Characterisation of novel influenza-derived HLA-B*18:01-restricted epitopes

Seasonal influenza viruses cause roughly 650 000 deaths annually despite available vaccines. CD8⁺ T cells typically recognise influenza-derived peptides from internal structural and non-structural influenza proteins and are an attractive avenue for future vaccine design as they could reduce the severity of disease following infection with diverse influenza strains. CD8⁺ T cells recognise peptides presented by the highly polymorphic Human Leukocyte Antigens class I molecules (HLA-I). Each HLA-I variant has distinct peptide binding preferences, representing a significant obstacle for designing vaccines that elicit CD8⁺ T cell responses across broad populations. Consequently, the rational design of a CD8⁺ T cell-mediated vaccine would require the identification of highly immunogenic peptides restricted to a range of different HLA molecules.

Here, we assessed the immunogenicity of six recently published novel influenza-derived peptides identified by mass-spectrometry and predicted to bind to the prevalent HLA-B*18:01 molecule.

Using CD8⁺ T cell activation assays and protein biochemistry, we showed that 3/6 of the novel peptides were immunogenic in several HLA-B*18:01⁺ individuals and confirmed their HLA-B*18:01 restriction. We subsequently compared CD8⁺ T cell responses towards the previously identified highly immunogenic HLA-B*18:01-restricted NP₂₁₉ peptide. Using X-ray crystallography, we solved the first crystal structures of HLA-B*18:01 presenting immunogenic influenza-derived peptides. Finally, we dissected the first TCR repertoires specific for HLA-B*18:01 restricted pathogen-derived peptides, identifying private and restricted repertoires against each of the four peptides.

Overall the characterisation of these novel immunogenic peptides provides additional HLA-B*18:01-restricted vaccine targets derived from the Matrix protein 1 and potentially the non-structural protein and the RNA polymerase catalytic subunit of influenza viruses.