Found in translation
Studying the genetics of fruit flies, nematodes and other model organisms may greatly speed the search for cures for human disease.
When cancer researcher Allen Bale, M.D., and his team discovered a gene associated with the development of basal cell carcinoma in 1996, he decided that if he really wanted this new knowledge to help his patients, the thing to do was learn more about fruit flies. So the associate professor of genetics and medicine and director of the DNA Diagnostics Laboratory went to work studying the genetics of Drosophila melanogaster in the laboratory of his genetics department colleague Tian Xu, Ph.D.
Until less than a decade ago, Dr. Bale’s move from humans to Drosophila would have seemed startling. “Those connections just weren’t made,” he says. “People were working on fruit flies and people were working on humans, but they weren’t working on both.” Today, moving between species has emerged as an increasingly necessary part of scientific research and an ever more common path at Yale. The result in Dr. Bale’s case was that he was able to open up entirely new ways of looking at the most common form of skin cancer in humans.
Although Dr. Bale’s laboratory had found a link between the occurrence of basal cell carcinoma and the gene—which they named NBCCS (for nevoid basal cell carcinoma syndrome)—they had no idea how this association gave rise to the cancer. Moreover, its function in a normal human cell was a complete mystery. Without this information, it was virtually impossible to assess how the cancer might be triggered through the workings of NBCCS. Pinpointing the function of a single gene in humans would be a monumental and expensive task. So Dr. Bale turned to Dr. Xu and Drosophila melanogaster, the tiny fruit fly.
By comparing the genetic sequence of NBCCS against other previously identified genes of the fruit fly, Dr. Bale eventually was able to find that it was structurally similar to a gene called Patched. Patched was known to produce a protein that controls the development of distinct anterior and posterior segments of the fly. Using this information, Dr. Bale had the key he needed to direct his own investigations into the human version of the gene. “Once we could show the human gene was similar to Patched,” he says, “we knew what other genes it would be likely to function with.” The NBCCS gene is now widely recognized as the key gene that causes basal cell carcinoma. Moreover, researchers have found that mutations in these other genes are also responsible for other cancers. Dr. Bale’s laboratory is now looking at the ways existing medicines for basal cell carcinoma affect the Patched gene in hopes of coming up with more effective treatments and, one day, a cure.
Dr. Bale’s approach—to switch hunting grounds from the human genome to that of the fruit fly—is an example of an ever-increasing trend within the medical community to use simple model systems to learn about the function and behavior of our own genes. Translational research, as this growing body of work has come to be known, is based on the notion that the genetic similarities among species—from single-cell organisms to humans—are far greater than the differences. By understanding the genetics of the simpler organism, investigators believe they can identify and understand the functioning of the shared genes in humans. Translating the complex activities of human genes into the activities of similar genes in simpler species makes it far easier to interpret the biology of humans and especially human diseases.
“Simple cells have much to teach us,” says Carolyn Slayman, Ph.D., a geneticist who is deputy dean for academic and scientific affairs at the medical school. “It is becoming increasingly clear that the basic pathways of cell growth and development arose very early in evolution and have remained virtually unchanged since.” The increasing availability of genome sequence information coming in from all over the world has provided a major impetus for the recent explosion in translational research. Scientists now believe that some 80 percent of all human genes appear to have a functional counterpart in the fruit fly. The nematode Caenorhabditis elegans, whose genome size is comparable to Drosophila, and even the single-cell yeast Saccharomyces cerevisiae are some other widely used model organisms for which most genes have human equivalents.
The resemblance goes beyond mere structural similarities of genes to entire networks and pathways inside the cells of different organisms. Like jigsaw puzzles that become more difficult and time-consuming as the number of pieces increases, complex organisms contain more genes than simpler organisms do. But the links between these pieces appear to be the same. So by learning how the pieces fit together in simpler puzzles, scientists are putting together a map to guide them through the labyrinth of human genetics as well. “The fundamental machinery that makes a cell a cell is essentially the same in all living organisms,” says cell biologist Peter Novick, Ph.D. “If one can understand the basic working of a simpler system such as the yeast, then the rest is just a matter of specialization.”
A simpler approach
The high degree of evolutionary conservation among all species allows scientists to substitute a gene in one organism with its counterpart from another. Moreover, experimentation on humans in most of these cases is simply not feasible, making animal models a necessary substitute. Using animal models can vastly speed up researchers’ capacities to analyze new genes and mutations associated with a huge range of human diseases. The savings can be tremendous. Where the estimated time and cost for the completion of a genetic experiment on a mammalian system might typically run one year at a cost of $10,000 and take about five to 10 technicians, the same test on C. elegans or Drosophila systems can take a single person a matter of weeks to complete at a fraction of the cost.
“As recently as 10 years ago we only had indications that the mechanisms used by these different organisms were related, but this is now an established fact,” says Michael Stern, Ph.D., associate professor of genetics in the Boyer Center for Molecular Medicine and a pioneer in demonstrating the importance of those relations. During his postdoctoral research at the Massachusetts Institute of Technology, he studied the migration of post-embryonic precursor muscle cells to their eventual locations in the adult nematode. After he arrived at Yale, he learned that SEM-5, a gene product of one of the crucial members of this pathway, looked much like a protein known to be important in human cell-to-cell communication. Probing into the sequence and structure of the gene, Dr. Stern found that the gene bore a remarkable resemblance to a human gene called GRB2 (Growth factor Receptor Binding protein) and also to a fly gene named Drk.
