COLUMN ONE : Genetic Detectives on a Roll : Researchers are zeroing in on genes that cause disease. The discoveries promise to revolutionize detection and treatment.
Imagine you work for the water company and you are called on to find the single leaking faucet in the United States.
That, says molecular biologist Francis Collins of the University of Michigan in Ann Arbor, is the magnitude of the task he faced when he set out in 1985 to find the defective gene that causes cystic fibrosis, a fatal disease that is characterized by a buildup of mucus in the lungs.
Collins and his colleagues needed to find a particular string of about 100,000 chemicals buried somewhere in the pool of 3 billion chemicals that make up the human genome--the complete set of instructions for making a human.
Using genetic technology developed during the 1980s, Collins and Lap-Chee Tsui of the Hospital for Sick Children in Toronto were able to locate their leaking faucet, announcing in August that they had finally identified the one defective gene that causes the disease.
They are not alone in their success. In the last three years, researchers have located four other equally perplexing genes: the defective genes that cause retinitis pigmentosa, Duchenne muscular dystrophy and chronic granulomatous lymphoma and the gene that determines the sex of children. “That’s quite an achievement,” Collins said.
Researchers agree that future prospects look just as bright. Biologists are on the verge of identifying the genes that cause many of the estimated 4,000 diseases caused by a single genetic defect, including Huntington’s disease, Wilms’ tumor, neurofibromatosis, polycystic kidney disease, hereditary colon cancer and a host of others.
“We are just beginning a golden age of genetics,” said UCLA medical geneticist Robert Sparks.
“It’s just an extraordinarily exciting time to be working in the field,” added molecular biologist Kenneth Kidd of Yale University. “Renaissance might be another good word to describe it.”
Many of these discoveries will have immediate impact. The identification of the gene that causes a disease, for example, makes possible prenatal screening of fetuses to determine if they are susceptible to it. Just last Tuesday, Integrated Genetics Inc. of Framingham, Mass., announced that it will begin marketing a prenatal test for cystic fibrosis.
For the present, such identification may lead only to termination of the pregnancy to forestall a life of suffering. But in the longer term, physicians may be able to identify fetuses or children who are potential victims of genetic diseases, allowing parents to take precautions to minimize the risk of the disease in their offspring.
Identification of genetic defects will also make possible new forms of therapy, particularly in cases such as cystic fibrosis, where nothing was previously known about the biochemical defect underlying the disease. This fall, for example, researchers around the country are beginning studies of a bold new treatment for Duchenne muscular dystrophy that was made possible, in large part, by the recent identification of the causative gene.
Geneticists are also becoming more sanguine about piecing together the riddle of diseases such as cancer, diabetes and heart disease, which involve several genes working together. In addition, they are discovering the genes that control a variety of normal processes in the body, yielding new insights into how life functions and promising the development of new techniques to promote health.
“We’ve seen only the beginning of this whole thing,” said UC Irvine geneticist Francisco Ayala. “We are going to live in a very different world in molecular biology and medicine 10 years hence.”
The rapid pace of progress is all the more remarkable because no one could have predicted it even as recently as the early 1970s. At a 1973 International Congress of Genetics in Berkeley, graduate students were complaining that genetics was a dead-end career, that few research positions in universities were open to them and that industrial jobs were non-existent.
Unknown to them at the time, however, molecular biologists Herbert Boyer of UC San Francisco and Paul Berg of Stanford University had only weeks before devised the first technique for transferring genes from one organism to another. That discovery triggered a revolution unlike any other in science. For the first time, researchers were able not only to study the intimate details of DNA (deoxyribonucleic acid, the blueprint of life), but to manipulate it as well.
DNA Replication
By putting genes or other fragments of DNA into bacteria and yeast, which were then grown in the laboratory, researchers were able to replicate DNA in large amounts for the first time, thereby making it vastly easier to sequence, or learn the precise order of, the individual chemicals, called bases, strung along the DNA strands like beads on a necklace.
A $3-billion national project to sequence the entire 3 billion bases in the human genome is getting under way. That project is expected to take 15 years, but for the short term, geneticists are concentrating on locating the estimated 100,000 human genes--which make up only 10% of the genome--and sequencing the 10,000 to 150,000 bases in each. Only after these are identified will they attack the 90% of remaining genetic material in the genome, whose function is unknown.
