Transcriptomics

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Epigenetic and transcriptional aberrations in human pluripotent stem cells reflect differences in reprogramming mechanisms [methylation array]


ABSTRACT: Human pluripotent stem cells hold great potential for regenerative medicine, but existing cell types have imitations. Human embryonic stem cells derived from fertilized embryos (IVF-ESCs) are considered the “gold standard”, but are allogeneic to potential recipients. Autologous induced pluripotent stem cells (iPSCs) can be produced from somatic cells by forced expression of pluripotency-associated factors, but are prone to genetic and epigenetic aberrations. To determine whether accumulation of such aberrations is intrinsic to somatic cell reprogramming, or secondary to the reprogramming method, we employed an alternative approach by somatic cell nuclear transfer (SCNT). SCNT-based reprogramming to NT-ESCs is mediated by factors present in oocyte’s cytoplasm, thus mimicking early embryogenesis. We generated genetically matched pluripotent stem cells and conducted genome-wide genetic, epigenetic and transcriptional analyses. We discovered that unlike iPSCs, NT-ESCs have a low burden of de novo copy number variations (CNVs), reflecting superior maintenance of genetic stability. Moreover, DNA methylation and transcriptome profiles of NT-ESCs corresponded closely to those of IVF-ESCs. In contrast, iPSCs harbored methylation abnormalities including residual CpG methylation typical of parental fibroblasts, suggesting incomplete reprogramming. We conclude that human somatic cells can be faithfully reprogrammed to pluripotency by SCNT with the potential to satisfy the clinical requirements for cell replacement therapies. Bisulphite converted DNAs of two IVF-ESCs, two sendai produced iPSC lines, two retro-virus produced iPSC lines, four NT-ESCs, and the parental fibroblast were hybridized to the Illumina Infinium HumanMethylation 450K Beadchip

ORGANISM(S): Homo sapiens  

SUBMITTER: Robert E Morey  

PROVIDER: E-GEOD-53060 | ArrayExpress | 2014-07-08

SECONDARY ACCESSION(S): GSE53060PRJNA230786

REPOSITORIES: GEO, ArrayExpress

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Publications

Generation of human induced pluripotent stem cells from dermal fibroblasts.

Lowry W E WE   Richter L L   Yachechko R R   Pyle A D AD   Tchieu J J   Sridharan R R   Clark A T AT   Plath K K  

Proceedings of the National Academy of Sciences of the United States of America 20080215 8


The generation of patient-specific pluripotent stem cells has the potential to accelerate the implementation of stem cells for clinical treatment of degenerative diseases. Technologies including somatic cell nuclear transfer and cell fusion might generate such cells but are hindered by issues that might prevent them from being used clinically. Here, we describe methods to use dermal fibroblasts easily obtained from an individual human to generate human induced pluripotent stem (iPS) cells by ect  ...[more]

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