Can a minimal replicating construct be identified as the embodiment of cancer?

BioEssays

Volumn 36, Issue 5, 2014, Pages 503-512

  Solé, Ricard V ^a,b,c   Valverde, Sergi ^a,b   Rodriguez Caso, Carlos ^a,b   Sardanyés, Josep ^a,b  

^a UNIVERSITAT POMPEU FABRA   (Spain)

^b INSTITUTE OF EVOLUTIONARY BIOLOGY CSIC UNIVERSITAT POMPEU FABRA   (Spain)

^c SANTA FE INSTITUTE   (United States)

Author keywords

Cancer; Error threshold; Microbial populations; Minimal cell; Mutator phenotype

Indexed keywords

APOPTOSIS; ARTICLE; CANCER CELL; CANCER GROWTH; CARCINOGENESIS; CELL ADHESION; CELL COMMUNICATION; CELL DIFFERENTIATION; CELL METABOLISM; CELL MOTILITY; CELL POPULATION; CHROMOSOME ABERRATION; DNA REPAIR; EPIGENETICS; GENOMIC INSTABILITY; GROWTH RATE; HOUSEKEEPING GENE; HUMAN; HUMAN CELL; HYPOTHESIS; NEOPLASM; PHASE TRANSITION; PRESSURE; STRESS; DNA REPLICATION; GENETIC EPIGENESIS; GENETICS;

DNA REPLICATION; EPIGENESIS, GENETIC; GENOMIC INSTABILITY; HUMANS; NEOPLASMS;

EID: 84897938697     PISSN: 02659247     EISSN: 15211878     Source Type: Journal    
DOI: 10.1002/bies.201300098     Document Type: Article

References (108)

