The Doric Column

May 26, 2003

Discovery Genomics Tools Up for Gene Therapy
A Fish Story
DNA on Tour & a "Tour de Force"
Gene Therapy: Perils and Promise

Discovery Genomics Tools Up for Gene Therapy

Willingly or unwillingly,
the ability to read the human gene code (genome)...
Makes us all explorers.

        As the Future Catches You
        Juan Enriquez

This marks my 20th year working in a Medical School.

I was hired in 1983 to do some editing and public relations for physician-scientist Jorge Yunis. He had built a solid international reputation in the fields of cancer genetics, genetic birth defects, and the comparative genetic evolution of the great primates and us.

When I started, all the talk was of the discovery of cancer genes, so-called cellular oncogenes. These were the culprits somehow involved in the early stages of cancer -- the opening act. They were viral DNA sequences, originally found in animals like chickens and rats, that had made their way into human chromosomes over the eons. Cellular oncogenes, when mutated by a carcinogen, when "turned on," could transform human cells in a culture dish -- could make them cancerous.

For the next seven years I tried to learn all I could about DNA, genes, and those curious objects in the cell nucleus that package the whole works and transfer it to the next generation during cell division. The chromosomes. I spent a lot of time in Diehl Hall, the University's Biomedical Library.

As it turned out, this experience yielded valuable early insight into what today is called "genomic geography." I learned where genes thought to be important in cancer, like oncogenes and "tumor suppressor genes," are located on the human chromosome map [see illustration, right], exactly where chromosomes tended to break and rearrange in different types of cancer [sometimes at the sites where oncogenes are located], and how certain viruses known to cause cancer insert themselves repeatedly at the same site on the same chromosome.

More or less on my own, I made genomic maps. Not terribly detailed maps, really, but maps that brought together things that I had learned. One of my maps caught the eye of Dr. Yunis. He wanted to see the scientific papers that backed it up. These I quickly produced for him. He liked what he saw so well that, after further verification, he incorporated a concept I was developing into his next scientific paper and made me co-author.

My experience making genomic maps is why I find the science of Perry Hackett and his colleagues Stephen Ekker, David Largaespada, and Scott McIvor at Discovery Genomics, Inc. and the University's Beckman Center for Genome Engineering so intriguing.

My interest is fueled by what I understand about their science. The facts are more sobering: the start-up firm, based on University of Minnesota technology, has entered the highly competitive biotechnology arena where success rests on good ideas, hard work, and blind luck. Lots of "interesting" technologies have been shelved in recent years for lack of a perceived future in the marketplace.

With that caveat, Discovery Genomics has the advantage of rowing with the current produced by three high-powered research fields: a model vertebrate animal system for genetic studies, gene identification, and gene therapy.

The future of the privately held company rests largely on its unique approach to genetic tool making for these fields.

A Fish Story

First a fish story.

While I was digging and photocopying in the Biomedical Library during the 1980s, Perry Hackett was developing "expression vectors" for the Minnesota Transgenic Fish Group, formed by University faculty members Kevin Guise, Anne Kapuscinski, Tony Faras and Hackett.

The group's main goal was to find a way to promote growth in commercially valuable fish such as walleye, northern pike and rainbow trout. What they found is that transferring genes from one species to another is tricky business: Much depends on where in the fish chromosomes the new gene is inserted and whether enzymes called integrases can be recruited to place the new DNA sequence in the appropriate regulatory environment.

In brief, the cooperation of signaling DNA sequences upstream and downstream from the inserted gene can make all the difference. Even in fish that expressed the new gene, usually the gene was not expressed uniformly in all tissues including what Hackett calls "the most important tissue," the gonads, which meant the trait would not be passed on to the offspring.

In their initial experiments, Hackett and his colleagues used integrase recognition systems from disabled retroviruses to construct their transgenes for delivery to fish chromosomes. They were hampered in their efforts because big fish spawn only once or twice a year. So in 1986 Hackett introduced zebrafish [Danio rerio] into his laboratory. Zebrafish spawn every couple months. That move "opened up new areas of research," as Hackett puts it modestly.

