Attempt at a systemic outlook on aging and carcinogenesis

Piwowar, M.; Dygut, J.; Piwowar, P.; Konieczny, L.; Roterman, I.

doi:10.1515/bams-2014-0012

Artykuł - szczegóły

Tytuł artykułu

Attempt at a systemic outlook on aging and carcinogenesis

Autorzy

Piwowar M. , Dygut J. , Piwowar P. , Konieczny L. , Roterman I.

Wybrane pełne teksty z tego czasopisma

Identyfikatory

DOI

10.1515/bams-2014-0012

Warianty tytułu

Języki publikacji

Abstrakty

Two of the key problems plaguing humanity – aging and carcinogenesis – are inexorably linked. While their nature seems different, their mechanisms have a lot in common. Evidence suggests that aging is the result of spontaneous synthesis and accumulation of improperly folded proteins in cells, leading to a variety of pathologies. As for carcinogenesis, it is tied to genetic mutations – permanent, covalent changes in the DNA. Both processes are random in character; however, unlike mutations, the accumulation of malformed proteins is not genetically determined. Instead, control over this process hinges upon regulating the protein exchange rate – a phenomenon that seems a likely candidate for the basic aging control mechanism. Although mutations themselves may be counteracted in a controlled manner, their effects typically cannot. The mechanisms of aging and carcinogenesis, while functionally different, remain correlated: an aging cell is rendered more susceptible to mutational changes. The rapidly growing body of information regarding aging and carcinogenesis enables a systemic approach to both these phenomena – an approach that is attempted in this review.

Słowa kluczowe

aging Congo red creation of organisms eukaryotic cells advent evolutionary time functionrelated mutations partly unfolded proteins systems biology tumorigenesis

Wydawca

Uniwersytet Jagielloński - Collegium Medicum
Index Copernicus Sp. z o.o.

Czasopismo

Bio-Algorithms and Med-Systems

Rocznik

2014

Tom

Vol. 10, no. 3

Strony

101--115

Opis fizyczny

Bibliogr. 101 poz., rys., wykr.

Twórcy

autor

Piwowar M.

Department of Bioinformatics and Telemedicine, Jagiellonian University – Medical College, Kraków, Poland

autor

Dygut J.

Hospital in Przemyśl, Przemyśl, Poland

autor

Piwowar P.

AGH University of Science and Technology, Pawilon B-1, Kraków, Poland

autor

Konieczny L.

Chair of Medical Biochemistry, Jagiellonian University – Medical College, Kraków, Poland

autor

Roterman I.

myroterm@cyf-kr.edu.pl

Department of Bioinformatics and Telemedicine, Jagiellonian University – Medical College, Łazarza 16, 31-530 Kraków, Poland

