Induced Pluripotent Stem Cells and Embryonic Stem Cells Are Distinguished by Gene Expression Signatures

By M. H. Chin, Mike J. Mason, Wei Xie, Stefano Volinia, M. Singer, C. Peterson, G. Ambartsumyan, Otaren Aimiuwu, Laura Richter, Jin Zhang and 13 more. Cell Stem Cell, 2009

1,024 citations recorded by the source corpus.

SUMMARY Induced pluripotent stem cells (iPSCs) outwardly appear to be indistinguishable from embryonic stem cells (ESCs). A study of gene expression profiles of mouse and human ESCs and iPSCs suggests that, while iPSCs are quite similar to their embryonic counterparts, a recurrent gene expression signature appears in iPSCs regardless of their origin or the method by which they were generated. Upon extended culture, hiPSCs adopt a gene expression profile more similar to hESCs; however, they still retain a gene expression signature unique from hESCs that extends to miRNA expression. Genome-wide data suggested that the iPSC signature gene expression differences are due to differential promoter binding by the reprogramming factors. High-resolution array profiling demonstrated that there is no common specific subkaryotypic alteration that is required for reprogramming and that reprogramming does not lead to genomic instability. Together, these data suggest that iPSCs should be considered a unique subtype of pluripotent cell.

Subfields: Biomedical Engineering, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/be34bc6649df493f4fa86165bb1ca8623cfa4ab7

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Citations in the corpus

Incomplete DNA methylation underlies a transcriptional memory of the somatic cell in human iPS cells (2011, neutral): “Transcriptional differences have also been described and proposed to represent a persistent memory of the original somatic cells in iPS cell”
Energy Metabolism in Human Pluripotent Stem Cells and Their Differentiated Counterparts (2011, background): “unique gene expression signature appears in IPSCs regardless of their origin [4].”
Epigenetic memory in induced pluripotent stem cells (2010, background): “Minor differences in mRNA and microRNA expression have been reported 40 , but removal of transgenes reduces the differences 43 .”
Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines (2011, positive): “To quantitatively address this issue, we reframed them as a classification problem: Can we use DNA methylation and gene expression profiles to accurately predict whether a specific cell line is an ES or iPS cell line? Several gene signatures of differences between human ES and iPS cell lines have be”
Distinct Epigenomic Landscapes of Pluripotent and Lineage-committed Human Cells (2010, background): “found 3947 genes differentially expressed between several iPSC and hESC lines (Chin et al., 2009).”
The tumorigenicity of human embryonic and induced pluripotent stem cells (2011, background): “However, HESCs and HiPSCs (as well as their mouse counterparts) are not identical, and rapidly accumulating evidence suggests that there are considerable differences between these two pluripotent cell types, including important aspects such as global gene expressio”
Induced pluripotent stem cells: past, present, and future. (2012, neutral): “(2009) compared three human ESC lines and five iPSC lines by expression microarrays and identified hundreds of genes that were differentially expressed (Chin et al., 2009).”
Somatic cell reprogramming and transitions between pluripotent states: facts, hypotheses, unresolved issues (2010, neutral): “However, some studies using global expression analyses concluded that iPSCs are a unique subtype of pluripotent cells that retain a consistent gene expression signature distinguishable from ESCs, even after extended passaging (Chin et al., 2009).”
Identification and classification of chromosomal aberrations in human induced pluripotent stem cells. (2010, background): “Detection of Chromosomal Aberrations in HiPSCs cell line, hiPSC18 (Chin et al., 2009; Lowry et al., 2008), was found normal by gene expression analysis at passage 9, whereas by passage 56 both PCF and Expander/EASE analyses predicted gains in chromosomes 3 and 12 (Figures S2D and S2E).”
Induced pluripotency: history, mechanisms, and applications. (2010, background): “2009) and in the expression of mRNAs and miRNAs (Chin et al. 2009; Wilson et al. 2009) have been reported between both mouse and human ESCs and iPSCs.”
Epigenetic memory and preferential lineage-specific differentiation in induced pluripotent stem cells derived from human pancreatic islet beta cells. (2011, positive): “…their ability to generate embryoid bodies (EBs) and teratomas, mounting evidence suggested that iPSCs differed from ESCs in gene expression proﬁles (Chin et al., 2009), persistence of donor-cell gene expression (Ghosh et al., 2010; Marchetto et al., 2009), differentiation abilities (Feng et al.,…”