Integrated analysis of high- resolution DNA methylation profiles, gene expression, germline genotypes and clinical end points in breast cancer patients

Breast cancer is a heterogeneous disease for which alterations in DNA methylation patterns have been shown to be of biological and clinical importance. Here we report on the integrated analysis of molecular alterations including the methylation status of 27 gene promoters analyzed by highly quantitative pyrosequencing, and the association to gene expression, germline genotype and clinical parameters including survival. Breast cancer specific deregulation of DNA methylation (both hyper- and hypomethylation) was found in twenty genes including ACVR1, OGG1, IL8 and TFF1. The methylation level in the promoter regions was significantly negatively correlated to gene expression for twelve genes (such as MST1R, ST6GAL1 and TFF1) indicating that a gain of aberrant methylation (hypermethylation) inhibits gene expression. Multiple associations between molecular and clinical parameters were identified, and multivariate statistical analysis demonstrated that methylation was more strongly associated to clinical parameters than gene expression for the investigated genes. The methylation level of BCAP31 and OGG1 showed significant association to survival, and these associations were validated in a larger patient cohort (The Cancer Genome Atlas). Our study provides evidence for the promise of DNA methylation alterations for clinical applications. What's new? The heterogenous nature of breast cancer is influenced by alterations in DNA methylation, deregulation of which may result in hypermethylation or hypomethylation. Here, DNA methylation was found to be specifically deregulated in breast cancer for 20 genes, in 12 of which hypermethylation was associated with the inhibition of gene expression. Methylation status was further associated with clinical parameters, including overall survival in breast cancer. The findings indicate that analyses of alterations in DNA methylation could be of clinical prognostic value for breast cancer.