The Breast Cancer Epigenome

Reviewer: John P. Plastaras, MD, PhD
The Abramson Cancer Center of the University of Pennsylvania
Last Modified: December 14, 2006

Presenter: M. Esteller
Affiliation: Spanish National Cancer Centre (CNIO), Madrid, Spain


  • Epigenetics is the study of information related to DNA that does not depend on the DNA sequence itself. Examples include methylation of DNA itself, modification of histones, and micro-RNA expression.
  • In general, the progression of normal cells to cancer cells involves a global decrease in cytosine methylation, but focused increase in cytosine methylation in the promoters of specific sequences.
  • Hypermethylation of CpG islands in these promoters can silence gene expression, hence a mechanism of turning off tumor suppressor genes without the requirement of a frank mutation


  • Whole genome-specific methylation of CpG islands can be studied by "ChIP on CHIP" analysis
    • The MBD protein binds to methylated DNA sequences
    • Using an antibody to MBD, chromatin immunoprecipitation (ChIP) can isolate hypermethlated DNA, which can be analyzed by microarray analysis on gene chips (ChIP on CHIP)


  • Like colon cancer, in breast cancer there is a global 40% loss of methylated cytosine, but hypermethylation (silencing) indicates which genes are turned off in tumors and tumor cell lines.
  • Every tumor type, has its own patter of hypermethylation
    • Cluster analysis of hypermethylated genes has implied that some cell lines thought to be breast cancer cell lines are more closely related to melanoma cell lines
  • Genes important in familial breast cancer are also epigenetically silenced
    • In sporatic tumors, BRCA1 expression was wiped out by a combination of loss of heterozygosity (gene deletion) and epigenetic silencing (hypermethylation)
    • In familial BRCA1 tumors, hypermethylation occasionally serves as an alternate mechanism for the "second hit," when there was not loss of heterozygosity.
    • Other known cancer genes are hypermethylated in breast cancers, such as those that affect DNA repair (hMLH1, MGMT, BRCA1), cell cycle (p16 INK4a, p14 ARF), and hormone receptors (ER, PR, AR), etc.
  • This approach revealed the novel importance of potential tumor suppressor genes.
    • In breast cancer specifically, the prolactin receptor is silenced
    • SRBC, a binding partner of BRCA1, is silenced in breast cancer as well, but only in tumors that had wild type BRCA1
    • WRN, the Werner syndrome gene associated with premature aging and increase cancer risk is silenced in a subset of breast cancers.
  • In addition to direct DNA hypermethylation, modification of histones is another epigenetic mechanism with implications in breast cancer
    • There is global loss of mono and trimethylation of histone H4 in cancer
    • Snail is a protein that induces methylation of histones, and its expression is associated with tumor progression

Author's Conclusions

  • Epigenetic effects are important in tumor progression
  • Unlike actual mutations in the DNA of tumor cells which can only be reversed with by gene therapy, epigenetic modifications may be amenable to drug therapy. This includes inhibitors of by DNA methylation (e.g. 5-azacytidine, Zebularine) and histone modification (e.g. the histone deacetylase inhibitor, SAHA)

Clinical/Scientific Implications

  • This was a general talk summarizing published work in the area of tumor epigenetics
    • Genetic tests have been useful clinically in breast cancer
    • Gene sequence tests are used in familial breast cancer (BRCA1, BRCA2) to guide therapy such as prophylactic mastectomy
    • RNA expression profiles, such as OncotypeDx, are used to determine prognosis
    • Epigenetic tests may complement these other test to inform prognosis and response to particular therapy
  • Pharmacologic modulators of epigenetic phenomenom are being tested clinically, but a limitation is the lack of genetic target specificity.