Epigenetic heterogeneity is far more dynamic
than genetic heterogeneity, and it is likely that
transcriptional plasticity driven by epigenetic regulators responding to environmental and therapeutic pressures underpins the failure of many
cancer drugs to induce durable disease remission
in patients. It has been hypothesized that therapeutic failures often arise from adaptive responses
in cancer stem cells. Consistent with this idea, it
was recently demonstrated in preclinical models
that resistance to epigenetic therapies in AML
emerges from a subpopulation of leukemia stem
cells (64). This model of resistance was not driven
by genetic evolution but rather by transcriptional
plasticity, an important emerging theme of epigenetic resistance in cancer biology (64–66).
These studies have answered some crucial
questions but have also raised new ones: Why
are some leukemia stem cells sensitive and others
resistant to the same therapeutic pressure? What
drives this transcriptional plasticity? Is the adaptive response equal in different tissues? The transcriptional plasticity by which some cancers evade
epigenetic therapies also potentially offers new
opportunities. In the absence of gatekeeper mutations and genetic evolution, the therapeutic
pressure exerted on a heterogeneous population
of cancer cells by epigenetic therapies provides
a unique bottleneck that helps to homogenize
the adaptive response to the therapy by invoking
the use of an alternative transcriptional program
to sustain the cancer cells. Although this adaptive
response is likely to be cell context–dependent,
it may be predictable and therefore of use in
exposing and exploiting new synthetic lethal
dependencies. These strategies may result in new
combination therapies that are more efficacious.
All too often, an empirical approach drives the
iteration of combination therapies in cancer.
Urgent clinical need will continue to fuel this
policy, but there have been some important lessons learned with epigenetic therapies that warrant a more cautious approach. Because normal
and malignant epigenetic regulation is cell context–
specific, empirical combinations of therapies that
substantially alter the epigenome may potentially
be detrimental. For example, monotherapy with a
DNMTi extends the survival of many patients
with MDS (51), and HDAC inhibitors in isolation
have also shown some benefit in MDS. However,
in contrast to the predicted synergy, several
studies have now demonstrated that the empirical combination of these agents results in no
discernible synergy and in fact may result in
functional antagonism; several patients have had
a poorer outcome with combination therapy than
those treated with a DNMTi alone (67, 68). These
findings highlight the need to thoroughly explore
the molecular rationale for combination epigenetic therapies and experimentally demonstrate
the synergistic effects of the combination therapy in appropriate preclinical models and primary
human cancer cells. Several recent examples of
this molecular approach, including the combination of BET inhibitors and DOT1L inhibitors (38)
and a synthetic lethal strategy of combining IDH
inhibitors with BCL2 inhibitors (69), have begun
to emerge and set the stage for future combination therapy trials.
Developing new epigenetic therapies
There is now great interest in generating small
molecules that are effective in modulating the
cancer epigenome. At present, however, there is
no clear strategy to establish what these therapeutic targets should be. Much of epigenetic drug
discovery is being driven by what is possible from
a medicinal chemistry viewpoint rather than what
is needed. To aid in this process, a number of
investigators have used genetic screens to identify novel targets that compromise the viability of
cancer cells both in vitro and in vivo (70, 71). Although a comprehensive discussion on the merits
of genetic knockout using methods such as CRISPR/
Cas9 versus knockdown using RNA interference
(RNAi) is beyond the scope of this review, some
caveats need to be acknowledged when using
such approaches to identify druggable epigenetic
regulators. First, it is important to recognize that
many epigenetic proteins function in the context
of multiprotein member complexes, and a single
epigenetic protein may have an essential scaffold/
targeting/catalytic role in several diverse complexes (13). Therefore, genetic ablation of a single
member may disrupt the entire complex and the
“real” druggable target may not be the one identified in the screen. Furthermore, epigenetic proteins often contain several functional protein
domains (Fig. 2). Some of these domains are used
to bind DNA or posttranslational histone modifications (epigenetic reader domains). Other domains have catalytic activity to either deposit
(epigenetic writer domain) or remove (epigenetic
eraser domain) histone/DNA modifications (13).
This is important because each of these domains
may have a distinct role in epigenetic regulation.
Therefore, identifying the precise domain responsible for the phenotype of interest is critical to
inform rational drug design. An elegant strategy
using genome editing to identify the protein
domain most critical for drug development has
recently been proposed. By designing guide RNAs
against the coding regions of epigenetic writer,
reader, or eraser domains, the authors could identify the most important functional domain because in-frame variants in the domain, which
preserve the full-length protein, were equally deleterious to genetic ablation of the epigenetic regulator (72). Perhaps the ideal method in future
studies seeking to identify new epigenetic therapies is to use a combination of these strategies in
sophisticated models of cancer (Fig. 2).
