Quantification of CpG methylation at the 5'-region of XIST by pyrosequencing from human serum

Aberrant methylation of X (inactive)-specific transcript (XIST) is common in serum derived from human prostate and testicular germ cell tumors. The direct quantification of XIST methylation is urgently required for clinical application because human serum contains both normal and cancer-originated XIST DNA. We directly quantitated the methylation percentage of three CpG sites (+947, +956, +971) from the 5'-region of XIST by pyrosequencing. The average methylation percentages at three CpG sites were 88% (+/-5.8) at CpG1, 98% (+/-3.4) at CpG2, and 92% (+/-5.6) at CpG3 from normal male (N = 19). From prostate cancer-derived sera, the average methylation percentage of XIST was 65% (+/-8.3) at CpG1, 82% (+/-10.9) at CpG2, and 74% (+/-4.4) at CpG3, which is lower than the normal XY serum DNA, but greater than normal XX serums. The methylation status of XIST also correlated with its gene expression in B-lymphoblastoid and prostate cancer cell lines. This method is sensitive for quantifying the small percentage change in the methylation status of XIST, and may be used for early diagnosis and monitoring of cancer in men using serum.