Researcher: Guoping Feng

A Google map of the brain

by Elizabeth Dougherty |

At the start of the twentieth century, Santiago Ramón y Cajal’s drawings of brain cells under the microscope revealed a remarkable diversity of cell types within the brain. Through sketch after sketch, Cajal showed that the brain was not, as many believed, a web of self-similar material, but rather that it is composed of billions of cells of many different sizes, shapes, and interconnections.

Yet more than a hundred years later, we still do not know how many cell types make up the human brain. Despite decades of study, the challenge remains daunting, as the brain’s complexity has overwhelmed attempts to describe it systematically or to catalog its parts.

Now, however, this appears about to change, thanks to an explosion of new technical advances in areas ranging from DNA sequencing to microfluidics to computing and microscopy. For the first time, a parts list for the human brain appears to be within reach.

Why is this important? “Until we know all the cell types, we won’t fully understand how they are connected together,” explains McGovern Investigator Guoping Feng. “We know that the brain’s wiring is incredibly complicated, and that the connections are key to understanding how it works, but we don’t yet have the full picture. That’s what we are aiming for. It’s like making a Google map of the brain.”

Identifying the cell types is also important for understanding disease. As genetic risk factors for different disorders are identified, researchers need to know where they act within the brain, and which cell types and connections are disrupted as a result. “Once we know that, we can start to think about new therapeutic approaches,” says Feng, who is also an institute member of the Broad Institute, where he leads the neurobiology program at the Stanley Center for Psychiatric Disorders Research.

Drop by drop

In 2012, computational biologist Naomi Habib arrived from the Hebrew University of Jerusalem to join the labs of McGovern Investigator Feng Zhang and his collaborator Aviv Regev at the Broad Institute. Habib’s plan was to learn new RNA methods as they were emerging. “I wanted to use these powerful tools to understand this fascinating system that is our brain,” she says.

Her rationale was simple, at least in theory. All cells of an organism carry the same DNA instructions, but the instructions are read out differently in each cell type. Stretches of DNA corresponding to individual genes are copied, sometimes thousands of times, into RNA molecules that in turn direct the synthesis of proteins. Differences in which sequences get copied are what give cells their identities: brain cells express RNAs that encode brain proteins, while blood cells express different RNAs, and so on. A given cell can express thousands of genes, providing a molecular “fingerprint” for each cell type.

Analyzing these RNAs can provide a great deal of information about the brain, including potentially the identities of its constituent cell types. But doing this is not easy, because the different cell types are mixed together like salt and pepper within the brain. For many years, studying brain RNA meant grinding up the tissue—an approach that has been compared to studying smoothies to learn about fruit salad.

As methods improved, it became possible to study the tiny quantities of RNA contained within single cells. This opened the door to studying the difference between individual cells, but this required painstaking manipulation of many samples, a slow and laborious process.

A breakthrough came in 2015, with the development of automated methods based on microfluidics. One of these, known as dropseq (droplet-based sequencing), was pioneered by Steve McCarroll at Harvard, in collaboration with Regev’s lab at Broad. In this method, individual cells are captured in tiny water droplets suspended in oil. Vast numbers of droplets are automatically pumped through tiny channels, where each undergoes its own separate sequencing reactions. By running multiple samples in parallel, the machines can process tens of thousands of cells and billions of sequences, within hours rather than weeks or months. The power of the method became clear when in an experiment on mouse retina, the researchers were able to identify almost every cell type that had ever been described in the retina, effectively recapitulating decades of work in a single experiment.

Dropseq works well for many tissues, but Habib wanted to apply it to the adult brain, which posed a unique challenge. Mature neurons often bear elaborate branches that become intertwined like tree roots in a forest, making it impossible to separate individual cells without damage.

Nuclear option

So Habib turned to another idea. RNA is made in the nucleus before moving to the cytoplasm, and because nuclei are compact and robust it is easy to recover them intact in large numbers, even from difficult tissues such as brain. The amount of RNA contained in a single nucleus is tiny, and Habib didn’t know if it would be enough to be informative, but Zhang and Regev encouraged her to keep going. “You have to be optimistic,” she says. “You have to try.”

Fortunately, the experiment worked. In a paper with Zhang and Regev, she was able to isolate nuclei from newly formed neurons in the adult mouse hippocampus (a brain structure involved in memory), and by analyzing their RNA profiles individually she could order them in a series according to their age, revealing their developmental history from birth to maturity.

Now, after much further experimentation, Habib and her colleagues have managed to apply the droplet method to nuclei, making it possible for the first time to analyze huge numbers of cells from adult brain—at least ten times more than with previous methods.

This opens up many new avenues, including the study of human postmortem tissue, given that RNA in nuclei can survive for years in frozen samples. Habib is already starting to examine tissue taken at autopsy from patients with Alzheimer’s and other neurodegenerative diseases. “The neurons are degenerating, but the other cells around them could also be contributing to the degenerative process,” she says. “Now we have these tools, we can look at what happens during the progression of the disease.”

Computing cells

Once the sequencing is completed, the results are analyzed using sophisticated computational methods. When the results emerge, data from individual cells are visualized as colored dots, clustered on a graph according to their statistical similarities. But because the cells were dissociated at the start of the experiment, information about their appearance and origin within the brain is lost.

To find out how these abstract displays correspond to the visible cells of the brain, Habib teamed up with Yinqing Li, a former graduate student with Zhang who is now a postdoc in the lab of Guoping Feng. Li began with existing maps from the Allen Institute, a public repository with thousands of images showing expression patterns for individual genes within mouse brain. By comparing these maps with the molecular fingerprints from Habib’s nuclear RNA sequencing experiments, Li was able to make a map of where in the brain each cell was likely to have come from.

It was a good first step, but still not perfect. “What we really need,” he says, “is a method that allows us to see every RNA in individual cells. If we are studying a brain disease, we want to know which neurons are involved in the disease process, where they are, what they are connected to, and which special genes might be involved so that we can start thinking about how to design a drug that could alter the disease.”

Expanding horizons

So Li partnered with Asmamaw (Oz) Wassie, a graduate student in the lab of McGovern Investigator Ed Boyden, to tackle the problem. Wassie had previously studied bioengineering as an MIT undergraduate, where he had helped build an electronic “artificial nose” for detecting trace chemicals in air. With support from a prestigious Hertz Fellowship, he joined Boyden’s lab, where he is now working on the development of a method known as expansion microscopy.

