Epigenetics primer: Why the clinician should care about epigenetics

Pharmacotherapy

Volumn 33, Issue 12, 2013, Pages 1362-1368

  Duarte, Julio D ^a  

^a UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

Author keywords

DNA methylation; epigenetics; epigenomics; histone modifications; miRNA; pharmacoepigenetics

Indexed keywords

5 AZA 2' DEOXYCYTIDINE; AZACITIDINE; DNA; FOMIVIRSEN; HISTONE; MIPOMERSEN; ROMIDEPSIN; UNTRANSLATED RNA; VORINOSTAT;

ALZHEIMER DISEASE; ARTICLE; ATAXIA; CUTANEOUS T CELL LYMPHOMA; CYTOMEGALOVIRUS RETINITIS; DNA METHYLATION; DNA MODIFICATION; DRUG INDICATION; DRUG MECHANISM; DRUG RESPONSE; EPIGENETICS; FAMILIAL HYPERCHOLESTEROLEMIA; GENE EXPRESSION; GENETIC REGULATION; HISTONE MODIFICATION; HUMAN; MULTIPLE SCLEROSIS; MYELODYSPLASTIC SYNDROME; NEOPLASM; PHARMACOGENETICS;

DNA METHYLATION; EPIGENETICS; EPIGENOMICS; HISTONE MODIFICATIONS; MIRNA; PHARMACOEPIGENETICS;

DNA; DRUG THERAPY; EPIGENESIS, GENETIC; EPIGENOMICS; HISTONES; HUMANS; PHARMACEUTICAL PREPARATIONS;

EID: 84892365365     PISSN: 02770008     EISSN: 18759114     Source Type: Journal    
DOI: 10.1002/phar.1325     Document Type: Article

References (54)

