title: Genome-wide DNA Methylation Profiling Reveals Methylation Markers Associated with 3q Gain for Detection of Cervical Precancer and Cancer.
abstract: Purpose:Epigenetic host cell changes involved in cervical cancer development following a persistent high-risk human papillomavirus (hrHPV) infection, provide promising markers for the management of hrHPV-positive women. In particular, markers based on DNA methylation of tumor suppressor gene promoters are valuable. These markers ideally identify hrHPV-positive women with precancer (CIN2/3) in need of treatment. Here, we set out to identify biologically relevant methylation markers by genome-wide methylation analysis of both hrHPV-transformed cell lines and cervical tissue specimens.Experimental Design and Results:Genome-wide discovery by next-generation sequencing (NGS) of methyl-binding domain-enriched DNA (MBD-Seq) yielded 20 candidate methylation target genes. Further verification and validation by multiplex-targeted bisulfite NGS and (quantitative) methylation-specific PCR (MSP) resulted in 3 genes (GHSR, SST, andZIC1) that showed a significant increase in methylation with severity of disease in both tissue specimens and cervical scrapes (P< 0.005). The area under the ROC curve for CIN3 or worse varied between 0.86 and 0.89. Within the group of CIN2/3, methylation levels of all 3 genes increased with duration of lesion existence (P< 0.0005), characterized by duration of preceding hrHPV infection, and were significantly higher in the presence of a 3q gain (P< 0.05) in the corresponding tissue biopsy.Conclusions:By unbiased genome-wide DNA methylation profiling and comprehensive stepwise verification and validation studies usingin vitroand patient-derived samples, we identified 3 promising methylation markers (GHSR, SST, andZIC1)associated with a 3q gain for the detection of cervical (pre)cancer.Clin Cancer Res; 23(14); 3813-22. ©2017 AACR.
authors.affiliation: Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands.
authors.forename: Wina
authors.initials: W
authors.lastname: Verlaat
authors.affiliation: Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands.
authors.forename: Peter J F
authors.initials: PJF
authors.lastname: Snijders
authors.affiliation: Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands.|Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, the Netherlands.
authors.forename: Putri W
authors.initials: PW
authors.lastname: Novianti
authors.affiliation: Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands.
authors.forename: Saskia M
authors.initials: SM
authors.lastname: Wilting
authors.affiliation: Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands.
authors.forename: Lise M A
authors.initials: LMA
authors.lastname: De Strooper
authors.affiliation: Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium.
authors.forename: Geert
authors.initials: G
authors.lastname: Trooskens
authors.affiliation: Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium.
authors.forename: Johan
authors.initials: J
authors.lastname: Vandersmissen
authors.affiliation: Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium.
authors.forename: Wim
authors.initials: W
authors.lastname: Van Criekinge
authors.affiliation: Department of Gynecologic Oncology, Cancer Research Center Groningen, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
authors.forename: G Bea A
authors.initials: GBA
authors.lastname: Wisman
authors.affiliation: Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands.
authors.forename: Chris J L M
authors.initials: CJLM
authors.lastname: Meijer
authors.affiliation: Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands.
authors.forename: Daniëlle A M
authors.initials: DAM
authors.lastname: Heideman
authors.affiliation: Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands. r.steenbergen@vumc.nl.
authors.forename: Renske D M
authors.initials: RDM
authors.lastname: Steenbergen
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics; D045744:Cell Line, Tumor; D002893:Chromosomes, Human, Pair 3 / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D005260:Female; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D027383:Papillomaviridae / Q000472:pathogenicity; D011230:Precancerous Conditions / Q000235:genetics* / Q000473:pathology; D054440:Receptors, Ghrelin / Q000235:genetics*; D013004:Somatostatin / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics*; D002583:Uterine Cervical Neoplasms / Q000235:genetics* / Q000473:pathology
chemical_list: D014408:Biomarkers, Tumor; D054440:Receptors, Ghrelin; D014157:Transcription Factors; C492123:ZIC1 protein, human; D013004:Somatostatin