SARS-CoV-2 mRNA vaccination elicits a robust and persistent T follicular helper cell response in humans

  1. Philip A. Mudd
  2. Anastasia A. Minervina
  3. Mikhail V. Pogorelyy
  4. Jackson S. Turner
  5. Wooseob Kim
  6. Elizaveta Kalaidina
  7. Jan Petersen
  8. Aaron J. Schmitz
  9. Tingting Lei
  10. Alem Haile
  11. Allison M. Kirk
  12. Robert C. Mettelman
  13. Jeremy Chase Crawford
  14. Thi H.O. Nguyen
  15. Louise C. Rowntree
  16. Elisa Rosati
  17. Katherine A. Richards
  18. Andrea J. Sant
  19. Michael K. Klebert
  20. Teresa Suessen
  21. William D. Middleton
  22. Jeremie H. Estepp
  23. Stacey Schultz-Cherry
  24. Maureen A. McGargill
  25. Aditya Gaur
  26. James Hoffman
  27. Motomi Mori
  28. Li Tang
  29. Elaine Tuomanen
  30. Richard Webby
  31. Randall T. Hayden
  32. Hana Hakim
  33. Diego R. Hijano
  34. Kim J. Allison
  35. E. Kaitlynn Allen
  36. Resha Bajracharya
  37. Walid Awad
  38. Lee-Ann Van de Velde
  39. Brandi L. Clark
  40. Taylor L. Wilson
  41. Aisha Souquette
  42. Ashley Castellaw
  43. Ronald H. Dallas
  44. Ashleigh Gowen
  45. Thomas P. Fabrizio
  46. Chun-Yang Lin
  47. David C. Brice
  48. Sean Cherry
  49. Ericka Kirkpatrick Roubidoux
  50. Valerie Cortez
  51. Pamela Freiden
  52. Nicholas Wohlgemuth
  53. Kendall Whitt
  54. Joshua Wolf
  55. Sharlene A. Teefey
  56. Jane A. O’Halloran
  57. Rachel M. Presti
  58. Katherine Kedzierska
  59. Jamie Rossjohn
  60. Paul G. Thomas
  61. Ali H. Ellebedy

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Abstract

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  1. Version published to 10.1016/j.cell.2021.12.026
  2. ScreenIT

