Cancerland

by David Scadden

  A newer technology is based on the discovery of something called CRISPR, which stands for clustered regularly interspaced short palindromic repeats. These are bits of DNA that repeat inside the genes of bacteria and are separated by short snatches of DNA called spacers. The early work on CRISPR was done mainly by Spanish microbiologist Francisco Mojica, who published a report on them in 1993. He collaborated with Ruud Jansen of Utrecht University on naming CRISPR in 2002. The chemical that seemed to enable this process—a protein called Cas9—was discovered by Alexander Bolotin of the French National Institute for Agricultural Research, who reported his work in May 2005. It was Bolotin who recognized that the CRISPR-Cas9 system functioned like a very precise genome-editing machine, snipping genes and creating openings where viral DNA could be inserted.

  It fell to a remarkably focused and intuitive scientist named Eugene Koonin, who immigrated to the United States from Russia in 1991, to recognize that bacteria retained bits of DNA from viruses so that in the future, invaders of the same sort could be recognized and defeated. Most people don’t realize that viruses attack bacteria and that this assault happens in and on our bodies in every moment of every day. CRISPR-Cas9 creates what Koonin calls a “mug shot” of a virus, and this imagery is used to establish immunity. In future encounters, bacteria check a virus against the mug shot and, when a match is made, handily defeat it.

  The CRISPR-Cas9 dynamic also clarified the remarkable role that viruses have played in evolution. In 2016, David Enard of Stanford University would report that almost one-third of the genetic changes that make humans different from chimpanzees were caused by viruses. Sometimes the change would occur as a result of the immune system’s response to an invader, but sometimes it happened spontaneously, without this intermediary step. Bits of virus would combine with bits of DNA to produce something entirely new. His coauthor, Dmitri Petrov, said, “The discovery that this constant battle with viruses has shaped us in every aspect—not just proteins that fight infection but everything—is profound. All organisms have been living with these viruses for billions of years. This work shows that the viruses have affected every part of the cell.”

  Petrov’s enthusiasm was merited, as work done around the globe, much of it inspired by the CRISPR-Cas9 discoveries, energized the fields of genetics and stem cell biology and offered hope to those working on cancer and other diseases driven by genetic abnormalities. Few tales of scientific discovery are more twisting and range as far afield as the story of CRISPR-Cas9. Among the more unexpected players in this drama were food industry researchers in Denmark who were curious about improving yogurt production, and a globetrotting scientist who was an expert in microbiology, genetics, and biochemistry. The well-traveled scientist, Emmanuelle Charpentier, of Berlin’s Max Planck Institute for Infection Biology, worked with Jennifer Doudna of the University of California–Berkeley to discover how to use CRISPR-Cas9 as a genome-editing tool. Charpentier would eventually describe the high point in her CRISPR work, which came when a colleague reached her cell phone. “I stood on the curbside for ages,” she would recall, “while we discussed when would be the right time to publish because by then we had actually got the story.”

  The story culminated in a successful experiment that proved the CRISPR-Cas9 process could reliably edit genes. Doudna would write about how this work affected her personally, recalling how startled she was by the success. This was December 2012. Soon, CRISPR-Cas9 had been used to edit the genes of wheat, fish, human stem cells, and mice. (The mice had benefited from the correction of a gene defect that caused a hereditary disease.) Most startling of all was an experiment that changed the genetic makeup of monkey embryos. Implanted in the uteri of surrogates, the embryos developed into monkeys that carried the new genetic code in most of their cells, including their sperm cells and egg cells, which means they would be able to pass along their genes to future generations.

  “Every day brought an influx of papers describing research using Crisper-Cas9,” wrote Doudna in 2015. “My inbox was full of requests from researchers seeking advice or collaboration. All this activity could have a direct impact on human life yet most people I knew outside of work—neighbors, extended family members, parents of my son’s classmates—remained largely oblivious. I felt as though I was living in two separate worlds.”

