The role of epigenetics in personalized medicine: Challenges and opportunities

BMC Genomics

Volumn 8, Issue 1, 2015, Pages

  Rasool, Mahmood ^a   Malik, Arif ^b   Naseer, Muhammad Imran ^a   Manan, Abdul ^b   Ansari, Shakeel Ahmed ^a   Begum, Irshad ^b   Qazi, Mahmood Husain ^b   Pushparaj, Peter Natesan ^a   Abuzenadah, Adel M ^a   Al Qahtani, Mohammed Hussein ^a   Kamal, Mohammad Amjad ^a   Gan, Siew Hua ^c  

^a KING ABDULAZIZ UNIVERSITY   (Saudi Arabia)

^b UNIVERSITY OF LAHORE   (Pakistan)

^c SCHOOL OF HEALTH SCIENCES   (Malaysia)

Author keywords

[No Author keywords available]

Indexed keywords

B RAF KINASE; DNA METHYLTRANSFERASE;

ALK GENE; BRAF GENE; CANCER THERAPY; CARCINOGENESIS; COPY NUMBER VARIATION; CPG ISLAND; DNA METHYLATION; EPIGENETICS; GENE; GENETIC SCREENING; GENETIC VARIABILITY; HUMAN; MOLECULARLY TARGETED THERAPY; ONCOGENE K RAS; PERSONALIZED MEDICINE; PHARMACOGENOMICS; REVIEW; GENETIC EPIGENESIS; GENOMICS; PHARMACOGENETICS; PROCEDURES;

EPIGENESIS, GENETIC; GENETIC TESTING; GENOMICS; HUMANS; PHARMACOGENETICS; PRECISION MEDICINE;

EID: 84928339162     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1755-8794-8-S1-S5     Document Type: Review

References (74)

