Neuroscience

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Posts tagged mutations

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(Image caption: Various functions of PINK1 within a representative dopaminergic neuron)
New discoveries place lack of energy at the basis of Parkinson’s Disease 
Neuroscientists Vanessa Moraïs and Bart De Strooper from VIB and KU Leuven have demonstrated how a defect in the gene Pink1 results in Parkinson’s disease. By mapping this process at a molecular level, they have provided the ultimate proof that a deficient energy production process in cells can result in Parkinson’s disease. These insights are so revolutionary that they have been published in the leading journal Science.
Vanessa Moraïs (VIB/KU Leuven):“Having Parkinson’s disease means that you can no longer tell your own body what to do. The hope of finding a solution to this has stimulated me for many years to unravel what goes wrong in the cells of Parkinson’s patients. This research is an important step forwards.”
Bart De Strooper (VIB/KU Leuven):“Parkinson’s disease is one of the research focuses in our department. It gives great satisfaction that we have unraveled a molecular process responsible for the faulty energy production process in cells of Parkinson’s patients. This confirms our belief that repairing the energy production in cells is a possible therapeutic strategy.”
Faulty energy production forms the basis of Parkinson’s diseaseMitochondria are cell components that produce the energy required by a cell to function. The action of these mitochondria – and therefore the energy production in cells – is disrupted in Parkinson’s disease. The exact mechanism was unknown. In recent years, scientists have described various gene defects (mutations) in Parkinson’s patients that result in decreased activity of the mitochondria, including a mutation in the Pink1 gene.
Molecular mechanism provides ultimate proofVanessa Moraïs studied the link between Pink1, mitochondria and Parkinson’s disease in fruit-flies and mice with a defective Pink1 gene. These model organisms exhibited symptoms of Parkinson’s disease as a result of this defect. She was able to demonstrate that the defect in Pink1 resulted in the so-called ‘Complex I’ – a protein complex with a crucial role in the energy production of mitochondria – not being phosphorylated adequately, resulting in decreased energy production. When Moraïs and her colleagues ensured correct phosphorylation of Complex I, the Parkinson’s symptoms decreased or disappeared in mice and in patient-derived stem cell lines. The scientists thereby demonstrated that the lack of phosphorylation causes Parkinson’s disease in patients with a defect Pin1 gene.
Further research in Parkinson’s patients with defective Pink1 geneThis study reveals that repairing the phosphorylation of Complex I could be a treatment strategy for Parkinson’s disease. The VIB scientists have already used cells from Parkinson’s patients with a defective Pink1 gene to demonstrate that repairing the phosphorylation results in increased energy production. However, will this cause the symptoms of Parkinson’s disease to decrease or disappear? Only tests on patients can answer this question. According to the scientists, the best strategy would be to start with the sub-group of patients with a defective Pink1 gene. But before starting clinical trials, a lot of aspects still have to be tested.

(Image caption: Various functions of PINK1 within a representative dopaminergic neuron)

New discoveries place lack of energy at the basis of Parkinson’s Disease

Neuroscientists Vanessa Moraïs and Bart De Strooper from VIB and KU Leuven have demonstrated how a defect in the gene Pink1 results in Parkinson’s disease. By mapping this process at a molecular level, they have provided the ultimate proof that a deficient energy production process in cells can result in Parkinson’s disease. These insights are so revolutionary that they have been published in the leading journal Science.

Vanessa Moraïs (VIB/KU Leuven):
“Having Parkinson’s disease means that you can no longer tell your own body what to do. The hope of finding a solution to this has stimulated me for many years to unravel what goes wrong in the cells of Parkinson’s patients. This research is an important step forwards.”

Bart De Strooper (VIB/KU Leuven):
“Parkinson’s disease is one of the research focuses in our department. It gives great satisfaction that we have unraveled a molecular process responsible for the faulty energy production process in cells of Parkinson’s patients. This confirms our belief that repairing the energy production in cells is a possible therapeutic strategy.”

Faulty energy production forms the basis of Parkinson’s disease
Mitochondria are cell components that produce the energy required by a cell to function. The action of these mitochondria – and therefore the energy production in cells – is disrupted in Parkinson’s disease. The exact mechanism was unknown. In recent years, scientists have described various gene defects (mutations) in Parkinson’s patients that result in decreased activity of the mitochondria, including a mutation in the Pink1 gene.

Molecular mechanism provides ultimate proof
Vanessa Moraïs studied the link between Pink1, mitochondria and Parkinson’s disease in fruit-flies and mice with a defective Pink1 gene. These model organisms exhibited symptoms of Parkinson’s disease as a result of this defect. She was able to demonstrate that the defect in Pink1 resulted in the so-called ‘Complex I’ – a protein complex with a crucial role in the energy production of mitochondria – not being phosphorylated adequately, resulting in decreased energy production. When Moraïs and her colleagues ensured correct phosphorylation of Complex I, the Parkinson’s symptoms decreased or disappeared in mice and in patient-derived stem cell lines. The scientists thereby demonstrated that the lack of phosphorylation causes Parkinson’s disease in patients with a defect Pin1 gene.

Further research in Parkinson’s patients with defective Pink1 gene
This study reveals that repairing the phosphorylation of Complex I could be a treatment strategy for Parkinson’s disease. The VIB scientists have already used cells from Parkinson’s patients with a defective Pink1 gene to demonstrate that repairing the phosphorylation results in increased energy production. However, will this cause the symptoms of Parkinson’s disease to decrease or disappear? Only tests on patients can answer this question. According to the scientists, the best strategy would be to start with the sub-group of patients with a defective Pink1 gene. But before starting clinical trials, a lot of aspects still have to be tested.

