Combination of methylated-DNA precipitation and methylation-sensitive restriction enzymes (COMPARE-MS) for the rapid, sensitive and quantitative detection of DNA methylation.
Hypermethylation of CpG island (CGI) sequences is a nearly universal somatic genome alteration in cancer. Rapid and sensitive detection of DNA hypermethylation would aid in cancer diagnosis and risk stratification. We present a novel technique, called COMPARE-MS, that can rapidly and quantitatively detect CGI hypermethylation with high sensitivity and specificity in hundreds of samples simultaneously. To quantitate CGI hypermethylation, COMPARE-MS uses real-time PCR of DNA that was first digested by methylation-sensitive restriction enzymes and then precipitated by methyl-binding domain polypeptides immobilized on a magnetic solid matrix. We show that COMPARE-MS could detect five genome equivalents of methylated CGIs in a 1000- to 10,000-fold excess of unmethylated DNA. COMPARE-MS was used to rapidly quantitate hypermethylation at multiple CGIs in >155 prostate tissues, including benign and malignant prostate specimens, and prostate cell lines. This analysis showed that GSTP1, MDR1 and PTGS2 CGI hypermethylation as determined by COMPARE-MS could differentiate between malignant and benign prostate with sensitivities >95% and specificities approaching 100%. This novel technology could significantly improve our ability to detect CGI hypermethylation.
Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine 1650 Orleans Street, CRB 116, Baltimore, MD 21231, USA.
Srinivasan
S
Yegnasubramanian
Xiaohui
X
Lin
Michael C
MC
Haffner
Angelo M
AM
DeMarzo
William G
WG
Nelson
D000818:Animals; D002460:Cell Line; D045744:Cell Line, Tumor; D011232:Chemical Precipitation; D018899:CpG Islands; D004247:DNA / Q000737:chemistry; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000737:chemistry; D019003:Deoxyribonuclease HpaII; D005454:Fluorescence Polarization; D051549:Glutathione S-Transferase pi / Q000235:genetics; D006801:Humans; D008297:Male; D025202:Molecular Diagnostic Techniques; D016133:Polymerase Chain Reaction / Q000379:methods*; D011467:Prostate / Q000378:metabolism; D011471:Prostatic Neoplasms / Q000175:diagnosis*; D017434:Protein Structure, Tertiary; D012372:ROC Curve; D018411:Spodoptera / Q000166:cytology; D013997:Time Factors
D004268:DNA-Binding Proteins; C489325:MBD2 protein, human; D004247:DNA; C496556:GSTP1 protein, human; D051549:Glutathione S-Transferase pi; D019003:Deoxyribonuclease HpaII