HHS Public Access

Author manuscript
Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
Author Manuscript

Published in final edited form as:

Expert Rev Precis Med Drug Dev. 2017 ; 2(1): 33–45. doi:10.1080/23808993.2017.1284557.

The role of epigenomics in personalized medicine

Mohamad M. Kronfola, Mikhail G. Dozmorovb, Rong Huangc, Patricia W. Slattuma, and
Joseph L. McClaya,*
aDepartment of Pharmacotherapy and Outcomes Science, Virginia Commonwealth University
School of Pharmacy, Richmond, Virginia, USA
bDepartment of Biostatistics, Virginia Commonwealth University School of Medicine, Richmond,
Author Manuscript

Virginia, USA
cDepartment of Medicinal Chemistry, Virginia Commonwealth University School of Pharmacy,
Richmond, Virginia, USA

Abstract
Introduction—Epigenetics is the study of reversible modifications to chromatin and their
extensive and profound effects on gene regulation. To date, the role of epigenetics in personalized
medicine has been under-explored. Therefore, this review aims to highlight the vast potential that
epigenetics holds.

Areas covered—We first review the cell-specific nature of epigenetic states and how these can
vary with developmental stage and in response to environmental factors. We then summarize
Author Manuscript

epigenetic biomarkers of disease, with a focus on diagnostic tests, followed by a detailed

description of current and pipeline drugs with epigenetic modes of action. Finally, we discuss
epigenetic biomarkers of drug response.

Expert commentary—Epigenetic variation can yield information on cellular states and

developmental histories in ways that genotype information cannot. Furthermore, in contrast to
fixed genome sequence, epigenetic patterns are plastic, so correcting aberrant, disease-causing
epigenetic marks holds considerable therapeutic promise. While just six epigenetic drugs are
currently approved for use in the United States, a larger number is being developed. However, a
drawback to current therapeutics is their non-specific effects. Development of locus-specific
epigenetic modifiers, used in conjunction with epigenetic biomarkers of response, will enable truly
precision interventions.
Author Manuscript

Keywords
Chromatin remodeling; DNA methylation; DNMT inhibitors; Epigenetic biomarkers; Epigenetic
drugs; HDAC inhibitors; Histone modifications; Oncology; Neuroscience; Pharmacokinetics

*
Correspondence to: Joseph L. McClay, Ph.D., Robert Blackwell Smith Building, 410 North 12th Street, Medical College of Virginia
Campus, Virginia Commonwealth University, Richmond, VA 23298-0533. Tel: +1 804-828 3428, [email protected].
Declaration of Interest
JL McClay received honoraria from the American College of Clinical Pharmacy to present on the topic of pharmacoepigenomics. The
authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or
financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.
 Kronfol et al. Page 2

1. Introduction
Author Manuscript

Personalized medicine is founded upon the concept that individual differences in therapeutic
success are the norm among patients that require pharmacological treatment. This concept is
not new. Hippocrates writing in the 5th century BCE is known to have commented, “give
different ones [drugs] to different patients, for the sweet ones do not benefit everyone, nor do
the astringent ones, nor are all the patients able to drink the same things.” (see [1]). Thus, the
concept of variable response to drugs has been discussed for at least two and a half
millennia. However, being able to predict who will respond to a given drug has proven an
enduring challenge. With the advent of modern genomic technologies, which enable us to
read each patient’s genetic make-up, the idea of personalized medicine is becoming a reality.

Pharmacogenetics, the core discipline of personalized medicine, has already delivered some
profound and meaningful successes. The effectiveness of Cytochrome P450 (CYP450)
Author Manuscript

genotypes in predicting an individual’s drug metabolizing phenotype is a notable example

[2]. This has led to several of these biomarkers being approved for clinical use by regulatory
bodies such as the US Federal Drug Administration (FDA) (www.fda.gov/Drugs/
ScienceResearch/ResearchAreas/Pharmacogenetics/ucm083378.htm). Beyond drug
metabolism, genetic variants at numerous other loci have shown robust associations
indicative of clinical relevance, with commercial kits and services now available to deliver
this information to health providers and consumers [3].

In the last decade, pharmacogenetics has harnessed the power of genome-wide association
studies (GWAS). This has enabled the field to move beyond the study of candidate genes to
scanning hundreds of thousands of genetic markers for each subject. Several promising new
leads have been discovered. Arguably, however, the success of GWAS in pharmacogenomics
Author Manuscript

has not mirrored that of complex disease studies. Primarily this may be an issue of statistical
power, whereby the clinical trials necessary to measure drug response are costly and so
sample sizes currently tend to be small. As studies grow in size and number and meta-
analyses are conducted across samples, we can expect GWAS to yield additional insight over
time [4]. However, GWAS will not yield all the answers for any given drug response
phenotype. Beyond the limitation where GWAS focuses on common polymorphisms, even if
all the relevant variants for response to a given drug were mapped, we would still be unable
to explain all the phenotypic variation in drug response [5]. Drug response is complex and,
like other complex traits, it likely arises from the interplay of multiple genetic and
environmental factors over the life course [6]. DNA sequence is just one component of this
complexity.

Most genotype associations in complex traits such as drug response are probabilistic
Author Manuscript

indicators of phenotype, which typically say little of certainty about the state of the organism
at the time of sampling. When treating an individual patient with a specific drug, substantial
supporting information in addition to genotype information may be required before making
a clinical decision. Even phenotypes that are strongly influenced by genetics, such as the
CYP450 drug metabolism phenotypes, will be modified by the effects of concurrent
medications or alcohol and tobacco use that may inhibit or interfere with CYP enzyme

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
 Kronfol et al. Page 3

activity [7,8]. This further illustrates the need to consider information beyond genotype
Author Manuscript

alone.

There are two broad complexities to living organisms that are not addressed by genotype
information. These are 1) spatial and 2) temporal variation in biological function or
phenotypic expression within the same organism. Consider that humans are composed of
multiple cell types with a diverse array of functions (spatial, or cell-specific variation) and
that we take on very different macroscopic forms in early versus later life (temporal, or
developmental variation). Yet essentially the same genome is present in all nucleated cells at
all time points. In this review, we will show how the processes that lead to cellular diversity
and organismal development, i.e. epigenetics, can be harnessed to provide more nuanced
DNA-based biomarkers and novel treatment strategies [9]. Indeed, epigenetics may also
yield an environmental exposure record of the patient that we are just beginning to
comprehend [10]. Epigenetic biomarkers are therefore fundamentally different to studies of
Author Manuscript

gene expression, proteins or metabolites, which provide snapshots of functional state at a

single time point. Epigenetics provides layers of regulatory and environmental exposure
information on top of each individual’s unique genome [11]. Thus, it indicates what
happened to you and you alone, and from this we may be able to determine your truly
personal drug regimen design and success, disease susceptibility and cure.

2. Epigenetics Overview
The term “epigenetics” was first described by the British developmental biologist Conrad
Waddington in the 1940s as “the branch of biology which studies the causal interactions
between genes and their products, which bring the phenotype into being” [12,13].
Waddington’s definition therefore predates the discovery of DNA and so the term
Author Manuscript

“epigenetics” has developed over time. Waddington was focused on organismal

development, whereby cells starting with the fertilized egg follow trajectories of increasing
specialization until terminal differentiation, which cannot be reversed. One of Waddington’s
visual metaphors for this process, where the cell is conceptualized as a marble rolling down
a rolling hillside with ravines and valleys, has an enduring intuitive appeal and is explained
in Figure 1.

Today, backed by knowledge of the genome and some core molecular processes, epigenetics
can be defined as the study of mitotically stable changes in genetic regulation that do not
involve changes to nucleotide sequence [14]. Mitotic stability, in this sense, means that the
epigenetic state of the parent cell is written to the daughter cell after mitosis, thereby
continuing the developmental trajectory of the parent. This regulation is enacted via
epigenetic marks, which are reversible regulatory modifications to chromatin.
Author Manuscript

2.1 Epigenetic modifications to chromatin

The most intensively studied epigenetic mark is the methylation of DNA cytosine residues at
the carbon 5 position (5mC). This mark is made via the DNA N-methyl transferase (DNMT)
enzymes and is most often found in the sequence context CpG [15]. DNA methylation is one
of the core epigenetic marks essential for regulating gene expression in normal cell
development and differentiation [16]. While 5mC is the most well-characterized, other

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
 Kronfol et al. Page 4

cytosine modifications have now been discovered, such as 5-hydroxymethycytosine (5hmC),

Author Manuscript

5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) [17,18]. The functions of these exotic
marks are still being elucidated, but 5hmC may play an important role in the central nervous
system, where it is prevalent, and in the regulation of pluripotency in stem cells [19,20].

Another major class of epigenetic mark involves the post-translational modification of

histones, the proteins that package DNA into nucleosomes [21]. Histones are the chief
protein components of chromatin, whereby 146 bp of DNA is wound around each histone
octamer [22]. There are five major classes of canonical histones, where each octamer is
typically formed of two H2A-H2B dimers and a H3-H4 tetramer while H1 serves as a linker
protein between nucleosomes. H3 and H4 have long tails that protrude from the nucleosome
that can be covalently modified in several places, while other histones can also be modified
to a lesser degree. The best characterized modifications include mono-, di- and tri-
methylation, acetylation and phosphorylation, although a growing number continue to be
Author Manuscript

reported [23]. Standard nomenclature abbreviates the histone, the modified residue and the
type of modification, such that histone 3 lysine 27 acetylation is written as “H3K27Ac”.
These modifications are written and erased by specific enzyme families, such as histone
acetyltransferases (HATs) and histone deacetylases (HDACs) in the case of acetylation
marks, or histone methyltransferases (HMTs) and demethylases (HDMs) in the case of
methylation marks [23].

