Distinct epigenetic changes in the stromal cells of breast cancers (original) (raw)

Nature Genetics volume 37, pages 899–905 (2005)Cite this article

Abstract

Increasing evidence suggests that changes in the cellular microenvironment contribute to tumorigenesis, but the molecular basis of these alterations is not well understood. Although epigenetic modifications of the neoplastic cells in tumors have been firmly implicated in tumorigenesis1, it is not known whether epigenetic modifications occur in the non-neoplastic stromal cells. To address this question in an unbiased and genome-wide manner, we developed a new method, methylation-specific digital karyotyping, and applied it to epithelial and myoepithelial cells, stromal fibroblasts from normal breast tissue, and in situ and invasive breast carcinomas. Our analyses showed that distinct epigenetic alterations occur in all three cell types during breast tumorigenesis in a tumor stage– and cell type–specific manner, suggesting that epigenetic changes have a role in the maintenance of the abnormal cellular microenvironment in breast cancer.

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References

  1. Fazzari, M.J. & Greally, J.M. Epigenomics: beyond CpG islands. Nat. Rev. Genet. 5, 446–455 (2004).
    Article CAS Google Scholar
  2. Allinen, M. et al. Molecular characterization of the tumor microenvironment in breast cancer. Cancer Cell 6, 17–32 (2004).
    Article CAS Google Scholar
  3. Bissell, M.J. & Radisky, D. Putting tumours in context. Nat. Rev. Cancer 1, 46–54 (2001).
    Article CAS Google Scholar
  4. Bissell, M.J., Radisky, D.C., Rizki, A., Weaver, V.M. & Petersen, O.W. The organizing principle: microenvironmental influences in the normal and malignant breast. Differentiation 70, 537–546 (2002).
    Article Google Scholar
  5. Tlsty, T.D. & Hein, P.W. Know thy neighbor: stromal cells can contribute oncogenic signals. Curr. Opin. Genet. Dev. 11, 54–59 (2001).
    Article CAS Google Scholar
  6. Jones, P.A. & Takai, D. The role of DNA methylation in mammalian epigenetics. Science 293, 1068–1070 (2001).
    Article CAS Google Scholar
  7. Feinberg, A.P. & Tycko, B. The history of cancer epigenetics. Nat. Rev. Cancer 4, 143–153 (2004).
    Article CAS Google Scholar
  8. Adany, R., Heimer, R., Caterson, B., Sorrell, J.M. & Iozzo, R.V. Altered expression of chondroitin sulfate proteoglycan in the stroma of human colon carcinoma. Hypomethylation of PG-40 gene correlates with increased PG-40 content and mRNA levels. J. Biol. Chem. 265, 11389–11396 (1990).
    CAS PubMed Google Scholar
  9. Adany, R. & Iozzo, R.V. Altered methylation of versican proteoglycan gene in human colon carcinoma. Biochem. Biophys. Res. Commun. 171, 1402–1413 (1990).
    Article CAS Google Scholar
  10. Adany, R. & Iozzo, R.V. Hypomethylation of the decorin proteoglycan gene in human colon cancer. Biochem. J. 276, 301–306 (1991).
    Article CAS Google Scholar
  11. Huang, T.H., Perry, M.R. & Laux, D.E. Methylation profiling of CpG islands in human breast cancer cells. Hum. Mol. Genet. 8, 459–470 (1999).
    Article CAS Google Scholar
  12. Shi, H. et al. Expressed CpG island sequence tag microarray for dual screening of DNA hypermethylation and gene silencing in cancer cells. Cancer Res. 62, 3214–3220 (2002).
    CAS PubMed Google Scholar
  13. Plass, C. Cancer epigenomics. Hum. Mol. Genet. 11, 2479–2488 (2002).
    Article CAS Google Scholar
  14. Wang, T.L. et al. Digital karyotyping. Proc. Natl. Acad. Sci. USA 99, 16156–16161 (2002).
    Article CAS Google Scholar
  15. Dai, Z. et al. An AscI boundary library for the studies of genetic and epigenetic alterations in CpG islands. Genome Res. 12, 1591–1598 (2002).
    Article CAS Google Scholar
  16. Rhee, I. et al. DNMT1 and DNMT3b cooperate to silence genes in human cancer cells. Nature 416, 552–556 (2002).
    Article CAS Google Scholar
  17. Paz, M.F. et al. Genetic unmasking of epigenetically silenced tumor suppressor genes in colon cancer cells deficient in DNA methyltransferases. Hum. Mol. Genet. 12, 2209–2219 (2003).
    Article CAS Google Scholar
  18. Shigematsu, H. et al. Aberrant methylation of HIN-1 (high in normal-1) is a frequent event in many human malignancies. Int. J. Cancer 113, 600–604 (2005).
    Article CAS Google Scholar
  19. Krop, I. et al. Frequent HIN-1 promoter methylation and lack of expression in multiple human tumor types. Mol. Cancer Res. 2, 489–494 (2004).
    CAS PubMed Google Scholar
  20. Krop, I.E. et al. HIN-1, a putative cytokine highly expressed in normal but not cancerous mammary epithelial cells. Proc. Natl. Acad. Sci. USA 98, 9796–9801 (2001).
    Article CAS Google Scholar
  21. Feinberg, A.P. & Vogelstein, B. Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301, 89–92 (1983).
    Article CAS Google Scholar
  22. Bocker, W. et al. Common adult stem cells in the human breast give rise to glandular and myoepithelial cell lineages: a new cell biological concept. Lab. Invest. 82, 737–746 (2002).
    Article Google Scholar
  23. Kremenskoy, M. et al. Genome-wide analysis of DNA methylation status of CpG islands in embryoid bodies, teratomas, and fetuses. Biochem. Biophys. Res. Commun. 311, 884–890 (2003).
    Article CAS Google Scholar
  24. Caron, H. et al. The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science 291, 1289–1292 (2001).
    Article CAS Google Scholar
  25. Ushijima, T. Detection and interpretation of altered methylation patterns in cancer cells. Nat. Rev. Cancer 5, 223–231 (2005).
    Article CAS Google Scholar
  26. Bell, A.C. & Felsenfeld, G. Methylation of a _CTCF_-dependent boundary controls imprinted expression of the IGF2 gene. Nature 405, 482–485 (2000).
    Article CAS Google Scholar
  27. Saha, S. et al. Using the transcriptome to annotate the genome. Nat. Biotechnol. 20, 508–512 (2002).
    Article CAS Google Scholar
  28. Cai, L. et al. Clustering analysis of SAGE data using a Poisson approach. Genome Biol. 5, R51 (2004).
    Article Google Scholar
  29. Herman, J.G., Graff, J.R., Myohanen, S., Nelkin, B.D. & Baylin, S.B. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc. Natl. Acad. Sci. USA 93, 9821–9826 (1996).
    Article CAS Google Scholar

