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Promise and Progress - The Story of Epigenetics

Reprogramming Cancer Cells - The Story of Epigenetics
Issue No. 1

The Story of Epigenetics

Date: July 16, 2014

steve baylin
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Stephen Baylin

What Is Epigenetics?

Literally translated, epigenetics means around genetics.  It refers to natural control mechanisms that influence gene expression.  Their role is often compared computer software.  Think of DNA, and the genes we are born with, as the human hard drive.  Everything a cell does is controlled by this hard drive.  But, a hard drive cannot work without software.  Epigenetics is the software package.  Researchers believe that every cancer may have 50 to several hundred genes that have working “hard drives,” but their epigenetic “software” is causing them to act in a way that can lead to cancer development.

In the world of cancer, epigenetics is considered an emerging field, but its study is not new.  Investigators Andrew Feinberg and Bert Vogelstein first reported epigenetic changes in human cancer in 1983. Renowned veteran cancer scientists like Donald Coffey, Stephen Baylin, Peter Jones, Jim Herman, William Nelson, and Dr. Feinberg have been studying this biological process for decades, but it did not gain widespread acceptance until the early 2000s. Dr. Nelson, Kimmel Cancer Center Director, recalls in the 1990s when it was difficult to get a scientific paper on the topic published.   Technologies that allowed science to analyze DNA at the molecular level and the tenacity of a relatively small group of scientists proved its validity.  The long concealed mysteries of what some have referred to as the “ghost in our genes,” referring to epigenetic mechanisms’ ability to alter gene expression without leaving a permanent mark on DNA, are beginning to be uncovered. Now, what was once an outcast in cancer research is being heralded as one of the most promising fields of study in cancer medicine.

With a group of epigenetic scientists, who Dr. Nelson characterizes as “second to none,” the Kimmel Cancer Center has become a hub for epigenetic discovery and clinical translation.

Converting Doubters to Believers

If history was to name a founder of epigenetics, C.H. Waddington would likely get that designation. In the early 1940s, Dr. Waddington, an embryologist, put forth a radical idea for its era. With the genetic knowledge we have today, it is difficult to imagine, but at the time, most embryologists did not believe genes were important in human development. Rather, they contended that they played a minor role, controlling inconsequential details like eye color.  Dr. Waddington disagreed and introduced the concept of genes, and their regulation via an epigenetic landscape, as controlling cell differentiation and cell fate.  Of course, we now know that our DNA-- the genes we are born with--control every physical element of who we are.  Not only do they control eye color; they control eye formation.  The second phase of that development—the primitive mechanisms that turn genes on and off and, for example, let an eye cell know it’s an eye cell, and a brain cell know it’s a brain cell, when to start growing, and when to stop growing—that epigenetic landscape that Dr. Waddington first referred to more than a half century ago—is just now beginning to be understood, particularly how it applies to cancer.

Findings by Dr. Feinberg, now director of the Johns Hopkins Center for Epigenetics, and Kimmel Cancer Center epigenetics expert Stephen Baylin were trailblazers in this area of science, helping to garner attention for the field.

Dr. Feinberg described a global demethylation of the cancer genome. To try to better understand how epigenetics contributed to disease, he dug deeper into the role of normal epigenetic controls in cell behavior. In normal human development, when the sperm and egg come together and form that first cell, how that one cell divides and determines what its fate will be to eventually form a complete human body, Dr. Feinberg showed, is controlled through epigenetic mechanisms. Gene expression is what makes a cell behave the way it behaves, but how a cell figures out what proteins to express is controlled through epigenetics.

Dr. Feinberg suspected that this process was somehow getting hijacked in cancer. Corruption of the mechanisms that makes an undifferentiated cell know to become a liver cell could be at the root of the transformation of that same liver cell into a cancer cell. “In cancer, cells are confused about their own identity,” says Dr. Feinberg.  “I think epigenetic instability may be a general, universal feature of solid tumors—not necessarily genes getting turned off or genes getting turned on, but genes getting randomized until a preference for the cancer cell results.”

Dr. Baylin’s focus was on the hyper- or over- methylation of cancer genes, mainly tumor suppressor genes.  The process turned off gene expression, and what’s more it provided a therapeutic target. Drugs that blocked methylation of the gene could, in principle, turn the gene back on.  This work began to inspire the research of young investigators entering the cancer field.

Kimmel Cancer Center Director William Nelson was one of them.  He did not set out to become an epigenetics researcher.  In the early 1990s, he was beginning his career as a prostate cancer clinician and scientist when his research on cancer drug resistance led him to what remains today as one of the most classic examples of gene silencing through hypermethylation driving the development of cancer.