Filed under parkinson's disease pink1 mitochondria mutations genetics neuroscience science

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Tiny Proteins Have Outsized Influence On Nerve Health
Mutations in small proteins that help convey electrical signals throughout the body may have a surprisingly large effect on health, according to results of a new Johns Hopkins study published in Proceedings of the National Academy of Sciences in December using spider, scorpion and sea anemone venom. 
The tiny conduits carrying those electrical signals are sodium channels that are vital to our well-being—they trigger action potentials, or spurts of electrical energy that course from body to brain to deliver messages that invoke feelings like pain or temperature sensitivity. When such channels go awry, they contribute to a slew of diseases, one of which is epilepsy.
In the new research, Frank Bosmans, Ph.D., an assistant professor of physiology at the Johns Hopkins University School of Medicine, has found that auxiliary “helper” proteins that interact with sodium channels also play a crucial role. And that, he says, could affect drug development for epilepsy, neurological diseases, muscular disorders and pain syndromes.  
“Nobody had thought these tiny molecules that don’t even form the main sodium channel were capable of changing the response of the channel to certain compounds,” Bosmans says. “But in what we consider a new concept, these auxiliary subunits can be considered as drug targets.”
Over the past few decades, there have been hints that these auxiliary proteins were influencing sodium channels, but few analyzed the problem very closely. John Gilchrist, a graduate student in Bosmans’ lab, began evaluating each of the four proteins, one at a time.
Gilchrist engineered frog eggs that made sodium channels and exposed them to the toxins released by tarantulas, scorpions, wasps and sea anemones, an extension of Bosmans’ earlier doctoral research studying the effect of animal venoms on sodium channels. He found that one auxiliary protein in particular, beta4, altered the whole sodium channel system. When exposed to tarantula venom, for instance, tissue in the presence of beta4 showed decreased sensitivity in the sodium channels, meaning that the protein changed the way the nerve fired. This denotes that if a human got bit by a tarantula in a region where beta4 was active, the whole experience might be just a little less painful, says Bosmans.
To figure out what was going on in the altered channels, Bosmans needed to know what the protein looked like, he says. He contacted Filip Van Petegem, a crystallographer at the University of British Columbia in Vancouver, Canada. Van Petegem was able to map the 3-D structure of beta4 down to 1.7 angstroms, the highest possible resolution. Crystal structure in hand, Bosmans could now mutate beta4 and watch what happened. 
Purely by chance, Van Petegem had already started that mutation process. To diagram the crystal, Van Petegem had been forced to substitute one protein for another due to quirks in the test system. Bosmans found that the tiny mutation thwarted beta4’s interaction with the sodium channel system.
That finding promptly overturned conventional wisdom into how these proteins behave, Bosmans says. 
Back in 1998, Bosmans says, physicians determined that a mutation in the beta1 protein seemed to be triggering a case of epilepsy. Epilepsy has hundreds of causes. It was known at the time that a chemical bridge within the sodium channel held the beta proteins together. If that bridge, known as a disulfide bond, is broken, the proteins fall apart. The physicians theorized that the mutation they found must have destroyed the bridge along with their accompanying proteins. That broken bridge theory has remained dominant ever since.
But when Bosmans introduced that same mutation in beta4, the structure stayed intact. The changes he saw were much more subtle. The position of the protein Van Petegem had mutated changed slightly so that it was farther away from the channel. And only when that mutated crystal was exposed to a toxin did beta4 lose its ability to communicate with the sodium channel.
Bosmans says that even with evidence of the auxiliary proteins’ importance mounting, such as in the epilepsy study, drug developers have continued to ignore the proteins rather than treatment opportunities. Most efforts to develop new drugs to treat epilepsy still focus exclusively on modifying the sodium channels, which don’t need the beta proteins to operate. But Bosmans believes this is only part of the story.
His new finding suggests that such an approach is shortsighted, because mutations in these beta proteins may very well be causing the disease at hand. Drugs that target the beta proteins have the potential to deliver a much more focused treatment, he says.
"That’s one of the new concepts that we’re trying to launch—keep an eye on these little guy proteins, because they are important. If they have a mutation in them, they can cause a disease,” Bosmans says. 
(Image credit)

Tiny Proteins Have Outsized Influence On Nerve Health

Mutations in small proteins that help convey electrical signals throughout the body may have a surprisingly large effect on health, according to results of a new Johns Hopkins study published in Proceedings of the National Academy of Sciences in December using spider, scorpion and sea anemone venom

The tiny conduits carrying those electrical signals are sodium channels that are vital to our well-being—they trigger action potentials, or spurts of electrical energy that course from body to brain to deliver messages that invoke feelings like pain or temperature sensitivity. When such channels go awry, they contribute to a slew of diseases, one of which is epilepsy.

In the new research, Frank Bosmans, Ph.D., an assistant professor of physiology at the Johns Hopkins University School of Medicine, has found that auxiliary “helper” proteins that interact with sodium channels also play a crucial role. And that, he says, could affect drug development for epilepsy, neurological diseases, muscular disorders and pain syndromes.  

“Nobody had thought these tiny molecules that don’t even form the main sodium channel were capable of changing the response of the channel to certain compounds,” Bosmans says. “But in what we consider a new concept, these auxiliary subunits can be considered as drug targets.”

Over the past few decades, there have been hints that these auxiliary proteins were influencing sodium channels, but few analyzed the problem very closely. John Gilchrist, a graduate student in Bosmans’ lab, began evaluating each of the four proteins, one at a time.

Gilchrist engineered frog eggs that made sodium channels and exposed them to the toxins released by tarantulas, scorpions, wasps and sea anemones, an extension of Bosmans’ earlier doctoral research studying the effect of animal venoms on sodium channels. He found that one auxiliary protein in particular, beta4, altered the whole sodium channel system. When exposed to tarantula venom, for instance, tissue in the presence of beta4 showed decreased sensitivity in the sodium channels, meaning that the protein changed the way the nerve fired. This denotes that if a human got bit by a tarantula in a region where beta4 was active, the whole experience might be just a little less painful, says Bosmans.

To figure out what was going on in the altered channels, Bosmans needed to know what the protein looked like, he says. He contacted Filip Van Petegem, a crystallographer at the University of British Columbia in Vancouver, Canada. Van Petegem was able to map the 3-D structure of beta4 down to 1.7 angstroms, the highest possible resolution. Crystal structure in hand, Bosmans could now mutate beta4 and watch what happened. 

Purely by chance, Van Petegem had already started that mutation process. To diagram the crystal, Van Petegem had been forced to substitute one protein for another due to quirks in the test system. Bosmans found that the tiny mutation thwarted beta4’s interaction with the sodium channel system.

