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Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band

Nature Genetics volume 38, pages 540–549 (2006)Cite this article

Abstract

We report a new mechanism in carcinogenesis involving coordinate long-range epigenetic gene silencing. Epigenetic silencing in cancer has always been envisaged as a local event silencing discrete genes. However, in this study of silencing in colorectal cancer, we found common repression of the entire 4-Mb band of chromosome 2q.14.2, associated with global methylation of histone H3 Lys9. DNA hypermethylation within the repressed genomic neighborhood was localized to three separate enriched CpG island 'suburbs', with the largest hypermethylated suburb spanning 1 Mb. These data change our understanding of epigenetic gene silencing in cancer cells: namely, epigenetic silencing can span large regions of the chromosome, and both DNA-methylated and neighboring unmethylated genes can be coordinately suppressed by global changes in histone modification. We propose that loss of gene expression can occur through long-range epigenetic silencing, with similar implications as loss of heterozygosity in cancer.

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Figure 1: Differential methylation of a region in colorectal cancer identified by AIMS.
Figure 2: DNA methylation profile of the 4-Mb region in colorectal cancer on chromosome 2q14.2.
Figure 3: DNA methylation of the CpG islands associated with EN1, SCTR and INHBB.
Figure 4: Gene suppression across 2q14.2 in colorectal cancer.
Figure 5: Effect of 5AzaC and TSA on gene expression across region 2q14.2.
Figure 6: Chromatin immunoprecipitation (ChIP) across the 2q14.2 region.
Figure 7: Relationship between DNA methylation and normal gene expression levels.
Figure 8: Epigenetic lesions in cancer.

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References

  1. Jones, P.A. & Baylin, S.B. The fundamental role of epigenetic events in cancer. Nat. Rev. Genet. 3, 415–428 (2002).

    Article  CAS  Google Scholar 

  2. Laird, P.W. Cancer epigenetics. Hum. Mol. Genet. 14, R65–R76 (2005).

    Article  CAS  Google Scholar 

  3. Gardiner-Garden, M. & Frommer, M. CpG islands in vertebrate genomes. J. Mol. Biol. 196, 261–282 (1987).

    Article  CAS  Google Scholar 

  4. Lander, E.S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).

    Article  CAS  Google Scholar 

  5. Clark, S.J. & Melki, J. DNA methylation and gene silencing in cancer: which is the guilty party? Oncogene 21, 5380–5387 (2002).

    Article  CAS  Google Scholar 

  6. Song, J.Z., Stirzaker, C., Harrison, J., Melki, J.R. & Clark, S.J. Hypermethylation trigger of the glutathione-S-transferase gene (GSTP1) in prostate cancer cells. Oncogene 21, 1048–1061 (2002).

    Article  CAS  Google Scholar 

  7. Baylin, S. & Bestor, T.H. Altered methylation patterns in cancer cell genomes: cause or consequence? Cancer Cell 1, 299–305 (2002).

    Article  CAS  Google Scholar 

  8. Bachman, K.E. et al. Histone modifications and silencing prior to DNA methylation of a tumor suppressor gene. Cancer Cell 3, 89–95 (2003).

    Article  CAS  Google Scholar 

  9. Melki, J.R., Vincent, P.C. & Clark, S.J. Concurrent DNA hypermethylation of multiple genes in acute myeloid leukaemia. Cancer Res. 59, 3730–3740 (1999).

    CAS  PubMed  Google Scholar 

  10. Costello, J.F. et al. Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nat. Genet. 24, 132–138 (2000).

    Article  CAS  Google Scholar 

  11. Rush, L.J. et al. Epigenetic profiling in chronic lymphocytic leukemia reveals novel methylation targets. Cancer Res. 64, 2424–2433 (2004).

    Article  CAS  Google Scholar 

  12. Feltus, F.A., Lee, E.K., Costello, J.F., Plass, C. & Vertino, P.M. Predicting aberrant CpG island methylation. Proc. Natl. Acad. Sci. USA 100, 12253–12258 (2003).

    Article  CAS  Google Scholar 

  13. Ushijima, T. Detection and interpretation of altered methylation patterns in cancer cells. Nat. Rev. Cancer 5, 223–231 (2005).

    Article  CAS  Google Scholar 

  14. Frigola, J., Ribas, M., Risques, R.A. & Peinado, M.A. Methylome profiling of cancer cells by amplification of inter-methylated sites (AIMS). Nucleic Acids Res. 30, e28 (2002).

    Article  Google Scholar 

  15. Stirzaker, C., Song, J.Z., Davidson, B. & Clark, S.J. Transcriptional gene silencing promotes DNA hypermethylation through a sequential change in chromatin modifications in cancer cells. Cancer Res. 64, 3871–3877 (2004).