Bibliografia

1. Chen F, Lam CH, Tsui OK. The surface mobility of glasses. Science 2014;343:975–6.
2. Walter P, Ron D. The unfolded protein response: from stress pathway to homeostatic regulation. Science 2011;334:1081–6.
3. Ross JM, Stewart JB, Hagström E, Brené S, Mourier A, Coppotelli G, et al. Germline mitochondrial DNA mutations aggravate ageing and can impair brain development. Nature 2013;01:412–5.
4. Gabuzda D, Yankner BA. Inflamation links ageing to the brain. Nature 2013;497:197–8.
5. Nemoto S, Finkel T. Ageing and the mystery at Arles. Nature 2004;429:149–52.
6. Burhans WC, Weinberger M. DNA replication stress, genome instability and aging. Nucleic Acids Res 2007;35:7545–56.
7. Marchewka A, Dąbrowski Z, Żołądź J. Fizjologia starzenia się. Wydawnictwo Naukowe PWN, Warszawa, 2013 (in Polish).
8. Shen EZ, Song CQ, Lin Y, Zhang WH, Su PF, Liu WY, et al. Mitoflash frequency in early adulthood predicts lifespan in Caenorhabditis elegans. Nature 2014;508:128–32.
9. King NP, Bale JB, Sheffler W, McNamara DE, Gonen S, Gonen T, et al. Accurate design of co-assembling multi-component protein nanomaterials. Nature 2014;510:103–8.
10. Dyson HJ, Wright PE. Equilibrium NMR studies of unfolded and partially folded proteins. Nat Struct Biol 1998;5(Suppl):499–503.
11. Neudecker P, Robustelli P, Cavalli A, Walsh P, Lundström P, Zarrine-Afsar A, et al. Structure of an intermediate state in protein folding and aggregation. Science 2012;336:362–6.
12. Eliezer D. Visualizing amyloid assembly. Science 2012;336:308–9.
13. Sunde M, Blake CC. From globular to the fibrous state: protein structure and structural conversion in amyloid formation. Q Rev Biophys 1998;31:1–39.
14. Stopa B, Jagusiak A, Konieczny L, Piekarska B, Rybarska J, Zemanek G, et al. The use of supramolecular structures as protein ligands. J Mol Model 2013;19:4731–40.
15. Konieczny L, Roterman I, Spólik P. Systems biology – strategy of living organisms. New York, Heidelberg, Dordrecht, London: Springer 2014.
16. Khan Z, Ford MJ, Cusanovich DA, Mitrano A, Pritchard JK, Gilad Y. Primate transcript and protein expression levels evolve under compensatory selection pressures. Science 2013;342:1100–4.
17. Wu L, Candille SI, Choi Y, Xie D, Jiang L, Li-Pook-Than J, et al. Variation and genetic control of protein abundance in humans. Nature 2013;499:79–82.
18. Gardner BM, Walter P. Unfolded proteins are Ire1-activating ligands that directly induce the unfolded protein response. Science 2011;333:1891–4.
19. Hollien J, Weissman JS. Decay of endoplasmic reticulumlocalized mRNAs during the unfolded protein response. Science 2006;313:104–7.
20. Bass J, Takahashi JS. Circadian integration of metabolism and energetics. Science 2010;330:1349–54.
21. Spólnik P, Konieczny L, Roterman I, Markiewicz M. Biological clock – is the need for a clock a common issue for cells and computers? Bio-Algorithms Med-Syst 2012;8:255–65.
22. Jiang H, Ju Z, Rudolph KL. Telomere shortening and aging. Z Gerontol Geriatr 2007;40:314–24.
23. Yang H, Rudge DG, Koos JD, Vaidialingam B, Yang HJ, Pavletich NP. mTOR kinase structure, mechanism and regulation. Nature 2013;97:217–23.
24. Johnson SC, Yanos ME, Kayser EB, Quintana A, Sangesland M, Castanza A, et al. mTOR inhibition alleviates mitochondrial disease in a mouse model of Leigh syndrome. Science 2013;342:1524–8.
25. Johnson SC, Rabinovitch PS, Kaeberlein M. mTOR is a key modulator of ageing and age-related disease. Nature 2013;493:338–45.
