Monday, January 26, 2009

On A High-fat Diet, Protective Gene Variant Becomes Bad Actor

New evidence in mice bolsters the notion that a version of a gene earlier shown to protect lean people against weight gain and insulin resistance can have the opposite effect in those who eat a high-fat diet and are heavier, reveals a report in the January 7th issue of the journal Cell Metabolism, a Cell Press publication.

The findings suggest that the 12 percent of people who carry the so-called Ala12 version of the gene that serves as a master controller of fat differentiation will be more sensitive than most to the amount of fat in their diets. (That fat-moderating gene is called peroxisome proliferator-activated receptor gamma isoform 2, or Pparg2.)

The Ala12 gene variant in question is less active and less efficient in driving fat cells' formation than the more common Pro12 version, the researchers explained. As a result, individuals carrying Ala12 are generally less obese and more sensitive to insulin, but that can change if they shift to a less sensible, fat-laden meal plan.

Genetic testing for the variant might therefore be used as a diagnostic tool, said Johan Auwerx of Université Louis Pasteur in France and the Ecole Polytechnique Fédérale de Lausanne in Switzerland. "Through dietary counseling, carriers could be informed that they really need to watch out for high fat in their diets," he said.

The findings also raise a potential caution about the long-term effects of drugs called thiazolidinediones (TZDs) now in use for the treatment of diabetes, he added. Those drugs stimulate activity of the Pparg2 receptor. The findings suggest it may be better—at least in some settings—to have a less active receptor.

Auwerx's team first described the Ala12 version of Pparg2 about 10 years ago when they found in a Finnish and a Japanese American population living in Hawaii that the mutation lowered the risk of diabetes. Others tried to reproduce the findings in Americans to no avail. Indeed, the Americans in the followup study, who were generally heavier than the groups Auwerx had examined earlier, showed the exact opposite pattern.

That led to the idea that effects of the gene might somehow be sensitive to initial body weight, but an animal study was needed to sort out the underlying details.

The researchers now show that mice with two copies of the Ala12 variant, when fed a balanced diet of normal mouse chow, are leaner and have improved insulin sensitivity and better plasma lipid profiles than mice with two copies of Pro12. They also live longer.

When mice with the same genetic background were instead sustained on a diet high in fat, those benefits disappeared. In fact, those Ala12 animals grew somewhat more obese than mice with the more common Pro12 variant of the gene, though not significantly so.

The result shows an important interaction between the Pparg2 gene and the environment, they report. The underlying basis for the effect seems to depend on changes in the way the Pparg2 receptor interacts with its cofactors and in its sensitivity to a fat-produced hormone known as adiponectin, which influences blood sugar control and fatty acid breakdown.

" Collectively, our results establish the diet-dependent influence of Pparg2 Pro12Ala variant on metabolic control via modulated cofactor interaction and changes in gene expression patterns in mice," the researchers concluded. "These data hence consolidate Pparg2 as an important factor at the interface between genes and the environment and may provide avenues to better, possibly Pro12Ala genotype-dependent treatment strategies for insulin resistance in type 2 diabetes and the metabolic syndrome."

Monday, January 19, 2009

Stem Cell Troops Called To Repair The Body Using New Drug Combinations

Scientists have tricked bone marrow into releasing extra adult stem cells into the bloodstream, a technique that they hope could one day be used to repair heart damage or mend a broken bone, in a new study published today in the journal Cell Stem Cell. When a person has a disease or an injury, the bone marrow mobilises different types of stem cells to help repair and regenerate tissue. The new research, by researchers from Imperial College London, shows that it may be possible to boost the body's ability to repair itself and speed up repair, by using different new drug combinations to put the bone marrow into a state of 'red alert' and send specific kinds of stem cells into action.

In the new study, researchers tricked the bone marrow of healthy mice into releasing two types of adult stem cells – mesenchymal stem cells, which can turn into bone and cartilage and that can also suppress the immune system, and endothelial progenitor cells, which can make blood vessels and therefore have the potential to repair damage in the heart.

