Identification of HLA-A*02:01-Restricted Candidate Epitopes Derived from the Nonstructural Polyprotein 1a of SARS-CoV-2 That May Be Natural Targets of CD8 + T Cell Recognition In Vivo
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Abstract
For the development of vaccines based on SARS-CoV-2-specific cytotoxic T lymphocytes (CTLs), we attempted to identify HLA-A*02:01-restricted CTL epitopes derived from the nonstructural polyprotein 1a of SARS-CoV-2. Out of 82 peptides predicted by bioinformatics, 54 peptides showed good binding affinities to HLA-A*02:01.
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SciScore for 10.1101/2020.09.18.304493: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IACUC: This study was approved by the Animal Research Committee of Saitama Medical University. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources After 3 hours’ incubation at 37°C, peptide-pulsed cells were stained with anti-HLA-A2 monoclonal antibody, BB7.2 (47), followed by FITC-labeled goat anti-mouse IgG antibody (Sigma-Aldrich, St. Louis, MO). anti-HLA-A2suggested: Noneanti-mouse IgGsuggested: NoneIn brief, after 1 wk following immunization, spleen cells were incubated with 50 μM of each peptide for 5 hours at 37°C … SciScore for 10.1101/2020.09.18.304493: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IACUC: This study was approved by the Animal Research Committee of Saitama Medical University. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources After 3 hours’ incubation at 37°C, peptide-pulsed cells were stained with anti-HLA-A2 monoclonal antibody, BB7.2 (47), followed by FITC-labeled goat anti-mouse IgG antibody (Sigma-Aldrich, St. Louis, MO). anti-HLA-A2suggested: Noneanti-mouse IgGsuggested: NoneIn brief, after 1 wk following immunization, spleen cells were incubated with 50 μM of each peptide for 5 hours at 37°C in the presence of brefeldin A (GolgiPlug™, BD Biosciences), and were stained with FITC-conjugated anti-mouse CD8 monoclonal antibody (mAb) (BioLegend, San Diego, CA). anti-mouse CD8suggested: NoneExperimental Models: Cell Lines Sentences Resources Briefly, RMA-S-HHD cells were pre-cultured overnight at 26°C in a CO2 incubator, and then pulsed with each peptide at various concentrations ranging from 0.01 μM to 100 μM for 1 hour at 26°C. RMA-S-HHDsuggested: NoneExperimental Models: Organisms/Strains Sentences Resources Mice: We used HLA-A*02:01 transgenic mice (37) that express a transgenic HLA-A*02:01 monochain, designated as HHD, in which human β2-microglobulin is covalently linked to a chimeric heavy chain composed of HLA-A*02:01 (α1 and α2 domains) and H-2Db (α3, transmembrane, and cytoplasmic domains). HLA-A*02:01suggested: RRID:IMSR_TAC:9659)Software and Algorithms Sentences Resources Prediction of CTL epitopes: Four computer-based programs including SYFPEITHI (31), nHLAPred (32), ProPred-I (33), and IEDB (34) were used to predict HLA-A*02:01-restricted CTL epitopes derived from pp1a of SARS-CoV-2 (GenBank accession numbers: LC528232.1 & LC528233.1). SYFPEITHIsuggested: NoneIn brief, after 1 wk following immunization, spleen cells were incubated with 50 μM of each peptide for 5 hours at 37°C in the presence of brefeldin A (GolgiPlug™, BD Biosciences), and were stained with FITC-conjugated anti-mouse CD8 monoclonal antibody (mAb) (BioLegend, San Diego, CA). BD Biosciencessuggested: (BD Biosciences, RRID:SCR_013311)Statistical analyses: One-way ANOVA followed by post-hoc tests was performed for statistical analyses among multiple groups using Graphpad Prism 5 software (GraphPad software, San Diego, CA). Graphpad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)GraphPadsuggested: (GraphPad Prism, RRID:SCR_002798)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 did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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