The SARS-CoV-2 pandemic has had unprecedented global impact. To date, there have been over 67 million confirmed infections and 1.5 million deaths worldwide. Diverse outcomes to infection are observed, with asymptomatic presentation and mild illness at one end of the spectrum, and pneumonia-like disease requiring intensive care at the other. Despite recent promising developments in vaccines, our understanding of the immune response to this novel pathogen, including why responses vary so greatly, remains immature.
The cellular immune response relies on cell surface presentation of pathogen-derived peptidic antigens by the Human Leukocyte Antigen (HLA) class I and II molecules (HLA-I and HLA-II) for surveillance by CD8+ and CD4+ T cells, respectively. We have employed an immunopeptidomics workflow to identify naturally processed and presented peptides derived from SARS-CoV-2 in infected airway epithelial cell lines. In brief, post-infection, cells were lysed, and the HLA-I and HLA-II immunoaffinity purified using a pan HLA-I (W6/32) monoclonal antibody (mAb) and a pan HLA-II mAb cocktail (combines anti HLA-DR, anti HLA-DQ and anti HLA-DP). Peptides were acid eluted and analysed by LC-MS/MS.
Our analyses have revealed HLA-I mediated presentation of Spike glycoprotein derived peptides incorporating deamidated asparagine (N) residues, a residual post-translational modification indicative of removal of prior N-linked glycosylation. In contrast, the majority of HLA-II restricted peptides mapped to the nucleoprotein, ORF3a, membrane protein and ORF9b, revealing differences in sampling of the SARS-CoV-2 proteome by the HLA-I and -II antigen processing pathways. Understanding which regions of the virus are responsible for eliciting protective immune responses will have applications in future vaccine design, work to define the correlation between specific T cell responses and infection outcome, and our ultimate understanding of this newly emerged pathogen.