1. Bird A,. Perceptions of epigenetics. Nature 2007; 447: 396-8.
2. Lawlor ER, Thiele CJ,. Epigenetic changes in pediatric solid tumors: promising new targets. Clin Cancer Res 2012; 18: 2768-79.
3. Kouzarides T,. Chromatin modifications and their function. Cell 2007; 128: 693-705.
4. Jones PA,. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 2012; 13: 484-92.
5. Maunakea AK, Nagarajan RP, Bilenky M, et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 2010; 466: 253-7.
6. Tahiliani M, Koh KP, Shen Y, et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 2009; 324: 930-5.
7. Williams K, Christensen J, Pedersen MT, et al. TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 2011; 473: 343-8.
8. Djebali S, Davis CA, Merkel A, et al. Landscape of transcription in human cells. Nature 2012; 489: 101-8.
9. Rana TM,. Illuminating the silence: understanding the structure and function of small RNAs. Nat Rev Mol Cell Biol 2007; 8: 23-36.
10. Esteller M,. Non-coding RNAs in human disease. Nat Rev Genet 2011; 12: 861-74.
11. Ding SW, Voinnet O,. Antiviral immunity directed by small RNAs. Cell 2007; 130: 413-26.
12. Aravin AA, Sachidanandam R, Girard A, Fejes-Toth K, Hannon GJ,. Developmentally regulated piRNA clusters implicate MILI in transposon control. Science 2007; 316: 744-7.
13. King TH, Liu B, McCully RR, Fournier MJ,. Ribosome structure and activity are altered in cells lacking snoRNPs that form pseudouridines in the peptidyl transferase center. Mol Cell 2003; 11: 425-35.
14. Lee JT,. Epigenetic regulation by long noncoding RNAs. Science 2012; 338: 1435-9.
15. Sigova AA, Mullen AC, Molinie B, et al. Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells. Proc Natl Acad Sci USA 2013; 110: 2876-81.
16. Ooi SK, Qiu C, Bernstein E, et al. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 2007; 448: 714-7.
17. Iorio MV, Piovan C, Croce CM,. Interplay between microRNAs and the epigenetic machinery: an intricate network. Biochim Biophys Acta 2010; 1799: 694-701.
18. Juttermann R, Li E, Jaenisch R,. Toxicity of 5-aza-2deoxycytidine to mammalian cells is mediated primarily by covalent trapping of DNA methyltransferase rather than DNA demethylation. Proc Natl Acad Sci USA 1994; 91: 11797-801.
19. Heijmans BT, Tobi EW, Stein AD, et al. Persistent epigenetic differences associated with prenatal exposure to famine in humans. Proc Natl Acad Sci USA 2008; 105: 17046-9.
20. Joubert BR, Haberg SE, Nilsen RM, et al. 450K epigenome-wide scan identifies differential DNA methylation in newborns related to maternal smoking during pregnancy. Environ Health Perspect 2012; 120: 1425-31.
21. Shih AH, Abdel-Wahab O, Patel JP, Levine RL,. The role of mutations in epigenetic regulators in myeloid malignancies. Nat Rev Cancer 2012; 12: 599-612.
22. Esteller M, Hamilton SR, Burger PC, Baylin SB, Herman JG,. Inactivation of the DNA repair gene O6-methylguanine-DNA methyltransferase by promoter hypermethylation is a common event in primary human neoplasia. Cancer Res 1999; 59: 793-7.
23. Morin RD, Mendez-Lago M, Mungall AJ, et al. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature 2011; 476: 298-303.
24. Schaefer A, O'Carroll D, Tan CL, et al. Cerebellar neurodegeneration in the absence of microRNAs. J Exp Med 2007; 204: 1553-8.
25. Shin D, Shin JY, McManus MT, Ptacek LJ, Fu YH,. Dicer ablation in oligodendrocytes provokes neuronal impairment in mice. Ann Neurol 2009; 66: 843-57.
26. Hebert SS, Papadopoulou AS, Smith P, et al. Genetic ablation of Dicer in adult forebrain neurons results in abnormal tau hyperphosphorylation and neurodegeneration. Hum Mol Genet 2010; 19: 3959-69.
27. Holdt LM, Beutner F, Scholz M, et al. ANRIL expression is associated with atherosclerosis risk at chromosome 9p21. Arterioscler Thromb Vasc Biol 2010; 30: 620-7.
28. Petronis A,. Epigenetics as a unifying principle in the aetiology of complex traits and diseases. Nature 2010; 465: 721-7.
29. Cowley AW Jr, Nadeau JH, et al. Report of the National Heart, Lung, and Blood Institute Working Group on epigenetics and hypertension. Hypertension 2012; 59: 899-905.
30. Nakajima M, Iwanari M, Yokoi T,. Effects of histone deacetylation and DNA methylation on the constitutive and TCDD-inducible expressions of the human CYP1 family in MCF-7 and HeLa cells. Toxicol Lett 2003; 144: 247-56.
