title: Global hypomethylation identifies Loci targeted for hypermethylation in head and neck cancer.
abstract: OBJECTIVE
  The human epigenome is profoundly altered in cancers, with a characteristic loss of methylation in repetitive regions and concomitant accumulation of gene promoter methylation. The degree to which these processes are coordinated is unclear so we investigated both in head and neck squamous cell carcinomas.
  
  
  METHODS
  Global methylation was measured using the luminometric methylation assay (LUMA) and pyrosequencing of LINE-1Hs and AluYb8 repetitive elements in a series of 138 tumors. We also measured methylation of more than 27,000 CpG loci with the Illumina HumanMethylation27 Microarray (n = 91).
  
  
  RESULTS
  LINE-1 methylation was significantly associated with LUMA and Infinium loci methylation (Spearman's ρ = 0.52/ρ = 0.56, both P < 0.001) but not that of AluYb8. Methylation of LINE-1, AluYb8, and Infinium loci differed by tumor site (each Kruskal-Wallis, P < 0.05). Also, LINE-1 and LUMA methylation were associated with HPV16 E6 serology (each Mann-Whitney, P < 0.05). Comparing LINE-1 methylation to gene-associated methylation, we identified a distinct subset of CpG loci with significant hypermethylation associated with LINE-1 hypomethylation. An investigation of sequence features for these CpG loci revealed that they were significantly less likely to reside in repetitive elements (Gene Set Enrichment Analysis, P < 0.02), enriched in CpG islands (P < 0.001) and were proximal to transcription factor-binding sites (P < 0.05). We validated the top CpG loci that had significant hypermethylation associated with LINE-1 hypomethylation (at EVI2A, IFRD1, KLHL6, and PTPRCAP) by pyrosequencing independent tumors.
  
  
  CONCLUSIONS
  These data indicate that global hypomethylation and gene-specific methylation processes are associated in a sequence-dependent manner, and that clinical characteristics and exposures leading to HNSCC may be influencing these processes.
authors.affiliation: Departments of Molecular Pharmacology and Physiology, Community Health-Center for Environmental Health and Technology, and Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA.
authors.forename: Graham M
authors.initials: GM
authors.lastname: Poage
authors.forename: E Andres
authors.initials: EA
authors.lastname: Houseman
authors.forename: Brock C
authors.initials: BC
authors.lastname: Christensen
authors.forename: Rondi A
authors.initials: RA
authors.lastname: Butler
authors.forename: Michele
authors.initials: M
authors.lastname: Avissar-Whiting
authors.forename: Michael D
authors.initials: MD
authors.lastname: McClean
authors.forename: Tim
authors.initials: T
authors.lastname: Waterboer
authors.forename: Michael
authors.initials: M
authors.lastname: Pawlita
authors.forename: Carmen J
authors.initials: CJ
authors.lastname: Marsit
authors.forename: Karl T
authors.initials: KT
authors.lastname: Kelsey
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D014408:Biomarkers, Tumor / Q000235:genetics / Q000378:metabolism; D002294:Carcinoma, Squamous Cell / Q000235:genetics / Q000378:metabolism* / Q000473:pathology; D018899:CpG Islands; D019175:DNA Methylation; D005260:Female; D006258:Head and Neck Neoplasms / Q000235:genetics / Q000378:metabolism* / Q000473:pathology; D006801:Humans; D008297:Male; D008875:Middle Aged; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA; D014407:Tumor Cells, Cultured
chemical_list: D014408:Biomarkers, Tumor