Epigenetic Drugs Take On Cancer

Armed with nearly $10 million raised by telethons, a research "dream team" hopes to prove that a new approach to cancer therapy can halt solid tumors.

Power couple. Cancer epigenetics pioneers Stephen Baylin (top) and Peter Jones are treating tumors with the drug Vidaza (green), which replaces cytosines in DNA, then prevents a key enzyme (red) from transferring methylation patterns to daughter cells.

When Stephen Baylin and Peter Jones began their research careersabout 3 decades ago, they found themselves challenging the cancerestablishment. Tumor cells are typically riddled with genetic mutations, and most cancer biologists suspected that these altered DNA sequences were driving the uncontrolled cell growth. But Baylin and Jones—initially rivals and later collaborators—suggested that another factor was a suite of chemical modifications to DNA and its accessory proteins that determines whether genes are turned on.

For years, they were virtually ignored at meetings. "There would be a sort of glaze in people's eyes," says Jones, who is at the University of Southern California in Los Angeles. But today, many cancer biologists agree that DNA methylation, a process in which enzymes tack methyl groups onto genes and block their activity, and other so-called epigenetic changes might be as important as genetic mutations in causing cancer. Last year, Baylin and Jones received an award from the American Association for Cancer Research (AACR); the presenter noted that "The two of us worked sort of like salmon swimming upstream," recalls Baylin wryly, in his sunny fifth-floor corner office at Johns Hopkins University overlooking downtown Baltimore, Maryland.

AACR has also helped select Baylin and Jones, as leaders of a so-called epigenetics dream team, to receive more than $9 million from Stand Up To Cancer, a glitzy Hollywood campaign that has raised nearly $200 million for research with star-laden telethons. The 3-year grant has helped fund the first phase II clinical trials to test DNA demethylating drugs—already used successfully to treat a blood cancer—for solid tumors such as lung cancer. The idea is not to kill cancer cells but to correct their DNA methylation and thereby "reprogram" them to behave more normally, Baylin says: "It really is a different way of looking at therapy."

The two are again running into skepticism in the cancer community. Some scientists worry that instead of resetting epigenetic patterns, the primary drug Baylin and Jones are testing simply kills cells, whether cancerous or healthy ones, and therefore has toxic side effects. Precisely how the treatment works isn't yet known. And because drugs that remove methyl groups from DNA can potentially switch on hundreds of genes in healthy cells, including knownoncogenes, there is concern that the drugs could cure one kind of cancer but cause another. "From a scientific point of view, you would like to know why these drugs sometimes work and develop more specific agents," says Johns Hopkins cancer geneticist Bert Vogelstein, whose lab neighbors Baylin's.

More specific versions of the drugs being tested by the epigenetics dream team are in fact in the pipeline. But molecular biologist Phillip Sharp of the Massachusetts Institute of Technology (MIT), who chaired the AACR committee that selected the Baylin and Jones–led effort for the Stand Up To Cancer funding, says the project seemed worth the investment to gauge the promise of cancer epigenetic therapies. Raising money to test the key drug was particularly important, Sharp says, because the U.S. patent will soon expire, dulling the interest of pharmaceuticalcompanies: "Very few companies will want to put serious money into this until someone shows it works."


Muffled genes

The field of cancer epigenetics took off in the 1970s, when Jones's lab was experimenting with a potent cancer cell–killing compound developed in Czechoslovakia. Jones noticed that this compound, azacitidine, could turn embryonic mouse cells into muscle and did so without mutating DNA. He showed that the compound was turning on a muscle-development gene that had been shut off by methylation. From this work, Jones suggested that changes in DNA methylation might be linked to aberrant gene expression in cancer.

Not long after, researchers began to document abnormal DNA methylation in most kinds of cancer cells. Some at Johns Hopkins, including Vogelstein, reported in 1983 that in colon cancer, much of a tumor cell's genome is stripped of these methyl groups. Yet Baylin noticed that certain genes in cancers tended to have too much methylation, particularly so-called tumor suppressor genes that normally check cell growth. Baylin's lab eventually showed that methylating such genes could be as effective at silencing genes as mutating them.

