Scientists Link ALS Progression to Increased Protein Instability

A new study by scientists from The Scripps Research Institute (TSRI), Lawrence Berkeley National Laboratory (Berkeley Lab) and other institutions suggests a cause of amyotrophic lateral sclerosis (ALS), also known as Lou Gehrig’s disease.

“Our work supports a common theme whereby loss of protein stability leads to disease,” said John A. Tainer, professor of structural biology at TSRI and senior scientist at Berkeley Lab, who shared senior authorship of the new research with TSRI Professor Elizabeth Getzoff.

Getzoff, Tainer and their colleagues, who focused on the effects of mutations to a gene coding for a protein called superoxide dismutase (SOD), report their findings this week in the online Early Edition of the Proceedings of the National Academy of Sciences. The study provides evidence that those proteins linked to more severe forms of the disease are less stable structurally and more prone to form clusters or aggregates.

“The suggestion here is that strategies for stabilizing SOD proteins could be useful in treating or preventing SOD-linked ALS,” said Getzoff.

Striking in the Prime of Life

ALS is notorious for its ability to strike down people in the prime of life. It first leapt into public consciousness when it afflicted baseball star Lou Gehrig, who succumbed to the disease in 1941 at the age of only 38. Recently, the ALS Association’s Ice Bucket Challenge has enhanced public awareness of the disease.

ALS kills by destroying muscle-controlling neurons, ultimately including those that control breathing. At any one time, about 10,000 Americans are living with the disease, according to new data from the Centers for Disease Control and Prevention, but it is almost always lethal within several years of the onset of symptoms.

SOD1 mutations, the most studied factors in ALS, are found in about a quarter of hereditary ALS cases and seven percent of ordinary “sporadic” ALS cases. SOD-linked ALS has nearly 200 variants, each associated with a distinct SOD1 mutation. Scientists still don’t agree, though, on just how the dozens of different SOD1 mutations all lead to the same disease.

One feature that SOD1-linked forms of ALS do have in common is the appearance of SOD clusters or aggregates in affected motor neurons and their support cells. Aggregates of SOD with other proteins are also found in affected cells, even in ALS cases that are not linked to SOD1 mutations.

In 2003, based on their and others’ studies of mutant SOD proteins, Tainer, Getzoff and their colleagues proposed the “framework destabilization” hypothesis. In this view, ALS-linked mutant SOD1 genes all code for structurally unstable forms of the SOD protein. Inevitably some of these unstable SOD proteins lose their normal folding enough to expose sticky elements that are normally kept hidden, and they begin to aggregate with one another, faster than neuronal cleanup systems can keep up—and that accumulating SOD aggregation somehow triggers disease.

Faster Clumping, Worse Disease

In the new study, the Tainer and Getzoff laboratories and their collaborators used advanced biophysical methods to probe how different SOD1 gene mutations in a particular genetic ALS “hotspot” affect SOD protein stability.

To start, they examined how the aggregation dynamics of the best-studied mutant form of SOD, known as SOD G93A, differed from that of non-mutant, “wild-type” SOD. To do this, they developed a method for gradually inducing SOD aggregation, which was measured with an innovative structural imaging system called SAXS (small-angle X-ray scattering) at Berkeley Lab’s SIBYLS beamline.

“We could detect differences between the two proteins even before we accelerated the aggregation process,” said David S. Shin, a research scientist in Tainer’s laboratories at Berkeley Lab and TSRI who continues structural work on SOD at Berkeley.

The G93A SOD aggregated more quickly than wild-type SOD, but more slowly than an SOD mutant called A4V that is associated with a more rapidly progressing form of ALS.

Subsequent experiments with G93A and five other G93 mutants (in which the amino acid glycine at position 93 on the protein is replaced with a different amino acid) revealed that the mutants formed long, rod-shaped aggregates, compared to the compact folded structure of wild-type SOD. The mutant SOD proteins that more quickly formed longer aggregates were again those that corresponded to more rapidly progressing forms of ALS.

What could explain these SOD mutants’ diminished stability? Further tests focused on the role of a copper ion that is normally incorporated within the SOD structure and helps stabilize the protein. Using two other techniques, electron-spin resonance (ESR) spectroscopy and inductively coupled plasma mass spectrometry (ICP-MS), the researchers found that the G93-mutant SODs seemed normal in their ability to take up copper ions, but had a reduced ability to retain copper under mildly stressing conditions—and this ability was lower for the SOD mutants associated with more severe ALS.