1. Heijmans BT, Tobi EW, Stein AD, Putter H, Blauw GJ, Susser ES, Slagboom PE, Lumey LH: Persistent epigenetic differences associated with prenatal exposure to famine in humans. Proc Natl Acad Sci 2008, 105:17046-17049.
2. McGowan PO, Sasaki A, D'Alessio AC, Dymov S, Labonté B, Szyf M, Turecki G, Meaney MJ: Epigenetic regulation of the glucocorticoid receptor in human brain associates with childhood abuse. Nat Neurosci 2009, 12:342-348.
3. Jirtle RL, Skinner MK: Environmental epigenomics and disease susceptibility. Nat Rev Genet 2007, 8:253-262.
4. Sadikoric B, Al-Romaih K, Squire JA, Zielinske M: Causes and Consequences of Genetic and Epigenetic Alterations in Human Cancer. Current Genomic 2008, 9:394-408.
5. Mikkelson TS: Genome-wide maps of chromatin state in Pluripotent and Lineage-committed cells. Nature 2007, 448:553-560.
6. Choi SW, Friso S: Epigenetics: A New Bridge between Nutrition and Health. American society for Nutrition. Adv Nutr 2010, 1:8-16.
7. Hirst M, Marra MA: Epigenetics and human disease. Int J Biochem Cell Biol 2009, 41:136-146.
8. Feinberg AP: Phenotypic plasticity and the epigenetics of human disease. Nature 2007, 447:433-440.
9. Bjornsson HT, Fallin MD, Feinberg AP: An integrated epigenetic and genetic approach to common human disease. Trends Genet 2004, 20:350-358.
10. Richardson B: Primer: epigenetics of autoimmunity. Nat Clin Pract Rheumatol 2007, 3:521-527.
11. Mehler MF: Epigenetics and the nervous system. Ann Neurol 2008, 64:602-617.
12. Petronis A: The origin of schizophrenia: genetic thesis, epigenetic antithesis, and resolving synthesis. Biol Psychiatry 2004, 55:965-970.
13. Esteller M: Epigenetics in cancer. N Engl J Med 2008, 358:1148-1159.
14. Feinberg AP, Tycko B: The history of cancer epigenetics. Nat Rev Cancer 2004, 4:143-153.
15. Esteller M: Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet 2007, 8:286-298.
16. Jones PA, Baylin SB: The epigenomics of cancer. Cell 2007, 128:683-692.
17. Wang Y: An evaluation of new criteria for CpG islands in the human genome as gene markers. Bioinformatics 2004, 20:1170-1177.
18. Momparler RL: Cancer Epigenetics. Oncogene 2003, 22:6479-6483.
19. Chang X, Blumenthal RM: Coordinated chromatin control: Structural and Functional linkage of DNA and histone methylation. Biochemistry 2010, 49:2999-3008.
20. Kim JK, Samaranayake M, Pradhan S: Epigenetic mechanisms in mammals. Cell Mol Life Sci 2009, 66:596-612.
21. Corti O, Lesage S, Brice A: What genetics tells us about the causes and mechanisms of Parkinson's disease. Physiol Rev 2011, 91:1161-1218.
22. Malzac P, Webber H, Moncla A, Graham JM, Kukolich M, Williams C, Pagon RA, Ramsdell LA, Kishino T, Wagstaff J: Mutation analysis of UBE3A in Angelman syndrome patients. Am J Hum Genet 1998, 62:1353-1360.
23. Parsons JL, Tait PS, Finch D, Dianova II, Edelmann MJ, Khoronenkova SV, Kessler BM, Sharma RA, McKenna WG, Dianov GL: Ubiquitin ligase ARF-BP1/Mule modulates base excision repair. EMBO J 2009, 28:3207-3215.
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, Gécz J: Submicroscopic duplications of the hydroxysteroid dehydrogenase HSD17B10 and the E3 ubiquitin ligase HUWE1 are associated with mental retardation. Am J Hum Genet 2008, 82:432-443.
25. Tzvetkov N, Breuer P: Josephin domain-containing proteins from a variety of species are active de-ubiquitination enzymes. Biol Chem 2007, 388:973-978.
26. Latif F, Tory K, Gnarra J, Yao M, Duh FM, Orcutt ML, Stackhouse T, Kuzmin I, Modi W, Geil L: Identification of the von Hippel-Lindau disease tumor suppressor gene. Science 1993, 260:1317-1320.
27. Bignell GR, Warren W, Seal S, Takahashi M, Rapley E, Barfoot R, Green H, Brown C, Biggs PJ, Lakhani SR: Identification of the familial cylindromatosis tumour-suppressor gene. Nat Genet 2000, 25:160-165.
28. Marine JC: Spotlight on the role of COP1 in tumorigenesis. Nat Rev Cancer 2012, 12:455-464.
29. Fraile JM, Quesada V, Rodriguez D, Freije JM, Lopez-Otin C: Deubiquitinases in cancer: new functions and therapeutic options. Oncogene 2012, 31:2373-2388.
30. Hussain S, Zhang Y, Galardy PJ: DUBs and cancer: the role of deubiquitinating enzymes as oncogenes, non-oncogenes and tumor suppressors. Cell Cycle 2009, 8:1688-1697.
31. Ginsburg GS, Willard HF: Genomic and personalized medicine: foundations and applications. Translational Research 2009, 154:277-287.
32. Willard H: Organization, variation and expression of the human genome as a foundation of genomic and personalized medicine. In Genomic and personalized medicine. 1st edition. Edited by: Willard H, Ginsburg GS. Durham, NC: Elsevier; 2009.
33. West M, Ginsburg GS, Huang A, Nevins J: Embracing the complexity of genomic data for personalized medicine. Genome Res 2006, 16:559-566.
34. Ginsburg GS, McCarthy J: Personalized medicine and the pharmaceutical industry. Trends Biotechnol 2001, 19:491-496.
35. Willard H, Angrist M, Ginsburg G: Genomic medicine: Genetic variation and its impact on the future of health care. Phil Trans R Soc B 2005, 360:1543-1550.
36. Pirmohamed M: Pharmacogenetics: Past, present and future. Drug Discov Today 2011, 16:852-861.
37. Snyderman R: The role of genomics in enabling prospective health care. In Genomic and personalized medicine. Edited by: Willard H, Ginsburg GS. Durham, NC: Elsevier; 2009:378-385.
38. Phillips KA, Veenstra DL, Oren E, Lee JK, Sadee W: Potential role of Pharmacogenomics in reducing adverse drug reactions: a systematic review. JAMA 2001, 286:2270-2279.
39. Huang Y, Anderle P, Bussey KJ, Barbacioru C, Shankavaram U, Dai Z, Reinhold WC, Papp A, Weinstein JN, Sadee W: Membrane transporters and channels: role of the transportome in cancer chemosensitivity and chemoresistance. Cancer Res 2004, 64:4294-4301.
