Fig. 7: VAED kinetic study: expression of selected genes and Th-2 skewing in lungs of infected hamsters.

Digital nCounter technology was used to survey expression patterns of n = 128 genes associated with either Th1, Th2, Th17 and Treg pathways or with different immune cells populations. a Principal component analysis based on ln(x)-transformed normalized count values obtained for all profiled genes in hamster lungs. Unit variance scaling was applied to rows and singular value decomposition with imputation was used to calculate principal components 1 (PC1) and 2 (PC2), which are plotted on the X and Y axis and explain 32.9% and 28.9% of the variance in the dataset, respectively. Colors indicate the different necropsy days and symbols represent different treatment groups. The ellipses in green are only for visualization purposes. b Immune response patterns on Th-pathway level. Pathway scores related to the indicated 4 different T cell subsets were plotted over time. Symbols represent individual scores, and the lines shows the group means; n = 3 per group per timepoint. Level of significance is illustrated with asterisks for the following p values: 0.01 to 0.05 - *; 0.001 to 0.01 - **; 0.0001 to 0.001 - ***; <0.0001 - ****. DPI days post challenge infection. c Differentially expressed genes on at least one of the necropsy days (p < 0.05; no fold change cut-off; n = 3 per group and DPI) when comparing vaccinated vs. mock-vaccinated AND vaccinated vs. re-challenge groups. n = 37 genes fulfilled these criteria: n = 28 were upregulated (upper cluster) and n = 9 were downregulated (lower cluster) in association with the vaccination. For any given gene, brown indicates higher expression relative to all samples’ average and blue indicates lower expression (difference of ±1 = values are one SD away from the average of the row). Note that expression levels can only be compared within a row (i.e. per gene across samples), not between different rows. The numbers in column “DPI” indicate the day(s), when a specific gene was significantly upregulated, as compared to both the mock-vaccinated and re-challenge group. Genes associated with Th2 pathway are shown in pink, genes associated with Th1 pathway are shown in green, and immune cells are highlighted with blue.