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Acknowledgements

We thank A. Richardson, G. Lodeiro and R. Gomes for their help with the acquisition of human tissue samples; R. Gelman for help with statistical analysis; B. Vogelstein and K. Kinzler for providing genomic DNA from HCT116 wild-type and DKO cells and their continuous support and encouragement; and B. Vogelstein, I. Krop and other members of the laboratory of K.P. for critical reading of the manuscript and their constructive criticism throughout the execution of this project. This work was supported by the National Cancer Institute Specialized Program in Research Excellence in Breast Cancer at Dana-Farber/Harvard Cancer Center, by Department of Defense Breast Cancer Center of Excellence grants awarded to K.P. and by a Department of Defense Postdoctoral Fellowship grant awarded to J.Y.

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Authors and Affiliations

  1. Department of Medical Oncology, Dana Farber Cancer Institute, 44 Binney Street, Boston, 02115, Massachusetts, USA
    Min Hu, Jun Yao & Kornelia Polyak
  2. Harvard Medical School, Boston, 02115, Massachusetts, USA
    Min Hu, Jun Yao & Kornelia Polyak
  3. Research Computing, Dana Farber Cancer Institute, 44 Binney Street, Boston, 02115, Massachusetts, USA
    Li Cai
  4. University of Maryland, Greenebaum Cancer Center, Baltimore, 21201, Maryland, USA
    Kurt E Bachman
  5. Laboratory of Biology and Developmental Biology, University of Liège, Sart Tilman, Liège, B-4000, Belgium
    Frédéric van den Brûle
  6. Sidney Kimmel Cancer Center at Johns Hopkins University, Baltimore, 21231, Maryland, USA
    Victor Velculescu

Authors

  1. Min Hu
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  2. Jun Yao
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  3. Li Cai
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  4. Kurt E Bachman
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  5. Frédéric van den Brûle
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  6. Victor Velculescu
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  7. Kornelia Polyak
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Corresponding author

Correspondence toKornelia Polyak.

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Competing interests

M.H. and K.P. submitted a patent application on the MSDK method and the findings described in this manuscript, in accordance with the policies of the Dana Farber Cancer Institute.

Supplementary information

Supplementary Fig. 1

SNP array analysis of genomic DNA samples used for MSDK analysis. (PDF 139 kb)

Supplementary Fig. 2

Genome-wide overview of the location of CpG islands, predicted AscI sites overlayed with methylation (MDSK), and gene expression (SAGE) patterns. (PDF 196 kb)

Supplementary Table 1

Statistical analysis of MSDK libraries generated from HCT116 WT and DKO cells. (PDF 143 kb)

Supplementary Table 2

List of breast tissue samples used for methylation assays. (PDF 81 kb)

Supplementary Table 3

Statistical analysis of MSDK libraries generated from normal (N-EPI-7) and tumor (I-EPI-7) breast epithelial cells. (PDF 128 kb)

Supplementary Table 4

Statistical analysis of MSDK libraries generated from normal (N-STR-I7) and tumor (I-STR-7) breast stromal cells. (PDF 142 kb)

Supplementary Table 5

Statistical analysis of MSDK libraries generated from normal (N-MYOEP-4) and DCIS tumor (D-MYOEP-6) breast myoepithelial cells. (PDF 134 kb)

Supplementary Table 6

Statistical analysis of MSDK libraries generated from normal breast myoepithelial (N-MYOEP-4) and epithelial (N-EPI-I7) cells. (PDF 136 kb)

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Hu, M., Yao, J., Cai, L. et al. Distinct epigenetic changes in the stromal cells of breast cancers.Nat Genet 37, 899–905 (2005). https://doi.org/10.1038/ng1596

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