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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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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

Authors
  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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