Passage number is a major contributor to genomic structural variations in mouse iPSCs

Stem Cells

Volumn 32, Issue 10, 2014, Pages 2657-2667

  Liu, Pengfei ^a   Kaplan, Anna ^b   Yuan, Bo ^a   Hanna, Jacob H ^b   Lupski, James R ^a,c   Reiner, Orly ^b  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^c TEXAS CHILDREN S HOSPITAL   (United States)

Author keywords

Chromosomal aberrations; DNA copy number variations; DNA replication; Induced pluripotent stem cells; Neural stem cells

Indexed keywords

ANEUPLOIDY; ANIMAL CELL; ARTICLE; B LYMPHOCYTE; BRAIN CELL; CELL EXPANSION; CHROMOSOME 11; CHROMOSOME 12; CHROMOSOME 19; CHROMOSOME 6; COPY NUMBER VARIATION; EMBRYO; EMBRYO CELL; FIBROBLAST; GENETIC VARIABILITY; GENOMIC INSTABILITY; MITOSIS; MOUSE; NEURAL STEM CELL; NONHUMAN; PLURIPOTENT STEM CELL; STEM CELL CULTURE; Y CHROMOSOME; ANIMAL; CELL CLONE; CELL PROLIFERATION; CHROMOSOME BREAKAGE; COMPARATIVE GENOMIC HYBRIDIZATION; CYTOLOGY; GENE LOCUS; GENETICS; METABOLISM; MOLECULAR GENETICS; MULTICELLULAR SPHEROID; NUCLEOTIDE SEQUENCE;

ANEUPLOIDY; ANIMALS; BASE SEQUENCE; CELL PROLIFERATION; CHROMOSOME BREAKAGE; CLONE CELLS; COMPARATIVE GENOMIC HYBRIDIZATION; DNA COPY NUMBER VARIATIONS; GENETIC LOCI; GENOMIC INSTABILITY; GENOMIC STRUCTURAL VARIATION; INDUCED PLURIPOTENT STEM CELLS; MICE; MOLECULAR SEQUENCE DATA; NEURAL STEM CELLS; SPHEROIDS, CELLULAR;

EID: 84908092597     PISSN: 10665099     EISSN: 15494918     Source Type: Journal    
DOI: 10.1002/stem.1779     Document Type: Article

References (29)

1. Marchetto MC, Brennand KJ, Boyer LF et al. Induced pluripotent stem cells (iPSCs) and neurological disease modeling: progress and promises. Hum Mol Genet 2011;20: R109-115.
2. Baker DE, Harrison NJ, Maltby E et al. Adaptation to culture of human embryonic stem cells and oncogenesis in vivo. Nat Biotechnol 2007;25:207-215.
3. 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.
4. Martins-Taylor K, Nisler BS, Taapken SM et al. Recurrent copy number variations in human induced pluripotent stem cells. Nat Biotechnol 2011;29:488-491.
5. Mayshar Y, Ben-David U, Lavon N et al. Identification and classification of chromosomal aberrations in human induced pluripotent stem cells. Cell Stem Cell 2010;7:521-531.
6. Hussein SM, Batada NN, Vuoristo S et al. Copy number variation and selection during reprogramming to pluripotency. Nature 2011;471:58-62.
7. 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.
8. Pasi CE, Dereli-Oz A, Negrini S et al. Genomic instability in induced stem cells. Cell Death Differentiat 2011;18:745-753.
9. Chen Y, Guo L, Chen J et al. Genomewide CNV analysis in mouse induced pluripotent stem cells reveals dosage effect of pluripotent factors on genome integrity. BMC Genom 2014;15:79.
10. Abyzov A, Mariani J, Palejev D et al. Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells. Nature 2012;492:438-442.
11. Laurent LC, Ulitsky I, Slavin I 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.
12. Taapken SM, Nisler BS, Newton MA et al. Karotypic abnormalities in human induced pluripotent stem cells and embryonic stem cells. Nat Biotechnol 2011;29:313-314.
13. Harrison NJ. Genetic instability in neural stem cells: an inconvenient truth? J Clin Invest 2012;122:484-486.
14. Arlt MF, Rajendran S, Birkeland SR et al. De novo CNV formation in mouse embryonic stem cells occurs in the absence of Xrcc4- dependent nonhomologous end joining. PLoS Genet 2012;8:e1002981.
15. Lee JA, Carvalho CM, Lupski JR. A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders. Cell 2007;131:1235-1247.
16. Hastings PJ, Ira G, Lupski JR. A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet 2009;5: e1000327.
17. Carey BW, Markoulaki S, Beard C et al. Single-gene transgenic mouse strains for reprogramming adult somatic cells. Nat Method. 2010;7:56-59.
18. Chojnacki A, Weiss S. Production of neurons, astrocytes and oligodendrocytes from mammalian CNS stem cells. Nat Protoc 2008; 3:935-940.
19. Kantor AB, Herzenberg LA. Origin of murine B cell lineages. Ann Rev Immunol 1993;11:501-538.
20. Biesecker LG, Spinner NB. A genomic view of mosaicism and human disease. Nat Rev Genet 2013;14:307-320.
21. Rehen SK, McConnell MJ, Kaushal D et al. Chromosomal variation in neurons of the developing and adult mammalian nervous system. Proc Natl Acad Sci USA 2001;98: 13361-13366.
22. McConnell MJ, Lindberg MR, Brennand KJ et al. Mosaic copy number variation in human neurons. Science 2013;342:632-637.
23. Arlt MF, Ozdemir AC, Birkeland SR et al. Hydroxyurea induces de novo copy number variants in human cells. Proc Natl Acad Sci USA 2011;108:17360-17365.
24. Quinlan AR, Boland MJ, Leibowitz ML et al. Genome sequencing of mouse induced pluripotent stem cells reveals retroelement stability and infrequent DNA rearrangement during reprogramming. Cell Stem Cell 2011;9: 366-373.
25. Lupski JR. Genetics. Genome mosaicism- one human, multiple genomes. Science 2013; 341:358-359.
26. Liang Q, Conte N, Skarnes WC et al. Extensive genomic copy number variation in embryonic stem cells. Proc Natl Acad Sci U S A 2008;105:17453-17456.
27. Dittwald P, Gambin T, Szafranski P et al. NAHR-mediated copy-number variants in a clinical population: Mechanistic insights into both genomic disorders and Mendelizing traits. Genome Res 2013;23:1395-1409.
28. Lu J, Li H, Hu M et al. The Distribution of Genomic Variations in Human iPSCs Is Related to Replication-Timing Reorganization during Reprogramming. Cell Rep 2014;7:70-78.
29. Benito-Sanz S, Royo JL, Barroso E et al. Identification of the first recurrent PAR1 deletion in Leri-Weill dyschondrosteosis and idiopathic short stature reveals the presence of a novel SHOX enhancer. J Med Genet 2012;49:442-450.