In this method, a sample of tissue is embedded with a polymer that swells when water is added. The entire sample expands in all directions, allowing scientists to see fine details such as connections between neurons, using an ordinary microscope. Wassie recently helped develop a way to anchor RNA molecules to the polymer matrix, allowing them to be physically secured during the expansion process. Now, within the expanded samples he can see the individual molecules using a method called fluorescent in situ hybridization (FISH), in which each RNA appears as a glowing dot under the microscope. Currently, he can label only a handful of RNA types at once, but by using special sets of probes, applied sequentially, he thinks it will soon be possible to distinguish thousands of different RNA sequences.

“That will help us to see what each cell looks like, how they are connected to each other, and what RNAs they contain,” says Wassie. By combining this information with the RNA expression data generated by Li and Habib, it will be possible to reveal the organization and fine structure of complex brain areas and perhaps to identify new cell types that have not yet been recognized.

Looking ahead

Li plans to apply these methods to a brain structure known as the thalamic reticular nucleus (TRN) – a sheet of tissue, about ten neurons thick in mice, that sits on top of the thalamus and close to the cortex. The TRN is not well understood, but it is important for controlling sleep, attention and sensory processing, and it has caught the interest of Feng and other neuroscientists because it expresses a disproportionate number of genes implicated in disorders such as autism, attention deficit hyperactivity disorder, and intelligence deficits. Together with Joshua Levin’s group at Broad, Li has already used nuclear RNA sequencing to identify the cell types in the TRN, and he has begun to examine them within intact brain using the expansion techniques. “When you map these precise cell types back to the tissue, you can integrate the gene expression information with everything else, like electrophysiology, connectivity, morphology,” says Li. “Then we can start to ask what’s going wrong in disease.”

Meanwhile, Feng is already looking beyond the TRN, and planning how to scale the approach to other structures and eventually to the entire brain. He returns to the metaphor of a Google map. “Microscopic images are like satellite photos,” he says. “Now with expansion microscopy we can add another layer of information, like property boundaries and individual buildings. And knowing which RNAs are in each cell will be like seeing who lives in those buildings. I think this will completely change how we view the brain.”

A new player in appetite control

Anne Trafton |

MIT neuroscientists have discovered that brain cells called glial cells play a critical role in controlling appetite and feeding behavior. In a study of mice, the researchers found that activating these cells stimulates overeating, and that when the cells are suppressed, appetite is also suppressed.

The findings could offer scientists a new target for developing drugs against obesity and other appetite-related disorders, the researchers say. The study is also the latest in recent years to implicate glial cells in important brain functions. Until about 10 years ago, glial cells were believed to play more of a supporting role for neurons.

“In the last few years, abnormal glial cell activities have been strongly implicated in neurodegenerative disorders. There is more and more evidence to point to the importance of glial cells in modulating neuronal function and in mediating brain disorders,” says Guoping Feng, the James W. and Patricia Poitras Professor of Neuroscience. Feng is also a member of MIT’s McGovern Institute for Brain Research and the Stanley Center for Psychiatric Research at the Broad Institute.

Feng is one of the senior authors of the study, which appears in the Oct. 18 edition of the journal eLife. The other senior author is Weiping Han, head of the Laboratory of Metabolic Medicine at the Singapore Bioimaging Consortium in Singapore. Naiyan Chen, a postdoc at the Singapore Bioimaging Consortium and the McGovern Institute, is the lead author.

Turning on appetite

It has long been known that the hypothalamus, an almond-sized structure located deep within the brain, controls appetite as well as energy expenditure, body temperature, and circadian rhythms including sleep cycles. While performing studies on glial cells in other parts of the brain, Chen noticed that the hypothalamus also appeared to have a lot of glial cell activity.

“I was very curious at that point what glial cells would be doing in the hypothalamus, since glial cells have been shown in other brain areas to have an influence on regulation of neuronal function,” she says.

Within the hypothalamus, scientists have identified two key groups of neurons that regulate appetite, known as AgRP neurons and POMC neurons. AgRP neurons stimulate feeding, while POMC neurons suppress appetite.

Until recently it has been difficult to study the role of glial cells in controlling appetite or any other brain function, because scientists haven’t developed many techniques for silencing or stimulating these cells, as they have for neurons. Glial cells, which make up about half of the cells in the brain, have many supporting roles, including cushioning neurons and helping them form connections with one another.

In this study, the research team used a new technique developed at the University of North Carolina to study a type of glial cell known as an astrocyte. Using this strategy, researchers can engineer specific cells to produce a surface receptor that binds to a chemical compound known as CNO, a derivative of clozapine. Then, when CNO is given, it activates the glial cells.

The MIT team found that turning on astrocyte activity with just a single dose of CNO had a significant effect on feeding behavior.

“When we gave the compound that specifically activated the receptors, we saw a robust increase in feeding,” Chen says. “Mice are not known to eat very much in the daytime, but when we gave drugs to these animals that express a particular receptor, they were eating a lot.”

The researchers also found that in the short term (three days), the mice did not gain extra weight, even though they were eating more.

“This raises the possibility that glial cells may also be modulating neurons that control energy expenditures, to compensate for the increased food intake,” Chen says. “They might have multiple neuronal partners and modulate multiple energy homeostasis functions all at the same time.”

When the researchers silenced activity in the astrocytes, they found that the mice ate less than normal.

Suzanne Dickson, a professor of neuroendocrinology at the University of Gothenburg in Sweden described the study as part of a “paradigm shift” toward the idea that glial cells have a less passive role than previously believed.

“We tend to think of glial cells as providing a support network for neuronal processes and that their activation is also important in certain forms of brain trauma or inflammation,” says Dickson, who was not involved in the research. “This study adds to the emerging evidence base that glial cells may also exert specific effects to control nerve cell function in normal physiology.”

Unknown interactions

Still unknown is how the astrocytes exert their effects on neurons. Some recent studies have suggested that glial cells can secrete chemical messengers such as glutamate and ATP; if so, these “gliotransmitters” could influence neuron activity.

Another hypothesis is that instead of secreting chemicals, astrocytes exert their effects by controlling the uptake of neurotransmitters from the space surrounding neurons, thereby affecting neuron activity indirectly.

Feng now plans to develop new research tools that could help scientists learn more about astrocyte-neuron interactions and how astrocytes contribute to modulation of appetite and feeding. He also hopes to learn more about whether there are different types of astrocytes that may contribute differently to feeding behavior, especially abnormal behavior.

