title: Nonpromoter methylation of the CDKN2A gene with active transcription is associated with improved locoregional control in laryngeal squamous cell carcinoma.
abstract: We previously reported a novel association between CDKN2A nonpromoter methylation and transcription (ARF/INK4a) in human papillomavirus associated oropharyngeal tumors. In this study we assessed whether nonpromoter CDKN2A methylation in laryngeal squamous cell carcinomas (LXSCC) conferred a similar association with transcription that predicted patient outcome. We compared DNA methylation and ARF/INK4a RNA expression levels for the CDKN2A locus using the Illumina HumanMethylation27 beadchip and RT-PCR in 43 LXSCC tumor samples collected from a prospective study of head and neck cancer patients treated at Montefiore Medical Center (MMC). Validation was performed using RNAseq data on 111 LXSCC tumor samples from the Cancer Genome Atlas (TCGA). The clinical relevance of combined nonpromoter CDKN2A methylation and transcription was assessed by multivariate Cox regression for locoregional recurrence on a subset of 69 LXSCC patients with complete clinicopathologic data from the MMC and TCGA cohorts. We found evidence of CDKN2A nonpromoter hypermethylation in a third of LXSCC from our MMC cohort, which was significantly associated with increased ARF and INK4a RNA expression (Wilcoxon rank-sum, P = 0.007 and 0.003, respectively). A similar association was confirmed in TCGA samples (Wilcoxon rank-sum test P < 0.0001 for ARF and INK4a). Patients with CDKN2A hypermethylation or high ARF/INK4a expression were significantly less likely to develop a locoregional recurrence compared to those with neither of the features, independent of other clinicopatholgic risk factors (adjusted hazard ratio=0.21, 95% confidence interval:0.05-0.81). These results support the conclusion that CDKN2A nonpromoter methylation is associated with increased ARF and INK4a RNA expression, and improved locoregional control in LXSCC.
authors.affiliation: Department of Pathology, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York.
authors.forename: Miriam M
authors.initials: MM
authors.lastname: Ben-Dayan
authors.affiliation: Department of Pathology, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York.|Department of Otorhinolaryngology-Head and Neck Surgery, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York.
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Ow
authors.affiliation: Department of Pathology, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York.|Dicipline of Oncology, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland.
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Belbin
authors.affiliation: Department of Pathology, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York.
authors.forename: Joshua
authors.initials: J
authors.lastname: Wetzler
authors.affiliation: Department of Otorhinolaryngology-Head and Neck Surgery, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York.
authors.forename: Richard V
authors.initials: RV
authors.lastname: Smith
authors.affiliation: Department of Pathology, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York.
authors.forename: Geoffrey
authors.initials: G
authors.lastname: Childs
authors.affiliation: Department of Epidemiology, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania.
authors.forename: Brenda
authors.initials: B
authors.lastname: Diergaarde
authors.affiliation: Department of Otolaryngology/Head and Neck Cancer Surgery, University of North Carolina, Chapel Hill, North Carolina.
authors.forename: D Neil
authors.initials: DN
authors.lastname: Hayes
authors.affiliation: Departments of Otolaryngology Head and Neck Surgery, University of California, San Francisco, California.|Department of Clinical and Translational Science Institute, University of California, San Francisco, California.
authors.forename: Jennifer R
authors.initials: JR
authors.lastname: Grandis
authors.affiliation: Department of Pathology, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York.
authors.forename: Michael B
authors.initials: MB
authors.lastname: Prystowsky
authors.affiliation: Departments of Epidemiology & Population Health and Medicine, Albert Einstein College of Medicine, Bronx, New York.
authors.forename: Nicolas F
authors.initials: NF
authors.lastname: Schlecht
mesh_terms: D002294:Carcinoma, Squamous Cell / Q000235:genetics*; D019941:Cyclin-Dependent Kinase Inhibitor p16; D050763:Cyclin-Dependent Kinase Inhibitor p18 / Q000235:genetics*; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008297:Male; D009364:Neoplasm Recurrence, Local / Q000235:genetics*; D009959:Oropharyngeal Neoplasms / Q000235:genetics*; D011379:Prognosis; D011446:Prospective Studies; D017423:Sequence Analysis, RNA; D015533:Transcriptional Activation; D015854:Up-Regulation
chemical_list: C000614131:CDKN2A protein, human; D019941:Cyclin-Dependent Kinase Inhibitor p16; D050763:Cyclin-Dependent Kinase Inhibitor p18
keywords: CDKN2A; gene transcription; larynx cancer; methylation; p14(ARF); p16(INK4a); tumor biomarkers