Fig. 3: Spatial inflammation in P. berghei infected and SGC sections.

a Pearson correlations between marker genes of spots belonging to periportal in cluster ST1 (blue), acute inflammation in cluster ST3 (yellow), pericentral in cluster ST4 (red), and acute pericentral in cluster ST2 (purple). Positive correlation values are indicated in orange and negative correlation values are indicated in blue. b Gene expression of genes highlighted in (a) as a function of the distance (Loess-smoothed) to the portal vein for marker genes of cluster ST1 and ST3 (top) or the central vein for marker genes of cluster ST2 and ST4. Ribbons around the curve indicate the standard error of the mean (SEM). c Representative H&E (top) and DAPI (bottom) images of Inflammatory hotspots (IHSs) observed in P. berghei infected section 12 hpi (n = 10). IHSs are highlighted with white dotted lines. The scale bar indicates 50 µm. d Change in expression (Δ) of the top four genes with the highest negative correlation as a function of the distance (Loess-smoothed) between 0 and 600 µm from IHSs neighborhoods (Methods for details) where IHSs were present (12, 24, and 38 hpi as well as 24 and 38 h after salivary gland challenge (control)). Ribbons around the curve indicate the standard error of the mean (SEM). e Projection of expression modules of genes in (d) on tissue sections across three conditions with the highest numbers of visually annotated IHSs (12 and 24 hpi as well as 38 h after salivary gland challenge (control)). Module scores are shown as a color gradient from low scores (dark purple) to high scores (yellow). IHSs are highlighted with white dotted lines. View fields measure 500 by 500 µm. The number of sections per time point and the average number of parasites for each section is indicated at the bottom of each time point.