Is Obama’s Plan to Map the Human Brain this Generation’s Equivalent to Landing a Man on the Moon?

President John F. Kennedy’s mission in the 1960s was to land a man on the moon. President Bill Clinton made cracking the human genome one of his top priorities. Now, President Barack Obama says a detailed map of the human brain is necessary to understand how it works and what needs to be done when it’s not working properly. The president is expected to unveil his plans for an estimated $3 billion, decade-long commitment to the Brain Activity Map project next month in his 2014 budget proposal.

Rutgers Today talked with Rutgers University behavioral neuroscientist Timothy Otto, professor and director of the Behavioral and Systems Neuroscience program in the Department of Psychology, about what we know about the brain, how much we still need to discover and if spending billions of dollars in research will enable scientists to develop new treatments for debilitating neurological diseases like Alzheimer’s, Parkinson’s and autism.

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Transmission routes of spreading protein particles

Study on cell cultures gives insights into the mechanisms of
neurodegenerative diseases

Bonn, Germany, March 27th, 2013. In diseases like Alzheimer’s and Parkinson’s endogenous proteins accumulate in the brain, eventually leading to the death of nerve cells. These deposits, which consist of abnormally formed proteins, are supposed to migrate between interconnected areas of the brain, thereby contributing to the development of the illness. Now, a new laboratory study by scientists from Germany and the US shows that certain protein particles are indeed capable of multiplying and spreading from one cell to the next. The investigation was conducted by researchers of the German Center for Neurodegenerative Diseases (DZNE) in Bonn and Munich who cooperated with scientists from the US and from other German institutions. The results are now published in the “Proceedings of the National Academy of Sciences of the USA“ (PNAS).

Are particles consisting of deformed proteins capable of moving from one cell’s interior to the next, multiplying and spreading as in a chain reaction? The team of scientists headed by Ina Vorberg, who is a researcher at the DZNE site in Bonn and a professor at the University of Bonn, investigated this hypothesis. The scientists did so with the help of cell cultures, which allowed them to adapt experiments to specific questions.

The researchers used cultured brain cells that originated from mice. The genetic code of a model protein was transferred into these cells, enabling the scientists to control production of the protein.

A yeast particle

The blueprint of the molecule was extracted from yeast DNA. This protein does not exist in humans. Nevertheless, the scientists chose this particular protein because it had several properties that were relevant for the study: In its natural environment – the yeast cell – it is capable of forming replicating “aggregates” (i. e. large protein particles). The protein deforms during this process. Now, the question was, whether something similar would happen in mammalian cells.

“At first, our mouse cells produced the protein, but no particles formed,” Vorberg reports. “The situation changed when we exposed the cells to aggregates of the same protein. Suddenly, the proteins which had been in solution started building clumps.”

Diffusing aggregates

Once this reaction had been triggered the cells went on producing aggregates. The researchers noticed that these clumps spread into neighboring cells, where they initiated synthesis of further aggregates.

“We have experimentally shown that certain protein particles originating from the cytosol, i. e. from inside the cells, are able to spread between cells. This means that in mammalian cells there are mechanisms capable of triggering such a chain reaction. Accordingly, what we have shown in our model system may be applicable to neurodegenerative diseases,” Vorberg comments.

Propagation of aggregates was most effective between adjacent cells. “At least in our model system, protein particles are not released efficiently into the medium and assimilated by neighboring cells. The most effective transmission happens by direct cell-to-cell contact. It is possible that cells form protrusions and that aggregates move from one cell to the next through this connection”, says the neuroscientist. What is happening here will be the focus of further research.

Basis for potential therapies

“It is important to know how protein particles disseminate”, Vorberg emphasizes. “Disease-related protein particles might propagate in a similar way to the model protein we investigated.”

Unraveling the mechanism for transmission between cells could lead to new methods for treatment. “If we find a way to prevent the spreading of disease-related protein particles, we might be able to interfere with the progression of the diseases,” Vorberg says.

The neuroscience of finding your lost keys

Ever find yourself racking your brain on a Monday morning to remember where you put your car keys?

When you do find those keys, you can thank the hippocampus, a brain region responsible for storing and retrieving memories of different environments-such as that room where your keys were hiding in an unusual spot.

Now, scientists have helped explain how the brain keeps track of the incredibly rich and complex environments people navigate on a daily basis. They discovered how the dentate gyrus, a subregion of the hippocampus, helps keep memories of similar events and environments separate, a finding they reported March 20 in eLife. The findings, which clarify how the brain stores and distinguishes between memories, may also help identify how neurodegenerative diseases, such as Alzheimer’s disease, rob people of these abilities.

