Representing Cancer Cell Trajectories in a Phase-Space Diagram: Switching Cellular States by Biological Phase Transitions

Applied Statistics for Network Biology: Methods in Systems Biology

Volumn 1, Issue , 2011, Pages 377-403

  Bizzarri, Mariano ^a   Giuliani, Alessandro ^b  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

^b ISTITUTO SUPERIORE DI SANITÀ   (Italy)

Author keywords

Anomalous attractor; Cancer; Cell shape; Fractal; Morphological phenotype; Phase transition; System descriptor

Indexed keywords

EID: 84885554291     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527638079.ch17     Document Type: Chapter

References (156)

1. Gilbert, S.F. and Sarkar, S. (2000) Embracing complexity: organicism for the twenty-first century. Dev. Dyn., 219, 1-9.
2. Goodwin, B. (1994) How the Leopard Changed its Spots, Princeton University Press, Princeton, NJ.
3. Van Speybroeck, L., De Waele, D., and van De Vijver, G. (2002) Theories in early embryology. Close connections between epigenesis, preformationism and self-organization. Ann.NYAcad. Sci., 981, 7-49.
4. Cumming, F.W. (1994) Aspects of growth and form. PhysicaD, 79, 146-163.
5. Ricard, J. (1999) Biological Complexity and the Dynamics of Life Processes, Elsevier, New York.
6. Salazar-Ciudad, I., Newman, S.A., and Solé, R.V. (2001) Phenotypic and dynamical transitions in model genetic networks. Emergence of patterns and genotype-phenotype relationships. Evol. Dev., 3, 84-94.
7. Turing, A.M. (1952) The chemical basis of morphogenesis. Trans. R. Soc. Lond. B Biol. Sci., 237, 37-72.
8. Wang, N. and Ingber, D.E. (1994) Control of cytoskeletal mechanics by extracellular matrix, cell shape and mechanical tension. Biophys. J., 66, 2181-2189.
9. Ben-Ze'ev, A. (1991) Animal cell shape changes and gene expression. BioEssays, 13, 207-212.
10. Huang, S., Chen, S.C., and Ingber, D.E. (1998) Cell shape-dependent control of p27Kip and cell cycle progression in human capillary endothelial cells. Mol. Biol. Cell, 9, 3179-3193.
11. Hughes-Fulford, M., Rodenacker, K., and Jütting, U. (2006) Reduction of anabolic signals and alteration of osteoblast nuclear morphology in microgravity. J. Cell Biochem., 99, 435-449.
12. Hammond, T.G., Benes, E., O'Reilly, K.C. et al. (2000) Mechanical culture conditions effect gene expression: gravity-induced changes on the space shuttle. Physiol. Genomics, 3, 163-173.
13. Ingber, D.E. (1997) Tensegrity: the architectural basis of cellular mechanotrasduction. Annu. Rev. Physiol., 59, 575-599.
14. Pourati, J., Maniotis, A., Speigel, D., Schaffer, J.L., Butler, J.P., Fredberg, J.J., Ingber, D.E., Stamenovic, D., and Wang, N. (1998) Is cytoskeletal tension a major determinant of cell deformability in adherent endothelial cells? Am. J. Physiol., 274, C1283-C1289.
15. Chen, C.S., Alonso, J.L., Ostuni, E., Whitesides, G.M., and Ingber, D.E. (2003) Cell shape provides global control of focal adhesion assembly. Biochem. Biophs. Res. Commun., 307, 355-361.
16. Davies, P.F., Spaan, J.A., and Krams, R. (2005) Shear stress biology of the endothelium. Ann. Biomed. Eng., 33, 1714-1718.
17. Paszek, M.J., Zahir, N., Johnson, K.R., Lakins, J.N., Rozenberg, G.I., Gefen, A., Reinhart-King, C.A., Margulies, S.S., Dembo, M., Boettiger, D.,Hammer, D.A., and Weaver, V.M. (2005) Tensional homeostasis and the malignant phenotype. Cancer Cell, 8, 241-254.
