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http://dx.doi.org/10.5483/BMBRep.2021.54.10.094

Single cell heterogeneity in human pluripotent stem cells  

Yang, Seungbok (Department of Life Sciences, Pohang University of Science and Technology (POSTECH))
Cho, Yoonjae (Department of Life Sciences, Pohang University of Science and Technology (POSTECH))
Jang, Jiwon (Department of Life Sciences, Pohang University of Science and Technology (POSTECH))
Publication Information
BMB Reports / v.54, no.10, 2021 , pp. 505-515 More about this Journal
Abstract
Human pluripotent stem cells (hPSCs) include human embryonic stem cells (hESCs) derived from blastocysts and human induced pluripotent stem cells (hiPSCs) generated from somatic cell reprogramming. Due to their self-renewal ability and pluripotent differentiation potential, hPSCs serve as an excellent experimental platform for human development, disease modeling, drug screening, and cell therapy. Traditionally, hPSCs were considered to form a homogenous population. However, recent advances in single cell technologies revealed a high degree of variability between individual cells within a hPSC population. Different types of heterogeneity can arise by genetic and epigenetic abnormalities associated with long-term in vitro culture and somatic cell reprogramming. These variations initially appear in a rare population of cells. However, some cancer-related variations can confer growth advantages to the affected cells and alter cellular phenotypes, which raises significant concerns in hPSC applications. In contrast, other types of heterogeneity are related to intrinsic features of hPSCs such as asynchronous cell cycle and spatial asymmetry in cell adhesion. A growing body of evidence suggests that hPSCs exploit the intrinsic heterogeneity to produce multiple lineages during differentiation. This idea offers a new concept of pluripotency with single cell heterogeneity as an integral element. Collectively, single cell heterogeneity is Janus-faced in hPSC function and application. Harmful heterogeneity has to be minimized by improving culture conditions and screening methods. However, other heterogeneity that is integral for pluripotency can be utilized to control hPSC proliferation and differentiation.
Keywords
Cell-to-cell variation; Heterogeneity; Human pluripotent stem cells; Pluripotency;
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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