31. Li Y, Cui Y, Hart SN, Klaassen CD, Zhong XB,. Dynamic patterns of histone methylation are associated with ontogenic expression of the Cyp3a genes during mouse liver maturation. Mol Pharmacol 2009; 75: 1171-9.
32. Ingelman-Sundberg M, Sim SC, Gomez A, Rodriguez-Antona C,. Influence of cytochrome P450 polymorphisms on drug therapies: pharmacogenetic, pharmacoepigenetic and clinical aspects. Pharmacol Ther 2007; 116: 496-526.
33. Pan YZ, Gao W, Yu AM,. MicroRNAs regulate CYP3A4 expression via direct and indirect targeting. Drug Metab Dispos 2009; 37: 2112-7.
34. Esteller M, Garcia-Foncillas J, Andion E, et al. Inactivation of the DNA-repair gene MGMT and the clinical response of gliomas to alkylating agents. N Engl J Med 2000; 343: 1350-4.
35. Hegi ME, Diserens AC, Gorlia T, et al. MGMT gene silencing and benefit from temozolomide in glioblastoma. N Engl J Med 2005; 352: 997-1003.
36. Fukuchi M, Nii T, Ishimaru N, et al. Valproic acid induces up- or down-regulation of gene expression responsible for the neuronal excitation and inhibition in rat cortical neurons through its epigenetic actions. Neurosci Res 2009; 65: 35-43.
37. D'Souza A, Onem E, Patel P, La Gamma EF, Nankova BB,. Valproic acid regulates catecholaminergic pathways by concentration-dependent threshold effects on TH mRNA synthesis and degradation. Brain Res 2009; 1247: 1-10.
38. Sharma RP, Rosen C, Kartan S, et al. Valproic acid and chromatin remodeling in schizophrenia and bipolar disorder: preliminary results from a clinical population. Schizophr Res 2006; 88: 227-31.
39. Chen Y, Sharma RP, Costa RH, Costa E, Grayson DR,. On the epigenetic regulation of the human reelin promoter. Nucleic Acids Res 2002; 30: 2930-9.
40. Perisic T, Zimmermann N, Kirmeier T, et al. Valproate and amitriptyline exert common and divergent influences on global and gene promoter-specific chromatin modifications in rat primary astrocytes. Neuropsychopharmacology 2010; 35: 792-805.
41. Dje N'Guessan P, Riediger F, Vardarova K, et al. Statins control oxidized LDL-mediated histone modifications and gene expression in cultured human endothelial cells. Arterioscler Thromb Vasc Biol 2009; 29: 380-6.
42. Lin YC, Lin JH, Chou CW, Chang YF, Yeh SH, Chen CC,. Statins increase p21 through inhibition of histone deacetylase activity and release of promoter-associated HDAC1/2. Cancer Res 2008; 68: 2375-83.
43. Vaughan CJ, Murphy MB, Buckley BM,. Statins do more than just lower cholesterol. Lancet 1996; 348: 1079-82.
44. Liao JK, Laufs U,. Pleiotropic effects of statins. Annu Rev Pharmacol Toxicol 2005; 45: 89-118.
45. Minami Y, Satoh M, Maesawa C, et al. Effect of atorvastatin on microRNA 221 / 222 expression in endothelial progenitor cells obtained from patients with coronary artery disease. Eur J Clin Invest 2009; 39: 359-67.
46. Poliseno L, Tuccoli A, Mariani L, et al. MicroRNAs modulate the angiogenic properties of HUVECs. Blood 2006; 108: 3068-71.
47. Arrowsmith CH, Bountra C, Fish PV, Lee K, Schapira M,. Epigenetic protein families: a new frontier for drug discovery. Nat Rev Drug Discov 2012; 11: 384-400.
48. Ungerstedt JS, Sowa Y, Xu WS, et al. Role of thioredoxin in the response of normal and transformed cells to histone deacetylase inhibitors. Proc Natl Acad Sci USA 2005; 102: 673-8.
49. Deleavey GF, Damha MJ,. Designing chemically modified oligonucleotides for targeted gene silencing. Chem Biol 2012; 19: 937-54.
50. Raal FJ, Santos RD, Blom DJ, et al. Mipomersen, an apolipoprotein B synthesis inhibitor, for lowering of LDL cholesterol concentrations in patients with homozygous familial hypercholesterolaemia: a randomised, double-blind, placebo-controlled trial. Lancet 2010; 375: 998-1006.
51. Kasinski AL, Slack FJ,. Epigenetics and genetics. MicroRNAs en route to the clinic: progress in validating and targeting microRNAs for cancer therapy. Nat Rev Cancer 2011; 11: 849-64.
52. Van Rooij E, Olson EN,. MicroRNA therapeutics for cardiovascular disease: opportunities and obstacles. Nat Rev Drug Discov 2012; 11: 860-72.
53. Cortez MA, Bueso-Ramos C, Ferdin J, Lopez-Berestein G, Sood AK, Calin GA,. MicroRNAs in body fluids-the mix of hormones and biomarkers. Nat Rev Clin Oncol 2011; 8: 467-77.
54. Garcia-Gimenez JL, Sanchis-Gomar F, Lippi G, et al. Epigenetic biomarkers: A new perspective in laboratory diagnostics. Clin Chim Acta 2012; 413: 1576-82.