Mass cytometry of early immune remodeling after mRNA booster vaccination reveals exploratory CD4 naive T-cell associations with documented breakthrough infection

Abstract

Messenger RNA (mRNA) vaccines rapidly engage innate and adaptive immunity, but the systemic immune changes occurring within 24 h of vaccination remain incompletely understood. We investigated whether early cellular and global H3K27ac/m6A changes were associated with subsequent documented breakthrough infection (BTI). We performed an exploratory longitudinal systems-immunology analysis of an outcome-balanced subset of 124 participants from a randomized trial of COVID-19 mRNA booster vaccination (62 BTI and 62 non-BTI). Peripheral blood mononuclear cells collected at Day 0 and Day 1 were profiled by high-dimensional mass cytometry. Seventeen major immune-cell populations were assessed for changes in relative abundance, marker profiles, and global H3K27ac/m6A signals. Neutralizing-antibody responses were measured through Day 180. Within 24 h, booster vaccination induced rapid lineage-specific remodeling of circulating immune composition. Classical and intermediate monocytes showed positive shifts in CLR-transformed relative abundance, whereas pDCs, NK cells, and selected CD8 and unconventional T-cell populations showed negative shifts. CD4 T-cell populations remained comparatively stable on this relative-composition scale. Early H3K27ac and m6A changes correlated with abundance changes in selected innate and T-cell populations. Associations with later humoral immunity were limited: after exclusion of antibody measurements obtained on or after documented BTI, no association between early H3K27ac/m6A changes and Day 14 or Day 180 neutralizing-antibody responses remained significant after multiple-testing correction. Major-cell abundance trajectories did not differ significantly by subsequent BTI status. In contrast, BTI was associated with smaller Day 0-to-Day 1 changes in CD4_Tn IFN–Th1 chemokine, cytotoxic–Th1-associated, and CCL2–CCR2-associated marker scores and in the m6A readout. mRNA booster vaccination induces rapid, cell-type-specific immune remodeling within 24 h. Major-cell abundance changes were broadly shared across BTI groups, whereas early CD4_Tn marker-associated and m6A signal changes were associated with subsequent documented BTI. These findings support further evaluation of dynamic early immune states as correlates of heterogeneity in vaccine responses.