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Volumn 10, Issue 89, 2013, Pages

Quantifying waddington landscapes and paths of non-adiabatic cell fate decisions for differentiation, reprogramming and transdifferentiation

Author keywords

Differentiation and reprogramming; Dynamical path; Non adiabatic; Potential landscape

Indexed keywords

BINS; CELLS; DECISION MAKING; DYNAMICAL SYSTEMS; GENES; STEM CELLS;

EID: 84899783682     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2013.0787     Document Type: Article
Times cited : (68)

References (52)
  • 1
    • 33747195353 scopus 로고    scopus 로고
    • Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors
    • DOI 10.1016/j.cell.2006.07.024, PII S0092867406009767
    • Takahashi K, Yamanaka S. 2006 Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663-676. (doi:10.1016/j.cell.2006.07.024). (Pubitemid 44233629)
    • (2006) Cell , vol.126 , Issue.4 , pp. 663-676
    • Takahashi, K.1    Yamanaka, S.2
  • 2
    • 77953466536 scopus 로고    scopus 로고
    • Nuclear reprogramming to a pluripotent state by three approaches
    • doi:10.1038/nature09229
    • Yamanaka S, Blau HM. 2010 Nuclear reprogramming to a pluripotent state by three approaches. Nature 465, 704-712. (doi:10.1038/nature09229).
    • (2010) Nature , vol.465 , pp. 704-712
    • Yamanaka, S.1    Blau, H.M.2
  • 3
    • 67650095196 scopus 로고    scopus 로고
    • Elite and stochastic models for induced pluripotent stem cell generation
    • doi:10.1038/nature08180
    • Yamanaka S. 2009 Elite and stochastic models for induced pluripotent stem cell generation. Nature 460, 49-52. (doi:10.1038/nature08180).
    • (2009) Nature , vol.460 , pp. 49-52
    • Yamanaka, S.1
  • 4
    • 52949127370 scopus 로고    scopus 로고
    • Extreme makeover: Converting one cell into another
    • doi:10.1016/j.stem.2008.09.015
    • Zhou Q, Melton D. 2008 Extreme makeover: converting one cell into another. Cell Stem Cell 3, 382-388. (doi:10.1016/j.stem.2008.09.015).
    • (2008) Cell Stem Cell , vol.3 , pp. 382-388
    • Zhou, Q.1    Melton, D.2
  • 5
    • 70450285340 scopus 로고    scopus 로고
    • Technical challenges in using human induced pluripotent stem cells to model disease
    • doi:10. 1016/j.stem.2009.11.009
    • Saha K, Jaenisch R. 2009 Technical challenges in using human induced pluripotent stem cells to model disease. Cell Stem Cell 5, 584-595. (doi:10. 1016/j.stem.2009.11.009).
    • (2009) Cell Stem Cell , vol.5 , pp. 584-595
    • Saha, K.1    Jaenisch, R.2
  • 6
    • 71449125977 scopus 로고    scopus 로고
    • Forcing cells to change lineages
    • doi:10.1038/nature08533
    • Graf T, Enver T. 2009 Forcing cells to change lineages. Nature 462, 587-594. (doi:10.1038/nature08533).
    • (2009) Nature , vol.462 , pp. 587-594
    • Graf T, E.T.1
  • 7
    • 0036790975 scopus 로고    scopus 로고
    • Intrinsic and extrinsic contributions to stochasticity in gene expression
    • USA,doi:10.1073/pnas.162041399
    • Swain PS, Elowitz MB, Siggia ED. 2002 Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc. Natl Acad. Sci. USA 99, 12 795-12 800. (doi:10.1073/pnas.162041399).
    • (2002) Proc. Natl Acad. Sci. , vol.99 , pp. 12795-12800
    • Swain, P.S.1    Elowitz, M.B.2    Siggia, E.D.3
  • 9
    • 68049139696 scopus 로고    scopus 로고
    • Regulated fluctuations in Nanog expression mediate cell fate decisions in embryonic stem cells
    • doi:10.1371/journal. pbio.1000149
    • Kalmar T, Lim C, Hayward P, Munoz-Descalzo S, Nichols J. 2009 Regulated fluctuations in Nanog expression mediate cell fate decisions in embryonic stem cells. PLoS Biol. 7, 7. (doi:10.1371/journal. pbio.1000149).
