Monday, February 23, 2009

Earlier Diagnosis Of Uterine Cancer Possible With New Findings

Cancer of the uterus (womb) is the commonest gynaecological malignancy in the West. Research carried out at the University of Gothenburg, Sweden, has now identified a gene that may simplify future diagnosis.

Cancer is a genetic disease. It occurs when changes take place in the genes that regulate cell division, cell growth, cell death, cell signalling and blood vessel formation – either due to mutations caused by external factors such as smoking or radiation – or due to inherited changes. This interaction between defective genes and environmental factors means that cancer is an extremely complex disease. Cancer of the uterus, or endometrial carcinoma, is no exception.

Cancer of the uterus is the commonest gynaecological malignancy in the West and accounts for between five and six per cent of all cancers in Swedish women. However, the symptoms are often vague, and we know little about the genetic factors that lead to the appearance and development of this form of cancer. It is therefore vital that these genes are identified, as this could enable doctors to make the diagnosis much more quickly and easily, allowing the development of more effective cancer treatment.

In her study, Sandra Karlsson, a researcher at the Department of Cell and Molecular Biology, has used inbred rats to locate the defective genes that cause uterine cancer. Like monozygotic (identical) twins, these inbred rats are genetically almost identical, which makes it much easier to study the influence of the environment in which they live.

“More than 90 per cent of the female rats in the study spontaneously developed uterine cancer. By using advanced techniques to analyse gene expression in the tumours, we succeeded in identifying a gene signature that could be used as a future diagnostic test for human uterine cancer,” says Sandra Karlsson.

The signature is made up of three genes. One of them protects the cell against oxygen free radicals. These free radicals are naturally and continuously produced in the cell, but excess amounts, which can damage the cell and the body’s DNA, are associated with over 200 diseases, from arteriosclerosis and dementia to rheumatism, cerebral haemorrhage and cancer. The studies carried out by Sandra Karlsson on human malignant tumours have confirmed that changes in this gene are present in early as well as late stage cancer.

“This shows that the identified gene has an important role in the origin and development of uterine cancer,” says Sandra Karlsson.

The thesis Gene Expression Patterns in a Rat Model of Human Endometrial Adenocarcinoma was publicly defended on the December 19th. Supervisor – Professor Karin Klinga Levan.

Monday, February 16, 2009

Shortened DATE Gene Region Linked To Breast Cancer

Reza Zarnegar and colleagues, at the University of Pittsburgh, Pittsburgh, have determined that genetic variation in a piece of DNA that regulates activity of the HGF gene might be a useful marker to identify individuals with an increased risk of developing breast cancer.

The HGF gene is not active in normal breast epithelial cells. However, its activity is not repressed in tumor samples from many patients with breast cancer. In the study, the authors identified a DNA region that controls the activity of the HGF gene and named it DATE (deoxyadenosine tract element).

Functional studies determined that shortening the DATE region led to activation of the HGF gene in cell lines. Further analysis indicated that a substantial proportion of patients with breast cancer have shortened DATE regions, and that these patients were markedly younger than patients with a DATE region of normal length.

Given these data, the authors suggest that future studies should investigate whether shortened DATE regions are also associated with other cancers that overexpress HGF, such as some forms of colon, stomach, pancreatic, endometrial, and cervical cancer.

Tuesday, February 10, 2009

Gene Therapy For Blindness Improves Vision, Safety Study Indicates

All three people who received gene therapy at the University of Florida to treat a rare, incurable form of blindness have regained some of their vision, according to a paper published online today in Human Gene Therapy. The patients — one woman and two men ranging from 21 to 24 years old with a type of hereditary blindness called Leber congenital amaurosis type 2 — volunteered to test the safety of an experimental gene-transfer technique in a phase 1 clinical research study conducted by UF and the University of Pennsylvania with support from the National Eye Institute of the National Institutes of Health.

