DNA demethylation – a new way of coming at cancers

I got into this topic indirectly, starting out by researching what is known about DNA demethylation in response to a comment by Res on my blog post Homicide by DNA methylation.  I found a great deal of interesting material related to epigenomics, cancers, DNA demethylation, histone acetylation and other topics  –  too much to cover in one blog post.  I am going to concentrate here mostly on cystine DNA demethylation as a new approach to preventing and treating cancers, leaving a number of other interesting epigenomic topics for other posts.  The path of the discussion leads around to an old longevity topic – drinking green tea.

1.      Cancer is an epigenetic disease

The point is made in the 2006 publication New therapeutic targets in cancer: the epigenetic connection “Cancer is an epigenetic disease, a combination of DNA modifications, chromatin organization and variations in its associated proteins configure a new entity that regulates gene function throughout methylation, acetylation and chromatin remodeling. Irregular de novo DNA methylation, mainly promoter hypermethylation, histone deacetylation or methylation are important means for the transcriptional repression of cancer-associated genes. Reverse these epigenetic processes restoring normal expression of malignancy- preventing-genes has consequently become a new therapeutic target in cancer treatment. Aberrant patterns of epigenetic modifications will be, in a near future, crucial parameters in cancer diagnosis, prognosis and therapy.”

2.     One of the key things that happen in cancers is aberrant methylation of the promoter region of tumor suppressor genes, rendering them inexpressive, that is, silencing them.

This kind of DNA methylation takes place at CpG dinucleotides.   “CpG islands, which are regions of more than 500 base pairs in size and with a GC content greater than 55% (ref. 3), have been conserved during evolution because they are normally kept free of methylation. These stretches of DNA are located within the promoter regions of about 40% of mammalian genes and, when methylated, cause stable heritable transcriptional silencing. Aberrant de novo methylation of CpG islands is a hallmark of human cancers and is found early during carcinogenesis(ref).”

I am talking about methylation-induced silencing of familiar anti-tumor genes like p53 and p16(INK4a), plus a number of others like BRCA1, BRCA2, APC, RB1. WIF1, MLH1, TIMP3, PTEN, APC, CD95, RASSF1A, E cadherin, RECK and GSTP1.  The role of methylation of tumor suppressor genes in cancers is pretty established knowledge by now. For example, this 2005 report looked at “DNA methylation patterns of the tumour suppressor gene p16INK4A promoter in colon carcinoma cell lines.” Around that time, microarray technology started to become available for efficient detection of DNA methylation(ref)(ref) and the microarray detection methods have continued to improve since allowing much research progress.

3.     There has been a significant amount of research aimed at developing cancer therapies that work by inhibiting methylation of tumor suppressor genes or by demethylating them and restoring their expression.

A number of substances have been effective in demethylating tumor suppressor cells in cancers and restoring their functionality in in-vitro and small animal experiments.  For example, one substance that does the trick is described in the 2006 paper Arsenic trioxide inhibits DNA methyltransferase and restores methylation-silenced genes in human liver cancer cells.  “In the present study, we investigated methylation status of the CpG islands of some major tumor suppressor genes both in human hepatocellular carcinoma and liver cancer cell lines and examined whether demethylation by arsenic trioxide (As2O3) could restore their expression in the cell lines. HepG2 and Huh-7 cells were treated with 2 to 10 micromol/L of AS2O3 and/or 1 micromol/L of 5-aza-2′-deoxycytidine for 24, 48, and 72 hours. The methylation status of the CpG island around the promoter regions of p161NK4a, RASSF1A, E cadherin, and GSTP1 was detected by a methylation-specific polymerase chain reaction (MSP). — In conclusion, a low concentration of As2O3 induces CpG island demethylation of tumor suppressor genes by inhibition of DNMT and reactivates the partially/fully silenced genes in liver cancer cells.”  Of course, arsenic trioxide may not be a very friendly substance to use in humans.

