Friday, March 14, 2008

The Future Of Genetic Research

The eminent British molecular biologist Sydney Brenner once got a hearty laugh from his audience by describing how some future graduate student will define a mouse: "ATC, GCC, AAG, GGT, GTA, ATA. . . ." But every year the idea of defining an organism by the sequence of its DNA bases seems a little less farfetched.

In the sharpest image ever obtained of the DNA double helix (above,right) DNA is magnified approximately 25 million times with the aid of a scanning tunneling microscope, a powerful tool invented in the early 1980s. The turns and grooves of the DNA segment shown in this image closely match those of a corresponding computer-graphics model (above, left).

Victor McKusick, of The Johns Hopkins University School of Medicine, notes that scientists' growing ability to read and write in the language of the genes has already explained some of the once-mysterious basic concepts of genetics. The difference between dominant and recessive traits as causes of genetic disease used to be just an abstraction based on a great deal of observation. If a genetic defect expressed itself only in patients who inherited the trait from both parents, it was called recessive; both copies of the gene coding for the trait were presumably defective, resulting in disease. If the trait was dominant, on the other hand, it meant that one defective copy of the gene was sufficient to spell disaster.

But why should some disorders require two mistakes, while others resulted from only one? Molecular biology has given a concrete and remarkably simple explanation.

"It now appears that these two categories [recessive and dominant] correspond pretty closely to the two fundamental categories of proteins: enzymatic and structural," McKusick said in a recent review of genetics research. Recessive disorders tend to result from failures in genes that code for enzymes, the biological catalysts that do much of the body's chemical work. A person who has inherited the defective gene from only one parent often goes disease-free because the normal gene inherited from the other parent produces enough of the enzyme to serve the body's needs. The disorder appears only when the person inherits the same defect from both parents and therefore lacks any working copy of the normal gene.

If the genetic defect affects structural proteins, however, for example, collagen, a key component of connective tissues and bones, one copy of the faulty gene is usually enough to cause disease. It is easy to see why. A four-engine airplane can still fly even if one of its engines fails, as long as the other engines provide enough power, but a single faulty strut that makes a wing fall off will cause the plane to crash.

The reason some genetic disorders are relatively common while most are extremely rare has also proved to be almost ridiculously obvious. The bigger the gene, the greater the chance that something will go wrong with part of it. In many cases, it seems as simple as that.

Sometimes rather subtle differences in the defects of a single gene can make a profound difference in a patient's fate, as Louis Kunkel of the HHMI unit at Harvard University learned after he and his team discovered the gene for Duchenne muscular dystrophy (DMD) in 1986. Major flaws in that huge gene result in the presently incurable DMD, a muscle-wasting disease that leaves young boys wheelchair-bound by age 12 and generally kills them by age 20, because the muscles that control breathing fail. By contrast, lesser defects in that same gene produce a much more benign disease, Becker's muscular dystrophy.

A year after discovering this gene, the team identified the protein it codes for - a previously unknown protein, now named dystrophin, which occurs in muscles in such small amounts that it would never have been found by ordinary means. Dystrophin plays a key role in muscle cells and may be involved in many other muscle diseases. Researchers are now analyzing how dystrophin functions, what other proteins it interacts with, and whether it might be replaced to interrupt the course of disease.

Experts see many more insights such as these in the future, as research in molecular genetics opens some of the "black boxes" of biology.

"I think we are going to have an explosion of understanding," says David Valle, of the HHMI unit at The Johns Hopkins University. For example, the causes of mental disorders certainly include environmental factors, but biological psychiatrists believe the genes are whispering an important message, if only it can be heard.

Genetic research will illuminate many disorders of single organs, such as the eye, teeth, skin, and cochlea (the hearing apparatus of the ear), Valle believes. The deafness of about two-thirds of patients with serious hearing problems has a genetic basis, he says. Molecular biologists can find genes that are expressed only in the cochlea and therefore are probably important in hearing. Once such genes have been identified, several strategies exist for determining their functions and suggesting treatments.

Valle's current research focuses on a rare genetic disorder of the eye, gyrate atrophy, which leads to blindness through degeneration of the retina. The basic fault is an enzyme defect that causes an abnormal buildup of the amino acid ornithine. Surprisingly, some 35 different mutations in a single gene are able to produce the disease. The excess ornithine is found almost everywhere in the body - blood, urine, tears, spinal fluid, but the serious ill-effects are limited almost entirely to the retina. As yet, nobody knows why.

