“Negative” genes, such as Rb, suppress cell division. In normal cells, these anti-oncogenes, or tumor suppressor genes, provide the “brakes” to cellular proliferation, shutting down cell division when the cell receives appropriate signals. In cancer cells, these brakes have been inactivated by mutations. In cells with missing brakes, to use Bishop’s analogy again, the “stop” signals for mitosis can no longer be registered. Again, the cell divides and keeps dividing, defying all signals to stop.
Both abnormalities, activated proto-oncogenes and inactivated tumor suppressors (“jammed accelerators” and “missing brakes”), represent the core molecular defects in the cancer cell. Bishop, Knudson, and Varmus did not know how many such defects were ultimately needed to cause human cancers. But a confluence of them, they postulated, causes cancer.
A Risky Prediction
They see only their own shadows or the shadows of one another, which the fire throws on the opposite wall of the cave.
—Plato
The philosopher of science Karl Popper coined the term risky prediction to describe the process by which scientists verify untested theories. Good theories, Popper proposed, generate risky predictions. They presage an unanticipated fact or event that runs a real risk of not occurring or being proven incorrect. When this unanticipated fact proves true or the event does occur, the theory gains credibility and robustness. Newton’s understanding of gravitation was most spectacularly validated when it accurately presaged the return of Halley’s comet in 1758. Einstein’s theory of relativity was vindicated in 1919 by the demonstration that light from distant stars is “bent” by the mass of the sun, just as predicted by the theory’s equations.
By the late 1970s, the theory of carcinogenesis proposed by Varmus and Bishop had also generated at least one such risky prediction. Varmus and Bishop had demonstrated that precursors of oncogenes—proto-oncogenes—existed in all normal cells. They had found activated versions of the src proto-oncogene in Rous sarcoma virus. They had suggested that mutations in such internal genes caused cancer—but a crucial piece of evidence was still missing. If Varmus and Bishop were right, then mutated versions of such proto-oncogenes must exist inside cancer cells. But thus far, although other scientists had isolated an assortment of oncogenes from retroviruses, no one had isolated an activated, mutated oncogene out of a cancer cell.
“Isolating such a gene,” as the cancer biologist Robert Weinberg put it, “would be like walking out of a cave of shadows. . . . Where scientists had previously only seen oncogenes indirectly, they might see these genes, in flesh and blood, living inside the cancer cell.”
Robert Weinberg was particularly concerned with getting out of shadows. Trained as a virologist in an era of great virologists, he had worked in Dulbecco’s lab at the Salk Institute in the sixties isolating DNA from monkey viruses to study their genes. In 1970, when Temin and Baltimore had discovered reverse transcriptase, Weinberg was still at the bench, laboriously purifying genes out of monkey viruses. Six years later, when Varmus and Bishop had announced the discovery of cellular src, Weinberg was still purifying DNA from viruses. Weinberg felt as if he was stuck in a perpetual penumbra, surrounded by fame but never famous himself. The retrovirus revolution, with all its mysteries and rewards, had quietly passed him by.
In 1972, Weinberg moved to MIT, to a small laboratory a few doors down from Baltimore’s lab to study cancer-causing viruses. “The chair of the department,” he said, “considered me quite a fool. A good fool. A hardworking fool, but still a fool.” Weinberg’s lab occupied a sterile, uninspiring space at MIT, in a sixties-style brutalist building served by a single creaking elevator. The Charles River was just far enough to be invisible from the windows, but just near enough to send freezing puffs of wind through the quadrangle in the winter. The building’s basement connected to a warren of tunnels with airless rooms where keys were cut and machines repaired for other labs.
Labs, too, can become machines. In science, it is more often a pejorative description than a complimentary one: an efficient, thrumming, technically accomplished laboratory is like a robot orchestra that produces perfectly pitched tunes but no music. By the mid-1970s, Weinberg had acquired a reputation among his colleagues as a careful, technically competent scientist, but one who lacked direction. Weinberg felt his work was stagnating. What he needed was a simple, clear question.
