Category Archives: Gene Medicine

ScienceDaily (Oct. 2, 2012) Cancerous tumors contain hundreds of mutations, and finding these mutations that result in uncontrollable cell growth is like finding the proverbial needle in a haystack. As difficult as this task is, it's exactly what a team of scientists from Cornell University, the University of North Carolina, and Memorial Sloan-Kettering Cancer Center in New York have done for one type of breast cancer. In a report appearing in the journal Genetics, researchers show that mutations in a gene called NF1 are prevalent in more than one-fourth of all noninheritable or spontaneous breast cancers.

In mice, NF1 mutations are associated with hyper-activation of a known cancer-driving protein called Ras. While researchers have found earlier evidence that NF1 plays a role in other types of cancer, this latest finding implicates it in breast cancer. This suggests that the drugs that inhibit Ras activity might prove useful against breast cancers with NF1 mutations.

"As we enter the era of personalized medicine, genomic technologies will be able to determine the molecular causes of a woman's breast cancer," said John Schimenti, Ph.D., a researcher involved in the work from the Center for Vertebrate Genomics at Cornell University College of Veterinary Medicine in Ithaca, New York. "Our results indicate that attention should be paid to NF1 status in breast cancer patients, and that drug treatment be adjusted accordingly both to reduce the cancer and to avoid less effective treatments."

To make this discovery, scientists analyzed the genome of mammary tumors that arise in a mouse strain prone to genetic instability -- whose activity closely resembles the activity in human breast cancer cells -- looking for common mutations that drive tumors. The gene NF1 was missing in 59 out of 60 tumors, with most missing both copies. NF1 is a suppressor of the oncogene Ras, and Ras activity was extremely elevated in these tumors as a consequence of the missing NF1 gene. Researchers then examined The Cancer Genome Atlas (TCGA) data, finding that NF1 was missing in more than 25 percent of all human breast cancers, and this was associated with a decrease in NF1 gene product levels, which in turn is known to increase Ras activity. "This research is compelling because it helps us understand why some breast cancers are more likely to respond to only certain types of treatment," said Mark Johnston, Editor-in-Chief of the journal GENETICS. "The findings reported in this article may guide clinicians to better treatments specific to the needs of each patient."

This study was supported by NIH training grants IT32HDO57854 and 5T32GM007617 that supported M.D.W.; Empire State Stem Cell Fund contract numbers C026442 and C024174 to J.C.S.; and C.M.P. and A.D.P. were supported by NCI Breast SPORE program (P50-CA58223-09A1), by U24-CA143848, and by the Breast Cancer Research Foundation.

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The above story is reprinted from materials provided by Genetics Society of America, via Newswise.

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Gene responsible for many spontaneous breast cancers identified

October 3, 2012 in Nation/World

Lauran Neergaard Associated Press

WASHINGTON (AP) Too often, newborns die of genetic diseases before doctors even know whats to blame. Now scientists have found a way to decode those babies DNA in just days instead of weeks, moving gene-mapping closer to routine medicalcare.

The idea: Combine faster gene-analyzing machinery with new computer software that, at the push of a few buttons, uses a babys symptoms to zero in on the most suspicious mutations. The hope would be to start treatment earlier, or avoid futile care for lethalillnesses.

Wednesdays study is a tentative first step: Researchers at Childrens Mercy Hospital in Kansas City, Mo., mapped the DNA of just five children, and the study wasnt done in time to help most ofthem.

But the hospital finds the results promising enough that by years end, it plans to begin routine gene-mapping in its neonatal intensive care unit and may offer testing for babies elsewhere, too while further studies continue, said Dr. Stephen Kingsmore, director of the pediatric genome center at ChildrensMercy.

For the first time, we can actually deliver genome information in time to make a difference, predicted Kingsmore, whose team reported the method in the journal Science TranslationalMedicine.

Even if the diagnosis is a lethal disease, the family will at least have an answer. They wont have false hope, headded.

