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Review

Effects of the in Vitro Manipulation of Stem Cells: Epigenetic Mechanisms as Mediators of Induced Metabolic Fluctuations

Pages 429-437 | Published online: 29 Jul 2013

References

  • Weissman IL . Stem cells: units of development, units of regeneration, and units in evolution. Cell100(1) , 157–168 (2000).
  • Ramalho-Santos M , WillenbringH. On the origin of the term ‘stem cell‘. Cell Stem Cell1(1) , 35–38 (2007).
  • Martin GR . Isolation of a pluripotent cell line from early mouse embryos cultured in medium conditioned by teratocarcinoma stem cells. Proc. Natl Acad. Sci. USA78(12) , 7634–7638 (1981).
  • Smith AG , HeathJK, DonaldsonDD et al. Inhibition of pluripotential embryonic stem cell differentiation by purified polypeptides. Nature 336(6200) , 688–690 (1988).
  • Williams RL , HiltonDJ, PeaseS et al. Myeloid leukaemia inhibitory factor maintains the developmental potential of embryonic stem cells. Nature 336(6200) , 684–687 (1988).
  • Zhang Y , LiW, LaurentT, DingS. Small molecules, big roles – the chemical manipulation of stem cell fate and somatic cell reprogramming. J. Cell Sci.125(Pt 23) , 5609–5620 (2012).
  • Narsinh KH , SunN, Sanchez-FreireV et al. Single cell transcriptional profiling reveals heterogeneity of human induced pluripotent stem cells. J. Clin. Invest. 121(3) , 1217–1221 (2011).
  • Hayashi K , LopesSM, TangF, SuraniMA. Dynamic equilibrium and heterogeneity of mouse pluripotent stem cells with distinct functional and epigenetic states. Cell Stem Cell3(4) , 391–401 (2008).
  • Singh AM , HamazakiT, HankowskiKE, TeradaN. A heterogeneous expression pattern for Nanog in embryonic stem cells. Stem Cells25(10) , 2534–2542 (2007).
  • Kalmar T , LimC, HaywardP et al. Regulated fluctuations in nanog expression mediate cell fate decisions in embryonic stem cells. PLoS Biol. 7(7) , e1000149 (2009).
  • Stockholm D , BenchaouirR, PicotJ et al. The origin of phenotypic heterogeneity in a clonal cell population in vitro. PLoS One 2(4) , e394 (2007).
  • Stockholm D , Edom-VovardF, CoutantS et al. Bistable cell fate specification as a result of stochastic fluctuations and collective spatial cell behavior. PLoS One 5(12) , e14441 (2010).
  • Chang HH , HembergM, BarahonaM, IngberDE, HuangS. Transcriptome-wide noise controls lineage choice in mammalian progenitor cells. Nature453(7194) , 544–547 (2008).
  • Ying QL , WrayJ, NicholsJ et al. The ground state of embryonic stem cell self-renewal. Nature 453(7194) , 519–523 (2008).
  • Hebert JM . FGFs: neurodevelopment‘s jack-of-all-trades – how do they do it? Front. Neurosci.5 , 133 (2011).
  • Lanner F , RossantJ. The role of FGF/Erk signaling in pluripotent cells. Development137(20) , 3351–3360 (2010).
  • Woodgett JR . Judging a protein by more than its name: GSK-3. Sci. STKE2001(100) , re12 (2001).
  • Folmes CD , NelsonTJ, Martinez-FernandezA et al. Somatic oxidative bioenergetics transitions into pluripotency-dependent glycolysis to facilitate nuclear reprogramming. Cell Metab. 14(2) , 264–271 (2011).
  • Zhu S , LiW, ZhouH et al. Reprogramming of human primary somatic cells by OCT4 and chemical compounds. Cell Stem Cell 7(6) , 651–655 (2010).
  • Yoshida Y , TakahashiK, OkitaK, IchisakaT, YamanakaS. Hypoxia enhances the generation of induced pluripotent stem cells. Cell Stem Cell5(3) , 237–241 (2009).
