Efficient Targeting and Activation of Antigen-Presenting Cells In Vivo after Modified mRNA Vaccine Administration in Rhesus Macaques

Abstract

mRNA vaccines are rapidly emerging as a powerful platform for infectious diseases because they are well tolerated, immunogenic, and scalable and are built on precise but adaptable antigen design. We show that two immunizations of modified non-replicating mRNA encoding influenza H10 hemagglutinin (HA) and encapsulated in lipid nanoparticles (LNP) induce protective HA inhibition titers and H10-specific CD4⁺ T cell responses after intramuscular or intradermal delivery in rhesus macaques. Administration of LNP/mRNA induced rapid and local infiltration of neutrophils, monocytes, and dendritic cells (DCs) to the site of administration and the draining lymph nodes (LNs). While these cells efficiently internalized LNP, mainly monocytes and DCs translated the mRNA and upregulated key co-stimulatory receptors (CD80 and CD86). This coincided with upregulation of type I IFN-inducible genes, including MX1 and CXCL10. The innate immune activation was transient and resulted in priming of H10-specific CD4⁺ T cells exclusively in the vaccine-draining LNs. Collectively, this demonstrates that mRNA-based vaccines induce type-I IFN-polarized innate immunity and, when combined with antigen production by antigen-presenting cells, lead to generation of potent vaccine-specific responses.

Keywords: antigen-presenting cells; mRNA vaccines; nonhuman primates.

Figure 1

LNP-Encapsulated Modified mRNA Platform Elicit Strong Vaccine Immunity by Distinct Vaccination Routes (A–D) Immunogenicity analysis of rhesus macaques after intradermal (i.d.) or intramuscular (i.m.) immunizations with LNPs containing mRNA encoding hemagglutinin of H10N8 influenza A virus (H10) alone or co-formulated with GLA adjuvant (i.m. + GLA) (n = 4/group). (A) H10-specific hemagglutination inhibition (HAI) titers. Immunizations (arrows) were given at weeks 0 and 4. The i.m. + GLA group was boosted again at week 15. Filled and open circles show mean and individual values, respectively. Dashed lines indicate the threshold for protective titers. (B) Gating strategy of cytokine⁺ total CD4 memory T cells. (C) Percentage of IFNγ⁺ CD4⁺ H10-specific memory T cells. (D) CD4⁺ T cell polyfunctionality as measured by IFNγ (G), IL-2 (2), and TNF (T) expression. Pie slivers in black, gray, and light gray indicate triple, double, or single cytokine⁺ cells, respectively, and arc shows IFNγ⁺ cells. Two-way Anova test with Tukey’s multiple comparison test. *p < 0.05, **p < 0.01, ***p < 0.001.

Figure 2

Rapid Immune Cell Infiltration in Response to LNP/mRNA Administration to Distinct Injection Sites (A–F) Cell suspensions obtained from muscle and skin injected with PBS or indicated formulations at 4 and 24 hr or 9 days post-immunization were used for enumeration of immune cells per gram tissue from the injection sites. (A) Gating of infiltrating live CD45⁺ immune cells in muscle (i.m.) and skin (i.d.) injected with PBS, LNP without mRNA (Empty), or with mRNA content at 4 and 24 hr. (B) Comparison of CD45⁺ immune cell levels in muscle versus skin at 4 or 24 hr after injection of empty LNP (–) or LNP with mRNA cargo (+). (C and D) Characterization of the CD45⁺ mobilized immune cell subsets: (C) CD66abce⁺ neutrophils and (D) CD14⁺ CD16⁻ classical monocytes, CD14⁺ CD16⁺ intermediate monocytes, and CD14⁻ CD16⁺ non-classical monocytes. (E) CD11c⁺ myeloid dendritic cells (DCs) and CD123⁺ plasmacytoid DCs. (F) CD1c (BDCA-1) + or – DCs in muscle and CD1a⁺ or CD209 (DC-SIGN)⁺ APCs in skin at 4 and 24 hr (n = 5/group) and day 9 (n = 2/group). Filled and open circles show the mean and individual values, respectively. *p < 0.05, **p < 0.01; ns, not significant. Wilcoxon signed-rank test.

