Exploring CD8⁺ T-Cell Immune Dynamics in SARS-CoV-2 Infection and COVID-19 Vaccine- Induced Responses in Hematological Cancers

Coronavirus disease 2019 (COVID-19), caused by the newly emergent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to significant global morbidity and mortality. The CD8+ T-cell immune response has been suggested to play a critical role in controlling SARS-CoV-2 infection by eliminating virus-infected cells and ensuring lasting protection against the virus. This function becomes even more crucial considering the observed decline in antibody responses a few months after infection. However, due to the novel nature of SARS-CoV-2, the antigen-specific immune response and its impact on both short- and long-term immune response remain inadequately understood. Addressing this gap, this thesis explores several of these areas using state-of-the-art Tcell analysis platforms. It examines the persistence of SARS-CoV-2-specific T-cell responses and their influence on the outcome of COVID-19, investigates vaccine-driven T-cell immunity in immunocompromised patients, as well as the potential influence of pre-existing T-cells on SARS-CoV-2 T-cell immunity.
In Manuscript I, we investigated the dynamics and durability of CD8+ T-cell responses in patients with severe or mild COVID-19 disease by simultaneously tracking 553 immunogenic epitopes from the acute phase of infection up to approximately 220 days post-infection. Using DNA-barcoded peptidemajor histocompatibility complex (pMHC) multimers, cell surface phenotype panel, single-cell analysis, and antigen-specific functional assessment we performed a comprehensive analysis of CD8+ T-cells in a cohort of 73 patients. Our study reveals that SARS-CoV-2-specific CD8+ T-cells are detectable early post-infection and persist throughout the investigated timespan, exhibiting severitydependent frequency and phenotypic profiles. Additionally, single-cell data highlighted a potential functional dysregulation of certain antigen-specific T-cells in severe COVID-19 patients, demonstrating the utility of longitudinal profiling of T-cells on individual antigen level.
We next evaluated the T-cell immunity of COVID-19 vaccines in immunocompromised patients. The current COVID-19 vaccine has elicited robust T-cell responses, contributing to protection against hospitalization and death. However, knowledge about vaccine-induced T-cell immunity in patients with chronic lymphocytic leukemia (CLL) and Myelodysplastic Syndrome (MDS), who typically experience immune deficiencies, is limited. Manuscript II focuses on BNT162b2 COVID-19 mRNA vaccine-induced T-cell immunity in these patients. We mapped the antigen-specific T-cells across the full SARS-CoV-2 spike protein and evaluated the impact of multiple vaccinations on CD8+ T-cell frequency and phenotype in patients and compared with a cohort of vaccinated healthy donors. In patients with CLL and MDS, vaccine-induced, antigen-specific CD8+ T-cell responses were notably present after the first dose of the BNT162b2 mRNA vaccine. Subsequent booster doses significantly enhanced the frequency and number of these T-cell responses. This pattern of immunogenicity, characterized by the emergence of immunodominant epitopes and an enriched immunogenic profile, persisted for at least six months post-vaccination, potentially providing long-term protection against COVID-19 in these high-risk populations.
Additionally, SARS-CoV-2-specific CD8⁺ T-cells have been detected in unexposed individuals to the virus as well as in those exposed but PCR-negative, indicating initial priming against other pathogens that cross-recognize SARS-CoV-2 antigens, especially to human common coronaviruses (HCoVs) with which they share high sequence homology. Building on these findings, we conducted additional experiments to assess CD8⁺ T-cell cross-reactivity between SARS-CoV-2 and HCoV epitopes, potentially elucidating mechanisms of cross-protection and the impact of pre-existing immunity on SARS-CoV-2 infection dynamics.
Together, this thesis focuses on the CD8⁺ T-cell-mediated immune landscape in COVID-19. It highlights the potential impact of the immune response on disease severity, the efficacy of mRNA vaccination in vulnerable populations, and the potential for cross-reactive T-cell responses. These insights are helpful for the development of future vaccine strategies and therapeutic interventions aimed at enhancing immune protection across diverse patient populations.