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Genetic Reprogramming: Epigenetics

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Newswise — To radiation, chemotherapy, surgery and biological therapies deployed to wage war on cancer, M. D. Anderson researchers have added a new approach – diplomacy.

“In this instance, we’re not trying to kill cancer cells, rather we talk to cells and remind them of their regular programming. We persuade them to return to their normal behavior,” says Jean-Pierre Issa, M.D., professor in M. D. Anderson’s Department of Leukemia.

The instruments of persuasion are drugs that awaken cancer-suppressing genes in cancer cells by sweeping away chemical “off” switches connected to those genes. Methyl groups – which consist of a carbon atom surrounded by hydrogen atoms – silence genes by attaching at a certain spot, hanging off the gene like a tag or bookmark.

Issa and Leukemia Department Chair Hagop Kantarjian, M.D., are pioneers in the emerging field of epigenetics, the study of changes in gene expression and cellular behavior that are not caused by physical damage or mutation of the genes themselves. DNA methylation, for example, is epigenetic.

Issa and Kantarjian revived a failed chemotherapy, for instance, by turning it from attack to diplomatic mode. Using a low-dose, low-toxicity, longer-term approach, they showed that decitabine extends the life of some leukemia patients by demethylating, or turning on, genes.

Based on a clinical trial led by Kantarjian, the U.S. Food and Drug Administration last year approved decitabine (Dacogen™) for treatment of myelodysplastic syndrome, a lethal failure of the bone marrow to produce enough normal blood cells. The latest research by the group shows 70% of patients experienced some relief from MDS, with 35% experiencing complete remission. The median time of remission was 20 months.

Only the Beginning 

Before the development of decitabine and another epigenetic agent called azacytidine (Vidaza™), MDS was a disease “with no treatment,” Issa says. There was no chance of putting it in remission with a drug. Only supportive care, such as a blood transfusion, was available. Bone marrow transplants worked for a small number of patients.

“I see this as the beginning of the development of epigenetic therapy,” Kantarjian says. “FDA approval of decitabine was just the beginning. This is when the real research starts, when the drug becomes accessible to investigators in an easy manner so they can develop new concepts and new strategies to optimize the use of the drug as a single agent, in combinations and across many tumors.”

The leukemia group has a leading program, investigating epigenetic agents in 18 clinical trials. Four of those trials involve azacytidine, a drug that acts in a similar manner as decitabine. The two medications are the first epigenetic therapies approved for cancer.

Kantarjian, Issa, MDS Section Chief Guillermo Garcia- Manero, M.D., and colleagues have pressed ahead refining the optimal decitabine dosage for MDS, exploring its use in other leukemias, in combination with other drugs, and addressing how cancer becomes resistant to the drug. Azacytidine trials explore similar issues. Issa also collaborates with a team from Duke University on the use of decitabine for melanoma and renal cell carcinoma.

Nearly one-half of the 32 epigenetic trials at M. D. Anderson study decitabine. Not bad for a drug that was left for dead 25 years ago.

Drug Revival

Kantarjian’s and Issa’s work to revive decitabine is a classic example of the major role academic medical institutions play in drug discovery and development.

Decitabine was discovered in Czechoslovakia and tested against leukemia as traditional high-dose, cell-killing chemotherapy in Europe. The drug showed activity against the disease but was dogged by dangerous and unpredictable myelosuppression – the shutting down of blood production in the bone marrow.

This side effect caused the drug’s manufacturer, Pharmachemie BV of Europe, to shelve it in the 1980s.

Decitabine still intrigued Kantarjian, who was following the newborn field of epigenetics and suspected the drug had potential if used properly.

Pharmachemie was not interested in sponsoring any more clinical trials, but agreed to provide Kantarjian with decitabine. He filed his own investigational new drug application with the FDA and went to work. Kantarjian recalls that it was the early 1990s and he was the only physician in the United States working with the drug.

At the time, Issa was on the faculty at Johns Hopkins studying epigenetics. His research in DNA methylation led him to believe that decitabine might work epigenetically as a demethylating agent.

The two met in 1993 at a scientific meeting when Issa sought out Kantarjian and his poster on use of decitabine for chronic myelogenous leukemia. A collaboration was born.

They developed a Phase I clinical trial using decitabine intravenously for MDS at doses ranging from one-twentieth to one-fiftieth of the doses employed in the European trials. The trial showed that the drug was safe and active, with the lower dose preventing dangerous incidents of myelosuppression. Lab research indicated it worked by wiping out methyl tags.

Issa came to M. D. Anderson in 1999, where he and Kantarjian developed and led a pivotal Phase III multi-center trial in 2001. Results were reported early last year in the journal Cancer, citing that 17% of patients had some response, with responders having a median time to disease progression or death of 17.8 months, compared with 9.8 months for patients who didn’t respond.

