Biochemistry and Bioinformatics

Whole Exome Sequencing Identifies Cause of Metabolic Disease

2012-02-11T05:12:00.000-08:00

Sequencing a patient's entire genome to discover the source of his or her disease is not routine -- yet. But geneticists are getting close.

A case report, published this week in the American Journal of Human Genetics, shows how researchers can combine a simple blood test with an "executive summary" scan of the genome to diagnose a type of severe metabolic disease.

Researchers at Emory University School of Medicine and Sanford-Burnham Medical Research Institute used "whole-exome sequencing" to find the mutations causing a glycosylation disorder in a boy born in 2004. Mutations in the gene (called DDOST) that is responsible for the boy's disease had not been previously seen in other cases of glycosylation disorders.

Whole-exome sequencing is a cheaper, faster, but still efficient strategy for reading the parts of the genome scientists believe are the most important for diagnosing disease. The report illustrates how whole-exome sequencing, which was first offered commercially for clinical diagnosis in 2011, is entering medical practice. Emory Genetics Laboratory is now gearing up to start offering whole exome sequencing as a clinical diagnostic service.

It is estimated that most disease-causing mutations (around 85 percent) are found within the regions of the genome that encode proteins, the workhorse machinery of the cell. Whole-exome sequencing reads only the parts of the human genome that encode proteins, leaving the other 99 percent of the genome unread.

The boy in the case report was identified by Hudson Freeze, PhD and his colleagues. Freeze is director of the Genetic Disease Program at Sanford-Burnham Medical Research Institute. A team led by Madhuri Hegde, PhD, associate professor of human genetics at Emory University School of Medicine and director of the Emory Genetics Laboratory, identified the gene responsible. Postdoctoral fellow Melanie Jones is the first author of the paper.

"This is part of an ongoing effort to develop diagnostic strategies for congenital disorders of glycosylation," Hegde says. "We have a collaboration with Dr. Freeze to identify new mutations."

Glycosylation is the process of attaching sugar molecules to proteins that appear on the outside of the cell. Defects in glycosylation can be identified through a relatively simple blood test that detects abnormalities in blood proteins. The sugars are important for cells to send signals and stick to each other properly. Patients with inherited defects in glycosylation have a broad spectrum of medical issues, such as developmental delay, digestive and liver problems and blood clotting defects.

The boy in this case report was developmentally delayed and had digestive problems, vision problems, tremors and blood clotting deficiencies. He did not walk until age 3 and cannot use language. The researchers showed that he had inherited a gene deletion from the father and a genetic misspelling from the mother. "Over the years, we've come to know many families and their kids with glycosylation disorders. Here we can tell them their boy is a true 'trail-blazer' for this new disease," Freeze said. "Their smiles -- that's our bonus checks."

The researchers went on to show that introducing the healthy version of the DDOST gene into the patient's cells in the laboratory could restore normal protein glycosylation. Thus, restoring normal function by gene therapy is conceivable, if still experimental. However, restoration of normal glycosylation would be extremely difficult to achieve for most of the existing cells in the body.

The research was supported by the National Institutes of Health and by the Rocket Fund.

Journal Reference:

Melanie A. Jones, Bobby G. Ng, Shruti Bhide, Ephrem Chin, Devin Rhodenizer, Ping He, Marie-Estelle Losfeld, Miao He, Kimiyo Raymond, Gerard Berry, Hudson H. Freeze, Madhuri R. Hegde. DDOST Mutations Identified by Whole-Exome Sequencing Are Implicated in Congenital Disorders of Glycosylation. The American Journal of Human Genetics, 2012; DOI: 10.1016/j.ajhg.2011.12.024

Courtesy: ScienceDaily

New 'Biopsy in a Blood Test' to Detect Cancer

2012-02-09T05:11:00.000-08:00

Scientists from The Scripps Research Institute, Scripps Health, and collaborating cancer physicians have successfully demonstrated the effectiveness of an advanced blood test for detecting and analyzing circulating tumor cells (CTCs) -- breakaway cells from patients' solid tumors -- from cancer patients. The findings, reported in five new papers, show that the highly sensitive blood analysis provides information that may soon be comparable to that from some types of surgical biopsies.

"It's a next-generation technology," said Scripps Research Associate Professor Peter Kuhn, PhD, senior investigator of the new studies and primary inventor of the high-definition blood test. "It significantly boosts our ability to monitor, predict, and understand cancer progression, including metastasis, which is the major cause of death for cancer patients."

The studies were published February 3, 2012, in the journal Physical Biology.

The new test, called HD-CTC, labels cells in a patient's blood sample in a way that distinguishes possible CTCs from ordinary red and white blood cells. It then uses a digital microscope and an image-processing algorithm to isolate the suspect cells with sizes and shapes ("morphologies") unlike those of healthy cells. Just as in a surgical biopsy, a pathologist can examine the images of the suspected CTCs to eliminate false positives and note their morphologies.

Kuhn emphasizes that this basic setup can be easily modified with different cell-labeling and image-processing techniques.

Five New Studies, Five Steps Forward

To test the new technology, members of the Kuhn lab at Scripps Research teamed up with pathologists and oncologists at Scripps Health in La Jolla, California; UC San Diego Moores Cancer Center at the University of California, San Diego; the Billings Clinic in Billings, Montana; the Division of Medical Oncology at the University of California, San Francisco; the Center for Applied Molecular Medicine at the University of Southern California, in Los Angeles; and the Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital in Amsterdam, the Netherlands.

The five new studies that resulted from the collaboration not only demonstrate the accuracy and effectiveness of the new test for a number of different cancer types, but also begin to explore the utility of the technology for diagnosing and monitoring patients and improving cancer research in the lab. While other tests for CTCs typically use "enrichment" steps in which suspected CTCs are concentrated -- and these methods inadvertently exclude some types of CTCs -- the new studies show HD-CTC works well as a no-cell-left-behind process and enables a more complete analysis.

Also striking is the quality of the images. "The high definition method gives a detailed portrait of these elusive cells that are caught in the act of spreading around the body," said diagnostic pathologist Kelly Bethel, MD, of Scripps Health, Scripps Research, and UC San Diego School of Medicine, who is the senior clinical investigator on Kuhn's team. "It's unprecedented -- we've never been able to see them routinely and in high definition like this before."

In the first study, the research team examined 83 advanced cancer patients using HD-CTC to document the test's sensitivity and accuracy for different cancer types. The scientists found that the test detected five or more CTCs per milliliter of blood in 80 percent of patients with metastatic prostate cancer, 70 percent of those with metastatic breast cancer, 50 percent of those with metastatic pancreatic cancer, and no healthy subjects. The current gold-standard CTC test, known as CellSearch, was notably less sensitive in detecting tumor cells in these samples.

Most patients whose CTC counts surpassed the detection threshold also showed small aggregates of CTCs, which cancer biologists term "microtumor emboli." These are widely suspected to be incipient metastatic tumors, as well as triggers for the blood clots that often kill advanced cancer patients. In the second study, the scientists showed that HD-CTC could detect these aggregates in 43 percent of 71 patients with advanced prostate, lung, pancreas, and breast cancers, and in none of a group of 15 healthy subjects. "This tells us that HD-CTC could be helpful in studying the origins of cancer metastases and related blood clots, and for predicting them, too," Kuhn said.

In the third study, the team used HD-CTC to compare circulating tumor cells from prostate cancer patients with cells from prostate cancer cell lines that researchers often use as convenient models for prostate cancer biology in the lab. The team found significant differences between the two classes of cells, in their cell morphology and in the way they were labeled by HD-CTC's fluorescent tags. "This underscores the need for studying cancer cells from patients, not just model cancer cells that in some ways may be utterly different from the real thing," Kuhn said.

In the fourth study, the researchers performed HD-CTC tests on 28 patients with advanced non-small-cell lung cancer over periods of up to a year. The team was able to detect CTCs in 68 percent of samples, and found that the numbers of detected CTCs tended to go up as other measures showed cancer progression.

In the fifth and final paper of the series, the team used HD-CTC in 78 patients who had just been diagnosed with various stages of non-small-cell lung cancer. "We demonstrated that we could sensitively detect CTCs even in patients with early-stage cancer," Kuhn said.

This result points to the possibility of using the HD-CTC blood test not only to evaluate already-diagnosed cancer, but also to help detect cancer in people who are unaware they have it. "If HD-CTC works on the day after cancer diagnosis, as we've shown, then one can easily imagine that it would work the day before diagnosis, too," Kuhn said.

Kuhn and his colleagues now intend to study the use of HD-CTC as a potential screening test and to develop it further for use in clinical monitoring and cancer research. Kuhn has founded a San Diego-based biotechnology company, Epic Sciences, Inc., to develop HD-CTC commercially for companion diagnostic products in personalized cancer care.

Journal References:

Jorge Nieva, MarcoWendel, Madelyn Luttgen, Dena Marrinucci, Lyudmila Bazhenova, Anand Kolatkar, Roger Santala, BrockWhittenberger, James Burke, Melissa Torrey, Kelly Bethel, and Peter Kuhn. High-- imaging of circulating tumor cells and associated cellular events in non-small cell lung cancer patients: a longitudinal analysis. Physical Biology, Feb 3, 2012
Dena Marrinucci1, Kelly Bethel, Anand Kolatkar, Madelyn Luttgen, Michael Malchiodi,, Franziska Baehring, Katharina Voigt, Daniel Lazar, Jorge Nieva, Lyudmilda Bazhenova, Andrew H Ko, W Michael Korn, Ethan Schram, Michael Coward, Xing Yang, Thomas Metzner, Rachelle Lamy, Meghana Honnatti, Craig Yoshioka, Joshua Kunken, Yelena Petrova, Devin Sok, David Nelson, and Peter Kuhn. Fluid biopsy in patients with metastatic prostate, pancreatic and breast cancers. Physical Biology, Feb 3, 2012
Daniel C Lazar, Edward H Cho, Madelyn S Luttgen, Thomas J Metzner, Maria Loressa Uson, Melissa Torrey, Mitchell E Gross, and Peter Kuhn. Cytometric comparisons between circulating tumor cells from prostate cancer patients and the prostate-tumor-derived LNCaP cell line. Physical Biology, Feb 3, 2012
Edward H Cho, MarcoWendel, Madelyn Luttgen1, Craig Yoshioka, Dena Marrinucci1, Daniel Lazar, Ethan Schram, Jorge Nieva, Lyudmila Bazhenova, Alison Morgan, Andrew H Ko, W Michael Korn, Anand Kolatkar, Kelly Bethel, and Peter Kuhn. Characterization of circulating tumor cell aggregates identified in patients with epithelial tumors. Physical Biology, Feb 3, 2012
Marco Wendel, Lyudmila Bazhenova, Rogier Boshuizen, Anand Kolatkar, Meghana Honnatti, Edward H. Cho, Dena Marrinucci, Ajay Sandhu, Anthony Perricone, Patricia Thistlethwaite, Kelly Bethel, Jorge Nieva, Michel van den Heuvel, and Peter Kuhn. Fluid biopsy for Circulating Tumor Cell identification in Patients with early and late stage Non-Small Cell Lung Cancer; a glimpse into lung cancer biology. Physical Biology, Feb 3, 2012

Courtesy: ScienceDaily

Why Do Cells Age? Discovery of Extremely Long-Lived Proteins May Provide Insight Into Cell Aging and Neurodegenerative Diseases

2012-02-07T05:09:00.000-08:00

One of the big mysteries in biology is why cells age. Now scientists at the Salk Institute for Biological Studies report that they have discovered a weakness in a component of brain cells that may explain how the aging process occurs in the brain.

The scientists discovered that certain proteins, called extremely long-lived proteins (ELLPs), which are found on the surface of the nucleus of neurons, have a remarkably long lifespan.

While the lifespan of most proteins totals two days or less, the Salk Institute researchers identified ELLPs in the rat brain that were as old as the organism, a finding they reported February 3 in Science.

The Salk scientists are the first to discover an essential intracellular machine whose components include proteins of this age. Their results suggest the proteins last an entire lifetime, without being replaced.

ELLPs make up the transport channels on the surface of the nucleus; gates that control what materials enter and exit. Their long lifespan might be an advantage if not for the wear-and-tear that these proteins experience over time. Unlike other proteins in the body, ELLPs are not replaced when they incur aberrant chemical modifications and other damage.

Damage to the ELLPs weakens the ability of the three-dimensional transport channels that are composed of these proteins to safeguard the cell's nucleus from toxins, says Martin Hetzer, a professor in Salk's Molecular and Cell Biology Laboratory, who headed the research. These toxins may alter the cell's DNA and thereby the activity of genes, resulting in cellular aging.

Funded by the Ellison Medical Foundation and the Glenn Foundation for Medical Research, Hetzer's research group is the only lab in the world that is investigating the role of these transport channels, called the nuclear pore complex (NPC), in the aging process.

Previous studies have revealed that alterations in gene expression underlie the aging process. But, until the Hetzer lab's discovery that mammals' NPCs possess an Achilles' heel that allows DNA-damaging toxins to enter the nucleus, the scientific community has had few solid clues about how these gene alterations occur.

"The fundamental defining feature of aging is an overall decline in the functional capacity of various organs such as the heart and the brain," says Hetzer. "This decline results from deterioration of the homeostasis, or internal stability, within the constituent cells of those organs. Recent research in several laboratories has linked breakdown of protein homeostasis to declining cell function."

The results that Hetzer and his team just report suggest that declining neuron function may originate in ELLPs that deteriorate as a result of damage over time.

"Most cells, but not neurons, combat functional deterioration of their protein components through the process of protein turnover, in which the potentially impaired parts of the proteins are replaced with new functional copies," says Hetzer.

"Our results also suggest that nuclear pore deterioration might be a general aging mechanism leading to age-related defects in nuclear function, such as the loss of youthful gene expression programs," he adds.

The findings may prove relevant to understanding the molecular origins of aging and such neurodegenerative disorders as Alzheimer's disease and Parkinson's disease.

In previous studies, Hetzer and his team discovered large filaments in the nuclei of neurons of old mice and rats, whose origins they traced to the cytoplasm. Such filaments have been linked to various neurological disorders including Parkinson's disease. Whether the misplaced molecules are a cause, or a result, of the disease has not yet been determined.

Also in previous studies, Hetzer and his team documented age-dependent declines in the functioning of NPCs in the neurons of healthy aging rats, which are laboratory models of human biology.

Hetzer's team includes his colleagues at the Salk Institute as well as John Yates III, a professor in the Department of Chemical Physiology of The Scripps Research Institute.

When Hetzer decided three years ago to investigate whether the NPC plays a role in initiating or contributing to the onset of aging and certain neurodegenerative diseases, some members of the scientific community warned him that such a study was too bold and would be difficult and expensive to conduct. But Hetzer was determined despite the warnings.

Journal Reference:

J. N. Savas, B. H. Toyama, T. Xu, J. R. Yates, M. W. Hetzer. Extremely Long-Lived Nuclear Pore Proteins in the Rat Brain. Science, 2012; DOI: 10.1126/science.1217421

Courtesy: ScienceDaily

Embryonic Signal Drives Pancreatic Cancer and Offers a Way to Kill It

2012-01-27T06:00:00.000-08:00

Pancreatic cancer is a particularly challenging one to beat; it has a tendency to spread and harbors cancer stem cells that stubbornly resist conventional approaches to therapy. Now, researchers reporting in the November issue of Cell Stem Cell, a Cell Press publication, have evidence to suggest there is a way to kill off those cancer stem cells. The target is a self-renewal pathway known for its role not in cancer but in embryonic stem cells.

"I don't think the cancer stem cells have any direct link to embryonic development, rather they are using this developmental pathway for their uncontrolled self-renewal capacity," said Christopher Heeschen of the Spanish National Cancer Research Centre in Madrid. "This pathway is completely inactive in adult tissue. We've checked many tissues and there is zero -- no detectable expression at all."

The so-called Nodal/Activin pathway's embryonic ties and absence from other tissues present a real opportunity. It suggests you could target the molecular pathway without harming other adult cells. Heeschen's team has now shown that approach to therapy does seem to work in mice.

They first demonstrated the important role of the Nodal/Activin pathway in cancer stem cells derived from human pancreatic cancer. When that signal was blocked, normally resistant pancreatic cancer stem cells became sensitive to chemotherapy.

The researchers then moved on to experiments in mice with established tumors seeded from human cancer cells. Treatment of those animals with the pathway inhibitor plus standard chemotherapy eliminated those stem cells.

"The dual combination therapy worked strikingly well," Heeschen said. "The mice responded with 100 percent survival after 100 days." That's compared to mice not receiving the therapy, which bore large tumors and died within 40 days of implantation.

That two-part treatment wasn't enough to tackle pancreatic cancer when intact tumor tissue was implanted into mice as opposed to just cancer cells, the researchers found. Heeschen says that's because those cells were nestled within a supportive "stroma." That protective tissue delivered the Activin signal and prevented the drug combination from reaching the cells.

To get around that, Heeschen and his colleagues added a third ingredient to therapy, an inhibitor intended to target the stroma. The three-pronged approach translated into long-term, progression-free survival for the mice.

Interestingly, Heeschen says the animals' tumors didn't show signs of shrinking even as they were defeated. "They were more or less dead tissue. They were senescent with no cancer stem cells -- just sitting there," he said.

Those tissues apparently had no ability to form new tumors. The findings suggest that tumor regression isn't always the key thing to look for. It also shows that drugs designed to target cancer stem cells alone are promising, but only in combination with other drugs.

"The concept that you can hit cancer stem cells and tumors will melt away must be abandoned," Heeschen said. "You have to treat the entire cancer -- the stroma, cancer stem cells and differentiated cells -- as a complex. "

Heeschen says there are hints that this embryonic pathway might have important roles in other forms of cancer, including breast, lung and colorectal cancers. That's something they will now test in further studies.

Journal Reference:

Enza Lonardo, Patrick C. Hermann, Maria-Theresa Mueller, Stephan Huber, Anamaria Balic, Irene Miranda-Lorenzo, Sladjana Zagorac, Sonia Alcala, Iker Rodriguez-Arabaolaza, Juan Carlos Ramirez, Raul Torres-Ruíz, Elena Garcia, Manuel Hidalgo, David Álvaro Cebrián, Rainer Heuchel, Matthias Löhr, Frank Berger, Peter Bartenstein, Alexandra Aicher, Christopher Heeschen. Nodal/Activin Signaling Drives Self-Renewal and Tumorigenicity of Pancreatic Cancer Stem Cells and Provides a Target for Combined Drug Therapy. Cell Stem Cell, 2011; 9 (5): 433 DOI: 10.1016/j.stem.2011.10.001

Courtesy: ScienceDaily

Advance Toward an Imaging Agent for Diagnosing Alzheimer's Disease

2012-01-25T05:59:00.000-08:00

Scientists are reporting development and initial laboratory tests of an imaging agent that shows promise for detecting the tell-tale signs of Alzheimer's disease (AD) in the brain -- signs that now can't confirm a diagnosis until after patients have died. Their report appears in the journal ACS Medicinal Chemistry Letters.

Masahiro Ono and colleagues explain that no proven laboratory test or medical scan now exists for AD, which is claiming an increasingly heavy toll with the graying of the world's population. Patients now get a diagnosis of AD based on their medical history and symptoms, and symptoms like memory loss often are identical to those of normal aging. Currently, the only definitive way to diagnose AD involves an autopsy with examination of brain samples for the presence of the clumps and tangles of abnormal protein that occur in the disease.

The scientists describe the synthesis and lab testing of a new imaging agent (called FPPDB), which bound tightly to ß-amyloid plaques and neurofibrillary tangles -- signs of AD -- in human brain samples. In normal laboratory mice, which served as stand-ins for humans, FPPDB stayed in the body long enough for a PET scan (a sophisticated medical imaging technique). With further development, the imaging agent may allow early AD diagnosis in humans, the scientists indicate.

The authors acknowledge funding from the Japan Society for the Promotion of Science and the Ministry of Education, Culture, Sports, Science and Technology, Japan.

Journal Reference:

Kenji Matsumura, Masahiro Ono, Hiroyuki Kimura, Masashi Ueda, Yuji Nakamoto, Kaori Togashi, Yoko Okamoto, Masafumi Ihara, Ryosuke Takahashi, Hideo Saji. 18F-Labeled Phenyldiazenyl Benzothiazole for in Vivo Imaging of Neurofibrillary Tangles in Alzheimer's Disease Brains. ACS Medicinal Chemistry Letters, 2012; 3 (1): 58 DOI: 10.1021/ml200230e

Courtesy: ScienceDaily

Genetic Mechanism Linked to Congenital Heart Disease Identified

2012-01-23T05:58:00.000-08:00

Scientists at the Gladstone Institutes have identified a finely tuned mechanism by which fetal heart muscle develops into a healthy and fully formed beating heart -- offering new insight into the genetic causes of congenital heart disease and opening the door to one day developing therapies to fight this chronic and potentially fatal disorder.

In a paper being published online in Nature Genetics, researchers in the laboratory of Gladstone Senior Investigator Benoit Bruneau, PhD, describe the roles that two genes -- Ezh2 and Six1 -- play in embryonic heart development, while also uncovering how the genetic basis of embryonic heart formation can have profound health consequences later in life.

This research highlights the emerging importance of a biological process called "epigenetics," in which a genetic change that is inherited by a cell or organism early during development has long-term consequences. Epigenetics is of particular interest in heart development, as the incorrect activation of genes in fetal development can lead to congenital heart disease into adulthood.

"Approximately 1.3 million children and adults in the United States live with congenital heart disease -- requiring daily medications, surgeries and for some, heart transplants," said Dr. Bruneau, who is also a professor of Pediatrics at the University of California, San Francisco, with which Gladstone is affiliated. "An understanding of the epigenetic regulation of heart development could someday bring us closer to improving the lives of these individuals."

At specific times during healthy heart development, Ezh2 acts as a "master regulator," shutting off genes that are no longer needed or that need to be kept off. In the past, the focus has been on which genes get switched on during normal heart development. But in this paper, Dr. Bruneau, along with Gladstone Postdoctoral Scholar Paul Delgado-Olguin, PhD, investigated which genes must remain off to ensure the development of a healthy heart.

In laboratory experiments, Drs. Bruneau and Delgado-Olguin removed Ezh2 from mice at various developmental stages, monitoring any ensuing genetic or physical changes and comparing them to mice whose Ezh2 remained intact. Surprisingly, mice without Ezh2 developed normally in the uterus. It wasn't until after birth that they began to show problems. Their hearts became enlarged and weakened and were unable to pump blood efficiently. An enlarged heart is a hallmark feature of cardiomyopathy, a form of congenital heart disease that afflicts thousands of children each year and for which the only manifestation may be sudden death.

Further analysis revealed that Six1 is normally on only for a brief period during heart development, after which Ezh2 shuts it off for good. But without Ezh2 to act as a regulator, Six1 remains on -- leading to heart problems later in life.

"When Six1 remains active for too long in Ezh2-deficient mice, it boosts the activity of other genes that shouldn't be activated in heart-muscle cells -- such as genes that make skeletal muscle," said Dr. Delgado-Olguin. "The enlargement and thickening of the mice's hearts over time eventually led to heart failure."

This breakthrough may help researchers improve their understanding of the genetic causes of congenital heart disease while also pointing the way to potential therapies. For example, a type of congenital heart disease called dilated cardiomyopathy is caused by mutations in Eya4, a gene that is also regulated by Ezh2 in the heart.

"Six1 is just one of many Ezh2-regulated genes that are vital for heart development," said Dr. Bruneau. "Our next goal is to find out exactly how Ezh2 regulates these other genes, so that we can begin to develop a complete genomic blueprint of how a heart becomes a heart."

Senior Research Technologist Yu Huang, MD, PhD, also participated in this research at Gladstone, which received funding from the National Institutes of Health, the California Institute for Regenerative Medicine, the DeGeorge Charitable Trust, the American Heart Association and William H. Younger.

Journal Reference:

Paul Delgado-Olguín, Yu Huang, Xue Li, Danos Christodoulou, Christine E Seidman, J G Seidman, Alexander Tarakhovsky, Benoit G Bruneau. Epigenetic repression of cardiac progenitor gene expression by Ezh2 is required for postnatal cardiac homeostasis. Nature Genetics, 2012; DOI: 10.1038/ng.1068

Courtesy: ScienceDaily

Brain Glia Cells Increase Their DNA Content to Preserve Vital Blood-Brain Barrier

2012-01-21T05:13:00.000-08:00

The blood-brain barrier is essential for maintaining the brain's stable environment -- preventing entry of harmful viruses and bacteria and isolating the brain's specific hormonal and neurotransmitter activity from that in the rest of the body.

In addition to nerve cells, the brain contains glia cells that support and protect the neurons. In the fruit fly, the blood-brain boundary is made by glia joined into an envelope sealed around the nerve cells. As the brain rapidly expands during development, the glial envelope must grow correspondingly to remain intact. However, little has been known about how the blood-brain barrier maintains its integrity as the brain it protects develops.

Now Whitehead Institute scientists report that as the developing larval fruit fly brain grows by cell division, it instructs subperineurial glia (SPG) cells that form the blood-brain barrier to enlarge by creating multiple copies of their genomes in a process known as polyploidization. The researchers report their work this month in the journal Genes and Development.

"We think that this may be the same developmental strategy that's used in other contexts, where you need an outer layer of cells to maintain a seal, yet you also need the organ to grow during development," says Whitehead Member Terry Orr-Weaver.

Like the larval fruit fly's blood-brain barrier, cell layers in the human placenta and skin may employ polyploidization to respond to the need to expand while maintaining a sound boundary between the fetus and its surroundings, and the body and the outside world, respectively.

For preserving such barriers, polyploidy is ideal, as the cells forming the boundary enlarge without undergoing full cell division, a process that would break the tight junctions between cells.

In the larval fruit fly, polyploid SPG are necessary for maintaining the blood-brain barrier. When Yingdee Unhavaithaya, a postdoctoral researcher in Orr-Weaver's lab and first author of the Genes and Development article, prevented the SPG from making additional genome copies and becoming polyploid, the blood-brain barrier shattered as the brain continued to expand and the SPG was unable to accommodate its growth.

When allowed to progress naturally, polyploidy is flexible enough to accommodate even unusual brain expansion. After Unhavaithaya enlarged the brain by inducing a brain tumor, the SPG responded by increasing their ploidy and the blood-brain barrier remained unbroken.

This experiment also indicates that somehow the expanding brain mass is telling the SPG to increase their ploidy, but only as much as necessary to maintain the tight junctions between the SPG.

"It's a glimpse of communication between tissues during organogenesis," says Unhavaithaya. "We see different tissues trying to make a properly sized organ together. And one of the ways is by receiving instruction from the growing tissue so the other tissue can scale its size to properly conform to this tissue ratio for the organism."

For Orr-Weaver, Unhavaithaya's work could lead to additional exciting research.

"It has really opened up a whole new area to look at, so we can understand the mechanistic basis by which this communication happens," says Orr-Weaver, who is also an American Cancer Society professor of biology at MIT. "Does it happen at the organ level, or does it happen locally? There's really a lot to sort out."

This work was supported the Harold and Leila Mathers Charitable Foundation and the American Cancer Society.

Journal Reference:

Y. Unhavaithaya, T. L. Orr-Weaver. Polyploidization of glia in neural development links tissue growth to blood-brain barrier integrity. Genes & Development, 2012; 26 (1): 31 DOI: 10.1101/gad.177436.111

Courtesy: ScienceDaily

The Microbiome and Disease: Gut Bacteria Influence the Severity of Heart Attacks in Rats

2012-01-19T05:15:00.000-08:00

New research published online in the FASEB Journal suggests that the types and levels of bacteria in the intestines may be used to predict a person's likelihood of having a heart attack, and that manipulating these organisms may help reduce heart attack risk. This discovery may lead to new diagnostic tests and therapies that physicians use to prevent and treat heart attacks. In addition, this research suggests that probiotics may be able to protect the heart in patients undergoing heart surgery and angioplasty.

"Our discovery is a revolutionary milestone in the prevention and treatment of heart attacks," said John E. Baker, Ph.D., study author from the Division of Cardiothoracic Surgery at the Medical College of Wisconsin in Milwaukee. "The biochemical link between intestinal bacteria, their metabolites, and injury to the heart will reduce the risk of death from a heart attack and, coupled with the use of probiotics, will ultimately be able to improve the overall cardiovascular health of the human population."

To make this discovery, Baker and colleagues conducted experiments involving three groups of rats. The first group was fed a standard diet. The second group was treated orally with the antibiotic vancomycin in the drinking water. The third group was fed a probiotic supplement that contains Lactobacillus plantarum, a bacterium that suppresses the production of leptin.

The group treated with the antibiotic had decreased levels of leptin (a protein hormone that plays a key role in appetite and metabolism), which resulted in smaller heart attacks, and improved recovery of mechanical function as compared to the group fed a standard diet. The antibiotic reduced total bacterial numbers in the intestines and altered the abundance of specific types of bacteria and fungi that live in the gut. Treating these rats with leptin was shown to offset the protection produced by the antibiotic treatment. The third group was fed a probiotic that also altered the numbers and types of bacteria and fungi living in the gut. Like those fed the antibiotic, these rats also had decreased leptin levels, resulting in smaller heart attacks and greater recovery of mechanical function as compared to the first group. Treating these rats with leptin also was shown to offset the protection produced by the probiotic.

"We may not be ready to prescribe yogurt to prevent heart attacks, but this research does gives us a much better understanding of how the microbiome affects our response to injury," said Gerald Weissmann, M.D., Editor-in-Chief of the FASEB Journal. "Just as physicians use cholesterol levels, blood pressure, and overall body composition as measures of heart disease risk, we may soon evaluate our body's susceptibility to disease by looking at the microbes that inhabit the gut."

Journal Reference:

Vy Lam, Jidong Su, Stacy Koprowski, Anna Hsu, James S. Tweddell, Parvaneh Rafiee, Garrett J. Gross, Nita H. Salzman, and John E. Baker. Intestinal microbiota determine severity of myocardial infarction in rats. FASEB J., 2012 DOI: 10.1096/fj.11-197921

Courtesy: ScienceDaily

New Method Keeps Normal Cells and Tumor Cells Taken from an Individual Cancer Patient Alive

2012-01-17T07:12:00.000-08:00

In a major step that could revolutionize biomedical research, scientists have discovered a way to keep normal cells as well as tumor cells taken from an individual cancer patient alive in the laboratory -- which previously had not been possible. Normal cells usually die in the lab after dividing only a few times, and many common cancers will not grow, unaltered, outside of the body.

This new technique, described December 29 online in the American Journal of Pathology, could be the critical advance that ushers in a new era of personalized cancer medicine, and has potential application in regenerative medicine, says the study's senior investigator, Richard Schlegel, M.D., Ph.D., chairman of the department of pathology at Georgetown Lombardi Comprehensive Cancer Center, a part of Georgetown University Medical Center.

"Because every tumor is unique, this advance will make it possible for an oncologist to find the right therapies that both kills a patient's cancer and spares normal cells from toxicity," he says. "We can test resistance as well chemosensitivity to single or combination therapies directly on the cancer cell itself."

The research team, which also includes several scientists from the National Institutes of Health, found that adding two different substances to cancer and normal cells in a laboratory pushes them to morph into stem-like cells -- adult cells from which other cells are made.