"Everyday, we have to remember subtle differences between how things are today, versus how they were yesterday - from where we parked our car to where we left our cellphone," says Fred H. Gage, senior author on the paper and the Vi and John Adler Chair for Research on Age-Related Neurodegenerative Disease at Salk. "We found how the brain makes these distinctions, by storing separate ‘recordings’ of each environment in the dentate gyrus."

The process of taking complex memories and converting them into representations that are less easily confused is known as pattern separation. Computational models of brain function suggest that the dentate gyrus helps us perform pattern separation of memories by activating different groups of neurons when an animal is in different environments.

However, previous laboratory studies found that in fact the same populations of neurons in the dentate gyrus are active in different environments, and that the way the cells distinguished new surroundings was by changing the rate at which they sent electrical impulses. This discrepancy between theoretical predictions and laboratory findings has perplexed neuroscientists and obscured our understanding of memory formation and retrieval.

To explore this mystery more deeply, the Salk scientists compared the functioning of the mouse dentate gyrus and another region of the hippocampus, known as CA1, using laboratory techniques for tracking the activity of neurons at multiple time points.

First, the researchers took mice from their original chamber and placed them in a novel chamber to learn about a new environment (episode 1). Meanwhile, they recorded which hippocampal neurons were active as the animals responded to their new surroundings. Subsequently, the mice were either returned to that same novel chamber to measure memory recall or to a slightly modified chamber to measure discrimination (episode 2). The active neurons in episode 2 were also labeled in order to determine if the neurons activated in episode 1 were used in the same way for recall and for discrimination of small differences between environments.

When the researchers compared the neural activity during the two episodes, they found that the dentate gyrus and CA1 sub-regions functioned differently. In CA1, the same neurons that were active during the initial learning episode were also active when the mice retrieved the memories. In the dentate gyrus, however, distinct groups of cells were active during the learning episodes and retrieval. Also, exposing the mice to two subtly different environments activated two distinct groups of cells in the dentate gyrus.

"This finding supported the predictions of theoretical models that different groups of cells are activated during exposure to similar, but distinct, environments," says Wei Deng, a Salk postdoctoral research and first author on the paper. "This contrasts with the findings of previous laboratory studies, possibly because they looked at different sub-populations of neurons in the dentate gyrus."

The Salk researchers’ findings suggest that recalling a memory-such as the location of missing keys-does not always involve reactivation of the same neurons that were active during encoding. More importantly, the results indicate that the dentate gyrus performs pattern separation by using distinct populations of cells to represent similar but non-identical memories.

The findings help clarify the mechanisms that underpin memory formation and shed light on systems that are disrupted by injuries and diseases of the nervous system.

The Unstable Repeats—Three Evolving Faces of Neurological Disease

Disorders characterized by expansion of an unstable nucleotide repeat account for a number of inherited neurological diseases. Here, we review examples of unstable repeat disorders that nicely illustrate three of the major pathogenic mechanisms associated with these diseases: loss of function typically by disrupting transcription of the mutated gene, RNA toxic gain of function, and protein toxic gain of function. In addition to providing insight into the mechanisms underlying these devastating neurological disorders, the study of these unstable microsatellite repeat disorders has provided insight into very basic aspects of neuroscience.

New structural insight into neurodegenerative disease

A research team from the Korea Advanced Institute of Science and Technology (KAIST) released their results on the structure and molecular details of the neurodegenerative disease-associated protein Ataxin-1. Mutations in Ataxin-1 cause the neurological disease, Spinocerebellar Ataxia Type 1 (SCA1), which is characterized by a loss of muscular coordination and balance (ataxia), as is seen in Parkinson’s, Alzheimer’s, and Huntington’s diseases.

SCA1-causing mutations in the ATAXIN1 gene alter the length of a glutamine stretch in the Ataxin-1 protein. The research team provides the first structural insight into the complex formation of ATAXIN-1 with its binding partner, Capicua (CIC). The team, led by Professor Ji-Joon Song from the Department of Biological Sciences at KAIST, solved the structure of Ataxin-1 and CIC complex in atomic level revealing molecular details of the interaction between Ataxin-1 and CIC.

Professor Song explained his recent research work, “We are able to see the intricate process of complex formation and reconfiguration of the two proteins when they interact with each other. Our work, we expect, will provide a new therapeutic target to modulate SCA1 neurodegenerative disease.”

Understanding structural and molecular details of proteins at the atomic level will help researchers to track the molecular pathogenesis of the disease and, ultimately, design targeted therapies or treatments for patients, rather than just relieving the symptoms of diseases.

