title: Unique DNA methylation loci distinguish anatomic site and HPV status in head and neck squamous cell carcinoma.
abstract: OBJECTIVE
  We have used a genome-wide approach to identify novel differentially methylated CpG dinucleotides that are seen in different anatomic sites of head and neck squamous cell carcinoma (HNSCC), as well as those that might be related to HPV status in the oropharynx.
  
  
  METHODS
  We conducted genome-wide DNA methylation profiling of primary tumor samples and corresponding adjacent mucosa from 118 HNSCC patients undergoing treatment at Montefiore Medical Center, Bronx, NY, using the Illumina HumanMethylation27 beadchip. For each matched tissue set, we measured differentially methylated CpG loci using a change in methylation level (M-value).
  
  
  RESULTS
  When datasets were individually analyzed by anatomic site of the primary tumor, we identified 293 differentially methylated CpG loci in oral cavity squamous cell carcinoma (SCC), 219 differentially methylated CpG loci in laryngeal SCC, and 460 differentially methylated in oropharyngeal SCC. A subset of these differentially methylated CpG loci was common across all anatomic sites of HNSCC. Stratification by HPV status revealed a significantly higher number of differentially methylated CpG loci in HPV+ patients.
  
  
  CONCLUSIONS
  Novel epigenetic biomarkers derived from clinical HNSCC specimens can be used as molecular classifiers of this disease, revealing many new avenues of investigation for this disease.
authors.affiliation: Authors' Affiliations: Departments of Pathology; Epidemiology & Population Health; Pediatrics, Microbiology & Immunology; Obstetrics, Gynecology & Women's Health, Albert Einstein College of Medicine; and Department of Otorhinolaryngology-Head and Neck Surgery, Montefiore Medical Center, Medical Arts Pavilion, Bronx, New York.
authors.forename: Roberto A
authors.initials: RA
authors.lastname: Lleras
authors.forename: Richard V
authors.initials: RV
authors.lastname: Smith
authors.forename: Leslie R
authors.initials: LR
authors.lastname: Adrien
authors.forename: Nicolas F
authors.initials: NF
authors.lastname: Schlecht
authors.forename: Robert D
authors.initials: RD
authors.lastname: Burk
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Harris
authors.forename: Geoffrey
authors.initials: G
authors.lastname: Childs
authors.forename: Michael B
authors.initials: MB
authors.lastname: Prystowsky
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Belbin
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D002294:Carcinoma, Squamous Cell / Q000235:genetics* / Q000473:pathology* / Q000821:virology; D018899:CpG Islands; D019175:DNA Methylation; D005260:Female; D020869:Gene Expression Profiling; D056426:Genetic Loci; D006258:Head and Neck Neoplasms / Q000235:genetics* / Q000473:pathology* / Q000821:virology; D006801:Humans; D008297:Male; D008875:Middle Aged; D009367:Neoplasm Staging; D027383:Papillomaviridae / Q000235:genetics; D030361:Papillomavirus Infections / Q000821:virology; D000077195:Squamous Cell Carcinoma of Head and Neck; D014412:Tumor Virus Infections / Q000821:virology; D043222:Ubiquitin Thiolesterase / Q000235:genetics; D055815:Young Adult
chemical_list: C482860:UCHL1 protein, human; D043222:Ubiquitin Thiolesterase
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