18. Rothman, S. (2002) Lessons from the Living Cell. The Limits of Reductionism, McGraw- Hill, New York.
19. Noble, D. (2006) TheMusic of Life, Oxford University Press, London.
20. Shapiro, J.A. (2009) Revisiting the central dogma in the 21st century. Ann. NYAcad Sci., 1178, 6-28.
21. Elowitz, M.B., Levine, A.J., Siggia, E.D., and Swain, P.S. (2002) Stochastic gene expression in a single cell. Science, 297, 1183-1186.
22. Laforge, B., Guez, D., Martinez, M., and Kupiec, J.-J. (2005) Modeling embryogenesis and cancer: an approach based on an equilibrium between the autostabilization of stochastic gene expression and the interdependence of cells for proliferation. Prog. Biophys. Mol. Biol., 89, 93-120.
23. McAdams, H.H. and Arkin, A. (1997) Stochastic mechanisms in gene expression. Proc. Natl.Acad. Sci.USA, 94, 814-819.
24. Wray, G.A. and Abouheif, E. (1998)When is homology not homology? Curr. Opin. Genet. Dev., 8, 675-680.
25. Nelson, C.M. and Bissell, M.J. (2006) Of extracellular matrix, scaffolds, and signaling: tissue architecture regulates development, homeostasis, and cancer. Annu. Rev. Cell Dev. Biol., 22, 287-309.
26. Newman, S.A., Forgas, G., and Muller, G.B. (2006) Before programs: the physical origination of multicellular forms. Int. J. Dev. Biol., 50, 289-299.
27. Belousov, L.V., Opitz, J.M., and Gilbert, S.F. (1997) Contributions to field theory and life of Alexander G. Gurwitsch. Int. J. Dev. Biol., 41, 771-779.
28. Gilbert, S.F., Opitz, J.M., and Raff, R.A. (1996) Resynthesizing evolutionary and developmental biology. Dev. Biol., 173, 357-372.
29. D'Arcy,W.T. (1992) On Growth and Form, Cambridge University Press,Cambridge.
30. Nelson, C.M. (2009)Geometric control of tissue morphogenesis. Biochem. Biophys. Acta, 1793, 903-910.
31. Watson, P.A. (1991) Function follows form: generation of intracellular signals by cell deformation. FASEB J., 5, 2013-2019.
32. Watt, F.M., Jordan, P.W., and O'Neill, C.H. (1988) Cell shape controls terminal differentiation of human epidermal keratinocytes. Proc. Natl. Acad. Sci. USA, 85, 5576-5580.
33. Chen, C.S., Mrksich, M., Huang, S., Withesides, G.M., and Ingber, D.E. (1997) Geometric control of cell life and death. Science, 276, 1425-1428.
34. Newman, S.A. and Comper, W.D. (1990) Generic physical mechanisms of morphogenesis and pattern formation. Development, 49, 1-18.
35. Harold, F.M. (1990) To shape a cell: an inquiry into the causes of morphogenesis of microorganisms. Microbiol. Rev., 54, 381-431.
36. Patwari, P. and Lee, R.T. (2008) Mechanical control of tissue morphogenesis. Circ. Res., 103, 234-243.
37. Joyce, A.R. and Palsson, B. (2006) The model organism as a system: integrating "omics" data sets. Nat. Rev., 7, 198-210.
38. Knox, S.S. (2010) From "omics" to complex disease: a systems biology approach to gene-environment interactions in cancer. Cancer Cell Int., 10, 1-13.
39. Conti, F., Valerio, M.C., Zbilut, J.P., and Giuliani, A. (2007) Will systems biology offer new holistic paradigms to life sciences? Syst. Synth. Biol., 1, 161-165.
40. Prigogine, I. and Nicolis, G. (1977) Self- Organization in Non-Equilibrium Systems, John Wiley & Sons, Inc., New York.