Professor Song’s research paper, entitled “Structural Basis of Protein Complex Formation and Reconfiguration by Polyglutamine Disease Protein ATAXIN-1 and Capicua,” will be published in the March 15th issue of Genes & Development

Tau Transmission Model Opens Doors for New Alzheimer’s, Parkinson’s Therapies

Injecting synthetic tau fibrils into animal models induces Alzheimer’s-like tau tangles and imitates the spread of tau pathology, according to research from the Perelman School of Medicine at the University of Pennsylvania being presented at the American Academy of Neurology’s 65th Annual Meeting in San Diego March 16-23, 2013.

This Alzheimer’s research, along with additional Parkinson’s research from Penn and beyond, further demonstrates the cell-to-cell transmission of neurodegenerative proteins. John Q. Trojanowski, MD, PhD, co-director of the Center for Neurodegenerative Disease Research (CNDR) and professor of Pathology and Laboratory Medicine at the Perelman School of Medicine, University of Pennsylvania, will present the research in the Hot Topics plenary session on Tuesday, March 19 starting at 5:15pm.

"The transmission model better explains the spread of disease within neurodegenerative disease, and has uncovered new therapeutic opportunities which we are exploring vigorously," said Dr. Trojanowski. “However, it is important to emphasize that the spread of Alzheimer’s and Parkinson’s pathology does not mean these diseases are infectious, like Mad Cow disease, based on data from another recent study from our group.”

For supplemental information on the transmission of tau pathology, the laboratory of senior author Virginia M.-Y. Lee, Ph.D., MBA, director of CNDR and professor of Pathology and Laboratory Medicine at the Perelman School of Medicine, University of Pennsylvania, published additional findings in the Journal of Neuroscience.

Discovery opens door to new drug options for serious diseases

Researchers have discovered how oxidative stress can turn to the dark side a cellular protein that’s usually benign, and make it become a powerful, unwanted accomplice in neuronal death.

This finding, reported in Proceedings of the National Academy of Sciences, could ultimately lead to new therapeutic approaches to many of the world’s debilitating or fatal diseases.

The research explains how one form of oxidative stress called tyrosine nitration can lead to cell death. Through the common link of inflammation, this may relate to health problems ranging from heart disease to chronic pain, spinal injury, cancer, aging, and amyotrophic lateral sclerosis, or Lou Gehrig’s disease.

As part of the work, the scientists also identified a specific “chaperone” protein damaged by oxidants, which is getting activated in this spiral of cellular decline and death. This insight will provide a new approach to design therapeutic drugs.

The findings were published by scientists from the Linus Pauling Institute at Oregon State University; Maria Clara Franco and Alvaro Estevez, now at the University of Central Florida; and researchers from several other institutions. They culminate a decade of work.

“These are very exciting results and could begin a major shift in medicine,” said Joseph Beckman.

Beckman is an LPI principal investigator, distinguished professor of biochemistry, and director of the OSU Environmental Health Sciences Center. He also last year received the Discovery Award from the Medical Research Foundation of Oregon, given to the leading medical scientist in the state.

“Preventing this process of tyrosine nitration may protect against a wide range of degenerative diseases,” Beckman said. “The study shows that drugs could effectively target oxidatively damaged proteins.”

Scientists have known for decades about the general concept of oxidative damage to cells, resulting in neurodegeneration, inflammation and aging. But the latest findings prove that some molecules in a cell are thousands of times more sensitive to attack.

In this case, heat shock protein 90, or HSP90, helps monitor and chaperone as many as 200 necessary cell functions. But it can acquire a toxic function after nitration of a single tyrosine residue.

“It was difficult to believe that adding one nitro group to one protein will make it toxic enough to kill a motor neuron,” Beckman said. “But nitration of HSP90 was shown to activate a pro-inflammatory receptor called P2X7. This begins a dangerous spiral that eventually leads to the death of motor neurons.”

The very specificity of this attack, however, is part of what makes the new findings important. Drugs that could prevent or reduce oxidative attack on these most vulnerable sites in a cell might have value against a wide range of diseases.

“Most people think of things like heart disease, cancer, aging, liver disease, even the damage from spinal injury as completely different medical issues,” Beckman said. “To the extent they can often be traced back to inflammatory processes that are caused by oxidative attack and cellular damage, they can be more similar than different.

“It could be possible to develop therapies with value against many seemingly different health problems,” Beckman added.

Beckman has spent much of his career studying the causes of amyotrophic lateral sclerosis, and this study suggested the processes outlined in this study might be relevant both to that disease and spinal cord injury.

