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Quantitative analysis of associations between DNA hypermethylation, hypomethylation, and DNMT RNA levels in ovarian tumors

Oncogene volume 25, pages 2636–2645 (2006)Cite this article

Abstract

How hypermethylation and hypomethylation of different parts of the genome in cancer are related to each other and to DNA methyltransferase (DNMT) gene expression is ill defined. We used ovarian epithelial tumors of different malignant potential to look for associations between 5′-gene region or promoter hypermethylation, satellite, or global DNA hypomethylation, and RNA levels for ten DNMT isoforms. In the quantitative MethyLight assay, six of the 55 examined gene loci (LTB4R, MTHFR, CDH13, PGR, CDH1, and IGSF4) were significantly hypermethylated relative to the degree of malignancy (after adjustment for multiple comparisons; P<0.001). Importantly, hypermethylation of these genes was associated with degree of malignancy independently of the association of satellite or global DNA hypomethylation with degree of malignancy. Cancer-related increases in methylation of only two studied genes, LTB4R and MTHFR, which were appreciably methylated even in control tissues, were associated with DNMT1 RNA levels. Cancer-linked satellite DNA hypomethylation was independent of RNA levels for all DNMT3B isoforms, despite the ICF syndrome-linked DNMT3B deficiency causing juxtacentromeric satellite DNA hypomethylation. Our results suggest that there is not a simple association of gene hypermethylation in cancer with altered DNMT RNA levels, and that this hypermethylation is neither the result nor the cause of satellite and global DNA hypomethylation.

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Acknowledgements

We thank Kazuko Arakawa for her excellent assistance in statistical computing. This work was supported in part by NIH Grants CA81506 (to ME), CA96958 (to PWL), and PO1CA46589 and PO1 CA70972 (to EF).

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Authors and Affiliations

  1. Department of Biochemistry, Tulane Cancer Center, and Human Genetics Program, Tulane Medical School, New Orleans, LA, USA

    M Ehrlich, C B Woods & F Yang

  2. University of Minnesota Cancer Center, Minneapolis, Minnesota, USA

    M C Yu

  3. Department of Pathology, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA, USA

    L Dubeau

  4. Department of Biochemistry, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA, USA

    M Campan, D J Weisenberger, Ti Long & P W Laird

  5. Department of Surgery and Molecular Biology, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA, USA

    D J Weisenberger, Ti Long & P W Laird

  6. Department of Biochemical Pharmacology, American Health Foundation, Valhalla, NY, USA

    B Youn

  7. New York University School of Medicine, Tuxedo, NY, USA

    E S Fiala

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  1. M Ehrlich
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  2. C B Woods
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Correspondence to M Ehrlich.

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Supplementary Information accompanies the paper on Oncogene website (http://www.nature.com/onc).

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Ehrlich, M., Woods, C., Yu, M. et al. Quantitative analysis of associations between DNA hypermethylation, hypomethylation, and DNMT RNA levels in ovarian tumors. Oncogene 25, 2636–2645 (2006). https://doi.org/10.1038/sj.onc.1209145

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