Signaling pathway cloud regulation for in silico screening and ranking of the potential geroprotective drugs

Frontiers in Genetics

Volumn 5, Issue MAR, 2014, Pages

  Zhavoronkov, Alex ^a,b,c,d   Buzdin, Anton A ^a,b,d,e   Garazha, Andrey V ^a,b,d,e   Borisov, Nikolay M ^a,b,f   Moskalev, Alexey A ^a,g,h  

^a MOSCOW INSTITUTE OF PHYSICS AND TECHNOLOGY   (Russian Federation)

^b First Oncology Research and Advisory Center   (Russian Federation)

^c The Biogerontology Research Foundation   (United Kingdom)

^d Clinical Center of Pediatric Hematology Oncology and Immunology   (Russian Federation)

^e SHEMYAKIN OVCHINNIKOV INSTITUTE OF BIOORGANIC CHEMISTRY   (Russian Federation)

^f INSTITUTE OF BIOPHYSICS   (Russian Federation)

^g SYKTYVKAR STATE UNIVERSITY   (Russian Federation)

^h INSTITUTE OF BIOLOGY   (Russian Federation)

Author keywords

Aging suppressive drug; Geroprotector; Signaling pathway cloud; Transcriptomics; Validation of drugs

Indexed keywords

DRUG; GEROPROTECTIVE DRUG; UNCLASSIFIED DRUG;

ALGORITHM; ARTICLE; BIOLOGICAL PHENOMENA AND FUNCTIONS CONCERNING THE ENTIRE ORGANISM; CELL FUNCTION; COMPUTER MODEL; DRUG SCREENING; EPIGENETICS; EXPERIMENTAL DESIGN; GENE EXPRESSION PROFILING; GEROPROTECTION; GROWTH, DEVELOPMENT AND AGING; HUMAN; METABOLIC PARAMETERS; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; SIMULATION; TRANSCRIPTOMICS;

EID: 84897979664     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2014.00049     Document Type: Article

References (50)

