Skip to main content

The Epigenomics of Cancer

  • Chapter
  • First Online:
An Omics Perspective on Cancer Research

Abstract

Epigenomics is the genome-wide study of epigenetics such as DNA methylation and histone modification. Epigenetic abnormality plays an important role in the pathogenesis of most cancers. Among these modifications, DNA methylation is the best-known and most important because of its heritable character. Here, recent advances in several technologies for genome-wide profiling of DNA methylation are reviewed.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Abujiang P, Mori TJ, Takahashi T et al (1998) Loss of heterozygosity (LOH) at 17q and 14q in human lung cancers. Oncogene 17:3029–3033

    Article  CAS  PubMed  Google Scholar 

  • Adorjan P, Distler J, Lipscher E et al (2002) Tumor class prediction and discovery by microarray-based DNA methylation analysis. Nucleic Acids Res 30:e21

    Article  PubMed  Google Scholar 

  • Ballestar E, Paz MF, Valle L et al (2003) Methyl-CpG binding proteins identify novel sites of epigenetic inactivation in human cancer. EMBO J 22:6335–6345

    Article  CAS  PubMed  Google Scholar 

  • Barski A, Cuddapah S, Cui K et al (2007) High-resolution profiling of histone methylations in the human genome. Cell 129:823–837

    Article  CAS  PubMed  Google Scholar 

  • Bernstein BE, Mikkelsen TS, Xie X et al (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125:315–326

    Article  CAS  PubMed  Google Scholar 

  • Bernstein BE, Meissner A, Lander ES (2007) The mammalian epigenome. Cell 128:669–681

    Article  CAS  PubMed  Google Scholar 

  • Bird A (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16:6–21

    Article  CAS  PubMed  Google Scholar 

  • Bjerkvig R, Tysnes BB, Aboody KS et al (2005) Opinion: the origin of the cancer stem cell: current controversies and new insights. Nat Rev Cancer 5:899–904

    Article  CAS  PubMed  Google Scholar 

  • Bracken AP, Pasini D, Capra M et al (2003) EZH2 is downstream of the pRB-E2F pathway, essential for proliferation and amplified in cancer. EMBO J 22:5323–5335

    Article  CAS  PubMed  Google Scholar 

  • Cloos PA, Christensen J, Agger K et al (2006) The putative oncogene GASC1 demethylates tri- and dimethylated lysine 9 on histone H3. Nature 442:307–311

    Article  CAS  PubMed  Google Scholar 

  • Cokus SJ, Feng S, Zhang X et al (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452:215–219

    Article  CAS  PubMed  Google Scholar 

  • Dobrovic A, Simpfendorfer D (1997) Methylation of the BRCA1 gene in sporadic breast cancer. Cancer Res 57:3347–3350

    CAS  PubMed  Google Scholar 

  • Eden A, Gaudet F, Waghmare A et al (2003) Chromosomal instability and tumors promoted by DNA hypomethylation. Science 300:455

    Article  CAS  PubMed  Google Scholar 

  • Esteller M (2006) Epigenetics provides a new generation of oncogenes and tumor-suppressor genes. Br J Cancer 94:179–183

    Article  CAS  PubMed  Google Scholar 

  • Feinberg AP, Vogelstein B (1983) Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301:89–92

    Article  CAS  PubMed  Google Scholar 

  • Feinberg AP, Tycko B (2004) The history of cancer epigenetics. Nat Rev Cancer 4:143–153

    Article  CAS  PubMed  Google Scholar 

  • Feinberg AP (2007) Phenotypic plasticity and the epigenetics of human disease. Nature 447:433–440

    Article  CAS  PubMed  Google Scholar 

  • Fryxell KJ, Zuckerkandl E (2000) Cytosine deamination plays a primary role in the evolution of mammalian isochores. Mol Biol Evol 17:1371–1383

    CAS  PubMed  Google Scholar 

  • Gitan RS, Shi H, Chen CM et al (2002) Methylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis. Genome Res 12:158–164