The growing understanding of epigenetics suggests a new way of treating cancers, because, unlike mutations, changes to a gene's methylation can be reversed. For example, silenced tumor suppressor genes might be turned back on. In theory, this might be done with compounds that lead to the loss of the methyl groups from DNA by interfering with the enzyme DNA methyltransferase (DNMT). As it happens, azacitidine, the DNMT inhibitor thatsparked Jones's interest in methylation, and a similar compound, decitabine, did undergo early clinical testing for cancers in the 1970s and 1980s, but both were abandoned at the time because they were too toxic.

Partly through "serendipity," says Jean-Pierre Issa of MD Anderson Cancer Center in Houston, Texas, he and a few other clinical researchers revisited these drugs in the 1990s. While searching for a treatment for myelodysplastic syndrome (MDS), a preleukemia condition, the investigators discovered that the two compounds could safely slow the cancer. The key, notes Issa, was to ignore the conventional practice of giving patients as much of a cancer drug as they can safely tolerate. A medical oncologist named Lewis Silverman at Mount Sinai School of Medicine in New York City was treating elderly MDS patients and found that relatively low doses of azacitadine improved health and extended survival in 30% to 60% of those treated and sent a few into remission.

Meanwhile, Issa followed up on lab observations suggesting that at low doses, decitabine might stop cancer cells from dividing by reactivating tumor suppressor genes. That, he and others realized, could offer a way to stop tumor growth that is gentler than killing cells outright. Issa started clinical trials of low-dose decitabine for MDS patients and was soon having success similar to Silverman's. Their trials led the U.S. Food and Drug Administration (FDA) to approve azacitidine (marketed as Vidaza) in 2004 and decitabine (Dacogen) in 2006 for treating MDS.

It makes sense, researchers say, that these two drugs help cancer patients only at low doses given the way they work. In structure, they mimic cytosine, one of the four bases of DNA. During cell replication, the fake cytosine swaps places with real cytosine in growing strands of DNA, then traps DNA methyltransferases, interfering with the ability of these enzymes to reproduce the cell's existing methylation in the new DNA of the daughter cell. If the drug dose is too high, the cells simply die. At low doses, the cells survive but with less DNA methylation.


Building on success

With the money from Stand Up To Cancer, the epigenetics dream team is now extending the clinical trials of DNMT inhibitors to lung, breast, and colon cancers. There's no reason why such drugs should not work on solid tumors as well, Baylin and Jones say.

The team is combining the DNMT inhibitors with histone deacetylase (HDAC) inhibitors, another class of compounds that target epigenetic changes in cancer cells. Within the cell's nucleus, DNA is wound around proteins called histones that are packed together to form a package called chromatin. Somewhat like DNA, these histones can also get chemically tagged by methyl groups and acetyl groups. These tags determine the chromatin's structure, influencing whether certain genes are on, and scientists have found abnormal histone acetylation patterns in various types of cancer cells. Indeed, a compound that in cell studies appeared promising as an anticancer drug ultimately turned out to be an HDAC inhibitor. This drug, known as SAHA (Zolinza), like other HDAC inhibitors, blocks the removal of acetyl groups from histones. It was approved in 2006 by FDA for treating a rare immune system cancer called cutaneous T-cell lymphoma.

Cell studies by Baylin's group have shown that the two types of epigenetic therapies should synergize, which is why the Stand Up To Cancer team is venturing ahead with a combination approach, initially testing Vidaza and the HDAC inhibitor Entinostat for advanced non–small cell lung cancer in a trial at Johns Hopkins. The unpublished results, says Baylin, are promising for patients with cancer that had spread despite several chemotherapy treatments. The drug combo has slowed or stopped tumor growth in 30% of 28 patients and has produced "very robust and durableresponses" in four people, he adds, shrinking or even eliminating their tumors for at least 1.5 years.

Two-thirds of the people in the trial were not helped by the treatment, however. Baylin and others offer several explanations. Not enough of the drug may be getting into the lung tumor cells, the researchers suggest, noting that a more stable DNMT inhibitor, which the team will use in a future trial, may help. Another possibility is that, because they have received chemotherapy, these advanced cancer patients may have already developed "resistance" to nucleus-targeting drugs (including the epigenetic treatment). Mutations in their tumor cells may have closed off the drugs' access points to the nucleus, Issa says. To test this idea, the Stand Up To Cancer team plans to try the epigenetic drugs on cancer patients who have had surgery but no chemotherapy.

