Copy number variation and selection during reprogramming to pluripotency

• Published in: Nature (London) Vol. 471; no. 7336; pp. 58 - 62
• Main Authors: Hussein, Samer M., Batada, Nizar N., Vuoristo, Sanna, Ching, Reagan W., Autio, Reija, Närvä, Elisa, Ng, Siemon, Sourour, Michel, Hämäläinen, Riikka, Olsson, Cia, Lundin, Karolina, Mikkola, Milla, Trokovic, Ras, Peitz, Michael, Brüstle, Oliver, Bazett-Jones, David P., Alitalo, Kari, Lahesmaa, Riitta, Nagy, Andras, Otonkoski, Timo
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 03.03.2011; Nature Publishing Group
• Subjects: 631/208/457/649/2157; 631/532/2064/2158; 631/532/2435; Biological and medical sciences; Cell cycle; Cell differentiation; Cell differentiation, maturation, development, hematopoiesis; Cell Line; Cell physiology; Cellular Reprogramming - genetics; Chromosome Fragile Sites - genetics; DNA Copy Number Variations - genetics; Embryonic Stem Cells - cytology; Embryonic Stem Cells - metabolism; Fibroblasts - cytology; Fibroblasts - metabolism; Fundamental and applied biological sciences. Psychology; Genetic aspects; Haplotypes - genetics; Humanities and Social Sciences; Humans; In Situ Hybridization, Fluorescence; Induced Pluripotent Stem Cells - cytology; Induced Pluripotent Stem Cells - metabolism; Induced Pluripotent Stem Cells - pathology; Methods; Molecular and cellular biology; Mosaicism; multidisciplinary; Mutagenesis - genetics; Mutation; Oligonucleotide Array Sequence Analysis; Polymorphism, Single Nucleotide - genetics; Propagation; Science; Science (multidisciplinary); Selection, Genetic - genetics; Stem cells; Canada; Human; Cell reprogramming; Pluripotent cell; Copy number; Stem cell; Selection; Variations
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature09871

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. Genetic abnormalities in iPS cells Epigenomic reprogramming of somatic cells to produce iPS (induced pluripotent stem) cells has important therapeutic potential and is the basis of potentially important disease models. Recent reports that the reprogramming and in vitro culture of iPS cells can induce genetic and epigenetic abnormalities raise concerns over the implications of these abnormalities for clinical applications of iPS cells. Three papers in this issue present genomics studies of human iPS and embryonic stem (ES) cells, and taken together, the results confirm that chromosomal, subchromosomal and single-base level anomalies do accumulate in iPS cells. Hussein et al . compare copy number alterations of early and intermediate passage human iPS cells and report a higher level of copy number variations associated with reprogramming. During moderate length culture, however, iPS cells undergo a selection process leading to a decreased mutation load equivalent to that seen in ES cells. Gore et al . report protein-coding point mutations in 22 human iPS cell lines reprogrammed using five different methods; some mutations were pre-existing in the somatic cells, others were new mutations linked to reprogramming. Lister et al . used whole-genome DNA methylation profiling of human ES, iPS and somatic progenitor cell lines to reveal 'hotspots' in the genomes of iPS cells that are aberrantly reprogrammed. Reprogramming of somatic cells to induced pluripotent stem (iPS) cells that can be differentiated into many cell types has great potential for personalized therapy. By comparing copy number variations of early- and intermediate-passage human iPS cells to their respective parental fibroblast cells and human embryonic stem (ES) cells, this study finds that a high mutation rate is associated with the reprogramming process. However, during moderate length culture, human iPS cells undergo a selection process leading to decreased mutation load of cells equivalent to that observed in human ES cells.