Robust immune response to the BNT162b mRNA vaccine in an elderly population vaccinated 15 months after recovery from COVID-19

Figures

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  Figure 1.. Experimental design. a-c. Schematic presentation of the experimental workflow. (a) elderly population recovered from COVID-19; (b) SARS-CoV-2 antigen-naïve population; the syringes indicate vaccinations; the test tubes indicate the blood drawing and the triangles the antibody testing. The asterisks indicate the days at which samples for RNA-seq was collected. (c) Peripheral blood mononuclear cells (PBMCs) were purified from blood drawn prior to and after the vaccination and RNA-seq was performed at a depth of 240 million reads per sample. d. Age distribution of participants in each cohort.

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  Figure 2.. Serum cytokine, chemokine and antibody levels. a-b. Volcano plots depict differentially expressed cytokines and chemokine between days 0, 1 and 7 at the 1st vaccination of the COVID-19 recovered cohort (a) and the 2nd vaccination of the SARS-CoV-2 naïve cohort (b). Red dots indicate significant upregulation; blue dots indicate significant downregulation (p-value < 0.05). See also Supplementary Figure 1 and Supplementary Tables 2. c-d. Cytokine and chemokine concentrations in serum prior to and post vaccination (pg/ml) of CXCL10 and IFN-γ. Boxes show median, 25th and 75th percentiles and whiskers show the range. p-value are from 2-way ANOVA with Tukey’s multiple comparisons test and Two-stage linear step-up procedure of Benjamini, Krieger and Yekutieli method and listed in Supplementary Table 2. *p < 0.05, ***p < 0.0001, ****p < 0.00001. e-f. IgG anti-Spike-RBD levels in the COVID-19 recovered (e) and SARS-CoV-2 antigen-naïve group (f). p-value are from 1-way ANOVA with Tukey’s multiple comparisons test. ****p < 0.00001. Vaccination of the COVID-19 recovered cohort occurred immediately after collecting blood for antibody measurements (15 months).

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  Figure 3.. Characteristics of immune transcriptome for vaccination. Principal-component analysis (PCA) of transcriptomes generated prior to (day 0) and after the vaccination (days 1 and 7) from COVID-19 recovered individuals. The variation in the global gene expression profiles across the three time points is shown. Principal components 1 (PC1) and 2 (PC2), which represent the greatest variation in gene expression, are shown. b. Volcano plots of DEGs comparing Day1 versus Day0, Day7 vs Day0 and Day7 vs Day1 in the COVID-19 recovered cohort. DEGs (adjusted p-value, P.adj < 0.05) with a log2 fold change (FC) of more than 1 or less than −1 are indicated in red and blue, respectively. Non-significant DEGs are indicated in gray. The numbers of upregulated and downregulated genes are listed in Supplementary Tables 4–6. c. PCA of transcriptomes from the SARS-CoV-2 antigen-naïve cohort prior to (day0) and day1 and day7 after the second (booster) vaccination. d. Volcano plot of DEGs comparing Day1 versus Day0, Day7 vs Day0 and Day7 vs Day1 in SARS-CoV-2 naïve cohort. The numbers of upregulated and downregulated genes are listed in Supplementary Tables 7–9. Volcano plots depict differentially…

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  Figure 4.. Comparison of immune transcriptomes between COVID-19 recovered and SARS-CoV-2 naïve cohorts after receiving the BNT162b booster. a. Heatmaps showing log2 FC (top, red) and corresponding P.adj (bottom, ocher) of significantly upregulated genes between Day0 and Day1 in COVID-19 recovered (left) and SARS-CoV-2 naïve (right) cohorts. The genes specifically activated between day0 and day1 and still induced by day7 are listed in Supplementary Table 11–12. b. Venn diagram displays the number of significantly induced genes between Day0 and Day1 in both cohorts. The genes in each part are listed in Supplementary Table 13 and their GSEA analysis is in Supplementary Figure 4. c. Heatmaps showing log2 FC (top) and corresponding P.adj (bottom) of genes significantly activated at day7 in COVID-19 recovered (left) and SARS-CoV-2 naïve (right) cohorts. The genes induced between day0 and day7 fall into different categories based on their activation pattern (Supplementary Table 11–12). Group A, genes whose activation progresses between day0 and day7; Group B, genes highly activated preferentially between day0 and day1; Group C, genes highly activated between day1 and day7. d. Genes categorized in…