    Article  CAS  PubMed  Google Scholar 

  • Hatada I, Hayashizaki Y, Hirotsune S et al (1991) A genomic scanning method for higher organisms using restriction sites as landmarks. Proc Natl Acad Sci USA 88:9523–9527

    Article  CAS  PubMed  Google Scholar 

  • Hatada I, Sugama T, Mukai T (1993) A new imprinted gene cloned by a methylation-sensitive genome scanning method. Nucleic Acids Res 21:5577–5582

    Article  CAS  PubMed  Google Scholar 

  • Hatada I, Fukasawa M, Kimura M et al (2006) Genome-wide profiling of promoter methylation in human. Oncogene 25:3059–3064

    Article  CAS  PubMed  Google Scholar 

  • Hayatsu H, Wataya Y, Kazushige K (1970) The addition of sodium bisulfite to uracil and to cytosine. J Am Chem Soc 92:724–726

    Article  CAS  PubMed  Google Scholar 

  • Hirotsune S, Hatada I, Komatsubara H et al (1992) New approach for detection of amplification in cancer DNA using restriction landmark genomic scanning. Cancer Res 52:3642–3647

    CAS  PubMed  Google Scholar 

  • Jenuwein T (2001) Re-SET-ting heterochromatin by histone methyltransferases. Trends Cell Biol 11:266–273

    Article  CAS  PubMed  Google Scholar 

  • Jones PA, Baylin SB (2007) The epigenomics of cancer. Cell 128:683–692

    Article  CAS  PubMed  Google Scholar 

  • Kaneda A, Kaminishi M, Yanagihara K et al (2002a) Identification of silencing of nine genes in human gastric cancers. Cancer Res 62:6645–6650

    PubMed  Google Scholar 

  • Kaneda A, Kaminishi M, Nakanishi Y et al (2002b) Reduced expression of the insulin-induced protein 1 and p41 Arp2/3 complex genes in human gastric cancers. Int J Cancer 100:57–62

    Article  CAS  PubMed  Google Scholar 

  • Kaghad M, Bonnet H, Yang A et al (1997) Monoallelically expressed gene related to p53 at 1p36, a region frequently deleted in neuroblastoma and other human cancers. Cell 90:809–819

    Article  CAS  PubMed  Google Scholar 

  • Karpf AR, Peterson PW, Rawlins JT et al (1999) Inhibition of DNA methyltransferase stimulates the expression of signal transducer and activator of transcription 1, 2, and 3 genes in colon tumor cells. Proc Natl Acad Sci USA 96:14007–14012

    Article  CAS  PubMed  Google Scholar 

  • Lee TI, Jenner RG, Boyer LA et al (2006) Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125:301–313

    Article  CAS  PubMed  Google Scholar 

  • Liang G, Gonzales FA, Jones PA et al (2002) Analysis of gene induction in human fibroblasts and bladder cancer cells exposed to the methylation inhibitor 5-aza-2′-deoxycytidine. Cancer Res 62:961–966

    CAS  PubMed  Google Scholar 

  • Lisitsyn N, Lisitsyn N, Wigler M (1993) Cloning the differences between two complex genomes. Science 259:946–951

    Article  CAS  PubMed  Google Scholar 

  • Liu K, Zhan M, Zheng P (2008) Loss of p73 expression in six non-small cell lung cancer cell lines is associated with 5′CpG island methylation. Exp Mol Pathol 84:59–63

    Article  CAS  PubMed  Google Scholar 

  • Mack GS (2006) Epigenetic cancer therapy makes headway. J Natl Cancer Inst 98:1443–1444

    PubMed  Google Scholar 

  • Marks PA, Breslow R (2007) Dimethyl sulfoxide to vorinostat: development of this histone deacetylase inhibitor as an anticancer drug. Nat Biotechnol 25:84–90

    Article  CAS  PubMed  Google Scholar 

  • Matsuyama T, Kimura MT, Koike K et al (2003) Global methylation screening in the Arabidopsis thaliana and Mus musculus genome: applications of virtual image restriction landmark genomic scanning (Vi-RLGS). Nucleic Acids Res 31:4490–4496

    Article  CAS  PubMed  Google Scholar 

  • Mikkelsen TS, Ku M, Jaffe DB et al (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448:553–560

