Evidence map›Paper›PMID 36332630›Full record

ArticleStem cell reports2023

Virtual cells in a virtual microenvironment recapitulate early development-like patterns in human pluripotent stem cell colonies.

Himanshu Kaul, Nicolas Werschler, Ross D Jones, M Mona Siu, Mukul Tewary, Andrew Hagner, Joel Ostblom, Daniel Aguilar-Hidalgo, Peter W Zandstra

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Stem cell reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.

0numbers the graph read from it
0cells of the map it votes in
14citing papers in PubMed
1.6field-weighted citation impact, top 17% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

14 citing papers in PubMed, 18 citations in OpenAlex.

  1. Review
  2. Review
  3. From genes to germ layers: virtual twins of gastruloids.NPJ systems biology and applications · 2026
    Review
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  5. Review
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  10. Review
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  12. Systems bioengineering approaches for developmental toxicology.Computational and structural biotechnology journal · 2023
    Review
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  14. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors at 2 institutions in 1 country.

Himanshu KaulSchool of Engineering, University of Leicester, Leicester, UK; Department of Respiratory Sciences, University of Leicester, Leicester, UK.
Nicolas WerschlerSchool of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.
Ross D JonesSchool of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
M Mona SiuMichael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
Mukul TewaryInstitute of Biomedical Engineering, University of Toronto, Toronto, ON, Canada.
Andrew HagnerSchool of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.
Joel OstblomInstitute of Biomedical Engineering, University of Toronto, Toronto, ON, Canada.
Daniel Aguilar-HidalgoSchool of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
Peter W ZandstraSchool of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada. Electronic address: peter.zandstra@ubc.ca.
University of British Columbia · CAUniversity of Toronto · CA

Funding

CIHR FDN-154283
6 · The paper itself

Abstract

The mechanism by which morphogenetic signals engage the regulatory networks responsible for early embryonic tissue patterning is incompletely understood. Here, we developed a minimal gene regulatory network (GRN) model of human pluripotent stem cell (hPSC) lineage commitment and embedded it into "cellular" agents that respond to a dynamic morphogenetic signaling microenvironment. Simulations demonstrated that GRN wiring had significant non-intuitive effects on tissue pattern order, composition, and dynamics. Experimental perturbation of GRN connectivities supported model predictions and demonstrated the role of OCT4 as a master regulator of peri-gastrulation fates. Our so-called GARMEN strategy provides a multiscale computational platform to understand how single-cell-based regulatory interactions scale to tissue domains. This foundation provides new opportunities to simulate the impact of network motifs on normal and aberrant tissue development.

Indexed as

Pluripotent Stem CellsCell DifferentiationEndodermGastrulationGene Expression Regulation, DevelopmentalGene Regulatory NetworksHumansMesodermSignal Transductionagent-based modeldevelopmentdigital twinectodermendodermgastrulationgene regulatory networkmesodermmultiscale modelreaction diffusion

Identifiers

PMID36332630
PMCPMC9859929
OpenAlexW4308017591

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.