mRNA vaccine-induced T cells respond identically to SARS-CoV-2 variants of concern but differ in longevity and homing properties depending on prior infection status
Curation statements for this article:-
Curated by eLife
Evaluation Summary:
This work will be of broad interest to those studying adaptive immunity to SARS-CoV-2, particularly with a focus on T cell immunology. The study confirms that mRNA vaccine-elicited T cell responses maintain recognition of peptides derived from VOC, and provides phenotypic characterisation of spike-specific T cells from both convalescent and infection-naive subjects.
(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)
This article has been Reviewed by the following groups
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Abstract
While mRNA vaccines are proving highly efficacious against SARS-CoV-2, it is important to determine how booster doses and prior infection influence the immune defense they elicit, and whether they protect against variants. Focusing on the T cell response, we conducted a longitudinal study of infection-naïve and COVID-19 convalescent donors before vaccination and after their first and second vaccine doses, using a high-parameter CyTOF analysis to phenotype their SARS-CoV-2-specific T cells. Vaccine-elicited spike-specific T cells responded similarly to stimulation by spike epitopes from the ancestral, B.1.1.7 and B.1.351 variant strains, both in terms of cell numbers and phenotypes. In infection-naïve individuals, the second dose boosted the quantity and altered the phenotypic properties of SARS-CoV-2-specific T cells, while in convalescents the second dose changed neither. Spike-specific T cells from convalescent vaccinees differed strikingly from those of infection-naïve vaccinees, with phenotypic features suggesting superior long-term persistence and ability to home to the respiratory tract including the nasopharynx. These results provide reassurance that vaccine-elicited T cells respond robustly to emerging viral variants, confirm that convalescents may not need a second vaccine dose, and suggest that vaccinated convalescents may have more persistent nasopharynx-homing SARS-CoV-2-specific T cells compared to their infection-naïve counterparts.
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Author Response:
Reviewer #1:
In this study, the authors use CyTOF-based analysis to characterise spike-specific T cell responses following mRNA vaccination. They seek to understand both the breadth of responses to 'wildtype'-like and variant spikes, as well as the differences between T cell responses from convalescent and previously uninfected subjects. Consistent with other studies, they find that spike-specific T cell responses are similar across different variants, both in frequency and phenotype. In contrast, however, they identify several phenotypic differences in the T cell response elicited by infection, vaccination, or vaccination following infection.
Despite a somewhat limited sample size, they clearly identify changes in memory phenotype and chemokine receptor expression that may affect T cell trafficking to mucosal …
Author Response:
Reviewer #1:
In this study, the authors use CyTOF-based analysis to characterise spike-specific T cell responses following mRNA vaccination. They seek to understand both the breadth of responses to 'wildtype'-like and variant spikes, as well as the differences between T cell responses from convalescent and previously uninfected subjects. Consistent with other studies, they find that spike-specific T cell responses are similar across different variants, both in frequency and phenotype. In contrast, however, they identify several phenotypic differences in the T cell response elicited by infection, vaccination, or vaccination following infection.
Despite a somewhat limited sample size, they clearly identify changes in memory phenotype and chemokine receptor expression that may affect T cell trafficking to mucosal tissues across infection and vaccination. While inclusion of additional chemokine receptors (such as CXCR3) in the CyTOF panel would have aided in characterising these cells, this data highlights how infection and vaccination may elicit distinct T cell responses.
In fact CXCR3 and CCR4 were chemokine receptors that were considered for the panel, but could not be included as antibodies against these antigens do not stain properly on cells fixed with paraformaldehyde (PFA), and for logistical and biosafety reasons the specimens analyzed in this study had to be PFA-fixed before CyTOF staining. Although we have previously analyzed expression of CXCR3 and CCR4 on T cells by CyTOF (Cavrois et al, Cell Reports 2017 20(4):984 PMID: 28746881; Xie et al, Cell Reports 2021 35(4):109038 PMID: 33910003), those studies were exclusively performed on viable cells, and not on COVID-19 patient specimens. All our prior CyTOF phenotyping studies using COVID-19 patient specimens (Neidleman et al, Cell Reports Medicine 2020 1(6):100081 PMID: 32839763; Neidleman et al, Cell Reports 2021 36(3):109414 PMID: 34260965; Ma et al, J Immunol 207(5):1344, PMID 34389625), as well as some of our non-COVID-19 studies (Ma et al, Elife 9:e55487 PMID: 32452381; Neidleman et al, Elife 2020 9:e60933 PMID: 32990219), were performed on fixed cells, where CXCR3 and CCR4 unfortunately could not be included as parameters analyzed.
Future studies will be required to better assess the functional impacts of these phenotypic differences on T cell recall and contribution to protective immunity.
