BNT162b2 vaccine induces divergent B cell responses to SARS-CoV-2 S1 and S2

  1. R. Camille Brewer
  2. Nitya S. Ramadoss
  3. Lauren J. Lahey
  4. Shaghayegh Jahanbani
  5. William H. Robinson
  6. Tobias V. Lanz

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Abstract

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  1. Version published to 10.1038/s41590-021-01088-9
  2. ScreenIT

    SciScore for 10.1101/2021.07.20.21260822: (What is this?)

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

    Table 1: Rigor

    EthicsField Sample Permit: Study design, sample collection, and storage: All studies were approved by the Institutional Review Board of Stanford University (IRB-3780), and the studies complied with the relevant ethical regulations.
    IRB: Study design, sample collection, and storage: All studies were approved by the Institutional Review Board of Stanford University (IRB-3780), and the studies complied with the relevant ethical regulations.
    Consent: All participants provided written informed consent before participating in the study.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    B cell samples without antigen enrichment were stained with CD19, IgD, CD27, CD38 TotalSeq-C antibodies (all Biolegend).
    CD19
    suggested: (Agilent Cat# TC67401, RRID:AB_579635)
    IgD
    suggested: None
    CD38 TotalSeq-C
    suggested: None
    For antigen-sorted B cell samples, cells were stained with the following fluorescently labeled antibodies according to standard protocols: CD19, CD20, CD38 (all BD Biosciences), CD3, CD27, IgM, IgD, (all BioLegend), IgA (Miltenyi Biotec)
    CD20
    suggested: None
    CD38
    suggested: None
    CD3
    suggested: None
    CD27
    suggested: None
    IgM , IgD
    suggested: (MyBioSource Cat# MBS531438, RRID:AB_10577295)
    Additionally, samples were labeled with TotalSeq-C hashtag 1-9 antibodies (Biolegend) for demultiplexing individual samples in downstream analysis.
    1-9
    suggested: None
    Secondary HRP-conjugated antibodies goat anti-human IgG (Bethyl Laboratories) or HRP-conjugated goat anti-human IgA (Bethyl Laboratories) were applied for 1h at RT, and plates were developed with TMB substrate (Thermo Fisher Scientific), and stopped with 2N sulfuric acid.
    Secondary HRP-conjugated antibodies goat anti-human IgG
    suggested: None
    anti-human IgG
    suggested: None
    anti-human IgA
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Lenti X 293T cells (Takara Bio) were cultured in DMEM (ATCC, 30-2002) with 10% heat-inactivated FBS (Corning) and 100 U/ml of penicillin–streptomycin (Gibco).
    Lenti X 293T
    suggested: None
    Briefly, LentiX 293T cells were seeded in 10cm plates.
    293T
    suggested: None
    Virus was titrated on HeLa-ACE2 cells.
    HeLa-ACE2
    suggested: None
    Recombinant DNA
    SentencesResources
    After 24 hours, cells were transfected using Fugene transfection reagent (Promega) with pHAGE-CMV-Luc2-IRES-ZsGreen-W, lentiviral helper plasmids (HDM-Hgpm2, HDM-tat1b, pRC-CMV-Rev1b), and wildtype or variant SARS-CoV-2 spike plasmids (parent plasmids publicly available from Jesse Bloom lab).
    pHAGE-CMV-Luc2-IRES-ZsGreen-W
    suggested: RRID:Addgene_164432)
    pRC-CMV-Rev1b
    suggested: RRID:Addgene_164443)
    Software and Algorithms
    SentencesResources
    FlowJo Version 10.7.1 (BD Biosciences) and R version 3.6.1 was used for flow cytometry data analysis.
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Statistics and software: GraphPad Prism version 8.4.1 and R version 3.6.1 were used for statistical analyses.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Graphical illustrations were created with BioRender.
    BioRender
    suggested: (Biorender, RRID:SCR_018361)

    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: Please consider improving the rainbow (“jet”) colormap(s) used on page 20. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

    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.

    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.

  3. Version published to 10.1101/2021.07.20.21260822 on medRxiv