Clarity came to him one morning in the midst of one of Boston’s infamously blinding blizzards. On a February day in 1978, walking to work, Weinberg was caught in an epic snowstorm. Public transportation had ground to a halt, and Weinberg, in a rubber hat and galoshes, had chosen to plod across the blustering Longfellow Bridge from his home to his lab, slowly planting his feet through the slush. The snow blotted out the landscape and absorbed all sounds, creating a silent, hypnotic interior. And as Weinberg crossed the frozen river, he thought about retroviruses, cancer, and human cancer genes.
Src had been so easy to isolate and identify as a cancer-causing gene, Weinberg knew, because Rous sarcoma virus possesses a measly four genes. One could scarcely turn around in the retroviral genome without bumping into an oncogene. A cancer cell, in contrast, has about twenty thousand genes. Searching for a cancer-causing gene in that blizzard of genes was virtually hopeless.
But an oncogene, by definition, has a special property: it provokes unbridled cellular proliferation in a normal cell. Temin had used this property in his cancer-in-a-dish experiment to induce cells to form “foci.” And as Weinberg thought about oncogenes, he kept returning to this essential property.
Of the twenty thousand genes in a cancer cell, Weinberg reasoned the vast majority were likely normal and only a small minority were mutated proto-oncogenes. Now imagine, for a moment, being able to take all twenty thousand genes in the cancer cell, the good, the bad, the ugly, and transferring them into twenty thousand normal cells, such that each cell receives one of the genes. The normal, unmutated genes will have little effect on the cells. But an occasional cell will receive an oncogene, and, goaded by that signal, it will begin to grow and reproduce insatiably. Reproduced ten times, these cells will form a little clump on a petri dish; at twelve cell divisions, that clump will form a visible “focus”—cancer distilled into its primordial, elemental form.
The snowstorm was Weinberg’s catharsis; he had rid himself of retroviruses. If activated oncogenes existed within cancer cells, then transferring these genes into normal cells should induce these normal cells to divide and proliferate. For decades, cancer biologists had relied on Rous sarcoma virus to introduce activated src into cells and thereby incite cell division. But Weinberg would bypass Rous’s virus; he would determine if cancer-causing genes could be transferred directly from cancer cells to normal cells. At the end of the bridge, with snow still swirling around him, he found himself at an empty intersection with lights still flashing. He crossed it, heading to the cancer center.
Weinberg’s immediate challenge was technical: how might he transfer DNA from a cancer cell to a population of normal cells? Fortunately, this was one of the technical skills that he had so laboriously perfected in the laboratory during his stagnant decade. His chosen method of DNA transfer began with the purification of DNA from cancer cells, grams of it precipitated out of cell extracts in a dense, flocculent suspension, like curdled milk. This DNA was then sheared into thousands of pieces, each piece carrying one or two genes. To transfer this DNA into cells, he next needed a carrier, a molecule that would slip DNA into the interior of a cell. Here, Weinberg used a trick. DNA binds to the chemical calcium phosphate to form minuscule white particles. These particles are ingested by cells, and as the cells ingest these particles, they also ingest the DNA pieces bound to the calcium phosphate. Sprinkled on top of a layer of normal cells growing in a petri dish, these particles of DNA and calcium phosphate resemble a snowglobe of swirling white flakes, the blizzard of genes that Weinberg had so vividly imagined in his walk in Boston.
Once that DNA blizzard had bee
n sprinkled on the cells and internalized by them, Weinberg envisioned a simple experiment. The cell that had received the oncogene would embark on unbridled growth, forming the proliferating focus of cells. Weinberg would isolate such foci and then purify the DNA fragment that had induced the proliferation. He would thus capture a real human oncogene.
In the summer of 1979, Chiaho Shih, a graduate student in Weinberg’s lab, began to barrel his way through fifteen different mouse cancer cells, trying to find a fragment of DNA that would produce foci out of normal cells. Shih was laconic and secretive, with a slippery, quicksilver temper, often paranoid about his experiments. He was also stubborn: when he disagreed with Weinberg, colleagues recalled him thickening his accent and pretending not to understand English, a language he spoke with ease and fluency under normal circumstances. But for all his quirks, Shih was also a born perfectionist. He had learned the DNA transfection technique from his predecessors in the lab, but even more important, he had an instinctive feel for his cells, almost a gardener’s instinct to discriminate normal versus abnormal growth.
