Fig. 2: Global and spatially distinct effects of P. berghei on tissue gene expression.

a Differentially expressed genes between P. berghei infected and SGC sections at 12 hpi and 38 hpi. Averaged expression is depicted from low (dark purple) to high (yellow) expression. b Expression of modules showing highest expression in 12 hpi and 38 hpi across tissue spots for infected and SGC sections. The scale bar denotes 500 µm and module values range from low (dark purple) to high values (yellow). c Expression of ISG module expression across spatial clusters. d Immunofluorescence (IF) and Hematoxylin and Eosin-stained (H&E) images of P. berghei infected tissue sections at 12, 24, and 38 h (n = 23). Colored boxes indicate time points (12 hpi = red, 24 hpi = green, 38 hpi = blue). Parasites (UIS4) are highlighted by white circles, scale bars indicate 100 µm and DAPI denotes DNA staining. The position of each parasite is indicated in black on H&E images. The number of sections per time point and average number of parasites per section is shown below. e Loess-smoothed module scores of P. berghei genes with negative correlation (r) to parasite distance. Ribbons around the curve indicate the standard error of the mean (SEM). Colors indicate conditions (12, 24, and 38 hpi) and white circles highlight parasites (UIS4). Module scores on corresponding H&E images show high expression on a scale from low (dark purple) to high (yellow). Scale bars indicate 100 µm. f Gene-ontology (GO) enrichment of top five GO-terms of genes associated with proximity (left) or distance to the parasite (right). g Loess-smoothed gene expression change (Δ) of host genes exhibiting negative correlation to distance to parasite neighborhoods within 400 µm to parasite neighborhoods across time points of infection. Ribbons around the curve indicate the standard error of the mean (SEM). h Change in gene expression (Δ) of host genes that exhibit a positive correlation to parasite neighborhood distances within 400 µm to parasite neighborhoods across time points of infection. Ribbons around the curve indicate the standard error of the mean (SEM).