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

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 ( DAPK, TWIST, HIN-1, RASSF1A, RAR beta 2 and APC) were 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, RAR beta 2 and APC). Only one of the individual genes studied, RAR beta 2, 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, RAR beta 2 and APC, was significantly increased in IBC ( n = 19) when compared to non-IBC ( n = 81): 53% vs. 23% for RAR beta 2 ( 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.