Indeed, that move helped to make Danio rerio what it is today at the dawn of the post-genomic era -- a star model organism for the study of development, organ formation, behavior, aging, and disease. Zebrafish reproduce rapidly and their bodies are transparent, so that the developmental consequences of genetic mutations introduced into their genomes can be observed and tracked. Indeed, they are literally windows on tissue, organ, and disease development.

Hackett is a professor in the Department of Genetics, Cell Biology, and Development, a joint department of the Medical School and the College of Biological Sciences. He is also chief scientific officer and founder of Discovery Genomics, Inc. In March he gave me a tour of the company's offices and laboratories at 614 McKinley Place in Minneapolis.

Although the building is new, the territory was familiar to me. I had worked for R&D Systems, Inc. in the late 1980s. R&D Systems, a leading supplier of biological reagents called cytokines for the research market, is part of Techne Corporation which is headquartered at 614 McKinley Place and which is an investor in Discovery Genomics.

Last century, the space on which Techne Corporation and Discovery Genomics reside, an industrial area just west of Stinson Boulevard in northeast Minneapolis, spawned the dried milk powder business of Land O'Lakes Creameries, Inc. The business quickly became the nation's largest.

I asked myself, will the land prove to be bountiful again? Will its yield help to make Minnesota a global biosciences hub that Governor Tim Pawlenty wants it to be?

Hackett took me into a small room that reminded me of the tropical fish alcove of my neighborhood pet store, except in this case the residents of the aquatic tanks looked strikingly alike. They were going about their business until Hackett brought an index finger close to the glass. It drew them close like a magnet. An abrupt motion then sent them scurrying.

He made a passing reference to herd behavior, a term that scientific brilliance looking for capital knows viscerally.

There's the rub. For Hackett and his colleagues. Perhaps for Minnesota's biosciences future, for our "genomic geography."


But finance is a problem nearly everywhere. From the beginning, Hackett said, he was "adamant that we stay here," adding that "if you go to the biotech centers on the east or west coast, employees can't afford to live there. I can't afford to live there."

Hackett graduated from high school in Palo Alto, California and attended college at Stanford University as an undergraduate. He knows Stanford well, including some of its luminaries such as Nobel laureate Paul Berg. And he knows the entrepreneurial culture of the San Francisco area.

In his view, Minnesota has a lot going for it. It has local talent and "a lot of terrific resources" at the University of Minnesota.

"Minnesota has all the infrastructure in place for us to be successful here, with one huge exception. Sophisticated business investors in biotechnology are not located here," Hackett said.

"We need sophisticated people to keep an eye on things."

DNA on Tour & a "Tour de Force"

Back in the days when human chromosomes swam about the backdrop of my mind like a screensaver, I remember reading a paper by Cold Spring Harbor geneticist Barbara McClintock entitled "The Significance of the Responses of the Genome to Challenge" [Science, 226:792, 1984]. It was the paper she delivered in Stockholm, Sweden when she received the Nobel Prize in 1983.

"In the future, attention undoubtedly will be centered on the genome, and with greater appreciation of its significance as a highly sensitive organ of the cell, monitoring genomic activities and correcting common errors, sensing the unusual and unexpected events, and responding to them, often by restructuring the genome," McClintock wrote. "We know about the components of genomes that could be made available for such restructuring."

One of the components constantly at work restructuring the genome, which McClintock discovered while studying the genetics of corn (Zea mays) in the 1940s, she called mobile or transposable elements.

These sequences of DNA-on-the-move, colloquially called "jumping genes," burrow into the organism's chromosomes and produce everything from "small changes involving a few nucleotides, to gross modifications involving large segments of chromosomes, such as duplications, deficiencies, inversions, and other more complex reorganizations."

I was interested because I was studying so-called fragile sites in human chromosomes. Fragile sites are specific places where chromosomes break and fracture when the chromosomes are subjected to ionizing radiation, chemical agents, or dietary deficiencies -- that is, when they are subjected to environmental "challenge."

It is the genomic "transposable element," or transposon, that Hackett and his scientific colleagues have recruited, refined and outfitted to do the work of gene delivery.

