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Reporter: Aviva Lev-Ari, PhD, RN

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Nature Reviews Drug Discovery 12, 92-93 (February 2013) doi:10.1038/nrd3943

Drugging the epigenome

Samia Burridge

Epigenetic alterations — for example, changes in the way that the genome is packaged by surrounding histone proteins, causing genes to be switched on or off — are linked to diseases including cancers and immunoinflammatory disorders. Such evidence, coupled with recent progress in showing that enzymes involved in epigenetic processes can be modulated by drug-like small molecules, has fuelled interest in exploiting the therapeutic potential of epigenetic targets.

“Epigenetic targets are increasingly recognized as highly selective entry points for disease intervention rather than generic controllers of bulk gene expression,” says James Audia, Chief Scientific Officer of Constellation Pharmaceuticals, an epigenetics-focused company based in Boston, Massachusetts, USA. “What makes epigenetic targets stand out in my mind is the potential to use them to reprogramme a cellular phenotype by altering the cellular transcriptional programme as a result of altering its epigenome,” adds Cheryl Arrowsmith, Professor at the University of Toronto, Canada, and Chief Scientist at the Toronto laboratory of the Structural Genomics Consortium (SGC). “An example of this is the recent ‘reprogramming’ of drug-resistant leukaemia cells to become drug-sensitive by inhibition of the lysine-specific histone demethylase LSD1 (Nature Med. 18, 605–611; 2012).”

Target watchDrugging the epigenomeDigital Vision/Punchstock

Novel epigenetic targets such as histone demethylases are now rapidly joining established target classes such as histone deacetylases (HDACs). With the aim of illuminating trends in the field, a data mining-based analysis of ~380 proteins that make up the ‘epigenome’ defined in a recent review (Nature Rev. Drug Discov. 11, 384–400; 2012) was conducted, which is highlighted in this article. The output of the analysis is designed to be explored through an interactive dashboard. Analysis details and guidance for using the dashboard are provided in Supplementary information S1 (box), and some example outputs are discussed here.

Analysis

Text-mining technology developed by Relay Technology Management, which is partly owned by Nature Publishing Group, was used to search over 3.7 million published documents indexed by Medline between 2001 and 2012 for information related to the set of epigenetic proteins, which fall into several families. A snapshot from the dashboard, with the parameters set to focus on two of these families — HDACs and histone methyltransferases — is shown in Fig. 1. Three further parameters (with values ranging from 0 to 1) are used to refine the output of the dashboard. The established index quantifies the degree to which epigenetics research has focused on each protein since 2001; the emerging index quantifies the degree to which the research has increasingly focused on each protein, relative to the historic level; and the targeting index quantifies the degree to which a protein has appeared in publications and grants in the context of molecular targeting applications or therapeutic concepts.

Figure 1 | Epigenetics dashboard snapshot.

Figure 1 : Epigenetics dashboard snapshot. Unfortunately we are unable to provide accessible alternative text for this. If you require assistance to access this image, or to obtain a text description, please contact npg@nature.comSelected members of the histone deacetylase (HDAC)–sirtuin (SIRT) family (red) and methyltransferase family (blue) that have both a high established index and a high target index are shown. The circle size indicates the number of issued US patents related to the target, shown within the circles; see Supplementary information S1 (box) for details. DNMT, DNA methyltransferase; MLL, mixed lineage leukaemia protein.

As expected, HDAC1, HDAC2 and HDAC3 — which are targeted by the approved anticancer drugs vorinostat and romidepsin, and have been researched extensively over the past decade — have both a high targeting index and a high established index. Among other proteins of interest in the two families, the histone methyltransferase EZH2 is an example of a protein for which the publication rate in the period analysed has been substantial overall and is also increasing, leading to high rankings in both the established index (Fig. 1) and the emerging index (not shown). Moreover, its activity has been implicated in various cancers and its small-molecule druggability has recently been demonstrated (Nature Chem. Biol. 8, 890–896; 2012), which contributes to its relatively high targeting index. A discussion of data for some more recently emerging targets in the histone demethylase family is presented in Box 1.

Dash Dhanak, who leads the epigenetics research programme at GlaxoSmithKline, believes that the recently demonstrated druggability of several proteins, including EZH2 and DOT1 (another histone methyltransferase), is encouraging for the next generation of epigenetic drugs. However, understanding the biology associated with modulating each target is a major challenge. “The target landscape is broad and the extent of validated (and valid) chemical matter is limited (and limiting), often requiring risky investment to develop the chemical tools necessary to conduct the translational experiments. We are elucidating the fundamental science in the course of doing drug discovery,” says Audia.