One key to this research involved new methods that allowed researchers to genetically engineer nitrotyrosine into HSP90. This allowed scientists to pin down the exact areas of damage, which may be important in the identification of drugs that could affect this process, the researchers said.

Adding to the list of disease-causing proteins in brain disorders

A multi-institution group of researchers has found new candidate disease proteins for neurodegenerative disorders. James Shorter, Ph.D., assistant professor of Biochemistry and Biophysics at the Perelman School of Medicine, University of Pennsylvania, Paul Taylor, M.D., PhD, St. Jude Children’s Research Hospital, and colleagues describe in an advanced online publication of Nature that mutations in prion-like segments of two RNA-binding proteins are associated with a rare inherited degeneration disorder affecting muscle, brain, motor neurons and bone (called multisystem proteinopathy) and one case of the familial form of amyotrophic lateral sclerosis (ALS).

"This study uses a variety of scientific approaches to provide powerful evidence that unregulated polymerization of proteins involved in RNA metabolism may contribute to ALS and related diseases," said Amelie Gubitz, Ph.D., a program director at the National Institute of Neurological Disorders and Stroke (NINDS).

ALS, or Lou Gehrig’s disease, is a universally fatal neurodegenerative disease. Previous studies found that mutations in two related RNA-binding proteins, TDP-43 and FUS, cause some forms of ALS, but more proteins were suspected of causing other forms of the disease. TDP-43 and FUS regulate how the genetic code is translated for the assembly of proteins.

There are over 200 human RNA-binding proteins, including FUS and TDP-43, raising the possibility that additional RNA-binding proteins might contribute to ALS pathology. Computer algorithms, based on protein sequences, designed to identify yeast prions predict that around 250 human proteins, including several RNA-binding proteins associated with neurodegenerative disease, harbor a distinctive prion-like segment. These segments are essential for the assembly of certain protein complexes. But, the interplay between human prion-like segments and disease is not well understood.

Using yeast as a model organism, co-author Aaron Gitler, while at Penn in 2011, surveyed 133 of 200-plus candidate human RNA-binding proteins to predict new ALS disease genes, other than TDP-43 and FUS. They further winnowed the candidates to about 10 proteins with prion-like segments, and selected two candidates, TAF15 and EWSR1, for further study. Both TAF15 and EWSR1 aggregated in the test tube and were toxic in yeast.

Remarkably, they also uncovered TAF15 and EWSR1 mutations in ALS patients that were not found in healthy individuals. Based on these findings, they proposed that RNA-binding proteins with prion-like segments might contribute very broadly to the pathology of ALS and related brain disorders.

Characterizing the Top-Ten

Taylor, Gitler, Shorter, and others continued to characterize the top-ten human RNA-binding proteins with prion-like segments. The Nature study describes that two more of the top-ten candidates, called hnRNPA1 and hnRNPA2B1, are mutated and cause familial cases of brain disease. The mutations in hnRNPA1 and hnRNPA2B1 were present in two families with an extremely rare inherited degeneration affecting muscle, brain, motor neuron, and bone and another from a person with familial ALS.

Mutations in these two proteins fell in the prion-like segments and coincided with “sticky” regions in the proteins, making these regions more prone to assemble into self-organizing fibrils. The normal form of the proteins shows a natural tendency to assemble into fibrils, which is exacerbated by the disease mutations.

"The mutations accelerate the formation of the fibrils that recruit normal protein to form more fibrils," noted co-first author Emily Scarborough, from Penn. This dysregulated assembly likely contributes to disease. Indeed, the disease mutations also promote excess incorporation of the proteins into stress granules within a cell and the formation of clumps in the cells of animal models of human neurodegenerative disease.

"Neurodegenerative disease could ensue from unregulated fibril formation initiated spontaneously by environmental stress or another factor that regulates a protein’s assembly," says Scarborough.

"This paper reflects an amazing collaborative effort and provides a great example of how understanding the underlying pure protein biochemistry can help explain how genetic mutations might cause pathology and disease," says Shorter.

"The findings confirm a strong prediction that the disease-causing mutations make the prion-like segment ‘stickier’ and more prone to clump," added co-first author Zamia Diaz, also from Penn.

Diseases associated with fibrils forming from prion-like domains in proteins frequently show “spreading” pathology, in which cellular degeneration via inclusions starts in one center of the brain and “spreads” to neighboring tissue. Although not directly addressed in the Nature study, the findings suggest that cell-to-cell transmission of a self-templating protein could contribute to the spreading pathology that is characteristic of these diseases.

"Related proteins with prion-like domains must be considered candidates for initiating and perhaps propagating similar pathologies in muscle, brain, motor neurons, and bone," concluded Shorter.