Exploratory analysis of the human breast DNA methylation profile upon soymilk

Upon soy consumption, isoflavone metabolites attain bioactive concentrations in breast tissue possibly affecting health. Though in vitro epigenetic activity of soy metabolites has been described, the in vivo impact on the epigenome is largely unknown. Therefore, in this case-control study, the breast glandular tissue DNA methylome was explored in women undergoing an aesthetic breast reduction. After a run-in phase, 10 generally healthy Belgian or Dutch women received soymilk for 5 days. MethylCap-seq methylation profiles were compared with those of 10 matched controls. Isoflavones and their microbial metabolites were quantified in urine, serum, and glandular breast tissue (liquid chromatography-mass spectrometry) and 17β-estradiol in glandular breast tissue (immunoassay). Global DNA methylation levels were obtained for 6 cases and 5 controls using liquid chromatography-mass spectrometry. Although lower MethylCap-seq coverages were observed, mass spectrometry results and computational LINE-1 methylation analysis did not provide evidence supporting global methylation alterations upon treatment. At a false discovery rate of 0.05, no differentially methylated loci were identified. Moreover, a set of previously identified loci was specifically tested, but earlier reported results could not be validated. In conclusion, after a 5 day soymilk treatment, no epigenetic reprogramming in breast tissue could be found in this exploratory study. This study was a randomized dietary intervention trial with a run-in phase of at least 4 days and a supplementation phase of 5 days before breast surgery. Following eligibility assessment, volunteers were randomly allocated to the soymilk (n = 10) or control (n = 20, of which 10 included in the epigenomics study) group. Please note that SB9 is the technical replicate of SB21, and SB17 is the technical replicate of SB22.