In so doing, they have produced a practical tool for science, a great promise for medicine, and a tour de force of creative ingenuity: the "Sleeping Beauty Transposon System."

It began with zebrafish.

In 1994 scientists discovered transposons in zebrafish, proving that "jumping genes" jumped in vertebrate genomes. The next year Hackett and his colleagues reported that they had characterized a family of transposons in Danio rerio. In some instances the transposons were not evolutionarily conserved or embedded. That meant they could potentially be "exploited for gene tagging and genome mapping."

That finding spurred them to take the next step. "We decided to make a transposon ourselves," Hackett said.

They turned to the salmon family. Transposons were known to be more active in salmon in recent evolutionary time than in zebrafish, meaning they were less embedded. Using a "cut and paste" approach that DNA transposons themselves use in moving around and across genomes "in order to avoid extinction," Hackett and his postdoctoral associates Zoltán Ivics and Zsuzsanna Izsvák set about to build a transposon.

They identified and eliminated DNA sequences, accumulated through evolution, that impaired the ability of the transposon to recognize and bind to potential receptor molecules in the host genome. With these out of the way, the transposon's enzymatic machinery -- its transposases and integrases -- possessed the recognition sequences they needed to carry out the binding, cutting and pasting in an efficient manner.

The transposon engineered by Hackett and his colleagues took up residence in fish and mammalian cells, including human cells. Its frequency of uptake in cells could be increased many fold by combining the transposon with a lipid.

The scientists dubbed their creation "Sleeping Beauty" because it was "awakened from a long evolutionary sleep" in the salmon genome, with the help, of course, of molecular tools, computer analysis, and informed guesswork.

In their breakthrough paper, published in the journal Cell in 1997 ["Molecular Reconstruction of Sleeping Beauty, a Tc1-like Transposon from Fish, and its Transposition in Human Cells," 91: 501-510], they observed that "Sleeping Beauty should prove useful as an efficient vector for transposon tagging, enhancer trapping, and transgenesis in species in which DNA transposon technology is currently not available."

And for delivering therapeutic genes safely and effectively to patients who need them.


Gene Therapy: Perils and Promise

Important dates in the history of DNA

1953: Crick and Watson discover the double-helix structure of DNA.

1962: Watson, Crick and Maurice Wilkins share the Nobel Prize.

1990: Launch of the Human Genome Project; first gene therapy trial starts.

1993: Researchers clone first human embryos.

1997: Dolly the sheep, the world’s first cloned mammal, is born.

2003: 50th anniversary of Crick and Watson’s discovery; Dolly dies; the future of gene therapy trials is discussed.

          The London Times
          February 28, 2003

On the day marking the 50th anniversary of when James Watson and Francis Crick launched the genetic revolution by deducing the three-dimensional structure of DNA, a headline in the Washington Post issued a cautionary note:

Dream Unmet 50 Years After DNA Milestone
Gene Therapy Debacle Casts Pall on Field

Two boys in France being treated for severe combined immunodeficiency [SCID] by gene therapy had developed cancer. Though some pediatric patients had been cured of the deadly immune disease through the new technique, the next day, March 1st, the Food and Drug Administration [FDA] put severe restrictions on its use. It looked as if parents of children with "bubble boy" disease -- named for the Houston boy who spent his entire life inside a plastic bubble with filtered air -- had a longer wait in store.

Practically all gene therapy protocols currently in use employ genetically engineered viruses to deliver new genes into the patient's cells. Currently, no way is known to direct the virus to a specific and safe site on a chromosome, that is, to ensure that it does not interfere with a healthy gene or trigger a cancer gene.

The latter is apparently what happened to the two young boys being treated in Paris. In one case the correcting gene landed inside a cancer-promoting gene called LMO-2; in the other it landed near the LMO-2 gene.

The LMO-2 gene is located on the short arm of chromosome 11 at band p13, its street address in the human genome where the virus carrying a therapeutic gene paid an unwelcome call. It is essential for the healthy development of the blood system. When LMO-2 is disrupted it can lead to T-cell leukemia.

