Rewriting Cancer’s Script

GW researchers are discovering new ways that aggressive cancers hijack healthy cells to fuel their growth. Their findings could lead to new cancer treatments.

Story // Sarah C. P. Williams

Every day, about 70 women in the U.S. are diagnosed with ovarian cancer, and more than 40 die from the disease. Deep inside their ovaries and fallopian tubes, clusters of cells multiply uncontrollably, forming an aggressive mass that pushes into other organs.

In an ultra-low temperature freezer in the GW Cancer Center Biobank, Kate Chiappinelli and her colleagues have dozens of tubes of these tumor cells, donated by ovarian cancer patients who have undergone surgery at GW University Hospital. When she zooms into the cells’ inner workings, she often finds mistakes in their DNA, muddling the cells’ usual instructions for how to grow and reproduce.

For decades, researchers developing new ways to detect and treat cancers have focused their efforts on this erroneous DNA. About 10 percent of ovarian cancers, for instance, contain mutations in the BRCA genes—which can also lead to breast cancer—and drugs have been developed that specifically weaken tumors with these mutations.

But alongside mutated DNA sequences, Chiappinelli frequently finds something else awry with patients’ ovarian cancer cells: molecular switches that change how the cells read their DNA. Switches that should signal “off” are jammed in the “on” position and vice versa. A switch in the “off” position might make a cell ignore genetic instructions to create a particular protein. If this protein’s job is to patrol the cell looking for dangerous changes, shutting it off may help a tumor avoid detection. Another switch might force a growth gene to remain constantly on, like a stuck gas pedal making a tumor grow, grow, grow.

These kinds of molecular switches are partly controlled by what scientists call epigenetics—chemical changes that determine gene activity without requiring changes to the underlying DNA. If the long strands of DNA inside every cell are like a recipe book for life, epigenetics are the notes in the margins telling the cell to skip a step, double the ingredients, or repeat the steps.

Chiappinelli, an associate professor of microbiology, immunology, and tropical medicine, is among a growing number of researchers studying how modifications to genes—rather than permanent changes to the DNA itself—fuel the growth of cancers. Much of her work focuses on aggressive tumors, like most ovarian cancers, that defy standard treatments. She thinks that epigenetic drugs, which could tweak molecular switches to return cells to their healthy states, could work for these cancers.

“The epigenetic changes in cancer cells are a big part of what allows the cells to keep dividing and to evade the immune system and take over the body,” says Chiappinelli. “And so trying to reverse these changes with epigenetic drugs makes a lot of sense.”

Edward Seto, a professor of biochemistry and molecular medicine and the King Fahd Professor of Cancer Biology at GW, agrees. His work over the decades has shaped the field of epigenetics.

“Targeting these kinds of changes is still a novel and alternative way of treating cancer, and it has a huge amount of potential,” says Seto. “I think it could give a lot of cancer patients new hope.”

At GW, Chiappinelli and Seto are learning how to design drugs that change the epigenetics of cancer cells. Their work has the potential to upend what we know about how cancer develops and lead to new ways of stopping and reversing tumor growth.

Tightly coiled inside every human cell is more than six feet of DNA—a molecule that carries the genetic instructions for building and maintaining a living organism. But these long threads of DNA don’t float freely. They are wrapped around tiny balls called histones, like thread wrapped around spools.

It’s an efficient system but also a precarious one: When the packaging is mismanaged, the wrong genes can be activated or silenced. If the DNA material is packed too tight, the cell can’t read certain genes; if it’s too loose, harmful genes might get turned on.

More than two decades ago, Seto helped uncover part of why this happens.      

He was among the first to identify proteins called histone deacetylases (HDACs), which cause histones to grip the DNA wrapped around them more tightly. That work helped launch the modern field of epigenetics. HDACs offered a clear example of how molecules other than DNA itself could control gene activity: The more active HDACs are, the more tightly DNA is wound around histones and the less able cells are to read a stretch of DNA that turns on a particular gene.

“We now know that there are 18 different HDACs, and they’re used differently in different tissues and different stages of development,” explains Seto. “They are at the core of why different cells look so different from each other, and why normal and cancer are so different.”

