The role of epigenetics in personalized medicine: challenges and opportunities

详细信息    查看全文

• 作者：Mahmood Rasool (19) (20)
  Arif Malik (21)
  Muhammad Imran Naseer (19)
  Abdul Manan (21)
  Shakeel Ahmed Ansari (19)
  Irshad Begum (21)
  Mahmood Husain Qazi (22)
  Peter Natesan Pushparaj (19)
  Adel M Abuzenadah (19) (20)
  Mohammed Hussein Al-Qahtani (19)
  Mohammad Amjad Kamal (23)
  Peter Natesan Pushparaj (19)
  Siew Hua Gan (24)
  
  19. Center of Excellence in Genomic Medicine Research (CEGMR) ; King Abdulaziz University ; Jeddah ; Saudi Arabia
  20. KACST Technology Innovation Center in Personalized Medicine ; King Abdulaziz University ; Jeddah ; Kingdom of Saudi Arabia
  21. Institute of Molecular Biology and Biotechnology ; (IMBB) ; the University of Lahore ; Lahore ; Pakistan
  22. Center for Research in Molecular Medicine (CRiMM) ; The University of Lahore ; Kragujevac ; Pakistan
  23. King Fahd Medical Research Center ; King Abdulaziz University ; Jeddah ; Saudi Arabia
  24. Human Genome Centre ; School of Medical Sciences ; Universiti Sains Malaysia ; 16150 ; Kubang Kerian ; Kelantan ; Malaysia
  
• 刊名：BMC Medical Genomics
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：8
• 期：1-supp
• 全文大小：406 KB
• 参考文献：1. Heijmans, BT, Tobi, EW, Stein, AD, Putter, H, Blauw, GJ, Susser, ES, Slagboom, PE, Lumey, LH (2008) Persistent epigenetic differences associated with prenatal exposure to famine in humans. Proc Natl Acad Sci 105: pp. 17046-17049 CrossRef
  2. McGowan, PO, Sasaki, A, D'Alessio, AC, Dymov, S, Labont茅, B, Szyf, M, Turecki, G, Meaney, MJ (2009) Epigenetic regulation of the glucocorticoid receptor in human brain associates with childhood abuse. Nat Neurosci 12: pp. 342-348 CrossRef
  3. Jirtle, RL, Skinner, MK (2007) Environmental epigenomics and disease susceptibility. Nat Rev Genet 8: pp. 253-262 CrossRef
  4. Sadikoric, B, Al-Romaih, K, Squire, JA, Zielinske, M (2008) Causes and Consequences of Genetic and Epigenetic Alterations in Human Cancer. Current Genomic 9: pp. 394-408 CrossRef
  5. Mikkelson, TS (2007) Genome-wide maps of chromatin state in Pluripotent and Lineage-committed cells. Nature 448: pp. 553-560 CrossRef
  6. Choi, SW, Friso, S (2010) Epigenetics: A New Bridge between Nutrition and Health. American society for Nutrition. Adv Nutr 1: pp. 8-16 CrossRef
  7. Hirst, M, Marra, MA (2009) Epigenetics and human disease. Int J Biochem Cell Biol 41: pp. 136-146 CrossRef
  8. Feinberg, AP (2007) Phenotypic plasticity and the epigenetics of human disease. Nature 447: pp. 433-440 CrossRef
  9. Bjornsson, HT, Fallin, MD, Feinberg, AP (2004) An integrated epigenetic and genetic approach to common human disease. Trends Genet 20: pp. 350-358 CrossRef
  10. Richardson, B (2007) Primer: epigenetics of autoimmunity. Nat Clin Pract Rheumatol 3: pp. 521-527 CrossRef
  11. Mehler, MF (2008) Epigenetics and the nervous system. Ann Neurol 64: pp. 602-617 CrossRef
  12. Petronis, A (2004) The origin of schizophrenia: genetic thesis, epigenetic antithesis, and resolving synthesis. Biol Psychiatry 55: pp. 965-970 CrossRef
  13. Esteller, M (2008) Epigenetics in cancer. N Engl J Med 358: pp. 1148-1159 CrossRef
  14. Feinberg, AP, Tycko, B (2004) The history of cancer epigenetics. Nat Rev Cancer 4: pp. 143-153 CrossRef
  15. Esteller, M (2007) Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet 8: pp. 286-298 CrossRef
  16. Jones, PA, Baylin, SB (2007) The epigenomics of cancer. Cell 128: pp. 683-692 CrossRef