“We really know very little about how astrocytes contribute to the modulation of appetite, eating, and metabolism,” he says. “In the future, dissecting out these functional difference will be critical for our understanding of these disorders.”

Finding a way in

by Elizabeth Dougherty |

Our perception of the world arises within the brain, based on sensory information that is sometimes ambiguous, allowing more than one interpretation. Familiar demonstrations of this point include the famous Necker cube and the “duck-rabbit” drawing (right) in which two different interpretations flip back and forth over time.

Another example is binocular rivalry, in which the two eyes are presented with different images that are perceived in alternation. Several years ago, this phenomenon caught the eye of Caroline Robertson, who is now a Harvard Fellow working in the lab of McGovern Investigator Nancy Kanwisher. Back when she was a graduate student at Cambridge University, Robertson realized that binocular rivalry might be used to probe the basis of autism, among the most mysterious of all brain disorders.

Robertson’s idea was based on the hypothesis that autism involves an imbalance between excitation and inhibition within the brain. Although widely supported by indirect evidence, this has been very difficult to test directly in human patients. Robertson realized that binocular rivalry might provide a way to perform such a test. The perceptual switches that occur during rivalry are thought to involve competition between different groups of neurons in the visual cortex, each group reinforcing its own interpretation via excitatory connections while suppressing the alternative interpretation through inhibitory connections. Thus, if the balance is altered in the brains of people with autism, the frequency of switching might also be different, providing a simple and easily measurable marker of the disease state.

To test this idea, Robertson recruited adults with and without autism, and presented them with two distinct and differently colored images in each eye. As expected, their perceptions switched back and forth between the two images, with short periods of mixed perception in between. This was true for both groups, but when she measured the timing of these switches, Robertson found that individuals with autism do indeed see the world in a measurably different way than people without the disorder. Individuals with autism cycle between the left and right images more slowly, with the intervening periods of mixed perception lasting longer than in people without autism. The more severe their autistic symptoms, as determined by a standard clinical behavioral evaluation, the greater the difference.

Robertson had found a marker for autism that is more objective than current methods that involve one person assessing the behavior of another. The measure is immediate and relies on brain activity that happens automatically, without people thinking about it. “Sensation is a very simple place to probe,” she says.

A top-down approach

When she arrived in Kanwisher’s lab, Robertson wanted to use brain imaging to probe the basis for the perceptual phenomenon that she had discovered. With Kanwisher’s encouragement, she began by repeating the behavioral experiment with a new group of subjects, to check that her previous results were not a fluke. Having confirmed that the finding was real, she then scanned the subjects using an imaging method called Magnetic Resonance Spectroscopy (MRS), in which an MRI scanner is reprogrammed to measure concentrations of neurotransmitters and other chemicals in the brain. Kanwisher had never used MRS before, but when Robertson proposed the experiment, she was happy to try it. “Nancy’s the kind of mentor who could support the idea of using a new technique and guide me to approach it rigorously,” says Robertson.

For each of her subjects, Robertson scanned their brains to measure the amounts of two key neurotransmitters, glutamate, which is the main excitatory transmitter in the brain, and GABA, which is the main source of inhibition. When she compared the brain chemistry to the behavioral results in the binocular rivalry task, she saw something intriguing and unexpected. In people without autism, the amount of GABA in the visual cortex was correlated with the strength of the suppression, consistent with the idea that GABA enables signals from one eye to inhibit those from the other eye. But surprisingly, there was no such correlation in the autistic individuals—suggesting that GABA was somehow unable to exert its normal suppressive effect. It isn’t yet clear exactly what is going wrong in the brains of these subjects, but it’s an early flag, says Robertson. “The next step is figuring out which part of the pathway is disrupted.”

A bottom-up approach

Robertson’s approach starts from the top-down, working backward from a measurable behavior to look for brain differences, but it isn’t the only way in. Another approach is to start with genes that are linked to autism in humans, and to understand how they affect neurons and brain circuits. This is the bottom-up approach of McGovern Investigator Guoping Feng, who studies a gene called Shank3 that codes for a protein that helps build synapses, the connections through which neurons send signals to each other. Several years ago Feng knocked out Shank3 in mice, and found that the mice exhibited behaviors reminiscent of human autism, including repetitive grooming, anxiety, and impaired social interaction and motor control.

These earlier studies involved a variety of different mutations that disabled the Shank3 gene. But when postdoc Yang Zhou joined Feng’s lab, he brought a new perspective. Zhou had come from a medical background and wanted to do an experiment more directly connected to human disease. So he suggested making a mouse version of a Shank3 mutation seen in human patients, and testing its effects.

Zhou’s experiment would require precise editing of the mouse Shank3 gene, previously a difficult and time-consuming task. But help was at hand, in the form of a collaboration with McGovern Investigator Feng Zhang, a pioneer in the development of genome-editing methods.

Using Zhang’s techniques, Zhou was able to generate mice with two different mutations: one that had been linked to human autism, and another that had been discovered in a few patients with schizophrenia.

The researchers found that mice with the autism-related mutation exhibited behavioral changes at a young age that paralleled behaviors seen in children with autism. They also found early changes in synapses within a brain region called the striatum. In contrast, mice with the schizophrenia-related gene appeared normal until adolescence, and then began to exhibit changes in behavior and also changes in the prefrontal cortex, a brain region that is implicated in human schizophrenia. “The consequences of the two different Shank3 mutations were quite different in certain aspects, which was very surprising to us,” says Zhou.

The fact that different mutations in just one gene can produce such different results illustrates exactly how complex these neuropsychiatric disorders can be. “Not only do we need to study different genes, but we also have to understand different mutations and which brain regions have what defects,” says Feng, who received funding from the Poitras Center for Affective Disorders research and the Simons Center for the Social Brain. Robertson and Kanwisher were also supported by the Simons Center.

Surprising plasticity

The brain alterations that lead to autism are thought to arise early in development, long before the condition is diagnosed, raising concerns that it may be difficult to reverse the effects once the damage is done. With the Shank3 knockout mice, Feng and his team were able to approach this question in a new way, asking what would happen if the missing gene were to be restored in adulthood.