A 2009 paper A New Class of Quinoline-Based DNA Hypomethylating Agents Reactivates Tumor Suppressor Genes by Blocking DNA Methyltransferase 1 Activity and Inducing Its Degradation mentions two demethylating drugs that have made it through the clinical trials process but that have toxic properties, Vidaza,and Decitabine.  “Reactivation of silenced tumor suppressor genes by 5-azacytidine (Vidaza) and its congener 5-aza-2′-deoxycytidine (decitabine) has provided an alternate approach to cancer therapy. We have shown previously that these drugs selectively and rapidly induce degradation of the maintenance DNA methyltransferase (DNMT) 1 by a proteasomal pathway. Because the toxicity of these compounds is largely due to their incorporation into DNA, it is critical to explore novel, nonnucleoside compounds that can effectively reactivate the silenced genes.”

So, there has been a continuing search for effective agents that can demethylate tumor suppressor genes and that are free of toxic side effects.  One class of potentially useful substances is described in the previously mentioned paper, substances based on Quinoline, a familiar organic substance. “Here, we report that a quinoline-based compound, designated SGI-1027, inhibits the activity of DNMT1, DNMT3A, and DNMT3B as well M. SssI with comparable IC50 (6-13 µmol/L) by competing with S-adenosylmethionine in the methylation reaction. — Prolonged treatment of RKO cells with SGI-1027 led to demethylation and reexpression of the silenced tumor suppressor genes P16, MLH1, and TIMP3. Further, this compound did not exhibit significant toxicity in a rat hepatoma (H4IIE) cell line. This study provides a novel class of DNA hypomethylating agents that have the potential for use in epigenetic cancer therapy.”

4.     Some familiar substances can demethylate DNA in tumor suppressor genes.

One of the directions of search is plant-derived substances, our old friends, phytochemicals.  A 2009 publication Modulation of DNA Methylation by a Sesquiterpene Lactone Parthenolide states “Modulation of DNA methylation with DNA methylation inhibitors has been shown to result in cancer cell differentiation or apoptosis and represents a novel strategy for chemotherapy. Currently, effective DNA methylation inhibitors are mainly limited to decitabine and 5-azacytidine, which still show unfavorable toxicity profiles in the clinical setting. Thus, discovery and development of novel hypomethylating agents, with a more favorable toxicity profile, is essential to broaden the spectrum of epigenetic therapy. — Furthermore, parthenolide has been shown to reactivate tumor suppressor HIN-1 gene in vitro possibly associated with its promoter hypomethylation. Hence, our study established parthenolide as an effective DNA methylation inhibitor, representing a novel prototype for DNMT1 inhibitor discovery and development from natural structural-diversified sesquiterpene lactones.”  

Parthenolide occurs naturally in the plant feverfew (Tanacetum parthenium), after which it is named.  “The plant is well known in natural medicine. Tablets and tinctures are used for the relief of migraine, to help prevent blood clots,^[  as an anti-inflammatory providing relief in cases of arthritis, to relieve some types of menstrual problems, and as a digestive aid. Parthenolide, the main active ingredient, is a potential anticancer drug. It destroys acute myelogenous leukemia (AML) cells by inducing apoptosis, leaving normal bone marrow cells relatively unscathed. Moreover, the compound may get at the root of the disease because it also kills stem cells that give rise to AML(ref).” Parthenolide is a powerful inhibitor of the expression of NF-kappaB(ref).

A couple of demethylating substances showing potential promise are surprisingly familiar: the anesthetic procaine, and the green tea polyphenol epigallocatechin-3-gallate.  

