Altered pre-existing SARS-CoV-2-specific T cell responses in elderly individuals

  1. Naoyuki Taira
  2. Sakura Toguchi
  3. Mio Miyagi
  4. Tomoari Mori
  5. Hiroaki Tomori
  6. Koichi Oshiro
  7. Osamu Tamai
  8. Mitsuo Kina
  9. Masatake Miyagi
  10. Kentaro Tamaki
  11. Mary K Collins
  12. Hiroki Ishikawa

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Abstract

No abstract available

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  1. Version published to 10.1016/j.clicom.2021.12.001
  2. ScreenIT

    SciScore for 10.1101/2021.07.26.21261082: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: Subjects: The study design was approved by the Okinawa Institute of Science and Technology, Graduate University (OIST) human subjects ethics committee (applications HSR-2020-024, HSR-2020-028).
    Consent: All donors provided informed written consent.
    Sex as a biological variableBased on antibody test results, donors were grouped into seronegative young (n=45, 40 % male, 60% female; mean age 38 years, age rage 23-49 years), seronegative elderly (n=41, 17 % male, 83% female; mean age 81 years, age rage 70-93 years), seropositive young (n=19, 63 % male, 37% female; mean age 41 years, age rage 20-50 years), and seropositive elderly (n=11, 45 % male, 55% female; mean age 78 years, age rage 70-91 years).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Then, cells were resuspended in RPMI1640 (Gibco) medium supplemented with 5% (v/v) human AB-serum (PAN-Biotech; P30-2901), seeded into 96-well, U-bottom culture plates (106 cells per well), and either left unstimulated (cells treated with equimolar amounts of DMSO) or stimulated with 1μg/mL SARS-CoV-2 M peptide pool for 7 h in the presence of 1μg/mL anti-CD40 (5C3; Biolegend; 334302) and 1 μg/mL anti-CD28 antibodies (CD28.2; Biolegend; 302934).
    anti-CD40
    suggested: (BioLegend Cat# 334302, RRID:AB_1236384)
    anti-CD28
    suggested: None
    After stimulation, cells were incubated with anti-Fc receptor-blocking antibody (Biolegend; 422301) and NIR-Zomibie (Biolegend; 423106) and stained with anti-CD3 (OKT3; Biolegend; 1:200), anti-CD4 (clone PPA-T4; Biolegend; 1:200), anti-CD8 (SK1; Biolegend; 1:200), anti-CD45RA (HI100; Biolegend; 1:100), and anti-CCR7 (G043H7; Biolegend; 1:100) antibodies.
    anti-Fc receptor-blocking
    suggested: None
    anti-CD3
    suggested: (BioLegend Cat# 317318, RRID:AB_1937212)
    anti-CD4
    suggested: None
    anti-CD8
    suggested: (BioLegend Cat# 980902, RRID:AB_2616623)
    anti-CD45RA
    suggested: (BioLegend Cat# 304106, RRID:AB_314410)
    anti-CCR7
    suggested: (Fluidigm Cat# 3159003, RRID:AB_2714155)
    For intracellular cytokine analysis, cells were subsequently fixed and permeabilized using Foxp3 Staining Buffer Sets (eBioscience; 00-5253-00) and stained with anti-IFN-γ (B27; BD; 1:100), anti-TNF-α (MAb11; Biolegend; 1:20) and anti-IL-2 (MQ1-17H12; Biolegend; 1:20) antibodies.
    Foxp3
    suggested: None
    anti-IFN-γ
    suggested: (BD Biosciences Cat# 564039, RRID:AB_2738557)
    anti-TNF-α
    suggested: (BioLegend Cat# 502913, RRID:AB_315265)
    anti-IL-2
    suggested: (BioLegend Cat# 500305, RRID:AB_315092)
    Software and Algorithms
    SentencesResources
    Samples were analyzed on a Fortessa X-20 (BD), and data were analyzed with FlowJo software version 10.7.1 (FlowJo LLC).
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Statistical analysis: Unpaired t tests or Mann-Whitney U tests were performed using GraphPad Prism 9.1.0 software.
    GraphPad Prism
    suggested: (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:
    • 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 10.1101/2021.07.26.21261082v1 on medRxiv