Genomic stability in reprogramming

Current Opinion in Genetics and Development

Volumn 22, Issue 5, 2012, Pages 444-449

  Ronen, Daniel ^a   Benvenisty, Nissim ^a  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

CELL CLONE; CHROMOSOME 11; CHROMOSOME 12; CHROMOSOME 14; CHROMOSOME 17; CHROMOSOME 20; CHROMOSOME ABERRATION; COPY NUMBER VARIATION; DNA METHYLATION; DYSKERATOSIS CONGENITA; EMBRYONIC STEM CELL; GENE MUTATION; GENETIC VARIABILITY; GENOMIC INSTABILITY; HETEROPLASMY; HETEROZYGOSITY; HUMAN; INDEL MUTATION; KARYOTYPE; KARYOTYPING; MISSENSE MUTATION; MULTIPLE INSERTION MUTATION; NONHUMAN; NONSENSE MUTATION; PLURIPOTENT STEM CELL; POINT MUTATION; PRIORITY JOURNAL; REVIEW; SOMATIC CELL; SOMATIC MUTATION; SUBCHROMOSOMAL ABERRATION; TELOMERE; TELOMERE HOMEOSTASIS; TELOMERE SHORTENING; TRISOMY; TRISOMY 11; TRISOMY 8;

ANIMALS; CELL DIFFERENTIATION; CHROMOSOME ABERRATIONS; DNA, MITOCHONDRIAL; GENOMIC INSTABILITY; HUMANS; INDUCED PLURIPOTENT STEM CELLS; MUTATION; NUCLEAR REPROGRAMMING; REGENERATIVE MEDICINE; TELOMERE;

IPS;

EID: 84868203369     PISSN: 0959437X     EISSN: 18790380     Source Type: Journal    
DOI: 10.1016/j.gde.2012.09.003     Document Type: Review

References (52)