That finding promptly overturned conventional wisdom into how these proteins behave, Bosmans says. 

Back in 1998, Bosmans says, physicians determined that a mutation in the beta1 protein seemed to be triggering a case of epilepsy. Epilepsy has hundreds of causes. It was known at the time that a chemical bridge within the sodium channel held the beta proteins together. If that bridge, known as a disulfide bond, is broken, the proteins fall apart. The physicians theorized that the mutation they found must have destroyed the bridge along with their accompanying proteins. That broken bridge theory has remained dominant ever since.

But when Bosmans introduced that same mutation in beta4, the structure stayed intact. The changes he saw were much more subtle. The position of the protein Van Petegem had mutated changed slightly so that it was farther away from the channel. And only when that mutated crystal was exposed to a toxin did beta4 lose its ability to communicate with the sodium channel.

Bosmans says that even with evidence of the auxiliary proteins’ importance mounting, such as in the epilepsy study, drug developers have continued to ignore the proteins rather than treatment opportunities. Most efforts to develop new drugs to treat epilepsy still focus exclusively on modifying the sodium channels, which don’t need the beta proteins to operate. But Bosmans believes this is only part of the story.

His new finding suggests that such an approach is shortsighted, because mutations in these beta proteins may very well be causing the disease at hand. Drugs that target the beta proteins have the potential to deliver a much more focused treatment, he says.

"That’s one of the new concepts that we’re trying to launch—keep an eye on these little guy proteins, because they are important. If they have a mutation in them, they can cause a disease,” Bosmans says. 

(Image credit)

Filed under sodium channels mutations epilepsy auxiliary proteins neuroscience science

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Diabetes Gene Common In Latinos Has Ancient Roots
When it comes to the rising prevalence of Type 2 diabetes, there are many factors to blame.
Diet and exercise sit somewhere at the top of the list. But the genes that some of us inherit from Mom and Dad also help determine whether we develop the disease, and how early it crops up.
Now an international team of scientists have identified mutations in a gene that suggests an explanation for why Latinos are almost twice as likely to develop Type 2 diabetes as Caucasians and African-Americans.
But here’s the kicker: You have to go further back on the family tree than your parents to find who’s to blame for this genetic link to diabetes. Think thousands of generations ago.
Harvard geneticist and his colleagues uncovered hints that humans picked up the diabetes mutations from Neanderthals, our ancient cousins who went extinct about 30,000 years ago.
"As far as I know, this is the first time a version of a gene from Neanderthal has been connected to a modern-day disease," Altshuler tells Shots. He and his colleagues the findings Wednesday in the journal Nature.
A few years ago, geneticists at the in Germany sent shock waves through the scientific community when they the genome of a Neanderthal from a fossil. Hidden in the genetic code were patterns that matched those in human DNA. And the data strongly suggested that humans were more than just friendly neighbors with Neanderthal.
"Now it’s well accepted that humans interbred with Neanderthals," Altshuler says. On average most of us carry about 2 percent of Neanderthal DNA in our genome. So it’s not surprising, he says, that 2 percent of our traits would be inherited from the ancient primates.
The new data don’t mean that Neanderthals had diabetes, Altshuler is quick to point out. “It just happens that this disease sequence came from them,” he says.
To identify genes that contribute to Latinos’ high rate of Type 2 diabetes, Altshuler and his team analyzed DNA from over 8,000 Mexicans and other Latinos.
The team found many genes already known to be involved with diabetes, such as one related to insulin production. But a new one also popped up in the analysis: a gene that’s likely involved in fat metabolism.
Mutations in this gene increase a person’s risk of getting Type 2 diabetes by about a 20 percent, Altshuler and the team found. If the person has two copies of the mutations, one from each parent, the risk rises by about 40 percent.
So for Mexican Americans, their for Type 2 diabetes goes from about 13 percent to 19 percent if they inherit two copies of the mutations. For other Americans, the risk gets boosted to about 11 percent from 8 percent.
"This is a genetic factor that has a modest affect on the risk of getting the disease. Not everybody that has it will have the disease," Altshuler says. "But the genes are very common in Latinos and Asians."
About half of Latinos carry the disease mutations, while 20 percent of Asians have it. On the other hand, only 2 percent of European Americans carry the mutations.
So the new genetic data help to explain a big chunk — perhaps almost a quarter — of the difference in Type 2 diabetes prevalence in Latinos versus European Americans.
"The findings are important because they give us a new biological clue about a gene involved in diabetes, which could lead to more treatments," Altshuler says. "The Neanderthal connection is interesting, but it’s not the essence of the work."

Diabetes Gene Common In Latinos Has Ancient Roots

When it comes to the rising prevalence of Type 2 diabetes, there are many factors to blame.

Diet and exercise sit somewhere at the top of the list. But the genes that some of us inherit from Mom and Dad also help determine whether we develop the disease, and how early it crops up.

Now an international team of scientists have identified mutations in a gene that suggests an explanation for why Latinos are almost twice as likely to develop Type 2 diabetes as Caucasians and African-Americans.

But here’s the kicker: You have to go further back on the family tree than your parents to find who’s to blame for this genetic link to diabetes. Think thousands of generations ago.

Harvard geneticist and his colleagues uncovered hints that humans picked up the diabetes mutations from Neanderthals, our ancient cousins who went extinct about 30,000 years ago.

"As far as I know, this is the first time a version of a gene from Neanderthal has been connected to a modern-day disease," Altshuler tells Shots. He and his colleagues the findings Wednesday in the journal Nature.

A few years ago, geneticists at the in Germany sent shock waves through the scientific community when they the genome of a Neanderthal from a fossil. Hidden in the genetic code were patterns that matched those in human DNA. And the data strongly suggested that humans were more than just friendly neighbors with Neanderthal.

"Now it’s well accepted that humans interbred with Neanderthals," Altshuler says. On average most of us carry about 2 percent of Neanderthal DNA in our genome. So it’s not surprising, he says, that 2 percent of our traits would be inherited from the ancient primates.

The new data don’t mean that Neanderthals had diabetes, Altshuler is quick to point out. “It just happens that this disease sequence came from them,” he says.