To find the answer, lab members Yuan Mei and Patricia Monteiro, along with Zhou, studied another strain of mice, in which the Shank3 gene was switched off but could be reactivated at any time by adding a drug to their diet. When adult mice were tested six weeks after the gene was switched back on, they no longer showed repetitive grooming behaviors, and they also showed normal levels of social interaction with other mice, despite having grown up without a functioning Shank3 gene. Examination of their brains confirmed that many of the synaptic alterations were also rescued when the gene was restored.

Not every symptom was reversed by this treatment; even after six weeks or more of restored Shank3 expression, the mice continued to show heightened anxiety and impaired motor control. But even these deficits could be prevented if the Shank3 gene was restored earlier in life, soon after birth.

The results are encouraging because they indicate a surprising degree of brain plasticity, persisting into adulthood. If the results can be extrapolated to human patients, they suggest that even in adulthood, autism may be at least partially reversible if the right treatment can be found. “This shows us the possibility,” says Zhou. “If we could somehow put back the gene in patients who are missing it, it could help improve their life quality.”

Converging paths

Robertson and Feng are approaching the challenge of autism from different starting points, but already there are signs of convergence. Feng is finding early signs that his Shank3 mutant mice may have an altered balance of inhibitory and excitatory circuits, consistent with what Robertson and Kanwisher have found in humans.

Feng is continuing to study these mice, and he also hopes to study the effects of a similar mutation in non-human primates, whose brains and behaviors are more similar to those of humans than rodents. Robertson, meanwhile, is planning to establish a version of the binocular rivalry test in animal models, where it is possible to alter the balance between inhibition and excitation experimentally (for example, via a genetic mutation or a drug treatment). If this leads to changes in binocular rivalry, it would strongly support the link to the perceptual changes seen in humans.

One challenge, says Robertson, will be to develop new methods to measure the perceptions of mice and other animals. “The mice can’t tell us what they are seeing,” she says. “But it would also be useful in humans, because it would allow us to study young children and patients who are non-verbal.”

A multi-pronged approach

The imbalance hypothesis is a promising lead, but no single explanation is likely to encompass all of autism, according to McGovern director Bob Desimone. “Autism is a notoriously heterogeneous condition,” he explains. “We need to try multiple approaches in order to maximize the chance of success.”

McGovern researchers are doing exactly that, with projects underway that range from scanning children to developing new molecular and microscopic methods for examining brain changes in animal disease models. Although genetic studies provide some of the strongest clues, Desimone notes that there is also evidence for environmental contributions to autism and other brain disorders. “One that’s especially interesting to us is a maternal infection and inflammation, which in mice at least can affect brain development in ways we’re only beginning to understand.”

The ultimate goal, says Desimone, is to connect the dots and to understand how these diverse human risk factors affect brain function. “Ultimately, we want to know what these different pathways have in common,” he says. “Then we can come up with rational strategies for the development of new treatments.”

Study reveals a basis for attention deficits

Anne Trafton |

More than 3 million Americans suffer from attention deficit hyperactivity disorder (ADHD), a condition that usually emerges in childhood and can lead to difficulties at school or work.

A new study from MIT and New York University links ADHD and other attention difficulties to the brain’s thalamic reticular nucleus (TRN), which is responsible for blocking out distracting sensory input. In a study of mice, the researchers discovered that a gene mutation found in some patients with ADHD produces a defect in the TRN that leads to attention impairments.

The findings suggest that drugs boosting TRN activity could improve ADHD symptoms and possibly help treat other disorders that affect attention, including autism.

“Understanding these circuits may help explain the converging mechanisms across these disorders. For autism, schizophrenia, and other neurodevelopmental disorders, it seems like TRN dysfunction may be involved in some patients,” says Guoping Feng, the James W. and Patricia Poitras Professor of Neuroscience and a member of MIT’s McGovern Institute for Brain Research and the Stanley Center for Psychiatric Research at the Broad Institute.

Feng and Michael Halassa, an assistant professor of psychiatry, neuroscience, and physiology at New York University, are the senior authors of the study, which appears in the March 23 online edition of Nature. The paper’s lead authors are MIT graduate student Michael Wells and NYU postdoc Ralf Wimmer.

Paying attention

Feng, Halassa, and their colleagues set out to study a gene called Ptchd1, whose loss can produce attention deficits, hyperactivity, intellectual disability, aggression, and autism spectrum disorders. Because the gene is carried on the X chromosome, most individuals with these Ptchd1-related effects are male.

In mice, the researchers found that the part of the brain most affected by the loss of Ptchd1 is the TRN, which is a group of inhibitory nerve cells in the thalamus. It essentially acts as a gatekeeper, preventing unnecessary information from being relayed to the brain’s cortex, where higher cognitive functions such as thought and planning occur.

“We receive all kinds of information from different sensory regions, and it all goes into the thalamus,” Feng says. “All this information has to be filtered. Not everything we sense goes through.”

If this gatekeeper is not functioning properly, too much information gets through, allowing the person to become easily distracted or overwhelmed. This can lead to problems with attention and difficulty in learning.

The researchers found that when the Ptchd1 gene was knocked out in mice, the animals showed many of the same behavioral defects seen in human patients, including aggression, hyperactivity, attention deficit, and motor impairments. When the Ptchd1 gene was knocked out only in the TRN, the mice showed only hyperactivity and attention deficits.

Toward new treatments

At the cellular level, the researchers found that the Ptchd1 mutation disrupts channels that carry potassium ions, which prevents TRN neurons from being able to sufficiently inhibit thalamic output to the cortex. The researchers were also able restore the neurons’ normal function with a compound that boosts activity of the potassium channel. This intervention reversed the TRN-related symptoms but not any of the symptoms that appear to be caused by deficits of some other circuit.

“The authors convincingly demonstrate that specific behavioral consequences of the Ptchd1 mutation — attention and sleep — arise from an alteration of a specific protein in a specific brain region, the thalamic reticular nucleus. These findings provide a clear and straightforward pathway from gene to behavior and suggest a pathway toward novel treatments for neurodevelopmental disorders such as autism,” says Joshua Gordon, an associate professor of psychiatry at Columbia University, who was not involved in the research.

Most people with ADHD are now treated with psychostimulants such as Ritalin, which are effective in about 70 percent of patients. Feng and Halassa are now working on identifying genes that are specifically expressed in the TRN in hopes of developing drug targets that would modulate TRN activity. Such drugs may also help patients who don’t have the Ptchd1 mutation, because their symptoms are also likely caused by TRN impairments, Feng says.