  In her professional world, Doudna would win awards and attract worldwide press attention. However, she and Charpentier would also become embroiled in a patent dispute with other scientists who had made CRISPR breakthroughs. Big institutions stood behind each of the parties, and the dispute seemed destined to go on for years. At one point, an insider who had worked with Doudna and Charpentier’s rivals even wrote them to promise bombshell evidence to help their case. He also sought employment. Patent conflicts are not unusual when hugely valuable advances are achieved by scientists, but no one enjoys the process of dealing with lawyers and scrambling to assert a claim. Scientists may be competitive types, but we also tend to eschew conflicts over who did what first. It distracts from the real work of research and discovery, and amid the argument and intrigue, productive relationships are threatened.

  Fortunately for those working on cancer and other genetic diseases, CRISPR-Cas9 was available, extremely inexpensive—ninety-nine dollars could get you started in the gene-editing business—and reliable. The magazine Popular Mechanics called this work “gene hacking,” which suggested that with the barest training almost anyone could get into it. One extremely effective nonprofit organization, Addgene of Cambridge, Massachusetts, collected and preserved variants on the CRISPR-Cas9 technology that performed different tasks. Scores of labs around the world contributed to what became a catalog of these chemicals, which were then supplied to labs worldwide. By 2017, the service had nearly one thousand contributors and had supplied hundreds of thousands of tools to scientists around the world. (This included special proteins that could make genes fluoresce for easy observation.) Addgene treated vectors and fluorescent proteins like open-source code in software engineering, as resources that could be easily accessed for the good of all.

  One of the first projects to use the new class of gene technology to develop a potential treatment for human disease was a partnership forged by Columbia University Medical Center and the University of Iowa. They used CRISPR-Cas9 and stem cells to create a potential treatment for one of the main causes of vision loss in adults, a heritable condition called retinitis pigmentosa. The early lab work was promising. Similarly, using CRISPR-Cas9 to fix genes has been tested in animal and shown to work in other disease settings caused by genetic abnormalities like muscular dystrophy. CRISPR-Cas9 can be used to both cut genes to make corrections in abnormal genes and to cut genes to damage them. Some genes are abnormal and cause problems like the oncogenes discussed earlier. Other genes are used for nefarious purposes by infections as is the case with HIV. That virus depends on a gene product that does not seem to be essential for humans. Since correcting a gene is much harder and much less efficient than cutting a gene to kill it, some, including a group I participate in, are planning to use CRISPR-Cas9 to render blood stem cell impervious to HIV infection. The idea of using CRISPR-Cas9 to cut and kill abnormal genes driving cancer, oncogenes, is an appealing one, but is not feasible. The problem is in the ability to accomplish that with sufficient efficiency to compromise all the tumor cells. We just don’t have the ability to do that and the remaining, uncut tumor cells would rapidly take over.

  Still, cancer was the focus of the first clinical trial using CRISPR-Cas9 to be given a green light to proceed in the U.S. In the summer of 2016, the National Institutes of Health approved the use of T cells edited with CRISPR-Cas9 to treat eighteen people with three different kinds of cancer, including melanoma, sarcoma, and multiple myeloma. The technology would be used to add a single powerful gene to help T cells find malignancies. It would also be used to remove genes that could inhibit the cancer-killing process and make the new T cells vulnerable to a chemical counterattack by t
he cancer. The University of Pennsylvania will run the trial, but the patients will come from around the country. Funding was supplied by the Parker Foundation and the Parker Institute for Cancer Immunotherapy. The hundreds of millions of dollars spent by the two entities came from Sean Parker, a self-taught computer scientist.

