Biosemiotic entropy of the genome: Mutations and epigenetic imbalances resulting in cancer

Entropy

Volumn 15, Issue 1, 2013, Pages 234-261

  Gryder, Berkley E ^a   Nelson, Chase W ^b   Shepard, Samuel S ^c  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

^b UNIVERSITY OF SOUTH CAROLINA   (United States)

^c CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

Author keywords

Biosemiotic entropy; Cancer; Chromatin architecture; Encode; Epigenetics; Gene mutations; Genetics; Homeostasis; Population genetics; Semiotics

Indexed keywords

EID: 84873128348     PISSN: None     EISSN: 10994300     Source Type: Journal    
DOI: 10.3390/e15010234     Document Type: Article

References (102)

1. Johnson, H.A. Information theory in biology after 18 years. Science 1970, 168, 1545-1550.
2. Sebeok, T.A. Biosemiotics: Its roots, proliferation, and prospects. Semiotica 2001, 134, 61-78.
3. Szostak, J.W. Functional information: Molecular messages. Nature 2003, 423, 689-689.
4. Sharov, A.A. Functional information: Towards synthesis of biosemiotics and cybernetics. Entropy 2010, 12, 1050-1070.
5. Stratton, M.R.; Campbell, P.J.; Futreal, P.A. The cancer genome. Nature 2009, 458, 719-724.
6. Merlo, L.M.F.; Pepper, J.W.; Reid, B.J.; Maley, C.C. Cancer as an evolutionary and ecological process. Nat. Rev. Cancer 2006, 6, 924-935.
7. Chin, L.; Meyerson, M.; Aldape, K.; Bigner, D.; Mikkelsen, T.; VandenBerg, S.; Kahn, A.; Penny, R.; Ferguson, M.L.; Gerhard, D.S.; et al. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008, 455, 1061-1068.
8. Gerstein, M.B.; Bruce, C.; Rozowsky, J.S.; Zheng, D.; Du, J.; Korbel, J.O.; Emanuelsson, O.; Zhang, Z.D.; Weissman, S.; Snyder, M. What is a gene, post-ENCODE? History and updated definition. Genome Res. 2007, 17, 669-681.
9. Yan, K.-K.; Fang, G.; Bhardwaj, N.; Alexander, R.P.; Gerstein, M. Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks. Proc. Natl. Acad. Sci. USA 2010, 107, 9186-9191.
10. D'Onofrio, D.J.; Abel, D.L.; Johnson, D.E. Dichotomy in the definition of prescriptive information suggests both prescribed data and prescribed algorithms: Biosemiotics applications in genomic systems. Theorl. Biol. Med. Model. 2012, 9, 8.
11. Emmeche, C.; Hoffmeyer, J. From language to nature, the semiotic metaphor in biology. Semiotica 1991, 84, 1-42.
12. D'Onofrio, D.; An, G. A comparative approach for the investigation of biological information processing: An examination of the structure and function of computer hard drives and DNA. Theorl. Biol. Med. Model. 2010, 7, 3.
13. Oller, J.W. The antithesis of entropy: Biosemiotic communication from genetics to human language with special emphasis on the immune systems. Entropy 2010, 12, 631-705.
14. Barbieri, M. A short history of biosemiotics. Biosemiotics 2009, 2, 221-245.
15. Peirce, C.S. Collected Papers of Charles Sanders Peirce; Harvard University Press: Cambridge, UK, 1958; Volume 7,8.
16. Barbieri, M. Three types of semiosis. Biosemiotics 2009, 2, 19-30.
17. Lasda, E.L.; Blumenthal, T. Trans-splicing. Wiley Interdiscip. Rev. RNA 2011, 2, 417-434.
18. Taft, R.J.; Pheasant, M.; Mattick, J.S. The relationship between non-protein-coding DNA and eukaryotic complexity. BioEssays 2007, 29, 288-299.
19. Adami, C. Introduction to artificial life. Trans. Evol. Comp. 1998, 2, 168-170.
20. Weinreich, D.M.; Delaney, N.F.; DePristo, M.A.; Hartl, D.L. Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 2006, 312, 111-114.