The researchers are also investigating when Ptchd1-related problems in the TRN arise and at what point they can be reversed. And, they hope to discover how and where in the brain Ptchd1 mutations produce other abnormalities, such as aggression.

The research was funded by the Simons Foundation Autism Research Initiative, the National Institutes of Health, the Poitras Center for Affective Disorders Research, and the Stanley Center for Psychiatric Research at the Broad Institute.

McGovern neuroscientists reverse autism symptoms

Anne Trafton |

Autism has diverse genetic causes, most of which are still unknown. About 1 percent of people with autism are missing a gene called Shank3, which is critical for brain development. Without this gene, individuals develop typical autism symptoms including repetitive behavior and avoidance of social interactions.

In a study of mice, MIT researchers have now shown that they can reverse some of those behavioral symptoms by turning the gene back on later in life, allowing the brain to properly rewire itself.

“This suggests that even in the adult brain we have profound plasticity to some degree,” says Guoping Feng, an MIT professor of brain and cognitive sciences. “There is more and more evidence showing that some of the defects are indeed reversible, giving hope that we can develop treatment for autistic patients in the future.”

Feng, who is the James W. and Patricia Poitras Professor of Neuroscience and a member of MIT’s McGovern Institute for Brain Research and the Stanley Center for Psychiatric Research at the Broad Institute, is the senior author of the study, which appears in the Feb. 17 issue of Nature. The paper’s lead authors are former MIT graduate student Yuan Mei and former Broad Institute visiting graduate student Patricia Monteiro, now at the University of Coimbra in Portugal.

Boosting communication

The Shank3 protein is found in synapses — the connections that allow neurons to communicate with each other. As a scaffold protein, Shank3 helps to organize the hundreds of other proteins that are necessary to coordinate a neuron’s response to incoming signals.

Studying rare cases of defective Shank3 can help scientists gain insight into the neurobiological mechanisms of autism. Missing or defective Shank3 leads to synaptic disruptions that can produce autism-like symptoms in mice, including compulsive behavior, avoidance of social interaction, and anxiety, Feng has previously found. He has also shown that some synapses in these mice, especially in a part of the brain called the striatum, have a greatly reduced density of dendritic spines — small buds on neurons’ surfaces that help with the transmission of synaptic signals.

In the new study, Feng and colleagues genetically engineered mice so that their Shank3 gene was turned off during embryonic development but could be turned back on by adding tamoxifen to the mice’s diet.
When the researchers turned on Shank3 in young adult mice (two to four and a half months after birth), they were able to eliminate the mice’s repetitive behavior and their tendency to avoid social interaction. At the cellular level, the team found that the density of dendritic spines dramatically increased in the striatum of treated mice, demonstrating the structural plasticity in the adult brain.

However, the mice’s anxiety and some motor coordination symptoms did not disappear. Feng suspects that these behaviors probably rely on circuits that were irreversibly formed during early development.
When the researchers turned on Shank3 earlier in life, only 20 days after birth, the mice’s anxiety and motor coordination did improve. The researchers are now working on defining the critical periods for the formation of these circuits, which could help them determine the best time to try to intervene.

“Some circuits are more plastic than others,” Feng says. “Once we understand which circuits control each behavior and understand what exactly changed at the structural level, we can study what leads to these permanent defects, and how we can prevent them from happening.”

Gordon Fishell, a professor of neuroscience at New York University School of Medicine, praises the study’s “elegant approach” and says it represents a major advance in understanding the circuitry and cellular physiology that underlie autism. “The combination of behavior, circuits, physiology, and genetics is state-of-the art,” says Fishell, who was not involved in the research. “Moreover, Dr. Feng’s demonstration that restoration of Shank3 function reverses autism symptoms in adult mice suggests that gene therapy may ultimately prove an effective therapy for this disease.”

Early intervention

For the small population of people with Shank3 mutations, the findings suggest that new genome-editing techniques could in theory be used to repair the defective Shank3 gene and improve these individuals’ symptoms, even later in life. These techniques are not yet ready for use in humans, however.

Feng believes that scientists may also be able to develop more general approaches that would apply to a larger population. For example, if the researchers can identify defective circuits that are specific for certain behavioral abnormalities in some autism patients, and figure out how to modulate those circuits’ activity, that could also help other people who may have defects in the same circuits even though the problem arose from a different genetic mutation.

“That’s why it’s important in the future to identify what subtype of neurons are defective and what genes are expressed in these neurons, so we can use them as a target without affecting the whole brain,” Feng says.

How a single gene contributes to autism and schizophrenia

Anne Trafton |

Although it is known that psychiatric disorders have a strong genetic component, untangling the web of genes contributing to each disease is a daunting task. Scientists have found hundreds of genes that are mutated in patients with disorders such as autism, but each patient usually has only a handful of these variations.

To further complicate matters, some of these genes contribute to more than one disorder. One such gene, known as Shank3, has been linked to both autism and schizophrenia.

MIT neuroscientists have now shed some light on how a single gene can play a role in more than one disease. In a study appearing in the Dec. 10 online edition of Neuron, they revealed that two different mutations of the Shank3 gene produce some distinct molecular and behavioral effects in mice.

“This study gives a glimpse into the mechanism by which different mutations within the same gene can cause distinct defects in the brain, and may help to explain how they may contribute to different disorders,” says Guoping Feng, the James W. and Patricia Poitras Professor of Neuroscience at MIT, a member of MIT’s McGovern Institute for Brain Research, a member of the Stanley Center for Psychiatric Research at the Broad Institute, and the senior author of the study.

The findings also suggest that identifying the brain circuits affected by mutated genes linked to psychiatric disease could help scientists develop more personalized treatments for patients in the future, Feng says.

The paper’s lead authors are McGovern Institute research scientist Yang Zhou, graduate students Tobias Kaiser and Xiangyu Zhang, and research affiliate Patricia Monteiro.

Disrupted communication

The protein encoded by Shank3 is found in synapses — the junctions between neurons that allow them to communicate with each other. Shank3 is a scaffold protein, meaning it helps to organize hundreds of other proteins clustered on the postsynaptic cell membrane, which are required to coordinate the cell’s response to signals from the presynaptic cell.

In 2011, Feng and colleagues showed that by deleting Shank3 in mice they could induce two of the most common traits of autism — avoidance of social interaction, and compulsive, repetitive behavior. A year earlier, researchers at the University of Montreal identified a Shank3 mutation in patients suffering from schizophrenia, which is characterized by hallucinations, cognitive impairment, and abnormal social behavior.

