title: Epigenetic determinants of ovarian clear cell carcinoma biology.
abstract: Targeted approaches have revealed frequent epigenetic alterations in ovarian cancer, but the scope and relation of these changes to histologic subtype of disease is unclear. Genome-wide methylation and expression data for 14 clear cell carcinoma (CCC), 32 non-CCC and four corresponding normal cell lines were generated to determine how methylation profiles differ between cells of different histological derivations of ovarian cancer. Consensus clustering showed that CCC is epigenetically distinct. Inverse relationships between expression and methylation in CCC were identified, suggesting functional regulation by methylation, and included 22 hypomethylated (UM) genes and 276 hypermethylated (HM) genes. Categorical and pathway analyses indicated that the CCC-specific UM genes were involved in response to stress and many contain hepatocyte nuclear factor (HNF) 1-binding sites, while the CCC-specific HM genes included members of the estrogen receptor alpha (ERalpha) network and genes involved in tumor development. We independently validated the methylation status of 17 of these pathway-specific genes, and confirmed increased expression of HNF1 network genes and repression of ERalpha pathway genes in CCC cell lines and primary cancer tissues relative to non-CCC specimens. Treatment of three CCC cell lines with the demethylating agent Decitabine significantly induced expression for all five genes analyzed. Coordinate changes in pathway expression were confirmed using two primary ovarian cancer datasets (p < 0.0001 for both). Our results suggest that methylation regulates specific pathways and biological functions in CCC, with hypomethylation influencing the characteristic biology of the disease while hypermethylation contributes to the carcinogenic process.
authors.affiliation: Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC; Department of Gynecology and Obstetrics Graduate School of Medicine, Kyoto University, Kyoto, Japan.
authors.forename: Ken
authors.initials: K
authors.lastname: Yamaguchi
authors.forename: Zhiqing
authors.initials: Z
authors.lastname: Huang
authors.forename: Noriomi
authors.initials: N
authors.lastname: Matsumura
authors.forename: Masaki
authors.initials: M
authors.lastname: Mandai
authors.forename: Takako
authors.initials: T
authors.lastname: Okamoto
authors.forename: Tsukasa
authors.initials: T
authors.lastname: Baba
authors.forename: Ikuo
authors.initials: I
authors.lastname: Konishi
authors.forename: Andrew
authors.initials: A
authors.lastname: Berchuck
authors.forename: Susan K
authors.initials: SK
authors.lastname: Murphy
mesh_terms: D018262:Adenocarcinoma, Clear Cell / Q000235:genetics* / Q000473:pathology; D019175:DNA Methylation; D057890:Epigenomics; D005260:Female; D051537:Hepatocyte Nuclear Factor 1 / Q000235:genetics / Q000378:metabolism; D006801:Humans; D009367:Neoplasm Staging; D010051:Ovarian Neoplasms / Q000235:genetics* / Q000473:pathology; D060888:Real-Time Polymerase Chain Reaction; D014407:Tumor Cells, Cultured
chemical_list: D051537:Hepatocyte Nuclear Factor 1
keywords: ERalpha; HNF1; epigenetic characterization; methylation; ovarian clear cell carcinoma