1. Merlo LMF, Pepper JW, Reid BJ, Maley CC. 2006. Cancer as an evolutionary and ecological process. Nat Rev Cancer 6: 924-35.
2. Gatenby RA. 1996. Application of competition theory to tumour growth: implications for tumour biology and treatment. Eur J Cancer 32: 722-6.
3. Duesberg P, Mandrioli D, McCormack A, Nicholson JM. 2011. Is carcinogenesis a form of speciation? Cell Cycle 10: 2100-14.
4. Solé RV. 2003. Phase transitions in unstable cancer cell populations. Eur J Phys B 35: 117-24.
5. Solé RV, Deisboeck T. 2004. An error catastrophe in cancer? J Theor Biol 228: 47-54.
6. Israel L. 1996. Tumor progression: random mutations or an integrated survival response to cellular stress conserved from unicellular organisms? J Theor Biol 178: 375-80.
7. Lambert G, Estevez-Salmeron L, Oh S, Liao D, et al. 2011. An analogy between the evolution of drug resistance in bacterial communities and malignant tissues. Nat Rev Cancer 11: 375-82.
8. Amdam GV, Seehuu S-C. 2006. Order, disorder, death: lessons from a superorganism. Adv Cancer Res 95: 31-60.
9. Deisboeck TS, Couzin IS. 2009. Collective behavior in cancer cell populations. BioEssays 31: 190-7.
10. Vincent M. 2011. Cancer: a de-repression of a default survival program common to all cells? BioEssays 34: 72-82.
11. Lengauer C, Kinzler KW, Vogelstein B. 1998. Genetic instabilities in human cancers. Nature 396: 643-9.
12. Negrini S, Gorgoulis VG, Halazonetis TD. 2010. Genomic instability: an evolving hallmark of cancer. Nat Rev Mol Cell Biol 11: 220-8.
13. Loeb LA. 1991. Mutator phenotype may be required for multistage carcinogenesis. Cancer Res 51: 3075-9.
14. Loeb LA. 1997. Transient expression of a mutator phenotype in cancer cells. Science 277: 1449-50.
15. Loeb LA. 2011. Human cancers express mutator phenotypes: origin, consequences and targeting. Nat Rev Cancer 11: 450-7.
16. Sheltzer JM, Blank HM, Pfau SJ, Tange Y, et al. 2011. Aneuploidy drives genomic instability in yeast. Science 333: 1026-30.
17. Kolodner RD, Cleveland DW, Putnam CD. 2011. Aneuploidy drives a mutator phenotype in cancer. Science 333: 942-3.
18. Weaver BAA, Silk AD, Montagna C, Verdier-Pinard P, et al. 2007. Aneuploidy acts both oncogenically and as a tumor supressor. Cancer Cell 11: 25-36.
19. Gillies RJ, Verduzco D, Gatenby RA. 2012. Evolutionary dynamics of carcinogenesis and why targeted therapy does not work. Nat Rev Cancer 12: 487-93.
20. Greaves M, Maley CC. 2012. Clonal evolution in cancer. Nature 481: 306-13.
21. Gatenby RA. 2009. A change of strategy in the war on cancer. Nature 459: 508-9.
22. Nowell P. 1976. The clonal evolution of tumor cell populations. Science 194: 23-8.
23. Gatenby RA, Frieden BR. 2002. Application of information theory and extreme physical information to carcinogenesis. Cancer Res 62: 3675-84.
24. Gatenby RA, Frieden BR. 2004. Information dynamics in carcinogenesis and tumor growth. Mutat Res 568: 259-73.
25. Tarabichi M, Antoniou A, Saiselet M, Pita JM, et al. 2013. Systems biology of cancer: entropy, disorder and selection-driven evolution to independence, invasion and swarm intelligence. Cancer Metastasis Rev 568: 259-73.
26. Fernandes J, Guedes PG, Lage CL, Cola J, et al. 2012. Tumor malignancy is engaged to prokaryotic homolog toolbox. Med Hypotheses 78: 435-41.
27. Gottesman MM, Fojo T, Bates SE. 2002. Multidrug resistance in cancer: role of ATP-dependent transporters. Nat Rev Cancer 2: 48-58.
28. Hollenstein K, Dawson RJP, Locher KP. 2007. Structure and mechanism of ABC transporter proteins. Curr Opin Struct Biol 17: 412-8.
29. Cahill DP, Kinzler KW, Vogelstein B, Lengauer C. 1999. Genetic instability and Darwinian selection in tumors. Trends Genet 15: M57-61.
30. Solé V. 2011. Phase Transitions. New York: Princeton University Press.
31. Bak P. 1996. How Nature Works. New York: Copernicus.
32. Frigyesi A, Gisselsson D, Mitelman F, Höglund M. 2003. Power law distribution of chromosome aberrations in cancer. Cancer Res 63: 7094-7.
33. Oliver A, Canton R, Campo P, Baquero F, et al. 2000. High frequency of hypermutable Pseudomonas aeruginosa in cystic fibrosis lung infection. Science 288: 1251-4.
34. Bjedov I, Tenaillon O, Gérard B, Souza V, et al. 2003. Stress-induced mutagenesis in bacteria. Science 300: 1404-9.
35. Sniegowski PD, Gerrish PJ, Lenski RE. 1997. Evolution of high mutation rates in experimental populations of E. coli. Nature 387: 703-5.
36. Bielas JH, Loeb KR, Rubin BP, True LD, et al. 2006. Human cancers express a mutator phenotype. Proc Natl Acad Sci USA 103: 18238-42.
37. Anderson GR, Stoler DL, Brenner BM. 2001. Cancer as an evolutionary consequence of a destabilized genome. BioEssays 23: 1037-46.
