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6 Epigenetic Diagnosis & Therapy, 2015, Vol. 1, No. 1 Sajadian and Nussler
mechanisms of the DNA demethylation [15, 16]. One
potential DNA demethylation pathway is enabled by the ten-
eleven-translocation proteins (TETs), which are named after
the ten-eleven-translocation (q22, q23) (10, 11) that occurs
in rare cases of acute myeloid and lymphocytic leukemia
[17, 18]. 5-mC is oxidized by TET proteins and thereby
converted to 5-hmC, 5-fC, and 5-CaC, which all belong to
the family of Fe (II)/2-oxygluttarate-dependent dioxgenases
. DNA methylation is reversible either through passive
demethylation via DNA replication or by active
demethylation via DNA repair followed by base excision
repair of modified nucleotides or DNA glycosidase [15, 17]
TET proteins play different roles in diverse biological
processes, including epigenetic regulation of gene
transcription, embryonic development, stem cell functions,
and cancer. They mediate the DNA demethylation process
and change the epigenetic state of DNA. A loss of 5-hmC,
together with a down-regulation or mutation of TET
proteins, has been reported in numerous types of cancer, like
melanoma, breast, prostate, myeloid, brain, and liver cancer
. It has been demonstrated that in patients suffering from
acute myeloid leukemia (AML), TET1 protein influences
mixed lineage leukemia (MLL) development .
Furthermore, several changes in TET2 proteins, like e.g.
deletion and deactivation of TET2, have been identified in
30% of all patients suffering from different kinds of myeloid
malignancies. Several work groups have reported an
alteration of a TET2 gene in a variety of myeloid
malignancies and the majority of the TET2 alterations
include single or double copy defects and nonsense/frame
shift mutation suggesting that TET2 lesions cause a loss of
function. Therefore, it has been suggested that TET2 is a
possible tumor suppressor gene that is responsible for
myeloid malignancies . Furthermore, the loss of 5-hmC
in correlation with clinical progression and relapse of
melanoma has been reported .
DNA METHYLATION AND CANCER
Numerous studies have reported that tumor cells exhibit a
major disruption in the regulation of the DNA methylation
pattern in cancer. Therefore, over the last few years, studies
have particularly focused on changes in DNA methylation.
. Earlier studies have demonstrated that the
hypomethylation of interspersed repetitive DNA is a
common feature of numerous types of cancer that causes
genomic instability and aberrant transcription initiation.
However, researchers have proven that the hypermethylation
of focal CpG islands is elevated in cancer and may result in
Fig. (1). Epigenetic machinery and interplay between epigenetic factors (modified from ). Epigenetic regulation depends on the three
following epigenetic factors: (a) DNA methylation, (b) histone modification, and (c) nucleosome positioning. The interaction between these
factors results in the final outcome, but disturbances of this balance lead to several diseases. Abbreviations: DNMT: DNA Methyl
Transferase, HAT: Histone Acetylation Transferase, HDAC: Histone Deacetylase, HMT: Histone Methyltransferase, HDM: Histone
DNMT3A & DNMT3B
(de novo DNMT)
HAT & HDAC
HAT & HDAC
HMT & HDM
Kinase & Phosphor
• Autoimmune disorder
• Neural disorder
DNA Methylation: Possible Target for Studies on Cancer Epigenetic Diagnosis & Therapy, 2015, Vol. 1, No. 1 7
inhibition of various miRNAs, tumor suppressor and
functional genes [23, 24].
Moreover, it has become evident that different pathways
target DNMT at the specific CpG Island. Moreover, four
different mechanisms target DNA methyltransferase. Firstly,
DNMT3A and DNMT3L recognize DNA or chromatin with
specific domains and they interact with the LYS4 of histone
3 (H3K4). Secondly, DNMT interacts with different
chromatin modifiers such as KMT and HDACs. Thirdly, the
Piwi-PiRNA complex, a class of ncRNAs, guides DNMTs to
transposon elements. Finally, the direct interaction of
promoter-associated RNA (pRNA) with the promoter of the
rRNA gene might recruit DNMT3b and enable methylation
. In addition, it has been shown that, in an alteration
between methylation and phosphorylation, an adjacent lysine
and serine determine the stability of DNMT1 thus preserving
the methylation pattern during cell division .