Shih grew enormous numbers of normal cells in petri dishes and sprinkled them weekly with genes derived from his panel of cancer cells. Plate after plate of transfected cells piled up in the laboratory. As Weinberg had imagined in his walk across the river, Shih soon stumbled upon a crucial early result. He found that transferring DNA from mouse cancer cells invariably produced foci in normal cells, proof that oncogenes could be discovered through such a method.*
Excited and mystified, Weinberg and Shih performed a bolder variant of the experiment. Thus far they had been using mouse cancer cell lines to obtain their DNA. Changing tactics and species, they moved on to human cancer cells. “If we were going to trap a real oncogene so laboriously,” Weinberg recalled, “we thought that we might as well find it in real human cancers.” Shih walked over to the Dana-Farber Cancer Institute and carried back a cancer cell line derived from a patient, Earl Jensen, a long-term smoker who had died of bladder cancer. DNA from these cells was sheared into fragments and transfected into the normal human cell line. Shih returned to his microscope, scouring plate after plate for foci.
The experiment worked yet again. As with the mouse cancer cell lines, prominent, disinhibited foci appeared in the dishes. Weinberg pushed Shih to find the precise gene that could convert a normal cell to a cancer cell. Weinberg’s laboratory was now racing to isolate and identify the first native human oncogene.
He soon realized the race had other contenders. At the Farber, across town, Geoff Cooper, a former student of Temin’s, had also shown that DNA from cancer cells could induce transformation in cells. So had Michael Wigler at the Cold Spring Harbor Lab in New York. And Weinberg, Cooper, and Wigler had yet other competitors. At the NCI, a little-known Spanish researcher named Mariano Barbacid had also found a fragment of DNA from yet another cancer cell line that would transform normal cells. In the late winter of 1981, all four laboratories rushed to the finish line. By the early spring, each lab had found its sought-after gene.
In 1982, Weinberg, Barbacid, and Wigler independently published their discoveries and compared their results. It was a powerful, unexpected convergence: all three labs had isolated the same fragment of DNA, containing a gene called ras, from their respective cancer cells.† Like src, ras was also a gene present in all cells. But like src again, the ras gene in normal cells was functionally different from the ras present in cancer cells. In normal cells, the ras gene encoded a tightly regulated protein that turned “on” and “off” like a carefully modulated switch. In cancer cells, the gene was mutated, just as Varmus and Bishop had predicted. Mutated ras encoded a berserk, perpetually hyperactive protein permanently locked “on.” This mutant protein produced an unquenchable signal for a cell to divide—and to keep dividing. It was the long-sought “native” human oncogene, captured in flesh and blood out of a cancer cell. “Once we had cloned a cancer gene,” Weinberg wrote, “the world would be at our feet.” New insights into carcinogenesis, and new therapeutic inroads would instantly follow. “It was,” as Weinberg would later write, all “a wonderful pipe dream.”
In 1983, a few months after Weinberg had purified mutant ras out of cancer cells, Ray Erikson traveled to Washington to receive the prestigious General Motors prize for his research on src activity and function. The other awardee that evening was Tom Frei, being honored for his advancement of the cure for leukemia.
It was a resplendent evening. There was an elegant candlelit dinner in a Washington banquet hall, followed by congratulatory speeches and toasts. Scientists, physicians, and policymakers, including many of the former Laskerites,* gathered around linen-covered tables. Talk turned frequently to the discovery of oncogenes and the invention of curative chemotherapy. But the two conversations seemed to be occurring in sealed and separate universes, much as they had at Temin’s conference in Houston more than a decade earlier. Frei’s award, for curing leukemia, and Erikson’s award, for identifying the function of a critical oncogene, might almost have been given to two unconnected pursuits. “I don’t remember any enthusiasm among the clinicians to reach out to the cancer biologists to synthesize the two poles of knowledge about cancer,” Erikson recalled. The two halves of cancer, cause and cure, having feasted and been feted together, sped off in separate taxis into the night.