In this form of LCA disease, photoreceptor cells cannot respond to light because a gene called RPE65 does not properly produce a protein necessary for healthy vision. In the study, researchers used an adeno-associated virus — an apparently harmless virus that already exists in most people — to deliver RPE65 to a small area of the retina.

Not only were there no ill effects other than routine postsurgical soreness, the subjects said the vision in their treated eyes was slightly improved in dim lighting conditions.

"The patients report seeing brighter areas and perhaps some images, but basically the message is that this is treatment is fully safe," said William W. Hauswirth, Ph.D., a professor of ophthalmology and member of UF's Powell Gene Therapy Center and the UF Genetics Institute.

"One thing we did not do is suppress the patients' immune systems, which was done in two other LCA clinical trials that were under way," said Hauswirth, who began studying the adeno-associated virus as a vehicle to deliver genes into living animals more than 30 years ago. "Theoretically, the idea was that it might be necessary to suppress the immune system because we are using a vector that might activate the body's defenses and cause a harmful response. However, immune suppression itself carries a risk of infections and other problems. Clearly we have shown there is no need to do that in this case."

Samuel G. Jacobson, M.D., Ph.D., a professor of ophthalmology with the Scheie Eye Institute at the University of Pennsylvania, is the study's principal investigator.

"This groundbreaking gene therapy trial builds on 15 years of research sponsored by the National Eye Institute of NIH," said Paul A. Sieving, M.D., Ph.D., director of the NEI. "The study has partially restored vision in three young adults, and it demonstrates that gene therapy can be effective in treating human vision disease. Many human diseases are inherited in families and result from mutations in single genes. These genetic conditions are particularly suited to potential treatment by gene therapy. This trial to treat vision loss from the condition of Leber congenital amaurosis is an important demonstration of proof of principle and shows that we are on the right track. We can now invest in further work to refine, and ultimately to expand, genetic treatment approaches."

Results published today focus on the health of the entire retina, not just the tiny portion that received the gene therapy. A detailed examination of the therapy's effectiveness in the treated portion of the eye will appear in an upcoming issue of the Proceedings of the National Academy of Sciences. Two other recent LCA clinical trial reports appeared recently in The New England Journal of Medicine.

"The safety study itself is a milestone, but when we see a benefit to the subject — that is a truly a welcome bonus," said Barry J. Byrne, M.D., Ph.D., a professor of molecular genetics and microbiology and director of UF's Powell Gene Therapy Center, which manufactured the viral vectors used in the study. "Improvements in someone's medical condition are ultimately what we are after."

LCA2 affects about 2,000 people in the United States and is one of several incurable forms of blindness collectively known as retinitis pigmentosa, which in turn affects about 200,000 Americans.

Children with LCA2 experience major visual disability that can lead to total vision loss in adulthood. Although vision loss is severe, the structure of the retina — including its connection to the brain — can remain relatively intact for decades before the photoreceptor cells degenerate.

Sunday, February 08, 2009

Numerous Undiscovered Gene Alterations In Pancreatic And Brain Cancers Detected

HHMI investigators have detected a multitude of broken, missing, and overactive genes in pancreatic and brain tumors, in the most detailed genetic survey yet of any human tumor. Some of these genetic changes were previously unknown and could provide new leads for improved diagnosis and therapy for these devastating cancers.

The discoveries, described in two reports published September 4, 2008, in Science Express, which provides early electronic publication of selected Science papers, emerged from the sequencing of nearly all the known protein-making genes in pancreatic cancers and in the most common form of brain tumors, glioblastomas. The study adds numerous items to the known "parts list" of these cancers, though further research is needed to determine which gene changes actually trigger development or spread of the disease.

HHMI investigator Bert Vogelstein and colleagues at the Johns Hopkins Kimmel Cancer Center, in collaboration with investigators at Duke University and elsewhere, sequenced 20,661 genes in cells from 24 patients with pancreatic cancer and 22 patients with glioblastoma. The team identified hundreds of gene mutations associated with the cancers.