In addition to histone modifications, histone variants can have significant transcriptional

regulatory roles. Histone variants replace canonical histones to alter nucleosome structure
and ultimately DNA accessibility [24]. An example histone variant is H2A.Z, which replaces
nucleosomal H2A to perform several complex regulatory roles in gene expression and
development [25]. Finally, for the purposes of this article, we also mention polycomb
Author Manuscript

epigenetic repressors and bromodomain-containing proteins. Polycomb proteins can remodel

chromatin and typically function as epigenetic gene silencers [26], while bromodomain
proteins are transducers of the acetylation signal on histones [27]. These chromatin-
interacting proteins are relevant for epigenetic personalized medicine because they are
targets for epigenetic drugs that we mention below in Section 3.2. Other putatively
epigenetic regulatory mechanisms exist, most notably the non-coding RNAs (ncRNAs),
which are beyond the scope of the current article. NcRNAs primarily function as post-
transcriptional regulators of gene expression, but also play roles in regulating chromatin
accessibility. They have been extensively reviewed elsewhere (http://www.cell.com/cell/
collections/noncoding-rna).

2.2 Epigenetic effects on gene expression and regulation

Author Manuscript

The “textbook”, or classic, view of epigenetic regulation is focused on DNA methylation at

gene promoters. In this view, hypomethylated CpGs are typically associated with active,
expressed genes, while hypermethylated CpGs are typically associated with silenced genes.
This effect arises because methylation of cytosine inhibits transcription factor binding [28].
Subsequent research has indicated that methylated cytosine, in addition to methylated
histone H3K9, and deacetylated H3 combine to form a repressive epigenetic signature, while
unmethylated DNA, methylated H3K4, and acetylated H3 combine to form an activating

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
 Kronfol et al. Page 5

epigenetic signature [29], although not all histone modifications are coupled with DNA
Author Manuscript

methylation [30]. An overview is provided in Figure 2. During development, epigenetic

patterns change and differentiated cells develop a stable and unique epigenetic pattern that
regulates tissue-specific gene transcription. While this view is broadly consistent with
current findings, waves of new genomic data have yielded a more nuanced view.

Massive studies such as ENCODE [31] and Roadmap Epigenomics [32] have significantly
advanced our understanding of genetic and epigenetic regulation. The ENCODE project
aims to identify all functional elements in the genome, while RoadMap Epigenomics aims to
elucidate epigenetic processes that contribute to human biology and disease. Both projects
make extensive use of next-generation sequencing (NGS) to profile reference epigenomes
and genome-wide protein-DNA binding patterns, including binding patterns for specific
modified histones. The most recent culmination of these efforts was the publication of 111
reference epigenomes by RoadMap Epigenomics [32]. This study revealed epigenetic
Author Manuscript

regulatory modules of coordinated activity, which are specific combinations of DNA

methylation, histone modifications and other proteins that shape chromatin structure, which
in turn determine transcriptional activity. These multi-layer data were used to classify
genomic regions according to functional state [33]. The working models produced by
RoadMap Epigenomics include a core 15 chromatin state model [32] and an expanded 18
chromatin state model (http://egg2.wustl.edu/roadmap/web_portal/chr_state_learning.html),
the latter including twelve active and six inactive states. Active states include transcribed
regions, active transcription start sites and their flanking regions, active enhancers and zinc
finger protein binding sites. Inactive states include heterochromatin and repressed polycomb
regions. This model, although complex, has already proven powerful for understanding
regulation of gene expression.
Author Manuscript

2.3 Individual differences in epigenetic states and developmental plasticity

Epigenetic modifications to chromatin are affected by exposure to environmental factors,
and any changes so induced are inherited mitotically in somatic cells [11]. Studies in human
twins have shown that, while their epigenomes are very similar in early life, they diverge as
the twins become older as a result of differing environmental exposures across the life
course, in addition to stochastic effects [34]. Epigenetic changes in response to
environmental factors may have evolved to provide plasticity in adaptation to environmental
cues [11]. Through the phenomena of de novo epigenetic writing and mitotic stability, the
effects of environmental factors can become embedded in the genome and persist to produce
long-term phenotypic changes [35]. Example environmental factors with demonstrated
developmental consequences include diet, toxins and stress. There is increasing recognition
of the importance of this phenomenon for epigenetic translational research, because it
Author Manuscript

provides concrete biological pathways that are involved in the persistence of environmental
effects [36].

Epigenetic states can also vary between individuals because of genetic differences. In the
case of methylation, one of the simplest examples involves polymorphic CpG sites [37]. If a
nucleotide substitution ablates a CpG in some individuals, those individuals cannot be
methylated at that locus. There are several examples of disease-associated polymorphic

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
 Kronfol et al. Page 6

CpGs, suggesting that this is a significant contributor to individual differences in disease risk
Author Manuscript

[38,39]. In addition to polymorphic CpGs, DNA sequence variation may also affect the
binding of chromatin-interacting proteins and thus influence epigenetic states [40]. Thus,
individual differences in epigenetic states, whether arising via genotype or maladaptive
responses to environmental factors, can lead to disease.

3. Epigenetic Applications in Personalized Medicine

Epigenetic disease associations provide not only mechanistic clues to disease etiology, but
can also function as diagnostic biomarkers. The developmental stage- and tissue-specificity
of epigenetic marks has led to considerable interest in developing biomarkers that capitalize
on these unique properties [41]. Furthermore, the fact that epigenetic marks are reversible
has led to significant interest in the development of drugs with epigenetic modes of action
[42,43].
Author Manuscript

3.1 Epigenetic biomarkers of disease

The largest body of work in disease epigenetics to date is on cancer. Since the first links
between DNA methylation and cancer were established in the early 1980s, a number of
epigenetic findings have been described, implicating several aspects of the epigenetic
machinery. Some excellent reviews of cancer epigenetics have been published recently
[44,45], so here we limit ourselves to epigenetic marks in cancer showing evidence or
potential as diagnostic or prognostic biomarkers.

Current epigenetic biomarker applications predominantly involve DNA methylation [46]. In

the United States, nucleic acid based tests intended for general clinical use are regulated by
the Federal Drug Administration (FDA) as medical devices. Currently there are no FDA-
Author Manuscript

approved tests that rely exclusively on epigenetic biomarkers. However, one commercially
available test with an epigenetic component has received full FDA approval. This is
ColoGuard®, a screening test for colorectal cancer in adults over 50. The test uses DNA
methylation levels at BMP3 and NDRG4, in combination of mutated KRAS and an
immunochemical assay for hemoglobin (Table 1). This test was reported to have superior
sensitivity but slightly lower specificity for colorectal cancer compared to the traditional
screening method, fecal immunochemical testing (FIT) [47]. However, more recent results
suggest FIT may be more effective and less costly than ColoGuard®, the latter necessitating
either very high patient uptake or a 60% reduction in cost per test to become the preferred
testing method [48]. This illustrates the economic barriers that diagnostic tests must
overcome, beyond the demonstration of efficacy and reproducibility, in order to become
widespread.
Author Manuscript

Two other epigenetic tests are currently available in the US, classified as Laboratory
Developed Tests (LDTs) and regulated under the Clinical Laboratory Improvement
Amendments (CLIA) program. This means that the test may only be conducted “in house”
in the laboratory where it was developed, once the lab meets CLIA performance standards.
The two tests are ConfirmMDx and AssureMDx, for prostate cancer and bladder cancer
respectively. Hypermethylation of the glutathione S-transferase gene (GSTP1) promoter in
prostrate cancer was first shown in the 1990s [49]. This marker, plus APC and RASSF1, are

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
 Kronfol et al. Page 7

now components of the ConfirmMDx test (Table 1), which is used to address false-negative
Author Manuscript

prostate biopsy concerns [50]. The AssureMDx test for bladder cancer involves the analysis
of DNA methylation levels of three genes (TWIST1, ONECUT2 and OTX1) in combination
with mutation analysis of three others [51].

In lung cancer, the DNA methylation of the SHOX2 gene was reported to be an accurate
marker for identifying lung cancer based on analysis of bronchial aspirates [52]. In Europe,
this biomarker is now commercially available as the Epi proLungVR BL Reflex Assay [53].
However, this test has not yet received regulatory approval for use in the USA.

In breast and ovarian cancer, hypermethylation of the BRCA1 promoter region has been
observed repeatedly [54,55]. BRCA1 is also thought to epigenetically repress expression of
the oncogenic microRNA miR-155 via a mechanism involving histone deacetylase 2
(HDAC2) [56]. A recent study by Anjum et al. (2014) identified a blood cell DNA
Author Manuscript

methylation signature at BRCA1 that was able to predict breast cancer risk several years
prior to diagnosis [57]. However, this biomarker is not yet available in a commercial kit or
test.

The biomarker potential of circulating cell-free DNA (cfDNA) has been investigated in
breast cancer and other cancers. Circulating cfDNA is extracted from plasma or serum and is
derived from dying tumor cells that release their DNA into the bloodstream. Kloten et al
(2013) used a panel of three genes (ITIH5, DKK3 and RASSF1A) that showed
hypermethylation in serum cfDNA from breast cancer patients and found these could
discriminate between patients and controls with a sensitivity of 67% and specificity of 69%
[58]. Fackler et al. (2014) followed this with a panel of 10 genes and cancer-specific DNA
was detected in sera with a sensitivity of 91% and specificity of 96% in the test samples
Author Manuscript

[59]. The researchers of the latter study are reportedly working with the diagnostics
company Cepheid to bring this test to market [60].

While epigenetic studies of cancer are arguably the most advanced relative to other areas,
several diseases have shown promising findings, particularly with respect to DNA
methylation. These include neurological disorders such as Alzheimer’s Disease [61,62] and
Parkinson’s Disease [63], autoimmune disorders such as systemic lupus erythematosus [64],
and psychiatric disorders such as schizophrenia [65,66] and autism [67]. Despite these
advances, there are no currently available diagnostic kits for these diseases that employ
epigenetic markers. Nevertheless, it is hoped that the clinical value of epigenomics already
seen in oncology will be replicated in these areas [68].