The finding was useful in learning about the conservation of these pathways among different species, and it also had important implications for understanding how cancers grow. Further investigation showed that these genes helped activate the human Ras gene, which is found to be mutated in some 30 percent of human cancers. What was perhaps most surprising of all was that either the human gene or the fly gene could functionally replace the worm gene. “This underscored the remarkable conservation of entire pathways that are important for cellular communication,” says Dr. Stern. “The knowledge that we gain about how these pathways work in both systems can now be used to derive a comprehensive understanding of the pathway in humans. This will help us put together the pieces of a jumbled genetic puzzle that we didn’t know would fit together so elegantly.”
By moving genes from one model organism to another as Dr. Stern is doing, investigators can get an ever more precise understanding of the fundamentals of cell life and, from there, cell dysfunction and human disease.
This multi-lane, two-way street between humans and simple models has become a familiar path for other researchers around Yale. Much of the credit goes to Dr. Xu, who is an associate professor of genetics in Yale’s Boyer Center and an assistant investigator in the Howard Hughes Medical Institute. In his own work, he employs fruit flies and mice to understand the molecular mechanisms of human diseases. With a new genetic approach that he developed during his postdoctoral research at the University of California Berkeley, Dr. Xu developed fruit fly models that develop tumors and neurodegenerative disease. He then demonstrated that mice and humans also contain homologues of the fly genes that he identified, and that mice lacking these genes also develop these diseases. These models, Dr. Xu says, are useful not only to study the function of known proteins, but also to discover important regulators not yet revealed by other methods.
Oxygen and the brain
Cancer is not the only domain in which translational research holds promise. Gabriel Haddad, M.D., chief of respiratory medicine in the Department of Pediatrics, frequently sees children experiencing breathing difficulties and associated problems due to respiratory ailments. Also a professor of cellular and molecular physiology, he has long been exploring how and why the different types of cells in the body respond differently to a lack of oxygen. “Nerve cells in particular are sensitive to oxygen deprivation,” he says. “The brain for example will suffer irreversible damage if the oxygen or blood supply is cut off for even five to 10 minutes. In contrast, the cells of a newly born animal and cancer cells show considerable tolerance to the lack of oxygen.”
In the hope of developing ways to prevent or minimize the damage to brain cells under conditions of hypoxia (low oxygen), such as happens during a stroke, Dr. Haddad began to investigate the molecular pathways triggered by these conditions. “We were able to carry out some tests in tissue cultures but in order to understand the true progression of events we needed living systems,” he recalls. He began his studies on a species of turtle able to withstand oxygen deprivation for several months. His aim was to understand how its cells could withstand such a long period without oxygen. While these animals were useful for figuring out some of the physiological aspects of tissue hypoxia, they were not easily amenable to advanced molecular approaches. Consequently, he considered alternative models. Six years ago, he began looking into the Drosophila system. “It not only had the advantage of being an ideal genetic system,” he says, “but also was extremely tolerant to hypoxia—demonstrating the ability to recover even after hours of oxygen deprivation.”
A clinician by training, Dr. Haddad needed to broaden his knowledge. Like Dr. Bale, he turned to Dr. Xu’s lab to learn the practicalities of working with the fruit fly before launching a full scale investigation in his own laboratory. He is now investigating the hypoxia response on the fruit fly model via a number of approaches. He explains: “One of the methods is to try and identify genes that help the flies recover from oxygen depletion. To this end, we have selected for mutants that are highly sensitive to oxygen deprivation and we are zooming in at the moment on a few mutations that produce this effect.” His laboratory is also trying to identify similar genes in the mammalian and human genome. “Given the fact that flies and mammals have very similar genes for so many different functions such as ion channels and embryonic development, it is quite likely that they will also share genes in pathways that are relevant to oxygen deprivation.” Eventually, Dr. Haddad envisions the development of biochemical therapies for stroke and other conditions that could induce anoxia tolerance in human cells to minimize damage in sensitive areas of the body.
Basic researchers also find they can benefit from switching between model systems. Lynn Cooley, Ph.D., associate professor of genetics, studies the building of the cytoskeleton during development in fruit flies. Her findings may have fundamental implications in understanding the behavior of cancer cells in humans, because they undergo significant rearrangements in their structure during the growth and metastasis of a tumor. “To understand the underlying biology,” she says, “one really has no choice but to turn to a model system.”
Even the most basic, one-cell organism shares fundamental genetic properties with humans. The complete yeast genome sequence is now available. Furthermore most of the expressed genes of mammalian cells have been identified. “Once we are able to see what a gene does in the yeast,” says cell biologist Dr. Novick, “we can apply principles of reverse genetics to look for the function of the homologues.”
Dr. Novick’s own research explores the mechanisms by which the yeast cell secretes different proteins from specific locations on the cell membrane. “This property of cellular polarization has very obvious relevance in cells like neurons and epithelial cells,” he says. “For instance, if an epithelial cell in the lining of the digestive tract were to secrete the enzymes in the wrong direction, you would destroy your own tissues rather than digest the food.”
To date, his investigations in yeast have turned up more than a dozen genes with human homologues for polarization alone. Six of these genes are produced as one big complex, which have been found to be involved in the polarization of cells in the lining of the kidney. Mutations in other proteins that interact with these gene products have been implicated in diseases such as retinal degeneration leading to blindness and one form of mental retardation.
What of the future? By all indications the different model systems continue to yield useful results with increasing relevance to many human diseases. Says Dr. Slayman: “These days a researcher who finds a new human gene will immediately look for homologues in fruit flies, yeasts or nematodes where functional experiments are much easier. Conversely, a scientist who finds a new yeast or nematode gene will rush to find a human homologue which may offer a clue to a known human disease.” It’s all there, it seems, if only the right translations can be found.