The Philadelphia Chromosome

by Jessica Wapner

  Finally, in 1977, Erikson and one of his students, Marc Collett, found the protein product of src, a discovery that generated excitement even among colleagues who’d teased Erikson for focusing his energy on cancer in chickens. But the satisfaction of the breakthrough was fleeting. After all, as nice as it was to be able to point to a protein and know that this was the one made by src, that information was actually fairly useless. What science really needed to know was the function of the protein. What did it actually do in the cell? Was it responsible for cell division? Did it help power the cell? If the cell is like a house, then identifying src’s product was like pointing to a single part of the house and declaring it important. Identifying its function meant knowing whether you were pointing to a fuse box, a radiator, or a water pipe. A year later, Collett and Erikson had figured it out. The product of src was an enzyme called a protein kinase.†

  Finding a kinase at the other end of src came as a surprise to Erikson and Collett and every other scientist studying viruses and cancer. Kinases are enzymes, a class of proteins that act as catalysts, facilitating processes in the cell that are essential to survival. In the years following Erikson and Collett’s finding, more than 500 kinases would be found inside the human body. They would eventually be found in nearly every living species (paramecia, those single-celled organisms usually seen on our first glimpse through a microscope, hold the world record with about 2,600 kinases). But in 1977, only a few had been identified. And as far as anyone knew, none of them had anything to do with cancer.

  Much of how kinases operate had been unraveled by Sir Philip Cohen at the University of Dundee in Scotland. There was only one known kinase when Cohen entered the field in the 1960s, and his lab had been largely responsible for illuminating the role kinases played in “all aspects of how living cells work,” he said. The term “kinase” itself hinted at their importance: The root is the same as in “kinetic,” from the Greek kinesis, meaning “motion.” What Cohen and others had found is that most cellular processes occur in a cascade of events. Insulin, for example, triggers one signal, which triggers another and then another. Charting these signaling pathways—signal transduction, the chain would come to be called—for a given process is a hallmark of the basic research behind understanding human diseases. Kinases, Cohen was finding, were almost always at the starting point of that cascade.

  What’s more, biologists had managed to figure out the exact mechanism that kinases use to set those pathways in motion, the flag the enzymes wave to start the race. Inside every living cell float molecules of ATP, or adenosine triphosphate, the container of energy inside our cells. The adenosine is a sugar-based chemical that serves as the backbone for three molecules of phosphate, hanging like beads on a string, with powerful bonds holding the beads together. ATP is, essentially, fuel.

  To launch a signaling cascade, kinases pluck a phosphate from ATP—one bead is removed from the string—and stick it to a protein. The phosphate wakes up the protein, which immediately starts performing whatever job it’s encoded to do. Once those duties are complete, another enzyme comes along and removes the phosphate, and the protein settles back into its more dormant state.

  “Kinases deliver the right materials at the right moment to the right place in a cell at minimum energy cost to a cell,” said Cohen, who has been knighted twice for his contributions to science. The process of delivering a phosphate to a protein, known as protein phosphorylation, is incredibly efficient, launching a chain of crucial events in one swift motion. The kinase, it turns out, is a model of sustainable energy.

  It is also, as scientists would soon discover, the perfect tool for cancer to proliferate.

  IN THE 1970S, Cohen’s lab had become a magnet for kinase-inclined scientists. He’d been a lead researcher in parsing the role kinases played in converting glucose, the sugar into which food is converted in our cells, into glycogen, the stored form of that sugar. After work, these scientists, mostly young single men, would tromp through the cold Scottish evening to a now-long-gone pub on the Hawk Hill Road to hash over their research. They were often accompanied by Nick Lydon, a postdoc from the next lab down the hall.