41. Waddington, C.H. (1957) The Strategy of the Genes: A Discussion of Some Aspects of Theoretical Biology, Allen & Unwin, London.
42. Huang, S. and Ingber, D.E. (2007) A nongenetic basis for cancer progression and metastasis: self-organizing attractors in cell regulatory networks. Breast Dis., 26, 27-54.
43. Chang, H.H., Hemberg, M., Barahona, M., Ingber, D.E., and Huang, S. (2008) Transcriptome wide noise controls lineage choice in mammalian progenitor cells. Nature, 453, 544-547.
44. Albert, R. and Othmer, H.G. (2003) The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. J. Theor. Biol., 223, 1-18.
45. Kauffman, S.A. (1993) Origins of Order: Self-Organization and Selection in Evolution, Oxford University Press, New York.
46. Huang, S. (1999) Gene expression profiling, genetic networks, and cellular states: an integrating concept for tumorigenesis and drug discovery. J. Mol. Med., 77, 469-480.
47. Aldana-Gonzalez, M., Coppersmith, S., and Kadanoff, L.P. (2003) Boolean dynamics with random couplings, in Perspectives and Problems in Non-Linear Science (eds E. Kaplan, J.E. Marsden, and K.R. Sreenivasan), Springer, New York, pp. 23-89.
48. Li, F., Long, T., Lu, Y., Ouyang, Q., and Tang, C. (2004) The yeast cell-cycle network is robustly designed. Proc. Natl. Acad. Sci. USA, 101, 4781-4786.
49. Tsuchiya, M., Piras, V., Choi, S., Akira, S., Tomita, M., Giuliani, A., and Selvarajoo, K. (2009) Emergent genome-wide control in wildtype and genetically mutated lipopolysaccharides-stimulated macrophages. PLoS ONE, 4, 1-13.
50. Sjoblom, T., Jones, S., Wood, L.D., Parsons, D.W., Lin, J., Barber, T.D. et al. (2006) The consensus coding sequences of human breast and colorectal cancers. Science, 314, 268-274.
51. Greenman, C., Stephens, P., Smith, R., Dalgliesh, G.L., Hunter, C., Bignell, G. et al. (2007) Patterns of somatic mutation in human cancer genomes. Nature, 446, 153-158.
52. Wood, L.D., Parsons, D.W., Jones, S., Lin, J., Sjoblom, T., Leary, R.J. et al. (2007) The genomic landscapes of human breast and colorectal cancers. Science, 318, 1108-1113.
53. Rhee, S.Y., Wood, V., Dolinski, K., and Draghici, S. (2008) Use and misuse of the gene ontology 710 annotations. Nat. Rev. Genet., 9, 509-515.
54. Huang, S., Ernberg, I., and Kauffman, S. (2009) Cancer attractors: A systems view of tumours from a gene network dynamics and developmental perspective. Semin. Cell Dev. Biol., 20, 869-876.
55. Guo, Y., Eichler, G.S., Feng, Y., Ingber, D.E., and Huang, S. (2006) Towards a holistic, yet gene-centered analysis of gene expression profiles: a case study of human lung cancers. J. Biomed. Biotechnol., 2006, 1-11.
56. Su, AI., Wiltshire, T., Batalov, S., Lapp, H., Ching, KA., Block, D. et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. USA, 101, 6062-6067.
57. Fearon, ER. and Vogelstein, B. (1990) A genetic model for colorectal tumorigenesis. Cell, 61, 759-767.
58. Hahn, W.C., Counter, C.M., Lundberg, A.S., Beijersbergen, R.L., Brooks, M.W., and Weinberg, R. (1999) Creation of human tumor cells with defined genetic elements. Nature, 400, 464-648.
59. Folkman, J.,Hahnfeldt, P., and Hlatky, L. (2000) Cancer: looking outside of the genome. Nat. Rev. Mol. Cell Biol., 1, 76-79.
