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Virchows Archiv
Published in: Virchows Archiv 1/2010

01-01-2010 | Review and Perspective

Genome-scale approaches to the epigenetics of common human disease

Author: Andrew P. Feinberg

Published in: Virchows Archiv | Issue 1/2010

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Abstract

Traditionally, the pathology of human disease has been focused on microscopic examination of affected tissues, chemical and biochemical analysis of biopsy samples, other available samples of convenience, such as blood, and noninvasive or invasive imaging of varying complexity, in order to classify disease and illuminate its mechanistic basis. The molecular age has complemented this armamentarium with gene expression arrays and selective analysis of individual genes. However, we are entering a new era of epigenomic profiling, i.e., genome-scale analysis of cell-heritable nonsequence genetic change, such as DNA methylation. The epigenome offers access to stable measurements of cellular state and to biobanked material for large-scale epidemiological studies. Some of these genome-scale technologies are beginning to be applied to create the new field of epigenetic epidemiology.
Literature
1.
Van Speybroeck L (2002) From epigenesis to epigenetics: the case of C. H. Waddington. Ann N Y Acad Sci 981:61–81PubMedCrossRef
2.
3.
Poirier LA (2002) The effects of diet, genetics and chemicals on toxicity and aberrant DNA methylation: an introduction. J Nutr 132:2336S–2339SPubMed
4.
5.
6.
Riggs AD, Pfeifer GP (1992) X-chromosome inactivation and cell memory. Trends Genet 8:169–174PubMed
7.
Strichman-Almashanu LZ, Lee RS, Onyango PO et al (2002) A genome-wide screen for normally methylated human CpG islands that can identify novel imprinted genes. Genome Res 12:543–554PubMed
8.
Song F, Smith JF, Kimura MT et al (2005) Association of tissue-specific differentially methylated regions (TDMs) with differential gene expression. Proc Natl Acad Sci USA 102:3336–3341CrossRefPubMed
9.
Shiota K, Kogo Y, Ohgane J et al (2002) Epigenetic marks by DNA methylation specific to stem, germ and somatic cells in mice. Genes Cells 7:961–969CrossRefPubMed
10.
Eckhardt F, Lewin J, Cortese R et al (2006) DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 38:1378–1385CrossRefPubMed
11.
Hark AT, Schoenherr CJ, Katz DJ et al (2000) CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus. Nature 405:486–489CrossRefPubMed
12.
Cui H, Niemitz EL, Ravenel JD et al (2001) Loss of imprinting of insulin-like growth factor-II in Wilms’ tumor commonly involves altered methylation but not mutations of CTCF or its binding site. Cancer Res 61:4947–4950PubMed
13.
Silva AJ, White R (1988) Inheritance of allelic blueprints for methylation patterns. Cell 54:145–152CrossRefPubMed
14.
Sandovici I, Naumova AK, Leppert M et al (2004) A longitudinal study of X-inactivation ratio in human females. Hum Genet 115:387–392CrossRefPubMed
15.
Feinberg AP (2007) Phenotypic plasticity and the epigenetics of human disease. Nature 447(7143):433–440CrossRefPubMed
16.
Feinberg AP, Vogelstein B (1983) Hypomethylation of ras oncogenes in primary human cancers. Biochem Biophys Res Commun 111:47–54CrossRefPubMed
17.
Cui H, Cruz-Correa M, Giardiello FM et al (2003) Loss of IGF2 imprinting: a potential marker of colorectal cancer risk. Science 299:1753–1755CrossRefPubMed
18.
Sakatani T, Kaneda A, Iacobuzio-Donahue CA et al (2005) Loss of imprinting of Igf2 alters intestinal maturation and tumorigenesis in mice. Science 307:1976–1978CrossRefPubMed
19.
Kaneda A, Wang CJ, Cheong R, et al (2007) Enhanced sensitivity to IGF-II signaling links loss of imprinting of IGF2 to increased cell proliferation and tumor risk. Proc Natl Acad Sci USA 104:20926–20931CrossRefPubMed
20.
Horsthemke B, Buiting K (2008) Genomic imprinting and imprinting defects in humans. Adv Genet 61:225–246CrossRefPubMed
21.
22.
Petronis A, Gottesman II, Crow TJ et al (2000) Psychiatric epigenetics: a new focus for the new century. Mol Psychiatry 5:342–346CrossRefPubMed
23.
Bjornsson HT, Fallin MD, Feinberg AP (2004) An integrated epigenetic and genetic approach to common human disease. Trends Genet 20:350–358CrossRefPubMed
24.
Weaver IC, Cervoni N, Champagne FA et al (2004) Epigenetic programming by maternal behavior. Nat Neurosci 7:847–854CrossRefPubMed
25.