“There were indications that the mutant SODs are more flexible than wild-type SOD, and we think that explains their relative inability to retain the copper ions,” said Ashley J. Pratt, the first author of the study, who was a student in the Getzoff laboratory and postdoctoral fellow with Tainer at Berkeley Lab.

Toward New Therapies

In short, the G93-mutant SODs appear to have looser, floppier structures that are more likely to drop their copper ions—and thus are more likely to misfold and stick together in aggregates.

Along with other researchers in the field, Getzoff and Tainer suspect that deviant interactions of mutant SOD trigger inflammation and disrupt ordinary protein trafficking and disposal systems, stressing and ultimately killing affected neurons.

“Because mutant SODs get bent out of shape more easily,” said Getzoff, “they don’t hold and release their protein partners properly. By defining these defective partnerships, we can provide new targets for the development of drugs to treat ALS.”

The researchers also plan to confirm the relationship between structural stability and ALS severity in other SOD mutants.

“If our hypothesis is correct,” said Shin, “future therapies to treat SOD-linked ALS need not be tailored to each individual mutation—they should be applicable to all of them.”

How gut bacteria ensure a healthy brain – and could play a role in treating depression

One of medicine’s greatest innovations in the 20th century was the development of antibiotics. It transformed our ability to combat disease. But medicine in the 21st century is rethinking its relationship with bacteria and concluding that, far from being uniformly bad for us, many of these organisms are actually essential for our health.

Nowhere is this more apparent than in the human gut, where the microbiome – the collection of bacteria living in the gastrointestinal tract – plays a complex and critical role in the health of its host. The microbiome interacts with and influences organ systems throughout the body, including, as research is revealing, the brain. This discovery has led to a surge of interest in potential gut-based treatments for neuropsychiatric disorders and a new class of studies investigating how the gut and its microbiome affect both healthy and diseased brains.

The microbiome consists of a startlingly massive number of organisms. Nobody knows exactly how many or what type of microbes there might be in and on our bodies, but estimates suggest there may be anywhere from three to 100 times more bacteria in the gut than cells in the human body. The Human Microbiome Project, co-ordinated by the US National Institutes of Health (NIH), seeks to create a comprehensive database of the bacteria residing throughout the gastrointestinal tract and to catalogue their properties.

The lives of the bacteria in our gut are intimately entwined with our immune, endocrine and nervous systems. The relationship goes both ways: the microbiome influences the function of these systems, which in turn alter the activity and composition of the bacterial community. We are starting to unravel this complexity and gain insight into how gut bacteria interface with the rest of the body and, in particular, how they affect the brain.

Read more

New front in war on Alzheimer’s, other protein-folding diseases

A surprise discovery that overturns decades of thinking about how the body fixes proteins that come unraveled greatly expands opportunities for therapies to prevent diseases such as Alzheimer’s and Parkinson’s, which have been linked to the accumulation of improperly folded proteins in the brain.

“This finding provides a whole other outlook on protein-folding diseases; a new way to go after them,” said Andrew Dillin, the Thomas and Stacey Siebel Distinguished Chair of Stem Cell Research in the Department of Molecular and Cell Biology and Howard Hughes Medical Institute investigator at the University of California, Berkeley.

Dillin, UC Berkeley postdoctoral fellows Nathan A. Baird and Peter M. Douglas and their colleagues at the University of Michigan, The Scripps Research Institute and Genentech Inc., will publish their results in the Oct. 17 issue of the journal Science.

Cells put a lot of effort into preventing proteins – which are like a string of beads arranged in a precise three-dimensional shape – from unraveling, since a protein’s activity as an enzyme or structural component depends on being properly shaped and folded. There are at least 350 separate molecular chaperones constantly patrolling the cell to refold misfolded proteins. Heat is one of the major threats to proteins, as can be demonstrated when frying an egg – the clear white albumen turns opaque as the proteins unfold and then tangle like spaghetti.

Heat shock

For 35 years, researchers have worked under the assumption that when cells undergo heat shock, as with a fever, they produce a protein that triggers a cascade of events that field even more chaperones to refold unraveling proteins that could kill the cell. The protein, HSF-1 (heat shock factor-1), does this by binding to promoters upstream of the 350-plus chaperone genes, upping the genes’ activity and launching the army of chaperones, which originally were called “heat shock proteins.”

