The antibody response induced FMDV vaccines in sheep correlates with early transcriptomic responses in blood

Fig. 1. Humoral responses induced by iFMDV, Ad5-FMDV, and Ad5-FMDV+ISA206VG vaccine in sheep. a Experimental design: Three groups of 10 sheep each were immunized with iFDMV (intramuscular route), or Ad5-FMDV with or without ISA206VG (half intramuscular and half subcutaneous route). Blood was collected on PAXgene® Blood RNA tubes at T0H, T4H, and T24H and processed to RNA-seq. Sera were collected at T0H and every 2 weeks for 365 days. b The mean percent inhibition values provided by the PrioCHECK ELISA in each group at each time point are plotted over time (365 days), and the standard errors of the mean are shown above the mean (10 sheep per group). Differences between the areas under the curve over time of the three groups are statistically significant (p < 0.001, Wilcoxon test). The doubtful and positivity thresholds (42% and 58% respectively) are shown with a dashed line. c The mean VNT titer per group are plotted over time and the s.e.m. are shown above the mean. Differences between the areas under the curve of the iFMDV group and the other groups are statistically significant (p < 0.005, Wilcoxon test). The differences between the areas under the curve of the Ad5-FMDV and…

Fig. 2. Humoral responses induced by the iFMDV vaccine in sheep individuals. The percent inhibition values obtained with the PrioCHECK and SPCE tests (linear scale) and the VNT titers (inverse of dilutions, log2 scale) are reported over time (D0 to D365) for each sheep, identified with its number. The doubtful and positive thresholds are indicated by dashed lines as in Fig. 1. Sheep were qualified positive responders and represented in red plots when the test values were considered positive in at least 30% of the time points, which is the case in all sheep vaccinated with iFMDV.

Fig. 3. Humoral responses induced by the Ad5-FMDV vaccine in sheep individuals. The percent inhibition values obtained with the PrioCHECK and SPCE tests (linear scale) and the VNT titers (inverse of dilutions, log2 scale) are reported over time (D0 to D365) for each sheep, identified with its number. The doubtful and positive thresholds are indicated by dashed lines as in Fig. 1. Sheep were qualified positive responders and represented in red plots when the test values were considered positive in at least 30% of the time points. Sheep were qualified negative responders and represented in blue plots when the test values were considered negative (below the doubtful threshold) in at least 80% of the time points. They were qualified ambiguous in all other cases and represented in orange.

Fig. 4. Humoral responses induced by Ad5-FMDV+ISA206VG vaccine in sheep individuals. The percent inhibition values obtained with the PrioCHECK and SPCE tests and the VNT titers (inverse of dilutions, log2 scale) are reported over time (D0 to D365) for each sheep, identified with its number. The doubtful and positive thresholds are indicated by dashed lines as in Fig. 1. Sheep were qualified positive responders and represented in red plots when the test values were considered positive in at least 30% of the time points. Sheep were qualified negative responders and represented in blue plots when the test values were considered negative (below the doubtful threshold) in at least 80% of the time points. They were qualified ambiguous in all other cases and represented in orange.

Fig. 5. Modulated BTMs in sheep blood at T24H vs. T0H. Enriched BTMs were identified from the ranked list of the differentially expressed genes between T24H and T0H in sheep blood post-vaccination. The enrichment p values are represented by graded red (upregulated BTMs) and by graded blue (downmodulated BTMs). BTMs are grouped in functional families (cell cycle (1), mononuclear phagocytes (2), antiviral response (3), inflammation (4), neutrophils (5), immune response (6), B cell (7), cell metabolism (8)).The lists of the enriched BMTs and their statistical values are provided in Supplementary Data Set 2 (iFMDV), Supplementary Data Set 3 (Ad5-FMDV), Supplementary Data Set 4 (Ad5-FMDV+ISA206VG).

Fig. 6. Transcriptomic signatures of the Ab response magnitude induced by the iFMDV vaccine. A PLS algorithm was used to retrieve the genes with fold changes (T24H vs. T0H) related to the VNT area under the curve. The ranked gene list of the first PLS component was processed through a GSEA to identify enriched BTMs (nominal p value of the GSEA < 0.05, FDR < 0.25). The gene fold changes contributing to each BTM were computed into a single activity score and a Spearman correlation test with VNT was performed across the 10 sheep (p < 0.05). a The BTMs positively correlating with the Ab response magnitude are in graded red according to the Spearman rho coefficient, and the negatively correlating ones are in graded blue. The BTMs are grouped in functional families (T cell (1), cell cycle (2), inflammation (3), Chaperonin-mediated folding (4), metabolism (5)). b The fold changes of genes contributing to the selected BTM (y-axis) are represented in a violin plot for each sheep which are ordered (x-axis) according to their VNT area under the curve values (sheep 828, 730, 862,014, 001, 658, 022, 726, 836, 989). Each sheep was attributed a color within a progressive gradient with red in the…

Fig. 7. Transcriptomic signatures of the Ab response magnitude induced by the Ad5-FMDV vaccine. A PLS algorithm was used to retrieve the genes with fold changes (T24H vs. T0H) related to the PrioCHECK area under the curve. The ranked gene list of the first PLS component was processed through a GSEA to identify enriched BTMs (nominal p value of the GSEA < 0.05, FDR < 0.25). The gene fold changes contributing to each BTM were computed into a single activity score and a Spearman correlation test to VNT was performed across the 10 sheep (p < 0.05). a The BTMs negatively correlating with the Ab response are in graded blue. The BTMs are grouped in functional families (cell migration (1), inflammation (2), cell cycle (3)). b The fold changes of genes contributing to the selected BTM (y-axis) are represented in a violin plot for each sheep which are ordered (x-axis) according to their PrioCHECK area under the curve values (sheep 930, 610, 851, 797, 661, 942, 000, 613, 771, 597). Each sheep was attributed a color within a progressive gradient with red in the maximal responder and blue in the lowest responder (see Fig. 3). Six modulated BTMs, selected on their biological meaning, are illustrated.…

Fig. 8. Transcriptomic signatures of the Ab response magnitude induced by the Ad5-FMDV+ISA206VG vaccine. A PLS algorithm was used to retrieve the genes with fold changes (T24H vs. T0H) related to the PrioCHECK area under the curve. The ranked gene list of the first PLS component was processed through a GSEA to identify enriched BTMs (nominal p value of the GSEA < 0.05, p < 0.25). The gene fold changes contributing to each BTM were computed into a single activity score and a Spearman correlation test to VNT was performed across the 10 sheep (p < 0.05). a The BTMs positively correlating with the Ab response magnitude are in graded red according to the Spearman rho coefficient, and the negatively correlating ones are in graded blue. The BTMs are grouped in functional families (T cell (1), B cell (2), neutrophils (3)). b The fold changes of genes contributing to the selected BTM (y-axis) are represented in a violin plot for each sheep which are ordered (x-axis) according to their PrioCHECK area under the curve values (720, 772, 021, 757, 662, 673, 743, 796, 751, 024). Each sheep was attributed a color, red in the maximal responders, yellow in intermediate responders, and blue in the lower…