title: Novel epigenetic changes in CDKN2A are associated with progression of cervical intraepithelial neoplasia.
abstract: To conduct a comprehensive mapping of the genomic DNA methylation in CDKN2A, which codes for the p16(INK4A) and p14(ARF) proteins, and 14 of the most promising DNA methylation marker candidates previously reported to be associated with progression of low-grade cervical intraepithelial neoplasia (CIN1) to cervical cancer.
  
  
  
  We analyzed DNA methylation in 68 HIV-seropositive and negative women with incident CIN1, CIN2, CIN3 and invasive cervical cancer, assaying 120 CpG dinucleotide sites spanning APC, CDH1, CDH13, CDKN2A, CDKN2B, DAPK1, FHIT, GSTP1, HIC1, MGMT, MLH1, RARB, RASSF1, TERT and TIMP3 using the Illumina Infinium array. Validation was performed using high resolution mapping of the target genes with HELP-tagging for 286 CpGs, followed by fine mapping of candidate genes with targeted bisulfite sequencing. We assessed for statistical differences in DNA methylation levels for each CpG loci assayed using univariate and multivariate methods correcting for multiple comparisons.
  
  
  
  In our discovery sample set, we identified dose dependent differences in DNA methylation with grade of disease in CDKN2A, APC, MGMT, MLH1 and HIC1, whereas single CpG locus differences between CIN2/3 and cancer groups were seen for CDH13, DAPK1 and TERT. Only those CpGs in the gene body of CDKN2A showed a monotonic increase in methylation between persistent CIN1, CIN2, CIN3 and cancers.
  
  
  
  Our data suggests a novel link between early cervical disease progression and DNA methylation in a region downstream of the CDKN2A transcription start site that may lead to increased p16(INK4A)/p14(ARF) expression prior to development of malignant disease.
authors.affiliation: Department of Genetics and Center for Epigenomics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
authors.forename: N Ari
authors.initials: NA
authors.lastname: Wijetunga
authors.affiliation: Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Belbin
authors.affiliation: Department of Pediatrics (Genetics), Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
authors.forename: Robert D
authors.initials: RD
authors.lastname: Burk
authors.affiliation: Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
authors.forename: Kathleen
authors.initials: K
authors.lastname: Whitney
authors.affiliation: Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
authors.forename: Maria
authors.initials: M
authors.lastname: Abadi
authors.affiliation: Department of Genetics and Center for Epigenomics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Pediatrics (Genetics), Albert Einstein College of Medicine, Bronx, NY 10461, USA. Electronic address: john.greally@einstein.yu.edu.
authors.forename: John M
authors.initials: JM
authors.lastname: Greally
authors.affiliation: Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA. Electronic address: mark.einstein@einstein.yu.edu.
authors.forename: Mark H
authors.initials: MH
authors.lastname: Einstein
authors.affiliation: Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine (Oncology), Albert Einstein College of Medicine, Bronx, NY 10461, USA. Electronic address: nicolas.schlecht@einstein.yu.edu.
authors.forename: Nicolas F
authors.initials: NF
authors.lastname: Schlecht
mesh_terms: D000328:Adult; D000368:Aged; D019941:Cyclin-Dependent Kinase Inhibitor p16 / Q000096:biosynthesis / Q000235:genetics; D050763:Cyclin-Dependent Kinase Inhibitor p18 / Q000096:biosynthesis / Q000235:genetics*; D019175:DNA Methylation; D018450:Disease Progression; D044127:Epigenesis, Genetic; D005260:Female; D016147:Genes, Tumor Suppressor; D019942:Genes, p16; D006801:Humans; D008875:Middle Aged; D015513:Oncogene Proteins / Q000096:biosynthesis / Q000235:genetics; D002583:Uterine Cervical Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D055815:Young Adult; D002578:Uterine Cervical Dysplasia / Q000235:genetics* / Q000378:metabolism / Q000473:pathology
chemical_list: C401561:CDK2AP2 protein, human; C000614131:CDKN2A protein, human; D019941:Cyclin-Dependent Kinase Inhibitor p16; D050763:Cyclin-Dependent Kinase Inhibitor p18; D015513:Oncogene Proteins
keywords: Biomarker; CIN; Cervical cancer; Methylation; p14; p16