Epigenetic profiling of
tumor DNAs may reveal important new
theranostic targets to improve prognosis and treatment of advanced
cancer patients. In this study, we performed a genome-wide profile of DNA methylation patterns in sporadic
breast tumors by using the HumanMethylation27 BeadChips to assess relationships between DNA methylation changes and patient
tumor characteristics. The arrays identified 264 hypermethylated loci/genes present in genomic CpG islands. Hierarchical clustering based on methylation levels divided the specimens into three distinct groups, within which certain clinical features also clustered. Statistically significant differences were determined between overall methylation levels of these clusters and
estrogen receptor and
progesterone receptor (ER/PR) status (P = 0.001),
tumor relapse (P = 0.035), and
lymph node metastasis (P = 0.042). We identified several individual methylated genes associated with clinical features, including six genes (RECK, SFRP2, UAP1L1, ACADL, ITR, and UGT3A1) that showed statistical significance between methylation and relapse-free survival. Notably, the RECK gene in this group has been associated in other
cancers with poorest prognosis. Among the leading relapse-associated genes and the genes associated with ER/PR status, we sequenced an independent set of paired normal/
tumor breast DNA samples to confirm
tumor specificity of methylation. Further, we carried out quantitative real-time
reverse transcriptase PCR to confirm reduced expression in methylated
tumors. Our findings suggest the utility for the DNA methylation patterns in these genes as clinically useful
surrogate markers in
breast cancer, as well as new molecular pathways for further investigation as therapeutic targets.