In normal cells, for instance, HDACs make sure the genes associated with making tumor-promoting proteins are turned “off”—their DNA is tightly wound around histones—and the genes associated with making tumor-suppressing proteins are turned “on”—their DNA is loosely wound—ready to be read. But in cancer cells, that control system breaks down. HDACs become aberrantly activated, tightly gripping and hiding from view tumor-suppressing genes that should be on, like those that stop cells from growing too quickly and dividing too often, or those that alert the immune system to damage. Without these safeguards, cells begin to grow more aggressively than usual.

In the early 2000s, researchers showed that blocking HDACs in a variety of tumor cells could slow or stop cancer cell growth. Drugs that block HDACs, known as HDAC inhibitors, loosen the tightly packed DNA, letting cells regain access to genes that had been hidden from view.

“That really broke the whole field open,” says Seto.

Four HDAC inhibitors are now approved for treating certain blood cancers; these drugs are taken by patients with lymphomas and multiple myelomas that have not responded to other treatments. But Seto is working to expand their use to more challenging solid tumors like melanoma, prostate, breast, lung and colorectal cancer.

Supported by decades of federal funding, Seto has shown that blocking HDACs can kill cancer cells by loosening histones’ grip on DNA and turning back on vital programs that can sense danger and put the brakes on cell growth.

“Rather than shutting everything down, we’re trying to restore balance,” Seto says. “To take the system back to a state where it can regulate itself again.”

Importantly, HDAC blockers—like many existing chemotherapy drugs—work most strongly on quickly dividing cells, affecting how they package DNA around histones when they are newly copied. This means most cells in an adult human, which rarely divide, are unaffected by the drugs, and they can be discontinued when a cancer is in remission.

Already, Seto and collaborators at the University of Chicago have carried out early tests in isolated cells to show that a new HDAC inhibitor is especially potent against melanoma, lung, breast and liver cancers. Seto is working with the GW Technology Commercialization Office to patent the compound, referred to as TD047. This will let GW license the drug to pharmaceutical companies for continued research and clinical trials.

Histones are not the only way that healthy cells regulate which genes they use. Another form of epigenetic control is DNA methylation—tiny chemical tags (like molecular sticky notes) that attach directly to strands of DNA. When a cell’s DNA-reading machinery encounters a methyl tag as it scans a strand of DNA, the tag instructs it to skip ahead and ignore the gene or genes that come next. Cells contain millions of methyl tags, and they change over time.

In healthy cells, this process helps shape a cell’s identity by telling its machinery to ignore unneeded genes. Methylation might signal brain cells to skip liver genes, for instance. But in cancer, methylation can go haywire, silencing the same kinds of genes that histones might mistakenly shut off—those important for slowing unchecked growth and launching immune responses.

“Methylation is a red stoplight,” says Chiappinelli. “It tells the cell to stop expressing certain genes. In cancer, a lot of the stoplights are in the wrong places.”

Scientists don’t know exactly how or why those red lights turn on in tumor cells, but Chiappinelli has shown that switching them back to green can help treat cancer. Her lab works extensively with methylation blockers—chemicals that prevent duplicating cells from adding methyl tags to all new strands of DNA. Some have already been approved by the FDA to treat leukemia and bone marrow disorders.

Chiappinelli’s team uses these chemicals to treat the ovarian cancer tumor cells stored in their freezer, letting them study how and why the drugs work—information that may eventually help them design new, more targeted methylation blockers. They’ve already found one surprising reason the chemicals weaken cancer cells: They activate long-silenced stretches of DNA known as the “dark genome”—regions of genetic material that don’t code for known proteins and were once dismissed as junk.

“When scientists sequenced the whole human genome for the first time, they realized that only 2 to 3 percent of it actually contains the codes for making proteins,” explains Chiappinelli. “The rest of it we know much less about.”

Much of this dark genome remains constantly methylated and ignored by cells throughout the body. Some sections of it, Chiappinelli has discovered, are the remaining bits and pieces of ancient viruses that once infected humans many generations ago. Her methylation blockers can wake up this viral debris for the first time.

The result is a powerful immune response. Cells sound the alarm, calling on the immune system to destroy them—just as they would if they were infected with an active virus. In mouse models of ovarian cancer, Chiappinelli’s team has shown that this immune activation leads to smaller tumors and longer survival.

