Multivariate meta-analysis reveals global transcriptomic signatures underlying distinct human naive-like pluripotent states

The ground or naive pluripotent state of human pluripotent stem cells (hPSCs), which was initially established in mouse embryonic stem cells (mESCs), is an emerging and tentative concept. To verify this vital concept in hPSCs, we performed a multivariate meta-analysis of major hPSC datasets via the...

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Bibliographic Details
Published in:PloS one 2021-05, Vol.16 (5), p.e0251461-e0251461
Main Authors: Johnson, Kory R, Mallon, Barbara S, Fann, Yang C, Chen, Kevin G
Format: Article
Language:English
Subjects:
Analysis
Bioinformatics
Biology and Life Sciences
Computer programs
Data analysis
Datasets
Editing
Electronic mail
Embryonic stem cells
Embryos
Genetic transcription
Genomes
Hypoxia
Kinases
Laboratories
Mail
Meta-analysis
Neurological diseases
Physical Sciences
Pluripotency
Research and Analysis Methods
Reviews
RNA sequencing
Stem cell transplantation
Stem cells
Stroke
Vitronectin
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Summary:The ground or naive pluripotent state of human pluripotent stem cells (hPSCs), which was initially established in mouse embryonic stem cells (mESCs), is an emerging and tentative concept. To verify this vital concept in hPSCs, we performed a multivariate meta-analysis of major hPSC datasets via the combined analytic powers of percentile normalization, principal component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE), and SC3 consensus clustering. This robust bioinformatics approach has significantly improved the predictive values of our meta-analysis. Accordingly, we revealed various similarities or dissimilarities between some naive-like hPSCs (NLPs) generated from different laboratories. Our analysis confirms some previous studies and provides new evidence concerning the existence of three distinct naive-like pluripotent states. Moreover, our study offers global transcriptomic markers that define diverse pluripotent states under various hPSC growth protocols.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0251461