Biopeer

Genes show the way

American researchers have deciphered the role genes play in three cases: breast cancer, Noonan syndrome (NS) and septic shock sensitivity.

Researchers from the University of California, San Francisco, have identified the gene GATA–3 as having a role in the development of breast cancer. This gene is vital for mature mammary cells to retain their maturity in the adult. In the study, conducted on adult mice, they found that when activity of GATA–3 was halted, the cells primarily involved in breast cancer regressed to a state distinctive of metastatic cancer. They multiplied uncontrollably and then died. This new study has helped researchers to understand why breast cancer patients with high GATA–3 expression do better than those with low expression.

While mutations in the PTPN11 gene and KRAS oncogene have been identified as causes for Noonan syndrome, scientists have now recognized mutations in the gene SOS1 as causing NS in certain cases. The findings were based on a study of the genetic analysis of more than 100 children suffering from NS but who did not have either of the known mutations as the cause. Mutations of SOS1 were found in about 20 per cent of the cases. When the scientists tested on mammalian cells, they found that, like the PTPN11 mutations, it encouraged the activities of RAS and MAP kinase. The researchers hope that their findings will aid prenatal diagnosis and genetic counseling for NS.

Also, researchers from New York have isolated the gene that makes some people more susceptible to septic shock. A septic shock is characterized by "cytokine storm," an uncontrollable surge of immune system components. This rush of immune system components destroys vital organs rather than destroying bacteria. Researchers have identified AUF1 as the gene that switches off the rush of immune system components. However, its level of activity differs from person to person, making some people more susceptible to septic shock. Having identified the gene, the researchers believe that now drugs can be developed to control its activity.

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New landmarks in gene research

Researchers at Pennsylvania University have found that gene therapy can be used to treat HIV patients who have not responded well to drug therapy. In the preliminary test conducted on five HIV patients, it was observed that HIV levels in the patients’ blood dropped significantly on infusing genetically modified T cells carrying an altered version of HIV virus into the patients’ blood stream. The research is an important step in the future scope of gene therapy for the treatment of AIDS.

Meanwhile, a missing genetic link in the structural and electrical part of the heart has been discovered to explain the cause for sudden heart failure in many people. Researchers at Baylor College of Medicine (BCM) and Texas Children’s Hospital in Houston have found a gene called Caveolin-3, that has an instrumental impact on the heart’s electrical make up which governs the heart’s rhythm. An absence or a mutation of this gene can disturb the electrical balance thus causing structural changes in the heart, which can lead to heart arrest. The same results were observed in a similar study conducted by researchers at the Mayo Clinic in Rochester, Maryland and at the University of Wisconsin.

In a landmark development in the sphere of gene research and diagnosis, the world’s first gene-based test for diagnosis of breast cancer has been introduced. A Johnson & Johnson company called Veridex has introduced the test in Europe. The GeneSearch™ Breast LymphNode (BLN) test will not only provide early detection but will also aid in patient staging and monitoring.

Role of genes in SIDS and premature birth unraveled

In a breakthrough study, researchers from the University of Manchester have found that abnormal lung development could be one of the causes for cot death. The researchers analyzed DNA from 25 babies who had died from Sudden Infant Death Syndrome (SIDS). They then compared the samples to DNA taken from normal babies. Remarkable differences were found in a gene that produces VEGF, a growth-factor protein important for lung development. There were striking differences also in the gene for cytokine IL-6, a cell-signaling chemical that promotes an inflammatory immune response. With this study, now there are three genes that are strongly associated with SIDS.

Meanwhile, genes have also been tied to premature birth in African-Americans. Researchers from Virginia Commonwealth University's School of Medicine have identified a variation in the SERPINH1 gene as increasing the risk of an early break in the amniotic sac, resulting in premature delivery. Dr Jerome F Strauss III and his colleagues studied the gene variation called the minor "T" allele polymorphism. They found that this polymorphism leads to decreased levels of a protein that stabilizes collagen, leading to weakened fetal membranes. They believe that if the amount of collagen produced could be increased in such cases, then premature birth could be prevented.