Conclusions and perspective
The recognition that epigenetic regulators play a
central role in the initiation and maintenance of
cancer and can be therapeutically targeted has
presented a myriad of opportunities. Thus far, as
is customary, all of the new epigenetic therapies
have been tested in early-stage clinical trials in
patients with relapsed and chemorefractory can-
cers. The fact that some of these patients have
achieved a complete response, albeit transiently
on single-agent therapy, offers hope for the future
of these agents. It is unlikely that epigenetic thera-
pies as single agents will provide a panacea for any
aggressive malignancy, and therefore the future
lies in rational patient selection and combination
therapies. Even in aggressive and often incurable
diseases such as AML, combination chemotherapy
using two cytotoxic drugs is very effective in in-
ducing a complete response. The problem lies
in maintaining this response by eradicating the
tumor-initiating cells that persist as minimal re-
sidual disease and serve as the nidus for a later
relapse. The fact that mutations in epigenetic
regulators are often early events seen in pre-
malignant cells raises the possibility that thera-
pies targeted to these mutations may have a role
as maintenance therapies to consolidate the gains
from combination chemotherapy. Epigenetic ther-
apies may also achieve success when used to
exploit synthetic lethal vulnerabilities exposed by
therapeutic pressure from other targeted therapies
or the de novo mutational landscape; for example,
preclinical models of cancers containing SWI/
SNF mutations have been shown to be more re-
sponsive to EZH2 inhibitors (15).
A rapidly increasing body of evidence demonstrates the interdependence of cancer epigenetics
and cancer immunology. It is clear that epigenetic
therapies induce an immunological response that
contributes to their efficacy (55), and accumulating data also demonstrate that epigenetic therapies
potentiate the effects of adoptive immunotherapies
(73) and immune checkpoint inhibitors (74). As
such, the next frontier—combinations of immunotherapies and epigenetic therapies—is set for
clinical evaluation. Despite the challenges posed
by the incessant evolution of cancer under therapeutic pressure, our increasing understanding of
these diverse trajectories and the fundamental
role that epigenetic regulation plays in this process has offered several innovative therapeutic
opportunities. This field looks forward with optimism as we continue our quest to change the
natural history of aggressive malignancies with
combination therapies that include epigenetic
agents as a cornerstone.
REFERENCES AND NOTES
1. K. Luger, M. L. Dechassa, D. J. Tremethick, Nat. Rev. Mol. Cell
Biol. 13, 436–447 (2012).
2. E. Segal, J. Widom, Trends Genet. 25, 335–343 (2009).
3. C. D. Allis, M.-L. Caparros, T. Jenuwein, D. Reinberg, Epigenetics
(Cold Spring Harbor Laboratory Press, ed. 2, 2015).
4. A. J. Bannister, T. Kouzarides, Cell Res. 21, 381–395 (2011).
5. Z. Gao et al., Mol. Cell 45, 344–356 (2012).
6. A. Piunti, A. Shilatifard, Science 352, aad9780 (2016).
7. L. Di Croce, K. Helin, Nat. Struct. Mol. Biol. 20, 1147–1155 (2013).
8. K. Klauke et al., Nat. Cell Biol. 15, 353–362 (2013).
9. L. Morey et al., Cell Stem Cell 10, 47–62 (2012).
10. A. M. Schmitt, H. Y. Chang, Cancer Cell 29, 452–463 (2016).
11. K. V. Morris, J. S. Mattick, Nat. Rev. Genet. 15, 423–437 (2014).
12. L. A. Garraway, E. S. Lander, Cell 153, 17–37 (2013).
13. M. A. Dawson, T. Kouzarides, Cell 150, 12–27 (2012).
14. B. Vogelstein et al., Science 339, 1546–1558 (2013).
15. C. Kadoch, G. R. Crabtree, Sci. Adv. 1, e1500447 (2015).
16. D. Sturm et al., Nat. Rev. Cancer 14, 92–107 (2014).
17. C. Lu et al., Science 352, 844–849 (2016).
18. R. P. Halley-Stott, J. B. Gurdon, Brief. Funct. Genomics 12,
19. G. Q. Daley, Cell 151, 1151–1154 (2012).