More than 20 percent of infant deaths are due to a birth defect or genetic diseases, the kind caused by a problem with a single gene. While there are thousands of such diseases from Tay-Sachs to the lesser known Pompe disease, standard newborn screening tests detect only a few of them. And once a baby shows symptoms, fast diagnosis becomescrucial.

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Two-day test can spot gene diseases in newborns - Wed, 03 Oct 2012 PST

Washington, October 3 (ANI): A team of scientists has shown that mutations in a gene called NF1 are prevalent in more than one-fourth of all noninheritable or spontaneous breast cancers.

The team include scientists from Cornell University, the University of North Carolina, and Memorial Sloan-Kettering Cancer Center in New York.

In mice, NF1 mutations are associated with hyper-activation of a known cancer-driving protein called Ras. While researchers have found earlier evidence that NF1 plays a role in other types of cancer, this latest finding implicates it in breast cancer.

This suggests that the drugs that inhibit Ras activity might prove useful against breast cancers with NF1 mutations.

"As we enter the era of personalized medicine, genomic technologies will be able to determine the molecular causes of a woman's breast cancer," said John Schimenti, Ph.D., a researcher involved in the work from the Center for Vertebrate Genomics at Cornell University College of Veterinary Medicine in Ithaca, New York.

"Our results indicate that attention should be paid to NF1 status in breast cancer patients, and that drug treatment be adjusted accordingly both to reduce the cancer and to avoid less effective treatments," he added.

To make this discovery, scientists analyzed the genome of mammary tumors that arise in a mouse strain prone to genetic instability-whose activity closely resembles the activity in human breast cancer cells-looking for common mutations that drive tumors.

The gene NF1 was missing in 59 out of 60 tumors, with most missing both copies. NF1 is a suppressor of the oncogene Ras, and Ras activity was extremely elevated in these tumors as a consequence of the missing NF1 gene.

Researchers then examined The Cancer Genome Atlas (TCGA) data, finding that NF1 was missing in more than 25 percent of all human breast cancers, and this was associated with a decrease in NF1 gene product levels, which in turn is known to increase Ras activity.

The research was published in the journal GENETICS.(ANI)

Continued here:
Gene behind many spontaneous breast cancers identified

CHICAGO (Reuters) - U.S. scientists have sequenced the entire genetic code of four gravely ill newborns and identified genetic diseases in three of them in two days, quick enough to help doctors make treatment decisions.

Doctors behind the preliminary study released on Wednesday say it demonstrates a practical use for whole genome sequencing, in which researchers analyze all 3.2 billion chemical "bases" or "letters" that make up the human genetic code.

"It is now feasible to decode an entire genome and provide interim results back to the physician in two days," said Dr. Stephen Kingsmore, director of the Center for Pediatric Genomic Medicine at Children's Mercy medical center in Kansas City, Missouri, whose study was published in the journal Science Translational Medicine.

The study tested two software programs developed at Children's Mercy that were used in conjunction with a high-speed gene sequencer from Illumina called HiSeq 2500, which can sequence an entire genome in about 25 hours.

The company helped pay for the study and company researchers took part in it.

Next-generation gene sequencing machines have driven down the cost of whole genome sequencing, but making practical use of the data has been more challenging, largely because of the time it takes to analyze all of the data.

As many as a third of babies admitted to a neonatal intensive care unit in the United States have some form of genetic disease. Treatments are currently available for more than 500 diseases, but identifying them quickly has been a problem.

Typically, genetic testing on newborns using conventional methods takes four to six weeks, long enough that the infant has either died or been sent home.

"Up until now, they have really had to practice medicine blindfolded," Kingsmore said in a telephone briefing with reporters.

Dr. Neil Miller, director of informatics at Children's Mercy, said the software programs help doctors identify which genes to test, and analyze the data quickly.