  Parker created his institute to great fanfare in the spring of 2016 with the announcement of $250 million in grants to fund work at six universities, including Penn. The money represented about 10 percent of his wealth, which he had derived from his work in the tech industry. Parker got his start at age nineteen with a music file-sharing service called Napster, which outraged record company execs because it permitted free copying of music. He started other companies, served as president of Facebook, and was a billionaire by age thirty. Although his initiative was one of the most ambitious, Parker was just one of many tech entrepreneurs who made big investments in charities, research projects, and development to benefit the world’s poor. At the time, he explained that his interest began with a concern about allergies (he has food allergies and asthma), but his investigation of immunotherapies soon led him to encouraging immunotherapies for cancer. He imagined his institute as a way to fund promising ideas without burdening scientists with the usual grant processes. He also thought he could maintain support for research in the face of disappointments that would discourage other funders.

  In addition to the money from philanthropists like Parker, funding for immunotherapy research came from foundations, the government, and pharmaceutical firms. For example, Novartis, which makes Gleevec, put $20 million into the Penn Center for Advanced Cellular Therapeutics. These types of commercial investments, as well as many that come from foundations, involve profit-sharing arrangements that nonprofits hope will supply future grants, and corporations expect to contribute to their bottom lines. The money pouring into immunotherapy research indicated the wide agreement on its potential, especially in oncology. Add the dynamic potential created by CRISPR-Cas9 and you get such enormous potential that labs around the world raced to try out new ideas.

  Governments, investors, and scientists worldwide understand that biotechnology may hold the greatest promise for mankind of any field of science and that for generations to come, treatments based on genetic and molecular interventions could cure a host of deadly and debilitating illnesses. As I write this, I am attending an international meeting of hematologists where remarkable results of gene therapy to correct hemophilia are being presented. The results are truly breathtaking. People who otherwise had lifelong risks of massive bleeding and a dependence on regular infusions of clotting factors appear to become free of both. It is early days, but it looks as if we are witnessing the transformation of this disease and the lives of the individuals affected by it. What this will mean to the families carrying this genetic abnormality is incalculable. Literally generations of uncertainty and suffering may be relieved. That is what biomedical science is doing and doing now.

  Jim Allison looked at big advances in the science and compared them with Sputnik, the first-ever man-made satellite that circled Earth in 1957 and set off the space race. That competition to conquer space pitted the United States against the Soviet Union. But as these two countries notched ever-greater achievements in the pursuit of prestige, they also sparked the development of advanced electronics, computers, specialized materials, and many other new technologies. Indeed, the greatest legacy of the space race was not the image of men on the moon but the scientific and engineering excellence that made space missions possible. Combine those achievements with the spirit and management of such complex endeavors and you see a template for the future of research. Except cancer isn’t going to be solved by engineers. Biologists work differently and think differently. Though they too stand on the shoulders of giants who worked before them, the progress of discovery is far less linear and step-wise in biology. The fitful stops, turns, and jumps of biology take determined visionaries who can also tolerate a lot more pondering and a lot less calculating.

  The iconoclastic Texan is a good example. Allison had pointed out the importance of immune checkpoints in the 1980s, but it took thirty years for things to play out as he envisioned. A bit eccentric, even for a biologist, Jim is a man who pursues his interest with great enthusiasm. For example, he turned his love for the harmonica into a jam session with Willie Nelson, which in turn led to the creation of a blues band called the Checkpoints. All the members are immunologists and oncologists.

  In 1996, Jim published a paper in Science that reported on the use of a “checkpoint blockade” to release T cells from a go-slow signal sent by a molecule called CTLA-4. Swimming against the academic mainstream, which largely focused cancer treatments on gene mutations, not immunology, Jim continued this work until it produced a drug that could be tested in trials with patients who had reached the end of conventional treatments for melanoma. In a typical year, doctors diagnose roughly seventy-five thousand new cases of melanoma in the United States, and as many as ten thousand Americans die because it has spread from the initial skin site to other organs. Common sites for this kind of metastasis include other portions of tissue beneath the skin, the lymphatic system, liver, lungs, and brain.