Figure 3

Gene Expression Analysis of the LNP/mRNA Injection Sites and the Draining LNs (A–E) Gene regulation at the LNP/mRNA vaccine injection sites and in the draining LNs relative to corresponding PBS controls at 24 hr. log₂ fold change (FC) represents log₂ (ratio of the mean expressions at vaccine and PBS sites) (n = 4/group). (A and B) Heatmaps of selected genes at the injection sites (A) and draining LNs (B) that are primarily involved in inflammation, migration, antigen uptake, and presentation. Examples of these genes are in the dashed boxes. (C) The number of selected genes with log₂ (FC) ≥ 2 exclusively or mutually expressed in i.m. and i.d. groups and involved in inflammation (orange), migration (blue), or antigen uptake and presentation (gray). Boxes show upregulated genes only in i.m. or i.d. group. (D and E) log₂ (FC) of specific genes of interest at the vaccine injection sites (D) and in the draining LNs (E) related to the indicated pathways. Gray asterisks are genes involved in IFN signaling, and black asterisks are IFN-inducible genes.

Figure 4

LNP/mRNA Induce Cellular Activation with Type I IFN Response Signature (A–F) Analysis of cellular activation in situ post-immunization and in vitro. (A and B) Type I IFN-inducible MxA expression (red) in LNs draining PBS, LNP/mRNA, or empty LNP injection sites at the indicated time points (A) and the number of MxA⁺ cells per mm² LN area in i.m. and i.d. group combined (B). n = 4/group. Mean ± SEM is shown. DAPI⁺ cell nuclei in blue. Scale bars, 200 μm. (C) Serum CXCL10 (IP-10) prior and 24 hr after immunization (n = 4/group). Bar represents the mean. (D) IFNα production in vitro by rhesus CD123⁺ PDCs stimulated for 16 hr with the indicated conditions. n = 8. Mean ± SEM is shown. (E) Expression of co-stimulatory CD80 at 24 hr on lineage (CD3/CD8/CD20)⁻ HLA-DR⁺ APCs at the injection sites and in the draining LNs. Gray-filled histogram are PBS control sites, and blue (i.m.) and red (i.d.) lines denote LNP/mRNA sites from the same animal. (F) Compiled background (i.e., PBS site) subtracted from the mean fluorescence intensity (MFI) of CD80 on APC subsets at 4 and 24 hr. n = 4/group. Mean ± SEM is shown. *p < 0.05, **p < 0.01, ***p < 0.001, ns (not significant). Wilcoxon signed-rank test.

Figure 5

Efficient LNP Uptake and Vaccine mRNA Translation Coincide with Cellular Activation (A–F) Animals received mRNA-encoding fluorescent mCitrine protein encapsulated in Atto-655-labeled LNP at the indicated time points for analysis of LNP uptake and mCitrine mRNA translation per gram tissue from the injection sites and the draining LNs. (A) Uptake of LNP and translation of the delivered mRNA by lineage⁻ HLA-DR⁺ APCs in suspensions of muscle (i.m.) and skin (i.d.) injection sites and the draining LNs at 4 versus 24 hr post-injection. Empty LNPs indicate unlabeled LNPs without mRNA. (B–D) Compiled data of LNP uptake and mRNA translation by neutrophils (B) and monocyte (C) or DC (D) subsets at 4 or 24 hr (n = 4/group) and day 9 (n = 2/group). Open and closed circles denote mean ± SEM of LNP⁺ and mCitrine⁺ cells, respectively. Asterisks indicate significantly higher mCitrine⁺ subsets compared to the opposing group or cell subset at the same time point. Mann-Whitney test. (E) Proportions of LNP⁺ or mCitrine⁺ cell subsets. Doughnut and pie charts represent the more versus less frequent cell subsets, respectively. (F) CD80 expression on HLA-DR⁺ Lin⁻ APCs according to their LNP uptake (L) and mCitrine mRNA translation (M) as indicted by the quadrant gate. CD80 MFI and the percentage of CD80⁺ of these populations are compiled, and asterisks indicate significant differences compared to the L^– M^– population. n = 4/group. Mean ± SEM is shown. Wilcoxon signed-rank test. *p < 0.05, **p < 0.01.

Figure 6

Priming of H10-Specific CD4⁺ T Cells Is Restricted to Draining LNs (A and B) H10-naive animals received i.m. or i.d. immunizations with LNP with H10 mRNA upon which LNs draining vaccine injection or irrelevant non-vaccine draining LNs were harvested 9 days later for evaluation of H10-specific of CD4⁺ T cell responses. (A) CFSE-labeled suspensions of LNs draining i.m. or i.d. LNP/H10 mRNA injection sites or irrelevant gut draining control LNs at day 9 post-immunization were cultured for 3 days with H10 peptides for CFSE dilution by responding and proliferating H10-specific CD4⁺ T cells. (B) IFNγ production after 6 hr H10 peptide stimulation by H10-specific CD4⁺ T cells in the indicated LN cell suspensions that were cultured for 3 days with H10-peptides (i.e., to allow expansion of H10-specific CD4⁺ T cells) or with media only. n = 2/group. Mean ± SD is shown.