Improved measurement of LINE-1 sequence methylation for cancer detection

Clin Chim Acta. 2011 Jan 30;412(3-4):314-21. doi: 10.1016/j.cca.2010.10.030. Epub 2010 Nov 12.


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).

Conclusion: LINE-1 partial methylation represents hypomethylation in normal cells but hypermethylation in cancer cells. This information improves LINE-1 methylation detection in cancer.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Aged, 80 and over
  • Carcinoma, Squamous Cell / blood
  • Carcinoma, Squamous Cell / diagnosis*
  • Carcinoma, Squamous Cell / genetics*
  • DNA Methylation*
  • DNA Restriction Enzymes / metabolism
  • Female
  • Genetic Techniques*
  • Humans
  • Leukocytes / metabolism
  • Long Interspersed Nucleotide Elements / genetics*
  • Male
  • Middle Aged
  • Mouth Neoplasms / blood
  • Mouth Neoplasms / diagnosis*
  • Mouth Neoplasms / genetics*
  • Sulfites / metabolism


  • Sulfites
  • DNA Restriction Enzymes
  • hydrogen sulfite