  Lydon had never been considered particularly brilliant. He was dyslexic, and so he never excelled in his classes at the Strathallan boarding school in Perth, Scotland. With its lack of prose to wade through, science proved much easier for him than literature or language. Because in those days the UK educational system required students to choose a specialty early on, Lydon ended up sticking with the hard sciences. He attended the University of Leeds, where he majored in biochemistry and zoology, and followed his undergraduate degree with a PhD in biochemistry. He arrived at the University of Dundee for postdoctoral training in 1978, just as Erikson was rattling the field with his report about the Src kinase.

  Lydon was studying hormonal regulation, but the work lacked the bite of practical relevance. By contrast, the sounds of science emanating from the Cohen lab piqued his interest to no end. Lydon, his piercing blue eyes reflecting his active mind, began hovering around the lab benches of Cohen’s postdocs—Brian Hemmings, Peter Parker, and Colin Picton, in particular—to soak up all he could about how kinases were involved in glucose metabolism, the breakdown of glycogen, and all other aspects of the signaling pathway that began with insulin. He sat in on seminars held by the lab and regularly joined Hemmings and the rest for pints.

  The potential for this research to be useful in a tangible way excited Lydon. “I’d always been interested in application more than basic research,” said Lydon. And there was something about kinases that he couldn’t ignore, like the lamp from a distant lighthouse on some unknown shore. As he chatted with Cohen’s postdocs about the field, he heard about the discovery that the cancer-causing gene src encoded a kinase. It was the first time this family of enzymes had been found in cancer. Lydon had to know more. Their involvement in the insulin pathway was intriguing enough. But for a scientist wanting to make sure his work had a practical application, studying a protein involved in cancer seemed a gold mine. Gradually, after watching from the sidelines, Lydon knew he wanted to turn his focus to kinases. Figuring out how he would do that was another matter entirely.

  6

  _______

  CONSUMMATE INSTIGATORS

  Bishop and Varmus’s discovery of the cellular origin of the src gene spurred a chase for other similarly derived oncogenes. If RSV achieved this odd feat, could other viruses do the same? As luck would have it, the technology to do an expansive, rapid search for oncogene candidates became available at just the right moment. In the early 1970s, a group of graduate students at Stanford University discovered several different enzymes that allowed them to join together DNA from different sources, recombining it into a single strand. Recombinant DNA, as it came to be called, enabled scientists to investigate individual genes in a way much easier than creating radioactive probes. The technique became so integral to so many aspects of science that it even seeped into mainstream knowledge, but under its more easily grasped name: cloning.

  The invention of cloning in the early 1970s was nothing short of a revolution for the field of genetics. It allowed for individual DNA molecules to be propagated in a cell culture, and it allowed viral DNA to be duplicated outside of the natural host. Most relevant to this story, recombinant DNA technology enabled scientists to take apart viral genomes and test the cancer-causing potential of each individual gene. Viruses usually comprise just four or five genes, and with recombinant DNA, each of those few genes could be cloned individually, revealing which single gene was responsible for inducing transformation. It was like lifting up each cup to find out which one hid the magician’s coin.‡ This line of inquiry—Were there other oncogenes like src out there?—quickly bore fruit. The list of such proto-oncogenes continued to expand: myc, ras, and, later, hundreds of other human genes. A few years later, in the early 1980s, some scientists made another conceptual leap: If a virus can turn a normal gene into an oncogene, could enviro
nmental factors do the same thing? “Why wouldn’t cigarette smoke be able to do that? Why wouldn’t sunlight be able to do that?” said Bishop, recalling the questions of the day. The notion that a proto-oncogene could be converted into an oncogene by something other than a virus was taking root. No one was sure what the exact trigger might be, or how to even search for the trigger. But slowly, oncogenes were pried loose from their historical ties with viruses. The research into oncogenes was taking on a life all its own.

  IN 1977, WHEN Erikson and Collett pronounced that the product of the src gene was a kinase, these ideas remained almost entirely unimagined. Many scientists working in this vein assumed that the discoveries they were making were relevant to human cancer, but there was no concrete link. Making the leap from proto-oncogenes in chickens to proto-oncogenes in people meant crossing an enormous chasm.