1. Robinton D.A., Daley G.Q. The promise of induced pluripotent stem cells in research and therapy. Nature 2012, 481:295-305.
2. Unternaehrer J.J., Daley G.Q. Induced pluripotent stem cells for modelling human diseases. Philos Trans R Soc Lond B: Biol Sci 2011, 366:2274-2285.
3. Tiscornia G., Vivas E.L., Belmonte J.C. Diseases in a dish: modeling human genetic disorders using induced pluripotent cells. Nat Med 2011, 17:1570-1576.
4. Hochedlinger K., Plath K. Epigenetic reprogramming and induced pluripotency. Development 2009, 136:509-523.
5. Meissner A. Epigenetic modifications in pluripotent and differentiated cells. Nat Biotechnol 2010, 28:1079-1088.
6. Bock C., Kiskinis E., Verstappen G., Gu H., Boulting G., Smith Z.D., Ziller M., Croft G.F., Amoroso M.W., Oakley D.H., et al. Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell 2011, 144:439-452.
7. Guenther M.G., Frampton G.M., Soldner F., Hockemeyer D., Mitalipova M., Jaenisch R., Young R.A. Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells. Cell Stem Cell 2010, 7:249-257.
8. Phanstiel D.H., Brumbaugh J., Wenger C.D., Tian S., Probasco M.D., Bailey D.J., Swaney D.L., Tervo M.A., Bolin J.M., Ruotti V., et al. Proteomic and phosphoproteomic comparison of human ES and iPS cells. Nat Methods 2011, 8:821-827.
9. Ohi Y., Qin H., Hong C., Blouin L., Polo J.M., Guo T., Qi Z., Downey S.L., Manos P.D., Rossi D.J., et al. Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells. Nat Cell Biol 2011, 13:541-549.
10. Kim K., Doi A., Wen B., Ng K., Zhao R., Cahan P., Kim J., Aryee M.J., Ji H., Ehrlich L.I., et al. Epigenetic memory in induced pluripotent stem cells. Nature 2010, 467:285-290.
11. Lister R., Pelizzola M., Kida Y.S., Hawkins R.D., Nery J.R., Hon G., Antosiewicz-Bourget J., O'Malley R., Castanon R., Klugman S., et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 2011, 471:68-73.
12. Chin M.H., Mason M.J., Xie W., Volinia S., Singer M., Peterson C., Ambartsumyan G., Aimiuwu O., Richter L., Zhang J., et al. Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell 2009, 5:111-123.
13. Bar-Nur O., Russ H.A., Efrat S., Benvenisty N. Epigenetic memory and preferential lineage-specific differentiation in induced pluripotent stem cells derived from human pancreatic islet beta cells. Cell Stem Cell 2011, 9:17-23.
14. Urbach A., Bar-Nur O., Daley G.Q., Benvenisty N. Differential modeling of fragile X syndrome by human embryonic stem cells and induced pluripotent stem cells. Cell Stem Cell 2010, 6:407-411.
15. Evans M.J., Kaufman M.H. Establishment in culture of pluripotential cells from mouse embryos. Nature 1981, 292:154-156.
16. Stadtfeld M., Hochedlinger K. Induced pluripotency: history, mechanisms, and applications. Genes Dev 2010, 24:2239-2263.
17. Thomson J.A., Itskovitz-Eldor J., Shapiro S.S., Waknitz M.A., Swiergiel J.J., Marshall V.S., Jones J.M. Embryonic stem cell lines derived from human blastocysts. Science 1998, 282:1145-1147.
18. Papapetrou E.P., Sadelain M. Generation of transgene-free human induced pluripotent stem cells with an excisable single polycistronic vector. Nat Protoc 2011, 6:1251-1273.
19. Taapken S.M., Nisler B.S., Newton M.A., Sampsell-Barron T.L., Leonhard K.A., McIntire E.M., Montgomery K.D. Karotypic abnormalities in human induced pluripotent stem cells and embryonic stem cells. Nat Biotechnol 2011, 29:313-314.
20. Chen Q., Shi X., Rudolph C., Yu Y., Zhang D., Zhao X., Mai S., Wang G., Schlegelberger B., Shi Q. Recurrent trisomy and Robertsonian translocation of chromosome 14 in murine iPS cell lines. Chromosome Res 2011, 19:857-868.
21. Pasi C.E., Dereli-Oz A., Negrini S., Friedli M., Fragola G., Lombardo A., Van Houwe G., Naldini L., Casola S., Testa G., et al. Genomic instability in induced stem cells. Cell Death Differ 2011, 18:745-753.
22. Sommer C.A., Sommer A.G., Longmire T.A., Christodoulou C., Thomas D.D., Gostissa M., Alt F.W., Murphy G.J., Kotton D.N., Mostoslavsky G. Excision of reprogramming transgenes improves the differentiation potential of iPS cells generated with a single excisable vector. Stem Cells 2010, 28:64-74.
23. Ben-David U., Benvenisty N. High prevalence of evolutionarily-conserved and species-specific genomic aberrations in mouse pluripotent stem cells. Stem Cells 2012, 30:612-622.
24. Martins-Taylor K., Nisler B.S., Taapken S.M., Compton T., Crandall L., Montgomery K.D., Lalande M., Xu R.H. Recurrent copy number variations in human induced pluripotent stem cells. Nat Biotechnol 2011, 29:488-491.
25. Mayshar Y., Ben-David U., Lavon N., Biancotti J.C., Yakir B., Clark A.T., Plath K., Lowry W.E., Benvenisty N. Identification and classification of chromosomal aberrations in human induced pluripotent stem cells. Cell Stem Cell 2010, 7:521-531.
26. Amps K., Andrews P.W., Anyfantis G., Armstrong L., Avery S., Baharvand H., Baker J., Baker D., Munoz M.B., Beil S., et al. Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage. Nat Biotechnol 2011, 29:1132-1144.
27. Gore A., Li Z., Fung H.L., Young J.E., Agarwal S., Antosiewicz-Bourget J., Canto I., Giorgetti A., Israel M.A., Kiskinis E., et al. Somatic coding mutations in human induced pluripotent stem cells. Nature 2011, 471:63-67.
28. Ben-David U., Mayshar Y., Benvenisty N. Large-scale analysis reveals acquisition of lineage-specific chromosomal aberrations in human adult stem cells. Cell Stem Cell 2011, 9:97-102.