The two substances are a Rho kinase (ROCK) inhibitor and fibroblast feeder cells. ROCK inhibitors help stop cell movement, but it is unclear why this agent turns on stem cell attributes, Schlegel says. His co-investigator Alison McBride, Ph.D., of the National Institute of Allergy and Infectious Diseases, had discovered that a ROCK inhibitor allowed skin cells (keratinocytes) to reproduce in the laboratory while feeder cells kept them alive.

The Georgetown researchers -- 13 investigators in the departments of pathology and oncology -- tried ROCK inhibitors and fibroblast feeder cells on the non-keratinocyte epithelial cells that line glands and organs to see if they had any effect. They found that both were needed to produce a dramatic effect in which the cells visibly changed their shape as they reverted to a stem-like state.

"We tried breast cells and they grew well. We tried prostate cells and their growth was fantastic, which is amazing because it is normally impossible to grow these cells in the lab," Schlegel says. "We found the same thing with lung and colon cells that have always been difficult to grow."

"In short, we discovered we can grow normal and tumor cells from the same patient forever, and nobody has been able to do that," he says. "Normal cell cultures for most organ systems can't be established in the lab, so it wasn't possible previously to compare normal and tumor cells directly."

The ability to immortalize cancer cells will also make biobanking both viable and relevant, Schlegel says. The researchers further discovered that the stem-like behavior in these cells is reversible. Withdrawing the ROCK inhibitor forces the cells to differentiate into the adult cells that they were initially. This "conditional immortalization" could help advance the field of regenerative medicine, Schlegel says.

However, the most immediate change in medical practice from these findings is the potential they have in "revolutionizing what pathology departments do," Schlegel says.

"Today, pathologists don't work with living tissue. They make a diagnosis from biopsies that are either frozen or fixed and embedded in wax," he says. "In the future, pathologists will be able to establish live cultures of normal and cancerous cells from patients, and use this to diagnose tumors and screen treatments. That has fantastic potential."

This research was funded by grants from the National Institutes of Health, Department of Defense fellowship funding, and an internal grant from Georgetown Lombardi's Cancer Center Support Grant from the National Cancer Institute.

Georgetown University and the National Institutes of Health have filed two patent applications on technologies described in this paper. The inventors for the patent application related to immortalization of non-keratinocyte technology described in this paper which is jointly owned by Georgetown and NIH include Schlegel, Xuefeng Liu and Alison McBride. Sandra Chapman and McBride are co-inventors on a separate patent application filed by the National Institutes of Health related to keratinocyte technology described in this paper.

Journal Reference:

Xuefeng Liu, Virginie Ory, Sandra Chapman, Hang Yuan, Chris Albanese, Bhaskar Kallakury, Olga A. Timofeeva, Caitlin Nealon, Aleksandra Dakic, Vera Simic, Bassem R. Haddad, Johng S. Rhim, Anatoly Dritschilo, Anna Riegel, Alison McBride, Richard Schlegel. ROCK Inhibitor and Feeder Cells Induce the Conditional Reprogramming of Epithelial Cells. The American Journal of Pathology, 2011; DOI: 10.1016/j.ajpath.2011.10.036

Courtesy: ScienceDaily

Changes Seen in Cerebrospinal Fluid Levels Before Onset of Alzheimer's Disease

2012-01-13T05:18:00.000-08:00

Cerebrospinal fluid levels of Aβ42 appear to be decreased at least five to 10 years before some patients with mild cognitive impairment develop Alzheimer disease (AD) dementia whereas other spinal fluid levels seem to be later markers of disease, according to a report in the January issue of Archives of General Psychiatry, one of the JAMA/Archives journals.

The researchers note as background in the study that disease-modifying therapies, such as immunotherapy, are more likely to be successful if started in the early stages of the disease so there is a need to identify patients with Alzheimer disease before neurodegeneration is not too severe.

Peder Buchhave, M.D., Ph.D, who is affiliated with Lund University and Skane University, Sweden, and colleagues conducted an extended follow-up of the cohort from a previous study of 137 patients with mild cognitive impairment (MCI) at baseline. The median follow-up was 9.2 years.

During the follow-up, 72 patients (53.7 percent) developed AD and 21 (15.7 percent) progressed to other forms of dementia. At the baseline, cerebrospinal fluid Aβ42 levels were reduced and other biomarkers T-tau and P-tau levels were elevated in patients who converted to AD during follow-up compared with levels in patients who did not develop AD.

The study indicates baseline CSF Aβ42 levels were equally reduced in patients with MCI who converted to AD within five years (the early converters) compared to those who converted later between five and 10 years. However, T-tau and P-tau levels were significantly higher in early converters compared to later ones.

Researchers suggest that "approximately 90 percent of patients with MCI and pathologic CSF biomarkers at baseline will develop AD within 9.2 years."

"Therefore, these markers can identify individuals at high risk for future AD least five to 10 years before conversion to dementia. Hopefully, new therapies that can retard or even halt progression of the disease will soon be available. Together with an early and accurate diagnosis, such therapies could be initiated before neuronal degeneration is too widespread and patients are already demented," the authors conclude.

Journal Reference:

P. Buchhave, L. Minthon, H. Zetterberg, A. K. Wallin, K. Blennow, O. Hansson. Cerebrospinal Fluid Levels of β-Amyloid 1-42, but Not of Tau, Are Fully Changed Already 5 to 10 Years Before the Onset of Alzheimer Dementia. Archives of General Psychiatry, 2012; 69 (1): 98 DOI: 10.1001/archgenpsychiatry.2011.155

Courtesy: ScienceDaily

Anti-Sense Might Make Sense for Treating Liver Cancer

2012-01-11T05:17:00.000-08:00

A new study shows that it is possible to selectively target and block a particular microRNA that is important in liver cancer. The finding might offer a new therapy for this malignancy, which kills an estimated 549,000 people worldwide annually.

The animal study, by researchers at The Ohio State University Comprehensive Cancer Center -- Arthur G. James Cancer Hospital and Richard J. Solove Research Institute (OSUCCC -- James) and at Mayo Clinic, focused on microRNA-221 (miR-221), a molecule that is consistently present at abnormally high levels in liver cancer.

To control the problem molecule, the researchers designed a second molecule as a kind of mirror image of the first. That mirror molecule is called an antisense oligonucleotide, and it selectively bound to and blocked the action of miR-221 in human liver cancer transplanted into mice. The treatment significantly prolonged the animals' lives and promoted the activity of important tumor-suppressor genes.

"This study is significant because hepatocellular carcinoma, or liver cancer, generally has a poor prognosis, so we badly need new treatment strategies," says principal investigator Thomas Schmittgen, associate professor and chair of pharmaceutics at Ohio State's College of Pharmacy and a member of the OSUCCC -- James Experimental Therapeutics program.

The findings are published in the journal Cancer Research.

For the study, Schmittgen and his colleagues injected liver cancer cells labeled with the luminescent lighting-bug protein luciferase into the livers of mice. The researchers used bioluminescence imaging to monitor tumor growth.

When the tumors reached the appropriate size, they gave one group of animals the molecule designed to block miR-221; the other group received a control molecule.

Key findings include the following:

After treatment with the antisense oligonucleotide, half the treated animals were alive at 10 weeks versus none of the controls.
The antisense oligonucleotide significantly reduced levels of miR-221 in both tumor and normal liver samples.
Treatment with the antisense oligonucleotide caused a three-fold increase in the activity of three important tumor-suppressor genes that are blocked by miR-221 in liver cancer. (The tumor suppressors were p27, p57 and PTEN.)

"Overall, this study provides proof-of-principle for further development of microRNA-targeted therapies for hepatocellular carcinomas," Schmittgen says.

Funding from the National Cancer Institute and from the National Institute of Diabetes and Digestive and Kidney Diseases supported this research.

Other researchers involved in this study were Jong-Kook Park, Jinmai Jiang, Lei He, Ji Hye Kim, Mitch A. Phelps, Tracey L. Papenfuss and Carlo M. Croce of Ohio State; Takayuki Kogure and Tushar Patel of Mayo Clinic, Jacksonville, Florida; and Gerard J. Nuovo.

Journal Reference:

J.-K. Park, T. Kogure, G. J. Nuovo, J. Jiang, L. He, J. H. Kim, M. A. Phelps, T. L. Papenfuss, C. M. Croce, T. Patel, T. D. Schmittgen. miR-221 Silencing Blocks Hepatocellular Carcinoma and Promotes Survival. Cancer Research, 2011; 71 (24): 7608 DOI: 10.1158/0008-5472.CAN-11-1144

Courtesy: ScienceDaily

World’s First Primate Chimeric Offspring Produced: Research Demonstrates Not All Embryonic Stem Cells Are Equal

2012-01-09T05:15:00.000-08:00

Newly published research by scientists at Oregon Health & Science University provides significant new information about how early embryonic stem cells develop and take part in formation of the primate species. The research, which took place at OHSU's Oregon National Primate Research Center, has also resulted in the first successful birth of chimeric monkeys -- monkeys developed from stem cells taken from two separate embryos.

The research is being published this week in the online edition of the journal Cell and will be published in a future printed copy of the journal.

The research was conducted to gain a better understanding of the differences between natural stem cells residing in early embryos and their cultured counterparts called embryonic stem cells. This study also determined that stem cell functions and abilities are different between primates and rodents.

Here's more information about the early primate stem cells that were studied: The first cell type was totipotent cells -- cells from the early embryo that have the ability to divide and produce all of the differentiated cells in the placenta and the body of organism. These were compared with pluripotent cells -- cells derived from the later stage embryo that have only the ability to become the body but not placenta.

In mice, either totipotent or pluripotent cells from two different animals can be combined to transform into an embryo that later becomes a chimeric animal. However, the current research demonstrated that for reasons yet unknown, chimeric animals can only develop from totipotent cells in a higher animal model: the rhesus macaque. OHSU showed this to be the case by successfully producing the world's first primate chimeric offspring, three baby rhesus macaques named Roku, Hex and Chimero.

"This is an important development -- not because anyone would develop human chimeras -- but because it points out a key distinction between species and between different kind of stem cells that will impact our understanding of stem cells and their future potential in regenerative medicine," explained Shoukhrat Mitalipov, Ph.D., an associate scientist in the Division of Reproductive and Developmental Sciences at ONPRC.

"Stem cell therapies hold great promise for replacing damaged nerve cells in those who have been paralyzed due to a spinal cord injury or for example, in replacing dopamine-producing cells in Parkinson's patients who lose these brain cells resulting in disease. As we move stem cell therapies from the lab to clinics and from the mouse to humans, we need to understand what these cells do and what they can't do and also how cell function can differ in species."

The OHSU Oregon National Primate Research Center and the National Institutes of Health funded the research.

Journal Reference:

Masahito Tachibana, Michelle Sparman, Cathy Ramsey, Hong Ma, Hyo-Sang Lee, Maria Cecilia T. Penedo, Shoukhrat Mitalipov. Generation of Chimeric Rhesus Monkeys. Cell, 2012; DOI: 10.1016/j.cell.2011.12.007

Courtesy: ScienceDaily

Computer Assisted Design (CAD) for RNA: Researchers Develop CAD-Type Tools for Engineering RNA Control Systems

2012-01-07T05:53:00.000-08:00

The computer assisted design (CAD) tools that made it possible to fabricate integrated circuits with millions of transistors may soon be coming to the biological sciences. Researchers at the U.S. Department of Energy (DOE)'s Joint BioEnergy Institute (JBEI) have developed CAD-type models and simulations for RNA molecules that make it possible to engineer biological components or "RNA devices" for controlling genetic expression in microbes. This holds enormous potential for microbial-based sustainable production of advanced biofuels, biodegradable plastics, therapeutic drugs and a host of other goods now derived from petrochemicals.

"Because biological systems exhibit functional complexity at multiple scales, a big question has been whether effective design tools can be created to increase the sizes and complexities of the microbial systems we engineer to meet specific needs," says Jay Keasling, director of JBEI and a world authority on synthetic biology and metabolic engineering. "Our work establishes a foundation for developing CAD platforms to engineer complex RNA-based control systems that can process cellular information and program the expression of very large numbers of genes. Perhaps even more importantly, we have provided a framework for studying RNA functions and demonstrated the potential of using biochemical and biophysical modeling to develop rigorous design-driven engineering strategies for biology."

Keasling, who also holds appointments with the Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California (UC) Berkley, is the corresponding author of a paper in the journal Science that describes this work. The paper is titled "Model-driven engineering of RNA devices to quantitatively-program gene expression." Other co-authors are James Carothers, Jonathan Goler and Darmawi Juminaga.

Synthetic biology is an emerging scientific field in which novel biological devices, such as molecules, genetic circuits or cells, are designed and constructed, or existing biological systems, such as microbes, are re-designed and engineered. A major goal is to produce valuable chemical products from simple, inexpensive and renewable starting materials in a sustainable manner. As with other engineering disciplines, CAD tools for simulating and designing global functions based upon local component behaviors are essential for constructing complex biological devices and systems. However, until this work, CAD-type models and simulation tools for biology have been very limited.

Identifying the relevant design parameters and defining the domains over which expected component behaviors are exerted have been key steps in the development of CAD tools for other engineering disciplines," says Carothers, a bioengineer and lead author of the Science paper who is a member of Keasling's research groups with both JBEI and the California Institute for Quantitative Biosciences. "We've applied generalizable engineering strategies for managing functional complexity to develop CAD-type simulation and modeling tools for designing RNA-based genetic control systems. Ultimately we'd like to develop CAD platforms for synthetic biology that rival the tools found in more established engineering disciplines, and we see this work as an important technical and conceptual step in that direction."

Keasling, Carothers and their co-authors focused their design-driven approach on RNA sequences that can fold into complicated three dimensional shapes, called ribozymes and aptazymes. Like proteins, ribozymes and aptazymes can bind metabolites, catalyze reactions and act to control gene expression in bacteria, yeast and mammalian cells. Using mechanistic models of biochemical function and kinetic biophysical simulations of RNA folding, ribozyme and aptazyme devices with quantitatively predictable functions were assembled from components that were characterized in vitro, in vivo and in silico. The models and design strategy were then verified by constructing 28 genetic expression devices for the Escherichia coli bacterium. When tested, these devices showed excellent agreement -- 94-percent correlation -- between predicted and measured gene expression levels.

"We needed to formulate models that would be sophisticated enough to capture the details required for simulating system functions, but simple enough to be framed in terms of measurable and tunable component characteristics or design variables," Carothers says. "We think of design variables as the parts of the system that can be predictably modified, in the same way that a chemical engineer might tune the operation of a chemical plant by turning knobs that control fluid flow through valves. In our case, knob-turns are represented by specific kinetic terms for RNA folding and ribozyme catalysis, and our models are needed to tell us how a combination of these knob-turns will affect overall system function."

JBEI researchers are now using their RNA CAD-type models and simulations as well as the ribozyme and aptazyme devices they constructed to help them engineer metabolic pathways that will increase microbial fuel production. JBEI is one of three DOE Bioenergy Research Centers established by DOE's Office of Science to advance the technology for the commercial production of clean, green and renewable biofuels. A key to JBEI's success will be the engineering of microbes that can digest lignocellulosic biomass and synthesize from the sugars transportation fuels that can replace gasoline, diesel and jet fuels in today's engines.

"In addition to advanced biofuels, we're also looking into engineering microbes to produce chemicals from renewable feedstocks that are difficult to produce cheaply and in high yield using traditional organic chemistry technology," Carothers says.

While the RNA models and simulations developed at JBEI to date fall short of being a full-fledged RNA CAD platform, Keasling, Carothers and their coauthors are moving towards that goal.

"We are also actively trying to make our models and simulations more accessible to researchers who may not want to become RNA control system experts but would nonetheless like to use our approach and RNA devices in their own work," Carothers says.

While the work at JBEI focused on E. coli and the microbial production of advanced biofuels, the authors of the Science paper believe that their concepts could also be used for programming function into mammalian systems and cells.

"We recently initiated a research project to investigate how we can use our approach to engineer RNA-based genetic control systems that will increase the safety and efficacy of regenerative medicine therapies that use cultured stem cells to treat diseases such as diabetes and Parkinson's," Carothers says.

This research was supported in part by grants from the DOE Office of Science through JBEI, and the National Science Foundation through the Synthetic Biology Engineering Research Center (SynBERC).

Journal Reference:

James M. Carothers, Jonathan A. Goler, Darmawi Juminaga, Jay D. Keasling. Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression. Science, December 2011: Vol. 334 no. 6063 pp. 1716-1719 DOI: 10.1126/science.1212209

Courtesy: ScienceDaily

Self-Regulation of the Immune System Suppresses Defense Against Cancer

2012-01-05T01:51:00.000-08:00

Regulatory T cells (Tregs), which are part of the body's immune system, downregulate the activity of other immune cells, thus preventing the development of autoimmune diseases or allergies. Scientists at the German Cancer Research Center (DKFZ) have now found the activation steps that are blocked by Tregs in immune cells. Since Tregs can also suppress the body's immune defense against cancer, the findings obtained by the DKFZ researchers are important for developing more efficient cancer treatments.

It is vital that the body's own immune system does not overreact. If its key players, the helper T cells, get out of control, this can lead to autoimmune diseases or allergies. An immune system overreaction against infectious agents may even directly damage organs and tissues.

Immune cells called regulatory T cells ("Tregs") ensure that immune responses take place in a coordinated manner: They downregulate the dividing activity of helper T cells and reduce their production of immune mediators. "This happens through direct contact between regulatory cell and helper cell," says Prof. Peter Krammer of DKFZ. "But we didn't know yet what this contact actually causes in helper cells." The researchers' hypothesis was that the contact with the Tregs affects certain steps in the complex signaling cascade that leads to the activation of the helper T cells.

If the T cell receptor, a sensor molecule on the surface of helper cells, senses foreign or damaged protein molecules, this will trigger a cascade of biochemical activation reactions. At the end of this signaling cascade, genes that are required for an immune attack will be read in the nucleus of helper cells.

Jointly with colleagues from several German research institutes, Peter Krammer, Angelika Schmidt and co-workers have now compared the signaling cascades in helper cells with and without contact to Tregs. The immunologists found out that a short contact of the two types of cells in the culture dish is sufficient to suppress the helper cells. Following Treg contact, the typical release of calcium ions into the plasma of helper cells does not occur. As a result, two important transcription factors, NFkappaB and NFAT, do no longer function. They normally activate genes for immune mediators, thus alerting the immune system.

"The mode of action of Tregs is of great importance for cancer medicine. Many of our colleagues have shown in various types of cancer that Tregs can downregulate the immune response against tumors so that transformed cells escape the immune defense. This can contribute to the development and spread of cancer. We are therefore searching for ways to reactivate such suppressed helper cells," said Krammer, explaining the goals of his work. For developing immune therapies against cancer it is also crucial to understand how Tregs work. The researchers are trying to prevent that immune cells which have been painstakingly activated against cancer in the culture dish are immediately suppressed again by Tregs.

Journal Reference:

A. Schmidt, N. Oberle, E.-M. Weiss, D. Vobis, S. Frischbutter, R. Baumgrass, C. S. Falk, M. Haag, B. Brugger, H. Lin, G. W. Mayr, P. Reichardt, M. Gunzer, E. Suri-Payer, P. H. Krammer. Human Regulatory T Cells Rapidly Suppress T Cell Receptor-Induced Ca2 , NF- B, and NFAT Signaling in Conventional T Cells. Science Signaling, 2011; 4 (204): ra90 DOI: 10.1126/scisignal.2002179

Courtesy: ScienceDaily

Alzheimer's: Diet Patterns May Keep Brain from Shrinking

2012-01-03T01:50:00.000-08:00

People with diets high in several vitamins or in omega 3 fatty acids are less likely to have the brain shrinkage associated with Alzheimer's disease than people whose diets are not high in those nutrients, according to a new study published in the December 28, 2011, online issue of Neurology®, the medical journal of the American Academy of Neurology.

Those with diets high in omega 3 fatty acids and in vitamins C, D, E and the B vitamins also had higher scores on mental thinking tests than people with diets low in those nutrients. These omega 3 fatty acids and vitamin D are primarily found in fish. The B vitamins and antioxidants C and E are primarily found in fruits and vegetables.

In another finding, the study showed that people with diets high in trans fats were more likely to have brain shrinkage and lower scores on the thinking and memory tests than people with diets low in trans fats. Trans fats are primarily found in packaged, fast, fried and frozen food, baked goods and margarine spreads.

The study involved 104 people with an average age of 87 and very few risk factors for memory and thinking problems. Blood tests were used to determine the levels of various nutrients present in the blood of each participant. All of the participants also took tests of their memory and thinking skills. A total of 42 of the participants had MRI scans to measure their brain volume.

Overall, the participants had good nutritional status, but seven percent were deficient in vitamin B12 and 25 percent were deficient in vitamin D.

Study author Gene Bowman, ND, MPH, of Oregon Health & Science University in Portland and a member of the American Academy of Neurology, said that the nutrient biomarkers in the blood accounted for a significant amount of the variation in both brain volume and thinking and memory scores. For the thinking and memory scores, the nutrient biomarkers accounted for 17 percent of the variation in the scores. Other factors such as age, number of years of education and high blood pressure accounted for 46 percent of the variation. For brain volume, the nutrient biomarkers accounted for 37 percent of the variation.

"These results need to be confirmed, but obviously it is very exciting to think that people could potentially stop their brains from shrinking and keep them sharp by adjusting their diet," Bowman said.

The study was the first to use nutrient biomarkers in the blood to analyze the effect of diet on memory and thinking skills and brain volume. Previous studies have looked at only one or a few nutrients at a time or have used questionnaires to assess people's diet. But questionnaires rely on people's memory of their diet, and they also do not account for how much of the nutrients are absorbed by the body, which can be an issue in the elderly.

The study was supported by the National Institutes of Health, the National Institute on Aging and National Center for Complementary and Alternative Medicine and the U.S. Department of Veteran Affairs, Portland VA Medical Center.

Story Source:

The above story is reprinted from materials provided by American Academy of Neurology.

Courtesy: ScienceDaily

Preventing Cancer Development Inside the Cell Cycle

2011-10-28T08:22:00.000-07:00

Researchers from the NYU Cancer Institute, an NCI-designated cancer center at NYU Langone Medical Center, have identified a cell cycle-regulated mechanism behind the transformation of normal cells into cancerous cells. The study shows the significant role that protein networks can play in a cell leading to the development of cancer. The study results, published in the October 21 issue of the journal Molecular Cell, suggest that inhibition of the CK1 enzyme may be a new therapeutic target for the treatment of cancer cells formed as a result of a malfunction in the cell's mTOR signaling pathway.

In the study, NYU Cancer Institute researchers examined certain multi-protein complexes and protein regulators in cancer cells. Researchers identified a major role for the multi-protein complex called SCF^βTrCP. It assists in the removal from cancer cells the recently discovered protein DEPTOR, an inhibitor of the mTOR pathway. SCF (Skp1, Cullin1, F-box protein) ubiquitin ligase complexes are responsible for the removal of unnecessary proteins from a cell. This degradation of proteins by the cell's ubiquitin system controls cell growth and prevents malignant cell transformation. Researchers show that inhibiting the ability of SCF^βTrCPto degrade DEPTOR in cells can result in blocking the proliferation of cancer cells. In addition, researchers discovered that the activity of CK1 (Casein Kinase 1), a protein that regulates signaling pathways in most cells, is needed for SCF^βTrCPto successfully promote the degradation of DEPTOR.

"Low levels of DEPTOR and high levels of mTOR activity are found in many cancers, including cancers of the breast, prostate, and lung," said senior study author Michele Pagano, MD, the May Ellen and Gerald Jay Ritter Professor of Oncology and Professor of Pathology at NYU Langone Medical Center and a Howard Hughes Medical Institute Investigator. "It is critical for researchers to better understand how the protein DEPTOR is regulated.Our study shows it would be advantageous to increase the levels of DEPTOR in many types of cancer cells to inhibit mTOR and prevent cell proliferation."

The mTOR pathway (mammalian Target Of Rapamycin) regulates the growth, proliferation, and survival of a cell, and its proper regulation is essential to prevent the formation of cancer cells. DEPTOR interrupts the mTOR pathway by binding to mTOR protein complexes and blocking their enzymatic activities, restraining cell growth. This helps support the proliferation and survival of cancer cells.

Study experiments showed that a reduction of SCF^βTrCPand CK1 proteins in cells resulted in accumulation of DEPTOR. Also, DEPTOR was destroyed in cells only when SCF^βTrCP and CK1 were both present. Thus, inhibition of SCF^βTrCPor CK1 represents a novel and promising way to inhibit the mTOR pathway. A pharmacologic inhibitor of CK1 was tested by researchers and shown to successfully stabilize DEPTOR in cells, while other pharmacological agents had no effect.

"Our study findings demonstrate that DEPTOR is regulated by the SCF^βTrCPprotein complex in cells reentering the cell cycle, and deregulation of this event could contribute to the aberrant activation of the mTOR pathway in cancer," said lead author Shanshan Duan, PhD, a post-doctoral fellow in the Department of Pathology at NYU School of Medicine in Dr. Pagano's Laboratory. "This study suggests a novel approach to stop the deregulation of the mTOR pathway in cancer cells with promising small molecule inhibitors of CK1.This study is another step forward in the translation of laboratory findings into more effective approaches to cancer prevention and treatment."

Journal References:

Shanshan Duan, Jeffrey R. Skaar, Shafi Kuchay, Alfredo Toschi, Naama Kanarek, Yinon Ben-Neriah, Michele Pagano. mTOR Generates an Auto-Amplification Loop by Triggering the βTrCP- and CK1α-Dependent Degradation of DEPTOR. Molecular Cell, 2011; 44 (2): 317-324 DOI: 10.1016/j.molcel.2011.09.005
Shanshan Duan, Jeffrey R. Skaar, Shafi Kuchay, Alfredo Toschi, Naama Kanarek, Yinon Ben-Neriah, Michele Pagano. mTOR Generates an Auto-Amplification Loop by Triggering the βTrCP- and CK1α-Dependent Degradation of DEPTOR. Molecular Cell, 21 October 2011; 44(2) pp. 317 - 324 DOI: 10.1016/j.molcel.2011.09.005

Courtesy: ScienceDaily

Antiviral Drugs May Slow Alzheimer's Progression

2011-10-26T08:21:00.000-07:00

Antiviral drugs used to target the herpes virus could be effective at slowing the progression of Alzheimer's disease (AD), a new study shows.

The University of Manchester scientists have previously shown that the herpes simplex virus type 1 (HSV1) is a risk factor for Alzheimer's when it is present in the brains of people who have a specific genetic risk to the disease.

AD is an incurable neurodegenerative condition affecting about 18 million people worldwide. The causes of the disease or of the abnormal protein structures seen in AD brains -- amyloid plaques and neurofibrillary tangles -- are completely unknown.

The Manchester team has established that the herpes virus causes accumulation of two key AD proteins -- β-amyloid (Aβ) and abnormally phosphorylated tau (P-tau) -- known to be the main components of plaques and tangles respectively. Both proteins are thought by many scientists to be involved in the development of the disease.

"We have found that the viral DNA in AD brains is very specifically located within amyloid plaques," said Professor Ruth Itzhaki, who led the team in the University's Faculty of Life Sciences. "This, together with the production of amyloid that the virus induces, suggests that HSV1 is a cause of toxic amyloid products and of plaques.

"Our results suggest that HSV1, together with the host genetic factor, is a major risk for AD, and that antiviral agents might be used for treating patients to slow disease progression."

Currently available antiviral agents act by targeting replication of HSV1 DNA, and so the researchers considered that they might be successful in treating AD only if the accumulation of β-amyloid and P-tau accumulation caused by the virus occurs at or after the stage at which viral DNA replication occurs.

"If these proteins are produced independently of HSV1 replication, antivirals might not be effective," said Professor Itzhaki. "We investigated this and found that treatment of HSV1-infected cells with acyclovir, the most commonly used antiviral agent, and also with two other antivirals, did indeed decrease the accumulation of β-amyloid and P-tau, as well as decreasing HSV1 replication as we would expect.

"This is the first study investigating antiviral effects on AD-like changes and we conclude that since antiviral agents reduce greatly β-amyloid and P-tau levels in HSV1-infected cells, they would be suitable for treating Alzheimer's disease. The great advantage over current AD therapies is that acyclovir would target only the virus, not the host cell or normal uninfected cells. Further, these agents are very safe and are relatively inexpensive.

"Also, by targeting a cause of Alzheimer's disease, other viral damage, besides β-amyloid and P-tau, which might be involved in the disease's pathogenesis, would also be inhibited.

"The next stage of our research -- subject to funding -- will focus on finding the most suitable antiviral agent -- or combination of two agents that operate via different mechanisms -- for use as treatment. We then need to investigate the way in which the virus and the genetic risk factor interact to cause the disease, as that might lead to further novel treatments.

"Eventually, we hope to begin clinical trials in humans but this is still some way off yet and again will require new funding."

The study, carried out with Dr Matthew Wozniak and other colleagues in the Faculty of Life Sciences, is published in the Public Library of Science (PLoS) One journal.

Journal Reference:

Matthew A. Wozniak, Alison L. Frost, Chris M. Preston, Ruth F. Itzhaki. Antivirals Reduce the Formation of Key Alzheimer's Disease Molecules in Cell Cultures Acutely Infected with Herpes Simplex Virus Type 1. PLoS ONE, 2011; 6 (10): e25152 DOI: 10.1371/journal.pone.0025152

Courtesy: ScienceDaily

Newly Discovered Reservoir of Antibiotic Resistance Genes

2011-10-24T08:20:00.000-07:00

Waters polluted by the ordure of pigs, poultry, or cattle represent a reservoir of antibiotic resistance genes, both known and potentially novel. These resistance genes can be spread among different bacterial species by bacteriophage, bacteria-infecting viruses, according to a paper in the October Antimicrobial Agents and Chemotherapy.

"We found great quantities of bacteriophages carrying different antibiotic resistance genes in waters with fecal pollution from pigs, cattle, and poultry," says Maite Muniesa of the University of Barcelona, Spain, an author on the study. "We demonstrated that the genes carried by the phages were able to generate resistance to a given antibiotic when introduced into other bacteria in laboratory conditions," says Muniesa.

Although we often think of antibiotic resistance genes as evolving into existence in response to the antibiotics that doctors use to fight human disease and that agribusiness uses to fatten farm animals, microbes had undoubtedly been using both antibiotics and resistance genes to compete with each other for millions of years before antibiotics revolutionized human medicine and resistance genes threatened their efficacy to the point where the World Health Organization considers them to be one of the biggest risks to human health.

Thus, the Spanish researchers suspect, based on their study, that these resistance gene reservoirs are the product of microbial competition, rather than pressure from human use of antibiotics. They note that the pasture-fed cattle in their study are not fed antibiotics, and they suggest that even if antibiotic feed additives were banned, new resistance genes might emerge while old ones spread from these reservoirs into bacteria that infect humans.

And if resistance genes are being mobilized from these reservoirs, it becomes important to understand how the resistance genes are transmitted from phage to new bacterial species, in order to develop strategies that could hinder this transmission, limiting the emergence of new resistance genes, says Muniesa.