  The fact that Src was a kinase had come as a complete shock. Only a handful of kinases had been found in human cells, and they were assumed to be involved in only a few very specific processes in the cell. What on earth could they have to do with cancer? The discovery brought instant recognition to Erikson and Collett and launched a frenzy of new research about kinases. “It was quite a zoo for a while,” recalled Erikson. The search was on to figure out whether any other cancer-causing viruses were also abusing the natural kinase mechanism.

  If scientists were at first baffled by the appearance of a kinase on the stage of cancer research, the logic of their involvement slowly became clear. As research continued to pull back the curtain, kinases were found to have roles in all manner of cellular processes: cell division, metabolism, insulin breakdown, and numerous other pathways and actions that are essential for living. As consummate instigators, setting off cascades of signals by the simple bestowal of a phosphate onto a protein, kinases suddenly seemed like the obvious place for cancer to begin. This kind of general mechanism, with the power to guide so many crucial functions, science would later realize, is perfectly suited for the development of cancer, a disease of unchecked cell growth. If cancer is like a gun, then the kinase is like the finger behind the trigger.

  But so much mystery still remained. Normal cells had normal src genes and, therefore, normal Src kinases. When the Rous sarcoma virus picked up the src gene from a chicken and integrated it into its own genome, the gene became an oncogene, an abnormal version that caused cancer. Clearly, then, the protein encoded by the gene—the Src kinase—was also abnormal. An onco-protein, so to speak. But how? What was the difference between the Src kinase in healthy cells and the Src kinase in cancer cells?

  JUST AS THE world of cancer treatment was about to enter its modern era, Brian Druker was entering medical school, where he would soon be forced to admit his interest in cancer, something he’d tried to deny since his first undergraduate years at University of California–San Diego. He’d always done well in school; academic excellence had always been strongly encouraged in the tight-knit household where he and his three siblings had grown up in St. Paul, Minnesota. But he’d resisted pigeonholing himself into medicine, and his applications to med school had lacked the hallmarks of the students who’d shaped their every decision around becoming a doctor, their résumés littered with hospital volunteer hours and early anatomy courses. Rather than marching steadily into the medical profession, Druker had stumbled forward one step at a time, charting his course according to what was appealing to him at the time. He’d delved into laboratory research out of curiosity, and when the time came to apply to medical school, he’d amassed far more hours in the lab than at a hospital, a track record he assumed would be a strike against him. So it came as a surprise when his interviewer at University of California—San Diego Medical School, a man named Russell Doolittle, who was one of the most highly regarded scientists on the campus and known to be impossible to please, told Druker at their first meeting, “You’re exactly the kind of person I like to see in our medical school.” At the time, Druker was just relieved for some recognition, having bumbled his way through his previous interviews. Only later did he realize the future that he’d secured for himself by following his interest in the lab bench. “It was the path I had chosen for medical school that he wanted to assist,” Druker said.

  Still, for the moment he was keeping quiet about his interest in cancer. “You have to realize, cancer was a devastating disease,” said Druker. “Everybody died.” The disease was a grim, dark domain where only the most morbid physician dared tread, and Druker was unwilling to admit, even to himself, that he was fascinated by it. “Everybody was afraid of it, and people in oncology [were] weird because this disease was so hopeless,” he recalled. “Why would you go take care of patients with no hope? You were crazy if you were going to do that.”

  7

  _______

  WHERE THE KINASE HANGS THE KEYS

  Just a year after the Src kinase was discovered came the next significant moment in kinase research. While Erikson was working out the src product, Tony Hunter, a British scientist doing his postdoctoral training at the Salk Institute in La Jolla, California, was examining a virus known as polyomavirus, which causes multiple types of tumors in rodents. The DNA sequence of the virus was just being made available. Just as with the Rous sarcoma virus, polyomavirus included some genes that could render cells cancerous and others that allowed the virus to successfully infect its host. By the late 1970s, Hunter knew that those responsibilities were equally distributed among the polyomavirus genome, with about half of the genes related to replication and the other half related to cancer transformation. Hunter had been trying to understand how the cancer-related genes induced cancer. It was the same question Erikson had been asking: What was the protein product of the gene, and how did that protein spur tumor growth?