3.2 Epigenetic drugs

Author Manuscript

The dynamic and reversible nature of epigenetic modifications is of particular relevance to

drug development, as it implies that specific disease-associated epigenetic states may be
reversible with pharmacological treatment [69]. This segment will summarize current and
potential “epidrugs”, or drugs with epigenetic modes of action. Epidrugs are classified
according to their respective target enzymes, and include the following: DNA N-methyl
transferase inhibitors (DNMTi), histone acetyltransferase inhibitors (HATi/KATi), histone
methyltransferase inhibitors (HMTi/KMTi), histone N-methyl lysine demethylase inhibitors

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
 Kronfol et al. Page 8

(HDMi/KDMi), histone deacetylase inhibitors (HDACi/KDACi), and bromodomain

Author Manuscript

inhibitors. Currently there are two classes of epigenetic drugs that have been approved by
FDA for clinical use in the United States: DNMTi and HDACi (see Table 2).

The first approved epidrug in the US was azacitidine (Vidaza, Azadine), a DNMTi indicated
to treat chronic myelomonocytic leukemia and myelodysplastic syndrome. Azacitidine was
approved in 2004 and quickly followed by decitabine (Dacogen) with same indication two
years later. Both drugs cause broad hypomethylation that leads to cellular dysregulation that
most seriously affects rapidly dividing cells. It is important to note that these drugs are not
highly locus-specific and these agents can cause hypomethylation at many genomic sites.
Even though current drugs are designed to favorably induce genes that have been silenced in
cancer [70], they may also activate the expression of prometastatic genes as well as
oncogenes [71]. There remains a need to develop more selective DNMTi to improve the
efficacy and reduce side effects for this class of drug.
Author Manuscript

The potential application of DNMTi to other diseases is also under investigation and
examples include multiple sclerosis [72], HIV [73], pain [74] and memory [75]. For
example, DNMT activity was observed in HIV-1 infection of CD4(+) T-cells in vitro and
induced hypermethylation of distinct cellular promoters [73]. Studies from Rajasethupathy
et al. suggested that DNA methylation is necessary for serotonin-dependent long-term
facilitation in memory formation [76]. For a curative therapy of AIDS patients, a
combination of antiretroviral drugs and epidrugs has been suggested for the reactivation of
latent HIV-1 genomes. These epidrugs include DNMTi, HDACi, histone methyltransferase
inhibitors (HMTi) and histone demethylase inhibitors [73].

The HDAC inhibitors suberoylanilide hydroxamic acid (SAHA, vorinostat, in 2006) and
Author Manuscript

romidepsin (depsipeptide, in 2009) have proven to be successful in cancer therapeutics

[77,78]. These agents cause the accumulation of acetylated histones and prevent progression
of tumor cells. Vorinostat was the first HDACi to be approved by the FDA, indicated for
cutaneous manifestations in patients with cutaneous T-cell lymphoma (CTCL). Panobinostat
is the latest HDACi approved by the FDA in 2015 and is indicated for the treatment of
multiple myeloma in combination with bortezomib and dexamethasone. Outside the US,
HDACi approvals vary. In Europe, for example, only panobinostat has been approved for
general clinical use (to treat multiple myeloma), while belinostat received orphan
designation for peripheral T-cell lymphoma (PTCL). In China, an additional HDACi known
as chidamide (Epidaza®), was approved for treatment of PTCL by the Chinese FDA in
2015. Although most HDACi are approved for cancer type indications, studies have
suggested potential roles in schizophrenia [79] and Type2 diabetes [80]. However, similar to
Author Manuscript

the DNMTi drugs, current HDACi have broad effects across the genome and lack locus-
specificity. These drugs can have serious side effects [43] and use of currently approved
HDACi in cancer is often indicated only after other treatments have failed, or as combination
therapies (Table 2).

Besides these two approved epidrug classes, HMTi and bromodomain inhibitors are other
emerging epidrug classes under development. Pinometostat is a small molecule inhibitor of
the histone methyltransferase DOT1L for the treatment of MLL-r leukemia [81].

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
 Kronfol et al. Page 9

Tazemetostat is an orally administered, first-in-class small molecule HMTi that targets the
Author Manuscript

EZH2 transcriptional repressor to treat multiple types of hematological malignancies and

genetically defined solid tumors [82]. GSK3326595, an inhibitor of the transcriptional
regulator protein arginine methyltransferase 5 (PRMT5), is also in phase 1 clinical trial.
Bromodomain proteins are readers that recognize acetylated lysine and transduce the gene
activation signal [27]. OTX-015 and CPI-0610 are bromodomain protein inhibitors both in
phase I trials for cancers. These drugs target a specific family of bromodomain proteins,
known as Bromodomain Extra-Terminal motif (BET) proteins [83]. Another BET inhibitor,
Apabetalone (RVX-208), is in Phase III clinical trials for cardiovascular events in Type 2
diabetes subjects with coronary artery disease. These example epidrugs, and several more
are advancing through the clinical trial pipeline, are summarized in Table 3. In this table, we
focus only on epidrugs in active or planned clinical trials registered in the US
(clinicaltrials.gov) and show the latest phase trial for each drug, plus any trials for
Author Manuscript

indications outside oncology. We restrict our listing of early phase cancer indications
because these are too numerous to list concisely.

Finally, several HATi are in preclinical studies at time of writing. Aberrant function of
HATs, also called lysine acetyltransferases (KATs), is correlated with cancer and other
diseases [84]. HATi are great candidates with potential therapeutic utility, but current HATi
only have moderate potency and specificity and none are in clinical trial at time of writing.
Nevertheless, some HATi have shown efficacy in preclinical studies. Compound C646 is a
pyrazolone-containing small molecule inhibitor of the p300/CBP HAT subfamily [85]. It has
been shown to cause growth arrest in melanoma cell lines and inhibit cancer cell growth in
prostate and lung cancer cell lines. PU139 is a pyridoisothiazolone that inhibits several HAT
subfamilies and was shown to block neuroblastoma xenograft growth in mice [86]. These
agents and others in development are indicative that HATi are still in infancy relative to other
Author Manuscript

epigenetic drugs, but they show enormous promise and need further investment to reach
their potential as therapeutic compounds.

3.3 Epigenetic biomarkers of drug response

As a natural extension of pharmacogenetics, it is possible to use epigenetic biomarkers to
predict drug response. While none have yet achieved regulatory approval for clinical use, a
small number of examples are established in the literature. Among the best known is DNA
methylation of the MGMT promoter. This gene encodes a DNA repair enzyme (O6-
alkylguanine DNA alkyltransferase). Methylation in the promoter region of MGMT is
associated with better response to alkylating neoplastic agents like temozolomide, as first
shown in glioblastoma by Esteller et al. (2000) [87] and later by Hegi et al. (2005) [88]. The
mechanism of effect is as follows. Temozolamide alkylates or methylates DNA at the N-7 or
Author Manuscript

O-6 positions of guanine residues and the resulting DNA damage triggers tumor cell death.
Hypomethylation of MGMT leads to expression of O6-alkylguanine DNA alkyltransferase,
which can repair the DNA damage, whereas hypermethylation leads to silencing of the gene
and thus greater susceptibility to the drug. In addition to glioma, a role for MGMT in
predicting response to metastatic colorectal cancer (mCRC) treatment has also been
suggested [89].

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
 Kronfol et al. Page 10

Other published epigenetic biomarker examples include GSTP1 and BRCA1. Methylation of
Author Manuscript

the promoter of GSTP1 is correlated with survival in breast cancer patients and may be
predictive of treatment efficacy with doxorubicin [90] or DNA methyltransferase (DNMT)
inhibitors [91]. The BRCA1 gene plays a role in DNA damage response and
hypermethylation of the BRCA1 promoter region may be predictive of enhanced sensitivity
to platinum-derived drugs in cancer cell lines and xenografted tumors; it also may be
predictive of increased time to relapse and survival in ovarian cancer patients under cisplatin
treatment [92].

The impact of epigenetics in drug response has been investigated beyond oncology. For
example, methylation of the P2 promoter of the IGF1 gene affects transcriptional response to
growth hormone (GH) [93]. GH is mainly used to treat children with short stature due to
growth hormone deficiency. Ouni et al. [93] measured P2-driven and total IGF1 transcripts
before and 12 h after the GH injection and found an increase in P2-driven transcripts with a
Author Manuscript

very strong inverse correlation with CG-137 methylation. This correlation accounted for ~
25% of the variability in the response to GH.

3.4 Epigenetic modification of drug absorption, distribution, metabolism and excretion

(ADME) genes
ADME genes encode transporters, plasma proteins, and drug metabolizing enzymes that are
responsible for absorption, distribution, metabolism and excretion of xenobiotics. Genetic
variation at ADME genes has proven extremely successful in predicting individual
differences in pharmacokinetics, particularly in the case of drug metabolizing phenotypes
associated with the CYP450s, as mentioned above. However, there remain large individual
differences in drug metabolism unexplained by genetic variation that have led to the
suggestion that epigenetics may substantially influence these phenotypes [94].
Author Manuscript

Unfortunately, research to date has not yet directly addressed this question, but individual
variation in epigenetic states of ADME genes has been correlated with a range of outcomes.
For example, Parkinson’s disease has been associated with hypomethylation of the CYP2E1
gene promoter in the brain [95]. Methylation levels at CYP1B1 [96] and CYP1A1 [97] have
been associated with prostate cancer, and CYP2W1 with colon cancer [98]. Methylation
levels at the drug transporter genes OCT1 [99] and OCT2 [100], responsible for the renal
excretion of drugs, have been associated with renal carcinoma. These findings demonstrate
the existence of inter-patient variability in ADME gene epigenetic states, some of which
have functional effects on gene expression. However, the extent of normal epigenetic
variation at these loci in the population and the extent to which it will affect pharmacokinetic
phenotypes remains to be determined.
Author Manuscript

3.5 Conclusion
Epigenomic medicine is already here, with numerous epigenetic disease associations
reported, six epidrugs and a handful of epigenetic biomarker tests available the US, plus a
small number of other products available worldwide. The largest number of findings and
applications to date is in the field of oncology. However, the field of epigenetics is only a
few decades old and epigenomic medicine is a very recent arrival, so we are still in early
days. The perceived benefits that epigenomics will bring to healthcare are emphatically

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
 Kronfol et al. Page 11

illustrated by the large number of epidrugs currently in development and the large sums of
Author Manuscript

research dollars spent on large-scale discovery efforts such as RoadMap Epigenomics. To

drive the field forward, epigenomic medicine needs to expand beyond cancer. Also, while
significant efforts are being devoted to bringing new epidrugs to market, more efforts must
be devoted to developing new epigenetic biomarkers, of which there are few.

