Abstract
Aberrant DNA methylation is a frequent epigenetic alteration in cancer cells that has emerged as a pivotal mechanism for tumorigenesis. Accordingly, novel therapies targeting the epigenome are being explored with the aim to restore normal DNA methylation patterns on oncogenes and tumor suppressor genes. A limited number of studies indicate that dietary compound resveratrol modulates DNA methylation of several cancer-related genes; however a complete view of changes in methylome by resveratrol has not been reported yet. In this study we performed a genome-wide survey of DNA methylation signatures in triple negative breast cancer cells exposed to resveratrol. Our data showed that resveratrol treatment for 24 h and 48 h decreased gene promoter hypermethylation and increased DNA hypomethylation. Of 2476 hypermethylated genes in control cells, 1,459 and 1,547 were differentially hypomethylated after 24 h and 48 h, respectively. Remarkably, resveratrol did not induce widespread non-specific DNA hyper- or hypomethylation as changes in methylation were found in only 12.5% of 27,728 CpG loci. Moreover, resveratrol restores the hypomethylated and hypermethylated status of key tumor suppressor genes and oncogenes, respectively. Importantly, the integrative analysis of methylome and transcriptome profiles in response to resveratrol showed that methylation alterations were concordant with changes in mRNA expression. Our findings reveal for the first time the impact of resveratrol on the methylome of breast cancer cells and identify novel potential targets for epigenetic therapy. We propose that resveratrol may be considered as a dietary epidrug as it may exert its anti-tumor activities by modifying the methylation status of cancer -related genes which deserves further in vivo characterization.
Highlights
Epigenetic aberrations and specific alterations in DNA methylation patterns resulting in altered gene expression programs may greatly contribute to tumorigenesis [1]
Hypomethylation of CpG islands can result in genome instability, reactivation of transposons, and upregulation of proto-oncogenes [3], whilst promoter hypermethylation may suppress the transcription of tumor suppressor genes, including genes involved in DNA repair, detoxification, apoptosis, cell cycle, cell proliferation, metastasis and angiogenesis [4]
The methylated DNA regions were enriched using the array-based profiling of reference-independent methylation status method which is based on the differential restriction of DNA by methylation-specific and methylation-sensitive restriction enzymes [12], followed by whole-genome hybridization of human DNA methylation 3x720 K CpG Island Plus RefSeq promoter array HG18 CpG (NimbleGen) that covers 22,532 gene promoters and 27,728 annotated CpG islands
Summary
Epigenetic aberrations and specific alterations in DNA methylation patterns resulting in altered gene expression programs may greatly contribute to tumorigenesis [1]. Novel therapies targeting the epigenome are being explored with the aim to restore normal DNA methylation patterns on oncogenes and tumor suppressor genes. In this context, increasing experimental evidence suggest that dietary compounds may exert health benefits through the modulation of the epigenetic status of cells during the lifespan [5]. Many phytochemicals found in vegetables and plants have potent antioxidant and antitumor activities with low toxicity These nutraceuticals may alter the epigenetic marks involved in the early steps of carcinogenesis, such as global DNA hypomethylation, tumor suppressor gene promoter hypermethylation and modifications of the histones code [6]. The search and discovery of novel dietary epigenetic modulators and their clinical application in patients is an emerging therapeutic strategy against human cancers
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