  By 1978, Hunter had figured out that the polyomavirus made three proteins that were responsible for causing rodent cancer. Elsewhere, researchers studying the same virus showed that one of these proteins, the middle one, known as “middle T,” was behind the conversion of skin cells into tumor cells. Now the question was: What kind of protein was it? It was the same question that had led Erikson on an eight-year trek down a rabbit hole.

  When Erikson and Collett’s Src kinase report came out, Hunter immediately wondered whether his polyoma protein was the same variety. “Maybe it was a universal mechanism of transformation,” Hunter recalled thinking at the time. And that was exactly what he and two other research groups found: The crucial protein was a kinase. “That was obviously incredibly exciting,” says Hunter. “It pretty much proved that kinase activity was going to be important, although we didn’t know how.”

  But his restless mind wasn’t done asking questions about this protein. As the role of kinases in cancer was becoming more apparent, Hunter wanted to know how, exactly, they accomplished this devilish feat.

  Over several years, Phil Cohen, at Dundee, and others had parsed the process of phosphorylation, the crucial placement of a phosphate by a kinase onto another protein in the cell to catalyze a stream of microscopic events. Scientists had figured out that when the kinase delivers a phosphate to a protein, the phosphate can’t land just anywhere. Just like having a spot in a house where the keys are kept, the kinase needs a specific target location on which to deposit the phosphate it removes from ATP, the triplet of phosphates that serves as the main storehouse of energy within the cell like a battery.

  That target location, the place where the kinase always hangs the keys, was a single amino acid, one of the many strung together to form a particular protein. Only certain amino acids can serve this function. During the time that Hunter was investigating polyomavirus, two amino acids were known to be the targets: serine and threonine. Every known kinase placed phosphates onto either serine or threonine.

  Once Hunter had confirmed that the protein responsible for the cancer induced by the polyomavirus was a kinase, he wanted to connect the dots further, to describe exactly how and why that kinase caused cancer. As a first step, he planned to
check which amino acid the kinase phosphorylated, serine or threonine.

  To find out which amino acid was the target of any kinase, researchers immersed a protein in a solution that separated out the amino acids at a pH of 1.9. When the amino acids were separated, it was possible to see which one carried the phosphate. If the solution got old, though, and a lazy researcher didn’t refresh it, the pH changed, and different amino acids would emerge.

  Hunter was feeling particularly lazy one day in 1979, and he used old buffer solution as he continued his search for the amino acid phosphorylated by the middle T kinase. One of the amino acids that emerged as a result was tyrosine. Tyrosine wasn’t a very popular amino acid in scientific research, and Hunter had hardly been on the lookout for it, especially considering that every other kinase known at that time brought phosphate only to either serine or threonine. But when he took a closer look, he saw that the tyrosine was phosphorylated.

  Hunter was taken aback. It was like hearing a foreign language for the first time and realizing that there are other ways to communicate. Tyrosine kinase is exceptionally rare in the human body. Of the more than 500 kinases known today, only about ninety attach phosphates to tyrosine. And those ninety kinases activate less than 1 percent of the proteins in the human body. In other words, fewer than ten of every 1,000 proteins in the body have tyrosine as their receiving dock. The other 900-plus proteins use serine, threonine, or a combination of both. Hunter didn’t know just how rare tyrosine phosphorylation was at the time, but he knew he’d stumbled onto an oddity. Of the several kinases known at that point, all stuck their phosphates onto serine or threonine. Why would this one target tyrosine? And was that fact important?