Feng wanted to find out how these two different mutations in the Shank3 gene could play a role in such different disorders. To do that, he and his colleagues engineered mice with each of the two mutations: The schizophrenia-related mutation results in a truncated version of the Shank3 protein, while the autism-linked mutation leads to a total loss of the Shank3 protein.

Behaviorally, the mice shared many defects, including strong anxiety. However, the mice with the autism mutation had very strong compulsive behavior, manifested by excessive grooming, which was rarely seen in mice with the schizophrenia mutation.

In the mice with the schizophrenia mutation, the researchers saw a type of behavior known as social dominance. These mice trimmed the whiskers and facial hair of the genetically normal mice sharing their cages, to an extreme extent. This is a typical way for mice to display their social dominance, Feng says.

By activating the mutations in different parts of the brain and at different stages of development, the researchers found that the two mutations affected brain circuits in different ways. The autism mutation exerted its effects early in development, primarily in a part of the brain known as the striatum, which is involved in coordinating motor planning, motivation, and habitual behavior. Feng believes that disruption of synapses in the striatum contributes to the compulsive behavior seen in those mice.

In mice carrying the schizophrenia-associated mutation, early development was normal, suggesting that truncated Shank3 can adequately fill in for the normal version during this stage. However, later in life, the truncated version of Shank3 interfered with synaptic functions and connections in the brain’s cortex, where executive functions such as thought and planning occur. This suggests that different segments of the protein — including the stretch that is missing in the schizophrenia-linked mutation — may be crucial for different roles, Feng says.

The new paper represents an important first step in understanding how different mutations in the same gene can lead to different diseases, says Joshua Gordon, an associate professor of psychiatry at Columbia University.

“The key is to identify how the different mutations alter brain function in different ways, as done here,” says Gordon, who was not involved in the research. “Autism strikes early in childhood, while schizophrenia typically arises in adolescence or early adulthood. The finding that the autism-associated mutation has effects at a younger age than the schizophrenia-associated mutation is particularly intriguing in this context.”

Modeling disease

Although only a small percentage of autism patients have mutations in Shank3, many other variant synaptic proteins have been associated with the disorder. Future studies should help to reveal more about the role of the many genes and mutations that contribute to autism and other disorders, Feng says. Shank3 alone has at least 40 identified mutations, he says.

“We cannot consider them all to be the same,” he says. “To really model these diseases, precisely mimicking each human mutation is critical.”

Understanding exactly how these mutations influence brain circuits should help researchers develop drugs that target those circuits and match them with the patients who would benefit most, Feng says, adding that a tremendous amount of work needs to be done to get to that point.

His lab is now investigating what happens in the earliest stages of the development of mice with the autism-related Shank3 mutation, and whether any of those effects can be reversed either during development or later in life.

The research was funded by the Simons Center for the Social Brain at MIT, the Stanley Center for Psychiatric Research at the Broad Institute of MIT and Harvard, the Poitras Center for Affective Disorders Research at MIT, and National Institute of Mental Health.

Bold new microscopies for the brain

by Elizabeth Doherty |

McGovern researchers create unexpected new approaches to microscopy that are changing the way scientists look at the brain.

Ask McGovern Investigator Ed Boyden about his ten-year plan and you’ll get an immediate and straight-faced answer: “We would like to understand the brain.”

He means it. Boyden intends to map all of the cells in a brain, all of their connections, and even all of the molecules that form those connections and determine their strengths. He also plans to study how information flows through the brain and to use this to generate a working model. “I’d love to be able to load a map of an entire brain into a computer and see if we can simulate the brain,” he says.

Boyden likens the process to reverse-engineering a computer by opening it up and looking inside. The analogy, though not perfect, provides a sense of the enormity of the task ahead. As complicated as computers are, brains are far more complex, and they are also much harder to visualize, given the need to see features at multiple scales. For example, signals travel from cell to cell through synaptic connections that are measured in nanometers, but the signals are then propagated along nerve fibers that may span several centimeters—a difference of more than a million-fold. Modern microscopes make it possible to study features at one scale or the other, but not both together. Similarly, there are methods for visualizing electrical activity in single neurons or in whole brains, but there is no way to see both at once. So Boyden is building his own tools, and in the process is pushing the limits of imagination. “Our group is often trying to do the opposite of what other people do,” Boyden says.

Boyden’s new methods are part of a broader push to understand the brain’s connectivity, an objective that gained impetus two years ago with the President’s BRAIN Initiative, and with allied efforts such as the NIH-funded Human Connectome Project. Hundreds of researchers have already downloaded Boyden’s recently published protocols, including colleagues at the McGovern Institute who are using them to advance their studies of brain function and disease.

Just add water

Under the microscope, the brain section prepared by Jill Crittenden looks like a tight bundle of threads. The nerve fibers are from a mouse brain, from a region known to degenerate in humans with Parkinson’s disease. The loss of the tiny synaptic connections between these fibers may be the earliest signs of degeneration, so Crittenden, a research scientist who has been studying this disease for several years in the lab of McGovern Investigator Ann Graybiel, wants to be able to see them.

But she can’t. They are far too small— smaller than a wavelength of light, meaning they are beyond the limit for optical microscopy. To bring these structures into view, one of Boyden’s technologies, called expansion microscopy (ExM), simply makes the specimen bigger, allowing it to be viewed on a conventional laboratory microscope.

The idea is at once obvious and fantastical. “Expansion microscopy is the kind of thing scientists daydream about,” says Paul Tillberg, a graduate student in Boyden’s lab. “You either shrink the scientist or expand the specimen.”

Leaving Crittenden’s sample in place, Tillberg adds water. Minutes later, the tissue has expanded and become transparent, a ghostly and larger version of its former self.

Crittenden takes another look through the scope. “It’s like someone has loosened up all the fibers. I can see each one independently, and see them interconnecting,” she says. “ExM will add a lot of power to the tools we’ve developed for visualizing the connections we think are degenerating.”

It took Tillberg and his fellow graduate student Fei Chen several months of brainstorming to find a plausible way to make ExM a reality. They had found inspiration in the work of MIT physicist Toyoichi Tanaka, who in the 1970s had studied smart gels, polymers that rapidly expand in response to a change in environment. One familiar example is the absorbent material in baby diapers, and Boyden’s team turned to this substance for the expansion technique.

