Germinal center responses to SARS-CoV-2 mRNA vaccines in healthy and immunocompromised individuals

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1. Version published to 10.1016/j.cell.2022.01.027

   Mar 1, 2022
2. 

   ScreenIT

   Sep 27, 2021

   SciScore for 10.1101/2021.09.16.21263686: (What is this?)

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

   Table 1: Rigor

   Ethics	Consent: Written informed consent for participation was obtained according to the Declaration of Helsinki and protocols were approved by the Institutional Review Board of the University of Pennsylvania. IRB: Written informed consent for participation was obtained according to the Declaration of Helsinki and protocols were approved by the Institutional Review Board of the University of Pennsylvania.
   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
   After resting overnight, CD40 blocking antibody was added to both duplicate wells for 15 minutes …

   SciScore for 10.1101/2021.09.16.21263686: (What is this?)

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

   Table 1: Rigor

   Ethics	Consent: Written informed consent for participation was obtained according to the Declaration of Helsinki and protocols were approved by the Institutional Review Board of the University of Pennsylvania. IRB: Written informed consent for participation was obtained according to the Declaration of Helsinki and protocols were approved by the Institutional Review Board of the University of Pennsylvania.
   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
   After resting overnight, CD40 blocking antibody was added to both duplicate wells for 15 minutes prior to stimulation.	CD40 suggested: None
   Plates were then washed again with PBS-T three times and 50 µl of horseradish peroxidase (HRP)–labeled goat anti-human IgG (1:5000; Jackson ImmunoResearch Laboratories) secondary antibodies was added.	anti-human IgG suggested: None
   Serum antibody concentrations were reported as arbitrary units relative to the CR3022 monoclonal antibody.	CR3022 suggested: None
   Also included in this mixture to neutralize any potential VSV-G carryover virus was 1E9F9, a mouse anti-VSV Indiana G, at a concentration of 600 ng/ml (Absolute Antibody).	anti-VSV suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   SARS-CoV-2 RBD and FL proteins were produced in 293F cells and purified using nickel–nitrilotriacetic acid (Ni-NTA) resin (Qiagen).	293F suggested: RRID:CVCL_D615)
   Pseudovirus neutralization assay: Production of VSV pseudotypes with SARS-CoV-2 S: 293T cells plated 24 hours previously at 5 × 106 cells per 10 cm dish were transfected using calcium phosphate with 35 µg of pCG1 SARS-CoV-2 S D614G delta18 or pCG1 SARS-CoV-2 S B.1.351 delta 18 expression plasmid encoding a codon optimized SARS-CoV2 S gene with an 18 residue truncation in the cytoplasmic tail (kindly provided by Stefan Pohlmann).	293T suggested: None
   Vero E6 cells stably expressing TMPRSS2 were seeded in 100 µl at 2.5×104 cells/well in a 96 well collagen coated plate.	Vero E6 suggested: None
   The serum-virus mixture was then used to replace the media on VeroE6 TMPRSS2 cells.	VeroE6 TMPRSS2 suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
   Recombinant DNA
   Sentences	Resources
   Pseudovirus neutralization assay: Production of VSV pseudotypes with SARS-CoV-2 S: 293T cells plated 24 hours previously at 5 × 106 cells per 10 cm dish were transfected using calcium phosphate with 35 µg of pCG1 SARS-CoV-2 S D614G delta18 or pCG1 SARS-CoV-2 S B.1.351 delta 18 expression plasmid encoding a codon optimized SARS-CoV2 S gene with an 18 residue truncation in the cytoplasmic tail (kindly provided by Stefan Pohlmann).	pCG1 SARS-CoV-2 suggested: None pCG1 suggested: None
   Software and Algorithms
   Sentences	Resources
   . viSNE analysis: viSNE analysis was performed on Cytobank (https://cytobank.org).	Cytobank suggested: (Cytobank, RRID:SCR_014043)
   AIM assay data were visualized using RStudio.	RStudio suggested: (RStudio, RRID:SCR_000432)
   Statistical analysis: GraphPad Prism software version 9 was used for generating dot plots, bar plots and the correlation images presented in this work.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)

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   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).

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   Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

   These limitations emphasize the need for directly probing GC responses by adopting minimally invasive approaches, such as fine-needle-aspiration, that allow longitudinal sampling of the vaccine draining lymph nodes without requiring their surgical excision. Only two published studies ever described human GC responses to vaccination (against influenza or SARS-CoV-2) in humans by using the FNA technique (Turner et al., 2020, 2021). One study (Turner et al., 2021), reported S-specific GC B cell responses to SARS-CoV-2 mRNA vaccination in lymph nodes, but did not investigate the generation of RBD-specific GC B cells or the connection between SARS-CoV-2-specific GC B cells and Tfh cells, nAbs, and SARS-CoV-2-specific memory B cells. Our study sought to address these open questions by performing an in-depth profiling of the GC responses elicited by SARS-CoV-2 mRNA vaccines directly in lymphoid tissue. We found that these vaccines prompted the formation of robust Full S and RBD-specific GC B cell as well as Tfh cell responses localized in draining axillary lymph nodes. Importantly, our study revealed that lymphoid tissue SARS-CoV-2-specific GC B cell populations were strongly associated with the ability to produce SARS-CoV-2 nAbs, as further supported by the evidence that immunosuppressed individuals, who cannot form GCs, present a deeply blunted nAb production (Results in KTX are discussed at length below). Although to a lower degree, we also found that bona fide Tfh cells in drain...

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   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.

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   Results from scite Reference Check: We found no unreliable references.

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3. 

   Version published to 10.1101/2021.09.16.21263686v1 on medRxiv

   Sep 21, 2021