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Promise and Progress - The Gene Team
The Gene Team
Date: January 2, 2014
A Look Inside the Ludwig Center Lab That Defined Cancer
Feel a sneeze coming on? Reach for a Kleenex. Need to wrap a package? Scotch tape is a must-have. Looking for answers on the Internet? “Google” it, of course. There are certain go-to brands that are so equated with excellence that their trademark has become synonymous with the product itself.
Cancer science and medicine are no different. Though they are not household names, the best of the best are Bert Vogelstein and Kenneth Kinzler when cancer genes are at issue. Drs. Vogelstein and Kinzler are the quintessential cancer gene finders. With more than 200,000 scientific journal references and counting, the pair’s work in deciphering the genetic causes of cancer is universally regarded as the most relevant in the study of the disease. They developed the model for cancer initiation and progression, first with colon cancer, and then applied their methods to other cancers and cracked the genetic codes of more forms of the disease than any other research team in the world. Their work is now considered classic, the paradigm for much of modern cancer research.
In 2006, this cancer research powerhouse drew the attention of Ludwig Cancer Research and earned a transformational $20 million gift and the distinction of being named one of only six Ludwig Centers in the United States.
“The long list of accomplishments made by Drs. Vogelstein and Kinzler are a shining example of high-impact philanthropy,” says Dr. William Nelson, director of the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins. “Clearly, they are brilliant scientists, but funding is as critical to making scientific advances as great ideas, and Ludwig Cancer Research has provided that essential component.”
Drs. Vogelstein and Kinzler, directors of the Ludwig Center at Johns Hopkins, had already firmly established their reputation as leaders in cancer research. The important discoveries that unfolded one by one in the their laboratory led the world to understand that cancer is a genetic disease. However, until this point, their findings came by painstakingly looking at just a few suspect genes at a time. The Ludwig gift brought automated gene-sequencing equipment to their laboratory, which allowed the scientists to simultaneously sequence millions of genes. Research that once took years could now be done in months and for a fraction of the cost of earlier studies. An unprecedented and all-encompassing view of precisely what was happening inside the cancer cell was at last possible.
This first comprehensive view inside the immortal cell revealed an intricate convolution of genetic errors. If not for the cell’s menacing purpose, its ability to hijack and exploit normal cellular functions to its benefit would be something to marvel. The phenomenon of this corrupted cell was, however, outdone—and more importantly, undone—by the virtuosity of the Ludwig Center scientific sleuths who amazingly deciphered its game plan.
A Genetic Tutorial
To truly appreciate the scale and complexity of the accomplishments of the Vogelstein/Kinzler team, it is important to understand the series of genetic events involved in cancer formation. Dr. Vogelstein compares it to an encyclopedia. “Each of us has an encyclopedia in our cells, and each page of that encyclopedia represents one gene,” he says. A set of genetic encyclopedias comprises 46 books, and each of these books represents chromosomes—23 books are inherited from our mother and 23 are inherited from our father. Each “chromosome” book has about 1,000 pages—one for each gene on that chromosome. Every page is filled with about 1,500 letters. However, the letters on the “gene” pages are not the 26 A through Z alphabet characters. Rather, just four characters represent the “gene” alphabet: A, C, G and T, an abbreviation for the chemicals that make up genes.
Mistakes that occur in this genetic encyclopedia are like misspelled words. For example, if a book contains letters to form the word “feet,” it means one thing to the reader. If two letters are transposed, and the word appears as “feat,” it means something completely different. The same is true of the characters that make up the genetic alphabet. The cancer cell genome may have an “A” instead of a “C,” or a “G” instead of a “T.” This, he says, is a mutation, and when they occur, they change the way a cell interprets its instructions and, as a result, how it behaves.
A few other types of errors can occur. Sometimes a page is repeated, in a process known as gene amplification. In other cases, the page is missing. This is a genetic deletion. Dr. Vogelstein says that of these possible errors, by far the most common is the typographical character substitutions known as point mutations.
Save for about 50 of these errors among the millions of characters that make up the genes, cancer cells are nearly identical to normal cells, and that is what makes cancer such a complex disease. Teasing out these errors from a sea of normal cells has confounded both scientists and the human body’s own checks and balances.