Drs. Baylin and Herman had already introduced a scenario in which tumor suppressor genes could be rendered inactive through the epigenetic process of hypermethylation, but they had not yet uncovered a good real life example of it they could point to.  When Dr. Nelson’s research led him to a gene called GSTP1, which he found was recognizably and verifiably hypermethylated in prostate cancer, still, the scientific world, except for a few, remained unconvinced of this purported epigenetic involvement in cancer.  Dr. Nelson struggled to get his research published. 

In some ways, Dr. Nelson believes it may have been the early detractors that helped propel the field forward.  “It created a higher level of rigor among those of us who believed,” says Dr. Nelson.  They set out to prove what they were convinced—what their research was showing them—that epigenetics played a key role in cancer initiation and progression.

Dr. Nita Ahuja, a Kimmel Cancer Center surgeon and clinician-scientist was among the small group of investigators involved in epigenetics research. “I was not a basic scientist, but I understood enough to know that all of the things we were seeing in medicine couldn’t just be bad genes,” she says.

While Drs. Nelson, Ahuja, and others were having difficulty getting their research published and felt like outcasts in the larger world of academic medicine, it was not that way at Johns Hopkins.  “The unique part of Johns Hopkins and the Kimmel Cancer Center is the collaborative nature.  It is the culture here,” says Dr. Ahuja.  “The exploration of novel ideas is celebrated here, and we are able to develop cooperative relationships spanning many departments and specialties.  This doesn’t exist at other places.  But, it’s what I love about Johns Hopkins.  There are no silos or territories.  I am a cancer surgeon who has an appointment in the Department of Surgery and laboratory space in the Kimmel Cancer Center, and directors of both programs support this.  Money can’t buy that. It has to exist in the fabric of the institution.”

It is this collegiality that maintained the momentum of epigenetics research at the Kimmel Cancer Center despite an inhospitable environment among the greater cancer research community.   Drs. Baylin and Herman built a tool that allowed scientists to look laterally at many genes across many cancers and establish a pattern of silencing through gene methylation. These hypermethylated genes were the subjects of promising innovation in the form of biomarker tests that could tease out aggressive cancers from more indolent forms and provide new targets for novel treatment strategies.  The origination of personalized cancer medicine was at hand.

Dr. Nelson’s colleagues describe him as a problem solver with an uncanny ability to see complex problems in a straightforward and logical way, and he saw an unmet medical need for men at risk of prostate cancer in his epigenetic discovery. In a disease where overtreatment is a major problem, Dr. Nelson’s discovery was used to create the first, noninvasive, epigenetic-based test for the disease.  The GSTP1 gene is only hypermethylated in cancer.  The epigenetic marker is not found in any normal cell, says Dr. Nelson.  As a result, it is being translated into a simple urine test.  It is most useful for men who are suspected to have prostate cancer because of an abnormal exam or rising PSA (prostate specific antigen) levels, despite a negative biopsy.  Prostate biopsies miss about 25 percent of cancers, and the test helps address this uncertainty.  If the urine test is positive, it predicts the presence of prostate cancer with almost 100 percent certainty.  If results are negative, it confirms the biopsy results with less than a five percent error rate. Dr. Nelson is now collaborating with epigenetics expert Vasan Yegnasubramanian to further refine the technology for use as a general prostate cancer screening test and as a tool to identify men who may have lower risk forms of the disease and could safely forgo treatment.  Conversely, such a test, given the right epigenetic markers, could distinguish men who have more aggressive forms of the cancer who would benefit from treatment.

The promising work of this group of researchers was at last gaining acceptance for the field of epigenetics. When Dr. Baylin first began his research some three decades earlier, the term epigenetics did not exist.  Now, he is viewed as the leader in the field, and his research in epigenetics is the most frequently cited in the established and rapidly growing specialty.  The pioneering work of Dr. Baylin and team in this emerging field of epigenetics, coupled with breakthroughs in cancer genetics made by Ludwig Center scientists, resulted in the Kimmel Cancer Center being dubbed in media reports a “cancer research powerhouse.”

But accolades and laboratory success have never been what the Kimmel Cancer Center is about.  Translational science—the ability to transfer laboratory knowledge to the benefit of patients—was the goal. The most exciting aspect for Dr. Baylin was that his life’s work was about to become a treatment for cancer.  The perseverance and innovative thinking by Dr. Baylin and others had laid the groundwork for an Epigenetic Dream Team.

A Dream Team

Few would dispute the amount of epigenetic research talent amassed at the Kimmel Cancer Center. Laboratory findings in leukemia and lung cancer paved the way for clinical trials of a drug that appeared to have the ability to fix some of the epigenetic initiated changes to genetic code that helped cancers grow and thrive. 

