title: Global alterations of DNA methylation in cholangiocarcinoma target the Wnt signaling pathway.
abstract: The molecular mechanisms underlying the genesis of cholangiocarcinomas (CCs) are poorly understood. Epigenetic changes such as aberrant hypermethylation and subsequent atypical gene expression are characteristic features of most human cancers. In CC, data regarding global methylation changes are lacking so far. We performed a genome-wide analysis for aberrant promoter methylation in human CCs. We profiled 10 intrahepatic and 8 extrahepatic CCs in comparison to non-neoplastic biliary tissue specimens, using methyl-CpG immunoprecipitation (MCIp) combined with whole-genome CpG island arrays. DNA methylation was confirmed by quantitative mass spectrometric analysis and functional relevance of promoter hypermethylation was shown in demethylation experiments of two CC cell lines using 5-aza-2'deoxycytidine (DAC) treatment. Immunohistochemical staining of tissue microarrays (TMAs) from 223 biliary tract cancers (BTCs) was used to analyze candidate gene expression at the protein level. Differentially methylated, promoter-associated regions were nonrandomly distributed and enriched for genes involved in cancer-related pathways including Wnt, transforming growth factor beta (TGF-β), and PI3K signaling pathways. In CC cell lines, silencing of genes involved in Wnt signaling, such as SOX17, WNT3A, DKK2, SFRP1, SFRP2, and SFRP4 was reversed after DAC administration. Candidate protein SFRP2 was substantially down-regulated in neoplastic tissues of all BTC subtypes as compared to normal tissues. A significant inverse correlation of SFRP2 protein expression and pT status was found in BTC patients.
  
  
  CONCLUSIONS
  We provide a comprehensive analysis to define the genome-wide methylation landscape of human CC. Several candidate genes of cancer-relevant signaling pathways were identified, and closer analysis of selected Wnt pathway genes confirmed the relevance of this pathway in CC. The presented global methylation data are the basis for future studies on epigenetic changes in cholangiocarcinogenesis.
authors.affiliation: Institute of Pathology, University Hospital Heidelberg, Germany.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Goeppert
authors.forename: Carolin
authors.initials: C
authors.lastname: Konermann
authors.forename: Christopher Roman
authors.initials: CR
authors.lastname: Schmidt
authors.forename: Olga
authors.initials: O
authors.lastname: Bogatyrova
authors.forename: Lea
authors.initials: L
authors.lastname: Geiselhart
authors.forename: Christina
authors.initials: C
authors.lastname: Ernst
authors.forename: Lei
authors.initials: L
authors.lastname: Gu
authors.forename: Natalia
authors.initials: N
authors.lastname: Becker
authors.forename: Manuela
authors.initials: M
authors.lastname: Zucknick
authors.forename: Arianeb
authors.initials: A
authors.lastname: Mehrabi
authors.forename: Mohammadreza
authors.initials: M
authors.lastname: Hafezi
authors.forename: Frederick
authors.initials: F
authors.lastname: Klauschen
authors.forename: Albrecht
authors.initials: A
authors.lastname: Stenzinger
authors.forename: Arne
authors.initials: A
authors.lastname: Warth
authors.forename: Kai
authors.initials: K
authors.lastname: Breuhahn
authors.forename: Marcus
authors.initials: M
authors.lastname: Renner
authors.forename: Wilko
authors.initials: W
authors.lastname: Weichert
authors.forename: Peter
authors.initials: P
authors.lastname: Schirmacher
authors.forename: Christoph
authors.initials: C
authors.lastname: Plass
authors.forename: Dieter
authors.initials: D
authors.lastname: Weichenhan
mesh_terms: D000328:Adult; D000368:Aged; D001650:Bile Duct Neoplasms / Q000235:genetics / Q000473:pathology / Q000503:physiopathology*; D017734:Bile Ducts, Extrahepatic; D001653:Bile Ducts, Intrahepatic; D045744:Cell Line, Tumor; D018281:Cholangiocarcinoma / Q000235:genetics / Q000473:pathology / Q000503:physiopathology*; D018899:CpG Islands / Q000235:genetics / Q000502:physiology; D019175:DNA Methylation / Q000235:genetics / Q000502:physiology*; D004273:DNA, Neoplasm / Q000235:genetics / Q000502:physiology*; D044127:Epigenesis, Genetic / Q000235:genetics / Q000502:physiology; D005260:Female; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics / Q000502:physiology; D055106:Genome-Wide Association Study; D006801:Humans; D008099:Liver / Q000378:metabolism / Q000473:pathology; D008297:Male; D008565:Membrane Proteins / Q000378:metabolism; D008875:Middle Aged; D015398:Signal Transduction / Q000235:genetics / Q000502:physiology*; D051153:Wnt Proteins / Q000235:genetics / Q000502:physiology*; D000094742:Secreted Frizzled-Related Proteins
chemical_list: D004273:DNA, Neoplasm; D008565:Membrane Proteins; D051153:Wnt Proteins; C109618:SFRP2 protein, human; D000094742:Secreted Frizzled-Related Proteins