38. Domingo E, Sheldon J, Perales C. 2012. Viral quasispecies evolution. Microbiol Mol Biol 7: 159-216.
39. Bull JJ, Meyers LA, Lachmann M. 2005. Quasispecies made simple. PLoS Comput Biol 1: e61.
40. Schuster P. 1994. How do RNA molecules viruses explore their worlds? In Cowan GA, Pines D, Meltzer D (eds); Complexity: Metaphors, Models Reality. Reading, MA: Addison-Wesley. p. 383-418.
41. Fox JF, Loeb LA. 2010. Lethal mutagenesis: targeting the mutator phenotype in cancer. Semin Cancer Biol 20: 353-9.
42. Beckman RA. 2009. Mutator mutations enhance tumorigenic efficiency across fitness landscapes. PLoS One 4: e5860.
43. Koonin EV. 2000. How many genes can make a cell: the minimal-gene-set concept. Annu Rev Genomics Hum Genet 1: 99-116.
44. Gil R, Silva FJ, Pereto J, Moya A. 2004. Determination of the core of a minimal bacterial gene set. Microbiol Mol Biol Rev 68: 518-37.
45. Solé RV, Munteanu A, Rodriguez-Caso C, Macia J. 2007. Synthetic protocell biology: from reproduction to computation. Phil Trans R Soc B 362: 1727-37.
46. Nijhawan D, Zack TI, Ren Y, Strickland MR, et al. 2012. Cancer vulnerabilities unveiled by genomic loss. Cell 150: 842-54.
47. Parker HG, Ostrander EA. 2014. Hiding in plain view - an ancient dog in the modern world. Science 343: 376-8.
48. Murchison EP, Wedge DC, Alexandrov LB, Fu B, et al. 2014. Transmissible dog cancer genome reveals the origin and history of an ancient cell lineage. Science 343: 437-40.
49. Loeb LA, Essigmann JM, Kazazi F, Zhang J, et al. 1999. Lethal mutagenesis of HIV with mutagenic nucleoside analogs. Proc Natl Acad Sci USA 96: 1492-7.
50. Domingo E, Sheldon J, Perales C. 2012. Viral quasispecies evolution. Microbiol Mol Biol 76: 159-216.
51. Mas A, Lopez-Galindez C, Cacho I, Gomez J, et al. 2010. Unfinished stories on viral quasispecies and Darwinian views of evolution. J Mol Biol 397: 865-77.
52. Helleday H, Petermann E, Lundin C, Hodgson B, et al. 2008. DNA repair pathways as targets for cancer therapy. Nat Rev Cancer 8: 193-200.
53. Malgorzata E, Jonkers J. 2011. Studying therapy response and resistance in mouse models for BRCA1-deficient breast cancer. J Mammary Gland Biol Neoplasia 16: 41-50.
54. Bouwman P, Jonkers J. 2012. The effects of deregulated DNA damage signalling on cancer chemotherapy response and resistance. Nat Rev Cancer 12: 587-98.
55. O'Neil NJ, van Pel DM, Hieter P. 2013. Synthetic lethality and cancer: cohesin and PARP at the replication fork. Trends Genet 8: e1002574.
56. Kauffman SA. 1971. Differentiation of malignant to benign cells. J Theor Biol 31: 429-31.
57. Kauffman SA. 1993. Origins of Order. New York: Oxford University Press.
58. Huang S, Ernberg I, Kauffman SA. 2009. Cancer attractors. Semin Cell Dev Biol 20: 869-76.
59. Huang S. 2001. Genomics, complexity and drug discovery: insights from Boolean network models. Pharmacogenomics 2: 203-22.
60. Pe'er D, Hacohen N. 2011. Principles and strategies for developing network models in cancer. Cell 144: 864-73.
61. Creixell P, Schoof EM, Erler JT, Linding R. 2012. Navigating cancer network attractors for tumor-specific therapy. Nat Biotechnol 30: 842-8.
62. Waddington CH. 1947. The Strategy of Genes. London: Allen and Unwinm.
63. Huang S. 2012. The molecular and mathematical basis of Waddington's epigenetic landscape: a framework for post-Darwinian biology? BioEssays 34: 149-57.
64. Solé RV. 2012. Catastrophes and complex networks in genomically unstable tumorigenesis. In Deisboeck TS, Stakamatos GS (eds); Multiscale Cancer Modeling. Boca Raton, Florida: CRC Press. p. 67-86.
65. Stratton MR, Campbell PJ, Futreal PA. 2009. The cancer genome. Nature 458: 719-24.
66. Podlaha O, Riester M, Subhajyoti D, Michor F. 2012. Evolution of the cancer genome. Trends Genet 28: 155-61.
67. Huang S. 2012. Tumor progression: chance and necessity in Darwinian and Lamarckian somatic (mutationless) evolution. Prog Biophys Mol Biol 110: 69-86.
68. Crespi B, Summers K. 2005. Evolutionary biology of cancer. Trends Ecol Evol 20: 545-52.
69. Gonzalez-Garcia I, Solé RV, Costa J. 2001. Metapopulation dynamics and spatial heterogeneity in cancer. Proc Natl Acad Sci USA 99: 13085-9.
70. Maley CC, Galipeau PC, Finley JC, Wongsurawat VJ. 2006. Genetic clonal diversity predicts progression to esophageal adenocarcinoma. Nat Genet 38: 468-73.
71. Solé RV, Bascompte J. 2007. Self-Organization in Complex Ecosystems. Princeton, New Jersey: Princeton U. Press.
72. Martens EA, Kostadinov R, Maley CC, Hallatschek O. 2011. Spatial structure increases the waiting tie for cancer. New J Phys 13: 115014.
73. Toyabe S, Sano M. 2005. Spatial suppression of error catastrophe in a growing pattern. Physica D 203: 1-8.