60. Capp, J.P. (2005) Stochastic gene expression, disruption of tissue averaging effects and cancer as a disease of development. BioEssays, 27, 1277-1285.
61. Sonnenschein, C. and Soto, A.M. (1999) The Society of Cells: Cancer and Control of Cell Populations, Springer, New York.
62. Baker, S.G. and Kramer, B.S. (2007) Paradoxes in carcinogenesis: new opportunities for research directions. BMC Cancer, 7, 151-157.
63. Bizzarri, M., Cucina, A., Conti, F., and D'Anselmi, F. (2008) Beyond the oncogenic paradigm: understanding complexity in cancerogenesis. Acta Biotheor., 56, 173-196.
64. Miklos, G.L.G. (2005) The Human Cancer Genome Project - one more misstep in the war on cancer. Nat. Biotechnol., 3, 535-537.
65. Olumi, A.F., Grossfeld, G.D., Hayward, S.W., Carroll, P.R., Tlsty, T.D., and Cunha, G.R. (1999) Carcinomaassociated fibroblasts direct tumor progression of initiated human prostatic epithelium. Cancer Res., 59, 5002-5011.
66. Barcellos-Hoff, M.H. and Ravani, S.A. (2000) Irradiatedmammarygland stroma promotes the expression of tumorigenic potential by unirradiated epithelial cells. Cancer Res., 60, 1254-1260.
67. Maffini, M.V., Soto, A.M., Calabro, J.M., Ucci, A.A., and Sonnenschein, C. (2004) The stroma as a crucial target in rat mammary gland carcinogenesis. J. Cell Sci., 117, 1495-1502.
68. Weaver,V.M. andGilbert, P. (2004)Watch the neighbour: cancer is a communal affair. J. Cell Sci., 117, 1495-1502.
69. Sonnenscheim, C. and Soto, A.M. (2000) Somatic mutation theory of carcinogenesis: why it should be dropped and replaced. Mol. Carcinogen., 29, 205-211.
70. Suresh, S. (2007) Biomechanics and biophysics of cancer cells. Acta Biomater., 3, 413-438.
71. Soto, A.M. and Sonnenschein, C. (2005) Emergentism as a default: cancer as a problem of tissue organization. J. Biosci., 30, 103-118.
72. Ronnov-Jessen, L. and Bissell, M.J. (2008) Breast cancer by proxy: can the microenvironment be both the cause and consequence? Trends Mol. Med., 15, 5-13.
73. Anderson, A.R.A., Weaver, A.M., Cummings, P.T., and Quaranta, V. (2006) Tumor morphology and phenotypic evolution driven by selective pressure from the microenvironment. Cell, 127, 905-915.
74. Huang, S. and Ingber, D.E. (2005) Cell tension, matrix mechanics, and cancer development. Cancer Cell, 2, 175-176.
75. Butcher, D.T., Alliston, T., and Weaver, V.M. (2009) A tense situation: forcing tumour progression. Nat. Rev. Cancer, 9, 108-122.
76. Tilghman, R.W. and Parsons, J.T. (2008) Focal adhesion kinase as a regulator of cell tension in the progression of cancer. Semin. Cancer Biol., 18, 45-52.
77. Zaman, M.H., Trapani, L.M., Sieminski, A.L., Mackellar, D., Gong, H., Kamm, R.D.,Wells, A., Lauffenburger, D.A., and Matsudaira, P. (2006) Migration of tumor cells in 3D matrices is governed by matrix stiffness along with cell-matrix adhesion and proteolysis. Proc. NatlAcad. Sci.USA, 103, 10889-10894.
78. Weaver, V.M., Petersen, O.W., Wang, F., Larabell, C.A., Briand, P., Damsky, C., and Bissell, M.J. (1997) Reversion of the malignant phenotype of human breast cells in three dimensional culture and in vivo by integrin blocking antibodies. J. Cell Biol., 137, 231-245.