However, the detailed mechanism(s) leading to hyper- or
hypomethylation shall be decorticated in the future.
HYPERMETHYLATION IN CANCER
The CpG islands are protected by various defense
mechanisms by accessing the DNA methyltransferase, such
as DNA replication timing, active demethylation, or active
transcription. Most genes that are susceptible to
hypermethylation are associated with the regulation of DNA
repair, apoptosis, cell cycle, drug resistance, metastasis, and
differentiation . Many tumors are hypermethylated in
one or more genes. For instance, in lung cancer, it has been
demonstrated that alterations of DNA methylation have been
found in more than 40 genes .
Regarding breast cancer, it has been shown that several
critical genes, which seem to be important in tumorigenesis,
are hypermethylated. Among those genes, cell adhesion
genes, inhibitors of matrix metalloproteinases, as well as the
ER and PR steroid receptor genes can be found and have
been linked to breast cancer development .
It has also been reported that DNA methylation is one of
the reasons for the inactivation of BRCA1 in breast cancer,
which is one of the genes most commonly associated with
breast cancer . Moreover, the hypermethylation of other
cell cycle genes may result in acute lymphoblastic leukemia
which is an undesirable clinical outcome .
HYPOMETHYLATION IN MALIGNANCIES
Hypomethylation is an alteration in DNA methylation
which is frequently seen in solid tumors [31-33], and is a
sign of a progressive malignancy . Furthermore, it has
been reported that the hypomethylation status contributes to
oncogenesis through up-regulation of some oncogenes, like
H-RAs and c-MYC , as well as by chromosome
instability [35, 36].
During cancer development, aberrations not only occur in
the DNA methylation, but also in the regulation of histone
modifications . For instance, numerous studies have
demonstrated that histone deacytylases (HDACs) are
overexpressed in different types of cancer. This
overexpression leads to a deacetylation of the Transcription
Starting Site (TSS) of important genes and subsequently to
the assembly of silenced genes into more compact structures
Fig. (2). Active demethylation pathway through the conversion of 5mC to 5hmC by recruiting TET proteins. Following 5mC oxidation,
demethylation occurs by dilution of oxidized base or by removal through DNA glycosidase- and DNA repair-mediated excision of modified
nucleotides (modified from ). Abbreviations: C: Cytosine, 5mC: 5-methylcytosine, 5hmC: 5-hydroxymethylcytosine; 5fC: 5-
formylcytosine, 5caC: 5-carboxylcytosine, TDG: Thymine DNA Glucosidase, BER: Base Excision Repair.
8 Epigenetic Diagnosis & Therapy, 2015, Vol. 1, No. 1 Sajadian and Nussler
In summary, there exists an epigenetic crosstalk between
histone modification, micro-RNAs, and DNA methylation.
Post-transcriptionally, miR-29 and miR-148 regulate the
DNA demethylases [40, 41]. Moreover, it has been proven
that DNMTs interact with HDAC . In particular, the
combination of DNMT and HDAC inhibitors is a primary
target for potential therapeutics against cancer [42, 43],
because these inhibitors are capable of targeting the
epigenetic status of DNA and histones simultaneously,
which may enable the development of more effective
EPIGENETICS AND CANCER STEM CELL
Recently, the concept has arisen that cancer stem cells
are to be classified as a subpopulation of cancer cells with a
different tumorigenic potential. This side population, which
is usually named cancer-initiating cells or cancer stem cells
(CSC), has a characteristic potential for self-renewal that
may sustain and perpetuate tumors and is known to dispose
of a higher drug resistance. Firstly, it has been observed that
CD34+CD38- leukemic stem cells disposing of a
differentiation and proliferation capacity are able to trigger
human leukemia in NOD/SCID mice . Furthermore, it
has been proven that a landscape of solid tumors, such as
glioblastoma , breast cancer , prostate cancer ,
and hepatocellular carcinoma , contain CSCs. A growing
number of studies prove that the cancer-initiating cells are
mostly resistant to chemotherapy or radiotherapy, which
results in the recurrence of tumors , and in the formation
of metastases .