40. Jain KK: Applications of AmpliChip® CYP450. Mol Diag 2005, 9:119-127.
41. Druker BJ, Talpaz M, Resta DJ, Peng B, Buchdunger E, Ford JM, Lydon NB, Kantarjian H, Capdeville R, Ohno-Jones S, Sawyers CL: Efficacy and safety of a specific inhibitor of the BCR-ABL tyrosine kinase in chronic myeloid leukemia. N Engl J Med 2001, 344:1031-1037.
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: Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. N Engl J Med 2004, 350:2129-2139.
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: Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that over-expresses HER2. N Engl J Med 2001, 344:783-792.
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: Current View from Alzheimer Disease to Type 2 Diabetes Mellitus. CNS Neurol Disord Drug Targets 2014,13(3):533-42.
45. Modrek B, Lee C: A genomic view of alternative splicing. Nat Genet 2002, 30:13-19.
46. Bray NJ, Buckland PR, Williams NM, Williams HJ, Norton N, Owen MJ, O'Donovan MC: A haplotype implicated in schizophrenia susceptibility is associated with reduced COMT expression in human brain. Am J Hum Genet 2003, 73:152-161.
47. Petronis A: Epigenetics and bipolar disorder: new opportunities and challenges. Am J Med Genet 2003, 123:65-75.
48. Rakyan VK, Blewitt ME, Druker R, Preis JI, Whitelaw E: Metastable epialleles in mammals. Trends Genet 2002, 18:348-351.
49. Laird PW: Cancer epigenetics. Hum Mol Genet 2005, 14:65-76.
50. Byrd JC, Marcucci G, Parthun MR, Xiao JJ, Klisovic RB, Moran M, Lin TS, Liu S, Sklenar AR, Davis ME: A phase 1 and pharmacodynamic study of depsipeptide (FK228) in chronic lymphocytic leukemia and acute myeloid leukemia. Blood 2005, 105:959-967.
51. Dowell JE, Minna JD: Cancer chemotherapy targeted at reactivating the expression of epigenetically inactivated genes. J Clin Oncol 2004, 22:1353-1355.
52. Esteller M, Garcia-Foncillas J, Andion E, Goodman SN, Hidalgo OF, Vanaclocha V, Baylin SB, Herman JG: Inactivation of the DNA-repair gene MGMT and the clinical response of gliomas to alkylating agents. N Engl J Med 2000, 343:1350-1354.
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, López-Guillermo A, Grogan TM, Miller TP, LeBlanc M, Ott G, Kvaloy S, Delabie J, Holte H, Krajci P, Stokke T, Staudt LM: The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. N Engl J Med 2002, 346:1937-1947.
54. Van't 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: Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002, 415:530-536.
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: A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med 2004, 351:2817-2826.
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: Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet 2005, 365:671-679.
57. Dave SS, Fu K, Wright GW, Lam LT, Kluin P, Boerma EJ, Greiner TC, Weisenburger DD, Rosenwald A, Ott G, Müller-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: Molecular diagnosis of Burkitt's lymphoma. N Engl J Med 2006, 354:2431-2442.
58. Lo SS, Mumby PB, Norton J, Rychlik K, Smerage J, Kash J, Chew HK, Gaynor ER, Hayes DF, Epstein A, Albain KS: 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 2010, 28:1671-1676.
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: 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 2010, 28:3937-3944.
60. Paez JG, Jänne 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: EGFR mutations in lung cancer: Correlation with clinical response to gefitinib therapy. Science 2004, 304:1497-1500.
61. Gomes AR, Zhao F, Lam EWF: Role and regulation of the forkhead transcription factors FOXO3a and FOXM1 in carcinogenesis and drug resistance. Chin J Cancer 2013, 32:366-371.
62. Maria E, Gil C: Targeting the PI3K/AKT/mTOR pathway in estrogen receptor-positive breast cancer. Cancer treatment reviews 2014. 10.1016/j.ctrv.2014.03. 004
63. Yan M, Liu QQ: Targeted therapy: tailoring cancer treatment. Chin J Cancer 2013,32(7):363-364.
64. Couzin-Frankel J: NIH Wants to Hear About Genetic Tests. Science Insider 2010.
65. Mangravite LM, Thorn CF, Krauss RM: Clinical implications of pharmacogenomics of statin treatment. Pharmacogenomics J 2006, 6:360-74.
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: Beta1-adrenergic receptor polymorphisms and left ventricular remodeling changes in response to beta-blocker therapy. Pharmacogenet Genomics 2005, 15:227-234.
67. Rieder MJ, Reiner AP, Gage BF, Nickerson DA, Eby CS, McLeod HL, Blough DK, Thummel KE, Veenstra DL, Rettie AE: Effect of VKORC1 haplotypes on transcriptional regulation and warfarin dose. N Engl J Med 2005, 352:2285-2293.
68. Winslow R: Major shift in war on cancer. Wall Street Journal 2011.
69. Ries LAG, Harkins D, Krapcho M, et al.: SEER Cancer Statistics Review, 1975-2003. 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, Láng I, Nitz U, Iwata H, Thomssen C, Lohrisch C, Suter TM, Rüschoff J, Suto T, Greatorex V, Ward C, Straehle C, McFadden E, Dolci MS, Gelber RD: Trastuzumab after adjuvant chemotherapy in HER2-positive breast cancer. N Engl J Med 2005, 353:1659-1672.
72. Romond EH, Perez EA, Bryant J, Suman VJ, Geyer CE Jr, 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: Trastuzumab plus adjuvant chemotherapy for operable HER2-positive breast cancer. N Engl J Med 2005, 353:1673-1684.
73. Lièvre A, Bachet JB, Le Corre D, Boige V, Landi B, Emile JF, Côté JF, Tomasic G, Penna C, Ducreux M, Rougier P, Penault-Llorca F, Laurent-Puig P: KRAS mutation status is predictive of response to cetuximab therapy in colorectal cancer. Cancer Res 2006, 66:3992-3995.
74. National Comprehensive Cancer Network: Guidelines in Oncology: Colon Cancer. v.2. NCCN website 2009. Available at: http://www.nccn.org/professionals/physician_gls/PDF/colon.pdf