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Background: Genome-wide association studies have identified that multiple singlenucleiotide polymorphisms on chromosome 9p21 are tightly associated with (coronaryartery disease) CAD. However, the mechanism linking this risk locus to CAD remainsunclear.Methodology/Principal Findings: The methylation status of six candidate genes (BAX,BCL-2, TIMP3, p14ARF, p15INK4b and p16INK4a) in 205 patients and controls who underwentcoronary angiography were analyzed by quantitative MethyLight assay. Rs10757274 wasgenotyped and expression of INK4/ARF and antisense non-coding RNA in the INK4 locus(ANRIL) was determined by real-time RT-PCR. Serum levels of TGF-β1 were measured byELISA. Compared with controls, DNA methylation levels at p15INK4b significantly increasedin CAD patients (P=0.006). To validate and dissect the methylation percentage of each targetCpG site at p15INK4b, Pyrosequencing was performed, finding CpG +314 remarkablyhypermethylated in CAD patients. The rs10757274 genotype was significantly associatedwith CAD (P=0.003) and GG genotype carriers had a higher level of ANRIL exon 1-5expression compared among three genotypes (P=0.009). There was a stepwise increase inp15INK4b and p16INK4a methylation as ANRIL exon 1-5 expression elevated (r=0.23, P=0.001and r=0.24, P=0.001, respectively), although neither of two loci methylation was directlylinked to rs10757274 genotype.Conclusions/Significance: p15INK4b methylation is associated with CAD and ANRILexpression. The epigenetic changes in p15INK4b methylation and ANRIL expression mayinvolve in the mechanisms of chromosome 9p21 on CAD development.