Quantitative and qualitative features of adaptive immune responses after SARS-CoV-2 mRNA vaccination

Vaccination is one of the greatest achievements in global health, a fact underscored once again during the SARS-CoV-2 pandemic. Among the vaccines developed to combat this pandemic, the mRNA-based vaccine BNT162b2 (Comirnaty®) played a central role in the global vaccination campaign. While prior studies have extensively characterized the antibody immune response elicited by mRNA vaccines, a comprehensive understanding of the quality of the immune response, especially with regard to T cell responses, has been lacking. Such insights are essential for evaluating vaccine immunogenicity and advancing next-generation vaccine technologies, including mRNA-based platforms. Furthermore, the effectiveness of Comirnaty® became increasingly important in heterologous vaccination regimens due to reports of thromboembolic events after application of the adenoviral vector-based vaccine Vaxzevria®. Beyond its medical significance, the global vaccination effort also provided a unique opportunity to study systematically de novo adaptive immune responses in humans before and after repeated antigen exposures. This thesis aimed to provide an in-depth characterization of the immunogenicity of mRNA-based vaccines across different vaccination regimens, with a particular focus on the quality and longitudinal dynamics of humoral and T cell immune responses. To achieve this, we established the longitudinal cohort ‘CoVa-Adapt,’ consisting of 29 healthcare workers who received three doses of the mRNA vaccine Comirnaty®. Additionally, we analyzed further cohorts of healthy individuals with different homologous or heterologous vaccination regimens at selected time points post-vaccination. Peripheral blood mononuclear cells (PBMCs) and serum were isolated in our lab for subsequent analyses of vaccine-induced immunity. While the groups of Matthias Tenbusch and Thomas Winkler conducted an in-depth assessment of the humoral immune response, we focused on characterizing the T cell response. We evaluated the magnitude, cytokine expression profile, and proliferative potential of spike-specific T cells through in vitro re-stimulation using ELISpot and flow cytometry, including peptide-human leukocyte antigen (pHLA) multimers. To provide a more comprehensive characterization, we examined the phenotype and clonal composition of the CD8+ T cell response across 16 epitope specificities using single-cell RNA sequencing, T cell receptor (TCR) sequencing, and surface protein (CITE) sequencing. Finally, to assess functionality, we re-expressed 106 TCRs from five epitope-specific repertoires and evaluated their peptide sensitivity as well as their cross-reactivity to altered peptide ligands (APLs). We first identified the mRNA-based vaccine Comirnaty® as highly immunogenic in heterologous prime-boost regimens following adenoviral vector-based primary vaccination. The induced humoral immune response was non-inferior and, in some aspects, superior to homologous vaccination regimens. Additionally, across all vaccination strategies, polyfunctional spike-specific T cells were induced and maintained long-term (Publication 1). Using the longitudinal cohort CoVa-Adapt, we further identified the induction of IgG4 antibodies following repeated mRNA immunizations, a phenomenon unique to homologous mRNA vaccine regimens. This shift was associated with a significant reduction in Fc-mediated effector functions, including antibody-dependent cellular phagocytosis and complement deposition (Publication 2). To further explore the effects of repeated immunization, we analyzed, in a unique case study, a hypervaccinated individual from Magdeburg (HIM), who voluntarily, outside of a clinical study context, received 217 SARS-CoV-2 vaccinations. This extraordinary case demonstrated a substantial quantitative increase in adaptive immune responses compared to the standard three-dose mRNA vaccination regimen. However, despite these quantitative changes, the quality of the immune response remained largely unchanged. For instance, specific T cells preserved their proliferative potential, polyfunctionality, and peptide sensitivity, comparable to controls (Publication 3). Lastly, within the CoVa-Adapt cohort, the three-dose mRNA vaccination regimen elicited a prominent T cell response, with selected epitopes emerging as immunodominant. At acute time points (10 days post-vaccination), T cells specific for these epitopes exhibited a common activation and cycling gene signature, prominently featuring genes of a type-I interferon response. Clonotype analysis revealed the recruitment of highly functional TCR repertoires post-vaccination, exceeding an initial avidity threshold. Notably, there was no predominance of T cell clones with maximal TCR avidity. Instead, spike-specific T cell repertoires remained polyclonal, ensuring robust protection against potential mutational escape (Publication 4). Overall, this thesis underscores the importance of a detailed characterization of the immune response quality following vaccination, revealing previously unrecognized immunological outcomes of repeated mRNA vaccinations. It further highlights T cell functionality and polyclonality as critical yet underrepresented dimensions of vaccine-induced immune quality. These findings have the potential to extend beyond SARS-CoV-2 given the expanding role of mRNA vaccine technology in combating diverse pathogens and advancing personalized therapies.