Yet another explanation is that only some patients' tumors are driven by epigenetic changes (see sidebar). Indeed, the team is examining the DNA methylation and gene expression of each patient in their trials, with the hope of finding a pattern that predicts whether a person will respond to the drug combo. Others are also taking this approach. In the 20 October issue of Science Translational Medicine, researchers at the U.S. National Cancer Institute report that they have used epigenetic and gene-expression signatures to classify liver cancer cell lines into two distinct types: one that dies when treated with a DNMT inhibitor and one that does not.


Room for improvement?

As the Stand Up To Cancer team pushes ahead with its solid-tumortrials, skepticism continues about the drugs being tested, most of it centering on questions about the mechanism. "The drugs do work at low doses, and they do change epigenetic modification patterns, but it is not clear whether the clinical benefits are due to the epigenetic changes," says molecular biologist Frank Lyko of the German Cancer Research Center in Heidelberg. DNA-demethylating drugs such as azacitidine and decitabine may simply be killing cells, he suggests. And HDAC inhibitors, which act on many cell pathways, may be changing some that have nothing to do with epigenetics, such as acetylation patterns in proteinsin cytoplasm. Paul Marks of Memorial Sloan-Kettering Cancer Center in New York City, who developed the first HDAC inhibitors, agrees: "We're still in the very early stages of trying to understand how best to use these inhibitors in a clinical setting."

And even if DMNT inhibitors do epigenetically reprogram cancer cells, they could also turn on genes that cause cancer. Rudolf Jaenisch, a developmental biologist at MIT, has conducted mouse studies that illustrate this potential problem. He and his colleagues have shown that if they disable the gene for a DNA methyltransferase, the mice eventually develop a type of lymphoma (Science, 18 April 2003, p. 489). "One has to be cautious playing with amechanism that could have several potential effects," he says.

Jaenisch says his group's mouse results may not be relevant to adult cancer patients undergoing treatment with DNMT inhibitors because the clinical doses don't seem high enough to match knocking down the gene for a methylating enzyme. Still, Jaenisch lauds efforts by researchers such as Lyko, a former postdoc in his lab, to develop drugs that demethylate DNA by blocking one or more of the DNA methyltransferase enzymes rather than globally suppressing methylation by incorporating a fake cytosine into DNA. Such specific enzyme inhibitors should demethylate fewer genes and perhaps reduce the potential for side effects.

Baylin and other members of the epigenetics dream team are quick to respond to such criticisms. They say there is plenty of evidence that the drugs they're testing aren't mere cell killers. "You see things in the clinic that you never see with cytotoxic drugs," says Issa. He points to MDS patients' slow response time—some show no change in cancer growth for months—and he notes that people can stay on the drugs a long time without serious toxicity. Jones says that because most normal cells aren't dividing and don't have messed-up methylation patterns, they should be little affected. The drugs "are targeting an abnormal chromatin state not present in normal cells," Jones says.

Whether more specific drugs will work better is debatable, says Baylin, who calls himself "agnostic" on the issue. The wide-ranging effects of the older drugs may actually make them more effective, he and Jones suggest.

Baylin says that how DNMT inhibitors stymie cancer should soon become clearer. His own lab hopes to publish a study showing that when very low doses of decitabine and azacitidine—similar to those given to MDS and lung cancer patients—are added to cultured leukemia and breast cancer cells, the cells don't die right away. Instead, the cells die days or weeks later, perhaps because they act more like normal cells and can't survive in the foreign environment in a tumor. Most intriguing, says Baylin, is that his experiments suggest that the drugs reprogramcancer stemlike cells, a much-debated type of tumor-initiating cell that resists traditional cancer drugs.

Nonetheless, he and Jones may still have a long way to go to convince colleagues that low doses of DNA-demethylating drugs can control cancer in people. "This is not going to be easy," Baylin says. "Maybe we'll continue to swim upriver."