title: Genome-wide methylation screen in low-grade breast cancer identifies novel epigenetically altered genes as potential biomarkers for tumor diagnosis.
abstract: Aberrant DNA methylation constitutes a well-established epigenetic marker for breast cancer. Changes in methylation early in cancer development may be clinically relevant for cancer detection and prognosis-based therapeutic decisions. In the present study, a combination of methyl-CpG immunoprecipitation (MCIp) and human CpG island (CGI) arrays was applied to compare genome-wide DNA methylation profiles in 10 low-grade in situ and invasive breast cancers against 10 normal breast samples. In total, 214 CGIs were found to be hypermethylated in ≥6 of 10 tumors. Functional term enrichment analyses revealed an overrepresentation of homeobox genes and genes involved in transcription and regulation of transcription. Significant hypermethylation of 11 selected genes in tumor vs. normal tissue was validated in two independent sample sets (45 tumors and 11 controls, 43 tumors and 8 controls) using quantitative EpiTyper technology. In tumors, median methylation levels of BCAN, HOXD1, KCTD8, KLF11, NXPH1, POU4F1, SIM1, and TCF7L1 were ≥30% higher than in normal samples, representing potential biomarkers for tumor diagnosis. Using the 90th percentile of methylation levels in normal tissue as cutoff value, 62-92% of in situ samples (n=13), 72-97% of invasive samples from the first validation set (n=32), and 86-100% of invasive samples from the second validation set (n=43) were classified as hypermethylated. Hypermethylation of KLF11 and SIM1 might also be associated with increased risk of developing metastases. In summary, early methylation changes are frequent in the low-grade pathway of breast cancer and may be useful in the development of differential diagnostic and possibly also prognostic markers.
authors.affiliation: German Cancer Research Center (DKFZ), Division of Epigenomics and Cancer Risk Factors, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
authors.forename: Marta
authors.initials: M
authors.lastname: Faryna
authors.forename: Carolin
authors.initials: C
authors.lastname: Konermann
authors.forename: Sebastian
authors.initials: S
authors.lastname: Aulmann
authors.forename: Justo Lorenzo
authors.initials: JL
authors.lastname: Bermejo
authors.forename: Markus
authors.initials: M
authors.lastname: Brugger
authors.forename: Sven
authors.initials: S
authors.lastname: Diederichs
authors.forename: Joachim
authors.initials: J
authors.lastname: Rom
authors.forename: Dieter
authors.initials: D
authors.lastname: Weichenhan
authors.forename: Rainer
authors.initials: R
authors.lastname: Claus
authors.forename: Michael
authors.initials: M
authors.lastname: Rehli
authors.forename: Peter
authors.initials: P
authors.lastname: Schirmacher
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Sinn
authors.forename: Christoph
authors.initials: C
authors.lastname: Plass
authors.forename: Clarissa
authors.initials: C
authors.lastname: Gerhauser
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D051017:Apoptosis Regulatory Proteins; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics; D014408:Biomarkers, Tumor / Q000235:genetics*; D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology; D058581:Brevican / Q000235:genetics; D018797:Cell Cycle Proteins / Q000235:genetics; D019175:DNA Methylation; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D055106:Genome-Wide Association Study / Q000379:methods*; D006023:Glycoproteins / Q000235:genetics; D018398:Homeodomain Proteins / Q000235:genetics; D006801:Humans; D061986:MCF-7 Cells; D008875:Middle Aged; D060787:Neoplasm Grading; D009367:Neoplasm Staging; D009479:Neuropeptides / Q000235:genetics; D012097:Repressor Proteins / Q000235:genetics; D058125:Transcription Factor 7-Like 1 Protein / Q000235:genetics; D050819:Transcription Factor Brn-3A / Q000235:genetics
chemical_list: D051017:Apoptosis Regulatory Proteins; D051792:Basic Helix-Loop-Helix Proteins; D014408:Biomarkers, Tumor; D058581:Brevican; D018797:Cell Cycle Proteins; D006023:Glycoproteins; D018398:Homeodomain Proteins; D009479:Neuropeptides; D012097:Repressor Proteins; D058125:Transcription Factor 7-Like 1 Protein; D050819:Transcription Factor Brn-3A; C546938:BCAN protein, human; C442019:HOXD1 protein, human; C115117:KLF11 protein, human; C494188:POU4F1 protein, human; C491094:SIM1 protein, human; C544912:TCF7L1 protein, human; C112162:neurexophilin