We absolutely agree that future studies should be pursued to better assess the functional impacts of the phenotypic differences on T cell recall, and on contribution to protective immunity. Such studies will most certainly require use of animal models, and in fact are studies that we have just begun (mouse model) or will soon begin (non-human primate model). To fully acknowledge the need for such functional studies, we have now added to multiple sections of the Discussion the need for future studies to incorporate animal models (Line 472 and Lines 488-491), including the statement “Such follow-up studies should also examine the functional outcomes of the discoveries made here (e.g., effect of chemokine receptor expression on homing of infection- and vaccine-elicited SARS-CoV-2-specific T cells), including in animal models of SARS-CoV-2 infection.”
Reviewer #2:
The authors address an important question, whether it people who have had Covid19 and are then vaccinated with one mRNA Spike vaccines made better immune responses than those who had not previously been infected and have two shots of the vaccine. They also compare responses to different virus variants and find extensive cross reactions and no differences between the groups - an important result.Their main finding is a difference in the quality of the CD4+ T cells in the 'Covid-vaccinees' compared to the 'naive double vaccines'. They suggest that T cells in the former may home better to the respiratory tract and persist longer.
The major strengths are:
• The methodology used, based on Cytof multiparameter analysis of antigen responding CD4 and CD8 T cells.
• Demonstration that the second vaccine dose in the naive group 'improves' the T cell response.
• Demonstration that a second vaccination in the Covid19 group does not improve the T cells.
We thank the Reviewer for the nice summary and for the positive comments.
Weaknesses:
Fully (and commendably) acknowledged in the manuscript:
• The study groups are small
• The antigen specific T cells are stimulated in vitro so may be distorted, nevertheless there were still differences
We agree with the Reviewer about the listed weaknesses of the study. We note that we had in our original manuscript acknowledged all these weaknesses within our “Limitations” section, including the fact that we had to stimulate our samples to identify and characterize the SARS- CoV-2-specific T cells. We have now expanded the part about our having stimulated the samples, by proposing that future studies should take advantage of tetramer technology to characterize cells in their baseline (non-stimulated) states, whilst acknowledging that such studies would for the most part be limited to CD8+ T cell responses as tetramer reagents for CD4+ T cells are less robust (Lines 500-506).
Not acknowledged but possibly outside the scope of this study:
• The reader will wonder how this affects the antibody response which ultimately is the main protector from reinfection and also how the T cell responses might impact on disease severity after post vaccination (re)-inrfection
Serological assays were not performed in this study; however we fully agree with the importance of associating the in-depth phenotypes of vaccine-elicited SARS-CoV-2-specific T cells with the antibody response. In fact, just as we went very “deep” into the phenotypes of SARS-CoV-2-specific T cells in this study, we are at the moment optimizing techniques to, in an analogous fashion, deeply characterize the serological response to vaccination. This entails optimizing a flow cytometry-based approach we recently introduced and implemented on a small number of specimens (Ma et al, J Immunol 207(5):1344, PMID 34389625), to be able to simultaneously assess the levels of IgA1, IgA2, IgE, IgG1, IgG2, IgG3, IgG4, and IgM against the S1, S2, and RBD domains of the SARS-CoV-2 spike protein in a large number of patient specimens. Once we’ve optimized the assay and applied it on the vaccine specimens, we plan to associate the resulting 24-parameter serological datasets (8 isotypes of antibodies each against 3 antigens = 24 parameters total) with the high-dimensional SARS-CoV-2-specific T cell datasets from this study, but that will be its own separate (and large) study and beyond the scope of this current one. As generating such serological data will take at least 3-6 months to complete, and the focus of this study is on SARS-CoV-2-specific T cells (and all conclusions we drew were based only on the T cell data), we think it appropriate that we limit this study to deep-phenotyping of the T cells. We have now brought up in the last part of our “Limitations” section the lack of serological analysis in this current study as a limitation, and how follow-up studies should associate serological responses with the T cell responses characterized here. (Lines 506-511: “A final limitation is that serological analyses were not performed in this study. As coordination between the humoral and cellular arms of immunity are likely key to effectively controlling viral replication, future studies should assess to what extent the breadth, isotypes, and functional features of spike-specific antibodies elicited by vaccination associate with the herein described phenotypic features of vaccine-elicited SARS-CoV-2-specific T cells.”)
With regards to how T cell responses might impact disease severity and breakthrough infections, this is an aspect we are very interested in investigating, as detailed in our final response further below.
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Evaluation Summary:
This work will be of broad interest to those studying adaptive immunity to SARS-CoV-2, particularly with a focus on T cell immunology. The study confirms that mRNA vaccine-elicited T cell responses maintain recognition of peptides derived from VOC, and provides phenotypic characterisation of spike-specific T cells from both convalescent and infection-naive subjects.