“Cancer is a very difficult disease to treat because basically the enemy here is our own cells,” says Dr. Kinzler. “Cancer cells are very similar to us. There may be only a hundred specific genetic changes in coding genes that distinguish a normal cell from a cancer cell, and we need to figure out how to use that to specifically kill cancer cells.”
Compare the cancer genome to the bacterial genome. Bacterial infections are easily recognized by the body’s immune system and treatable with drugs known as antibiotics. The reason, Dr. Kinzler says, is that bacterial genomes are so different from the human genome. Bacteria have 1,000 to 2,000 genes, all of which are vastly different from the 20,000 or so genes in the human genome. These differences make it possible to develop drugs that target gene products made by bacteria and impact infections without affecting the genes of human cells.
“In cancer, 19,950 genes are the same in most cases, and the other 50 have just slight changes that distinguish them from normal cells,” says Dr. Vogelstein. To further complicate matters, “Two cancers can be from the same organ and look similar under the microscope, but genetically they are distinct.” That is why therapies that work in one patient may not work in another.
Despite this complexity, in the last six years, they have accomplished something that would have been impossible just a decade ago. Using the most advanced technology, the team has analyzed all of the genes in a cancer cell—more than 30 million base pairs of DNA—and provided the first-ever comprehensive blueprint of cancer: what goes wrong in the cellular instruction manual to cause cancer. This task of superhuman scope has taken the cancer world by storm, opened new vistas of research and, for the first time, presented a full genetic understanding of one of humankind’s greatest threats.
As complex and transforming as these firsts are, they started humbly and quietly in 1983 in a converted supermarket on the Johns Hopkins East Baltimore medical campus.
At the time, little was understood about cancer. There were lots of theories, but no real answers. All that was really known was that it was an unstable disease that got worse with time. Inspired by the National Cancer Act’s “War on Cancer” initiative that promised a cure for cancer, most scientists were searching for a magic bullet—a unilateral approach that would conquer cancer. Many were looking for quick fixes—drug treatments they hoped would rein in this vicious killer. Drs. Vogelstein and Kinzler took a different approach. Successfully treating cancer, they believed, would require an understanding of what it was. Their research was revealing a much more complicated, multifarious genetic disease than most scientists of the time—or the public—had appreciated. They were uncovering a genetic infrastructure unlike anything that had ever been described in human disease. It centered on a delicate balance between cell-growth accelerators known as oncogenes and the cancer-controlling genes called tumor suppressor genes that kept them in check.
Alterations to these genes, either inherited or acquired throughout life, disrupted the delicate balance, giving an advantage to cell growth. In essence, cancer is nothing more than a normal cell that does not die. As this immortal cell divides, it eventually reveals itself in the form of a tumor. While many focused on the tumor, Dr. Vogelstein realized very early on that it was what precipitated the tumor that mattered. He compared it to an iceberg. The tumor was the tip of the iceberg that could be seen, and the genetic alterations were the layers that began forming beneath the water decades earlier. The hidden layers, what happened inside the cell before the tumor developed, was what he was interested in learning about, and he was certain it was the key to controlling cancer.
Dr. Benjamin Baker, a Johns Hopkins internist, was intrigued by Dr. Vogelstein’s revolutionary concept that cancer was caused by genes gone awry. He helped Dr. Vogelstein form the Bowel Tumor Working Group, which proved to be a turning point, bringing together seasoned clinicians and investigators and bright, young scientists to explore this visionary gene-centered hypothesis in colorectal cancer.
Dr. Vogelstein and team were about to break open Pandora’s box. Without the benefit of today’s automated gene-sequencing technology, the researchers accomplished the near impossible. They were among the first scientists to apply molecular biology to the study of cancer. They developed tools to look inside the submicroscopic molecules of the cell and found rare, uncorrected errors to DNA that set the cancer process in motion.
One by one, they uncovered a series of genetic mistakes that revealed how colorectal cancer started and progressively became more and more dangerous as these genetic alterations accumulated. They identified the genes responsible for the major forms of inherited colorectal cancer as well as genes that initiated the more common noninherited form of the disease.
The mystery was solved. Cancer was a genetic disease. Drs. Vogelstein and Kinzler’s breakthrough discoveries sent reverberations throughout the world of science as research teams at institutions throughout the country scrambled to look for similar genetic alterations in other cancers.
