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Gene silencing in cancer by histone H3 lysine 27 trimethylation independent of promoter DNA methylation

Nature Genetics volume 40, pages 741–750 (2008)Cite this article

Abstract

Epigenetic silencing in cancer cells is mediated by at least two distinct histone modifications, polycomb-based histone H3 lysine 27 trimethylation (H3K27triM) and H3K9 dimethylation. The relationship between DNA hypermethylation and these histone modifications is not completely understood. Using chromatin immunoprecipitation microarrays (ChIP-chip) in prostate cancer cells compared to normal prostate, we found that up to 5% of promoters (16% CpG islands and 84% non-CpG islands) were enriched with H3K27triM. These genes were silenced specifically in prostate cancer, and those CpG islands affected showed low levels of DNA methylation. Downregulation of the EZH2 histone methyltransferase restored expression of the H3K27triM target genes alone or in synergy with histone deacetylase inhibition, without affecting promoter DNA methylation, and with no effect on the expression of genes silenced by DNA hypermethylation. These data establish EZH2-mediated H3K27triM as a mechanism of tumor-suppressor gene silencing in cancer that is potentially independent of promoter DNA methylation.

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Figure 1: Two distinct histone codes at loci silenced in cancer.
Figure 2: Global assessment of H3K27 modifications in cancer.
Figure 3: H3K27triM and its related gene silencing as a cancer-specific event in prostate cancers.
Figure 4: Global assessment of DNA methylation and H3K27triM in normal and cancer cell lines.
Figure 5: Reactivation of silenced gene expression by inhibition of DNA methylation, histone deacetylation or EZH2 expression.
Figure 6: H3K27triM and its related gene silencing are cancer-relevant events in prostate and breast cancers.
Figure 7: Effects of EZH2 knockdown (EZH2 KD) in cancer cell lines.

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References

  1. Jenuwein, T. & Allis, C.D. Translating the histone code. Science 293, 1074–1080 (2001).

    Article  CAS  Google Scholar 

  2. Herman, J.G. & Baylin, S.B. Gene silencing in cancer in association with promoter hypermethylation. N. Engl. J. Med. 349, 2042–2054 (2003).

    Article  CAS  Google Scholar 

  3. Cao, R. & Zhang, Y. The functions of E(Z)/EZH2-mediated methylation of lysine 27 in histone H3. Curr. Opin. Genet. Dev. 14, 155–164 (2004).

    Article  CAS  Google Scholar 

  4. Lachner, M. & Jenuwein, T. The many faces of histone lysine methylation. Curr. Opin. Cell Biol. 14, 286–298 (2002).

    Article  CAS  Google Scholar 

  5. Levine, S.S. et al. The core of the polycomb repressive complex is compositionally and functionally conserved in flies and humans. Mol. Cell. Biol. 22, 6070–6078 (2002).

    Article  CAS  Google Scholar 

  6. Dellino, G.I. et al. Polycomb silencing blocks transcription initiation. Mol. Cell 13, 887–893 (2004).

    Article  CAS  Google Scholar 

  7. Shao, Z. et al. Stabilization of chromatin structure by PRC1, a Polycomb complex. Cell 98, 37–46 (1999).

    Article  CAS  Google Scholar 

  8. Varambally, S. et al. The polycomb group protein EZH2 is involved in progression of prostate cancer. Nature 419, 624–629 (2002).

    Article  CAS  Google Scholar 

  9. Kleer, C.G. et al. EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells. Proc. Natl. Acad. Sci. USA 100, 11606–11611 (2003).

    Article  CAS  Google Scholar 

  10. Leung, C. et al. Bmi1 is essential for cerebellar development and is overexpressed in human medulloblastomas. Nature 428, 337–341 (2004).

    Article  CAS  Google Scholar 

  11. 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 

  12. Toyota, M. et al. CpG island methylator phenotype in colorectal cancer. Proc. Natl. Acad. Sci. USA 96, 8681–8686 (1999).

    Article  CAS  Google Scholar 

  13. Toyota, M. et al. Identification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification. Cancer Res. 59, 2307–2312 (1999).

    CAS  PubMed  Google Scholar 

  14. Cross, S.H., Charlton, J.A., Nan, X. & Bird, A.P. Purification of CpG islands using a methylated DNA binding column. Nat. Genet. 6, 236–244 (1994).

    Article  CAS  Google Scholar 

  15. Kirmizis, A. et al. Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27. Genes Dev. 18, 1592–1605 (2004).

    Article  CAS  Google Scholar 

  16. Bracken, A.P. et al. EZH2 is downstream of the pRB-E2F pathway, essential for proliferation and amplified in cancer. EMBO J. 22, 5323–5335 (2003).

    Article  CAS  Google Scholar 

  17. Bernstein, B.E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315–326 (2006).

    CAS  Google Scholar 

  18. Brennan, K.R. & Brown, A.M. Wnt proteins in mammary development and cancer. J. Mammary Gland Biol. Neoplasia 9, 119–131 (2004).

    Article  Google Scholar 

  19. Asatiani, E. et al. Deletion, methylation, and expression of the NKX3.1 suppressor gene in primary human prostate cancer. Cancer Res. 65, 1164–1173 (2005).