To identify genes that contribute to Latinos’ high rate of Type 2 diabetes, Altshuler and his team analyzed DNA from over 8,000 Mexicans and other Latinos.

The team found many genes already known to be involved with diabetes, such as one related to insulin production. But a new one also popped up in the analysis: a gene that’s likely involved in fat metabolism.

Mutations in this gene increase a person’s risk of getting Type 2 diabetes by about a 20 percent, Altshuler and the team found. If the person has two copies of the mutations, one from each parent, the risk rises by about 40 percent.

So for Mexican Americans, their for Type 2 diabetes goes from about 13 percent to 19 percent if they inherit two copies of the mutations. For other Americans, the risk gets boosted to about 11 percent from 8 percent.

"This is a genetic factor that has a modest affect on the risk of getting the disease. Not everybody that has it will have the disease," Altshuler says. "But the genes are very common in Latinos and Asians."

About half of Latinos carry the disease mutations, while 20 percent of Asians have it. On the other hand, only 2 percent of European Americans carry the mutations.

So the new genetic data help to explain a big chunk — perhaps almost a quarter — of the difference in Type 2 diabetes prevalence in Latinos versus European Americans.

"The findings are important because they give us a new biological clue about a gene involved in diabetes, which could lead to more treatments," Altshuler says. "The Neanderthal connection is interesting, but it’s not the essence of the work."

Filed under diabetes type ii diabetes mutations genetics genomics neuroscience science

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Gene linked to common intellectual disability

University of Adelaide researchers have taken a step forward in unravelling the causes of a commonly inherited intellectual disability, finding that a genetic mutation leads to a reduction in certain proteins in the brain.

ARX is among the top four types of intellectual disability linked to the X-chromosome in males. So far, 115 families, including many large Australian families, have been discovered to carry an ARX (Aristaless related homeobox) mutation that gives rise to intellectual disability.

"There is considerable variation in the disability across families, and within families with a single mutation. Symptoms among males always include intellectual disability, as well as a range of movement disorders of the hand, and in some cases severe seizures," says Associate Professor Cheryl Shoubridge, Head of Molecular Neurogenetics with the University of Adelaide’s Robinson Institute.

ARX mutations were first discovered by the University of Adelaide’s Professor Jozef Gecz in 2002. To date, researchers have detected 52 different ARX mutations and 10 distinct clinical syndromes.

Associate Professor Shoubridge is lead author of a new paper on ARX intellectual disability published in the journal Human Molecular Genetics.

In laboratory studies, Associate Professor Shoubridge’s team has shown that mutations lead to a significant reduction in ARX proteins in the brain, but the actual causes and mechanisms involved in this remain unknown. Her team tested six genes that the ARX protein interacts with, and found that one of them - a gene likely to be important to early brain development - appears to be adversely affected by the reduction of ARX proteins.

"This plays an important role in setting up architecture and networks in the brain, which become disrupted due to the mutation", Associate Professor Shoubridge says.

"The discovery of this genetic link is an important step forward but there is still much work to be done. We’re now looking further at the mechanism of the reduction in ARX protein and what that means for the brain at a functional level."

Associate Professor Shoubridge says up to 3% of the population is affected by some kind of intellectual disability, costing $14.7 billion each year in Australia alone.

"The personal cost to families is enormous, especially in the most severe cases. Being able to unravel why and how these disabilities occur is very important to us and to the many people whose lives are affected by these conditions," she says.

(Source: adelaide.edu.au)

Filed under intellectual disability x chromosome ARX brain mapping mutations genetics neuroscience science

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Scientists fish for new epilepsy model and reel in potential drug

NIH-funded study finds zebrafish model may help identify treatments for a severe form of childhood epilepsy

image

According to new research on epilepsy, zebrafish have certainly earned their stripes. Results of a study in Nature Communications suggest that zebrafish carrying a specific mutation may help researchers discover treatments for Dravet syndrome (DS), a severe form of pediatric epilepsy that results in drug-resistant seizures and developmental delays.

Scott C. Baraban, Ph.D., and his colleagues at the University of California, San Francisco (UCSF), carefully assessed whether the mutated zebrafish could serve as a model for DS, and then developed a new screening method to quickly identify potential treatments for DS using these fish. This study was supported by the National Institute of Neurological Disorders and Stroke (NINDS), part of the National Institutes of Health and builds on pioneering epilepsy zebrafish models first described by the Baraban laboratory in 2005.

Dravet syndrome is commonly caused by a mutation in the Scn1a gene, which encodes for Nav1.1, a specific sodium ion channel found in the brain. Sodium ion channels are critical for communication between brain cells and proper brain functioning.

The researchers found that the zebrafish that were engineered to have the Scn1a mutation that causes DS in humans exhibited some of the same characteristics, such as spontaneous seizures, commonly seen in children with DS. Unprovoked seizure activity in the mutant fish resulted in hyperactivity and whole-body convulsions associated with very fast swimming. These types of behaviors are not seen in normal healthy zebrafish.

“We were also surprised at how similar the mutant zebrafish drug profile was to that of Dravet patients,” said Dr. Baraban. “Antiepileptic drugs shown to have some benefits in patients (such as benzodiazepines or stiripentol) also exhibited some antiepileptic activity in these mutants. Conversely, many of the antiepileptic drugs that do not reduce seizures in these patients showed no effect in the mutant zebrafish.”

In this study, the researchers developed a fast and automated drug screen to quickly test the effectiveness of various compounds in mutant zebrafish. The researchers tracked behavior and measured brain activity in the mutant zebrafish to determine if the compounds had an impact on seizures.

“Scn1a mutants seize often, so it is relatively easy to monitor their seizure behavior at baseline and then again after a drug application,” said Dr. Baraban. “Using zebrafish placed individually in a 96-part petri dish we can accurately quantify this seizure behavior. In this way, we can test almost 100 fish at one time and quickly determine whether a drug candidate has any effect on these spontaneous seizures.”

In the first such application of this approach, UCSF researchers screened 320 compounds and found that clemizole was most effective in inhibiting seizure activity. Clemizole is approved by the U.S. Food and Drug Administration and has a safe toxicology profile. “This finding was completely unexpected. Based on what is currently known about clemizole, we did not predict that it would have antiepileptic effects,” said Dr. Baraban.

