Epigenetic therapy for breast cancer.

Abstract

Both genetic and epigenetic alterations can control the progression of cancer. Genetic alterations are impossible to reverse, while epigenetic alterations are reversible. This advantage suggests that epigenetic modifications should be preferred in therapy applications. DNA methyltransferases and histone deacetylases have become the primary targets for studies in epigenetic therapy. Some DNA methylation inhibitors and histone deacetylation inhibitors are approved by the US Food and Drug Administration as anti-cancer drugs. Therefore, the uses of epigenetic targets are believed to have great potential as a lasting favorable approach in treating breast cancer.

Full text

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Int. J. Mol. Sci. 2011, 12, 4465-4476; doi:10.3390/ijms12074465

International Journal of
Molecular Sciences
ISSN 1422-0067
www.mdpi.com/journal/ijms
Review
Epigenetic Therapy for Breast Cancer
Feng-Feng Cai 1, Corina Kohler 1, Bei Zhang 1, Ming-Hong Wang 2, Wei-Jie Chen 1
and Xiao-Yan Zhong 1,*
1 Laboratory for Gynecological Oncology, Department of Biomedicine, Women’s Hospital,
University of Basel, Hebelstrasse 20, Room 420, Basel, CH 4031, Switzerland;
E-Mails: fcai@uhbs.ch (F.-F.C.); kohlerc@uhbs.ch (C.K.); zhangb@uhbs.ch (B.Z.);
wchen@uhbs.ch (W.-J.C.)
2 Department of General Practice Medicine, Zhongda Hospital of Southeast University, Nanjing
210009, Jiangsu, China; E-Mail: wangminghong@medmail.com.cn
* Author to whom correspondence should be addressed; E-Mail: zhongx@uhbs.ch;
Tel.: +41-612-659-248; Fax: +41-612-659-399.
Received: 20 May 2011; in revised form: 30 June 2011 / Accepted: 1 July 2011 /
Published: 11 July 2011

Abstract: Both genetic and epigenetic alterations can control the progression of cancer.
Genetic alterations are impossible to reverse, while epigenetic alterations are reversible.
This advantage suggests that epigenetic modifications should be preferred in therapy
applications. DNA methyltransferases and histone deacetylases have become the primary
targets for studies in epigenetic therapy. Some DNA methylation inhibitors and histone
deacetylation inhibitors are approved by the US Food and Drug Administration as
anti-cancer drugs. Therefore, the uses of epigenetic targets are believed to have great
potential as a lasting favorable approach in treating breast cancer.
Keywords: breast cancer; epigenetic therapy; DNA methylation inhibitors; Histone
deacetylation inhibitors

