Genetic heterogeneity of induced pluripotent stem cells: Results from 24 clones derived from a single C57BL/6 mouse

PLoS ONE

Volumn 10, Issue 3, 2015, Pages

  Li, Cheng ^a,b   Klco, Jeffery M ^a,c   Helton, Nichole M ^a   George, Daniel R ^a   Mudd, Jacqueline L ^a   Miller, Christopher A ^a   Lu, Charles ^a   Fulton, Robert ^a   O'Laughlin, Michelle ^a   Fronick, Catrina ^a   Wilson, Richard K ^a   Ley, Timothy J ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b ONYX PHARMACEUTICALS   (United States)

^c ST JUDE CHILDREN S RESEARCH HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

ANIMAL CELL; ARTICLE; C57BL 6 MOUSE; CELL CLONE; CELL DIFFERENTIATION; COLONY FORMING UNIT; CONTROLLED STUDY; EXOME; GENE FREQUENCY; GENE MUTATION; GENETIC HETEROGENEITY; GENETIC VARIABILITY; HEMATOPOIESIS; HEMATOPOIETIC STEM CELL; HETEROZYGOTE; IN VITRO STUDY; MALE; MOUSE; NONHUMAN; NUCLEAR REPROGRAMMING; PLURIPOTENT STEM CELL; SEQUENCE ANALYSIS; SKIN FIBROBLAST; ANIMAL; C57BL MOUSE; CYTOLOGY; FIBROBLAST; GENE EXPRESSION; GENE EXPRESSION PROFILING; HIGH THROUGHPUT SEQUENCING; INDUCED PLURIPOTENT STEM CELL; METABOLISM;

ANIMALS; CELL DIFFERENTIATION; CLONE CELLS; FIBROBLASTS; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC HETEROGENEITY; HEMATOPOIESIS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INDUCED PLURIPOTENT STEM CELLS; MALE; MICE; MICE, INBRED C57BL;

EID: 84925728955     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0120585     Document Type: Article

References (29)