29. Laurent L.C., Ulitsky I., Slavin I., Tran H., Schork A., Morey R., Lynch C., Harness J.V., Lee S., Barrero M.J., 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 2011, 8:106-118.
30. Hussein S.M., Batada N.N., Vuoristo S., Ching R.W., Autio R., Narva E., Ng S., Sourour M., Hamalainen R., Olsson C., et al. Copy number variation and selection during reprogramming to pluripotency. Nature 2011, 471:58-62.
31. Howden S.E., Gore A., Li Z., Fung H.L., Nisler B.S., Nie J., Chen G., McIntosh B.E., Gulbranson D.R., Diol N.R., et al. Genetic correction and analysis of induced pluripotent stem cells from a patient with gyrate atrophy. Proc Natl Acad Sci USA 2011, 108:6537-6542.
32. Cheng L., Hansen N.F., Zhao L., Du Y., Zou C., Donovan F.X., Chou B.K., Zhou G., Li S., Dowey S.N., et al. Low incidence of DNA sequence variation in human induced pluripotent stem cells generated by nonintegrating plasmid expression. Cell Stem Cell 2012, 10:337-344.
33. Ji J., Ng S.H., Sharma V., Neculai D., Hussein S., Sam M., Trinh Q., Church G.M., McPherson J.D., Nagy A., et al. Elevated coding mutation rate during the reprogramming of human somatic cells into induced pluripotent stem cells. Stem Cells 2012, 30:435-440.
34. Young M.A., Larson D.E., Sun C.W., George D.R., Ding L., Miller C.A., Lin L., Pawlik K.M., Chen K., Fan X., et al. Background mutations in parental cells account for most of the genetic heterogeneity of induced pluripotent stem cells. Cell Stem Cell 2012, 10:570-582.
35. Quinlan A.R., Boland M.J., Leibowitz M.L., Shumilina S., Pehrson S.M., Baldwin K.K., Hall I.M. Genome sequencing of mouse induced pluripotent stem cells reveals retroelement stability and infrequent DNA rearrangement during reprogramming. Cell Stem Cell 2011, 9:366-373.
36. Suhr S.T., Chang E.A., Rodriguez R.M., Wang K., Ross P.J., Beyhan Z., Murthy S., Cibelli J.B. Telomere dynamics in human cells reprogrammed to pluripotency. PLoS ONE 2009, 4:e8124.
37. Agarwal S., Loh Y.H., McLoughlin E.M., Huang J., Park I.H., Miller J.D., Huo H., Okuka M., Dos Reis R.M., Loewer S., et al. Telomere elongation in induced pluripotent stem cells from dyskeratosis congenita patients. Nature 2010, 464:292-296.
38. Vaziri H., Chapman K.B., Guigova A., Teichroeb J., Lacher M.D., Sternberg H., Singec I., Briggs L., Wheeler J., Sampathkumar J., et al. Spontaneous reversal of the developmental aging of normal human cells following transcriptional reprogramming. Regen Med 2010, 5:345-363.
39. Yehezkel S., Rebibo-Sabbah A., Segev Y., Tzukerman M., Shaked R., Huber I., Gepstein L., Skorecki K., Selig S. Reprogramming of telomeric regions during the generation of human induced pluripotent stem cells and subsequent differentiation into fibroblast-like derivatives. Epigenetics 2011, 6:63-75.
40. Mathew R., Jia W., Sharma A., Zhao Y., Clarke L.E., Cheng X., Wang H., Salli U., Vrana K.E., Robertson G.P., et al. Robust activation of the human but not mouse telomerase gene during the induction of pluripotency. FASEB J 2010, 24:2702-2715.
41. Batista L.F., Pech M.F., Zhong F.L., Nguyen H.N., Xie K.T., Zaug A.J., Crary S.M., Choi J., Sebastiano V., Cherry A., et al. Telomere shortening and loss of self-renewal in dyskeratosis congenita induced pluripotent stem cells. Nature 2011, 474:399-402.
42. Marion R.M., Strati K., Li H., Tejera A., Schoeftner S., Ortega S., Serrano M., Blasco M.A. Telomeres acquire embryonic stem cell characteristics in induced pluripotent stem cells. Cell Stem Cell 2009, 4:141-154.
43. Gourronc F.A., Klingelhutz A.J. Therapeutic opportunities: Telomere maintenance in inducible pluripotent stem cells. Mutat Res 2012, 730:98-105.
44. Marion R.M., Blasco M.A. Telomere rejuvenation during nuclear reprogramming. Curr Opin Genet Dev 2010, 20:190-196.
45. Prigione A., Lichtner B., Kuhl H., Struys E.A., Wamelink M., Lehrach H., Ralser M., Timmermann B., Adjaye J. Human induced pluripotent stem cells harbor homoplasmic and heteroplasmic mitochondrial DNA mutations while maintaining human embryonic stem cell-like metabolic reprogramming. Stem Cells 2011, 29:1338-1348.
46. Blum B., Benvenisty N. The tumorigenicity of diploid and aneuploid human pluripotent stem cells. Cell Cycle 2009, 8:3822-3830.
47. Ben-David U., Benvenisty N. The tumorigenicity of human embryonic and induced pluripotent stem cells. Nat Rev Cancer 2011, 11:268-277.
48. Kinde I., Wu J., Papadopoulos N., Kinzler K.W., Vogelstein B. Detection and quantification of rare mutations with massively parallel sequencing. Proc Natl Acad Sci USA 2011, 108:9530-9535.
49. Araten D.J., Golde D.W., Zhang R.H., Thaler H.T., Gargiulo L., Notaro R., Luzzatto L. A quantitative measurement of the human somatic mutation rate. Cancer Res 2005, 65:8111-8117.
50. Lynch M. Rate, molecular spectrum, and consequences of human mutation. Proc Natl Acad Sci USA 2010, 107:961-968.
51. Baker D.E., Harrison N.J., Maltby E., Smith K., Moore H.D., Shaw P.J., Heath P.R., Holden H., Andrews P.W. Adaptation to culture of human embryonic stem cells and oncogenesis in vivo. Nat Biotechnol 2007, 25:207-215.
52. Draper J.S., Smith K., Gokhale P., Moore H.D., Maltby E., Johnson J., Meisner L., Zwaka T.P., Thomson J.A., Andrews P.W. Recurrent gain of chromosomes 17q and 12 in cultured human embryonic stem cells. Nat Biotechnol 2004, 22:53-54.