title: DNA methylation profiling across the spectrum of HPV-associated anal squamous neoplasia.
abstract: BACKGROUND
  Changes in host tumor genome DNA methylation patterns are among the molecular alterations associated with HPV-related carcinogenesis. However, there is little known about the epigenetic changes associated specifically with the development of anal squamous cell cancer (SCC). We sought to characterize broad methylation profiles across the spectrum of anal squamous neoplasia.
  
  
  RESULTS
  Twenty-nine formalin-fixed paraffin embedded samples from 24 patients were evaluated and included adjacent histologically normal anal mucosa (NM; n = 3), SCC-in situ (SCC-IS; n = 11) and invasive SCC (n = 15). Thirteen women and 11 men with a median age of 44 years (range 26-81) were included in the study. Using the SFP(10) LiPA HPV-typing system, HPV was detected in at least one tissue from all patients with 93% (27/29) being positive for high-risk HPV types and 14 (93%) of 15 invasive SCC tissues testing positive for HPV 16. Bisulfite-modified DNA was interrogated for methylation at 1,505 CpG loci representing 807 genes using the Illumina GoldenGate Methylation Array. When comparing the progression from normal anal mucosa and SCC-IS to invasive SCC, 22 CpG loci representing 20 genes demonstrated significant differential methylation (p<0.01). The majority of differentially methylated gene targets occurred at or close to specific chromosomal locations such as previously described HPV methylation "hotspots" and viral integration sites.
  
  
  CONCLUSIONS
  We have identified a panel of differentially methlylated CpG loci across the spectrum of HPV-associated squamous neoplasia of the anus. To our knowledge, this is the first reported application of large-scale high throughput methylation analysis for the study of anal neoplasia. Our findings support further investigations into the role of host-genome methylation in HPV-associated anal carcinogenesis with implications towards enhanced diagnosis and screening strategies.
authors.affiliation: Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America.
authors.forename: Jonathan M
authors.initials: JM
authors.lastname: Hernandez
authors.forename: Erin M
authors.initials: EM
authors.lastname: Siegel
authors.forename: Bridget
authors.initials: B
authors.lastname: Riggs
authors.forename: Steven
authors.initials: S
authors.lastname: Eschrich
authors.forename: Abul
authors.initials: A
authors.lastname: Elahi
authors.forename: Xiaotao
authors.initials: X
authors.lastname: Qu
authors.forename: Abidemi
authors.initials: A
authors.lastname: Ajidahun
authors.forename: Anders
authors.initials: A
authors.lastname: Berglund
authors.forename: Domenico
authors.initials: D
authors.lastname: Coppola
authors.forename: William M
authors.initials: WM
authors.lastname: Grady
authors.forename: Anna R
authors.initials: AR
authors.lastname: Giuliano
authors.forename: David
authors.initials: D
authors.lastname: Shibata
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001003:Anal Canal / Q000473:pathology / Q000821:virology; D001005:Anus Neoplasms / Q000235:genetics* / Q000473:pathology / Q000821:virology*; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation; D005260:Female; D056426:Genetic Loci / Q000235:genetics; D060005:Genotyping Techniques; D006801:Humans; D008297:Male; D008875:Middle Aged; D009361:Neoplasm Invasiveness; D018307:Neoplasms, Squamous Cell / Q000235:genetics* / Q000473:pathology / Q000821:virology*; D020411:Oligonucleotide Array Sequence Analysis; D027383:Papillomaviridae / Q000235:genetics / Q000502:physiology*; D011786:Quality Control; D017422:Sequence Analysis, DNA; D013447:Sulfites / Q000494:pharmacology
chemical_list: D013447:Sulfites; C042345:hydrogen sulfite