These findings suggest that Scn1a mutant zebrafish may serve as a good model of DS and that the drug screen may be effective in quickly identifying novel therapies for epilepsy. 

Dr. Baraban also noted that someday these experiments can be “personalized,” by looking at mutated zebrafish that use genetic information from individual patients. 

(Source: ninds.nih.gov)

Filed under Dravet syndrome epilepsy zebrafish ion channels Scn1a gene mutations neuroscience science

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Hospital scientists identify ALS disease mechanism

Study strengthens link between amyotrophic lateral sclerosis (ALS) and problems in protein production machinery of cells and identifies possible treatment strategy

Researchers have tied mutations in a gene that causes amyotrophic lateral sclerosis (ALS) and other neurodegenerative disorders to the toxic buildup of certain proteins and related molecules in cells, including neurons. The research, published recently in the scientific journal Cell, offers a new approach for developing treatments against these devastating diseases.

Scientists at St. Jude Children’s Research Hospital and the University of Colorado, Boulder, led the work.

The findings provide the first evidence that a gene named VCP plays a role in the break-up and clearance of protein and RNA molecules that accumulate in temporary structures called RNA granules. RNAs perform a variety of vital cell functions, including protein production. RNA granules support proper functioning of RNA.

In ALS and related degenerative diseases, the process of assembling and clearing RNA granules is impaired. The proteins and RNAs associated with the granules often build up in nerve cells of patients. This study shows how mutations in VCP might contribute to that process and neurodegenerative disease.

“The results go a long way to explaining the process that links a variety of neurodegenerative diseases, including ALS, frontotemporal dementia and related diseases of the brain, muscle and bone known as multisystem proteinopathies,” said the study’s co-corresponding author, J. Paul Taylor, M.D., Ph.D., a member of the St. Jude Department of Developmental Neurobiology. Roy Parker, Ph.D., of the University of Colorado’s Department of Chemistry and Biochemistry and the Howard Hughes Medical Institute (HHMI), is the other corresponding author.

ALS, also known as Lou Gehrig’s disease, is diagnosed in about 5,600 Americans annually and is associated with progressive deterioration of nerve cells in the brain and spine that govern movement, including breathing. There is no effective treatment, and death usually occurs within five years.

“A strength of this study is that it provides a unifying hypothesis about how different genetic mutations all affect stress granules, which suggests that understanding stress granule dynamics and how they can be manipulated might be beneficial for treatment of these diseases,” Parker said.

Earlier work from Taylor’s laboratory identified mutations in VCP as a cause of ALS and related multisystem proteinopathies. Until now, however, little was known about how those mistakes caused disease. The latest findings appeared in the June 20 issue and are highlighted in a review article published in the August 15 issue of Cell.

The research also ties VCP mutations to disruption of RNA regulation, which prior studies have connected to the progression of neurodegenerative diseases, said Regina-Maria Kolaitis, Ph.D., a postdoctoral fellow in Taylor’s laboratory. She and Ross Buchan, Ph.D., a postdoctoral fellow in Parker’s laboratory, are co-first authors.

The work focused on a class of RNA granules called stress granules. They are formed by proteins and an RNA molecule called mRNA that accumulates in the cell cytoplasm in response to stress. Stressed cells do not want to waste energy producing unnecessary proteins. Stress granules are one mechanism cells use to halt production until the cellular environment normalizes, which is when stress granules typically dissolve.

Proteins found in stress granules include RNA-binding proteins like TDP-43, FUS, hnRNPA1 and hnRNPA2B1 that regulate gene activity. Mutations in those proteins can also cause ALS and related disorders.

VCP has many functions in cells, but it is not an RNA-binding protein and until now it was not connected to stress granules or RNA processing,” Kolaitis said. “This study provides a new window into the disease process, highlighting VCP’s role in keeping cells healthy.”

For this study, researchers used yeast to identify a network of 125 genes that affect the formation and behavior of stress granules. One of the genes that appeared to play a central role in the network was CDC48, which functions like VCP in yeast. In addition, many of the genes identified are involved in a process called autophagy that cells use to break down and recycle unneeded molecules, including proteins.

Working in yeast and mammalian cells, researchers showed that stress granules are cleared by autophagy, which stalled when VCP was mutated. Researchers also reported that stress granules accumulated following mutation of either CDC48 or VCP.

“This work suggests that activating autophagy to help rid cells of stress granules offers a new approach to neurodegenerative disease treatment,” Taylor said.

(Source: stjude.org)

Filed under ALS neurodegenerative diseases stress granules mRNA mutations neuroscience science

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Researchers discover a potential cause of autism
Key enzymes are found to have a ‘profound effect’ across dozens of genes linked to autism. The insight could help illuminate environmental factors behind autism spectrum disorder and contribute to a unified theory of how the disorder develops. 
Problems with a key group of enzymes called topoisomerases can have profound effects on the genetic machinery behind brain development and potentially lead to autism spectrum disorder (ASD), according to research announced today in the journal Nature. Scientists at the University of North Carolina School of Medicine have described a finding that represents a significant advance in the hunt for environmental factors behind autism and lends new insights into the disorder’s genetic causes.
“Our study shows the magnitude of what can happen if topoisomerases are impaired,” said senior study author Mark Zylka, PhD, associate professor in the Neuroscience Center and the Department of Cell Biology and Physiology at UNC. “Inhibiting these enzymes has the potential to profoundly affect neurodevelopment — perhaps even more so than having a mutation in any one of the genes that have been linked to autism.”
The study could have important implications for ASD detection and prevention.
“This could point to an environmental component to autism,” said Zylka. “A temporary exposure to a topoisomerase inhibitor in utero has the potential to have a long-lasting effect on the brain, by affecting critical periods of brain development. ”
This study could also explain why some people with mutations in topoisomerases develop autism and other neurodevelopmental disorders.
Topiosomerases are enzymes found in all human cells. Their main function is to untangle DNA when it becomes overwound, a common occurrence that can interfere with key biological processes.
Most of the known topoisomerase-inhibiting chemicals are used as chemotherapy drugs. Zylka said his team is searching for other compounds that have similar effects in nerve cells. “If there are additional compounds like this in the environment, then it becomes important to identify them,” said Zylka. “That’s really motivating us to move quickly to identify other drugs or environmental compounds that have similar effects — so that pregnant women can avoid being exposed to these compounds.”
Zylka and his colleagues stumbled upon the discovery quite by accident while studying topotecan, a topoisomerase-inhibiting drug that is used in chemotherapy. Investigating the drug’s effects in mouse and human-derived nerve cells, they noticed that the drug tended to interfere with the proper functioning of genes that were exceptionally long — composed of many DNA base pairs. The group then made the serendipitous connection that many autism-linked genes are extremely long.
“That’s when we had the ‘Eureka moment,’” said Zylka. “We realized that a lot of the genes that were suppressed were incredibly long autism genes.”
Of the more than 300 genes that are linked to autism, nearly 50 were suppressed by topotecan. Suppressing that many genes across the board — even to a small extent — means a person who is exposed to a topoisomerase inhibitor during brain development could experience neurological effects equivalent to those seen in a person who gets ASD because of a single faulty gene.
The study’s findings could also help lead to a unified theory of how autism-linked genes work. About 20 percent of such genes are connected to synapses — the connections between brain cells. Another 20 percent are related to gene transcription — the process of translating genetic information into biological functions. Zylka said this study bridges those two groups, because it shows that having problems transcribing long synapse genes could impair a person’s ability to construct synapses.
“Our discovery has the potential to unite these two classes of genes — synaptic genes and transcriptional regulators,” said Zylka. “It could ultimately explain the biological mechanisms behind a large number of autism cases.”