Studies on the epigenetic modifications in stem cells and
in cancer cells have directed interest to stem/progenitor cells,
which are at the origin of cancer. It is believed that the
genetic and epigenetic changes in these cells provide the
ability for their survival, protecting them from toxic
environment, which then contributes to tumor initiation .
Interestingly, the Polycomb repressive complex, which
causes abnormal gene silencing in cancer, represses CpG
island genes in Emberyonic Stem Cells (ESCs) in the same
way as in cancer [52, 53]. Following this abnormal
hypermethylation due to DNA damage, inflammation or
stress caused by ROS, tumor suppressor genes become
silenced. This may lead to the activation of stem cell
pathways and provide the ability of self-renewal for cancer
cells . For example, in stem cells, like e.g. the CD133+
cells, promoter hypermethylation of some tumor suppressor
genes, such as SFRP1 and SOX17, was identified ,
proving the stem cell origin of epigenetic abnormalities in
APPLICATION OF EPIGENETIC DRUGS
As was described above, the application of epigenetic
drugs is being increasingly focused on in the field of
biomedicine and drug development research. Like numerous
other diseases, cancer causes aberrancies in the epigenetic
regulation. Most importantly, the pattern of DNA
demethylation and histone modification has been related to
tumor genesis and metastasis [10, 57]. Therefore, it is
believed that these two biomechanical processes have a high
potential for being used in clinical applications, such as e.g.
in cancer detection, tumor prognosis, and
pharmacoepigenetics (prediction of treatment response). For
example, hypermethylation of glutathione transferase
(GSTP1) constitutes a promising epigenetic marker in
prostate cancer . It has to be pointed out that 80-90% of
men suffering from prostate cancer exhibit a
hypermethylation of GSTP1 and that this hypermethylation
does not occur in benign hyperplastic prostate tissue .
Therefore, GSTP1 methylation is a helpful prognostic
marker, which enables the discrimination of benign tumor
tissue in prostate cancer. As a matter of fact, GSTP1 is also
hypermethylated in other cancers such as in kindney, liver
and breast cancer . Interestingly, the screening of single
markers through global DNA methylation offers great
clinical potential, as for example, it allows for the prediction
of metastases in colorectal cancer, recurrence in lung cancer,
and progression in virus-associated neoplasms [57, 61]. In
addition to DNA methylation markers, histone-based
markers have been suggested as epigenetic biomarkers. In
particular, aberrant histone modifications have been linked to
recurring prostate cancer .
Nowadays, most studies focus on the development of
epigenetic drugs, which can reverse the abnormal epigenetic
state to the normal epigenetic state in cancer cells. Up to
now, the US Food and Drug Administration (FDA) has
approved four epigenetic small molecule drugs for the
treatment of cancer: 5-Azacytidine (5-Aza) and 5-Aza-2´-
deoxycytidine (DNMT inhibitors) which have been used for
patients suffering from myelodyplastic syndrome and from
acute leukemia, as well as Varinostat and Romidepsin
(HDAC inhibitors) which are used for treatment of T-cell
lymphoma and some hematological tumors . It has to be
pointed out that each DNMT inhibitor possesses its own way
of action on the gene transcription.
Although 5-Aza and 5-Aza-2´-deoxycytidine have the
same therapeutic effect, their mode of action in tumor cells is
different. It has been demonstrated that 5-Aza-2´-
deoxycytidine is able to induce senescence in tumor cells,
while 5-Aza induces cell death in tumor cells in vitro and in
vivo. These two DNMT inhibitors differ from each other on
the molecular and the cellular level: For instance, 5-Aza can
be integrated in both DNA and RNA (20-40% and 60-80%
respectively), while 5-Aza-2´-deoxycytidine can only be
incorporated in DNA. Moreover, 5-Aza-2´-deoxycytidine
induces more DNA damage and micronuclei formation than
Furthermore, it has been rported that Azacytidine
increases the antitumor effect sensitivity of Docetaxel (DTX)
and Cisplation in aggressive and chemoresistant prostate
cancer . In addition, it has been shown that Pyrazofurin
(PF), an inhibitor of orotidylate decarboxylase improved the
anti-tumoral activity of 5-Aza in human leukemia cells .
