title: Genome-wide methylome analysis using MethylCap-seq uncovers 4 hypermethylated markers with high sensitivity for both adeno- and squamous-cell cervical carcinoma.
abstract: BACKGROUND
  Cytology-based screening methods for cervical adenocarcinoma (ADC) and to a lesser extent squamous-cell carcinoma (SCC) suffer from low sensitivity. DNA hypermethylation analysis in cervical scrapings may improve detection of SCC, but few methylation markers have been described for ADC. We aimed to identify novel methylation markers for the early detection of both ADC and SCC.
  
  
  RESULTS
  Genome-wide methylation profiling for 20 normal cervices, 6 ADC and 6 SCC using MethylCap-seq yielded 53 candidate regions hypermethylated in both ADC and SCC. Verification and independent validation of the 15 most significant regions revealed 5 markers with differential methylation between 17 normals and 13 cancers. Quantitative methylation-specific PCR on cervical cancer scrapings resulted in detection rates ranging between 80% and 92% while between 94% and 99% of control scrapings tested negative. Four markers (SLC6A5, SOX1, SOX14 and TBX20) detected ADC and SCC with similar sensitivity. In scrapings from women referred with an abnormal smear (n=229), CIN3+ sensitivity was between 36% and 71%, while between 71% and 93% of adenocarcinoma in situ (AdCIS) were detected; and CIN0/1 specificity was between 88% and 98%. Compared to hrHPV, the combination SOX1/SOX14 showed a similar CIN3+ sensitivity (80% vs. 75%, respectively, P>0.2), while specificity improved (42% vs. 84%, respectively, P < 10-5).
  
  
  CONCLUSIONS
  SOX1 and SOX14 are methylation biomarkers applicable for screening of all cervical cancer types.
authors.affiliation: Department of Gynecologic Oncology, University of Groningen, University Medical Centre Groningen, Cancer Research Centre Groningen, Groningen, The Netherlands.|Department of Laboratory Medicine, Tianjin Medical University, Tianjin, China.
authors.forename: Rong
authors.initials: R
authors.lastname: Wang
authors.affiliation: Department of Gynecologic Oncology, University of Groningen, University Medical Centre Groningen, Cancer Research Centre Groningen, Groningen, The Netherlands.
authors.forename: Robert W
authors.initials: RW
authors.lastname: van Leeuwen
authors.affiliation: Department of Gynecologic Oncology, University of Groningen, University Medical Centre Groningen, Cancer Research Centre Groningen, Groningen, The Netherlands.
authors.forename: Aniek
authors.initials: A
authors.lastname: Boers
authors.affiliation: Department of Gynecologic Oncology, University of Groningen, University Medical Centre Groningen, Cancer Research Centre Groningen, Groningen, The Netherlands.
authors.forename: Harry G
authors.initials: HG
authors.lastname: Klip
authors.affiliation: Department of Mathematical Modeling, Statistics and Bio-informatics, University of Ghent, Ghent, Belgium.
authors.forename: Tim
authors.initials: T
authors.lastname: de Meyer
authors.affiliation: Department of Pathology, VU University Medical Centre, Amsterdam, The Netherlands.
authors.forename: Renske D M
authors.initials: RD
authors.lastname: Steenbergen
authors.affiliation: Department of Mathematical Modeling, Statistics and Bio-informatics, University of Ghent, Ghent, Belgium.
authors.forename: Wim
authors.initials: W
authors.lastname: van Criekinge
authors.affiliation: Department of Gynecologic Oncology, University of Groningen, University Medical Centre Groningen, Cancer Research Centre Groningen, Groningen, The Netherlands.
authors.forename: Ate G J
authors.initials: AG
authors.lastname: van der Zee
authors.affiliation: Department of Pathology, University of Groningen, University Medical Centre Groningen, Cancer Research Centre Groningen, Groningen, The Netherlands.
authors.forename: Ed
authors.initials: E
authors.lastname: Schuuring
authors.affiliation: Department of Gynecologic Oncology, University of Groningen, University Medical Centre Groningen, Cancer Research Centre Groningen, Groningen, The Netherlands.
authors.forename: G Bea A
authors.initials: GB
authors.lastname: Wisman
mesh_terms: D065311:Adenocarcinoma in Situ / Q000235:genetics* / Q000473:pathology; D000328:Adult; D000368:Aged; D014408:Biomarkers, Tumor / Q000235:genetics*; D018196:Carcinoma, Adenosquamous / Q000235:genetics* / Q000473:pathology; D002294:Carcinoma, Squamous Cell / Q000235:genetics* / Q000473:pathology; D016022:Case-Control Studies; D019175:DNA Methylation; D055088:Early Detection of Cancer; D005260:Female; D020869:Gene Expression Profiling; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D051097:Glial Cell Line-Derived Neurotrophic Factor Receptors / Q000235:genetics; D050487:Glycine Plasma Membrane Transport Proteins / Q000235:genetics; D006801:Humans; D008875:Middle Aged; D010641:Phenotype; D011237:Predictive Value of Tests; D011379:Prognosis; D015203:Reproducibility of Results; D055748:SOXB1 Transcription Factors / Q000235:genetics; D055749:SOXB2 Transcription Factors / Q000235:genetics; D020825:T-Box Domain Proteins / Q000235:genetics; D002583:Uterine Cervical Neoplasms / Q000235:genetics* / Q000473:pathology; D014626:Vaginal Smears; D002578:Uterine Cervical Dysplasia / Q000235:genetics* / Q000473:pathology
chemical_list: D014408:Biomarkers, Tumor; C494987:GFRA1 protein, human; D051097:Glial Cell Line-Derived Neurotrophic Factor Receptors; D050487:Glycine Plasma Membrane Transport Proteins; C493271:SLC6A5 protein, human; C490906:SOX1 protein, human; C117478:SOX14 protein, human; D055748:SOXB1 Transcription Factors; D055749:SOXB2 Transcription Factors; D020825:T-Box Domain Proteins; C420984:TBX20 protein, human
keywords: (quantitative) methylation-specific PCR ((Q)MSP); DNA methylation biomarkers; MethylCap-seq; adenocarcinoma (in situ); uterine cervical neoplasms