Intensive single-cell analysis reveals immune-cell diversity among healthy individuals

  1. Yukie Kashima
  2. Keiya Kaneko
  3. Patrick Reteng
  4. Nina Yoshitake
  5. Lucky Ronald Runtuwene
  6. Satoi Nagasawa
  7. Masaya Onishi
  8. Masahide Seki
  9. Ayako Suzuki
  10. Sumio Sugano
  11. Mamiko Sakata-Yanagimoto
  12. Yumiko Imai
  13. Kaori Nakayama-Hosoya
  14. Ai Kawana-Tachikawa
  15. Taketoshi Mizutani
  16. Yutaka Suzuki

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Abstract

Immune responses are different between individuals and personal health histories and unique environmental conditions should collectively determine the present state of immune cells. However, the molecular systems underlying such heterogeneity remain elusive. Here, we conducted a systematic time-lapse single-cell analysis, using 171 single-cell libraries and 30 mass cytometry datasets intensively for seven healthy individuals. We found substantial diversity in immune-cell profiles between different individuals. These patterns showed daily fluctuations even within the same individual. Similar diversities were also observed for the T-cell and B-cell receptor repertoires. Detailed immune-cell profiles at healthy statuses should give essential background information to understand their immune responses, when the individual is exposed to various environmental conditions. To demonstrate this idea, we conducted the similar analysis for the same individuals on the vaccination of influenza and SARS-CoV-2. In fact, we detected distinct responses to vaccines between individuals, although key responses are common. Single-cell immune-cell profile data should make fundamental data resource to understand variable immune responses, which are unique to each individual.

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  1. Version published to 10.26508/lsa.202201398
  2. ScreenIT

    SciScore for 10.1101/2021.10.18.464926: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: Ethics approval and consent to participate: The human materials were collected and analyzed following the procedure approved by the ethical committee of the University of Tokyo as examination number: 20-351.
    IRB: Ethics approval and consent to participate: The human materials were collected and analyzed following the procedure approved by the ethical committee of the University of Tokyo as examination number: 20-351.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    In the SARS-CoV-2 vaccination study, we measured the antibody titer anti-SARS-CoV-2 S IgG and anti-SARS-CoV-2 S IgM.
    anti-SARS-CoV-2 S IgG
    suggested: None
    anti-SARS-CoV-2 S IgM
    suggested: None
    Software and Algorithms
    SentencesResources
    We employed BD FACSCanto (BD) and the sort logic was set by gating lymphocytes by forward scatter and side scatter and then gating on CD3+ CD4+ cells and CD3+ CD8+ cells.
    BD FACSCanto
    suggested: None
    The dataset was analyzed by FlowJo sofetware.
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)

    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 50. 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

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  3. Version published to 10.1101/2021.10.18.464926v1 on bioRxiv