    SciScore for 10.1101/2021.09.08.459485: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: Written informed consent was obtained from each subject.
    IRB: The study was approved by the Washington University in St. Louis Institutional Review Board (approval # 2020-12-081).
    Field Sample Permit: Blood samples were collected in 8 mL CPT tubes; and PBMC was isolated and frozen within 24 hours of collection.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Cells were then stained with 1 µL Ghost Dye Violet 510 Viability Dye (Tonbo Biosciences 13-0870-T100) and a cocktail of fluorescent antibodies: 1 µL each of anti-human CD3 (Brilliant Violet 421-conjugated, Biolegend 344834, clone SK7)
    anti-human CD3
    suggested: (BioLegend Cat# 344834, RRID:AB_2565675)
    Cells were surface stained in an additional 50 uL FACS containing 1 µL Ghost Dye Violet 510 Viability Dye (Tonbo Biosciences 13-0870-T100) and a cocktail of fluorescent anti-human antibodies: CXCR5 SuperBright 436 (Thermo, 62-9185-42, clone MU5UBEE), CD45RA eFluor 450 (Thermo, 48-0458-42, clone HI100), CD19 BV510 (Biolegend, 302242, clone HIB19), CD8 BV570 (Biolegend, 301038, clone RPA-T8), CD3 BV750 (Biolegend, 344846, clone SK7), CD4 BB515 (BD, 565996, clone SK3)
    anti-human antibodies: CXCR5 SuperBright 436
    suggested: None
    CD45RA eFluor 450
    suggested: (Thermo Fisher Scientific Cat# 48-0458-42, RRID:AB_1272059)
    CD19
    suggested: (BioLegend Cat# 302242, RRID:AB_2561668)
    CD8
    suggested: (BD Biosciences Cat# 564526, RRID:AB_2744458)
    CD3
    suggested: (BioLegend Cat# 344846, RRID:AB_2800923)
    CD4
    suggested: (BD Biosciences Cat# 565996, RRID:AB_2739447)
    For detection of intracellular cytokines, cells were resuspended in 50 µL Perm/Wash buffer containing a cocktail of anti-human antibodies including IFNγ BV480 (BD, 566100, clone B27), TNFα BV605 (Biolegend, 502936, clone MAb11), IL17 BV785 (Biolegend, 512338, clone BL168), IL21 PE (Biolegend, 513004, clone 3A3-N2), and IL2 APC (Thermo, 17-7029-82, clone MQ1-17H12) and were incubated for 30 min at 4°C.
    anti-human antibodies including IFNγ BV480
    suggested: None
    TNFα
    suggested: None
    IL17
    suggested: (BioLegend Cat# 512338, RRID:AB_2566765)
    IL2 APC
    suggested: (Thermo Fisher Scientific Cat# 17-7029-82, RRID:AB_469492)
    Experimental Models: Cell Lines
    SentencesResources
    To generate the lentivirus we transfected 293T packaging cell line (ATCC CRL-3216) with the pLVX lentiviral vector containing TCR_4.1-mCherry or TCR_6.3-mCherry insert, psPAX2 packaging plasmid (Addgene plasmid #12260), and pMD2.
    293T
    suggested: None
    Jurkat peptide stimulation: Jurkat 76.7 cells expressing TCRs 4.1 and 6.3 (2.5×105) were co-cultured with PBMCs from SARS-CoV-2 naive DPB1*:04:01-positive donor (6×105) pulsed with 1 µM of CTFEYVSQPFLMDLE peptide, 1 µg/mL each of anti-human CD28 (BD Biosciences 555725) and CD49d (BD Biosciences 555501)
    Jurkat
    suggested: None
    Jurkat 76.7
    suggested: None
    Recombinant DNA
    SentencesResources
    These sequences were cloned into the pLVX-EF1α-IRES-Puro lentiviral expression vector (Clontech).
    pLVX-EF1α-IRES-Puro
    suggested: None
    To generate the lentivirus we transfected 293T packaging cell line (ATCC CRL-3216) with the pLVX lentiviral vector containing TCR_4.1-mCherry or TCR_6.3-mCherry insert, psPAX2 packaging plasmid (Addgene plasmid #12260), and pMD2.
    pLVX
    suggested: RRID:Addgene_101121)
    psPAX2
    suggested: RRID:Addgene_12260)
    pMD2
    suggested: None
    Briefly, HLA-DP4 CLIP was expressed in Trichoplusia Ni (Hi5) insect cells via a pFastBac-Dual construct encoding HLA-DP4 α- and β- chains with C-terminal fos/jun zipper domain.
    pFastBac-Dual
    suggested: RRID:Addgene_135584)
    Software and Algorithms
    SentencesResources
    Samples were then run on a Cytek Aurora spectral flow cytometer using SpectroFlo v2.2 software (Cytek) and analyzed using FlowJo software (v10.8.0, BD).
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Tetramer responses over time in Figures 3 and 4 were graphed in Prism (v9.1.0,
    Prism
    suggested: (PRISM, RRID:SCR_005375)
    GraphPad Software,
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Cells were analyzed by flow cytometry on a custom-configured BD Fortessa using FACSDiva software (Becton Dickinson)
    FACSDiva
    suggested: (BD FACSDiva Software, RRID:SCR_001456)
    Cells were washed twice in FACS and analyzed by flow cytometry on a Cytek Aurora spectral flow cytometer using SpectroFlo v2.2 software (Cytek) and analyzed using FlowJo v10.7.1 software (TreeStar).
    SpectroFlo
    suggested: None
    stringdist and igraph R packages were used to build TCR similarity network, gephi software was used for TCR similarity networks layout and visualisation and ggplot2 library for other visualisations.
    ggplot2
    suggested: (ggplot2, RRID:SCR_014601)

    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:
    Our study has several limitations, including the small number of subjects and the lack of comprehensive epitope mapping beyond the immunodominant response we identified. There are several questions that we did not address that will be useful topics for future studies, including the extent of clonal overlap between the blood and lymph node CD4+ T cell compartments, and the transcriptional profiles of the lymph node TFH response over the long period of clonal stability. In conclusion, we find that mRNA vaccine technology has an exceptional ability to induce high-frequency antigen-specific B cell (Turner et al., 2021) and antigen-specific CD4+ TFH cell responses in the human lymph node following prime-boost administration. These characteristics underlie the development of high titer neutralizing antibodies and protection from infection in vaccinated individuals. The selective enhancement of lymph node TFH responses induced by vaccine regimens represents a broad strategy for improving future vaccines.

    Results from TrialIdentifier: We found the following clinical trial numbers in your paper:

    IdentifierStatusTitle
    NCT04362995RecruitingSt. Jude Tracking of Viral and Host Factors Associated With …

    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 10.1101/2021.09.08.459485 on bioRxiv