Pathway activation profiling reveals new insights into Age-related Macular Degeneration and provides avenues for therapeutic interventions

Aging

Volumn 6, Issue 12, 2014, Pages 1064-1075

  Makarev, Evgeny ^a   Cantor, Charles ^b,c   Zhavoronkov, Alex ^a,d   Buzdin, Anton ^a,e   Aliper, Alexander ^a   Csoka, Antonei Benjamin ^f,g  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b BOSTON UNIVERSITY   (United States)

^c Retrotope Inc   (United States)

^d Biogerontology Research Foundation   (United Kingdom)

^e Pathway Pharmaceuticals Limited   (Hong Kong)

^f Vision Genomics LLC   (United States)

^g HOWARD UNIVERSITY   (United States)

Author keywords

Age related Macular Degeneration; AMD; gene expression; signaling pathway activation strength; Transcriptome profiling

Indexed keywords

GENETIC MARKER;

BIOLOGY; CASE CONTROL STUDY; COMPUTER PROGRAM; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC DATABASE; GENETIC MARKER; GENETIC PREDISPOSITION; GENETICS; HUMAN; IMMUNOLOGY; MACULAR DEGENERATION; METABOLISM; PATHOLOGY; PHENOTYPE; PIGMENT EPITHELIUM; PROCEDURES;

CASE-CONTROL STUDIES; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; HUMANS; MACULAR DEGENERATION; PHENOTYPE; RETINAL PIGMENT EPITHELIUM; SOFTWARE DESIGN;

EID: 84920935309     PISSN: 19454589     EISSN: None     Source Type: Journal    
DOI: 10.18632/aging.100711     Document Type: Article

References (57)

