Global BioID-based SARS-CoV-2 proteins proximal interactome unveils novel ties between viral polypeptides and host factors involved in multiple COVID19-associated mechanisms

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   ScreenIT

   Sep 1, 2020

   SciScore for 10.1101/2020.08.28.272955: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Transfected cells were then incubated overnight at 4°C with monoclonal anti-FLAG M2 mouse antibody (dilution 1:2,000, Sigma-Aldrich).	anti-FLAG suggested: None
   After 3 washes for 10 min with PBS 0.01% Triton X-100, cells were incubated for 1 h at 37 °C with the Alexa Fluor 647-conjugated secondary antibody donkey anti mouse IgG (H+L) (1:2,000	anti mouse IgG suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   T-REx™ HEK293 cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Sigma-Aldrich), GlutaMAX™ and Penicillin-Streptomycin (1x).	H…

   SciScore for 10.1101/2020.08.28.272955: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Transfected cells were then incubated overnight at 4°C with monoclonal anti-FLAG M2 mouse antibody (dilution 1:2,000, Sigma-Aldrich).	anti-FLAG suggested: None
   After 3 washes for 10 min with PBS 0.01% Triton X-100, cells were incubated for 1 h at 37 °C with the Alexa Fluor 647-conjugated secondary antibody donkey anti mouse IgG (H+L) (1:2,000	anti mouse IgG suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   T-REx™ HEK293 cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Sigma-Aldrich), GlutaMAX™ and Penicillin-Streptomycin (1x).	HEK293 suggested: None
   Software and Algorithms
   Sentences	Resources
   BioID data analysis: The proteins were identified by comparing all MS/MS data with the Homo sapiens proteome database (Uniprot, release March 2020, Canonical+Isoforms, comprising 42,360 entries + viral bait protein sequences added manually), using the MaxQuant software version 1.5.8.3.	MaxQuant suggested: (MaxQuant, RRID:SCR_014485)
   The statistical analysis was done by Perseus software (version 1.6.2.3).	Perseus suggested: (Perseus, RRID:SCR_015753)
   The tabs ‘Enrichment basal condition’ and ‘Enrichment poly(I:C)’ have been generated entering the lists of high confidence proximal interactors of each viral bait protein in the ToppCluster online tool4 (	ToppCluster suggested: ( ToppCluster , RRID:SCR_001503)
   All interactors individual annotations are shown in Supplemental Table 2, which was generated using the Metascape annotation tool5 (https://metascape.org/).	Metascape suggested: (Metascape, RRID:SCR_016620)
   Processing of the images was performed using Zeiss Zen 2 software and assembled using Adobe Illustrator.	Adobe Illustrator suggested: (Adobe Illustrator, RRID:SCR_010279)
   Our code is written in Python 3.87 and makes use of several modules, primarily: NetworkX8 for graph operations, NumPy9 for array manipulation and numerical computations, pandas10 for data handling and Plotly11 for visualization.	Python suggested: (IPython, RRID:SCR_001658)

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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:

   We thus do think that this apparent limitation could be also seen as an asset of our study; (ii) In our opinion, the main limitation sits in the expression of a single protein at a time. Knowing that several viral proteins require viral cofactors, infected context and/or the presence viral RNA to function properly (e.g. NSP10-NSP14 or NSP10-NSP16), the present analysis almost certainly misses cooperative viral interactions. Similar studies performed in infected cells will thus bring highly valuable additional information on putative SARS-CoV-2 pathogenesis mechanisms. As an attempt to mimic a physiopathological context, we artificially induced an anti-viral response by transfecting poly(I:C) and repeating the proximal interactome analysis. These experiments already revealed novel interactions of the utmost importance; and (iii), the proximal interactions are not necessarily physical and should therefore be considered as a discovery step systematically requiring orthogonal or functional validation. However, the proximal interactomics multiple analysis generated by us and others have been at the basis of fundamental mechanism discoveries, supporting the validity of the approach for identifying new biology (see177 for review). This first proximal interaction mapping of SARS-CoV-2 proteins provides a plethora of novel research tracks to better understand this virus pathogenesis. Although for a few proteins our approach did not lead to satisfying results (NSP3, NSP5, NSP8, ORF8 an...

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   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).

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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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2. 

   Version published to 10.1101/2020.08.28.272955v1 on bioRxiv

   Aug 29, 2020