In a similar study, Dr Xiaobin Wang, at Children's Memorial Hospital, Chicago, found that a genetic variant of the Prolylcarboxypeptidase gene had a considerable connection with preeclampsia. The only known cure for preeclampsia is delivery of the baby. Often, preeclampsia develops by the 20th week and so the baby is born prematurely. Women having the gene variant, and had chronic hypertension before becoming pregnant, were at an increased risk of developing preeclampsia. It is hoped that this will help doctors to identify and intervene in premature delivery.

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Researchers widen genetic horizons

Three separate studies have made significant contributions to the field of genetics enabling possibly better treatments for Parkinson's disease and muscular dystrophy.

Researchers at the Karolinska Institute, Sweden, have zeroed in on mechanisms that may be one of the causes for Parkinson's disease. The team generated a mouse model in which the gene TFAM is automatically deleted from the genome in the dopamine nerve cells. Without TFAM, mitochondria cannot function properly. It was found that the mice born from genetically modified parents develop the disease slowly in adulthood, like humans with Parkinson's disease. The dopamine producing nerve cells in the brain stem slowly degenerated and that too, in a particular order. The researchers hope that the mouse model will help them to develop drugs that delay, or even stop the death of the nerve cells.

Meanwhile, researchers from the University of Virginia, USA, have found a way to reverse myotonic dystrophy, the most common form of muscular dystrophy (MD), in mice. They created mice with faulty DNA that could be turned on and off by adding or removing an antibiotic to their drinking water. In the "on" phase the mice showed all the cardinal features of myotonic dystrophy. When the DNA was turned off, normal skeletal and cardiac muscle function was restored. Although the treatment was not 100 per cent effective, the researchers believe that their results prove that it might be possible to reverse muscular dystrophy.

In another study, researchers from the University of Florida, USA, have found a new method of gene therapy for hereditary heart conditions, which has been proved successful in animal tests. The approach delivers corrective genes with a single injection into the veins. Tests conducted on mice and monkeys have been successful.

Genetic research continues to advance

In separate studies, researchers from two countries have widened the scope of genetics.

US scientists have found a mutation in a gene that is a major cause of Parkinson’s disease among Eastern European (Ashkenazi) Jews. Researchers from the Albert Einstein College of Medicine of Yeshiva University and Beth Israel Medical Center studied the gene LRRK2 in 120 unrelated Ashnekazi Jewish Parkinson’s disease patients. The participants were compared to a control group comprising 317 Ashenazi Jews who did not have the disease. The researchers extracted DNA from the participants and examined them for mutations. It was found that 18.3 per cent of the Jews suffering from the disease had the G2019S mutation while only 1.3 per cent of the control group had it. The mutation was also detected in 29.7 per cent of those who had a family history of the disease and in 13.3 per cent of the nonfamilial cases. The researchers believe that their findings establish the need for genetic counseling for Parkinson’s disease.

Meanwhile, in a first-of-its-kind achievement, US scientists have managed to reconstruct an ancient gene. Segments of two modern mouse genes, which descended from the ancient one, were combined to reconstruct the 530-million-year-old gene. The genes scrutinized in the study were Hox genes. The scientists claim that the reconstruction is further evidence of the steps of evolution and helps to demystify the process. They also hope that it will give way to a new kind of gene therapy that will be able to cure more diseases.

British researchers have identified why second hand smoke does not affect all children. The research team from the University of Dundee found that defects in the genes that produce glutathione-S-transferase (GST) make children susceptible to the harmful effects of environmental tobacco smoke exposure.

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Your personal genome for $1000

One of the promises of genomics is the ability to have your own genome analyzed and then for you to receive personalized treatments.  Sounds great, but at $20 million a shot, a tad pricey.  A group of researchers have cut that my almost a factor of ten, brining the cost down to $2.2 million.  How?  Drop the fancy and expensive lab equipment and look for ways to use more common tools.