74. Axelrod R, Axelrod DE, Pienta KJ. 2006. Evolution of cooperation among tumor cells. Proc Natl Acad Sci USA 103: 13474-9.
75. Haruta S, Kato S, Yamamoto K, Igarashi Y. 2009. Intertwined interspecies relationships: approaches to untangle the microbial network. Environ Microbiol 11: 2963-9.
76. Pazos F, Valencia A, De Lorenzo V. 2003. The organization of the microbial biodegradation network from a systems-biology perspective. EMBO Rep 4: 994-9.
77. Camacho DF, Pienta KJ. 2012. Disrupting the networks of cancer. Clin Cancer Res 18: 2801-8.
78. Gatenby RA, Brown J, Vincent T. 2009. Lessons from applied ecology: cancer control using an evolutionary double bind. Cancer Res 69: 7499-502.
79. Solé RV, Montoya J. 2001. Complexity and fragility in ecological networks. Proc R Soc Lond B 268: 2039-45.
80. Montoya JM, Pimm SL, Solé RV. 2006. Ecological networks and their fragility. Nature 442: 259-64.
81. Buldyrev SV, Parshani R, Paul G, Stanley EH, et al. 2010. Catastrophic cascade of failures in interdependent networks. Nature 464: 1025-8.
82. Gao J, Buldyrev SV, Stanley EH, Havlin S. 2012. Networks formed by interdependent networks. Nat Phys 8: 40-8.
83. Jones PA, Baylin SB. 2007. The epigenomics of cancer. Cell 128: 683-92.
84. Timp W, Feinberg AP. 2013. Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host. Nat Rev Cancer 13: 497-510.
85. Serra R, Villani M, Barbieri A, Kauffman SA, et al. 2010. On the dynamics of random Boolean networks subject to noise: attractors, ergodic sets and cell types. J Theor Biol 265: 185-93.
86. Villani M, Barbieri A, Serra R. 2011. A dynamical model of genetic networks for cell differentiation. PLoS One 6: e17703.
87. Marusyk A, Almendro V, Polyak K. 2012. Intra-tumor heterogeneity: a looking-glass for cancer? Nat Rev Cancer 12: 323-4.
88. Hahn WC, Weinberg RA. 2002. Modelling the molecular circuitry of cancer. Nat Rev Cancer 2: 331-41.
89. Cui Q, Ma Y, Jaramillos M, Bari H, et al. 2007. A map of human cancer signaling. Mol Syst Biol 3: e152.
90. Essaghir A, Demoulin J-P. 2012. A minimal connected network of transcription factors regulated in human tumors and its application to the quest of universal cancer biomarkers. PLoS One 7: 39666.
91. Eyfjord JE, Bodvarsdottir SK. 2005. Genomic instability and cancer: networks involved in response to DNA damage. Fund Mol Mec Mutagen 592: 18-28.
92. Rodriguez-Caso C, Corominas-Murtra B, Solé RV. 2009. On the basic computational structure of gene regulatory networks. Mol Biosyst 5: 1617-29.
93. Kim J-R, Kim J, Kwon Y, Lee H-Y, et al. 2011. Reduction of complex signaling networks to a representative kernel. Sci Sign 4: 1-10.
94. Kim J, Park S-M, Cho K-H. 2013. Discovery of a kernel for controlling biomolecular regulatory networks. Nat Sci Rep 3: 2223.
95. Scheffer M. 2009. Critical Transitions in Nature and Society. Princeton, New Jersey: Princeton U. Press.
96. Chen L, Liu R, Liu Z-P, Li M, et al. 2012. Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers. Nat Sci Rep 2: 342.
97. Maguran AE. 1988. Ecological Diversity Its Measurement. Princeton, New Jersey: Princeton U. Press.
98. Maley CC, Galipeau PC, Finley JC, Jon Wongsurawat V, et al. 2006. Genetic clonal diversity predicts progression to esophageal adenocarcinoma. Nat Genet 38: 468-73.
99. Preziosi L (ed). 2003. Cancer Modeling and Simulation. Boca Raton, Florida: Chapman & Hall.
100. Anderson A, Quaranta V. 2008. Integrative mathematical oncology. Nat Rev Cancer 8: 227-34.
101. Byrne HM, Alarcon T, Owen MR, Webb SD, et al. 2006. Modelling aspects of cancer dynamics: a review. Phil Trans R Soc Lond B 364: 1563-78.
102. D'Onofrio A, Cerrai Pand Gandolfi A (eds). 2012. New Challenges for Cancer Systems Biomedicine. Berlin: Springer.
103. Gusev Y, Kagansky V, Dooley WC. 2000. A stochastic model of chromosome segregation errors with reference to cancer cells. Math Comp Model 32: 97-111.
104. Komarova N, Wodarz D. 2004. The optimal rate of chromosome loss for the inactivation of tumor supressor genes in cancer. Proc Natl Acad Sci USA 101: 7017-21.
105. Höglund M, Frigyesi A, Gisselsson D, Mitelman F. 2005. Statistical behavior of complex cancer karyotypes. Genes Chromosomes Cancer 42: 327-41.
106. Vincent MD. 2010. The animal within: carcinogenesis and the clonal evolution of cancer cells are speciation events sensu stricto. Evolution 64: 1173-83.
107. Glassman ML, Hochberg A. 1997. Time reversal in biological systems. Med Hypotheses 49: 505-8.
108. Ciriello G, Miller ML, Aksoy BA, Senbabaoglu Y, et al. 2013. Emerging landscape of oncogenic signatures across human cancers. Nat Genet 45: 1127-33.