Mathematical approaches to modeling development and reprogramming

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 14, 2014, Pages 5076-5082

  Morris, Rob ^a   Sancho Martinez, Ignacio ^a   Sharpee, Tatyana O ^a   Belmonte, Juan Carlos Izpisua ^a  

^a SALK INSTITUTE FOR BIOLOGICAL STUDIES   (United States)

Author keywords

Dedifferentiation; Elite model; Stochastic model; Waddington landscape

Indexed keywords

KRUPPEL LIKE FACTOR 4; MYC PROTEIN; OCTAMER TRANSCRIPTION FACTOR 4; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR NANOG; TRANSCRIPTION FACTOR SOX2;

BIOTECHNOLOGY; CANCER CELL; CELL COUNT; CELL DIFFERENTIATION; CELL FUNCTION; CELL MATURATION; CELL PROLIFERATION; CELL TYPE; CHROMATIN ASSEMBLY AND DISASSEMBLY; EPIGENETICS; GENE EXPRESSION; GENE REGULATORY NETWORK; HUMAN; MATHEMATICAL MODEL; NONHUMAN; NUCLEAR REPROGRAMMING; PLURIPOTENT STEM CELL; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STABILITY; REGENERATIVE MEDICINE; REVIEW; SOMATIC CELL; TRANSLATIONAL RESEARCH;

DEDIFFERENTIATION; ELITE MODEL; STOCHASTIC MODEL; WADDINGTON LANDSCAPE;

CELL DIFFERENTIATION; HUMANS; MODELS, BIOLOGICAL; PLURIPOTENT STEM CELLS; TRANSCRIPTION FACTORS;

EID: 84898043400     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1317150111     Document Type: Review

References (55)

