Hussein, SM, Batada, NN, Vuoristo, S, Ching, RW, Autio, R, Närvä, E et al.. Copy number variation and selection during reprogramming to pluripotency. Nature 471: 58-62

Samuel Lunenfeld Research Institute, Toronto, Ontario M5T 3H7, Canada.
Nature (Impact Factor: 41.46). 03/2011; 471(7336):58-62. DOI: 10.1038/nature09871
Source: PubMed


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.

Download full-text


Available from: Reagan Ching,
  • Source
    • "However, recent reports imply that genetic and epigenetic aberrations occur during the derivation and reprogramming processes (Liang and Zhang, 2013; Pera, 2011; Lund et al., 2012). These range from chromosomal abnormalities (Laurent et al., 2011),''de novo'' copy number variations (CNVs) (Hussein et al., 2011), and point mutations in protein-coding regions (Gore et al., 2011). Such changes may complicate their use for regenerative medicine purposes (Bayart and Cohen-Haguenauer, 2013). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Despite the enormous replication potential of the human liver, there are currently no culture systems available that sustain hepatocyte replication and/or function in vitro. We have shown previously that single mouse Lgr5+ liver stem cells can be expanded as epithelial organoids in vitro and can be differentiated into functional hepatocytes in vitro and in vivo. We now describe conditions allowing long-term expansion of adult bile duct-derived bipotent progenitor cells from human liver. The expanded cells are highly stable at the chromosome and structural level, while single base changes occur at very low rates. The cells can readily be converted into functional hepatocytes in vitro and upon transplantation in vivo. Organoids from α1-antitrypsin deficiency and Alagille syndrome patients mirror the in vivo pathology. Clonal long-term expansion of primary adult liver stem cells opens up experimental avenues for disease modeling, toxicology studies, regenerative medicine, and gene therapy. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.
    Cell 01/2015; 160(1-2):299-312. DOI:10.1016/j.cell.2014.11.050 · 32.24 Impact Factor
  • Source
    • "Several research groups have found that those proclaimed induced stem cells had more abnormal chromosomes [7] , more protein-coding point mutations [8] , more abnormal epigenomic reprogramming and DNA methylation [9] [10] [11] , and more copy number variations [12] [13] than normal somatic cells or embryonic stem cells; those supposed induced pluripotent stem cells had more chances to develop tumors, and they could form tumors more rapidly than human embryonic stem cells [14] . "
    [Show abstract] [Hide abstract]
    ABSTRACT: The claimed human induced pluripotent stem cells (iPSCs) are not equivalent to human embryonic or adult stem cells. These should be redefined as induced pluripotent stem cell-like cells. We do not think that those so-called induced pluripotent stem cells will be a reliable and feasible source of stem cells for the foreseeable future.
    01/2015; 29(1):1-2. DOI:10.7555/JBR.29.20140166
  • Source
    • "[96] of transcriptome data (Illumina HT-12v4 array) and by the capacity to form embryoid bodies that spontaneously differentiate into the three germ layers (ectoderm, endoderm, and mesoderm) (Fig. 2B). More extensive characterization includes aberrant genetic/epigenetic modification [97] , reprogramming-induced point mutations [98] and CNVs [99] , Fig. 2 "
    [Show abstract] [Hide abstract]
    ABSTRACT: Schizophrenia (SZ) is a devastating mental disorder afflicting 1% of the population. Recent genome-wide association studies (GWASs) of SZ have identified >100 risk loci. However, the causal variants/genes and the causal mechanisms remain largely unknown, which hinders the translation of GWAS findings into disease biology and drug targets. Most risk variants are noncoding, thus likely regulate gene expression. A major mechanism of transcriptional regulation is chromatin remodeling, and open chromatin is a versatile predictor of regulatory sequences. MicroRNA-mediated post-transcriptional regulation plays an important role in SZ pathogenesis. Neurons differentiated from patient-specific induced pluripotent stem cells (iPSCs) provide an experimental model to characterize the genetic perturbation of regulatory variants that are often specific to cell type and/or developmental stage. The emerging genome-editing technology enables the creation of isogenic iPSCs and neurons to efficiently characterize the effects of SZ-associated regulatory variants on SZ-relevant molecular and cellular phenotypes involving dopaminergic, glutamatergic, and GABAergic neurotransmissions. SZ GWAS findings equipped with the emerging functional genomics approaches provide an unprecedented opportunity for understanding new disease biology and identifying novel drug targets.
    Neuroscience Bulletin 01/2015; 31(1). DOI:10.1007/s12264-014-1488-2 · 2.51 Impact Factor
Show more