4. Expert Commentary
Several factors are currently driving innovation in epigenomic medicine. First is the general
level of interest in the field, which is high. Second is the ongoing characterization of
reference epigenomes to enrich and accelerate research efforts. Third is the availability of
powerful methods such as next-generation sequencing (NGS) to characterize epigenomes.
Discussion of technical methods is largely outside the scope of this article and reviews have
been published elsewhere [101,102]. However, with NGS approaches already in use to
Author Manuscript

characterize genome-wide DNA methylation and protein-DNA binding patterns, we would

argue that technology is not a bottleneck for the advancement of epigenomic medicine.

Considering epigenomic biomarker research, among the most significant difficulties are data
complexity and the clean interpretation of findings [103]. Unlike studies of genotype,
epigenomics has a direction of causality problem. While epigenetic biomarkers may be
predictive of disease state or drug response, epigenetic changes are also inducible by
pharmacological treatments [11,104]. As a result, there is the risk that epigenetic differences
between cases and controls in an epigenome-wide association study could be the result of
drug treatment in cases, rather than causal variation. Furthermore, evidence from genome-
wide studies suggests that not all epigenetic changes are functional or cause identifiable
changes to gene expression [105]. Targeting specific populations, such as drug-naïve
Author Manuscript

patients, may go some way to solving issues related to the direction of causality, but it is
certain that experimental model systems will be needed to adequately disentangle causality
and establish functionality of epigenetic changes.

Another complexity is that epigenetic modifications are cell-specific. While this is in many
ways an advantage, and can give precise insight into the workings of the cell of origin, it
also leads to some challenges in sample collection, particularly with respect to clinical
studies. Blood DNA is the most readily-accessible source from humans, but the extent to
which blood DNA methylation is reflective of methylation changes in other tissues is
debated and it seems there may not be a hard and fast rule with respect to which changes are
reflected in blood as compared to which are not. Aging epigenetic signatures, also known as
the “epigenetic clock”, appear to transcend tissue barriers [106], but the extent to which a
blood DNA methylation mark is informative about a disease of, for example, the lung or
Author Manuscript

heart remains an open question. Circulating cfDNA is an exception, since it is sourced from
the diseased tissue of interest and is merely liberated into the bloodstream.

While these considerations apply to the discovery of novel epigenetic biomarkers, a separate
set of considerations apply to novel epigenetic drugs. Paramount among priorities for future
epidrug development is improving target specificity. This can be viewed in two ways. First,
as mentioned above, current drugs lack genomic locus specificity and affect DNA

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
 Kronfol et al. Page 12

methylation or histone modifications somewhat indiscriminately. To truly enable precision

Author Manuscript

correction of aberrant changes, some sort of nucleic acid targeting adjunct is likely to be
required. While antisense RNA (MG98) has already been used to modulate DNMT activity
with some success [107], it is difficult to speculate how this could be used to target
epigenetic modifications at specific target loci. On the other hand, it may be possible to
capitalize on the locus targeting abilities of CRISPR/Cas9 systems to deliver epigenetic
modifying agents to specific loci. Indeed, epigenome editing has already been demonstrated
using this broad approach [108]. A second consideration involves the specificity of epidrugs
to specific members of families of chromatin modifying enzymes. For example, there are
numerous human DNMTs and HDAC enzymes with somewhat different functions and
substrate specificities but currently available DNMTi and HDACi are non-selective and
inhibit many isozymes. However, some drugs currently in clinical trials appear to be more
selective, e.g. mocetinostat that inhibits only HDAC 1 and 4 (see Table 3). Thus, the problem
Author Manuscript

of specificity does not appear to be insurmountable. To conclude, we mention two areas, one
technological and one clinical, that we consider to be of significant interest going forward.

The advent of chromatin conformation capture (3C) sequencing technology marked the
beginning of a new era in precision medicine and our understanding of epigenomic
regulation. Its evolution into Hi-C technology allows insight into the well-organized 3D
structure of the human genome within the nucleus [109]. Numerous studies demonstrated
highly conserved topologically associated domains (TADs) - spatially close units of
chromatin bringing together enhancers, promoters of genes, and other regulatory elements.
These TADs have well-defined boundaries marked by strongly interacting chromatin regions
(chromatin loops) [110]. TADs harbor multiple active RNA polymerases anchored to a
nuclear substructure, with genes within TADs showing co-expression patterns [111]. TADs
are increasingly recognized as regulatory units orchestrating expression of thousands of
Author Manuscript

genes, thus implying a new “druggable nucleosome” paradigm. Disruption of TAD

boundaries due to genetic variants leads to fusion of TADs and/or formation of smaller
TADs [112,113]. This is a frequent event in cancer, leading to coordinated expression of
oncogenes [114,115]. With the dropping costs of sequencing using personalized TAD
abnormalities for diagnostic, prognostic and, potentially, treatment purposes will soon
complement traditional gene expression and epigenetic tests.

In the clinical arena, aging is an area where epigenomic medicine may make an impact.
Older adults are at increased risk for adverse drug events and this may be partly because
aging is associated with changes in physiology that can affect drug pharmacokinetics and
pharmacodynamics [116]. The clinical challenge is to identify those patients who are more
likely to experience an adverse drug event or altered drug response among the older adult
Author Manuscript

population when weighing the risk versus the benefit of a drug therapy. Chronologic age
alone is insufficient as an indicator that dosage adjustment or avoidance of a particular
therapeutic agent is warranted. Pharmacogenetic information alone is also insufficient, as
altered drug response and risk of adverse drug events changes across the lifespan while
genotype remains constant [117,118]. Epigenetic alterations may be a better indicator than
chronological age for personalizing drug therapy for the older population. For example, it
has been proposed that epigenetic regulation of cytochrome P450 (CYP) enzymes
responsible for drug metabolism through DNA methylation may result in altered drug

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
 Kronfol et al. Page 13

exposure in geriatric patients [119]. More research is needed to elucidate the relationships
Author Manuscript

between epigenetics and drug exposure and response during senescence, but is a promising
alternative to chronologic age for adjusting pharmacotherapy in older adults.

Five-year view
We expect to see the introduction of several new epidrugs in the next five years, given that
many are currently in later stage clinical trials. Perhaps the most significant change in this
area will be the introduction of epidrugs with indications outside cancer. For example,
Apabetalone (RVX-208) from Resverlogix is in Phase III trials for high risk Type 2 diabetes
mellitus patients with coronary artery disease (Table 3). Resverlogix also reports the
planning of Phase II trials for Alzheimer’s disease (www.resverlogix.com/programs/
rvx-208-clinical-development/). Successful approval for either of these indications would be
a first step for epidrugs outside oncology. We also expect to see new classes of epidrug enter
Author Manuscript

clinical trials. As mentioned above, several HATi are in preclinical development and show
therapeutic promise. There is growing recognition of the importance of histone acetylation
in many diseases, including cancer, so we expect the first HATi to enter clinical trials in
three to five years.

Given the high level of current research interest, we expect a number of epigenetic
biomarker tests to become commercially available on a five-year horizon. There are
numerous clinical trials currently ongoing to evaluate epigenetic biomarkers. In addition to
the developments cited in Sections 3.1 and 3.3 above, clinical trials of DNA methylation
biomarkers for disease diagnosis, prediction of treatment efficacy and even quantifying toxin
exposure (see for example clinical trial NCT01815385) are ongoing or planned. One area
that should see significant growth is the use of epigenetic markers on cfDNA. As mentioned
in Section 3.1, cfDNA is sourced from dead cells that have released their contents into the
Author Manuscript

bloodstream. Diseased tissue DNA contributes significantly to circulating cfDNA, so cfDNA

is a more direct assay of the diseased tissue methylation levels than surrogate markers from
readily accessible cell types such as lymphocytes. Double stranded DNA from tumor
exosomes also has this property [120]. This is important given the cell-specific nature of
methylation patterns. With cfDNA biomarker tests under development (Section 3.1), we
expect more research in this area and perhaps clinical introduction of cfDNA methylation
tests within five years.

As researchers continue to seek out new epigenetic biomarkers, we will see more large-scale
epigenome-wide studies of complex diseases. These studies will primarily focus on DNA
methylation but we expect the current, prevailing use of high density microarrays to largely
give way to NGS as costs continue to fall. Whole genome bisulfite shotgun sequencing
Author Manuscript

(WGBS) is poised to become the dominant method of choice, because it is the only way to
assay DNA methylation at single base resolution. Correlation between neighboring
methylated sites is low beyond very short distances [40], so this level of resolution is
necessary for a comprehensive genome-wide DNA methylation analysis. While cost is the
primary factor limiting large-scale implementation of WGBS, improved analysis methods
will be needed to extract maximum information from these complex data. Research into
whole genome sequence analysis methods will intensify over the next five years with efforts

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
 Kronfol et al. Page 14

such as the US Precision Medicine Initiative, a >$200 million program to develop

Author Manuscript

individualized therapy on a large scale. Analytical developments made in sequence variant

analysis will likely bleed over to advance NGS methods for epigenetic studies.

