title: Global analysis of DNA methylation changes during progression of oral cancer.
abstract: OBJECTIVE
  Earlier studies involving a priori gene selection have identified promoter regions deregulated by DNA methylation changes in oral squamous cell cancers (OSCCs) and precancers. Interrogation of global DNA methylation patterns for such specimens has not been reported, though such analyses are needed to uncover novel molecular factors driving disease.
  
  
  METHODS
  We evaluated global DNA methylation patterns for 30 biopsies obtained from 10 patients undergoing surgical removal of an OSCC or carcinoma in situ (CIS). From a disease field in each patient, we collected (i) dysplastic, (ii) CIS or OSCC, and (iii) adjacent normal biopsies. DNA isolated from each biopsy was profiled for methylation status using the Illumina HumanMethylation27K platform.
  
  
  RESULTS
  Our data demonstrate that aberrant methylation of promoter CpG islands exists across oral precancer and OSCC genomes. Non-hierarchical clustering of all methylation data revealed distinct methylation patterns between the normal and the CIS/OSCC tissues (with results for dysplastic biopsies split between groups). Multiple genes exhibiting recurrent aberrant DNA methylation were found for both dysplastic and CIS/OSCC groups, and included enrichment for genes found in the WNT and MAPK signaling pathways.
  
  
  CONCLUSIONS
  In identifying aberrant DNA methylation at the earliest stages of oral precancer and finding recurring epigenetic disruption of specific genes/pathways across our analyzed cohort, we see evidence that CpG methylation changes may play a role in oral cancer progression and that global DNA methylation analyses may have significant utility in wider studies that seek to derive biomarkers or potentially druggable targets to improve oral cancer outcomes.
authors.affiliation: Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Rebecca
authors.initials: R
authors.lastname: Towle
authors.forename: Danielle
authors.initials: D
authors.lastname: Truong
authors.forename: Kirsten
authors.initials: K
authors.lastname: Hogg
authors.forename: Wendy P
authors.initials: WP
authors.lastname: Robinson
authors.forename: Catherine F
authors.initials: CF
authors.lastname: Poh
authors.forename: Cathie
authors.initials: C
authors.lastname: Garnis
mesh_terms: D000328:Adult; D000368:Aged; D002278:Carcinoma in Situ / Q000235:genetics* / Q000473:pathology; D002294:Carcinoma, Squamous Cell / Q000235:genetics* / Q000473:pathology; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D018450:Disease Progression; D057890:Epigenomics / Q000379:methods; D005260:Female; D006801:Humans; D020935:MAP Kinase Signaling System / Q000235:genetics; D008297:Male; D008875:Middle Aged; D009062:Mouth Neoplasms / Q000235:genetics* / Q000473:pathology; D017346:Protein Serine-Threonine Kinases / Q000235:genetics; D051153:Wnt Proteins / Q000235:genetics; D060449:Wnt Signaling Pathway / Q000235:genetics
chemical_list: D051153:Wnt Proteins; D017346:Protein Serine-Threonine Kinases
keywords: CIS; Dysplasia; Epigenetics; FV; Field effect; Methylation; OPL; OSCC; Oral cancer; Progression; carcinoma in situ; fluorescence visualization; oral premalignant lesion; oral squamous cell carcinoma