One reason why the fruit fly has been a favorite model organism for genetics research is that it has only 4 chromosomes, and in some tissue like the salivary gland the chromosomal DNA is replicated many times without cell division, leading to giant chromosomes, large and thick. In addition, those giant, amplified, chromosomes have a distinct banding pattern, somewhat like laser tags, that help distinguish one chromosome from another, and they identify even specific regions within chromosomes. The pattern is thought to result from the complex folding of chromatin within the chromosome.
In contrast, human chromosomes are many (43 pairs) and small, and do not have a banding pattern. But in the 1960’s, in an experiment in which chromosomes removed from a cell and splayed on a microscope slide were treated with a protein-digesting enzyme (trypsin), suddenly a banding pattern emerged. This was hardly expected, but very welcomed because now specific human chromosomes and chromosome regions could be readily recognized.
The discovery of the banding pattern of chromosomes was one of the lynchpins in working through the first discovery of the genetic cause of cancer in humans, the first “miracle drug” for the treatment of Chronic Myeloid Leukemia, and the ongoing revolution in personalized medicine.
This discovery involved the observation that patients with CML often had an unusual looking chromosome in their leukemic cells. It became known as the Philadelphia chromosome, for the city in which the observation was made.
By observing the banding pattern of that unusual chromosome, Janet Rowley, a young geneticist at the University of Chicago, was able to conclude that the Philadelphia chromosome was actually comprised of a portion of chromosome 22, and portion of chromosome. The two chromosomes had apparently each broken and the broken pieces were rejoined incorrectly, like a piece of a hot dog joining on it broken end to the broken end of a piece of sausage.
The joining point, it turned out – after several years of research – brought together two pieces of unrelated genes, one a regulatory fragment, the other a coding region for a gene for tyrosine kinase, and the two together resulted in a gene that was no longer regulated, belting out a continuous supply of the enzyme, whether needed or not. Tyrosine kinase proved to be a stimulant for driving the cell division cycle, leading to cancerous growth.
Once the gene was discovered it took 50 years before the remarkably specific drug, Gleevec, entered the market, changing the prospects for leukemia patients from grim to hopeful.
The full history of this remarkable story has been published in an appropriately named book, The Philadelphia Chromosome, by Jessica Wapner. A terrific review of the book appeared in Science magazine on June 21, and I attach it here. In the same issue Janet Rowley gives a really interesting personal perspective of this great scientific and medical success story. The book review and perspective together offer us a rich picture as a prelude to reading the book.
1. Review of The Philadelphia Chromosome
From Science 2013 342:1412.
Aditi Nadkarni –Tracing a Translocation’s Impact
The reviewer is at the Department of Biology, 1009 Silver Center, New York University, 100 Washington Square East, New York, NY 10003-6688, USA. E-mail: firstname.lastname@example.org
The Philadelphia Chromosome A Mutant Gene and the Quest to Cure Cancer at the Genetic Level by Jessica Wapner The Experiment, New York, 2013. 327 pp. $25.95. ISBN 9781615190676.
Most of us love an underdog’s success story. Jessica Wapner’s The Philadelphia Chromosome includes several such stories. Wapner, a freelance science writer, describes the path from the first description of a chromosomal abnormality in cancer cells to the successful deployment of a gene-targeted medicine against what had previously been a lethal leukemia. Along the way, she pays homage to various scientific underdogs: a graduate student who spent 10-hour days peering through a microscope for the sheer love of observation; a postdoctoral fellow who risked “the judgment and ridicule of [his] peers” in negating the findings of a world-famous scientist; a junior researcher who doggedly pursued a goal dismissed as unfeasible; a physician who urged a drug company to set aside commercialism for a cure; and, most important, a patient brought back from the brink of death by a new cancer drug. Wapner aptly compares the investigators to “a hundred painters applying brushes to a canvas at some time or another over twenty-five years, driven only by curiosity and, sometimes, a vague hope that their work might eventually be relevant to human cancer.” Without knowing what the end result would look like, she notes, they ended up creating a “scientific masterpiece.”
A half century ago, a diagnosis of cancer was devastating because it meant death was likely imminent. Most available treatments were ineffective and often put patients through immense suffering before they succumbed to their disease. One such cancer was chronic myeloid leukemia (CML), which rendered patients sallow as it rapidly poisoned their immune systems, flooding them with abnormal white blood cells. The survival rate was a mere 14%, and most patients died within six years. In 1960, Peter Nowell and his graduate student David Hungerford noticed a genetic abnormality in a chromosome of CML patients (1), a discovery that eventually led to the idea that rogue genes could be a cause of cancer. The genetic abnormality, the Philadelphia chromosome, would become the first genetic defect identified as a direct culprit in cancer initiation.
Wapner’s narrative begins with the discovery of the Philadelphia chromosome and continues through the 30 years that it took to develop a drug that successfully targeted this genetic abnormality, thus turning a once fatal disease into a manageable condition that can be treated with a pill. Today, 12 years after the drug, imatinib mesylate (Gleevec), entered the market, the survival rate of CML patients is 95.2%. Told in the manner of a thriller with a dash of history, The Philadelphia Chromosome describes the events that went into the “rational design” of that pharmaceutical treatment for CML.