Although epigenetic biomarker research will continue to focus on DNA methylation, it is of

note that the first epigenome-wide association study focusing on histone modifications was
recently published. In this study, Sun et al. (2016) compared genome-wide histone
acetylation levels in autism spectrum disorder cases to control subjects [121]. Following this
initial demonstration, it is certain that epigenome-wide association studies of histone
modifications will follow shortly for other disorders. In addition to histones, inroads may be
made into large-scale epidemiological studies of 5-hydroxymethylcytosine or other
methylation variants.

In sum, the next five years should see intensifying research efforts in personalized epigenetic
Author Manuscript

medicine, the introduction of several new epidrugs, initiation of clinical trials for new drug
classes, and the clinical introduction of novel DNA methylation biomarker tests. Overall it
should prove an exciting time for this nascent area.

Acknowledgments
Funding

JL McClay was partially supported by grant R21MH099419 from the US National Institutes of Health. MG
Dozmorov was supported in part by the Virginia Commonwealth University Presidential Research Quest award. R
Huang was supported by an American Cancer Society Institutional Research Grant. Sponsors had no role in the
preparation of this manuscript.

References
Author Manuscript

1. Sykiotis GP, Kalliolias GD, Papavassiliou AG. Pharmacogenetic Principles in the Hippocratic
Writings. J Clin Pharmacol. 2005; 45:1218–1220. [PubMed: 16239353]
2. Ingelman-Sundberg M. Pharmacogenetics of cytochrome P450 and its applications in drug therapy:
the past, present and future. Trends Pharmacol Sci. 2004; 25:193–200. [PubMed: 15063083]
3. McCarthy JJ, McLeod HL, Ginsburg GS. Genomic medicine: a decade of successes, challenges, and
opportunities. Sci Transl Med. 2013; 5:189sr4. [PubMed: 23761042]
4. Ritchie MD. The success of pharmacogenomics in moving genetic association studies from bench to
bedside: study design and implementation of precision medicine in the post-GWAS era. Hum Genet.
2012; 131:1615–1626. [PubMed: 22923055]
5. Manolio TA, Collins FS, Cox NJ, et al. Finding the missing heritability of complex diseases. Nature.
2009; 461:747–753. [PubMed: 19812666]
6. Cardon LR, Harris T. Precision medicine, genomics and drug discovery. Hum Mol Genet. 2016;
25:R166–R172. [PubMed: 27538422]
7. Tracy TS, Chaudhry AS, Prasad B, et al. Interindividual Variability in Cytochrome P450-Mediated
Author Manuscript

Drug Metabolism. Drug Metab Dispos Biol Fate Chem. 2016; 44:343–351. [PubMed: 26681736]
8. He Z-X, Chen X-W, Zhou Z-W, et al. Impact of physiological, pathological and environmental
factors on the expression and activity of human cytochrome P450 2D6 and implications in precision
medicine. Drug Metab Rev. 2015; 47:470–519. [PubMed: 26574146]
9. Bock C. Epigenetic biomarker development. Epigenomics. 2009; 1:99–110. [PubMed: 22122639]
10. Ladd-Acosta C. Epigenetic Signatures as Biomarkers of Exposure. Curr Environ Health Rep. 2015;
2:117–125. [PubMed: 26231361]
11. Feinberg AP. Phenotypic plasticity and the epigenetics of human disease. Nature. 2007; 447:433–
440. [PubMed: 17522677]

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
 Kronfol et al. Page 15

12. Goldberg AD, Allis CD, Bernstein E. Epigenetics: A Landscape Takes Shape. Cell. 2007;
128:635–638. [PubMed: 17320500]
Author Manuscript

13. Noble D. Conrad Waddington and the origin of epigenetics. J Exp Biol. 2015; 218:816–818.
[PubMed: 25788723]
14. Riggs, A., Russo, V., Martiensen, R. Epigenetic Mechanisms of Gene Regulation. Plainview, NY:
Cold Spring Harbor Laboratory Press; 1996.
15. Irizarry RA, Ladd-Acosta C, Wen B, et al. The human colon cancer methylome shows similar
hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet. 2009;
41:178–186. [PubMed: 19151715]
16. Reik W, Dean W, Walter J. Epigenetic reprogramming in mammalian development. Science. 2001;
293:1089–1093. [PubMed: 11498579]
17. Ito S, Shen L, Dai Q, et al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-
carboxylcytosine. Science. 2011; 333:1300–1303. [PubMed: 21778364]
18. Bachman M, Uribe-Lewis S, Yang X, et al. 5-Formylcytosine can be a stable DNA modification in
mammals. Nat Chem Biol. 2015; 11:555–557. [PubMed: 26098680]
19. Kriaucionis S, Heintz N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje
Author Manuscript

neurons and the brain. Science. 2009; 324:929–930. [PubMed: 19372393]

20. Pastor WA, Pape UJ, Huang Y, et al. Genome-wide mapping of 5-hydroxymethylcytosine in
embryonic stem cells. Nature. 2011; 473:394–397. [PubMed: 21552279]
21. Jenuwein T, Allis CD. Translating the histone code. Science. 2001; 293:1074–1080. [PubMed:
11498575]
22. Luger K, Mäder AW, Richmond RK, et al. Crystal structure of the nucleosome core particle at 2.8
A resolution. Nature. 1997; 389:251–260. [PubMed: 9305837]
23. Bannister AJ, Kouzarides T. Regulation of chromatin by histone modifications. Cell Res. 2011;
21:381–395. [PubMed: 21321607]
24. Weber CM, Henikoff S. Histone variants: dynamic punctuation in transcription. Genes Dev. 2014;
28:672–682. [PubMed: 24696452]
25. Marques M, Laflamme L, Gervais AL, et al. Reconciling the positive and negative roles of histone
H2A.Z in gene transcription. Epigenetics. 2010; 5:267–272. [PubMed: 20364108]
26. Entrevan M, Schuettengruber B, Cavalli G. Regulation of Genome Architecture and Function by
Author Manuscript

Polycomb Proteins. Trends Cell Biol. 2016; 26:511–525. [PubMed: 27198635]

27. Filippakopoulos P, Knapp S. Targeting bromodomains: epigenetic readers of lysine acetylation. Nat
Rev Drug Discov. 2014; 13:337–356. [PubMed: 24751816]
28. Jaenisch R, Bird A. Epigenetic regulation of gene expression: how the genome integrates intrinsic
and environmental signals. Nat Genet. 2003; 33(Suppl):245–254. [PubMed: 12610534]
29. Ivanov M, Barragan I, Ingelman-Sundberg M. Epigenetic mechanisms of importance for drug
treatment. Trends Pharmacol Sci. 2014; 35:384–396. [PubMed: 24993164]
30. Hansen K, Helin K. Epigenetic inheritance through self-recruitment of the polycomb repressive
complex 2. Epigenetics. 2009; 4:133–138. [PubMed: 19377285]
31. ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human
genome. Nature. 2012; 489:57–74. [PubMed: 22955616]
32**. Kundaje A, Meuleman W, et al. Roadmap Epigenomics Consortium. Integrative analysis of 111
reference human epigenomes. Nature. 2015; 518:317–330. A tour de force revealing baseline
epigenetic patterns and regulation in human tissues. [PubMed: 25693563]
Author Manuscript

33. Ernst J, Kheradpour P, Mikkelsen TS, et al. Mapping and analysis of chromatin state dynamics in
nine human cell types. Nature. 2011; 473:43–49. [PubMed: 21441907]
34. Fraga MF, Ballestar E, Paz MF, et al. Epigenetic differences arise during the lifetime of
monozygotic twins. Proc Natl Acad Sci U S A. 2005; 102:10604–10609. [PubMed: 16009939]
35. Feil R, Fraga MF. Epigenetics and the environment: emerging patterns and implications. Nat Rev
Genet. 2011; 13:97–109.
36. Rutter M. Why is the topic of the biological embedding of experiences important for translation?
Dev. Psychopathol. 2016; 28:1245–1258.

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
 Kronfol et al. Page 16

37. Zhi D, Aslibekyan S, Irvin MR, et al. SNPs located at CpG sites modulate genome-epigenome
interaction. Epigenetics. 2013; 8:802–806. [PubMed: 23811543]
Author Manuscript

38. Zhou D, Li Z, Yu D, et al. Polymorphisms involving gain or loss of CpG sites are significantly
enriched in trait-associated SNPs. Oncotarget. 2015; 6:39995–40004. [PubMed: 26503467]
39. Cazaly E, Charlesworth J, Dickinson JL, et al. Genetic Determinants of Epigenetic Patterns:
Providing Insight into Disease. Mol Med. 2015; 21:400–409. [PubMed: 25822796]
40. McClay JL, Shabalin AA, Dozmorov MG, et al. High density methylation QTL analysis in human
blood via next-generation sequencing of the methylated genomic DNA fraction. Genome Biol.
2015; 16:291. [PubMed: 26699738]
41. García-Giménez, JL. Epigenetic Biomarkers and Diagnostics. Academic Press; 2015.
42. Szyf M. Epigenetics, DNA methylation, and chromatin modifying drugs. Annu Rev Pharmacol
Toxicol. 2009; 49:243–263. [PubMed: 18851683]
43. Hunter P. The second coming of epigenetic drugs: a more strategic and broader research framework
could boost the development of new drugs to modify epigenetic factors and gene expression.
EMBO Rep. 2015; 16:276–279. [PubMed: 25662153]
44. Suvà ML, Riggi N, Bernstein BE. Epigenetic reprogramming in cancer. Science. 2013; 339:1567–
Author Manuscript

1570. [PubMed: 23539597]

45. Feinberg AP, Koldobskiy MA, Göndör A. Epigenetic modulators, modifiers and mediators in
cancer aetiology and progression. Nat Rev Genet. 2016; 17:284–299. [PubMed: 26972587]
46. Amacher DE. A 2015 survey of established or potential epigenetic biomarkers for the accurate
detection of human cancers. Biomarkers. 2016; 21:387–403. [PubMed: 26983778]
47. Imperiale TF, Ransohoff DF, Itzkowitz SH, et al. Multitarget stool DNA testing for colorectal-
cancer screening. N Engl J Med. 2014; 370:1287–1297. [PubMed: 24645800]
48. Ladabaum U, Mannalithara A. Comparative Effectiveness and Cost Effectiveness of a Multitarget
Stool DNA Test to Screen for Colorectal Neoplasia. Gastroenterology. 2016; 151:427–439. e6.
[PubMed: 27311556]
49. Lee WH, Morton RA, Epstein JI, et al. Cytidine methylation of regulatory sequences near the pi-
class glutathione S-transferase gene accompanies human prostatic carcinogenesis. Proc Natl Acad
Sci U S A. 1994; 91:11733–11737. [PubMed: 7972132]
50. Partin AW, Van Neste L, Klein EA, et al. Clinical validation of an epigenetic assay to predict
Author Manuscript

negative histopathological results in repeat prostate biopsies. J Urol. 2014; 192:1081–1087.

