1 |
Madden DT, Davila-Kruger D, Melov S and Bredesen DE (2011) Human embryonic stem cells express elevated levels of multiple pro-apoptotic BCL-2 family members. PLoS One 6, e28530
DOI
|
2 |
Dumitru R, Gama V, Fagan BM et al (2012) Human embryonic stem cells have constitutively active Bax at the golgi and are primed to undergo rapid apoptosis. Molecular Cell 46, 573-583
DOI
|
3 |
Imreh MP, Gertow K, Cedervall J et al (2006) In vitro culture conditions favoring selection of chromosomal abnormalities in human ES cells. J Cell Biochem 99, 508-516
DOI
|
4 |
Rouhani FJ, Nik-Zainal S, Wuster A et al (2016) Mutational history of a human cell lineage from somatic to induced pluripotent stem cells. PLoS Genet 12, e1005932
DOI
|
5 |
Thompson O, Von Meyenn F, Hewitt Z et al (2020) Low rates of mutation in clinical grade human pluripotent stem cells under different culture conditions. Nat Commun 11, 1528
DOI
|
6 |
Markouli C, Couvreu De Deckersberg E, Regin M et al (2019) Gain of 20q11.21 in human pluripotent stem cells impairs TGF-β-dependent neuroectodermal commitment. Stem Cell Reports 13, 163-176
DOI
|
7 |
Blum B, Bar-Nur O, Golan-Lev T and Benvenisty N (2009) The anti-apoptotic gene survivin contributes to teratoma formation by human embryonic stem cells. Nat Biotechnol 27, 281-287
DOI
|
8 |
Suzuki MM and Bird A (2008) DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 9, 465-476
DOI
|
9 |
Hackett JA and Surani MA (2013) DNA methylation dynamics during the mammalian life cycle. Philos Trans R Soc Lond B Biol Sci 368, 20110328
DOI
|
10 |
Liao J, Karnik R, Gu H et al (2015) Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells. Nat Genet 47, 469-478
DOI
|
11 |
Bock C, Kiskinis E, Verstappen G et al (2011) Reference maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell 144, 439-452
DOI
|
12 |
Desmarais JA, Unger C, Damjanov I, Meuth M and Andrews P (2016) Apoptosis and failure of checkpoint kinase 1 activation in human induced pluripotent stem cells under replication stress. Stem Cell Res Ther 7, 17
DOI
|
13 |
Lee CT, Raphael, Abigail et al (2015) Functional consequences of 17q21.31/WNT3-WNT9B amplification in hPSCs with respect to neural differentiation. Cell Rep 10, 616-632
DOI
|
14 |
Calvanese V, Horrillo A, Hmadcha A et al (2008) Cancer genes hypermethylated in human embryonic stem cells. PLoS One 3, e3294
DOI
|
15 |
Pauklin S and Vallier L (2013) The cell-cycle state of stem cells determines cell fate propensity. Cell 155, 135-147
DOI
|
16 |
Luo LZ, Gopalakrishna-Pillai S, Nay SL et al (2012) DNA repair in human pluripotent stem cells is distinct from that in non-pluripotent human cells. PLoS One 7, e30541
DOI
|
17 |
Jang J, Wang Y, Matthew et al (2016) Primary ciliumautophagy-nrf2 (pan) axis activation commits human embryonic stem cells to a neuroectoderm fate. Cell 165, 410-420
DOI
|
18 |
Saretzki G, Walter T, Atkinson S et al (2008) Downregulation of multiple stress defense mechanisms during differentiation of human embryonic stem cells. Stem Cells 26, 455-464
DOI
|
19 |
Hyka-Nouspikel N, Desmarais J, Gokhale PJ et al (2012) Deficient DNA damage response and cell cycle checkpoints lead to accumulation of point mutations in human embryonic stem cells. Stem Cells 30, 1901-1910
DOI
|
20 |
Julia, Guan X, Jeremy et al (2013) High mitochondrial priming sensitizes hESCs to DNA-damage-induced apoptosis. Cell Stem Cell 13, 483-491
DOI
|
21 |
Lee J, Hyeon DY and Hwang D (2020) Single-cell multiomics: technologies and data analysis methods. Exp Mol Med 52, 1428-1442
DOI
|
22 |
Nakanishi M, Mitchell RR, Benoit YD et al (2019) Human pluripotency is initiated and preserved by a unique subset of founder cells. Cell 177, 910-924.e922
DOI
|
23 |
Shelley, Thornton M, Mason E, Jessica, Christine and Martin (2014) Single-cell gene expression profiles define self-renewing, pluripotent, and lineage primed states of human pluripotent stem cells. Stem Cell Reports 2, 881-895
