Abd El-Baky Nawal, Amara Amro A, Redwan Elrashdy M
Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Alexandria P.O. Box 21934, Egypt.
Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah P.O. Box 80203, Saudi Arabia.
Vaccines (Basel). 2023 Feb 25;11(3):548. doi: 10.3390/vaccines11030548.
The adaptive (T-cell-mediated) immune response is a key player in determining the clinical outcome, in addition to neutralizing antibodies, after SARS-CoV-2 infection, as well as supporting the efficacy of vaccines. T cells recognize viral-derived peptides bound to major histocompatibility complexes (MHCs) so that they initiate cell-mediated immunity against SARS-CoV-2 infection or can support developing a high-affinity antibody response. SARS-CoV-2-derived peptides bound to MHCs are characterized via bioinformatics or mass spectrometry on the whole proteome scale, named immunopeptidomics. They can identify potential vaccine targets or therapeutic approaches for SARS-CoV-2 or else may reveal the heterogeneity of clinical outcomes. SARS-CoV-2 epitopes that are naturally processed and presented on the human leukocyte antigen class I (HLA-I) and class II (HLA-II) were identified for immunopeptidomics. Most of the identified SARS-CoV-2 epitopes were canonical and out-of-frame peptides derived from spike and nucleocapsid proteins, followed by membrane proteins, whereby many of which are not caught by existing vaccines and could elicit effective responses of T cells in vivo. This review addresses the detection of SARS-CoV-2 viral epitopes on HLA-I and HLA-II using bioinformatics prediction and mass spectrometry (HLA peptidomics). Profiling the HLA-I and HLA-II peptidomes of SARS-CoV-2 is also detailed.
适应性（T细胞介导的）免疫反应是决定新冠病毒感染后临床结果的关键因素，除了中和抗体外，还对疫苗的效力起支持作用。T细胞识别与主要组织相容性复合体（MHC）结合的病毒衍生肽，从而启动针对新冠病毒感染的细胞介导免疫，或支持产生高亲和力抗体反应。与MHC结合的新冠病毒衍生肽通过生物信息学或全蛋白质组规模的质谱进行表征，即免疫肽组学。它们可以识别新冠病毒的潜在疫苗靶点或治疗方法，否则可能揭示临床结果的异质性。通过免疫肽组学鉴定了在人类白细胞抗原I类（HLA-I）和II类（HLA-II）上自然加工和呈递的新冠病毒表位。大多数鉴定出的新冠病毒表位是源自刺突蛋白和核衣壳蛋白的典型和移码肽，其次是膜蛋白，其中许多未被现有疫苗捕获，并且可以在体内引发T细胞的有效反应。本综述探讨了使用生物信息学预测和质谱（HLA肽组学）检测HLA-I和HLA-II上的新冠病毒病毒表位。还详细介绍了新冠病毒HLA-I和HLA-II肽组的分析。
