During the first days of fall, the Boston weather initially cooperated but quickly grew colder over the course of a packed 3 days at the Westin Waterfront hotel for the Histone Deacetylase Inhibitor track of the Discovery On Target 2013 conferences. This year a record number of attendees from basic science, clinical research, and industry presented their latest work in the rapidly expanding field of epigenetics. A few short years ago, spurred by the discovery of chemical inhibitors, the HDAC field was dominated by pre-clinical and clinical cancer work and the development of novel technologies to understand and target HDACs. Those attending the HDAC track saw that this research has entered an extended second act, maturing and spreading well beyond cancer research.
Chemogenomic Approaches to Spatiotemporal Regulation of HDAC Activity
Ralph Mazitschek, Massachusetts General Hospital
Shortly after their development, HDAC inhibitors took off as potential cancer therapies. In vitro, these inhibitors displayed a near-universal ability to kill or slow the growth of numerous cancerous cell lines, while showing relatively minor effects on non-cancerous lines. Moreover, these inhibitors seemed to be fairly well-tolerated in pre-clinical mouse models, which led to hundreds of clinical trials investigating the therapeutic potential of these compounds on a wide variety of cancers in people. However, aside from some early victories against myeloid malignancies, the early promise of HDAC inhibitors as cancer therapies has been unrealized. One proposed reason for this has been that HDAC inhibitors have significant dose-limiting toxicities in the clinic, limiting the exposure of cancerous cells to sub-lethal levels of HDAC inhibitors.
Dr Mazitschek presented the intriguing possibility of HDAC inhibitors that could be exclusively activated in cancerous tissue. Using molecules which change their conformation when activated by light, Dr Mazitchek is working to develop compounds that switch from inactive to active inhibitors of HDACs by simply shining a light on them, allowing for spatial and temporal control of HDAC inhibitors in vivo. Nearly equally as impressive, Dr Mazitchek showcased the lab’s ingenuity with a variety of increasingly complex lighting rigs for controlling these molecules, developed rapidly with inexpensive off-the-shelf components. Although still in early stages, this technology could potentially offer the therapeutic benefits of HDAC inhibitors without the side-effects, and could usher in a new HDAC revolution in cancer.
Novel Lysine Acylation Pathways and Acetylation-Independent Mechanisms of HDACs
Yingming Zhao, University of Chicago
The first day of the Histone Deacetylase conference had a bit of a marathon session, ending well after the Epigenetic Reader conference had the previous day. However, those that were able to remain until the very end were rewarded with an eye-opening presentation on additional capabilities of the now clearly mis-named histone deacetylases. Although histone deacetylases are named for their capability to deacetylate histones, it is now understood that many and perhaps most proteins are regulated by acetylation of lysine side chains. Moreover it has become increasingly appreciated that non-histone substrates may actually be more critical targets of histone deacetylases than histones themselves.
Dr Zhao presented research showing that even the deacetylase function of a “histone deacetylase” is not completely accurate. In acetylating lysines, histone acetyltransferases (HATs) use the metabolite acetyl-CoA as an acetyl group donor. Dr Zhao demonstrated that HATs can also use a plethora of other metabolites, such as malonyl, succinyl, propionyl, and crotonyl-CoA as a donor, creating malonyl-lysine, succinyl-lysine, etc… Dr Zhao identified the “deacetylase” Sirt5 as a key eraser of these modifications.
What function these modifications play and the full suite of enzymes that control them is still not clear, however Dr Zhao showed that they are affected by cellular metabolism (glucose flux) and that this function is conserved from bacteria to mammals. This talk closed out the first day of the histone deacetylase conference with the possibility that the most interesting future research on histone deacetylases may have no relation to histones or acetylation.
HDAC Inhibitor Treatment of Pathological Muscle Remodeling
Timothy A. McKinsey, University of Colorado, Denver
Heart disease is the leading cause of death in the US, and as such is one of the most critical areas of unmet need. Dr McKinsey’s work focuses on developing therapies to block cardiac fibrosis and hypertrophy as a result of injury or pathological condition. He presented work investigating the mechanism by which HDAC inhibitors are able to block fibrosis and hypertrophy following cardiac injury through inhibition of JNK and ERK pathway signaling.