1. Bourne RR, Stevens GA, White RA, Smith JL, Flaxman SR, Price H, Jonas JB, Keeffe J, Leasher J, Naidoo K, Pesudovs K, Resnikoff S and Taylor HR. Causes of vision loss worldwide, 1990-2010: a systematic analysis. The Lancet Global health. 2013; 1:e339-349.
2. Zhavoronkov A and Cantor CR. Methods for structuring scientific knowledge from many areas related to aging research. PloS one. 2011; 6:e22597.
3. Chakravarthy U, Wong TY, Fletcher A, Piault E, Evans C, Zlateva G, Buggage R, Pleil A and Mitchell P. Clinical risk factors for age-related macular degeneration: a systematic review and meta-analysis. BMC ophthalmology. 2010; 10:31.
4. Wong WL, Su X, Li X, Cheung CM, Klein R, Cheng CY and Wong TY. Global prevalence of age-related macular degeneration and disease burden projection for 2020 and 2040: a systematic review and meta-analysis. The Lancet Global health. 2014; 2:e106-116.
5. Zhavoronkov A and Litovchenko M. Biomedical progress rates as new parameters for models of economic growth in developed countries. International journal of environmental research and public health. 2013; 10:5936-5952.
6. Blagosklonny MV. How to save Medicare: the anti-aging remedy. Aging (Albany NY). 2012; 4:547-552.
7. Yonekawa Y and Kim IK. Clinical Characteristics and Current Treatment of Age-Related Macular Degeneration. Cold Spring Harbor perspectives in medicine. 2014; Epub ahead of print.
8. Cook HL, Patel PJ and Tufail A. Age-related macular degeneration: diagnosis and management. British medical bulletin. 2008; 85:127-149.
9. Cameron DJ, Yang Z, Gibbs D, Chen H, Kaminoh Y, Jorgensen A, Zeng J, Luo L, Brinton E, Brinton G, Brand JM, Bernstein PS, Zabriskie NA, et al. HTRA1 variant confers similar risks to geographic atrophy and neovascular age-related macular degeneration. Cell cycle (Georgetown, Tex). 2007; 6:1122-1125.
10. Zhu D, Deng X, Xu J and Hinton DR. What determines the switch between atrophic and neovascular forms of age related macular degeneration? - the role of BMP4 induced senescence. Aging (Albany NY). 2009; 1:740-745.
11. Li CM, Chung BH, Presley JB, Malek G, Zhang X, Dashti N, Li L, Chen J, Bradley K, Kruth HS and Curcio CA. Lipoprotein-like particles and cholesteryl esters in human Bruch's membrane: initial characterization. Investigative ophthalmology & visual science. 2005; 46:2576-2586.
12. Neale BM, Fagerness J, Reynolds R, Sobrin L, Parker M, Raychaudhuri S, Tan PL, Oh EC, Merriam JE, Souied E, Bernstein PS, Li B, Frederick JM, et al. Genome-wide association study of advanced age-related macular degeneration identifies a role of the hepatic lipase gene (LIPC). Proceedings of the National Academy of Sciences of the United States of America. 2010; 107:7395-7400.
13. Baird PN, Guida E, Chu DT, Vu HT and Guymer RH. The epsilon2 and epsilon4 alleles of the apolipoprotein gene are associated with age-related macular degeneration. Investigative ophthalmology & visual science. 2004; 45:1311-1315.
14. Yu Y, Reynolds R, Fagerness J, Rosner B, Daly MJ and Seddon JM. Association of variants in the LIPC and ABCA1 genes with intermediate and large drusen and advanced age-related macular degeneration. Investigative ophthalmology & visual science. 2011; 52:4663-4670.
15. Larrayoz IM, Huang JD, Lee JW, Pascual I and Rodriguez IR. 7-ketocholesterol-induced inflammation: involvement of multiple kinase signaling pathways via NFkappaB but independently of reactive oxygen species formation. Investigative ophthalmology & visual science. 2010; 51:4942-4955.
16. Tuo J, Grob S, Zhang K and Chan CC. Genetics of immunological and inflammatory components in age-related macular degeneration. Ocular immunology and inflammation. 2012; 20:27-36.
17. Sparrow JR, Ueda K and Zhou J. Complement dysregulation in AMD: RPE-Bruch's membrane-choroid. Molecular aspects of medicine. 2012; 33:436-445.
18. Huang Y, Li W and Kong AN. Anti-oxidative stress regulator NF-E2-related factor 2 mediates the adaptive induction of antioxidant and detoxifying enzymes by lipid peroxidation metabolite 4-hydroxynonenal. Cell & bioscience. 2012; 2:40.
19. Erridge C, Webb DJ and Spickett CM. Toll-like receptor 4 signalling is neither sufficient nor required for oxidised phospholipid mediated induction of interleukin-8 expression. Atherosclerosis. 2007; 193:77-85.
