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Genome-wide methylation analysis identifies genes specific to breast cancer hormone receptor status and risk of recurrence.

Publication ,  Journal Article
Fackler, MJ; Umbricht, CB; Williams, D; Argani, P; Cruz, L-A; Merino, VF; Teo, WW; Zhang, Z; Huang, P; Visvananthan, K; Marks, J; Ethier, S ...
Published in: Cancer Res
October 1, 2011

To better understand the biology of hormone receptor-positive and-negative breast cancer and to identify methylated gene markers of disease progression, we carried out a genome-wide methylation array analysis on 103 primary invasive breast cancers and 21 normal breast samples, using the Illumina Infinium HumanMethylation27 array that queried 27,578 CpG loci. Estrogen and/or progesterone receptor-positive tumors displayed more hypermethylated loci than estrogen receptor (ER)-negative tumors. However, the hypermethylated loci in ER-negative tumors were clustered closer to the transcriptional start site compared with ER-positive tumors. An ER-classifier set of CpG loci was identified, which independently partitioned primary tumors into ER subtypes. A total of 40 (32 novel and 8 previously known) CpG loci showed differential methylation specific to either ER-positive or ER-negative tumors. Each of the 40 ER subtype-specific loci was validated in silico, using an independent, publicly available methylome dataset from the Cancer Genome Atlas. In addition, we identified 100 methylated CpG loci that were significantly associated with disease progression; the majority of these loci were informative particularly in ER-negative breast cancer. Overall, the set was highly enriched in homeobox containing genes. This pilot study shows the robustness of the breast cancer methylome and illustrates its potential to stratify and reveal biological differences between ER subtypes of breast cancer. Furthermore, it defines candidate ER-specific markers and identifies potential markers predictive of outcome within ER subgroups.

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Published In

Cancer Res

DOI

EISSN

1538-7445

Publication Date

October 1, 2011

Volume

71

Issue

19

Start / End Page

6195 / 6207

Location

United States

Related Subject Headings

  • Recurrence
  • Receptors, Estrogen
  • Oncology & Carcinogenesis
  • Humans
  • Genome-Wide Association Study
  • Genes, Neoplasm
  • Female
  • Disease Progression
  • DNA Methylation
  • CpG Islands
 

Citation

APA
Chicago
ICMJE
MLA
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Fackler, M. J., Umbricht, C. B., Williams, D., Argani, P., Cruz, L.-A., Merino, V. F., … Sukumar, S. (2011). Genome-wide methylation analysis identifies genes specific to breast cancer hormone receptor status and risk of recurrence. Cancer Res, 71(19), 6195–6207. https://doi.org/10.1158/0008-5472.CAN-11-1630
Fackler, Mary Jo, Christopher B. Umbricht, Danielle Williams, Pedram Argani, Leigh-Ann Cruz, Vanessa F. Merino, Wei Wen Teo, et al. “Genome-wide methylation analysis identifies genes specific to breast cancer hormone receptor status and risk of recurrence.Cancer Res 71, no. 19 (October 1, 2011): 6195–6207. https://doi.org/10.1158/0008-5472.CAN-11-1630.
Fackler MJ, Umbricht CB, Williams D, Argani P, Cruz L-A, Merino VF, et al. Genome-wide methylation analysis identifies genes specific to breast cancer hormone receptor status and risk of recurrence. Cancer Res. 2011 Oct 1;71(19):6195–207.
Fackler, Mary Jo, et al. “Genome-wide methylation analysis identifies genes specific to breast cancer hormone receptor status and risk of recurrence.Cancer Res, vol. 71, no. 19, Oct. 2011, pp. 6195–207. Pubmed, doi:10.1158/0008-5472.CAN-11-1630.
Fackler MJ, Umbricht CB, Williams D, Argani P, Cruz L-A, Merino VF, Teo WW, Zhang Z, Huang P, Visvananthan K, Marks J, Ethier S, Gray JW, Wolff AC, Cope LM, Sukumar S. Genome-wide methylation analysis identifies genes specific to breast cancer hormone receptor status and risk of recurrence. Cancer Res. 2011 Oct 1;71(19):6195–6207.

Published In

Cancer Res

DOI

EISSN

1538-7445

Publication Date

October 1, 2011

Volume

71

Issue

19

Start / End Page

6195 / 6207

Location

United States

Related Subject Headings

  • Recurrence
  • Receptors, Estrogen
  • Oncology & Carcinogenesis
  • Humans
  • Genome-Wide Association Study
  • Genes, Neoplasm
  • Female
  • Disease Progression
  • DNA Methylation
  • CpG Islands