Genes and gene expression are affected by epigenetics, a stable, heritable, but reversible form of gene control. Three principal forms of epigenetics are DNA methylation, histone post-transcriptional modification, and non-coding RNA. The study of these epigenetic phenomena has led to a few epigenetic treatments for cancer. However, there seems to be a lag in the rate of FDA approval for new epigenetic therapies and additional indications for existing ones. This article will look at what is happening in epigenetics and try to ascertain the future for epigenetic drugs.
DNA methylation regulates gene expression by preventing the binding of transcription factors or by recruiting non-transcribing protein complexes to DNA. It is catalyzed by the methyltransferase enzyme, which works at CpG sites near the transcription domain to inhibit gene expression. DNA methylation is reversible. Active and passive forms of DNA methylation are crucial for normal cell development and differentiation.
Cancer cells show abnormal DNA methylation patterns. Cancer is marked by global hypermethylation, which destabilizes the genome and activates oncogenes. Paradoxically, it is also marked by hypermethylation at specific sites. This turns off tumor suppressor genes. One goal of epigenetics, therefore, is to restore normal DNA methylation patterns.
Histone post-translational modifications of N-terminal histone tails are an epigenetic form of regulation of gene expression. Histone protein organizes the long fibers of DNA. Protruding N-terminal tails undergo post-translational modifications of acetylation, methylation, phosphorylation, ubiquitinization, and sumoylation.
The packaging of genetic information in the cell is an epigenetic phenomenon, and these post-translational modifications are reversible. Histones with different covalent modifications are associated with activation or repression of chromatin and gene expression. Loss of acetylation on the N-terminal histone tail is the first step in gene silencing, and histone de-acetylases have been a key target of epigenetic therapy.
Cell differentiation and development depends on non-coding RNA. This is RNA that is not translated to protein and includes miRNA (micro RNA), siRNA (small interfering RNA), piRNA (piwi-interacting RNA), and lncRNA (long non-coding RNA). Non-coding RNA mediates the recruitment of DNA methyltransferases to provide methylation and transcriptional silencing.
Protein translation is inhibited by miRNA, which pairs with complementary RNA sequences. It influences cancer cell proliferation, apoptosis, and metabolism by affecting the expression of epigenetic enzymes. The mechanism of siRNA is similar to miRNA. Epigenetic control is also affected by piRNA, which interacts with piwi proteins. A wide range of functions in cellular and developmental processes is carried out by lncRNA. These molecules carry epigenetic information that interacts with enzymes regulating histone and DNA methylation, chromatin condensation, and gene silencing.
Epigenetic drugs and the U.S. FDA
The inhibition of specific epigenetic enzymes can reverse the incorporation of an epigenetic mutation. Therefore epigenetic enzymes are attractive targets for cancer therapy. Seven epigenetic drugs have been approved by the U.S. FDA to treat hematological malignancies, including two methyltransferase inhibitors and five histone inhibitors.
Azacytidine (Vidanza) and Decitabine (Dacogen) are epigenetic inhibitors targeting DNMT1 (DNA dimethyltransferase 1). These two drugs are for treatment of AML (adult myeloid leukemia), CML (chronic myelogenous leukemia), and MDS (myodysplastic syndrome).
Veronistat (Zolina) is a histone deacetylase inhibitor used to treat CTCL (cutaneous T-cell lymphoma). Belinastat (Baleodaq) is used for PTCL (peripheral T-cell lymphoma), and Romidepsin (Istodax) is for both CTCL and PTCL. Panobistat (Farydak) is another histone deacetylase inhibitor for multiple myeloma.
All the indications for which epigenetic drugs are approved are hematological malignancies. None are for solid tumors, although testing is ongoing. The difference in drug response between hematological malignancies and solid tumors has been ascribed to different pathological characteristics, phenotype conversion, epigenetic and genomic features, and the tumor microenvironment.
Some epigenetic regulators are only slightly more expressed in tumor tissue compared to normal tissue. Most epigenetic drugs have nonselective effects on the genome; they may activate the expression of oncogenes. Many epigenetic functions also depend on certain components in protein complexes. Targeting one epigenetic molecule may destroy the function of the complex, resulting in off-target side effects.
Image: All the indications for which epigenetic drugs are approved are hematological malignancies. None are for solid tumors, although testing is ongoing. Image from Dreamstime.
The microenvironment of solid tumors is different from hematological malignancies. Rapid cellular proliferation in solid tumors produces hypoxia and tissue acidification, affecting the expression and post-translational modification of epigenetic molecules and the effectiveness of anticancer drugs.
Epigenetic futures
Perhaps where epigenetic drugs will do best is in combination therapy with chemotherapy and radiation. For instance, DNMT1 or HDAC (histone deacetylase) inhibitors increase cancer cell sensitivity to the chemotherapy drugs cisplatin and doxorubicin. The epigenetic agents work by increasing chromatin accessibility through chromatin decomposition. Indications under investigation for these combinations include metastatic melanoma and non-small cell lung cancer.
Epigenetic drugs combined with radiotherapy promote DNA damage and cell apoptosis. Histone deacetylase inhibitors make cancer cells sensitive to radiotherapy by amplifying DNA damage signaling and inhibiting double-strand DNA break repair. Indications under investigation include gastrointestinal tract carcinoma, high-grade glioma, non-small cell lung cancer, prostate cancer, esophageal cancer, and head and neck cancer.
In combination with molecular-target drugs, epigenetic drugs were significantly more effective at promoting their anticancer effects. Studies are underway for non-small cell lung cancer, breast and ovarian cancer, metastatic melanoma, and refractory lymphoma.
Immunotherapy drugs received a boost from epigenetic drugs too, with improvements to the anticancer effects against squamous cell carcinoma, lung cancer, glioma, and breast, bladder, prostate, and colon cancer.
Making use of the research
Part of the problem with synthetic epigenetic drugs is their lack of specificity. Some researchers are taking a different approach and seeking those reversible epigenetic factors that are affected by diet and lifestyle changes.
A large cohort study conducted in The Netherlands looked at the DNA methylation response to drinking. Analysis of DNA methylation showed promoter methylation of several genes was higher in a group with high alcohol intake than it was it the lower alcohol intake group.
DNA methylation marks of smoking showed a difference between cases and controls consistent with the interaction between maternal smoking and the risk of cancer in offspring. Several studies have demonstrated hypermethylation and silencing of several genes associated with lung cancer. This may be due to histone code modifications, which are known to be induced by tobacco smoke.
Image: A study that looked at DNA methylation response to drinking found that promoter methylation of several genes was higher in a group with high alcohol intake than it was it the lower alcohol intake group. Image from Pexel.
Obesity is a well-known risk factor for colorectal cancer. Obesity leads to CpG methylation changes that result in differentially expressed genes relevant to metabolism and tumorigenicity. A whole-genome bisulfite sequencing study of mice revealed thousands of differentially methylated regions between CpG sites of obese versus lean mice. When obese mice were shifted from a high-fat to a low-fat diet, body weight dropped to that of lean controls, and most of the differentially expressed genes returned to normal.
The degree to which environmental factors influence carcinogenesis depends on the type of factors and the duration of exposure. Early stages of cancer development might best be influenced by diet and lifestyle factors, which may be implemented immediately, rather than by the slow, uncertain arrival of epigenetic drugs.