    Article  CAS  Google Scholar 

  16. Kondo, Y., Shen, L., Yan, P.S., Huang, T.H. & Issa, J.P. Chromatin immunoprecipitation microarrays for identification of genes silenced by histone H3 lysine 9 methylation. Proc. Natl. Acad. Sci. USA 101, 7398–7403 (2004).

    Article  CAS  Google Scholar 

  17. Frigola, J. et al. Differential DNA hypermethylation and hypomethylation signatures in colorectal cancer. Hum. Mol. Genet. 14, 319–326 (2005).

    Article  CAS  Google Scholar 

  18. Kangas, M. et al. Structure and chromosomal localization of the human and murine genes for the macrophage MARCO receptor. Genomics 58, 82–89 (1999).

    Article  CAS  Google Scholar 

  19. Gui, C.Y., Ngo, L., Xu, W.S., Richon, V.M. & Marks, P.A. Histone deacetylase (HDAC) inhibitor activation of p21WAF1 involves changes in promoter-associated proteins, including HDAC1. Proc. Natl. Acad. Sci. USA 101, 1241–1246 (2004).

    Article  CAS  Google Scholar 

  20. Archer, S.Y., Meng, S., Shei, A. & Hodin, R.A. p21(WAF1) is required for butyrate-mediated growth inhibition of human colon cancer cells. Proc. Natl. Acad. Sci. USA 95, 6791–6796 (1998).

    Article  CAS  Google Scholar 

  21. Zhu, W.G. et al. 5-aza-2′-deoxycytidine activates the p53/p21Waf1/Cip1 pathway to inhibit cell proliferation. J. Biol. Chem. 279, 15161–15166 (2004).

    Article  CAS  Google Scholar 

  22. Huschtscha, L.I. et al. Loss of p16INK4 expression by methylation is associated with lifespan extension of human mammary epithelial cells. Cancer Res. 58, 3508–3512 (1998).

    CAS  PubMed  Google Scholar 

  23. Weber, M. et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet. 37, 853–862 (2005).

    Article  CAS  Google Scholar 

  24. Nie, Y. et al. DNA hypermethylation is a mechanism for loss of expression of the HLA class I genes in human esophageal squamous cell carcinomas. Carcinogenesis 22, 1615–1623 (2001).

    Article  CAS  Google Scholar 

  25. van Noesel, M.M. et al. Clustering of hypermethylated genes in neuroblastoma. Genes Chromosom. Cancer 38, 226–233 (2003).

    Article  CAS  Google Scholar 

  26. Palmisano, W.A. et al. Aberrant promoter methylation of the transcription factor genes PAX5 alpha and beta in human cancers. Cancer Res. 63, 4620–4625 (2003).

    CAS  PubMed  Google Scholar 

  27. Brockdorff, N. X-chromosome inactivation: closing in on proteins that bind Xist RNA. Trends Genet. 18, 352–358 (2002).

    Article  CAS  Google Scholar 

  28. Latham, K.E. X chromosome imprinting and inactivation in preimplantation mammalian embryos. Trends Genet. 21, 120–127 (2005).

    Article  CAS  Google Scholar 

  29. Plath, K., Mlynarczyk-Evans, S., Nusinow, D.A. & Panning, B. Xist RNA and the mechanism of X chromosome inactivation. Annu. Rev. Genet. 36, 233–278 (2002).

    Article  CAS  Google Scholar 

  30. Lippman, Z. & Martienssen, R. The role of RNA interference in heterochromatic silencing. Nature 431, 364–370 (2004).

    Article  CAS  Google Scholar 

  31. O'Neill, M.J. The influence of non-coding RNAs on allele-specific gene expression in mammals. Hum. Mol. Genet. 14, R113–R120 (2005).

    Article  CAS  Google Scholar 

  32. Jaffrey, R.G. et al. Genomic instability at the BUB1 locus in colorectal cancer, but not in non-small cell lung cancer. Cancer Res. 60, 4349–4352 (2000).

    CAS  PubMed  Google Scholar 

  33. Moon, R.T., Kohn, A.D., De Ferrari, G.V. & Kaykas, A. WNT and beta-catenin signalling: diseases and therapies. Nat. Rev. Genet. 5, 691–701 (2004).

    Article  CAS  Google Scholar 

  34. Adamska, M., MacDonald, B.T., Sarmast, Z.H., Oliver, E.R. & Meisler, M.H. En1 and Wnt7a interact with Dkk1 during limb development in the mouse. Dev. Biol. 272, 134–144 (2004).

    Article  CAS  Google Scholar 

  35. Pang, R.T., Lee, L.T., Ng, S.S., Yung, W.H. & Chow, B.K. CpG methylation and transcription factors Sp1 and Sp3 regulate the expression of the human secretin receptor gene. Mol. Endocrinol. 18, 471–483 (2004).

