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JBS, December 2011, 16 (10)

Epigenetics: Working Toward the Answers

Epigenetics. You can hardly glance at the scientific literature – and even mainstream media – without seeing something about epigenetics pop up. A simple Google search turns up more than 3 million entries. It has been heralded by most as "so much larger than the genome space." But, what does epigenetics mean to SLAS members involved in laboratory science and technology?

 

The Journal of Biomolecular Screening (JBS) is helping SLAS members answer that question. The two-part JBS special issue, "Epigenetic-Targeted Drug Discovery," focuses on relevant advances in the field. Guest editors are Tom Heightman, Astex Pharmaceuticals and Andrew Pope, GlaxoSmithKline.

As stated by JBS Editor-in-Chief Bob Campbell, "Both Tom and Andy have a deep understanding of epigenetic targeted drug discovery and the underlying issues in this new research area. They have compiled an impressive body of work in the JBS epigenetics special issues." Pope indicates that he and Heightman, originally tasked with filling one issue, were unexpectedly overwhelmed with quality manuscript submissions and that it was decided to publish two issues (December 2011 and January 2012).

"This special issue topic of epigenetics was selected because it has experienced a boom in interest, especially in the drug discovery community," Heightman explains. "In the last few years, scientists have begun to realize the therapeutic potential of manipulating epigenetic systems, and those in both academic and industrial sectors are trying to harness that fabulous potential."

Say the editors in their December column:

"In its broadest sense, epigenetics describes the complex molecular processes that control the regulation and inheritance of gene expression patterns in healthy development and disease. It holds the potential to revolutionize basic science, medicine and drug discovery, much like the discovery of the genetic code almost 60 years ago. The significance of epigenetics is magnified when one considers that it defines mechanisms for dynamic, semi-reversible biochemical responses to environmental conditions ranging from diet to psychological stress, or in other words, a developmental plasticity in which early life experiences influence disease susceptibility in later life and even in subsequent generations. Epigenetic mechanisms provide the basis for the extraordinary complexity and specialization that occurs within differentiated cells, which goes well beyond the answers provided by the (relatively simple) genetic code. As such, the area is poised for major discoveries, many of which are likely to be underpinned by the assay and screening approaches described in two special issues of JBS."

The Beginnings

Pope explains that epigenetics, which simply means acting upon genetics, has been around for quite awhile. However what has burst to the forefront in the last couple of years is the expanded discovery of epigenetic systems and the resultant therapeutic implications.

"Looking back to the ‘90s when the human genome was being sequenced, people had a quite naïve view of the implications for biomedical science; they kind of thought there would be a gene for everything and that the biological complexity and the cause of many diseases would be explained at the level of genetic variation," Pope says. "Actually, there turned out to be a relatively modest number of genes; nowhere near enough to explain the incredible complexity of higher organisms and specialization in cells, let alone the causes of disease. There had to be something else. Epigenetic systems provide that additional complexity and therefore the key to understanding how the genetic code is actually used in practice. Also, discovering that epigenetic processes were dynamic and could be modified, and also to some extent be inherited in subsequent generations, really opened up the fascinating idea that the way in which your genetic code is read out can be affected by your environment.

"We are still in the very early stages of understanding the incredible complexity of processes which control gene expression," Pope continues. "Solving the human genome was the end of one road – it provided a very crude map. There are a number of clear cases where the genetic basis for disease is understood, but these tend to be relatively rare diseases. The majority of major diseases are more complex and prevalence is almost certainly more the result of a byzantine combination of gene expression (i.e., genome plus epigenetics) and environmental effects (e.g., diet, lifestyle etc.). The idea that the environment that impacted your grandparents may be affecting your health outcomes (and, by extension that what you have been exposed to may affect subsequent generations of your progeny) is pretty mind blowing."

"The phenomenon of DNA methylation and gene silencing is a very broad-ranging science that has been studied for decades in diverse living organisms – plants, insects and others – but it maintained a relatively low profile in drug discovery," Heightman adds. "It was not obvious how the findings could be harnessed. The discovery of the genetic code 60 years ago has allowed scientists to map out the roles of proteins required by living organisms, but it didn't make clear how that genetic code was read or interpreted in different circumstances both for development of organisms and responses to environmental stimuli. It's only very recently that things have become clearer, as we're getting a molecular understanding of the epigenetic processes to read that genetic code and interpret it in appropriate ways. This is why the field has suddenly hit a peak of interest."

Burning Questions

The guest editors surmise that as more is discovered, more questions are raised.