Tsankova NM, Berton O, Renthal W et al (2006) Sustained hippocampal chromatin regulation in a mouse model of depression and antidepressant action. Nat Neurosci 9:519–525CrossRefPubMed
26.
Shimabukuro M, Jinno Y, Fuke C et al (2006) Haloperidol treatment induces tissue- and sex-specific changes in DNA methylation: a control study using rats. Behav Brain Funct 2:37CrossRefPubMed
27.
McMahon FJ, Stine OC, Meyers DA et al (1995) Patterns of maternal transmission in bipolar affective disorder. Am J Hum Genet 56:1277–1286PubMed
28.
Skuse DH, James RS, Bishop DV et al (1997) Evidence from Turner’s syndrome of an imprinted X-linked locus affecting cognitive function. Nature 387:705–708CrossRefPubMed
29.
Hansen RS, Wijmenga C, Luo P et al (1999) The DNMT3B DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome. Proc Natl Acad Sci USA 96:14412–14417CrossRefPubMed
30.
Sutcliffe JS, Nelson DL, Zhang F et al (1992) DNA methylation represses FMR-1 transcription in fragile X syndrome. Hum Mol Genet 1:397–400CrossRefPubMed
31.
Amir RE, Van den Veyver IB, Wan M et al (1999) Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2. Nat Genet 23:185–188CrossRefPubMed
32.
Fan G, Beard C, Chen RZ et al (2001) DNA hypomethylation perturbs the function and survival of CNS neurons in postnatal animals. J Neurosci 21:788–797PubMed
33.
Nelson ED, Kavalali ET, Monteggia LM (2008) Activity-dependent suppression of miniature neurotransmission through the regulation of DNA methylation. J Neurosci 28:395–406CrossRefPubMed
34.
Roohi J, Montagna C, Tegay DH et al (2008) Disruption of contactin 4 in 3 subjects with autism spectrum disorder. J Med Genet 46(3):176–182CrossRefPubMed
35.
Bakkaloglu B, O’Roak BJ, Louvi A et al (2008) Molecular cytogenetic analysis and resequencing of contactin associated protein-like 2 in autism spectrum disorders. Am J Hum Genet 82:165–173CrossRefPubMed
36.
Arking DE, Cutler DJ, Brune CW et al (2008) A common genetic variant in the neurexin superfamily member CNTNAP2 increases familial risk of autism. Am J Hum Genet 82:160–164CrossRefPubMed
37.
Alarcon M, Abrahams BS, Stone JL et al (2008) Linkage, association, and gene-expression analyses identify CNTNAP2 as an autism-susceptibility gene. Am J Hum Genet 82:150–159CrossRefPubMed
38.
Strauss KA, Puffenberger EG, Huentelman MJ et al (2006) Recessive symptomatic focal epilepsy and mutant contactin-associated protein-like 2. N Engl J Med 354:1370–1377CrossRefPubMed
39.
Wareham KA, Lyon MF, Glenister PH et al (1987) Age related reactivation of an X-linked gene. Nature 327:725–727CrossRefPubMed
40.
Brown S, Rastan S (1988) Age-related reactivation of an X-linked gene close to the inactivation centre in the mouse. Genet Res 52:151–154CrossRefPubMed
41.
Bennett-Baker PE, Wilkowski J, Burke DT (2003) Age-associated activation of epigenetically repressed genes in the mouse. Genetics 165:2055–2062PubMed
42.
Bandeen-Roche K, Xue QL, Ferrucci L et al (2006) Phenotype of frailty: characterization in the women’s health and aging studies. J Gerontol A Biol Sci Med Sci 61:262–266PubMed
43.
Fraga MF, Ballestar E, Paz MF et al (2005) Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci USA 102:10604–10609CrossRefPubMed
44.
45.
46.
Esteller M (2007) Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet 8:286–298CrossRefPubMed
47.
48.
Bibikova M, Fan JB (2009) GoldenGate assay for DNA methylation profiling. Methods Mol Biol 507:149–163CrossRefPubMed
49.
Clark SJ, Harrison J, Paul CL et al (1994) High sensitivity mapping of methylated cytosines. Nucleic Acids Res 22:2990–2997CrossRefPubMed
50.
Bibikova M, Lin Z, Zhou L et al (2006) High-throughput DNA methylation profiling using universal bead arrays. Genome Res 16:383–393CrossRefPubMed
51.
Weber M, Davies JJ, Wittig D et al (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37:853–862CrossRefPubMed
52.
Irizarry RA, Ladd-Acosta C, Carvalho B et al (2008) Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res 18:780–790CrossRefPubMed
53.
Irizarry RA, Ladd-Acosta C, Wen B et al (2009) The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 41:178–186CrossRefPubMed
54.
Costello JF, Smiraglia DJ, Plass C (2002) Restriction landmark genome scanning. Methods 27:144–149CrossRefPubMed
55.
Jorgensen HF, Adie K, Chaubert P et al (2006) Engineering a high-affinity methyl-CpG-binding protein. Nucleic Acids Res 34:e96CrossRefPubMed
56.
Illingworth R, Kerr A, Desousa D et al (2008) A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol 6:e22CrossRefPubMed
57.
