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Dynamic Changes in the Copy Number of Pluripotency and Cell Proliferation Genes in Human ESCs and iPSCs during Reprogramming and Time in Culture
Louise C. Laurent, Igor Ulitsky, Ileana Slavin, Ha Tran, Andrew Schork, Robert Morey, Candace Lynch, Julie V. Harness, Sunray Lee, Maria J. Barrero, Sherman Ku, Marina Martynova, Ruslan Semechkin, Vasiliy Galat, Joel Gottesfeld, Juan Carlos Izpisua Belmonte, Chuck Murry, Hans S. Keirstead, Hyun-Sook Park, Uli Schmidt, Andrew L. Laslett, Franz-Josef Muller, Caroline M. Nievergelt, Ron Shamir, Jeanne F. Loring
The tremendous self-renewal and differentiation capabilities of human pluripotent stem cells (hPSCs) make them potential sources of differentiated cells for cell therapy. Cell therapies are subject to rigorous safety trials, and high priority is placed on demonstrating that the cells are nontumorigenic (Fox, 2008). Because genetic aberrations have been strongly associated with cancers, it is important that preparations destined for clinical use are free from cancer-associated genomic alterations. Human embryonic stem cell (hESC) lines have been shown to become aneuploid in culture (Baker et al., 2007,Draper et al., 2004,Imreh et al., 2006,Maitra et al., 2005,Mitalipova et al., 2005), and the most frequent changes, trisomies of chromosomes 12 and 17, are also characteristic of malignant germ cell tumors (Atkin and Baker, 1982,Rodriguez et al., 1993,Skotheim et al., 2002). Aneuploidies can be detected by karyotyping, but less easily detectable subchromosomal genetic changes may also have adverse effects. Small abnormalities have been detected in hESCs by using comparative genomic hybridization (CGH) and single-nucleotide polymorphism (SNP) genotyping (Lefort et al., 2008,N?rv? et al., 2010,Spits et al., 2008). These studies lacked sufficient resolution and power to identify cell type-associated duplications and deletions. A recent study has reported the use of gene expression data to detect genomic aberrations in a large number of hESCs and hiPSCs (Mayshar et al., 2010). However, the methods used could reliably detect only relatively large (≥10 megabase) aberrations, and the lack of nonpluripotent samples for comparison precluded the authors from determining which regions of genomic aberration were specific to pluripotent stem cells.
In this study, we performed high-resolution SNP genotyping on a large number of hESC lines, induced human pluripotent stem cell lines (hiPSCs), somatic stem cells, primary cells, and tissues. We found that hESC lines had a higher frequency of genomic aberrations compared to the other cell types. Furthermore, we identified regions in the genome that had a greater tendency to be aberrant in the hESCs when compared to the other cell types examined. Recurrent regions of duplication were seen on chromosome 12, encompassing the pluripotency-associated transcription factor NANOG and a nearby NANOG pseudogene, and on chromosome 20, upstream of the DNA methyltransferase DNMT3B. Although the frequency of genomic aberrations seen in the hiPSC lines was similar to those of cultured somatic cells and tissues, we observed one of the recurrent areas of duplication characteristic of hESCs in one of the hiPSC lines.
Furthermore, comparison of 12 hiPSC lines generated from the same primary fibroblast cell line identified genomic aberrations that were present in the hiPSC lines and absent from the original fibroblast line. Analysis of early- and late-passage samples from these hiPSC lines allowed us to distinguish between events that arose during the process of reprogramming and those that accumulated during long-term passage. In general, deletions tended to occur with reprogramming and involve tumor-suppressor genes, whereas duplications accumulated with passaging and tended to encompass tumor-promoting genes. These results suggest that human pluripotent stem cell populations are prone to genomic aberrations that could compromise their stability and utility for clinical applications and that reprogramming and expansion in culture may lead to selection for particular genomic changes.