DOI
|
24 |
Catalina P, Montes R, Ligero G et al (2008) Human ESCs predisposition to karyotypic instability: is a matter of culture adaptation or differential vulnerability among hESC lines due to inherent properties? Molecular Cancer 7, 76
DOI
|
25 |
Jang J, Han D, Golkaram M et al (2019) Control over single-cell distribution of G1 lengths by WNT governs pluripotency. PLoS Biol 17, e3000453
DOI
|
26 |
Rossant J and Tam PPL (2017) New insights into early human development: lessons for stem cell derivation and differentiation. Cell Stem Cell 20, 18-28
DOI
|
27 |
Peerani R, Rao BM, Bauwens C et al (2007) Niche-mediated control of human embryonic stem cell self-renewal and differentiation. EMBO Rep 26, 4744-4755
DOI
|
28 |
Bedzhov I and Zernicka-Goetz M (2014) Self-organizing properties of mouse pluripotent cells initiate morphogenesis upon implantation. Cell 156, 1032-1044
DOI
|
29 |
Xu C, Inokuma MS, Denham J et al (2001) Feeder-free growth of undifferentiated human embryonic stem cells. Nat Biotechnol 19, 971-974
DOI
|
30 |
Toh YC, Xing J and Yu H (2015) Modulation of integrin and E-cadherin-mediated adhesions to spatially control heterogeneity in human pluripotent stem cell differentiation. Biomaterials 50, 87-97
DOI
|
31 |
Yoshihara M, Araki R, Kasama Y et al (2017) Hotspots of de novo point mutations in induced pluripotent stem cells. Cell Reports 21, 308-315
DOI
|
32 |
Warmflash A, Sorre B, Etoc F, Siggia ED and Brivanlou AH (2014) A method to recapitulate early embryonic spatial patterning in human embryonic stem cells. Nat Methods 11, 847-854
DOI
|
33 |
Wang J, Xie G, Singh M et al (2014) Primate-specific endogenous retrovirus-driven transcription defines naivelike stem cells. Nature 516, 405-409
DOI
|
34 |
Liu Y, Mi Y, Mueller T et al (2019) Multi-omic measurements of heterogeneity in HeLa cells across laboratories. Nat Biotechnol 37, 314-322
DOI
|
35 |
Taapken SM, Nisler BS, Newton MA et al (2011) Karyotypic abnormalities in human induced pluripotent stem cells and embryonic stem cells. Nat Biotechnol 29, 313-314
DOI
|
36 |
Merkle FT, Ghosh S, Kamitaki N et al (2017) Human pluripotent stem cells recurrently acquire and expand dominant negative P53 mutations. Nature 545, 229-233
DOI
|
37 |
Simara P, Tesarova L, Rehakova D et al (2017) DNA double-strand breaks in human induced pluripotent stem cell reprogramming and long-term in vitro culturing. Stem Cell Res Ther 8, 73
DOI
|
38 |
Zhang J, Hirst AJ, Duan F et al (2019) Anti-apoptotic mutations desensitize human pluripotent stem cells to mitotic stress and enable aneuploid cell survival. Stem Cell Reports 12, 557-571
DOI
|
39 |
Maynard S, Swistowska AM, Lee JW et al (2008) Human embryonic stem cells have enhanced repair of multiple forms of DNA damage. Stem Cells 26, 2266-2274
DOI
|
40 |
Initiative ISC (2011) Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage. Nat Biotechnol 29, 1132-1144
DOI
|
41 |
Draper JS, Smith K, Gokhale P et al (2004) Recurrent gain of chromosomes 17q and 12 in cultured human embryonic stem cells. Nat Biotechnol 22, 53-54
DOI
|
42 |
Baker D, Adam, Paul et al (2016) Detecting genetic mosaicism in cultures of human pluripotent stem cells. Stem Cell Reports 7, 998-1012
DOI
|
43 |
Narva E, Autio R, Rahkonen N et al (2010) High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity. Nat Biotechnol 28, 371-377
DOI
|
44 |
Kucab JE, Zou X, Morganella S et al (2019) A compendium of mutational signatures of environmental agents. Cell 177, 821-836.e816
DOI
|
45 |
Halliwell JA, Frith TJR, Laing O et al (2020) Nucleosides rescue replication-mediated genome instability of human pluripotent stem cells. Stem Cell Reports 14, 1009-1017
DOI
|
46 |
Cannan WJ and Pederson DS (2016) Mechanisms and consequences of double-strand DNA break formation in chromatin. J Cell Physiol 231, 3-14
DOI
|
47 |