By the time the FDA approved decitabine in May 2006, the drug had been held by four companies: Pharmachemie, TEVA, SuperGen and finally MGI Pharma, which purchased the drug from SuperGen in September 2004 and shepherded it through the FDA fast-track process. The frequent change of companies was another challenge in keeping decitabine alive, Kantarjian says.

Azacytidine, developed on a parallel track by a team at Mount Sinai Medical Center in New York, and owned by Pharmion, was approved by the FDA in 2004.

Decitabine, researchers note, is the more potent demethylating agent of the two.

Thinking Outside the Box

“Dr. Issa and Dr. Kantarjian brought a unique assimilation of scientific and clinical expertise that enabled them to think about developing decitabine in a different way,” says Mary Lynne Hedley, Ph.D., chief scientific officer of MGI Pharma. “And that’s really why decitabine ended up being so useful for patients.”

They upset three dogma of drug development and patient care, Hedley notes. First, they took a general cell-killing drug and by understanding its biological activity, transformed it into an early version of targeted therapy.

Second, they rejected the common practice of administering the maximum tolerated dose of a medication. And third, they focused on longer-term courses of therapy and disease management, rather than short courses of treatment.

The key to improved outcomes seen in the MDS follow-up study was prolonged treatment at low doses, Kantarjian says. “The best results with decitabine will be achieved by giving the drug to patients for one or two years, consisting of 20 to 24 courses of treatment, rather than three or four courses.”

Beyond MDS

Kantarjian leads a Phase III clinical trial of decitabine for acute myelogenous leukemia – the most common form of the disease in adults. Kantarjian notes that AML also is a leukemia that has shown the least improvement in treatment outcomes over the last 30 years.

A Phase II trial for decitabine as frontline therapy for AML in elderly patients, those with the grimmest prospects, also is under way.

Most patients over 65 go untreated, except for receiving supportive care, because of the toxicities associated with chemotherapy used against the disease. Their median survival is 1.7 months.

A poster presented by the team at the 2007 American Society of Clinical Oncology meeting showed how decitabine, with its low-intensity and minimal side effects, might help older AML patients. Total response rate was 52%, with 24% having complete remissions. Median survival time at the 20-month mark of the study was 12.6 months.

A study published this year comparing the effectiveness of decitabine to that of high-intensity chemotherapy in high-risk MDS patients showed comparable remission rates for each option, but those receiving decitabine had nearly doubled the mean survival time – 22 months versus 12 months. “Chemotherapy gets patients to remission, but it’s very toxic and remissions tend to be short-lived,” Issa says.

Other M. D. Anderson researchers also are testing epigenetic drugs alone or in combinations against solid tumors as well as myeloma and lymphoma.

David Stewart, M.D., professor in the Department of Thoracic/Head and Neck Medical Oncology, for example, is exploring in a Phase I trial the use of the drug for solid tumors and lymphomas that have resisted other treatment.

Some solid tumors, such as colon and head and neck cancers, are known to have a great deal of methylation. Issa notes that earlier clinical trials of decitabine against these cancers also failed, but they repeated the same mistake as the European trials, using maximum tolerated doses for short periods.

“This drug really hasn’t been properly tested at low doses over longer periods as a demethylating agent against those cancers,” Issa says.

More to Learn

There is still plenty to understand about how demethylating agents such as decitabine work. Their effect is global because they demethylate and switch on many genes. The research team is pinpointing specific cancer-suppressing genes that are silenced by methylation.

MDS eventually becomes resistant to decitabine. Issa says resistance starts as early as six months or as late as 3.5 years. The drug strips away all methyl tags, both normal and abnormal. The normal tags come back quickly, while the abnormal tags return more slowly. “If they come back, the drug stops working,” Issa notes.

Initial research in DNA methylation indicated that removing the tags might promote cancer by turning on oncogenes. However, Issa notes, subsequent research showed that methylation silenced hundreds of genes, inactivating those involved in tumor suppression and programmed cell death of cancerous cells.

Since tumors rely more on gene silencing to survive than normal adult cells do, the overall effect of demethylation is favorable for treatment.

Two for One

One potential answer to the problem of resistance is to combine agents, explains Garcia-Manero, M.D., an expert in epigenetics and associate professor of leukemia.

Garcia-Manero was lead author of a major study published in the journal Blood late last year. It combined decitabine with valproic acid, an anti-convulsant drug used for epilepsy.

Valproic acid hits a different epigenetic target, Garcia-Manero explains, inhibiting the removal of chemical “on” switches – acetyl tags – that activate genes.

Combining the two drugs in a group of 54 AML and MDS patients was shown to be safe and effective, Garcia-Manero notes. Methyl “off” switches were stripped from DNA, and two types of histone acetylation were achieved and an important tumor-suppressing gene was reactivated.

Of 10 elderly MDS and AML patients, five responded to the combination, with four of them experiencing remission. Overall, 22% of patients got some relief from the combination, with 19% having complete remission. While the study was too small to draw conclusions about the drugs’ effectiveness, it points to the need for follow-up clinical trials.

