title: Novel approaches to global mining of aberrantly methylated promoter sites in squamous head and neck cancer.
abstract: OBJECTIVE
  Promoter hypermethylation is emerging as a promising molecular strategy for early detection of cancer. We examined promoter methylation status of 1143 cancer-associated genes to perform a global but unbiased inspection of methylated regions in head and neck squamous cell carcinoma (HNSCC).
  
  
  METHODS
  Laboratory-based study.
  
  
  METHODS
  Integrated health care system.
  
  
  METHODS
  Five samples, two frozen primary HNSCC biopsies and three HNSCC cell lines, were examined. Whole genomic DNA was interrogated using a combination of DNA immunoprecipitation (IP) and Affymetrix whole-genome tiling arrays.
  
  
  RESULTS
  Of the 1143 unique cancer genes on the array, 265 were recorded across five samples. Of the 265 genes, 55 were present in all five samples, and 36 were common to four of five samples, 46 to three of five, 56 to two of five, and 72 to one of five samples. Hypermethylated genes in the five samples were cross-examined against those in PubMeth, a cancer methylation database combining text mining and expert annotation (http://www.pubmeth.org). Of the 441 genes in PubMeth, only 33 are referenced to HNSCC. We matched 34 genes in our samples to the 441 genes in the PubMeth database. Of the 34 genes, eight are reported in PubMeth as HNSCC associated.
  
  
  CONCLUSIONS
  This pilot study examined the contribution of global DNA hypermethylation to the pathogenesis of HNSCC. The whole-genome methylation approach indicated 231 new genes with methylated promoter regions not yet reported in HNSCC. Examination of this comprehensive gene panel in a larger HNSCC cohort should advance selection of HNSCC-specific candidate genes for further validation as biomarkers in HNSCC.
authors.affiliation: Department of Otolaryngology-Head and Neck Surgery, Henry Ford Hospital, Detroit, MI 48202, USA. mworsha1@hfhs.org
authors.forename: Maria J
authors.initials: MJ
authors.lastname: Worsham
authors.forename: Kang Mei
authors.initials: KM
authors.lastname: Chen
authors.forename: Josena K
authors.initials: JK
authors.lastname: Stephen
authors.forename: Shaleta
authors.initials: S
authors.lastname: Havard
authors.forename: Michael S
authors.initials: MS
authors.lastname: Benninger
mesh_terms: D000368:Aged; D002294:Carcinoma, Squamous Cell / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D045744:Cell Line, Tumor; D015331:Cohort Studies; D019175:DNA Methylation / Q000235:genetics*; D005240:Feasibility Studies; D005260:Female; D052138:Genes, Neoplasm / Q000502:physiology*; D006258:Head and Neck Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D006801:Humans; D047468:Immunoprecipitation; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D010865:Pilot Projects; D016133:Polymerase Chain Reaction; D011401:Promoter Regions, Genetic / Q000235:genetics*