“What the community really needs is a set of tool compounds that can be used to explore the biology of each target and for target validation in disease models,” says Arrowsmith. “Traditionally, such compounds (potent, selective, cell-active and not cytotoxic) have not been widely available to academics who publish the majority of the literature that is used to make decisions on the therapeutic potential of a target.” With this in mind, the SGC has an ongoing project to develop and disseminate ‘open-access’ epigenetic chemical probes, especially for community-wide use to validate targets, explore target biology and also to identify potentially negative effects of target inhibition (see the SGC website). “The field is too large and the potential too vast for any single company or sector to be able to explore all the possibilities,” concludes Arrowsmith.

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Supplementary information

Supplementary information accompanies this paper.

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Histone Deacetylase Inhibitors Induce Epithelial-to-Mesenchymal Transition in Prostate Cancer Cells(1)

Authors: Dejuan Kong, Aamir Ahmad, Bin Bao, Yiwei Li, Sanjeev Banarjee, Fazlul H. Sarkar, Wayne State University School of Medicine

Reporter-Curator: Stephen J. Williams, Ph.D.

Clinically, there has not been much success in treating solid tumors with histone deacetylase inhibitors (HDACi). Histone acetylation and deacetylation play an important role in transcriptional regulation of genes and increased activity is associated with many cancers, therefore it was thought that HDAC inhibition might be fruitful as a therapy.  There have been several phase I and II clinical trials using HDACi for treatment of various malignancies, including hematological and solid malignancies(2), with most success seen in hematologic malignancies such as cutaneous T-cell lymphoma and peripheral T-cell lymphoma and little or no positive outcome with solid tumors.  Many mechanisms of resistance to HDACi in solid tumors have been described, most of which are seen with other chemotherapeutics such as increased multidrug resistance gene MDR1, increased anti-apoptotic proteins and activation of cell survival pathways(3).

A report in PLOS One by Dr. Dejuan Kong, Dr. Fazlul Sarkar, and colleagues from Wayne State University School of Medicine, demonstrate another possible mechanism of resistance to HDACi in prostate cancer, by induction of the epithelial-to-mesenchymal transition (EMT), which has been associated with the development of resistance to chemotherapies in other malignancies of epithelial origin(4,5).

EMT is an important differentiation process in embryogenesis and felt to be important in progression of cancer.  Epithelial cells will acquire a mesenchymal morphology (on plastic this looks like a cuboidal epithelial cell gaining a more flattened, elongated, tri-corner morphology; see paper Figure 1) and down-regulate epithelial markers such as cytokeratin, up-regulation of mesenchymal markers, increased migration and invasiveness in standard assays, and increased resistance to chemotherapeutics, and similarity to cancer stem cells(6-10).

ImageFigure 1. HDACis led to the induction of EMT phemotype. (A and B) PC3 cells treated with TSA and SAHA for 24 h at indicated doses.  The photomicrographs of PC3 cells treated with TSA and SAHA exhibited a fibroblastic-type phenotype, while cells treated with DMAO control displayed rounded epithelial cell morphology (original magnification, x 100). (C) Treated PC3 cells show increased mesenchymal markers vimentin and ZEB1 and F-actin reorganization.  Figure taken from Kong, D., Ahmad, A., Bao, B., Li, Y., Banerjee, S., and Sarkar, F. H. (2012) PloS one 7, e45045

In this study the authors found that treatment of prostate carcinoma cells with two different HDACis (trichostatin A (TSA) and suberoylanilide hydroxamic acid (SAHA)) induced EMT phenotype mediated through up-regulation of transcription factors ZEB1, ZEB2 and Slug, increased expression of mesenchymal markers vimentin, N-cadherin and fibronectin by promoting histone 3 acetylation on gene promoters.  In addition TSA increased the stem cell markers Sox2 and Nanog with concomitant EMT morphology and increased cell motility.

Below is the abstract of this paper(1):

ABSTRACT

Clinical experience of histone deacetylase inhibitors (HDACIs) in patients with solid tumors has been disappointing; however, the molecular mechanism of treatment failure is not known. Therefore, we sought to investigate the molecular mechanism of treatment failure of HDACIs in the present study. We found that HDACIs Trichostatin A (TSA) and Suberoylanilide hydroxamic acid (SAHA) could induce epithelial-to-mesenchymal transition (EMT) phenotype in prostate cancer (PCa) cells, which was associated with changes in cellular morphology consistent with increased expression of transcription factors ZEB1, ZEB2 and Slug, and mesenchymal markers such as vimentin, N-cadherin and Fibronectin. CHIP assay showed acetylation of histone 3 on proximal promoters of selected genes, which was in part responsible for increased expression of EMT markers. Moreover, TSA treatment led to further increase in the expression of Sox2 and Nanog in PCa cells with EMT phenotype, which was associated with cancer stem-like cell (CSLC) characteristics consistent with increased cell motility. Our results suggest that HDACIs alone would lead to tumor aggressiveness, and thus strategies for reverting EMT-phenotype to mesenchymal-to-epithelial transition (MET) phenotype or the reversal of CSLC characteristics prior to the use of HDACIs would be beneficial to realize the value of HDACIs for the treatment of solid tumors especially PCa.