Having identified the gene alterations that caused inherited colon cancers, such as familial colon cancer and familial adenomatous polyposis, they developed tests to detect the alterations and radically changed how these patients were managed in the clinic. For the first time, clinicians could know which family members had inherited colorectal-cancer-causing mutations, so that those at risk could be monitored closely for cancer. As important, the tests also revealed family members who did not have the gene mutations so they could be spared unnecessary screening measures. It was the first example of personalized, genome-based cancer medicine for patients with typical forms of cancer.
The Ludwig Difference
Harnessing the power of these cancer gene discoveries and applying them to the general population was a much greater challenge. The $20 million-plus gift from Ludwig Cancer Research would prove to be another turning point for the Vogelstein/Kinzler team. The donation established the Ludwig Center at Johns Hopkins and provided a steady stream of income to fund the laboratory and its scientists.
“In many ways, the establishment of the Ludwig Center was the beginning of our work,” says Dr. Vogelstein. Although they had already made unprecedented discoveries, the Ludwig funding allowed the team to pursue gene sequencing on a massive scale and, once again, to lead the world in making pioneering cancer discoveries.
The Vogelstein/Kinzler team had already revealed to the world that cancer was a genetic disease, and uncovered some of the genes involved. Now, cancer type by cancer type, they would study every gene in the cancer genome and lay out a specific blueprint of the alterations that caused each cancer to start, grow and spread. “For the first time in the history of medicine, we had the technology to define the mistakes in that genetic code that occur in human cancers,” explains Dr. Kinzler.
With this new support from Ludwig Cancer Research, these investigators, arguably the most brilliant in cancer research, have revealed to the world answers that had remained elusive for decades.
Dr. Vogelstein is even-tempered, soft-spoken and deliberate. He is as humble as he is smart. He listens intently when his laboratory scientists, students and trainees discuss their research, present problems and ask questions. Likewise, they listen intently when he responds. They seem to recognize and appreciate that they are among the few who have earned an opportunity to study with the master. One of his former trainees, who now co-directs the gastrointestinal cancer program at the Kimmel Cancer Center, once said of him, “Bert Vogelstein is the smartest person I have ever met.” He describes him as a scientific compass of sorts. “If Bert is heading in a certain direction scientifically, you can be sure that it’s the right one, and that’s usually the direction I go.”
Dr. Vogelstein’s brilliance goes beyond his scientific prowess. As the architect of the laboratory that led the world to understand the origins of cancer, his brilliance is also reflected in the investigators he has hand picked to join his team and mission.
The first of them was Dr. Kinzler, a pharmacology and molecular sciences expert, who has worked with Dr. Vogelstein since 1983 and played a central role in the cancer gene discoveries. He pioneered the discovery of cancer genes in their group and became the world’s foremost expert on the APC gene, the most frequently mutated tumor suppressor gene in colon cancer. Energetic, fast-talking and equally reflective, Dr. Kinzler is the perfect complement to Dr. Vogelstein. A solution finder, he is able to overcome deficiencies in technology to move research forward, inventing methods like SAGE, a predecessor to today’s automated gene-sequencing technology. SAGE reads DNA much like a grocery store scanner reads and monitors product quantities. It provided some of the first high-tech analysis of gene expression, showing which genes were overexpressed or underexpressed in cancer. Dr. Vogelstein says Dr. Kinzler is “an out-and-out genius, with intuitions and talents that continue to amaze me, even after working so closely with him for two decades.”
Dr. Nickolas Papadopoulos is calm with a comforting smile and an engaging Greek accent. His expertise is in cancer genetics. He trained with Drs. Vogelstein and Kinzler and then left to work in industry where he developed gene-based diagnostics. He rejoined the research team in 2006 with the opening of the Ludwig Center. His aim is to translate what he and his colleagues have learned about cancer genetics into better diagnostics for cancer. His top priority is sketched out on his office wall, a formula that he hopes will improve next-generation sequencing. The technology works well for basic research, but the error rate currently makes it unreliable for patient care. Dr. Papadopoulos’ combined cancer genetics expertise and industry experience position the Ludwig Center team to make the critical bridge between genetic discoveries and personalized cancer prevention, diagnostics and treatment.
