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.
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