  17. Wang, Y (2004) An evaluation of new criteria for CpG islands in the human genome as gene markers. Bioinformatics 20: pp. 1170-1177 CrossRef
  18. Momparler, RL (2003) Cancer Epigenetics. Oncogene 22: pp. 6479-6483 CrossRef
  19. Chang, X, Blumenthal, RM (2010) Coordinated chromatin control: Structural and Functional linkage of DNA and histone methylation. Biochemistry 49: pp. 2999-3008 CrossRef
  20. Kim, JK, Samaranayake, M, Pradhan, S (2009) Epigenetic mechanisms in mammals. Cell Mol Life Sci 66: pp. 596-612 CrossRef
  21. Corti, O, Lesage, S, Brice, A (2011) What genetics tells us about the causes and mechanisms of Parkinson鈥檚 disease. Physiol Rev 91: pp. 1161-1218 CrossRef
  22. Malzac, P, Webber, H, Moncla, A, Graham, JM, Kukolich, M, Williams, C, Pagon, RA, Ramsdell, LA, Kishino, T, Wagstaff, J (1998) Mutation analysis of UBE3A in Angelman syndrome patients. Am J Hum Genet 62: pp. 1353-1360 CrossRef
  23. Parsons, JL, Tait, PS, Finch, D, Dianova, II, Edelmann, MJ, Khoronenkova, SV, Kessler, BM, Sharma, RA, McKenna, WG, Dianov, GL (2009) Ubiquitin ligase ARF-BP1/Mule modulates base excision repair. EMBO J 28: pp. 3207-3215 CrossRef
  24. Froyen, G, Corbett, M, Vandewalle, J, Jarvela, I, Lawrence, O, Meldrum, C, Bauters, M, Govaerts, K, Vandeleur, L, Van Esch, H, Chelly, J, Sanlaville, D, van Bokhoven, H, Ropers, HH, Laumonnier, F, Ranieri, E, Schwartz, CE, Abidi, F, Tarpey, PS, Futreal, PA, Whibley, A, Raymond, FL, Stratton, MR, Fryns, JP, Scott, R, Peippo, M, Sipponen, M, Partington, M, Mowat, D, Field, M, Hackett, A, Marynen, P, Turner, G, G茅cz, J (2008) Submicroscopic duplications of the hydroxysteroid dehydrogenase HSD17B10 and the E3 ubiquitin ligase HUWE1 are associated with mental retardation. Am J Hum Genet 82: pp. 432-443 CrossRef
  25. Tzvetkov, N, Breuer, P (2007) Josephin domain-containing proteins from a variety of species are active de-ubiquitination enzymes. Biol Chem 388: pp. 973-978 CrossRef
  26. Latif, F, Tory, K, Gnarra, J, Yao, M, Duh, FM, Orcutt, ML, Stackhouse, T, Kuzmin, I, Modi, W, Geil, L (1993) Identification of the von Hippel-Lindau disease tumor suppressor gene. Science 260: pp. 1317-1320 CrossRef
  27. Bignell, GR, Warren, W, Seal, S, Takahashi, M, Rapley, E, Barfoot, R, Green, H, Brown, C, Biggs, PJ, Lakhani, SR (2000) Identification of the familial cylindromatosis tumour-suppressor gene. Nat Genet 25: pp. 160-165 CrossRef
  28. Marine, JC (2012) Spotlight on the role of COP1 in tumorigenesis. Nat Rev Cancer 12: pp. 455-464 CrossRef
  29. Fraile, JM, Quesada, V, Rodriguez, D, Freije, JM, Lopez-Otin, C (2012) Deubiquitinases in cancer: new functions and therapeutic options. Oncogene 31: pp. 2373-2388 CrossRef
  30. Hussain, S, Zhang, Y, Galardy, PJ (2009) DUBs and cancer: the role of deubiquitinating enzymes as oncogenes, non-oncogenes and tumor suppressors. Cell Cycle 8: pp. 1688-1697 CrossRef
  31. Ginsburg, GS, Willard, HF (2009) Genomic and personalized medicine: foundations and applications. Translational Research 154: pp. 277-287 CrossRef
  32. Willard, H Organization, variation and expression of the human genome as a foundation of genomic and personalized medicine. In: Willard, H, Ginsburg, GS eds. (2009) Genomic and personalized medicine. Elsevier, Durham, NC
  33. West, M, Ginsburg, GS, Huang, A, Nevins, J (2006) Embracing the complexity of genomic data for personalized medicine. Genome Res 16: pp. 559-566 CrossRef
  34. Ginsburg, GS, McCarthy, J (2001) Personalized medicine and the pharmaceutical industry. Trends Biotechnol 19: pp. 491-496 CrossRef
