Synopsis: Biotechnology

Same Genes, Different Doses
Distant DNA controls gene activity

Context: Even in cases where two people share the same gene, they can produce widely differing amounts of the protein the gene codes for. This can lead to differences in physical characteristics, and it can also mean the difference between sickness and health. Segments of DNA called regulatory elements are one factor controlling how much of a particular protein the body produces. While researchers today can use algorithms to pick out genes from sequences of DNA, they have previously been unable to accurately distinguish regulatory elements from other non-coding DNA, let alone match those elements with the genes that they regulate. Researchers at the University of Pennsylvania, led by Vivian Cheung, have found a way to do just that.

Methods and Results: Using white blood cells from 94 people, the researchers identified more than 3,500 genes whose expression was similar among relatives but varied widely among people who were unrelated. These patterns of expression were then correlated with patterns of known genetic markers across the genome. Hundreds of genes’ expression was linked to particular genetic markers – far more than the number predicted by chance. About four-fifths of these markers were located more than 5,000 base pairs from the genes that they regulated; many were even on other chromosomes. Researchers found that some “hot spot” regions apparently influence the expression of more than 30 genes. In addition, many genes seem to be regulated by more than one region.

Why it matters: Researchers can finally study the genetic differences governing gene expression. The hot spots, which Cheung’s team calls “master regulators,” will help to tease out some of the mysteries that surround gene expression. More immediately, the techniques may allow researchers to use variation within genes and within regulatory elements to understand and treat disease. For years, geneticists have scoured the human genome for genes that contribute to complex traits, like susceptibility to depression or heart disease. Finding factors that control the genes is just as important but much more difficult. Now scientists should be better equipped to find the genetic variations that make a difference in matters of life and death.

Source: Morley, M. et al. (2004) Genetic analysis of genome-wide variation in human gene expression. Nature 430:743-7.

On Again, Off Again
A gene comes with a handy switch

Context: Good health requires more than the right genes; those genes must also be able to switch on and off at the right time. In research involving animals or cell cultures, fi guring out a gene’s function is much easier when scientists can turn it on at will. Led by Richard Mulligan, a group of researchers at Harvard Medical School and Children’s Hospital in Boston have crafted genes that come with an easily controlled on/off switch – a powerful research tool that has the potential to off er a new kind of gene therapy.

Methods and Results: The switch consists of a ribozyme, an enzyme made up of RNA. Laising Yen, a postdoc in Mulligan’s lab, and colleagues inserted a ribozyme sequence into a gene that coded for an easily detectable protein. Cells with the altered gene made long stretches of messenger RNA; part of the RNA made the ribozyme, while the rest carried instructions for making the protein. The researchers tinkered with diff erent ribozymes, eventually creating ones that were able to chop up the RNA before the protein it coded for could be made. In the cell cultures and living mice containing the ribozyme sequence, protein production dropped to nearly undetectable levels. What’s more, the researchers were able to deactivate the ribozyme using certain drugs – essentially turning on the inserted gene by turning off the off switch. Such treatments succeeded in restoring gene expression by up to 50 percent.

Why it matters: The researchers imagine creating genetic therapies in which the onset of a physiological condition would activate the genes necessary to manage it. Genetically engineered cells might be able to secrete insulin in accordance with glucose levels, freeing diabetics from constant blood monitoring and insulin injection. For the moment, however, such dreams are far from reality. Closer at hand and still very exciting are discovery techniques that would allow researchers to monitor the effects produced by several genes in a single animal, or to analyze how a gene adjusts to an organism’s aging or to different stages of a disease.

Source: Yen, L. et al. (2004) Exogenous control of mammalian gene expression through modulation of RNA self-cleavage. Nature 431:471-6.

Drug Bug
Genetically engineered bacteria treatintestinal disease

Context: Finding ways to get drugs to the right part of the body is a constant challenge for drugmakers. The intestines would seem easier to treat than other areas, as drugs taken orally should eventually arrive there. But a number of promising drugs for the treatment of colitis, an intensely uncomfortable infl ammation of the large intestine, become waylaid in the mucus of the small intestine and never reach their target. Now, a group of researchers led by Lothar Steidler from Ghent University in Belgium has genetically modified bacteria to secrete such a drug as they travel through the gut.

Methods and Results: The researchers engineered Lactococcus lactis so that it would produce trefoil factors, shamrock-shaped proteins that hasten healing and protect the gut from injury. The modified bacteria proved more effective than the purified protein alone at preventing and treating colitis in mice. Outside the body, the bacteria do not survive.

Why it matters: The use of genetically modified (GM) organisms as drug delivery devices is moving toward the mainstream. Another GM bacterium produced by these researchers, one that secretes the anti-inflammatory drug interleukin-10, is being tested in European clinical trials as a treatment for infl ammatory bowel disease. Other GM bacteria, to be delivered to the nose and vaginal tract, are being studied to prevent infectious disease. Still another may deliver a cancer vaccine. In the 1980s and ’90s, recombinant DNA technology ushered in an era of new protein drugs; despite substantial regulatory and technical obstacles, bacteria may prove an effective way to deliver them.

Source: Vandenbroucke, K. et al. (2004) Active delivery of trefoil factors by genetically modifi ed Lactococcus lactis prevents and heals acute colitis in mice. Gastroenterology 127:502-513.

New Strike against Stroke
Neuronal damage has a new culprit

Context: Strokes kill neurons by depriving them of oxygen. Without oxygen, neurons have difficulty producing the molecule ATP, their source of energy. This prevents them from performing housekeeping chores, including the important task of pulling glutamate, a message-transmitting chemical, back into the neuron after its message has been received; glutamate keeps sending signals to neighboring neurons, resulting in a deadly influx of calcium ions. However, drugs designed to curb stroke damage by blocking glutamate’s effects have shown disappointing results in clinical trials. New research, led by Zhigang Xiong at the Legacy Clinical Research and Technology Center in Portland, OR, shows another strategy that seems more promising.

Methods and Results: To make ATP without oxygen, cells use an inefficient method that produces lactic acid and protons as by-products. Neurons using this method become more acidic; they also become more susceptible to damage, but it wasn’t clear why. Xiong and his colleagues speculated that acid-sensing ion channels (ASICs) might move calcium into the cell, thereby accelerating neuronal damage. After showing that strokelike conditions activated ASICs, and that ASICs allowed calcium into the neuron, they studied mice lacking the gene for ASIC1a, which is highly expressed in the brain. When subjected to simulated strokes, mice without the gene fared better than mice with it, even when treated with memantine, a drug that blocks the actions of glutamate. The researchers also discovered that small molecules that block ASICs can protect against stroke injury. In rats treated with one such molecule before simulated strokes, the rate of neuronal death was less than half that among untreated rats.

Why it matters: Drugs that block ASICs will likely face many of the same challenges as those that block glutamate: they must be administered quickly after a stroke and could have unintended effects on brain function. Nonetheless, small molecules have already shown the capacity to prevent the type of brain damage caused by this newly described mechanism. Thus, these results offer hope against a devastating cause of disability and the third-leading cause of death in the United States.

Source: Xiong, Z. G. et al. (2004) Neuroprotection in ischemia: blocking calcium-permeable acid-sensing ion channels. Cell 118: 687-698.