The world was beginning to take notice, and Dr. Baylin’s laboratory model was becoming a clinical model.  Crucial to these advances was a type of drug called a demethylating agent.  Too much methylation in the active regions of tumor suppressor genes was found to shut the genes down, giving advantage to one of the cancer cell’s iconic behaviors–uncontrolled growth. Blocking the methylation of the gene turned it back on.

In 1980, another leading epigenetics expert, Peter Jones, a University of Southern California researcher, provided some of the first evidence that demethylating agents might have unique and unexpected anticancer properties. He was studying the drug 5-azacytidine as a potential chemotherapy agent, when he observed that in low doses the drug didn’t brutally destroy cancer cells as most chemotherapy drugs did, but rather gently nudged the cell into behaving differently.

Years later, Dr. Baylin and team decided to take another look at the drug, which had largely been abandoned because of its toxicity.  Laboratory studies in lung cancer and leukemia led to a clinical trial for patients with a pre-leukemia condition called myelodysplastic syndrome (MDS).  It worked so well, with some patients disease-free for ten years and counting, that the drug received FDA approval for treatment of MDS.  Dr. Baylin wondered if the drug might also work against other cancers.

Then in 2008, the Entertainment Industry Foundation and Major League Baseball formed Stand Up To Cancer (SU2C) to mobilize the public to donate money for cancer research and to motivate the scientific community to collaborate on promising areas of research that could quickly be moved to clinical trials.  “Dream Teams” made up of clinicians and scientists from around the country—the best in their fields were formed—selected after rigorous review by another panel of esteemed cancer experts and directed to take on specific cancer research projects. When the epigenetics dream team was announced, Drs. Baylin and Jones were the natural choices to lead it.

Dr. Baylin’s research of the role of DNA methylation in cancer had led him to a molecular co-conspirator.  He observed that it wasn’t just DNA methylation that affected gene expression but also how the DNA was packaged in the cell.  If the DNA contained within one cell was extracted and stretched out, end-to-end it would extend six feet.  Yet all of that molecular material is compacted and packed inside the nucleus of a human cell. The nucleus is a structure so tiny that more than 50,000 of them can fit on the head of a pin. 

Chromatin, a complex combination of proteins, mainly histones, is responsible for compressing the DNA to fit inside a cell.  This packaging also plays a role in gene expression and the copying of DNA as cells divide.  A loose chromatin results in normal gene expression, but add methylation to the mix, and histones hold the DNA together tightly and interfere with the gene expression. This tightened chromatin, Dr. Baylin and team found, can keep genes, including tumor suppressor genes, in a constant state of non-expression.   It can cause cancer cells to behave in a primitive, embryonic-like manner.  Unlike normal embryonic cells, which receive and respond to signals that tell them to stop making new cells, epigenetically altered cancer cells seem to maintain their ability to replicate, renew and divide.

Scientists do not know what prompts the cancer-promoting changes in chromatin structure.  They suspect it may be a repair mechanism engaged in response to cell injury, such as chronic inflammation.  While the cause is uncertain, Dr. Baylin’s research has identified a way that may fix it.  In the laboratory, when he and his team combined a demethylating drug with a histone-blocking drug  (HDAC inhibitor) in human cancer cell lines, the chromatin structure loosened and some gene expression was restored.  This discovery became the focus of the first SU2C Epigenetic Dream Team patient study.

Few scientists have devoted as much time to epigenetic research as Dr. Baylin.  Mild mannered and soft-spoken, he smiles and nods his head in an expression of tempered optimism and wonder.  Belying  his calm exterior is a feeling of intensity and resolve. These trials are the culmination of his life’s work, but that’s not why he so desperately wants what he and his team have found in the laboratory to work in patients. “It’s not about me.  It’s all about the patients,” he says.  “It is a luxury and privilege to get to a point where your research has resulted in something that could help patients.”

It may seem reasonable to suppose that a laboratory researcher would become disconnected from the patient.  After all, the scientist’s day-to-day relationship is with the cancer cell, the mouse model, the experiment.  It is not with the patient.  We hear of academic institutions where science is performed for the sake of science and success is measured by the scope and size of the project. While all learning has value, at the Kimmel Cancer Center, where scientists work side by side with clinicians and many perform both research and patient care, people like Dr. Baylin measure success by the contributions their science makes to advancing patient care.  It is not always a new treatment or grand discovery, but all work is aimed at figuring out, discovery by discovery, how the cancer cell works and how to break its grip.  Far from disconnected from the patient, laboratory research at the Kimmel Cancer Center is inextricably aligned with the patient.

For Dr. Baylin, the roots run deep.  He is a third generation physician. His father was a radiologist at Duke University, and his grandfather was a general practitioner in Baltimore.  He chose his own path in medicine, but his family’s inspiration is evident. Old family photos are found throughout his office.  A microscope and a cherished old, weathered chair that belonged to his father also are there.