    Article  CAS  Google Scholar 

  36. Tang, C. et al. Expression of receptors for gut peptides in pancreata of BOP-treated and control hamsters. Carcinogenesis 17, 2171–2175 (1996).

    Article  CAS  Google Scholar 

  37. Tang, C., Biemond, I. & Lamers, C.B. Expression of peptide receptors in human endocrine tumours of the pancreas. Gut 40, 267–271 (1997).

    Article  CAS  Google Scholar 

  38. Reis, F.M. et al. Activin, inhibin and the human breast. Mol. Cell. Endocrinol. 225, 77–82 (2004).

    Article  CAS  Google Scholar 

  39. Mylonas, I. et al. Inhibin/activin subunits (inhibin-alpha, -betaA and -betaB) are differentially expressed in human breast cancer and their metastasis. Oncol. Rep. 13, 81–88 (2005).

    CAS  PubMed  Google Scholar 

  40. Sims, R.J., III, Nishioka, K. & Reinberg, D. Histone lysine methylation: a signature for chromatin function. Trends Genet. 19, 629–639 (2003).

    Article  CAS  Google Scholar 

  41. Mutskov, V. & Felsenfeld, G. Silencing of transgene transcription precedes methylation of promoter DNA and histone H3 lysine 9. EMBO J. 23, 138–149 (2004).

    Article  CAS  Google Scholar 

  42. Gius, D. et al. Distinct effects on gene expression of chemical and genetic manipulation of the cancer epigenome revealed by a multimodality approach. Cancer Cell 6, 361–371 (2004).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  44. Lorincz, M.C., Schubeler, D., Hutchinson, S.R., Dickerson, D.R. & Groudine, M. DNA methylation density influences the stability of an epigenetic imprint and Dnmt3a/b-independent de novo methylation. Mol. Cell. Biol. 22, 7572–7580 (2002).

    Article  CAS  Google Scholar 

  45. Nguyen, C. et al. Susceptibility of nonpromoter CpG islands to de novo methylation in normal and neoplastic cells. J. Natl. Cancer Inst. 93, 1465–1472 (2001).

    Article  CAS  Google Scholar 

  46. Lorincz, M.C., Dickerson, D.R., Schmitt, M. & Groudine, M. Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nat. Struct. Mol. Biol. 11, 1068–1075 (2004).

    Article  CAS  Google Scholar 

  47. Clark, S.J., Harrison, J., Paul, C.L. & Frommer, M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res. 22, 2990–2997 (1994).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank J. Rodriguez for LOH analysis, G. Aiza and M. Muñoz for technical help, P. Molloy for reading the manuscript and A. Statham for help with figures. This work was supported in part by a grant from the Australian National Health and Medical Research Council (NH&MRC; grants 293810 and 325622) and a grant from the Spanish Ministry of Education and Science (SAF2003/5821). J.F. is a fellow of the Spanish Ministry of Education and Science (FPU program) at the Universitat Autonoma de Barcelona and S.J.C. is a principal research fellow of NH&MRC (293811).

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Authors and Affiliations

  1. Cancer Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, 2010, New South Wales, Australia

    Jordi Frigola, Jenny Song, Clare Stirzaker, Rebecca A Hinshelwood & Susan J Clark

  2. Institut d'Investigacio Biomedica de Bellvitge (IDIBELL)-Institut de Recerca Oncologia, Hospital Duran i Reynals, 08907 L'Hospitalet, Barcelona, Spain

    Jordi Frigola & Miguel A Peinado

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Correspondence to Susan J Clark.

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Supplementary information

Supplementary Fig. 1

Identification of a differentially methylated region in colorectal cancer using AIMS. (PDF 353 kb)

Supplementary Fig. 2

Ten defined genes are located in 2q14.2. (PDF 285 kb)

Supplementary Fig. 3

Direct genomic bisulfite sequencing across chromosome 2q14.2 (PDF 1176 kb)

Supplementary Fig. 4

Genomic bisulfite sequencing of individual clones of the CpG islands across 2q14.2. (PDF 1154 kb)

Supplementary Fig. 5

Real-time RT-PCR and temperature dissociation profiles. (PDF 1176 kb)

Supplementary Fig. 6

Chromatin immunoprecipitation real-time PCR and temperature dissociation profiles. (PDF 1068 kb)

Supplementary Table 1

Primers used for bisulfite sequencing, RT-PCR and ChIP analysis. (PDF 67 kb)

Supplementary Methods (PDF 60 kb)

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Frigola, J., Song, J., Stirzaker, C. et al. Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band. Nat Genet 38, 540–549 (2006). https://doi.org/10.1038/ng1781

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