Key to that transition is Dr. Luis Diaz, the only practicing oncologist on the Ludwig Center team. He is driven, compassionate, and always moving, dividing his time between the laboratory and the clinic. Dr. Diaz completed his residency and fellowship at Johns Hopkins, came to the Vogelstein/Kinzler lab as a trainee in 2002 and joined the faculty in 2005. He makes sure the team’s research is on course to benefit patients. Dr. Diaz, who specializes in gastrointestinal cancers, primarily colon cancer and pancreas cancer, quips, “You never want to see me because that means you have a bad cancer.” In truth, he is precisely who these patients want and need to see. Backed by some of the most significant cancer discoveries ever made, he is the essential connection between cancer research and cancer medicine.
Dr. Shibin Zhou has a big smile, quiet voice, and a completely different scientific background than that of his Ludwig Center colleagues. He came to the Vogelstein/Kinzler laboratory nearly 20 years ago as a postdoctoral fellow. He is the member of the Ludwig Center team focused on novel therapeutics. Like a landscape artist, he sees beauty in how all aspects of a cell’s biology function together. He has an image of how the rogue cancer cell develops and begins breaking all of the rules that govern normal cell behavior and has devised innovative ways to beat it. In one such inventive approach, Dr. Zhou genetically engineered bacteria that grows only in the oxygen-starved core of malignant tumors. The bacteria safely colonizes inside the tumor, developing an abscess that eats away at the tumor from inside out. When it reaches the outside rim of the tumor, the area connected to oxygen-rich blood supply, it no longer works. Dr. Zhou then uses other agents to finish off the crippled tumor. Laboratory and animal models have been successful, and Johns Hopkins has now licensed his technology to industry so that patient clinical studies can be conducted around the world.
The team also includes students, trainees and technicians from a wide variety of backgrounds. Each person contributes a necessary expertise and a unique perspective. Just as a good recipe requires the finest ingredients, the Ludwig Center team has just the right mix of people and ideas. It is immediately recognizable that this laboratory is different. The drive of super-focused scientists who have made some of the most significant cancer discoveries is tempered by a feeling of comfort and collegiality. A row of tabletop candy dispensers, comic strip cutouts, a pool table, and random toys are oddly conspicuous in this world of top-notch science. They provide silent testimony that these researchers with seemingly superhuman intellectual capacities are, in fact, real people. Like the intricate and complex cancer cell they study, they do not fit a mold. It is this willingness to walk outside of the lines and to think in ways no one has thought before that has given rise to their unprecedented success.
“We’re not interested in hammering the nail into the weakest part of the wood. We’re interested in hammering the nail into the foundation of the wood—the hardest part,” says Dr. Vogelstein.
Hammer they did, providing insights into cancer that had never been understood, never even imagined. Collaborating with the internationally recognized Kimmel Cancer Center pancreatic cancer program, this cancer was one of the first cancer genomes the Ludwig Center team deciphered. For this study, the scientists examined 24 pancreas cancers and determined the sequence of all of the genes in these cancers. On average, they found just 50 mutations (genetic mistakes that are present only in cancer cells) among the 20,000 genes in each cell. Other than these 50 differences, the genes in the cancer cell were identical to those in normal cells. It is no wonder then that progress has come slower than the public would like and that general curative treatments have been elusive. These studies also revealed a staggering complexity. While every cancer had a similar number of alterations, not every cancer had the same alterations. They varied from patient to patient. “No two cancers are genetically the same, even though they may look the same under the most powerful microscope,” says Dr. Kinzler.
Personal, Genome-Based Medicine
If ever a disease required a personalized approach to treatment, it would be cancer. Cancer is not a one-size-fits-all disease. If each patient’s cancer is genetically unique, then diagnostic and clinical methods need to take that fact into consideration for screening, detection and treatment plans. These differences from cancer to cancer pose significant obstacles. However, now that they are better understood, the roadblocks to effective treatment can potentially be exploited to improve treatment. “I call this genome-based medicine,” says Dr. Vogelstein. “Even though each patient’s cancer genome is different, these differences can sometimes be targeted with drugs.”
For decades, the world searched desperately for a picture of what cancer really was. What was driving this disease that appeared to come out of nowhere, for a time seemed submissive to treatment and then mounted a second, often-lethal, vengeful attack? Drs. Vogelstein, Kinzler and team painted that picture.
