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Human pluripotent stem cells hold potential for regenerative medicine, but available cell types have significant limitations. Although embryonic stem cells (ES cells) from in vitro fertilized embryos (IVFES cells) represent the 'gold standard', they are allogeneic to patients. Autologous induced pluripotent stem cells (iPS cells) are prone to epigenetic and transcriptional aberrations. To determine whether such abnormalities are intrinsic to somatic cell reprogramming or secondary to the reprogramming method, genetically matched sets of human IVF ES cells, iPS cells and nuclear transfer ES cells (NT ES cells) derived by somatic cell nuclear transfer (SCNT) were subjected to genome-wide analyses. Both NT ES cells and iPS cells derived from the same somatic cells contained comparable numbers of de novo copy number variations. In contrast, DNA methylation and transcriptome profiles of NT ES cells corresponded closely to those of IVF ES cells, whereas iPS cells differed and retained residual DNA methylation patterns typical of parental somatic cells. Thus, human somatic cells can be faithfully reprogrammed to pluripotency by SCNT and are therefore ideal for cell replacement therapies.
The derivation of human ES cells from in vitro fertilized embryos1 is relevant for cell-based therapies, and while iPS cell technology2,3 overcomes allogenicity issues, a high frequency of genetic and epigenetic abnormalities have been observed, including subchromosomal duplications and deletions detected as copy number variations (CNVs)4,5, protein-coding mutations6 anddefects in DNA methylationand gene expression at regionssubject to imprinting and X-chromosome inactivation7-10. Although it is not yet understood whether these aberrant epigenetic marks reflect errors aris- ing during reprogramming or incomplete reversion to pluripotency, they could impact the accuracy of in vitro disease modelling or, more impor- tantly, the utility of iPS cells for regenerative medicine. With the avail- ability of somatic cell nuclear transfer as an alternative approach to somatic cell reprogramming11, we explored the mechanisms underlying transcrip- tion factor- and SCNT-based reprogramming.
Genetically matched cell lines
In addition to four NT ES cell lines derived from fetal human dermal fibroblasts (HDFs),designated NT1-NT4 (ref. 11),wegenerated seven iPS cell lines from the same HDFs using retroviral vectors12 (two lines, named iPS-R1 and iPS-R2) and Sendai-virus-based vectors13 (five lines, named iPS-S1,iPS-S2, iPS-S3, iPS-S4 and iPS-S5). Two IVF ES cell lines (human ES Oregon (hESO)-7 and hESO-8) were derived following IVF ofoocytesfrom...