The combination of PF and 5-Aza may provide a useful
treatment for patients who do not respond to standard anti-
leukemic therapies . Furthermore, it has been proven that
5-Aza-2´-deoxycytidine inhibits telomerase activity and
reactivates p16 and c-Myc in hepatocellular carcinoma cells
(HCC), such as the MMC-7721 and the HepG2 cell line .
Other DNMT inhibitors, such as 5-fuoro-2´-
deoxycytidine, in combination with other drugs are currently
DNA Methylation: Possible Target for Studies on Cancer Epigenetic Diagnosis & Therapy, 2015, Vol. 1, No. 1 9
undergoing clinical trials regarding the treatment of different
types of cancers . The DNA methyltransferase inhibitor
Zebularin provoked the demethylation of tumor suppressor
genes by inducing apoptosis, cell cycle regulation in HCC
cell lines (Huh7, KMCH, and HepG2), and in vivo inhibition
of tumor growth in a xenograft model .
It has been discussed if the expression of specific
DNMTs might influence the differentiation status in
Fig. (3). Epigenetic drugs for cancer therapy. It has been described that scores of small molecules participate in the fight against cancer cells
by inducing changes in the epigenetic machineries. This figure illustrates some of the most important epigenetic drugs, which are classified
in relation to their epigenetic target. Abbreviations: DNMT1: DNA Methyltransferase 1, HDAC: Histone Deacetylase, PcG: Polycomb
Group, Me: Methylated, HAT: Histone Acetylase.
HDAC Inhibitors:HDAC Inhibitors: SIRTSIRT
Pol IIPol II
10 Epigenetic Diagnosis & Therapy, 2015, Vol. 1, No. 1 Sajadian and Nussler
developing and dedifferentiating cells. It has been shown
that 5-Aza triggers differentiation in mesenchymal stem cells
(MSCs) [8, 71, 72]. Furthermore, we have reported that
pretreatment of fat-derived old MSCs with 5-Aza improves
osteogenic differentiation by DNA demethylation. We have
observed a reduction of 5hmC in Ad-MSCs from older
donors (> 60 years) compared to young donors (< 45 years).
After stimulation of cells with 5-Azacytidine the osteogenic
potential of the cells improved. It has been observed that the
increase of AP activity and matrix mineralization is
associated with an inducement of the expression of 5hmC as
well as with the expression of TET2 and TET3 .
Therefore, we have concluded that 5-Azacytidine induces the
rejuvenating process of older Ad-MSCs (Fig. 4).
Furthermore, it has been demonstrated in various studies that
the treatment of human Adipose Stem Cells (ADSC) and
human bone marrow MSCs with 20 µM 5-Azacytidine
improves their hepatic differentiation [73-75]. In the same
line of evidence, it has been shown that the incubation of
human bone marrow MSCs with 1 µM TSA which had been
pretreated with hepatogenic-stimulating agents, improves the
hepatogenic differentiation of these cells . Moreover, a
combination of TSA and 5-Aza-dc has improved the
differentiation of human CD34+ to CD34/ CD90 cells .
Regarding the influence of the epigenetic status on the
reprogramming mechanism of the cells, it has been reported
that vitamin C induces the active demethylation pathway
through the induction TET enzyme activity in mouse
embryonic stem cells (ES) . In the same line of evidence,
it has been demonstrated that TET2 facilitates the
differentiation of hematopoietic stem cells . Therefore,
vitamin C can be used for reprogramming stem cells, as it
induces TET-dependent demethylation.
OTHER EPIGENETIC MODIFYING DRUGS
In the past years, many anticancer drugs targeting the
acetylation or methylation status of histones through
different mechanisms have been developed, such as HDAC
inhibitors class I, II, III (sirtuins), and IV, HATs, HMTs,
HDMs, and various kinds of kinases. Based on their
chemical properties, the HDACs are branched into the four
Fig. (4). Reprogrammation and differentiation of cells through a DNA methylation pattern. Changes in the methylation status of cells may
lead to differentiation either through passive demethylation [8, 72] by inhibition of DNMT or through active demethylation by inducing TET
proteins to produce 5hmC [78, 79]. Abbreviations: 5mC: 5-methylcytosine 5hmC: 5-hydroxymethylcytosine; 5fC: 5-formylcytosine; 5caC:
5-carboxylcytosine; TDG: Thymine DNA Glucosidase; BER: Base Excision Repair, TET: Ten eleven translocation, DNMT: DNA
Methyltransferase, SAH: S-adenosylhomocysteine, Hcy: Homocysteine SAM: S-Adenosylmethionin.
