title: DNA methylation and hormone receptor status in breast cancer.
abstract: BACKGROUND
  We examined whether differences in tumor DNA methylation were associated with more aggressive hormone receptor-negative breast cancer in an ethnically diverse group of patients in the Breast Cancer Care in Chicago (BCCC) study and using data from The Cancer Genome Atlas (TCGA).
  
  
  RESULTS
  DNA was extracted from formalin-fixed, paraffin-embedded samples on 75 patients (21 White, 31 African-American, and 23 Hispanic) (training dataset) enrolled in the BCCC. Hormone receptor status was defined as negative if tumors were negative for both estrogen and progesterone (ER/PR) receptors (N = 22/75). DNA methylation was analyzed at 1505 CpG sites within 807 gene promoters using the Illumina GoldenGate assay. Differential DNA methylation as a predictor of hormone receptor status was tested while controlling for false discovery rate and assigned to the gene closest to the respective CpG site. Next, those genes that predicted ER/PR status were validated using TCGA data with respect to DNA methylation (validation dataset), and correlations between CpG methylation and gene expression were examined. In the training dataset, 5.7 % of promoter mean methylation values (46/807) were associated with receptor status at P < 0.05; for 88 % of these (38/46), hypermethylation was associated with receptor-positive disease. Hypermethylation for FZD9, MME, BCAP31, HDAC9, PAX6, SCGB3A1, PDGFRA, IGFBP3, and PTGS2 genes most strongly predicted receptor-positive disease. Twenty-one of 24 predictor genes from the training dataset were confirmed in the validation dataset. The level of DNA methylation at 19 out 22 genes, for which gene expression data were available, was associated with gene activity.
  
  
  CONCLUSIONS
  Higher levels of promoter methylation strongly correlate with hormone receptor positive status of breast tumors. For most of the genes identified in our training dataset as ER/PR receptor status predictors, DNA methylation correlated with stable gene expression level. The predictors performed well when evaluated on independent set of samples, with different racioethnic distribution, thus providing evidence that this set of DNA methylation biomarkers will likely generalize to prospective patient samples.
authors.affiliation: Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago (UIC), M/C 669, 900 S. Ashland Ave., Chicago, 60607 IL USA.
authors.forename: Elizaveta V
authors.initials: EV
authors.lastname: Benevolenskaya
authors.affiliation: Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh.
authors.forename: Abul B M M K
authors.initials: AB
authors.lastname: Islam
authors.affiliation: Department of Health Sciences, The University of Chicago, Chicago, USA.
authors.forename: Habibul
authors.initials: H
authors.lastname: Ahsan
authors.affiliation: Department of Health Sciences, The University of Chicago, Chicago, USA.
authors.forename: Muhammad G
authors.initials: MG
authors.lastname: Kibriya
authors.affiliation: Department of Health Sciences, The University of Chicago, Chicago, USA.
authors.forename: Farzana
authors.initials: F
authors.lastname: Jasmine
authors.affiliation: Loyola University, Chicago, USA.
authors.forename: Ben
authors.initials: B
authors.lastname: Wolff
authors.affiliation: Division of Epidemiology and Biostatistics, School of Public Health, University of Illinois at Chicago (UIC), M/C 923, Chicago, 60612 IL USA.
authors.forename: Umaima
authors.initials: U
authors.lastname: Al-Alem
authors.affiliation: Department of Pathology, University of Illinois at Chicago, Chicago, USA.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Wiley
authors.affiliation: Department of Pathology, University of Illinois at Chicago, Chicago, USA.
authors.forename: Andre
authors.initials: A
authors.lastname: Kajdacsy-Balla
authors.affiliation: Department of Pathology, University of Illinois at Chicago, Chicago, USA.
authors.forename: Virgilia
authors.initials: V
authors.lastname: Macias
authors.affiliation: Division of Epidemiology and Biostatistics, School of Public Health, University of Illinois at Chicago (UIC), M/C 923, Chicago, 60612 IL USA.
authors.forename: Garth H
authors.initials: GH
authors.lastname: Rauscher
mesh_terms: D000368:Aged; D001943:Breast Neoplasms / Q000235:genetics* / Q000503:physiopathology; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005260:Female; D005819:Genetic Markers; D006801:Humans; D008875:Middle Aged; D011960:Receptors, Estrogen / Q000235:genetics / Q000502:physiology*; D011980:Receptors, Progesterone / Q000235:genetics / Q000502:physiology*
chemical_list: D005819:Genetic Markers; D011960:Receptors, Estrogen; D011980:Receptors, Progesterone
keywords: Breast cancer; DNA methylation; ER/PR hormone receptor status