1. Alcedo, J., Flatt, T., and Pasyukova, E. G. (2013). Neuronal inputs and outputs of aging and longevity. Front. Genet. 4:71. doi: 10.3389/fgene.2013.00071
2. Bernardes De Jesus, B., Vera, E., Schneeberger, K., Tejera, A. M., Ayuso, E., Bosch, F., et al. (2012). Telomerase gene therapy in adult and old mice delays aging and increases longevity without increasing cancer. EMBO Mol. Med. 4, 691-704. doi: 10.1002/emmm.201200245
3. Blalock, E. M., Chen, K. C., Sharrow, K., Herman, J. P., Porter, N. M., Foster, T. C., et al. (2003). Gene microarrays in hippocampal aging: statistical profiling identifies novel processes correlated with cognitive impairment. J. Neurosci. 23, 3807-3819.
4. Borisov, N., Aksamitiene, E., Kiyatkin, A., Legewie, S., Berkhout, J., Maiwald, T., et al. (2009). Systems-level interactions between insulin-EGF networks amplify mitogenic signaling. Mol. Syst. Biol. 5, 256. doi: 10.1038/msb.2009.19
5. Chowers, I., Liu, D., Farkas, R. H., Gunatilaka, T. L., Hackam, A. S., Bernstein, S. L., et al. (2003). Gene expression variation in the adult human retina. Hum. Mol. Genet. 12, 2881-2893. doi: 10.1093/hmg/ddg326
6. Danilov, A., Shaposhnikov, M., Plyusnina, E., Kogan, V., Fedichev, P., and Moskalev, A. (2013). Selective anticancer agents suppress aging in Drosophila. Oncotarget 4, 1507-1526.
7. De Magalhaes, J. P., Curado, J., and Church, G. M. (2009). Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics 25, 875-881. doi: 10.1093/bioinformatics/btp073
8. Gaman, L., Stoian, I., and Atanasiu, V. (2011). Can ageing be slowed?: Hormetic and redox perspectives. J. Med. Life 4, 346-351.
9. Gems, D., and Partridge, L. (2008). Stress-response hormesis and aging: "that which does not kill us makes us stronger." Cell Metab. 7, 200-203. doi: 10.1016/j.cmet.2008.01.001
10. Hong, M. G., Myers, A. J., Magnusson, P. K., and Prince, J. A. (2008). Transcriptome-wide assessment of human brain and lymphocyte senescence. PLoS ONE 3:e3024. doi: 10.1371/journal.pone.0003024
11. Horvath, S. (2013). DNA methylation age of human tissues and cell types. Genome Biol. 14:R115. doi: 10.1186/gb-2013-14-10-r115
12. Horvath, S., Zhang, Y., Langfelder, P., Kahn, R. S., Boks, M. P., Van Eijk, K., et al. (2012). Aging effects on DNA methylation modules in human brain and blood tissue. Genome Biol. 13:R97. doi: 10.1186/gb-2012-13-10-r97
13. Imoto, S., Savoie, C. J., Aburatani, S., Kim, S., Tashiro, K., Kuhara, S., et al. (2003). Use of gene networks for identifying and validating drug targets. J. Bioinform. Comput. Biol. 1, 459-474. doi: 10.1142/S0219720003000290
14. Kamburov, A., Pentchev, K., Galicka, H., Wierling, C., Lehrach, H., and Herwig, R. (2011). ConsensusPathDB: toward a more complete picture of cell biology. Nucleic Acids Res. 39, D712-D717. doi: 10.1093/nar/gkq1156
15. Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., and Hattori, M. (2004). The KEGG resource for deciphering the genome. Nucleic Acids Res. 32, D277-D280. doi: 10.1093/nar/gkh063
16. Kennedy, B. (2012). Gerontology: more funding for studies of ageing. Nature 487:39. doi: 10.1038/487039a
17. Kennedy, B. K., and Pennypacker, J. K. (2013). Drugs that modulate aging: the promising yet difficult path ahead. Transl. Res. doi: 10.1016/j.trsl.2013.11.007. [Epub ahead of print].
18. Kim, E. B., Fang, X., Fushan, A. A., Huang, Z., Lobanov, A. V., Han, L., et al. (2011). Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature 479, 223-227. doi: 10.1038/nature10533
19. Kiyatkin, A., Aksamitiene, E., Markevich, N. I., Borisov, N. M., Hoek, J. B., and Kholodenko, B. N. (2006). Scaffolding protein Grb2-associated binder 1 sustains epidermal growth factor-induced mitogenic and survival signaling by multiple positive feedback loops. J. Biol. Chem. 281, 19925-19938. doi: 10.1074/jbc. M600482200
20. Kuzmin, D., Gogvadze, E., Kholodenko, R., Grzela, D. P., Mityaev, M., Vinogradova, T., et al. (2010). Novel strong tissue specific promoter for gene expression in human germ cells. BMC Biotechnol. 10:58. doi: 10.1186/1472-6750-10-58
21. Kuzmina, N. B., and Borisov, N. M. (2011). Handling complex rule-based models of mitogenic cell signaling (on the example of ERK Activation upon EGF Stimulation). Int. Proc. Chem. Biol. Environ. Eng. 5, 67-82.
22. Lehmann, G., Muradian, K. K., and Fraifeld, V. E. (2013). Telomere length and body temperature-independent determinants of mammalian longevity? Front. Genet. 4:111. doi: 10.3389/fgene.2013.00111
23. Loram, J., and Bodnar, A. (2012). Age-related changes in gene expression in tissues of the sea urchin Strongylocentrotus purpuratus. Mech. Ageing Dev. 133, 338-347. doi: 10.1016/j.mad.2012.03.012
24. Mendelsohn, A. R., and Larrick, J. W. (2013). The DNA methylome as a biomarker for epigenetic instability and human aging. Rejuvenation Res. 16, 74-77. doi: 10.1089/rej.2013.1414
25. Mityaev, M. V., Kopantzev, E. P., Buzdin, A. A., Vinogradova, T. V., and Sverdlov, E. D. (2010). Enhancer element potentially involved in human survivin gene promoter regulation in lung cancer cell lines. Biochemistry (Mosc.) 75, 182-191. doi: 10.1134/S0006297910020082