The process they devised involves several steps. The tissue is first labeled using fluorescent antibodies that bind to molecules of interest, and then it is impregnated with the gel-forming material. Once the gel has set, the fluorescent markers are anchored to the gel, and the original tissue sample is digested, allowing the gel to stretch evenly in all directions.

When water is added, the gel expands and the fluorescent markers spread out like a picture on a balloon. Remarkably, the 3D shapes of even the finest structures are faithfully preserved during the expansion, making it possible to see them using a conventional microscope. By labeling molecules with different colors, the researchers can even distinguish pre-synaptic from post-synaptic structures. Boyden plans eventually to use hundreds, possibly thousands, of colors, and to increase the expansion factor to 10 times original size, equivalent to a 1000-fold increase in volume.

ExM is not the only way to see fine structures such as synapses; they can also be visualized by electron microcopy, or by recently-developed ‘super-resolution’ optical methods that garnered a 2014 Nobel Prize. These techniques, however, require expensive equipment, and the images are very time-consuming to produce.

“With ExM, because the sample is physically bigger, you can scan it very quickly using just a regular microscope,” says Boyden.

Boyden is already talking to other leading researchers in the field, including Kwanghun Chung at MIT and George Church at Harvard, about ways to further enhance the ExM method. Within the McGovern Institute, among those who expect to benefit from these advances is Guoping Feng, who is developing mouse models of autism, schizophrenia and other disorders by introducing some of the same genetic changes seen in humans with these disorders. Many of the genes associated with autism and schizophrenia play a role in the formation of synapses, but even with the mouse models at his disposal, Feng isn’t sure what goes wrong with them because they are so hard to see. “If we can make parts of the brain bigger, we might be able to see how the assembly of this synaptic machinery changes in different disorders,” he says.

3D Movies Without Special Glasses

Another challenge facing Feng and many other researchers is that many brain functions, and many brain diseases, are not confined to one area, but are widely distributed across the brain. Trying to understand these processes by looking through a small microscopic window has been compared to watching a soccer game by observing just a single square foot of the playing field.

No current technology can capture millisecond-by-millisecond electrical events across the entire living brain, so Boyden and collaborators in Vienna, Austria, decided to develop one. They turned to a method called light field microscopy (LFM) as a way to capture 3D movies of an animal’s thoughts as they flash through the entire nervous system.

The idea is mind-boggling to imagine, but the hardware is quite simple. The instrument records images in depth the same way humans do, using multiple ‘eyes’ to send slightly offset 2D images to a computer that can reconstruct a 3D image of the world. (The idea had been developed in the 1990s by Boyden’s MIT colleague Ted Adelson, and a similar method was used to create Google Street View.) Boyden and his collaborators started with a microscope of standard design, attached a video camera, and inserted between them a six-by-six array of miniature lenses, designed in Austria, that projects a grid of offset images into the camera and the computer.

The rest is math. “We take the multiple, superimposed flat images projected through the lens array and combine them into a volume,” says Young-Gyu Yoon, a graduate student in the Boyden lab who designed and wrote the software.

Another graduate student, Nikita Pak, used the new method to measure neural activity in C. elegans, a tiny worm whose entire nervous system consists of just 302 neurons. By using a worm that had been genetically engineered so that its neurons light up when they become electrically active, Pak was able to make 3D movies of the activity in the entire nervous system. “The setup is just so simple,” he says. “Every time I use it, I think it’s cool.”

The team then tested their method on a larger brain, that of the larval zebra fish. They presented the larvae with a noxious odor, and found that it triggered activity in around 5000 neurons, over a period of about three minutes. Even with this relatively simple example, activity is distributed widely throughout the brain, and would be difficult to detect with previous techniques. Boyden is now working towards recording activity over much longer timespans, and he also envisions scaling it up to image the much more complex brains of mammals.

He hopes to start with the smallest known mammal, the Etruscan shrew. This animal resembles a mouse, but it is ten times smaller, no bigger than a thimble. Its brain is also much smaller, with only a few million neurons, compared to 100 million in a mouse.

Whole brain imaging in this tiny creature could provide an unprecedented view of mammalian brain activity, including its disruption in disease states. Feng cites sensory overload in autism as an example. “If we can see how sensory activity spreads through the brain, we can start to understand how overload starts and how it spills over to other brain areas,” he says.

Visions of Convergence

While Boyden’s microscopy technologies are providing his colleagues with new ways to study brain disorders, Boyden himself hopes to use them to understand the brain as a whole. He plans to use ExM to map connections and identify which molecules are where; 3D whole-brain imaging to trace brain activity as it unfolds in real time, and optogenetics techniques to stimulate the brain and directly record the resulting activity. By combining all three tools together, he hopes to pin stimuli and activity to the molecules and connections on the map and then use that to build a computational model that simulates brain activity.

The plan is grandiose, and the tools aren’t all ready yet, but to make the scheme plausible in the proposed timeframe, Boyden is adhering to a few principles. His methods are fast, capturing information-dense images rapidly rather than scanning over days, and inclusive, imaging whole brains rather than chunks that need to be assembled. They are also accessible, so researchers don’t need to spend large sums to acquire specialized equipment or expertise in-house.

The challenges ahead might appear insurmountable at times, but Boyden is undeterred. He moves forward, his mind open to even the most far-fetched ideas, because they just might work.

From genes to brains

by Elizabeth Dougherty |

Many brain disorders are strongly influenced by genetics, and researchers have long hoped that the identification of genetic risk factors will provide clues to the causes and possible treatments of these mysterious conditions. In the early years, progress was slow. Many claims failed to replicate, and it became clear that in order to identify the important risk genes with confidence, researchers would need to examine the genomes of very large numbers of patients.

Until recently that would have been prohibitively expensive, but genome research has been accelerating fast. Just how fast was underlined by an announcement in January from a California-based company, Illumina, that it had achieved a long-awaited milestone: sequencing an entire human genome for under $1000. Seven years ago, this task would have cost $10M and taken weeks of work. The new system does the job in a few hours, and can sequence tens of thousands of genomes per year.

In parallel with these spectacular advances, another technological revolution has been unfolding over the past several years, with the development of a new method for editing the genome of living cells. This method, known as CRISPR, allows researchers to make precise changes to a DNA sequence—an advance that is expected to transform many areas of biomedical research and may ultimately form the basis of new treatments for human genetic disease.