20. Carneiro AM, Costa R, Falcao MS, Barthelmes D, Mendonca LS, Fonseca SL, Goncalves R, Goncalves C, Falcao-Reis FM and Soares R. Vascular endothelial growth factor plasma levels before and after treatment of neovascular age-related macular degeneration with bevacizumab or ranibizumab. Acta ophthalmologica. 2012; 90:e25-30.
21. Nozaki M, Raisler BJ, Sakurai E, Sarma JV, Barnum SR, Lambris JD, Chen Y, Zhang K, Ambati BK, Baffi JZ and Ambati J. Drusen complement components C3a and C5a promote choroidal neovascularization. Proceedings of the National Academy of Sciences of the United States of America. 2006; 103:2328-2333.
22. Bandyopadhyay M and Rohrer B. Matrix metalloproteinase activity creates pro-angiogenic environment in primary human retinal pigment epithelial cells exposed to complement. Investigative ophthalmology & visual science. 2012; 53:1953-1961.
23. Moreira EF, Larrayoz IM, Lee JW and Rodriguez IR. 7-Ketocholesterol is present in lipid deposits in the primate retina: potential implication in the induction of VEGF and CNV formation. Investigative ophthalmology & visual science. 2009; 50:523-532.
24. Zhao C and Vollrath D. mTOR pathway activation in agerelated retinal disease. Aging. 2011; 3:346-347.
25. Zarbin MA and Rosenfeld PJ. Pathway-based therapies for age-related macular degeneration: an integrated survey of emerging treatment alternatives. Retina (Philadelphia, Pa). 2010; 30:1350-1367.
26. Kolosova NG, Muraleva NA, Zhdankina AA, Stefanova NA, Fursova AZ and Blagosklonny MV. Prevention of age-related macular degeneration-like retinopathy by rapamycin in rats. The American journal of pathology. 2012; 181:472-477.
27. Buzdin AA, Zhavoronkov A, Korzinkin M, Roumiantsev SA, Aliper AM, Venkova LS, Smirnov P and Borisov NM. The OncoFinder algorithm for minimizing the errors introduced by the high-throughput methods of transcriptome analysis. Frontiers in Molecular Biosciences. 2014; 1.
28. Borisov NM, Terekhanova NV, Aliper AM, Venkova LS, Smirnov PY, Roumiantsev S, Korzinkin MB, Zhavoronkov AA and Buzdin AA. Signaling pathway activation profiles make better markers of cancer than expression of individual genes. Oncotarget. 2014; 5:10198-10205.
29. Drier Y, Sheffer M and Domany E. Pathway-based personalized analysis of cancer. Proceedings of the National Academy of Sciences of the United States of America. 2013; 110:6388-6393.
30. Maftouh M, Belo AI, Avan A, Funel N, Peters GJ, Giovannetti E and Van Die I. Galectin-4 expression is associated with reduced lymph node metastasis and modulation of Wnt/beta-catenin signalling in pancreatic adenocarcinoma. Oncotarget. 2014; 5:5335-5349.
31. Morozevich GE, Kozlova NI, Ushakova NA, Preobrazhenskaya ME and Berman AE. Integrin alpha5beta1 simultaneously controls EGFR-dependent proliferation and Akt-dependent prosurvival signaling in epidermoid carcinoma cells. Aging (Albany NY). 2012; 4:368-374.
32. Zamkova M, Khromova N, Kopnin BP and Kopnin P. Rasinduced ROS upregulation affecting cell proliferation is connected with cell type-specific alterations of HSF1/SESN3/p21Cip1/WAF1 pathways. Cell cycle (Georgetown, Tex). 2013; 12:826-836.
33. Aliper AM, Frieden-Korovkina VP, Buzdin A, Roumiantsev SA and Zhavoronkov A. Interactome analysis of myeloid-derived suppressor cells in murine models of colon and breast cancer. Oncotarget. 2014; 5:11345-11353.
34. Spirin PV, Lebedev TD, Orlova NN, Gornostaeva AS, Prokofjeva MM, Nikitenko NA, Dmitriev SE, Buzdin AA, Borisov NM, Aliper AM, Garazha AV, Rubtsov PM, Stocking C, et al. Silencing AML1-ETO gene expression leads to simultaneous activation of both pro-apoptotic and proliferation signaling. Leukemia. 2014; 28:2222-2228.
35. Lezhnina K, Kovalchuk O, Zhavoronkov AA, Korzinkin MB, Zabolotneva AA, Shegay PV, Sokov DG, Gaifullin NM, Rusakov IG, Aliper AM, Roumiantsev SA, Alekseev BY, Borisov NM, et al. Novel robust biomarkers for human bladder cancer based on activation of intracellular signaling pathways. Oncotarget. 2014; 5:9022-9032.
36. Blagosklonny MV. Validation of anti-aging drugs by treating age-related diseases. Aging (Albany NY). 2009; 1:281-288.
37. Blagosklonny MV. Answering the ultimate question "what is the proximal cause of aging?". Aging (Albany NY). 2012; 4:861-877.