  • Folmes CD , DzejaPP, NelsonTJ, TerzicA. Metabolic plasticity in stem cell homeostasis and differentiation. Cell Stem Cell11(5) , 596–606 (2012).
  • Yanes O , ClarkJ, WongDM et al. Metabolic oxidation regulates embryonic stem cell differentiation. Nat. Chem. Biol. 6(6) , 411–417 (2010).
  • Paldi A . What makes the cell differentiate? Prog. Biophys. Mol. Biol.110(1) , 41–43 (2012).
  • Jordan B . Are expression profiles meaningless for cancer studies? Bioessays34(9) , 730–733 (2012).
  • Williams R , SchuldtB, MullerFJ. A guide to stem cell identification: progress and challenges in system-wide predictive testing with complex biomarkers. Bioessays33(11) , 880–890 (2011).
  • Lund RJ , NarvaE, LahesmaaR. Genetic and epigenetic stability of human pluripotent stem cells. Nat. Rev. Genet.13(10) , 732–744 (2012).
  • Taapken SM , NislerBS, NewtonMA et al. Karotypic abnormalities in human induced pluripotent stem cells and embryonic stem cells. Nat. Biotechnol. 29(4) , 313–314 (2011).
  • Dean W , BowdenL, AitchisonA et al. Altered imprinted gene methylation and expression in completely ES cell-derived mouse fetuses: association with aberrant phenotypes. Development 125(12) , 2273–2282 (1998).
  • Humpherys D , EgganK, AkutsuH et al. Epigenetic instability in ES cells and cloned mice. Science 293(5527) , 95–97 (2001).
  • Lengner CJ , GimelbrantAA, ErwinJA et al. Derivation of pre-X inactivation human embryonic stem cells under physiological oxygen concentrations. Cell 141(5) , 872–883 (2010).
  • Tompkins JD , HallC, ChenVC et al. Epigenetic stability, adaptability, and reversibility in human embryonic stem cells. Proc. Natl Acad. Sci. USA 109(31) , 12544–12549 (2012).
  • Kim K , DoiA, WenB et al. Epigenetic memory in induced pluripotent stem cells. Nature 467(7313) , 285–290 (2010).
  • Lister R , PelizzolaM, KidaYS et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 471(7336) , 68–73 (2011).
  • Engler AJ , SenS, SweeneyHL, DischerDE. Matrix elasticity directs stem cell lineage specification. Cell126(4) , 677–689 (2006).
  • Fehrer C , BrunauerR, LaschoberG et al. Reduced oxygen tension attenuates differentiation capacity of human mesenchymal stem cells and prolongs their lifespan. Aging Cell 6(6) , 745–757 (2007).
  • Csete M , WalikonisJ, SlawnyN et al. Oxygen-mediated regulation of skeletal muscle satellite cell proliferation and adipogenesis in culture. J. Cell Physiol. 189(2) , 189–196 (2001).
  • Mohyeldin A , Garzon-MuvdiT, Quinones-HinojosaA. Oxygen in stem cell biology: a critical component of the stem cell niche. Cell Stem Cell7(2) , 150–161 (2010).
  • Glimm H , OhIH, EavesCJ. Human hematopoietic stem cells stimulated to proliferate in vitro lose engraftment potential during their S/G(2)/M transit and do not reenter G(0). Blood96(13) , 4185–4193 (2000).
  • Schellenberg A , LinQ, SchulerH et al. Replicative senescence of mesenchymal stem cells causes DNA-methylation changes which correlate with repressive histone marks. Aging 3(9) , 873–888 (2011).
  • Till JE , MccullochEA, SiminovitchL. A stochastic model of stem cell proliferation, based on the growth of spleen colony-forming cells. Proc. Natl Acad. Sci. USA51 , 29–36 (1964).
  • Socolovsky M , LodishHF, DaleyGQ. Control of hematopoietic differentiation: lack of specificity in signaling by cytokine receptors. Proc. Natl Acad. Sci. USA95(12) , 6573–6575 (1998).
  • Abkowitz JL , CatlinSN, GuttorpP. Evidence that hematopoiesis may be a stochastic process in vivo. Nat. Med.2(2) , 190–197 (1996).