Journal Reference:

M. Colomer-Lluch, L. Imamovic, J. Jofre, M. Muniesa. Bacteriophages Carrying Antibiotic Resistance Genes in Fecal Waste from Cattle, Pigs, and Poultry. Antimicrobial Agents and Chemotherapy, 2011; 55 (10): 4908 DOI: 10.1128/AAC.00535-11

Courtesy: ScienceDaily

Hidden Genetic Influence On Cancer Discovered

2011-10-21T08:28:00.000-07:00

In findings with major implications for the genetics of cancer and human health, researchers at Beth Israel Deaconess Medical Center (BIDMC) and two other science teams in New York City and Rome have uncovered evidence of powerful new genetic networks and showed how it may work to drive cancer and normal development.

Four papers published online Oct. 14 in the journal Cell describe aspects of what may be a fundamentally new dimension of genetic activity that involves a vast posse of RNA molecules interacting and manipulating the molecular endgame behind the scenes. Each paper used a different approach, strengthening the basic discovery of the new RNA network.

In the half-century old central dogma of molecular biology, DNA issues its genetic blueprint to messenger RNA, which relays the orders to the protein-making machinery of the cell. The new studies suggest a significant new role for RNA on top of its traditional middle-management job: The RNA of one gene can control and be controlled by dozens or hundreds of RNAs of other genes.

In the case of a major tumor suppressor gene, PTEN, a shift in the associated RNA network appears to be as malevolent as a mutation in the gene itself in human prostate and colon cancer cells, in glioblastoma cells, and in a mouse model of melanoma, according to three of the papers.

The findings may enlarge the framework for investigating how tumors form and progress, who is at risk for cancer, and how to find and disable the essential misbehaving molecules that drive the growth and spread of cancer.

"For instance, we now know that the PTEN tumor suppressor gene is talking to a vast unrecognized RNA network," said Pier Paolo Pandolfi MD PhD, director of the Cancer Genetics Program at BIDMC and George C. Reisman Professor of Medicine at Harvard Medical School, and the senior author of two of the papers. "The RNAs talk through a new language. If this language is broken and the RNA network is perturbed, PTEN goes down, and this has devastating consequences. But it's incredibly exciting for therapeutic possibilities. You may be able to rewire the crosstalk between the RNAs for cancer prevention and therapy."

Scientists typically use genetic studies to probe how changes in the DNA code influence the action of the proteins. Targeted therapies have arisen from efforts to counteract the effect of problematic proteins, yet most of the genetic determinants of cancer remain a vexing puzzle. The newly discovered RNA network could explain much of the elusive genetic variation underlying cancer and other diseases, say authors of the papers.

The new RNA regulatory network also appears to extend into the massive non-protein-coding region of the human genome and plays an important role in normal muscle development, suggests another related paper in Cell. Because humans share so many protein-coding genes with other organisms, including worms and yeast, this large portion that is transcribed into non-coding RNA makes the human genome distinctive. Much of the function of that non-coding RNA has been a mystery.

"Almost all of the scientific analysis of cancer genes focuses on the protein-coding genes," Pandolfi said, referring to the two percent of the human genome where instructions are passed from DNA to RNA to proteins. "We know that nearly half of the genome is transcribed into RNA that doesn't code for protein. Through this new 'language' of RNA, we can functionalize this space."

How it works

The newly discovered network of RNA molecules converse through tiny targeted molecules called microRNAs, Pandolfi and his colleagues have found. RNAs share a vocabulary composed of specific sequences along their strands called microRNA response elements (MREs). RNAs compete for certain matching microRNAs. Once attached, microRNAs disable their host RNA molecules. It works through simple math: An increase in RNA can sponge up more microRNA, allowing other RNA to go about their business unhindered.

Scientists have known for a decade that microRNA can block RNA and prevent it from being translated into proteins. Some research has advanced to harnessing specific small microRNA molecules as experimental therapeutic tools to block individual protein-coding genes. What's new in the Cell papers is the idea of reverse logic -- that a large RNA network uses microRNA as a regulatory language.

Tantalizing hints of this newfound regulatory network have shown up in recent studies from several labs. Last year, Pandolfi's group reported that both PTEN and its nemesis, the common cancer-promoting gene KRAS, have doppelgangers known as pseudogenes in the non-coding regions of the genome, which act as decoys for targeted microRNA, greatly influencing the activity of the two cancer genes.

This August, Pandolfi and his co-authors named this RNA language and network activity "competing endogenous RNA" (ceRNA, pronounced SIR-na) in a Cell essay. The paper synthesized the emerging experimental evidence in a new theory. They proposed that ceRNA activity greatly expanded the functional genetic information in the human genome and played important roles in diseases, including cancer.

The ceRNA hypothesis adds a major new layer to the highly regulated basic players defined by the central dogma of molecular biology -- DNA, RNA and proteins. Other more established regulatory networks that keep cells healthy -- and break down in disease -- include small molecules added to proteins, such as the recycling label called ubiquitin. Another layer called epigenetics acts on the DNA and its packaging to lock or unlock certain genes.

The findings in the papers

Two of the Cell papers use a combination of bioinformatics and experimental evidence to connect the PTEN tumor suppressor gene to a network of several hundred RNA molecules in close communication.

One of the new papers from the Pandolfi lab linked about 150 new genes to the tumor suppressor PTEN in human prostate and colon cancer cell lines. Working with a collaborator at Jefferson Medical College in Philadelphia, postdoctoral fellow Yvonne Tay and her co-authors scanned the RNA transcripts of protein-coding genes based on their MRE sequences and then tested a few of the results. "Surprisingly, PTEN can be regulated by a lot of other genes through the ceRNA network," Tay said.

In an independent paper, a team in the lab of Andrea Califano at Columbia University in New York evaluated glioblastoma RNA and microRNA expression data from The Cancer Genome Atlas, a public database. They found a network in which more than 500 genes regulate PTEN. Of these, 13 are frequently deleted in glioblastoma and seem to work together through the microRNA language to squelch the tumor suppressor activity as if the tumors had mutations or deletions of PTEN itself.

"All these papers address different aspects of this compelling story and reinforce each other," said Califano, who also found RNA networks that appeared to communicate by other means. "PTEN is just an example. In each cell, different cliques of genes are connected by this microRNA-mediated network, including all the established oncogenes and tumor suppressors. This layer explains a significant amount of genetic variability in cancer. It allows genes that have nothing to do with the typical oncogene or tumor suppressor to gang up and regulate it. The discovery of this network allows us to discover genes never before associated with a tumor type or disease."

In a second paper from the Pandolfi group, mutations in the PTEN RNA network speeded up the growth of cancer in a mouse model of melanoma. Postdoctoral fellow Florian Karreth and his co-authors discovered possible new PTEN ceRNAs in a mutagenesis screen of a mouse model of melanoma. With the help of a bioinformatics team from the University of Turin, they did an in-depth analysis of one ceRNA (ZEB2) that is reduced in human cancer and verified that its reduction accelerated cancer progression in the mice. Interestingly, while the ZEB2 ceRNA opposes melanoma by sponging the microRNAs that would otherwise repress PTEN's tumor suppression activity, the ZEB2 protein is known to promote other cancers. "It is astonishing that RNA and protein molecules encoded by the same gene can take part in opposing biological processes," Karreth said.

The final study extends functional evidence of the new RNA network phenomenon to the normal differentiation of human muscle cells and to the large realm of human non-coding RNAs. Irene Bozzoni's group at the Sapienza University of Rome found that a long non-protein coding RNA works similarly as a decoy for microRNAs in normal muscle differentiation in mice and humans. In Duchenne muscular dystrophy, the decoy RNA is missing at a crucial time, preventing muscle cells from maturing.

"This explains in part why Duchenne cells have trouble, and it gives us another circuitry to attack in order to cure the disease," said Bozzoni, who heard about Pandolfi's ceRNA hypothesis at a meeting last year. "We have been working on noncoding RNA and microRNA for quite a long time. This cross-talk of RNAs through microRNAs is a revolutionary idea."

Journal References:

Yvonne Tay, Lev Kats, Leonardo Salmena, Dror Weiss, Shen Mynn Tan, Ugo Ala, Florian Karreth, Laura Poliseno, Paolo Provero, Ferdinando Di Cunto, Judy Lieberman, Isidore Rigoutsos, Pier Paolo Pandolfi. Coding-Independent Regulation of the Tumor Suppressor PTEN by Competing Endogenous mRNAs. Cell, 2011; 147 (2): 344-357 DOI: 10.1016/j.cell.2011.09.029
Florian A. Karreth, Yvonne Tay, Daniele Perna, Ugo Ala, Shen Mynn Tan, Alistair G. Rust, Gina DeNicola, Kaitlyn A. Webster, Dror Weiss, Pedro A. Perez-Mancera, Michael Krauthammer, Ruth Halaban, Paolo Provero, David J. Adams, David A. Tuveson, Pier Paolo Pandolfi. In Vivo Identification of Tumor- Suppressive PTEN ceRNAs in an Oncogenic BRAF-Induced Mouse Model of Melanoma. Cell, 2011; 147 (2): 382-395 DOI: 10.1016/j.cell.2011.09.032
Pavel Sumazin, Xuerui Yang, Hua-Sheng Chiu, Wei-Jen Chung, Archana Iyer, David Llobet-Navas, Presha Rajbhandari, Mukesh Bansal, Paolo Guarnieri, Jose Silva, Andrea Califano. An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma. Cell, 2011; 147 (2): 370-381 DOI: 10.1016/j.cell.2011.09.041
Marcella Cesana, Davide Cacchiarelli, Ivano Legnini, Tiziana Santini, Olga Sthandier, Mauro Chinappi, Anna Tramontano, Irene Bozzoni. A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA. Cell, 2011; 147 (2): 358-369 DOI: 10.1016/j.cell.2011.09.028

Courtesy: ScienceDaily

Understanding the Beginnings of Embryonic Stem Cells Helps Predict the Future

2011-10-19T05:27:00.000-07:00

Scientists have shown that laboratory-grown cells express a protein called Blimp1, which represses differentiation to somatic or regular tissue cells during germ cell development. Studies of these cells show that they also express other genes associated with early germ cell specification.

Ordinarily, embryonic stem cells exist only a day or two as they begin the formation of the embryo itself. Then they are gone.

In the laboratory dish, however, they act more like perpetual stem cells -- renewing themselves and exhibiting the ability to form cells of almost any type, a status called totipotency.

Dr. Thomas Zwaka, associate professor in the Stem Cell and Regenerative Medicine Center at Baylor College of Medicine, and his colleagues here and abroad showed that laboratory-grown cells express a protein called Blimp1, which represses differentiation to somatic or regular tissue cells during germ cell development. Studies of these cells show that they also express other genes associated with early germ cell specification.

A report on their work published online October 13 in the journal Current Biology. It will appear in the October 25 print edition of the journal.

"What are embryonic stem cells?" said Zwaka, who is also part of the Center for Cell and Gene Therapy at BCM, Texas Children's Hospital and The Methodist Hospital. "It is quite a surprise that we have them. In the embryo, there is a mass of cells that eventually form the embryo, but they do not persist. They do not have a program built in that allows them to persist."

To study this, he examined mice. If you put the mass of cells in a Petri dish in the laboratory, they act as thought they are stem cells with the ability for self renewal and totipotency -- the ability to become almost any kind of cell.

Understanding what happens early in development of embryonic stem cells in the laboratory might help make the process of growing them and another, new kind of stem cell called induced pluripotent stem cells -- cells with the potential of becoming many different kinds of tissues that are derived from somatic or adult cells.

"These induced pluripotent stem cells are poorly understood," said Zwaka. "If we know what is happening when we derive embryonic stem cells in the laboratory, it will inform us when we make induced pluripotent stem cells. The end product is similar."

The process of making the induced pluripotent stem cells is noisy and random, he said.

"Every time, the clones look different and emerge at different time points," said Zwaka. By contrast, embryonic development is like clockwork, with events occurring at the same point with each embryo. However, development of embryonic stem cells in the laboratory becomes more disorganized as time goes on.

In the laboratory dish, the mouse embryo continues to develop at a fairly organized rate for two or three days, but when the single cells are separated and grown singly, the embryonic stem cells begin to emerge. Only a tiny subset -- roughly 1 percent -- of the cells become an embryonic stem cell in the laboratory."

"We found that these cells (from the embryonic stem cells come) resemble in almost every feature an early germ cell (primordial germ cell)," he said. (Primordial germ cells are the source of gametes -- eggs and sperm.)

"It seems that these seeming germ cells are the cells that make the embryonic stem cells in culture," he said.

"Germ cells in the embryo are unique and pluripotent (able to become many different kinds of cells) and have a very sophisticated program in them that protects the from becoming somatic cells (specific tissue cells)," he said. "They retain their primitive state." Blimp1 is a master regulator of germ cells.

In the future, he said, he hopes that investigators in both fields can collaborate and learn from one another.

Others who took part in this research include Li-Fang Chua of BCM, M. Azim Surani of the Wellcome Trust Cancer Research UK Gurdon Institute at the University of Cambridge, and Rudolf Jaenisch of Whitehead Institute for BiomedicaI Research at the Massachusetts Institute of Technology in Cambridge.

Funding for this work came from the Huffington Foundation and the National Institutes of Health.

For more information on basic science research at Baylor College of Medicine, please go to From the Lab at Baylor College of Medicine.

Journal Reference:

Li-Fang Chu, M. Azim Surani, Rudolf Jaenisch, Thomas P. Zwaka. Blimp1 Expression Predicts Embryonic Stem Cell Development In Vitro. Current Biology, 13 October 2011 DOI: 10.1016/j.cub.2011.09.010

Courtesy: ScienceDaily

Uncharted Territory: Scientists Sequence the First Carbohydrate Biopolymer

2011-10-16T08:25:00.000-07:00

DNA and protein sequencing have forever transformed science, medicine, and society. Understanding the structure of these complex biomolecules has revolutionized drug development, medical diagnostics, forensic science, and our understanding of evolution and development. But, one major molecule in the biological triumvirate has remained largely uncharted: carbohydrate biopolymers.

Today, for the first time ever, a team of researchers led by Robert Linhardt of Rensselaer Polytechnic Institute has announced in the October 9 Advanced Online Publication edition of the journal Nature Chemical Biology the sequence of a complete complex carbohydrate biopolymer. The surprising discovery provides the scientific and medical communities with an important and fundamental new view of these vital biomolecules, which play a role in everything from cell structure and development to disease pathology and blood clotting.

The paper is titled "The proteoglycan bikunin has a defined sequence."

"Carbohydrate biopolymers, known as glycosaminoglycans, appear to be really important in how cells interact in higher organisms and could explain evolutionary differences and how development is driven. We also know that carbohydrate chains respond to disease, injury, and changes in the environment," said Linhardt, who is the Ann and John H. Broadbent Jr. '59 Senior Constellation Professor of Biocatalysis and Metabolic Engineering at Rensselaer. "In order to understand how and why this all happens, we first need to know their structure. And today, at least for the simplest glycosaminoglycan structure, we can now do this."

The first glycosaminoglycan sequenced was obtained from bikunin. Bikunin is a proteoglycan, a protein to which a single glycosaminoglycan chain is attached. Unlike less sophisticated carbohydrate biopolymers, such as starch and cellulose, the proteoglycans are decorated with structurally complex carbohydrates that enable them to perform more sophisticated and defined roles in the body. Bikunin, for example, is a natural anti-inflammatory that is used as a drug for the treatment of acute pancreatitis in Japan. It has the simplest chemical structure of any proteoglycan. Linhardt views the discovery of the structure of bikuin as the first step on the ladder to the discovery of the structure of more complex proteoglycans.

"The first genome sequences of DNA were on the simplest organisms such as bacteria. Once the technology was developed it ultimately led to the sequencing of the human genome," he said. "In our efforts to sequence carbohydrate biopolymers we don't yet know if the defined structure we observe for this simple protoglycan will hold for much more complex proteoglycans."

But, looking for structure in more complex proteoglycans will be among the next steps in the research for Linhardt and his team. The search for structure could help put to rest a long-running debate in the scientific community as to whether complex carbohydrate biopolymers require a defined structure to function.

"Despite all that is known about glycan formation, our understanding has not yet been deep enough to infer sequence or even determine if sequence occurs," Linhardt said. "These findings represent a new way of looking at these complex biomolecules as ordered structures."

Linhardt's research into carbohydrate sequencing began 30 years ago. In his previous work, he determined that some order existed in at least a portion of some carbohydrate biopolymers, but it did not represent the entire finished puzzle.

"Previously, we could see a pattern, but we could not see if all the chains were playing the same music. The tools did not yet exist. Now we can recognize it as a symphony."

To uncover the entire structure, Linhardt and his team, which was led by his doctoral student Mellisa Ly, borrowed a technique from the field of protein research called the proteomics top-down approach. As opposed to the bottom-up approach that first breaks apart a complex biopolymer into pieces and then rebuilds it piece by piece like a jigsaw puzzle, the top-down approach used by Linhardt and colleagues allows the researcher to picture the whole intact puzzle. This can only be accomplished with some of the most sophisticated technology available to the scientific community today, including very high-powered mass spectrometers.

Linhardt used a mass spectrometer located in the Rensselaer Center for Biotechnology and Interdisciplinary Studies (CBIS) to make his initial discoveries, and had these results independently confirmed on a separate and higher-level spectrometer at the University of Georgia. Mass spectrometers break down a molecule into separate charged particles or ions. These ions can then be categorized and analyzed based on their mass-to-charge ratio. These ratios then allow for sequencing of the entire molecule.

"This was truly the convergence of really sophisticated spectroscopy and its application to biology," Linhardt said. "We were fortunate to have a lot of time to play with the instrument at CBIS to understand its capabilities."

Beyond the technology it also took faith and determination. According to Linhardt, "It takes a student that is willing to try something even when the odds are pretty low. If it doesn't work, you make incremental progress. If it does work, you can make a great discovery. But, from the beginning you need to be a believer that it is worth taking the chance because it takes a lot of hard work in the lab."

And the odds weren't in Linhardt's favor. Despite being the most simple of proteoglycans, there were still 290 billion different possible sequences for the molecule.

"The first sample we looked at, we got the structure," Linhardt said. "In the end we did 15 chains and they all came back playing the same exact symphony."

The research is funded by the National Institutes of Health.

Linhardt and Ly were joined in the research by Tatiana Laremore of Rensselaer; Franklin Leach and Jonathan Amster of the University of Georgia; and Toshihiko Toida of Chiba University in Japan.

Journal Reference:

Mellisa Ly, Franklin E Leach, Tatiana N Laremore, Toshihiko Toida, I Jonathan Amster, Robert J Linhardt. The proteoglycan bikunin has a defined sequence. Nature Chemical Biology, 2011; DOI: 10.1038/nchembio.673

Courtesy: ScienceDaily

Compound Kills Highly Contagious Flu Strain by Activating Antiviral Protein

2011-09-30T05:55:00.000-07:00

A compound tested by UT Southwestern Medical Center investigators destroys several viruses, including the deadly Spanish flu that killed an estimated 30 million people in the worldwide pandemic of 1918.

This lead compound -- which acts by increasing the levels of a human antiviral protein -- could potentially be developed into a new drug to combat the flu, a virus that tends to mutate into strains resistant to anti-influenza drugs.

"The virus is 'smart' enough to bypass inhibitors or vaccines sometimes. Therefore, there is a need for alternative strategies. Current drugs act on the virus, but here we are uplifting a host/human antiviral response at the cellular level," said Dr. Beatriz Fontoura, associate professor of cell biology and senior author of the study available online in Nature Chemical Biology.

According to National Institutes of Health, influenza hospitalizes more than 200,000 people in the U.S. each year, with about 36,000 fatalities related to the illness. Worldwide, flu kills about 500,000 people annually.

In the latest cell testing, the compound successfully knocked out three types of influenza as well as a smallpox-related virus and an animal virus. Because of the highly contagious nature of the 1918 flu, those tests took place at Mount Sinai School of Medicine in New York, one of the few places that stores and runs tests on that flu strain.

The compound is among others that the research team is testing that induce an infection-fighting human protein called REDD1. Until this study, researchers had not demonstrated that REDD1 had this important antiviral function.

"We've discovered that REDD1 is a key human barrier for infection," said Dr. Fontoura, "Interestingly, REDD1 inhibits a signaling pathway that regulates cell proliferation and cancer."

The UT Southwestern-led research team tested 200,000 compounds for those that would inhibit flu virus infection. A total of 71 were identified.

Using the two most promising compounds, researchers at UT Southwestern and colleagues at Mount Sinai next will work to strengthen their potencies for further testing. Dr. Fontoura said it can take more than 10 years before successful compounds are developed into drugs.

UT Southwestern researchers involved in the study were lead author Miguel Mata and Neal Satterly, both graduate students in Dr. Fontoura's laboratory; Dr. Doug Frantz, former assistant professor of biochemistry; Shuguang Wei, a senior researcher in biochemistry; Dr. Noelle Williams, associate professor of biochemistry; Samuel Pena-Llopis, assistant instructor in developmental biology; Dr. James Brugarolas, assistant professor of internal medicine; Dr. Christian Forst, assistant professor of clinical sciences; Dr. Michael White, professor of cell biology; and Dr. Michael Roth, professor of biochemistry.

The research was supported by nine National Institutes of Health grants and by the Diane and Hal Brierley Distinguished Chair Fund.

Journal Reference:

Miguel A Mata, Neal Satterly, Gijs A Versteeg, Doug Frantz, Shuguang Wei, Noelle Williams, Mirco Schmolke, Samuel Peña-Llopis, James Brugarolas, Christian V Forst, Michael A White, Adolfo García-Sastre, Michael G Roth, Beatriz M A Fontoura. Chemical inhibition of RNA viruses reveals REDD1 as a host defense factor. Nature Chemical Biology, 2011; 7 (10): 712 DOI: 10.1038/nchembio.645

Courtesy: ScienceDaily

Edible Carbon Dioxide Sponge: All-Natural Nanostructures Could Address Pressing Environmental Problem

2011-09-28T05:53:00.000-07:00

A year ago Northwestern University chemists published their recipe for a new class of nanostructures made of sugar, salt and alcohol. Now, the same team has discovered the edible compounds can efficiently detect, capture and store carbon dioxide. And the compounds themselves are carbon-neutral.

The porous crystals -- known as metal-organic frameworks (MOFs) -- are made from all-natural ingredients and are simple to prepare, giving them a huge advantage over other MOFs. Conventional MOFs, which also are effective at adsorbing carbon dioxide, are usually prepared from materials derived from crude oil and often incorporate toxic heavy metals.

Other features of the Northwestern MOFs are they turn red when completely full of carbon dioxide, and the carbon capture process is reversible.

The findings, made by scientists working in the laboratory of Sir Fraser Stoddart, Board of Trustees Professor of Chemistry in the Weinberg College of Arts and Sciences, are published in the Journal of the American Chemical Society (JACS).

"We are able to take molecules that are themselves sourced from atmospheric carbon, through photosynthesis, and use them to capture even more carbon dioxide," said Ross S. Forgan, a co-author of the study and a postdoctoral fellow in Stoddart's laboratory. "By preparing our MOFs from naturally derived ingredients, we are not only making materials that are entirely nontoxic, but we are also cutting down on the carbon dioxide emissions associated with their manufacture."

The main component, gamma-cyclodextrin, is a naturally occurring biorenewable sugar molecule that is derived from cornstarch.

The sugar molecules are held in place by metals taken from salts such as potassium benzoate or rubidium hydroxide, and it is the precise arrangement of the sugars in the crystals that is vital to their successful capture of carbon dioxide.

"It turns out that a fairly unexpected event occurs when you put that many sugars next to each other in an alkaline environment -- they start reacting with carbon dioxide in a process akin to carbon fixation, which is how sugars are made in the first place," said Jeremiah J. Gassensmith, lead author of the paper and also a postdoctoral fellow in Stoddart's laboratory. "The reaction leads to the carbon dioxide being tightly bound inside the crystals, but we can still recover it at a later date very simply."

The fact that the carbon dioxide reacts with the MOF, an unusual occurrence, led to a simple method of detecting when the crystals have reached full capacity. The researchers place an indicator molecule, which detects changes in pH by changing its color, inside each crystal. When the yellow crystals of the MOFs are full of carbon dioxide they turn red.

The simplicity of the new MOFs, allied with their low cost and green credentials, have marked them as candidates for further commercialization. Ronald A. Smaldone, also a postdoctoral fellow in Stoddart's group and a co-author of the paper, added, "I think this is a remarkable demonstration of how simple chemistry can be successfully applied to relevant problems like carbon capture and sensor technology."

The National Science Foundation, the U.S. Department of Energy, the Engineering and Physical Sciences Research Council in the U.K., the King Abdulaziz City of Science and Technology (KACST) in Saudi Arabia and the Korea Advanced Institute of Science and Technology (KAIST) in Korea supported the research.

Journal Reference:

Jeremiah J. Gassensmith, Hiroyasu Furukawa, Ronald A. Smaldone, Ross S. Forgan, Youssry Y. Botros, Omar M. Yaghi, J. Fraser Stoddart. Strong and Reversible Binding of Carbon Dioxide in a Green Metal–Organic Framework. Journal of the American Chemical Society, 2011; 110913144109022 DOI: 10.1021/ja206525x

Courtesy: ScienceDaily

Targeting HIV's Sugar Coating: New Microbicide May Block AIDS Virus from Infecting Cells

2011-09-26T08:51:00.000-07:00

University of Utah researchers have discovered a new class of compounds that stick to the sugary coating of the AIDS virus and inhibit it from infecting cells -- an early step toward a new treatment to prevent sexual transmission of the virus.

Development and laboratory testing of the potential new microbicide to prevent human immunodeficiency virus infection is outlined in a study set for online publication in the journal Molecular Pharmaceutics.

Despite years of research, there is only one effective microbicide to prevent sexual transmission of HIV, which causes AIDS, or acquired immune deficiency syndrome. Microbicide development has focused on gels and other treatments that would be applied vaginally by women, particularly in Africa and other developing regions.

To establish infection, HIV must first enter the cells of a host organism and then take control of the cells' replication machinery to make copies of itself. Those HIV copies in turn infect other cells. These two steps of the HIV life cycle, known as viral entry and viral replication, each provide a potential target for anti-AIDS medicines.

"Most of the anti-HIV drugs in clinical trials target the machinery involved in viral replication," says the study's senior author, Patrick F. Kiser, associate professor of bioengineering and adjunct associate professor of pharmaceutics and pharmaceutical chemistry at the University of Utah.

"There is a gap in the HIV treatment pipeline for cost-effective and mass-producible viral entry inhibitors that can inactivate the virus before it has a chance to interact with target cells," he says.

Kiser conducted the study with Alamelu Mahalingham, a University of Utah graduate student in pharmaceutics and pharmaceutical chemistry; Anthony Geonnotti of Duke University Medical Center in Durham, N.C.; and Jan Balzarini of Catholic University of Leuven in Belgium.

The research was funded by the National Institutes of Health, the Bill and Melinda Gates Foundation, the Catholic University of Leuven, Belgium, and the Fund for Scientific Research, also in Belgium.

Synthetic Lectins Inhibit HIV from Entering Cells

Lectins are a group of molecules found throughout nature that interact and bind with specific sugars. HIV is coated with sugars that help to hide it from the immune system. Previous research has shown that lectins derived from plants and bacteria inhibit the entry of HIV into cells by binding to sugars found on the envelope coating the virus.

However, the cost of producing and purifying natural lectins is prohibitively high. So Kiser and his colleagues developed and evaluated the anti-HIV activity of synthetic lectins based on a compound called benzoboroxole, or BzB, which sticks to sugars found on the HIV envelope.

Kiser and his colleagues found that these BzB-based lectins were capable of binding to sugar residues on HIV, but the bond was too weak to be useful. To improve binding, they developed polymers of the synthetic lectins. The polymers are larger molecules made up of repeating subunits, which contained multiple BzB binding sites. The researchers discovered that increasing the number and density of BzB binding sites on the synthetic lectins made the substances better able to bind to the AIDS virus and thus have increased antiviral activity.

"The polymers we made are so active against HIV that dissolving about one sugar cube's weight of the benzoboroxole polymer in a bath tub of water would be enough to inhibit HIV infection in cells," says Kiser.

Depending on the strain, HIV displays significant variations in its viral envelope, so it is important to evaluate the efficacy of any potential new treatment against many different HIV strains.

Kiser and his colleagues found that their synthetic lectins not only showed similar activity across a broad spectrum of HIV strains, but also were specific to HIV and didn't affect other viruses with envelopes.

The scientists also tested the anti-HIV activity of the synthetic lectins in the presence of fructose, a sugar present in semen, which could potentially compromise the activity of lectin-based drugs because it presents an alternative binding site. However, the researchers found that the antiviral activity of the synthetic lectins was fully preserved in the presence of fructose.

"The characteristics of an ideal anti-HIV microbicide include potency, broad-spectrum activity, selective inhibition, mass producibility and biocompatibility," says Kiser. "These benzoboroxole-based synthetic lectins seem to meet all of those criteria and present an affordable and scalable potential intervention for preventing sexual transmission in regions where HIV is pandemic."

Kiser says future research will focus on evaluating the ability of synthetic lectins to prevent HIV transmission in tissues taken from the human body, with later testing in primates. Kiser and his colleagues are also developing a gel form of the polymers, which could be used as a topical treatment for preventing sexual HIV transmission.

Journal Reference:

Alamelu Mahalingam, Anthony R Geonnotti, Jan Balzarini, Patrick Franklin Kiser. Activity and Safety of Synthetic Lectins Based on Benzoboroxole-Functionalized Polymers for Inhibition of HIV Entry. Molecular Pharmaceutics, 2011; 110831135436035 DOI: 10.1021/mp2002957

Courtesy: ScienceDaily

Scientists Take First Step Towards Creating 'Inorganic Life'

2011-09-22T09:35:00.000-07:00

Scientists at the University of Glasgow say they have taken their first tentative steps towards creating 'life' from inorganic chemicals potentially defining the new area of 'inorganic biology'.

Professor Lee Cronin, Gardiner Chair of Chemistry in the College of Science and Engineering, and his team have demonstrated a new way of making inorganic-chemical-cells or iCHELLs.

Prof Cronin said: "All life on earth is based on organic biology (i.e. carbon in the form of amino acids, nucleotides, and sugars, etc.) but the inorganic world is considered to be inanimate.

"What we are trying do is create self-replicating, evolving inorganic cells that would essentially be alive. You could call it inorganic biology."

The cells can be compartmentalised by creating internal membranes that control the passage of materials and energy through them, meaning several chemical processes can be isolated within the same cell -- just like biological cells.

The researchers say the cells, which can also store electricity, could potentially be used in all sorts of applications in medicine, as sensors or to confine chemical reactions.

The research is part of a project by Prof Cronin to demonstrate that inorganic chemical compounds are capable of self-replicating and evolving -- just as organic, biological carbon-based cells do.

The research into creating 'inorganic life' is in its earliest stages, but Prof Cronin believes it is entirely feasible.

Prof Cronin said: "The grand aim is to construct complex chemical cells with life-like properties that could help us understand how life emerged and also to use this approach to define a new technology based upon evolution in the material world -- a kind of inorganic living technology.