A Tale of Three Responses

Dr. Baylin believed that the patients, not the scientists would tell the story of the study of epigenetics.  He was correct, and with twists befitting a mystery novel, the story was about to get very interesting.

The first clinical study of the combined demethylating agent and histone-blocking HDAC inhibitors was in patients with advanced lung, breast, and colon cancers.  The drugs were not given at the highest dose that patients could tolerate, as is usually the case in early studies of anticancer drugs.  Rather, low doses were given.  The goal was to kill the cancer cells by reprogramming their DNA, instead of obliterating them like most chemotherapy agents do.  In essence, the researchers were using the drugs to convert cancer cells back to normal cells—to change their destiny as Dr. Jones had done so many years ago in his laboratory studies of 5-azacytidine.  At high doses, the drug killed cancer cells, but at lower doses over time, it reprogramed cancer cells to behave like normal cells, a much less toxic and more permanent cancer fix. It was a radical departure from the standard approach of blasting cancer cells with as much poison as possible, but there was significant laboratory evidence to show that it could work.

It did, and remarkably, but only in a few lung cancer patients.  The responses, while small in number, were unprecedented.  Patients with resistant, lethal lung cancer that had spread to other organs and was resistant to other treatments were seeing their tumors melt away.   In a few other patients, tumors stopped growing.  The cancers didn’t go away, but they seemed to be dormant. Grow and spread is what cancer cells do best, so this response, though limited to just a handful of patients, made epigenetics fans and detractors alike take notice.

Still, most patients treated did not respond, and responses in breast cancer and colon cancer patients were not nearly as dramatic as those seen in the small group of lung cancer patients.  This did not surprise or deter Dr. Baylin and team.  Earlier work by his epigenetics colleagues James Herman and Malcolm Brock showed that specific epigenetic biomarkers provided a signature that could differentiate patients who were likely to respond from those who would not.   This trial was open to all patients with resistant cancers, and with no analysis for the epigenetic signature of their tumors, the expectation was that a small subset of patients would see results.  The analysis would come later with Dr. Baylin, basic scientist Cynthia Zahnow and cancer surgeon and translational scientist Nita Ahuja taking cells back to the laboratory for gene expression analyses.

What happened next, however, was not expected.  Because of funding provided through SU2C, Dr. Baylin and team had the opportunity to do something they typically never would get the chance to do. That was to follow up on patients who were taken off of the trial because their cancers continued to grow despite treatment with the experimental epigenetic therapy.  The team went back and reviewed the records of these patients. They expected to find that most of them had passed away.  These were patients with end-stage cancers that had spread and had not responded to three different attempts at chemotherapy.  When they learned that many of the lung cancer patients were still alive because their cancers had suddenly begun to respond to a wide variety of anticancer drugs, they were shocked.  Patients who seemed to progress while they were on the experimental therapy, some who had only received two or three treatments, were alive and doing well.  Cancers that had continued to grow and spread despite every effort were suddenly transformed.  Such responses were virtually unheard of, and the research team was eager to figure it out.

They pored over every scan, piece of clinical paperwork, and biopsy report available.  “There could only be two explanations,” says Dr. Baylin.  “Either the epigenetic therapy sensitized the cancers to subsequent treatment with standard drugs, or their improvement was a direct response to the epigenetic therapy.” The team needed to complete further studies in the laboratory to solve the mystery.

These new epigenetic targeted therapies do not work like the old cell-killing cytotoxic chemotherapies that do not discriminate between normal cells and cancer cells.  They specifically seek out and reprogram the epigenetic alterations that are allowing the cancer cell to survive and grow.  Dr. Baylin says the epigenetic therapies work slowly over time as they make repairs and return genes to normal function.  But Drs. Baylin, Herman, Brock, Ahuja and Zahnow, had another hunch.  They suspected that the epigenetic drugs had a priming affect on the tumor.  Altering the cancer cell’s gene expression with the demethylating agent and HDAC inhibitor had made the formerly resistant cells now vulnerable to treatment with anticancer drugs. 

As they began to study the cell lines in the laboratory, they found that the epigenetic drugs had the capability to impact almost every type of cell mechanism, including cell division, cell repair, and cell cycle and death.  Of particular interest to the researchers was the treatment’s affect on genes related to immune response.

Immune cells are on patrol at all times in the human body differentiating between foreign invaders and normal cells. Cancer cells are derived from normal cells, so they can fly beneath the radar of the immune system.  However, as the science of cancer immunology has advanced, researchers are finding that there is more to the cancer cell’s ability to evade the immune system than its similarities to normal cells.  Cancer cells use epigenetic controls to corrupt immune responses to cancer cells.  By hijacking the mechanisms that allow the immune system to differentiate an invading virus cell from a body’s own cells, it causes the immune system to tolerate cancer. 