Read more:
Rapid gene machines used to find cause of newborn illnesses

Is gene therapy finally becoming a reality? The European Commission is poised to authorize, for the first time in the Western world, the commercialization of a gene-therapy product. Called Glybera (alipogene tiparvovec), it is designed to treat a rare genetic defect involved in fat metabolism.

Success has been a long time coming. Gene therapy was first administered more than 20 years ago, to a child who had a rare disorder of the immune system called adenosine deaminase (ADA) deficiency. Since then, it has struggled to find its place in medicine amid a roller coaster of successes and setbacks, hype and scepticism that has little precedent in modern times. Although the approval of Glybera is a positive move, it is unlikely to herald a new age of gene therapies not without significant changes to the system. It is no coincidence that no gene therapy has yet been approved in the United States and that no other gene-therapy product is being considered by regulators in Europe.

Here is why. The design, development and manufacture of products such as Glybera a virus engineered to carry a correct copy of the defective gene is complex and done mostly in academic centres. Yet legislation introduced in the past decade in Europe and the United States demands that these products be produced under the same rules that cover conventional drugs, in establishments operated with industry-like standards and certified by government agencies.

This is a formidable challenge for academic centres, which tend to lack the necessary human and financial resources. So why is the development of gene therapy focused there, and not in industry, which seems better suited?

The first reason is the financial uncertainty generated by the complex, confused and poorly harmonized regulatory environment as the history of Glybera shows. At first, the application for its authorization received a negative opinion from two committees at the European Medicines Agency (EMA): the Committee for Advanced Therapies (CAT) and the Committee for Human Medicinal Products for Human Use (CHMP). Only when another body, the Standing Committee of the European Commission, asked the EMA to reconsider the application in a restricted indication did the CHMP eventually recommend approval under exceptional circumstances, requiring post-marketing studies and the set-up of a restricted-access programme. The Dutch firm Amsterdam Molecular Therapeutics, the inventor of Glybera, did not survive the process, and became known as uniQure after refinancing.

Lack of resources is a second reason. For many years, the drug industry stayed away from gene therapy, perceiving it as a dangerous technology of dubious efficacy that was too complex to develop and targeted too small a market.

There are some positive signs, because this last perception, at least, is changing: the industry now recognizes that rare diseases and orphan-drug legislation provide attractive opportunities. Some recombinant proteins and monoclonal antibodies originally developed as orphan drugs have been repurposed for larger indications.

The industry now recognizes that rare diseases and orphan-drug legislation provide attractive opportunities.

An example of how academia and industry could cooperate comes from the recent alliance between the drug giant GlaxoSmithKline (GSK) in London, and the charity-funded San Rafaelle Telethon Institute for Gene Therapy (TIGET) in Milan, Italy. GSK gained an exclusive licence to develop and commercialize the ADA treatment, and will co-develop with TIGET gene therapies for six more genetic diseases. The contribution of public or charity-funded organizations in early development phases lowers the cost and risk of investing in diseases with a tiny market, and gives the industry access to technologies that can be expanded to more profitable applications, thereby repaying the investment and allowing resources to be fed back into rare diseases. Unfortunately, promising therapies for hundreds of orphan diseases are unlikely to attract similar industrial interest.

So, how do we ensure that scientists will continue to develop such treatments? Should they all turn to the hospital exemption, which permits experimental therapies to be manufactured and used under the responsibility of a physician without regulatory supervision?

Originally posted here:
Gene therapies need new development models

A new method of genetic testing appears to be able to help doctors diagnose critically ill babies more quickly than ever before, according to a new study.

The method allows doctors for decode a baby's entire genome in two days -- breathtakingly fast compared to current methods that can take six weeks or more.

In the new study, the researchers report using the approach to decode the entire genomes of six acutely ill newborns admitted to neonatal intensive care units, two of whom had already been determined to have genetic diseases. What they found in this proof of concept, they said, could be used in the future to more quickly diagnose sick newborns and treat them early.

