KIM-1/TIM-1 is a Receptor for SARS-CoV-2 in Lung and Kidney

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1. 

   Version published to 10.1101/2020.09.16.20190694v2 on medRxiv

   Jan 11, 2022
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   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2020.09.16.20190694: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: The protocol was approved by the Institutional Review Board of the Ethics Committee of Partners Healthcare. IACUC: All mouse work was performed in accordance with the animal use protocol approved by the Institutional Animal Care and User Committee of the Harvard Medical School.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   After exposure to liposomes, the cells were washed with PBS and detached with 0.25% Trypsin/0.1% EDTA, fixed with 4% paraformaldehyde/5% FBS in PBS, and then immunostained with anti-KIM-1 …

   SciScore for 10.1101/2020.09.16.20190694: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: The protocol was approved by the Institutional Review Board of the Ethics Committee of Partners Healthcare. IACUC: All mouse work was performed in accordance with the animal use protocol approved by the Institutional Animal Care and User Committee of the Harvard Medical School.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   After exposure to liposomes, the cells were washed with PBS and detached with 0.25% Trypsin/0.1% EDTA, fixed with 4% paraformaldehyde/5% FBS in PBS, and then immunostained with anti-KIM-1 and anti-ACE2 antibodies.	anti-KIM-1 suggested: None
   In western blotting, primary antibodies against the following proteins were used: ACE2 (1:1000, as used in immunofluorescence staining); human KIM-1 cytoplasmic domain (rabbit, 1:1000, #195, developed in collaboration with BIOGEN Inc.	ACE2 suggested: (LSBio (LifeSpan Cat# LS-C347-1000, RRID:AB_1271963) KIM-1 cytoplasmic domain suggested: None
   As secondary antibodies, HRP-conjugated anti-rabbit IgG and anti-goat IgG (Dako, Denmark) were used.	anti-rabbit IgG suggested: None anti-goat IgG suggested: None
   For inhibition of KIM-1 by antibodies, purified anti-human KIM-1 IgG (both mouse monoclonal AKG7 and 3F4, developed by our group) or anti-mouse KIM-1 IgG (AF1817) were used.	anti-human KIM-1 IgG suggested: (R and D Systems Cat# AF1750, RRID:AB_2116561) 3F4 suggested: None anti-mouse KIM-1 IgG suggested: (R and D Systems Cat# AF1817, RRID:AB_2116446)
   Experimental Models: Cell Lines
   Sentences	Resources
   Cells were seeded onto 8-well chamber slide at a density of 1-1.5 × 105 cells/well (LLC-PK1 cells stably expressing human KIM-1 or empty pcDNA, A549 cells or mouse primary lung epithelial cells).	A549 suggested: NCI-DTP Cat# A549, RRID:CVCL_0023)
   LLC-PK1 cell lines and A549 cell lines were obtained from the ATCC.	LLC-PK1 suggested: None
   Experimental Models: Organisms/Strains
   Sentences	Resources
   C57BL/6 mice were purchased from Charles River Laboratories.	C57BL/6 suggested: None
   Software and Algorithms
   Sentences	Resources
   The protocol was approved by the Institutional Review Board of the Ethics Committee of Partners Healthcare.	Partners Healthcare suggested: (Partners HealthCare Biobank, RRID:SCR_001316)
   Processing of the raw data was done in Microsoft Excel, data points between 5 s and 10 s were averaged.	Microsoft Excel suggested: (Microsoft Excel, RRID:SCR_016137)
   The results were normalized between 0 and 1 and exported to GraphPad where nonlinear fitting and calculation of the EC50 was done.	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   For quantification of internalization from images taken by confocal microscopy, virosome-positive areas were measured by ImageJ and analyzed statistically.	ImageJ suggested: (ImageJ, RRID:SCR_003070)
   Data were analyzed using FLOWJO (FLOWJO).	FLOWJO suggested: (FlowJo, RRID:SCR_008520)
   Cambridge, MA); mouse KIM-1 (goat, 1:200, AF1817; R&D systems Inc, Minneapolis, MN); SARS Coronavirus Nucleocapsid (rabbit, 1:200, PA1-41098; Invitrogen, Thermo Fisher Scientific, Waltham, MA); ACE2 (rabbit, 1:200, ab15348; Abcam, Cambridge, MA); Prosurfactant Protein C (rabbit, 1:200, ab90716; Abcam, Cambridge, MA); IL-1β (goat, 1:200, AF-201; R&D systems Inc, Minneapolis, MN).	R&D systems Inc suggested: None
   For detection of IL-1β induced by treatment with Spike S1 subunit protein, tubuloids infected by adenovirus for GFP and KIM-1 or for control GFP and β-GAL were treated with biotinylated 2019-nCoV S1 protein, His, Avitag (AcroBiosystems, DE) for 24 hours and immunostained.	AcroBiosystems suggested: (ACRObiosystems, RRID:SCR_012550)

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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: Please consider improving the rainbow (“jet”) colormap(s) used on pages 26, 27 and 28. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

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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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3. 

   Version published to 10.1101/2020.09.16.20190694v1 on medRxiv

   Sep 18, 2020