Understanding the genetic cause of the disease has led to a medical treatment that seems effective: severely restricting the patient's diet to bring the ornithine levels down to nearly normal. Recently, the scientists have compared the effects of this treatment on children in whom it was started early and on siblings who did not receive it until an older age. The studies confirm that the dietary restriction minimizes damage to the retina, Valle reports. But the diet is only a stopgap solution.

Geneticists are searching for more effective remedies, including possible treatment for the gene defect itself.

"One of the really exciting things about modern molecular genetics is that we now have opportunities to make animal models of these diseases and to study what happens at the tissue level in a direct way," Valle says. "That is one of the big things that is going to be happening in the next decade or so.

Philip Sharp, director of the Center for Cancer Research at MIT, divides the benefits of genetics research into two categories: those that generate knowledge and those that generate treatment. He sees animal models as extremely important to both. Deliberately produced genetic diseases in animals will have pathologies like those of human diseases. "We will learn how to recognize them, treat them, and analyze them in animals," he says. "That is going to be the forefront of biomedical science, in one area of it at least."

In addition, many aspects of human development will be clarified by work with mice, flies, and worms, he says. Scientists have discovered that genes which are developmentally active in both Drosophila, the fruit fly, and C. elegans, the nematode worm, have direct counterparts in mammals, although the functions of these genes in humans are not yet entirely clear.

When genes of species that separated from each other many millions of years ago show so much similarity, there is every reason to believe they are related. Many molecular biologists have noticed that nature is quite frugal in preserving devices that have proved biologically effective. As an example, Valle points out that the human enzyme ornithine delta aminotransferase, which is defective in gyrate atrophy, is 54 percent identical to the comparable enzyme that functions in yeast.

"I think one of the real themes of biology is that Mother Nature uses things over and over again once she figures out how to solve a problem," Valle says.

This concept offers scientists a great opportunity, says Eric Lander of the Whitehead Institute. He thinks there is hope of compiling, eventually, a complete thesaurus of protein parts that function in Earth's myriad species. "That would be spectacular," Lander says. "If we had the thesaurus of all the moving parts, then we would understand life in a remarkable way."

Gene mapping and cloning are key to the assembly of the thesaurus, and progress in these areas is clearly accelerating. However most of the 50,000 to 100,000 human genes remain totally unknown, and there is still a long way to go.

To date, most of the progress in understanding the genetics of human disease has involved relatively rare conditions, such as cystic fibrosis or Duchenne muscular dystrophy, which are caused by errors in single genes. But science is also stalking the genes that contribute to heart disease, cancer, diabetes, and mental illness - the big killers and cripplers of mankind.

It may soon be possible to tell some people that they have certain genetic predispositions to a specific major illness and suggest that they tailor their lifestyles accordingly. Similarly, the use of drugs to treat some of the important diseases could be tailored to the genetically varied needs of patients, with benefits for them and for the health care system in general: "Different strokes for different strokes," as one scientist put it.

On the other hand, some scientists fear that people might be stigmatized or become uninsurable because of genetic traits, such as carrier states, that don't in themselves have any appreciable effect on health.

Genetic research is advancing steadily, often rapidly, on many fronts. It has long been known that some disorders affect males, others affect females primarily, while still others may appear in either sex. But a few years ago researchers discovered that, even in some of the latter disorders the gravity and sometimes even the nature of disease may depend on which parent provided the faulty gene. This phenomenon is called imprinting. Although it has been detected only in rare human conditions, imprinting is a subject of intense study as researchers look for other examples.

Other scientists have forsaken the genes that reside in cell nuclei and are finding new clues to disease in the genes of what are probably our oldest and most entrenched "parasites" - the mitochondria - tiny, energy-generating organs inside every cell. Mitochondria are thought to be the descendants of ancient bacteria that not only found a home in animal cells, but also adapted so thoroughly that they became indispensable functional parts of those cells. We inherit mitochondria only from our mothers; sperm leave their mitochondria behind when they enter the egg. Flaws in mitochondrial genes have been found to lead to certain types of blindness and epilepsy and may also contribute to some degenerative disorders, such as dementia, which are associated with aging.

"Mitochondrial DNA gives us a whole new way to think about genetic transmission of diseases," says Douglas Wallace of Emory University, a specialist in those vital intracellular power stations.

