Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs

Supplemental Tables related to the manuscript entitled: Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs Summary: T cell-mediated immunity plays an important role in controlling SARS-CoV-2 infection; yet the repertoire of naturally processed and presented viral epitopes on HLA class I remains uncharacterized. Here, we report the first HLA-I immunopeptidome of SARS-CoV-2 in two cell lines at different times post-infection using mass spectrometry. We found HLA-I peptides derived not only from canonical ORFs, but also from internal out-of-frame ORFs in Spike and Nucleocapsid not captured by current vaccines. Some peptides from out-of-frame ORFs elicited T cell responses in a humanized mouse model and COVID-19 patients that exceeded responses to canonical peptides including some of the strongest epitopes reported to date. Whole proteome analysis of infected cells revealed that early expressed viral proteins contribute more to HLA-I presentation and immunogenicity. These biological insights as well as the discovery of out-of-frame ORF epitopes will facilitate selection of peptides for immune monitoring and vaccine development.

与题为《分析严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）HLA-I类肽组揭示来自读码框外开放阅读框的T细胞表位》的论文相关的补充表格。摘要：T细胞介导的免疫在控制严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）感染中发挥关键作用，但目前仍未明确人类白细胞抗原I类（HLA-I）分子上天然加工呈递的病毒表位库。本研究利用质谱技术，首次在感染后不同时间点的两种细胞系中解析了SARS-CoV-2的HLA-I类免疫肽组。研究发现，HLA-I类肽段不仅源自经典开放阅读框（ORF），还来自刺突蛋白（Spike）和核衣壳蛋白（Nucleocapsid）内部的读码框外ORF，而当前疫苗并未涵盖这些序列。部分读码框外ORF来源的肽段在人源化小鼠模型和新型冠状病毒肺炎（COVID-19）患者体内诱导的T细胞反应，甚至强于经典肽段的反应，其中包括目前已报道的部分最强效表位。对感染细胞的全蛋白质组分析显示，早期表达的病毒蛋白对HLA-I类分子呈递及免疫原性的贡献更大。上述生物学见解以及读码框外ORF表位的发现，将为筛选用于免疫监测和疫苗开发的肽段提供助力。