The study was published Wednesday in the journal Science Translational Medicine.

"We think that we have come up with a solution for the tragic families who have a baby who's born and the doctors are not sure of what the cause of the baby's illness is," said the study's senior author, Dr. Stephen F. Kingsmore, director of the Center for Pediatric Genomic Medicine at Children's Mercy Hospitals and Clinics in Kansas City, Mo.

Many of the 3,500 known genetic diseases cause medical problems during the first month of life, the researchers wrote in their study. In the United States, over 20 percent of infant deaths are caused by genetic disorders and birth defects.

"Up to one third of babies admitted to a neonatal intensive care unit in the United States have genetic diseases," Kingsmore said, adding that babies with genetic problems often die or are sent home before a diagnosis is made.

For families coping with the tragedy of a sick newborn, the test may make a big difference.

"The family doesn't know what's going on," Kingsmore said. "The doctors are working heroically to figure out what's wrong. That can go on for weeks."

Armed with an early genetic diagnosis, Kingsmore said that doctors can communicate more clearly with the family.

Excerpt from:
Fast Gene Screen May Help Sick Babies

WASHINGTON (AP) Too often, newborns die of genetic diseases before doctors even know what's to blame. Now scientists have found a way to decode those babies' DNA in just days instead of weeks, moving gene-mapping closer to routine medical care.

The idea: Combine faster gene-analyzing machinery with new computer software that, at the push of a few buttons, uses a baby's symptoms to zero in on the most suspicious mutations. The hope would be to start treatment earlier, or avoid futile care for lethal illnesses.

Wednesday's study is a tentative first step: Researchers at Children's Mercy Hospital in Kansas City, Mo., mapped the DNA of just five children, and the study wasn't done in time to help most of them.

But the hospital finds the results promising enough that by year's end, it plans to begin routine gene-mapping in its neonatal intensive care unit and may offer testing for babies elsewhere, too while further studies continue, said Dr. Stephen Kingsmore, director of the pediatric genome center at Children's Mercy.

"For the first time, we can actually deliver genome information in time to make a difference," predicted Kingsmore, whose team reported the method in the journal Science Translational Medicine.

Even if the diagnosis is a lethal disease, "the family will at least have an answer. They won't have false hope," he added.

More than 20 percent of infant deaths are due to a birth defect or genetic diseases, the kind caused by a problem with a single gene. While there are thousands of such diseases from Tay-Sachs to the lesser known Pompe disease, standard newborn screening tests detect only a few of them. And once a baby shows symptoms, fast diagnosis becomes crucial.

Sequencing whole genomes all of a person's DNA can help when it's not clear what gene to suspect. But so far it has been used mainly for research, in part because it takes four to six weeks to complete and is very expensive.

Wednesday, researchers reported that the new process for whole-genome sequencing can take just 50 hours half that time to perform the decoding from a drop of the baby's blood, and the rest to analyze which of the DNA variations uncovered can explain the child's condition.

That's an estimate: The study counted only the time the blood was being decoded or analyzed, not the days needed to ship the blood to Essex, England, home of a speedy new DNA decoding machine made by Illumina, Inc. or to ship back the results for Children's Mercy's computer program to analyze. Kingsmore said the hospital is awaiting arrival of its own decoder, when 50 hours should become the true start-to-finish time.

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Two-day test can spot gene diseases in newborns

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Public release date: 1-Oct-2012 [ | E-mail | Share ]

Contact: Allison Elliott allison.elliott@uky.edu University of Kentucky

LEXINGTON, Ky. (Oct. 1, 2012) Usher syndrome is a hereditary disease in which affected individuals lose both hearing and vision. The impact of Usher syndrome can be devastating. In the United States, approximately six in every 100,000 babies born have Usher syndrome.

Several genes associated with different types of Usher syndrome have been identified. Most of these genes encode common structural and motor proteins that build sensory cells in the eye and inner ear.

