title: Improved measurement of LINE-1 sequence methylation for cancer detection.
abstract: BACKGROUND
  Methylation of long interspersed nuclear element-1 (LINE-1) sequences varies among normal cells and it is often decreased in cancer genomes and white blood cells (WBC) of cancer patients. Current measurement techniques of genome-wide level are inadequate because LINE-1 methylation is distinctive at each locus. Here, we improved the detection of cancer by combining information of LINE-1 methylation pattern and level.
  
  
  METHODS
  Combined bisulfite restriction analysis (COBRA) of LINE-1, COBRA LINE-1, was used to test cancer cell lines, two oral rinse cohorts, and WBC from normal and cancer patients. COBRA LINE-1 separated LINE-1 sequences into 4 products depending on the methylation statuses of 2 CpG dinucleotides, as follows: 2 unmethylated CpGs ((u)C(u)C), partial methylation ((m)C(u)C), 1 methylated CpG ((m)C), and 1 unmethylated CpG ((u)C).
  
  
  RESULTS
  The association between (m)C(u)C and (u)C(u)C was directly correlated in normal cells (r=0.4895, p=0.0009) but inversely correlated in cancer (r=-0.8979, p=0.0002). Oral rinse AUC values of (u)C(u)C were 0.763 and 0.926 and methylation levels were 0.707 and 0.621, respectively. (u)C(u)C, but not overall methylation level, differentiated cancer WBC from normal (p=0.0082 and p=0.4830, respectively).
  
  
  CONCLUSIONS
  LINE-1 partial methylation represents hypomethylation in normal cells but hypermethylation in cancer cells. This information improves LINE-1 methylation detection in cancer.
authors.affiliation: Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.
authors.forename: Tuangtong
authors.initials: T
authors.lastname: Pobsook
authors.forename: Keskanya
authors.initials: K
authors.lastname: Subbalekha
authors.forename: Phakdee
authors.initials: P
authors.lastname: Sannikorn
authors.forename: Apiwat
authors.initials: A
authors.lastname: Mutirangura
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D002294:Carcinoma, Squamous Cell / Q000097:blood / Q000175:diagnosis* / Q000235:genetics*; D019175:DNA Methylation; D004262:DNA Restriction Enzymes / Q000378:metabolism; D005260:Female; D005821:Genetic Techniques; D006801:Humans; D007962:Leukocytes / Q000378:metabolism; D020084:Long Interspersed Nucleotide Elements / Q000235:genetics*; D008297:Male; D008875:Middle Aged; D009062:Mouth Neoplasms / Q000097:blood / Q000175:diagnosis* / Q000235:genetics*; D013447:Sulfites / Q000378:metabolism
chemical_list: D013447:Sulfites; D004262:DNA Restriction Enzymes; C042345:hydrogen sulfite