Researchers discover a potential cause of autism

Key enzymes are found to have a ‘profound effect’ across dozens of genes linked to autism. The insight could help illuminate environmental factors behind autism spectrum disorder and contribute to a unified theory of how the disorder develops.

Problems with a key group of enzymes called topoisomerases can have profound effects on the genetic machinery behind brain development and potentially lead to autism spectrum disorder (ASD), according to research announced today in the journal Nature. Scientists at the University of North Carolina School of Medicine have described a finding that represents a significant advance in the hunt for environmental factors behind autism and lends new insights into the disorder’s genetic causes.

“Our study shows the magnitude of what can happen if topoisomerases are impaired,” said senior study author Mark Zylka, PhD, associate professor in the Neuroscience Center and the Department of Cell Biology and Physiology at UNC. “Inhibiting these enzymes has the potential to profoundly affect neurodevelopment — perhaps even more so than having a mutation in any one of the genes that have been linked to autism.”

The study could have important implications for ASD detection and prevention.

“This could point to an environmental component to autism,” said Zylka. “A temporary exposure to a topoisomerase inhibitor in utero has the potential to have a long-lasting effect on the brain, by affecting critical periods of brain development. ”

This study could also explain why some people with mutations in topoisomerases develop autism and other neurodevelopmental disorders.

Topiosomerases are enzymes found in all human cells. Their main function is to untangle DNA when it becomes overwound, a common occurrence that can interfere with key biological processes.

Most of the known topoisomerase-inhibiting chemicals are used as chemotherapy drugs. Zylka said his team is searching for other compounds that have similar effects in nerve cells. “If there are additional compounds like this in the environment, then it becomes important to identify them,” said Zylka. “That’s really motivating us to move quickly to identify other drugs or environmental compounds that have similar effects — so that pregnant women can avoid being exposed to these compounds.”

Zylka and his colleagues stumbled upon the discovery quite by accident while studying topotecan, a topoisomerase-inhibiting drug that is used in chemotherapy. Investigating the drug’s effects in mouse and human-derived nerve cells, they noticed that the drug tended to interfere with the proper functioning of genes that were exceptionally long — composed of many DNA base pairs. The group then made the serendipitous connection that many autism-linked genes are extremely long.

“That’s when we had the ‘Eureka moment,’” said Zylka. “We realized that a lot of the genes that were suppressed were incredibly long autism genes.”

Of the more than 300 genes that are linked to autism, nearly 50 were suppressed by topotecan. Suppressing that many genes across the board — even to a small extent — means a person who is exposed to a topoisomerase inhibitor during brain development could experience neurological effects equivalent to those seen in a person who gets ASD because of a single faulty gene.

The study’s findings could also help lead to a unified theory of how autism-linked genes work. About 20 percent of such genes are connected to synapses — the connections between brain cells. Another 20 percent are related to gene transcription — the process of translating genetic information into biological functions. Zylka said this study bridges those two groups, because it shows that having problems transcribing long synapse genes could impair a person’s ability to construct synapses.

“Our discovery has the potential to unite these two classes of genes — synaptic genes and transcriptional regulators,” said Zylka. “It could ultimately explain the biological mechanisms behind a large number of autism cases.”

Filed under autism ASD topoisomerases mutations brain development neuroscience science

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New insight into the human genome through the lens of evolution

By comparing the human genome to the genomes of 34 other mammals, Australian scientists have described an unexpectedly high proportion of functional elements conserved through evolution.

Less than 1.5% of the human genome is devoted to conventional genes, that is, encodes for proteins.  The rest has been considered to be largely junk.  However, while other studies have shown that around 5-8% of the genome is conserved at the level of DNA sequence, indicating that it is functional, the new study shows that in addition much more, possibly up to 30%, is also conserved at the level of RNA structure.

DNA is a biological blueprint that must be copied into another form before it can be actualised. Through a process known as ‘transcription’, DNA is copied into RNA, some of which ‘encodes’ the proteins that carry out the biological tasks within our cells. Most RNA molecules do not code for protein, but instead perform regulatory functions, such as determining the ways in which genes are expressed.

Like infinitesimally small Lego blocks, the nucleic acids that make up RNA connect to each other in very specific ways, which force RNA molecules to twist and loop into a variety of complicated 3D structures.

Dr Martin Smith and Professor John Mattick, from Sydney’s Garvan Institute of Medical Research, devised a method for predicting these complex RNA structures – more accurate than those used in the past – and applied it to the genomes of 35 different mammals, including bats, mice, pigs, cows, dolphins and humans. At the same time, they matched mutations found in the genomes with consistent RNA structures, inferring conserved function. Their findings are published in Nucleic Acids Research, now online.

