Evidence map›Paper›PMID 36801003›Full record

ArticleStem cell reports2023

In silico discovery of small molecules for efficient stem cell differentiation into definitive endoderm.

Gherman Novakovsky, Shugo Sasaki, Oriol Fornes, Meltem E Omur, Helen Huang, Carmen L Bayly, Dahai Zhang, Nathaniel Lim, Artem Cherkasov, Paul Pavlidis and 3 more

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 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing papers in PubMed
2.9field-weighted citation impact, top 9% 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

11 citing papers in PubMed, 19 citations in OpenAlex.

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  11. c-Jun N-terminal kinase signaling in aging.Frontiers in aging neuroscience · 2024
    Review
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

13 authors at 2 institutions in 2 countries.

Gherman NovakovskyBC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada; Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada; Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
Shugo SasakiBC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada; Department of Surgery, University of British Columbia, Vancouver, BC, Canada; School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.
Oriol FornesBC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada; Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
Meltem E OmurBC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada; Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada; Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
Helen HuangBC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada; Department of Surgery, University of British Columbia, Vancouver, BC, Canada; School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.
Carmen L BaylyBC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada; Department of Surgery, University of British Columbia, Vancouver, BC, Canada.
Dahai ZhangBC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada.
Nathaniel LimBioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada; Department of Psychiatry, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
Artem CherkasovDepartment of Urological Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada.
Paul PavlidisDepartment of Psychiatry, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
Sara MostafaviBC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada; Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; Department of Statistics, University of British Columbia, Vancouver, BC, Canada; Department of Computer Science, University of Washington, Seattle, WA, USA.
Francis C LynnBC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada; Department of Surgery, University of British Columbia, Vancouver, BC, Canada; School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada. Electronic address: francis.lynn@ubc.ca.
Wyeth W WassermanBC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada; Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada. Electronic address: wyeth@cmmt.ubc.ca.
University of British Columbia · CAUniversity of British Columbia Hospital · CA

Funding

Neuroinformatics for gene expression: networks, function and meta-analysisR01MH111099 · NIMH · UNIVERSITY OF BRITISH COLUMBIA · PI PAVLIDIS, PAUL · 2016 to 2025
$3.6M
CIHR PJT-156377CIHR PJT-162120NIMH NIH HHS R01 MH111099
6 · The paper itself

Abstract

Improving methods for human embryonic stem cell differentiation represents a challenge in modern regenerative medicine research. Using drug repurposing approaches, we discover small molecules that regulate the formation of definitive endoderm. Among them are inhibitors of known processes involved in endoderm differentiation (mTOR, PI3K, and JNK pathways) and a new compound, with an unknown mechanism of action, capable of inducing endoderm formation in the absence of growth factors in the media. Optimization of the classical protocol by inclusion of this compound achieves the same differentiation efficiency with a 90% cost reduction. The presented in silico procedure for candidate molecule selection has broad potential for improving stem cell differentiation protocols.

Indexed as

EndodermHuman Embryonic Stem CellsCell DifferentiationHumansbioinformaticsdefinitive endodermdifferentiationdrug repurposinggrowth factorpathway analysisstem celltranscription

Identifiers

PMID36801003
PMCPMC10031281
OpenAlexW4321116366

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.