"Bacteria are essentially single-cell micro-organisms made from organic chemicals, so why can't we make micro-organisms from inorganic chemicals and allow them to evolve?

"If successful this would give us some incredible insights into evolution and show that it's not just a biological process. It would also mean that we would have proven that non carbon-based life could exist and totally redefine our ideas of design."

The paper is published in the journal Angewandte Chemie.

Journal Reference:

Geoffrey J. T. Cooper, Philip J. Kitson, Ross Winter, Michele Zagnoni, De-Liang Long, Leroy Cronin. Modular Redox-Active Inorganic Chemical Cells: iCHELLs. Angewandte Chemie International Edition, 2011; DOI: 10.1002/anie.201105068

Courtesy: ScienceDaily

Potential Molecular Target to Prevent Growth of Cancer Cells Identified

2011-09-20T09:34:00.000-07:00

Researchers have shown for the first time that the protein fortilin promotes growth of cancer cells by binding to and rendering inert protein p53, a known tumor suppressor. This finding by researchers at the University of Texas Medical Branch may lead to treatments for a range of cancers and atherosclerosis, which p53 also helps prevent, and appears in the current print issue of the Journal of Biological Chemistry.

"The p53 protein is a critical defense against cancer because it activates genes that induce apoptosis, or the death of cells. However, p53 can be made powerless by mutations and inhibitors like fortilin," said Dr. Ken Fujise, lead author of the study and director, Division of Cardiology at UTMB.

Fortilin, an amino acid polypeptide protein, works in direct opposition to p53, protecting cells from apoptosis. Fujise discovered fortilin in 2000 and the protein has become a central focus of his research. This study marks the first time that scientists have been able to show the exact mechanism whereby fortilin exerts its anti-apoptotic activity.

Fujise and his team used cell cultures and animal models to show that fortilin binds to and inhibits p53, preventing it from activating genes, such as BAX and Noxa, that facilitate cell death. Thus, cells that would be killed are allowed to proliferate.

"When normal cells become cancer cells, our bodies' natural biological response is to activate p53, which eliminates the hopelessly damaged cells," said Fujise. "This process explains why the majority of people are able to stay cancer-free for most of their lives. Conversely, mutated p53 genes are seen in more than half of all human cancers, making them the most frequently observed genetic abnormality in cancer."

According to Fujise, upon further research and validation of the biological mechanism described in this study, scientists can begin exploring compounds that could modulate fortilin's activity on p53.

Such a compound would be a powerful chemotherapy agent and, because p53 inhibition has also been associated with atherosclerosis, could also protect against coronary disease and its many complications, including heart attack and stroke.

"Though we are in the early stages of this research, once screening for compounds is initiated, we could have a potential new drug to investigate in a very short period of time," said Fujise. With the support of National Institutes of Health high-throughput screening programs, which make it possible to screen very large numbers of compounds against a drug target, the process of identifying a new drug could potentially be shortened to months rather than years, he added.

Other authors include scientists at UTMB and other institutions: Yanjie Chen, Takayuki Fujita, Di Zhang, Hung Doan, Decha Pinkaew, Zhihe Liu, Jiaxin Wu, Yuichi Koide, Andrew Chiu, Curtis Chen Jun Lin, Jui-Yoa Chang; and Ke-He Ruan.

The study was supported in part by the National Institutes of Health, the American Heart Association, and MacDonald General Research Fund.

Journal Reference:

Y. Chen, T. Fujita, D. Zhang, H. Doan, D. Pinkaew, Z. Liu, J. Wu, Y. Koide, A. Chiu, C. C.-J. Lin, J.-Y. Chang, K.-H. Ruan, K. Fujise. Physical and Functional Antagonism between Tumor Suppressor Protein p53 and Fortilin, an Anti-apoptotic Protein. Journal of Biological Chemistry, 2011; 286 (37): 32575 DOI: 10.1074/jbc.M110.217836

Courtesy: ScienceDaily

World-First Viral Therapy Trial in Cancer Patients

2011-09-18T09:33:00.000-07:00

Researchers from the Ottawa Hospital Research Institute (OHRI), the University of Ottawa (uOttawa), Jennerex Inc. and several other institutions have just reported promising results of a world-first cancer therapy trial in journal Nature. The trial is the first to show that an intravenously-delivered viral therapy can consistently infect and spread within tumours without harming normal tissues in humans. It is also the first to show tumour-selective expression of a foreign gene after intravenous delivery.

The trial involved 23 patients (including seven at The Ottawa Hospital), all with advanced cancers that had spread to multiple organs and failed to respond to standard treatments. The patients received a single intravenous infusion of a virus called JX-594, at one of five dose levels, and biopsies were obtained eight to 10 days later. Seven of eight patients (87 per cent) in the two highest dose groups had evidence of viral replication in their tumour, but not in normal tissues. All of these patients also showed tumour-selective expression of a foreign gene that was engineered into the virus to help with detection. The virus was well tolerated at all dose levels, with the most common side effect being mild to moderate flu-like symptoms that lasted less than one day.

"We are very excited because this is the first time in medical history that a viral therapy has been shown to consistently and selectively replicate in cancer tissue after intravenous infusion in humans," said Dr. John Bell, a Senior Scientist at OHRI, Professor of Medicine at uOttawa and senior co-author on the publication. "Intravenous delivery is crucial for cancer treatment because it allows us to target tumours throughout the body as opposed to just those that we can directly inject. The study is also important because it shows that we can use this approach to selectively express foreign genes in tumours, opening the door to a whole new suite of targeted cancer therapies."

Dr. Bell and his team have been investigating cancer-fighting (oncolytic) viruses at OHRI for more than 10 years. JX-594 was developed in partnership with Jennerex Inc., a biotherpeutics company co-founded by Dr. Bell in Ottawa and Dr. David Kirn in San Francisco. JX-594 is derived from a strain of vaccinia virus that has been used extensively as a live vaccine against smallpox. It has a natural ability to replicate preferentially in cancer cells, but it has also been genetically engineered to enhance its anti-cancer properties.

"Oncolytic viruses are unique because they can attack tumours in multiple ways, they have very mild side effects compared to other treatments, and they can be easily customized for different kinds of cancer," said Dr. Bell. "We're still in the early stages of testing these viruses in patients, but I believe that someday, viruses and other biological therapies could truly transform our approach for treating cancer."

Although the current trial was designed primarily to assess safety and delivery of JX-594, anti-tumour activity was also evaluated. Six of eight patients (75%) in the two highest dose groups experienced a shrinking or stabilization of their tumour, while those in lower dose groups were less likely to experience this effect.

"These results are promising, especially for such an early-stage trial, with only one dose of therapy," said Dr. Bell. "But of course, we will need to do more trials to know if this virus can truly make a difference for patients. We are working hard to get these trials started, and at the same time, we are also working in the laboratory to advance our understanding of these viruses and figure out how best to use them."

This research was supported by Jennerex Inc., the Terry Fox Foundation, the Canadian Institutes of Health Research, the Ontario Institute for Cancer Research, The Ottawa Hospital Foundation, the Canada Foundation for Innovation, the Natural Sciences and Engineering Research Council of Canada and the Republic of Korea. OHRI / uOttawa authors on the paper include Dr. John Bell, Dr. Derek Jonker, Dr. Laura Chow, Dr. Fabrice Le Boeuf, Joe Burns, Laura Evgin, Naomi De Silva, Sara Cvancic, Dr. Kelley Parato, Dr. Jean-Simon Diallo and Dr. Manijeh Daneshmand, as well as alumnus Dr. Caroline Breitbach.

Journal Reference:

Caroline J. Breitbach, James Burke, Derek Jonker, Joe Stephenson, Andrew R. Haas, Laura Q. M. Chow, Jorge Nieva, Tae-Ho Hwang, Anne Moon, Richard Patt, Adina Pelusio, Fabrice Le Boeuf, Joe Burns, Laura Evgin, Naomi De Silva, Sara Cvancic, Terri Robertson, Ji-Eun Je, Yeon-Sook Lee, Kelley Parato, Jean-Simon Diallo, Aaron Fenster, Manijeh Daneshmand, John C. Bell, David H. Kirn. Intravenous delivery of a multi-mechanistic cancer-targeted oncolytic poxvirus in humans. Nature, 2011; 477 (7362): 99 DOI: 10.1038/nature10358

Courtesy: ScienceDaily

Nanosensors Made from DNA May Light Path to New Cancer Tests and Drugs

2011-09-15T10:00:00.000-07:00

Sensors made from custom DNA molecules could be used to personalize cancer treatments and monitor the quality of stem cells, according to an international team of researchers led by scientists at UC Santa Barbara and the University of Rome Tor Vergata.

The new nanosensors can quickly detect a broad class of proteins called transcription factors, which serve as the master control switches of life. The research is described in an article published in Journal of the American Chemical Society.

"The fate of our cells is controlled by thousands of different proteins, called transcription factors," said Alexis Vallée-Bélisle, a postdoctoral researcher in UCSB's Department of Chemistry and Biochemistry, who led the study. "The role of these proteins is to read the genome and translate it into instructions for the synthesis of the various molecules that compose and control the cell. Transcription factors act a little bit like the 'settings' of our cells, just like the settings on our phones or computers. What our sensors do is read those settings."

When scientists take stem cells and turn them into specialized cells, they do so by changing the levels of a few transcription factors, he explained. This process is called cell reprogramming. "Our sensors monitor transcription factor activities, and could be used to make sure that stem cells have been properly reprogrammed," said Vallée-Bélisle. "They could also be used to determine which transcription factors are activated or repressed in a patient's cancer cells, thus enabling physicians to use the right combination of drugs for each patient."

Andrew Bonham, a postdoctoral scholar at UCSB and co-first author of the study, explained that many labs have invented ways to read transcription factors; however, this team's approach is very quick and convenient. "In most labs, researchers spend hours extracting the proteins from cells before analyzing them," said Bonham. "With the new sensors, we just mash the cells up, put the sensors in, and measure the level of fluorescence of the sample."

This international research effort -- organized by senior authors Kevin Plaxco, professor in UCSB's Department of Chemistry and Biochemistry, and Francesco Ricci, professor at the University of Rome, Tor Vergata -- started when Ricci realized that all of the information necessary to detect transcription factor activities is already encrypted in the human genome, and could be used to build sensors. "Upon activation, these thousands of different transcription factors bind to their own specific target DNA sequence," said Ricci. "We use these sequences as a starting point to build our new nanosensors."

The key breakthrough underlying this new technology came from studies of the natural biosensors inside cells. "All creatures, from bacteria to humans, monitor their environments using 'biomolecular switches' -- shape-changing molecules made from RNA or proteins," said Plaxco. "For example, in our sinuses, there are millions of receptor proteins that detect different odor molecules by switching from an 'off state' to an 'on state.' The beauty of these switches is that they are small enough to operate inside a cell, and specific enough to work in the very complex environments found there."

Inspired by the efficiency of these natural nanosensors, the research group teamed with Norbert Reich, also a professor in UCSB's Department of Chemistry and Biochemistry, to build synthetic switching nanosensors using DNA, rather than proteins or RNA.

Specifically, the team re-engineered three naturally occurring DNA sequences, each recognizing a different transcription factor, into molecular switches that become fluorescent when they bind to their intended targets. Using these nanometer-scale sensors, the researchers could determine transcription factor activity directly in cellular extracts by simply measuring their fluorescence level.

The researchers believe that this strategy will ultimately allow biologists to monitor the activation of thousands of transcription factors, leading to a better understanding of the mechanisms underlying cell division and development. "Alternatively, since these nanosensors work directly in biological samples, we also believe that they could be used to screen and test new drugs that could, for example, inhibit transcription-factor binding activity responsible for the growth of tumor cells," said Plaxco.

This work was funded by the National Institute of Health, the Fond Québécois de la Recherche sur la Nature et les Technologies, the Italian Ministry of University and Research (MIUR) project "Futuro in Ricerca," and the Tri-County Blood Bank Santa Barbara Foundation.

Journal Reference:

Alexis Vallée-Bélisle, Andrew J. Bonham, Norbert O. Reich, Francesco Ricci, Kevin W. Plaxco. Transcription Factor Beacons for the Quantitative Detection of DNA Binding Activity. Journal of the American Chemical Society, 2011; 133 (35): 13836 DOI: 10.1021/ja204775k

Courtesy: ScienceDaily

Doctors' and Nurses' Hospital Uniforms Contain Dangerous Bacteria a Majority of the Time, Study Shows

2011-09-13T09:58:00.000-07:00

More than 60 percent of hospital nurses' and doctors' uniforms tested positive for potentially dangerous bacteria, according to a study published in the September issue of the American Journal of Infection Control, the official publication of APIC -- the Association for Professionals in Infection Control and Epidemiology.

A team of researchers led by Yonit Wiener-Well, MD, from the Shaare Zedek Medical Center in Jerusalem, Israel, collected swab samples from three parts of the uniforms of 75 registered nurses (RNs) and 60 medical doctors (MDs) by pressing standard blood agar plates at the abdominal zone, sleeves' ends and pockets.

The researchers at this 550-bed, university-affiliated hospital found that exactly half of all the cultures taken, representing 65 percent of the RN uniforms and 60 percent of the MD uniforms, harbored pathogens. Of those, 21 cultures from RN uniforms and six cultures from MD uniforms contained multi-drug resistant pathogens, including eight cultures that grew methicillin-resistant Staphylococcus aureus (MRSA). Although the uniforms themselves may not pose a direct risk of disease transmission, these results indicate a prevalence of antibiotic resistant strains in close proximity to hospitalized patients.

"It is important to put these study results into perspective," said APIC 2011 President Russell Olmsted, MPH, CIC. "Any clothing that is worn by humans will become contaminated with microorganisms. The cornerstone of infection prevention remains the use of hand hygiene to prevent the movement of microbes from these surfaces to patients."

"New evidence such as this study by Dr. Wiener-Well is helpful to improve the understanding of potential sources of contamination but, as is true for many studies, it raises additional questions that need to be investigated," added Olmsted.

According to the World Health Organization, the risk of healthcare-associated infection (HAI) in some developing countries is as much as 20 times higher than in developed countries. Even in hospitals in developed countries like Israel, the site of this investigation, and the U.S., HAIs occur too often, can be deadly, and are expensive to treat. HAI prevention is therefore the best approach for patient safety. Infection preventionists, in collaboration with direct care providers, can prevent more than half of HAIs by applying proven prevention practices as part of a comprehensive infection prevention and control program.

Journal Reference:

Yonit Wiener-Well, Margalit Galuty, Bernard Rudensky, Yechiel Schlesinger, Denise Attias, Amos M. Yinnon. Nursing and physician attire as possible source of nosocomial infections. American Journal of Infection Control, 2011; 39 (7): 555 DOI: 10.1016/j.ajic.2010.12.016

Courtesy: ScienceDaily

New Strategy for Overcoming Resistance to Targeted Cancer Drug

2011-09-11T10:02:00.000-07:00

Scientists at Dana-Farber Cancer Institute and colleagues overseas have discovered a pair of backup circuits in cancer cells that enable the cells to dodge the effect of a widely used cancer drug. Jamming those circuits with targeted therapies may heighten or restore the drug's potency, according to a study published in the Sept. 7 issue of Science Translational Medicine.

The research focused on the drug cetuximab, an antibody that interferes with cancer cell growth by blocking a structure known as the epidermal growth factor receptor (EGFR). Cetuximab is effective in many patients with colorectal cancer or squamous cell cancer of the head and neck, but the benefits rarely last longer than a year, and some patients receive no benefit from the drug.

Until now, scientists haven't known why cancers that initially respond to cetuximab become resistant to it, or how to overcome such resistance.

In the new study, researchers led by Pasi Janne, MD, PhD, of Dana-Farber and Kimio Yonesaka, MD, PhD, formerly of Dana-Farber and now at Kinki University School of Medicine, in Osaka, Japan, found that in some cetuximab-resistant cancer cells, a protein known as ERBB2 was actively sending "grow" signals, circumventing the "stop growing" signals triggered by cetuximab. The researchers discovered that ERBB2's activity sprang from an oversupply of the protein's parent gene, Her2/neu, or by a related protein, ERBB3, when prompted by high levels of the protein heregulin. In both cases, the new growth messages are unaffected by cetuximab.

"ERBB2 activates a critical signaling pathway that is not normally blocked by cetuximab, and in this way subverts cetuximab's function," says Janne, the study's co-senior author with Kazuhiko Nakagawa, MD, PhD, of Kinki University. "Because ERBB2 isn't affected by cetuximab, this is an easy way for cancers to become resistant to the drug."

The findings suggest that combining cetuximab with ERBB2-inhibiting drugs could be an effective therapy for cancers that are cetuximab-resistant from the start or for those that become resistant over time, the study authors say. Several such inhibitors have already been approved, while others are undergoing clinical study.

"We hope the findings of our study will inspire the development of clinical trials aimed at overcoming cetuximab resistance," Yonesaka remarks. "We've identified biomarkers that can be used to select cetuximab-resistant patients who may benefit from a combination of cetuximab and ERBB2 inhibitors."

Janne estimates that up to 40 percent of colorectal cancers are cetuximab-resistant when first diagnosed. He notes that although the ERBB2 pathway may be responsible for many cases of cetuximab resistance, there are undoubtedly other pathways, yet to be discovered, that play a similar role. Further research is needed to confirm ERBB2's role in cetuximab resistance and to develop strategies for testing ERBB2 inhibitors and cetuximab in clinical trials.

Funding for the study was provided by grants from the National Institutes of Health, the American Cancer Society, the William Randolph Hearst Foundation, and the Hazel and Samuel Bellin research fund.

Co-authors of the paper include Kreshnik Zejnullahu, Dalia Ercan, Andrew Rogers, Juliet Philips, MS, Jason Sun, Takafumi Okabe, MD, PhD, Jeffrey Swanson, MD, and Ramesh Shivdasani, MD, PhD, Dana-Farber; Isamu Okamoto, MD, PhD, Taroh Satoh, MD, Masayuki Takeda, MD, PhD, Yasuhito Fujisaka, MD, Toshio Shimizu, MD, PhD, Osamu Maenishi, Hiroyuki Itoh, MD, Kiyotaka Okuno, MD, Minoru Takada, MD, Masahiro Fukuoka, MD, and Kazuto Nishio, MD, PhD, Kinki University, Osaka, Japan; Federico Cappuzzo, MD, Massimo Roncalli, MD, and Annarita Destro, PhD, Instituto Clinico Humanitas, Rozzano, Italy; John Souglakos, MD, PhD, University of Crete, Heraklion, Greece; Yonggon Cho, and Marileila Varella-Garcia, University of Colorado Cancer Center, Denver; Koichi Taira, MD, and Koji Takeda, MD, Osaka City General Hospital, Japan; and Eugene Lifshits and Jeffrey Engelman, MD, PhD, Massachusetts General Hospital.

Journal Reference:

Kimio Yonesaka, Kreshnik Zejnullahu, Isamu Okamoto, Taroh Satoh, Federico Cappuzzo, John Souglakos, Dalia Ercan, Andrew Rogers, Massimo Roncalli, Masayuki Takeda, Yasuhito Fujisaka, Juliet Philips, Toshio Shimizu, Osamu Maenishi, Yonggon Cho, Jason Sun, Annarita Destro, Koichi Taira, Koji Takeda, Takafumi Okabe, Jeffrey Swanson, Hiroyuki Itoh, Minoru Takada, Eugene Lifshits, Kiyotaka Okuno, Jeffrey A. Engelman, Ramesh A. Shivdasani, Kazuto Nishio, Masahiro Fukuoka, Marileila Varella-Garcia, Kazuhiko Nakagawa, Pasi A. Jänne. Activation of ERBB2 Signaling Causes Resistance to the EGFR-Directed Therapeutic Antibody Cetuximab. Science Translational Medicine, 2011; 3 (99): 99ra86 DOI: 10.1126/scitranslmed.3002442

Courtesy: ScienceDaily

Scientists Pinpoint Shape-Shifting Mechanism Critical to Protein Signaling

2011-09-10T05:07:00.000-07:00

In a joint study, scientists from the California and Florida campuses of The Scripps Research Institute have shown that changes in a protein's structure can change its signaling function and they have pinpointed the precise regions where those changes take place.

The new findings could help provide a much clearer picture of potential drugs that would be both effective and highly specific in their biological actions.

The study, led by Patrick Griffin of Scripps Florida and Raymond Stevens of Scripps California, was published in a recent edition of the journal Structure.

The new study focuses on the β2-adrenergic receptor, a member of the G protein-coupled receptor family. G protein-coupled receptors convert extracellular stimuli into intracellular signals through various pathways. Approximately one third of currently marketed drugs (including for diabetes and heart disease) target these receptors.

Scientists have known that when specific regions of the receptor are activated by neurotransmitters or hormones, the structural arrangement (conformation) of the receptor is changed along with its function.

"While it's accepted that these receptors adopt multiple conformations and that each conformation triggers a specific type of signaling, the molecular mechanism behind that flexibility has been something of a black box," said Griffin, who is chair of the Scripps Research Department of Molecular Therapeutics and director of the Scripps Florida Translational Research Institute. "Our findings shed significant light to it."

The study describes in structural detail the various regions of the receptor that are involved in the changes brought about by selective ligands (ligands are molecules that bind to proteins to form an active complex), which, like a rheostat, run the gamut among activating the receptor, shutting it down, and reversing its function, as well as producing various states in between.

To achieve the results described in the study, the team used hydrogen-deuterium (HDX) mass spectrometry to measure the impact of interaction of various functionally selective ligands with the β2-adrenergic receptor. A mass spectrometer determines the mass of fragments from the receptor by measuring the mass-to-charge ratio of their ions. HDX has been used to examine changes in the shape of proteins and how these shape changes relate to protein function. The approach is often used to characterize protein-protein interactions that are critical for signal transduction in cells and to study protein-folding pathways that are critical to cell survival.

"At this early stage in understanding GPCR structure and function, it is important to view the entire receptor in combination with probing very specific regions," said Stevens, who is a professor in the Scripps Research Department of Molecular Biology. "Hydrogen-deuterium exchange mass spectrometry has the right timescale and resolution to asked important questions about complete receptor conformations in regards to different pharmacological ligand binding. The HDX data combined with the structural data emerging will really help everyone more fully understand how these receptors work."

"Using the HDX technology we can study the intact receptor upon interaction with ligands and pinpoint regions of the receptor that have undergone change in position or flexibility," Griffin said. "By studying a set of ligands one can start to develop patterns that are tied to activation of the receptor or shutting it down. Once we get a picture of what a functional ligand looks like, it might be possible to develop a drug to produce a highly selective therapeutic effect."

The lead author of the study, "Ligand-Dependent Perturbation of the Conformational Ensemble for the GPCR b2 Adrenergic Receptor Revealed by HDX," is Graham M. West of Scripps Research. Other authors include Ellen Y.T. Chien, Jovylyn Gatchalian, and Michael J. Chalmers of Scripps Research, and Vsevolod Katritch of the University of California, San Diego.

The study was supported by the National Institutes of Health.

Journal Reference:

Graham M. West, Ellen Y.T. Chien, Vsevolod Katritch, Jovylyn Gatchalian, Michael J. Chalmers, Raymond C. Stevens, Patrick R. Griffin. Ligand-Dependent Perturbation of the Conformational Ensemble for the GPCR β2 Adrenergic Receptor Revealed by HDX. Structure, 2011; DOI: 10.1016/j.str.2011.08.001

Courtesy: ScienceDaily

Cognitive Changes May Predict Alzheimer's Disease Development More Accurately Than Biomarkers

2011-09-09T11:05:00.000-07:00

Compared with changes in biomarkers, changes in cognitive abilities appear to be stronger predictors of whether an individual with mild cognitive impairment (MCI) will develop Alzheimer's disease, according to a report in the September issue of Archives of General Psychiatry, one of the JAMA/Archives journals.

Biomarkers such as changes in brain volume or in cerebrospinal fluid levels of some proteins have helped scientists learn about how Alzheimer's disease develops and whether treatments for it are effective, according to background information in the article. Behavioral markers such as cognitive changes, genetic risk factors and demographic variables also seem to be associated with the condition. However, the authors write, "despite formidable evidence for the predictive validity of individual biomarkers and behavioral markers, they have rarely been examined in combined models."

Jesus J. Gomar, Ph.D., from the Benito Menni Complex Assistencial en Salut Mental, Barcelona, Spain, and colleagues sought to determine how well different classes of biomarkers and cognitive markers could predict whether patients with MCI would develop Alzheimer's disease. They also wanted to assess whether any of these factors was associated with a disproportionate magnitude of decline. The longitudinal study used information from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. The study included 116 participants with MCI that converted to Alzheimer's disease in two years, 204 participants with MCI that did not convert to Alzheimer's disease and 197 cognitively healthy participants as controls.

The researchers used a variety of neuropsychological tests to assess participants' cognition and ability to function. They obtained cerebrospinal fluid samples when the study began and at annual visits for two years. At the beginning of the study, participants gave a blood sample which was examined for the presence of genes associated with Alzheimer's disease. The researchers also obtained information about participants' brain volume and cortical thickness from magnetic resonance imaging results included in the ADNI.

Analysis of the variables showed that two measures of delayed memory, as well as the cortical thickness of the left middle temporal lobe in the brain, were associated with a higher chance of converting from MCI to Alzheimer's disease at two years. A change in participants' scores on a measure of functional activities appeared to show a larger rate of decline than did changes in biomarkers. In particular, a decline in scores on the Functional Assessment Questionnaire and the Trail Making Test, part B, appeared to predict whether an individual with MCI would develop Alzheimer's disease within one year.

"Cognitive markers at baseline were more robust predictors of conversion than most biomarkers," write the authors. "Longitudinal analyses suggested that conversion appeared to be driven less by changes in the neurobiologic trajectory of the disease than by a sharp decline in functional ability and, to a lesser extent, by declines in executive function." The researchers add that in clinical practice and in clinical trials, the optimal way to accurately predict conversion to Alzheimer's disease is to use all available data.

Journal Reference:

J. J. Gomar, M. T. Bobes-Bascaran, C. Conejero-Goldberg, P. Davies, T. E. Goldberg. Utility of Combinations of Biomarkers, Cognitive Markers, and Risk Factors to Predict Conversion From Mild Cognitive Impairment to Alzheimer Disease in Patients in the Alzheimer's Disease Neuroimaging Initiative. Archives of General Psychiatry, 2011; 68 (9): 961 DOI: 10.1001/archgenpsychiatry.2011.96

Courtesy: ScienceDaily

Scientists Create Mammalian Cells With Single Chromosome Set

2011-09-07T11:03:00.000-07:00

Researchers have created mammalian cells containing a single set of chromosomes for the first time in research funded by the Wellcome Trust and EMBO. The technique should allow scientists to better establish the relationships between genes and their function.

Mammal cells usually contain two sets of chromosomes -- one set inherited from the mother, one from the father. The genetic information contained in these chromosome sets helps determine how our bodies develop. Changes in this genetic code can lead to or increase the risk of developing disease.

To understand how our genes function, scientists manipulate the genes in animal models -- such as the fruit fly, zebrafish and mice -- and observe the effects of these changes. However, as each cell contains two copies of each chromosome, determining the link between a genetic change and its physical effect -- or 'phenotype' -- is immensely complex.

Now, in research published in the journal Nature, Drs Anton Wutz and Martin Leeb from the Wellcome Trust Centre for Stem Cell Research at the University of Cambridge report a technique which enables them to create stem cells containing just a single set of chromosomes from an unfertilised mouse egg cell. The stem cells can be used to identify mutations in genes that affect the cells' behaviour in culture. In an additional step, the cells can potentially be implanted into the mouse for studying the change in organs and tissues.

The technique has previously been used in zebrafish, but this is the first time it has been successfully used to generate such mammalian stem cells.

Dr Wutz, a Wellcome Trust Senior Research Fellowship, explains: "These embryonic stem cells are much simpler than normal embryonic mammalian stem cells. Any genetic change we introduce to the single set of chromosomes will have an easy-to-determine effect. This will be useful for exploring in a systematic way the signalling mechanisms within cell and how networks of genes regulate development."

The researchers hope that this technique will help advance mammalian genetics and our understanding of the gene-function relationship in the same way that a similar technique has helped geneticists understand the simpler zebrafish animal model.

Understanding how our genetic make-up functions and how this knowledge can be applied to improve our health is one of the key strategic challenges set out by the Wellcome Trust. Commenting on this new study, Dr Michael Dunn, Head of Molecular and Physiological Sciences at the Wellcome Trust, says:

"This technique will help scientists overcome some of the significant barriers that have so far made studying the functions of genes so difficult. This is often the first step towards understanding why mutations lead to disease and, ultimately, to developing new drugs treatments."

Journal Reference:

Martin Leeb, Anton Wutz. Derivation of haploid embryonic stem cells from mouse embryos. Nature, 2011; DOI: 10.1038/nature10448

Courtesy: ScienceDaily

Research Aims to Starve Breast Cancer Cells

2011-09-03T05:04:00.000-07:00

The most common breast cancer uses the most efficient, powerful food delivery system known in human cells and blocking that system kills it, researchers report.

This method of starving cancer cells could provide new options for patients, particularly those resistant to standard therapies such as tamoxifen, Georgia Health Sciences University researchers said.

Human estrogen receptor-positive breast cancer cells thriving in a Petri dish or transplanted onto mice die when exposed to a drug that blocks the transporter, called SLC6A14, said Dr. Vadivel Ganapathy, Chairman of GHSU's Department of Biochemistry and Molecular Biology.

"It basically starves the cancer cell," said Ganapathy, corresponding author of the study published in the Journal of Biological Chemistry. The transporter can carry 18 of the known 20 amino acids, fuel all cells need in some combination. Amino acids enable cells to make proteins, which they need to function and survive. The cell type determines its amino acid needs and delivery system. Rapidly growing, dividing estrogen receptor-positive breast cancer needs nearly every amino acid so it makes the smart choice of utilizing the transporter that can deliver the biggest load, Ganapathy said.

SLC6A14 is the only transporter known to carry all 10 essential amino acids, essential because the body can't make them so they have to be delivered via the bloodstream from food. The transporter also takes eight of the nonessential amino acids along for the ride, Ganapathy said.

And it is a fast ride. The transporter has three energy sources instead of the usual one or two, he said.

Interestingly, SLC6A14 is expressed at low levels in most of the body. "There are specialized features of this transport system which could be used by every cell to its advantage but they do not seem to do that. It's expressed only at low levels in normal tissues," Ganapathy noted. While that may seem like a loss for healthy cells, it bolsters the cancer-fighting potential for drugs that block SLC6A14 by making it a more specific cancer target. "Since the normal cells do not depend on this transporter, you can use a drug that selectively blocks it to target cancer cells" Ganapathy said.

The compound they used is alpha-methyl-DL-tryptophan, already used in humans for short periods when they are getting a PET scan in certain areas of the brain. When the researchers treated estrogen receptor-positive breast cancer cells with it or put it in the drinking water of the mice with the cells, rapid growth stopped and the cancer cells died. Further studies showed alpha-methyl-DL-tryptophan seemed to impact only cells expressing the SLC6A14 transport system. Even another type of breast cancer, estrogen receptor-negative, wasn't impacted.

Researchers are now determining the most potent version of the compound.

The research was supported by the National Institutes of Health.