    • (2009) PLoS Biol. , vol.7 , pp. 7
    • Kalmar, T.1    Lim, C.2    Hayward, P.3    Munoz-Descalzo, S.4    Nichols, J.5
  • 10
    • 35348816062 scopus 로고    scopus 로고
    • A heterogeneous expression pattern for Nanog in embryonic stem cells
    • DOI 10.1634/stemcells.2007-0126
    • Singh AM, Hamazaki T, Hankowski KE, Terada N. 2007 A heterogeneous expression pattern for Nanog in embryonic stem cells. Stem Cells 25, 2534-2542. (doi:10.1634/stemcells.2007-0126). (Pubitemid 47582745)
    • (2007) Stem Cells , vol.25 , Issue.10 , pp. 2534-2542
    • Singh, A.M.1    Hamazaki, T.2    Hankowski, K.E.3    Terada, N.4
  • 13
    • 0037418265 scopus 로고    scopus 로고
    • Stochastic gene expression as a many-body problem
    • USA,doi:10.1073/pnas. 2627987100
    • Sasai M, Wolynes P. 2003 Stochastic gene expression as a many-body problem. Proc. Natl Acad. Sci. USA 100, 2374-2379. (doi:10.1073/pnas. 2627987100).
    • (2003) Proc. Natl Acad. Sci. , vol.100 , pp. 2374-2379
    • Sasai M, W.P.1
  • 16
    • 34548548655 scopus 로고    scopus 로고
    • Dynamics and intrinsic statistical fluctuations of a gene switch
    • DOI 10.1021/jp071735u
    • Lepzelter D, Kim K, Wang J. 2007 Dynamics and intrinsic statistical fluctuations of a gene switch. J. Phys. Chem. B 111, 10239-10247. (doi:10. 1021/jp071735u). (Pubitemid 47388030)
    • (2007) Journal of Physical Chemistry B , vol.111 , Issue.34 , pp. 10239-10247
    • Lepzelter, D.1    Kim, K.-Y.2    Wang, J.3
  • 17
    • 33846452487 scopus 로고    scopus 로고
    • Single molecule dynamics and statistical fluctuations of gene regulatory networks: A repressilator
    • DOI 10.1063/1.2424933
    • Kim K, Lepzelter D, Wang J. 2007 Single molecule dynamics and statistical fluctuations of gene regulatory networks: a repressilator. J. Chem. Phys. 126, 034702. (doi:10.1063/1.2424933). (Pubitemid 46146453)
    • (2007) Journal of Chemical Physics , vol.126 , Issue.3 , pp. 034702
    • Kim, K.-Y.1    Lepzelter, D.2    Wang, J.3
  • 19
    • 34547360659 scopus 로고    scopus 로고
    • Understanding stochastic simulations of the smallest genetic networks
    • DOI 10.1063/1.2741544
    • Schultz D, Onuchic JN, Wolynes PG. 2007 Understanding stochastic simulations of the smallest genetic networks. J. Chem. Phys. 126, 245102. (doi:10.1063/1.2741544). (Pubitemid 47141454)
    • (2007) Journal of Chemical Physics , vol.126 , Issue.24 , pp. 245102
    • Schultz, D.1    Onuchic, J.N.2    Wolynes, P.G.3
  • 20
    • 34548695666 scopus 로고    scopus 로고
    • Effects of the DNA state fluctuation on single-cell dynamics of self-regulating gene
    • DOI 10.1063/1.2768353
    • Okabe Y, Yagi Y, Sasai M. 2007 Effects of the DNA state fluctuation on single-cell dynamics of selfregulating gene. J. Chem. Phys. 127, 105107. (doi:10.1063/1.2768353). (Pubitemid 47416117)
    • (2007) Journal of Chemical Physics , vol.127 , Issue.10 , pp. 105107
    • Okabe, Y.1    Yagi, Y.2    Sasai, M.3
  • 21
    • 79951788338 scopus 로고    scopus 로고
    • Adiabatic and non-adiabatic non-equilibrium stochastic dynamics of single regulating genes
    • doi:10.1021/jp109036y
    • Feng H, Wang J. 2011 Adiabatic and non-adiabatic non-equilibrium stochastic dynamics of single regulating genes. J. Phys. Chem. B 115, 1254-1261. (doi:10.1021/jp109036y).
    • (2011) J. Phys. Chem. B , vol.115 , pp. 1254-1261
    • Feng, H.1    Wang, J.2
  • 22
    • 84863274610 scopus 로고    scopus 로고
    • Landscape and global stability of nonadiabatic and adiabatic oscillations in a gene network
    • doi:10.1016/j.bpj.2012.02.002
    • Feng H, Han B, Wang J. 2012 Landscape and global stability of nonadiabatic and adiabatic oscillations in a gene network. Biophys. J. 102, 1001-1010. (doi:10.1016/j.bpj.2012.02.002).