In their laboratory analyses of gene expression in cell lines derived from patients in the epigenetic treatment studies, one immune target was jumped out at them.  This target was a gene called PD-L1.

Cancer Immunity

Epigenetic treatment turns on a number of silenced genes.  Some of them encode molecules in the immune system that turn on immune responses and some that turn them off and lead to immune evasion. Immune inhibiting genes turned on by epigenetic therapy include PD-1, part of the intricate checkpoint system hardwired into the immune system, and its partner PD-L1. Normal human cells need the ability to communicate with immune cells that they are the good guys and should be left alone. Unfortunately, cancer cells exploit the same process to avoid an immune attack.

Drs. Baylin and Zahnow sought out the help of one of the world’s leading cancer immunology experts and their Kimmel Cancer Center colleague Drew Pardoll.  In some patients in the study, the PD-L1 gene was already active, and laboratory studies indicated that its expression by lung cancer cells might be enhanced by epigenetic therapy. Dr. Pardoll believed that using a drug to block PD-L1 or PD-1 in conjunction with epigenetic therapy could alter the balance of immune effects of the treatment toward an activated immune response right within the tumor. It was worth a try.

For that, Dr. Pardoll recruited the help of his wife and cancer immunology colleague at the Kimmel Cancer Center, Suzanne Topalian, and lung cancer expert Julie Brahmer.  It has been well established that cancer has an immune evasion signal.  To survive, cancer cells need to at least partially adapt to their environment.  They send out a “don’t look at me” signal to immune cells.  Treated with epigenetic drugs however, the ability to evade the immune system is broken and cancer cells send new signals—on one hand, they beckon the immune cells to come and get them, and on the other,  they shield against immune attack by expressing PD-L1. 

Drs. Baylin, Zahnow, Ahuja, and colleague John Wrangle went back to the laboratory to decipher the immune evasion signature for lung, breast, colon, and ovarian cancers.  To do this they looked at all of the genes that get turned on in cancer cells with demethylating drugs.  Lots of genes, they found, get reactivated, but about 20 percent of them are related to immune regulation.  “This is a much bigger component then we thought,” says Dr. Ahuja.  “A significant part of what the epigenome does is regulate the immune system.” 

Their research revealed a set of genes that are epigenetically programmed to evade detection by the immune system.  Using a drug to reverse this programming may force the cancer cells out of hiding and make them more vulnerable to treatment, or even better, allow the immune system to see the cancer and kill it.  “Imagine if we could get the immune system itself to fight the tumors and keep the cancer in check.  Then we might have a permanent cure,” says Dr. Zahnow.

They are now working to verify their laboratory findings by studying tumor samples from patients in the most recent SU2C lung cancer patient study who are receiving the epigenetic combined therapy of a demethylating agent, histone-blocking HDAC inhibitor and anti-PD-1 treatment.  Dr. Ahuja explains the imagery on the gene expression analysis array. Immune genes that are turned on appear red and those that are suppressed are labeled green.  If the epigenetic therapy is working, they should start to turn “green” tumors into “red” tumors.  “The promise is immense,” says Dr. Baylin.  “It’s a beautiful concept, and it represents translational science at its best.  We hope it is as beautiful in patients.  That’s what this trial will show us.”

At the same time, researchers like pediatric oncologist and cancer immunology expert Christopher Gamper are interested in deciphering what epigenetic therapy does to normal immune cells.  His hope is that these drugs may be used to augment the effectiveness of other immune treatments, such as cancer vaccines.  Rather than reprogramming cancer cells to make them more susceptible to immune attack, Dr. Gamper would like to reprogram immune soldiers called T-cells that patrol the body looking for danger to make them better at killing cancer cells.  Like PD-L1, the researchers are finding that other immune genes also are controlled epigenetically.

Epigenetics Frenzy

These early but promising results have transformed epigenetics into a booming industry. Understandably, clinicians wanted to get these promising treatments to their patients.  Drug companies want to see if their iteration of epigenetic agents might work even better, and laboratory scientists want to decipher exactly how the drugs are working to combat cancer.  Epigenetic therapy had now taken center stage in the cancer world.  For a disease in which time is the enemy, patience is a justifiably a rare commodity.

Everyone involved had the same mission—to bring better treatments to cancer patients. Some may argue that the drugs companies were in it to make money, but at the end of the day, the only way to make money is to develop a drug that works.  There are no bad guys. In fact, the trial would become a model for modern science with collaborative participation from science and medicine, industry, and philanthropy.