26. Lee IH, Kawai Y, Fergusson MM, Rovira II, Bishop AJ, Motoyama N, et al. Atg7 modulates p53 activity to regulate cell cycle and survival during metabolic stress. Science 2012;336:225–8.
27. Chin RM, Fu X, Pai MY, Vergnes L, Hwang H, Deng G, et al. The metabolite α-ketoglutarate extends lifespan by inhibiting ATP synthase and TOR. Nature 2014;509:397–401.
28. O’Neill LA, Hardie DG. Metabolism of inflammation limited by AMPK and pseudo-starvation. Nature 2013;493:346–55.
29. Michaelis S, Hrycyna CA. A protease for the ages. Science 2013;339:1529–30.
30. Conneely KN, Capell BC, Erdos MR, Sebastiani P, Solovieff N, Swift AJ, et al. Human longevity and common variations in the LMNA gene: a meta-analysis. Aging Cell 2012;11:475–81.
31. Paul S, Million-Weaver S, Chattopadhyay S, Sokurenko E, Merrikh H. Accelerated gene evolution through replicationtranscription conflicts. Nature 2013;495:512–5.
32. Wolff S, Dillin A. Ageing: beneficial miscommunication. Nature 2013;497:442–3.
33. Reiser KM. Nonenzymatic glycation of collagen in aging and diabetes. Proc Soc Exp Biol Med 1998;218:23–37.
34. Kasper M, Funk RH. Age-related changes in cells and tissues due to advanced glycation end products (AGEs). Arch Gerontol Geriatr 2001;32:2.
35. Vazquez A, Liu J, Zhou Y, Oltvai ZN. Catabolic efficiency of aerobic glycolysis: the Warburg effect revisited. BMC Syst Biol 2010;4:58.
36. Cairns RA, Harris IS, Mak TW. Regulation of cancer cell metabolism Nat Rev Cancer 2011;11:85–95.
37. de Lange T. Activation of telomerase in a human tumor. Proc Natl Acad Sci USA 1994;91:2882–5.
38. Shay JW, Reddel RR, Wright WE. Cancer and telomeres – an ALTernative to telomerase. Science 2012;336:1388–90.
39. Tomita M, Kami K. Systems biology, metabolomics, and cancer metabolism. Science 2012;336:990–1.
40. Vander Heiden MG, Cantley LC, Thompson CB. Understanding the Warburg effect: the metabolic requirements of cell proliferation. Science 2009;324:1029–33.
41. Vander Heiden MG, Locasale JW, Swanson KD, Sharfi H, Heffron GJ, Amador-Noguez D, et al. Evidence for an alternative glycolytic pathway in rapidly proliferating cells. Science 2010;329:1492–9.
42. Elsäser SJ, Allis CD, Lewis PW. New epigenetic drivers of cancers. Science 2011;331(6021), 1145–6.
43. Ramiro AR, Jankovic M, Callen E, Difilippantonio S, Chen HT, McBride KM, et al. Role of genomic instability and p53 in AIDinduced c-myc-Igh translocations. Nature 2006;440:105–9.
44. Lukas J, Lukas C. Molecular biology. Shielding broken DNA for a quick fix. Science 2013;339:652–3.
45. Krivtsov AV, Armstrong SA. Can one cell influence cancer heterogeneity? Science 2012;338:1035–6.
46. Fischer WW. Life before the rise of oxygen. Nature 2008;455:1051–2.
47. Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier ME, Mitros T, et al. The Amphimedon queenslandica genome and the evolution of animal complexity. Nature 2010;466:720–6.
48. Smith MP, Harper DA. Causes of the Cambrian explosion. Science 2013;341:1355–6.
49. Lyons TW, Reinhard CT, Planavsky NJ. The rise of oxygen in Earth’s early ocean and atmosphere. Nature 2014;506:307–15.
50. Eisenhoffer GT, Loftus PD, Yoshigi M, Otsuna H, Chien C-B, Morcos PA, et al. Crowding induces live cell extrusion to maintain homeostatic cell numbers in epithelia. Nature 2012;484:546–9.
51. Vogel G. How do organs know when they have reached the right size? Science 2013;340:1156–7.
52. Marinari E, Mehonic A, Curran S, Gale J, Duke T, Baum B. Livecell delamination counterbalances epithelial growth to limit tissue overcrowding. Nature 2012;484:542–5.
53. Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 2012;485:376–80.
54. Thellin O, Zorzi W, Lakaye B, De Borman B, Coumans B, Hennen G, et al. Housekeeping genes as internal standards: use and limits. J Biotechnol 1999;75:291–5.
55. Belle MD, Piggins HD. Circadian time redoxed. Science 2012;337:805–6.
56. Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, et al. Mutational landscape and significance across 12 major cancer types. Nature 2013;502:333–9.
57. Lawrence MS, Stojanov P, Mermel CH, Robinson JT, Garraway LA, Golub TR, et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 2014;505:495–501.
58. Muzny DM, Bainbridge MN, Chang K, Dinh HH, Drummond JA, Fowler G, et al. Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012;487:330–7.
59. Tamborero D, Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Kandoth C, Reimand J, et al. Comprehensive identification of mutational cancer driver genes across 12 tumor types. Sci Rep 2013;3:2650.
60. Weinstein JN, Akbani R, Broom BM, Wang W, Verhaak RG, McConkey D, et al. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature 2014;507:315–22.
61. Rahman N. Realizing the promise of cancer predisposition genes. Nature 2014;505:302–8. Erratum in: Nature 2014;510:176.
62. Hudson T. A clinical perspective. Nature 2013;502:306–7.
63. Ojesina AI, Lichtenstein L, Freeman SS, Pedamallu CS, Imaz-Rosshandler I, Pugh TJ, et al. Landscape of genomic alterations in cervical carcinomas. Nature 2014;506:371–5.
64. Aerts S, Cools J. Mutations close in on gene regulation. Nature 2013;499:35–6.
65. Dancer JY, Henry SP, Bondaruk J, Lee S, Ayala AG, de Crombrugghe B, et al. Expression of master regulatory genes controlling skeletal development in benign cartilage and bone forming tumors. Hum Pathol 2010;41:1788–93.
66. Yamada KM, Araki M. Tumor suppressor PTEN: modulator of cell signaling, growth, migration and apoptosis. J Cell Sci 2001;114(Pt 13):2375–82.
67. Burke JE, Perisic O, Masson GR, Vadas O, Williams RL. Oncogenic mutations mimic and enhance dynamic events in the natural activation of phosphoinositide 3-kinase p110α (PIK3CA). Proc Natl Acad Sci USA 2012;109:15259–64.
68. Harbour JW, Onken MD, Roberson ED, Duan S, Cao L, Worley LA, et al. Frequent mutation of BAP1 in metastasizing uveal melanomas. Science 2010;330:1410–3.
69. Ogawara Y, Kishishita S, Obata T, Isazawa Y, Suzuki T, Tanaka K, et al. Akt enhances Mdm2-mediated ubiquitination and degradation of p53. J Biol Chem 2002;277:21843–50.
70. Losman JA, Looper RE, Koivunen P, Lee S, Schneider RK, McMahon C, et al. (R)-2-Hydroxyglutarate is sufficient to promote leukemogenesis and its effects are reversible. Science 2013;339:1621–5.
71. Krall AS, Christofk HR. A metabolic metamorphosis. Nature 2013;496:38–40.
72. Chen Z, Odstrcil EA, Tu BP, McKnight SL. Restriction of DNA replication to the reductive phase of the metabolic cycle protects genome integrity. Science 2007;316:1916–9.
73. Son J, Lyssiotis CA, Ying H, Wang X, Hua S, Ligorio M, et al. Glutamine supports pancreatic cancer growth through a KRASregulated metabolic pathway. Nature 2013;496:101–5.
74. Levine AJ, Puzio-Kuter AM. The control of the metabolic switch in cancers by oncogenes and tumor suppressor genes. Science 2010;330:1340–4.
75. Gut P, Verdin E. The nexus of chromatin regulation and intermediary metabolism. Nature 2013;502:489–98.
76. Maddocks OD, Berkers CR, Mason SM, Zheng L, Blyth K, Gottlieb E, et al. Serine starvation induces stress and p53-dependent metabolic remodelling in cancer cells. Nature 2013;493:542–6.