[PubMed: 24747657]
51. van Kessel KEM, Neste LV, Lurkin I, et al. Evaluation of an Epigenetic Profile for the Detection of
Bladder Cancer in Patients with Hematuria. J Urol. 2016; 195:601–607. [PubMed: 26327355]
52. Schmidt B, Liebenberg V, Dietrich D, et al. SHOX2 DNA methylation is a biomarker for the
diagnosis of lung cancer based on bronchial aspirates. BMC Cancer. 2010; 10:600. [PubMed:
21047392]
53. Dietrich D, Kneip C, Raji O, et al. Performance evaluation of the DNA methylation biomarker
SHOX2 for the aid in diagnosis of lung cancer based on the analysis of bronchial aspirates. Int J
Oncol. 2012; 40:825–832. [PubMed: 22108652]
54. Stefansson OA, Esteller M. Epigenetic modifications in breast cancer and their role in personalized
medicine. Am J Pathol. 2013; 183:1052–1063. [PubMed: 23899662]
55. Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma.
Nature. 2011; 474:609–615. [PubMed: 21720365]
Author Manuscript

56. Chang S, Wang R-H, Akagi K, et al. Tumor suppressor BRCA1 epigenetically controls oncogenic
microRNA-155. Nat Med. 2011; 17:1275–1282. [PubMed: 21946536]
57. Anjum S, Fourkala E-O, Zikan M, et al. A BRCA1-mutation associated DNA methylation
signature in blood cells predicts sporadic breast cancer incidence and survival. Genome Med.
2014; 6:47. [PubMed: 25067956]
58. Kloten V, Becker B, Winner K, et al. Promoter hypermethylation of the tumor-suppressor genes
ITIH5, DKK3, and RASSF1A as novel biomarkers for blood-based breast cancer screening. Breast
Cancer Res BCR. 2013; 15:R4. [PubMed: 23320751]

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
 Kronfol et al. Page 17

59*. Fackler MJ, Lopez Bujanda Z, Umbricht C, et al. Novel methylated biomarkers and a robust assay
to detect circulating tumor DNA in metastatic breast cancer. Cancer Res. 2014; 74:2160–2170.
Author Manuscript

An important demonstration of circulating cell-free DNA methylation levels as diagnostic

biomarkers. [PubMed: 24737128]
60. Butkus, B. Hopkins Lab, Cepheid Developing Methylated DNA Panel for Breast Cancer Dx,
Monitoring. Genome Web [Internet]. 2015. Available from: https://www.genomeweb.com/
molecular-diagnostics/hopkins-lab-cepheid-developing-methylated-dna-panel-breast-cancer-dx
61. Lunnon K, Smith R, Hannon E, et al. Methylomic profiling implicates cortical deregulation of
ANK1 in Alzheimer’s disease. Nat Neurosci. 2014; 17:1164–1170. [PubMed: 25129077]
62. De Jager PL, Srivastava G, Lunnon K, et al. Alzheimer’s disease: early alterations in brain DNA
methylation at ANK1, BIN1, RHBDF2 and other loci. Nat Neurosci. 2014; 17:1156–1163.
[PubMed: 25129075]
63. Jowaed A, Schmitt I, Kaut O, et al. Methylation Regulates Alpha-Synuclein Expression and Is
Decreased in Parkinson’s Disease Patients’ Brains. J Neurosci. 2010; 30:6355–6359. [PubMed:
20445061]
64. Absher DM, Li X, Waite LL, et al. Genome-wide DNA methylation analysis of systemic lupus
Author Manuscript

erythematosus reveals persistent hypomethylation of interferon genes and compositional changes

to CD4+ T-cell populations. PLoS Genet. 2013; 9:e1003678. [PubMed: 23950730]
65. Pidsley R, Viana J, Hannon E, et al. Methylomic profiling of human brain tissue supports a
neurodevelopmental origin for schizophrenia. Genome Biol. 2014; 15:483. [PubMed: 25347937]
66. Aberg KA, McClay JL, Nerella S, et al. Methylome-wide association study of schizophrenia:
identifying blood biomarker signatures of environmental insults. JAMA Psychiatry. 2014; 71:255–
264. [PubMed: 24402055]
67. Ladd-Acosta C, Hansen KD, Briem E, et al. Common DNA methylation alterations in multiple
brain regions in autism. Mol Psychiatry. 2014; 19:862–871. [PubMed: 23999529]
68. Heyn H, Esteller M. DNA methylation profiling in the clinic: applications and challenges. Nat Rev
Genet. 2012; 13:679–692. [PubMed: 22945394]
69. DeWoskin VA, Million RP. The epigenetics pipeline. Nat Rev Drug Discov. 2013; 12:661–662.
[PubMed: 23989788]
70. Liang G, Gonzales FA, Jones PA, et al. Analysis of gene induction in human fibroblasts and
Author Manuscript

bladder cancer cells exposed to the methylation inhibitor 5-aza-2′-deoxycytidine. Cancer Res.
2002; 62:961–966. [PubMed: 11861364]
71. Cheishvili D, Boureau L, Szyf M. DNA demethylation and invasive cancer: implications for
therapeutics. Br J Pharmacol. 2015; 172:2705–2715. [PubMed: 25134627]
72. Peedicayil J. Epigenetic Drugs for Multiple Sclerosis. Curr Neuropharmacol. 2016; 14:3–9.
[PubMed: 26813117]
73. Abdel-Hameed EA, Ji H, Shata MT. HIV-Induced Epigenetic Alterations in Host Cells. Adv Exp
Med Biol. 2016; 879:27–38. [PubMed: 26659262]
74. Sun Y, Sahbaie P, Liang D, et al. DNA Methylation Modulates Nociceptive Sensitization after
Incision. PloS One. 2015; 10:e0142046. [PubMed: 26535894]
75. Singh P, Konar A, Kumar A, et al. Hippocampal chromatin-modifying enzymes are pivotal for
scopolamine-induced synaptic plasticity gene expression changes and memory impairment. J
Neurochem. 2015; 134:642–651. [PubMed: 25982413]
76. Rajasethupathy P, Antonov I, Sheridan R, et al. A role for neuronal piRNAs in the epigenetic
control of memory-related synaptic plasticity. Cell. 2012; 149:693–707. [PubMed: 22541438]
Author Manuscript

77. Lane AA, Chabner BA. Histone Deacetylase Inhibitors in Cancer Therapy. J Clin Oncol. 2009;
27:5459–5468. [PubMed: 19826124]
78. Falkenberg KJ, Johnstone RW. Histone deacetylases and their inhibitors in cancer, neurological
diseases and immune disorders. Nat Rev Drug Discov. 2014; 13:673–691. [PubMed: 25131830]
79. Kurita M, Holloway T, García-Bea A, et al. HDAC2 regulates atypical antipsychotic responses
through the modulation of mGlu2 promoter activity. Nat Neurosci. 2012; 15:1245–1254.
[PubMed: 22864611]
80. Sharma S, Taliyan R. Histone deacetylase inhibitors: Future therapeutics for insulin resistance and
type 2 diabetes. Pharmacol Res. 2016; 113:320–326. [PubMed: 27620069]

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
 Kronfol et al. Page 18

81*. Daigle SR, Olhava EJ, Therkelsen CA, et al. Potent inhibition of DOT1L as treatment of MLL-
fusion leukemia. Blood. 2013; 122:1017–1025. An interesting paper demonstrating the
Author Manuscript

application of an epidrug to a genetically distinct cancer subset. [PubMed: 23801631]

