Article | Published:

Increased methylation variation in epigenetic domains across cancer types

Nature Genetics volume 43, pages 768775 (2011) | Download Citation

Abstract

Tumor heterogeneity is a major barrier to effective cancer diagnosis and treatment. We recently identified cancer-specific differentially DNA-methylated regions (cDMRs) in colon cancer, which also distinguish normal tissue types from each other, suggesting that these cDMRs might be generalized across cancer types. Here we show stochastic methylation variation of the same cDMRs, distinguishing cancer from normal tissue, in colon, lung, breast, thyroid and Wilms' tumors, with intermediate variation in adenomas. Whole-genome bisulfite sequencing shows these variable cDMRs are related to loss of sharply delimited methylation boundaries at CpG islands. Furthermore, we find hypomethylation of discrete blocks encompassing half the genome, with extreme gene expression variability. Genes associated with the cDMRs and large blocks are involved in mitosis and matrix remodeling, respectively. We suggest a model for cancer involving loss of epigenetic stability of well-defined genomic domains that underlies increased methylation variability in cancer that may contribute to tumor heterogeneity.

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Acknowledgements

We thank C. Adams and Applied Biosystems, Inc. for supplying reagents for the sequencing experiments, B. Vogelstein, F. Giardiello and M. Zeiger for tumor samples and M. Newhouse for computer assistance. This work was supported by US National Institutes of Health grants R37CA054358, R01HG005220, 5P50HG003233, F32CA138111, 5R01GM083084 and R01DA025779 (K.Z.).

Author information

Author notes

    • Kasper Daniel Hansen
    • , Winston Timp
    • , Héctor Corrada Bravo
    • , Sarven Sabunciyan
    •  & Benjamin Langmead

    These authors contributed equally to this work.

Affiliations

  1. Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA.

    • Kasper Daniel Hansen
    • , Benjamin Langmead
    •  & Rafael A Irizarry
  2. Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

    • Kasper Daniel Hansen
    • , Winston Timp
    • , Héctor Corrada Bravo
    • , Sarven Sabunciyan
    • , Benjamin Langmead
    • , Oliver G McDonald
    • , Bo Wen
    • , Yun Liu
    • , Eirikur Briem
    • , Rafael A Irizarry
    •  & Andrew P Feinberg
  3. Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

    • Winston Timp
    • , Bo Wen
    • , Yun Liu
    • , Eirikur Briem
    •  & Andrew P Feinberg
  4. Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA.

    • Winston Timp
  5. Center for Bioinformatics and Computational Biology, Department of Computer Science, University of Maryland, College Park, Maryland, USA.

    • Héctor Corrada Bravo
  6. Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

    • Sarven Sabunciyan
  7. Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

    • Oliver G McDonald
  8. Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA.

    • Hao Wu
  9. Department of Bioengineering, Institute for Genomic Medicine and Institute of Engineering in Medicine, University of California at San Diego, San Diego, California, USA.

    • Dinh Diep
    •  & Kun Zhang

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Contributions

K.D.H. and R.A.I. wrote the DMR finder and smoothing algorithms. W.T. performed and analyzed the arrays with H.C.B., who wrote new software for this purpose. S.S. made the libraries and performed validation. B.L. wrote new methylation sequence alignment software. O.G.M. performed the histopathologic analysis. B.W. and H.W. performed LOCK experiments. Y.L. performed copy number experiments. D.D. and K.Z. performed bisulfite capture. E.B. performed the sequencing. R.A.I. and A.P.F. conceived and led the experiments and wrote the paper with the predominant assistance of K.D.H., W.T., H.C.B. and B.L.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Rafael A Irizarry or Andrew P Feinberg.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Note, Supplementary Tables 1, 2, 4–6, 8–10 and 13–19 and Supplementary Figures 1–24.

Excel files

  1. 1.

    Supplementary Table 3

    List of block locations

  2. 2.

    Supplementary Table 7

    List of small DMRs

  3. 3.

    Supplementary Table 11

    List of genes showing statistically significant over-expression in cancer compared to normal samples and are within 2,000 bp from an outward methylation boundary shift.

  4. 4.

    Supplementary Table 12

    Genes with higher gene expression variability in cancer compared to normal.

  5. 5.

    Supplementary Table 20

    As Supplementary Table 3, but for sample-specific blocks.

  6. 6.

    Supplementary Table 21

    As Supplementary Table 7, but for sample-specific small DMRs.

  7. 7.

    Supplementary Table 22

    Primers used for bisulfite pyrosequencing

  8. 8.

    Supplementary Table 23

    List of microarrays used to identify tissue-specific genes

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DOI

https://doi.org/10.1038/ng.865

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