Fig. 6: scRNA-seq analysis of immune cells in the PP in a mouse model of typhoid fever.
From: Salmonella Typhi gut invasion drives hypoxic immune subsets associated with disease outcomes
a, b tSNE visualization of scRNA-seq data from naïve and infected PP at 72 hpi. Cells are colored by infection status (naïve or infected) in (a), and by cell clusters in (b), with cluster annotations indicating cell types. c Comparison of cell-type composition between naïve and infected PP shows macrophage (Mϕ) infiltration and a reduction in Germinal center (GC) B cells in infected PP. Colors correspond to clusters in (b), with cell-type annotations shown in the legend on the right. d Dot plot showing expression levels of marker genes across clusters for each cell type. The size of each dot represents the percentage of cells in a cluster expressing a given gene, and the color indicates relative expression levels (legend on the right). e Dot plot showing expression levels of the six-gene hypoxia signature in immune cells from the PP of infected mice. f, g Analysis of public bulk RNA-seq data from the PP of naïve and Yersinia pseudotuberculosis-infected mice (72 hpi)23. f PCA projection based on the two leading principal components, showing separation between PP of naïve and Yersinia infected mice. g GSEA comparing gene expression in Yersinia infected versus naïve PP identifies up-regulated (right) and down-regulated (left) pathways. The hypoxia pathway is highlighted and significantly up-regulated in Yersinia-infected PP relative to naïve PP.