Highlights of the research include:

  • TSA and SAHA induce morphologic changes  in prostate carcinoma LNCaP and PC3 cells related to EMT by microscopy as well as accumulation of mesenchymal markers ZEB1, vimentin, and F-actin reorganization shown by immunofluorescence microscopy and increased expression of these markers shown by real-time PCR
  • Western blotting showed TSA treatment resulted in hyperacetyulation of histone 3 whi8le CHIP analysis revealed increased histone 3 acetylation on the promoters of vimentin, ZEB2, Slug, and MMP2
  • Western analysis revealed that HDACi not only induced EMT but increased the expression of cancer stem cell markers associated with increased motility such as Sox2 and Nanog.  Increased cell migration was measured by Transwell migration assays and increased cell motility was measured via cell detachment assays

1.            Kong, D., Ahmad, A., Bao, B., Li, Y., Banerjee, S., and Sarkar, F. H. (2012) PloS one 7, e45045

2.            Bertino, E. M., and Otterson, G. A. (2011) Expert opinion on investigational drugs 20, 1151-1158

3.            Robey, R. W., Chakraborty, A. R., Basseville, A., Luchenko, V., Bahr, J., Zhan, Z., and Bates, S. E. (2011) Molecular pharmaceutics 8, 2021-2031

4.            Wang, Z., Li, Y., Kong, D., Banerjee, S., Ahmad, A., Azmi, A. S., Ali, S., Abbruzzese, J. L., Gallick, G. E., and Sarkar, F. H. (2009) Cancer research 69, 2400-2407

5.            Wang, Z., Li, Y., Ahmad, A., Azmi, A. S., Kong, D., Banerjee, S., and Sarkar, F. H. (2010) Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy 13, 109-118

6.            Hugo, H., Ackland, M. L., Blick, T., Lawrence, M. G., Clements, J. A., Williams, E. D., and Thompson, E. W. (2007) Journal of cellular physiology 213, 374-383

7.            Thiery, J. P. (2002) Nature reviews. Cancer 2, 442-454

8.            Kong, D., Banerjee, S., Ahmad, A., Li, Y., Wang, Z., Sethi, S., and Sarkar, F. H. (2010) PloS one 5, e12445

9.            Kong, D., Li, Y., Wang, Z., and Sarkar, F. H. (2011) Cancers 3, 716-729

10.          Bao, B., Wang, Z., Ali, S., Kong, D., Li, Y., Ahmad, A., Banerjee, S., Azmi, A. S., Miele, L., and Sarkar, F. H. (2011) Cancer letters 307, 26-36

Other research papers on Cancer and Cancer Therapeutics were published on this Scientific Web site as follows:

PIK3CA mutation in Colorectal Cancer may serve as a Predictive Molecular Biomarker for adjuvant Aspirin therapy

Nanotechnology Tackles Brain Cancer

Response to Multiple Cancer Drugs through Regulation of TGF-β Receptor Signaling: a MED12 Control

Personalized medicine-based cure for cancer might not be far away

GSK for Personalized Medicine using Cancer Drugs needs Alacris systems biology model to determine the in silico effect of the inhibitor in its “virtual clinical trial”

Lung Cancer (NSCLC), drug administration and nanotechnology

Non-small Cell Lung Cancer drugs – where does the Future lie?

Cancer Innovations from across the Web

arrayMap: Genomic Feature Mining of Cancer Entities of Copy Number Abnormalities (CNAs) Data

How mobile elements in “Junk” DNA promote cancer. Part 1: Transposon-mediated tumorigenesis.

Cancer Genomics – Leading the Way by Cancer Genomics Program at UC Santa Cruz

Closing the gap towards real-time, imaging-guided treatment of cancer patients.

Closing the gap towards real-time, imaging-guided treatment of cancer patients.

mRNA interference with cancer expression

Search Results for ‘cancer’ on this web site

Cancer Genomics – Leading the Way by Cancer Genomics Program at UC Santa Cruz

Closing the gap towards real-time, imaging-guided treatment of cancer patients.

Lipid Profile, Saturated Fats, Raman Spectrosopy, Cancer Cytology

mRNA interference with cancer expression

Pancreatic cancer genomes: Axon guidance pathway genes – aberrations revealed

Biomarker tool development for Early Diagnosis of Pancreatic Cancer: Van Andel Institute and Emory University

Is the Warburg Effect the cause or the effect of cancer: A 21st Century View?

Crucial role of Nitric Oxide in Cancer

Targeting Glucose Deprived Network Along with Targeted Cancer Therapy Can be a Possible Method of Treatment

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