79. Krause, S., Maffini, M.V., Soto, A.M., and Sonnenschein, C. (2010) The microenvironment determines the breast cancer cells' phenotype: organization of MCF7 cells in 3D cultures. BMC Cancer, 10, 263-270.
80. Needham, J. (1936) New advances in the chemistry and biology of organized growth. Proc. R. Soc. London B. Biol. Sci., 29, 1577-1626.
81. Ruiz-Vela, A., Aguilar-Gallardo, C., and Simön, C. (2009) Building a framework for embryonic microenvironments and cancer stem cells. Stem Cell Rev., 5, 319-327.
82. Pierce, G.B. (1983) The cancer cell and its control by the embryo. Am. J. Pathol., 113, 116-124.
83. Cooper, M. (2009) Regenerative pathologies: stem cells, teratomas and theories of cancer. Med. Stud., 1, 55-66.
84. Ingber, D.E. (2008) Can cancer be reversed by engineering the tumour microenvironment? Semin. Cancer Biol., 18, 356-364.
85. Baker, S.G., Soto, A.M., Sonnenschein, C., Cappuccio, A., Potter, J.D., and Kramer, B.S. (2009) Plausibility of stromal initiation of epithelial cancers without a mutation in the epithelium: a computer simulation of morphostats. BMC Cancer, 9, 89-95.
86. Singhvi, R., Kumar, A., Lopez, G.P., Stephanopoulos, G.N., Wang, D.I., Whitesides, G.M., and Ingber, D.E. (1994) Engineering cell shape and function. Science, 264, 696-698.
87. Parker, K.K., Brock, A.L., Brangwynne, C., Mannix, R.J., Wang, N., Ostuni, E., Geisse, N.A., Adams, J.C., Whitesides, G.M., and Ingber, D.E. (2002) Directional control of lamellipodia extension by constraining cell shape and orienting cell tractional forces. FASEB J., 16, 1195-1204.
88. Jiang, X., Bruzewicz, D.A., Wong, A.P., Piel, M., and Whitesides, G.M. (2005) Directing cell migration with asymmetric micropatterns. Proc. Natl.Acad. Sci.USA, 102, 975-978.
89. Bissell, M.J., Farson, D., and Tung, A.S. (1977) Cell shape and hexose transport in normal and virus-transformed cells in culture. J. Supramol. Struct., 6, 1-12.
90. Wittelsberger, S.C., Kleene, K., and Penman, S. (1981) Progressive loss of shape-responsive metabolic controls in cells with increasingly transformed phenotype. Cell, 24, 859-866.
91. Chicurel, M.E., Singer, R.H.,Meyer, C.J., and Ingber, D.E. (1998) Integrin binding and mechanical tension induce movement of mRNA and ribosomes to focal adhesions. Nature, 392, 730-733.
92. Muschler, J., Lochter, A., Roskelley, C.D., Yurchenco, P., and Bissell, M.J. (1999) Division of labor among the alpha6beta4 integrin, beta1 integrins, and an E3 laminin receptor to signal morphogenesis and beta-casein expression in mammary epithelial cells. Mol. Biol. Cell, 10, 2817-2828.
93. Shannon, J.M. and Pitelka, D.R. (1981) The influence of cell shape on the induction of functional differentiation in mouse mammary cells in vitro. In Vitro, 17, 1016-1028.
94. Nelson, C.M., Khauv, D., Bissell, M.J., and Radisky, D.C. (2008) Change in cell shape is required for matrix metalloproteinase-induced epithelial-mesenchymal transition of mammary epithelial cells. J. Cell. Biochem., 105, 25-33.
95. McBeath, R., Pirone, D.M., Nelson, C.M., Bhadriraju, K., and Chen, C.S. (2004)Cell shape, cytoskeletal tension, and RhoA regulate stem cell lineage commitment. Dev. Cell, 6, 483-495.