    • (2012) Biophys. J. , vol.102 , pp. 1001-1010
    • Feng, H.1    Han, B.2    Wang, J.3
  • 23
    • 84864833626 scopus 로고    scopus 로고
    • A new mechanism of stem cell differentiation through slow binding/unbinding of regulators to genes
    • Feng H, Wang J. 2012 A new mechanism of stem cell differentiation through slow binding/unbinding of regulators to genes. Sci. Rep. 2, 550.
    • (2012) Sci. Rep. , vol.2 , pp. 550
    • Feng, H.1    Wang, J.2
  • 25
    • 77952914558 scopus 로고    scopus 로고
    • The potential landscape of genetic circuits imposes the arrow of time in stem cell differentiation
    • doi:10.1016/j.bpj.2010.03.058
    • Wang J, Xu L, Wang EK, Huang S. 2010 The potential landscape of genetic circuits imposes the arrow of time in stem cell differentiation. Biophys. J. 99, 29-39. (doi:10.1016/j.bpj.2010.03.058).
    • (2010) Biophys. J. , vol.99 , pp. 29-39
    • Wang, J.1    Xu, L.2    Wang, E.K.3    Huang, S.4
  • 26
    • 79957710315 scopus 로고    scopus 로고
    • Quantifying the Waddington landscape and biological paths for development and differentiation, 108
    • USA,doi:10.1073/pnas. 1017017108
    • Wang J, Zhang K, Xu L, Wang EK. 2011 Quantifying the Waddington landscape and biological paths for development and differentiation. Proc. Natl Acad. Sci. USA 108, 8257-8262. (doi:10.1073/pnas. 1017017108).
    • (2011) Proc. Natl Acad. Sci. , pp. 8257-8262
    • Wang, J.1    Zhang, K.2    Xu, L.3    Wang, E.K.4
  • 27
    • 84883349635 scopus 로고    scopus 로고
    • Quantifying cell fate decisions for differentiation and reprogramming of a human stem cell network: Landscape and biological paths
    • doi:10.1371/journal.pcbi.1003165
    • Li CH, Wang J. 2013 Quantifying cell fate decisions for differentiation and reprogramming of a human stem cell network: landscape and biological paths. PLoS Comput. Biol. 9, e1003165. (doi:10.1371/journal.pcbi.1003165).
    • (2013) PLoS Comput. Biol. , vol.9
    • Li, C.H.1    Wang, J.2
  • 28
    • 71149116163 scopus 로고    scopus 로고
    • Simple, realistic models of complex biological processes: Positive feedback and bistability in a cell fate switch and a cell cycle oscillator
    • doi:10.1016/j.febslet.2009.10.068
    • Ferrell JJ, Pomerening J, Kim S, Trunnell N, Xiong W, Huang C, Machleder E. 2009 Simple, realistic models of complex biological processes: positive feedback and bistability in a cell fate switch and a cell cycle oscillator. FEBS Lett. 583, 3999-4005. (doi:10.1016/j.febslet.2009.10.068).
    • (2009) FEBS Lett. , vol.583 , pp. 3999-4005
    • Ferrell, J.J.1    Pomerening, J.2    Kim, S.3    Trunnell, N.4    Xiong, W.5    Huang, C.6    Machleder, E.7
  • 29
    • 84861865440 scopus 로고    scopus 로고
    • Bistability, bifurcations, and Waddington's epigenetic landscape
    • doi:10.1016/j.cub.2012.03.045
    • Ferrell J. 2012 Bistability, bifurcations, and Waddington's epigenetic landscape. Curr. Biol. 22, R458-R66. (doi:10.1016/j.cub.2012.03.045).
    • (2012) Curr. Biol. , vol.22
    • Ferrell, J.1
  • 31
    • 84855274655 scopus 로고    scopus 로고
    • Systematic search for recipes to generate induced pluripotent stem cells
    • doi:10. 1371/journal.pcbi.1002300
    • Chang R, Shoemaker R, Wang W. 2011 Systematic search for recipes to generate induced pluripotent stem cells. PLoS Comput. Biol. 7, e1002300. (doi:10. 1371/journal.pcbi.1002300).
    • (2011) PLoS Comput. Biol. , vol.7
    • Chang, R.1    Shoemaker, R.2    Wang, W.3
  • 32
    • 55649104699 scopus 로고    scopus 로고
    • A computational model for understanding stem cell, trophectoderm and endoderm lineage determination
    • doi:10.1371/journal.pone.0003478
    • Chickarmane V, Peterson C. 2008 A computational model for understanding stem cell, trophectoderm and endoderm lineage determination. PLoS ONE 3, e3478. (doi:10.1371/journal.pone.0003478).
