Human cardiac organoids to model COVID‐19 cytokine storm induced cardiac injuries

Jun 11, 2022

SciScore for 10.1101/2022.01.31.478497: (What is this?)

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

Table 1: Rigor

Ethics	not detected.
Sex as a biological variable	not detected.
Randomization	For each donor, ventricular cardiomyocytes (CMs), ventricular fibroblasts (FBs), cardiac endothelial cells (ECs), and pericytes were chosen as representative cell types and maximally randomly sampled to reach the human cardiac organoid ratios of 55% CMs, 24% FBs, 14% ECs, and 7% pericytes.
Blinding	not detected.
Power Analysis	not detected.
Cell Line Authentication	not detected.

Table 2: Resources

Antibodies
Sentences	Resources
The sections were then washed 2 times (5 minutes) with PBST and stained for primary antibody at 1:200 in PBST for 1 hour at room temperature: mouse anti-alpha sarcomeric actinin (ab9465, Lot: GR3174517-4, Abcam), …

SciScore for 10.1101/2022.01.31.478497: (What is this?)

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

Table 1: Rigor

Ethics	not detected.
Sex as a biological variable	not detected.
Randomization	For each donor, ventricular cardiomyocytes (CMs), ventricular fibroblasts (FBs), cardiac endothelial cells (ECs), and pericytes were chosen as representative cell types and maximally randomly sampled to reach the human cardiac organoid ratios of 55% CMs, 24% FBs, 14% ECs, and 7% pericytes.
Blinding	not detected.
Power Analysis	not detected.
Cell Line Authentication	not detected.

Table 2: Resources

Antibodies
Sentences	Resources
The sections were then washed 2 times (5 minutes) with PBST and stained for primary antibody at 1:200 in PBST for 1 hour at room temperature: mouse anti-alpha sarcomeric actinin (ab9465, Lot: GR3174517-4, Abcam), mouse anti-alpha smooth muscle actin, (A6228, Lot: 056M4828V, Sigma)	anti-alpha sarcomeric actinin suggested: (Biorbyt Cat# orb18280, RRID:AB_10766997) anti-alpha smooth muscle actin suggested: None
Next, sections were blocked with 3% bovine serum albumin / TBS and then incubated with primary antibodies (rabbit anti α-actinin (Cell Signaling, 3134)) overnight at 4 °C at 1:30.	anti α-actinin suggested: None
The secondary antibody (donkey anti-rabbit-alexafluor-488 (Thermo Fisher, A-21206)), was incubated for 2h at room temperature at 1:500 together with alexa-coupled wheat germ agglutinin (WGA, 1:500, Thermofisher).	anti-rabbit-alexafluor-488 suggested: None WGA suggested: None
Experimental Models: Cell Lines
Sentences	Resources
In the instance of the HUVEC Deficient Organoids (HDOs) the 14% of the HUVEC cell content was replaced with cardiomyocytes in its cell suspension.	HUVEC suggested: KCB Cat# KCB 200648YJ, RRID:CVCL_2959)
Experimental Models: Organisms/Strains
Sentences	Resources
Eve Tech Cytokine Plexing: Supernatants were collected from organoid culture on day 4 and were analyzed for cytokine levels using a Human Cytokine Array Proinflammatory Focused 13 – plex (Eve Technologies, Calgary, AB)	AB suggested: RRID:BDSC_203)
Software and Algorithms
Sentences	Resources
Recording of the videos was performed with a Carl Zeiss Axiovert a1 Inverted Microscope and Zen 2011 software (Zeiss)	Zen suggested: None
125 ng of total RNA was used for the construction of the library using the New England Biolabs NEBNext® Poly(A	Poly(A suggested: None
Paired-end reads were aligned to the hg38 human reference genome (Genecode GRCh38.p13) using RNA STAR72 (v2.7.8a) and subsequent gene counts were generated using htseq-count (v13.5) utilizing the Galaxy Project online platform (v21.01, https://galaxyproject.org/).	Galaxy suggested: (Galaxy, RRID:SCR_006281)
Differential Gene Expression: The R package, DESeq2 (v1.24.0) [doi: 10.1186/s13059-014-0550-8], was used to perform the differential gene expression analysis.	DESeq2 suggested: (DESeq, RRID:SCR_000154)
Health’s Gene Expression Omnibus (GEO), GSE169241.	Gene Expression Omnibus suggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)
Differential gene expression analysis was performed using Rstudio (v1.3.1093) (R language v3.6.1).	Rstudio suggested: (RStudio, RRID:SCR_000432)
Volcano plots for each study were generated using the ggplot2 package (v3.3.5)73.	ggplot2 suggested: (ggplot2, RRID:SCR_014601)
To measure co-localization of F-actin and α-smooth muscle actin, a Color Threshold was applied to each image using ImageJ to account for the superimposition of each stain (yellow to measure for green and red overlap).	ImageJ suggested: (ImageJ, RRID:SCR_003070)
Statistical Analysis: Differences between experimental groups were analyzed using Microsoft Excel (v13.7) and GraphPad Prism (v9.1.1) statistical tools.	Microsoft Excel suggested: (Microsoft Excel, RRID:SCR_016137) GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)

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).

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

A limitation of our system is the lack of immune cells. To address this, we introduced the concept of in silico hCOs by leveraging the publicly available scRNAseq data of COVID-19 hearts and well-defined cell type and composition of our hCOs (Supplementary Fig. 3). The IL-1 β treated hCOs showed higher similarity with COVID-19 hearts than the in silico COVID-19 organoids in multiple GSVA analyses (Fig. 3B, 4A, 4H, and 5B). While this can be attributed to patient variation and the use of bulk RNAseq (used on the hCOs and in vivo heart samples) rather than scRNAseq (used to construct the in silico hCOs), our findings indicate the significance of the immunomodulatory properties (e.g., cytokine release) of cardiomyocytes, endothelial cells, and stromal cells in the organoids and in COVID-19 hearts. Additionally, because we utilized hPSC-CMs, it is possible the hCOs can better withstand IL-1 β mediated damage. However, we noticed similar trends in cardiac contractile structure and function upon exposure to IL-1 β, demonstrating that hPSC-CMs recapitulate the key phenotypic shifts seen in adult human cardiomyocytes. Though our findings are consistent with hPSC models of direct SARS-CoV-2 infection 6, direct comparisons are needed to validate our findings.

Results from TrialIdentifier: No clinical trial numbers were referenced.

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.

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Human cardiac organoids to model COVID‐19 cytokine storm induced cardiac injuries

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