Journal Reference:

S. Karunakaran, S. Ramachandran, V. Coothankandaswamy, S. Elangovan, E. Babu, S. Periyasamy-Thandavan, A. Gurav, J. P. Gnanaprakasam, N. Singh, P. V. Schoenlein, P. D. Prasad, M. Thangaraju, V. Ganapathy. SLC6A14 (ATB0, ), a highly concentrative and broad-specific amino acid transporter, is a novel and effective drug target for treatment of estrogen receptor-positive breast cancer. Journal of Biological Chemistry, 2011; DOI: 10.1074/jbc.M111.229518

Courtesy: ScienceDaily

New Method Reveals Parts of Bacterial Genome Essential to Life

2011-09-01T05:02:00.000-07:00

A team at the Stanford University School of Medicine has cataloged, down to the letter, exactly what parts of the genetic code are essential for survival in one bacterial species, Caulobacter crescentus.

They found that 12 percent of the bacteria's genetic material is essential for survival under laboratory conditions. The essential elements included not only protein-coding genes, but also regulatory DNA and, intriguingly, other small DNA segments of unknown function. The other 88 percent of the genome could be disrupted without harming the bacteria's ability to grow and reproduce.

The study, which was enabled by the team's development of an extremely efficient new method of genetic analysis, paves the way for better understanding of how bacterial life evolved and for improving identification of DNA elements that are essential for many bacterial processes, including the survival of pathogenic bacteria in an infected person. It will be published online Aug. 30 in Molecular Systems Biology.

"This work addresses a fundamental question in biology: What is essential for life?" said Beat Christen, PhD, one of the co-first authors of the new paper and a postdoctoral scholar in developmental biology. "We came up with a method to identify all the parts of the genome required for life."

The bacteria studied is a non-pathogenic freshwater species that has long been used in molecular biology research. Its complete genome was sequenced in 2001, but knowing the letters in its genetic code did not tell the researchers which bits of DNA were important to the bacteria.

"There were many surprises in the analysis of the essential regions of Caulobacter's genome," said Lucy Shapiro, PhD, the paper's senior author. "For instance, we found 91 essential DNA segments where we have no idea what they do. These may provide clues to lead us to new and completely unknown bacterial functions." Shapiro is a professor of developmental biology and the director of the Beckman Center for Molecular and Genetic Medicine at Stanford.

Caulobacter's DNA, like that of most bacteria, is a single, ring-shaped chromosome. To perform their experiment, the researchers mutated many Caulobacter cells so that each cell incorporated one piece of artificial DNA at a random location in its chromosome. The artificial DNA, which was labeled so the scientists could find it later, disrupted the function of the region of bacterial DNA where it landed. Over two days, the researchers grew these mutants until they had about 1 million bacterial cells, and then sequenced their DNA. After intensive computer analysis, they created a detailed map of the entire bacterial genome to show exactly where the artificial DNA segments had been inserted in the chromosome of the surviving cells.

This mutation map contained many gaps -- the regions of the DNA where no living bacteria had survived with an artificial DNA insertion. These regions, the researchers reasoned, must be essential for bacterial life since disrupting them prevented bacterial survival.

"We were looking for the dog that didn't bark," Shapiro said.

Scientists have used a similar mapping strategy to find essential genetic elements before, but the Stanford team added several innovations that greatly improved the speed and resolution of the method.

"Our method is very streamlined," Christen said. "We can do an analysis that would have taken years in a few weeks. We can immediately go to the answer."

The new method collapses into a single experiment work that used to take dozens of experimental steps, and shifts the majority of the time needed for the research from laboratory work to data analysis.

In total, the essential Caulobacter genome was 492,941 base pairs long and included 480 protein-coding genes that were clustered in two regions of the chromosome. The researchers also identified 402 essential promoter regions that increase or decrease the activity of those genes, and 130 segments of DNA that do not code for proteins but have other roles in modifying bacterial metabolism or reproduction. Of the individual DNA regions identified as essential, 91 were non-coding regions of unknown function and 49 were genes coding proteins whose function is unknown. Learning the functions of these mysterious regions will expand our knowledge of bacterial metabolism, the team said.

The research team anticipates that the new technique will have several interesting uses in both basic and applied research. For instance, the technique provides a rapid and economical method to learn which genetic elements are essential in any microbial species.

"This would give fundamental information so we could determine which essential genetic elements are conserved through evolution," said co-author Harley McAdams, PhD, professor of developmental biology.

The scientists also pointed out that the method could be used to examine which DNA segments are essential for bacterial survival in specific circumstances, such as when pathogenic bacteria invade a host animal or plant. Developing a comprehensive list of genetic elements that make a bacterial species infectious could lead to the identification of new anti-infective agents including new antibiotics.

The research team included co-first author Eduardo Abeliuk, an electrical engineering graduate student; research associate John Collier, PhD; senior research scientist Virginia Kalogeraki, PhD; Ben Passarelli, director of computing at the Stanford Functional Genomics Facility; John Coller, PhD, director of the Stanford Functional Genomics Facility; and Michael Fero, PhD, a National Institute of General Medical Sciences Quantitative Research Fellow at Stanford.

The research was funded by grants from the Department of Energy's Office of Science, the National Institutes of Health, the Swiss National Foundation and a LaRoche Foundation Fellowship.

Journal Reference:

Beat Christen, Eduardo Abeliuk, John M Collier, Virginia S Kalogeraki, Ben Passarelli, John A Coller, Michael J Fero, Harley H McAdams and Lucy Shapiro. The essential genome of a bacterium. Molecular Systems Biology, 2011; DOI: 10.1038/msb.2011.58

Courtesy: ScienceDaily

Sutureless Method for Joining Blood Vessels Invented

2011-08-30T08:57:00.000-07:00

Reconnecting severed blood vessels is mostly done the same way today -- with sutures -- as it was 100 years ago, when the French surgeon Alexis Carrel won a Nobel Prize for advancing the technique. Now, a team of researchers at the Stanford University School of Medicine has developed a sutureless method that appears to be a faster, safer and easier alternative.

In animal studies, a team led by Stanford microsurgeon Geoffrey Gurtner, MD, used a poloxamer gel and bioadhesive rather than a needle and thread to join together blood vessels, a procedure called vascular anastomosis. Results of the research are published online Aug. 28 in Nature Medicine. Lead authors of the study were Stanford postdoctoral scholar Edward Chang, MD, and surgery resident Michael Galvez, MD.

The big drawback of sutures is that they are difficult to use on blood vessels less than 1 millimeter wide. Gurtner began thinking about alternatives to sutures about a decade ago. "Back in 2002, I was chief of microsurgery at Bellevue in New York City, and we had an infant -- 10 to 12 months old -- who had a finger amputated by the spinning wheel of an indoor exercise bike," said Gurtner, senior author of the study and professor of surgery. "We struggled with reattaching the digit because the blood vessels were so small -- maybe half a millimeter. The surgery took more than five hours, and at the end we were only able to get in three sutures.

"Everything turned out OK in that case," he continued. "But what struck me was how the whole paradigm of sewing with a needle and thread kind of falls apart at that level of smallness."

Sutures are troublesome in other ways, too. They can lead to complications, such as intimal hyperplasia, in which cells respond to the trauma of the needle and thread by proliferating on the inside wall of the blood vessel, causing it to narrow at that point. This increases the risk of a blood clot getting stuck and obstructing blood flow. In addition, sutures may trigger an immune response, leading to inflamed tissue that also increases the risk of a blockage.

The new method could sidestep these problems. "Ultimately, this has the potential to improve patient care by decreasing amputations, strokes and heart attacks while reducing health-care costs," the authors write in the study.

Earlier in his career, as Gurtner contemplated a better way of joining together blood vessels, he considered whether ice could be used to fill the lumen, the inner space of the blood vessel, to keep both ends open to their full diameter long enough to glue them together. Not feasible, he concluded. "Water turns to ice quite slowly and you would have to drop the temperature of the surgical site a lot -- from 98.6 degrees to 32 degrees Fahrenheit," he said.

Shortly after arriving at Stanford in 2005, Gurtner approached fellow faculty member Gerald Fuller, PhD, professor of chemical engineering and the Fletcher Jones II Professor in the School of Engineering, about whether he knew of a substance that could be turned easily from a liquid to a solid and back to a liquid again, and that would also be safe to use in vascular surgery. Fuller immediately suggested a Food and Drug Administration-approved thermoreversible poloxamer called Poloxamer 407. It is constructed of polymer blocks whose properties can be reversed by heating.

Fuller teamed up with Jayakumar Rajadas, PhD, director of the Stanford Biomaterials and Advanced Drug Delivery Laboratory, to modify the poloxamer so that it would become solid and elastic when heated above body temperature but dissolve harmlessly into the bloodstream when cooled. The poloxamer then was used to distend both openings of a severed blood vessel, allowing researchers to glue them together precisely.

The researchers used a simple halogen lamp to heat the gel. In tests on animals, the technique was found to be five times faster than the traditional hand-sewn method, according to the study. It also resulted in considerably less inflammation and scarring after two years. The method even worked on extremely slim blood vessels -- those only 0.2 mm wide -- which would have been too tiny and delicate for sutures. "That's where it really shines," Gurtner said.

Dermabond, a surgical sealant, was used to attach the ends of the blood vessels together.

Poloxamers have been used before as a vehicle for delivering drugs, including chemotherapeutics, vaccines and anti-viral therapies. Researchers have used Poloxamer 407 to occlude blood vessels in experimental animals for the purpose of evaluating the gel's safety and efficacy in so-called "beating heart surgery," in which certain vessels need to be temporarily blocked to improve visibility for the surgeons performing a coronary artery bypass.

Although other sutureless methods have been developed, they generally have not produced better outcomes, the authors said. "Often, the use of microclips, staples or magnets is itself traumatic to blood vessels leading to failure rates comparable to or higher than sutured anastomoses," they wrote.

"This is a novel approach to anastomosis that could play a valuable role in microvascular surgery," said Frank Sellke, MD, chief of cardiothoracic surgery at Brown University Medical Center and associate editor of the Journal of Thoracic and Cardiovascular Surgery, who was not involved in the study. "But it really needs to show that it holds up in clinical trials."

The authors say further testing on large animals is needed before human trials can begin, but they note that all of the components used in the technique are already approved by the FDA. "This technology has the potential to progress rapidly from the 'bench to bedside,'" they write.

Gurtner said he believes the new technique could satisfy a huge unmet need and prove especially useful in minimally invasive surgeries, in which manipulating sutures takes on a whole new level of difficulty.

Michael Longaker, MD, the Deane P. and Louise Mitchell Professor in the School of Medicine and a co-author of the study, called the technique a "potential game-changer."

"When you're bringing together hollow tubes, whether they're large structures, like the colon or the aorta, or a small structure, like a vein in the finger of a child, you're always worried about lining them up directly and effectively sealing them," Longaker said. "The technique that Dr. Gurtner has pioneered could allow surgeons to perform anastomosis more quickly and with improved precision."

He continued: "Coming up with this solution was the result of the classic Stanford model of bringing together researchers from a variety of disciplines."

Other Stanford co-authors of the study were postdoctoral scholars Jason Glotzbach, MD, Kristin-Maria Sommer, PhD, Oscar Abilez, MD, PhD, and Cynthia Hamou, MD; medical student Samyra El-ftesi; and technician Travis Rappleye.

The work was supported by a Stanford Bio-X Interdisciplinary Initiatives Research Award and the Oak Foundation. Stanford University has patented the technology.

Gurtner and Longaker are also members of the Stanford Cancer Institute.

"Everything turned out OK in that case," he continued. "But what struck me was how the whole paradigm of sewing with a needle and thread kind of falls apart at that level of smallness."

Dermabond, a surgical sealant, was used to attach the ends of the blood vessels together.

Michael Longaker, MD, the Deane P. and Louise Mitchell Professor in the School of Medicine and a co-author of the study, called the technique a "potential game-changer."

He continued: "Coming up with this solution was the result of the classic Stanford model of bringing together researchers from a variety of disciplines."

The work was supported by a Stanford Bio-X Interdisciplinary Initiatives Research Award and the Oak Foundation. Stanford University has patented the technology.

Gurtner and Longaker are also members of the Stanford Cancer Institute.

Journal Reference:

Edward I Chang, Michael G Galvez, Jason P Glotzbach, Cynthia D Hamou, Samyra El-ftesi, C Travis Rappleye, Kristin-Maria Sommer, Jayakumar Rajadas, Oscar J Abilez, Gerald G Fuller, Michael T Longaker, Geoffrey C Gurtner. Vascular anastomosis using controlled phase transitions in poloxamer gels. Nature Medicine, 2011; DOI: 10.1038/nm.2424

Courtesy: ScienceDaily

Deaths from Strong Prescription Painkillers Are On the Increase, Experts Say

2011-08-28T05:41:00.000-07:00

Action is needed to tackle the increasing number of deaths in the United States and Canada from prescription painkillers known as opioids, say experts in an article published online in the British Medical Journal.

Opioids are prescription painkillers that contain compounds derived from the opium poppy.

While they have long been used to control the symptoms of cancer and acute medical conditions, they are increasingly being used to control chronic pain, for example in patients suffering from osteoarthritis, say Dr Irfan Dhalla and colleagues at the University of Toronto.

They describe how in the US, deaths involving opioid painkillers increased from 4,041 in 1999 to 14,459 in 2007 and are now more common than deaths from skin cancer, HIV and alcoholic liver disease. They add that between 1.4 million and 1.9 million Germans are addicted to prescription drugs and that some authorities have suggested that the UK may face a similar epidemic to that of North America in five to ten years time. Indeed, the use of strong opioids for chronic non-cancer pain in the UK has been described as a "disaster in the making" by Dr. Des Spence previously on bmj.com.

Dr. Dhalla and colleagues add that "deaths involving methadone and codeine roughly doubled in England and Wales between 2005 and 2009, while deaths involving heroin or morphine remained unchanged."

In order to tackle the crisis in the US and Canada, the authors put forward several strategies.

They say staff working for drug companies should not get commission for marketing prescription opioid drugs and that regulators should evaluate adverts for them before they are disseminated. Another initiative would be to introduce real-time electronic databases to reduce the frequency with which opioids are obtained from multiple doctors or pharmacies.

Dhalla and colleagues also call for educational outreach programmes for doctors to improve opioid prescribing, as well as more research to guide practice. They note that the evidence for the use of opioids to control chronic pain is very limited and the risks may outweigh the benefits.

In conclusion, they say that maintaining access to opioids for appropriately selected patients while striving for major reductions in overdose deaths must be a major priority for physicians and policymakers.

Journal Reference:

I. A. Dhalla, N. Persaud, D. N. Juurlink. Facing up to the prescription opioid crisis. BMJ, 2011; 343 (aug23 1): d5142 DOI: 10.1136/bmj.d5142

Courtesy: ScienceDaily

Blood Vessels Participate in the Eradication of Tumors

2011-08-26T05:38:00.000-07:00

Breast cancer: for the first time, very specific blood vessels have been discovered in tumors. These vessels facilitate the access of certain white blood cells, known as "killer lymphocytes," into tumor tissues and thus lead to the efficient destruction of tumors. This work, led by Jean-Philippe Girard, Inserm senior researcher at the Institut de Pharmacologie et de Biologie Structurale (CNRS/Université Toulouse III -- Paul Sabatier), in collaboration with the Institut Claudius Regaud, is published in the journal Cancer Research.

A category of white blood cells, called "killer lymphocytes," has the function of recognizing and destroying cancerous cells in the body. However, the eradication of the disease requires the presence of a large number of killer cells in contact with the tumors. How do these lymphocytes manage to penetrate the tumors in order to destroy them?

Although the mechanism has been shrouded in mystery until now, Girard's team at the Institut de Pharmacologie et de Biologie Structurale (CNRS / Université Toulouse III -- Paul Sabatier), in collaboration with researchers from the Institut Claudius Regaud (Centre de Lutte Contre le Cancer de Toulouse)[1], has lifted the veil on how lymphocytes infiltrate into tumors. By carrying out a study involving nearly 150 patients suffering from breast cancer, the scientists discovered the presence of a particular type of blood vessel, known as HEVs (High Endothelial Venules), in tumors. Normally, these HEV vessels are present in the lymph nodes[2] where they serve as port of entry for lymphocytes from the blood. The cells lining the walls of these HEV vessels are bulging and rounded and this very characteristic morphology facilitates the passage of lymphocytes from the blood into the tissue.

The Toulouse-based team discovered that the presence of a large number of killer lymphocytes in breast tumors was linked to the presence of a large number of HEV vessels in these tumors. This suggests that, as in lymph nodes, HEVs constitute the port of entry for lymphocytes into tumors. In addition, the researchers observed that when a tumor contains many HEV vessels, the patients are more likely to recover. The presence of these HEV vessels in a tumor could thus be a favorable prognosis factor.

The next steps for the researchers will be to confirm these results on larger groups of patients and to study the influence of HEV vessels on the response to therapeutics (chemo- and radiotherapy) widely used in breast cancer treatment. Studies are also underway to examine the role of HEV vessels in melanoma and cancer of the ovaries and the colon. The longer-term objective is to increase the quantity of HEVs in tumors and/or to make them form in tumors that do not have them, so as to enable a massive recruitment of killer lymphocytes for eradicating cancerous cells.

[1] This work benefited from financial support from the Ligue Nationale Contre le Cancer (Equipe Labellisée Ligue 2009), of the Fondation RITC (Recherche et Innovation Thérapeutique en Cancérologie) and the Région Midi-Pyrénées.

[2] Lymph nodes are where immune cells proliferate and differentiate. The lymphatic vessels bring an antigen (often from a pathogen) from the tissue to the ganglions, thus making it possible to bring about a specific immune response by activating the T and B lymphocytes.

Journal Reference:

Ludovic Martinet, Ignacio Garrido, Thomas Filleron, Sophie Le Guellec, Elisabeth Bellard, Jean-Jacques Fournie, Philippe Rochaix and Jean-Philippe Girard. Human solid tumors contain high endothelial venules (HEVs): association with T and B lymphocyte infiltration and favourable prognosis in breast cancer. Cancer Research, 16 August 2011 DOI: 10.1158/0008-5472.CAN-11-0431

Courtesy: ScienceDaily

New Target for Treatment of Type 2 Diabetes and Prediabetes Identified

2011-08-24T05:37:00.000-07:00

Researchers at the Joslin Diabetes Center have shown that an enzyme found in the mitochondria of cells is decreased in the skeletal muscle of those with diabetes, a finding that could lead to the development of drugs to boost the activity of this enzyme in an effort to fight the disease.

A paper in published online in the Proceedings of the National Academy of Sciences, showed that the enzyme, Sirt3, is decreased in the skeletal muscle of humans and animals with diabetes by at least half, compared to those without diabetes and that this may contribute to development of insulin resistance, one of the earliest manifestations of the disease. Sirt3 is found in the mitochondria, the power producers of cells that convert energy into usable forms.

"Ours is perhaps the first study to understand what is going wrong in the mitochondria of those with diabetes," said senior author C. Ronald Kahn, M.D., Head of the Joslin Section on Integrative Physiology and Metabolism and the Mary K. Iacocca Professor of Medicine at Harvard Medical School. "Many studies have shown that the mitochondria don't work well in those with diabetes. This points to a cause of why they don't work well."

Dr. Kahn said the study sought to look at how decreased Sirt3 levels might affect the metabolism of cells, particularly how it could affect insulin action in cells. "We know that one of the hallmarks of early diabetes is insulin resistance in muscle, but we didn't know what caused it," he said.

He said the study showed that when Sirt3 levels are low, as they are in the case of diabetes, the mitochondria of the cells are not as efficient in energy metabolism as they should be.

When the mitochondria become inefficient, they generate what are known as reactive oxygen species (ROS), chemically reactive molecules containing oxygen, which create insulin resistance in the muscles, he said.

"This is the first time this has been shown," Dr. Kahn said.

The goal for the future will be to find ways to restore levels of Sirt3 or increase the activity of the existing Sirt3, perhaps with a drug, in a bid to improve insulin resistance in the muscle and improve muscle metabolism, he said.

"It is a new target," he said.

Dr. Kahn noted that this study is one of the first demonstrations of a single defect that could affect mitochondrial metabolism and insulin signaling in the muscle.

"In further studies we will try to understand what proteins Sirt3 acts on," he said.

He noted that one of the earliest hallmarks of diabetes is insulin resistance in the skeletal muscle. As a result, a drug to boost Sirt3 levels could be useful in the treatment of prediabetes or in those newly diagnosed with the disease, he said.

"Agents which increase Sirt3 activity could, therefore, potentially reverse at least some of the adverse effects of type 2 diabetes," the paper concludes.

Co-authors included Enxuan Jing, lead author, as well as Brice Emanuelli, Jeremie Boucher and Kevin Lee, all of Joslin; Matthew D. Hirschey and Eric M. Verdin, both of Gladstone Institute of Virology and Immunology and the University of California, San Francisco; and David Lombard, formerly of the Department of Genetics at Harvard Medical School and currently at the Department of Pathology and Institute of Gerontology at the University of Michigan.

Dr. Verdin noted that by "uncovering the multi-faceted role of SIRT3, we are laying important groundwork to better combat this widespread disease at the cellular level."

The study was supported by research grants to Kahn and Verdin as well as a grant from the Ellison Foundation and the Mary K. Iacocca Professorship. The study also received support from the Joslin DERC cores laboratories.

Journal Reference:

Enxuan Jing, Brice Emanuelli, Matthew D. Hirschey, Jeremie Boucher, Kevin Y. Lee, David Lombard, Eric M. Verdin, C. Ronald Kahn. Sirtuin-3 (Sirt3) regulates skeletal muscle metabolism and insulin signaling via altered mitochondrial oxidation and reactive oxygen species production. Proceedings of the National Academy of Sciences, 2011; DOI: 10.1073/pnas.1111308108

Courtesy: ScienceDaily

Salmonella Stays Deadly With a 'Beta' Version of Cell Behavior

2011-08-21T06:28:00.000-07:00

Salmonella cells have hijacked the protein-building process to maintain their ability to cause illness, new research suggests. Scientists say that these bacteria have modified what has long been considered typical cell behavior by using a beta form of an amino acid -- as opposed to an alpha form -- during the act of making proteins.

Beta versions of amino acids occur in nature under rare and specific circumstances, but have never been observed as part of protein synthesis. Before this finding, in fact, researchers had determined that virtually all proteins were constructed with the alpha forms of amino acids.

This work has shown that when researchers delete any one of three genes from the process that makes use of the beta form of the amino acid, or if they insert the alpha form in the beta version's place, Salmonella cells are no longer able to cause disease. The amino acid in question is lysine, one of 22 genetically encoded amino acids that are strung together in cells to make proteins.

"When these genes were knocked out, the cells became sensitive to antibiotics. And if we put beta lysine into the medium where cells were growing, they became resistant to antibiotics," said Michael Ibba, professor of microbiology at Ohio State University and a senior author of the study. "So we could see the beta amino acid being taken up and used. The cells really do need the beta amino acid to be resistant to antibiotics, and for other aspects of their virulence."

This finding suggests that the process using this specific beta amino acid could be an attractive antibiotic target for this common pathogen, the researchers say.

The Centers for Disease Control and Prevention estimates that about 1.4 million people in the United States are infected with Salmonella each year, though only 40,000 cases are reported. Most people infected with Salmonella develop diarrhea, fever and abdominal cramps. Though recovery can occur within a week without treatment, some severe cases require antibiotic treatment and hospitalization.

The study is published in the Aug. 14 online edition of the journal Nature Chemical Biology.

This work began when University of Toronto scientists exploring the origins of Salmonella's virulence identified three genes that were clear players in the process. These three genes -- called YjeK, PoxA and EF-P -- were unusual in this context.

Genes that confer virulence in bacteria typically have a specific job, such as producing toxins or transporters. But these three virulence genes all looked like they should have a role in the protein synthesis machinery -- which is Ibba's expertise.

Under normal circumstances in cells, an enzyme will select amino acids in the cell and place them on a molecule called transfer RNA, or tRNA, which leads to translation of the genetic code into proteins.

In Salmonella cells, these steps are similar, but with a few surprising twists, Ibba said. He and colleagues confirmed that the YjeK gene makes beta lysine, and showed that the PoxA gene takes that beta lysine and attaches it to EF-P -- a protein that partially mimics the shape and function of tRNA.

"It's a really unexpected pathway," said Ibba, also an investigator in Ohio State's Center for RNA Biology. "It is a mimic of what normally makes protein in a cell. Where a cell would normally be expected to use an alpha amino acid, Salmonella puts on a beta amino acid. And it ends up making molecules that lead to the cells being virulent."

The research team first reconstructed this unusual protein synthesis process in test tube experiments, and then followed with studies in cell cultures. Even before they took on studying the mechanism, however, they knew that the effects of these virulence genes were powerful: In earlier animal studies, deleting any one of the three genes and then infecting mice with these altered Salmonella cellshad no effect on the animals. When the genes were left intact and cells were injected into mice, the resulting Salmonella infection killed the animals.

In addition, when the researchers tricked Salmonella cells into using alpha lysine for this pathway instead of beta lysine, the cells lost their ability to cause illness.

"This tells us the cell is not going to be able to easily replace the beta amino acid," Ibba said. "It is essential for virulence in Salmonella."

And that, he said, is why that amino acid might be such an effective drug target, especially as humans don't seem to make beta amino acids at all. "You have to make an antibiotic look like something natural, only different. If you have something that's already different like a beta amino acid, you've potentially got a much better drug target because it involves chemistry that's comparatively rare in the cell. It's harder for the cell to try to alter its own chemistry to develop resistance," Ibba said.

From here, the researchers are observing cell behavior later in the protein-building process to figure out how this hijacked system actually gives Salmonella its virulence.

This work is supported by the National Institutes of Health, the Canada Institutes of Health Research, the Natural Sciences and Engineering Research Council of Canada and Ohio State.

Co-authors include Hervé Roy, a former Ohio State research scientist now at the University of Central Florida; S. Betty Zou and William Navarre of the University of Toronto; Tammy Bullwinkle of Ohio State's Department of Microbiology; and Benjamin Wolfe and Craig Forsyth of Ohio State's Department of Chemistry.

Written by Emily Caldwell, (614) 292-8310; Caldwell.151@osu.edu

Journal Reference:

Hervé Roy, S Betty Zou, Tammy J Bullwinkle, Benjamin S Wolfe, Marla S Gilreath, Craig J Forsyth, William W Navarre & Michael Ibba. The tRNA synthetase paralog PoxA modifies elongation factor-P with (R)-β-lysine. Nature Chemical Biology, 14 August 2011 DOI: 10.1038/nchembio.632

Courtesy: ScienceDaily

Five Inherited Genetic Variants Linked to the Most Lethal Prostate Cancers

2011-08-19T06:26:00.000-07:00

An international team of researchers led by Fred Hutchinson Cancer Research Center has identified five inherited genetic variants that are strongly associated with aggressive, lethal prostate cancer. The discovery ultimately could lead to the development of a simple blood test that could be given upon diagnosis to determine which men should receive aggressive treatment versus a more conservative "watchful waiting" approach.

The findings, by Janet L. Stanford, Ph.D., co-director of the Hutchinson Center's Program in Prostate Cancer Research and a member of its Public Health Sciences Division, are published online Aug. 16 ahead of the September issue of Cancer Epidemiology, Biomarkers and Prevention.

A substantial number of men with indolent tumors -- which have a low probability of progressing to clinically significant, lethal prostate cancer -- are overtreated and, as a result, suffer side effects such as sexual impotence and urinary incontinence. In addition to its personal toll, overtreatment of indolent prostate cancer also carries a substantial economic burden, with an average of $2 billion to $3 billion spent annually in the U.S. on initial therapy alone.

"Biomarkers that could distinguish between patients with indolent versus more-aggressive tumors are urgently needed," Stanford said. "The panel of markers we've identified provides the first validated evidence that inherited genetic variants play a role in prostate cancer progression and mortality. Ultimately these markers could be used in the clinic, along with other known predictors that are used to assess tumor aggressiveness, such as a high Gleason score, to identify men with a high-risk profile."

The Hutchinson Center has filed a patent on the panel of five single-nucleotide polymorphisms, or SNPs (pronounced "snips"), which are single-letter variations within the four-letter DNA alphabet that serve as markers of genetic variation across the genome which may play a role in the development or progression of disease. "We chose to study SNPs in genes that potentially play a key role in biological pathways that may contribute to prostate cancer progression such as inflammation, steroid-hormone production and metabolism, DNA repair, circadian rhythm and vitamin D activity," Stanford said.

For the study, the researchers analyzed DNA in blood samples taken from a population-based group of 1,309 Seattle-area prostate cancer patients who were age 35 to 74 at the time of diagnosis. They evaluated 937 SNPs in 156 candidate genes and, of these, 22 SNPs emerged as being significantly associated with prostate cancer-specific mortality.

A subsequent validation study of these 22 SNPs was conducted in another population-based group of 2,875 prostate cancer patients in Sweden who were age 35 to 74 at diagnosis. Upon genotyping DNA from their blood, five of the 22 SNPs emerged as being significantly associated with death from prostate cancer. A higher proportion of patients from Sweden (17.4 percent) had died of prostate cancer relative to those from Seattle (4.6 percent) during a median follow-up period of 6.5 years, which is consistent with the higher prostate cancer mortality rate in Sweden relative to the U.S.

The five SNPs were located in or tagged, one each, to five genes that may affect prostate cancer progression:

LEPR -- The strongest marker associated with prostate cancer mortality in the study was the leptin receptor gene, which helps control tissue growth, inflammation, blood-vessel development and bone density. The latter effect makes LEPR an interesting candidate for understanding disease progression, since the primary metastatic site for prostate cancer is bone, and such metastases are predictive of fatal disease.
RNASEL -- This gene is associated with hereditary prostate cancer and is associated with apoptosis (programmed cell death), inflammation and the ability of cells to proliferate and stick to each other (hallmarks of cancer growth).
IL4 -- This Interleukin 4 gene is associated with tumor growth, blood vessel development and cancer cell migration.
CRY1 -- Cytochrome 1 is a gene that impacts the circadian rhythm and thereby may affect androgen levels, which are known to be involved in prostate cancer progression.
ARVCF -- This gene is a member of the catenin family of proteins, which help the inside and outside of cells "talk" to each other. Increased expression of ARVCF has been shown to disrupt cell adhesion, which may facilitate cancer progression.

Patients who carried four or all five of these genetic markers had a 50 percent higher risk of dying from their prostate cancer than patients who had two or fewer. The risk of dying from prostate cancer increased with the number of SNP genetic variants a patient carried.

"While previous studies have suggested that genetic background influences prostate cancer outcomes, this is the first study to validate genetic markers associated with lethal disease," Stanford said.

"The ability to distinguish patients at elevated risk for having aggressive, life-threatening prostate cancer at the time of diagnosis could improve care for the subset of cases most likely to benefit from aggressive therapy and help avoid overtreatment of patients whose tumors are likely to remain indolent," the authors wrote.

The potential usefulness of the panel of five SNPs in the clinic to stratify patients at higher risk for disease progression now needs to be evaluated in other patient populations. Stanford and colleagues are also planning additional studies of this set of genetic markers to predict adverse prostate cancer outcomes.