  • Kupiec JJ . The Origin of Individuals. World Scientific, NJ, USA (2009).
  • Kupiec JJ . A chance-selection model for cell differentiation. Cell Death Differ.3(4) , 385–390 (1996).
  • Kupiec JJ . A Darwinian theory for the origin of cellular differentiation. Mol. General Genet.255(2) , 201–208 (1997).
  • Gandrillon O , Kolesnik-AntoineD, KupiecJJ, BeslonG. Chance at the heart of the cell. Prog. Biophys. Mol. Biol.110(1) , 1–4 (2012).
  • Simons BD , CleversH. Strategies for homeostatic stem cell self-renewal in adult tissues. Cell145(6) , 851–862 (2011).
  • Yamanaka S . Elite and stochastic models for induced pluripotent stem cell generation. Nature460(7251) , 49–52 (2009).
  • Buganim Y , FaddahDA, ChengAW et al. Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase. Cell 150(6) , 1209–1222 (2012).
  • Hanna J , SahaK, PandoB et al. Direct cell reprogramming is a stochastic process amenable to acceleration. Nature 462(7273) , 595–601 (2009).
  • Elowitz MB , LevineAJ, SiggiaED, SwainPS. Stochastic gene expression in a single cell. Science297(5584) , 1183–1186 (2002).
  • Kaern M , ElstonTC, BlakeWJ, CollinsJJ. Stochasticity in gene expression: from theories to phenotypes. Nat. Rev. Genet.6(6) , 451–464 (2005).
  • Balazsi G , Van Oudenaarden A, Collins JJ. Cellular decision making and biological noise: from microbes to mammals. Cell144(6) , 910–925 (2011).
  • Neildez-Nguyen TM , ParisotA, VignalC et al. Epigenetic gene expression noise and phenotypic diversification of clonal cell populations. Differ. Res. Biol. Div. 76(1) , 33–40 (2008).
  • Misteli T . Protein dynamics: implications for nuclear architecture and gene expression. Science291(5505) , 843–847 (2001).
  • Meshorer E , YellajoshulaD, GeorgeE, ScamblerPJ, BrownDT, MisteliT. Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells. Dev. Cell10(1) , 105–116 (2006).
  • Melcer S , HezroniH, RandE et al. Histone modifications and lamin A regulate chromatin protein dynamics in early embryonic stem cell differentiation. Nat. Commun. 3 , 910 (2012).
  • Imamura T , KerjeanA, HeamsT, KupiecJJ, ThenevinC, PaldiA. Dynamic CpG and non-CpG methylation of the Peg1/Mest gene in the mouse oocyte and preimplantation embryo. J. Biol. Chem.280(20) , 20171–20175 (2005).
  • Yamagata Y , SzaboP, SzutsD, BacquetC, AranyiT, PaldiA. Rapid turnover of DNA methylation in human cells. Epigenetics7(2) , 141–145 (2012).
  • Paldi A . Stochastic gene expression during cell differentiation: order from disorder? Cell. Mol. Life Sci.60(9) , 1775–1778 (2003).
  • Kaelin WG Jr, Mcknight SL. Influence of metabolism on epigenetics and disease. Cell153(1) , 56–69 (2013).
  • Lu C , ThompsonCB. Metabolic regulation of epigenetics. Cell Metab.16(1) , 9–17 (2012).
  • Cyr AR , DomannFE. The redox basis of epigenetic modifications: from mechanisms to functional consequences. Antioxid. Redox Signal.15(2) , 551–589 (2011).
  • Huang S . The molecular and mathematical basis of Waddington‘s epigenetic landscape: a framework for post-Darwinian biology? Bioessays34(2) , 149–157 (2012).
  • Frost J , MonkD, MoschidouD et al. The effects of culture on genomic imprinting profiles in human embryonic and fetal mesenchymal stem cells. Epigenetics 6(1) , 52–62 (2011).
  • Yamagata Y , PariettiV, StockholmD et al. Lentiviral transduction of CD34+ cells induces genome-wide epigenetic modifications. PLoS One 7(11) , e48943 (2012).

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