By David N. Leff

Like the share averages on a bullish stock market, the estimated total number of genes on the human genome keeps going up. Its latest quotation is 140,000, of which, observed molecular geneticist Samuel Driver, "the genes for which we know the functions number from 1,000 to a paltry 5,000, depending on whose estimate you listen to."

James Thompson, research director at Atugen USA in Boulder, Colo., commented: "Current tools for determining gene function simply cannot keep pace with the rapid accumulation of new sequence information produced by the various genome projects."

Driver, who is co-founder and chief operating officer of Boston-based QIK Technology Inc., pointed out that the current preferred method of determining what a gene encodes, and what that expressed product does, "is to knock that gene out of embryonic mice, and see what happens." What happens, he went on, "is that generating a single recombinant, transgenic knockout [KO] mouse takes many months and much money. And once that gene is knocked out, its product missing, that gene is gone forever. That often kills the animal before its gene function can be determined." QIK, which stands for "quantitative informational knockdown, aims to knock genes down but not out.

"It's a fact," Driver continued, "that better than 90 percent of the main disorders that drug discovery programs target - cardiovascular disease, cancer, Alzheimer's disease - are polygenic. Looking for inhibitors of these multigenes one KO mouse at a time is counterproductive. What's more, the rate at which mammalian genomes are being sequenced these days, with most of their gene functions unknown, calls urgently for high-efficiency, low-unit-cost gene determination."

The December issue of Nature Biotechnology carries Driver's answer to this predicament in an article titled: "Oligonucleotide-based inhibition of embryonic gene expression." He is the paper's senior author. Like five of its seven co-authors, Driver is a former antisense researcher at Hybridon Inc., which put antisense oligonucleotides on the map some years ago in clinical trials of cancer. Another author is research ophthalmologist Lois Smith, of Harvard-affiliated Children's Hospital in Boston. Her field is retinopathy - the overgrowth of blood vessels in the retina, which afflicts premature infants and diabetics and causes macular degeneration in the elderly.

These three age-related, vision-degrading retinopathies have a single common denominator - the vascular endothelial growth factor (VEGF), which promotes the proliferation and maintenance of blood vessels.

Meet Celebrity Molecule VEGF

"VEGF is a very popular molecule these days," Driver told BioWorld Today. "It's a big player in angiogenesis and anti-angiogenesis, and has a major role in ocular neovascularization and solid-tumor growth. But VEGF's gene is very unusual. If an embryo inherits a chromosome from one parent containing a mutant VEGF gene, the other parent's intact VEGF is not sufficient to grow arteries, veins and capillaries. In fact, the embryo will die."

As described in their paper, Driver and his team matched QIK's antisense inhibition technique against traditional KO methods of analyzing the VEGF gene. Their compound consisted of methylating the gene- targeting oligonucleotide with proprietary chemicals designed to penetrate the placenta enveloping their mouse embryos. Injected into the tail veins of pregnant animals, at various times during gestation, the prototype drug suffused the circulation, then headed into its embryonic target, and suppressed VEGF's angiogenic function.

But "timing was everything," Driver recounted. "A mouse's gestation typically lasts 19 days," he explained. "When we injected the compound between days 7.5 and 8.5 following fertilization, blood vessel formation did not take place. This successful inhibition depended on our hitting the critical window of opportunity." On day 10.5, conventional VEGF-minus KO mice died in utero as a result of disruption in their blood-vessel development.

From Angiogenic To Neural Development Genes

After demonstrating function determination of VEGF, a promoter of blood vessel endothelium, the co-authors turned to growth-promoting neural epithelial-cadherin, a cell-cell adhesion molecule. Traditional recombinant E-cadherin KO mice also died in utero on day 4 to 4.5, because their morula-stage mass of cells failed to implant in the uterine wall. But those who got the QIK compound survived, and on day 12 disclosed a neural-tube defect, indicative of the E-cadherin gene's function. Thus, the knockdown approach not only allowed the co-authors to study the function of essential genes throughout prenatal development, but also to uncover completely unexpected roles for genes under investigation.

Driver and his fellow Hybridon alumni founded QIK in January 1998. "It's funded to date by its founders, a few private investors and contracts," he stated. "We are currently in the process of negotiating for money to move from our current facility to a larger one in Boston, because we need to increase staff and space to handle the work load that we've got right now. Right now we have six people working in the lab.

"Under contract," Driver said, "QIK is identifying antisense inhibitors for three mammalian genes in cell culture and finding active antisense inhibitors for biotech companies as well as academic institutions. Also doing a lot of polymorphism or gene expression analysis on particular genes of interest.

"We're an operational technology platform for the identification of gene function in mammals," he continued, "and we are looking for interesting applications to develop. In terms of a biotech company, QIK is unconventional," Driver added. "Rather than hunkering down and grabbing on to a particular group of genes and trying to develop a drug or diagnostic test we can market - just being a toolbox company - what we've done is develop a cross-platform technology that can be applied to a variety of different research programs in pharmaceutical, veterinary, agricultural or human drug development."