Proteins Enable Essential Enzyme to Maintain Its Grip On DNA

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:

1. 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

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:

1. 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

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:

1. 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

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

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:

1. 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

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:

1. 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

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:

1. 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

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:

1. 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

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

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:

1. 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

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:

1. 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

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:

1. 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

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:

1. 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