A needle in a haystack Antigen-specific CD4T cell responses in physiological and pathological contexts

This doctoral thesis investigates antigen-specific CD4 T cell responses and their role in adaptive immunity under both physiological and pathological conditions. The work examines these responses during natural SARS-CoV-2 infection, following vaccination, and under immunosuppressive therapies, while addressing challenges in monitoring low-frequent T cells.
Immune correlates of sustained antibody responses following mild SARS-CoV-2 infection were investigated. Individuals with long-lasting antibodies showed distinct memory B cell profiles, stronger B-T cell interactions, and improved antibody quality, suggesting enhanced germinal center activity. We then assessed how immunosuppressive treatments affect vaccine-induced immunity. Methotrexate therapy led to delayed antibody responses and reduced spike-specific CD4 T cells, indicating impaired T-B cell cooperation. Conversely, patients receiving B cell-depleting therapy failed to produce antibodies but exhibited strong activation of memory CD4 and CD8 T cells, revealing altered immune dynamics in the absence of B cells.
To improve detection of antigen-specific T cells, activation-induced marker (AIM) assays were optimized, demonstrating that multi-marker strategies enhance sensitivity and phenotyping accuracy. Additionally, novel high-valent peptide–MHC class II multimers were developed, enabling direct detection of antigen-specific CD4 T cells with high sensitivity and specificity. Combining these multimers with single-cell transcriptomics, we characterized how B cell depletion reshapes de novo CD4 T cell differentiation, uncovering distinct activation profiles and transcriptional programs in spike-specific CD4 T cells.