Computational multiscale modeling of embryo development

Current Opinion in Genetics and Development

Volumn 22, Issue 6, 2012, Pages 613-618

  Krupinski, Pawel ^a   Chickarmane, Vijay ^b   Peterson, Carsten ^a  

^a LUND UNIVERSITY   (Sweden)

^b CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; OCTAMER TRANSCRIPTION FACTOR 4; TRANSCRIPTION FACTOR CDX2; TRANSCRIPTION FACTOR GATA 6; TRANSCRIPTION FACTOR NANOG;

ALGORITHM; CDX2 GENE; CELL INTERACTION; CELL REGENERATION; EMBRYO DEVELOPMENT; GENE; GENE EXPRESSION; INTRACELLULAR SIGNALING; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MOLECULAR EVOLUTION; MOLECULAR INTERACTION; MOLECULAR MODEL; MONTE CARLO METHOD; NONHUMAN; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN EXPRESSION; REVIEW;

ANIMALS; BODY PATTERNING; CELL COMMUNICATION; COMPUTER SIMULATION; EMBRYONIC DEVELOPMENT; MAMMALS; MODELS, THEORETICAL; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

MAMMALIA;

EID: 84872662899     PISSN: 0959437X     EISSN: 18790380     Source Type: Journal    
DOI: 10.1016/j.gde.2012.08.006     Document Type: Review

References (49)