1. Takahashi K, Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. 2006; 126: 663-676. PMID: 16904174
2. Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K, et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell. 2007; 131: 861-872. PMID: 18035408
3. Yu J, Vodyanik MA, Smuga-Otto K, Antosiewicz-Bourget J, Frane JL, Tian S, et al. Induced pluripotent stem cell lines derived from human somatic cells. Science. 2007; 318: 1917-1920. PMID: 18029452
4. Bellin M, Marchetto MC, Gage FH, Mummery CL. Induced pluripotent stem cells: the new patient? Nat Rev Mol Cell Biol. 2012; 13: 713-726. doi: 10.1038/nrm3448 PMID: 23034453
5. Gore A, Li Z, Fung H-L, Young JE, Agarwal S, Antosiewicz-Bourget J, et al. Somatic coding mutations in human induced pluripotent stem cells. Nature. 2011; 471: 63-67. doi: 10.1038/nature09805 PMID: 21368825
6. Laurent LC, Ulitsky I, Slavin I, Tran H, Schork A, Morey R, 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. doi: 10.1016/j.stem.2010.12.003 PMID: 21211785
7. Abyzov A, Mariani J, Palejev D, Zhang Y, Haney MS, Tomasini L, et al. Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells. Nature. 2012; 492: 438-442. doi: 10. 1038/nature11629 PMID: 23160490
8. Young MA, Larson DE, Sun C-W, George DR, Ding L, Miller CA, 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. doi: 10.1016/j.stem.2012.03.002 PMID: 22542160
9. Mills JA, Wang K, Paluru P, Ying L, Lu L, Galvão AM, et al. Clonal genetic and hematopoietic heterogeneity among human-induced pluripotent stem cell lines. Blood. 2013; 122: 2047-2051. doi: 10.1182/blood-2013-02-484444 PMID: 23940280
10. Cahan P, Daley GQ. Origins and implications of pluripotent stem cell variability and heterogeneity. Nat Rev Mol Cell Biol. 2013; 14: 357-368. doi: 10.1038/nrm3584 PMID: 23673969
11. Liang G, Zhang Y. Genetic and epigenetic variations in iPSCs: potential causes and implications for application. Cell Stem Cell. 2013; 13: 149-159. doi: 10.1016/j.stem.2013.07.001 PMID: 23910082
12. Chang CW, Lai YS, Pawlik KM, Liu K, Sun CW, Li C, et al. Polycistronic Lentiviral Vector for "'Hit and Run'" Reprogramming of Adult Skin Fibroblasts to Induced Pluripotent Stem Cells. Stem Cells. 2009; 27: 1042-1049. doi: 10.1002/stem.39 PMID: 19415770
13. Vodyanik MA, Slukvin II. Hematoendothelial differentiation of human embryonic stem cells. Curr Protoc cell Biol; 2007. Chapter 23: Unit 23.6.
14. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25: 1754-1760. doi: 10.1093/bioinformatics/btp324 PMID: 19451168
15. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25: 2078-2079. doi: 10.1093/bioinformatics/btp352 PMID: 19505943
16. Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE, Dooling DJ, et al. SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinformatics 2012: 28(3): 311-317: doi: 10.1093/bioinformatics/btr665 PMID: 22155872
17. Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 2012; 22: 568-576. doi: 10.1101/gr.129684.111 PMID: 22300766
18. Saunders CT, Wong WSW, Swamy S, Becq J, Murray LJ, Cheetham RK. Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics 2012: 28: 1811-1817. doi: 10.1093/bioinformatics/bts271 PMID: 22581179
19. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010; 20: 1297-1303. doi: 10.1101/gr.107524.110 PMID: 20644199
20. Ye K, Schulz MH, Long Q, Apweiler R, Ning Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 2009: 25: 2865-2871. doi: 10.1093/bioinformatics/btp394 PMID: 19561018
21. Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, et al. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods 2013; 6: 677-681.
22. Yang SH, Cheng PH, Sullivan RT, Thomas JW, Chan AW. Lentiviral integration preferences in transgenic mice. Genesis 2008; 46: 711-718. doi: 10.1002/dvg.20435 PMID: 18821598
23. Boulting GL, Kiskinis E, Croft GF, Amoroso MW, Oakley DH, Wainger BJ, et al. A functionally characterized test set of human induced pluripotent stem cells. Nat Biotechnol 2011; 29: 279-288. doi: 10.1038/nbt.1783 PMID: 21293464
24. Kajiwara M, Aoi T, Okita K, Takahashi R, Inoue H, Takayama N, et al. Donor-dependent variations in hepatic differentiation from human-induced pluripotent stem cells. Proc Natl Acad Sci 2012; 109: 12538-12543. doi: 10.1073/pnas.1209979109 PMID: 22802639
25. Bock C, Kiskinis E, Verstappen G, Gu H, Boulting G, Smith ZD, et al. Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell 2011: 144: 439-452. doi: 10.1016/j.cell.2010.12.032 PMID: 21295703
26. Polo JM, Liu S, Figueroa ME, KulalertW, Eminli S, Tan KY, et al. Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells. Nat Biotechnol 2010; 28: 848-855. doi: 10.1038/nbt.1667 PMID: 20644536
27. Kim K, Doi A, Wen B, Ng K, Zhao R, Cahan P, et al. Epigenetic memory in induced pluripotent stem cells. Nature 2010; 467: 285-290. doi: 10.1038/nature09342 PMID: 20644535
28. Kim K, Zhao R, Doi A, Ng K, Unternaehrer J, Cahan P, et al. Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells. Nat Biotechnol 2011; 29: 1117-1119. doi: 10.1038/nbt.2052 PMID: 22119740
29. Klco JM, Spencer DH, Miller CA, Griffith M, Lamprecht TL, O'Laughlin M, et al. Functional heterogeneity of genetically defined subclones in acute myeloid leukemia. Cancer Cell 2014; 25: 379-392. doi:10.1016/j.ccr.2014.01.031 PMID: 24613412