This study, funded by the British Heart Foundation and the Wellcome Trust, is the first to selectively mobilise mesenchymal stem cells and endothelial progenitor cells from the bone marrow. Previous studies have only been able to mobilise the haematopoietic type of stem cell, which creates new blood cells. This technique is already used in bone marrow transplants in order to boost the numbers of haematopoietic stem cells in a donor's bloodstream.

The researchers were able to choose which groups of stem cells the bone marrow released, by using two different therapies. Ultimately, the researchers hope that their new technique could be used to repair and regenerate tissue, for example when a person has heart disease or a sports injury, by mobilising the necessary stem cells.

The researchers also hope that they could tackle autoimmune diseases such as rheumatoid arthritis, where the body is attacked by its own immune system, by kicking the mesenchymal stem cells into action. These stem cells are able to suppress the immune system.

Dr Sara Rankin, the corresponding author of the study from the National Heart & Lung Institute at Imperial College London, said: "The body repairs itself all the time. We know that the skin heals over when we cut ourselves and, similarly, inside the body there are stem cells patrolling around and carrying out repair where it's needed. However, when the damage is severe, there are limits to what the body can do of its own accord.

"We hope that by releasing extra stem cells, as we were able to do in mice in our new study, we could potentially call up extra numbers of whichever stem cells the body needs, in order to boost its ability to mend itself and accelerate the repair process. Further down the line, our work could lead to new treatments to fight various diseases and injuries which work by mobilising a person's own stem cells from within," added Dr Rankin.

The scientists reached their conclusions after treating healthy mice with one of two different 'growth factors' – proteins that occur naturally in the bone marrow – called VEGF and G-CSF. Following this treatment, the mice were given a new drug called Mozobil.

The researchers found that the bone marrow released around 100 times as many endothelial and mesenchymal stem cells into the bloodstream when the mice were treated with VEGF and Mozobil, compared with mice that received no treatment. Treating the mice with G-CSF and Mozobil mobilised the haematopoietic stem cells – this treatment is already used in bone marrow transplantation.

The researchers now want to investigate whether releasing repair stem cells into the blood really does accelerate the rate and degree of tissue regeneration in mice that have had a heart attack. Depending on the outcome of this work, they hope to conduct clinical trials of the new drug combinations in humans within the next ten years.

The researchers are also keen to explore whether ageing or having a disease affects the bone marrow's ability to produce different kinds of adult stem cells. They want to investigate if the new technique might help to reinvigorate the body's repair mechanisms in older people, to help them fight disease and injury.

Saturday, January 17, 2009

How Did Life Begin? RNA That Replicates Itself Indefinitely Developed For First Time

One of the most enduring questions is how life could have begun on Earth. Molecules that can make copies of themselves are thought to be crucial to understanding this process as they provide the basis for heritability, a critical characteristic of living systems. New findings could inform biochemical questions about how life began.

Now, a pair of Scripps Research Institute scientists has taken a significant step toward answering that question. The scientists have synthesized for the first time RNA enzymes that can replicate themselves without the help of any proteins or other cellular components, and the process proceeds indefinitely.

The work was recently published in the journal Science.

In the modern world, DNA carries the genetic sequence for advanced organisms, while RNA is dependent on DNA for performing its roles such as building proteins. But one prominent theory about the origins of life, called the RNA World model, postulates that because RNA can function as both a gene and an enzyme, RNA might have come before DNA and protein and acted as the ancestral molecule of life. However, the process of copying a genetic molecule, which is considered a basic qualification for life, appears to be exceedingly complex, involving many proteins and other cellular components.

For years, researchers have wondered whether there might be some simpler way to copy RNA, brought about by the RNA itself. Some tentative steps along this road had previously been taken by the Joyce lab and others, but no one could demonstrate that RNA replication could be self-propagating, that is, result in new copies of RNA that also could copy themselves.