The discovery of ras brought one challenge to a close for cancer geneticists: they had purified a mutated oncogene from a cancer cell. But it threw open another challenge. Knudson’s two-hit hypothesis had also generated a risky prediction: that retinoblastoma cancer cells contained two inactivated copies of the Rb gene. Weinberg, Wigler, and Barbacid had proved Varmus and Bishop right. Now someone had to prove Knudson’s prediction by isolating his fabled tumor suppressor gene and demonstrating that both its copies were inactivated in retinoblastoma.
This challenge, though, came with an odd conceptual twist. Tumor suppressor genes, by their very nature, are asserted in their absence. An oncogene, when mutated, provides an “on” signal for the cells to grow. A tumor suppressor gene when mutated, in contrast, removes an “off” signal for growth. Weinberg and Chiaho Shih’s transfection assay had worked because oncogenes can cause the normal cells to divide uncontrollably, thus forming a focus of cells. But an anti-oncogene, transfected into a cell, cannot be expected to create an “anti-focus.” “How can one capture genes that behave like ghosts,” Weinberg wrote, “influencing cells from behind some dark curtain?”
In the mid-1980s, cancer geneticists had begun to glimpse shadowy outlines behind retinoblastoma’s “dark curtain.” By analyzing chromosomes from retinoblastoma cancer cells using the technique pioneered by Janet Rowley, geneticists had demonstrated that the Rb gene “lived” on chromosome thirteen. But a chromosome contains thousands of genes. Isolating a single gene from that vast set—particularly one whose functional presence was revealed only when inactive—seemed like an impossible task. Large laboratories professionally equipped to hunt for cancer genes—Webster Cavenee’s lab in Cincinnati, Brenda Gallie’s in Toronto, and Weinberg’s in Boston—were frantically hunting for a strategy to isolate Rb. But these efforts had reached a standstill. “We knew where Rb lived,” Weinberg recalled, “but we had no idea what Rb was.”
Across the Charles River from Weinberg’s lab, Thad Dryja, an ophthalmologist-turned-geneticist, had also joined the hunt for Rb. Dryja’s laboratory was perched on the sixth floor of the Massachusetts Eye and Ear Infirmary—the Eyeball, as it was known colloquially among the medical residents. The ophthalmological infirmary was well-known for its clinical research on eye diseases, but was barely recognized for laboratory-based research. Weinberg’s Whitehead Institute boasted the power of the latest technologies, an army of machines that could sequence thousands of DNA samples and powerful fluorescent microscopes that could look down into the very heart of the cell. In contrast, the Eyeball, with its proud display of nineteenth-century eyeglasses and lenses in lacquered wooden vitrines, was al
most self-indulgently anachronistic.
Dryja, too, was an unlikely cancer geneticist. In the mid-1980s, having completed his clinical fellowship in ophthalmology at the infirmary in Boston, he had crossed town to the science laboratories at Children’s Hospital to study the genetics of eye diseases. As an ophthalmologist interested in cancer, Dryja had an obvious target: retinoblastoma. But even Dryja, an inveterate optimist, was hesitant about taking on the search for Rb. “Brenda [Gallie] and Web [Cavenee] had both stalled in their attempts [to clone Rb]. It was a slow, frustrating time.”
Dryja began his hunt for Rb with a few key assumptions. Normal human cells, he knew, have two copies of every chromosome (except the sex chromosomes), one from each parent, twenty-three pairs of chromosomes in all, a total of forty-six. Every normal cell thus has two copies of the Rb gene, one in each copy of chromosome thirteen.
Assuming Knudson was right in his two-hit hypothesis, every eye tumor should possess two independent inactivating mutations in the Rb gene, one in each chromosome. Mutations, Dryja knew, come in many forms. They can be small changes in DNA that can activate a gene. Or they can be large structural deletions in a gene, stretching over a large piece of the chromosome. Since the Rb gene had to be inactivated to unleash retinoblastoma, Dryja reasoned that the mutation responsible was likely a deletion of the gene. Deleting a sizable piece of a gene, after all, is perhaps the quickest, crudest way to paralyze and inactivate it.
The Emperor of All Maladies Page 45