The 2003 paper Procaine Is a DNA-demethylating Agent with Growth-inhibitory Effects in Human Cancer Cells was ahead of its time, before the wave of strong interest in demethylation-based cancer therapeutics. “Using the MCF-7 breast cancer cell line, we have found that procaine is a DNA-demethylating agent that produces a 40% reduction in 5-methylcytosine DNA content as determined by high-performance capillary electrophoresis or total DNA enzyme digestion. Procaine can also demethylate densely hypermethylated CpG islands, such as those located in the promoter region of the RARß2 gene, restoring gene expression of epigenetically silenced genes. This property may be explained by our finding that procaine binds to CpG-enriched DNA. Finally, procaine also has growth-inhibitory effects in these cancer cells, causing mitotic arrest. Thus, procaine is a promising candidate agent for future cancer therapies based on epigenetics.”  This was followed by a 2007 study Procaine inhibits the proliferation and DNA methylation in human hepatoma cells. “All the genes transcriptionally suppressed by DNA hypermethylation were demethylated and reactivated with PCA treatment. PCA treatment led to partial demethylation and significant reduction in tumor volume in vivo.”

This leads me to wonder if something as familiar as procaine could become an important anti-cancer tool.  Another relevant paper in this regard are Procaine and procainamide inhibit the Wnt canonical pathway by promoter demethylation of WIF-1 in lung cancer cells.  “Our results provide the first evidence that procaine and procainamide reactivate WIF-1 in these cancer cells and downregulate the Wnt canonical pathway. These results further suggest that procaine and procainamide may have a potential use for preventing the development of lung cancer.”

Finally, if you read this blog, you are likely to have a powerful tumor suppressor gene demethylating agent already sitting on your kitchen shelf – green tea.  The 2003 publication Tea polyphenol (-)-epigallocatechin-3-gallate inhibits DNA methyltransferase and reactivates methylation-silenced genes in cancer cell lines tells the basic story.  “Hypermethylation of CpG islands in the promoter regions is an important mechanism to silence the expression of many important genes in cancer. The hypermethylation status is passed to the daughter cells through the methylation of the newly synthesized DNA strand by 5-cytosine DNA methyltransferase (DNMT). We report herein that (-)-epigallocatechin-3-gallate (EGCG), the major polyphenol from green tea, can inhibit DNMT activity and reactivate methylation-silenced genes in cancer cells. — EGCG dose-dependently inhibited DNMT activity, showing competitive inhibition with a K(i) of 6.89 microM. — Treatment of human esophageal cancer KYSE 510 cells with 5-50 microM of EGCG for 12-144 h caused a concentration- and time-dependent reversal of hypermethylation of p16(INK4a), retinoic acid receptor beta (RARbeta), O(6)-methylguanine methyltransferase (MGMT), and human mutL homologue 1 (hMLH1) genes as determined by the appearance of the unmethylation-specific bands in PCR. This was accompanied by the expression of mRNA of these genes as determined by reverse transcription-PCR. The re-expression of RARbeta and hMLH1 proteins by EGCG was demonstrated by Western blot. Reactivation of some methylation-silenced genes by EGCG was also demonstrated in human colon cancer HT-29 cells, esophageal cancer KYSE 150 cells, and prostate cancer PC3 cells. The results demonstrate for the first time the inhibition of DNA methylation by a commonly consumed dietary constituent and suggest the potential use of EGCG for the prevention or reversal of related gene-silencing in the prevention of carcinogenesis.” 

A 2008 paper Effects of green tea polyphenol on methylation status of RECK gene and cancer cell invasion in oral squamous cell carcinoma cells provides an additional take.  “RECK is a novel tumour suppressor gene that negatively regulates matrix metalloproteinases (MMPs) and inhibits tumour invasion, angiogenesis and metastasis. In the present study, we investigated the effects of epigallocatechin-3-gallate (EGCG), a major polyphenol in green tea, on the methylation status of the RECK gene and cancer invasion in oral squamous cell carcinoma cell lines. Our results showed that treatment of oral cancer cells with EGCG partially reversed the hypermethylation status of the RECK gene and significantly enhanced the expression level of RECK mRNA.”

So, some of the substances that can demethylate and reactivate tumor suppressor genes appear to be procaine, polyphenols in green tea and the herb feverfew.  Research in this area is quite new and I would bet that a number of other very familiar phyto substances will turn out to also have this property.  Hey, I have been systematically demethylating my tumor suppressor genes every day (by consuming lots of green tea) without even knowing that I was doing that!