One possible solution, according to the physician treating the SCID disease patients in Paris, is to build a "buffer zone" around the virus to diminish its effect on nearby genes, such as LMO-2.

Which brings us back to Perry Hackett & Company at Discovery Genomics and their hopes to enter the multibillion-dollar gene therapy market.

Like viruses used to deliver therapeutic genes, the Sleeping Beauty transposon integrates into many different sites in fish and mammalian chromosomes. But the system Hackett and his colleagues are developing possesses protective features that viral systems do not have, at least not yet.

They are called "border elements."

Border elements may provide the "buffer zone" the French physician overseeing the gene therapy trials for SCID disease called for.

Hackett describes border elements as DNA sequences that "insulate normal genes and transgenes from chromosomal 'position effects' that can alter the specificity and stability of expression of transgenic DNA." He concedes that "no one knows how they work" or exactly why they provide a protective effect.

In short, border elements allow foreign genes or transposons delivering them to take up residence at any genomic street address without anybody really knowing or caring. Gene transcription, expression, and regulation in the neighborhood goes on as if nothing has changed -- as if no one has moved in. The new resident, the transgene, carries out its own transcription, expression, and regulation without causing a stir.

In experiments with zebrafish, Hackett's team is now incorporating border elements into its transgenic vectors. What they are finding is that dressing up Sleeping Beauty with border elements is a beautiful thing to behold. The gene carried by the transposon is highly expressed with this bit of technical powder-room touching up.

Some scientists are finding a relationship between border or insulator elements and the architecture of chromosomes; others find them associated with "chromatin hypersensitive sites."

Chromatin - the mass of DNA and proteins that condenses to make chromosomes during cell division -- forms loops, as illustrated below. In the model, a gene's promoters and enhancers, which control everything it does, cannot interact with the promoters and enhancers of other genes (colored in yellow and orange). Border-element proteins may serve to keep the loops separate (blue) or cordon them off by attachment to the nuclear matrix (red).

From Bell et al., "Insulators and Boundaries: Versatile Regulatory Elements in the Eukaryotic Genome," Science: 291, 5503 (2001).


Which transports me, loop-like, back to my work with human chromosome authority Jorge Yunis.

It takes me back to my experience as a would-be scientist and the countless hours I spent studying "chromatin hypersensitive sites" in the Biomedical Library, for which I was awarded co-authorship of a scientific paper. It reminds me of my efforts to find a relationship between fragile sites and these relatively unprotected sites in chromatin, home to promoters and enhancers, that are vulnerable to attack by enzymes, chemicals, and radiation. Is it the "looping," fostered by border elements, that makes them vulnerable?

I, for one, am excited about the scientific work being done by Perry Hackett, Stephen Ekker, David Largaespada, Scott McIvor and others at Discovery Genomics and the University's Beckman Institute.

And it's my hunch -- albeit merely a hunch, as I am a nonscientist and, alas, have no investment capital to speak of -- that they are really on to something....

That the restorative promise of human gene therapy has a better chance of being realized with the goings-on at the University and at 614 McKinley Place in Minneapolis.

    --William Hoffman

Disclaimer: The opinions expressed herein are the writer's own.

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Danio rerio, the zebrafish, the post-genomic star of the animal kingdom. The reputation of the pet fish is surging in the scientific community because it is a model organism for genetic studies of vertebrate development and disease. Image from Trans-NIH Zebrafish Initiative, National Institutes of Health.

Perry Hackett, PhD., a professor in the Department of Genetics, Cell Biology, and Development and chief scientific officer and founder of Discovery Genomics, Inc. Visit the Hackett Lab at the University of Minnesota.

Human chromosomes, carriers of our genes and mediators of our genetic destiny. Delivering a therapeutic gene safely and effectively to a chromosome has proven to be a major challenge for the emerging field of gene therapy. Discovery Genomics, Inc. uses the "Sleeping Beauty Transposon System" it developed to deliver genes to chromosomes without using viruses as delivery vehicles. Fluorescent in-situ hybridization [FISH] image from the Office of Science Education, National Institutes of Health.