Khulan B, Thompson RF, Ye K et al (2006) Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res 16:1046–1055CrossRefPubMed
58.
Oda M, Glass JL, Thompson RF et al (2009) High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers. Nucleic Acids Res 37(12):3829–3839CrossRefPubMed
59.
Yamada Y, Watanabe H, Miura F et al (2004) A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 21q. Genome Res 14:247–266CrossRefPubMed
60.
Ordway JM, Bedell JA, Citek RW et al (2006) Comprehensive DNA methylation profiling in a human cancer genome identifies novel epigenetic targets. Carcinogenesis 27:2409–2423CrossRefPubMed
61.
Margulies M, Egholm M, Altman WE et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380PubMed
62.
Shendure J, Porreca GJ, Reppas NB et al (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309:1728–1732CrossRefPubMed
63.
Meissner A, Gnirke A, Bell GW et al (2005) Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res 33:5868–5877CrossRefPubMed
64.
Frazer KA, Ballinger DG, Cox DR et al (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449:851–861CrossRefPubMed
65.
Manolio TA, Brooks LD, Collins FS (2008) A HapMap harvest of insights into the genetics of common disease. J Clin Invest 118:1590–1605CrossRefPubMed
66.
Cooper GM, Nickerson DA, Eichler EE (2007) Mutational and selective effects on copy-number variants in the human genome. Nat Genet 39:S22–S29CrossRefPubMed
67.
68.
69.
Pogribny IP, Basnakian AG, Miller BJ et al (1995) Breaks in genomic DNA and within the p53 gene are associated with hypomethylation in livers of folate/methyl-deficient rats. Cancer Res 55:1894–1901PubMed
70.
Pogribny IP, Miller BJ, James SJ (1997) Alterations in hepatic p53 gene methylation patterns during tumor progression with folate/methyl deficiency in the rat. Cancer Lett 115:31–38CrossRefPubMed
71.
Wainfan E, Poirier LA (1992) Methyl groups in carcinogenesis: effects on DNA methylation and gene expression. Cancer Res 52:2071s–2077sPubMed
72.
Jhaveri MS, Wagner C, Trepel JB (2001) Impact of extracellular folate levels on global gene expression. Mol Pharmacol 60:1288–1295PubMed
73.
Fowler BM, Giuliano AR, Piyathilake C et al (1998) Hypomethylation in cervical tissue: is there a correlation with folate status? Cancer Epidemiol Biomarkers Prev 7:901–906PubMed
74.
Jacob RA, Gretz DM, Taylor PC et al (1998) Moderate folate depletion increases plasma homocysteine and decreases lymphocyte DNA methylation in postmenopausal women. J Nutr 128:1204–1212PubMed
75.
Rampersaud GC, Kauwell GP, Hutson AD et al (2000) Genomic DNA methylation decreases in response to moderate folate depletion in elderly women. Am J Clin Nutr 72:998–1003PubMed
76.
DeBaun MR, Niemitz EL, Feinberg AP (2003) Association of in vitro fertilization with Beckwith–Wiedemann syndrome and epigenetic alterations of LIT1 and H19. Am J Hum Genet 72:156–160CrossRefPubMed
77.
Gicquel C, Gaston V, Mandelbaum J et al (2003) In vitro fertilization may increase the risk of Beckwith–Wiedemann syndrome related to the abnormal imprinting of the KCN1OT gene. Am J Hum Genet 72:1338–1341CrossRefPubMed
78.
Niemitz EL, Feinberg AP (2004) Epigenetics and assisted reproductive technology: a call for investigation. Am J Hum Genet 74:599–609CrossRefPubMed
79.
Bjornsson HT, Cui H, Gius D et al (2004) The new field of epigenomics: implications for cancer and other common disease research. Cold Spring Harb Symp Quant Biol 69:447–456CrossRefPubMed
80.
Harris TB, Launer LJ, Eiriksdottir G et al (2007) Age, gene/environment susceptibility—Reykjavik study: multidisciplinary applied phenomics. Am J Epidemiol 165:1076–1087CrossRefPubMed
81.
Bjornsson HT, Sigurdsson MI, Fallin MD et al (2008) Intra-individual change in DNA methylation over time with familial clustering. JAMA 299(24):2877–2883CrossRefPubMed
82.
Boks MP, Derks EM, Weisenberger DJ et al (2009) The relationship of DNA methylation with age, gender and genotype in twins and healthy controls. PLoS ONE 4:e6767CrossRefPubMed
83.
Zilliox MJ, Irizarry RA (2007) A gene expression bar code for microarray data. Nat Methods 4:911–913CrossRefPubMed
Metadata
Title
Genome-scale approaches to the epigenetics of common human disease
Author
Andrew P. Feinberg
Publication date
01-01-2010
Publisher
Springer-Verlag
Published in
Virchows Archiv / Issue 1/2010
Print ISSN: 0945-6317
Electronic ISSN: 1432-2307
DOI
https://doi.org/10.1007/s00428-009-0847-2

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