1. Introduction
Breast cancer is one of the most common cancers among women [1]. Although early detection and
improved treatment have increased breast cancer survival rates during the last decade, the 10 year survival
rate is still about 80% [2]. This shows that there is still need for developing novel therapeutic strategies.
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Genetic and epigenetic alterations have both been shown to play an important role in a variety of
cellular processes which include chromatin remodeling, imprinting, X chromosome inactivation, and
carcinogenesis [3]. The most common types of epigenetic alterations include DNA methylation and
histone modifications. Unlike genetic mutations, epigenetic changes are reversible making them a
more promising and safer alternative in breast cancer therapy.
The treatments of breast cancer demand multidisciplinary therapies. The state-of-the-art treatment
options usually include a combination of surgery therapy, radiation therapy, cytotoxic chemotherapy,
and molecularly targeted endocrine therapy depending on the type of breast cancer diagnosed [4].
During recent years, a lot of effort has been put into improving targeted therapy, in particular the
following two therapies: trastuzumab (Herceptin), directed against the human epidermal growth factor
receptor 2 (HER2); and bevacizumab, directed against vascular endothelial growth factor (VEGF). Both
targeted therapies have been approved as milestones [5].
Recently, new treatment strategies focusing on epigenetic alterations have been suggested over gene
mutation because of reversibility. The establishment and maintenance of epigenetic modifications rely
on the operations of special enzymes, DNA methyltransferases and histone deacetylases, which have
become the primary targets for epigenetic therapy [6,7]. Epigenetic therapies using the inhibitors of
these enzymes have anti-tumorigenic effects on malignant conditions [8]. Therefore, this review will
mainly focus on DNA methylation inhibitors and histone deacetylation inhibitors evaluating their
potential for future application in epigenetic therapy.
2. DNA Methylation Inhibitors (DNMT Inhibitors)
DNA methylation in regulatory regions of genes has been shown to influence gene expression.
5-hydroxymethylcytosine (5hmC), a novel DNA modification in mammalian genomic DNA, can lead
to demethylation of DNA and may contribute to the dynamics of DNA methylation [9,10].
Hypermethylation at GpG islands has been linked to transcriptional inactivation of genes. In cancer,
these instances of hypermethylation often can be found in genes’ promoter regions, which are involved
in cell cycle regulation, apoptosis, DNA repair, and informally known as tumor suppressor genes.
DNA hypermethylations at CpG islands have been found in a variety of malignancies including acute
myelogenous leukemia (AML), myelodysplastic syndrome (MDS) and other malignancies [11,12].
DNA methylation patterns are established and maintained by a family of enzymes called DNA
methyltransferases [13]. During the methylation process, these enzymes catalyze the transfer of a
methyl group to the 5 position of cytosin. In mammals, there are three active human DNA
methyltransferases, DNMT1, DNMT3A, and DNMT3B. DNMT1 has importance in post-replicative
maintenance of DNA methylation patterns in mammalian cells. DNMT3A and DNMT3B, two closely
related enzymes, are considered to play a critical role in the de novo establishment of methylation
patterns [14]. DNA demethylation can be achieved either by the failure of maintenance methylation
after DNA replication, or by replication-independent processes involving base excision repair (BER)
and nucleotide excision repair (NER) [15,16]. Tahiliani et al. suggested that the enzyme TET1, an
iron-dependent a-ketoglutarate dioxygenase, may be responsible for the conversion of 5-methylcytosine
(5mC) to 5-hydroxymethylcytosine (5hmC). It provided potential possibilities for demethylation [9].

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Recent drug developments mainly focus on DNMT inhibitors (DNMTi) including nucleoside
analogues and non-nucleoside analogues. By inhibiting DNMTs, genes that might have been silenced
by DNA methylation in the course of the carcinogenic process could be reactivated, and the
non-carcinogenic status of the cell could be reconstituted. The advantages of DNMT inhibitors are that
they are not cancer type specific and could be used to treat various cancers [17].
2.1. Nucleoside Analogues
Nucleosides analogues are inhibitors of DNA synthesis and imputed in direct or indirect regulation
of DNA methylation [18]. The mechanism of action in nucleoside analogues is based on their
transformation to nucleotides and their subsequent incorporation into DNA. The formation of covalent
complexes with DNMTs results in enzyme depletion and finally, a reversal of the methylation
pattern [19]. There are four well-characterized nucleoside analogue methylation inhibitors, 5-azacytidine,
5-aza-2’-deoxycytidine (5-Aza-CdR), 5’-fluoro-2’-deoxycytidine and Zebularine.
2.1.1. 5-Azacytidine
5-azacytidine (5-Aza-CR; Vidaza; azacitidine), a global DNMTi, was approved by FDA for the
treatment of myelodysplastic syndrome (MDS). The clinical trials that use this product against
different solid tumors have been carried out [20]. Azacitidine has two mechanisms of antineoplastic
action—cytotoxicity and DNA demethylation [21]. It can be incorporated into both DNA and RNA.
5-Aza-CR treatment of mammalian cells also leads to defective tRNAs and rRNAs, and inhibits protein
synthesis [22]. It is considered to cause chromosomal rearrangements and contribute to cytotoxicity [23].
2.1.2. 5’-Aza-2’-Deoxycytidine
5’-aza-2’-deoxycytidine (5-azaCdR; DAC; decitabine), a cytosine analogue, is also incorporated
into DNA during replication. 5’-aza-2’-deoxycytidine inhibits both DNMT1 and DNMT3B. It also
leads to enhanced acetylation of histones H3 and H4 at the promoter regions. The use of the activating
histone mark dimethylated lysine 4 of H3 was found to be enhanced by DAC by modulating gene
expression [24]. 5’-aza-2’-deoxycytidine activates both silenced tumor suppressor genes and
pro-metastatic genes by demethylation [20]. PDZ-LIM domain-containing protein 2 (PDLIM2)
contains a tumor suppression function and has been shown to be repressed in breast cancer cells. The
treatment of breast cancer cells with 5-aza-2’-deoxycytidine reversed the methylation of the
PDLIM2 promoter, restored PDLIM2 expression, and suppressed tumorigenicity of human breast
cancer cells [25].
5-aza-CdR induces tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) in human
breast cancer MDA-231 cells [26]. 5-aza-CdR is pivotal in enhancing chemosensitivity of breast
cancer cells to anticancer agents [27].
2.1.3. 5’-Fluoro-2’-Deoxycytidine
The nucleoside analogue 5’-fluoro-2’-deoxycytidine (5-F-dC; 5-F-CdR) is being evaluated
clinically as a DNA methyltransferase inhibitor. It has an inhibitive effect on the action of the methyl