21. Nelson, C.W.; Sanford, J.C., The effects of low-impact mutations in digital organisms. Theor. Biol. Med. Model. 2011, 8, 9.
22. Kuehn, B.M. Massive study compilation illuminates regulatory role of non-gene-encoding dna. JAMA 2012, 308, 1419-1420.
23. Collins, F.S.; McKusick, V.A. Implications of the human genome project for medical science. JAMA 2001, 285, 540-544.
24. Kuilman, T.; Michaloglou, C.; Mooi, W.J.; Peeper, D.S. The essence of senescence. Genes Dev. 2010, 24, 2463-2479.
25. Lynch, M., Rate, molecular spectrum, and consequences of human mutation. Proc. Natl. Acad. Sci. USA 2010, 107, 961-968.
26. Higgins, K.; Lynch, M. Metapopulation extinction caused by mutation accumulation. Proc. Natl. Acad. Sci. USA 2001, 98, 2928-2933.
27. Birney, E.; Stamatoyannopoulos, J.A.; Dutta, A.; Guigo, R.; Gingeras, T.R.; Margulies, E.H.; Weng, Z.P.; Snyder, M.; Dermitzakis, E.T.; Thurman, R.E.; et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447, 799-816.
28. The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489, 57-74.
29. Eyre-Walker, A.; Keightley, P.D. The distribution of fitness effects of new mutations. Nat. Rev. Genet. 2007, 8, 610-618.
30. Sauna, Z.E.; Kimchi-Sarfaty, C. Understanding the contribution of synonymous mutations to human disease. Nat. Rev. Genet. 2011, 12, 683-691.
31. Hughes, A.L.; Packer, B.; Welch, R.; Bergen, A.W.; Chanock, S.J.; Yeager, M. Widespread purifying selection at polymorphic sites in human protein-coding loci. Proc. Natl. Acad. Sci. USA 2003, 100, 15754-15757.
32. Suh, Y.; Vijg, J. Snp discovery in associating genetic variation with human disease phenotypes. Mutat. Res. 2005, 573, 41-53.
33. Mills, R.E.; Luttig, C.T.; Larkins, C.E.; Beauchamp, A.; Tsui, C.; Pittard, W.S.; Devine, S.E. An initial map of insertion and deletion (indel) variation in the human genome. Genome Res. 2006, 16, 1182-1190.
34. Hughes, A.L. The evolution of functionally novel proteins after gene duplication. P. Roy. Soc. B-Biol. Sci. 1994, 256, 119-124.
35. Kondrashov, A.S. Contamination of the genome by very slightly deleterious mutations: Why have we not died 100 times over? J. Theor. Biol. 1995, 175, 583-594.
36. Loeb, L.A.; Essigmann, J.M.; Kazazi, F.; Zhang, J.; Rose, K.D.; Mullins, J.I. Lethal mutagenesis of hiv with mutagenic nucleoside analogs. Proc. Natl. Acad. Sci. USA 1999, 96, 1492-1497.
37. Bull, J.J.; Sanjuan, R.; Wilke, C.O. Theory of lethal mutagenesis for viruses. J. Virol. 2007, 81, 2930-2939.
38. Galvani, A.P. The role of mutation accumulation in hiv progression. Proc. R. Soc. Lond. Ser. B Biol. Sci. 2005, 272, 1851-1858.
39. Haldane, J.B.S. The cost of natural selection. J. Genet. 1957, 55, 511-524.
40. Kimura, M. Optimum mutation rate and degree of dominance as determined by the principle of minimum genetic load. J. Genet. 1960, 57, 21-34.
41. Nei, M. Molecular Population Genetics and Evolution; North-Holland Publishing Company: Amsterdam, The Netherlands, 1975.
42. Ide, S.; Miyazaki, T.; Maki, H.; Kobayashi, T. Abundance of ribosomal rna gene copies maintains genome integrity. Science 2010, 327, 693-696.
43. Agarwal, V.; Nair, S.K. Aminoacyl trna synthetases as targets for antibiotic development. MedChemComm 2012, 3, 887-898.
44. Schlünzen, F.; Harms, J.M.; Franceschi, F.; Hansen, H.A.S.; Bartels, H.; Zarivach, R.; Yonath, A. Structural basis for the antibiotic activity of ketolides and azalides. Structure 2003, 11, 329-338.
45. Audi, J.; Belson, M.; Patel, M.; Schier, J.; Osterloh, J. Ricin poisoning-A comprehensive review. JAMA 2005, 294, 2342-2351.