To confirm the findings from the first trial, Dr. Baylin knew he must use the same drugs in the subsequent trial.  If the team switched the drugs around now, and the results were different, they would never know if variations in outcomes were related to the drugs or epigenetic mechanisms.  Three different competing drug companies, all with their own versions of the each type of drug and all eager to get them into patient studies, agreed to work together to maintain the integrity of the trial.  SU2C, which had fulfilled its grant commitment to the epigenetics Dream Team, was also eager to see this trial through.  After all, the work had achieved SU2C’s goal to rapidly bring new cancer therapies to patients through science and collaboration. Aided by a generous donation from Hollywood agent Jim Toth, whose father died of lung cancer, SU2C extended funding, and study of the three-drug epigenetic therapy is ongoing in patients.

For Dr. Baylin, who is in the front riding the wave, the challenge was managing expectations and waiting for science to reveal the answers.

There are two components to the trial.  One aimed at verifying the immune responses and the other at further testing the priming effect—the ability of epigenetic therapy to sensitize cancers to subsequent chemotherapy.  At the same time, a number of trials were being launched at the Kimmel Cancer Center and elsewhere studying a wide variety of epigenetic drug combinations and single agents. Whatever drug or drugs clinical trialists could get their hands on were being studied.

Drs. Zahnow and Ahuja were gathering the evidence and the data.  Collaborating with other Kimmel Cancer Center experts, they had 70 cell lines from breast, colon, ovary, and lung cancers as well as patient biopsies that they were comparing to the cell lines. Gene expression data, methylation data, proteomics data—anything that could be measured in a cancer cell was being analyzed.

“There was still so much we needed to learn,” says Dr. Zahnow. “What is the best way to give the drugs? Should they be given simultaneously or consecutively?  What are all of the targets the drugs hit?”  There is some evidence that demethylating agents have a stronger effect on the epithelial cells where cancers most often originate.  The histone blocking, HDAC inhibitors appear to influence the immune cells and microenvironment. “We need to figure all of this out so we can better inform drug development and figure out the best way to administer them,” says Dr. Zahnow.

Then there was the aspect of personalized therapy.  “If everyone’s cancer is different, and each patient has different genes silenced in his or her cancer, then the genes turned back on with epigenetic therapy will be different for each patient,” explains Dr. Zahnow.  Therefore, the way a demethylating agent, HDAC inhibitor, or immune blockade acts in one patient may likely be different than the way it acts in another patient. 

In the SU2C trials, the three-drug study that includes the anti-PD-1 drug has enrolled the most patients.  The priming trial is enrolling patients more slowly, as many are reluctant to gamble with chemotherapy again.  They’ve had chemotherapy, and it didn’t work.  Their cancers progressed.  While there is  evidence to show that the epigenetic drugs will make some patients’ cancers more sensitive to chemotherapy, most patients want the immune drug.  “The last thing cancer patients want to hear is that they need more chemotherapy,” says Dr. Zahnow.  “If we can get the immune system to function in a way that we could keep a cancer at bay forever, that’s huge.  Then we may have a permanent cure,” she says.  “Chemotherapy can’t do that.  There are always some tumor cells left behind, and they will grow the tumor back.”

Doctor as Patient

Dr. Zahnow recalls how happy she was when Dr. Baylin invited her to join the SU2C Epigenetics Dream Team.  “Dream Team” had more than one meaning to Dr. Zahnow.  For her, it truly felt like a dream come true. “Every basic scientist’s goal is to make a difference, to learn something about cancer cells that will help improve care for patients,” she says.  Her work with Dr. Baylin analyzing the affects of demethylating agents and HDAC inhibitors on cancer cells was being used by clinicians and drug companies to develop the next set of clinical studies.  “I could have almost stopped my career at that point, and said, ‘Okay, I’ve done more than I ever thought I could have done.  Maybe I’ve made a difference for patients,’” she says.

She was in her office discussing with Dr. Baylin her plans to test the epigenetic drugs in all of the cancer cell lines she had amassed.  The most promising responses had been in lung cancer, but what if they could learn more from studying the drugs in breast, colon, ovarian, pancreatic, and other cancers?  Dr. Baylin liked the approach, but a telephone call interrupted their meeting.

Dr. Baylin returned to his office while Dr. Zahnow took the call, and a few minutes later, noticeably shaken, she stood in his doorway. “That was my doctor,” she told him. “He said I have breast cancer.”  The full reality of the words she had just uttered had not fully sunk in. The menacing, despicable cells she had spent her entire professional life battling were now battling her.  In her mind, the first fight had already begun. This was personal now, and she was not about to let cancer rob her of her chance to be a part of the epigenetics Dream Team.

“I have cancer.  I will have to take some time off for surgery and chemo, but I don’t want to leave my work and the SU2C team.”   You are going to replace me.” The words came out frantically with Dr. Zahnow reeling as her brain tried to process her enthusiasm for working on the dream team against the horror of learning, only moments ago, she had cancer. 

