Impaired humoral immunity to SARS-CoV-2 BNT162b2 vaccine in kidney transplant recipients and dialysis patients

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1. Version published to 10.1126/sciimmunol.abj1031

   Jun 15, 2021
2. 

   ScreenIT

   Apr 24, 2021

   SciScore for 10.1101/2021.04.15.21255550: (What is this?)

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

   Table 1: Rigor

   Ethics	Consent: All participants gave written informed consent according to the approval of the ethics committee at the Charité University Hospital Berlin (EA2/010/21, EA4/188/20), the ethics committee of Saxony-Anhalt (EA7/21) and the ethics committee of the University of Greifswald (BB019/21). IRB: All participants gave written informed consent according to the approval of the ethics committee at the Charité University Hospital Berlin (EA2/010/21, EA4/188/20), the ethics committee of Saxony-Anhalt (EA7/21) and the ethics committee of the University of Greifswald (BB019/21).
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line …

   SciScore for 10.1101/2021.04.15.21255550: (What is this?)

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

   Table 1: Rigor

   Ethics	Consent: All participants gave written informed consent according to the approval of the ethics committee at the Charité University Hospital Berlin (EA2/010/21, EA4/188/20), the ethics committee of Saxony-Anhalt (EA7/21) and the ethics committee of the University of Greifswald (BB019/21). IRB: All participants gave written informed consent according to the approval of the ethics committee at the Charité University Hospital Berlin (EA2/010/21, EA4/188/20), the ethics committee of Saxony-Anhalt (EA7/21) and the ethics committee of the University of Greifswald (BB019/21).
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	Authentication: Annotation of clusters was performed manually by visual inspection of typical marker genes for cell-types and cell-states.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   For flow cytometric analysis, the following fluorochrome-labeled antibodies were used: BUV737 anti-CD11c (BD, clone B-ly6, 1:50),	anti-CD11c suggested: None
   APC-Cy7 anti-CD38 (Biolegend, clone HIT2, 1:1000)	APC-Cy7 suggested: (BD Biosciences Cat# 338430, RRID:AB_647374) anti-CD38 suggested: (LSBio (LifeSpan Cat# LS-C84991-1000, RRID:AB_10967217)
   After incubation for 60 minutes at 37°C, wells were washed 3 times and the peroxidase-labelled anti-IgG or anti-IgA antibody solution was added, followed by a second incubation step for 30 min.	anti-IgG suggested: None anti-IgA suggested: None
   Surrogate SARS-CoV-2 neutralization test (GenScript): This blocking ELISA qualitatively detects anti-SARS-CoV-2 antibodies suppressing the interaction between the receptor binding domain (RBD) of the viral spike glycoprotein (S) and the angiotensin-converting enzyme 2 (ACE2) protein on the surface of cells.	anti-SARS-CoV-2 suggested: None ACE2 suggested: None
   The absorbance of the sample is inversely correlated with the amount of SARS-CoV-2 neutralizing antibodies.	SARS-CoV-2 neutralizing antibodies . suggested: None
   Enriched cells were incubated with Fc Blocking Reagent (Milteniy Biotec) following manufacturer’s instructions and subsequently stained up to 107 lymphocytes per 100µL for 30min at 4°C with the following fluorophore-conjugated anti-human antibodies:, VioBlue anti-CD14 (Miltenyi Biotec, Clone TÜK4, 1:200), VioBlue anti-CD16 (Miltenyi Biotec, clone VEP13, 1:50)	anti-human antibodies: , VioBlue anti-CD14 ( Miltenyi Biotec , suggested: None anti-CD16 suggested: (Miltenyi Biotec Cat# 130-098-102, RRID:AB_2661280)
   , clone HIT2, 1:25), and the following TotalSeq-C oligomer-conjugated anti-human antibodies: CD138 (clone DL-1021, 1:50),	anti-human antibodies: CD138 suggested: None
   To allow for sequencing of pools of cells from different donors, cells were also incubated with TotalSeq oligomer-conjugated hashtag antibodies (TotalSeq-C anti-human Hashtag antibody 1 to 4 from BioLegend, 1:250).	anti-human Hashtag antibody 1 to 4 suggested: None
   Software and Algorithms
   Sentences	Resources
   Study participants: Peripheral blood samples (EDTA anti-coagulated or serum-tubes, BD Vacutainersystem, BD Diagnostics, Franklin Lakes, NJ, USA) from 25 healthy controls, 40 hemodialysis patients, 4 peritoneal dialysis patients and 40 kidney transplant recipients were collected at 7 ± 2 days after the second dose of SARS-CoV-2 BNT162b2 vaccination.	BD Diagnostics suggested: None
   Single Cell RNA-library preparation and sequencing: Single cell suspensions were obtained by cell sorting and applied to the 10x Genomics workflow for cell capturing and scRNA gene expression (GEX) and CiteSeq library preparation using the Chromium Single Cell 5’ Library & Gel Bead Kit as well as the Single Cell 5’ Feature Barcode Library Kit (10x Genomics).	CiteSeq suggested: None
   The cellranger output was further analyzed in R using the Seurat package (version 3.2.2) (39).	Seurat suggested: (SEURAT, RRID:SCR_007322)
   Flow cytometric data were analyzed by FlowJo software 10.7.1 (TreeStar, Ashland, OR, USA).	FlowJo suggested: (FlowJo, RRID:SCR_008520)
   GraphPad Prism Version 5 (GraphPad software, San Diego, CA, USA) was used for statistical analysis.	GraphPad 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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

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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: Please consider improving the rainbow (“jet”) colormap(s) used on pages 24, 20 and 22. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

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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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3. 

   Version published to 10.1101/2021.04.15.21255550v1 on medRxiv

   Apr 20, 2021