Injecting animals with HSF-1 has been shown not only to increase their tolerance of heat stress, but to increase lifespan.

Because an accumulation of misfolded proteins has been implicated in aging and in neurodegenerative diseases such as Alzheimer’s, Parkinson’s and Huntington’s diseases, scientists have sought ways to artificially boost HSF-1 in order to reduce the protein plaques and tangles that eventually kill brain cells. To date, such boosters have extended lifespan in lab animals, including mice, but greatly increased the incidence of cancer.

Dillin’s team found in experiments on the nematode worm C. elegans that HSF-1 does a whole lot more than trigger release of chaperones. An equal if not more important function is to stabilize the cell’s cytoskeleton, which is the highway that transports essential supplies – healing chaperones included – around the cell.

“We are suggesting that, rather than making more of HSF-1 to prevent diseases like Huntington’s, we should be looking for ways to make the actin cytoskeleton better,” Dillin said. Such tactics might avoid the carcinogenic side effects of upping HSF-1.

Dillin is codirector of the Paul F. Glenn Center for Aging Research, a new collaboration between UC Berkeley and UC San Francisco supported by the Glenn Foundation for Medical Research. Center investigators will study the many ways that proteins malfunction within cells, ideally paving the way for novel treatments for neurodegenerative diseases.

A cell at war

Dillin compares a cell experiencing heat shock to a country under attack. In a war, an aggressor first cuts off all communications, such as roads, train and bridges, which prevents the doctors from treating the wounded. Similarly, heat shock disrupts the cytoskeletal highway, preventing the chaperone “doctors” from reaching the patients, the misfolded proteins.

“We think HSF-1 not only makes more chaperones, more doctors, but also insures that the roadways stay intact to keep everything functional and make sure the chaperones can get to the sick and wounded warriors,” he said.

The researchers found specifically that HSF-1 up-regulates another gene, pat-10, that produces a protein that stabilizes actin, the building blocks of the cytoskeleton.

By boosting pat-10 activity, they were able to cure worms that had been altered to express the Huntington’s disease gene, and also extend the lifespan of normal worms.

Dillin suspects that HSF-1’s main function is, in fact, to protect the actin cytoskeleton. He and his team mutated HSF-1 so that it no longer boosted chaperones, demonstrating, he said, that “you can survive heat shock with the normal level of heat shock proteins, as long as you make your cytoskeleton work better.”

He noted that the team’s results – that boosting chaperones is not essential to surviving heat stress – were so contradictory to current thinking that “I made my post-docs’ lives hell for three years” insisting on more experiments to rule out errors. Yet, when Dillin presented the results recently to members of the protein-folding community, he said the first reaction of many was, “That makes perfect sense.”

Presence of Enzyme May Worsen Effects of Spinal Cord Injury and Impair Long-term Recovery

Traumatic spinal cord injury (SCI) is a devastating condition with few treatment options. Studies show that damage to the barrier separating blood from the spinal cord can contribute to the neurologic deficits that arise secondary to the initial trauma. Through a series of sophisticated experiments, researchers reporting in The American Journal of Pathology suggest that matrix metalloproteinase-3 (MMP-3) plays a pivotal role in disruption of the brain/spinal cord barrier (BSCB), cell death, and functional deficits after SCI. This link also presents new therapeutic possibilities.

“Matrix metalloproteinases (MMPs) are enzymes known to degrade the extracellular matrix and other extracellular proteins and are essential for remodeling of the extracellular matrix and wound healing. Excessive proteolytic activity of MMPs can be detrimental, leading to numerous pathological conditions, including blood brain barrier (BBB)/BSCB disruption after injury,” explains Tae Young Yune, PhD, of the Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, Korea. Although other MMPs have been linked to SCI (i.e. MMP-2, MMP-9, and MMP-12), there has been no previous direct evidence of a similar role for MMP-3.

By comparing mice that underwent spinal cord injury to a control group, investigators found that both MMP3 messenger RNA (mRNA) and MMP-3 protein levels in spinal cord segments were increased after SCI, peaking one day after surgery in the experimental group, whereas no changes were seen in the controls. MMP-3 immunoreactivity was detected in cells within the lesion site, invading neutrophils, and blood vessel endothelial cells in the area outside of the initial injured area (the penumbra).

