Epitherapy: Combating Disease with Epigenetic Drugs

The human genome is comprised of some 3 billion bases. Those bases are organized into approximately 20,000 genes. And these genes are controlled by our epigenetics, so-called “on/off” switches that regulate gene expression through a variety of chemical modifications to the DNA and its associated components. Our epigenetic code, not to be confused with our genetic code or DNA sequence, directs normal biological processes such as cell development and specialization. It can determine when and where genes are expressed, aptly repressing or activating expression at specific times (e.g, during stem cell differentiation) and in specific cell types (e.g., insulin expression localized to pancreatic islet β-cells)^[1].

In addition to being heritable, the epigenetic landscape of our bodies can be influenced by non-inborn factors like environmental cues and lifestyle habits (food, sleep, exercise). Aberrant changes by these or other factors to our epigenome may contribute to or cause disease. Inflammatory, metabolic, infectious, cardiovascular, and neurological disorders, as well as cancers, all display epigenetic abnormalities as part of their pathologies. Interestingly, this epigenomic dysregulation is reversible, and epigenetic modifications have been pursued as suitable biomarkers for pharmaceutical treatments and epigenetic drug discovery research.

According to recent market intelligence data, the global epigenomic market, valued at $5.28 billion in 2017, will be at $16.3 billion by 2026. FDA-approved epigenetic drugs currently on the market are categorized into two classes, based on their mechanism of action. The first class is comprised of the histone deacetylase (HDAC) inhibitors^[2], constituting the bulk of the epigenetic drug market. HDACs are a class of enzymes that remove acetyl groups on lysine residues in the N-terminal tail and on the nucleosome-core surface of histones. Deacetylated histones compact chromatin structure and thereby reduce gene transcription levels. Deviations from normal HDAC activity can induce irregular transcription of genes regulating cell proliferation and apoptosis, promoting tumor growth and metastasis. Marketed HDAC inhibitors include Novartis’s Farydak (panobinostat) for multiple myeloma, Celgene’s Istodax (romidepsin) and Merck’s Zolinza (vorinostat) for cutaneous T-cell lymphoma, and TopoTarget’s Beleodaq (belinostat) for peripheral T-cell lymphoma.

To conduct your own experiment to measure the activity or inhibition of total histone deacetylase (HDAC) in a convenient, sensitive and fast assay, we recommend the Epigenase HDAC Activity/Inhibition Direct Assay Kit (Colorimetric). This kit takes just 3.5 hours to complete thanks to its versatile strip-well microplate format and is sensitive enough to detect activity from as low as 0.5 ng of purified HDAC enzyme.

Inhibitors of DNA methyltransferase (DNMT) make up the second class of epigenetic drugs, which include Otsuka Pharmaceutical’s Dacogen (decitabine) and Celgene’s Vidaza (azacytidine) for myelodysplastic syndrome. DNMTs serve as DNA methylating agents, covalently adding methyl groups to the 5-carbon position of cytosines that project into the major grooves of DNA and inhibit transcription. Abnormal DNA methylation associated with increased DNMT expression or activity has been found in many different diseases, especially in cancer. For example, transcriptional silencing of tumor suppressor genes via promoter region hypermethylation is known to occur during oncogenesis^[3]. Inhibition of DNMTs may lead to demethylation and expression of silenced genes.

Aside from HDAC and DNMT inhibitors, drugs targeting other epigenetic modifiers are actively being pushed through the biopharmaceutical pipeline and in various clinical trial stages. These targets include histone methyltransferases (HMTs) like EZH2 and DOT1L; HMT binding partner interactions like that between menin and the histone methyltransferase MLL; histone demethylases like LSD1; histone ubiquitination-mediating proteins like PRC1; and BETs, proteins that interact with acetylated histones^[4]. Interest in epigenetic therapy is expanding, as is the growth of biotech startups focused on identifying new epigenetic targets and the next “epi-pharmaceutical” blockbuster. Flagship Pioneering’s Omega Therapeutics, which was recently launched in September, has made headlines lately for its in silico approach to identifying potential targets using computational biology. Additionally, the incorporation of epigenetic drugs in combination therapies to improve the activity of other medicinal agents rendered ineffective by drug resistance is an emerging field with great potential.

A major setback for these drugs is their lack of specificity. Off-target issues such as global hypomethylation and non-histone protein modification, along with their accompanying side effects, are a concern. Due to the complexity of the epigenome, the identification of disease-specific epigenetic biomarkers is paramount to developing novel drugs with precise targets, thereby lowering doses, minimizing toxicity, and increasing efficacy. Innovations in nanotechnology and single-cell sequencing will undoubtedly facilitate advancements in personalized-targeted therapy, providing customized treatment tailored to an individual’s unique epigenome. EpiGentek is continually striving to improve upon the speed, sensitivity, accuracy, and simplicity by which these biomarkers are assessed and quantified. EpiGentek’s next generation MethylFlash and EpiQuik technologies provide for rapid and direct measurements of the most commonly studied epigenetic modifications, including DNA methylation, RNA methylation, histone modifications, and protein-DNA interactions. Although epigenetic drugs at present are primarily geared toward treating patients with cancer, other diseases like diabetes, rheumatoid arthritis, Alzheimer’s disease, schizophrenia, and atherosclerosis, to name a few, have been linked to epigenetic anomalies and present new opportunities for therapeutic intervention.

References:

1. Olsen JA, Kenna LA, Spelios MG, Hessner MJ, Akirav EM. Circulating differentially methylated amylin DNA as a biomarker of β-cell loss in type 1 diabetes. PLoS One 2016;11:e0152662
2. Katarzyna R, Lucyna B. Epigenetic therapies in patients with solid tumors: focus on monotherapy with deoxyribonucleic acid methyltransferase inhibitors and histone deacetylase inhibitors. J Can Res Ther 2019;15:961-70
3. Subramaniam D, Thombre R, Dhar A, Anant S. DNA methyltransferases: a novel target for prevention and therapy. Front Oncol 2014;4:80
4. Ye F, Huang J, Wang H, Luo C, Zhao K. Targeting epigenetic machinery: Emerging novel allosteric inhibitors. Pharmacol Ther 2019;107406