Perspective is an interesting dynamic.  We consider different situations, and we think we have an idea of how we would react; how we would feel. It’s one thing to imagine.  It’s quite another to have a firsthand experience.  The 50-year-old scientist was well acquainted with the breast cancer cell.  It had been the primary focus of her work for nearly two decades.  Now, however, her reality; her view of cancer was taking on a different dimension.

She continued her work on the Dream Team.  There were days when she traded her lab coat for an IV in the chemotherapy infusion clinic as she received treatment for her breast cancer. “I wanted to keep working,” she says. One would think her work would be a constant, tortuous reminder of her own illness, but Dr. Zahnow said when she was in her laboratory, she felt a sense of freedom from her own illness. “When I was running my lab, I wouldn’t think about my cancer,” she recalls.

One of the less glamorous aspects of the basic scientist’s job is obtaining tumor samples to study in the laboratory.  In some ways, they are like the puppy under the dinner table gathering scraps.  As procedures are being done in the care of patients, scientists work with clinicians and pathologists to collect fluids and tissue samples to use in their research. These patient samples are critical to research as they give scientists insights into the inner workings of the cancer cell.  In this molecular era of scientific research, even a drop of fluid can be used to extract cancer cells.

Dr. Zahnow was working with breast cancer clinicians Vered Stearns and Roisin Connolly to collect fluid drained from the lungs of patients with advanced breast cancer.  When breast cancer spreads to the lungs, many patients develop a condition called pleural effusion in which fluid accumulates around lungs.  Doctors must drain the fluid so that it doesn’t impair patients’ breathing. Dr. Zahnow could pull breast cancer cells from the fluids to use in her research.   

“I was so passionate about the work.  I wanted to observe and see how the procedure was done,” says Dr. Zahnow. One of the first patients who volunteered  her cells for research  looked like Dr. Zahnow, middle aged with short, blonde hair.  For Dr. Zahnow, it was like looking in a mirror, or worse yet possibly an undesired glimpse into her future. Dr. Zahnow was anything but naïve when it came to her cancer.  How could she be?  She knew far too much about cancer to have even the slightest protection from the reality of her disease. “Although I hope that I’ve been cured, breast cancer is one of those cancers that often comes back later,” she says.  “Breast cancer patients learn to live with their cancers but always worry about recurrence.”

These patients had recurrent cancer that had now spread beyond the breast to their lungs. There were few treatments that could help these women.  The epigenetic treatments the team was researching held promise.  She saw the faces behind the cells she was taking back to the laboratory. “If I saw a response in their cells in the laboratory, I would get really excited because I would hope they would do well on the trial,” she says.  “The truth is, often it doesn’t work as well in the patient as it did in the laboratory.” That’s why clinical studies are so painstakingly structured. They are designed to eliminate any bias, randomness, or even wishful thinking to reveal the scientific truth. Does this drug have a safe therapeutic effect on cancer and extend the life of patients?

Dr. Zahnow thought of all of the breast cancer cells she had killed in the laboratory with epigenetic drugs.  She thought of friends who were dying of breast cancer. She was more determined than ever to decipher how these drugs worked against cancer and how she and her team could get them to work even better, but she felt she could no longer collect the samples herself.  She had a new perspective.  “I know what these women are feeling,” says Dr. Zahnow. She understood what it was to wonder, ‘Will I grow old?  Will I have the privilege of living long enough to see my grandchildren?’” She wanted so desperately to help these women.  The research and clinical trials cannot move fast enough for her. 

It is one of the many reasons she enjoys working with Dr. Baylin.  “Steve [Baylin] is fiercely passionate about this work and has an amazing urgency about this,” she says.  “I do too, but now even more. We can’t waste time. Absolutely, we have to do things right, and we have to keep patient safety in mind.  But at the same time we have to push forward and find better treatments for patients because time is not on their side.  Too many are dying, and the pace is too slow for them.

At the Intersection of Genetics and Epigenetics

Cancer genetic and epigenetic research has advanced dramatically in the last decade, and with the leading experts in both disciplines at the Kimmel Cancer Center, investigators have uncovered a convergence of the two fields.  Many of the genes mutated in cancer are genes that regulate epigenetic processes.  This provides a link between genetic mutations and epigenetic abnormalities.  Like a volume control, this process can amplify or dampen a series of genes, changing the global expression pattern and dramatically altering the behavior of cells.

“It’s inter-related,” says Dr. Yegnasubramanian, who runs the Kimmel Cancer Center Next Generation Gene Sequencing laboratory. “Many epigenetic problems may have their basis in genetic abnormalities. The genes that get mutated in cancer are often genes that control DNA packaging.”

