Temporal associations of B and T cell immunity with robust vaccine responsiveness in a 16-week interval BNT162b2 regimen

  1. Manon Nayrac
  2. Mathieu Dubé
  3. Gérémy Sannier
  4. Alexandre Nicolas
  5. Lorie Marchitto
  6. Olivier Tastet
  7. Alexandra Tauzin
  8. Nathalie Brassard
  9. Raphaël Lima-Barbosa
  10. Guillaume Beaudoin-Bussières
  11. Dani Vézina
  12. Shang Yu Gong
  13. Mehdi Benlarbi
  14. Romain Gasser
  15. Annemarie Laumaea
  16. Jérémie Prévost
  17. Catherine Bourassa
  18. Gabrielle Gendron-Lepage
  19. Halima Medjahed
  20. Guillaume Goyette
  21. Gloria-Gabrielle Ortega-Delgado
  22. Mélanie Laporte
  23. Julia Niessl
  24. Laurie Gokool
  25. Chantal Morrisseau
  26. Pascale Arlotto
  27. Jonathan Richard
  28. Justin Bélair
  29. Alexandre Prat
  30. Cécile Tremblay
  31. Valérie Martel-Laferrière
  32. Andrés Finzi
  33. Daniel E. Kaufmann

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Abstract

No abstract available

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  1. Version published to 10.1016/j.celrep.2022.111013
  2. ScreenIT

    SciScore for 10.1101/2021.12.18.473317: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: EXPERIMENTAL MODEL AND SUBJECT DETAILS: Ethics Statement: All work was conducted in accordance with the Declaration of Helsinki in terms of informed consent and approval by an appropriate institutional board.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    CXCR3, CCR6, CXCR6 and CXCR5 antibodies were added in culture 15 min before stimulation.
    CXCR3
    suggested: None
    CCR6
    suggested: None
    CXCR6
    suggested: None
    CXCR5
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Cell lines: 293T human embryonic kidney and HOS cells (obtained from ATCC) were maintained at 37°C under 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) (Wisent) containing 5% fetal bovine serum (FBS) (VWR) and 100 μg/mL of penicillin-streptomycin (Wisent).
    HOS
    suggested: None
    293T-ACE2 cell line was previously reported (Prevost et al., 2020).
    293T-ACE2
    suggested: None
    Briefly, 293T cells were transfected with the lentiviral vector pNL4.3 R-E-Luc plasmid (NIH AIDS Reagent Program) and a plasmid encoding for the full-length SARS-CoV-2 Spike D614G glycoprotein (Beaudoin-Bussieres et al., 2020; Prevost et al., 2020) at a ratio of 10:1.
    293T
    suggested: None
    Recombinant DNA
    SentencesResources
    Briefly, 293T cells were transfected with the lentiviral vector pNL4.3 R-E-Luc plasmid (NIH AIDS Reagent Program) and a plasmid encoding for the full-length SARS-CoV-2 Spike D614G glycoprotein (Beaudoin-Bussieres et al., 2020; Prevost et al., 2020) at a ratio of 10:1.
    pNL4.3
    suggested: None
    R-E-Luc
    suggested: None
    Software and Algorithms
    SentencesResources
    Stained PBMC samples were acquired on Symphony cytometer (BD Biosciences) and analyzed using FlowJo v10.8.0 software.
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Statistics were analyzed using GraphPad Prism version 8.4.3 (GraphPad, San Diego, CA).
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Software scripts and visualization: Graphics and pie charts were generated using GraphPad PRISM version 8.4.1 and ggplot2 (v3.3.3) in R (v4.1.0).
    GraphPad PRISM
    suggested: (GraphPad Prism, RRID:SCR_002798)
    ggplot2
    suggested: (ggplot2, RRID:SCR_014601)
    Heat maps were generated in R (v4.1.0) using the pheatmap package (v1.0.12).
    pheatmap
    suggested: (pheatmap, RRID:SCR_016418)
    Uniform manifold approximation and projection (UMAP) was performed using package M3C (v1.14.0) on gated FCS files loaded through the flowCore package (v2.4.0).
    flowCore
    suggested: (flowCore, RRID:SCR_002205)
    Scaling and logicle transformation of the flow cytometry data was applied using the FlowSOM (Quintelier et al., 2021) R package (v2.0.0).
    FlowSOM
    suggested: (FlowSOM, RRID:SCR_016899)
    Clustering was achieved using Phenograph (v0.99.1) with the hyperparameter k (number of nearest-neighbors) set to 150).
    Phenograph
    suggested: (Phenograph, RRID:SCR_016919)

    Results from OddPub: Thank you for sharing your code.

    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:
    • 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 10.1101/2021.12.18.473317v1 on bioRxiv