Induced pluripotent stem cell generation-associated point mutations arise during the initial stages of the conversion of these cells

Stem Cell Reports

Volumn 2, Issue 1, 2014, Pages 52-63

  Sugiura, Mayumi ^a   Kasama, Yasuji ^a   Araki, Ryoko ^a   Hoki, Yuko ^a   Sunayama, Misato ^a   Uda, Masahiro ^a   Nakamura, Miki ^a   Ando, Shunsuke ^a   Abe, Masumi ^a  

^a NATIONAL INSTITUTE OF RADIOLOGICAL SCIENCES   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; CELL CLONE; EMBRYO; EMBRYONIC STEM CELL; GENE FREQUENCY; GENE MUTATION; HUMAN; HUMAN CELL; PLURIPOTENT STEM CELL; POINT MUTATION; PRIORITY JOURNAL; REGENERATIVE MEDICINE; SINGLE NUCLEOTIDE POLYMORPHISM; SOMATIC CELL; ANIMAL; C57BL MOUSE; CELL LINE; CHROMOSOME MAP; CYTOLOGY; DNA SEQUENCE; GENETIC HETEROGENEITY; GENOME; HIGH THROUGHPUT SEQUENCING; METABOLISM; MOUSE;

ANIMALS; CELL LINE; CHROMOSOME MAPPING; EMBRYONIC STEM CELLS; GENE FREQUENCY; GENETIC HETEROGENEITY; GENOME; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INDUCED PLURIPOTENT STEM CELLS; MICE; MICE, INBRED C57BL; POINT MUTATION; SEQUENCE ANALYSIS, DNA;

EID: 84892567493     PISSN: 22136711     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.stemcr.2013.11.006     Document Type: Article

References (32)