Bar-Nur O, Holger, Efrat S and Benvenisty N (2011) Epigenetic memory and preferential lineage-specific differentiation in induced pluripotent stem cells derived from human pancreatic islet beta cells. Cell Stem Cell 9, 17-23
DOI
|
48 |
Lamm N, Ben-David U, Golan-Lev T, Storchova Z, Benvenisty N and Kerem B (2016) Genomic instability in human pluripotent stem cells arises from replicative stress and chromosome condensation defects. Cell Stem Cell 18, 253-261
DOI
|
49 |
Ji J, Ng SH, Sharma V et al (2012) Elevated coding mutation rate during the reprogramming of human somatic cells into induced pluripotent stem cells. Stem Cells 30, 435-440
DOI
|
50 |
Weissbein U, Plotnik O, Vershkov D and Benvenisty N (2017) Culture-induced recurrent epigenetic aberrations in human pluripotent stem cells. PLoS Genet 13, e1006979
DOI
|
51 |
Bartolomei MS and Ferguson-Smith AC (2011) Mammalian genomic imprinting. Cold Spring Harb Perspect Biol 3, a002592-a002592
DOI
|
52 |
Surani MAH, Barton SC and Norris ML (1984) Development of reconstituted mouse eggs suggests imprinting of the genome during gametogenesis. Nature 308, 548-550
DOI
|
53 |
Lim DH and Maher ER (2010) Genomic imprinting syndromes and cancer. Adv Genet 70, 145-175
DOI
|
54 |
Initiative TISC (2007) Characterization of human embryonic stem cell lines by the International Stem Cell Initiative. Nat Biotechnol 25, 803-816
DOI
|
55 |
Nichols J and Smith A (2009) Naive and primed pluripotent states. Cell Stem Cell 4, 487-492
DOI
|
56 |
Niwa H, Ogawa K, Shimosato D and Adachi K (2009) A parallel circuit of LIF signalling pathways maintains pluripotency of mouse ES cells. Nature 460, 118-122
DOI
|
57 |
Desmarais JA, Hoffmann MJ, Bingham G, Gagou ME, Meuth M and Andrews PW (2012) Human embryonic stem cells fail to activate CHK1 and commit to apoptosis in response to DNA replication stress. Stem Cells 30, 1385-1393
DOI
|
58 |
Milholland B, Dong X, Zhang L, Hao X, Suh Y and Vijg J (2017) Differences between germline and somatic mutation rates in humans and mice. Nat Commun 8, 15183
DOI
|
59 |
Toyooka Y, Shimosato D, Murakami K, Takahashi K and Niwa H (2008) Identification and characterization of subpopulations in undifferentiated ES cell culture. Development 135, 909-918
DOI
|
60 |
Adams BR, Golding SE, Rao RR and Valerie K (2010) Dynamic dependence on ATR and ATM for doublestrand break repair in human embryonic stem cells and neural descendants. PLoS One 5, e10001
DOI
|
61 |
Petropoulos S, Edsgard D, Reinius B et al (2016) Single-cell RNA-Seq reveals lineage and X chromosome dynamics in human preimplantation embryos. Cell 165, 1012-1026
DOI
|
62 |
Bruck T and Benvenisty N (2011) Meta-analysis of the heterogeneity of X chromosome inactivation in human pluripotent stem cells. Stem Cell Research 6, 187-193
DOI
|
63 |
Ma H, Morey R, O'Neil RC et al (2014) Abnormalities in human pluripotent cells due to reprogramming mechanisms. Nature 511, 177-183
DOI
|
64 |
Vallabhaneni H, Lynch PJ, Chen G et al (2018) High basal levels of γH2AX in human induced pluripotent stem cells are linked to replication-associated DNA damage and repair. Stem Cells 36, 1501-1513
DOI
|
65 |
Yamazawa K, Ogata T and Ferguson-Smith AC (2010) Uniparental disomy and human disease: An overview. Am J Med Genet C Semin Med Genet 154C, 329-334
DOI
|
66 |
Thorold, Friedli M, He Y et al (2016) Molecular criteria for defining the naive human pluripotent state. Cell Stem Cell 19, 502-515
DOI
|
67 |
Lengner CJ, Gimelbrant AA, Erwin JA et al (2010) Derivation of pre-X inactivation human embryonic stem cells under physiological oxygen concentrations. Cell 141, 872-883
DOI
|
68 |
Amar, Chappell J, Trost R et al (2013) Cell-cycle control of developmentally regulated transcription factors accounts for heterogeneity in human pluripotent cells. Stem Cell Reports 1, 532-544
DOI
|
69 |
Dvash T, Lavon N and Fan G (2010) Variations of X chromosome inactivation occur in early passages of female human embryonic stem cells. PLoS One 5, e11330
DOI
|
70 |