  The drug was called ipilimumab, and the work of testing it was taken on by Bristol-Myers Squibb. In 2010, they reported good results, with almost a quarter of patients living more than two years, compared with 14 percent of those who didn’t get the drug. In all, 540 people got the drug, and continued to demonstrate far superior outcomes compared with standard approaches. This doesn’t mean the drug was found to be a magic bullet. More than 60 percent of people who got it suffered significant side effects as their immune systems targeted their own healthy organs. Seven people died from this effect. However, the risks associated with the new drug were no greater than the risks of traditional chemotherapy, and for most people, the side effects were far less troubling. And of course, many patients hoped to be among those for whom ipilimumab worked remarkably well. One man posted a testimonial online about how, six years after starting the drug, doctors could locate no cancer in his body. He rightly declared that the drug “saved my life!”

  Success with Allison’s discovery set off an avalanche of other efforts to unleash the immune system against cancer. Work in the 1990s on mouse models of autoimmune disease had led to the discovery by a Harvard colleague, Gordon Freeman, of a molecule that could turn down a T cell’s ability to get activated. Despite having the proper signal to become active, the presence of this molecule, PD-L1, kept the T cells relatively quiescent, as if they were exhausted. If PD-L1 was out of the picture, the T cells were vigorous. Antibodies against PD-L1 or its receptor, PD-1, have made an enormous impact on patients’ lives and are now approved by the FDA for treatment of some lung cancers, kidney cancer, bladder cancer, head and neck cancer, Hodgkin’s lymphoma, and others. Some of these were essentially untreatable by standard cancer chemotherapy. The so-called checkpoint inhibitors are a major step forward. Medicines targeting new or recently defined immune checkpoints are entering the clinic with clinical trials numbered in the dozens. It is not hyperbole to say that these immune-based therapies represent a revolution in cancer care. They have their limitations—patients do relapse or not respond, and complications are not trivial—but the number of years of life given to those previously with a death sentence is awe inspiring. And we are still at the beginning of the so-called immune-oncology field. Immune harnessing to fight cancer is here to stay and it came from basic research that initially did not have cancer as its focus.

  A far bigger target of research could be found in a family of genes responsible for regulating cell growth. First discovered in rats with a type of sarcoma (hence the term Ras for “rat sarcoma”), these genes drive switches that control a host of activities, including the proliferation of cells and their migration around the body. They also switch off these functions. Trouble arises when mutations disrupt their normally well-regulated activity. About 30 percen
t of all cancers involve Ras mutations, which transform them into oncogenes, which means they cause cancer, particularly pancreatic, lung, colon, and thyroid. Within the Ras family, three main ones—KRas, HRas, and NRas—are the main drivers of cancer.

  Ras oncogenes were deemed so significant that the National Cancer Institute funded an independent Ras initiative in 2013, which was intended to end decades of failed efforts to find ways to block Ras gene functions. Many researchers came to believe these oncogenes are undruggable, meaning they couldn’t be treated. They have chemical structures that are just not amenable to having a drug dock into it and turn off its function in a stable manner. Unwilling to accept defeat, immunology experts redoubled their efforts on the three big Ras oncogenes. In Bethesda, Maryland, Steven Rosenberg focused on mutations in KRas (named for discoverer W. H. Kirsten), which is implicated in lung, colon, and pancreatic cancers. Indeed, doctors have noticed that these three types of cancer seem to occur in the same patients.

  Rosenberg had long studied cancer-fighting immune cells, including T cells, and had been using immunotherapy to treat melanoma since 2002. He developed processes that would allow him to isolate the immune cells that were found in a person’s tumor. Reasoning that the immune cells were attracted to the tumor in a failed attempt to kill it, he harvested those cells, grew more of them in a lab, and then returned them to the body where they could pursue their mission. Rosenberg saw long-term remissions in as many as a quarter of his patients. Although melanoma is a serious problem, the KRas cancers affect far more people and an immune-based treatment for them would bring a new era in oncology. Rosenberg began a trial with a small number of people who had been tested to determine that their tumors involved KRas mutation and had reached the end of the line with standard care.