(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)
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Reviewer #1 (Public Review):
In this study, the authors use CyTOF-based analysis to characterise spike-specific T cell responses following mRNA vaccination. They seek to understand both the breadth of responses to 'wildtype'-like and variant spikes, as well as the differences between T cell responses from convalescent and previously uninfected subjects. Consistent with other studies, they find that spike-specific T cell responses are similar across different variants, both in frequency and phenotype. In contrast, however, they identify several phenotypic differences in the T cell response elicited by infection, vaccination, or vaccination following infection.
Despite a somewhat limited sample size, they clearly identify changes in memory phenotype and chemokine receptor expression that may affect T cell trafficking to mucosal tissues …
Reviewer #1 (Public Review):
In this study, the authors use CyTOF-based analysis to characterise spike-specific T cell responses following mRNA vaccination. They seek to understand both the breadth of responses to 'wildtype'-like and variant spikes, as well as the differences between T cell responses from convalescent and previously uninfected subjects. Consistent with other studies, they find that spike-specific T cell responses are similar across different variants, both in frequency and phenotype. In contrast, however, they identify several phenotypic differences in the T cell response elicited by infection, vaccination, or vaccination following infection.
Despite a somewhat limited sample size, they clearly identify changes in memory phenotype and chemokine receptor expression that may affect T cell trafficking to mucosal tissues across infection and vaccination. While inclusion of additional chemokine receptors (such as CXCR3) in the CyTOF panel would have aided in characterising these cells, this data highlights how infection and vaccination may elicit distinct T cell responses. Future studies will be required to better assess the functional impacts of these phenotypic differences on T cell recall and contribution to protective immunity.
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Reviewer #2 (Public Review):
The authors address an important question, whether it people who have had Covid19 and are then vaccinated with one mRNA Spike vaccines made better immune responses than those who had not previously been infected and have two shots of the vaccine. They also compare responses to different virus variants and find extensive cross reactions and no differences between the groups - an important result.Their main finding is a difference in the quality of the CD4+ T cells in the 'Covid-vaccinees' compared to the 'naive double vaccines'. They suggest that T cells in the former may home better to the respiratory tract and persist longer.
The major strengths are:
• The methodology used, based on Cytof multiparameter analysis of antigen responding CD4 and CD8 T cells.
• Demonstration that the second vaccine dose in the …
Reviewer #2 (Public Review):
The authors address an important question, whether it people who have had Covid19 and are then vaccinated with one mRNA Spike vaccines made better immune responses than those who had not previously been infected and have two shots of the vaccine. They also compare responses to different virus variants and find extensive cross reactions and no differences between the groups - an important result.Their main finding is a difference in the quality of the CD4+ T cells in the 'Covid-vaccinees' compared to the 'naive double vaccines'. They suggest that T cells in the former may home better to the respiratory tract and persist longer.
The major strengths are:
• The methodology used, based on Cytof multiparameter analysis of antigen responding CD4 and CD8 T cells.
• Demonstration that the second vaccine dose in the naive group 'improves' the T cell response.
• Demonstration that a second vaccination in the Covid19 group does not improve the T cells.
Weaknesses:
Fully (and commendably) acknowledged in the manuscript:
• The study groups are small
• The antigen specific T cells are stimulated in vitro so may be distorted, nevertheless there were still differences
Not acknowledged but possibly outside the scope of this study:
• The reader will wonder how this affects the antibody response which ultimately is the main protector from reinfection and also how the T cell responses might impact on disease severity after post vaccination (re)-inrfection
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SciScore for 10.1101/2021.05.12.443888: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
No key resources detected.
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: As this study was aimed at using in-depth phenotypic characterization as a discovery tool, it focused on deeply interrogating many different conditions (e.g., spike variants, longitudinal sampling) rather than many donors. Therefore, although a …
SciScore for 10.1101/2021.05.12.443888: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
No key resources detected.
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: As this study was aimed at using in-depth phenotypic characterization as a discovery tool, it focused on deeply interrogating many different conditions (e.g., spike variants, longitudinal sampling) rather than many donors. Therefore, although a total of 120 CyTOF specimens were run, only 8 donors were analyzed. The findings reported here should be confirmed in larger cohorts. A second limitation of the study was the need to stimulate the specimens in order to identify and characterize the vaccine-elicited T cells. We limited peptide exposure to 6 hours to minimize phenotypic changes caused by the stimulation. We note that at this time, stimulation with peptides is the only way to identify SARS-CoV-2-specific CD4+ T cells as robust MHC class II multimer reagents for SARS-CoV-2 are not available currently. Finally, the analysis focused on CD4+ T cells because the overall numbers of detectable spike-specific CD8+ T cells were low. Nonetheless, the main findings we made with the CD4+ T cells – that they recognize variants equivalently, and that the phenotypes of the responding cells differ by prior SARS-CoV- 2 natural infection status – were recapitulated among CD8+ T cells. Additional studies in a larger number of participants testing more cells, and implementing the use of MHC class I tetramers, would increase the ability to characterize in greater depth the vaccine-elicited CD8+ T cell response.
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.
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