    Article  CAS  PubMed  Google Scholar 

  • Miyamoto K, Asada K, Fukutomi T et al (2003) Methylation-associated silencing of heparan sulfate D-glucosaminyl 3-O-sulfotransferase-2 (3-OST-2) in human breast, colon, lung and pancreatic cancers. Oncogene 22:274–280

    Article  CAS  PubMed  Google Scholar 

  • Müller CI, Rüter B, Koeffler HP et al (2006) DNA hypermethylation of myeloid cells, a novel therapeutic target in MDS and AML. Curr Pharm Biotechnol 7:315–321

    Article  PubMed  Google Scholar 

  • Oki Y, Aoki E, Issa JP (2007) Decitabine–bedside to bench. Crit Rev Oncol Hematol 61:140–152

    Article  PubMed  Google Scholar 

  • Ren B, Robert F, Wyrick JJ (2000) Genome-wide location and function of DNA binding proteins. Science 290:2306–2309

    Article  CAS  PubMed  Google Scholar 

  • Ringrose L, Paro R (2004) Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu Rev Genet 38:413–443

    Article  CAS  PubMed  Google Scholar 

  • Schatz P, Dietrich D, Schuster M (2004) Rapid analysis of CpG methylation patterns using RNase T1 cleavage and MALDI-TOF. Nucleic Acids Res 32:e167

    Article  PubMed  Google Scholar 

  • Toyota M, Ho C, Ahuja N et al (1999) Identification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification. Cancer Res 59:2307–2312

    CAS  PubMed  Google Scholar 

  • Uhlmann K, Brinckmann A, Toliat MR et al (2002) Evaluation of a potential epigenetic biomarker by quantitative methyl-single nucleotide polymorphism analysis. Electrophoresis 23:4072–4079

    Article  CAS  PubMed  Google Scholar 

  • Ushijima T, Morimura K, Hosoya Y et al (1997) Establishment of methylation-sensitive-representational difference analysis and isolation of hypo- and hypermethylated genomic fragments in mouse liver tumors. Proc Natl Acad Sci USA 94:2284–2289

    Article  CAS  PubMed  Google Scholar 

  • Wakasugi T, Izumi H, Uchiumi T et al (2007) ZNF143 interacts with p73 and is involved in cisplatin resistance through the transcriptional regulation of DNA repair genes. Oncogene 26:5194–5203

    Article  CAS  PubMed  Google Scholar 

  • Watanabe T, Huang H, Nakamura M et al (2002) Methylation of the p73 gene in gliomas. Acta Neuropathol 104:357–362

    CAS  PubMed  Google Scholar 

  • 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 37:853–862

    Article  CAS  PubMed  Google Scholar 

  • Weber M, Hellmann I, Stadler MB et al (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39:457–466

    Article  CAS  PubMed  Google Scholar 

  • Widschwendter M, Fiegl H, Egle D et al (2007) Epigenetic stem cell signature in cancer. Nat Genet 39:157–158

    Article  CAS  PubMed  Google Scholar 

  • Yoshikawa H, Matsubara K, Qian GS et al (2001) SOCS-1, a negative regulator of the JAK/STAT pathway, is silenced by methylation in human hepatocellular carcinoma and shows growth-suppression activity. Nat Genet 28:29–35

    Article  CAS  PubMed  Google Scholar 

  • Yu L, Liu C, Vandeusen J et al (2005) Global assessment of promoter methylation in a mouse model of cancer identifies ID4 as a putative tumor-suppressor gene in human leukemia. Nat Genet 37:265–274

    Article  CAS  PubMed  Google Scholar 

  • Zardo G, Tiirikainen MI, Hong C et al (2002) Integrated genomic and epigenomic analyses pinpoint biallelic gene inactivation in tumors. Nat Genet 32:453–458

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Izuho Hatada .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer Science+Business Media B.V.

About this chapter

Cite this chapter

Hatada, I. (2010). The Epigenomics of Cancer. In: Cho, W. (eds) An Omics Perspective on Cancer Research. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-2675-0_4

Download citation

Publish with us

Policies and ethics