  35. Willard, H, Angrist, M, Ginsburg, G (2005) Genomic medicine: Genetic variation and its impact on the future of health care. Phil Trans R Soc B 360: pp. 1543-1550 CrossRef
  36. Pirmohamed, M (2011) Pharmacogenetics: Past, present and future. Drug Discov Today 16: pp. 852-861 CrossRef
  37. Snyderman, R The role of genomics in enabling prospective health care. In: Willard, H, Ginsburg, GS eds. (2009) Genomic and personalized medicine. Elsevier, Durham, NC, pp. 378-385
  38. Phillips, KA, Veenstra, DL, Oren, E, Lee, JK, Sadee, W (2001) Potential role of Pharmacogenomics in reducing adverse drug reactions: a systematic review. JAMA 286: pp. 2270-2279 CrossRef
  39. Huang, Y, Anderle, P, Bussey, KJ, Barbacioru, C, Shankavaram, U, Dai, Z, Reinhold, WC, Papp, A, Weinstein, JN, Sadee, W (2004) Membrane transporters and channels: role of the transportome in cancer chemosensitivity and chemoresistance. Cancer Res 64: pp. 4294-4301 CrossRef
  40. Jain, KK (2005) Applications of AmpliChip庐 CYP450. Mol Diag 9: pp. 119-127
  41. Druker, BJ, Talpaz, M, Resta, DJ, Peng, B, Buchdunger, E, Ford, JM, Lydon, NB, Kantarjian, H, Capdeville, R, Ohno-Jones, S, Sawyers, CL (2001) Efficacy and safety of a specific inhibitor of the BCR-ABL tyrosine kinase in chronic myeloid leukemia. N Engl J Med 344: pp. 1031-1037 CrossRef
  42. Lynch, TJ, Bell, DW, Sordella, R, Gurubhagavatula, S, Okimoto, RA, Brannigan, BW, Harris, PL, Haserlat, SM, Supko, JG, Haluska, FG, Louis, DN, Christiani, DC, Settleman, J, Haber, DA (2004) Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. N Engl J Med 350: pp. 2129-2139 CrossRef
  43. Slamon, DJ, Leyland-Jones, B, Shak, S, Fuchs, H, Paton, V, Bajamonde, A, Fleming, T, Eiermann, W, Wolter, J, Pegram, M, Baselga, J, Norton, L (2001) Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that over-expresses HER2. N Engl J Med 344: pp. 783-792 CrossRef
  44. Rasool, M, Malik, A, Qazi, A, Sheikh, IA, Manan, A, Shaheen, S, Qazi, MH, Chaudhary, AG, Abuzenadah, AM, Asif, M, Alqahtani, MH, Iqbal, Z, Shaik, MM, Gan, SH, Kamal, MA (2014) Current View from Alzheimer Disease to Type 2 Diabetes Mellitus. CNS Neurol Disord Drug Targets 13: pp. 533-42 CrossRef
  45. Modrek, B, Lee, C (2002) A genomic view of alternative splicing. Nat Genet 30: pp. 13-19 CrossRef
  46. Bray, NJ, Buckland, PR, Williams, NM, Williams, HJ, Norton, N, Owen, MJ, O鈥橠onovan, MC (2003) A haplotype implicated in schizophrenia susceptibility is associated with reduced COMT expression in human brain. Am J Hum Genet 73: pp. 152-161 CrossRef
  47. Petronis, A (2003) Epigenetics and bipolar disorder: new opportunities and challenges. Am J Med Genet 123: pp. 65-75 CrossRef
  48. Rakyan, VK, Blewitt, ME, Druker, R, Preis, JI, Whitelaw, E (2002) Metastable epialleles in mammals. Trends Genet 18: pp. 348-351 CrossRef
  49. Laird, PW (2005) Cancer epigenetics. Hum Mol Genet 14: pp. 65-76 CrossRef
  50. Byrd, JC, Marcucci, G, Parthun, MR, Xiao, JJ, Klisovic, RB, Moran, M, Lin, TS, Liu, S, Sklenar, AR, Davis, ME (2005) A phase 1 and pharmacodynamic study of depsipeptide (FK228) in chronic lymphocytic leukemia and acute myeloid leukemia. Blood 105: pp. 959-967 CrossRef
  51. Dowell, JE, Minna, JD (2004) Cancer chemotherapy targeted at reactivating the expression of epigenetically inactivated genes. J Clin Oncol 22: pp. 1353-1355 CrossRef
