MicroRNAs and Epigenetics Strategies to Reverse Breast Cancer

Abstract

Breast cancer is a sporadic disease with genetic and epigenetic components. Genomic instability in breast cancer leads to mutations, copy number variations, and genetic rearrangements, while epigenetic remodeling involves alteration by DNA methylation, histone modification and microRNAs (miRNAs) of gene expression profiles. The accrued scientific findings strongly suggest epigenetic dysregulation in breast cancer pathogenesis though genomic instability is central to breast cancer hallmarks. Being reversible and plastic, epigenetic processes appear more amenable toward therapeutic intervention than the more unidirectional genetic alterations. In this review, we discuss the epigenetic reprogramming associated with breast cancer such as shuffling of DNA methylation, histone acetylation, histone methylation, and miRNAs expression profiles. As part of this, we illustrate how epigenetic instability orchestrates the attainment of cancer hallmarks which stimulate the neoplastic transformation-tumorigenesis-malignancy cascades. As reversibility of epigenetic controls is a promising feature to optimize for devising novel therapeutic approaches, we also focus on the strategies for restoring the epistate that favor improved disease outcome and therapeutic intervention.

Keywords: epigenetic editing; epigenetics diet; estrogen receptor; hTERT; microRNAs.

Figure 1

Molecular mechanism of miRNA dysregulation during cancer. Here, “Me” indicates CpG methylation, “TFs” indicates transcription factors. The expression of miRNA genes is regulated at three different levels: Genetic and/or epigenetic, transcriptional, and bioprocessing level. At the genetic level, the copy number of miRNA genes may change due to the amplification/deletion of miRNA genes. CpG hypermethylation, a common epigenetic change during cancer, may control the miRNA genes expression aberrantly. At the transcriptional level, cancer-associated shuffling of transcription factors may alter miRNA expression profiles. Finally, miRNA expression is influenced by any dysregulation of components of the miRNA biosynthesis cascade (e.g., Drosha, Dicer, DGCR8, Argonaute proteins and exprotin 5).

Figure 2

Proposed model for coordinated epigenetics regulation of ER isotype (ERα and ERβ) expression dynamics in breast cancer. A reciprocal expression profile of ERα verses ERβ on ductal and lobular epithelial cells establishes initial low ERα: ERβ expression. The resultant ERα: ERβ sustains an ER cistrome supportive of normal cellular growth and proliferation. The original ERα: ERβ is set by several layers of epigenetic control; ERα promoter demethylation, ERα promoter acetylation, miRNA homeostasis, and ERβ2 induced proteasome degradation of ERα [175]. Neoplastic transformation moves the ERα: ERβ from low to high score which, in turn, results in ER cistrome shift favorable for neoplastic grow and proliferation. ERα promoter methylation, loss of ERβ2 assisted ERα level control, ERα promoter deacetylation and miRNA expression profile shift together lead to ERα down-regulation as the cells undergo neoplastic transformation. Though ERβ down-regulation contributes profoundly to the ERα:ERβ score, the exact epigenetic regulations of ERβ expression decrease are yet to be studied. However, the cancer cells acquire more aggressive cancerous phenotypes like estrogen-independent growth as the tumor proceeds through a malignant transformation pathway.

Figure 3

The histone modifications landscape of hTERT ectopic expression. Here, asterisk (*) denotes an apparently different modification mark. An overview of DNA methylation and histone modifications associated with hTERT ectopic expression is represented in two different hTERT-immortalized human mammary epithelial cell lines (MCF-10A cells and 184-hTERT-L9) [202]. Usually, the 184-hTERT-L9 cell line expresses hTERT more aggressively than the MCF10A cell line, whereas DNA methylation and histone modifications exhibited assorted patterns relatively exclusive to the cell type. Both of the cell lines show CpG methylation in the promoter and first exon. All the activating histone modification marks (H3K27ac, H3K36me3, H3K4me1, and H3K4me3) showed distinct patterns within the promoter region in terms of coverage and magnitude of deposition. Though the profile of repressive histone modification marks (H3K9me3 and H3K27me3) matched grossly, the magnitude of methyl-deposition was different for MCF10A cells and 184-hTERT-L9 cell line.

Figure 4

Interaction network of predicted miRNAs against TERT. The network was constructed using Cytoscape taking predicted miRNAs with a high score from mirDIP [187,216]. During network building, predicted miRNAs were targeted to interact with TERT. The length between the TERT and a subject miRNA indicates an integrated prediction score.

Figure 5

The epigenetic changes associated with breast cancer hallmarks. Here, PHyperMet means promoter hypermethylation, PHypoMet means promoter hypomethylation, miR means microRNA. Every single cancer hallmark could be controlled by an epigenetic regulation alone or in coordination with genetic regulation. Besides the epigenetic alteration of oncogene and tumor suppressor gene regulation [25,30,52,53], microRNAs have been attributed to different oncogenic hallmarks [13,61] of breast cancer.

Figure 6

Comparison of clinical trials completed for chemotherapeutic and epigenetic drugs. (A) A summary of the accomplished clinical trials on breast cancer from 2001. Here, the ash circle represents medicines that reached phase II clinical trials, the purple circle represents chemotherapeutic drugs, the pink circle represents DNMT inhibitors, the yellow circle represents HDAC inhibitors and the white rectangle represents the total number of clinical trials on breast cancer from 2001. (B) The status of the epigenetic drugs that have undergone complete clinical trials for breast cancer therapy from 2001. Here, the green crescent represents combination cases when the epigenetic drug was applied with other chemotherapeutic drugs/targeted therapy and the blue crescent represents epigenetic drugs applied alone. The data were collected from ClinicalTrials.gov [226].

Figure 7

The effect of epigenetic phytochemicals on breast cancer. Here, blue color phytochemicals indicate primarily HDAC inhibitors, green color phytochemicals indicate DNMT inhibitors, red color phytochemicals indicate miRNA profile modulators and black color phytochemicals indicate global epigenetics modulators. During tumorigenesis, cells undergo neoplastic transformation to favor uncontrolled neoplastic growth avoiding cell cycle regulation and apoptosis. As the cells proceed to malignancy, the neoplastic cells become motile through epithelial–mesenchymal transition [EMT], invade the surrounding tissue and metastasize to the distal anatomic location. The epigenetic phytochemicals interfere with tumorigenesis to either enhance apoptosis or prevent neoplastic growth. A number of epigenetic phytochemicals also halt the metastasis.