Systematic integrated analyses of methylomic and transcriptomic impacts of early combined botanicals on estrogen receptor-negative mammary cancer

Abstract

Dietary botanicals such as the cruciferous vegetable broccoli sprouts (BSp) as well as green tea polyphenols (GTPs) have shown exciting potential in preventing or delaying breast cancer (BC). However, little is known about their impact on epigenomic aberrations that are centrally involved in the initiation and progression of estrogen receptor-negative [ER(−)] BC. We have investigated the efficacy of combined BSp and GTPs diets on mammary tumor inhibition in transgenic Her2/neu mice that were administered the diets from prepubescence until adulthood. Herein, we present an integrated DNA methylome and transcriptome analyses for defining the early-life epigenetic impacts of combined BSp and GTPs on mammary tumors and our results indicate that a combinatorial administration of BSp and GTPs have a stronger impact at both transcriptome and methylome levels in comparison to BSp or GTPs administered alone. We also demonstrated a streamlined approach by performing an extensive preprocessing, quality assessment and downstream analyses on the genomic dataset. Our identification of differentially methylated regions in response to dietary botanicals administered during early-life will allow us to identify key genes and facilitate implementation of the subsequent downstream functional analyses on a genomic scale and various epigenetic modifications that are crucial in preventing ER(−) mammary cancer. Furthermore, our realtime PCR results were also found to be consistent with our genome-wide analysis results. These results could be exploited as a comprehensive resource for understanding understudied genes and their associated epigenetic modifications in response to these dietary botanicals.

Genome-Wide Analysis on Transcriptome and Methylome in Prevention of Mammary Tumor Induced by Early Life Combined Botanicals

“…The control group (N Control = 9) was administered control AIN-93G diet. In the BSp group (N BSp = 7), mice were administered a modified 26% (w/w) BSp diet (TestDiet, St. Louis, MO, USA) as used previously [8]. In the GTPs group, mice (N GTPs = 7) were orally administered with 0.5% GTPs Sunphenon 90D (Sunphenon 90D, Taiyo International, Inc., Minneapolis, MN, USA) in drinking water, which contains > 90% polyphenols.…”

“…Lastly, in the combination group, mice (N Combination = 7) were fed with a combination BSp and GTPs diet as described above. The BSp and GTPs concentrations incorporated in this study were pharmacologically achievable and also possessed translational potential [8,16,[20][21][22].…”

“…Previous studies have demonstrated that bioactive diets such as green tea polyphenols (GTPs) that contain a major polyphenol, epigallocatechin-3-gallate (EGCG), are efficacious in preventing and inhibiting various human cancers [5][6][7]. Additionally, cruciferous vegetables such as broccoli sprouts (BSp) that contain the bioactive isothiocyanate, sulforaphane (SFN), play an active role in the prevention of tumorigenesis [8].…”

“…We have previously shown that the combined administration of EGCG in GTPs and SFN in BSp can synergistically inhibit BC proliferation in vitro and in vivo [16]. We further tested the effects of GTPs and BSp in a transgenic mouse model, Her2/neu, and determined the impact of this combinatorial regimen on an epigenome [8]. To test whether the potent anticancer properties and essential regulatory roles of this novel dietary regimen on an epigenome are ubiquitous, we extended our study to investigate the combined effects of BSp and GTPs on BC in a different transgenic mouse model, SV40, and explored the potential epigenetic mechanisms.…”

Therapeutic Effects of Dietary Soybean Genistein on Triple-Negative Breast Cancer via Regulation of Epigenetic Mechanisms

“…To further discover the underlying mechanisms, we performed comprehensive genomewide transcriptomic analysis to identify key genes that expression changes may link soybean GE to its therapeutic effects against TNBC. We used PDX tumors from NSG mice engrafted with BCM-3204 and performed RNA-seq analysis as carried out previously [36,37]. The obtained RNA-seq data were transformed for linear modeling and a boxplot was generated to identify the samples' outliers across different treatment groups (Figure S2a).…”