Another series of experiments focused on the role of MMP-3 in BSCB permeability, using dye to visualize leakage through the BSCB. Similar to MMP-3 mRNA and protein levels, dye leakage reached a maximum one day after SCI. Leakage was lower in Mmp3 knockout mice that were genetically altered to be deficient in MMP-3 as well as in mice injected with either Mmp3 small interfering RNA (siRNA) or a general MMP inhibitor. Injection of MMP-3 into normal spinal cord also significantly increased dye leakage.

MMP-3 was found to contribute to the degradation of tight junction proteins that are responsible for maintaining the integrity of the BSCB barrier. In addition, the researchers reported that MMP-3 induced blood cell infiltration and hemorrhage after SCI in wild-type mice, but not in Mmp3 knockout mice.  MMP-3 also mediated activation of other MMPs (MMP-2 and MMP-9) that are up-regulated after SCI. “This is the first study to demonstrate that MMP-3 is involved in MMP-9 activation in central nervous system injury,” says Dr. Yune.

A significant finding was that mice deficient in MMP-3 showed significantly better functional recovery 14 and 28 days after injury than non-deficient mice. Histological analysis showed that after SCI the mice deficient in MMP-3 had smaller volumes of injured tissue and more healthy axons than non-deficient wild-type mice.

“The evidence suggests that BBB/BSCB disruption plays a pivotal role in acute and chronic neurological disorders. The inhibition of MMP-3 may be a promising therapeutic target for human central nervous system disease, including SCI,” notes Dr. Yune.

How the brain leads us to believe we have sharp vision

We assume that we can see the world around us in sharp detail. In fact, our eyes can only process a fraction of our surroundings precisely. In a series of experiments, psychologists at Bielefeld University have been investigating how the brain fools us into believing that we see in sharp detail. The results have been published in the scientific magazine ‘Journal of Experimental Psychology: General.’ Its central finding is that our nervous system uses past visual experiences to predict how blurred objects would look in sharp detail.

"In our study we are dealing with the question of why we believe that we see the world uniformly detailed," says Dr. Arvid Herwig from the Neuro-Cognitive Psychology research group of the Faculty of Psychology and Sports Science. The group is also affiliated to the Cluster of Excellence Cognitive Interaction Technology (CITEC) of Bielefeld University and is led by Professor Dr. Werner X. Schneider.

Only the fovea, the central area of the retina, can process objects precisely. We should therefore only be able to see a small area of our environment in sharp detail. This area is about the size of a thumb nail at the end of an outstretched arm. In contrast, all visual impressions which occur outside the fovea on the retina become progressively coarse. Nevertheless, we commonly have the impression that we see large parts of our environment in sharp detail.

Herwig and Schneider have been getting to the bottom of this phenomenon with a series of experiments. Their approach presumes that people learn through countless eye movements over a lifetime to connect the coarse impressions of objects outside the fovea to the detailed visual impressions after the eye has moved to the object of interest. For example, the coarse visual impression of a football (blurred image of a football) is connected to the detailed visual impression after the eye has moved. If a person sees a football out of the corner of her eye, her brain will compare this current blurred picture with memorised images of blurred objects. If the brain finds an image that fits, it will replace the coarse image with a precise image from memory. This blurred visual impression is replaced before the eye moves. The person thus thinks that she already sees the ball clearly, although this is not the case.

The psychologists have been using eye-tracking experiments to test their approach. Using the eye-tracking technique, eye movements are measured accurately with a specific camera which records 1000 images per second. In their experiments, the scientists have recorded fast balistic eye movements (saccades) of test persons. Though most of the participants did not realise it, certain objects were changed during eye movement. The aim was that the test persons learn new connections between visual stimuli from inside and outside the fovea, in other words from detailed and coarse impressions. Afterwards, the participants were asked to judge visual characteristics of objects outside the area of the fovea. The result showed that the connection between a coarse and detailed visual impression occurred after just a few minutes. The coarse visual impressions became similar to the newly learnt detailed visual impressions.

"The experiments show that our perception depends in large measure on stored visual experiences in our memory," says Arvid Herwig. According to Herwig and Schneider, these experiences serve to predict the effect of future actions ("What would the world look like after a further eye movement"). In other words: "We do not see the actual world, but our predictions."

