Single-cell profiling of T and B cell repertoires following SARS-CoV-2 mRNA vaccine

  1. Suhas Sureshchandra
  2. Sloan A. Lewis
  3. Brianna M. Doratt
  4. Allen Jankeel
  5. Izabela Coimbra Ibraim
  6. Ilhem Messaoudi

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Abstract

No abstract available

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  1. Version published to 10.1172/jci.insight.153201
  2. ScreenIT

    SciScore for 10.1101/2021.07.14.452381: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: Ethics Statement: This study was approved by the University of California Irvine Institutional Review Boards.
    Consent: Informed consent was obtained from all enrolled subjects.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Number of infected foci was determined using anti-SARS-CoV-2 Nucleocapsid antibody (Novus Biologicals NB100-56576) and HRP anti-rabbit IgG antibody (BioLegend).
    anti-SARS-CoV-2
    suggested: None
    anti-rabbit IgG
    suggested: None
    T cell phenotyping was conducted using an additional panel of antibodies – CD4 (OKT4, Biolegend), CD8b (2ST8.5H7, Beckman Coulter), CCR7 (G043H7, Biolegend), CD45RA (T6D11, Miltenyi Biotec), CD38 (HIT2, Tonbo Biosciences)
    CD4
    suggested: (RayBiotech Cat# CS-11-0132, RRID:AB_1228050)
    CD8b
    suggested: (Abcam Cat# ab34397, RRID:AB_2291359)
    CCR7
    suggested: None
    CD45RA
    suggested: None
    CD38
    suggested: None
    Plates were spun, surface stained using an antibody cocktail containing CD4 (OKT4, BioLegend), CD8b (2ST8.5H7, Beckman Coulter), CD28 (CD28.2, eBioscience), CD95 (DX2, eBioscience).
    OKT4
    suggested: None
    CD28
    suggested: None
    CD95
    suggested: None
    DX2
    suggested: None
    FACS for repertoire analysis: Cryopreserved PBMC from each person (n=4 for pre- and post-vaccine samples; n=3 for baseline and convalescent samples) were thawed, washed, and stained with 1 ug/test cell-hashing antibody (TotalSeq C0251, C0254, C0256, C0260, clones LNH-95, 2M2, BioLegend) for 30 minutes at 4C.
    C0254
    suggested: (Assay Biotech Cat# C0254, RRID:AB_10684215)
    C0256
    suggested: (Assay Biotech Cat# C0256, RRID:AB_10684216)
    C0260
    suggested: (Assay Biotech Cat# C0260, RRID:AB_10684622)
    2M2
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    The diluted plasma was pre-incubated with SARS-CoV-2 (100 PFU) for 1 hour before being transferred onto Vero E6 cells (ATCC C1008) seeded in a 96-well plate followed by overlay using 1% methylcellulose (Sigma Aldrich).
    Vero E6
    suggested: RRID:CVCL_XD71)
    Software and Algorithms
    SentencesResources
    The half maximum inhibitory concentration (IC50) was calculated by non-linear regression analysis using normalized counted foci on Prism 7 (Graphpad Software). 100% of infectivity was obtained normalizing the number of foci counted in the wells derived from the cells infected with SARS-CoV-2 virus in the absence of plasma.
    Prism
    suggested: (PRISM, RRID:SCR_005375)
    Graphpad
    suggested: (GraphPad, RRID:SCR_000306)
    Data were analyzed using FlowJo v10 (TreeStar
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Single cell RNA-Seq data analysis: Raw reads were aligned and quantified using the Cell Ranger Single-Cell Software Suite with Feature Barcode addition (version 4.0, 10X Genomics) against the GRCh38 human reference genome using the STAR aligner.
    STAR
    suggested: (STAR, RRID:SCR_004463)
    Differential expression analysis was performed using MAST using default settings in Seurat.
    MAST
    suggested: (MAST, RRID:SCR_016340)
    Germline sequences were reconstructed using IgBlast.
    IgBlast
    suggested: (IgBLAST, RRID:SCR_002873)

    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: We detected the following sentences addressing limitations in the study:
    Limitations of our study include small sample size, and restriction to participants receiving mRNA vaccine. Due to limited blood samples collected, we were unable to perform additional analysis such as phenotyping of circulating T follicular helper cells (cTfh) following vaccination. Given such few memory B cells from each subject, we were unable to perform rigorous somatic hypermutation analysis at the single cell level. Finally, future studies will have to focus on long-term protection (both cellular and humoral) of two doses of mRNA vaccine against the numerous variants of SARS-CoV-2 and mechanisms of decline in quality of protection (if any) in the elderly.

    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 10.1101/2021.07.14.452381v1 on bioRxiv