1. McDole K., Xiong Y., Iglesias P.A., Zheng Y. Lineage mapping the pre-implantation mouse embryo by two-photon microscopy, new insights into the segregation of cell fates. Dev Biol 2011, 355:239-249.
2. Luengo-Oroz M., Ledesma-Carbayo M., Peyrieras N., Santos A. Image analysis for understanding embryo development: a bridge from microscopy to biological insights. Curr Opin Genet Dev 2011, 21:630-637.
3. Khairy K., Keller P.J. Reconstructing embryonic development. Genesis 2010, 49:488-513.
4. Artus J., Hadjantonakis A. Troika of the mouseblastocyst: lineage segregation and stem cells. Curr Stem Cell Res Ther 2012, 7:78-91.
5. Bruce A.W., Zernicka-Goetz M. Developmental control of the early mammalian embryo: competition among heterogeneous cells that biases cell fate. Curr Opin Genet Dev 2010, 20:485-491.
6. Cockburn K., Rossant J. Making the blastocyst: lessons from the mouse. J Clin Invest 2010, 120:995-1003.
7. Chickarmane, Troein C., Nuber U., Sauro H.M., Peterson C. Transcriptional dynamics of the embryonic stem cell switch. PLoS Comp Biol 2006, 2:e123.
8. Chickarmane V., Peterson C. A computational model for understanding stem cell, trophectoderm and endoderm lineage determination. PLoS ONE 2008, 3:e3478.
9. Kalmar T., Lim C., Hayward P., Muñoz-Descalzo S., Nichols J., Garcia-Ojalvo J., Martinez∼Arias A. Regulated Fluctuations in nanog expression mediate cell fate decisions in embryonic stem cells. PLoS Biol 2009, 7:e1000149.
10. Glauche I., Herberg M., Roeder I. Nanog variability and pluripotency regulation of embryonic stem cells-insights from a mathematical model analysis. PLoS ONE 2010, 5:e11238.
11. Wray J., Kalkan T., Smith A.G. The ground state of pluripotency. Biochem Soc Trans 2010, 38:1027-1032.
12. Cross M.A., Enver T. The lineage commitment of haematopoietic stem cells. Curr Opin Genes Dev 1997, 7:609-613.
13. Pina C., Fugazza C., Tipping A.J., Brown J., Soneji S., Teles J., Peterson C., Enver T. Inferring rules of commitment in haematopoiesis. Nat Cell Biol 2012, 14:287-294.
14. Stephenson R.O., Yamanaka Y., Rossant J. Disorganized epithelial polarity and excess trophectoderm cell fate in preimplantation embryos lacking E-cadherin. Development 2010, 137:3383-3391.
15. Grabarek J.B., Zyzynska K., Saiz N., Piliszek A., Frankenberg S., Nichols J., Hadjantonakis A.K., Plusa B. Differential plasticity of epiblast and primitive endoderm precursors within the ICM of the early mouse embryo. Development 2012, 139:129-139.
16. Meilhac S.M., Adams R.J., Morris S.A., Danckaert A., Le Garrec J., Zernicka-Goetz M. Active cell movements coupled to positional induction are involved in lineage segregation in the mouse blastocyst. Dev Biol 2009, 331:210-221.
17. Stolarska M.A., Kim Y., Othmer H.G. Multi-scale models of cell and tissue dynamics. Philos Trans Roy Soc A 2009, 367:3525-3553.
18. Roeder A.H.K., Tarr P.T., Tobin C., Zhang X., Chickarmane V., Cunha A., Meyerowitz E.M. Computational morphodynamics of plants: integrating development over space and time. Nat Rev Mol Cell Biol 2011, 12:265-273.
19. Setty Y. Multi-scale computational modeling of developmental biology. Bioinformatics 2012, published online: May 24, 2012. 10.1093/bioinformatics/bts307.
20. Qu Z., Garfinkel A., Weiss J.N., Nivala M. Multi-scale modeling in biology: how to bridge the gaps between scales?. Prog Biophys Mol Biol 2011, 107:21-31.
21. Home P., Saha B., Ray S., Dutta D., Gunewardena S., Yoo B., Pal A., Vivian J.L., Larson M., Petroff M., et al. Altered subcellular localization of transcription factor TEAD4 regulates first mammalian cell lineage commitment. Proc Natl Acad Sci U S A 2012, 109:7362-7367.
22. Jedrusik A., Parfitt D.E., Guo G., Skamagki M., Grabarek J.B., Johnson M.H., Robson P., Zernicka-Goetz M. Role of Cdx2 and cell polarity in cell allocation and specification of trophectoderm and inner cell mass in the mouse embryo. Genes Dev 2008, 22:2692-2706.
23. Ralston A., Rossant J. Cdx2 acts downstream of cell polarization to cell-autonomously promote trophectoderm fate in the early mouse embryo. Dev Biol 2008, 313:614-629.
24. Yamanaka Y., Lanner F., Rossant J. FGF signal-dependent segregation of primitive endoderm and epiblast in the mouse blastocyst. Development 2010, 137:715-724.
25. Sasaki H. Mechanisms of trophectoderm fate specification in preimplantation mouse development. Dev Growth Differ 2010, 52:263-273.
26. Peltier J., Schaffer D.V. Systems biology approaches to understanding stem cell fate choice. IET Syst Biol 2010, 4:1-11.
27. Niwa H., Toyooka Y., Shimosato D., Strumpf D., Takahashi K., Yagi R., Rossant J. Interaction between Oct3/4 and Cdx2 determines trophectoderm differentiation. Cell 2005, 123:917-929.
28. Nishioka N., Inoue K., Adachi K., Kiyonari H., Ota M., Ralston A., Yabuta N., Hirahara S., Stephenson R.O., Ogonuki N., et al. The Hippo signaling pathway components Lats and Yap pattern Tead4 activity to distinguish mouse trophectoderm from inner cell mass. Dev Cell 2009, 16:398-410.
29. Barone V., Heisenberg C. Cell adhesion in embryo morphogenesis. Curr Opin Cell Biol 2012, 24:148-153.
30. Hamant O., Heisler M.G., Jonsson H., Krupinski P., Uyttewaal M., Bokov P., Corson F., Sahlin P., Boudaoud A., Meyerowitz E.M., et al. Developmental patterning by mechanical signals in Arabidopsis. Science 2008, 322:1650-1655.
31. Chiou K.K., Hufnagel L., Shraiman B.I. Mechanical stress inference for two dimensional cell arrays. PLoS Comput Biol 2012, 8:e1002512.
32. Shirinifard A., Glazier J.A., Swat M., Gens J.S., Family F., Jiang Y., Grossniklaus H.E. Adhesion failures determine the pattern of choroidal neovascularization in the eye: a computer simulation study. PLoS Comput Biol 2012, 8:e1002440.
33. Honda H., Motosugi N., Nagai T., Tanemura M., Hiiragi T. Computer simulation of emerging asymmetry in the mouse blastocyst. Development 2008, 135:1407-1414.
34. Graner F., Glazier J.A. Simulation of biological cell sorting using a two-dimensional extended Potts model. Phys Rev Lett 1992, 69:2013-2016.
35. Le Guillou L., Dard N., Glisse J., Maro B., Louvet-Vallée S., Laforge B. A 3D mechanical model of the early mammalian embryo. J Biol Phys Chem 2009, 9:11.
36. Fleming T.P., Sheth B., Fesenko I. Cell adhesion in the preimplantation mammalian embryo and its role in trophectoderm differentiation and blastocyst morphogenesis. Front Biosci 2001, 6:D1000-D1007.
37. Krupinski P., Chickarmane V., Peterson C. Simulating the mammalian blastocyst-molecular and mechanical interactions pattern the embryo. PLoS Comput Biol 2011, 7:e1001128.
38. Yamanaka Y., Ralston A., Stephenson R.O., Rossant J. Cell and molecular regulation of the mouse blastocyst. Dev Dyn 2006, 235:2301-2314.
39. Boehm B., Westerberg H., Lesnicar-Pucko G., Raja S., Rautschka M., Cotterell J., Swoger J., Sharpe J. The role of spatially controlled cell proliferation in limb bud morphogenesis. PloS Biol 2010, 8:e1000420.
40. Xie M., Tataw M., Venugopala Reddy G. Towards a functional understanding of cell growth dynamics in shoot meristem stem-cell niche. Semin Cell Dev Biol 2009, 20:1126-1133.
41. Uyttewaal M., Traas J., Hamant O. Integrating physical stress, growth, and development. Curr Opin Plant Biol 2010, 13:46-52.
42. Shirinifard A., Gens J.S., Zaitlen B.L., Poplawski N.J., Swat M., Glazier J.A. 3D multi-cell simulation of tumor growth and angiogenesis. PLoS ONE 2009, 4:e7190.
43. Katira P., Zaman M.H., Bonnecaze R.T. How changes in cell mechanical properties induce cancerous behavior. Phys Rev Lett 2012, 108:28103.
44. Deisboeck T.S., Wang Z., Macklin P., Cristini V. Multiscale cancer modeling. Annu Rev Biomed Eng 2010, 13:127-155.
45. Ashton R.S., Keung A.J., Peltier J., Schaffer D.V. Progress and prospects for stem cell engineering. Annu Rev Chem Biomol Eng 2011, 2:479-502.
46. High-throughput approaches for the analysis of extrinsic regulators of stem cell fate. Curr Opin Cell Biol 2012, 24:236-244.
47. Kobel S., Lutolf M.P. Biomaterials meet microfluidics: building the next generation of artificial niches. Curr Opin Biotechnol 2011, 22:690-697.
48. Diaz-Zuccarini V., Lawford P.V. An in-silico future for the engineering of functional tissues and organs. Organogenesis 2010, 6:245-251.
49. Wennekamp S., Hiiragi T. Stochastic processes in the development of pluripotency in vivo. Biotechnol J 2012, 7:737-744.