CD8+ T cell epitope variations suggest a potential antigen presentation deficiency for spike protein of SARS-CoV-2
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Abstract
COVID-19 is caused by a newly identified coronavirus, SARS-CoV-2, and has become a pandemic around the world. The illustration of the immune responses against SARS-CoV-2 is urgently needed for understanding the pathogenesis of the disease and its vaccine development. CD8+ T cells are critical for virus clearance and induce long lasting protection in the host. Here we identified specific HLA-A2 restricted T cell epitopes in the spike protein of SARS-CoV-2. Seven epitope peptides (n-Sp1, 2, 6, 7, 11, 13, 14) were confirmed to bind with HLA-A2 and potentially be presented by antigen presenting cells to induce host immune responses. Tetramers containing these peptides could interact with specific CD8+ T cells from convalescent COVID-19 patients, and one dominant epitope (n-Sp1) was defined. In addition, these epitopes could activate and generate epitope-specific T cells in vitro , and those activated T cells showed cytotoxicity to target cells. Meanwhile, all these epitopes exhibited high frequency of variations. Among them, n-Sp1 epitope variation 5L>F significantly decreased the proportion of specific T cell activation; n-Sp1 epitope 8L>V variant showed significantly reduced binding to HLA-A2 and decreased the proportion of n-Sp1-specific CD8+ T cell, which potentially contributes to the immune escape of SAR-CoV-2.
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SciScore for 10.1101/2021.01.22.427863: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Human subject enrollment: The Institutional Review Board of the Affiliated Huaqiao Hospital of Jinan University approved this study.
Consent: All subjects provided informed consent at the time of enrollment that their samples could be used for this study.Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Antibodies Sentences Resources Briefly, 106 PBMC were stained with FITC anti-human HLA-A2 antibody at 4 °C in the dark for 30 min, and acquired by using flow cytometer. anti-human HLA-A2suggested: NoneHLA-A2 positive PBMC samples were further stained with PE labelled tetramer … SciScore for 10.1101/2021.01.22.427863: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Human subject enrollment: The Institutional Review Board of the Affiliated Huaqiao Hospital of Jinan University approved this study.
Consent: All subjects provided informed consent at the time of enrollment that their samples could be used for this study.Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Antibodies Sentences Resources Briefly, 106 PBMC were stained with FITC anti-human HLA-A2 antibody at 4 °C in the dark for 30 min, and acquired by using flow cytometer. anti-human HLA-A2suggested: NoneHLA-A2 positive PBMC samples were further stained with PE labelled tetramer (home-made) and APC labelled human CD8+ antibody (BioLegend Cat#344721), and acquired with flow cytometer FACS Canto (BD). CD8+suggested: None0.5×106 CD8+ T cells from health donors were co-cultured with 0.5×106 mixed peptide-loaded T2A2 cells stained with CFSE, and stimulated with 1μg/mL anti-human CD28 antibodies (BioLegend Cat#302901) and 50 IU/mL IL-2 (SL PHARM, Recombinant Human Interleukin-2(125Ala) Injection). anti-human CD28suggested: (BioLegend Cat# 302901, RRID:AB_314303)Software and Algorithms Sentences Resources The spike protein sequences of all four virus strains were aligned with Clustal Omega with SARS-CoV-2 as reference, and potential peptide candidates specific to SARS-CoV-2 were selected for further validation. Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)The sequences of each epitope were extracted for further analysis with Microsoft Office Excel 2010 and Graphic Prism (Version 7). Microsoft Office Excelsuggested: (Microsoft Excel, RRID:SCR_016137)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).
Results from JetFighter: We did not find any issues relating to colormaps.
Results from scite Reference Check: We found no unreliable references.
About SciScore
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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SciScore for 10.1101/2021.01.22.427863: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement All subjects provided informed consent at the time of enrollment that their samples could be used for this study. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Antibodies Sentences Resources Cells were stained with FITC anti-human HLA-A2 antibody at 4 °C in the dark for 30 min, and acquired in flow cytometer FACS Canto (BD). anti-human HLA-A2suggested: NoneHLA-A2 positive PBMC samples were further stained with PE labelled tetramer （home-made）and APC labelled human … SciScore for 10.1101/2021.01.22.427863: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement All subjects provided informed consent at the time of enrollment that their samples could be used for this study. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Antibodies Sentences Resources Cells were stained with FITC anti-human HLA-A2 antibody at 4 °C in the dark for 30 min, and acquired in flow cytometer FACS Canto (BD). anti-human HLA-A2suggested: NoneHLA-A2 positive PBMC samples were further stained with PE labelled tetramer （home-made）and APC labelled human CD8+ antibody (BioLegend Cat#344721), and acquired with flow cytometer FACS Canto (BD). APCsuggested: (BioLegend Cat# 344721, RRID:AB_2075390)CD8+suggested: None0.5x106 CD8+ T cells from health donors were co-cultured with 0.5x106 mixed peptide-loaded T2A2 cells stained with CFSE, and stimulated with 1µg/mL anti-human CD28 antibodies (BioLegend Cat#302901) and 50 IU/mL IL-2 (SL PHARM, Recombinant Human Interleukin-2(125Ala) Injection). anti-human CD28suggested: (BioLegend Cat# 302901, RRID:AB_314303)Software and Algorithms Sentences Resources The spike protein sequences of all four virus strains were aligned with Clustal Omega with SARS-CoV-2 as reference, and potential peptide candidates specific to SARS-CoV-2 were selected for further validation. Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)The sequences of each epitope were extracted for further analysis with Microsoft Office Excel 2010 and Graphic Prism (Version 7). Microsoft Office Excelsuggested: (Microsoft Excel, RRID:SCR_016137)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).
Results from JetFighter: We did not find any issues relating to colormaps.
About SciScore
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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