Hippo signaling pathway activation during SARS-CoV-2 infection contributes to host antiviral response

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1. Version published to 10.1371/journal.pbio.3001851

   Nov 8, 2022
2. 

   ScreenIT

   Apr 11, 2022

   SciScore for 10.1101/2022.04.07.487520: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: Ethics Statement: For human tissue procurement, large airways and bronchial tissues were acquired after lung transplantations at the Ronald Reagan UCLA Medical Center from deidentified normal human donors following Institutional Review Board (IRB) IACUC: Use of these established cell lines for the study was approved by the Institutional Biosafety Committee at UCLA. shRNA-mediated gene silencing: hPSC-CM cells (1 × 105 cells/well) were added in a 48-well plate.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	Using a double blinded approach to count the positively stained cells, Image J’s plugin Cell Counter program was used.
   Power Analysis	not detected.
   Cell Line …

   SciScore for 10.1101/2022.04.07.487520: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: Ethics Statement: For human tissue procurement, large airways and bronchial tissues were acquired after lung transplantations at the Ronald Reagan UCLA Medical Center from deidentified normal human donors following Institutional Review Board (IRB) IACUC: Use of these established cell lines for the study was approved by the Institutional Biosafety Committee at UCLA. shRNA-mediated gene silencing: hPSC-CM cells (1 × 105 cells/well) were added in a 48-well plate.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	Using a double blinded approach to count the positively stained cells, Image J’s plugin Cell Counter program was used.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Fixed cells were immunostained with anti-spike antibody (NR-616 Monoclonal Antibody) to assess virus replication.	anti-spike suggested: None
   Viral infection was examined by immunostaining or western blot analysis using SARS-CoV-2 antibodies [BEI Resources: NR-10361	SARS-CoV-2 suggested: None
   The slides were then stained with YAP (S127) antibody (Cell Signaling, 13008, 1-100) and CD68 antibody (Dako, m0876, 1-200) at 4 degree overnight, the signal was detected using Bond Polymer Refine Detection Kit (Leica Microsystems, catalogue #DS9800) with a diaminobenzidine reaction to detect antibody labeling and hematoxylin counterstaining.	S127 suggested: None CD68 suggested: (Agilent Cat# M0876, RRID:AB_2074844)
   Experimental Models: Cell Lines
   Sentences	Resources
   SARS-CoV-2 was passaged once in Vero E6 cells and viral stocks were aliquoted and stored at −80°C.	Vero E6 suggested: RRID:CVCL_XD71)
   Infection: Calu-3 cells were seeded at 30 × 103 cells per well in 0.2 ml volumes using a 96-well plate and hPSC-CMs were replated at 1 × 105 cells per well in a 48-well plate.	Calu-3 suggested: IZSLER Cat# BS TCL 103, RRID:CVCL_0609)
   Recombinant DNA
   Sentences	Resources
   The pLKO.1-puro sh-RNA targeting YAP1 (5’-CCGGCCCAGTTAAATGTTCACCAATCTCGAGATTGGTGAACATTTAACTGGGTTTTTG-3’), LATS1 (5’-CCGGCAAGTCAGAAATCCACCCAAACTCGAGTTTGGGTGGATTTCTGACTTGTTTTT-3’) or pLKO.	pLKO.1-puro suggested: RRID:Addgene_125778) pLKO suggested: None
   Software and Algorithms
   Sentences	Resources
   Image Analysis/Quantification: The confocal images were obtained using the Leica Application Suite X (LAS X) and/or the Zeiss LSM 700 Confocal Microscopy by Zeiss Software Program with maximum intensity projection feature.	Zeiss Software Program suggested: None
   Total number of cells in each image was obtained by manually counting all the DAPI stained nuclei using ImageJ program (Version 1.8.0;	ImageJ suggested: (ImageJ, RRID:SCR_003070)
   The raw read counts per gene were used as inputs for differential expression gene analysis using DESeq2 v1.28.1 in R v4.0.355.	DESeq2 suggested: (DESeq, RRID:SCR_000154)
   (KEGG) pathway database was used to examine the hippo signaling pathway in the DEG datasets58.	KEGG suggested: (KEGG, RRID:SCR_012773)
   The gene expression data used in this study were retrieved at Gene Expression Omnibus with accession numbers GSE150316 54 and GSE15039257.	Gene Expression Omnibus suggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)

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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: 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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   Results from scite Reference Check: We found no unreliable references.

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3. 

   Version published to 10.1101/2022.04.07.487520v1 on bioRxiv

   Apr 8, 2022