The researchers also found numerous cases where tumor cells had extra or too few copies of a gene. The typical pancreatic cancer contained 63 genetic alterations, while the average brain tumor contained 60. Using "next generation" sequencing, the researchers also comprehensively assessed changes in levels of gene activity.

Taken together, the two studies suggest that a small number of commonly mutated genes - or "mountains" - and a much larger number of rarer, low-frequency gene changes - "hills" - cause these cancers, said the researchers.

The authors said their results demonstrate that "genome-wide genetic analyses…can identify the precise genetic alterations that are likely to be responsible for pathway disregulation in each patient's tumor." They found that each individual tumor had its own particular assortment of gene changes. "If you have 100 patients, you have 100 different diseases," said Vogelstein, who is a co-corresponding author of the Science paper with Johns Hopkins researchers Victor E. Velculescu and Kenneth W. Kinzler. "But this will not surprise clinical oncologists, because they see how different every patient is" in the way their tumor behaves and responds to treatment.

Cancer biologist Tyler Jacks, a Howard Hughes Medical Institute investigator at the Massachusetts Institute of Technology who was not involved in the studies, said he was not surprised by the large number of infrequent gene mutations — primarily because Vogelstein and his colleagues reported in 2007 that they had found breast and colon cancers to be similarly complex genetically. "But if you had asked me three years ago, I would have given a different answer," Jacks said.

Vogelstein said the sheer number and variability of genetic changes in the tumors pose a challenge to one of the main goals of "personalized medicine" — identifying as many cancer-causing mutations as possible and developing an array of targeted drugs, each designed to strike a specific mutation.

Jacks agreed that cancer researchers would have preferred that tumors' mutational landscapes be dominated by the high-frequency "mountains," as these make attractive targets for the design of new drugs. With conventional DNA sequencing technologies, these prominent mountains were the mutations most readily linked to cancer, he said. But as new methods make it feasible to sequence nearly all the genes in a tumor sample, researchers are beginning to recognize that "the landscape is crowded with changes, mostly occurring at low frequency."

"It's suggesting that maybe we shouldn't even be focusing so much on the individual genes that are mutated," Vogelstein said. "Instead, we should be thinking about the functional pathways in which these genes operate. This is a different way of looking at how cancer develops."

Indeed, many of the gene abnormalities could be grouped into functional units. For example, when they analyzed the DNA in 24 pancreatic cancers, the scientists identified 12 core signaling pathways that were each abnormal in the great majority of tumors. Some of those pathways regulate apoptosis - the programmed death of abnormal cells - or repair of damaged DNA. Other altered pathways control the rate of cell division, influence how tightly cells stick together, or determine their ability to invade nearby tissues.

In the brain tumor samples, the survey found that the mutated genes could be grouped into similar pathways, such as those controlling growth and apoptosis. However, some of the newly found mutations occurred in pathways involved in nervous system signaling processes not previously known to be altered in any form of cancer. The scientists speculate that this pathway may be specific for glial cell tumorigenesis.

Similarly, one particular genetic change netted by the survey was found exclusively in brain tumors. That mutation was particularly intriguing because of its potential near-term clinical importance. Specific mutations in the isocitrate dehydrogenase gene IDH1 were found in 12 percent of the brain tumors. They were found in almost all cases of secondary glioblastomas - developing from lower-grade tumors - but rarely in primary high-grade glioblastomas. They also tended to affect younger patients (average age 33 compared to age 53 for patients without the mutations). Patients whose brain tumors had the IDH1mutation lived significantly longer with their cancer than those who did not.

Although it is not known how the IDH1 mutation contributes to cancer, Vogelstein said that it could help single out individuals who are likely to have better outcomes. With further research, it is conceivable that the mutation could have relevance for therapy, he said.