“Genomes accumulate mutations over time, some of which don’t change the structure of associated RNAs. If the sequence changes during evolution, yet the RNA structure stays the same, then the principles of natural selection suggest that the structure is functional and is required for the organism,” explained Dr Martin Smith.

“Our hypothesis is that structures conserved in RNA are like a common template for regulating gene expression in mammals – and that this could even be extrapolated to vertebrates and less complex organisms.”

“We believe that RNA structures probably operate in a similar way to proteins, which are composed of structural domains that assemble together to give the protein a function.”

“We suspect that many RNA structures recruit specific molecules, such as proteins or other RNAs, helping these recruited elements to bond with each other. That’s the general hypothesis at the moment – that non-coding RNAs serve as scaffolds, tethering various complexes together, especially those that control genome organization and expression during development.”

“We know that many RNA transcripts are associated with diseases and developmental conditions, and that they are differentially expressed in distinct cells.”

“Our structural predictions can serve as an annotative tool to help researchers understand the function of these RNA transcripts.”

“That is the first step – the next is to describe the structures in more detail, figure out exactly what they do in the cell, then work out how they relate to our normal development and to disease.”

(Source: garvan.org.au)

Filed under mammals human genome evolution mutations gene expression science

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Suspicions confirmed: Common cause for brain tumors in children
An overactive signaling pathway is a common cause in cases of pilocytic astrocytoma, the most frequent type of brain cancer in children. This was discovered by a network of scientists coordinated by the German Cancer Research Center (as part of the International Cancer Genome Consortium, ICGC). In all 96 cases studied, the researchers found defects in genes involved in a particular pathway. Hence, drugs can be used to help affected children by blocking components of the signaling cascade. The project is funded by the German Cancer Aid (Deutsche Krebshilfe) and the Federal Ministry of Education and Research (BMBF). The findings are published in the latest issue of the journal “Nature Genetics”. 
Brain cancer is the primary cause of cancer mortality in children. Even in cases when the cancer is cured, young patients suffer from the stress of a treatment that can be harmful to the developing brain. In a search for new target structures that would create more gentle treatments, cancer researchers are systematically analyzing all alterations in the genetic material of these tumors. This is the mission of the PedBrain consortium, which was launched in 2010. Led by Professor Stefan Pfister from the German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ), the PedBrain researchers have now published the results of the first 96 genome analyses of pilocytic astrocytomas.
Pilocytic astrocytomas are the most common childhood brain tumors. These tumors usually grow very slowly. However, they are often difficult to access by surgery and cannot be completely removed, which means that they can recur. The disease may thus become chronic and have debilitating effects for affected children.
In previous work, teams of researchers led by Professor Dr. Stefan Pfister and Dr. David Jones had already discovered characteristic mutations in a major proportion of pilocytic astrocytomas. All of the changes involved a key cellular signaling pathway known as the MAPK signaling cascade. MAPK is an abbreviation for “mitogen-activated protein kinase.” This signaling pathway comprises a cascade of phosphate group additions (phosphorylation) from one protein to the next – a universal method used by cells to transfer messages to the nucleus. MAPK signaling regulates numerous basic biological processes such as embryonic development and differentiation and the growth and death of cells.
“A couple of years ago, we had already hypothesized that pilocytic astrocytomas generally arise from a defective activation of MAPK signaling,” says David Jones, first author of the publication. “However, in about one fifth of the cases we had not initially discovered these mutations. In a whole-genome analysis of 96 tumors we have now discovered activating defects in three other genes involved in the MAPK signaling pathway that have not previously been described in astrocytoma.”
“Aside from MAPK mutations, we do not find any other frequent mutations that could promote cancer growth in the tumors. This is a very clear indication that overactive MAPK signals are necessary for a pilocytic astrocytoma to develop,” says study director Stefan Pfister. The disease thus is a prototype for rare cancers that are based on defects in a single biological signaling process.
In total, the genomes of pilocytic astrocytomas contain far fewer mutations than are found, for example, in medulloblastomas, a much more malignant pediatric brain tumor. This finding is in accordance with the more benign growth behavior of astrocytomas. The number of mutations increases with the age of the affected individuals.
About one half of pilocytic astrocytomas develop in the cerebellum, the other 50 percent in various other brain regions. Cerebellar astrocytomas are genetically even more homogenous than other cases of the disease: In 48 out of 49 cases that were studied, the researchers found fusions between the BRAF gene, a central component of the MAPK signaling pathway, and various other fusion partners.
“The most important conclusion from our results,” says study director Stefan Pfister, “is that targeted agents for all pilocytic astrocytomas are potentially available to block an overactive MAPK signaling cascade at various points. We might thus in the future be able to also help children whose tumors are difficult to access by surgery.”

Suspicions confirmed: Common cause for brain tumors in children

An overactive signaling pathway is a common cause in cases of pilocytic astrocytoma, the most frequent type of brain cancer in children. This was discovered by a network of scientists coordinated by the German Cancer Research Center (as part of the International Cancer Genome Consortium, ICGC). In all 96 cases studied, the researchers found defects in genes involved in a particular pathway. Hence, drugs can be used to help affected children by blocking components of the signaling cascade. The project is funded by the German Cancer Aid (Deutsche Krebshilfe) and the Federal Ministry of Education and Research (BMBF). The findings are published in the latest issue of the journal “Nature Genetics”.

Brain cancer is the primary cause of cancer mortality in children. Even in cases when the cancer is cured, young patients suffer from the stress of a treatment that can be harmful to the developing brain. In a search for new target structures that would create more gentle treatments, cancer researchers are systematically analyzing all alterations in the genetic material of these tumors. This is the mission of the PedBrain consortium, which was launched in 2010. Led by Professor Stefan Pfister from the German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ), the PedBrain researchers have now published the results of the first 96 genome analyses of pilocytic astrocytomas.

Pilocytic astrocytomas are the most common childhood brain tumors. These tumors usually grow very slowly. However, they are often difficult to access by surgery and cannot be completely removed, which means that they can recur. The disease may thus become chronic and have debilitating effects for affected children.

