A Peptide Vaccine Candidate Tailored to Individuals' Genetics Mimics the Multi-Targeted T Cell Immunity of COVID-19 Convalescent Subjects

  1. Eszter Somogyi
  2. Zsolt Csiszovszki
  3. Levente Molnár
  4. Orsolya Lőrincz
  5. József Tóth
  6. Sofie Pattijn
  7. Jana Schockaert
  8. Aurélie Mazy
  9. István Miklós
  10. Katalin Pántya
  11. Péter Páles
  12. Enikő R. Tőke

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Abstract

Long-term immunity to coronaviruses likely stems from T cell activity. We present here a novel approach for the selection of immunoprevalent SARS-CoV-2-derived T cell epitopes using an in silico cohort of HLA-genotyped individuals with different ethnicities. Nine 30-mer peptides derived from the four major structural proteins of SARS-CoV-2 were selected and included in a peptide vaccine candidate to recapitulate the broad virus-specific T cell responses observed in natural infection. PolyPEPI-SCoV-2-specific, polyfunctional CD8 + and CD4 + T cells were detected in each of the 17 asymptomatic/mild COVID-19 convalescents' blood against on average seven different vaccine peptides. Furthermore, convalescents' complete HLA-genotype predicted their T cell responses to SARS-CoV-2-derived peptides with 84% accuracy. Computational extrapolation of this relationship to a cohort of 16,000 HLA-genotyped individuals with 16 different ethnicities suggest that PolyPEPI-SCoV-2 vaccination will likely elicit multi-antigenic T cell responses in 98% of individuals, independent of ethnicity. PolyPEPI-SCoV-2 administered with Montanide ISA 51 VG generated robust, Th1-biased CD8 + , and CD4 + T cell responses against all represented proteins, as well as binding antibodies upon subcutaneous injection into BALB/c and hCD34 + transgenic mice modeling human immune system. These results have implications for the development of global, highly immunogenic, T cell-focused vaccines against various pathogens and diseases.

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  1. Version published to 10.3389/fgene.2021.684152
  2. ScreenIT

    SciScore for 10.1101/2020.10.16.339937: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board StatementConsent: All donors provided written informed consent.
    IRB: All procedures described in this study have been reviewed and approved by the local ethic committee (CELEAG) and validated by the French Ministry of Research.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variableLarge, US cohort (n=16,000) The database comprising anonymized HLA-genotype data from 16,000 individuals was created by obtaining 1,000 donors from each of 16 ethnic groups (500 male and 500 female) from the National Marrow Donor Program (NMDP).
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Thereafter, cells were incubated in FcR blocking reagent at 4°C for 5 min, and then staining mixture (containing anti-CD3, Biolegend, anti-CD4, and anti-CD8 antibodies; BD Biosciences) was added to each well.
    anti-CD3
    suggested: None
    anti-CD4
    suggested: None
    anti-CD8
    suggested: None
    After fixation, cytokine staining mixture (containing anti-IFN-γ, anti-IL-2, anti-IL-4, anti-IL-10 and anti-TNF-α antibodies, Biolegend) was added to each well.
    anti-IFN-γ
    suggested: (Bio-Rad Cat# M6000007NY, RRID:AB_2784537)
    anti-IL-2
    suggested: None
    anti-IL-4 ,
    suggested: None
    anti-IL-10
    suggested: None
    anti-TNF-α
    suggested: None
    The Anti-SARS-CoV-2 ELISA plates ere coated with recombinant S-1 structural protein from SARS-CoV-2 to which antibodies against SARS-CoV-2 bind.
    Anti-SARS-CoV-2
    suggested: None
    ELISAs were performed by Mikromikomed Kft (Budapest, Hungary) using a DiaPro COVID-19 IgM Enzyme Immunoassay for the determination of IgM antibodies to COVID-19 in human serum and plasma, DiaPro COVID-19
    IgM
    suggested: None
    IgG Enzyme Immunoassay for the determination of IgG antibodies to COVID-19 in human serum and plasma, and DiaPro COVID-19 IgA Enzyme Immunoassay for the determination of IgA antibodies to COVID-19 in human serum and plasma according to the manufacturer’s instructions (Dia.Pro Diagnostic Bioprobes S.r.l., Italy).
    IgA
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Vero E6 cells expressing the ACE-2 receptor (Vero C1008 [ATCC No. CRL-1586, US]), were seeded at 20 000 cells/well to reach a cell confluence of 80%.
    Vero E6
    suggested: None
    Vero
    suggested: ATCC Cat# CRL-1586, RRID:CVCL_0574)
    C1008
    suggested: ATCC Cat# CRL-1586, RRID:CVCL_0574)
    Experimental Models: Organisms/Strains
    SentencesResources
    ) Peptides and PolyPEPI-SCoV-2 vaccine preparation: The 9-mer (s2, s5, s9, n1, n2, n3, n4, e1, m1) and 30-mer (S2, S5, S7, N1, N2, N3, N4, E1, M1) peptides were manufactured by Intavis Peptide Services GmbH&Co. KG (Tübingen, Germany) and PEPScan (Lelystad, The Netherlands) using solid-phase peptide synthesis.
    e1
    suggested: None
    The following stains were used for BALB/c mice cohorts: 11B11 562915 (BD)
    BALB/c
    suggested: None
    Software and Algorithms
    SentencesResources
    Then, the translated coding sequences of the four structural protein sequences were aligned and compared using a multiple sequence alignment (Clustal Omega, EMBL-EBI, United Kingdom).
    Clustal Omega
    suggested: (Clustal Omega, RRID:SCR_001591)
    (47–49) Characterization of the Model Population was reported previously.(34) A second cohort of 356 individuals with characterized HLA class II genotypes (2 × HLA-DRB, 2 × HLA-DP, and 2 × HLA-DQ) at four-digit allele resolution was obtained from the dbMHC database(50), an online available repository operated by the National Center for Biotechnology Information (NCBI).
    dbMHC
    suggested: (dbMHC, RRID:SCR_002302)
    Large, US cohort (n=16,000) The database comprising anonymized HLA-genotype data from 16,000 individuals was created by obtaining 1,000 donors from each of 16 ethnic groups (500 male and 500 female) from the National Marrow Donor Program (NMDP).
    National Marrow Donor Program
    suggested: None
    Flow-cytometry was performed using a BD Cytofix/Cytoperm Plus Kit with BD GolgiStop™
    BD GolgiStop™
    suggested: None
    Spot counts ≥25 were background corrected by subtracting unstimulated (DMSO) control.
    Spot
    suggested: (Spot, RRID:SCR_018915)
    All flow cytometry data were acquired with LSRFortessa™ X-20 and analyzed using FlowJo V10 software.
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Absorbance were read on an Epoch Microplate Reader (Biotech) and analyzed using Gen5 software.
    Gen5
    suggested: (Gen5, RRID:SCR_017317)
    Luminescence results for each dilution were used to generate a titration curve using a 4-parameter logistic regression (4PL) using Microsoft Excel (for Microsoft Office 365).
    Microsoft Excel
    suggested: (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 rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • 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.

    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.

  3. Version published to 10.1101/2020.10.16.339937v1 on bioRxiv