A systematic, unbiased mapping of CD8⁺and CD4⁺T cell epitopes in Yellow Fever vaccinees

Abstract

Keywords: Yellow Fever vaccination, immunogenicity, CD4 + and CD8 + T cell epitope discovery, forward-reverse immunology, immunodominance and immunodomination, peptide-MHC tetramers, peptide-MHC predictors. Current word count:≈ 11500 words Comprehensive identification of CD8 + and CD4 + T cell epitopes from Yellow Fever virus AbstractExamining CD8 + and CD4 + T cell responses after primary Yellow Fever vaccination in a cohort of 210 volunteers, we have identified and tetramer-validated 92 CD8 + and 50 CD4 + T cell epitopes, many inducing strong and prevalent (i.e. immunodominant) T cell responses. Restricted by 40 and 14 HLA-class I and II allotypes, respectively, these responses have wide population coverage and might be of considerable academic, diagnostic and therapeutic interest. The broad coverage of epitopes and HLA overcame the otherwise confounding effects of HLA diversity and non-HLA background providing the first evidence of T cell immunodomination in humans. Also, double-staining of CD4 + T cells with tetramers representing the same HLA-binding core, albeit with different flanking regions, demonstrated an extensive diversification of the specificities of many CD4 + T cell responses. We suggest that this could reduce the risk of pathogen escape, and that multi-tetramer staining is required to reveal the true magnitude and diversity of CD4 + T cell responses. Our T cell epitope discovery approach uses a combination of 1) overlapping peptides representing the entire Yellow Fever virus proteome to search for peptides containing CD4 + and/or CD8 + T cell epitopes, 2) predictors of peptide-HLA binding to suggest epitopes and their restricting HLA allotypes, 3) generation of peptide-HLA tetramers to identify T cell epitopes, and 4) analysis of ex vivo T cell responses to validate the same. This approach is systematic, exhaustive, and can be done in any individual of any HLA haplotype. It is all-inclusive in the sense that it includes all protein antigens and peptide epitopes, and encompasses both CD4 + and CD8 + T cell epitopes. It is efficient and, importantly, reduces the false discovery rate. The unbiased nature of the T cell epitope discovery approach presented here should support the refinement of future peptide-HLA class I and II predictors and tetramer technologies, which eventually should cover all HLA class I and II isotypes. We believe that future investigations of emerging pathogens (e.g. SARS-CoV-2) should include population-wide T cell epitope discovery using blood samples from patients, convalescents and/or long-term survivors, who might all hold important information on T cell epitopes and responses.Primary vaccination with the attenuated YFV vaccine, 17D-204, is known to trigger a prompt and vigorous cellular immune reaction (25,26). Here, 210 vaccinees were recruited, and peripheral blood mononuclear cells (PBMC) were prepared from 50-and 200-ml blood samples obtained before and ≈ 2 weeks after primary vaccination, respectively (26). The typical yield from the latter was ≈ 450 million PBMC. A...

Measles-mumps-rubella vaccine at 6 months of age, immunology, and childhood morbidity in a high-income setting: study protocol for a randomized controlled trial

“…In explorative analyses, cellular immunity against measles after early MMR vaccination and again after routine MMR vaccination at 15 months of age is evaluated as activated (interferon gamma producing) T cells recognizing selected measles-epitopes through ELIspot analyses [20]. Maternal antibodies, stress, and pollution have the potential to interfere with the immune response.…”