One example of the far-reaching interest in epigenetics can be found in northern Sweden preventive health specialist Lars Olov Bygren's study of the long-term effects the feast and famine years had on children growing up in Norrbotten in the 19th century, as well as on their children and grandchildren. Bygren found that kids who over ate in even a single season of abundant crops produced children found to die decades earlier than their peers. A January 2010 Time article explains how Bygren had become fascinated with research showing that conditions in the womb could affect your health not only when you were a fetus but well into adulthood. That begged the question – does what your mom does to her body even before pregnancy play a role in your health? The results challenged long-standing notions that the effects of nurture and nature were not supposed to happen so quickly. According to the Time article:

"The answer lies beyond both nature and nurture. Bygren's data — along with those of many other scientists working separately over the past 20 years — have given birth to a new science called epigenetics. At its most basic, epigenetics is the study of changes in gene activity that do not involve alterations to the genetic code but still get passed down to at least one successive generation. These patterns of gene expression are governed by the cellular material — the epigenome — that sits on top of the genome, just outside it (hence the prefix epi-, which means above). It is these epigenetic "marks" that tell your genes to switch on or off, to speak loudly or whisper. It is through epigenetic marks that environmental factors like diet, stress and prenatal nutrition can make an imprint on genes that is passed from one generation to the next."

Another example published late in 2011 in Human Molecular Genetics shows a role for epigenetic factors related to disease etiology in monozygotic twins.

"This study represents the first comprehensive analysis of disease-associated DNA methylation differences in MZ twins discordant for SZ [schizophrenia] and BD [bipolar disorder], using a genome-wide approach. We found no alterations in global DNA methylation between affected and unaffected twins, but considerable disease-associated between-twin differences at specific loci across the genome. Some differences were consistently altered across a combined discordant psychosis group, whereas others appear to be specific to either SZ or BD. Furthermore, although many differences were identified across all discordant twin pairs for each diagnostic category, others were specific to one or a couple of pairs. Our hypothesis-free experimental design allowed us to identify disease-associated DNA methylation differences at loci not previously implicated in psychiatric disorders, but we also found evidence for DNA methylation differences at genes previously implicated in psychosis, such as GPR24 and CTNNA2 in BD. Pathway analysis of our top loci highlighted a significant enrichment of epigenetic disruption to biological networks and pathways relevant to psychiatric disease and neurodevelopment. Overall, our data provide further evidence to support a role for DNA methylation differences in the etiology of both SZ and BD."

"This area of science is evolving very rapidly," Pope expounds. "What's captured in the JBS special issues is that for the first time, people are generating drug-like molecules that interact with these systems and asking, what do they do? This is raising very interesting questions. For example, how specific are these effects at the level of different cell types? When you perturb these systems and change expression of a set of genes in a certain way, what happens when you remove the drug? Will the cell happily revert back to what it was before?

"We are in relatively unknown territory here," Pope continues. "It is not going to be like conventional pharmacology where you inhibit the function of an enzyme or receptor, and activity returns to normal immediately after the drug is washed out. Obviously, each cell in your body is to some extent specialized. Some are very active with rapid protein turnover so it makes sense that epigenetic control mechanisms are active at a different level in different cell types. This is one reason why cancer is the first disease being targeted by epigenetic drugs; tumor cells are growing uncontrollably and in a way that may often be dependent upon epigenetic processes. Having the ability to selectively prevent those cells from proliferating and, in fact, causing selective death of tumor cells is obviously attractive. However, given the universality of epigenetic control of gene expression, we will need to be careful about establishing the safety of new medicines that work via these mechanisms. Of course this issue is not just restricted to drugs which target epigenetics; it might possibly underlie the action and side effects of other drugs also."

JBS Special Issues

In the December issue guest editors' column, Heightman and Pope say the approval of epigenetic drugs for haematological cancers (DNA methylation [DNMT] inhibitors azacitidine and decitabine for myelodysplastic syndrome, and histone deacetylase [HDAC] inhibitors vorinostat and romidepsin for cutaneous T-cell lymphoma) has demonstrated that modulation of relatively broad epigenetic regulatory processes can show beneficial efficacy and safety profiles in defined patient groups. The impact of these early drugs is likely to widen as combination trials with targeted anticancer agents progress. This precedent has attracted the interest of a large and growing number of pharmaceutical and biotech companies (currently estimated at around 40 companies worldwide) working on refinements in DNA methyltransferase and HDAC inhibition, as well as exploring the effects of modulating additional histone modifying proteins including lysine or arginine methyltransferases, lysine demethylases, and domains that recruit transcriptional regulators to histone modifications, particularly acetyl-lysine and methyl-lysine. These efforts are mirrored by wide-ranging public sector initiatives aimed at unraveling the complex interplay of combinatorial DNA and histone modifications in transcriptional regulation, and collecting epidemiological epigenomic fingerprint data leading to biomarker development for diagnostic, prognostic and theranostic patient assessment, as well as clinical association for potential new molecular targets.

In addition, offers Campbell, the development of not-for-profit, private-public partnerships such as the Structural Genomics Consortium (SGC), have been established with the primary goal of identifying epigenetic tool compounds and deciphering x-ray crystal structures to improve our understanding of this "pre-competitive" scientific space. SGC members currently include the University of Toronto, Oxford University, Karolinska Institute, Canadian granting agencies and Wellcome Trust, together with Eli Lilly, GlaxoSmithKline, Novartis Research Foundation and Pfizer.