Dr. Vogelstein says there are probably not many surprises left in cancer genetics. “It is unlikely that there are many more genes frequently mutated in cancer. These types of common mutations would likely have been found by now,” he says. “It’s time to take what we’ve learned and put it into action.”
The real beauty of the Ludwig Center team’s research is its potential for broad applications. With the cost of genome sequencing plummeting, soon every patient of the Kimmel Cancer Center will have his or her cancer’s genome sequenced to reveal its unique genetic signature and determine the best course of treatment, he predicts. When Dr. Vogelstein and team deciphered the pancreas cancer genome in 2006, the research cost about $200,000 per patient and took several months to complete. Today, to sequence a cancer genome, he says, it takes about a week and costs only a few thousand dollars. Right now, the gene-alteration-targeted treatments do not provide cures. Tumors that initially respond tend to recur. Ongoing research focused on combining these targeted therapies with other drugs may lead to better and longer-lasting responses.
As promising is the potential to engage the immune system. “Every one of these mutations that alters a gene should make it foreign to the immune system. The body has never seen these particular genes. In this way, it is similar to a bacterial or viral infection,” says Dr. Vogelstein. Cancer genome sequencing has revealed genetic mutations that should be susceptible to an immune attack. Cancer immunologists can now find and exploit these mutant proteins within cancer cells to the benefit of patients. “This is a cancer immunologist’s dream,” says Dr. Vogelstein.
“Knowing the roadmap of a cancer is the key to attacking it. Now that we have identified the key gene mutations, we can focus on determining at what point in the cancer process they occur, whether they guide prognosis, and if they might be good targets for prevention or treatment,” adds Dr. Kinzler.
Prevention Is Cure
What the Ludwig Center team provided was the detailed schematic for how a tumor starts and how it becomes progressively more dangerous. As the result of heredity or outside cell-damaging exposures, like cigarette smoke or high-fat diets, cell DNA is changed. Over the course of up to 30 years, genetic alterations amass until the cancer makes a lethal transformation in which cancer cells can travel from the original tumor site and invade other vital organs and tissue. This process is known as metastasis, and in cancer, it represents the point of no return, often the line between curable and incurable.
Take colon cancer, for example. According to Dr. Vogelstein, of the 55,000 people who die each year, nearly all of the deaths occur because the cancers were not detected until this final stage. He believes that if the cancers are detected before cancer cells spread, most patients can be cured with surgery and drug treatment or potentially even surgery alone.
“It takes about 30 years for a cancer to go from its submicroscopic stage to a full-blown metastatic cancer capable of killing a patient,” says Dr. Vogelstein. “The last stage, metastasis, where the cancer spreads is the stage that actually kills people, and this stage occurs only in the last few years of this 30-year process.” Unfortunately, this is when many cancers are diagnosed. By this time, they have acquired so many gene alterations that they are often resistant to treatment.
This revelation that cancer is in place for decades before it enters its final, lethal stage led the Ludwig team to focus their efforts on cancer prevention. Their goal is not necessarily to prevent a cancer from occurring, but to use what they have learned about the cancer genome to keep it from killing people. They are creating safe, simple and inexpensive tests that detect early genetic changes that precipitate cancer development. Such tests would allow doctors to find, diagnose and eradicate cancers in their very earliest stages.
This is easier said than done, Dr. Vogelstein admits, but he and his team are now focused on developing such cancer screening tests. If past accomplishments are any indicator, it is likely they will be successful.
The tests they are developing are different than the cancer screening tests currently being used, such as PSA for prostate cancer and fecal occult blood for colon cancer. These tests are undeniably useful, but they are not specific. Many noncancer conditions can cause a positive result. The tests the Ludwig team has invented are definitive indicators of cancer, as they detect the genetic alterations that actually cause the cancer. The challenge is determining the blood and body fluids from which this cancer DNA could be easily extracted and ensuring the test is sensitive enough so it does not miss genetic alterations.
The First True Tests for Cancer
As tumor cells divide, they develop their own blood supply to get the nutrients they need to survive and grow. As a result, cancer cell DNA gets carried into the bloodstream, providing evidence of the cancer’s existence. Similarly, cancer cells also may shed this DNA in other body fluids and secretions. For example, a colorectal cancer would shed DNA into stool, a bladder cancer into urine, a lung cancer into sputum or an endometrial cancer in cervical excretions. Sensitive tests that could easily, safely and inexpensively detect these early changes would permit early interventions and could potentially make many cancers curable.
