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).深入理解并诱导针对严重急性呼吸综合征冠状病毒2（SARS-CoV-2）的保护性免疫应答是当前的紧迫任务。为达成上述研究目标，本研究对经SARS-CoV-2刺突（S）蛋白脉冲处理的、表达多样HLA-DR亚型的单核细胞衍生树突状细胞所呈递的人类白细胞抗原II类（HLA-II）结合肽库进行了表征分析。本研究共鉴定得到209条独特的HLA-II结合肽序列，其中多数形成嵌套簇集结构，这些肽段可映射至S蛋白的多个区域，包括糖基化修饰区域。通过对比S蛋白与HLA-II结合肽段的糖基化谱型，研究发现后者的聚糖残基发生了显著修剪，该过程极可能在抗原加工阶段被诱导发生。本研究数据同时揭示，S1亚基的受体结合基序是富含HLA-DR结合肽的区域；此外还鉴定出若干源自S2亚基的肽段，有望成为交叉保护性疫苗诱导应答的靶向靶点。本研究成果将有助于解析感染个体与疫苗接种者体内的CD4+ T细胞应答，并可应用于下一代疫苗的研发设计。 表S1 对应图2与图3：免疫肽组学数据分析补充数据集，涵盖所有供体中映射至S蛋白序列的、经Peaks搜索引擎鉴定的肽段的鉴定指标、嵌套簇信息以及NetMHCIIpan预测结果。 表S2 对应图3与图4：纯化S蛋白的弹性蛋白酶消化及在H2O18存在下经PNGnase F处理的补充数据集，提供修饰位点、修饰类型、肽段鉴定得分及修饰占有率信息。 表S3 对应图4：纯化S蛋白弹性蛋白酶消化的补充数据集，涵盖经Byonic搜索引擎鉴定的、映射至S蛋白的糖肽序列的糖肽鉴定指标。 表S4 对应图4：免疫肽组学样本补充数据集，涵盖所有供体中映射至S蛋白的糖肽序列经Byonic搜索引擎鉴定的肽段的鉴定指标、嵌套簇信息以及NetMHCIIpan预测结果。 表S5 对应图6：补充数据集展示了四项近期T细胞表位定位研究（Mateus等，2020；Tarke等，2020；Peng等，2020；Nelde等，2020）中检测到CD4+ T细胞应答的刺突蛋白肽段。