title: Quantitative methylation-specific PCR for the detection of aberrant DNA methylation in liquid-based Pap tests.
abstract: BACKGROUND
  Aberrant promoter methylation of selective tumor suppressor genes has been detected in squamous intraepithelial lesions (SIL) and invasive cervical cancer. Identification of methylation profiles of genes that can distinguish high-grade SIL (HSIL) from low-grade SIL (LSIL), and cytologically negative for intraepithelial lesion or malignancy (NILM) residual liquid-based Papanicolaou (Pap) tests may be potentially useful as an ancillary test for cervical cancer screening.
  
  
  METHODS
  Using real-time quantitative methylation-specific polymerase chain reaction (PCR) (QMSP), the authors analyzed the frequency and relative level of promoter methylation for DAPK1, IGSF4, SPARC, and TFPI2 in biopsy-confirmed HSIL and LSIL, and NILM residual liquid-based Pap tests. The percentage of methylation (%M) for each gene was calculated using the reference gene, ACTB. The cumulative methylation score for each sample, defined as the sum of %M of all 4 genes, was used to analyze the genes in combination.
  
  
  RESULTS
  For each gene analyzed the frequency and relative level of methylation were increased in HSIL compared with combined NILM/LSIL samples. The cumulative methylation scores were significantly higher in HSIL samples (P < .0001). Area under the receiver operating characteristic (ROC) curve (AUC) demonstrated that methylation of each gene could distinguish HSIL from NILM/LSIL samples (AUC range, 0.6-0.67; P < or = .0028). The combination of 4 genes showed improved test performance (AUC = 0.76; P < .0001). There was no significant difference in cumulative methylation in HSIL cases with histologic outcomes of cervical intraepithelial neoplasia grade 2 (CIN2) versus CIN3. There was no association between the methylation of any gene and the presence of human papillomavirus.
  
  
  CONCLUSIONS
  The methylation profile of multiple genes in combination can better distinguish HSIL from combined NILM/LSIL samples. Although aberrant DNA methylation has the potential to function as a molecular biomarker of HSIL in liquid-based Pap tests, additional genes that are selectively methylated in HSIL are needed to improve the clinical performance.
authors.affiliation: Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.
authors.forename: Steven L
authors.initials: SL
authors.lastname: Kahn
authors.forename: Brigitte M
authors.initials: BM
authors.lastname: Ronnett
authors.forename: Patti E
authors.initials: PE
authors.lastname: Gravitt
authors.forename: Karen S
authors.initials: KS
authors.lastname: Gustafson
mesh_terms: D000328:Adult; D014408:Biomarkers, Tumor / Q000032:analysis*; D019175:DNA Methylation; D005260:Female; D006801:Humans; D008875:Middle Aged; D065006:Papanicolaou Test; D016133:Polymerase Chain Reaction / Q000379:methods*; D012680:Sensitivity and Specificity; D002583:Uterine Cervical Neoplasms / Q000175:diagnosis*; D014626:Vaginal Smears / Q000379:methods*; D002578:Uterine Cervical Dysplasia / Q000175:diagnosis*
chemical_list: D014408:Biomarkers, Tumor