96. Denton, M. andMarshall, C. (2001) Laws of form revisited. Nature, 410, 417.
97. Rosai, J. (2001) The continuing role of morphology in the molecular age. Mod. Pathol., 14, 258-260.
98. Virchow, R.L.K. (1978) Cellular Pathology 1859 (Special Edition). Churchill, London, pp. 204-207.
99. Mandelbrot, B.B. (1975) Stochastic models for the Earth's relief, the shape and the fractal dimension of the coastlines, and the number-area rule for islands. Proc. Natl. Acad. Sci. USA, 72, 3825-3828.
100. Mandelbrot, B.B. (1982) The Fractal Geometry of Nature, Freeman, New York.
101. Smith, T.G., Lange, G.D., and Marks, W.B. (1996) Fractal methods and results in cellular morphology - dimensions, lacunarity and multifractals. J. Neurosci. Methods, 69, 123-136.
102. Cutting, J.E. andGarvin, J.J. (1987) Fractal curves and complexity. Percept. Psychophys., 42, 365-370.
103. Normant, F. and Tricot, C. (1991) Methods for evaluating the fractal dimension of curves using convex hulls. Phys. Rev. A, 43, 6518-6525.
104. Poincaré, H. and Bendixson, I. (1901) Sur les courbes définies par des équations différentielles. Acta Math., 24, 1-88.
105. Scheck, F. (1990) Mechanics, Springer, Heidelberg.
106. Toussaint, O. and Schneider, E.D. (1998) The thermodynamics and evolution of complexity in biological systems. Comp. Biochem. Physiol., 120, 3-9.
107. Rangayyan, R.M. and Nguyen, T.M. (2007) Fractal analysis of contours of breast masses in mammograms. J. Dig. Imag., 20, 223-237.
108. Rangayyan, R.M., El-Faramawy, N.M., Desautels, J.E.L., and Alim, O.A. (1997) Measures of acutance and shape for classification of breast tumors. IEEE Trans. Med. Imag., 16, 799-810.
109. Losa, G.A., Merlini, D., Nonnenmacher, T.F., andWeibel, E.R. (eds) (2002) Fractals in Biology andMedicine, Birkhauser, Basel.
110. Baish, J.W. and Jain, R.K. (2000) Fractals and cancer. Cancer Res., 60, 3683-3688.
111. Cross, S.S. (1997) Fractals in pathology. J. Pathol., 182, 1-8.
112. Cross, S.S., McDonagh, A.J.G., and Stephenson, T.J. (1995) Fractal and integer-dimensional analysis of pigmented skin lesions. Am. J. Dermatol., 17, 374-378.
113. Claridge, E., Hall, P.N., and Keefe, M. (1992) Shape analysis for classification of malignant melanoma. J. Biomed. Eng., 14, 229-324.
114. Gazit, Y., Berk, D.A., Leunig, M., Baxter, L.T., and Jain, R.K. (1995) Scale-invariant behavior and vascular network formation in normal and tumor tissue. Phys. Rev. Lett., 75, 2428-2431.
115. Michaelson, J.S., Cheongsiatmoy, J.A., Dewey, F. et al. (2005) Spread of human cancer cells occurs with probabilities indicative of a nongenetic mechanism. Br. J. Cancer, 93, 1244-1249.
116. Landini, G. and Rippin, J.W. (1996) How important is tumour shape? Quantification of the epithelial connective tissue interface in oral lesions using local connected fractal dimension analysis. J. Pathol., 179, 210-217.
117. Eid, R.A. and Landini, G. (2003) Quantification of the global and local complexity of the epithelial-connective tissue interface of normal, dysplastic, and neoplastic oral mucosa using digital imaging. Pathol. Res. Pract., 199, 475-482.