Like the Vogelstein group's 2007 findings on breast and colon cancer, the new study suggests that many these diseases are caused not by a few major genetic kingpins, but instead by a large cast of minor culprits. How this multiplicity of cancer triggers can best be confronted is uncertain, but the authors of the two papers say it may force a shift in drug development emphasis. The best hope for new therapies, they wrote, "may lie in the discovery of agents that target the physiologic effects of the altered pathways and processes, rather than their individual genetic components."

Friday, February 06, 2009

For Fats, Longer May Not Be Better

Researchers have uncovered why some dietary fats, specifically long-chain fats, such as oleic acid (found in olive oil), are more prone to induce inflammation. Long-chain fats, it turns out, promote increased intestinal absorption of pro-inflammatory bacterial molecules called lipopolysaccharides (LPS).

While dietary fats that have short chains (such as those found in milk and cheese products) can be absorbed directly into the bloodstream from the intestines, long-chain fats need to be first packaged by the intestinal cells into particles known as chylomicrons (large complexes similar to HDL and LDL particles). Erik Eckhardt and colleagues at the University of Kentucky wondered whether some unwanted LPS particles, routinely shed by the bacteria that inhabit the human gut, might also be sneaking in the chylomicrons.

Their hypothesis turned out to be correct; when they treated cultured human intestinal cells with oleic acid they observed significant secretion of LPS together with the chylomicron particles, a phenomenon that was not observed when the cells were treated with short-chain butyric acid. Similar findings were found in mouse studies; high amounts of dietary oleic acid, but not butyric acid, promoted significant absorption of LPS into the blood and lymph nodes and subsequent expression of inflammatory genes.

Eckhardt and colleagues believe these findings may pave the way for future therapies for Crohn's disease and other inflammatory bowel disorders. In addition, they note that this study once again highlights the importance of the diverse bacteria that call our intestines home.

Treatment For Hearing Loss? Scientists Grow Hair Cells Involved in Hearing

Oregon Health & Science University scientists have successfully produced functional auditory hair cells in the cochlea of the mouse inner ear. The breakthrough suggests that a new therapy may be developed in the future to successfully treat hearing loss. The results of this research was recently published by the journal Nature.   

“One approach to restore auditory function is to replace defective cells with healthy new cells,” said John Brigande, Ph.D., an assistant professor of otolaryngology at the Oregon Hearing Research Center in the OHSU School of Medicine. “Our work shows that it is possible to produce functional auditory hair cells in the mammalian cochlea.”

The researchers specifically focused on the tiny hair cells located in a portion of the ear’s cochlea called the organ of Corti. It has long been understood that as these hair cells die, hearing loss occurs. Throughout a person’s life, a certain number of these cells malfunction or die naturally leading to gradual hearing loss often witnessed in aging persons. Those who are exposed to loud noises for a prolonged period or suffer from certain diseases lose more sensory hair cells than average and therefore suffer from more pronounced hearing loss.

Brigande and his colleagues were able to produce hair cells by transferring a key gene, called Atoh1, into the developing inner ears of mice. The gene was inserted along with green florescent protein (GFP) which is the molecule that makes a species of jellyfish glow. GFP is often used in research as a “marker” that a scientist can use to determine, in this case, the exact location of the Atoh1 expression.  Remarkably, the gene transfer technique resulted in Atoh1 expression in the organ of Corti, where the sensory hair cells form.

Using this method, the researchers were able to trace how the inserted genetic material successfully led to hair cell production resulting in the appearance of more hair cells than are typically located in the ears of early postnatal mice. Crucially, Dr. Anthony Ricci, associate professor of otolaryngology at the Stanford University School of Medicine, demonstrated that the hair cells have electrophysiological properties consistent with wild type or endogenous hair cells, meaning that the hair cells appear to be functional. Based on these data, the scientists concluded that Atoh1 expression generates functional auditory hair cells in the inner ear of newborn mammals.

“It remains to be determined whether gene transfer into a deaf mouse will lead to the production of healthy cells that enable hearing. However, we have made an important step toward defining an approach that may lead to therapeutic intervention for hearing loss,” Brigande said.