    • (2008) PLoS ONE , vol.3
    • Chickarmane, V.1    Peterson, C.2
  • 33
    • 33947308285 scopus 로고    scopus 로고
    • How is pluripotency determined and maintained?
    • DOI 10.1242/dev.02787
    • Niwa H. 2007 How is pluripotency determined and maintained? Development 134, 635-646. (doi:10. 1242/dev.02787). (Pubitemid 46437906)
    • (2007) Development , vol.134 , Issue.4 , pp. 635-646
    • Niwa, H.1
  • 34
    • 50449104011 scopus 로고    scopus 로고
    • Potential landscape and flux framework of non-equilibrium networks: Robustness, dissipation and coherence of biochemical oscillations
    • USA, (doi:10.1073/pnas. 0800579105
    • Wang J, Xu L, Wang EK. 2008 Potential landscape and flux framework of non-equilibrium networks: robustness, dissipation and coherence of biochemical oscillations. Proc. Natl Acad. Sci. USA 105, 12271-12276. (doi:10.1073/pnas. 0800579105).
    • (2008) Proc. Natl Acad. Sci. , vol.105 , pp. 12271-12276
    • Wang, J.1    Xu, L.2    Wang, E.K.3
  • 35
    • 77952334362 scopus 로고    scopus 로고
    • Potential and flux landscapes quantify the stability and robustness of budding yeast cell cycle network
    • USA, (doi:10.1073/pnas. 0910331107
    • Wang J, Li CH, Wang EK. 2010 Potential and flux landscapes quantify the stability and robustness of budding yeast cell cycle network. Proc. Natl Acad. Sci. USA 107, 8195-8200. (doi:10.1073/pnas. 0910331107).
    • (2010) Proc. Natl Acad. Sci. , vol.107 , pp. 8195-8200
    • Wang, J.1    Li, C.H.2    Wang, E.K.3
  • 36
    • 79952619659 scopus 로고    scopus 로고
    • Landscape and flux decomposition for exploring global natures of nonequilibrium dynamical systems under intrinsic statistical fluctuations
    • doi:10.1016/j.cplett.2011.02.020
    • Li CH, Wang J, Wang EK. 2011 Landscape and flux decomposition for exploring global natures of nonequilibrium dynamical systems under intrinsic statistical fluctuations. Chem. Phys. Lett. 505, 75-80. (doi:10.1016/j.cplett. 2011.02.020).
    • (2011) Chem. Phys. Lett. , vol.505 , pp. 75-80
    • Li, C.H.1    Wang, J.2    Wang, E.K.3
  • 37
    • 84861691830 scopus 로고    scopus 로고
    • Potential flux landscapes determine the global stability of a Lorenz chaotic attractor under intrinsic fluctuations
    • doi:10.1063/1.4716466
    • Li CH, Wang EK, Wang J. 2012 Potential flux landscapes determine the global stability of a Lorenz chaotic attractor under intrinsic fluctuations. J. Chem. Phys. 136, 194108. (doi:10.1063/1.4716466).
    • (2012) J. Chem. Phys. , vol.136 , pp. 194108
    • Li, C.H.1    Wang, E.K.2    Wang, J.3
  • 38
    • 20344364613 scopus 로고    scopus 로고
    • Laws in Darwinian evolutionary theory
    • DOI 10.1016/j.plrev.2005.03.002, PII S1571064505000126
    • Ao P. 2005 Laws in Darwinian evolutionary theory. Phys. Life Rev. 2, 117-156. (doi:10.1016/j.plrev. 2005.03.002). (Pubitemid 40792433)
    • (2005) Physics of Life Reviews , vol.2 , Issue.2 , pp. 117-156
    • Ao, P.1
  • 39
    • 33748096830 scopus 로고    scopus 로고
    • Open-system nonequilibrium steady state: Statistical thermodynamics, fluctuations, and chemical oscillations
    • DOI 10.1021/jp061858z
    • Qian H. 2006 Open-system nonequilibrium steady state: statistical thermodynamics, fluctuations, and chemical oscillations. J. Phys. Chem. B 110, 15063-15074. (doi:10.1021/jp061858z). (Pubitemid 44334760)
    • (2006) Journal of Physical Chemistry B , vol.110 , Issue.31 , pp. 15063-15074
    • Qian, H.1
  • 40
    • 84869799148 scopus 로고    scopus 로고
    • Attractor landscape analysis reveals feedback loops in the p53 network that control the cellular response to DNA damage
    • r, (doi:10.1126/scisignal.2003363
    • Choi M, Shi J, Jung SH, Chen X, Cho KH. 2012 Attractor landscape analysis reveals feedback loops in the p53 network that control the cellular response to DNA damage. Sci. Signal. 5, ra83. (doi:10.1126/scisignal.2003363).