1. Waddington CH (1957) The Strategy of the Genes: A Discussion of Some Aspects of Theoretical Biology (Allen & Unwin, London).
2. Takahashi K, Yamanaka S (2006) Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126(4):663-676.
3. Takahashi K, et al. (2007) Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131(5):861-872.
4. Aasen T, et al. (2008) Efficient and rapid generation of induced pluripotent stem cells from human keratinocytes. Nat Biotechnol 26(11):1276-1284.
5. Anokye-Danso F, et al. (2011) Highly efficient miRNA-mediated reprogramming of mouse and human somatic cells to pluripotency. Cell Stem Cell 8(4):376-388.
6. Aoi T, et al. (2008) Generation of pluripotent stem cells from adult mouse liver and stomach cells. Science 321(5889):699-702.
7. Giorgetti A, et al. (2009) Generation of induced pluripotent stem cells from human cord blood using OCT4 and SOX2. Cell Stem Cell 5(4):353-357.
8. Jopling C, Boue S, Izpisua Belmonte JC (2011) Dedifferentiation, transdifferentiation and reprogramming: Three routes to regeneration. Nat Rev Mol Cell Biol 12(2):79-89.
9. Yamanaka S (2009) Elite and stochastic models for induced pluripotent stem cell generation. Nature 460(7251):49-52.
10. Hanna J, et al. (2009) Direct cell reprogramming is a stochastic process amenable to acceleration. Nature 462(7273):595-601.
11. Li Y, Shen Z, Shelat H, Geng YJ (2013) Reprogramming somatic cells to pluripotency: A fresh look at Yamanaka's model. Cell Cycle 12(23):3594-3598.
12. Rais Y, et al. (2013) Deterministic direct reprogramming of somatic cells to pluripotency. Nature 502(7469):65-70.
13. Ruiz S, et al. (2011) A high proliferation rate is required for cell reprogramming and maintenance of human embryonic stem cell identity. Curr Biol 21(1):45-52.
14. Chen J, et al. (2013) H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs. Nat Genet 45(1):34-42.
15. Watanabe A, Yamada Y, Yamanaka S (2013) Epigenetic regulation in pluripotent stem cells: A key to breaking the epigenetic barrier. Philos Trans R Soc Lond B Biol Sci 368(1609):20120292.
16. Choi YJ, et al. (2011) miR-34 miRNAs provide a barrier for somatic cell reprogramming. Nat Cell Biol 13(11):1353-1360.
17. Ang YS, Gaspar-Maia A, Lemischka IR, Bernstein E (2011) Stem cells and reprogramming: Breaking the epigenetic barrier? Trends Pharmacol Sci 32(7):394-401.
18. Bhutani N, et al. (2010) Reprogramming towards pluripotency requires AID-dependent DNA demethylation. Nature 463(7284): 1042-1047.
19. Utikal J, et al. (2009) Immortalization eliminates a roadblock during cellular reprogramming into iPS cells. Nature 460(7259): 1145-1148.
20. Wang J, Li C, Wang E (2010) Potential and flux landscapes quantify the stability and robustness of budding yeast cell cycle network. Proc Natl Acad Sci USA 107(18):8195-8200.
21. Wang J, Xu L, Wang E, Huang S (2010) The potential landscape of genetic circuits imposes the arrow of time in stem cell differentiation. Biophys J 99(1):29-39.
22. Furusawa C, Kaneko K (2012) A dynamical-systems view of stem cell biology. Science 338(6104):215-217.
23. Zhou JX, Aliyu MD, Aurell E, Huang S (2012) Quasi-potential landscape in complex multi-stable systems. J R Soc Interface 9(77): 3539-3553.
24. Wang J, Zhang K, Xu L, Wang E (2011) Quantifying the Waddington landscape and biological paths for development and differentiation. Proc Natl Acad Sci USA 108(20):8257-8262.
25. Li C, 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(8):e1003165.
26. Ladewig J, Koch P, Brustle O (2013) Leveling Waddington: The emergence of direct programming and the loss of cell fate hierarchies. Nat Rev Mol Cell Biol 14(4):225-236.
27. Polo JM, et al. (2012) A molecular roadmap of reprogramming somatic cells into iPS cells. Cell 151(7):1617-1632.
28. Hansson J, et al. (2012) Highly coordinated proteome dynamics during reprogramming of somatic cells to pluripotency. Cell Rep 2(6): 1579-1592.
29. Vierbuchen T, Wernig M (2011) Direct lineage conversions: Unnatural but useful? Nat Biotechnol 29(10):892-907.
30. Sancho-Martinez I, Baek SH, Izpisua Belmonte JC (2012) Lineage conversion methodologies meet the reprogramming toolbox. Nat Cell Biol 14(9):892-899.
31. Efe JA, et al. (2011) Conversion of mouse fibroblasts into cardiomyocytes using a direct reprogramming strategy. Nat Cell Biol 13(3):215-222.
32. Kim J, et al. (2011) Direct reprogramming of mouse fibroblasts to neural progenitors. Proc Natl Acad Sci USA 108(19):7838-7843.
33. Kurian L, et al. (2013) Conversion of human fibroblasts to angioblast-like progenitor cells. Nat Methods 10(1):77-83.
34. Ring KL, et al. (2012) Direct reprogramming of mouse and human fibroblasts into multipotent neural stem cells with a single factor. Cell Stem Cell 11(1):100-109.
35. Thier M, et al. (2012) Direct conversion of fibroblasts into stably expandable neural stem cells. Cell Stem Cell 10(4):473-479.
36. Soufi A, Zaret KS (2013) Understanding impediments to cellular conversion to pluripotency by assessing the earliest events in ectopic transcription factor binding to the genome. Cell Cycle 12(10): 1487-1491.
37. Soufi A, Donahue G, Zaret KS (2012) Facilitators and impediments of the pluripotency reprogramming factors' initial engagement with the genome. Cell 151(5):994-1004.
38. Zaret KS, Carroll JS (2011) Pioneer transcription factors: Establishing competence for gene expression. Genes Dev 25(21): 2227-2241.
39. Buganim Y, et al. (2012) Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase. Cell 150(6):1209-1222.
40. Golipour A, et al. (2012) A late transition in somatic cell reprogramming requires regulators distinct from the pluripotency network. Cell Stem Cell 11(6):769-782.
41. Samavarchi-Tehrani P, et al. (2010) Functional genomics reveals a BMP-driven mesenchymal-to-epithelial transition in the initiation of somatic cell reprogramming. Cell Stem Cell 7(1):64-77.
42. Visvader JE, Lindeman GJ (2012) Cancer stem cells: Current status and evolving complexities. Cell Stem Cell 10(6):717-728.
43. Visvader JE (2011) Cells of origin in cancer. Nature 469(7330): 314-322.
44. Medema JP (2013) Cancer stem cells: The challenges ahead. Nat Cell Biol 15(4):338-344.
45. Fessler E, Dijkgraaf FE, De Sousa E Melo F, Medema JP (2013) Cancer stem cell dynamics in tumor progression and metastasis: Is the microenvironment to blame? Cancer Lett 341(1):97-104.
46. Gupta PB, et al. (2011) Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells. Cell 146(4): 633-644.
47. MacArthur BD, Lemischka IR (2013) Statistical mechanics of pluripotency. Cell 154(3):484-489.
48. Amps K, et al.; International Stem Cell Initiative (2011) Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage. Nat Biotechnol 29(12):1132-1144.
49. Cahan P, Daley GQ (2013) Origins and implications of pluripotent stem cell variability and heterogeneity. Nat Rev Mol Cell Biol 14(6): 357-368.
50. Liang G, Zhang Y (2013) Genetic and epigenetic variations in iPSCs: Potential causes and implications for application. Cell Stem Cell 13(2):149-159.
51. Montserrat N, et al. (2013) Reprogramming of human fibroblasts to pluripotency with lineage specifiers. Cell Stem Cell 13(3):341-350.
52. Shu J, et al. (2013) Induction of pluripotency in mouse somatic cells with lineage specifiers. Cell 153(5):963-975.
53. Sisan DR, Halter M, Hubbard JB, Plant AL (2012) Predicting rates of cell state change caused by stochastic fluctuations using a datadriven landscape model. Proc Natl Acad Sci USA 109(47): 19262-19267.
54. Buganim Y, Faddah DA, Jaenisch R (2013) Mechanisms and models of somatic cell reprogramming. Nat Rev Genet 14(6): 427-439.
55. Hu Z, Cheng L, Berne BJ (2010) First passage time distribution in stochastic processes with moving and static absorbing boundaries with application to biological rupture experiments. J Chem Phys 133(3):034105.