Their work has been made easier by the development of new techniques that greatly speed up the scientific detective work. One of the most important of these is an enzyme-based technique called polymerase chain reaction (PCR), which enables researchers to replicate DNA much more simply and quickly than with conventional genetic engineering techniques.
Conventional methods require researchers to insert a gene or DNA fragment into a bacterium, grow large quantities of the bacteria in the laboratory and isolate and purify the desired DNA, a process that can take days or weeks.
PCR avoids the need to work with bacteria. Researchers simply place their desired DNA in a test tube with an enzyme called DNA polymerase and the raw materials from which DNA is formed. Within hours, the enzyme will manufacture millions or billions of copies of the original DNA in relatively pure form.
The sequencing of DNA has also been automated. Ten years ago, an average graduate student might have been able to sequence one or two bases per day. Now, automatic machines can sequence 10,000 bases per day and newer machines promise to sequence 200,000 per day.
One of the most unusual of the new techniques is called the “zoo blot.” It is used when researchers have identified a long DNA segment that contains the gene they seek but are having difficulty separating the gene from the extraneous DNA that surrounds it.
The zoo blot relies on the fact that similar functions in animals and man are usually carried out by similar or identical proteins. If a gene codes for a protein with a normal function, it is usually present in more than one species of animals, according to USC geneticist Norman Arnheim. The hemoglobin in the blood of a cow or rabbit, for example, is very similar to the hemoglobin in human blood; hence, their genes are also very similar.
Geneticists thus compare the DNA fragment they are studying to DNA from other animals, including cows, pigs, rodents, rabbits, frogs, and even insects, such as fruit flies. If they find that a portion of their DNA is identical to DNA from other animals, they can be fairly confident that that portion is the gene.
A Crucial Step
Zoo blots were a crucial step in identifying the cystic fibrosis gene, Collins said.
With these new techniques, researchers have greatly accelerated the pace of genetic research. That pace was displayed at the 10th International Workshop on Gene Mapping at Yale in June.
At that meeting, researchers reported for the first time the approximate locations of 53 genetic abnormalities, raising to 164 the number of such defects whose precise or approximate locations on the human genome have been discovered.
Among the genetic defects whose locations were reported, Kidd of Yale said, were those that cause manic-depressive illness, schizophrenia, dwarfism, cleft palate and epilepsy.
At the same meeting, researchers also reported locations for 700 normal genes, bringing the number of known normal gene locations to 1,700. By contrast, when the first such meeting was held in 1973, the number of genes whose location was known was only 50, Kidd said.
Perhaps a more graphic example of the accelerated pace of research was provided by geneticist C. Thomas Caskey of Baylor University in Waco, Tex. In 1980, he said, six people worked in his laboratory for 18 months to identify a single human gene. The process required “horrific manpower and effort,” he said.
But this summer, Caskey noted, a single graduate student in his lab designed an experiment to locate and sequence an animal gene for a protein called urokase and completed the project in only seven days.
Armed with these new techniques, geneticists are searching avidly for the defective genes that cause such conditions as Huntington’s disease, as well as for the oncogenes that cause cancer, the anti-oncogenes that provide protection against cancer and the myriad genes that are thought to produce susceptibility to heart disease. Most researchers expect a continuing stream of new discoveries over the coming decades.
But the research is also taking them down unexpected pathways. “We are finding new genes with functions we hadn’t even imagined existed before,” Kidd said. “We can look at a DNA sequence and say ‘This structure is a gene,’ but we don’t know what it does.”
Kidd noted, for example, that researchers have discovered genes for several hormone receptors-- proteins on a cell’s surface to which hormones bind--”that were identified because they have a common element that defines them as receptor genes. But when they were initially identified, it wasn’t known what they were receptors for.”
Turning On and Off
Ultimately, added UC Irvine’s Ayala, researchers hope to learn how groups of genes are turned on and off. Geneticists already know how individual genes are turned on, he said, “but we don’t know how the whole organism and the environment interacts to produce noses and ears and legs and brains--how groups of genes are (activated) as opposed to individual genes.”
Such knowledge might lead to the ability to regrow lost arms and legs or even internal organs. “These interactions may be much simpler than we anticipate,” he said.
Concluded UCLA’s Sparks: “We are just beginning to see the fruits of these new developments. . . . There will be much more in the future.”