    Article  CAS  Google Scholar 

  20. Boyer, L.A. et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947–956 (2005).

    Article  CAS  Google Scholar 

  21. Schlesinger, Y. et al. Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat. Genet. 39, 232–236 (2007).

    Article  CAS  Google Scholar 

  22. Widschwendter, M. et al. Epigenetic stem cell signature in cancer. Nat. Genet. 39, 157–158 (2007).

    Article  CAS  Google Scholar 

  23. Ohm, J.E. et al. A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing. Nat. Genet. 39, 237–242 (2007).

    Article  CAS  Google Scholar 

  24. Vire, E. et al. The Polycomb group protein EZH2 directly controls DNA methylation. Nature 439, 871–874 (2006).

    Article  CAS  Google Scholar 

  25. Estecio, M.R. et al. High-throughput methylation profiling by MCA coupled to CpG island microarray. Genome Res. 17, 1529–1536 (2007).

    Article  CAS  Google Scholar 

  26. Shen, L. et al. Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters. PLoS Genet. 3, 2023–2036 (2007).

    Article  CAS  Google Scholar 

  27. Dey, A., Minucci, S. & Ozato, K. Ligand-dependent occupancy of the retinoic acid receptor beta 2 promoter in vivo. Mol. Cell. Biol. 14, 8191–8201 (1994).

    Article  CAS  Google Scholar 

  28. Benetti, R. et al. The death substrate Gas2 binds m-calpain and increases susceptibility to p53-dependent apoptosis. EMBO J. 20, 2702–2714 (2001).

    Article  CAS  Google Scholar 

  29. Issa, J.P. CpG island methylator phenotype in cancer. Nat. Rev. Cancer 4, 988–993 (2004).

    Article  CAS  Google Scholar 

  30. Plath, K. et al. Role of histone H3 lysine 27 methylation in X inactivation. Science 300, 131–135 (2003).

    Article  CAS  Google Scholar 

  31. Kondo, Y. & Issa, J.-P. Enrichment for histone H3 lysine 9 methylation at Alu repeats in human cells. J. Biol. Chem. 278, 27658–27662 (2003).

    Article  CAS  Google Scholar 

  32. Martens, J.H. et al. The profile of repeat-associated histone lysine methylation states in the mouse epigenome. EMBO J. 24, 800–812 (2005).

    Article  CAS  Google Scholar 

  33. Weinmann, A.S., Yan, P.S., Oberley, M.J., Huang, T.H. & Farnham, P.J. Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev. 16, 235–244 (2002).

    Article  CAS  Google Scholar 

  34. Pokholok, D.K. et al. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122, 517–527 (2005).

    Article  CAS  Google Scholar 

  35. 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 

  36. Colella, S., Shen, L., Baggerly, K.A., Issa, J.-P. & Krahe, R. Sensitive and quantitative universal Pyrosequencing methylation analysis of CpG sites. Biotechniques 35, 146–150 (2003).

    Article  CAS  Google Scholar 

  37. Campisi, J. Analysis of tumor suppressor gene-induced senescence. Methods Mol. Biol. 223, 155–172 (2003).

    CAS  PubMed  Google Scholar 

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Acknowledgements

This work was supported in part by US National Institutes of Health by grants P50CA100632, R33CA89837 and RO1CA098006 to J.-P.J.I. and grant P50CA058204 to B.K.-A. J.-P.J.I. is an American Cancer Society Clinical Research Professor supported by a generous gift from the F.M. Kirby Foundation. Y.K. was supported by an Odyssey Fellowship at the M.D. Anderson Cancer Center and the Cell Science Research Foundation. We especially thank Y. Guo and X. Chen for their technical assistance.

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Author notes

  1. Alfred S Cheng

    Present address: Present address: Institute of Digestive Disease, Faculty of Medicine, Chinese University of Hong Kong, Li Ka Shing Medical Sciences Building, Prince of Wales Hospital, Shatin, N.T. Hong Kong SAR.,

  2. Yutaka Kondo and Lanlan Shen: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Leukemia, University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, 77030, Texas, USA

    Yutaka Kondo, Lanlan Shen, Saira Ahmed, Yanis Boumber, Chantale Charo & Jean-Pierre J Issa

  2. Division of Molecular Oncology, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, 464-8681, Nagoya, Japan

    Yutaka Kondo & Yoshitaka Sekido

  3. Department of Molecular Virology, Human Cancer Genetics Program, Immunology, and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, 420 West 12th Avenue, Columbus, 43210, Ohio, USA

    Alfred S Cheng & Tim Hui-Ming Huang

  4. Department of Lymphoma/Myeloma, University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, 77030, Texas, USA

    Tadanori Yamochi

  5. Department of Biochemistry II, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, 466-8550, Nagoya, Japan

    Takeshi Urano & Koichi Furukawa

  6. Department of Pathology, Department of Veterans Affairs Medical Center, Baylor College of Medicine and Michael E. DeBakey, 1 Baylor Plaza, Houston, 77030, Texas, USA

    Bernard Kwabi-Addo

  7. Department of Biostatistics and Applied Mathematics, University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, 77030, Texas, USA

    David L Gold

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  1. Yutaka Kondo
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Contributions

Y.K. and J.-P.J.I. designed the research; Y.K., L.S., A.S.C., S.A., Y.B. and C.C. performed the research; T.Y., T.U., K.F., Y.S. and T.H.-M.H. designed the assays; D.L.G. analyzed microarray data; B.K.-A. collected and analyzed clinical samples; and Y.K. and J.-P.J.I. wrote the paper.

Corresponding author

Correspondence to Jean-Pierre J Issa.

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Kondo, Y., Shen, L., Cheng, A. et al. Gene silencing in cancer by histone H3 lysine 27 trimethylation independent of promoter DNA methylation. Nat Genet 40, 741–750 (2008). https://doi.org/10.1038/ng.159

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