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Reprogramming: The Prize for the Best
Pluripotent Stem Cell Goes To………
Induced pluripotent stem cell (iPSC) technology aims to provide patient-specific stem cells to
be used in the replacement of cells and tissues in human diseases and disorders. However,
high levels of genetic and epigenetic abnormalities have been observed in iPSCs, and it is
not fully understood if these errors arise during the reprogramming process or if they
represent an incomplete reprogramming stage. Now in a gargantuan effort, researchers from
the laboratories of Joseph R. Ecker, Louise C. Laurent, and Shoukhrat Mitalipov have
subjected genetically matched sets of human in vitro fertilization-derived embryonic stem
cells (IVF ESCs), iPSCs and nuclear transfer ESCs (NT ESCs) to genome-wide analyses
and report these findings in Nature [1].
The group investigated 4 different types of pluripotent cells:
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four NT ESC lines derived from fetal human dermal fibroblasts (HDFs) - NT1–NT4 [2]
two iPSC lines from the same HDFs using retroviral vectors - iPS-R1 and iPS-R2 [3]
five iPSC lines from the same HDFs using Sendai-virus-based vectors - iPS-S1-5 [4]
two IVF ESC lines (human ES Oregon (hESO)-7 and hESO-8) derived using IVF of
oocytes from the same egg donor used for SCNT [2]
For each cell type, an in depth genome wide analysis of the cells to investigate the scale of
differences in the NT ESCs and iPSCs as compared to the “gold standard” IVF ESCs. Their
findings, in brief, were:
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Copy Number Variations (CNVs) – using high-throughput single nucleotide
polymorphism (SNP) analysis
No statistically significant differences between the three cell types (although
limited by small sample number)
Global DNA Methylation - using Infinium HumanMethylation450 BeadChip
Methylation of NT ESCs are more similar to IVF ESCs, than to iPSCs
iPSCs retain higher levels of residual somatic epigenetic memory
DNA methylation at imprinted and X-chromosome inactivation (XCI) regions
NT ESCs are more similar to IVF ESCs, than to iPSCs
XCI loci methylation levels displayed variation across the lines
Autosomal non-imprinted loci
iPSCs generally displayed higher methylation levels than NT ESCs as
compared to IVF ESCs
High-coverage base-resolution methylation – using Methyl C-sequencing
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iPSCs displayed higher levels of differentially methylated regions (DMRs)
than NT ESCs as compared to IVF ESCs
Non-CG Methylation in NT ESCs
Analysis suggests that NT ESCs are reprogrammed to a state nearing that of
IVF ESCs, compared to iPSCs
Global gene expression – using strand specific RNA-sequencing
iPSCs aberrantly expressed more genes than NT ESCs as compared to IVF
ESCs
Overall, their findings suggest that transcription factor-mediated iPSC-generation suffers
from incomplete epigenetic reprogramming, while NT-ESCs are highly similar to IVF ESC
controls. Specifically, iPSCs suffer the persistence of somatic patterns of CpG methylation
[5], higher aberrations in non-CpG methylation, and so an affected gene expression profile.
The authors therefore suggest that the study of oocyte-based reprogramming may allow us
to elucidate reprogramming conditions which more faithfully recapitulate the conditions of the
ooplasm. The next questions is whether this research will shift the focus, both in funding and
research, away from iPSC-based technologies and towards NT-based ESC production.
References
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Ma H, Morey R, O'Neil RC, et al. Abnormalities in human pluripotent cells due to
reprogramming mechanisms. Nature 2014;511:177-183.
Tachibana M, Amato P, Sparman M, et al. Human embryonic stem cells derived by
somatic cell nuclear transfer. Cell 2013;153:1228-1238.
Lowry WE, Richter L, Yachechko R, et al. Generation of human induced pluripotent
stem cells from dermal fibroblasts. Proc Natl Acad Sci U S A 2008;105:2883-2888.
Fusaki N, Ban H, Nishiyama A, et al. Efficient induction of transgene-free human
pluripotent stem cells using a vector based on Sendai virus, an RNA virus that does not
integrate into the host genome. Proc Jpn Acad Ser B Phys Biol Sci 2009;85:348-362.
Kim K, Doi A, Wen B, et al. Epigenetic memory in induced pluripotent stem cells.
Nature 2010;467:285-290.