Generation of SARS-CoV-2 S1 Spike Glycoprotein Putative Antigenic Epitopes in Vitro by Intracellular Aminopeptidases

  1. George Stamatakis
  2. Martina Samiotaki
  3. Anastasia Mpakali
  4. George Panayotou
  5. Efstratios Stratikos

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Abstract

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  1. Version published to 10.1021/acs.jproteome.0c00457
  2. ScreenIT

    SciScore for 10.1101/2020.06.22.164681: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (23) partner repository with the dataset identifier PXD019901.
    PRIDE
    suggested: (Pride-asap, RRID:SCR_012052)
    Database Search: We employed the MaxQuant computational proteomics platform version 1.6.14.0 to search the peak lists against the Spike glycoprotein SARS2 FASTA file (Swissprot accession number P0DTC2) and a file containing 247 frequently observed contaminants.
    MaxQuant
    suggested: (MaxQuant, RRID:SCR_014485)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    While our experimental approach has limitations as discussed below, this finding suggests that intracellular antigen processing by aminopeptidases may constitute a major filter in determining which peptides will be presented by MHCI. Indeed, it has been recently proposed that the main function of ERAP1 is to limit the peptide pool available for MHCI (31). In this context, this experimental approach could be useful in optimizing bioinformatic predictions. Our findings provide new information on both the general biological functions of intracellular aminopeptidases that generate antigenic peptides as well as on specific processing of a key antigen from SARS-CoV-2. Specifically, our results highlight that each enzyme bears a unique trimming fingerprint to antigen processing. Although this has been suggested before based on differences in specificity towards specific peptide substrates (26, 32–34), it has not been observed in the context of peptide ensembles. This is potentially important since competition of different peptides for the cavity in these enzymes could result in complex substrate interactions. At first glance, major differences in trimming fingerprints between each or the three enzymes, may appear to impose an unnecessary complication to antigenic peptide generation. It is conceivable, however, that this trimming variability is desirable for the immune system, since it can expand the breadth of possible antigenic peptides detected in different immunological settings ...

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    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.
    • No funding statement was detected.
    • No protocol registration statement was detected.

    About SciScore

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  3. Version published to 10.1101/2020.06.22.164681v1 on bioRxiv