In Vitro Evolution

A few years after Tracey Lincoln arrived at Scripps Research from Jamaica to pursue her Ph.D., she began exploring the RNA-only replication concept along with her advisor, Professor Gerald Joyce, M.D., Ph.D., who is also Dean of the Faculty at Scripps Research. Their work began with a method of forced adaptation known as in vitro evolution. The goal was to take one of the RNA enzymes already developed in the lab that could perform the basic chemistry of replication, and improve it to the point that it could drive efficient, perpetual self-replication.

Lincoln synthesized in the laboratory a large population of variants of the RNA enzyme that would be challenged to do the job, and carried out a test-tube evolution procedure to obtain those variants that were most adept at joining together pieces of RNA.

Ultimately, this process enabled the team to isolate an evolved version of the original enzyme that is a very efficient replicator, something that many research groups, including Joyce's, had struggled for years to obtain. The improved enzyme fulfilled the primary goal of being able to undergo perpetual replication. "It kind of blew me away," says Lincoln.

Immortalizing Molecular Information

The replicating system actually involves two enzymes, each composed of two subunits and each functioning as a catalyst that assembles the other. The replication process is cyclic, in that the first enzyme binds the two subunits that comprise the second enzyme and joins them to make a new copy of the second enzyme; while the second enzyme similarly binds and joins the two subunits that comprise the first enzyme. In this way the two enzymes assemble each other — what is termed cross-replication. To make the process proceed indefinitely requires only a small starting amount of the two enzymes and a steady supply of the subunits.

"This is the only case outside biology where molecular information has been immortalized," says Joyce.

Not content to stop there, the researchers generated a variety of enzyme pairs with similar capabilities. They mixed 12 different cross-replicating pairs, together with all of their constituent subunits, and allowed them to compete in a molecular test of survival of the fittest. Most of the time the replicating enzymes would breed true, but on occasion an enzyme would make a mistake by binding one of the subunits from one of the other replicating enzymes. When such "mutations" occurred, the resulting recombinant enzymes also were capable of sustained replication, with the most fit replicators growing in number to dominate the mixture. "To me that's actually the biggest result," says Joyce.

The research shows that the system can sustain molecular information, a form of heritability, and give rise to variations of itself in a way akin to Darwinian evolution. So, says Lincoln, "What we have is non-living, but we've been able to show that it has some life-like properties, and that was extremely interesting."

Knocking on the Door of Life

The group is pursuing potential applications of their discovery in the field of molecular diagnostics, but that work is tied to a research paper currently in review, so the researchers can't yet discuss it.

But the main value of the work, according to Joyce, is at the basic research level. "What we've found could be relevant to how life begins, at that key moment when Darwinian evolution starts." He is quick to point out that, while the self-replicating RNA enzyme systems share certain characteristics of life, they are not themselves a form of life.

The historical origin of life can never be recreated precisely, so without a reliable time machine, one must instead address the related question of whether life could ever be created in a laboratory. This could, of course, shed light on what the beginning of life might have looked like, at least in outline. "We're not trying to play back the tape," says Lincoln of their work, "but it might tell us how you go about starting the process of understanding the emergence of life in the lab."

Joyce says that only when a system is developed in the lab that has the capability of evolving novel functions on its own can it be properly called life. "We're knocking on that door," he says, "But of course we haven't achieved that."

The subunits in the enzymes the team constructed each contain many nucleotides, so they are relatively complex and not something that would have been found floating in the primordial ooze. But, while the building blocks likely would have been simpler, the work does finally show that a simpler form of RNA-based life is at least possible, which should drive further research to explore the RNA World theory of life's origins.

Thursday, January 15, 2009

Protein's Essential Role In Repairing Damaged Cells Revealed

University of Michigan researchers have discovered that a key protein in cells plays a critical role in not one, but two processes affecting the development of cancer.