In previous work, teams of researchers led by Professor Dr. Stefan Pfister and Dr. David Jones had already discovered characteristic mutations in a major proportion of pilocytic astrocytomas. All of the changes involved a key cellular signaling pathway known as the MAPK signaling cascade. MAPK is an abbreviation for “mitogen-activated protein kinase.” This signaling pathway comprises a cascade of phosphate group additions (phosphorylation) from one protein to the next – a universal method used by cells to transfer messages to the nucleus. MAPK signaling regulates numerous basic biological processes such as embryonic development and differentiation and the growth and death of cells.

“A couple of years ago, we had already hypothesized that pilocytic astrocytomas generally arise from a defective activation of MAPK signaling,” says David Jones, first author of the publication. “However, in about one fifth of the cases we had not initially discovered these mutations. In a whole-genome analysis of 96 tumors we have now discovered activating defects in three other genes involved in the MAPK signaling pathway that have not previously been described in astrocytoma.”

“Aside from MAPK mutations, we do not find any other frequent mutations that could promote cancer growth in the tumors. This is a very clear indication that overactive MAPK signals are necessary for a pilocytic astrocytoma to develop,” says study director Stefan Pfister. The disease thus is a prototype for rare cancers that are based on defects in a single biological signaling process.

In total, the genomes of pilocytic astrocytomas contain far fewer mutations than are found, for example, in medulloblastomas, a much more malignant pediatric brain tumor. This finding is in accordance with the more benign growth behavior of astrocytomas. The number of mutations increases with the age of the affected individuals.

About one half of pilocytic astrocytomas develop in the cerebellum, the other 50 percent in various other brain regions. Cerebellar astrocytomas are genetically even more homogenous than other cases of the disease: In 48 out of 49 cases that were studied, the researchers found fusions between the BRAF gene, a central component of the MAPK signaling pathway, and various other fusion partners.

“The most important conclusion from our results,” says study director Stefan Pfister, “is that targeted agents for all pilocytic astrocytomas are potentially available to block an overactive MAPK signaling cascade at various points. We might thus in the future be able to also help children whose tumors are difficult to access by surgery.”

Filed under brain cancer pilocytic astrocytoma brain tumor genes mutations genetics neuroscience science

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Decoding Rett syndrome: New pieces to the puzzle

Rett Syndrome is a neurological disorder that affects about 1 in 10,000 girls. Back in 1992, University of Edinburgh researcher Adrian Bird discovered that the protein, MeCP2, plays a major role in the disease. The story of MeCP2 is in many ways a microcosm of human genetics. It has become the showcase gene for many complex epi-genetic phenomena including X-linked inactivation, DNA methylation, and genomic imprinting. These gender-specific bargaining chips provide compatibility in an evolutionary system where sex-chromosome provisioning is inherently assymetric. In two new papers, one in Nature and the the other in Nature Neuroscience, Bird and collaborator Michael Greenberg, show how mutations found in Rett Syndrome affect the interaction of MeCP2 with a key regulatory protein known as NCoR.

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Nearly all cases of Rett Syndrome are caused by mutations at various postions in the MeCP2 gene. Bird and Greenberg analyzed the locations of these mutations using the RettBase MeCp2 database, and found they cluster to two primary locations—the well-known methyl-CpG binding domain, and a new hotspot within a transcriptional repressor domain (TRD). When they compared these locations with mutations found in the general population by using the Exome Variant Server, they found no overlap. This suggests the that the MeCP2 and TRD regions are the primary regions involved in Rett’s.

The researchers hypothesized that the newly found TRD region must act through a unknown regulator of MeCP2 function. Using mass spectrometry, they were able to identify several factors which they had purified from Mecp2-EGFP “knock-in” mice. Most of these factors turned out to be subunits of the co-repressor, NCoR, which was previously known to interact with MeCP2. This is the first identified example of a protein-protein interaction known to be disrupted in Rett’s.

In the Nature paper, the researchers further report that activity-dependent phosphorylation of MeCP2 mediates its interaction with NCoR. They used a technique known as phosphotryptic mapping to identify three sites that are directly phosphorylated in MeCP2 as a result of elevation in cAMP or BDNF. More generally, they showed that membrane depolarization, and therefore activity, results in the phosporylation.

One confounding factor in trying to pinpoint the mechanisms underlying Rett Syndrome is that both loss of MeCP2, and overexpression of MeCP2, can lead to the disease. In mouse models of the disease, this could be accounted for by the observation that both loss of NCoR binding, and constitutive binding of NCoR can lead to disease symptoms. While not a complete explanation of the role of MeCP2 in the disease, it provides some clues to help dissect the involvement of the many different kinds of mutations involved.

Despite the rarity of Rett’s syndrome, its impact on our understanding of human genetics and neural development should not be underestimated. As one of the autistic spectrum disorders, research on Rett’s helps connect molecular mechanics to behavior. For example, when MeCP2 is bound to DNA it can cause condensation of the chromatin structure, and also form complexes with histone deacetylaces. In demostrating that neural activity, and subsequent signal tranduction pathways, lead to modifications of MeCP2, the researchers have revealed a path from the environment directly to the genes.

The X-linked inactivation of one copy of the MeCP2 gene in females adds another layer of complexity to the disease. The celluar mosiac formed by the pattern of inactivation, particularly in the brain, needs more study to be undersatood. The fact that Rett’s symptoms can be “rescued” in mice by the expression of MeCP2 in postmitotic neurons is encouraging. In humans, Rett’s is frequently not observed untill the first or second year of life. As MeCP2 activation correlates with this period of rapid neural maturation, Rett’s is generally considered to be neurodevelopmental disease, as opposed to a neurodegenerative disease.

Rett’s is hardly ever observed in males for the simple reason that they fail to thrive long before birth. In those rare cases that a presumably XXY male child is rescued by the additional X chromsome, as in Klinefelder’s disease, rare opportunity to study the disease etiology is afforded. The efforts of these researchers, and the larger Rett’s community, together with the insights afforded by massive data collation have turned a rare disease into a primary source of knowledge about how evolution proceeds through the interplay of the sexes at the genetic and epigenetic levels.

(Source: medicalxpress.com)

Filed under neurodevelopmental diseases Rett syndrome MeCP2 gene mutations neuroscience science

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