Using a combination of genetic knockdown and isoform-specific HDAC inhibitors, Dr McKinsey was able to elegantly demonstrate that different HDAC isoforms contribute in different ways to this effect. HDAC1 deacetylates a regulatory protein to activate JNK signaling, while HDAC3 blocks transcription of a negative regulator of ERK signaling. Dr McKinsey also detailed preliminary work connecting Brd4 to fibrosis and heart failure, as well as an intriguing suggestion that HDAC inhibitors and BET bromodomain inhibitors may be acting via similar mechanisms in treating fibrosis.
Design of Class I Isoform Selective Inhibitors for Use in Metabolic Indications
Edward Holson, Broad Institute
Nearly all HDAC inhibitors, including those being used clinically have fairly broad activity against multiple HDAC isoforms – particularly the Class I HDACs that are involved in histone deacetylation. It is generally agreed that the future of HDAC inhibitors lies in creating drugs that can target a particular HDAC isoform, in order to maximize therapeutic efficacy while minimizing unwanted side-effects. While exciting progress has been made in creating an HDAC6-specific inhibitor, until recently no inhibitors have been able to specifically target a single Class I HDAC. Such an inhibitor would be highly desirable, as the broad inhibition of Class I HDACs is thought to underlie the dose-limiting toxicities HDAC inhibitors in the clinic.
Dr Holson presented his work using developing BRD3308, one of the first inhibitors that preferentially targets HDAC3. Using insights gained from crystal structures of HDACs bound to inhibitors, Dr Holson was able to derivatize a benzamide Class I HDAC inhibitor to specifically target HDAC3. This opens up exciting new areas not just in therapeutic development, but also in understanding the enzymatic functionality of HDACs.
Prior to isoform specific inhibitors, genetic knockdown of specific isoforms was used to investigate function. However it has become clear that HDACs play many biological roles that are unrelated to their enzymatic activity, and thus knockdown is a poor surrogate for what happens in vivo when a particular HDAC is inhibited pharmacologically. Thus BRD3308 opens up an entirely new avenue of research in understanding HDACs and the role they play in disease – undoubtedly we are in for a wealth of new research using this compound as a tool to understand a wide range of biological processes.
Zinc Binding Groups Inhibit Class IIa HDAC and Alters Immune Responses
Mercedes Lobera, Tempero Pharmaceuticals, Inc.
The conference ended with one of the most eagerly anticipated breakthroughs in the HDAC field – the development and characterization of a Class IIa HDAC inhibitor. Of all the HDACs, Class IIa HDACs have undergone perhaps the most profound transition in our understanding of them. It was once believed that these HDACs deacetylated histones, and that they were inhibited by broad-spectrum HDAC inhibitors like Vorinostat and Panobinostat. Over time, this model has been chipped away – it is now believed that these HDACs function largely outside the nucleus and likely are not involved in deacetylating histones at all.
The targets and effects of these deacetylases are still largely a mystery and furthermore it has been called into question whether these “deacetylases” even have deacetylase activity. Thus, Dr Lobera’s talk was particularly ground-breaking as she demonstrated that not only do Class IIa HDACs have deacetylase activity, but that this activity seems to be exclusively targeted towards non-histone substrates, that this activity can in fact be specifically targeted with pharmacological inhibitors, and that inhibiting this activity has biological consequences.
The research is still in early stages, but the effect of inhibiting these enzymes in patient-derived cells seems to be extremely subtle in that it produces little transcriptional effect on several different types of cells. This is perhaps to be expected as these HDACs do not target histones, and moreover is almost certainly desirable in terms of producing therapeutics with minimal toxicities. After a great deal of work characterizing the subtle effects of this inhibitor, Dr Lobera showed that this inhibitor is able to block inflammation by limiting the differentiation of monocytes into macrophages. The mechanism is still not clear and a great deal of research remains in characterizing Class IIa inhibition under different contexts, however this early work has already answered several pressing questions in the field and opened investigation into even more.
**EpiGenie would like to thank Ryan Kuzmickas, who is a student in the Cichowski lab at Brigham and Women’s Hospital, for this conference coverage***