"Most proteins involved in responding to DNA damage that can cause cancer either help detect the damage and warn the rest of the cell, or help repair the damage," says David O. Ferguson, M.D., Ph.D., the study's lead author. Ferguson is an assistant professor of pathology at the U-M Medical School and a member of U-M's Comprehensive Cancer Center.

Prior research has shown that the protein, Mre11, functioned as a "gatekeeper" to signal injury to the cell and prevent damaged cells from proliferating. Now, Ferguson and colleagues have discovered that in mammals, a function of the Mre11 protein also serves as a "caretaker," by repairing DNA.

Their findings, published in the journal Cell, could have important implications for cancer treatment by someday allowing oncologists to predict a tumor's sensitivity to radiation and other therapies, making it more vulnerable to treatment.

Under normal circumstances, the body's cells grow, divide and eventually die. When something damages a healthy cell's DNA -- such as radiation or exposure to a toxin -- a multiprotein complex steps in to repair the breakage and activate other fundamental cellular processes.

The MRN complex, comprised of the Mre11, Rad50 and NBS1 proteins, senses DNA damage, known as double-strand breaks, within the cell. The complex then transmits that information to an enzyme called the ATM (ataxia-telangiectasia mutated) checkpoint kinase.

The ATM kinase controls the cell's response to double-strand breaks, and slows cell growth to give the cell opportunities to repair them, says Ferguson.

When the MRN complex doesn't work properly, inherited human neurological diseases, such as ataxia-telangiectasia-like syndrome and Nijmegen breakage syndrome, result. Both feature MRN mutations and significantly predispose a person to immunodeficiency and cancer.

What Ferguson and colleagues discovered is that Mre11 not only senses and communicates damage, it also repairs DNA double-strand breaks by acting as a nuclease, an enzyme that modifies and processes the broken DNA ends.

Saturday, January 10, 2009

The Ribosome: Perfectionist Protein-maker Trashes Errors

The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist.Johns Hopkins researchers, reporting in the journal Nature January 7, have discovered a new "proofreading step" during which the suite of translational tools called the ribosome recognizes errors, just after making them, and definitively responds by hitting its version of a "delete" button.

It turns out, the Johns Hopkins researchers say, that the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products which, as workhorses of the cell, carry out the very business of life.

"What we now know is that in the event of miscoding, the ribosome cuts the bond and aborts the protein-in-progress, end of story," says Rachel Green, a Howard Hughes Medical Institute investigator and professor of molecular biology and genetics in the Johns Hopkins University School of Medicine. "There's no second chance." Previously, Green says, molecular biologists thought the ribosome tightly managed its actions only prior to the actual incorporation of the next building block by being super-selective about which chemical ingredients it allows to enter the process.

Because a protein's chemical "shape" dictates its function, mistakes in translating assembly codes can be toxic to cells, resulting in the misfolding of proteins often associated with neurodegenerative conditions. Working with bacterial ribosomes, Green and her team watched them react to lab-induced chemical errors and were surprised to see that the protein-manufacturing process didn't proceed as usual, getting past the error and continuing its "walk" along the DNA's protein-encoding genetic messages.

"We thought that once the mistake was made, it would have just gone on to make the next bond and the next," Green says. "But instead, we noticed that one mistake on the ribosomal assembly line begets another, and it's this compounding of errors that leads to the partially finished protein being tossed into the cellular trash," she adds.

To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction that Green says is "shocking" and reveals just how much of a stickler the ribosome is about high-fidelity protein synthesis.

"These are not subtle numbers," she says, noting that there's a clear biological cost for this ribosomal editing and jettisoning of errors, but a necessary expense.

"The cell is a wasteful system in that it makes something and then says, forget it, throw it out," Green concedes. "But it's evidently worth the waste to increase fidelity. There are places in life where fidelity matters."