1. R. Araki, M. Uda, Y. Hoki, M. Sunayama, M. Nakamura, S. Ando, M. Sugiura, H. Ideno, A. Shimada, A. Nifuji, and M. Abe Negligible immunogenicity of terminally differentiated cells derived from induced pluripotent or embryonic stem cells Nature 494 2013 100 104
2. L. Cheng, N.F. Hansen, L. Zhao, Y. Du, C. Zou, F.X. Donovan, B.K. Chou, G. Zhou, S. Li, S.N. Dowey NISC Comparative Sequencing Program Low incidence of DNA sequence variation in human induced pluripotent stem cells generated by nonintegrating plasmid expression Cell Stem Cell 10 2012 337 344
3. R. Doan, N.D. Cohen, J. Sawyer, N. Ghaffari, C.D. Johnson, and S.V. Dindot Whole-genome sequencing and genetic variant analysis of a Quarter Horse mare BMC Genomics 13 2012 78
4. P. Ghosh, C. Hsu, E.J. Alyamani, M.M. Shehata, M.A. Al-Dubaib, A. Al-Naeem, M. Hashad, O.M. Mahmoud, K.B. Alharbi, and K. Al-Busadah et al. Genome-wide analysis of the emerging infection with Mycobacterium avium subspecies paratuberculosis in the Arabian camels (Camelus dromedarius) PLoS ONE 7 2012 e31947
5. A. Gore, Z. Li, H.L. Fung, J.E. Young, S. Agarwal, J. Antosiewicz-Bourget, I. Canto, A. Giorgetti, M.A. Israel, and E. Kiskinis et al. Somatic coding mutations in human induced pluripotent stem cells Nature 471 2011 63 67
6. K. Hayashida, T. Abe, W. Weir, R. Nakao, K. Ito, K. Kajino, Y. Suzuki, F. Jongejan, D. Geysen, and C. Sugimoto Whole-genome sequencing of Theileria parva strains provides insight into parasite migration and diversification in the African continent DNA Res. 20 2013 209 220
7. S.E. Howden, A. Gore, Z. Li, H.L. Fung, B.S. Nisler, J. Nie, G. Chen, B.E. McIntosh, D.R. Gulbranson, and N.R. Diol et al. Genetic correction and analysis of induced pluripotent stem cells from a patient with gyrate atrophy Proc. Natl. Acad. Sci. USA 108 2011 6537 6542
8. S.M. Hussein, N.N. Batada, S. Vuoristo, R.W. Ching, R. Autio, E. Närvä, S. Ng, M. Sourour, R. Hämäläinen, and C. Olsson et al. Copy number variation and selection during reprogramming to pluripotency Nature 471 2011 58 62
9. S.M. Hussein, J. Elbaz, and A.A. Nagy Genome damage in induced pluripotent stem cells: assessing the mechanisms and their consequences Bioessays 35 2013 152 162
10. J. Ji, S.H. Ng, V. Sharma, D. Neculai, S. Hussein, M. Sam, Q. Trinh, G.M. Church, J.D. McPherson, A. Nagy, and N.N. Batada Elevated coding mutation rate during the reprogramming of human somatic cells into induced pluripotent stem cells Stem Cells 30 2012 435 440
11. L.C. Laurent, I. Ulitsky, I. Slavin, H. Tran, A. Schork, R. Morey, C. Lynch, J.V. Harness, S. Lee, and M.J. Barrero et al. Dynamic changes in the copy number of pluripotency and cell proliferation genes in human ESCs and iPSCs during reprogramming and time in culture Cell Stem Cell 8 2011 106 118
12. H. Li, and R. Durbin Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25 2009 1754 1760
13. W.E. Lowry, L. Richter, R. Yachechko, A.D. Pyle, J. Tchieu, R. Sridharan, A.T. Clark, and K. Plath Generation of human induced pluripotent stem cells from dermal fibroblasts Proc. Natl. Acad. Sci. USA 105 2008 2883 2888
14. N. Maherali, R. Sridharan, W. Xie, J. Utikal, S. Eminli, K. Arnold, M. Stadtfeld, R. Yachechko, J. Tchieu, and R. Jaenisch et al. Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution Cell Stem Cell 1 2007 55 70
15. K. Martins-Taylor, and R.H. Xu Concise review: genomic stability of human induced pluripotent stem cells Stem Cells 30 2012 22 27
16. K. Martins-Taylor, B.S. Nisler, S.M. Taapken, T. Compton, L. Crandall, K.D. Montgomery, M. Lalande, and R.H. Xu Recurrent copy number variations in human induced pluripotent stem cells Nat. Biotechnol. 29 2011 488 491
17. Y. Mayshar, U. Ben-David, N. Lavon, J.C. Biancotti, B. Yakir, A.T. Clark, K. Plath, W.E. Lowry, and N. Benvenisty Identification and classification of chromosomal aberrations in human induced pluripotent stem cells Cell Stem Cell 7 2010 521 531
18. A. McKenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis, A. Kernytsky, K. Garimella, D. Altshuler, S. Gabriel, M. Daly, and M.A. DePristo The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data Genome Res. 20 2010 1297 1303
19. A. Nagy, J. Rossant, R. Nagy, W. Abramow-Newerly, and J.C. Roder Derivation of completely cell culture-derived mice from early-passage embryonic stem cells Proc. Natl. Acad. Sci. USA 90 1993 8424 8428
20. K. Okita, T. Ichisaka, and S. Yamanaka Generation of germline-competent induced pluripotent stem cells Nature 448 2007 313 317
21. K. Okita, M. Nakagawa, H. Hyenjong, T. Ichisaka, and S. Yamanaka Generation of mouse induced pluripotent stem cells without viral vectors Science 322 2008 949 953
22. I.H. Park, R. Zhao, J.A. West, A. Yabuuchi, H. Huo, T.A. Ince, P.H. Lerou, M.W. Lensch, and G.Q. Daley Reprogramming of human somatic cells to pluripotency with defined factors Nature 451 2008 141 146
23. M.C. Puri, and A. Nagy Concise review: embryonic stem cells versus induced pluripotent stem cells: the game is on Stem Cells 30 2012 10 14
24. A.R. Quinlan, M.J. Boland, M.L. Leibowitz, S. Shumilina, S.M. Pehrson, K.K. Baldwin, and I.M. Hall Genome sequencing of mouse induced pluripotent stem cells reveals retroelement stability and infrequent DNA rearrangement during reprogramming Cell Stem Cell 9 2011 366 373
25. S.M. Taapken, B.S. Nisler, M.A. Newton, T.L. Sampsell-Barron, K.A. Leonhard, E.M. McIntire, and K.D. Montgomery Karotypic abnormalities in human induced pluripotent stem cells and embryonic stem cells Nat. Biotechnol. 29 2011 313 314
26. K. Takahashi, and S. Yamanaka Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors Cell 126 2006 663 676
27. K. Takahashi, K. Tanabe, M. Ohnuki, M. Narita, T. Ichisaka, K. Tomoda, and S. Yamanaka Induction of pluripotent stem cells from adult human fibroblasts by defined factors Cell 131 2007 861 872
28. W. Wang, J. Yang, H. Liu, D. Lu, X. Chen, Z. Zenonos, L.S. Campos, R. Rad, G. Guo, and S. Zhang et al. Rapid and efficient reprogramming of somatic cells to induced pluripotent stem cells by retinoic acid receptor gamma and liver receptor homolog 1 Proc. Natl. Acad. Sci. USA 108 2011 18283 18288
29. L.D. Wartman, D.E. Larson, Z. Xiang, L. Ding, K. Chen, L. Lin, P. Cahan, J.M. Klco, J.S. Welch, and C. Li et al. Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression J. Clin. Invest. 121 2011 1445 1455
30. M. Wernig, A. Meissner, R. Foreman, T. Brambrink, M. Ku, K. Hochedlinger, B.E. Bernstein, and R. Jaenisch In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state Nature 448 2007 318 324
31. M.A. Young, D.E. Larson, C.W. Sun, D.R. George, L. Ding, C.A. Miller, L. Lin, K.M. Pawlik, K. Chen, and X. Fan et al. Background mutations in parental cells account for most of the genetic heterogeneity of induced pluripotent stem cells Cell Stem Cell 10 2012 570 582
32. J. Yu, M.A. Vodyanik, K. Smuga-Otto, J. Antosiewicz-Bourget, J.L. Frane, S. Tian, J. Nie, G.A. Jonsdottir, V. Ruotti, and R. Stewart et al. Induced pluripotent stem cell lines derived from human somatic cells Science 318 2007 1917 1920