Bats are a major reservoir of emerging infectious diseases that pose a serious threat to animal and human health. Bats harbour deadly viruses such as Ebola, SARS and Hendra virus (HeV) without clinical signs of disease. Vaccines are not available against many of these viruses and a better understanding of the bat immune system could aid vaccine development. We hypothesise that the bat adaptive immune system contributes to the ability of bats to co-exist asymptomatically with viruses. One of the key adaptive immune responses is the presentation of antigens by major histocompatibility complex (MHC) class I molecules to CD8+ T cells. We sought to understand antigen processing and presentation in bats by characterising the first bat MHC class I molecules using a proteogenomics approach.
We immunoaffinity-purified bat MHC class I molecules and bound proteins and peptide cargo was analysed by LC-MS/MS. We show for the first time that bat MHC class I molecules associate with a peptide-loading complex. Furthermore, we characterised the first endogenous peptide repertoires of three distinct bat MHC class I molecules. These peptides ranged from 8 to 15 amino acid residues and motif analysis revealed strong amino acid biases at various anchor positions. Lastly, we identified HeV-derived peptides from infected bat cells which also displayed similar amino acid biases. We exploited these motifs to predict viral epitopes in silico and 20 novel HeV peptide ligands were confirmed by LC-MRM analysis.
In conclusion, this study describes the functional characterisation of the first bat MHC class I molecules and their respective peptide repertoires. We have also identified the first viral peptides presented by bat MHC class I molecules. Our results provide fundamental insights into the antigen processing and presentation pathways of bats, which ultimately can be used to understand viral control.