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transfer reaction [28,29]. However it has a lesser underlying effect as a drug since it leads to
potentially toxic products [30].
2.1.4. Zebularine
Zebularine is characterized as an inhibitor of cytidine deaminase with antitumor characteristics
inhibiting DNA methylation and reactivating silenced genes similarly to 5-aza-CdR. The mechanism
of action of zebularine as a DNMTi also requires incorporation into DNA after phosphorylation of
zebularine to the diphosphate level and conversion to a deoxynucleotide [31]. It acts through
post-transcriptional inhibition of DNMTs, inhibition of methyl CpG binding proteins, and alteration of
global histone acetylation status. In contrast to other DNMTi, Zebularine is relatively less toxic to
breast cancer cell lines [32]. The ability to manage zebularine with other epigenetic therapeutics with the
least additive effect has also been established. Zebularine has antimitogenic and angiostatic activities [33].
2.2. Non-Nucleoside Analogues
A few non-nucleoside analogues are known to inhibit DNA methylation and rarely made it to
clinical trials but active research in this field will possibly lead to the introduction of more compounds
of this class in the near future. Non-nucleoside analogues inhibit DNA methylation by binding directly
to the catalytic region of the DNMT without incorporating into DNA [34].
RG108, was first characterized by Brueckner et al. in 2005. They showed that it effectively
prevented DNA methyltransferases in vitro in human cell lines. It causes demethylation and reactivation
of tumor suppressor genes while not affecting the methylation pattern of centromeric satellite
sequences [35]. So far, RG108 has not yet entered clinical trials.
Epigallocatechin-3-gallate (EGCG) is the main polyphenol compound of green tea. Treating cancer
cells with micromolar concentrations of EGCG showed reduced DNA methylation and elevated
transcription of tumor suppressor genes [36]. EGCG is currently being tested in Phase I trials and will
be evaluated in phase II and III trials in the near future [37,38].
Psammaplins are derived from the sponge Psseudoceratina purpurea. They are inhibitors of both
DNMTs and HDACs [39]. NVP-LAQ824, a Psammapalin derivative, has shown antitumor activity in
preclinical studies [40]. It is currently undergoing Phase I clinical trials for hematologic malignancies.
MG98 is an antisense oligonucleotide which prevents translation of DNMT1 mRNA by hybridizing
to the 3’ untranslated region of the DNMT1 mRNA. In addition to MG98’s great advantage due to its
low toxicity, MG98 also demonstrates no antitumor activity in various solid cancers and no
dose-related effects in Phase I studies; however, a Phase II study is currently underway [41,42].
The cardiovascular drug, hydralazine, promotes demethylation and tumor suppressor gene
transcriptional reactivation. Hydrazine is also most likely to increase the efficacy of current biological
or chemotherapeutic treatments [43]. In Phase I clinical trials, the drug has been shown to be
well-tolerated and devoid of the common side effects of cytotoxic chemotherapy agents.
Zambrano et al. additionally showed up to 52% demethylation of promoter regions in selected tumor
suppressor genes upon treatment with different dose levels of the compound. A phase II clinical study
using hydralazine in combination with standard cytotoxic chemotherapy is being planned as proof of