Now, her group is mapping exactly which other regions of the poorly understood “dark genome” are unveiled by the methylation blockers in ovarian cancer cells. The work is funded by the National Cancer Institute, the Department of Defense and the Ovarian Cancer Research Association.

“Unlike many other solid tumors, ovarian cancer has low response rates to immune therapies,” says Chiappinelli. “We think the dark genome has huge potential as a drug target. It’s an exciting area to be working in.”

At the same time, Loretta Wang, a senior neuroscience major who works in Chiappinelli’s lab, is testing the effect of methylation blockers on blood samples from some of the same ovarian cancer patients at GW University Hospital who donated tumor biopsies. She has shown that the drugs also act directly on the patient’s immune cells, turning on genes that make them more active than usual.

“We think we can make immune cells more effective with these drugs,” she says. “We increase the rate at which they recognize cancer and prolong their response.”

The findings mean that the methylation blockers have the potential to offer a three-punch against cancer: They remove problematic methyl tags and turn back on protective genes that check cancer cell growth; they activate parts of the dark genome in cancer cells that grab the attention of the immune system; and they make the immune system itself more responsive to cancer.

The broad effects on the immune system mean that the methylation blockers may pair well with existing immunotherapies—treatments that aim to turn a patient’s own immune system against a tumor.

“Immunotherapy has absolutely revolutionized cancer treatment, but it doesn’t work for all tumors,” says Chiappinelli. “I think the combination of epigenetic drugs with immunotherapy could change that.”

No two cancer patients are alike. Among the ovarian cancer patients treated at GW, some have genetic risk factors—like mothers or sisters with cancer—that might explain the origins of their cancer, but many don’t. They come from different backgrounds, have worked different jobs, experienced different stressors and lived in different places. Researchers have long struggled to explain how these characteristics impact who develops cancer and how aggressive their cancer is. Epigenetics might explain it.

Even when two tumors have the same genetic mutations, their methylation tags and histone behavior can vary. Trace Walker, a fifth-year graduate student in Chiappinelli’s lab, is studying what gives rise to those differences. He’s especially focused on the gene p53, which is mutated in a wide range of cancers, and is investigating whether those mutations influence patterns of DNA methylation.

Walker is supported by GW’s Cancer Biology T32 Training Program, a federally funded initiative co-led by Seto and Norman Lee, director of the Integrated Biomedical Sciences Ph.D. Program, that provides mentorship and additional coursework to early-career researchers. Through the program, Walker says he has gained a broader perspective on the social and environmental forces that shape cancer risk and outcomes.

“T32 training gives you this different perspective of understanding not only the molecular biology of cancer but how environmental and socioeconomic factors contribute,” he says.

These influences—such as stress, pollution and nutrition—can leave lasting chemical marks on DNA. Over time, these shifts in a person’s epigenome—the entire collection of epigenetic marks in their cells—could impact their cancer risk.

“We’re learning that the epigenome isn’t just static,” says Walker, who received a prestigious award from the National Cancer Institute to continue his research at GW as he transitions from graduate school to postdoctoral work. “It’s shaped by the environment, by stress and by the cancer’s own mutations. That gives us a chance to intervene.”

No one yet knows exactly how or when methylation tags and histone modifications change during a tumor’s life cycle. Do they arise early, helping the cancer slip past immune surveillance? Or do they come later, cementing a tumor’s resistance to treatment?

These are the questions driving Chiappinelli’s and Seto’s next steps. Both researchers see a future where epigenetic profiling helps guide clinical decisions, where doctors could run a test not just to see what mutations a tumor carries but also what gene programs have been turned on or off by changes to methylation or HDACs. And because epigenetic drugs don’t alter the genetic code itself, they offer a flexible, reversible way to reshape how DNA is read.

“It’s far easier to use drugs to change gene expression than to edit the DNA itself,” says Chiappinelli. “That gives us an incredible opportunity.”

For decades, Seto envisioned himself as a basic scientist driven by fundamental questions about how cells control their identities. Today, he is energized by the medical applications that are emerging as a result of his interrogations.

“Seeing that this work actually has the potential to benefit patients is incredibly rewarding,” he says.