California Pacific Currents 2002
Laying the Foundations for Gene Transfer
Robert J. Debs, MD
DNA from all living organisms is made up of the same chemical and physical components. DNA sequencing, the side-by-side arrangement of these component parts along the well known DNA double helix, spells out the exact instructions required to create a particular organism with its own unique traits. The genome — an organism’s complete set of sequenced DNA — has been almost completely defined in humans. Yet few therapies based on this new genetic knowledge have delivered the miraculous results many people, perhaps naively, expected.
Cancer, heart disease, and AIDS will not be cured anytime soon, but the promise of gene-based therapy may not be that far off. Hundreds of researchers around the world are working to refine their understanding of disease at the molecular level to advance DNA-based therapies that will benefit patients directly.
One such researcher is Robert J. Debs, MD, a senior scientist at California Pacific Medical Center Research Institute. He and his small team of PhD scientists are exploring the possibilities of gene transfer (more commonly called gene therapy) as a way to treat fatal cancers.
“Basically what causes most severe or fatal human diseases,” says Dr. Debs, “are genetic errors — specific alterations of our DNA. My group is focused on developing tools that will allow us to fix genetic errors in people.” Cancer, for example, usually results from a combination of genetic errors. These can be inherited or can be acquired through interaction with the environment: the result of years of smoking tobacco or exposure to other toxins.
Challenges of Gene Transfer
When Debs says he wants to “fix genetic errors directly in people,” he places special emphasis on people. Many of the gene-therapy strategies tried to date worked fine in cell culture but proved ineffective or even toxic in animal models. (Therapies that fail in animal models are either abandoned or, to be suitable for eventual testing in humans, are further researched, developed, and then retested in animals.)
The location of a genetic error may be well known and and still evade correction. This is true of the minuscule error on human chromosome 7 that causes cystic fibrosis. “Even though we know exactly what DNA sequence must be altered to cure most cystic fibrosis patients, nobody has yet developed DNA delivery techniques that can fix the error or even improve the quality of life for these patients,” says Dr. Debs. “Right now, nobody can effectively correct genetic errors in humans in a safe and lasting way.”
Imagine a single kind of tumor cell growing in a Petri dish as one model and a mouse — an animal nearly as complex as a human — as another. Thousands of different kinds of cells in the mouse interact and change from second to second to maintain the body’s delicate balance, unlike the relatively uncomplicated life of the homogeneous tumor cells living in a dish. “We’re lucky when cell models tell us anything important about the whole animal model. In some fundamental ways, these two models are really apples and oranges,” he says.
As such, Debs and his team are working to develop tried-and-true methods for delivering corrective genes or other therapeutic genetic material to the nucleus of DNA-damaged cells in animals (this is what is meant by gene transfer or gene therapy). The genetic material being introduced must reach the cell nucleus, This is where the cell’s own genetic material is located and from which the functional activity of the cell is directed, to have any effect. Better techniques to deliver transferred genes to cell nuclei and to make these genes work well once they are in place are on the agenda — among a host of other research projects Debs and his team pursue.
Underlying Themes in Cancer
One area of special interest to the group is how cancer spreads (metastasizes) to other organs of the body. “What kills patients is not the development of the cancer but its spread. I’m trained as a cancer specialist. I’ve been on the front lines, so I know how powerless we are with most common tumors once they’ve spread. We usually can’t treat them effectively.”
Although no cancer is exactly like another in its genetic cause, Debs and other cancer researchers are discovering that certain of the same genetic mutations or deletions occur in many different types of tumors. For example, breast, colon, and lung cancer are different cancers, but their tumor cells may harbor some of the same harmful genetic anomalies.
This suggests that there may be underlying genetic similarities that cause cancers to metastasize. “If you know what those genes are, and if those genes are required by many cancers to spread, then it doesn’t matter so much if you’re dealing with lung, colon, or breast cancer,” says Dr. Debs. He and his team are working to discover and fully understand common factors in metastasis and to develop gene-transfer techniques for correcting them.
Genetic errors that cause cancer generally fall into two categories. One type occur in normal genes that have mutated and become hyperactive, causing the cells they inhabit to become cancerous and possibly aggressively metastatic. These are called oncogenes. The other type involves tumor-suppressor genes. Their natural function is to control cell processes. When one of these genes mutates, the cell may grow unrestrainedly or metastasize.
The Inner Life of Cancer Cells
The Debs team is using a new science called functional genomics to investigate the very complicated nature of metastasis and the genetic errors responsible for producing this deadly event. Functional genomics is the effort to identify what each of the thousands of now sequenced genes actually do. It involves sophisticated laboratory techniques that enable researchers to study the inner activities of cells and their interactions at the molecular level.
“For example, we modify the level of expression of targeted genes and see what effect this has on the ability of cancer to spread. We might take a gene and make too much of it in the cell, or we might completely delete a gene of interest,” says Dr. Debs. Through studies like these, Debs and his team are learning much about the function of certain genes involved in cancer. They are discovering, for example, which genes regulate the cell’s life cycle, which promote the formation of blood vessels to feed the tumor, and which enable metastasis.
Knowledge of this kind will benefit Debs’s goal of creating tools for gene transfer. “We’re trying to develop techniques that can fix diseases. Concurrently, these same techniques will help us to better understand the genetic basis that underlies essentially all common fatal human diseases. In other words, as we get more powerful ways to fix DNA, we’ll know better what specific genes we need to fix,” he says.
Tools for Gene Transfer
Debs hopes the techniques his team is developing and the discoveries it is making will lead to their primary objective: the creation of a “generic technology platform” for gene transfer. He is referring to techniques that will serve a wide variety of gene-transfer purposes in a broad range of tissue types and diseases. “For instance, someone interested in ALS [amyotrophic lateral sclerosis] might come to us and say, ‘We need to turn off this gene in the brain to see if it is important in ALS.’ Our team would help them do that,” he says. “In the same way, someone interested in coronary artery disease might ask us to help them make more or less of a lipoprotein through gene transfer. Our platform would apply to virtually everything.”
It will take more long hours of painstaking work to get there. But once the platform is developed, says Dr. Debs, “we might see metastatic cancer change from a fatal disease to either a curable one or, in the worst case, a chronic disease that can be treated, like diabetes.”