A prime example of a genetic mutation having epigenetic consequences is the brain cancer gene called IDH1, identified by Ludwig Center cancer genetics researcher Nickolas Papdapolous and team in 2008. IDH1 produces an enzyme that regulates cell metabolism, but a mutation in the gene results in increased production of a metabolite that can affect DNA methylation. [deletion] IDH1 mutations are very simple genetic changes, but they cause a cascading effect of alterations to the epigenetic landscape that ultimately become a major driving force behind the cancer.  Investigators believe there are many more examples of the genetic/epigenetic collaboration in cancer.  Although it is impossible to fix a mutated gene, the epigenetic changes can be targeted and disrupted with drugs. 

Pediatric oncologist Patrick Brown has found a pattern of genetic/epigenetic collusion in infant leukemia, one of the most treatment-resistant forms of leukemia and one that attacks the youngest of victims.  This cancer of blood and bone marrow cells occurs in babies during the first year of life and is set in motion by a rearrangement in a gene called MLL.  The gene gets cut and fused to one of about 70 other partner genes. Dr. Brown has found that all of these partner genes have a common relationship with another gene called DOT1L, an epigenetic gene that modifies DNA packaging in the cell. This morphed fusion gene, begins sending epigenetic miscommunications to all of the normal genes in the MLL pathway and causes activation of genes that should be turned off and silences genes that should be turned on. Dr. Brown is beginning a patient study of epigenetic therapy using demethylating and chromatin-modifying drugs to shut down the effects of the fusion gene.  Another approach, he says, may be to find a drug that inhibits or deactivates DOT1L, the gene MLL uses to modify the epigenome.

Dr. Yegnasubramanian has uncovered a similar scenario in prostate cancer.  In a study of prostate cancers from men who died of the disease, he found increased methylation in genes not methylated in normal tissue.  In each patient studied, this pattern of hypermethylation was consistently maintained across all of the metastatic prostate tumors and occurred near genes in cancer-related pathways that control development and differentiation.  “We need to do more research, but it looks like the areas that have increased methylation are being selected for by the cancer cell to keep its advantage,” says Dr. Yegnasubramanian.   “We know these were resistant cancers because we obtained the tumor samples from men who died of prostate cancer.  Perhaps if these methylation alterations could have been reversed, the cancer cells might become sensitized to treatments.”

The opportunity to offset the collateral damage to epigenetic functions caused by broken genes is one of the newest and most promising iterations of epigenetic research and one that is rapidly revealing new targets for treatment. Driving this progress is new technology that allows investigators to catalog epigenetic changes and align them back to the genome.  “There are striking differences in how DNA is organized in the cancer cell and how it is organized in the normal cell,” says Dr. Yegnasubramanian. “Now we have the technology to go in and look at this at the molecular level.” 

This ability has become critically important with growing evidence that some mutated tumor suppressor genes establish cancers through many subsequent epigenetic alterations. He says, “Although the mutation is the initiating event, it is the epigenetic alterations that are involved in driving the cancer, and unlike mutations, the epigenetic changes can be targeted and halted with drugs.”

The Future of Epigenetics

In this era of personalized cancer medicine, many experts believe that epigenetics could be a master control of sorts, so intrinsic to the initiation and spread of cancer that it could potentially provide opportunities to globally reset cancer cells. The panel of epigenetic alterations that drive a particular cancer may vary, but if they can be identified in individual patients, then maybe we have found the Achilles’s heel of cancer.

The word “cure” is used frequently in the context of cancer. But, how do we define cure?  Some might say that it is not obtained until every cancer cell is obliterated. Others wonder if rendering cancers harmless is just as good.   They envision using these mechanisms to keep cancers, of all types, in a chronic or dormant phase, by reprogramming cancer cells to be normal or by tweaking immune cells to engage and kill them.  Kimmel Cancer Center investigators are changing the paradigm, providing a new way of thinking about cancer.

The floodgates have opened. Decades of science have fueled the success of epigenetic clinical studies. No one anticipated the interplay between genetics and epigenetics, but it was revealed because of Kimmel Cancer Center excellence in both fields.  With this preponderance of expertise here, our center is uniquely positioned to set the course for continuing advances.

Still, most experts agree that science has only scraped the surface when it comes to epigenetics. The understanding of the full power of epigenetic mechanisms to read, write, erase, and move genetic code is just beginning to be understood, but already we have promising treatments.  “If we looked at all of the genes silenced epigenetically in cancer and could turn them all back on, no cancer cell could withstand it,” says Dr. Nelson.  “We can do that in the laboratory, and now we are learning how to do it safely and effectively in humans.  We have tremendous opportunity and unparalleled ingenuity.  All we need to do is connect the dots.”

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