In the early 1970s, geneticist Janet Rowley, using recently developed chromosome banding techniques, observed that the lopped-off head of the Philadelphia chromosome in CML patients had somehow perched onto another chromosome. Going against established views about cancer, Rowley argued that this chromosomal translocation could be the cause of the cancer. Her finding opened the door to the discovery of the cancer-causing oncogene affected by this change in CML patients. It took several years and the concerted efforts of many researchers to uncover the precise mechanism by which the translocated Philadelphia chromosome causes the brakes to fail on a runaway kinase, resulting in uncontrolled cell division—a hallmark of cancer. The discovery of this culprit oncogene, as Wapner describes, ultimately revealed the relation between the Philadelphia chromosome and CML and presented the kinase as a target for therapy. A specific kinase inhibitor could bind to and stop the uncontrolled kinase in its tracks, “[l]ike a gloved hand fitting perfectly over a mouth to block the next breath.”
Much of the second half of the book focuses on the frantic struggle to get the life-saving drug to patients. Here Brian Druker, a clinical oncologist turned researcher, emerges as a hero through his inspiring commitment to patients and his unyielding determination to save people from the clutches of a fierce disease.
Reading Wapner’s account suggests that while the scientists involved in the discovery and development of Gleevec were underdogs in their field, the drug was somewhat of a stepchild for the company. “There were too few patients with CML to make developing this new drug worthwhile for the company.” In short, the drug would not profit the company as much as one that targeted some disease affecting a larger population. This problem of market-driven policy remains a subject of debate. Drug companies are often criticized for shifting their research focus to diseases with a higher incidence to ensure that they have a larger demand for their products.
The author covers a lot of ground in describing the politics of science and dissecting the inner workings of a pharmaceutical company’s drug development process. She withholds judgment, instead providing two sides of the story: In one, a physician coaxes a drug company focused on commercial interest to think about patients. In the other, a drug company, bombarded with sudden demand from the market, rushes to complete the toxicity studies required for Food and Drug Administration clearance. Wapner also describes the impact of the CML community’s 1999 online petition urging increased production of the drug for clinical trials.
In the last chapter, Wapner surveys the current landscape of cancer research, noting hurdles to continued progress such as difficulties in sequencing tumors and the unintended effects of technology transfer agreements on collaborations. She also mentions the pressing issues of poverty, limited access to medical care, and ever-rising drug prices that patients face. In her concluding comments she notes that although targeted drugs have changed cancer treatment and “medicine as a whole,” their failure “to transform other cancers into tolerable chronic conditions has generated skepticism about the future of the approach.”
As a young cancer researcher, I especially appreciate Wapner’s mention of the current abysmal funding situation—which does not reward new or risky ideas and is extremely stingy in supporting those early in their careers. She points out that in 2010, less than 4% of the U.S. National Institutes of Health’s R01 funding went to scientists under age 36. On the contrary, in the 1960s and 1970s (when many of the discoveries described in the book occurred), being a young scientist with novel ideas was an asset. Some key contributions to the Philadelphia chromosome story, as the author notes, came from young researchers given the freedom to pursue their own ideas. Support for such freedom of thought and creativity is now hard to come by in academic bioscience.
Wapner’s use of analogies to describe difficult scientific concepts makes her narrative accessible to lay readers. Still, the jargon in some portions that detail experimental hurdles may overwhelm those lacking firsthand experience in the laboratory. Nonetheless, I appreciate that her artful storytelling does not dilute the complexity of the science or sensationalize the subject. By recounting personal stories of the researchers and patients, Wapner helps readers identify with the story. The Philadelphia Chromosome offers powerful testimony on what the cancer research and pharmaceutical fields are capable of when academic scientists, physicians, and drug companies work together.
PERSPECTIVE by Janet D. Rowley (Science 2013 342:1412)
Forty years ago, a chromosomal translocation was discovered to cause leukemia and revealed cancer as a genetic disease.It was dubbed the Philadelphia chro-mosome, named after the city where the abnormal chromosome was first described in 1960 (1). Peter Nowell, of the University of Pennsylvania, and David Hungerford, at the Fox Chase Cancer Center, had taken a close look at patients with chronic myeloid leuke-mia (CML) and found that regardless of sex, they had a very small chromosome. It was a turning point in cancer biology, the beginning of a story that would draw new attention to chromosome abnormalities as a cause of cancer, a phenomenon that still influences our under-standing of the disease.
To appreciate the importance of the discovery of Nowell and Hungerford, it is necessary to understand the state of biomedical science in the 1950s. The prevailing view from studies of experimentally induced cancer was that chromosome abnormalities were the result of genomic instability in cancer cells, not the cause. It was assumed that loss of DNA from the Philadelphia (Ph) chromosome (originally thought to be a deletion in chromosome 21) included genes that regulate cell growth, thereby leading to unrestrained proliferation of leukocytes. The situation was complicated because some patients with CML lacked the Ph chromosome and surprisingly, they had a shorter survival than did those with a Ph chromosome (2). Nonetheless, the presence of the Ph chromosome became an important diagnostic tool in hematology, and it appeared to be the exception to the established view that chromosome changes were variable and irrelevant in cancer.
