Chromatin as a Cancer Target – Part I: Chromatin Writers

August 19, 2014

By Garrett Rhyasen, PhD

Introduction

The epigenetic machinery of the cell has emerged as an attractive target in treating a myriad of human diseases. Of course, here at Oncology Discovery, I’m primarily interested in writing about cancer biology. Luckily, there have been a flurry of recent developments, which are beginning to validate epigenetic targets in oncology – scientists, industry players, and investors alike should take note. This is my inaugural first post, and the beginning of a three part series, where I will take you through the current landscape of epigenetic cancer targets, sharing some of my own thoughts along the way.

Let’s begin with a brief primer. The experienced reader may want to jump to the next section. Chromatin is the essence of epigenetics. It is a mixture of histone proteins, DNA, and RNA. The organization of chromatin is responsible for the efficient packaging of genomic information within every mammalian cell. Not surprisingly, the dynamic nature of chromatin packaging is highly regulated. Reversible chemical modifications on chromatin allow variegated access to, and expression of, specific genes. These modifications can be recognized and modified by various protein complexes. I’ll be elaborating on an example from one of three major classes of chromatin-associated proteins – all of which are exciting nascent cancer targets (1). The first two – ‘writers’ and ‘erasers’ – are responsible for enzymatic deposition, and removal of various chromatin modifications, respectively. Chromatin ‘readers’ represent a curious third class of targets, and unlike ‘writers’ and ‘erasers,’ they lack enzymatic activity, and instead simply bind to histones that have been marked by an appropriate modification. Histone binding can result in recruitment of additional protein complexes, resulting in gene transcription modulation. Great. With that background out of the way, let’s jump into the meat of today’s discussion.

Chromatin Writers

Writers catalyze the deposition of chemical modifications onto chromatin. This class is comprised of histone acetylases, kinases, histone methyltransferases, and ubiquitin ligases. The dynamic modifications catalyzed by writers can result in rapid changes in local chromatin structure, allowing for the expression – or repression of – certain sets of genes. In some cases these genes are important for normal development processes, and misregulation can result in the development of cancer. Let us dive deeper, and examine an interesting example.

EZH2

EZH2 is a histone methyltransferase, and catalytic component of the Polycomb Repressive Complex 2 (PRC2), which also contains cofactors RbAp46/48, SUZ12, and EED (Figure 1). PRC2 is involved in silencing genes involved in development and differentiation processes, through catalyzing the methylation of H3K27 (2). If the Polycomb complex sounds like your cup of tea, I’d advise you to take a look at an excellent review by Margueron and Reinberg (3). But I stray. You should be intrigued in EZH2 as a cancer target because somatic mutations and deletions have been reported in several hematologic malignancies. And here’s where things get interesting…

Almost paradoxically EZH2 appears to act as both a tumor suppressor and oncogene, depending on disease context. For example, in Myelodysplastic Syndromes (MDS) deletions of chromosome 7q correlate with poor prognosis. EZH2 is located within a commonly deleted region on 7q, and is targeted by misssense and frameshift mutations in approximately 6% of MDS patients (4). Myeloid cell lines that harbor these kinds of EZH2 mutations show decreased H3K27 methylation, which is consistent with EZH2 loss-of-function (5). Furthermore, in mice, EZH2 loss can promote the development of MDS (6), thus in myeloid neoplasia EZH2 seems to be acting as a tumor suppressor.

Conversely, in some lymphoid malignancies, EZH2 mutations result in an acquired neomorphic function. Neowhat?! A ‘neomorphic’ mutation results in a dominant gain of function. The resulting neomorphic enzyme has altered activity relative to the wild-type protein. In my view, neomorphic oncogenes make excellent cancer targets. In a perfect world, with the identification of cancer-dependent neomorphs, one would be able to eliminate cancer cells with exquisite selectivity. I’m not alone with this line of thinking. Folks from both Epizyme and Agios have employed such a strategy. For example, the Agios IDH2 inhibitor (AG-221) acts against a neomorphic mutant. This program has recently been granted Fast Track Designation by the FDA, which could be interpreted as early validation of this approach. I digress… Let’s get back to EZH2.

So how does this relate to EZH2? Well, in about 22% of Diffuse Large B-Cell Lymphoma (DLBCL) and in 7% of follicular lymphomas (FL) there is a recurring mutation (Y641X) within the SET domain of EZH2 (7). This mutation is different from the ones I described in MDS. In this context, mutant EZH2 (Y641X) gains neomorphic function through altered substrate recognition. Because of a single amino acid substitution the SET domain of EZH2 ‘sees’ its substrate a bit differently. What’s more, DLBCL cells harboring the Y641X mutation display increased levels of H3K27me3 – upregulated H3K27me3 is thought to stimulate malignant transformation (8), perhaps through transcriptional repression of important tumor suppressors.

So EZH2 mutations – both activating and inactivating – can contribute to cancer development. Is the concept contradictory? No. Is it confusing? Yes. In the strange world of epigenetic targets, context is king – cellular context to be exact. Thus the differential transcriptional architecture in myeloid versus lymphoid neoplasia can probably account for what appears to be a contradiction.

Table 1. Publicly Disclosed EZH2 inhibitor programs.