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concept that the reactivation of tumor suppressor genes silenced by DNA methylation increases
chemotherapy efficacy in solid tumors [44].
3. Histone Deacetylation Inhibitors (HDAC Inhibitors)
Histone deacetylation inhibitors (HDAC inhibitors) inhibit histone deacetylase enzymes leading to
the accumulation of acetylation in histones and then changing cellular processes that have become
defective in cancerous cells. They have been shown to accumulate hyper-acatetylated histones and
inhibit tumors [45]. HDAC inhibitors can be divided into four groups: shortchain fatty acids,
hydroxamic acids, cyclic tetrapeptides and benzamides [46]. In humans, there are 11 zinc-dependent
HDAC inhibitors. Different classes of HDAC inhibitors are now in clinical development for the
treatment of both hematologic and solid tumors. Isoform selective HDAC inhibitors in combination
with anti-cancer agents may serve as a future strategy for breast cancer therapy [47].
3.1. Shortchain Fatty Acids
Butyrate was the first HDAC inhibitor that was shown to inhibit cell growth and induce apoptosis [48].
Butyrate causes hyperacetylation of H3 and H4. Sodium butyrate can enhance radiosensitivity in MCF-7
breast cancer cell lines and can trigger apoptosis by the induction of caspase-10 expression [49].
Valproic acid (VPA), a well-tolerated antiepileptic drug with anti-tumor effects, is the only clinically
available histone deacetylase inhibitor on both estrogen-sensitive and estrogen-insensitive breast
cancer cells. VPA is a powerful antiproliferative agent in estrogen-sensitive breast cancer cells, making
this drug of clinical interest as a new approach in treating breast cancer. Valproic acid inhibits HDAC
activity in vitro and in vivo, and relieves HDAC-dependent transcriptional repression and causes
hyperacetylation of histones. It is most likely that the acid achieves this through binding to the catalytic
center of HDACs. Valproic acid induces differentiation of carcinoma cells. Tumor growth and
metastasis formation have been shown to be significantly reduced in animal experiments [50].
Valproic acid induces proteasomal degradation of HDAC2 by selectively inhibiting the catalytic
activity of class I HDACs. It induces ERα mRNA and protein without modifying ERβ in breast cancer
cells. It reprograms the cells to a more differentiated and physiologic phenotype in both ERα-positive
and ERα-negative malignant mammary epithelial cells that can improve the sensitivity to endocrine
therapy and chemotherapy in breast cancer patients [51].
3.2. Hydroxamic Acids
Hydroxamates are active at micromolar to subnanomolar concentrations. Trichostatin A (TSA) is
the first hydroxamic acid HDAC inhibitor identified, and most efficiently alters breast cancer cell
viability. TSA, which is derived from Streptomyces, possesses anti-HDAC activity. The effect of TSA
on cell proliferation and differentiation can be attributed to the inhibition of HDAC. TSA inhibits
growth of ERα-positive breast cancer cells in vitro and also inhibits breast tumor growth in vivo. TSA
enhances acetylation as well as the stability of the ERα protein and p300 protein; proteins that may
contribute to the treatment of human breast cancer [52]. TSA synergizes with the demethylating agent
5-Aza-CdR in the re-expression of genes silenced in the process of carcinogenesis. Additionally, TSA