In even more fundamental ways, discoveries in genetics have led to novel strategies for treating disease. Decades ago, scientists learned that DNA is mainly the archive of genetic information. Its orders are translated into action by segments of ribonucleic acid (RNA), which serve as the working blueprints for all proteins. Today, chemists are beginning to create valuable new drugs by fabricating "anti-sense" segments of RNA, whose sequence is the exact opposite of an unwanted sequence, to combine with certain existing strands of RNA and thus block the action of specific genes.

The bottom line in any kind of biomedical research lies in the realm of treatment and prevention. The ultimate step in that direction is gene therapy - the deliberate transplantation of genes to treat or even prevent human disease. Many geneticists dismiss gene therapy as a distant prospect, but others disagree. "We are going to have gene therapy," Philip Sharp says. "We are probably going to have it soon."

Gene therapy was actually tried in 1970 and again in 1980 without success, but the knowledge and techniques were primitive by today's standards. The first attempt in what might be called the modern era of gene therapy began in September 1990 at the National Institutes of Health (NIH), when doctors treated a 4-year-old girl. The child suffered from a grave immune deficiency because she lacked the enzyme adenosine deaminase. The doctors took her own white blood cells, altered them by adding the gene for the missing enzyme and transplanted the altered cells back into her.

Next on the NIH agenda was a substantially different strategy introducing a cancer-fighting substance, tumor necrosis factor, into the genetic repertoire of melanoma patients' own cancer-fighting white blood cells. Ultimately the same approach may be applied to other types of cancer.

Philip Sharp suggests one possibility that might be tried as soon as techniques are sufficiently refined. Instead of treating an AIDS patient for the rest of his or her life with a drug to protect the immune system against the HIV virus, doctors might use gene transplants to render the patient's immune system permanently resistant to the virus.

W. French Anderson of the NIH, one of the architects of the new attempts at gene therapy, sees a bright future. By the early years of the next century, he predicts, gene therapy will have become a highly sophisticated drug delivery system. Doctors will give the patient one, or perhaps several, transplants of his or her own cells that have been genetically engineered to manufacture a drug. In many cases this might replace the conventional practice of injecting drugs at regular intervals. How far in the future is this new application of genetic medicine? Five to ten years for the essential techniques, he estimates, somewhat longer to achieve a high degree of sophistication.

The first gene therapy attempts at NIH used the patient's white blood cells as the target for gene insertion. In the future, scientists hope to perfect techniques for using bone marrow cells. Several research centers are making progress in animal experiments using liver cells and endothelial cells, such as those that line blood vessels, to deliver valuable genes to the tissues where they would be useful. Another strategy that would have seemed sheer fantasy a few years ago is being discussed by serious scientists today. That is the idea of using inhalant spray to deliver copies of a good gene to airway tissues of cystic fibrosis patients.

The transplantation and manipulation of genes in other species has already proved valuable in genetics research and will probably play an even larger role in the future.

Mario Capecchi and his team at the University of Utah have recently used the method of gene manipulation known as homologous recombination to discover the function of a mouse gene. The gene first attracted notice because it produced breast cancer in the animals when it became activated abnormally. By developing mice in which that gene, and only that gene, had been knocked out, the scientists showed that the gene's normal function is crucial to the development of two regions of the animals' brain: the midbrain and cerebellum. The discovery opens an important door to studies of brain development and brain function.

To use homologous recombination, scientists must be able to identify and grow embryonic stem (ES) cells, the unspecialized precursors of all other cells in an organism. In Capecchi's mouse experiments, ES cells are modified to alter the specific gene under study and then implanted in a very early mouse embryo and used to breed animals that have the desired trait or flaw. Some experts consider this technique among the most exciting recent advances in genetics research.

But the excitement in genetics is general and pervasive. "Having been part of genetics research for 30 years, I find it almost stupefying that it is every bit as exciting and maybe even more so than it has seemed in the past," says Leon Rosenberg, dean of the Yale University School of Medicine. "I continue to be dazzled by the pace and surprise of new information in the field."

Studies of microbes, plants, animals, and many normal human beings are all contributing to the explosion of new knowledge. In recent years, molecular genetics has given important insights into the origin of life and its evolution, the emergence of humans, and our intimate relatedness to every other species on Earth. We can expect many more advances as geneticists continue to explore the wonder of life.

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