26. Moskalev, A. A., and Shaposhnikov, M. V. (2010). Pharmacological inhibition of phosphoinositide 3 and TOR kinases improves survival of Drosophila melanogaster. Rejuvenation Res. 13, 246-247. doi: 10.1089/rej.2009.0903
27. Moskalev, A., and Shaposhnikov, M. (2011). Pharmacological inhibition of NF-kappaB prolongs lifespan of Drosophila melanogaster. Aging (Albany NY) 3, 391-394.
28. Murphy, G. G., Shah, V., Hell, J. W., and Silva, A. J. (2006). Investigation of age-related cognitive decline using mice as a model system: neurophysiological correlates. Am. J. Geriatr. Psychiatry 14, 1012-1021. doi: 10.1097/01.JGP.0000209404.54310.b3
29. Park, S. K., Kim, K., Page, G. P., Allison, D. B., Weindruch, R., and Prolla, T. A. (2009). Gene expression profiling of aging in multiple mouse strains: identification of aging biomarkers and impact of dietary antioxidants. Aging Cell 8, 484-495. doi: 10.1111/j.1474-9726.2009.00496.x
30. Park, S. K., and Prolla, T. A. (2005). Gene expression profiling studies of aging in cardiac and skeletal muscles. Cardiovasc. Res. 66, 205-212. doi: 10.1016/j.cardiores.2005.01.005
31. Rattan, S. (2013). Aging is not a disease: implications for intervention. Aging Dis. 5. [Epub ahead of print].
32. Rodgerson, D. O., and Harris, A. G. (2011). A comparison of stem cells for therapeutic use. Stem Cell Rev. 7, 782-796. doi: 10.1007/s12015-011-9241-y
33. Savoie, C. J., Aburatani, S., Watanabe, S., Eguchi, Y., Muta, S., Imoto, S., et al. (2003). Use of gene networks from full genome microarray libraries to identify functionally relevant drug-affected genes and gene regulation cascades. DNA Res. 10, 19-25. doi: 10.1093/dnares/10.1.19
34. Tacutu, R., Craig, T., Budovsky, A., Wuttke, D., Lehmann, G., Taranukha, D., et al. (2013). Human ageing genomic resources: integrated databases and tools for the biology and genetics of ageing. Nucleic Acids Res. 41, D1027-D1033. doi: 10.1093/nar/gks1155
35. Trindade, L. S., Aigaki, T., Peixoto, A. A., Balduino, A., Manica Da Cruz, I. B., and Heddle, J. G. (2013). A novel classification system for evolutionary aging theories. Front. Genet. 4:25. doi: 10.3389/fgene.2013.00025
36. Tu, C.-T., and Chen, B.-S. (2013). New measurement methods of network robustness and response ability via microarray data. PLoS ONE 8:e55230. doi: 10.1371/journal.pone.0055230
37. Vaiserman, A. M., and Pasyukova, E. G. (2012). Epigenetic drugs: a novel anti-aging strategy? Front. Genet. 3:224. doi: 10.3389/fgene.2012.00224
38. Voronkov, A., and Krauss, S. (2013). Wnt/beta-catenin signaling and small molecule inhibitors. Curr. Pharm. Des. 19, 634-664. doi: 10.2174/138161213804581837
39. Weindruch, R., Kayo, T., Lee, C.-K., and Prolla, T. A. (2002). Gene expression profiling of aging using DNA microarrays. Mech. Ageing Dev. 123, 177-193. doi: 10.1016/S0047-6374(01)00344-X
40. Welle, S., Brooks, A. I., Delehanty, J. M., Needler, N., and Thornton, C. A. (2003). Gene expression profile of aging in human muscle. Physiol. Genomics 14, 149-159. doi: 10.1152/physiolgenomics.00049.2003
41. Wolters, S., and Schumacher, B. (2013). Genome maintenance and transcription integrity in aging and disease. Front. Genet. 4:19. doi: 10.3389/fgene.2013.00019
42. Xue, H., Xian, B., Dong, D., Xia, K., Zhu, S., Zhang, Z., et al. (2007). A modular network model of aging. Mol. Syst. Biol. 3, 147. doi: 10.1038/msb4100189
43. Ye, X., Linton, J. M., Schork, N. J., Buck, L. B., and Petrascheck, M. (2013). A pharmacological network for lifespan extension in Caenorhabditis elegans. Aging Cell. doi: 10.1111/acel.12163. [Epub ahead of print].
44. Yizhak, K., Gabay, O., Cohen, H., and Ruppin, E. (2013). Model-based identification of drug targets that revert disrupted metabolism and its application to ageing. Nat. Commun. 4:2632. doi: 10.1038/ncomms3632.
45. Zabolotneva, A. A., Bantysh, O., Suntsova, M. V., Efimova, N., Malakhova, G. V., Schumann, G. G., et al. (2012a). Transcriptional regulation of human-specific SVAF(1) retrotransposons by cis-regulatory MAST2 sequences. Gene 505, 128-136. doi: 10.1016/j.gene.2012.05.016
46. Zabolotneva, A. A., Zhavoronkov, A., Garazha, A. V., Roumiantsev, S. A., and Buzdin, A. A. (2012b). Characteristic patterns of microRNA expression in human bladder cancer. Front. Genet. 3:310. doi: 10.3389/fgene.2012.00310
47. Zahn, J. M., Poosala, S., Owen, A. B., Ingram, D. K., Lustig, A., Carter, A., et al. (2007). AGEMAP: a gene expression database for aging in mice. PLoS Genet. 3:e201. doi: 10.1371/journal.pgen.0030201
48. Zhavoronkov, A., and Cantor, C. R. (2011). Methods for structuring scientific knowledge from many areas related to aging research. PLoS ONE 6:e22597. doi: 10.1371/journal.pone.0022597
49. Zhavoronkov, A., and Litovchenko, M. (2013). Biomedical progress rates as new parameters for models of economic growth in developed countries. Int. J. Environ. Res. Public Health 10, 5936-5952. doi: 10.3390/ijerph10115936
50. Zhavoronkov, A., Smit-Mcbride, Z., Guinan, K. J., Litovchenko, M., and Moskalev, A. (2012). Potential therapeutic approaches for modulating expression and accumulation of defective lamin A in laminopathies and age-related diseases. J. Mol. Med. (Berl.) 90, 1361-1389. doi: 10.1007/s00109-012-0962-4