Comparable Frequencies of Coding Mutations and Loss of Imprinting in Human Pluripotent Cells Derived by Nuclear Transfer and Defined Factors

Abstract

The recent finding that reprogrammed human pluripotent stem cells can be derived by nuclear transfer into human oocytes as well as by induced expression of defined factors has revitalized the debate on whether one approach might be advantageous over the other. Here we compare the genetic and epigenetic integrity of human nuclear-transfer embryonic stem cell (NT-ESC) lines and isogenic induced pluripotent stem cell (iPSC) lines, derived from the same somatic cell cultures of fetal, neonatal, and adult origin. The two cell types showed similar genome-wide gene expression and DNA methylation profiles. Importantly, NT-ESCs and iPSCs had comparable numbers of de novo coding mutations, but significantly more than parthenogenetic ESCs. As iPSCs, NT-ESCs displayed clone- and gene-specific aberrations in DNA methylation and allele-specific expression of imprinted genes. The occurrence of these genetic and epigenetic defects in both NT-ESCs and iPSCs suggests that they are inherent to reprogramming, regardless of derivation approach.

From cloned frogs to patient matched stem cells: induced pluripotency or somatic cell nuclear transfer?

“…Both iPS cells and ntES cells showed more de novo coding mutations, 10 on average, than parthenogenetic stem cell lines with a germ line origin, which contained 1.25 de novo mutations [19 ].…”

“…Johannesson and colleagues compared human ntES cell lines to iPS cell lines derived from the same somatic cell cultures of fetal, neonatal, and adult origin [19 ]. The two cell types of ntES and iPS cell lines showed no systematic differences in gene expression and DNA methylation patterns.…”

“…(b) SCNT blastocyst and stem cell line (reproduced with permission from CSC, modified from[16 ]). (c) Cluster diagram of DNA methylation patterns comparing iPSCs and NT-ESCs (from[19 ]). …”

Present and future challenges of induced pluripotent stem cells

“…They found that iPSCs have aberrant DNA methylation statuses for some imprinted genes, such as DIRAS3, MEG3 and PEG3, and regions of X-chromosome inactivation. However, Johannesson et al concluded that human SCNT-ESCs and iPSCs have no significant differences in gene expression, DNA methylation or frequency of de novo coding mutations [81]. In addition, imprinting loss was shown to occur in both SCNT-ESC and iPSC lines with a similar frequency.…”

The silver lining of induced pluripotent stem cell variation

“…Due to the considerable costs of these tests, the stem cells community should agree on the minimal standard requirements for legitimate research purposes. However, we strongly advocate for a rigorous and more in-depth analysis of iPSC lines for clinical applications to identify genetic and epigenetic alterations, including mitochondrial DNA mutations (15) copy number variations (CNVs) (16) and histone tail modifications (17), at least until we achieve a clear understanding of the safety profile. Of note, the first clinical trial using iPSC-derived cells was put on hold because the genetic analysis revealed presence of new CNVs in the cells differentiated for transplantation.…”