Research article

Methylation of homeobox genes is a frequent and early epigenetic event in breast cancer

Stella Tommasi¹ , Deborah L Karm¹ , Xiwei Wu² , Yun Yen³ and Gerd P Pfeifer¹

¹  Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA

²  Division of Information Sciences, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA

³  Department of Clinical and Molecular Pharmacology, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA

author email corresponding author email

Breast Cancer Research 2009, 11:R14doi:10.1186/bcr2233

Published:	27 February 2009

Abstract

Introduction

Aberrant methylation of CpG islands is a hallmark of cancer and occurs at an early stage in breast tumorigenesis. However, its impact on tumor development is not fully determined, and its potential as a diagnostic biomarker remains to be validated. Methylation profiling of invasive breast carcinoma has been largely explored. Conversely, very little and sparse information is available on early-stage breast cancer. To gain insight into the epigenetic switches that may promote and/or contribute to the initial neoplastic events during breast carcinogenesis, we have analyzed the DNA methylation profile of ductal carcinoma in situ, a premalignant breast lesion with a great potential to progress toward invasive carcinoma.

Methods

We have utilized a comprehensive and sensitive array-based DNA mapping technique, the methylated-CpG island recovery assay, to profile the DNA methylation pattern in ductal carcinoma in situ. Differential methylation of CpG islands was compared genome-wide in tumor DNA versus normal DNA utilizing a statistical linear model in the LIMMA software package.

Results

Using this approach, we have identified 108 significant CpG islands that undergo aberrant DNA methylation in ductal carcinoma in situ and stage I breast tumors, with methylation frequencies greater than or comparable with those of more advanced invasive carcinoma (50% to 93%). A substantial fraction of these hypermethylated CpG islands (32% of the annotated CpG islands) is associated with several homeobox genes, such as the TLX1, HOXB13, and HNF1B genes. Fifty-three percent of the genes hypermethylated in early-stage breast cancer overlap with known Polycomb targets and include homeobox genes and other developmental transcription factors.

Conclusions

We have identified a series of new potential methylation biomarkers that may help elucidate the underlying mechanisms of breast tumorigenesis. More specifically, our results are suggestive of a critical role of homeobox gene methylation in the insurgence and/or progression of breast cancer.