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. 2022 Nov 22;7(22):e163347.
doi: 10.1172/jci.insight.163347.

Consecutive BNT162b2 mRNA vaccination induces short-term epigenetic memory in innate immune cells

Affiliations

Consecutive BNT162b2 mRNA vaccination induces short-term epigenetic memory in innate immune cells

Yuta Yamaguchi et al. JCI Insight. .

Abstract

Consecutive mRNA vaccinations against SARS-CoV-2 reinforced both innate and adaptive immune responses. However, it remains unclear whether the enhanced innate immune responses are mediated by epigenetic regulation and, if so, whether these effects persist. Using mass cytometry, RNA-Seq, and ATAC-Seq, we show that BNT162b2 mRNA vaccination upregulated antiviral and IFN-stimulated gene expression in monocytes with greater effects after the second vaccination than those after the first vaccination. Transcription factor-binding motif analysis also revealed enriched IFN regulatory factors and PU.1 motifs in accessible chromatin regions. Importantly, although consecutive BNT162b2 mRNA vaccinations boosted innate immune responses and caused epigenetic changes in isolated monocytes, we show that these effects occurred only transiently and disappeared 4 weeks after the second vaccination. Furthermore, single-cell RNA-Seq analysis revealed that a similar gene signature was impaired in the monocytes of unvaccinated patients with COVID-19 with acute respiratory distress syndrome. These results reinforce the importance of the innate immune response in the determination of COVID-19 severity but indicate that, unlike adaptive immunity, innate immunity is not unexpectedly sustained even after consecutive vaccination. This study, which focuses on innate immune memory, may provide novel insights into the vaccine development against infectious diseases.

Keywords: COVID-19; Cellular immune response; Epigenetics; Innate immunity; Vaccines.

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Conflict of interest statement

Conflict of interest: The authors have declared that no conflict of interest exists.

