Copy number variation and selection during reprogramming to pluripotency

Abstract

The mechanisms underlying the low efficiency of reprogramming somatic cells into induced pluripotent stem (iPS) cells are poorly understood. There is a clear need to study whether the reprogramming process itself compromises genomic integrity and, through this, the efficiency of iPS cell establishment. Using a high-resolution single nucleotide polymorphism array, we compared copy number variations (CNVs) of different passages of human iPS cells with their fibroblast cell origins and with human embryonic stem (ES) cells. Here we show that significantly more CNVs are present in early-passage human iPS cells than intermediate passage human iPS cells, fibroblasts or human ES cells. Most CNVs are formed de novo and generate genetic mosaicism in early-passage human iPS cells. Most of these novel CNVs rendered the affected cells at a selective disadvantage. Remarkably, expansion of human iPS cells in culture selects rapidly against mutated cells, driving the lines towards a genetic state resembling human ES cells.

Concise Review: Induced Pluripotent Stem Cells Versus Embryonic Stem Cells: Close Enough or Yet Too Far Apart?

“…Besides epigenetic aberrations it is reported that iPSC also bear genomic mutations [69][70][71][72]. These could arise from the reprogramming itself and from the in vitro expansion of cells afterward.…”

“…Another interesting study showed that early passage iPSC bear a significant number of CNV that actually attenuates during subsequent intermediate length passaging, finally descending to the average number of CNV per ESC lines or fibroblasts [71]. The elimination of the CNV in iPSC population is possible because many are present in mosaic fashion (i.e., only a certain part of the cell population has the mutation).…”

Genetics of Human Sleep Behavioral Phenotypes

“…DNA can then be extracted from iPSC cultures for use in genetic analyses. However, it should be noted that the reprogramming procedure can induce de novo genomic alterations such as copy-number variation (CNV; Hussein et al, 2011). Also, it is currently time and money consuming to generate human iPSCs.…”

Can we grow sperm? A translational perspective on the current animal and human spermatogenesis models

“…Chromosomal abnormalities seem to appear earlier in iPSCs cultures, 70 and higher frequency of mutations and greater number of novel copy number variants are also present in iPSCs. 70,71 Aberrant DNA methylation and retention of epigenetic markers from the cell of origin also suggest significant reprogramming variability in human iPSCs. 72 As it stands, the lack of genetic stability in iPSCs precludes their use in clinical applications in humans until further research defines the effect of this recent finding.…”