Allotypic variation in antigen processing controls antigenic peptide generation from SARS-CoV-2 S1 spike glycoprotein

  1. George Stamatakis
  2. Martina Samiotaki
  3. Ioannis Temponeras
  4. George Panayotou
  5. Efstratios Stratikos

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Abstract

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  1. Version published to 10.1016/j.jbc.2021.101329
  2. ScreenIT

    SciScore for 10.1101/2021.07.03.450989: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Database Search: The generated raw files were processed by the Proteome Discoverer software (Thermo
    Proteome Discoverer
    suggested: (Proteome Discoverer, RRID:SCR_014477)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Limitations of the study: While our study highlights the potential importance of ERAP1 allotypes in immune response variability between individuals, it has some important limitations that need to be taken into account when interpreting results. The in vitro nature of the digestions may not be an optimal surrogate for cellular antigen processing, either due to missing components (such as other peptidases) or due to cellular compartmentalization. HLA-restriction is only indirectly simulated and thus does not take into account kinetic components of peptide competition for binding inside the ER. Furthermore, although antigenic peptide destruction is evident when comparing the two reaction conditions, it is difficult to analyze statistically without an explicit set of 9mer peptides in the initial reaction. Finally, although our approach of concurrently analyzing hundreds of peptide-trimming reactions proved invaluable in identifying difference between trimming patterns of ERAP1 allotypes, the number of peptides used was not sufficient to allow for the explicit identification of sequence motifs in trimming preferences. The latter however may not be readily feasible given the large substrate cavity of ERAP1 that allows for a complex landscape of peptide-enzyme interactions30. Cytotoxic responses after vaccination – different response depending on ERAP1 allotype?: Although vaccines developed for COVID-19 had as a primary goal the induction of robust antibody responses, the generation...

    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.

    About SciScore

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  3. Version published to 10.1101/2021.07.03.450989v1 on bioRxiv