46. Ferreras, J.M.; Citores, L.; Iglesias, R.; Jimenez, P.; Girbes, T. Use of ribosome-inactivating proteins from sambucus for the construction of immunotoxins and conjugates for cancer therapy. Toxins 2011, 3, 420-441.
47. Neznanov, N.; Komarov, A.P.; Neznanova, L.; Stanhope-Baker, P.; Gudkov, A.V. Proteotoxic stress targeted therapy (pstt): Induction of protein misfolding enhances the antitumor effect of the proteasome inhibitor bortezomib. Oncotarget 2011, 2, 209-221.
48. Adams, J. The development of proteasome inhibitors as anticancer drugs. Cancer cell 2004, 5, 417-421.
49. Lin, G.; Li, D.; de Carvalho, L.P.S.; Deng, H.; Tao, H.; Vogt, G.; Wu, K.; Schneider, J.; Chidawanyika, T.; Warren, J.D.; et al. Inhibitors selective for mycobacterial versus human proteasomes. Nature 2009, 461, 621-626.
50. Gryder, B.E.; Guerrant, W.; Chen, C.H.; Oyelere, A.K. Oxathiazole-2-one derivative of bortezomib: Synthesis, stability and proteasome inhibition activity. MedChemComm 2011, 2, 1083-1086.
51. Bell, D.; Berchuck, A.; Birrer, M.; Chien, J.; Cramer, D.W.; Dao, F.; Dhir, R.; DiSaia, P.; Gabra, H.; Glenn, P.; et al. Integrated genomic analyses of ovarian carcinoma. Nature 2011, 474, 609-615.
52. Ellwood-Yen, K.; Graeber, T.G.; Wongvipat, J.; Iruela-Arispe, M.L.; Zhang, J.F.; Matusik, R.; Thomas, G.V.; Sawyers, C.L. Myc-driven murine prostate cancer shares molecular features with human prostate tumors. Cancer cell 2003, 4, 223-238.
53. Riley, T.; Sontag, E.; Chen, P.; Levine, A. Transcriptional control of human p53-regulated genes. Nat. Rev. Mol. Cell Biol. 2008, 9, 402-412.
54. Hyytinen, E.R.; Haapala, K.; Thompson, J.; Lappalainen, K.; Roiha, M.; Rantala, I.; Helin, H.J.; Janne, I.A.; Vihinen, M.; Palvimo, J.J.; et al. Pattern of somatic androgen receptor gene mutations in patients with hormone-refractory prostate cancer. Lab. Invest. 2002, 82, 1591-1598.
55. Strahl, B.D.; Allis, C.D. The language of covalent histone modifications. Nature 2000, 403, 41-45.
56. Sengupta, N.; Seto, E. Regulation of histone deacetylase activities. J. Cell. Biochem. 2004, 93, 57-67.
57. Bannister, A.J.; Kouzarides, T. Regulation of chromatin by histone modifications. Cell Res. 2011, 21, 381-395.
58. Roy, R.; Chun, J.; Powell, S.N. Brca1 and brca2: Different roles in a common pathway of genome protection. Nat. Rev. Cancer 2012, 12, 68-78.
59. Helleday, T.; Petermann, E.; Lundin, C.; Hodgson, B.; Sharma, R.A. DNA repair pathways as targets for cancer therapy. Nat. Rev. Cancer 2008, 8, 193-204.
60. Negrini, S.; Gorgoulis, V.G.; Halazonetis, T.D. Genomic instability [mdash] an evolving hallmark of cancer. Nat. Rev. Mol. Cell Biol. 2010, 11, 220-228.
61. Hegi, M.E.; Sciuscio, D.; Murat, A.; Levivier, M.; Stupp, R. Epigenetic deregulation of DNA repair and its potential for therapy. Clin. Cancer Res. 2009, 15, 5026-5031.
62. Ghobrial, I.M.; Witzig, T.E.; Adjei, A.A. Targeting apoptosis pathways in cancer therapy. CA Cancer J. Clin. 2005, 55, 178-194.
63. Bisson, W.H.; Abagyan, R.; Cavasotto, C.N. Molecular basis of agonicity and antagonicity in the androgen receptor studied by molecular dynamics simulations. J. Mol. Graph. Model. 2008, 27, 452-458.
64. Scher, H.I.; Fizazi, K.; Saad, F.; Taplin, M.E.; Sternberg, C.N.; Miller, K.; de Wit, R.; Mulders, P.; Chi, K.N.; Shore, N.D.; et al. Increased survival with enzalutamide in prostate cancer after chemotherapy. New Engl. J. Med. 2012, 367, 1187-1197.
