Single-cell profiling of the antigen-specific response to BNT162b2 SARS-CoV-2 RNA vaccine
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Abstract
RNA-based vaccines against SARS-CoV-2 have proven critical to limiting COVID-19 disease severity and spread. Cellular mechanisms driving antigen-specific responses to these vaccines, however, remain uncertain. Here we identify and characterize antigen-specific cells and antibody responses to the RNA vaccine BNT162b2 using multiple single-cell technologies for in depth analysis of longitudinal samples from a cohort of healthy participants. Mass cytometry and unbiased machine learning pinpoint an expanding, population of antigen-specific memory CD4 + and CD8 + T cells with characteristics of follicular or peripheral helper cells. B cell receptor sequencing suggest progression from IgM, with apparent cross-reactivity to endemic coronaviruses, to SARS-CoV-2-specific IgA and IgG memory B cells and plasmablasts. Responding lymphocyte populations correlate with eventual SARS-CoV-2 IgG, and a participant lacking these cell populations failed to sustain SARS-CoV-2-specific antibodies and experienced breakthrough infection. These integrated proteomic and genomic platforms identify an antigen-specific cellular basis of RNA vaccine-based immunity.
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SciScore for 10.1101/2021.07.28.453981: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Consent: Informed consent was obtained, and a baseline health questionnaire was also completed. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources In vitro characterization of CD38+ICOS+ Cells: Quantification of CD38+ICOS+ CD4 and CD8 T cells by flow cytometry: To quantify CD38+ICOS+ CD4 and CD8 T cells, PBMCs were first resuspended with Human TruStain Fcx (Biolegend) for 10 minutes at room temperature and then stained with the following antibodies in FACS buffer (PBS+ 2% fetal bovine serum): CD8a e450 (Invitrogen 48-0086-42, CD38+ICOS+suggested: NoneSciScore for 10.1101/2021.07.28.453981: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Consent: Informed consent was obtained, and a baseline health questionnaire was also completed. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources In vitro characterization of CD38+ICOS+ Cells: Quantification of CD38+ICOS+ CD4 and CD8 T cells by flow cytometry: To quantify CD38+ICOS+ CD4 and CD8 T cells, PBMCs were first resuspended with Human TruStain Fcx (Biolegend) for 10 minutes at room temperature and then stained with the following antibodies in FACS buffer (PBS+ 2% fetal bovine serum): CD8a e450 (Invitrogen 48-0086-42, CD38+ICOS+suggested: NoneCD4suggested: NoneAdditional intracellular antibodies were: TNF-a AF488 (Biolegend 502915, 1:100) AF488suggested: NoneExperimental Models: Cell Lines Sentences Resources Triplicate wells containing virus only (maximal CPE in the absence of mAb) and wells containing only Vero cells in medium (no-CPE wells) were included as controls. Verosuggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)Software and Algorithms Sentences Resources Mass cytometry datasets in this manuscript have been deposited in FlowRepository (http://flowrepository.org/). FlowRepositorysuggested: (FLOWRepository, RRID:SCR_013779)Comparisons of population frequencies pre- and post-vaccination as well as correlations between post-vaccine cell frequencies and IgG titers were done in GraphPad Prism version 9.0. GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)Cells were analyzed on a Miltenyi MACSQuant16 Analyzer with single-stain control PBMC samples used for compensation conducted in FlowJo v10.6.2. FlowJosuggested: (FlowJo, RRID:SCR_008520)) sequencing core at an appropriate target concentration for 10X Genomics library preparation and subsequent sequencing. Genomicssuggested: (UTHSCSA Genomics Core, RRID:SCR_012239)Briefly, 50 μL of cell culture medium (DMEM supplemented with 2% FBS) was added to each well of a 96-well E-plate using a ViaFlo384 liquid handler (Integra Biosciences) to obtain background reading. Integra Biosciencessuggested: NoneRTCA IC50 values were determined by nonlinear regression analysis using Prism software. Prismsuggested: (PRISM, RRID:SCR_005375)Single-Cell RNA-Seq analysis: Single-cell analysis was performed using Seurat v4.0.0 (14) Seuratsuggested: (SEURAT, RRID:SCR_007322)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: Please consider improving the rainbow (“jet”) colormap(s) used on pages 34, 35, 36 and 50. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
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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