Journal Reference:

Daniel W. Lin, Liesel M. FitzGerald, Rong Fu, Erika M. Kwon, Siqun Lilly Zheng, Suzanne Kolb, Fredrik Wiklund, Pär Stattin, William B. Isaacs, Jianfeng Xu, Elaine A. Ostrander, Ziding Feng, Henrik Grönberg, and Janet L. Stanford. Genetic Variants in the LEPR, CRY1, RNASEL, IL4, and ARVCF Genes Are Prognostic Markers of Prostate Cancer-Specific Mortality. Cancer Epidemiol Biomarkers Prev, August 16, 2011 DOI: 10.1158/1055-9965.EPI-11-0236

Courtesy: ScienceDaily

Antibody Discovered That May Help Detect Ovarian Cancer in Earliest Stages

2011-08-17T06:24:00.000-07:00

Using a new approach to developing biomarkers for the very early detection of ovarian cancer, researchers at Rush University Medical Center have identified a molecule in the bloodstream of infertile women that could one day be used to screen for those at high risk for the disease -- or even those with early-stage ovarian cancer.

The molecule, an antibody that the human body manufactures, is an autoimmune response to mesothelin. This well-studied protein is found in abundance on the surface of ovarian cancer cells but present only in limited amounts in normal human tissue.

The study is published in the online version issue of Cancer Epidemiology, Biomarkers & Prevention, published by the American Society for Cancer Research.

"The finding is extremely important because at present medical tests are unable to detect ovarian cancer in its early stages, which is why death rates from this disease are so high," said Judith Luborsky, PhD, professor of pharmacology, obstetrics and gynecology and preventive medicine at Rush and lead author of the study.

"Our approach to discovering cancer biomarkers was unique in this study. Instead of investigating molecules specific to ovarian cancer alone, we asked what molecules women with a risk of ovarian cancer and those with ovarian cancer had in common," Luborsky said.

The study enabled the researchers to explain the link between infertility and ovarian cancer that has been established in numerous epidemiological surveys.

"More important, with the discovery of the mesothelin antibody, we now have what appears to be a biomarker that can potentially be used in screening tests to help us conquer ovarian cancer," Luborsky said.

According to the American Cancer Society's most recent estimates, there are expected to be about 21,900 new cases of ovarian cancer in the U.S. in 2011 and about 15,460 deaths from the disease. Ovarian cancer is the ninth most common cancer in women (not counting skin cancer) and ranks fifth as the cause of cancer death in women. The poor prognosis for women with ovarian cancer is due to the lack of both clinical symptoms when the cancer first develops and the absence of laboratory tests specific to the disease.

In the study at Rush, researchers tested for mesothelin antibodies in the bloodstream of 109 women who were infertile, 28 women diagnosed with ovarian cancer, 24 women with benign ovarian tumors or cysts, and 152 healthy women. Infertility was due to endometriosis, ovulatory dysfunction or premature ovarian failure or was unexplained.

Significant levels of mesothelin antibodies were found in women with premature ovarian failure, ovulatory dysfunction and unexplained infertility, as well as in women with ovarian cancer, although not in women with endometriosis and not in healthy women or women with benign disease. Endometriosis is generally associated with a different kind of ovarian carcinoma than other types of infertility, which may explain why mesothelin antibodies were not found in these cases.

Why the presence of mesothelin antibodies in the bloodstream should be linked with ovarian cancer is not clear.

"It has been hypothesized that an autoimmune response precedes or somehow contributes to the development and progression of malignant tumors," Luborsky said. "We think that antibodies may arise in response to very early abnormal changes in ovarian tissue that may or may not progress to malignancy, depending on additional triggering events. Or, alternatively, antibodies may bind to normal cells in the ovary, causing dysfunction and leading to infertility -- and, in a subpopulation of women, to the development of ovarian cancer."

Other researchers involved in the study were Yi Yu, MS, and Seby Edassery, MS, both from Rush, and a group led by Ingegerd Hellstrom, MD, PhD, and Karl Eric Hellstrom, MD, PhD, and including Yuan Yee Yip, BS, Jade Jaffar, BS, and Pu Liu, PhD, from Harborview Medical Center at the University of Washington.

The study was supported by funding from the National Institutes of Health and Fujirebio Diagnostics, Inc.

Journal Reference:

Judith L. Luborsky, Yi Yu, Seby L. Edassery, Jade Jaffar, Yuan Yee Yip, Pu Liu, Karl Eric Hellstrom, and Ingegerd Hellstrom. Autoantibodies to Mesothelin in Infertility. Cancer Epidemiol Biomarkers Prev, August 16, 2011 DOI: 10.1158/1055-9965.EPI-11-0139

Courtesy: ScienceDaily

Scientists Map Genes for Common Form of Brain Cancer; Findings Reveal Cause of the Tumors

2011-08-12T05:53:00.000-07:00

Johns Hopkins Kimmel Cancer Center scientists have completed a comprehensive map of genetic mutations occurring in the second-most common form of brain cancer, oligodendroglioma. The findings, reported in the Aug. 4 issue of Science, also appear to reveal the biological cause of the tumors, they say.

To create the map, the scientists sequenced protein-coding genes in seven oligodendroglioma tissue samples, and focused attention on recurring mutations in two genes not previously associated with these tumors -- CIC and FUBP1. The investigators say that CIC and FUBP1 are known to regulate cell-signaling processes, and CIC mutations have been rarely linked to sarcoma, breast and prostate cancers.

More mutations in the two genes were found in an additional 27 oligodendroglioma samples. In all, two-thirds of the samples studied had CIC and FUBP1 mutations.

"Whenever we find genes mutated in a majority of tumors, it is likely that the pathway regulated by that gene is critical for the development and biology of the tumor," says Nickolas Papadopoulos, Ph.D., associate professor of oncology at the Johns Hopkins Kimmel Cancer Center.

In brain cancer, the Hopkins investigators say CIC and FUBP1 mutations may be the "missing link" in what scientists describe as a "two-hit" theory of cancer development. The theory is based on the fact that each cell in the human body has two copies of 23 chromosomes containing thousands of protein-producing genes. If a gene on one chromosome is damaged or deleted, the other copy makes up for the loss of protein. But if the second copy fails as well, the cell cannot make the proper protein and may become cancerous.

In oligodendrogliomas, the "first hit" has long been known to occur in regions of chromosome 1 and 19, which fuse together resulting in a loss of many genes on both chromosomes. Up to 70 percent of oligodendroglioma patients have these DNA fusions, and most of them respond better to chemotherapy and radiation than those who lack the deletions in the chromosomes. For more than a decade, researchers have been looking for evidence of a "second hit" in specific mutated genes that allow oligodendrogliomas to develop.

In the current study, the Johns Hopkins investigators found mutations in the remaining copies of the CIC and FUBP1 genes on chromosomes 1 and 19, suggesting that these mutations represent the second hit needed to create cancer.

"Thanks to the Human Genome Project and advances in cancer genome sequencing, a single study can now resolve decade-old questions and reveal the genetics of this brain cancer," says Kenneth Kinzler, Ph.D., professor and co-director of the Ludwig Center at Johns Hopkins. "Knowing the genetic roadmap of a cancer is the key to attacking it."

Oligodendrogliomas account for up to 20 percent of brain cancers and more commonly occur in younger people aged 30 to 45. The cancer forms most often in the frontal lobe of the brain in cells that coat neurons. Median survival of 10 years is considered far better than other brain cancers. Oligodendrogliomas are treated initially with surgery, followed by chemotherapy and radiation.

The research team says its next step will be to test whether patients with CIC and FUBP1 mutations have the same favorable prognosis as those who have the chromosome 1 and 19 fusion, says Chetan Bettegowda, M.D., Ph.D., chief resident in the Department of Neurosurgery at Johns Hopkins.

"We can focus now on when these mutations develop during tumor formation, whether they can guide prognosis, and how they might form targets for therapy," says Bettegowda.

Bettegowda says the gene map uncovered mutations in other genes, such as PIK3CA, which have been well-studied in cancer. It is possible, he says, that oligodendroglioma patients with mutations in PIK3CA or other genes could be enrolled in current clinical trials using experimental therapies that target these mutations.

Funding for the research was provided by the Virginia and D.K. Ludwig Fund for Cancer Research, the Pediatric Brain Tumor Foundation, the Duke Comprehensive Cancer Center Core, the Burroughs Wellcome Fund, the James S. McDonnell Foundation, state funding from Sao Paulo (FAPESP), the National Cancer Institute and National Institutes of Health.

Contributors to the research include Nishant Agrawal, Yuchen Jiao, Mark Sausen, Laura D. Wood, Ralph H. Hruban, Fausto J. Rodriguez, Daniel P. Cahill, Gregory Riggins, Victor Velculescu and Bert Vogelstein of Johns Hopkins; Roger McLendon, Darell Bigner and Hai Yan of Duke University; and Sueli Mieko Oba-Shinjo and Suely Kazue Nagahashi Marie of the University of Sao Paulo, Brazil.

Under agreements between the Johns Hopkins University, Genzyme, Exact Sciences, Inostics, Qiagen, Invitrogen and Personal Genome Diagnostics, Papadopoulos, Vogelstein, Kinzler and Velculescu are entitled to a share of the royalties received by the University on sales of products related to genes and technologies described in this manuscript. Papadopoulos, Vogelstein, Kinzler, and Velculescu are co-founders of Inostics and Personal Genome Diagnostics stock, which is subject to certain restrictions under Johns Hopkins University policy.

Journal Reference:

Chetan Bettegowda, Nishant Agrawal, Yuchen Jiao, Mark Sausen, Laura D. Wood, Ralph H. Hruban, Fausto J. Rodriguez, Daniel P. Cahill, Roger Mclendon, Gregory Riggins, Victor E. Velculescu, Sueli Mieko Oba-Shinjo, Suely Kazue Nagahashi Marie, Bert Vogelstein, Darell Bigner, Hai Yan, Nickolas Papadopoulos, Kenneth W. Kinzler. Mutations in CIC and FUBP1 Contribute to Human Oligodendroglioma. Science, 2011; DOI: 10.1126/science.1210557

Courtesy: ScienceDaily

Making Sperm from Stem Cells in a Dish

2011-08-10T05:51:00.000-07:00

Researchers have found a way to turn mouse embryonic stem cells into sperm. This finding, reported in the journal Cell in a special online release on August 4th, opens up new avenues for infertility research and treatment. A Kyoto University team has coaxed mouse embryonic stem cells into sperm precursors, called primordial germ cells (PGCs), and shown that these cells can give rise to healthy sperm.

The researchers say that such in vitro reconstitution of germ cell development represents one of the most fundamental challenges in biology.

When transplanted into mice that were unable to produce sperm normally, the stem cell derived PGCs produced normal-looking sperm, which were then used to successfully fertilize eggs. These fertilized eggs, when transplanted into a recipient mother, produced healthy offspring that grew into fertile male and female adult mice. The same procedure could produce fertile offspring from induced pluripotent stem cells that are often derived from adult skin cells.

"Continued investigations aimed at in vitro reconstitution of germ cell development, including the induction of female PGCLCs and their descendants, will be crucial for a more comprehensive understanding of germ cell biology in general, as well as for the advancement of reproductive technology and medicine," the researchers wrote.

Journal Reference:

Katsuhiko Hayashi, Hiroshi Ohta, Kazuki Kurimoto, Shinya Aramaki, Mitinori Saitou. Reconstitution of the Mouse Germ Cell Specification Pathway in Culture by Pluripotent Stem Cells. Cell, 04 August 2011 DOI: 10.1016/j.cell.2011.06.052

Courtesy: ScienceDaily

Why Plant 'Clones' Aren't Identical

2011-08-08T05:49:00.000-07:00

A new study of plants that are reproduced by 'cloning' has shown why cloned plants are not identical.Scientists have known for some time that 'clonal' (regenerant) organisms are not always identical: their observable characteristics and traits can vary, and this variation can be passed on to the next generation. This is despite the fact that they are derived from genetically identical founder cells.

Now, a team from Oxford University, UK, and King Abdullah University of Science and Technology, Saudi Arabia, believe they have found out why this is the case in plants: the genomes of regenerant plants carry relatively high frequencies of new DNA sequence mutations that were not present in the genome of the donor plant.

The team report their findings in this week's Current Biology.

'Anyone who has ever taken a cutting from a parent plant and then grown a new plant from this tiny piece is actually harnessing the ability such organisms have to regenerate themselves,' said Professor Nicholas Harberd of Oxford University's Department of Plant Sciences, lead author of the paper. 'But sometimes regenerated plants are not identical, even if they come from the same parent. Our work reveals a cause of that visible variation.'

Using DNA sequencing techniques that can decode the complete genome of an organism in one go (so-called 'whole genome sequencing') the researchers analysed 'clones' of the small flowering plant 'thalecress' (Arabidopsis). They found that observable variations in regenerant plants are substantially due to high frequencies of mutations in the DNA sequence of these regenerants, mutations which are not contained in the genome of the parent plant.

'Where these new mutations actually come from is still a mystery,' said Professor Harberd. 'They may arise during the regeneration process itself or during the cell divisions in the donor plant that gave rise to the root cells from which the regenerant plants are created. We are planning further research to find out which of these two processes is responsible for these mutations. What we can say is that Nature has safely been employing what you might call a 'cloning' process in plants for millions of years, and that there must be good evolutionary reasons why these mutations are introduced.'

The new results suggest that variation in clones of plants may have different underlying causes from that of variation in clones of animals -- where it is believed that the effect of environmental factors on how animal genes are expressed is more important and no similar high frequencies of mutations have been observed.

Professor Harberd said: 'Whilst our results highlight that cloned plants and animals are very different they may give us insights into how both bacterial and cancer cells replicate themselves, and how mutations arise during these processes which, ultimately, have an impact on human health.'

Journal Reference:

Caifu Jiang, Aziz Mithani, Xiangchao Gan, Eric J. Belfield, John P. Klingler, Jian-Kang Zhu, Jiannis Ragoussis, Richard Mott, Nicholas P. Harberd. Regenerant Arabidopsis Lineages Display a Distinct Genome-Wide Spectrum of Mutations Conferring Variant Phenotypes. Current Biology, 2011; DOI: 10.1016/j.cub.2011.07.002

Courtesy: ScienceDaily

Increasing Potency of HIV-Battling Proteins

2011-08-05T05:11:00.000-07:00

If one is good, two can sometimes be better. Researchers at the California Institute of Technology (Caltech) have certainly found this to be the case when it comes to a small HIV-fighting protein.

The protein, called cyanovirin-N (CV-N), is produced by a type of blue-green algae and has gained attention for its ability to ward off several diseases caused by viruses, including HIV and influenza. Now Caltech researchers have found that a relatively simple engineering technique can boost the protein's battling prowess.

"By linking two cyanovirins, we were able to make significantly more potent HIV-fighting molecules," says Jennifer Keeffe, a staff scientist at Caltech and first author of a new paper describing the study in the Proceedings of the National Academy of Sciences (PNAS). "One of our linked molecules was 18 times more effective at preventing infection than the naturally occurring, single protein."

The team's linked pairs, or dimers, were able to neutralize all 33 subtypes of HIV that they were tested against. The researchers also found the most successful dimer to be similar or more potent than seven well-studied anti-HIV antibodies that are known to be broadly neutralizing.

CV-N binds well to certain carbohydrates, such as the kind found in high quantities connected to the proteins on the envelope that surrounds the HIV virus. Once attached, CV-N prevents a virus from infecting cells, although the mechanism by which it accomplishes this is not well understood.

What is known is that each CV-N protein has two binding sites where it can bind to a carbohydrate and that both sites are needed to neutralize HIV.

Once the Caltech researchers had linked two CV-Ns together, they wanted to know if the enhanced ability of their engineered dimers to ward off HIV was related to the availability of additional binding sites. So they engineered another version of the dimers -- this time with one or more of the binding sites knocked out -- and tested their ability to neutralize HIV.

It turns out that the dimers' infection-fighting potency increased with each additional binding site -- three sites are better than two, and four are better than three. The advantages seemed to stop at four sites, however; the researchers did not see additional improvements when they linked three or four CV-N molecules together to create molecules with six to eight binding sites.

Although CV-N has a naturally occurring dimeric form, it isn't stable at physiological temperatures, and thus mainly exists in single-copy form. To create dimers that would be stable under such conditions, the researchers covalently bound together two CV-N molecules in a head-to-tail fashion, using flexible polypeptide linkers of varying lengths.

Interestingly, by stabilizing the dimers and locking them into a particular configuration, it seems that the group created proteins with distances between binding sites that are very similar to those between the carbohydrate binding sites in a broadly neutralizing anti-HIV antibody.

"It is possible that we have created a dimer that has its carbohydrate binding sites optimally positioned to block infection," says Stephen Mayo, Bren Professor of Biology and Chemistry, chair of the Division of Biology, and corresponding author of the new paper.

Because it is active against multiple disease-causing viruses, including multiple strains of HIV, CV-N holds unique promise for development as a drug therapy. Other research groups have already started investigating its potential application in prophylactic gels and suppositories.

"Our hope is that those who are working to make prophylactic treatments using cyanovirin will see our results and will use CVN2L0 instead of naturally occurring cyanovirin," Keeffe says. "It has higher potency and may be more protective."

The work was funded by the National Security Science and Engineering Faculty Fellowship program, the Defense Advanced Research Projects Agency Protein Design Processes program, and the Bill and Melinda Gates Foundation through the Grand Challenges in Global Health Initiative.

Journal Reference:

J. R. Keeffe, P. N. P. Gnanapragasam, S. K. Gillespie, J. Yong, P. J. Bjorkman, S. L. Mayo. Designed oligomers of cyanovirin-N show enhanced HIV neutralization. Proceedings of the National Academy of Sciences, 2011; DOI: 10.1073/pnas.1108777108

Courtesy: ScienceDaily

A Cellular Protein Can Reduce the Growth and Spread of Cancer Cells

2011-08-03T05:10:00.000-07:00

According to the Canadian Cancer Society, one in four Canadians will die of cancer. This year alone, the disease will kill an estimated 75,000 people. With incidence rates on the rise, more cancer patients are facing grave prognoses. Fortunately, Lawson Health Research Institute's Dr. John Lewis, Dr. Ann Chambers, and colleagues have found new hope for survival. Their new study released July 28 in Laboratory Investigation shows that maspin, a cellular protein, can reduce the growth and spread of cancer cells -- but only when it is in the nucleus.

Maspin is believed to inhibit the formation, development, and spread of tumors in several aggressive cancers, including breast, ovarian, and head and neck cancers. Yet efforts to use this information to predict how cancer patients will fare have been challenging; the presence of maspin has been linked to both good and bad prognoses. Dr. Lewis, Dr. Chambers, and their team believed that this inconsistency was caused by the location of maspin in the cell, whether in the nucleus or in the cytoplasm, and sought to test this theory.

To assess the effects of maspin on tumor growth and development, they tested two aggressive cancers: a highly invasive head and neck cancer, and a breast cancer known to spread to the lymph nodes and the lungs. The team introduced two forms of maspin into the cancer cells, one that went into the nucleus and one that was blocked from the nucleus. Then they injected the cells into both chicken embryo and mouse models of cancer and asked the simple question: which one slowed the cancer down?

It turned out the answer was simple: when maspin was allowed to get into the nucleus of the cancer cells, the disease's ability to spread was significantly limited. In fact, the incidence of metastasis was lowered from 75% to 40%. When maspin was not established in the nucleus; however, this ability was reversed and cancer cells were far more likely to spread. These findings demonstrate that the location of maspin within the cell significantly influences cancer cells' behavior, determining how aggressive the disease will be and how positive patient outcomes will be.

"The difference is night and day," Dr. Lewis says. "Metastasis is the cause of 90% of cancer deaths. We can now clearly see that maspin is working in the nucleus to dramatically reduce both the extent and the size of distant metastases."

"This study resolves a mystery in which maspin was sometimes linked with poor patient prognosis and sometimes with good patient prognosis," Dr. Chambers explains. "Our new work suggests that when maspin is located in the nucleus it blocks cancer growth and spread. This study may help doctors to understand how aggressive a patient's cancer will be, and may also lead to new targets for drug development."

The study was funded through a Postdoctoral Fellowship Award from the Terry Fox Foundation, the Canadian Breast Cancer Research Alliance, the Canadian Cancer Society Research Institute, and the Canadian Institutes of Health Research.

Journal Reference:

Brigitte Goulet, Wendy Kennette, Amber Ablack, Carl O Postenka, M Nicole Hague, Joe S Mymryk, Alan B Tuck, Vincent Giguère, Ann F Chambers, John D Lewis. Nuclear localization of maspin is essential for its inhibition of tumor growth and metastasis. Laboratory Investigation, 2011; 91 (8): 1181 DOI: 10.1038/labinvest.2011.66

Courtesy: ScienceDaily

Bacterial Resistance to Antibiotics: The More They Resist, the More They Divide

2011-08-01T10:08:00.000-07:00

The number of multiresistant strains of bacteria in hospitals is increasing. Bacteria acquire resistance to antibiotics through mutations in their chromosomes and by incorporating new genes, either from the surrounding environment or from other bacteria. Now, a research team at the Portuguese CBA research (University of Lisbon) and the Instituto Gulbenkian de Ciência has shown that, surprisingly, when both mechanisms of resistance are playing out in the bacterium Escherichia coli (E. coli), its ability to survive and reproduce is increased.

These results are now published in the open-access journal PLoS Genetics.

Usually, the acquisition of new genes, either through the insertion of pieces of DNA -- called plasmids -- or through mutations, comes at a cost to the bacteria, reflected in a reduction in its rate of cell division, for example. Francisco Dionísio, senior author of the paper, describes the process using the following analogy: "If you disassembled your computer and randomly changed connections and pieces, you wouldn't expect it to work better than before."

However, Francisco and his colleagues show that, when a mutation occurs in the chromosome of a bacterium that has already incorporated a resistance-carrying plasmid, the bacteria divide faster in 10% of the mutation-plasmid combinations tested. Similarly, bacteria that first acquire resistance to antibiotics through mutation of their chromosome and then gain further resistance by insertion of plasmids into their DNA show reproduction rate increases in 32% of combinations.

In 2009, the same research groups showed, for the first time, the importance of interactions between random genes in determining antibiotic resistance in bacteria. This latest study takes their initial findings a step further, by demonstrating that this is a general phenomenon, and thus may help to predict how a bacterial population will evolve after receiving a plasmid that confers resistance to a certain antibiotic.

Francisco Dionísio adds: "These results are, at least, unexpected in light of what we previously knew about genetic interactions, and may underlie the mechanism whereby rapid resistance to antibiotics appeared.

Journal Reference:

Rui F. Silva, Sílvia C. M. Mendonça, Luís M. Carvalho, Ana M. Reis, Isabel Gordo, Sandra Trindade, Francisco Dionisio. Pervasive Sign Epistasis between Conjugative Plasmids and Drug-Resistance Chromosomal Mutations. PLoS Genetics, 2011; 7 (7): e1002181 DOI: 10.1371/journal.pgen.1002181

Courtesy: ScienceDaily

Proteins Enable Essential Enzyme to Maintain Its Grip On DNA

2011-07-31T05:08:00.000-07:00

Scientists have identified a family of proteins that close a critical gap in an enzyme that is essential to all life, allowing the enzyme to maintain its grip on DNA and start the activation of genes.

The enzyme, called RNA polymerase, is responsible for setting gene expression in motion in all cells. RNA polymerase wraps itself around the double helix of DNA, using one strand to match nucleotides and make a copy of genetic material.

RNA polymerase cannot fall off of the DNA or stop this process once it starts. If it does, no proteins will be made, and the cell will die.

A team led by Ohio State University researchers demonstrated in a bacterial model that a specific protein binds to two sides of a space in the RNA polymerase molecule at a critical point in its connection to DNA, effectively closing the gap and creating a clamp around the two strands.

In bacteria, two related proteins perform this function. One is NusG, which is required for bacterial growth. Another is RfaH, a virulence factor that gives bacteria their ability to infect and cause disease. Depending on the gene, either NusG or RfaH bridges the critical gap in RNA polymerase in bacteria to maintain the enzyme's attachment to DNA, the researchers found.

"DNA could be imagined as a cylinder, and RNA polymerase encircles it," said Irina Artsimovitch, associate professor of microbiology at Ohio State and senior author of the research. "Before, we had a structural model where these proteins sit at a site where RNA polymerase contacts the DNA. But even if you see something binding, you still have to prove this binding has a functional consequence. We show here that RNA polymerase forms two halves of a clamp, and these proteins bind in the middle and make the clamp complete."

Though understanding this mechanism was the main goal of the study, the findings could contribute to research in antibiotic development. With these proteins known to have a critical role in supporting cell life, they could function as targets for drugs designed to either kill bacteria or take away their ability to cause disease.

The research is published in the July 22, 2011, issue of the journal Molecular Cell.

RNA polymerase is an unusual enzyme because of its processivity, a quality that both requires and enables it to do its extremely long and complicated job perfectly every time, without pausing or making a mistake. Scientists have known that RNA polymerase is processive, but until now didn't know how it remained so. Because RNA polymerase is universally conserved -- meaning it is present and has the same function in all living organisms and has for generations -- these findings in bacteria apply to all other forms of life, including humans.

"RNA polymerase has to make very long messages. In humans, RNA chains can be up to 1 million nucleotides long. If RNA polymerase stops prematurely, it loses the RNA chain and has to start over again. To prevent this futile cycle, some factor has to help RNA polymerase to stay bound to the DNA and RNA," Artsimovitch said. "Our major argument is that RNA polymerase can run longer if it makes a ring around the DNA."

Artsimovitch pursued the roles of RfaH and NusG because these proteins, too, are universally conserved, just as the RNA polymerase enzyme is. In other single-celled and also more complex organisms, they have different names than those found in bacteria, but their roles as transcription factors -- proteins that control gene expression -- are the same. And they are the only family of transcription factors known to be universally conserved.

"It makes sense -- if something is universally conserved, it is likely doing something very important," said Artsimovitch, also an investigator in Ohio State's Center for RNA Biology.

She and colleagues conducted a series of genetic and biochemistry experiments in cells and test tubes, respectively, to define the roles of the RfaH and NusG proteins in Escherichia coli, their model system. Their findings helped confirm recent reports from other researchers studying single-celled Archaea organisms suggesting that the structures of these proteins allow them to close the clamp on RNA polymerase and contribute to its processivity.

There is additional context from Artsimovitch's work, however, that determines which protein fills the gap.

"So we know the mechanism by which these proteins work is similar in all organisms, but you can have different scenarios," said Anastasia Sevostyanova, a postdoctoral researcher in microbiology at Ohio State and first author of the study.

In most cases, a bacterial cell needs to turn on genes just so it can continue to grow. In those cases, NusG would close the gap. However, under circumstances when specialized control of genes is in order -- such as when bacteria infect their human host -- then RfaH, the virulence factor, will fill that gap in the RNA polymerase clamp instead.

The researchers hope to further elucidate how other factors from the same universally conserved family of proteins orchestrate the gene expression programs that control cell life.

This work was supported by grants from the National Institutes of Health.

Study co-authors include Georgiy Belogurov, formerly of Ohio State's Department of Microbiology and now with the University of Turku in Finland; and Rachel Mooney and Robert Landick of the University of Wisconsin-Madison.

Journal Reference:

Anastasia Sevostyanova, Georgiy A. Belogurov, Rachel A. Mooney, Robert Landick, Irina Artsimovitch. The β Subunit Gate Loop Is Required for RNA Polymerase Modification by RfaH and NusG. Molecular Cell, Volume 43, Issue 2, 253-262, 22 July 2011 DOI: 10.1016/j.molcel.2011.05.026

Courtesy: ScienceDaily

Anti-Malaria Drug Chloroquine Finding May Lead to Treatments for Arthritis, Cancer and Other Diseases

2011-07-29T05:07:00.000-07:00

In a study published recently in the journal Science Signaling, Van Andel Research Institute (VARI) scientists demonstrate on the molecular level how the anti-malaria drug chloroquine represses inflammation, which may provide a blueprint for new strategies for treating inflammation and a multitude of autoimmune diseases such as arthritis, multiple sclerosis, and certain cancers.

Chloroquine is a widely used anti-malaria drug that inhibits the growth of parasites. For decades, chloroquine and its derivative amodiaquine have also been used as anti-inflammation drugs to treat diseases such as rheumatoid arthritis, though the exact mechanism of how chloroquine affects the immune system has remained unclear.

By providing an understanding of these basic functions, researchers may now have the necessary tools to develop improved treatments for a myriad of common autoimmune disorders.

"The implications of this study are significant," said Henry F. McFarland, Ph.D., former Chief of the Neuroimmunology Branch of the National Institute of Neurological Disorders and Stroke (NINDS). "These results provide a mechanistic basis for therapeutic strategies for treating inflammation and autoimmune diseases and should provide exciting new approaches which can be tested in clinical trials."

Autoimmune diseases arise when the body's immune system mistakes otherwise healthy cells, tissues, and organs for pathogens and attacks them. These diseases can afflict any part of the body, but one symptom common to most autoimmune diseases is that of inflammation.

The National Institutes of Health (NIH) lists more than 80 common autoimmune diseases including asthma, Crohn's disease, Guillain-Barré syndrome, multiple sclerosis, myasthenia gravis, psoriasis, rheumatoid arthritis, and some types of cancers among many others.

Dr. H. Eric Xu, Head of the VARI Center for Structural Biology and Drug Discovery, and his colleagues showed that chloroquine represses inflammation through synergistic activation of glucocorticoid signaling. Glucocorticoids are a class of steroid hormones that bind to the glucocorticoid receptor present in almost every vertebrate animal cell. They are among the most potent and effective agents for treating inflammation and autoimmune diseases.

Synthetic glucocorticoids are used for treating asthma, allergies, and rheumatoid arthritis. Since glucocorticoids also interfere with some of the abnormal mechanisms in cancer cells, they are also used in high doses to treat certain cancers such as leukemia and lymphoma. However, at therapeutic dosages, glucocorticoids can cause a range of debilitating side effects including diabetes, osteoporosis, skin atrophy, and growth retardation.

"The discovery and development of novel uses of glucocorticoids that retain their beneficial therapeutic effects but reduce undesired adverse side effects remains a major medical challenge," said VARI Research Scientist Yuanzheng He, Ph.D., lead author of the study.

The VARI research revealed an unexpected regulation of glucocorticoid signaling by lysosomal functioning. Lysosomes are organelles found in animal cells that use enzymes to break down waste materials and cellular debris.

Researchers found that they could mimic the effect of chloroquine by inhibiting lysosomes in the cell. They believe that the development of new therapies for treating inflammation and autoimmune disease will involve strategies that combine both glucocorticoid and lysosomal inhibitors.

"We have known for some time that both steroids and lysosomes affect the immune system, but we didn't know that they worked together," said VARI President and Research Director Jeffrey Trent, Ph.D. "Researchers now have a clear path forward for undertaking projects to develop glucocorticoid and lysosomal inhibitors, and to improve the efficacy and potency of chloroquine as a therapeutic agent."