Sahakyan A, Kim R, Chronis C et al (2017) Human naive pluripotent stem cells model X chromosome dampening and X inactivation. Cell Stem Cell 20, 87-101
DOI
|
71 |
Becker KA, Ghule PN, Therrien JA et al (2006) Self-renewal of human embryonic stem cells is supported by a shortened G1 cell cycle phase. J Cell Physiol 209, 883-893
DOI
|
72 |
Singh AM and Dalton S (2009) The cell cycle and myc intersect with mechanisms that regulate pluripotency and reprogramming. Cell Stem Cell 5, 141-149
DOI
|
73 |
Sakaue-Sawano A, Kurokawa H, Morimura T et al (2008) Visualizing spatiotemporal dynamics of multicellular cell-cycle progression. Cell 132, 487-498
DOI
|
74 |
Pauklin S, Madrigal P, Bertero A and Vallier L (2016) Initiation of stem cell differentiation involves cell cycle-dependent regulation of developmental genes by cyclin D. Genes Dev 30, 421-433
DOI
|
75 |
Moreira de Mello JC, Fernandes GR, Vibranovski MD and Pereira LV (2017) Early X chromosome inactivation during human preimplantation development revealed by single-cell RNA-sequencing. Sci Rep 7, 10794
DOI
|
76 |
Patel S, Bonora G, Sahakyan A et al (2017) Human embryonic stem cells do not change their X inactivation status during differentiation. Cell Rep 18, 54-67
DOI
|
77 |
Silva SS, Rowntree RK, Mekhoubad S and Lee JT (2008) X-chromosome inactivation and epigenetic fluidity in human embryonic stem cells. Proc Natl Acad Sci U S A 105, 4820-4825
DOI
|
78 |
Leick MB, Shoff CJ, Wang EC, Congress JL and Gallicano GI (2011) Loss of imprinting of IGF2 and the epigenetic progenitor model of cancer. Am J Stem Cells 1, 59-74
|
79 |
William, Chen D, Liu W et al (2016) Naive human pluripotent cells feature a methylation landscape devoid of blastocyst or germline memory. Cell Stem Cell 18, 323-329
DOI
|
80 |
Jelinic P and Shaw P (2007) Loss of imprinting and cancer. J Pathol 211, 261-268
DOI
|
81 |
Johannesson B, Sagi I, Gore A et al (2014) Comparable frequencies of coding mutations and loss of imprinting in human pluripotent cells derived by nuclear transfer and defined factors. Cell Stem Cell 15, 634-642
DOI
|
82 |
Chambers I, Silva J, Colby D et al (2007) Nanog safeguards pluripotency and mediates germline development. Nature 450, 1230-1234
DOI
|
83 |
Rodriguez S, Jafer O, Goker H et al (2003) Expression profile of genes from 12p in testicular germ cell tumors of adolescents and adults associated with i(12p) and amplification at 12p11.2-p12.1. Oncogene 22, 1880-1891
DOI
|
84 |
Jo HY, Lee Y, Ahn H et al (2020) Functional in vivo and in vitro effects of 20q11.21 genetic aberrations on hPSC differentiation. Sci Rep 10, 18582
DOI
|
85 |
Lyon MF (1961) Gene Action in the X-chromosome of the mouse (Mus musculus L.). Nature 190, 372-373
DOI
|
86 |
Pick M, Stelzer Y, Bar-Nur O, Mayshar Y, Eden A and Benvenisty N (2009) Clone- and gene-specific aberrations of parental imprinting in human induced pluripotent stem cells. Stem Cells 27, 2686-2690
DOI
|
87 |
Geens M, Seriola A, Barbe L et al (2016) Female human pluripotent stem cells rapidly lose X chromosome inactivation marks and progress to a skewed methylation pattern during culture. Mol Hum Reprod 22, 285-298
DOI
|
88 |
Weinberger L, Ayyash M, Novershtern N and Hanna JH (2016) Dynamic stem cell states: naive to primed pluripotency in rodents and humans. Nat Rev Mol Cell Biol 17, 155-169
DOI
|
89 |
Roost MS, Slieker RC, Bialecka M et al (2017) DNA methylation and transcriptional trajectories during human development and reprogramming of isogenic pluripotent stem cells. Nat Commun 8, 908
DOI
|
90 |
Shen Y, Matsuno Y, Fouse SD et al (2008) X-inactivation in female human embryonic stem cells is in a nonrandom pattern and prone to epigenetic alterations. Proc Natl Acad Sci U S A 105, 4709-4714
DOI
|
91 |
Fleming TP et al (2001) Cell junctions and cell interactions in animal and human blastocyst development. ART and the Human Blastocyst. Springer, New York, NY, 2001. 91-102.