82. Kurmasheva RT, Sammons M, Favours E, et al. Initial testing (stage 1) of tazemetostat (EPZ-6438),
a novel EZH2 inhibitor, by the Pediatric Preclinical Testing Program. Pediatr Blood Cancer. 2016
83. Chung C, Coste H, White JH, et al. Discovery and Characterization of Small Molecule Inhibitors
of the BET Family Bromodomains. J Med Chem. 2011; 54:3827–3838. [PubMed: 21568322]
84. Khan SN, Khan AU. Role of histone acetylation in cell physiology and diseases: An update. Clin
Chim Acta Int J Clin Chem. 2010; 411:1401–1411.
85. Bowers EM, Yan G, Mukherjee C, et al. Virtual ligand screening of the p300/CBP histone
acetyltransferase: identification of a selective small molecule inhibitor. Chem Biol. 2010; 17:471–
482. [PubMed: 20534345]
86. Gajer JM, Furdas SD, Gründer A, et al. Histone acetyltransferase inhibitors block neuroblastoma
cell growth in vivo. Oncogenesis. 2015; 4:e137. [PubMed: 25664930]
87*. Esteller M, Garcia-Foncillas J, Andion E, et al. Inactivation of the DNA-Repair Gene MGMT and
the Clinical Response of Gliomas to Alkylating Agents. N Engl J Med. 2000; 343:1350–1354. A
Author Manuscript

landmark study that was one of the first to show association between epigenetic factors and
therapeutic drug response. [PubMed: 11070098]
88. Hegi ME, Diserens A-C, Gorlia T, et al. MGMT gene silencing and benefit from temozolomide in
glioblastoma. N Engl J Med. 2005; 352:997–1003. [PubMed: 15758010]
89. Fornaro L, Vivaldi C, Caparello C, et al. Pharmacoepigenetics in gastrointestinal tumors: MGMT
methylation and beyond. Front Biosci Elite Ed. 2016; 8:170–180. [PubMed: 26709653]
90. Chiam, K., Centenera, MM., Butler, LM., et al. GSTP1 DNA Methylation and Expression Status Is
Indicative of 5-aza-2′-Deoxycytidine Efficacy in Human Prostate Cancer Cells. In: Agoulnik, I.,
editor. PLoS ONE. Vol. 6. 2011. p. e25634
91. Dejeux E, Rønneberg J, Solvang H, et al. DNA methylation profiling in doxorubicin treated
primary locally advanced breast tumours identifies novel genes associated with survival and
treatment response. Mol Cancer. 2010; 9:68. [PubMed: 20338046]
92. Stefansson OA, Villanueva A, Vidal A, et al. BRCA1 epigenetic inactivation predicts sensitivity to
platinum-based chemotherapy in breast and ovarian cancer. Epigenetics. 2012; 7:1225–1229.
Author Manuscript

[PubMed: 23069641]
93. Ouni M, Belot MP, Castell AL, et al. The P2 promoter of the IGF1 gene is a major epigenetic locus
for GH responsiveness. Pharmacogenomics J. 2016; 16:102–106. [PubMed: 25869012]
94. Ivanov M, Kacevska M, Ingelman-Sundberg M. Epigenomics and interindividual differences in
drug response. Clin Pharmacol Ther. 2012; 92:727–736. [PubMed: 23093317]
95. Kaut O, Schmitt I, Wüllner U. Genome-scale methylation analysis of Parkinson’s disease patients’
brains reveals DNA hypomethylation and increased mRNA expression of cytochrome P450 2E1.
Neurogenetics. 2012; 13:87–91. [PubMed: 22238121]
96. Tokizane T, Shiina H, Igawa M, et al. Cytochrome P450 1B1 is overexpressed and regulated by
hypomethylation in prostate cancer. Clin Cancer Res Off J Am Assoc Cancer Res. 2005; 11:5793–
5801.
97. Okino ST, Pookot D, Li L-C, et al. Epigenetic inactivation of the dioxin-responsive cytochrome
P4501A1 gene in human prostate cancer. Cancer Res. 2006; 66:7420–7428. [PubMed: 16885337]
98. Gomez A, Karlgren M, Edler D, et al. Expression of CYP2W1 in colon tumors: regulation by gene
methylation. Pharmacogenomics. 2007; 8:1315–1325. [PubMed: 17979506]
Author Manuscript

99. Schaeffeler E, Hellerbrand C, Nies AT, et al. DNA methylation is associated with downregulation
of the organic cation transporter OCT1 (SLC22A1) in human hepatocellular carcinoma. Genome
Med. 2011; 3:82. [PubMed: 22196450]
100. Liu Y, Zheng X, Yu Q, et al. Epigenetic activation of the drug transporter OCT2 sensitizes renal
cell carcinoma to oxaliplatin. Sci Transl Med. 2016; 8:348ra97.
101. Laird PW. Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet.
2010; 11:191–203. [PubMed: 20125086]
102. Krueger F, Kreck B, Franke A, et al. DNA methylome analysis using short bisulfite sequencing
data. Nat Methods. 2012; 9:145–151. [PubMed: 22290186]

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
 Kronfol et al. Page 19

103. Ledford H. Epigenetics: The genome unwrapped. Nature. 2015; 528:S12–S13. [PubMed:
26630592]
Author Manuscript

104. Wang Y, Krishnan HR, Ghezzi A, et al. Drug-induced epigenetic changes produce drug tolerance.
PLoS Biol. 2007; 5:e265. [PubMed: 17941717]
105*. Stricker SH, Köferle A, Beck S. From profiles to function in epigenomics. Nat Rev Genet. 2016
advance online publication. An outstanding and up-to-date review of complex epigenomic
regulation.
106. Horvath S. DNA methylation age of human tissues and cell types. Genome Biol. 2013; 14:R115.
[PubMed: 24138928]
107. Reid GK, Besterman JM, MacLeod AR. Selective inhibition of DNA methyltransferase enzymes
as a novel strategy for cancer treatment. Curr Opin Mol Ther. 2002; 4:130–137. [PubMed:
12044034]
108. Thakore PI, Black JB, Hilton IB, et al. Editing the epigenome: technologies for programmable
transcription and epigenetic modulation. Nat Methods. 2016; 13:127–137. [PubMed: 26820547]
109*. Lieberman-Aiden E, van Berkum NL, Williams L, et al. Comprehensive mapping of long-range
interactions reveals folding principles of the human genome. Science. 2009; 326:289–293. A
Author Manuscript

landmark paper in understanding the 3D genome. [PubMed: 19815776]

110. Rao SSP, Huntley MH, Durand NC, et al. A 3D map of the human genome at kilobase resolution
reveals principles of chromatin looping. Cell. 2014; 159:1665–1680. [PubMed: 25497547]
111. Symmons O, Uslu VV, Tsujimura T, et al. Functional and topological characteristics of
mammalian regulatory domains. Genome Res. 2014; 24:390–400. [PubMed: 24398455]
112. Fudenberg G, Imakaev M, Lu C, et al. Formation of Chromosomal Domains by Loop Extrusion.
Cell Rep. 2016; 15:2038–2049. [PubMed: 27210764]
113. Sanborn AL, Rao SSP, Huang S-C, et al. Chromatin extrusion explains key features of loop and
domain formation in wild-type and engineered genomes. Proc Natl Acad Sci U S A. 2015;
112:E6456–6465. [PubMed: 26499245]
114. Rickman DS, Soong TD, Moss B, et al. Oncogene-mediated alterations in chromatin
conformation. Proc Natl Acad Sci U S A. 2012; 109:9083–9088. [PubMed: 22615383]
115. Valton A-L, Dekker J. TAD disruption as oncogenic driver. Curr Opin Genet Dev. 2016; 36:34–
40. [PubMed: 27111891]
Author Manuscript

116. Slattum, P., Peron, E., Ogbonna, K. The Pharmacology of Aging. In: Fill, HM.Rockwood,
K.Woodhouse, K., Young, JB., editors. Brocklehursts Textb Geriatr Med Gerontol. 8. Philadephia
PA: Saunders/Elsevier; 2016. p. Chapter 26
117. Pal S, Tyler JK. Epigenetics and aging. Sci Adv. 2016; 2:e1600584. [PubMed: 27482540]
118. Brunet A, Berger SL. Epigenetics of aging and aging-related disease. J Gerontol A Biol Sci Med
Sci. 2014; 69(Suppl 1):S17–20. [PubMed: 24833581]
119. Seripa D, Panza F, Daragjati J, et al. Measuring pharmacogenetics in special groups: geriatrics.
Expert Opin Drug Metab Toxicol. 2015; 11:1073–1088. [PubMed: 25990744]
120. Thakur BK, Zhang H, Becker A, et al. Double-stranded DNA in exosomes: a novel biomarker in
cancer detection. Cell Res. 2014; 24:766–769. [PubMed: 24710597]
121*. Sun W, Poschmann J, Cruz-Herrera Del Rosario R, et al. Histone Acetylome-wide Association
Study of Autism Spectrum Disorder. Cell. 2016; 167:1385–1397. e11. The first study, to our
knowledge, to systematically compare epigenome-wide histone modification profiles in disease
cases versus controls. [PubMed: 27863250]
Author Manuscript

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
 Kronfol et al. Page 20

Key issues
Author Manuscript

• Epigenetic data has distinct information content to genotype information

because epigenetic marks, including DNA methylation and histone
modifications, are developmentally dynamic and tissue-specific.

• Epigenetic marks have profound effects on genetic regulation.

• Aberrant epigenetic regulation may cause disease. Aberrant epigenetic marks

may arise from genetic differences or may arise over the life course via
maladaptive response to environmental factors.

• There are numerous specific examples of epigenetic marks associated with

disease and some are validated as diagnostic biomarkers for cancer.

• Epigenetic marks are reversible, therefore much effort has been expended in
Author Manuscript

developing drugs with epigenetic modes of action. All current epigenetic

drugs are indicated for cancer but many more are in development.

• A small number of epigenetic biomarkers of drug response have been

reported but none are yet approved for general clinical use.

• Next-generation sequencing will enable the discovery of new biomarkers,

with the expectation this area will continue to focus on DNA methylation in
the near future

• A major challenge in epigenetic drug development is targeting specific

genetic loci. Solutions may involve adaptations of the CRISPR/dCas9 system
of epigenome editing.
Author Manuscript

• Future directions may include the “druggable nucleosome” concept and life
stage-specific biomarkers of drug response.
Author Manuscript

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
 Kronfol et al. Page 21
Author Manuscript

Figure 1.
Waddington represented the developmental process as a series of “decisions” made by
differentiating cells that could be represented as forks in the valleys of the “developmental
landscape”. Panels A and B represent the alternate fates of the cell, or ball by analogy. As
the pluripotent stem cell of the egg (ball at the top), begins to specialize, the differentiation
Author Manuscript

“decisions” made are irreversible. Its pattern of epigenetic regulation is established by the
point of terminal differentiation at the bottom of the landscape. With epigenetic drugs and
therapies, the aim is to artificially reverse maladaptive epigenetic states and essentially “push
the ball back up the hill”. Figure from Noble (2015) [13] reproduced with permission.
Author Manuscript
Author Manuscript

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
 Kronfol et al. Page 22
Author Manuscript
Author Manuscript
Author Manuscript

Figure 2.
Epigenetic regulation of gene expression via chromatin remodeling. The diagram shows two
generic chromatin activity states. At the top, active chromatin is open and accessible to
transcription factors and polymerases, with nucleosomes spread apart, DNA typically in an
unmethylated state and acetylation marks on histones. HAT is histone acetyltransferase,
SWI/SNF is a nucleosome remodeling complex, RNA Pol II is RNA polymerase II. The
Author Manuscript

lower panel shows the opposite inactive chromatin scenario, where the nucleosomes are
tightly packed, the DNA is methylated and inaccessible to transcription factors, while
histones have their acetylation marks removed. HDAC is histone deacetylase, HMT is
histone methyltransferase. Figure is adapted from Luong, P. Basic Principles of Genetics,
Connexions Web site. [http://cnx.org/content/m26565/1.1/] (2009) under a Creative
Commons Attribution License ([http://creativecommons.org/licenses/by/3.0/CC-BY 3.0]).

