Subcellular mapping of the protein landscape of SARS-CoV-2 infected cells for target-centric drug repurposing

Article activity feed

1. 

   ScreenIT

   Apr 1, 2022

   SciScore for 10.1101/2022.03.29.482838: (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
   Proteins with more than 60% identity across the whole length of the antigen sequences used to generate the HPA antibody were selected.	HPA suggested: None
   Secondary antibodies goat anti□mouse Alexa Fluor 555 (A21424), goat anti□rabbit Alexa Fluor 488 (A11034), and goat anti□chicken Alexa Fluor 647 (A21449), were diluted to 2.5 µg/ml in PBS containing 4% FBS.	anti□rabbit suggested: None anti□chicken suggested: None
   Primary antibodies generated at the HPA were diluted to 2 µg/ml, commercial Sigma-1 R antibody to 3 µg/ml (MAB1076, R&D systems) chicken Calreticulin (Abcam, ab2908) to 1 µg/ml and mouse SARS-CoV-2 …

   SciScore for 10.1101/2022.03.29.482838: (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
   Proteins with more than 60% identity across the whole length of the antigen sequences used to generate the HPA antibody were selected.	HPA suggested: None
   Secondary antibodies goat anti□mouse Alexa Fluor 555 (A21424), goat anti□rabbit Alexa Fluor 488 (A11034), and goat anti□chicken Alexa Fluor 647 (A21449), were diluted to 2.5 µg/ml in PBS containing 4% FBS.	anti□rabbit suggested: None anti□chicken suggested: None
   Primary antibodies generated at the HPA were diluted to 2 µg/ml, commercial Sigma-1 R antibody to 3 µg/ml (MAB1076, R&D systems) chicken Calreticulin (Abcam, ab2908) to 1 µg/ml and mouse SARS-CoV-2 Spike monoclonal antibody (GTX632604 GeneTex) to 1 µg/ml.	Calreticulin ( Abcam , suggested: None
   Secondary antibodies goat anti□mouse Alexa Fluor 555 (A21424), goat anti□rabbit Alexa Fluor 488 (A11034), and goat anti□chicken Alexa Fluor 647 (A21449), were diluted to 2.5 µg/ml in PBS containing 4% BSA.	anti□mouse suggested: (C. Birchmeier - Max Delbruck Center for Molecular Medicine, Berlin, Germany Cat# Guinea pig anti-mouse Tlx3 polyclonal antibody, RRID:AB_2532145)
   Experimental Models: Cell Lines
   Sentences	Resources
   Cell culture and virus infection: Vero E6 cell line was grown at 37°C in a 5% CO2 condition in Dulbecco’ modified Eagle’s medium (DMEM) containing 10% FBS (Gibco).	Vero E6 suggested: None
   Software and Algorithms
   Sentences	Resources
   Antibody selection: Validated antibodies from the HPA project were blasted against the Chlorocebus sabaeus sequence from Ensembl.	Ensembl suggested: (Ensembl, RRID:SCR_002344)
   Generation of virus and host protein interaction network: Viral bait - host protein and host protein-protein interaction network was visualized with Cytoscape (63).	Cytoscape suggested: (Cytoscape, RRID:SCR_003032)
   Human protein - protein interactions were derived from String database (64)	String suggested: (STRING, RRID:SCR_005223)
   , KEGG database (	KEGG suggested: (KEGG, RRID:SCR_012773)
   , Reactome database (66), WikiPathways and Human Phenotype Ontology.	WikiPathways suggested: (WikiPathways, RRID:SCR_002134)
   Data was plotted using Graphpad Prism software.	Graphpad Prism suggested: (GraphPad Prism, RRID:SCR_002798)

   ---

   Results from OddPub: Thank you for sharing your data.

   ---

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

   A limitation of this study is that results are based on data from the non-human cell line Vero E6, originating from the African green monkey. This cell line is known for its dampened innate immune response and permissiveness to SARS-CoV-2, which makes it a feasible but a limiting virology model (62). When comparing subcellular localization of the hits from the host-response screen between non-infected Vero E6 cells and the immunofluorescence data on human cell lines as previously generated within the HPA, 80% of the patterns overlap between the species (data publicly available at www.proteinatlas.org). Looking at staining similarities across all proteins (n=546) stained in Vero E6 in addition to human cell lines within the HPA, 75% show overlap in subcellular localization. Due to the inter-species similarities, we speculate that host proteome landscape responses to SARS-CoV-2 infection in a partially similar manner in human cell lines. In this work we performed targeted phenotyping of disease relevant proteins as a funnel to guide target selection for drug repurposing or discovery. Further, we suggest that “targeted phenotyping” can be used to prioritize host targets for novel drugs, in this case for the treatment of COVID-19. Our approach can be applied as a stand-alone filter or as an integrated layer in multi-omics study for the selection of relevant host responses in infectious diseases. Given that the approach is easily scalable and transferable for infectious agents or ...

   ---

   Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
   

   Identifier	Status	Title
   NCT04890509	Completed	A Study of Bemcentinib for the Treatment of COVID-19 in Hosp…

   ---

   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.

   ---

   Read the original source
2. 

   Version published to 10.1101/2022.03.29.482838v1 on bioRxiv

   Mar 29, 2022