  52. Esteller, M, Garcia-Foncillas, J, Andion, E, Goodman, SN, Hidalgo, OF, Vanaclocha, V, Baylin, SB, Herman, JG (2000) Inactivation of the DNA-repair gene MGMT and the clinical response of gliomas to alkylating agents. N Engl J Med 343: pp. 1350-1354 CrossRef
  53. Rosenwald, A, Wright, G, Chan, WC, Connors, JM, Campo, E, Fisher, RI, Gascoyne, RD, Muller-Hermelink, HK, Smeland, EB, Giltnane, JM, Hurt, EM, Zhao, H, Averett, L, Yang, L, Wilson, WH, Jaffe, ES, Simon, R, Klausner, RD, Powell, J, Duffey, PL, Longo, DL, Greiner, TC, Weisenburger, DD, Sanger, WG, Dave, BJ, Lynch, JC, Vose, J, Armitage, JO, Montserrat, E, L贸pez-Guillermo, A, Grogan, TM, Miller, TP, LeBlanc, M, Ott, G, Kvaloy, S, Delabie, J, Holte, H, Krajci, P, Stokke, T, Staudt, LM (2002) The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. N Engl J Med 346: pp. 1937-1947 CrossRef
  54. Van鈥檛 Veer, LJ, Dai, H, Van de Vijver, MJ, He, YD, Hart, AA, Mao, M, Peterse, HL, van der Kooy, K, Marton, MJ, Witteveen, AT, Schreiber, GJ, Kerkhoven, RM, Roberts, C, Linsley, PS, Bernards, R, Friend, SH (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature 415: pp. 530-536 CrossRef
  55. Paik, S, Shak, S, Tang, G, Kim, C, Baker, J, Cronin, M, Baehner, FL, Walker, MG, Watson, D, Park, T, Hiller, W, Fisher, ER, Wickerham, DL, Bryant, J, Wolmark, N (2004) A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med 351: pp. 2817-2826 CrossRef
  56. Wang, Y, Klijn, JG, Zhang, Y, Sieuwerts, AM, Look, MP, Yang, F, Talantov, D, Timmermans, M, Meijer-van Gelder, ME, Yu, J, Jatkoe, T, Berns, EM, Atkins, D, Foekens, JA (2005) Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet 365: pp. 671-679 CrossRef
  57. Dave, SS, Fu, K, Wright, GW, Lam, LT, Kluin, P, Boerma, EJ, Greiner, TC, Weisenburger, DD, Rosenwald, A, Ott, G, M眉ller-Hermelink, HK, Gascoyne, RD, Delabie, J, Rimsza, LM, Braziel, RM, Grogan, TM, Campo, E, Jaffe, ES, Dave, BJ, Sanger, W, Bast, M, Vose, JM, Armitage, JO, Connors, JM, Smeland, EB, Kvaloy, S, Holte, H, Fisher, RI, Miller, TP, Montserrat, E, Wilson, WH, Bahl, M, Zhao, H, Yang, L, Powell, J, Simon, R, Chan, WC, Staudt, LM (2006) Molecular diagnosis of Burkitt鈥檚 lymphoma. N Engl J Med 354: pp. 2431-2442 CrossRef
  58. Lo, SS, Mumby, PB, Norton, J, Rychlik, K, Smerage, J, Kash, J, Chew, HK, Gaynor, ER, Hayes, DF, Epstein, A, Albain, KS (2010) Prospective multi-center study of the impact of the 21-gene recurrence score assay on medical oncologist and patient adjuvant breast cancer treatment selection. J Clin Oncol 28: pp. 1671-1676 CrossRef
  59. O'Connell, MJ, Lavery, I, Yothers, G, Paik, S, Clark-Langone, KM, Lopatin, M, Watson, D, Baehner, FL, Shak, S, Baker, J, Cowens, JW, Wolmark, N (2010) Relationship between tumor gene expression and recurrence in four independent studies of patients with stage II/III colon cancer treated with surgery alone or surgery plus adjuvant fluorouracil plus leucovorin. J Clin Oncol 28: pp. 3937-3944 CrossRef
  60. Paez, JG, J盲nne, PA, Lee, JC, Tracy, S, Greulich, H, Gabriel, S, Herman, P, Kaye, FJ, Lindeman, N, Boggon, TJ, Naoki, K, Sasaki, H, Fujii, Y, Eck, MJ, Sellers, WR, Johnson, BE, Meyerson, M (2004) EGFR mutations in lung cancer: Correlation with clinical response to gefitinib therapy. Science 304: pp. 1497-1500 CrossRef
  61. Gomes, AR, Zhao, F, Lam, EWF (2013) Role and regulation of the forkhead transcription factors FOXO3a and FOXM1 in carcinogenesis and drug resistance. Chin J Cancer 32: pp. 366-371 CrossRef
  62. Maria, E, Gil, C (2014) Targeting the PI3K/AKT/mTOR pathway in estrogen receptor-positive breast cancer. Cancer treatment reviews.
