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

Stella Tommasi, Deborah L. Karm, Xiwei Wu, Yun Yen, Gerd P. Pfeifer

Research output: Contribution to journalArticle

106 Citations (Scopus)

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.

Original languageEnglish
Article numberR14
JournalBreast Cancer Research
Volume11
Issue number1
DOIs
Publication statusPublished - Feb 27 2009
Externally publishedYes

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CpG Islands
Homeobox Genes
Epigenomics
Methylation
Breast Neoplasms
Carcinoma, Intraductal, Noninfiltrating
Breast
DNA Methylation
Carcinogenesis
Biomarkers
Carcinoma
Neoplasms
DNA
Statistical Models
Oligonucleotide Array Sequence Analysis
Genes
Linear Models
Transcription Factors
Software
Genome

ASJC Scopus subject areas

  • Cancer Research
  • Oncology
  • Medicine(all)

Cite this

Methylation of homeobox genes is a frequent and early epigenetic event in breast cancer. / Tommasi, Stella; Karm, Deborah L.; Wu, Xiwei; Yen, Yun; Pfeifer, Gerd P.

In: Breast Cancer Research, Vol. 11, No. 1, R14, 27.02.2009.

Research output: Contribution to journalArticle

Tommasi, Stella ; Karm, Deborah L. ; Wu, Xiwei ; Yen, Yun ; Pfeifer, Gerd P. / Methylation of homeobox genes is a frequent and early epigenetic event in breast cancer. In: Breast Cancer Research. 2009 ; Vol. 11, No. 1.
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AB - 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.

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