Myth-conceptions: How myths about the brain are hampering teaching

Teachers in the UK, Holland, Turkey, Greece and China were presented with seven so-called ‘neuromyths’ and asked whether they believe them to be true.

A quarter or more of teachers in the UK and Turkey believe a student’s brain would shrink if they drank less than six to eight glasses of water a day, while around half or more of those surveyed believe a student’s brain is only 10 per cent active and that children are less attentive after sugary drinks and snacks.

Over 70 per cent of teachers in all countries wrongly believe a student is either left-brained or right-brained, peaking at 91 per cent in the UK.

And almost all teachers (over 90 per cent in each country) feel that teaching to a student’s preferred learning style - auditory, kinaesthetic or visual - is helpful, despite no convincing evidence to support this approach.

The new research from the University of Bristol, published in Nature Reviews Neuroscience, calls for better communication between neuroscientists and educators.

Dr Paul Howard-Jones, author of the article from Bristol University’s Graduate School of Education, said: “These ideas are often sold to teachers as based on neuroscience – but modern neuroscience cannot be used support them. These ideas have no educational value and are often associated with poor practice in the classroom.”

The report blames wishfulness, anxiety and a bias towards simple explanations as typical factors that distort neuroscientific fact into neuromyth.

Such factors also appear to be hampering recent efforts of neuroscientists to communicate the true meaning of their work to educators.

Dr Howard-Jones added: “Although the increased dialogue between neuroscience and education is encouraging, we see new neuromyths on the horizon and old ones returning in new forms.

“Sometimes, transmitting ‘boiled-down’ messages about the brain to educators can just lead to misunderstanding, and confusions about concepts such as brain plasticity are common in discussions about education policy.”

The report highlights several areas where new findings from neuroscience are becoming misinterpreted by education, including brain-related ideas regarding early educational investment, adolescent brain development and learning disorders such as dyslexia and ADHD.

Hopes that education will draw genuine benefit from neuroscience may rest on a new but rapidly growing field of ‘neuroeducational’ research that combines both fields.

The review concludes that, in the future, such collaboration will be greatly needed if education is to be enriched rather than misled by neuroscience.

Male and female brains aren’t equal when it comes to fat

Researchers have found that male and female brains respond in remarkably different ways to high-fat meals. Those differences in the brain lead to greater inflammation and increased health risks in males that indulge on fatty foods in comparison to females, a new study in mice shows. The findings reported in the Cell Press journal Cell Reports on October 16th may help to explain observed differences in obesity outcomes between women and men – premenopausal women carrying extra weight fare better than men do – and suggest that dietary advice should be made more sex-specific.

"Our findings, for the first time, suggest that males and females respond to high-fat diets differently," said Deborah Clegg of the Cedar-Sinai Diabetes And Obesity Research Institute in Los Angeles. "The data would suggest that is probably ‘ok’ for females to occasionally have a high-fat meal, where it is not recommended for males.

"The way we treat patients and provide dietary and nutritional advice should be altered. We might be less concerned about an occasional hamburger for women, but for men, we might more strongly encourage avoidance, especially if they have pre-existing diseases such as heart disease or type 2 diabetes."

Earlier data from Clegg’s team and others had suggested that inflammation in the brain is tied to overeating, blood sugar imbalances, and increased inflammation in other parts of the body, including fat tissue. Those effects can be triggered, in males in particular, by short-term exposure to a high-fat diet.

The researchers say they were initially shocked to discover that male and female brains differ in their fatty acid composition. When they manipulated male mouse brains to have the fatty acid profile of females, they found that those animals were protected from the ill effects of a diet high in fat.

When males with average male brains entered an inflammatory state after eating diets high in fat, they also suffered from reduced cardiac function in a way that female animals in the study did not. Those sex differences in the brain’s response to fat are related to differences between females and males in estrogen and estrogen receptor status.

Clegg says her team is now working out a strategy to confirm whether the findings in mice apply to people too. If they do, there will be some very immediate practical implications for what men and women should put on their plates.

"We have always had ‘one size fits all’ with respect to our nutritional information and our pharmaceutical approach," Clegg said. "Our data begin to suggest that sex should be factored in, and men should be more closely monitored for fat intake and inflammation than women."

(Image: Shutterstock)