In a paper to be published in the November 2012 issue of Nature Genetics, a team of researchers from multiple institutions, led by Zubair M. Ahmed from the University of Cincinnati and Cincinnati Children's Hospital Medical Center, and including Gregory Frolenkov, associate professor in the University of Kentucky College of Medicine Department of Physiology, reported a novel type of gene associated with Usher syndrome - a calcium and integrin binding protein 2 (CIB2).

Zubair M. Ahmed, Saima Riazuddin, Thomas B. Friedman and their teams have identified this gene on chromosome 15 and determined that its mutations are responsible for nonsyndromic deafness and Usher syndrome type I. CIB2 was found to be interacting with other proteins associated with Usher syndrome.

Suzanne Leal and her team at the Baylor College of Medicine found that in Pakistan, CIB2 mutations are one of the prevalent genetic causes of nonsyndromic hearing loss.

Inna Belyantseva at the National Institute on Deafness and Other Communication Disorders, the National Institutes of Health, established that CIB2 is localized at the tips of mechanosensory stereocilia of the inner ear hair cells, exactly where the conversion of sound waves into electrical signals occurs.

Frolenkov and his team at UK demonstrated that disease-associated mutations in CIB2 change the ability of this protein to bind intracellular calcium; in a zebra fish model, its loss disrupts mechanosensitivity in the hair cells.

Furthermore, Tiffany Cook, Elke Buschback and their team at University of Cincinnati knockdown CIB2 analog in Drosophila (fruit fly) eyes and observed calcium-dependent degeneration of photoreceptors and loss of sensitivity to repetitive light pulses.

Read the original here:
Novel gene associated with Usher syndrome identified

ScienceDaily (Sep. 30, 2012) Researchers at the University of Cincinnati and Cincinnati Children's Hospital Medical Center have found a new genetic mutation responsible for deafness and hearing loss associated with Usher syndrome type 1.

These findings, published in the Sept. 30 advance online edition of the journal Nature Genetics, could help researchers develop new therapeutic targets for those at risk for this syndrome.

Partners in the study included the National Institute on Deafness and other Communication Disorders (NIDCD), Baylor College of Medicine and the University of Kentucky.

Usher syndrome is a genetic defect that causes deafness, night-blindness and a loss of peripheral vision through the progressive degeneration of the retina.

"In this study, researchers were able to pinpoint the gene which caused deafness in Usher syndrome type 1 as well as deafness that is not associated with the syndrome through the genetic analysis of 57 humans from Pakistan and Turkey," says Zubair Ahmed, PhD, assistant professor of ophthalmology who conducts research at Cincinnati Children's and is the lead investigator on this study.

Ahmed says that a protein, called CIB2, which binds to calcium within a cell, is associated with deafness in Usher syndrome type 1 and non-syndromic hearing loss.

"To date, mutations affecting CIB2 are the most common and prevalent genetic cause of non-syndromic hearing loss in Pakistan," he says. "However, we have also found another mutation of the protein that contributes to deafness in Turkish populations.

"In animal models, CIB2 is found in the mechanosensory stereocilia of the inner ear -- hair cells, which respond to fluid motion and allow hearing and balance, and in retinal photoreceptor cells, which convert light into electrical signals in the eye, making it possible to see," says Saima Riazuddin, PhD, assistant professor in UC's department of otolaryngology who conducts research at Cincinnati Children's and is co-lead investigator on the study.

Researchers found that CIB2 staining is often brighter at shorter row stereocilia tips than the neighboring stereocilia of a longer row, where it may be involved in calcium signaling that regulates mechano-electrical transduction, a process by which the ear converts mechanical energy -- or energy of motion -- into a form of energy that the brain can recognize as sound.

"With this knowledge, we are one step closer to understanding the mechanism of mechano-electrical transduction and possibly finding a genetic target to prevent non-syndromic deafness as well as that associated with Usher syndrome type 1," Ahmed says.

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Gene that causes a form of deafness discovered