|
92 |
Etoc F, Metzger J, Ruzo A et al (2016) A Balance between secreted inhibitors and edge sensing controls gastruloid self-organization. Dev Cell 39, 302-315
DOI
|
93 |
Jain AK and Barton MC (2018) p53: emerging roles in stem cells, development and beyond. Development 145, dev158360
DOI
|
94 |
Tahiliani M, Koh KP, Shen Y et al (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930-935
DOI
|
95 |
Calder A, Roth-Albin I, Bhatia S et al (2013) Lengthened G1 phase indicates differentiation status in human embryonic stem cells. Stem Cells Dev 22, 279-295
DOI
|
96 |
Kevin, Liang H, Lim YS et al (2015) Deterministic restriction on pluripotent state dissolution by cell-cycle pathways. Cell 162, 564-579
DOI
|
97 |
Thomson JA (1998) Embryonic stem cell lines derived from human blastocysts. Science 282, 1145-1147
DOI
|
98 |
Kallas-Kivi A, Trei A, Stepanjuk A et al (2018) The role of integrin β1 in the heterogeneity of human embryonic stem cells culture. Biol 7, bio034355
|
99 |
Kristopher, Altun G, Lynch C et al (2012) Recurrent variations in DNA methylation in human pluripotent stem cells and their differentiated derivatives. Cell Stem Cell 10, 620-634
DOI
|
100 |
Messerschmidt DM, Knowles BB and Solter D (2014) DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos. Genes Dev 28, 812-828
DOI
|
101 |
McGrath J and Solter D (1984) Completion of mouse embryogenesis requires both the maternal and paternal genomes. Cell 37, 179-183
DOI
|
102 |
Weksberg R (2010) Imprinted genes and human disease. Am J Med Genet C Semin Med Genet 154C, 317-320
DOI
|
103 |
Rugg-Gunn PJ, Ferguson-Smith AC and Pedersen RA (2007) Status of genomic imprinting in human embryonic stem cells as revealed by a large cohort of independently derived and maintained lines. Hum Mol Genet 16, R243-R251
DOI
|
104 |
Bar S, Schachter M, Eldar-Geva T and Benvenisty N (2017) Large-scale analysis of loss of imprinting in human pluripotent stem cells. Cell Rep 19, 957-968
DOI
|
105 |
Davies W, Isles AR and Wilkinson LS (2005) Imprinted gene expression in the brain. Neurosci Biobehav Rev 29, 421-430
DOI
|
106 |
Korkola JE, Houldsworth J, Chadalavada RSV et al (2006) Down-regulation of stem cell genes, including those in a 200-kb gene cluster at 12p13.31, is associated with in vivo differentiation of human male germ cell tumors. Cancer Res 66, 820-827
DOI
|
107 |
Vallot C, Patrat C, Collier AJ et al (2017) XACT noncoding RNA competes with XIST in the control of X chromosome activity during human early development. Cell Stem Cell 20, 102-111
DOI
|
108 |
Ben-David U, Arad G, Weissbein U et al (2014) Aneuploidy induces profound changes in gene expression, proliferation and tumorigenicity of human pluripotent stem cells. Nat Commun 5, 4825
DOI
|
109 |
Darr H, Mayshar Y and Benvenisty N (2006) Overexpression of NANOG in human ES cells enables feeder-free growth while inducing primitive ectoderm features. Development 133, 1193-1201
DOI
|
110 |
Avery S, Adam, Baker D et al (2013) BCL-XL mediates the strong selective advantage of a 20q11.21 amplification commonly found in human embryonic stem cell cultures. Stem Cell Reports 1, 379-386
DOI
|