Journal Reference:

Y. He, Y. Xu, C. Zhang, X. Gao, K. J. Dykema, K. R. Martin, J. Ke, E. A. Hudson, S. K. Khoo, J. H. Resau, A. S. Alberts, J. P. MacKeigan, K. A. Furge, H. E. Xu. Identification of a Lysosomal Pathway That Modulates Glucocorticoid Signaling and the Inflammatory Response. Science Signaling, 2011; 4 (180): ra44 DOI: 10.1126/scisignal.2001450

Courtesy: ScienceDaily

Researchers Identify Seventh and Eighth Bases of DNA

2011-07-27T05:04:00.000-07:00

For decades, scientists have known that DNA consists of four basic units -- adenine, guanine, thymine and cytosine. Those four bases have been taught in science textbooks and have formed the basis of the growing knowledge regarding how genes code for life. Yet in recent history, scientists have expanded that list from four to six.

Now, with a finding published online in the July 21, 2011, issue of the journal Science, researchers from the UNC School of Medicine have discovered the seventh and eighth bases of DNA.

These last two bases -- called 5-formylcytosine and 5 carboxylcytosine -- are actually versions of cytosine that have been modified by Tet proteins, molecular entities thought to play a role in DNA demethylation and stem cell reprogramming.

Thus, the discovery could advance stem cell research by giving a glimpse into the DNA changes -- such as the removal of chemical groups through demethylation -- that could reprogram adult cells to make them act like stem cells.

"Before we can grasp the magnitude of this discovery, we have to figure out the function of these new bases," said senior study author Yi Zhang, Ph.D., Kenan Distinguished Professor of biochemistry and biophysics at UNC and an Investigator of the Howard Hughes Medical Institute. "Because these bases represent an intermediate state in the demethylation process, they could be important for cell fate reprogramming and cancer, both of which involve DNA demethylation."

Much is known about the "fifth base," 5-methylcytosine, which arises when a chemical tag or methyl group is tacked onto a cytosine. This methylation is associated with gene silencing, as it causes the DNA's double helix to fold even tighter upon itself.

Last year, Zhang's group reported that Tet proteins can convert 5 methylC (the fifth base) to 5 hydroxymethylC (the sixth base) in the first of a four step reaction leading back to bare-boned cytosine. But try as they might, the researchers could not continue the reaction on to the seventh and eighth bases, called 5 formylC and 5 carboxyC.

The problem, they eventually found, was not that Tet wasn't taking that second and third step, it was that their experimental assay wasn't sensitive enough to detect it. Once they realized the limitations of the assay, they redesigned it and were in fact able to detect the two newest bases of DNA. The researchers then examined embryonic stem cells as well as mouse organs and found that both bases can be detected in genomic DNA.

The finding could have important implications for stem cell research, as it could provide researchers with new tools to erase previous methylation patterns to reprogram adult cells.

It could also inform cancer research, as it could give scientists the opportunity to reactivate tumor suppressor genes that had been silenced by DNA methylation.

The research was funded by the Howard Hughes Medical Institute and the National Institutes of Health.

Study co-authors from UNC include Shinsuke Ito, Ph.D.; Li Shen, Ph.D.; Susan C. Wu, Ph.D.; Leonard B. Collins and James A. Swenberg, Ph.D.

Journal Reference:

Shinsuke Ito, Li Shen, Qing Dai, Susan C. Wu, Leonard B. Collins, James A. Swenberg, Chuan He, Yi Zhang. Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine. Science, 2011; DOI: 10.1126/science.1210597

Courtesy: ScienceDaily

Astronomers Discover Largest and Most Distant Reservoir of Water Yet

2011-07-25T05:02:00.000-07:00

Water really is everywhere. Two teams of astronomers, each led by scientists at the California Institute of Technology (Caltech), have discovered the largest and farthest reservoir of water ever detected in the universe. Looking from a distance of 30 billion trillion miles away into a quasar -- one of the brightest and most violent objects in the cosmos -- the researchers have found a mass of water vapor that's at least 140 trillion times that of all the water in the world's oceans combined, and 100,000 times more massive than the sun.

Because the quasar is so far away, its light has taken 12 billion years to reach Earth. The observations therefore reveal a time when the universe was just 1.6 billion years old. "The environment around this quasar is unique in that it's producing this huge mass of water," says Matt Bradford, a scientist at NASA's Jet Propulsion Laboratory (JPL), and a visiting associate at Caltech. "It's another demonstration that water is pervasive throughout the universe, even at the very earliest times." Bradford leads one of two international teams of astronomers that have described their quasar findings in separate papers that have been accepted for publication in the Astrophysical Journal Letters.

A quasar is powered by an enormous black hole that is steadily consuming a surrounding disk of gas and dust; as it eats, the quasar spews out huge amounts of energy. Both groups of astronomers studied a particular quasar called APM 08279+5255, which harbors a black hole 20 billion times more massive than the sun and produces as much energy as a thousand trillion suns.

Since astronomers expected water vapor to be present even in the early universe, the discovery of water is not itself a surprise, Bradford says. There's water vapor in the Milky Way, although the total amount is 4,000 times less massive than in the quasar, as most of the Milky Way's water is frozen in the form of ice.

Nevertheless, water vapor is an important trace gas that reveals the nature of the quasar. In this particular quasar, the water vapor is distributed around the black hole in a gaseous region spanning hundreds of light-years (a light-year is about six trillion miles), and its presence indicates that the gas is unusually warm and dense by astronomical standards. Although the gas is a chilly -53 degrees Celsius (-63 degrees Fahrenheit) and is 300 trillion times less dense than Earth's atmosphere, it's still five times hotter and 10 to 100 times denser than what's typical in galaxies like the Milky Way.

The water vapor is just one of many kinds of gas that surround the quasar, and its presence indicates that the quasar is bathing the gas in both X-rays and infrared radiation. The interaction between the radiation and water vapor reveals properties of the gas and how the quasar influences it. For example, analyzing the water vapor shows how the radiation heats the rest of the gas. Furthermore, measurements of the water vapor and of other molecules, such as carbon monoxide, suggest that there is enough gas to feed the black hole until it grows to about six times its size. Whether this will happen is not clear, the astronomers say, since some of the gas may end up condensing into stars or may be ejected from the quasar.

Bradford's team made their observations starting in 2008, using an instrument called Z-Spec at the Caltech Submillimeter Observatory (CSO), a 10-meter telescope near the summit of Mauna Kea in Hawaii. Z-Spec is an extremely sensitive spectrograph, requiring temperatures cooled to within 0.06 degrees Celsius above absolute zero. The instrument measures light in a region of the electromagnetic spectrum called the millimeter band, which lies between infrared and microwave wavelengths. The researchers' discovery of water was possible only because Z-Spec's spectral coverage is 10 times larger than that of previous spectrometers operating at these wavelengths. The astronomers made follow-up observations with the Combined Array for Research in Millimeter-Wave Astronomy (CARMA), an array of radio dishes in the Inyo Mountains of Southern California.

This discovery highlights the benefits of observing in the millimeter and submillimeter wavelengths, the astronomers say. The field has developed rapidly over the last two to three decades, and to reach the full potential of this line of research, the astronomers -- including the study authors -- are now designing CCAT, a 25-meter telescope to be built in the Atacama Desert in Chile. CCAT will allow astronomers to discover some of the earliest galaxies in the universe. By measuring the presence of water and other important trace gases, astronomers can study the composition of these primordial galaxies.

The second group, led by Dariusz Lis, senior research associate in physics at Caltech and deputy director of the CSO, used the Plateau de Bure Interferometer in the French Alps to find water. In 2010, Lis's team was looking for traces of hydrogen fluoride in the spectrum of APM 08279+5255, but serendipitously detected a signal in the quasar's spectrum that indicated the presence of water. The signal was at a frequency corresponding to radiation that is emitted when water transitions from a higher energy state to a lower one. While Lis's team found just one signal at a single frequency, the wide bandwidth of Z-Spec enabled Bradford and his colleagues to discover water emission at many frequencies. These multiple water transitions allowed Bradford's team to determine the physical characteristics of the quasar's gas and the water's mass.

The other authors on Lis's paper, "Discovery of water vapor in the high-redshift quasar APM 08279+5255 at Z=3.91," are Tom Phillips, Caltech's John D. MacArthur Professor of Physics and director of the CSO; David Neufeld of Johns Hopkins University; Maryvonne Gerin of the Paris Observatory and the French National Center for Scientific Research; and Roberto Neri of the Institute of Millimeter Radio Astronomy in France. Funding was provided by the National Science Foundation (NSF).

The authors on Bradford's paper, "The water vapor spectrum of APM 08279+5255: X-ray heating and infrared pumping over hundreds of parsecs," include Caltech's Hien Nguyen, a visiting associate and lecturer in physics; Jamie Bock, senior faculty associate in physics and scientist at JPL; and Jonas Zmuidzinas, the Merle Kingsley Professor of Physics and chief technologist at JPL. The other authors are Alberto Bolatto of the University of Maryland, College Park; Philip Maloney, Jason Glenn, and Julia Kamenetzky of the University of Colorado, Boulder; James Aguirre, Roxana Lupu, and Kimberly Scott of the University of Pennsylvania; Hideo Matsuhara of the Institute of Space and Astronautical Science in Japan; Eric Murphy of the Carnegie Institution for Science; and Bret Naylor of JPL.

Funding for Z-Spec was provided by the NSF, NASA, the Research Corporation, and partner institutions. The CSO is operated by Caltech under contract from the NSF. CARMA was built and is operated by Caltech, UC Berkeley, the University of Maryland, College Park, the University of Illinois at Urbana-Champaign, and the University of Chicago. CARMA is funded by a combination of state and private sources, as well as the NSF and its University Radio Observatories program.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by California Institute of Technology. The original article was written by Marcus Woo.

Courtesy: ScienceDaily

An Unexpected Actor in Vaccination: Our Own DNA

2011-07-22T05:59:00.000-07:00

The teams of Doctor Christophe Desmet and Professor Fabrice Bureau, of the Laboratory of Cellular and Molecular Physiology within the University of Liège's GIGA-Research centre, and of Professor Ken Ishii at the University of Osaka in Japan have just discovered an unexpected mode of action for the vaccine adjuvant alum. When a vaccine containing alum is injected, contact with alum apparently pushes certain cells of the body to release their own DNA.

The presence of this DNA outside the cells, a place where it is not to be found in normal conditions, thus acts as a stimulant of the immune system and strongly boosts the response to the vaccine.

Alum, a salt of aluminium, is currently by far the most widely used vaccine adjuvant. Developed in the middle of the 20^th century, alum has largely demonstrated its effectiveness and safety of use. That it is why it is found in numerous vaccines. Tens of millions of doses of alum are thus administered each year, and each person in our Western societies has probably received alum at least once in their life. Nevertheless, alum was developed in a relatively empirical manner; the way it helps the immune system to respond to vaccines had not been properly understood up until now.

The discovery by the Belgian and Japanese researchers thus enables a better understanding of the way current vaccines work, and should help in the creation of new adjuvants for future vaccines. The response mechanisms to DNA brought to light in this study could in particular eventually allow the development of new adjuvants with extremely targeted and effective activity.

The researchers are this week publishing their results in the journal Nature Medicine.

Journal Reference:

Thomas Marichal, Keiichi Ohata, Denis Bedoret, Claire Mesnil, Catherine Sabatel, Kouji Kobiyama, Pierre Lekeux, Cevayir Coban, Shizuo Akira, Ken J Ishii, Fabrice Bureau, Christophe J Desmet. DNA released from dying host cells mediates aluminum adjuvant activity. Nature Medicine, 2011; DOI: 10.1038/nm.2403

Courtesy: ScienceDaily

Genetic Mutation Linked to Parkinson's Disease

2011-07-20T06:58:00.000-07:00

Researchers have discovered a new gene mutation they say causes Parkinson's disease. The mutation was identified in a large Swiss family with Parkinson's disease, using advanced DNA sequencing technology.

The study, published July 15 in the American Journal of Human Genetics, was led by neuroscientists at the Mayo Clinic campus in Florida and included collaborators from the U.S., Canada, Europe, United Kingdom, Asia and the Middle East.

"This finding provides an exciting new direction for Parkinson's disease research," says co-author Zbigniew Wszolek, M.D., a Mayo Clinic neuroscientist. "Every new gene we discover for Parkinson's disease opens up new ways to understand this complex disease, as well as potential ways of clinically managing it."

The team found that mutations in VPS35, a protein responsible for recycling other proteins within cells, caused Parkinson's disease in the Swiss family. Mutated VPS35 may impair the ability of a cell to recycle proteins as needed, which could lead to the kind of errant buildup of protein seen in some Parkinson's disease brains and in other diseases like Alzheimer's disease says co-author Owen Ross, Ph.D., a neuroscientist at Mayo Clinic in Florida. "In fact, expression of this gene has been shown to be reduced in Alzheimer's disease, and faulty recycling of proteins within cells has been linked to other neurodegenerative diseases," he says.

So far, mutations in six genes have been linked to familial forms of Parkinson's disease, with many mutations identified as a direct result of Mayo Clinic's collaborative research efforts. Dr. Wszolek has built a worldwide network of Parkinson's disease investigators, many of whom have conducted research at Mayo Clinic. The study's first author, Carles Vilariño-Güell, Ph.D., and the senior investigator, Matthew Farrer, Ph.D., worked on this study while at Mayo Clinic in 2010; they have since moved to the University of British Columbia in Vancouver. The joint first author, neurologist Christian Wilder, M.D., first identified the Swiss Parkinson's disease family and continued to study them while he was a research fellow at Mayo Clinic; he has now returned to Centre Hospitalier Universitaire Vaudois in Lausanne, Switzerland.

Investigators used a new genetic sequencing technique to find the VPS35 mutation, according to Dr. Ross. They used 'exome' sequencing to look for shared variations in a pair of first cousins within a large Swiss family affected by Parkinson's disease. Collectively, exons, which provide the genetic blueprint used in the production of proteins, make up only 1 percent of the entire genome and so it is much easier to look for novel variations, causing changes in the protein sequence, that would represent possible disease-causing mutations, he says. "Cousins only share about 10 percent of their genome, whereas parents and children or siblings share much more. This narrowed the field of novel variations for us," says Dr. Wszolek, with VPS35 emerging as the latest Parkinson's disease gene.

"There is much more we need to know about this gene," Dr. Ross says. "Although it appears to be a rare cause of Parkinson's disease, it seems to be very important from a mechanistic viewpoint for this disease and possibly other neurodegenerative disorders."

The study was funded by grants from the National Institutes of Health, the Swiss Parkinson's Disease Foundation, the Michael J. Fox Foundation, a gift from Carl Edward Bolch, Jr., and Susan Bass Bolch. The sequencing work was financed by the Parkinson's Disease Foundation. This work and Dr. Vilariño-Güell received the AD/Parkinson's Disease Conference Award donated by Ms. Evelyn Greenberg in memory of Prof. Moshe Greenberg.

Journal Reference:

Carles Vilariño-Güell, Christian Wider, Owen A. Ross, Justus C. Dachsel, Jennifer M. Kachergus, Sarah J. Lincoln, Alexandra I. Soto-Ortolaza, Stephanie A. Cobb, Greggory J. Wilhoite, Justin A. Bacon, Bahareh Behrouz, Heather L. Melrose, Emna Hentati, Andreas Puschmann, Daniel M. Evans, Elizabeth Conibear, Wyeth W. Wasserman, Jan O. Aasly, Pierre R. Burkhard, Ruth Djaldetti, et al. VPS35 Mutations in Parkinson Disease. American Journal of Human Genetics, Volume 89, Issue 1, 15 July 2011, Pages 162-167 DOI: 10.1016/j.ajhg.2011.06.001

Courtesy: ScienceDaily

Stem Cells: Nearing Goal of Using Patient's Own Cells to Make Stem Cells to Replace Lost or Diseased Tissue

2011-07-18T06:56:00.000-07:00

Scientists at the Salk Institute for Biological Studies have developed an improved technique for generating large numbers of blood cells from a patient's own cells. The new technique will be immediately useful in further stem cell studies, and when perfected, could be used in stem cell therapies for a wide variety of conditions including cancers and immune ailments.

"There are further improvements that we need to make, but this takes us a significant step closer to the ultimate goal, which is to be able to take ordinary cells from a patient, induce them to become stem cells, and then use those stem cells to rebuild lost or diseased tissues, for example the patient's bone marrow," says Inder M. Verma, PhD, Irwin and Joan Jacobs Chair in Exemplary Life Science and American Cancer Society Professor of Molecular Biology at the Salk Institute Laboratory of Genetics. Verma is senior author of the report, which is published in the July edition of the journal Stem Cells.

Stem cell researchers have been racing towards this goal since 2006, when techniques for turning ordinary skin cells into induced pluripotential stem cells (iPSCs) were first reported. In principle, iPSCs mimic the embryonic stem cells (ESCs) from which organisms develop. Researchers now want to find the precise mixes and sequences of chemical compounds needed to coax iPSCs to mature into the tissue-specific stem cells of their choice. The latter are self-renewing, and can be transplanted into the body to produce the 'progenitor' cells that multiply locally and produce mature tissue cells.

However, researchers don't know yet how to induce iPSCs to become tissue-specific stem cells or mature tissue cells with high efficiency. "We've been producing these cells in quantities that are too low to enable them to be studied easily, much less used for therapies," says Aaron Parker, PhD, a former graduate student and now a postdoctoral researcher in Verma's lab. Parker is a co-lead-author of the paper, with Niels-Bjarne Woods, PhD, who was a postdoctoral researcher in the Verma lab at the outset of the project, and is now an assistant professor at Lund University in Sweden.

Like many other stem cell research laboratories, the Verma lab has been trying to find more efficient ways to turn iPSCs into blood-forming 'hematopoietic' stem cells (HSCs). These may be more valuable medically than any other tissue-specific stem cell, because they can supply not only oxygen-carrying red blood cells but also all the white blood cells of the immune system. "There would be an almost unlimited number of usages for true HSCs," says Verma.

For the present study, the research team sought to do a better job of mimicking the changing conditions that naturally direct ESCs to become HSCs in the womb. "We took seven lines of human ESCs and iPSCs, and experimented with different combinations and sequences of growth factors and other chemical compounds that are known to be present as ESCs move to the HSC state in a developing human," says Parker.

Applying cocktails of these factors, Parker and Woods and their colleagues induced the iPSCs and ESCs to form colonies of cells that bore the distinctive molecular markers of blood cells. With their best such cocktail they were able to detect blood-specific markers on 84% of their cells after three weeks. "That's a big jump in efficiency from what we saw in the field just a few years ago," says Parker.

The technique still has room for improvement. The researchers detected progenitor cells and mature cells from only one category or lineage: myeloid cells, which include red blood cells and primitive immune cells such as macrophages. "We didn't see any cells from the lymphoid lineage, meaning T-cells and B-cells," Parker says.

Another drawback was that the blood cell population they produced from ESCs and iPSCs contained short-lived progenitors and mature blood cells but no indefinitely renewing, transplantable HSCs. Their cocktail, they believed, either pushed the cells past the HSC state to the progenitor state too quickly, or made the maturing cells skip the HSC state entirely.

From this and other labs' results, the team hypothesized the existence of an intermediate, pre-hematopoietic type of stem cell, produced by ESCs and iPSCs and in turn producing HSCs. "We know that HSCs appear in a particular region of mammals during embryonic development, and our idea is that these pre-hematopoietic stem cells are there and are somehow made to mature into HSCs," says Parker. "So our lab is now going to focus on finding the precise maturation signals provided by that embryonic region to produce these true, transplantable HSCs."

Once that is done, researchers will need to make a number of further refinements to improve the safety of HSCs intended for human patients. "But we're now tantalizingly close to our ultimate goal," says Verma.

The other authors who contributed to the work were Roksana Moraghebi, of Lund University's Stem Cell Center; Margaret K. Lutz, Amy L. Firth, Kristen J. Brennand, W. Travis Berggren and Fred H. Gage of the Salk Institute Laboratory for Genetics; Juan Carlos Izpisúa Belmonte of the Salk Institute Gene Expression Laboratory; and Angel Raya of the Center of Regenerative Medicine in Barcelona, Spain.

Funding for this research was provided by the National Institutes for Health, the California Institute for Regenerative Medicine, the Leducq Foundation, the Merieux Foundation, the Ellison Medical Foundation, Ipsen/Biomeasure, Sanofi Aventis, the Prostate Cancer Foundation, the H.N. and Frances C. Berger Foundation, The Royal Physiographic Society of Sweden, the Lund University Medical Faculty, and the Lars Hierta Memorial Foundation, and the H.A. and Mary K. Chapman Charitable Trust.

Journal Reference:

Niels-Bjarne Woods, Aaron S. Parker, Roksana Moraghebi, Margaret K. Lutz, Amy L. Firth, Kristen J. Brennand, W.Travis Berggren, Angel Raya, Juan Carlos Izpisúa Belmonte, Fred H. Gage, Inder M. Verma. Brief Report: Efficient Generation of Hematopoietic Precursors and Progenitors from Human Pluripotent Stem Cell Lines. Stem Cells, 2011; 29 (7): 1158 DOI: 10.1002/stem.657

Courtesy: ScienceDaily

Targeted Agent Addition to Herceptin Has Positive Effect On Metastatic HER-2 Breast Cancer, Study Finds

2011-07-15T05:11:00.000-07:00

Adding Afinitor® to Herceptin®, the main treatment for HER2-positive metastatic breast cancer, helps some women with disease that has been resistant to previous Herceptin-based therapies, according to a study led by researchers at The University of Texas MD Anderson Cancer Center and published in the Journal of Clinical Oncology.

The Phase I/II study demonstrated that a combination of the targeted therapies, which play different roles in cancer, offers a personalized therapy approach that can help some patients with advanced disease. Thirty-four percent of the women in the study benefited from the regimen.

About one in four breast cancer tumors is HER2-positive, which means it makes too much of the protein HER2, a human epidermal growth factor. This type of breast cancer often is more aggressive and difficult to treat.

"Herceptin (trastuzumab) works well for many patients, but about 30 percent of those with advanced disease do not respond to the drug, even combined with chemotherapy," said PK Morrow, M.D., assistant professor in the Department of Breast Medical Oncology and lead co-author of the study. "Even if metastatic HER2-positive breast cancer initially responds to Herceptin, the disease usually eventually progresses on standard Herceptin-based therapy."

Resistance to Herceptin has been linked to activation of the PI3K/mTOR cancer pathway. PTEN, a protein that acts as a tumor suppressor, can counteract P13K. However in the absence of PTEN, the mTOR cancer pathway may be activated. Afinitor (everolimus) overcomes resistance by inhibiting the mTOR pathway.

Bench-to-Bedside Research

"Combining these two agents offers patients with metastatic HER2-positive breast cancer a chemotherapy-free option," Morrow said. "Despite the fact that most of these women had received multiple chemotherapy regimens, this regimen offered additional clinical benefit and less toxicity for many of patients."

Built on preclinical studies at MD Anderson that showed mTOR inhibition makes mice with HER2-positive and PTEN-deficient breast tumors more sensitive to Herceptin, the study was part of MD Anderson's and Dana- Farber Cancer Institute's breast cancer SPORE (Specialized Program of Research Excellence) grant from the National Cancer Institute.

"This study is important to breast cancer treatment, and it represents a crucial step toward personalized cancer therapy by increasing our understanding of cancer pathways," said Francisco J. Esteva, M.D., Ph.D., professor in MD Anderson's Department of Breast Medical Oncology and corresponding author. "It's the culmination of more than five years, starting with basic research and animal studies, and an excellent example of bench-to-bedside research."

Approach Shows Promise

Presented in part at the 2010 annual meeting of the American Society of Clinical Oncology, the study stemmed from two concurrent trials at MD Anderson and Dana-Farber. Forty-seven women with HER2-positive metastatic breast cancer that had progressed on Herceptin-based therapy were given Herceptin every three weeks and Afinitor daily. Almost half the women had previously received two or more chemotherapy regimens.

The combination therapy resulted in partial responses in 15 percent of patients and persistent stable disease in 19 percent of patients, resulting in a clinical benefit rate of 34 percent. Median progression-free survival was four months. Treatment was well tolerated, and side effects, which included fatigue, infection and mouth sores, were manageable.

Patients with PTEN loss had lower rates of overall survival, but progression-free survival was not affected, suggesting that PTEN loss enables activation of pathways that promote cancer growth. However, PIK3 mutations did not significantly affect progression-free survival or overall survival. The finding that progression-free survival was not significantly affected by PTEN loss or PIK3 mutation suggests that the addition of Afinitor may slow tumor progression through inhibition of mTOR.

MD Anderson researchers are recruiting HER-2 positive breast cancer patients for BOLERO-3, a randomized multi-center trial of a regimen including the two agents and a chemotherapy drug (vinorelbine).

Researchers for this study included Joe Ensor, Ph.D., Daniel Booser, M.D., Julia Moore, R.N., B.S.N., Peter Flores, Yan Xiong, Ph.D., Siyuan Zhang, M.D., Ph.D., Aysegul Sahin, M.D., Rodolfo Nuñez, M.D., Gabriel Hortobagyi, M.D., and Dihua Yu, M.D., Ph.D. at MD Anderson; Gerburg Wulf, M.D. and Jeanna Coviello at Beth Israel Deaconess Medical Center; Ian Krop, M.D., Ph.D. and Eric Winer, M.D. at Dana-Farber Cancer Institute; and David Kindelberger, M.D. at Brigham and Women's Hospital.

In addition to MD Anderson's and the Dana-Farber's SPORE grant from the National Cancer Institute, the research was supported by Novartis Pharmaceuticals and the AVON Foundation.

Journal Reference:

P. Khanh Morrow, G. M. Wulf, J. Ensor, D. J. Booser, J. A. Moore, P. R. Flores, Y. Xiong, S. Zhang, I. E. Krop, E. P. Winer, D. W. Kindelberger, J. Coviello, A. A. Sahin, R. Nunez, G. N. Hortobagyi, D. Yu, F. J. Esteva. Phase I/II Study of Trastuzumab in Combination With Everolimus (RAD001) in Patients With HER2-Overexpressing Metastatic Breast Cancer Who Progressed on Trastuzumab-Based Therapy. Journal of Clinical Oncology, 2011; DOI: 10.1200/JCO.2010.32.2321

Courtesy: ScienceDaily

First Whole-Genome Lung Cancer Study: Review of Lung Tumor from a Patient Who Never Smoked

2011-07-13T05:10:00.000-07:00

A first-of-its-kind study of a patient with lung cancer who never smoked is being presented by TGen (The Translational Genomics Research Institute) and the Virginia G. Piper Cancer Center at Scottsdale Healthcare at the 14th World Conference on Lung Cancer, July 3-7 in Amsterdam.

Researchers for the first time sequenced the entire DNA and RNA of a patient with metastatic adenocarcinoma of the lung, said Dr. Glen Weiss, the first author of the study, which will be published in a special supplement of the Journal of Thoracic Oncology. Dr. Weiss also is Director of Thoracic Oncology at Virginia G. Piper Cancer Center Clinical Trials, a partnership between TGen and Scottsdale Healthcare that treats cancer patients with promising new drugs.

The patient is a 61-year-old woman who never smoked whose lung cancer had entered her bloodstream and spread to other parts of her body. She had been treated with several types of chemotherapy.

The study, Advanced Never Smoker Adenocarcinoma of the Lung: Report of paired normal and tumor whole genome and transcriptome sequencing, used Whole Genome Sequencing (WGS), also called Next-Generation Sequencing (NGS), to look at all 3 billion chemical bases of the patient's normal, as well as the patient's tumor, DNA.

The study went further by examining the normal and tumor RNA for whole transcriptome sequencing, which can reveal the possible defects in how proteins are synthesized. This provided an even more intricate view of the tumors biological make up and what might have led to her cancer.

"Evidently, this is very exciting. Next-Generation Sequencing now offers us the ability to survey the global landscape of cancer," said Dr. John Carpten, Director of TGen's Integrated Cancer Genomics Division and senior author of the presentation.

The results of the patient's sequencing were discussed with her treating oncologist and may be used along with other information to help decide the best course of future treatment.

A review of well-characterized cancer-related genes found that a mutation resided in the TP53 gene, a mutation in the tumor (one base change in the genetic code), and that the mutation was always present in both the DNA and RNA. Such a mutation can halt the creation of tumor suppressor genes and result in the generation of a tumor. Interestingly, the cancer specimen showed no loss of heterozygosity (LOH), in which one side of the DNA's chromosome becomes inactive because of a mutation.

"This observation highlights the complexity of cancer and how different genetic mechanisms can alter a gene. This novel finding would not have been readily determined without the combined DNA and RNA integration approach," said Dr. David Craig, Associate Director of TGen's Neurogenomics Division, and also a senior author of the presentation.

Dr. Weiss said these investigative techniques will be used more often to pinpoint the origins of disease.

"In the future, with improved infrastructure and decreased costs, we anticipate that using NGS techniques will become more commonplace," Dr. Weiss said. "NGS has the potential to identify unique tumor aberrations at an unprecedented depth."

The conference is sponsored by the International Association for the Study of Lung Cancer (IASLC), which hosts a meeting every two years.

The study was funded, in part, by the National Foundation for Cancer Research.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by The Translational Genomics Research Institute, via EurekAlert!, a service of AAAS.

Courtesy: ScienceDaily

Discovery of Natural Antibody Brings a Universal Flu Vaccine a Step Closer

2011-07-11T05:07:00.000-07:00

Annually changing flu vaccines with their hit-and-miss effectiveness may soon give way to a single, near-universal flu vaccine, according to a new report from scientists at The Scripps Research Institute and the Dutch biopharmaceutical company Crucell. They describe an antibody that, in animal tests, can prevent or cure infections with a broad variety of influenza viruses, including seasonal and potentially pandemic strains.

The finding, published in the journal Science Express on July 7, 2011, shows the influenza subtypes neutralized with the new antibody include H3N2, strains of which killed an estimated one million people in Asia in the late 1960s.

"Together this antibody and the one we reported in 2009 have the potential to protect people against most influenza viruses," said Ian Wilson, who is the Hansen Professor of Structural Biology and a member of the Skaggs Institute for Chemical Biology at Scripps Research, as well as senior author of the new paper with Crucell's chief scientific officer Jaap Goudsmit.

Tackling a Major Shortcoming

Wilson's laboratory has been working with Crucell scientists since 2008 to help them overcome the major shortcoming of current influenza vaccines: They work only against the narrow set of flu strains that the vaccine makers predict will dominate in a given year, so their effectiveness is temporary. In addition, current influenza vaccines provide little or no protection against unforeseen strains.

These shortcomings reflect a basic flu-virus defense mechanism. The viruses come packaged in spherical or filamentous envelopes that are studded with mushroom-shaped hemagglutinin (HA) proteins, whose more accessible outer structures effectively serve as decoys for a normal antibody response. "The outer loops on the HA head seem to draw most of the antibodies, but in a given strain these loops can mutate to evade an antibody response within months," said Wilson. Antiviral drugs aimed at these and other viral targets also lose effectiveness as flu virus populations evolve.

"The major goal of this research has been to find and attack relatively unvarying and functionally important structures on flu viruses," said Damian Ekiert, a graduate student in the Scripps Research Kellogg School of Science and Technology who is working in the Wilson laboratory. Ekiert and Crucell's Vice President for Antibody Discovery Robert H. E. Friesen are co-first authors of the Science Express report.