“We’re testing a number of epigenetic agents that have exciting potential,” Garcia-Manero notes. His team has a paper pending in Blood that shows promising results with the combination of valproic acid, azacytidine and all-trans retinoic acid for AML and MDS patients. Overall, 42% of 53 patients showed some response to the three-drug combination, with 22% having complete remissions.

Garcia-Manero also is testing three other epigenetic agents, all of which protect acetyl “on” switches: vorinostat, MGCD0103 and LBH589.

Razelle Kurzrock, M.D., professor in the Department of Experimental Therapeutics and director of M. D. Anderson’s Phase I Clinical Trials Program, leads a clinical trial testing azacytidine and valproic acid in advanced metastatic cancers.

Issa remembers presenting a research poster on epigenetics to the 1992 annual meeting of the American Association for Cancer Research, “There was one other poster on the subject out of 4,000,” he says.

At this year’s AACR meeting, there were 500 posters on epigenetic approaches – genetic diplomacy marches on.

Genes Misbehaving

Cancer remains a disease of genes and genetic mutations, changes that drive cancer and make it hard to treat. But it’s also a disease of genetic expression – genes behaving badly – and that, Jean-Pierre Issa, M.D., explains, is where epigenetics comes in.

To understand epigenetics, you have to start at the beginning, at the embryonic stage. An embryo’s cells all have an identical set of genes. Its next job is to use those genes to differentiate cells into varied organs and tissues to build the body. This is accomplished with epigenetic signals that turn on the genes needed to create an organ while blocking other genes, explains Issa, professor in M. D. Anderson’s Department of Leukemia.

The crucial actors here are methyl groups (off switches) and acetyl groups (on switches). Methyl tags attach to specific areas of genes. Acetyl tags have a more complex story, connecting with histone proteins to turn genes on.

Histones wrap around DNA. This histone-DNA combination forms the chromatin complex, which in turn composes chromosomes. When acetyl groups attach to histones, they turn on the accompanying gene. When acetyl tags are removed, the histone tightens around genes, turning them off.

Epigenetic drugs wipe out the methyl groups temporarily or block the stripping of acetyl groups from histones.

While some cancers are tied to inherited genetic variations, others are launched by damage to DNA. Mutated or damaged genes generally are impervious to repair by treatment. Therapies generally target these cells for death. Genes that are suppressed, Issa notes, can be manipulated through epigenetics – a more diplomatic approach.

“Our genome is set. It can’t be modified. Our epigenome is more dynamic. It’s something we can affect with epigenetic drugs or by our behavior,” Issa says.

Think of genes as hardware and epigenetics as the operating system software, explains Cheryl Lyn Walker, Ph.D., professor in M. D. Anderson’s Department of Carcinogenesis at the Virginia Harris Cockrell Cancer Research Center in Smithville, Texas.

External carcinogenic factors such as diet, tobacco use or environmental toxins can cause cancer both via direct DNA damage and epigenetic effects, Walker says. She and her colleagues are focusing on all suspects that turn normal cells into cancer cells.

Walker, for example, studies genetic predisposition to cancer and how cancer-causing chemicals, or carcinogens, interact with genetic factors to cause cancer.

She examines the impact of xenoestrogens – chemicals present in our environment that act like estrogens – which are taken in through environmental exposures or in food, such as a plant phytoestrogen that is present in soy. Walker studies how exposure to xenoestrogens affects the development of uterine fibroids. Fibroids occur in upwards of 50% to 75% of women, and these tumors are the principal reason for hysterectomy in women of reproductive age.

Working in a rodent model, Walker found that those with a genetic predisposition to develop fibroids and who are exposed to environmental estrogens at crucial times during development have dramatically increased risk of developing tumors later.

“This is called developmental reprogramming. When you disrupt a tissue while it’s developing, you worsen the risk of disease in adulthood,” Walker says. “We’re finding that for this type of environmental exposure, it’s all about timing.”

Reprogramming probably is accomplished through an epigenetic mechanism, Walker says, and so may be susceptible to epigenetic treatment.

Interestingly, Issa has found that methyl tags accumulate over time, shutting down genes. It’s a tantalizing possible connection to aging, he says, but that’s another story.

Epigenetics — By Definition:

Acetylation: a reaction that introduces an acetyl group into a molecule of an organic compound. Acetyl tags work by connecting to specific proteins and act as a genetic on switch.

Demethylation: the chemical process of removing a methyl group from a molecule, which, in turn, can reactivate tumor-suppressor genes that are silenced by methylation.

Epigenetics: the study of changes in gene expression and cellular behavior that are not caused by physical damage or mutation of the genes themselves.

Methylation: an enzyme-mediated chemical modification that adds methyl groups at selected sites on proteins, DNA and RNA. Methyl tags work by attaching to specific areas of genes and act as a genetic off switch.

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(NewsWise, Medical News, Source: University of Texas MD Anderson Cancer Center, April 3, 2008)


The information contained in these articles may or may not be in agreement with my own opinions. They are not posted as medical advice of any kind.

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