title: Methylation of human papillomavirus type 16 genome and risk of cervical precancer in a Costa Rican population.
abstract: BACKGROUND
  Previous studies have suggested an association between human papillomavirus type 16 (HPV16) genome methylation and cervical intraepithelial neoplasia grade 3 (CIN3) (ie, cervical precancer) and cancer, but the results have been inconsistent.
  
  
  METHODS
  We designed a case-control study within a large prospective cohort of women who underwent multiple screenings for cervical cancer in Guanacaste, Costa Rica. Diagnostic specimens were collected at the time of CIN3 diagnosis (n = 30 case subjects) and persistent HPV16 infection (persistence; n = 35 case subjects), prediagnostic specimens at the first HPV16-positive screening visit (n = 20 CIN3 case subjects; n = 35 persistence case subjects), and control specimens from women with infection clearance within 2 years (n = 34 control subjects). DNA extracted from specimens (cervical cells) was analyzed for methylation levels at 67 CpG sites throughout the HPV16 genome using pyrosequencing. Benjamini-Hochberg method was used to account for multiple testing. Associations between methylation levels and risk of CIN3 or persistence were assessed using logistic regression models to estimate odds ratios (ORs) and 95% confidence intervals (CIs).
  
  
  RESULTS
  Increased methylation in diagnostic vs control specimens at nine CpG sites, three in each L1, L2, and E2/E4 genomic regions, was associated with an increased risk of CIN3 (third tertile [high] vs first and second tertiles combined [low], OR = 3.29 [95% CI = 1.16 to 9.34] to 11.12 [95% CI = 2.29 to 76.80]) and persistence. High methylation at three of these CpG sites was associated with a much higher risk when combined compared with low methylation at these sites (OR = 52, 95% CI = 4.0 to 670). In prediagnostic vs control specimens, increased methylation at a CpG site (nucleotide position 4261) in L2 was associated with an increased risk of CIN3.
  
  
  CONCLUSIONS
  In this HPV16-infected cohort, increased methylation of CpG sites within the HPV16 genome before diagnosis and at the time of diagnosis was associated with cervical precancer.
authors.affiliation: Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, 6120 Executive Blvd, EPS/7101, Rockville, MD 20892, USA. mirabellol@mail.nih.gov
authors.forename: Lisa
authors.initials: L
authors.lastname: Mirabello
authors.forename: Chang
authors.initials: C
authors.lastname: Sun
authors.forename: Arpita
authors.initials: A
authors.lastname: Ghosh
authors.forename: Ana C
authors.initials: AC
authors.lastname: Rodriguez
authors.forename: Mark
authors.initials: M
authors.lastname: Schiffman
authors.forename: Nicolas
authors.initials: N
authors.lastname: Wentzensen
authors.forename: Allan
authors.initials: A
authors.lastname: Hildesheim
authors.forename: Rolando
authors.initials: R
authors.lastname: Herrero
authors.forename: Sholom
authors.initials: S
authors.lastname: Wacholder
authors.forename: Attila
authors.initials: A
authors.lastname: Lorincz
authors.forename: Robert D
authors.initials: RD
authors.lastname: Burk
mesh_terms: D000328:Adult; D000368:Aged; D016022:Case-Control Studies; D003364:Costa Rica / Q000453:epidemiology; D018899:CpG Islands / Q000235:genetics*; D019175:DNA Methylation; D055088:Early Detection of Cancer; D005260:Female; D016679:Genome, Viral / Q000235:genetics*; D052162:Human papillomavirus 16 / Q000235:genetics*; D006801:Humans; D016015:Logistic Models; D008875:Middle Aged; D016017:Odds Ratio; D011446:Prospective Studies; D018570:Risk Assessment; D012307:Risk Factors; D002583:Uterine Cervical Neoplasms / Q000175:diagnosis / Q000453:epidemiology / Q000821:virology*; D002578:Uterine Cervical Dysplasia / Q000175:diagnosis / Q000453:epidemiology / Q000821:virology*