Bladder cancer is a prime example. Nearly 75,000 people in the United States are diagnosed with bladder cancer each year. Although the majority of patients initially respond to cancer treatment, at least half will have their cancers come back. As a result, patients with bladder cancer require lifelong monitoring. Currently, there is no screening test for bladder cancer, and costs to treat and monitor patients exceed $3 billion a year. Per person, experts say, it is the most expensive cancer to treat. Dr. Papadopoulos says a test that detects cancer DNA in urine could be used to discover cancers very early and also to monitor existing patients for recurrence. Such a test, he says, would greatly reduce the need for invasive and quality-of-life-altering treatments and dramatically slash health care costs.
Another example is a new test being developed by Ludwig Center scientists Dr. Diaz and Isaac Kinde, M.D., Ph.D. It uses Pap tests, routinely performed since the 1950s in gynecologists’ offices throughout the country to detect and prevent cervical cancer. Drs. Diaz, Kinde, and their colleagues have been able to develop a test that detects not just cervical cancers, but also uterine and ovarian cancers. The test, called PapGene, captures DNA that is shed from cancer cells and contains genetic alterations that lead to endometrial and ovarian cancer development. It extracts the endometrial and ovarian cancer-specific DNA from the same cervical fluid collected during conventional Pap tests to warn of developing cervical cancers. This new test could one day make it possible to test for three female cancers at a woman’s annual wellness exam. “This discovery is an example of the innovation the Ludwig support has produced,” says Dr. Diaz. “This type of funding sparks ideas that save lives.”
In early small-scale studies of PapGene, the test detected 100 percent of endometrial cancers and 40 percent of ovarian cancers. The difference in test sensitivity is really a matter of geography, specifically the proximity of each organ to the cervix. The endometrium is in the uterus and closer to the cervix, so it sheds a greater number of cells into the cervical fluid collected during a Pap test. On the other hand, cells from the ovaries must travel through the fallopian tubes to reach the uterus and cervix and, therefore, are diminished in numbers and quality. The Ludwig Center investigators are working to improve PapGene’s sensitivity to ovarian cancer, but even at 40 percent, it could help many women. Currently, there is no test for early detection of ovarian cancer, a lethal disease often referred to as the silent killer because it does not cause symptoms and frequently goes undiagnosed until it is well-advanced. Similarly, there is no screening test for uterine cancers. If the team finds similar results in larger studies, the $100 test could begin to be introduced in doctors’ offices in three to five years.
Dr. Kinzler envisions tests like these becoming a regular part of annual physical exams. “People normally give blood, stool, urine when they visit their doctors. Women have Pap smears, and smokers may provide sputum samples. All of these could be examined for mutations,” says Dr. Kinzler. He is hopeful that the ongoing work in the Ludwig Center laboratory will result in gene-based cancer screening tests that will make possible the detection of many cancers in early and highly treatable stages.
If he is right, the coming decades will see dramatic decreases in cancer deaths. Some of the change will come through improved gene and immune-targeted therapies, but the biggest differences will be made, Dr. Kinzler predicts, through early detection and prevention. “The history of medicine shows that when a disease is understood, it eventually becomes manageable,” says Dr. Vogelstein. Because of the work of Drs. Vogelstein, Kinzler and their Ludwig Center team, the world now understands what cancer is, better than many other human diseases. “This understanding truly has been revolutionary,” says Dr. Vogelstein.
In public health, he points out, preventive techniques, not cures, have been most effective at reducing deaths. “We still can’t cure polio. We can’t cure a massive heart attack or stroke, but we can prevent them, and that has led to their decreased incidence,” says Dr. Vogelstein. “I think the same will happen with cancer. That is the next revolution—the most important one—to take this knowledge we have gathered and help patients in ways that could only be imagined before.”
He and Dr. Kinzler believe that their Ludwig Center team is poised to make that leap. “The Ludwig gift enabled our generation to decipher cancer, to become the first generation in the history of mankind to know what cancer is. It enabled us to make this progress, and it inspires us and charges us to go farther, to conquer cancer,” says Dr. Vogelstein. “It’s a commitment we intend to make to good on.”