Hormone therapy use and breast tissue DNA methylation: analysis of epigenome wide data from the normal breast study

Abstract

Hormone therapy (HT) is associated with increased risk of breast cancer, strongly dependent on type, duration, and recency of use. HT use could affect cancer risk by changing breast tissue transcriptional programs. We hypothesize that these changes are preceded by changes in DNA methylation. To explore this hypothesis we used histologically normal-appearing breast tissue from the Normal Breast Study (NBS). DNA methylation β-values were obtained using the Illumina HumanMethylation 450 BeadChips for 90 samples including all NBS-participants who used HT within 5 y before surgery. Data were analyzed using the reference-free cell mixture method. Cancer Genome Atlas (TCGA) mRNA-Seq data were used to assess correlation between DNA methylation and gene expression. We identified 527 CpG sites in 403 genes that were associated with ever using HT at genome wide significance (FDR q < 0.05), of these, 68 sites were also significantly associated with duration of use or recency of use. Twelve sites reached significance in all analyses one of which was cg01382688 in ARHGEF4 (p < 1.2x10 −7). Mutations in ARHGEF4 have been reported in breast tumors, but this is the first report of possible breast cancer-related DNA methylation changes. In addition, 22 genes included more than one significant CpG site and a majority of these sites were significantly correlated with gene expression. Although based on small numbers, these findings support the hypothesis that HT is associated with epigenetic alterations in breast tissue, and identifies genes with altered DNA methylation states which could be linked to breast cancer development.

Associations of breast cancer related exposures and gene expression profiles in normal breast tissue—The Norwegian Women and Cancer normal breast tissue study

“… 61 Changes in gene expression patterns in normal breast tissue after treatment with HT was observed in one experimental study, 62 and a recent study on DNA methylation showed association between HT use and epigenetic changes in normal breast tissue. 63 We did not observe similar changes in our data. Few participants exposed and lack of information on prior HT use, as well as duration of use, could partially explain these results.…”

“…Hall et al found a distinct gene expression profile in breast cancer tissue associated with HT use, and linked HT use to better recurrence‐free survival 61 . Changes in gene expression patterns in normal breast tissue after treatment with HT was observed in one experimental study, 62 and a recent study on DNA methylation showed association between HT use and epigenetic changes in normal breast tissue 63 . We did not observe similar changes in our data.…”

Menopausal hormone-replacement therapy and breast cancer risk: An updated and simplified view

“…These epigenetic modifications triggered by MHT might contribute to BC development and progression. [54] Table 5 summarizes the molecular effectors of MHT contributing to increased BC risk.…”

Ten Years of EWAS

“…[ 151 ] Another EWAS illustrated 527 CpG sites with altered levels of DNA methylation in HT users. [ 152 ] Twelve of these loci were all highly significant, such as cg01382688 ( ARHGEF4 ). These findings all confirm that hormone exposure and epigenetic alterations are correlated, providing assistance in the prevention of breast cancer.…”