Company	Drug Name	Development Stage	Trial Number	Indication	Formulation
Aurigene Discovery Technologies	–	Pre-clinical	–	–	–
Constellation Pharmaceuticals	CPI-169; CPI-360	Pre-clinical	–	–	–
Epizyme; Eisai	EPZ-6483 (E-7438)	Phase I	NCT01897571	Non-Hodgkin Lymphoma; Sarcoma	Oral
GlaxoSmithKline	GSK-2816126	Phase I	NCT02082977	Diffuse Large B-Cell Lymphoma; Follicular Lymphoma	Intravenous
Kainos Medicine	KM-301	Pre-clinical	–	–	–
OncoFusion Therapeutics	–	Pre-clinical	–	–	–

EZH2 inhibitors

Not surprisingly, EZH2 has emerged as a hot cancer drug target. Although I only managed to find six publicly disclosed EZH2 programs (Table 1), it’s likely that most oncology-focused pharmaceutical companies are kicking the tires on EZH2. There’s plenty of reason to get excited! The promise of a selective, and less toxic, cancer medicine seems to be one of them. In fact, small molecule inhibitors against EZH2 selectively kill Lymphoma cells bearing neomorphic EZH2 mutations, while having little effect on the proliferation of wild-type cells (9, 10). Impressive.

Make no mistake, the approval of EZH2-targeted agents is not yet certain; however, two EZH2 inhibitors have entered phase I human clinical trials: EPZ-6438 (E-7438) and GSK-2816126. Both trials are currently recruiting participants and have not yet reached the maximum tolerated dose. On August 12th, Epizyme disclosed early Phase I clinical data on EPZ-6438 at the ASH meeting on Lymphoma Biology. Importantly, they see target inhibition in patients, and perhaps most encouragingly, there have already been objective responses reported from two patients. Keep in mind these responses occurred below MTD. These trials represent a pivotal moment in the development of epigenetic agents targeted to specific patient mutations.

To recap, we’ve learned that chromatin ‘writers,’ like EZH2, can deposit chemical modifications on chromatin. These modifications can alter the structure of chromatin and subsequently modulate gene transcription. Mutations which affect the function of chromatin writers can result in aberrant accumulation certain chromatin modifications, resulting in cancer development. Inhibitors targeting these mutations therefore appear to be an effective means to selectively target cancer cells. Although the early evidence is encouraging, time will tell if this is a viable anti-cancer strategy in humans.

Thanks for stopping by. Stay tuned for the sequel: Chromatin as a cancer target – Part II: Chromatin Erasers

References

1. Simo-Riudalbas L, and Esteller M. Targeting the histone orthography of cancer: drugs for writers, erasers and readers. British journal of pharmacology. 2014.
2. Morey L, and Helin K. Polycomb group protein-mediated repression of transcription. Trends in biochemical sciences. 2010;35(6):323-32.
3. Margueron R, and Reinberg D. The Polycomb complex PRC2 and its mark in life. Nature. 2011;469(7330):343-9.
4. Nikoloski G, Langemeijer SM, Kuiper RP, Knops R, Massop M, Tonnissen ER, van der Heijden A, Scheele TN, Vandenberghe P, de Witte T, et al. Somatic mutations of the histone methyltransferase gene EZH2 in myelodysplastic syndromes. Nature genetics. 2010;42(8):665-7.
5. Ernst T, Chase AJ, Score J, Hidalgo-Curtis CE, Bryant C, Jones AV, Waghorn K, Zoi K, Ross FM, Reiter A, et al. Inactivating mutations of the histone methyltransferase gene EZH2 in myeloid disorders. Nature genetics. 2010;42(8):722-6.
6. Sashida G, Harada H, Matsui H, Oshima M, Yui M, Harada Y, Tanaka S, Mochizuki-Kashio M, Wang C, Saraya A, et al. Ezh2 loss promotes development of myelodysplastic syndrome but attenuates its predisposition to leukaemic transformation. Nature communications. 2014;5(4177.
7. Morin RD, Johnson NA, Severson TM, Mungall AJ, An J, Goya R, Paul JE, Boyle M, Woolcock BW, Kuchenbauer F, et al. Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nature genetics. 2010;42(2):181-5.
8. Sneeringer CJ, Scott MP, Kuntz KW, Knutson SK, Pollock RM, Richon VM, and Copeland RA. Coordinated activities of wild-type plus mutant EZH2 drive tumor-associated hypertrimethylation of lysine 27 on histone H3 (H3K27) in human B-cell lymphomas. Proceedings of the National Academy of Sciences of the United States of America. 2010;107(49):20980-5.
9. Knutson SK, Wigle TJ, Warholic NM, Sneeringer CJ, Allain CJ, Klaus CR, Sacks JD, Raimondi A, Majer CR, Song J, et al. A selective inhibitor of EZH2 blocks H3K27 methylation and kills mutant lymphoma cells. Nature chemical biology. 2012;8(11):890-6.
10. McCabe MT, Graves AP, Ganji G, Diaz E, Halsey WS, Jiang Y, Smitheman KN, Ott HM, Pappalardi MB, Allen KE, et al. Mutation of A677 in histone methyltransferase EZH2 in human B-cell lymphoma promotes hypertrimethylation of histone H3 on lysine 27 (H3K27). Proceedings of the National Academy of Sciences of the United States of America. 2012;109(8):2989-94.

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