Unique molecular signatures sustained in circulating monocytes and regulatory T cells in convalescent COVID-19 patients

  1. Andrew D. Hoffmann
  2. Sam E. Weinberg
  3. Suchitra Swaminathan
  4. Shuvam Chaudhuri
  5. Hannah Faisal Almubarak
  6. Matthew J. Schipma
  7. Chengsheng Mao
  8. Xinkun Wang
  9. Lamiaa El-Shennawy
  10. Nurmaa K. Dashzeveg
  11. Juncheng Wei
  12. Paul J. Mehl
  13. Laura J. Shihadah
  14. Ching Man Wai
  15. Carolina Ostiguin
  16. Yuzhi Jia
  17. Paolo D'Amico
  18. Neale R. Wang
  19. Yuan Luo
  20. Alexis R. Demonbreun
  21. Michael G. Ison
  22. Huiping Liu
  23. Deyu Fang

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Abstract

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  1. Version published to 10.1016/j.clim.2023.109634
  2. ScreenIT

    SciScore for 10.1101/2022.03.26.485922: (What is this?)

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

    Table 1: Rigor

    EthicsField Sample Permit: Human subject study and biosafety approvals for blood draws: All research activities with human blood specimens of pre-COVID-19, sero-negative (healthy) donors and convalescent COVID-19 patients were implemented under NIH guidelines for human subject studies and the protocols approved by the Northwestern University Institutional Review Board (STU00205299) as well as the Institutional Biosafety Committee for COVID-19 research.
    IRB: Human subject study and biosafety approvals for blood draws: All research activities with human blood specimens of pre-COVID-19, sero-negative (healthy) donors and convalescent COVID-19 patients were implemented under NIH guidelines for human subject studies and the protocols approved by the Northwestern University Institutional Review Board (STU00205299) as well as the Institutional Biosafety Committee for COVID-19 research.
    Consent: For collecting human blood specimens, patients and donors were recruited at Northwestern Memorial Hospital based on their availability and willingness to consent and participate in the research.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Results were normalized to the CR3022 antibody with known affinity to the receptor binding domain of SARS-CoV2 (Creative Biolabs, MRO-1214LC)(29, 52).
    CR3022
    suggested: (Imported from the IEDB Cat# CR3022, RRID:AB_2848080)
    Cells were stained for surface antigens using fluorescence-conjugated monoclonal Abs specific to human CD45, CD3, CD4, CD127 and CD25 antibodies for Treg identification and sorting as well as CD45, CD3, CD64, CD14 and CD16 for monocyte characterization and sorting.
    CD45
    suggested: (RayBiotech Cat# CS-11-0019, RRID:AB_1227882)
    CD4
    suggested: (BD Biosciences Cat# 560249, RRID:AB_1645496)
    CD127
    suggested: (BD Biosciences Cat# 560249, RRID:AB_1645496)
    CD25
    suggested: None
    CD3
    suggested: None
    CD64
    suggested: None
    CD14
    suggested: (BioLegend Cat# 348805, RRID:AB_2889063)
    CD16
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Neutralization assays with 10 μL or 80 μL of plasma were performed using HEK293 cells with stable expression of human ACE2.
    HEK293
    suggested: CLS Cat# 300192/p777_HEK293, RRID:CVCL_0045)
    0.5 μL RBD-647 was then pre-incubated with PBS as a control or 80 μL patient-derived plasma for 45 minutes on ice, after which it was combined with 106 HEK/ACE2 cells.
    HEK/ACE2
    suggested: None
    The levels of RBD-647 binding to HEK293/ACE2 cells were then assessed BD FACSAria Cell Sorter and analyzed using FlowJo v10software.
    HEK293/ACE2
    suggested: None
    Software and Algorithms
    SentencesResources
    The levels of RBD-647 binding to HEK293/ACE2 cells were then assessed BD FACSAria Cell Sorter and analyzed using FlowJo v10software.
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Quality control of the libraries was performed using an Invitrogen Qubit DNA high sensitivity kit (ThermoFisher Scientific, Q32851) and Agilent Bioanalyzer high sensitivity DNA kit (Agilent, 5067-4626).
    Agilent Bioanalyzer
    suggested: None
    scRNA-seq data acquisition and analysis: Data from scRNA-seq was demultiplexed and mapped to hg38 (refdata-gex-GRCh38-2020-A) using Cell Ranger software version 4.0.0 (10x genomics).
    Cell Ranger
    suggested: (Cell Ranger , RRID:SCR_017344)

    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 10.1101/2022.03.26.485922v1 on bioRxiv