title: Next-Generation Sequencing Approach in Methylation Analysis of HNF1B and GATA4 Genes: Searching for Biomarkers in Ovarian Cancer.
abstract: DNA methylation is well-known to be associated with ovarian cancer (OC) and has great potential to serve as a biomarker in monitoring response to therapy and for disease screening. The purpose of this study was to investigate methylation ofHNF1BandGATA4and correlate detected methylation with clinicopathological characteristic of OC patients. The study group consisted of 64 patients with OC and 35 control patients. To determine the most important sites ofHNF1BandGATA4, we used next-generation sequencing. For further confirmation of detected methylation of selected regions, we used high-resolution melting analysis and methylation-specific real-time polymerase chain reaction (PCR). Selected regions ofHNF1BandGATA4were completely methylation free in all control samples, whereas methylation-positive pattern was observed in 32.8% (HNF1B) and 45.3% (GATA4) of OC samples. Evaluating both genes together, we were able to detect methylation in 65.6% of OC patients. We observed a statistically significant difference inHNF1Bmethylation between samples with different stages of OC. We also detected subtype specific methylation inGATA4and a decrease of methylation in late stages of OC. The combination of unmethylatedHNF1Band methylatedGATA4was associated with longer overall survival. In our study, we employed innovative approach of methylation analysis ofHNF1BandGATA4to search for possible epigenetic biomarkers. We confirmed the significance of theHNF1BandGATA4hypermethylation with emphasis on the need of selecting the most relevant sites for analysis. We suggest selected CpGs to be further examined as a potential positive prognostic factor.
authors.affiliation: Institute of Clinical Biochemistry and Diagnostics, Charles University Faculty of Medicine and University Hospital Hradec Kralove, 500 05 Hradec Kralove, Czech Republic. ivana.bubancova@fnhk.cz.
authors.forename: Ivana
authors.initials: I
authors.lastname: Bubancova
authors.affiliation: Institute of Clinical Biochemistry and Diagnostics, Charles University Faculty of Medicine and University Hospital Hradec Kralove, 500 05 Hradec Kralove, Czech Republic. kovarikovahe@lfhk.cuni.cz.
authors.forename: Helena
authors.initials: H
authors.lastname: Kovarikova
authors.affiliation: The Fingerland Department of Pathology, Charles University Faculty of Medicine and University Hospital Hradec Kralove, 500 05 Hradec Kralove, Czech Republic. lacoj@lfhk.cuni.cz.
authors.forename: Jan
authors.initials: J
authors.lastname: Laco
authors.affiliation: Department of Clinical Genetics, University Hospital Hradec Kralove, 500 05 Hradec Kralove, Czech Republic. ema.ruszova@fnhk.cz.
authors.forename: Ema
authors.initials: E
authors.lastname: Ruszova
authors.affiliation: Department of Obstetrics and Gynecology, Charles University Faculty of Medicine and University Hospital Hradec Kralove, 500 05 Hradec Kralove, Czech Republic. ondrej.dvorak@fnhk.cz.
authors.forename: Ondrej
authors.initials: O
authors.lastname: Dvorak
authors.affiliation: Institute of Clinical Biochemistry and Diagnostics, Charles University Faculty of Medicine and University Hospital Hradec Kralove, 500 05 Hradec Kralove, Czech Republic. palicka@lfhk.cuni.cz.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Palicka
authors.affiliation: Institute of Clinical Biochemistry and Diagnostics, Charles University Faculty of Medicine and University Hospital Hradec Kralove, 500 05 Hradec Kralove, Czech Republic. marcela.chmelarova@fnhk.cz.
authors.forename: Marcela
authors.initials: M
authors.lastname: Chmelarova
mesh_terms: D000328:Adult; D000368:Aged; D014408:Biomarkers, Tumor; D019175:DNA Methylation; D005260:Female; D005500:Follow-Up Studies; D050991:GATA4 Transcription Factor / Q000235:genetics* / Q000378:metabolism; D015972:Gene Expression Regulation, Neoplastic; D051539:Hepatocyte Nuclear Factor 1-beta / Q000235:genetics* / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D053208:Kaplan-Meier Estimate; D008875:Middle Aged; D060787:Neoplasm Grading; D009367:Neoplasm Staging; D010051:Ovarian Neoplasms / Q000175:diagnosis / Q000235:genetics* / Q000378:metabolism / Q000401:mortality; D011379:Prognosis; D011401:Promoter Regions, Genetic
chemical_list: D014408:Biomarkers, Tumor; D050991:GATA4 Transcription Factor; D051539:Hepatocyte Nuclear Factor 1-beta
keywords: GATA4; HNF1B; biomarker; methylation; next-generation sequencing; ovarian cancer