Epigenetic modifications as therapeutic targets

Abstract

Epigenetic modifications work in concert with genetic mechanisms to regulate transcriptional activity in normal tissues and are often dysregulated in disease. Although they are somatically heritable, modifications of DNA and histones are also reversible, making them good targets for therapeutic intervention. Epigenetic changes often precede disease pathology, making them valuable diagnostic indicators for disease risk or prognostic indicators for disease progression. Several inhibitors of histone deacetylation or DNA methylation are approved for hematological malignancies by the US Food and Drug Administration and have been in clinical use for several years. More recently, histone methylation and microRNA expression have gained attention as potential therapeutic targets. The presence of multiple epigenetic aberrations within malignant tissue and the abilities of cells to develop resistance suggest that epigenetic therapies are most beneficial when combined with other anticancer strategies, such as signal transduction inhibitors or cytotoxic treatments. A key challenge for future epigenetic therapies will be to develop inhibitors with specificity to particular regions of chromosomes, thereby potentially reducing side effects.

Figure 1. Epigenetic Aberrations of CpG Island Promoters in Cancer and the Epigenetic Therapies That Target Them

Tumor suppressor genes (e.g. FBXO32, MLH1 & RUNX3) are expressed in normal cells and become silenced in cancer cells. This can occur by PRC reprogramming (e.g. FBXO32), where the polycomb group protein EZH2 catalyses the methylation of H3K27 or by 5mC reprogramming (e.g. MLH1, RUNX3) due to de-novo DNA methylation by DNMT3A and DNMT3B. Polycomb mediated repression can be targeted by inhibitors of PRC2, like DZNep and re-expression of these genes can be enhanced by HDAC and LSD1 inhibitors allowing acetylation of H3/4 and methylation of H3K4, respectively. Polycomb mediated repression can also be reversed by inducing miR-101 expression, which inhibits the expression and function of EZH2. 5mC reprogramming can be reversed, mainly by DNMT inhibitors, but also by re-expression of miR-143 and miR-29, two miRNAs that target de-novo DNMTs. LSD1 inhibitors may also reactivate tumor suppressor genes by inhibiting DNMT1 stabilization leading to loss of DNA methylation maintenance. Genes, which are polycomb repressed in normal cells (e.g. PAX7), can undergo epigenetic switching by gaining DNA methylation, thus losing their plasticity during transformation. Currently it is not known whether the treatment of cancer cells with DNMTi alone will reverse epigenetic switching to restore the polycomb repressed state or whether it will re-activate this set of genes. Cancer-Testis Antigens (CTAs, e.g. NY-ESO-1) can become silenced by DNA methylation in cancer. Treatment with DNMT inhibitors can induce CTA expression, allowing the immune system to recognize and kill the cancer cells. Black arrows represent epigenetic alterations during transformation and gray arrows represent the reversion of this alteration by epigenetic therapy.

Figure 2. Chemical structure of selected compounds that target epigenetic modifications

At the present time, several molecules, which target epigenetic alterations in pathological states are at different stages of drug development. The nucleoside analogs 5-Azacytidine and 5-Aza-2′-deoxycytidine are FDA approved to treat high-risk myelodysplastic syndromes (MDS) patients and successful clinical results have been reported. The drug Hydralazine is currently being investigated in clinical trials as a putative demethylating agent against solid tumors and S110, a dinucleotide containing 5-aza-CdR, has been shown, in vitro, to demethylate DNA with a decreased deamination by cytidine deaminase. Targeting histone acetylation has also been a successful example of epigenetic therapy. Several histone deacetylase inhibitors are FDA approved such as the hydroxamic acid-based compound SAHA and the depsipeptide, Romidepsin, while others are currently in clinical trials for cancer (Phenylbutyrate and Entinostat) and neurologic diseases (Entinostat) and new molecules targeting specific HDACs are under pre-clinical investigations (e.g. PCI-34051, which targets HDAC8). More recently, significant effort is underway to find new molecules able to target histone methylation. To our knowledge there are no drugs targeting histone methylation which are FDA approved or in clinical trials. However, pre-clinical trials suggest anti-tumor activity of the oligoamine analogue SL-11144, a LSD1 inhibitor and the S-adenosylhomocysteine hydrolase inhibitor 3-Deazaneplanocin A (DZNep), a drug that depletes cellular levels of PRC2 components.