The situation changed dramatically in the 1970s when several new staining techniques revealed chromosomes with unique banding patterns (transverse stripes) that allowed them to be distinguished individually and precisely ( 3, 4). Having learned a banding technique at Oxford University, I returned to the University of Chicago to apply the method to chromosome samples from leukemia patients.
Among these patients were two with acute myeloid leukemia (AML), where banding revealed that a piece of chromosome 8 had broken off and joined chromosome 21. This was the first recurring chromosomal translocation [t(8;21)] to be identified (5) . Were chromosomal changes consistent in other leukemias? It was already known that CML patients in terminal blast crisis showed a gain in middle-size chromosomes; these, I discovered, all turned out to be chromosome 8. What was even more startling was that chromosome 9 had an extra piece of material whose stain-ing resembled that of the missing piece of the Ph chromosome (by then, known to be chromosome 22). This suggested that the Ph chromosome could be the result of a translocation involving the swapped ends of chromosome 9 and chromosome 22. Leukemia cells from the same patients in the chronic phase of CML showed the same (9;22) translocation, whereas non-leukemia cells from their peripheral blood had a normal karyotype. It seemed quite likely that the Ph chromosome was an acquired translocation, a finding I reported 40 years ago (6).
There the matter stood for a decade. In the meantime, Herbert Abelson had isolated a virus that induced B cell leukemia. The ”Abelson” virus could transform normal murine lymphocytes and fibroblasts, and the causative viral factor was a protein with tyrosine kinase activity (v-Abl). The human counterpart of the Abelson viral gene, ABL,was mapped to chromosome 9 (7). Moreover, the only additional DNA found in the Ph chromosome was from chromosome 9 (8).The laborious task of cloning the chromosomal breakpoint in CML revealed that the ABL gene on chromosome 9 was translocated into part of a gene called the breakpoint cluster region (BCR) in chromosome 22, creating a BCR-ABL gene fusion (9, 11).
The only previously cloned translocation breakpoints, namely the t(8;14) in Burkitt lymphoma (B cells), had involved an onco-gene called MYC(the human counterpart of the viral oncogene v-myc), and the immuno-globulin gene on chromosome 14 (12,13).The discovery that oncogenes were involved in translocation breakpoints proved to be a remarkable validation of virology and of cytogenetics, fields that were struggling to show their relevance to human cancer. That CML involved the human oncogene ABL was welcome corroboration. Additional translocations were found to involve oncogenes as well, a few of which encoded tyrosine kinases like ABL; others involved genes that activate transcription factors that function in cell growth, differentiation, and even cell death. It was fortuitous that at the same time, drug companies were developing tyrosine kinase inhibitors. From this focus emerged imatinib (marketed as Gleevec), the compound eventually approved in 2001 to treat CML (and later, for other cancers). Like all tyrosine kinase inhibitors, imatinib prevents the protein (BCR-ABL, in the case of CML) from phosphorylating proteins that promote cancer development (14). This pharmaceutical breakthrough came almost 50 years after the discovery of the Ph chromosome. Imatinib changed CML from a disease with a 3- to 5-year average life span to one where patients have an almost normal life expectancy, especially with the advent of new second- and third-generation tyrosine kinase inhibitors. These later drugs, especially ponatinib, have been designed to be effective despite mutations in the activation domain of the ABL protein.
Whereas translocations were first identified in leukemias, lymphomas, and sarcomas, they are now cropping up in many common epithelial tumors, prostate cancer, and lung cancer, among others. Next-generation sequencing of leukemias and solid tumors has revealed a host of translocations (often small deletions or inversions) (15), some of which involve genes that are targets of drugs already approved for therapy of other conditions. It took only a few years from the discovery of the EML4-ALK translocation in lung cancer to the development of the tyrosine kinase inhibitor crizotinib (16), indicating that the discovery of new translocations may be more rapidly translatable to drug discovery. Although data on the occurrence and types of new translocations, based on karyotype analysis, are more frequently reported for hematologic cancers (75%) than for solid cancers (mainly epithelial) (25%), the proportion of malignancies that have recurring chromosomal translocations is the same in both. Moreover, the genes involved have the same function in both cases
(17). Thus, translocations are remarkably similar in function, though not necessarily in their frequency in individual cancers.
It is likely that next-generation sequencing will reveal a much higher incidence of gene fusions in solid tumors. But this method is a two-edged sword. It has identified numerous chromosomal translocations and deletions, but which of these lead to altered gene function and which are inconsequential? It will be difficult to distinguish them in the future without characterizing RNA from the tumors.
A goal of personalized medicine is to identify virtually all of the targetable genetic and epigenetic abnormalities in a patient’s tumor through next-generation sequencing and other technologies. To evolve targeted treatments for cancer, we also need a more sophisticated understanding of tumor-specific antigens and chromatin modifications, for example. There likely will be many surprises along the way, and paradigms will be discarded. Nevertheless, the goal will always be the same – to treat disease and benefit the patient.
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