Peripheral and lung resident memory T cell responses against SARS-CoV-2

  1. Judith Grau-Expósito
  2. Nerea Sánchez-Gaona
  3. Núria Massana
  4. Marina Suppi
  5. Antonio Astorga-Gamaza
  6. David Perea
  7. Joel Rosado
  8. Anna Falcó
  9. Cristina Kirkegaard
  10. Ariadna Torrella
  11. Bibiana Planas
  12. Jordi Navarro
  13. Paula Suanzes
  14. Daniel Álvarez-Sierra
  15. Alfonso Ayora
  16. Irene Sansano
  17. Juliana Esperalba
  18. Cristina Andrés
  19. Andrés Antón
  20. Santiago Ramón y Cajal
  21. Benito Almirante
  22. Ricardo Pujol-Borrell
  23. Vicenç Falcó
  24. Joaquín Burgos
  25. María J. Buzón
  26. Meritxell Genescà

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Abstract

Resident memory T cells (T RM ) positioned within the respiratory tract are probably required to limit SARS-CoV-2 spread and COVID-19. Importantly, T RM are mostly non-recirculating, which reduces the window of opportunity to examine these cells in the blood as they move to the lung parenchyma. Here, we identify circulating virus-specific T cell responses during acute infection with functional, migratory and apoptotic patterns modulated by viral proteins and associated with clinical outcome. Disease severity is associated predominantly with IFNγ and IL-4 responses, increased responses against S peptides and apoptosis, whereas non-hospitalized patients have increased IL-12p70 levels, degranulation in response to N peptides and SARS-CoV-2-specific CCR7 + T cells secreting IL-10. In convalescent patients, lung-T RM are frequently detected even 10 months after initial infection, in which contemporaneous blood does not reflect tissue-resident profiles. Our study highlights a balanced anti-inflammatory antiviral response associated with a better outcome and persisting T RM cells as important for future protection against SARS-CoV-2 infection.

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  1. Version published to 10.1038/s41467-021-23333-3
  2. Version published to 10.21203/rs.3.rs-198819/v1 on Research Square
  3. Version published to 10.1101/2020.12.02.20238907v3 on medRxiv
  4. Version published to 10.1101/2020.12.02.20238907v2 on medRxiv
  5. ScreenIT

    SciScore for 10.1101/2020.12.02.20238907: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Ethics statement: This study was performed in accordance with the Declaration of Helsinki and approved by the corresponding Institutional Review Board (PR(AG)192/2020 and PR(AG)212/2020) of the Vall d’Hebron University Hospital (HUVH), Barcelona, Spain.
    Consent: Written informed consent was provided by all patients recruited to this study and samples were prospectively collected and cryopreserved in the Vall d’Hebron Research Institute.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Cell surface antibody staining included anti-CD3 (Per-CP), anti-CD4 (BV605) and anti-CD56 (FITC) (all from BD Biosciences).
    anti-CD4
    suggested: None
    anti-CD56
    suggested: None
    , anti-CD3 (BV650, BD Biosciences) and anti-CD45 (BV605, BD Biosciences) antibodies.
    anti-CD3
    suggested: None
    anti-CD45
    suggested: None
    Cells were subsequently fixed and permeabilized using the FoxP3 Fix/Perm kit (BD Biosciences) and stained with anti-IL-4 (PE-Cy7, eBioscience), anti-IL-10 (PE, BD Biosciences), anti-T-bet (BV421, Biolegend) and anti-IFNg (AF700, Invitrogen) antibodies.
    anti-IL-4
    suggested: None
    PE-Cy7
    suggested: (Bioss Cat# bs-0698R-PE-Cy7, RRID:AB_11041615)
    anti-IL-10
    suggested: None
    anti-T-bet ( BV421
    suggested: None
    anti-IFNg
    suggested: None
    2 serology: Serological status of HL24, HL27, HL52, HL65 and HL69 patients was determined in serum using two commercial chemiluminescence immunoassays (CLIA) targeting specific SARS-CoV-2 antibodies: 1) Elecsys® Anti-SARS-CoV-2 (Roche Diagnostics, USA) was performed on the Cobas 8800 system (Roche Diagnostics, USA) for qualitative determination of total antibodies (including IgG, IgM and IgA) against nucleocapsid SARS-CoV-2 protein; and 2) Liaison SARS- CoV-2 S1/S2 IgG (DiaSorin, Italy) was performed on the LIAISON® XL Analyzer (DiaSorin, Italy) for quantitative determination of IgG against the spike (S) glycoprotein subunits 1 and 2 (S1/S2).
    Anti-SARS-CoV-2
    suggested: None
    glycoprotein subunits 1
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    The experiment controls used were infected and non-infected HeLA cells.
    HeLA
    suggested: CLS Cat# 300194/p772_HeLa, RRID:CVCL_0030)
    Software and Algorithms
    SentencesResources
    COVID-19 diagnosis was performed by two commercial RT-PCR-based assays, Allplex™ 2019- nCoV (Seegene, Korea) or Cobas® SARS-CoV-2 (Roche Diagnostics, USA) tests.
    Allplex™
    suggested: None
    Statistical analyses: Flow cytometry data was analyzed using FlowJo v10.7.1 software (TreeStar).
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Data and statistical analyses were performed using Prism 7.0 (GraphPad Software, La Jolla, CA, USA), unless otherwise stated.
    Prism
    suggested: (PRISM, RRID:SCR_005375)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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:
    We acknowledge that our study has several limitations, one being that sample size for the different groups was small to be conclusive. However, this was compensated by a narrow window of sampling during acute infection (7-16 days, post-symptoms onset) and by a comprehensive clinical characterization to stratify patients to study groups. In this sense, multiple correlations support our main findings and provide strength to our data, which is also largely supported by current literature. Further, identification of the precise phenotypes generating antigen-specific T responses, such as Tregs for IL-10, or the consideration of other T lymphocytes such as gdT cells should also be considered in future studies. Last, only five lung biopsies obtained from very different COVID-19 convalescent patients could be studied. While these patients are so far scarce, the immune responses identified in those samples not only contributed to round out the present report, but also represent the first evidence to our knowledge of persisting SARS-CoV-2- specific TRM in the lung. Disease severity during acute SARS-CoV-2 infection is associated with strong peripheral T and B cell responses4, 27, which not only may relate to antigenic burden but, also could potentially translate into a significant proportion of antigen-specific TRM in the lung once the patient recovers. Remaining important questions concern the level of viral replication and associated symptomatology that will stimulate an effective im...

    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.

    About SciScore

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  6. Version published to 10.1101/2020.12.02.20238907v1 on medRxiv