DNA Methylation: Possible Target for Studies on Cancer Epigenetic Diagnosis & Therapy, 2015, Vol. 1, No. 1 11
following groups: hydroxamic acid, short fatty acids, cyclic
peptide and benzamide enzymes . HDACs inhibitors
mainly arrest the cell cycle in G1 and G2-M phases, which,
in turn, induces apoptosis and cell differentiation. However,
they are able to inhibit angiogenesis and metastasis, and to
decrease the resistance of tumor cells to chemotherapy .
Recently, a new epigenetic drug called Suberoylanilide
hydroxamic acid (SAHA) has been approved for treating T-
cell cutaneous lymphoma by the Federal Drug
Administration (FDA) . Furthermore, a large number of
HDAC inhibitors, like e.g. TSA (Tricostatin A), PXD101
(Belinostat), and LBH589 (Panobinostat), are currently being
developed and are undergoing clinical trials [82, 83].
Class III HDAC inhibitors, so called Sirtuins (SIRT), are
important for the regulation of senescence, survival, and cell
proliferation. An increasing number of effective SIRT
inhibitors have recently been generated . SIRT1 and
SIRT2 inhibitors are likely to stop p53 activity, thereby
inducing growth arrest in cancer cells and increasing
sensitivity of tumor cells towards anticancer drugs .
Salermide - another SIRT1 and SIRT2 inhibitor - induces p-
53-independent apoptosis in tumor cells and reactivates
proapoptotic genes by deacytelation of H4K16Ac at the
epigenetic level which is mediated by SIRT1 .
It has been shown that curcumin, garcinol, and anacaridic
acid may act as HAT inhibitors with an anti-cancer effect in
ovarian and colon cancer. It has been demonstrated that all
three substances are able to inhibit EP300-mediated p53
acetylation [86, 87].
DZNep, Chaetocin, and BIX-01294 are known to be
lysine HMT inhibitors. It has been shown that DZNep
promotes apoptosis in the MCF7 cell line (breast cancer) and
in the HCT116 cell line (colorectal cancer) . Chaetocine
has an anti-cancer effect on multiple myeloma (MM) .
BIX-01294 deactivates the histone H3 lysine 9 (H3K9)
methyltransferases G9a and G9a-like protein by promoting
the apoptotic cell death .
It has been demonstrated that BIX-01294 induces
endothelial differentiation in Ad-MSCs. We have been able
to demonstrate that BIX modifies DNA and histone
methylation and remarkably increases the expression of
various endothelial markers that are required for blood vessel
formation, such as VCAM-1, PECAM, VEGFR-2, and
PDGF . From our studies, we conclude that drugs that
modify the DNA or histone methylation also induce changes
in the pluripotency [8, 72].
SUMMARY AND FUTURE PERSPECTIVES
In the present overview, we have presented numerous
encouraging findings demonstrating that so called small
molecules exert anti-tumoral activity through epigenetic
changes within target cells. Interestingly, even molecules,
like e.g. polyphenols, which are considered to be anti-
oxidative drugs, dispose of a potent epigenetic modifying
activity, and therefore slow down tumor growth. However,
the large variety among the structures of different molecules
that exert epigenetic modifying activity bears a high risk.
The mechanisms by which epigenetically modifying drugs
reduce growth or damage tumor cells are not very specific
and may therefore damage normal/healthy cells as well. In
this avenue, it is mandatory to develop new and more
specific small molecules against specific enzymes of the
epigenetic machinery in order to reduce damage on healthy
CONFLICT OF INTEREST
The authors declare that they do not have any conflict of
We like to thank Dr. Luc Koster for editing the
manuscript. The authors would also like to thank the
Ministry of Rural Affairs, and Consumer Protection Baden-
Württemberg for supporting our study and hence promoting
important research projects.
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Received: September 17, 2014 Revised: December 3, 2014 Accepted: December 8, 2014