Together, the guest editors continue by stating that the growing epigenetics research community has demonstrated epigenetic differences between healthy cells and those from patients with a variety of diseases beyond cancer, including immuno-inflammatory, metabolic, neurological and psychiatric diseases. In many cases, genetic knockdown, mutation and/or overexpression have been used to demonstrate the roles of individual epigenetic modulatory proteins in these differences, together with the therapeutic potential of reversing the epigenetic aberrations. As in other areas of biomedical research, it remains to be seen whether such promising outcomes can be recapitulated with small molecule modulators and translated to clinical benefit. To this end, early efforts to generate small molecules that can be used as probes in chemical biology experiments are essential to speed the process of identifying the key players in the epigenetic cast.

Heightman and Pope say that given the central role of epigenetic mechanisms, these classes of targets seem certain to provide opportunities for understanding and treating diseases well beyond the current focus in cancer. The potential of epigenetic-modulator compounds to alter gene expression in an unexpected and perhaps durable manner (i.e., long after drug elimination, perhaps even inheritable in some cases) may also result in some unique challenges with respect to drug safety.

In JBS's two special issues on epigenetic-targeted drug discovery, contributions from leading public sector, technology/life sciences/vendor, biotech and pharmaceutical groups who are applying 21st century drug discovery techniques to allow the generation and characterization of small molecule inhibitors of epigenetic regulatory proteins are featured. The December issue includes reviews covering the area of assays for epigenetic targets generally and, from JBS Editor-in-Chief Campbell, the fascinating and sometimes controversial area of sirtuins. Other papers in December focus mainly on systems that interact with histone acetyl marks: writers, readers and erasers of histone acetyl marks. This coverage is combined with some exciting new ways to assay these targets and reports of successful hit discovery efforts.

In the January 2012 issue, the papers focus on systems that interact with methyl marks, including methyl writers and erasers. It also includes papers describing methods to measure histone marks in cells.

What's Ahead

"The next year or two will be a very exciting time for epigenetics," Pope offers. "Currently there are only a few molecules for a very few indications that are actually in the clinic. And one thing we don't know at this point is to what extent existing compounds or medicines might affect the epigenetic systems. We're on the cusp of discovery of new drug-like molecules that interact with these. Those working in academia and in industry are finding a lot of molecules that interact with these systems, which will open up that biology much more and unravel how these systems work. We are going to see a huge explosion in that area – it is exciting to think about what that might bring about.

"In the case of the simple genetic model we've had before, you knock that gene out or go and look at mutations and tie that to diseases," Pope continues. "In epigenetics, there is much more dependence on chemical matters to exploit and develop our understanding. There is a lot of great work being done. At the center of that activity is creating assays and doing screening – that's the unique place where JBS will contribute to an area of science."

"It started within cancer and now we're seeing opportunities in other areas," Heightman adds. "In some ways, cancer is the most obvious disease area to start with because in most cancers the regulation of multiple genes is disregulated so oncogenes become upregulated and gene suppressors become down regulated. So that's a fairly obvious place to go looking for epitherapeutic areas. It's all about capturing data on epigenetic marks and mechanisms and today there is an explosion in data showing that there are differences in epigenetic marking in cells from healthy patients as opposed to specific cells from diseased patients."

In the next year or two, Heightman expects meaningful discoveries within immuno-inflammatory, metabolic, neurological and psychiatric diseases.

"Significant epigenetic differences have been noticed between healthy cells and cells for example in autoimmune diseases such as allergic asthma," Heightman details. "Some researchers have now shown that epigenetic modulators can make a significant difference in models of disease. Similarly in other unrelated disease areas including neurology and psychiatry, some very interesting epigenetic data show significant differences in patients with and without specific central nervous system conditions. These data beg the question, ‘If one treated those patients with an epigenetic modulator, could one reverse the symptoms, or even the progression, of the disease?' These are the questions provoked by epigenetic data and the community needs to address those challenges by coming forward with new biological and small molecule modulators of epigenetic processes."

Challenges

While certainly encouraged by the high quality advances reported in the JBS manuscripts, Heightman and Pope are clearly aware of the challenges still in front of scientists working in this field. Heightman shares that many of them are generic to other areas of drug discovery – demonstrating the roles of specific proteins that make them good drug targets, generating biological and chemical tools and selecting antibody or small molecule inhibitors that allow the study of the individual protein in biological systems both in diseased and healthy cells. From an assay development perspective, "understanding whether our biochemical assays are configured to properly identify screen actives in biologically relevant cellular systems, and subsequently whether this translates in vivo, will be key to early epigenetic drug discovery," comments Campbell.

"Then there are those more specific to epigenetics, such as achieving a meaningful therapeutic benefit," Heightman adds. "If we interrupt a process that is involved in regulating hundreds of genes or even thousands of genes, can we elicit a positive therapeutic response without also causing toxic or unwanted side effects that may arise from deregulating unwanted genes. It's a question of specificity – can we safely target those specific epigenetic processes that are responsible for disease?"

The December 2011 and January 2012 JBS authors have some ideas.

Editor's Note: The Lab Man addresses epigenetics in his January blog and podcast.

December 27, 2011