77. Zoncu R, Bar-Peled L, Efeyan A, Wang S, Sancak Y, Sabatini DM. mTORC1 senses lysosomal amino acids through an inside-out mechanism that requires the vacuolar H(+)-ATPase. Science 2011;334:678–83.
78. Purvis JE, Karhohs KW, Mock C, Batchelor E, Loewer A, Lahav G. p53 dynamics control cell fate. Science 2012;336:1440–4.
79. Hsieh AC, Liu Y, Edlind MP, Ingolia NT, Janes MR, Sher A, et al. The translational landscape of mTOR signalling steers cancer initiation and metastasis. Nature 2012;485:55–61.
80. Keller KE, Tan IS, Lee YS. SAICAR stimulates pyruvate kinase isoform M2 and promotes cancer cell survival in glucose-limited conditions. Science 2012;338:1069–72.
81. Mattaini KR, Vander Heiden MG. Glycosylation to adapt to stress. Science 2012;337:925–6.
82. Bass J. Circadian topology of metabolism. Nature 2012;491:348–56.
83. Starobinets H, Debnath J. A suppression switch. Nature 2013;504:225–6.
84. Dominissini D, He C. Damage prevention targeted Nature 2014;508:191–2.
85. Suva ML, Riggi N, Bernstein BE. Epigenetic reprogramming in cancer. Science 2013;339:1567–70.
86. Filippakopoulos P, Qi J, Picaud S, Shen Y, Smith WB, Fedorov O, et al. Selective inhibition of BET bromodomains. Nature 2010;468:1067–73.
87. Versteeg R. Tumours outside the mutation box. Nature 2014;506:438–9.
88. Kolodner RD, Cleveland DW, Putnam CD. Aneuploidy drives a mutator phenotype in cancer. Science 2011;333:942–3.
89. Martincorena I, Seshasayee AS, Luscombe NM. Evidence of non-random mutation rates suggests an evolutionary risk management strategy. Nature 2012;485:95–8.
90. Albert FW, Treusch S, Shockley AH, Bloom JS, Kruglyak L. Genetics of single-cell protein abundance variation in large yeast populations. Nature 2014;506:494–7.
91. Smagulova F, Gregoretti IV, Brick K, Khil P, Camerini-Otero RD, Petukhova GV. Genome-wide analysis reveals novel molecular features of mouse recombination hotspots. Nature 2011;472:375–8.
92. Ruark E, Snape K, Humburg P, Loveday C, Bajrami I, Brough R, et al. Mosaic PPM1D mutations are associated with predisposition to breast and ovarian cancer. Nature 2013;493:406–10.
93. Silvente-Poirot S, Poirot M. Cholesterol and cancer, in the balance. Science 2014;343:1445–6.
94. Nelson ER, Wardell SE, Jasper JS, Park S, Suchindran S, Howe MK, et al. 27-Hydroxycholesterol links hypercholesterolemia and breast cancer pathophysiology. Science 2013;342:1094–8.
95. Ryan KK, Seeley RJ. Food as a hormone. Science 2013;339:918–9.
96. Goossens T, Klein U, Küpers R. Frequent occurrence of deletions and duplications during somatic hypermutation: implications for oncogene translocations and heavy chain disease. Proc Natl Acad Sci USA 1998;95:2463–8.
97. Deweerdt S. Naked ambition. Nature 2014;509:S60–1.
98. Jones S, Wang TL, Shih Ie, Mao TL, Nakayama K, Roden R, et al. Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma. Science 2010;330:228–31.
99. Stieglitz B, Rana RR, Koliopoulos MG, Morris-Davies AC, Schaeffer V, Christodoulou E, et al. Structural basis for ligase-specific conjugation of linear ubiquitin chains by HOIP. Nature 2013;503:422–6.
100. Rivkin E, Almeida SM, Ceccarelli DF, Juang YC, MacLean TA, Srikumar T, et al. The linear ubiquitin-specific deubiquitinase gumby regulates angiogenesis. Nature 2013;498:318–24.
101. Matouschek A, Finley D. An ancient portal to proteolysis. An ancient portal to proteolysis. Science 2012;337:813-4.

Typ dokumentu

Bibliografia

Identyfikator YADDA

bwmeta1.element.baztech-62019a20-235e-4550-8ddc-f93e0b32acca