title: Comprehensive methylome analysis of ovarian tumors reveals hedgehog signaling pathway regulators as prognostic DNA methylation biomarkers.
abstract: Women with advanced stage ovarian cancer (OC) have a five-year survival rate of less than 25%. OC progression is associated with accumulation of epigenetic alterations and aberrant DNA methylation in gene promoters acts as an inactivating "hit" during OC initiation and progression. Abnormal DNA methylation in OC has been used to predict disease outcome and therapy response. To globally examine DNA methylation in OC, we used next-generation sequencing technology, MethylCap-sequencing, to screen 75 malignant and 26 normal or benign ovarian tissues. Differential DNA methylation regions (DMRs) were identified, and the Kaplan-Meier method and Cox proportional hazard model were used to correlate methylation with clinical endpoints. Functional role of specific genes identified by MethylCap-sequencing was examined in in vitro assays. We identified 577 DMRs that distinguished (p < 0.001) malignant from non-malignant ovarian tissues; of these, 63 DMRs correlated (p < 0.001) with poor progression free survival (PFS). Concordant hypermethylation and corresponding gene silencing of sonic hedgehog pathway members ZIC1 and ZIC4 in OC tumors was confirmed in a panel of OC cell lines, and ZIC1 and ZIC4 repression correlated with increased proliferation, migration and invasion. ZIC1 promoter hypermethylation correlated (p < 0.01) with poor PFS. In summary, we identified functional DNA methylation biomarkers significantly associated with clinical outcome in OC and suggest our comprehensive methylome analysis has significant translational potential for guiding the design of future clinical investigations targeting the OC epigenome. Methylation of ZIC1, a putative tumor suppressor, may be a novel determinant of OC outcome.
authors.affiliation: Department of Obstetrics and Gynecology; Tri-Service General Hospital; National Defense Medical Center; Taiwan, Republic of China; Laboratory of Epigenetics; Cancer Stem Cells; National Defense Medical Center; Taiwan, Republic of China; Institute of Biomedical Informatics of National Yang-Ming University at Taipei; Taiwan, Republic of China.
authors.forename: Rui-Lan
authors.initials: RL
authors.lastname: Huang
authors.forename: Fei
authors.initials: F
authors.lastname: Gu
authors.forename: Nameer B
authors.initials: NB
authors.lastname: Kirma
authors.forename: Jianhua
authors.initials: J
authors.lastname: Ruan
authors.forename: Chun-Liang
authors.initials: CL
authors.lastname: Chen
authors.forename: Hui-Chen
authors.initials: HC
authors.lastname: Wang
authors.forename: Yu-Ping
authors.initials: YP
authors.lastname: Liao
authors.forename: Cheng-Chang
authors.initials: CC
authors.lastname: Chang
authors.forename: Mu-Hsien
authors.initials: MH
authors.lastname: Yu
authors.forename: Jay M
authors.initials: JM
authors.lastname: Pilrose
authors.forename: Ian M
authors.initials: IM
authors.lastname: Thompson
authors.forename: Hsuan-Cheng
authors.initials: HC
authors.lastname: Huang
authors.forename: Tim Hui-Ming
authors.initials: TH
authors.lastname: Huang
authors.forename: Hung-Cheng
authors.initials: HC
authors.lastname: Lai
authors.forename: Kenneth P
authors.initials: KP
authors.lastname: Nephew
mesh_terms: D000818:Animals; D000970:Antineoplastic Agents / Q000008:administration & dosage; D000077216:Carcinoma, Ovarian Epithelial; D045744:Cell Line, Tumor; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D018572:Disease-Free Survival; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053823:Hedgehog Proteins / Q000378:metabolism*; D006801:Humans; D009375:Neoplasms, Glandular and Epithelial / Q000188:drug therapy / Q000235:genetics* / Q000378:metabolism* / Q000473:pathology; D009419:Nerve Tissue Proteins / Q000235:genetics* / Q000378:metabolism; D010051:Ovarian Neoplasms / Q000188:drug therapy / Q000235:genetics* / Q000378:metabolism* / Q000473:pathology; D011401:Promoter Regions, Genetic; D016016:Proportional Hazards Models; D015398:Signal Transduction; D016019:Survival Analysis; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
chemical_list: D000970:Antineoplastic Agents; D004268:DNA-Binding Proteins; D053823:Hedgehog Proteins; C489325:MBD2 protein, human; D009419:Nerve Tissue Proteins; D014157:Transcription Factors; C492123:ZIC1 protein, human; C492799:ZIC4 protein, human
keywords: DNA methylation; Hedgehog pathway; ZIC1; ZIC4; ovarian cancer