Genome-wide DNA methylation profiling of CpG islands in breast cancer identifies novel genes associated with tumorigenicity

Abstract

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 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 3 distinct groups, within which certain clinical features also clustered. Statistically significant differences were determined between overall methylation levels of these clusters and estrogen and progesterone receptor 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 6 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 estrogen/progesterone receptor (ER/PR) status, we sequenced an independent set of paired normal/tumor breast DNA samples to confirm tumor specificity of methylation. Further, we performed quantitative real-time RT-PCR to confirm reduced expression in methylated tumors. Our findings suggest 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.