Quantitative assessment of DNA hypermethylation in the inflammatory and non-inflammatory breast cancer phenotypes

Abstract

In this study, a comparative quantitative methylation profiling of inflammatory breast cancer (IBC) and non-IBC was set up for the identification of tumor-specific methylation patterns. Methylation ratios of six genes measured in benign breast tissues (n=9) and in tumor samples from non-IBC (n=81) and IBC (n=19) patients using quantitative methylation-specific PCR. Median methylation ratios observed in breast cancer (n=100) were significantly higher than those observed in benign breast tissues for 5 of 6 genes (TWIST, HIN-1, RASSF1A, RARβ2 and APC). Only one of the individual genes studied, RARβ2, showed differential methylation ratios in IBC and non-IBC (P=0.016). Using the maximal methylation ratio observed in benign breast tissue as a threshold, the methylation frequency of two genes, RARβ2 and APC, was significantly increased in IBC (n=19) when compared to non-IBC (n=81): 53% vs. 23% for RARβ2 (P=0.012) and 84% vs. 54% for APC (P=0.017). Using hierarchical clustering, methylation patterns could not classify breast cancers according to their phenotype. The finding of differential frequencies of methylation in IBC and non-IBC for 2 out of 6 genes suggests that gene-specific patterns of methylation could provide a basis for molecular classification of IBC Testing for additional genes could help to define the IBC phenotype based on patterns of aberrant gene promoter methylation.