ZFP may not be what it's cracked up to be...
How biotech tracks human uniqueness
Oakland Tribune, Oct 25, 2004 by Ian Hoffman, STAFF WRITER
The ingredients list for human life keeps shrinking.
Scientists' educated guess at the number of human genes has plummeted in just 10 years from 100,000 or more, to30,000 to 35,000 three years ago and to a new low -- issued this week by the International Human Genome Sequencing Consortium -- of 20,000 to 25,000.
Rats, mice, dogs and apes -- any mammal -- all have about the same number.
What distinguishes them is not so much their raw genetic ingredients, but when and how the genes are read to make the building blocks of life.
That bit of clerical ballet is the work of transcription factors. They are the operating systems for nearly all living things; without them, DNA would be a mass of unread data.
The most abundant by far are the 800 to 2,000 proteins shaped like fingers and bearing a bit of zinc. Exact roles for most of these zinc- finger proteins are a mystery. Biologists only have identified specific functions for about 50.
But evolution appears to have chosen zinc fingers to regulate an overwhelming array of life's machinery.
"I would expect that just about every gene in the genome has at least one zinc finger regulating it," said Lisa Stubbs, head of the genome biology division at Lawrence Livermore National Laboratory. "They're involved in almost every function imaginable. There are several generalones that are basically active in all cells that regulate cell growth."
They're implicated in cell death, cell division, the metabolism of fats, the immune system and on and on. They activate one set of genes to make kidneys and repress them to build nerve cells in the brain. Many are generalists and are shared among plants, flies, fish and mammals. But roughly half of human zinc fingers are unlike those in other living things. They have changed a lot in the last few million years, placing them at the cusp of human evolution.
A team of Livermore scientists is cataloguing all zinc fingers, partly out of conviction that these proteins may hold the biological secret of what it means to be human, what sets us apart from mice, primates and perhaps each other.
"We don't yet know whether the zinc fingers are variable between humans, but we think they are," said Stubbs.
In the Bay Area, a small biotech firm in Point Richmond is creating a different library of zinc fingers, most of them manmade. Scientists at Sangamo Biosciences are leapfrogging past the unknowns of natural zinc fingers by engineering their own from scratch.
They are mimicking evolution inside the laboratory, creating zinc fingers by the dozens and testing the ability to bind to a targeted DNA segment close to a gene. In theory, zinc fingers can latch virtually anywhere in the human genetic book.
"We can build zinc-finger proteins to bind to almost any gene sequence we want," said Casey Case, Sangamo vice president for research. "It's pretty wide open. We can turn on or off any kind of gene. There's no problem finding targets to work on."
This summer, after years of design and testing, the firm and medical-device maker Edwards Life Sciences, seller of the world's first artificial heart valve, launched the first-ever human experiments with a zinc finger-based drug.
The ailment they hope to defeat is peripheral artery disease, or PAD, that affects at least 8 million Americans. It's a close cousin of congestive heart disease that blocks blood flow in limbs.
Peter Cummins is one of them. As a Navy captain, he survived World War II, the Korean War and Vietnam. But in retirement, a new enemy arose to clog his arteries.
Cummins, 81, quit smoking and traded his steak dinners for steamed vegetables, rice and fruit. Vigorous exercise is out of the question. The arteries in his legs had stiffened and narrowed, so that even a short walk brings painful cramps and muscle ache. He no longer can walk the course for 18 holes of golf.
Bypasses unhelpful
Surgeons installed bypasses around his most clogged arteries in both legs, but to little avail.
This summer, Cummins received 20 injections into his calves and thighs. If he did not get a placebo, his cells were flooded with bits of DNA and began making a synthetic zinc-finger protein.
Sangamo scientists designed the zinc finger to lock onto a specific segment of DNA in front of a gene for producing a protein needed for building blood vessels. The gene and its products, which come in multiple forms, are known as vascular endothelial growth factor, or VEGF. It is hugely important for the growth of embryos and wound healing.
In the late 1990s, it looked as though VEGF was the holy grail for the field of angiogenesis, or artificially stimulating the growth of blood vessels. Yet human trials showed meager results. Medical researchers tried direct injections of VEGF. But the resulting blood vessels, when they grew much at all, often proved leaky.
"That was a huge disappointment," said Dr. Stephen Epstein, a researcher at Washington Hospital Center in Washington, D.C. and former chief of cardiology for the National Heart, Lung and Blood Institute. "Despite all of the excitement over angiogenesis over the last 12 or 14 years we have yet to see a robust, positive clinical trial."
Human trials are unpredictable. But there is tantalizing evidence in lab animals that the latest effort at switching genes on and off could be effective.
Reporting in Circulation, the leading journal of heart and blood science, Duke University Medical Center researchers said they grew a profusion of new vessels in the legs of blood-starved rabbits by injecting them with a zinc finger.
Blood flow doubles
Within days of the injection, multiple forms of VEGF were flowing in the rabbits' blood. Within a few weeks, twice as many blood vessels appeared in treated muscles as in untreated ones, and blood flow doubled in a month, the scientists found.
"The responses we saw were very, very good, very consistent and clearly significant," said Dr. Brian Annex, Duke's head of angiogenesis research.
He calls the zinc finger approach "a fascinating technology."
"It's a different strategy. This is using the body's strategy as opposed to producing what you think the body needs," he said. "I think this is a very powerful method and one that I think offers a lot of potential for a lot of different diseases."
Researchers are drawing up new experiments to try activating VEGF in heart muscle, to open new blood vessels around clogged arteries there.
Epstein of Washington Hospital Center is skeptical that activating a single gene will solve the mystery of angiogenesis. "There are probably dozens if not hundreds of genes whose products are involved in the development and maturation of blood vessels. What I would love to see is if there are a whole host of other genes that these zinc fingers activate," Epstein said. "I'd be encouraged by this study but I'd still be skeptical as to whether this translates into a successful clinical trial."
Yale University cardiology researcher Frank Giordano first speculated on using zinc fingers for angiogenesis. In 2002, he led researchers in treating mice with zinc fingers. The translucent ears of the mice filled with new blood vessels.
"The ability to manipulate those genes is very powerful with the zinc-finger proteins, and you can stimulate multiple genes at once," he said. "This angiogenic approach is only the tip of the iceberg."
Contact Ian Hoffman at ihoffman@angnewspapers.com |