  63. Yan, M, Liu, QQ (2013) Targeted therapy: tailoring cancer treatment. Chin J Cancer 32: pp. 363-364 CrossRef
  64. Couzin-Frankel, J (2010) NIH Wants to Hear About Genetic Tests. Science Insider.
  65. Mangravite, LM, Thorn, CF, Krauss, RM (2006) Clinical implications of pharmacogenomics of statin treatment. Pharmacogenomics J 6: pp. 360-74 CrossRef
  66. Terra, SG, Hamilton, KK, Pauly, DF, Lee, CR, Patterson, JH, Adams, KF, Schofield, RS, Belgado, BS, Hill, JA, Aranda, JM, Yarandi, HN, Johnson, JA (2005) Beta1-adrenergic receptor polymorphisms and left ventricular remodeling changes in response to beta-blocker therapy. Pharmacogenet Genomics 15: pp. 227-234 CrossRef
  67. Rieder, MJ, Reiner, AP, Gage, BF, Nickerson, DA, Eby, CS, McLeod, HL, Blough, DK, Thummel, KE, Veenstra, DL, Rettie, AE (2005) Effect of VKORC1 haplotypes on transcriptional regulation and warfarin dose. N Engl J Med 352: pp. 2285-2293 CrossRef
  68. Winslow, R (2011) Major shift in war on cancer. Wall Street Journal.
  69. Ries LAG, Harkins D, Krapcho M, / et al.: / SEER Cancer Statistics Review, 1975鈥?003. National Cancer Institute; http://www.seer.cancer.gov/csr/1975_2003/
  70. National Cancer Institute BRCA1 and BRCA2 fact sheet / NCI website Available at: http://www.cancer.gov/cancertopics/factsheet/risk/brca
  71. Piccart-Gebhart, MJ, Procter, M, Leyland-Jones, B, Goldhirsch, A, Untch, M, Smith, I, Gianni, L, Baselga, J, Bell, R, Jackisch, C, Cameron, D, Dowsett, M, Barrios, CH, Steger, G, Huang, CS, Andersson, M, Inbar, M, Lichinitser, M, L谩ng, I, Nitz, U, Iwata, H, Thomssen, C, Lohrisch, C, Suter, TM, R眉schoff, J, Suto, T, Greatorex, V, Ward, C, Straehle, C, McFadden, E, Dolci, MS, Gelber, RD (2005) Trastuzumab after adjuvant chemotherapy in HER2-positive breast cancer. N Engl J Med 353: pp. 1659-1672 CrossRef
  72. Romond, EH, Perez, EA, Bryant, J, Suman, VJ, Geyer, CE, Davidson, NE, Tan-Chiu, E, Martino, S, Paik, S, Kaufman, PA, Swain, SM, Pisansky, TM, Fehrenbacher, L, Kutteh, LA, Vogel, VG, Visscher, DW, Yothers, G, Jenkins, RB, Brown, AM, Dakhil, SR, Mamounas, EP, Lingle, WL, Klein, PM, Ingle, JN, Wolmark, N (2005) Trastuzumab plus adjuvant chemotherapy for operable HER2-positive breast cancer. N Engl J Med 353: pp. 1673-1684 CrossRef
  73. Li猫vre, A, Bachet, JB, Le Corre, D, Boige, V, Landi, B, Emile, JF, C么t茅, JF, Tomasic, G, Penna, C, Ducreux, M, Rougier, P, Penault-Llorca, F, Laurent-Puig, P (2006) KRAS mutation status is predictive of response to cetuximab therapy in colorectal cancer. Cancer Res 66: pp. 3992-3995 CrossRef
  Guidelines in Oncology: Colon Cancer. v.2. NCCN website.
  
• 刊物主题：Human Genetics; Microarrays;
• 出版者：BioMed Central
• ISSN：1755-8794

文摘

Epigenetic alterations are considered to be very influential in both the normal and disease states of an organism. These alterations include methylation, acetylation, phosphorylation, and ubiquitylation of DNA and histone proteins (nucleosomes) as well as chromatin remodeling. Many diseases, such as cancers and neurodegenerative disorders, are often associated with epigenetic alterations. DNA methylation is one important modification that leads to disease. Standard therapies are given to patients; however, few patients respond to these drugs, because of various molecular alterations in their cells, which may be partially due to genetic heterogeneity and epigenetic alterations. To realize the promise of personalized medicine, both genetic and epigenetic diagnostic testing will be required. This review will discuss the advances that have been made as well as the challenges for the future.