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
 Author Manuscript Author Manuscript Author Manuscript Author Manuscript

Table 1

Commercially available epigenetic diagnostic tests in the United States.

Product Proprietor/Launch year Disease Specimen Epigenetic Targets Regulation

Kronfol et al.

Cologuard Exact sciences/2014 Colorectal cancer Stool DNA methylation of NDRG4 and BMP3 (plus other genetic markers) FDA
ConfirmMDx MDxHealth/2012 Prostate cancer Tissue DNA methylation of GSTP1, RASSF1 and APC. LDT/CLIA
AssureMDx MDxHealth/2016 Bladder cancer Urine DNA methylation of TWIST, ONECUT2 and OTX1 (plus other genetic markers) LDT/CLIA

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
Page 23
 Kronfol et al. Page 24

Table 2

Classification of US FDA-approved epigenetic drug classes according to mechanism of action.

Author Manuscript

Mechanism of Action Active Ingredient (Trade name®, Proprietor) Date of Approval Indication(s)
DNA N-Methyltransferase Azacitidine (Vidaza®, Celgene) May 19, 2004 Chronic Myelomonocytic
Inhibitor (DNMTi) Leukemia. Myelodysplastic
Syndrome i.
Decitabine(Dacogen®, Otsuka) May 2, 2006 Chronic Myelomonocytic
Leukemia. Myelodysplastic
Syndromes ii.

Histone Deacetylase Vorinostat(Zolinza®, Merck) October 6, 2006 Cutaneous manifestations in

inhibitors (HDACi) patients with cutaneous T-Cell
Lymphoma (CTCL) who have
progressive, persistent or recurrent
disease on or following two
systemic therapies.
Romidepsin(Istodax®, Celgene) November 5,2009 Cutaneous T-cell Lymphoma
(CTCL) iii, Peripheral T-cell
Author Manuscript

Lymphoma (PTCL) iii

Belinostat(Beleodaq®, Spectrum Pharmaceuticals) July 3, 2014 Relapsed or Refractory Peripheral
T-cell Lymphoma (PTCL)
Panobinostat(Farydak®, Novartis) February 23, 2015 Multiple Myeloma after receiving at
least 2 prior regimens, including
bortezomib and an
immunomodulatory agent iv

i
Subtypes: refractory anemia or refractory anemia with ringed sideroblasts (if accompanied by neutropenia or thrombocytopenia or requiring
transfusions), refractory anemia with excess blasts, refractory anemia with excess blasts in transformation.
ii
Including 90 previously treated and untreated, de novo and secondary MDS of all French-American-British subtypes 91 (refractory anemia,
refractory anemia with ringed sideroblasts, refractory anemia with excess blasts, 92 refractory anemia with excess blasts in transformation, and 93
intermediate-1, intermediate-2, and high-risk International Prognostic Scoring System groups).
iii
In patients who have received at least one prior systemic therapy.
Author Manuscript

iv
In combination with bortezomib and dexamethasone.
Author Manuscript

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
 Author Manuscript Author Manuscript Author Manuscript Author Manuscript

Table 3

Classification of epigenetic drug classes in active clinical trials registered in the US (clinicaltrials.gov) according to mechanism of action.

Mechanism of action Active ingredient (Proprietor) Indication Clinical Trial Phase Trial Ref ID
Kronfol et al.

BET Bromodomain Inhibitors Apabetalone/RVX-208 (Resverlogix) High-risk type 2 diabetes mellitus with Phase III NCT02586155
coronary artery disease

CPI-0610 (Constellation Pharmaceuticals) Malignant Peripheral Nerve Sheath Tumor Phase II NCT02986919

INCB054329 (Incyte) Advanced malignancies Phase I/II NCT02431260

GSK525762 (GlaxoSmithKline) Carcinoma and hematological Phase I NCT01587703, NCT01943851

malignancies
GSK2820151 (GlaxoSmithKline) Advanced or recurrent solid tumors Phase I NCT02630251
ZEN-3694 (Zenith Epigenetics) Metastatic castration-resistant prostate Phase I NCT02711956i, NCT02705469
cancer (mCRPC) i
OTX015/MK-8628 (Merck) Selected advanced solid tumors Phase I NCT02698176
TEN-010/RO6870810 (Hoffmann-La Roche) Advanced Solid Tumors; Acute Myeloid Phase I NCT01987362, NCT02308761
Leukemia
FT-1101 (Forma therapeutics) Relapsed/Refractory Acute Leukemia Phase I NCT02543879
BMS-986158 (Bristol-Myers Squibb) Advanced Solid Tumors Phase I NCT02419417
Mivebresib/ABBV-075 (AbbVie) Advanced cancers Phase I NCT02391480

DNA N-Methyltransferase Inhibitor Guadecitabine (Astex) Acute Myeloid Leukemia Phase III NCT02920008
(DNMTi)
TdCyd (NCI) Advanced Solid Tumors Phase I NCT02423057

Histone Non-Selective Entinostat (Syndax) Advanced Hormone Receptor positive (HR Phase III NCT02115282
Deacetylase +) Breast Cancer ii
inhibitors
(HDACi)
Givinostat/ITF2357 (Italfarmaco) Chronic Myeloproliferative Neoplasms Phase II NCT01761968

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
Resminostat (4SC AG) Advanced Stage Mycosis Fungoides or Phase II NCT02953301
Sézary Syndrome
Quisinostat/JNJ-26481585 (Janssen) Ovarian cancer iii Phase II NCT02948075

Pracinostat/SB939 (NCIC Clinical Trials Acute Myeloid Leukemia iv, Myelofibrosis Phase II NCT01912274iv NCT02267278v
Group) v

Tefinostat (Chroma) Hepatocellular Carcinoma Phase I/II NCT02759601

Page 25
 Author Manuscript Author Manuscript Author Manuscript Author Manuscript

Mechanism of action Active ingredient (Proprietor) Indication Clinical Trial Phase Trial Ref ID
AR-42 (Celgene) Relapsed multiple myeloma vi Phase I NCT02569320

CUDC-907 (Curis) Multiple Myeloma Phase I NCT01742988

HDAC 1&4 Selective Mocetinostat (Mirati) Phase II NCT02954991

Kronfol et al.

Non-Small Cell Lung Cancer vii

HDAC 6 Selective ACY 241 (Acetylon) Non-Small Cell Lung Cancer vii Phase I NCT02635061

KA2507 (Karus) Solid tumor Phase I NCT03008018

Histone Lysine LSD1 inhibitors GSK2879552 (GlaxoSmithKline) Myelodysplastic Syndrome Phase II NCT02929498
De-methylases
(KDM/HDM)
Tranylcypromine (Martin Luther Universität) Relapsed/Refractory Acute Myeloid Phase I/II NCT02261779
Leukemia viii
INCB059872 (Incyte) Advanced Malignancies Phase I/II NCT02712905

IMG-7289 (Imago BioSciences) Acute Myeloid Leukemia Phase I NCT02842827

Histone Lysine DOT1L inhibitor Pinometostat/EPZ-5676 (Epizyme) Relapsed/Refractory Leukemias ix Phase I NCT01684150
Methyl
Transferase
(KMT/HMT) EZH1/2 inhibitor DS-3201b (Daiichi Sankyo) Lymphomas Phase I NCT02732275

EZH2 inhibitor Tazemetostat/EPZ-6438 (Epizyme) Advanced Solid Tumors or B-cell Phase I/II NCT01897571
lymphomas
MAK683 (Novartis) Diffuse Large B-cell Lymphoma Phase I/II NCT02900651

GSK2816126 (GlaxoSmithKline) Lymphomas, Multiple Myeloma, Solid Phase I NCT02082977

Tumors

PRMT5 inhibitor GSK3326595 (GlaxoSmithKline) Solid Tumors and Non-Hodgkin’s Phase I NCT02783300
Lymphoma

i
In combination with Enzalutamide.

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
ii
In combination with Aromasin (Exemestene).
iii
In combination with Paclitaxel and Carboplatin chemotherapy.
iv
In combination with Azacitidine.
v
In combination with Ruxolitinib.
vi
In combination with Pomalidomide.
Page 26
 Author Manuscript Author Manuscript Author Manuscript Author Manuscript
vii
In Combination with Nivolumab.
viii
In combination with all-trans-retinoic acid (ATRA) chemotherapy.
ix
Only patients with rearrangements involving the MLL gene.

LSD1: Lysine (K)-specific demethylase 1A, DOT1L: Disruptor of telomeric silencing 1-like, EZH1 or EZH2: Enhancer Of Zeste Homolog 1 or 2 Polycomb Respressive Complex 2 Subunit, PRMT5:
Protein Arginine Methyl Transferase 5.
Kronfol et al.

Expert Rev Precis Med Drug Dev. Author manuscript; available in PMC 2018 January 31.
Page 27