118. Tracqui, P. (2009) Biophysical model of tumor growth. Rep. Prog. Phys., 72, 1-30.
119. Waliszewski, P. and Konarski, J. (2002) Fractal structure of space and time is necessary for the emergence of selforganization, connectivity and collectivity in cellular system, in Fractals in Biology and Medicine (eds G.A. Losa, D. Merlini, T.F. Nonnenmacher, and E.R. Weibel), Birkhauser, Basel, pp. 15-24.
120. Lelièvre, S.A., Weaver, V.M., Nickerson, J.A., Larabell, C.A., Bhaumik, A., Petersen, O.W., and Bissell, M.J. (1998) Tissue phenotype depends on reciprocal interactions between the extracellular matrix and the structural organization of the nucleus. Proc. Natl. Acad. Sci. USA, 95, 14711-14716.
121. Thomas, C.H., Collier, J.H., Sfeir, C.S., and Healy, K.E. (2002) Engineering gene expression and protein synthesis by modulation of nuclear shape. Proc. Natl. Acad. Sci. USA, 99, 1972-1977.
122. Guilak, F. (1995) Compression-induced changes in the shape and volume of the chondrocyte nucleus. J. Biomech., 28, 1529-1541.
123. Wolf, K. and Friedl, P. (2006) Molecular mechanisms of cancer cell invasion and plasticity. Br. J. Dermatol., 154, 11-15.
124. Dahl, K.N., Ribeiro, A.J.S., and Lammerding, J. (2008) Nuclear shape, mechanics, and mechanotransduction. Circ Res., 102, 1307-1318.
125. Folkman, J. and Moscona, A. (1978) Role of cell shape in growth control. Nature, 273, 345-349.
126. Ingber, D.E. (1999) How cells (might) sense microgravity.FASEB J., 13, S3-S15.
127. Sonnenschein, C. and Soto, A.M. (2008) Theories of carcinogenesis: an emerging perspective. Semin. Cancer Biol., 18, 372-377.
128. Ingber, D.E. (2005)Mechanical control of tissue growth: function follows form. Proc. Natl. Acad. Sci. USA, 102, 11571-11572.
129. D'Anselmi, F., Valerio, M., Cucina, A., Galli, L., Proietti, S., Dinicola, S., Pasqualato, A., Manetti, C., Ricci, G., Giuliani, A., and Bizzarri, M. (2010) Metabolism and cell shape in cancer: a fractal analysis. Int. J. Biochem.Cell Biol., Epub ahead of print.
130. Bowie, J.E. and Young, I.T. (1977) An analysis technique for biological shape. Acta Cytol., 21, 739-746.
131. Young, I.T., Walker, J.E., and Bowie, J.E. (1974) An analysis technique for biological shape. Inform. Control, 25, 357-381.
132. Duncan, J.S., Lee, F.A., Smeulders, A.W.M., and Zaret, B.L. (1991) A bending energy model for measurement of cardiac shape deformity. IEEE Trans. Med. Imag., 10, 307-310.
133. Pernuš, F., Leonardis, A., and Kovačič, S. (1994) Two-dimensional object recognition using multiresolution non-information-preserving shape features. Pattern Recognit. Lett., 15, 1071-1076.
134. van Vliet, L.J. and Verbeeck, P.W. (1993) Curvature and bending energy in digitized 2D and 3D images. Eighth Scandinavian Conference on Image Analysis, Tromsø.
135. Castleman, K.R. (1996) Digital Image Processing, Prentice-Hall, Englewood Cliffs, NJ.
136. Cesar, R.M. Jr and Costa, L. daF. (1997) The application and assessment of multiscale bending energy for morphometric characterization of neural cells. Rev. Sci. Instrum., 68, 2177-2186.
137. Foty, R., Forgacs, G., Pfleger, C., and Steimberg, M. (1994) Liquid properties of embryonic tissues: measurement of interfacial tensions. Phys. Rev. Lett., 72, 2298-2301.
138. Foty, R., Pfleger, C., Forcas, G., and Steimberg, M. (1996) Surface tensions of embryonic tissues predict their mutual envelopment behaviour. Development, 122, 1611-1620.
