Mapping the SARS-CoV-2 spike glycoprotein-derived peptidome presented by HLA class II on dendritic cells. Parker et al

Understanding and eliciting protective immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an urgent priority. To facilitate these objectives, we profile the repertoire of human leukocyte antigen class II (HLA-II)-bound peptides presented by HLA-DR diverse monocyte-derived dendritic cells pulsed with SARS-CoV-2 spike (S) protein. We identify 209 unique HLA-II-bound peptide sequences, many forming nested sets, which map to sites throughout S including glycosylated regions. Comparison of the glycosylation profile of the S protein to that of the HLA-II-bound S peptides reveals substantial trimming of glycan residues on the latter, likely induced during antigen processing. Our data also highlight the receptor-binding motif in S1 as a HLA-DR-binding peptide-rich region and identify S2-derived peptides with potential for targeting by cross-protective vaccine-elicited responses. Results from this study will aid analysis of CD4+ T cell responses in infected individuals and vaccine recipients and have application in next-generation vaccine design. Table S1, relates to Figure 2 and 3: Supplementary data for immunopeptidomic data analysis, providing peptide identification metrics, nested clusters and NetMHCIIpan predictions for all peptides identified by the Peaks search engine for sequences that map to S protein in all donors. Table S2, relates to Figure 3 and 4: Supplementary data for elastase digestion of purified S protein and treatment with PNGnase F in the presence of H2O18, providing site, modification, peptide identification score and occupancy. Table S3, relates to Figure 4: Supplementary data for elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search engine for glycopeptide sequences that map to S protein. Table S4, relates to Figure 4: Supplementary data for immunopeptidomic samples, providing peptide identification metrics, nested clusters and NetMHCIIpan predictions for all peptides identified by Byonic search engine for glycopeptide sequences that map to S protein engine in all donors. Table S5, relates to Figure 6: Supplementary data showing the spike peptides to which CD4+ T cell responses were detected in four recent T cell epitope mapping studies (Mateus et al., 2020), (Tarke et al., 2020), (Peng et al., 2020), (Nelde et al., 2020).