Figures

Figure 1
Figure 1. BNT162b2 vaccine alters the innate immune response in monocytes after the first immunization.
(A) Study design and overview of the experiments. Healthy donors (n = 11) enrolled in this study received 2 doses of the BNT162b2 (30 μg/dose) vaccine at 3-week intervals. Blood samples were collected before (D0) and D1, D10, D20, D22, D31, and D49 days after the first vaccination. (B and C) Changes over time in the percentage of monocytes among PBMCs (B) and in the expression of IFNα/β-R2 on cMono, intMono, and ncMono (C). (D) Schematic overview of the RNA-Seq experiment performed using monocytes isolated from PBMCs collected from healthy individuals (n = 4) before and after vaccination (D0, D1, D20, and D22). (E) Numbers of DEGs in isolated monocytes on D1 and D22 compared with D0 and D20 (|log2 fold change| > 1 and Padj < 0.05). (F) Gene Ontology (GO) enrichment analysis of upregulated DEGs in isolated monocytes after BNT162b2 vaccination. All the significantly enriched terms are listed (Padj < 0.05). Left, comparison before (D0) and after (D1) the first vaccination; right, comparison before (D20) and after (D22) the second vaccination. The x axis shows number of genes included in each pathway. The dot color and size represent the statistical significance and the ratio of genes enriched in the pathway to the total enriched genes, respectively. GeneRatio shows the ratio of the number of genes included in each pathway to the total number of upregulated DEGs. WBCs, white blood cells; cMono, classical monocytes; intMono, intermediate monocytes; ncMono, nonclassical monocytes. Statistical analysis was performed using a repeated-measures 1-way ANOVA with a Greenhouse-Geisser correction and a Bonferroni post hoc test (B and C).
Figure 2
Figure 2. Epigenomic changes in monocytes regulate the innate immune responses to the BNT162b2 mRNA vaccine.
(A) Schematic overview of the ATAC-Seq experiment of monocytes magnetically separated from PBMCs collected from healthy individuals before (D0, n = 5) and after (D1 and D22, n = 4; D20 and D49, n = 5) vaccination. All 4 individuals included in the RNA-Seq analysis (in Figure 1) were included in the ATAC-Seq analysis. (B) Numbers of differentially accessible chromatin regions (DARs) (|log2 fold change| > 1 and P < 0.05) in isolated monocytes on D1, D20, D22, and D49 compared with those on D0 were identified using edgeR (n = 5 per group). (C) Heatmap of Z scores of the normalized read counts identified by ATAC-Seq of isolated monocytes on D0, D1, D20, D22, and D49. Annotated genes were related to the innate immune responses among the nearest genes in each cluster. (D) Enrichment analysis of the nearest genes detected in cluster 1 as conducted with Metascape (http://metascape.org). The top 20 significantly enriched terms are listed (P < 0.05). Innate immune response terms are marked in red. (E) PPI network analysis among the nearest genes in cluster 1 using molecular complex detection algorithm as conducted with Metascape (http://metascape.org). The components of each molecular complex detection (MCODE) are listed in Supplemental Figure 5B. (F) Changes in normalized peak counts nearest antiviral and IFN-stimulated genes identified by ATAC-Seq of isolated monocytes. Fold changes are represented compared with D0. (G) Enriched known motifs identified using hypergeometric optimization of motif enrichment (HOMER) among enhanced chromatin accessibility regions on D1, D20, D22, and D49 compared with those on D0. TF, transcription factor.
Figure 3
Figure 3. Dynamic changes in innate immune responses in monocytes after induction by the BNT162b2 mRNA vaccine.
(A) Overview of the experiments. Restimulation of monocytes isolated from PBMCs on D0, D20, and D49 with R848 for 6 or 24 hours (n =4 per group). All 4 individuals included in the ATAC-Seq analysis (in Figure 2) were included in the restimulation experiment. R848 is a ligand for TLR7 and TLR8, which mimics single-stranded RNA viral pathogens. (B) Concentrations of type I IFNs (IFN-α2 and IFN-β) in the culture supernatant after stimulation of isolated monocytes with R848 (100 ng/mL) for 24 hours (D0, D20, and D49; n = 4 per group). Type I IFN levels were measured by a bead-based immunoassay. Each dot represents an individual. (C) Antiviral and IFN-stimulated gene (APOBEC3A, IFITM1, ISG15, GBP5, TNFSF10, and WARS) expression levels were quantified by qPCR before and after stimulation of isolated monocytes with R848 (100 ng/mL) for 6 and 24 hours (n = 4 per group). The gene expression levels were normalized to those of GAPDH. Each dot represents an individual. ISGs, IFN-stimulated genes.
Figure 4
Figure 4. The strong relationship between the genes upregulated by vaccination and those downregulated during severe COVID-19.
(A) Overview of scRNA-Seq experiment on PBMCs from patients with COVID-19 with and without ARDS (n = 8 per group) and from healthy donors (n = 5). No participants were vaccinated against SARS-CoV-2 infection. (B) DEGs in monocytes identified by scRNA-Seq analysis of patients with COVID-19 with and without ARDS. Selected ISGs are annotated. (C) Circos plot of the overlapping genes among DEGs in monocytes detected for the BNT162b2 mRNA vaccine cohort and the unvaccinated COVID-19 cohort (Padj < 0.05). In the vaccine cohort, DEGs detected at D1 and D22 relative to D0 and D20, respectively, were analyzed. In the COVID-19 cohort, DEGs detected in monocytes of ARDS patients compared with non-ARDS patients were analyzed. Each segment of the outer circle represents a monocyte subclass (Pan Mono, pan monocytes; cMono, classical monocytes; intMono, intermediate monocytes; or ncMono, nonclassical monocytes) and gene expression pattern (upregulated or downregulated). The inner circle colored in red (upregulated genes) and blue (downregulated genes) represents the genes that are shared by multiple segments, and the gray circle represents genes that are unique to that segment. On the inside, each arc represents a gene list. The arcs linking the Pan Mono segment with the cMono, intMono, or ncMono segment are colored. (D, E, and F) Scatter plots showing the overlapping genes identified by Circos plot. The y axis represents DEGs in cMono (D), intMono (E), and ncMono (F) in the COVID-19 cohort (non-ARDS versus ARDS). The x axis represents DEGs in pan monocytes in the vaccine cohort (D20 versus D22). Genes with significantly changed expression are marked in red (|log2 fold change| > 1 and Padj < 0.05 in both analyses). ARDS, acute respiratory distress syndrome; cMono, classical monocytes; intMono, intermediate monocytes; ncMono, nonclassical monocytes.

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