysis (GSEA) of the ‘monocytes infection-induced genes’ in the genes that are higher in WT relative to TLR10 individuals 8 h post-infection (see methods) reveals partition of the gene signature into two sets which imply differences in sub-types activation following infection. Red to blue bar at the bottom represents the gene expression fold change between WT and TLR10 individuals (see also colorbar to the right); the black bars below indicate positions of the ‘monocytes infection-induced genes’ in the ordered list of genes. p-value is calculated by the maximal Enrichment Score (ES), which also defines the group of enriched genes (all genes to the left of the maximal ES position, i.e. the dashed line). e Expression matrix (scRNA-seq data) of the set of ‘monocytes infection-induced genes’ that were enriched in the genes that are higher in WT relative to TLR10 (genes to the left of the dashed line in d). Presented is the mean expression of these genes from each cell sub-type of the naive and exposed monocytes. The left bar represents the mean expression of these genes in each sub-types; monocytes sub-types color-coded as in Fig. 2b