Tuesday, February 03, 2009

Key Component In Cell Replication Identified

Last week, a presidential limousine shuttled Barack Obama to the most important job in his life. Scientists at the Stanford University School of Medicine have now identified a protein that does much the same for the telomerase enzyme — ferrying the critically important clump of proteins around to repair the ends of chromosomes that are lost during normal replication. Without such ongoing maintenance, stem cells would soon cease dividing and embryos would fail to develop.

"This is the first new protein component of telomerase that has been identified in 10 years," said Steven Artandi, MD, PhD, associate professor of hematology. "And it's likely to be a valuable target for anti-cancer therapies."

Artandi is the senior author of the research, which will be published in the Jan. 30 issue of Science. Graduate student Andrew Venteicher is the first author. The two collaborated with scientists at the National Cancer Institute-Frederick and the University of Georgia to conduct the research.

Telomerase is normally expressed in adult stem cells and immune cells, as well as in cells of the developing embryo. In these cells, the enzyme caps off the ends of newly replicated chromosomes, allowing unfettered cell division. Without telomerase, cells stop dividing or die within a limited number of generations. Unfortunately, the enzyme is also active in many cancer cells. Artandi and his collaborators found that blocking the inappropriate expression of the protein, called TCAB1, in human cancer cells keeps telomerase from reaching its DNA targets, called telomeres, and may limit the cell's life span.

"There are currently no effective telomerase inhibitors," said Artandi. "We've never really understood before how the enzyme gets to the telomeres; it's been a complete black box. Now we're starting to piece together how it happens, and that gives us more opportunities to interfere with its function."

Telomerase has been subject of intense research for years, but scientists have been stymied by the enzyme's large size and extreme rarity. Few cells in the adult body make the huge protein complex, and even they make only tiny amounts. As a result, only some members have been identified.

"It's been incredibly challenging to figure out all the protein components of telomerase," said Artandi, who refers to the unknown members of the complex as "dark matter." "We know how big the enzyme is, and it's clear that the known components don't add up to the total. Now we've identified one more member."

The researchers used a highly sensitive protein identification technique called mass spectrometry to ferret out TCAB1's presence in telomerase based on its ability to bind to another, known component of the enzyme. Early last year, Artandi's lab used the same technique to identify for the first time two other proteins — pontin and reptin — that are important for assembling the massive complex. This time around they identified TCAB1, a protein of previously unknown function.

Unlike pontin and reptin, TCAB1 is a true component of telomerase. But it's not required for the enzyme's activity. Rather, it recruits the telomerase complex to processing and holding areas in the nucleus of the cell called Cajal (pronounced "cuh-hall") bodies. Like a high-end garage, Cajal bodies apply the finishing touches to a variety of proteins that use small molecules of RNA to conduct their activities (telomerase, for example, uses an RNA molecule as a template for the DNA chain it tacks onto the ends of chromosomes). When appropriate, TCAB1 then chauffeurs the telomerase complex to the waiting end of a newly replicated chromosome.

"TCAB1 is absolutely necessary for the telomerase to make this jump from Cajal bodies to telomeres," said Artandi. "When we inhibited its activity in human cancer cells, the telomeres grew shorter," implying the cancer cells would die more quickly.

Prior to this study, TCAB1 had no known function. "Andy [Venteicher] found that TCAB1 binds not only telomerase, but also a specific class of small, non-coding RNA molecules that also end up in the Cajal bodies," said Artandi. He added that the protein may be a common biological shuttle responsible for delivering a variety of molecules to their destinations. He and his collaborators plan to continue their study of TCAB1 and also to identify other telomerase components.

"This is a story that's been unfolding over decades," said Artandi. "Telomerase is such a high-priority target for many diseases, but it's hard to attack when you know very little about it. But that's changing now."

The research was funded by the National Cancer Institute and the Leukemia and Lymphoma Society. Stanford graduate student Kelly McCann also participated in the research.