By sifting through the blood of people who had been immunized with flu vaccines, Goudsmit and his colleagues several years ago discovered an antibody that bound to one such vulnerable structure. In mice, an injection of the antibody, CR6261, could prevent or cure an otherwise-lethal infection by about half of flu viruses, including H1 viruses such as H1N1, strains of which caused deadly global pandemics in 1918 and 2009.

The Crucell researchers approached Wilson, whose structural biology lab has world-class expertise at characterizing antibodies and their viral targets. Ekiert, Wilson, and their colleagues soon determined the three-dimensional molecular structure of CR6261 and its binding site on HA, as they reported in Science in 2009. That binding site, or "epitope," turned out to be on HA's lower, less-accessible stalk portion. The binding of CR6261 to that region apparently interferes with flu viruses' ability to deliver their genetic material into host cells and start a new infection. That antibody is about to begin tests in human volunteers.

The Missing Piece

Crucell researchers subsequently searched for an antibody that could neutralize some or all of the remaining flu viruses unaffected by CR6261, and recently found one, CR8020, that fits this description. As the team now reports in the Science Express paper, CR8020 powerfully neutralizes a range of human-affecting flu viruses in lab-dish tests and in mice. The affected viruses include H3 and H7, two subtypes of great concern for human health that have already caused a pandemic (H3) or sporadic human infections (H7).

As with the CR6261 project, Ekiert and colleagues were able to grow crystals of the new antibody bound to an HA protein from a deadly strain of H3N2, and to use X-ray crystallography techniques to determine the antibody's structure and its precise epitope on the viral HA protein.

"It's even lower on the HA stalk than the CR6261 epitope; in fact it's closer to the viral envelope than any other influenza antibody epitope we've ever seen," said Ekiert.

Crucell is about to begin initial clinical trials of CR6261 in human volunteers, and the company expects eventually to begin similar trials of CR8020. If those trials succeed, aside from a vaccine the two antibodies could be combined and used in a "passive immunotherapy" approach. "This would mainly be useful as a fast-acting therapy against epidemic or pandemic influenza viruses," said Wilson. "The ultimate goal is an active vaccine that elicits a robust, long-term antibody response against those vulnerable epitopes; but developing that is going to be a challenging task."

The research was supported by the US National Institute of Allergy and Infectious Diseases, National Institutes of Health; the US Department of Energy; and by Crucell Holland BV.

Journal Reference:

Damian C. Ekiert, Robert H. E. Friesen, Gira Bhabha, Ted Kwaks, Mandy Jongeneelen, Wenli Yu, Carla Ophorst, Freek Cox, Hans J.W.M. Korse, Boerries Brandenburg, Ronald Vogels, Just P.J. Brakenhoff, Ronald Kompier, Martin H. Koldijk, Lisette A.H.M. Cornelissen, Leo L. M. Poon, Malik Peiris, Wouter Koudstaal, Ian A. Wilson, and Jaap Goudsmit. A Highly Conserved Neutralizing Epitope on Group 2 Influenza A Viruses. Science, July 7, 2011 DOI: 10.1126/science.1204839

Courtesy: ScienceDaily

HIV-Inhibiting Mechanism Identified

2011-07-08T02:12:00.000-07:00

Researchers at Case Western Reserve University School of Medicine have discovered a long-sought cellular factor that works to inhibit HIV infection of myeloid cells, a subset of white blood cells that display antigens and hence are important for the body's immune response against viruses and other pathogens.

The factor, a protein called SAMHD1, is part of the nucleic acid sensing machinery within the body's own immune system. It keeps cells from activating immune responses to the cells own nucleic acids, thus preventing certain forms of autoimmunity from developing.

SAMHD1 factor, researchers have found, can also sense and interfere with infection of myeloid cells, such as macrophages and dendritic cells, with HIV-1 and related immunodeficiency viruses. As such, SAMHD1 prevents the synthesis of virus copies in these cells, according to research led by Jacek Skowronski, PhD, a professor in the Department of Molecular Biology and Microbiology and member of the Center for AIDS Research at the Case Western Reserve University School of Medicine.

The findings appear in a manuscript published in the June 30 issue of Nature featuring Dr. Skowronski as the paper's senior author. The research was carried out in his lab at Case Western Reserve in collaboration with a research group led by Michael P. Washburn, PhD, at the Stowers Institute for Medical Research in Kansas City.

This issue of Nature also carries an independent report by a team from France headed by Monsef Benkirane, PhD, that identifies SAMHD1 as a factor that limits HIV growth in myeloid cells. The research broadens the understanding of how the immune system of the infected people handles HIV, and how HIV evades the immune system's response.

"The identification of SAMHD1 and its function may help to explain why some infected individuals can control HIV infection better than others," Dr. Skowronski says. "Ultimately, it could also provide a basis for conceiving of new therapies and treatment approaches to block HIV infection and/or its replication in infected individuals, and to stimulate body's own immune response to HIV."

Prior to this research the normal function of SAMHD1 was thought to be the prevention of the inappropriate activation of a class of the anti-viral responses mediated by production of anti-viral factors termed interferons, in the absence of virus infection. Mutations in SAMHD1, as well as two other cellular genes that encode nucleases, TREX1 and RNAse H2, cause a condition called Acairdi-Goutieres syndrome (AGS). The condition mimics congenital viral infection, and is due to unwarranted induction of the immune system's interferons in the absence of the virus. SAMHD1 and other AGS-causing cell proteins work to dispose cellular nucleic acid debris, thereby preventing inappropriate activation of the interferon system.

In the work described in the Nature manuscript, the researchers led by Dr. Skowronski discovered that in addition to preventing inappropriate autoimmune responses such as those seen in AGS, SAMHD1 possesses the ability to inhibit infection of myeloid cells by HIV by effectively interfering with the production of viral nucleic acids. Through this action SAMHD1 may prevent efficient activation of immune responses to HIV-1 virus in infected individuals, Dr. Skowronski explains.

The research also shows HIV-2 and related simian immunodeficiency viruses (SIVsm/mac) are able to overcome the protective mechanism within myeloid cells by using the protein Vpx they encode, to dispose of SAMHD1, thereby allowing infection with these viruses. Interestingly, viruses possessing Vpx, such as HIV-2, are much less pathogenic than HIV-1. This could be because by being able to establish infection in myeloid cells they provoke much more robust immune responses that HIV-1 does, since HIV-1 can not infect these cells efficiently, Dr. Skowronski says.

As a result, "One might expect that manipulation of SAMHD1 function in the context of HIV-1 infection may lead to more robust immune response to this virus" according to Dr. Skowronski.

Moving forward, researchers will focus on better understanding the molecular pathway SAMHD1 uses to inhibit HIV-1 infection. They will likewise strive to learn more about how SAMHD1 shapes the development of AIDS in HIV-infected individuals, Dr. Skowronski says.

ournal Reference:

Kasia Hrecka, Caili Hao, Magda Gierszewska, Selene K. Swanson, Malgorzata Kesik-Brodacka, Smita Srivastava, Laurence Florens, Michael P. Washburn, Jacek Skowronski. Vpx relieves inhibition of HIV-1 infection of macrophages mediated by the SAMHD1 protein. Nature, 2011; 474 (7353): 658 DOI: 10.1038/nature10195

Courtesy: ScienceDaily

Cancer Genome Atlas Completes Detailed Ovarian Cancer Analysis

2011-07-06T02:09:00.000-07:00

An analysis of genomic changes in ovarian cancer has provided the most comprehensive and integrated view of cancer genes for any cancer type to date. Ovarian serous adenocarcinoma tumors from 500 patients were examined by The Cancer Genome Atlas (TCGA) Research Network and analyses are reported in the June 30, 2011, issue of Nature.

Serous adenocarcinoma is the most prevalent form of ovarian cancer, accounting for about 85 percent of all ovarian cancer deaths. TCGA researchers completed whole-exome sequencing, which examines the protein-coding regions of the genome, on an unprecedented 316 tumors. They also completed other genomic characterizations on these tumors and another 173 specimens.

TCGA is jointly funded and managed by the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI), both part of the National Institutes of Health.

"This landmark study is producing impressive insights into the biology of this type of cancer," said NIH Director Francis Collins, M.D., Ph.D. "It will significantly empower the cancer research community to make additional discoveries that will help us treat women with this deadly disease. It also illustrates the power of what's to come from our investment in TCGA."

Among the specific findings is the confirmation that mutations in a single gene, TP53, are present in more than 96 percent of all such cancers. TP53 encodes a tumor suppressor protein that normally prevents cancer formation. Mutations in the gene disrupt this protein's function, which contributes to uncontrolled growth of ovarian cells. In addition, TCGA identified a multitude of less-frequent mutations in other genes.

TCGA researchers also established how sets of genes are expressed in a fashion that can predict patient survival -- identifying patterns for 108 genes associated with poor survival and 85 genes associated with better survival. Patients whose tumors had a gene-expression signature associated with poor survival lived for a period that was 23 percent shorter than patients whose tumors did not have such a signature. The overall five-year survival rate for ovarian cancer is 31 percent, which means that 69 percent of patients diagnosed this year will not be alive in 2016, highlighting the urgent need for a better understanding of the disease.

"The new knowledge of the genomic changes in ovarian cancer has revealed that the molecular catalysts of this disease are not limited to small changes affecting individual genes," said NCI Director Harold E. Varmus, M.D. "Also important are large structural changes that occur in these cancer genomes. Cancer researchers can use this comprehensive body of information to better understand the biology of ovarian cancer and improve the diagnosis and treatment of this dreaded disease."

To identify opportunities for targeted treatment, the investigators searched for existing drugs that might inhibit amplified or over-expressed genes that were suggested to play a role in ovarian cancer. The search identified 68 genes that could be targeted by existing Food and Drug Administration-approved or experimental therapeutic compounds. The investigators noted that one type of drug, a PARP (Poly ADP ribose polymerase) inhibitor, might be able to counteract the DNA repair gene observed in half of the ovarian tumors studied. While researchers have known that these drugs could be effective against the disease, this study revealed that 50 percent of tumors might be responsive to drugs that exploit the genetic instability of the tumors and induce the cancer cells to die.

"Like all cancers, ovarian cancer results from genomic derangements," said Eric D. Green, M.D., Ph.D., NHGRI director. "The efforts of TCGA are confirming that the more we learn about genomic changes in tumor cells, the more we will be able to care for the people affected by cancer."

The results of this study support the existence of four distinct subtypes of the disease, based on the patterns seen in the transcription of RNA from DNA. They also support the existence of four related subtypes based on the patterns of DNA methylation -- a chemical reaction in which a small molecule called a methyl group is added to DNA, changing the activity of individual genes. These patterns likely reflect the functional changes associated with ovarian serous adenocarcinoma, but are not strongly associated with survival duration.

Mutations in BRCA1 and BRCA2 genes, which are associated with some forms of breast cancer, also confer increased risk for ovarian cancer. In this study, approximately 21 percent of the tumors showed mutations in these genes. Analysis of these tumors confirmed observations that patients with mutated BRCA1 and BRCA2 genes have better survival odds than patients without mutations in these genes. Importantly, investigators identified that the mechanism by which the BRCA1 and BRCA2 genes become defective also relates to survival. If either of the BRCA1 and BRCA2 genes is mutated, there is improved survival duration. However, if BRCA1 activity is instead reduced by methylation, there is no improved survival duration.

"The integration of complex genomic data sets enabled us to discover an intricate array of genomic changes and validate one specific change that occurs in the vast majority of all ovarian cancers," said lead author Paul T. Spellman, Ph.D., Lawrence Berkeley Lab, Berkeley, Calif. "Significantly, we have also found new information regarding the role that the BRCA1 and BRCA2 genes play in determining survival."

In this latest study, the TCGA researchers built upon the approach they used in 2008 to characterize the genome of gliobastoma multiforme, the most common form of brain cancer.

TCGA, launched in 2006, is a comprehensive and coordinated effort to accelerate the understanding of the molecular basis of cancer through the application of genome analysis technologies, including large-scale genome sequencing. TCGA data are being made rapidly available to the research community through a database, http://tcga-data.nci.nih.gov/tcga. The database provides direct access to most analytic datasets, with other data, such as patient treatment records and raw DNA sequence data, available to qualified researchers through an NIH review and approval process. Future TCGA analyses of over 20 other tumor types will be primarily funded using American Recovery and Reinvestment Act (ARRA) monies.

Journal Reference:

Bell et al. Integrated genomic analyses of ovarian carcinoma. Nature, 2011; 474 (7353): 609 DOI: 10.1038/nature10166

Courtesy: ScienceDaily

Novel Genetic Variation Linked to Increased Risk of Sudden Cardiac Arrest

2011-07-04T02:07:00.000-07:00

A study by a global consortium of physician-scientists has identified a genetic variation that may predispose people to double the risk of having a sudden cardiac arrest, a disorder that gives little warning and is fatal in about 95 percent of cases. Although previous, smaller studies have identified some genes with a potential association with sudden cardiac arrest, this is the first study large enough to enable scientists to apply results to the general population.

Findings are published by the Public Library of Science in the online journal PLoS Genetics.

"We are at the beginning of unraveling the mystery of what causes sudden cardiac arrest and how to prevent it," said senior author Sumeet S. Chugh, MD, associate director of the Cedars-Sinai Heart Institute and a specialist in cardiac electrophysiology. "If we wait until someone has a sudden cardiac arrest, it is usually too late for treatment. That is why knowing who is genetically susceptible is so important."

Unlike heart attacks (myocardial infarction), which are typically caused by clogged coronary arteries reducing blood flow to the heart muscle, sudden cardiac arrest is the result of defective electrical impulses. Patients may have little or no warning, and the disorder usually causes nearly instantaneous death. Every year, 250,000 to 300,000 people in the U.S. and up to 5 million worldwide die from sudden cardiac arrest.

Despite years of significant advances in emergency medicine and resuscitation, just five percent of those who suffer sudden cardiac arrest survive. For patients at known risk for this or other heart rhythm abnormalities, an implantable cardioverter-defibrillator (ICD) may be placed in the chest or abdomen to detect faulty electrical impulses and provide a shock to return normal rhythm. Better genetic predictors of risk may someday enable the accurate prediction of which patients are most likely to benefit from costly ICD therapy.

The discovery came from a genome-wide association study, which examines the entire set of human genes to detect possible links between genetic variations and specific conditions or diseases. In this study, researchers from the Cedars-Sinai Heart Institute, Johns Hopkins University School of Medicine, along with researchers from the National Institutes of Health, Harvard University, Wake Forest University School of Medicine, Oregon Health and Science University, Finland, Canada and the Netherlands compared the genetic makeup of 4,402 subjects who had experienced sudden cardiac arrest to the DNA of 30,000 control subjects who had no history of the disorder.

Based on a comparison of the two groups, a genetic variation in the BAZ2B gene was found to be associated with a significantly increased risk of sudden cardiac arrest.

"If you have this genetic variation in your DNA, it appears that you may have a two-fold higher likelihood of sudden cardiac arrest," said Chugh, the Pauline and Harold Price Chair in Cardiac Electrophysiology Research.

The researchers also studied the link between other genetic variations that account for EKG abnormalities and were able to pinpoint several that can also be used for improving the prediction of sudden cardiac arrest in the community.

Journal Reference:

Dan E. Arking, M. Juhani Junttila, Philippe Goyette, Adriana Huertas-Vazquez, Mark Eijgelsheim, Marieke T. Blom, Christopher Newton-Cheh, Kyndaron Reinier, Carmen Teodorescu, Audrey Uy-Evanado, Naima Carter-Monroe, Kari S. Kaikkonen, Marja-Leena Kortelainen, Gabrielle Boucher, Caroline Lagacé, Anna Moes, XiaoQing Zhao, Frank Kolodgie, Fernando Rivadeneira, Albert Hofman, Jacqueline C. M. Witteman, André G. Uitterlinden, Roos F. Marsman, Raha Pazoki, Abdennasser Bardai, Rudolph W. Koster, Abbas Dehghan, Shih-Jen Hwang, Pallav Bhatnagar, Wendy Post, Gina Hilton, Ronald J. Prineas, Man Li, Anna Köttgen, Georg Ehret, Eric Boerwinkle, Josef Coresh, W. H. Linda Kao, Bruce M. Psaty, Gordon F. Tomaselli, Nona Sotoodehnia, David S. Siscovick, Greg L. Burke, Eduardo Marbán, Peter M. Spooner, L. Adrienne Cupples, Jonathan Jui, Karen Gunson, Y. Antero Kesäniemi, Arthur A. M. Wilde, Jean-Claude Tardif, Christopher J. O'Donnell, Connie R. Bezzina, Renu Virmani, Bruno H. C. h. Stricker, Hanno L. Tan, Christine M. Albert, Aravinda Chakravarti, John D. Rioux, Heikki V. Huikuri, Sumeet S. Chugh. Identification of a Sudden Cardiac Death Susceptibility Locus at 2q24.2 through Genome-Wide Association in European Ancestry Individuals. PLoS Genetics, 2011; 7 (6): e1002158 DOI: 10.1371/journal.pgen.1002158

Courtesy: ScienceDaily

Screen Developed to Identify New Anticancer Drug Targets

2011-06-30T05:13:00.000-07:00

Tumor suppressor genes normally control the growth of cells, but cancer can spring up when these genes are silenced by certain chemical reactions that modify chromosomes. Among the most common culprits responsible for inactivating these genes are histone deacetylases, a class of enzymes that remove acetyl groups from DNA-scaffolding proteins, and DNA methyltransferases, a family of enzymes that add methyl groups to DNA.

Drugs that counteract these enzymes, and thus reactivate tumor suppressor genes, are promising cancer therapies. For example, histone deacetylase inhibitors have been approved for the treatment of a type of T cell lymphoma, and are being tested in clinical trials for the treatment of a wide range of cancers. Similarly, DNA methyltransferase inhibitors have been approved to treat a certain kind of leukemia, and are undergoing clinical studies for the treatment of other cancers. But these medications can have serious side effects.

Now, Fox Chase Cancer Center postdoctoral associate Andrey Poleshko, PhD, along with Research Professor Richard A. Katz, PhD, and their colleagues have developed a screen to identify proteins that work in conjunction with these enzymes to repress gene expression. They will present their results at the AACR 102nd Annual Meeting 2011 on Tuesday, April 5.

Finding additional proteins that inactivate tumor suppressor genes, and understanding how they work, could lead to the broadening of this class of therapies beyond the two enzyme families, Poleshko said. "If we can find a way to block the action of such proteins, it may be possible to reactivate aberrantly silenced tumor suppressor genes and restore controlled growth in certain cancer cells," he noted. Such an approach would avoid interfering directly with the vital chromosome-modifying enzymes.

The researchers genetically programmed human cells to glow fluorescent green upon reactivation of the silent genes they harbor. By shutting down the activity of genes one by one and observing whether cells turned green, they were able to identify factors that help to suppress gene expression.

The method was efficient enough to permit screening of the entire genome, including 21,122 genes, and revealed 128 factors that are involved in regulating gene expression.

Research Assistant Professor Margret B. Einarson and Professor Anna Marie Skalka from Fox Chase are co-authors on the study.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by Fox Chase Cancer Center, via EurekAlert!, a service of AAAS.

Courtesy: ScienceDaily

Computational Software Provides Rapid Identification of Disease-Causing Gene Variations

2011-06-28T05:11:00.000-07:00

Scientists from the University of Utah and Omicia, Inc., a privately held company developing tools to interpret personal genome sequences, have announced the publication in Genome Research of a new software tool called VAAST, the Variant Annotation, Analysis and Selection Tool -- a probabilistic disease-causing mutation finder for individual human genomes.'

The dramatic decline in DNA sequencing costs is making personal genome sequencing a reality. Already, significant progress has been made in applying whole genome sequencing to cancer prognosis and early childhood disease. Examples include the 2010 publications on Miller Syndrome in Nature Genetics and Science, and similar studies aimed at identifying the unknown genetic defects responsible for some early childhood diseases.

However, a data interpretation bottleneck has limited the utility of personal genome information for medical diagnosis and preventive care. VAAST is a new algorithm to assist in overcoming this bottleneck. VAAST is the product of a collaboration between Mark Yandell, Ph.D., Associate Professor of Human Genetics at the University of Utah School of Medicine, and colleagues, and the Omicia scientific team under the leadership of Martin Reese, Ph.D., the company's CEO and Chief Scientific Officer.

In the Genome Research paper, Yandell and colleagues show that VAAST provides a highly accurate, statistically robust means to rapidly search personal genomes for genes with disease-causing mutations. The authors demonstrate that as few as three genomes from unrelated children, or those of the parents and their two children, are sufficient to identify disease causing mutations.

"The big challenge in genomic medicine today is how to sift through the millions of variants in a personal genome sequence to identify the disease-relevant variations," said Dr. Reese. "It's a classic needle in a haystack problem, and VAAST goes a long way toward solving it. We look forward to integrating VAAST into the Omicia Genome Analysis System currently under development for clinical applications."

Dr. Yandell added: "VAAST solves many of the practical and theoretical problems that currently plague mutation hunts using personal genome sequences. Our results demonstrate that this tool substantially improves upon existing methods with regard to statistical power, flexibility, and scope of use. Further, VAAST is automated, fast, works across all variant population frequencies and is sequencing platform independent."

In a separate paper published this week in the American Journal of Human Genetics, Gholson Lyon, M.D., Ph.D., previously at University of Utah and now at the Children's Hospital of Philadelphia, and colleagues report the use of VAAST as part of an international effort to identify the mutation responsible for a newly discovered childhood disease. This new illness, which they are tentatively calling Ogden Syndrome, is characterized by aged appearance, craniofacial abnormalities, cardiac arrhythmias and other symptoms. The team used X-chromosome exon capture and next-generation sequencing and the VAAST tool to quickly and unambiguously identify the disease-causing mutation in the NAA10 gene that has resulted in this fatal disease in children of two unrelated families.

"VAAST can identify disease-causing mutations with greater accuracy, using far fewer individuals and more rapidly than was previously possible," said Dr. Lyon. "We are now applying VAAST to many other unknown conditions, including rare Mendelian disorders and other common disorders such as ADHD and autism."

Commenting on the significance of this development, Eric J. Topol, M.D., Director, Scripps Translational Science Institute and Chief Academic Officer, Scripps Health, commented: "One of most important and exciting opportunities in genomic medicine is the newfound ability to pinpoint the root cause of an unknown idiopathic disease in an individual. The VAAST tool will markedly facilitate this and represents a major advance in the field. It fulfills a significant unmet need of interpreting whole genome sequences and will have a remarkable impact on accurate genomic diagnosis of many individuals going forward."

The development of VAAST was funded by the National Human Genome Research Institute through an American Recovery and Reinvestment Act Grand Opportunity (GO) grant. GO grants focus on transformative technologies and large, potentially high-impact projects.

Journal References:

Mark Yandell, Chad D. Huff, Hao Hu, Marc Singleton, Barry Moore, Jinchuan Xing, Lynn B. Jorde, Martin G. Reese. A probabilistic disease-gene finder for personal genomes. Genome Research, 2011; DOI: 10.1101/gr.123158.111
Alan F. Rope, Kai Wang, Rune Evjenth, Jinchuan Xing, Jennifer J. Johnston, Jeffrey J. Swensen, W. Evan Johnson, Barry Moore, Chad D. Huff, Lynne M. Bird, John C. Carey, John M. Opitz, Cathy A. Stevens, Tao Jiang, Christa Schank, Heidi Deborah Fain, Reid Robison, Brian Dalley, Steven Chin, Sarah T. South, Theodore J. Pysher, Lynn B. Jorde, Hakon Hakonarson, Johan R. Lillehaug, Leslie G. Biesecker, Mark Yandell, Thomas Arnesen, Gholson J. Lyon. Using VAAST to Identify an X-Linked Disorder Resulting in Lethality in Male Infants Due to N-Terminal Acetyltransferase Deficiency. American Journal of Human Genetics, 2011; DOI: 10.1016/j.ajhg.2011.05.017

Courtesy: ScienceDaily

Artificial Pancreas Being Developed to Ease Diabetes Burden

2011-06-26T05:10:00.000-07:00

The 25.8 million Americans who have diabetes may soon be free of finger pricks and daily insulin dosing. Mayo Clinic endocrinologists Yogish Kudva, M.B.B.S., and Ananda Basu, M.B.B.S., M.D., are developing an artificial pancreas that will deliver insulin automatically and with an individualized precision never before possible.

As part of this effort, Drs. Kudva and Basu will present their latest findings on how the mundane movements of everyday life affect blood sugar to the American Diabetes Association meeting this month in San Diego.

"The effects of low-intensity physical activity, mimicking activities of daily living, measured with precise accelerometers on glucose variability in type 1 diabetes had not been examined," says Dr. Kudva.

Among his newest findings is that even basic physical activity after meals has a profound impact on blood sugar levels for people with type 1 diabetes. "You would expect this result, but we wanted to know to what extent this phenomena would happen in people with type 1 diabetes," Dr. Kudva says.

Diabetics who engaged in low-grade physical activity after eating had blood sugar levels close to those of people with fully functioning pancreases. Those who remained sedentary after their meal, however, had elevated blood sugars.

The researchers plan to incorporate these findings into an artificial pancreas being developed at Mayo Clinic. The "Closed Loop System" under development includes a blood sugar monitor, an automatic insulin pump, a set of activity monitors that attach to the body and a central processing unit.

Clinical trials of the artificial pancreases are likely to begin in November with a handful of inpatient volunteers. Study participants will follow strict diet, exercise and insulin-delivery regimens in Mayo's Clinical Research Unit. Data will then be fed into an insulin-delivery algorithm, which mimics the body's natural process of monitoring and responding to glucose levels in the bloodstream.

"Physical activity enhances insulin action, hence lowering blood glucose concentration," Dr. Kudva says. "Real-time detection of physical activity -- and modeling of its effect on glucose dynamics -- is vital to design an automatic insulin delivery system."

Dr. Kudva and other Mayo researchers have spent nearly 15 years working on various aspects of diabetes and obesity. They are collaborating on the artificial pancreas and developing an algorithm that will afford patients the peace of mind to eliminate their daily routine of diabetes maintenance.

Dr. Basu will present findings that blood sugar levels decrease faster in the mornings in healthy adults than at dinner time, suggesting a diurnal pattern to natural insulin action. He proposes further study of this phenomenon and possible incorporation into the algorithm that drives the Closed Loop System.

The research has been funded by grants from the National Institutes of Health.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by Mayo Clinic.

Courtesy: ScienceDaily

Chirality: New Method to Consistently Make Left-Handed or Right-Handed Molecules

2011-06-24T05:04:00.000-07:00

Many organic molecules are non-superimposable with their mirror image. The two forms of such a molecule are called enantiomers and can have different properties in biological systems. The problem is to control which enantiomer you want to produce -- a problem that has proved to be important in the pharmaceutical industry. Researchers at the University of Gothenburg have now come up with a new method to control the process.

"Organic chemists think that it's impossible to create only one of the enantiomers without introducing some kind of optical activity into the reaction, but I've succeeded," says Theonitsa Kokoli at the University of Gothenburg's Department of Chemistry. "My method will allow the industry to produce the version they want without the use of a catalyst."

The phenomenon of non-superimposable mirror-image molecular structures is known as chirality. The two enantiomers can be compared to a pair of hands; they are non-superimposable mirror images of each other. A consequence of the different properties in biological systems is that a molecule can behave either as Dr Jekyll or Mr Hyde. The different characteristics in the enantiomers can be harmless, like in the limonene molecule. One enantiomer smells like orange and the other like lemon.

Thalidomide is a good example of how different forms of the same molecule can have disastrous consequences. One of the enantiomers was calming and eased nausea in pregnant women, while the other caused serious damage to the fetus. The thalidomide catastrophe is one of the reasons that a lot of research is devoted to chirality, as it is absolutely vital to be able to control which form of the molecule that is produced. Research on chirality has resulted in several Nobel Prizes over the years.

In biomolecules like DNA and proteins only one of the enantiomers exists in nature. In contrast to biomolecules, the same does not apply when chiral compounds are created synthetically in the lab. Generally an equal amount of both enantiomers is produced. One way of creating an excess of one enantiomer is to use a chiral catalyst, but this only transfers the properties that are already present in the catalyst.

"I've been working with absolute asymmetric synthesis instead, where optical activity is created," says Kokoli. "This is considered impossible by many organic chemists. I've used crystals in my reactions, where the two forms have crystallised as separate crystals, which in itself is fairly unusual. The product that was formed after the reactions comprised just one enantiomer."

While the results of Kokoli's research are particularly significant for the pharmaceuticals industry, they can also be used in the production of flavourings and aromas.

The thesis has been successfully defended on May 6, 2011.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by University of Gothenburg.

Courtesy: ScienceDaily

Tapeworm Drug Inhibits Colon Cancer Metastasis

2011-06-22T05:03:00.000-07:00

A compound that for about 60 years has been used as a drug against tapeworm infection is also apparently effective against colon cancer metastasis, as studies using mice have now shown. The compound silences a gene that triggers the formation of metastases in colon cancer.

Professor Ulrike Stein (Experimental and Clinical Research Center, a joint cooperation between the Charité Medical Faculty and the Max Delbrück Center for Molecular Medicine, (MDC)) and her research group made this discovery in collaboration with Professor Robert H. Shoemaker of the National Cancer Institute (NCI) in Frederick, Maryland. The results are reported in the Journal of the National Cancer Institute. Plans are already underway with Professor Peter M. Schlag (Charité Comprehensive Cancer Center) to conduct a clinical trial.

Colon cancer is one of the most common tumor diseases in Western countries. In Germany alone, there are approximated 73 000 new cases of the disease every year. Despite surgery, chemotherapy and radiation therapy, only about half of the affected patients are cured.

The reason is that around 20 percent of the colon cancer patients already have metastases at diagnosis and in about one third of the patients, metastasis occurs despite successful initial treatment. Of these patients with metastatic colon cancer, the five-year survival rate is only about 10 percent. By contrast, for nonmetastatic colon cancer patients the survival rate is 90 percent.

Scientists have known for several years that the gene S100A4/metastasin can initiate colon cancer metastasis. Five years ago Professor Stein, working together with Professor Schlag and Professor Walter Birchmeier (MDC), showed how this gene is regulated. They found that the beta-catenin gene, when mutant, activates this S100A4/metastasin gene, thus triggering colon cancer metastasis. Beta-catenin normally regulates cellular adhesion.

The scientists looked for compounds that block the expression of the metastasin gene. They screened 1280 compounds and found what they were looking for: niclosamide, a drug until now approved for use to treat intestinal parasite infections from tapeworms.

Surprisingly, the researchers discovered that niclosamide inhibits the beta catenin-driven expression of the S100A4/metastasin gene, both in the cell culture and in mice. The animals had fewer metastases. Next, the researchers want to conduct clinical trials to find out whether the compound is also effective in patients with metastasizing colon cancer.

Journal Reference:

Ulrike Sack, Wolfgang Walther, Dominic Scudiero, Mike Selby, Dennis Kobelt, Margit Lemm, Iduna Fichtner, Peter M. Schlag, Robert H. Shoemaker, Ulrike Stein. Novel Effect of Antihelminthic Niclosamide on S100A4-Mediated Metastatic Progression in Colon Cancer. Journal of the National Cancer Institute, 2011; DOI: 10.1093/jnci/djr190

Courtesy: ScienceDaily