65. Dreaden, E.C.; Gryder, B.E.; Austin, L.A.; Tene Defo, B.A.; Hayden, S.C.; Pi, M.; Quarles, L.D.; Oyelere, A.K.; El-Sayed, M.A. Antiandrogen gold nanoparticles dual-target and overcome treatment resistance in hormone-insensitive prostate cancer cells. Bioconjugate Chem. 2012.
66. Hara, T.; Miyazaki, J.; Araki, H.; Yamaoka, M.; Kanzaki, N.; Kusaka, M.; Miyamoto, M. Novel mutations of androgen receptor: A possible mechanism of bicalutamide withdrawal syndrome. Cancer Res. 2003, 63, 149-153.
67. Seruga, B.; Ocana, A.; Tannock, I.F. Drug resistance in metastatic castration-resistant prostate cancer. Nat. Rev. Clin. Oncol. 2011, 8, 12-23.
68. Gryder, B.E.; Sodji, Q.H.; Oyelere, A.K. Targeted cancer therapy: Giving histone deacetylase inhibitors all they need to succeed. Future Med. Chem. 2012, 4, 505-524.
69. Sadikovic, B.; Al-Romaih, K.; Squire, J.A.; Zielenska, M. Cause and consequences of genetic and epigenetic alterations in human cancer. Curr. Genomics 2008, 9, 394-408.
70. Ferguson-Smith, A.C. Genomic imprinting: The emergence of an epigenetic paradigm. Nat. Rev. Genet. 2011, 12, 565-575.
71. Peltomaki, P. Mutations and epimutations in the origin of cancer. Exp. Cell Res. 2012, 318, 299-310.
72. Furusawa, C.; Kaneko, K. A dynamical-systems view of stem cell biology. Science 2012, 338, 215-217.
73. Ruthenburg, A.J.; Li, H.T.; Milne, T.A.; Dewell, S.; McGinty, R.K.; Yuen, M.; Ueberheide, B.; Dou, Y.L.; Muir, T.W.; Patel, D.J.; et al. Recognition of a mononucleosomal histone modification pattern by bptf via multivalent interactions. Cell 2011, 145, 692-706.
74. Bogdanovic, O.; Veenstra, G.J.C. DNA methylation and methyl-cpg binding proteins: Developmental requirements and function. Chromosoma 2009, 118, 549-565.
75. Walker, C.L.; Ho, S.-M. Developmental reprogramming of cancer susceptibility. Nat. Rev. Cancer 2012, 12, 479-486.
76. Huang, Y.W.; Kuo, C.T.; Stoner, K.; Huang, T.H.Y.; Wang, L.S. An overview of epigenetics and chemoprevention. FEBS Lett. 2011, 585, 2129-2136.
77. Kang, S.K.; Park, J.B.; Cha, S.H. Multipotent, dedifferentiated cancer stem-like cells from brain gliomas. Stem Cells Dev. 2006, 15, 423-435.
78. Morin, R.D.; Mendez-Lago, M.; Mungall, A.J.; Goya, R.; Mungall, K.L.; Corbett, R.D.; Johnson, N.A.; Severson, T.M.; Chiu, R.; Field, M.; et al. Frequent mutation of histonemodifying genes in non-hodgkin lymphoma. Nature 2011, 476, 298-303.
79. Gibson, P.; Tong, Y.; Robinson, G.; Thompson, M.C.; Currle, D.S.; Eden, C.; Kranenburg, T.A.; Hogg, T.; Poppleton, H.; Martin, J.; et al. Subtypes of medulloblastoma have distinct developmental origins. Nature 2010, 468, 1095-1099.
80. Cao, L.A.; Yu, Y.K.; Bilke, S.; Walker, R.L.; Mayeenuddin, L.H.; Azorsa, D.O.; Yang, F.; Pineda, M.; Helman, L.J.; Meltzer, P.S. Genome-wide identification of pax3-fkhr binding sites in rhabdomyosarcoma reveals candidate target genes important for development and cancer. Cancer Res. 2010, 70, 6497-6508.
81. Khan, J.; Bittner, M.L.; Saal, L.H.; Teichmann, U.; Azorsa, D.O.; Gooden, G.C.; Pavan, W.J.; Trent, J.M.; Meltzer, P.S., Cdna microarrays detect activation of a myogenic transcription program by the pax3-fkhr fusion oncogene. Proc. Natl. Acad. Sci. USA 1999, 96, 13264-13269.
82. Mahoney, S.E.; Yao, Z.Z.; Keyes, C.C.; Tapscott, S.J.; Diede, S.J. Genome-wide DNA methylation studies suggest distinct DNA methylation patterns in pediatric embryonal and alveolar rhabdomyosarcomas. Epigenetics 2012, 7, 400-408.