    • (2012) Sci. Signal , vol.5
    • Choi, M.1    Shi, J.2    Jung, S.H.3    Chen, X.4    Cho, K.H.5
  • 41
    • 38449101120 scopus 로고    scopus 로고
    • Integration of biological networks and gene expression data using cytoscape
    • doi:10.1038/nprot.2007.324
    • Cline M, Smoot M, Cerami E, Kuchinsky A, Landys N. 2007 Integration of biological networks and gene expression data using cytoscape. Nat. Protoc. 2, 2366-2382. (doi:10.1038/nprot.2007.324).
    • (2007) Nat. Protoc. , vol.2 , pp. 2366-2382
    • Cline, M.1    Smoot, M.2    Cerami, E.3    Kuchinsky, A.4    Landys, N.5
  • 42
    • 79952846468 scopus 로고    scopus 로고
    • Progress in understanding reprogramming to the induced pluripotent state
    • doi:10. 1038/nrg2955
    • Plath K, Lowry WE. 2011 Progress in understanding reprogramming to the induced pluripotent state. Nat. Rev. Genet. 12, 253-265. (doi:10. 1038/nrg2955).
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 253-265
    • Plath, K.1    Lowry, W.E.2
  • 44
    • 59649110883 scopus 로고    scopus 로고
    • Cardiac fibroblasts regulate myocardial proliferation through [beta] 1 integrin signaling
    • doi:10.1016/j. devcel.2008.12.007
    • Ieda M, Tsuchihashi T, Ivey K, Ross R, Hong T, Shaw R, Srivastava D. 2009 Cardiac fibroblasts regulate myocardial proliferation through [beta] 1 integrin signaling. Dev. Cell 16, 233-244. (doi:10.1016/j. devcel.2008.12.007).
    • (2009) Dev. Cell , vol.16 , pp. 233-244
    • Ieda, M.1    Tsuchihashi, T.2    Ivey, K.3    Ross, R.4    Hong, T.5    Shaw, R.6    Srivastava, D.7
  • 45
    • 0034028901 scopus 로고    scopus 로고
    • Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells
    • DOI 10.1038/74199
    • Niwa H, Miyazaki J, Smith AG. 2000 Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells. Nat. Genet. 24, 372-376. (doi:10.1038/74199). (Pubitemid 30187435)
    • (2000) Nature Genetics , vol.24 , Issue.4 , pp. 372-376
    • Niwa, H.1    Miyazaki, J.-I.2    Smith, A.G.3
  • 46
    • 84878579948 scopus 로고    scopus 로고
    • A defined Oct4 level governs cell state transitions of pluripotency entry and differentiation into all embryonic lineages
    • doi:10.1038/ncb2742
    • Radzisheuskaya A, Chia G, Santos R, Theunissen T, Castro L, Nichols J, Silva J. 2013 A defined Oct4 level governs cell state transitions of pluripotency entry and differentiation into all embryonic lineages. Nat. Cell Biol. 15, 579-590. (doi:10.1038/ncb2742).
    • (2013) Nat. Cell Biol. , vol.15 , pp. 579-590
    • Radzisheuskaya, A.1    Chia, G.2    Santos, R.3    Theunissen, T.4    Castro, L.5    Nichols, J.6    Silva, J.7
  • 47
  • 49
    • 28344436489 scopus 로고    scopus 로고
    • Interaction between Oct3/4 and Cdx2 determines trophectoderm differentiation
    • DOI 10.1016/j.cell.2005.08.040, PII S0092867405009116
    • Niwa H, Toyooka Y, Shimosato D, Strumpf D, Takahashi K, Yagi R, Rossant J. 2005 Interaction between Oct3/4 and Cdx2 determines trophectoderm differentiation. Cell 123, 917-929. (doi:10.1016/j.cell.2005.08.040). (Pubitemid 41721036)
    • (2005) Cell , vol.123 , Issue.5 , pp. 917-929
    • Niwa, H.1    Toyooka, Y.2    Shimosato, D.3    Strumpf, D.4    Takahashi, K.5    Yagi, R.6    Rossant, J.7
  • 52
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • doi:10.1021/j100540a008
    • Gillespie DT. 1977 Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81, 2340-2361. (doi:10.1021/j100540a008).
    • (1977) J. Phys. Chem. , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1


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