 

A step toward the $1,000 personal genome using readily available lab equipment

A step toward the $1,000 personal genome using   readily available lab equipment

 

BOSTON-August 4, 2005-The theoretical price of having one's personal genome sequenced just fell from the prohibitive $20 million dollars to about $2.2 million, and the goal is to reduce the amount further--to about $1,000--to make individualized prevention and treatment realistic.

The sharp drop is due to a new DNA sequencing   technology developed by Harvard Medical School (HMS) researchers Jay Shendure,   Gregory Porreca, George Church, and their colleagues, reported on August 4 in   the online edition of Science. The team sequenced the E. coli bacterial genome   at a fraction of the cost of conventional sequencing using off-the-shelf   instruments and chemical reagents. Their technology appears to be even more   accurate and less costly than a commercial DNA decoding technology reported   earlier this week.

The Church group's technology is based on converting   a widely available and relatively inexpensive microscope with a digital camera   for use in a rapid automated sequencing process that does not involve the much   slower electrophoresis, a mainstay of the conventional Sanger sequencing   method.

This is, of course, how most research and manufacturing proceeds.  Making a prototype or a few custom one-offs or a single experiment and it's time consuming and expensive.  As time goes on people figure out how to do the same thing with cheaper materials or comment techniques or tools.  Such as the breakthrough in genomics.  With the goal of a $1000 genomic profile, there would be hope that more people will be able to be analyzed, treated, and add to a greater understanding of our genetic diversity (or lack thereof).

 

Technorati Tags : genomics, Harvard+medical+school, gene+sequencing, personal+genome

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Tristram Hussey, M.S. is a professional blogger and blog consultant, the Chief Blogging Officer for Qumana Software, and Managing Director of Qumana Services.  He holds a B.A. in Anthropology and a M.S. in Quaternary Studies.  He can be reached at tris AT qumana DOT com or tris AT trishussey DOT com.

 

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Whither the pharma blockbuster?

From Corante this week commenting on a NYT article—Pharmaceutical companies reconsider the future of blockbuster drugs.  Are the days of the mega blockbuster over?  The drug that everyone must have?  Is the future the custom compound?  With improvements in biotech I certainly think so.  Profit?  The profit is in reduced timelines and less distribution.

 

Perhaps this will a benefit of years genomics research.

 

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Tristram Hussey, M.S. was the webmaster for Glaxo Wellcome and GlaxoSmithKline.  Now he is a professional blogger and blog consultant, the Chief Blogging Officer for Qumana Software, and Managing Director of Qumana Services.  He can be reached at tris AT qumana DOT com or tris AT trishussey DOT com.

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Develop your custom microarrays online...for free

Agilent has announced a new, secure, online portal that allows genomics researchers to develop their own microarrays, for free.  This allows researchers who need to move beyond the pre-canned microarrays provided by many software companies, into the realm of custom microarrays with the click of a mouse.

 

No review or feedback was posted on this article.  If you have tried this service, please leave a comment on how good the service is.  Is it "you get what you pay for" or something that is a real tool that really helps.  Have your shout here.

 

Source:Agilent Technologies Introduces Secure Web Portal for Designing Custom Microarrarys for Genomic Research

 

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IT vendors can help lead the way in Genomics

According to a recent survey leading computer and IT companies like Apple, Microsoft, and Dell are perceived by genomics researchers as being well equipped to help them leverage technology in their field.  This is an interesting finding to me.  I think this shows almost a turning point for high-tech companies.  These companies see the benefit to them, even in a crass marketing sense, to having their products associated with as major breakthrough.  Take the example of Microsoft's anti-spam filter helping to find an HIV vaccine.

 

This is a partnership that certainly moves Microsoft from the realm of monopolistic giant to a company applying their technology in a very positive way.

 

Sources: BioInformatics, LLC  -- The Science Advisory Board  -- Leading IT Vendors Leverage Brand in the Genomics

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