139. Rohrschneider, M., Scheuermann, G., Hoehme, S., and Drasdo, D. (2007) Shape characterization of extracted and simulated tumor samples using topological and geometric measures. 29th Annual International Conference of the IEEE EMBS, Lyon.
140. Cristini, V., Frieboes, H.B., Gatenby, R., Caserta, S., Ferrari, M., and Sinek, J. (2005) Morphologic instability and cancer invasion. Clin. Cancer Res., 11, 6772-6779.
141. Ferriera, S.C., Martins, M.L., and Villa, M.J. (2003) Morphology transitions induced by chemotherapy in carcinomas in situ. Phys. Rev. E, 67, 1-9.
142. Trosko, J.E., Chang, C.-C., Upham, B.L., and Tai, M.-H. (2004) Ignored hallmarks of carcinogenesis: stem cells and cell-cell communication. Ann. NY Acad. Sci., 1028, 192-201.
143. Phillips, B.T. and Kimble, J. (2009) A new look at TCF and beta-catenin through the lens of a divergent C. elegans Wnt pathway. Dev. Cell, 17, 27-34.
144. Tepera, S.B., McCrea, P.D., and Rosen, J.M. (2003) A b-catenin survival signal is required for normal lobular development in the mammary gland. J. Cell Sci., 116, 1137-1149.
145. Rowlands, T.R., Pechenkina, I., Hatsell, S.J., Pestell, R.G., and Cowin, P. (2003) Dissecting the roles of b-catenin and cyclin D1 during mammary development and neoplasia. Proc. Natl. Acad. Sci. USA, 100, 11400-11405.
146. Sarrio, D., Perez-Mies, B.,Hardisson, D., Moreno-Bueno, G., Suarez, A., Cano, A., Martin-Perez, J., Gamallo, C., and Palacios, J. (2004) Cytoplasmic localization of p120ctn and E-cadherin loss characterize lobular breast carcinoma from preinvasive to metastatic lesions. Oncogene, 23, 3272-3283.
147. da Silva, E.C., Silva, A.C., de Paiva, A.C., and Nunes, R.A. (2008) Diagnosis of lung nodule using Moran's index and Geary's coefficient in computerized tomography images. Pattern Anal. Appl., 11, 89-99.
148. Christofori, G. and Semb, H. (1999) The role of cell-adhesion molecule E-cadherin as a tumour-suppressor gene. Trends Biochem. Sci., 24, 73-76.
149. Gumbiner, B.M. (1996) Cell adhesion: the molecular basis of tissue architecture and morphogenesis. Cell, 84, 345-357.
150. Prigogine, I. and Wiame, J.M. (1946) Biologie et Thermodynamique des phenomenes irreversibles. Experientia, 2, 451-453.
151. Zotin, A.I. (1990) Thermodynamic Bases of Biological Processes: Physiological Reactions and Adaptations, de Gruyter, Berlin.
152. Zotin, A.A. and Zotin, A.I. (1997) Phenomenological theory of ontogenesis. Int. J. Dev. Biol., 41, 917-921.
153. Palumbo, M.C., Farina, L., De Santis, A., Giuliani, A., Colosimo, A., Morelli, G., and Ruberti, I. (2008) Collective behavior in gene regulation: post-transcriptional regulation and the temporal compartmentalization of cellular cycles. FEBS J., 275, 2364-2371.
154. Huang, S. and Ingber, D.E. (2000) Shapedependent control of cell growth, differentiation, and apoptosis: switching between attractors in cell regulatory networks. Exp. Cell Res., 261, 91-103.
155. Griffin, J.L. (2004) Metabolic profiles to define the genome: can we hear the phenotypes? Trans. R. Soc. Lond. B Biol. Sci., 359, 857-871.
156. Ingber, D.E. (2008) Can cancer be reversed by engineering the tumour microenvironment? Semin. Cancer Biol., 18, 356-364.