Protective heterologous T cell immunity in COVID-19 induced by the trivalent MMR and Tdap vaccine antigens

  1. Vijayashree Mysore
  2. Xavier Cullere
  3. Matthew L. Settles
  4. Xinge Ji
  5. Michael W. Kattan
  6. Michaël Desjardins
  7. Blythe Durbin-Johnson
  8. Tal Gilboa
  9. Lindsey R. Baden
  10. David R. Walt
  11. Andrew H. Lichtman
  12. Lara Jehi
  13. Tanya N. Mayadas

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Abstract

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  1. Version published to 10.1016/j.medj.2021.08.004
  2. ScreenIT

    SciScore for 10.1101/2021.05.03.441323: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: Blood samples were obtained from consented healthy, self-reporting SARS-CoV-2 uninfected volunteers under a Mass General Brigham Institutional Review Board (IRB)-approved protocol (1999P001694).
    Consent: Patients signed informed consent to participate in a Mass General Brigham IRB-approved
    Sex as a biological variablenot detected.
    RandomizationtSNE was performed unsupervised from a maximum of 5,000 randomly selected cells from each sample, with a perplexity set to 80, using the implementation of tSNE plugin in flowJo.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Biotinylated anti-human IgG antibodies (Bethyl Laboratories A80-148B) were diluted in Homebrew Detector/Sample Diluent to final concentrations of 7.73ng/mL.
    Biotinylated anti-human IgG antibodies
    suggested: None
    anti-human IgG
    suggested: None
    To evaluate surface markers on nAPCs, antibodies to the following were used: CD15, CD66b, CD11c, HLA-DR, CD40, CD86 and CCR7 (Source Table).
    CD15
    suggested: None
    CD66b
    suggested: None
    CD11c
    suggested: None
    HLA-DR , CD40
    suggested: None
    CD86
    suggested: None
    To evaluate cell surface markers on T cells, antibodies to the following markers were used: CD3, CD4, CD8, CD45RA, CCR7, CD27, GPR56, CX3CR1, IFN-γ (Source Table).
    CD3
    suggested: (RayBiotech Cat# CS-11-0110, RRID:AB_1228004)
    CD4
    suggested: None
    CD8
    suggested: (Abcam Cat# ab34397, RRID:AB_2291359)
    CD45RA
    suggested: None
    CCR7
    suggested: None
    CD27
    suggested: None
    GPR56
    suggested: None
    CX3CR1
    suggested: None
    Experimental Models: Organisms/Strains
    SentencesResources
    Cell cytokine detection and analysis: nAPCs and monocyte-derived DCs (moDC) were cultured for 72h and supernatants were collected and analyzed for cytokine and chemokine levels using human cytokine 42-plex discovery assay (Eve Technologies, Calgary, AB).
    AB
    suggested: RRID:BDSC_203)
    Software and Algorithms
    SentencesResources
    FCS (flow cytometry standard format) 3.0 data file was used to export data that was analyzed using FlowJo (Mac version 10.7).
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Flow cytometric data analysis: Sample files were exported as FCS 3.0 files from FACSDiva and imported into flowJo v.
    FACSDiva
    suggested: (BD FACSDiva Software, RRID:SCR_001456)
    Intensities for markers of interest were overlaid on the dot-plot to show the expression of those markers on different cell islands and facilitate assignment of cell subsets to these islands using FlowSOM plugin.
    FlowSOM
    suggested: (FlowSOM, RRID:SCR_016899)
    Statistical analysis: Statistical analyses for cell-based assays were performed using Graphpad prism 8 (LaJolla, CA), and JMP10 software (SAS Institute, Inc, USA).
    Graphpad
    suggested: (GraphPad, RRID:SCR_000306)
    SAS Institute
    suggested: (Statistical Analysis System, RRID:SCR_008567)
    10X Genomics Cell Ranger Software Suite (v.4.0.0) (70) was used to process raw fastq files to expression tables and assemble V(D)J clonotypes, performing all the necessary barcode processing, mapping to the Human reference genome (GRCh38, GENCODE v32/Ensembl 98) and unique molecular identifier (UMI) expression counting; each batch contained an estimated > 7K cells.
    GENCODE
    suggested: (GENCODE, RRID:SCR_014966)
    The gene-cell matrix of all cells was analyzed in R v4.0.3 with Seurat v3.9.9 (71)
    Seurat
    suggested: (SEURAT, RRID:SCR_007322)
    The heatmap plot was created using the R package ComplexHeatmap, version 2.6.2.
    ComplexHeatmap
    suggested: (ComplexHeatmap, RRID:SCR_017270)
    The Circos plot was generated using the R package circlize, version 0.4.12.
    Circos
    suggested: (Circos, RRID:SCR_011798)
    circlize
    suggested: (circlize, RRID:SCR_002141)

    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 10.1101/2021.05.03.441323 on bioRxiv