83. Pennisi, E. Genomics ENCODE project writes eulogy for junk DNA. Science 2012, 337, 1159-1161.
84. Sumazin, P.; Yang, X.R.; Chiu, H.S.; Chung, W.J.; Iyer, A.; Llobet-Navas, D.; Rajbhandari, P.; Bansal, M.; Guarnieri, P.; Silva, J.; et al. An extensive microrna-mediated network of rna-rna interactions regulates established oncogenic pathways in glioblastoma. Cell 2011, 147, 370-381.
85. Marshall, L.; Kenneth, N.S.; White, R.J., Elevated trna(i)(met) synthesis can drive cell proliferation and oncogenic transformation. Cell 2008, 133, 78-89.
86. Kogo, R.; Shimamura, T.; Mimori, K.; Kawahara, K.; Imoto, S.; Sudo, T.; Tanaka, F.; Shibata, K.; Suzuki, A.; Komune, S.; et al. Long noncoding rna hotair regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res. 2011, 71, 6320-6326.
87. Candiloro, I.L.M.; Dobrovic, A. Detection of mgmt promoter methylation in normal individuals is strongly associated with the t allele of the rs16906252 mgmt promoter single nucleotide polymorphism. Cancer Prev. Res. 2009, 2, 862-867.
88. Pezer, Ž.; Ugarkovic, D. Role of non-coding rna and heterochromatin in aneuploidy and cancer. Semin. Cancer Biol. 2008, 18, 123-130.
89. Ioffe, Y.J.; Chiappinelli, K.B.; Mutch, D.G.; Zighelboim, I.; Goodfellow, P.J. Phosphatase and tensin homolog (pten) pseudogene expression in endometrial cancer: A conserved regulatory mechanism important in tumorigenesis? Gynecol. Oncol. 2012, 124, 340-346.
90. Hansotia, T.; Maida, A.; Flock, G.; Yamada, Y.; Tsukiyama, K.; Seino, Y.; Drucker, D.J. Extrapancreatic incretin receptors modulate glucose homeostasis, body weight, and energy expenditure. J. Clin. Invest. 2007, 117, 143-152.
91. Grecco, H.E.; Schmick, M.; Bastiaens, P.I.H. Signaling from the living plasma membrane. Cell 2011, 144, 897-909.
92. Davidson, R.M.; Lauritzen, A.; Lentz-Marino, L.; Seneff, S. Biological Water Structure and Biosemiotic Entropy: The Biophysical Etiology of Oncologic, Neurologic, and Infectious Disease. Entropy 2013, submitted for publication.
93. TCGA The cancer genome atlas. Available online: http://cancergenome.nih.gov/ (accessed on 15 December 2012).
94. Cortessis, V.; Thomas, D.; Levine, A.; Breton, C.; Mack, T.; Siegmund, K.; Haile, R.; Laird, P. Environmental epigenetics: Prospects for studying epigenetic mediation of exposure-response relationships. Human Genetics 2012, 131, 1565-1589.
95. Drouin, G.; Godin, J.R.; Page, B. The genetics of vitamin c loss in vertebrates. Curr. Genomics 2011, 12, 371-378.
96. Williams, T.N.; Mwangi, T.W.; Wambua, S.; Alexander, N.D.; Kortok, M.; Snow, R.W.; Marsh, K. Sickle cell trait and the risk of plasmodium falciparum malaria and other childhood diseases. J. Infect. Dis. 2005, 192, 178-186.
97. Koonin, E.V.; Novozhilov, A.S. Origin and evolution of the genetic code: The universal enigma. IUBMB Life 2009, 61, 99-111.
98. Mills, D.R.; Peterson, R.L.; Spiegelm, S An extracellular darwinian experiment with a selfduplicating nucleic acid molecule. Proc. Natl. Acad. Sci. USA 1967, 58, 217-224.
99. Barrick, J.E.; Yu, D.S.; Yoon, S.H.; Jeong, H.; Oh, T.K.; Schneider, D.; Lenski, R.E.; Kim, J.F., Genome evolution and adaptation in a long-term experiment with escherichia coli. Nature 2009, 461, 1243-1247.
100. Ohno, S. So much 'junk DNA' in our genome. Brookhaven Symp Biol. 1972, 366-370.
101. Muller, H.J. Our load of mutations. Am. J. hum. genet. 1950, 2, 111.
102. Crow, J.F. The high spontaneous mutation rate: Is it a health risk? Proc. Natl. Acad. Sci. USA 1997, 94, 8380-8386.