38. Newman AM, Gallo NB, Hancox LS, Miller NJ, Radeke CM, Maloney MA, Cooper JB, Hageman GS, Anderson DH, Johnson LV and Radeke MJ. Systems-level analysis of age-related macular degeneration reveals global biomarkers and phenotype-specific functional networks. Genome Medicine. 2012; 4:16.
39. Whitmore SS, Braun TA, Skeie JM, Haas CM, Sohn EH, Stone EM, Scheetz TE and Mullins RF. Altered gene expression in dry age-related macular degeneration suggests early loss of choroidal endothelial cells. Molecular vision. 2013; 19:2274-2297.
40. Hunter A, Spechler PA, Cwanger A, Song Y, Zhang Z, Ying GS, Hunter AK, Dezoeten E and Dunaief JL. DNA methylation is associated with altered gene expression in AMD. Investigative ophthalmology & visual science. 2012; 53:2089-2105.
41. Newman AM, Gallo NB, Hancox LS, Miller NJ, Radeke CM, Maloney MA, Cooper JB, Hageman GS, Anderson DH, Johnson LV and Radeke MJ. Systems-level analysis of age-related macular degeneration reveals global biomarkers and phenotype-specific functional networks. Genome Med. 2012; 4:16.
42. Segal E, Friedman N, Koller D and Regev A. A module map showing conditional activity of expression modules in cancer. Nature genetics. 2004; 36:1090-1098.
43. Mullins RF, Johnson MN, Faidley EA, Skeie JM and Huang J. Choriocapillaris vascular dropout related to density of drusen in human eyes with early age-related macular degeneration. Investigative ophthalmology & visual science. 2011; 52:1606-1612.
44. McLeod DS, Grebe R, Bhutto I, Merges C, Baba T and Lutty GA. Relationship between RPE and choriocapillaris in age-related macular degeneration. Investigative ophthalmology & visual science. 2009; 50:4982-4991.
45. Yuan X, Gu X, Crabb JS, Yue X, Shadrach K, Hollyfield JG and Crabb JW. Quantitative proteomics: comparison of the macular Bruch membrane/choroid complex from age-related macular degeneration and normal eyes. Molecular & cellular proteomics: MCP. 2010; 9:1031-1046.
46. Chao W and D'Amore PA. IGF2: epigenetic regulation and role in development and disease. Cytokine & growth factor reviews. 2008; 19:111-120.
47. Hamamura K, Zhang P and Yokota H. IGF2-driven PI3 kinase and TGFbeta signaling pathways in chondrogenesis. Cell biology international. 2008; 32:1238-1246.
48. Jonas JB, Tao Y, Neumaier M and Findeisen P. Monocyte chemoattractant protein 1, intercellular adhesion molecule 1, and vascular cell adhesion molecule 1 in exudative age-related macular degeneration. Archives of ophthalmology. 2010; 128:1281-1286.
49. Viola A and Luster AD. Chemokines and their receptors: drug targets in immunity and inflammation. Annual review of pharmacology and toxicology. 2008; 48:171-197.
50. Leung KW, Barnstable CJ and Tombran-Tink J. Bacterial endotoxin activates retinal pigment epithelial cells and induces their degeneration through IL-6 and IL-8 autocrine signaling. Molecular immunology. 2009; 46:1374-1386.
51. Wang ZY, Shen LJ, Tu L, Hu DN, Liu GY, Zhou ZL, Lin Y, Chen LH and Qu J. Erythropoietin protects retinal pigment epithelial cells from oxidative damage. Free radical biology & medicine. 2009; 46:1032-1041.
52. Shaw PX, Zhang L, Zhang M, Du H, Zhao L, Lee C, Grob S, Lim SL, Hughes G, Lee J, Bedell M, Nelson MH, Lu F, et al. Complement factor H genotypes impact risk of age-related macular degeneration by interaction with oxidized phospholipids. Proceedings of the National Academy of Sciences of the United States of America. 2012; 109:13757-13762.
53. Blagosklonny MV. Prospective treatment of age-related diseases by slowing down aging. The American journal of pathology. 2012; 181:1142-1146.
54. Moskalev AA, Aliper AM, Smit-McBride Z, Buzdin A and Zhavoronkov A. Genetics and epigenetics of aging and longevity. Cell cycle (Georgetown, Tex). 2014; 13:1063-1077.
55. Blagosklonny MV. Prevention of cancer by inhibiting aging. Cancer biology & therapy. 2008; 7:1520-1524.
56. Blagosklonny MV. Aging-suppressants: cellular senescence (hyperactivation) and its pharmacologic deceleration. Cell cycle (Georgetown, Tex). 2009; 8:1883-1887.
57. Bolstad BM, Irizarry RA, Astrand M and Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics (Oxford, England). 2003; 19:185-193.