The characteristics of immunogenic peptide:MHC class I complexes presented during viral infection

Abstract

The presentation of peptide:MHC Class I complexes (p:MHC-I) is a fundamental requirement for CD8+ T cell effector responses, which are important in antiviral immunity. To identify whether a peptide will be immunogenic, a key focus is typically on how a cell processes and presents peptide on MHC-I at sufficient levels to elicit a peptide-specific CD8+ T cell response. However, not all p:MHC-I presented during infection are immunogenic. The features of known epitopes that contribute towards peptide-specific CD8+ T cell responses are not well understood. In particular, although p:MHC-I abundance is assumed to be a key correlate of the magnitude of peptide-specific CD8+ T cell responses, p:MHC-I abundance is rarely directly measured to test this assumption. Moreover, systematic characterisation of p:MHC-I structural features contributing to immunogenicity is limited by the small number of known p:MHC-I identified in a well-established infection model. In this thesis, we use the recent description of a large set of vaccinia virus-derived p:MHC-I known to be presented in a mouse infection model to investigate the general features of defined p:MHC-I associated with immunogenicity. Using mass spectrometry, we directly quantified for the first time the abundance of vaccinia virus-derived p:MHC-I in the spleen of infected mice, which correlated with the magnitude of peptide-specific CD8+ T cell responses. In addition, we used structure prediction and molecular dynamics simulations to model the structural features of p:MHC-I presented during vaccinia virus infection and identify structural correlates of immunogenicity. Finally, using commercially available reagents, we developed a novel, accessible and cell-free assay to measure p:MHC-I affinity and stability that is particularly suited to replace current cell-based peptide loading assays. Show more