The CRISPR technology, which is based on a natural bacterial defense system against viruses, uses a short strand of RNA as a “search string” to locate a corresponding DNA target sequence. This RNA string can be synthesized in the lab and can be designed to recognize any desired sequence of DNA. The RNA carries with it a protein called Cas9, which cuts the target DNA at the chosen location, allowing a new sequence to be inserted—providing researchers with a fast and flexible “search-and-replace” tool for editing the genome.

One of the pioneers in this field is McGovern Investigator Feng Zhang, who along with George Church of Harvard, was the first to show that CRISPR could be used to edit the human genome in living cells. Zhang is using the technology to study human brain disorders, building on the flood of new genetic discoveries that are emerging from advances in DNA sequencing. The Broad Institute, where Zhang holds a joint appointment, is a world leader in human psychiatric genetics, and will be among the first to acquire the new Illumina sequencing machines when they reach the market later this year.

By sequencing many thousands of individuals, geneticists are identifying the rare genetic variants that contribute to risk of diseases such as autism, schizophrenia and bipolar disorder. CRISPR will allow neuroscientists to study those gene variants in cells and in animal models. The goal, says McGovern Institute director Bob Desimone, is to understand the biological roots of brain disorders. “The biggest obstacle to new treatments has been our ignorance of fundamental mechanisms. But with these new technologies, we have a real opportunity to understand what’s wrong at the level of cells and circuits, and to identify the pressure points at which therapeutic intervention may be possible.”

Culture Club

In other fields, the influence of genetic variations on disease has turned out to be surprisingly difficult to unravel, and for neuropsychiatric disease, the challenge may be even greater. The brain is the most complex organ of the body, and the underlying pathologies that lead to disease are not yet well understood. Moreover, any given disorder may show a wide variation in symptoms from patient to patient, and it may also have many different genetic causes. “There are hundreds of genes that can contribute to autism or schizophrenia,” says McGovern Investigator Guoping Feng, who is also Poitras Professor of Neuroscience.

To study these genes, Feng and collaborators at the Broad Institute’s Stanley Center for Psychiatric Research are planning to screen thousands of cultures of neurons, grown in the tiny wells of cell culture plates. The neurons, which are grown from stem cells, can be engineered using CRISPR to contain the genetic variants that are linked to neuropsychiatric disease. Each culture will contain neurons with a different variant, and these will be examined for abnormalities that might be associated with disease.

Feng and colleagues hope this high-throughput platform will allow them to identify cellular traits, or phenotypes, that may be related to disease and which can then be studied in animal models to see if they cause defects in brain function or in behavior. In the longer term, this high-throughput platform can also be used to screen for new drugs that can reverse these defects.

Animal Kingdom

Cell cultures are necessary for large-scale screens, but ultimately the results must be translated into the context of brain circuits and behavior. “That means we must study animal models too,” says Feng.

Feng has created several mouse models of human brain disease by mutating genes that are linked to these disorders and examining the behavioral and cellular defects in the mutant animals. “We have models of obsessive-compulsive disorder and autism,” he explains. “By studying these mice we want to learn what’s wrong with their brains.”

So far, Feng has focused on single-gene models, but the majority of human psychiatric disorders are triggered by multiple genes acting in combination. One advantage of the new CRISPR method is that it allows researchers to introduce several mutations in parallel, and Zhang’s lab is now working to create autistic mice with more than one gene alteration.

Perhaps the most important advantage of CRISPR is that it can be applied to any species. Currently, almost all genetic modeling of human disease is restricted to mice. But while mouse models are convenient, they are limited, especially for diseases that affect higher brain functions and for which there are no clear parallels in rodents. “We also need to study species that are closer to humans,” says Feng.

Accordingly, he and Zhang are collaborating with colleagues in Oregon and China to use CRISPR to create primate models of neuropsychiatric disorders. Earlier this year, a team in China announced that they had used CRISPR to create transgenic monkeys that will be used to study defects in metabolism and immunity.

Feng and Zhang are planning to use a similar approach to study brain disorders, but in addition to macacques, they will also work with a smaller primate species, the marmoset. These animals, with their fast breeding cycles and complex behavioral repertoires, are ideal for genetic studies of behavior and brain function. And because they are very social with highly structured communication patterns, they represent a promising new model for understanding the neural basis of social cognition and its disruption in conditions such as autism.

Given their close evolutionary relationship to humans, marmoset models could also help accelerate the development of new therapies. Many experimental drugs for brain disorders have been tested successfully in mice, only to prove ineffective in subsequent human trials. These failures, which can be enormously expensive, have led many drug companies to cut back on their neuroscience R&D programs. Better animal models could reverse this trend by allowing companies to predict more accurately which drug candidates are most promising, before investing heavily in human clinical trials.

Feng’s mouse research provides an example of how this approach can work. He previously developed a mouse model of obsessive-compulsive disorder, in which the animals engage in obsessive self-grooming, and he has now shown that this effect can be reversed when the missing gene is reintroduced, even in adulthood. Other researchers have seemed similar results with other brain disorders such as Rett Syndrome, a condition that is often accompanied by autism. “The brain is amazingly plastic,” says Feng. “At least in a mouse, we have shown that the damage can often be repaired. If we can also show this in marmosets or other primate models, that would really give us hope that something similar is possible in humans.”

Human Race

Ultimately, to understand the genetic roots of human behavior, researchers must sequence the genomes of individual subjects in parallel with measurements of those same individuals’ behavior and brain function.

Such studies typically require very large sample sizes, but the plummeting cost of sequencing is now making this feasible. In China, for instance, a project is already underway to sequence the genomes of many thousands of individuals to uncover genetic influences on cognition and intelligence.

The next step will be to link the genetics to brain activity, says McGovern Investigator John Gabrieli, who also directs the Martinos Imaging Center at MIT. “It’s a big step to go from DNA to behavioral variation or clinical diagnosis. But we know those genes must affect brain function, so neuroimaging may help us to bridge that gap.”

But brain scans can be time-consuming, given that volunteers must perform behavioral tasks in the scanner. Studies are typically limited to a few dozen subjects, not enough to detect the often subtle effects of genomic variation.

One way to enlarge these studies, says Gabrieli, is to image the brain during rest rather than in a state of prompted activity. This procedure is fast and easy to replicate from lab to lab, and patterns of resting state activity have turned out to be surprisingly reproducible; moreover, Gabrieli is finding that differences in resting activity are associated with brain disorders such as autism, and he hopes that in the future it will be possible to relate these differences to the genetic factors that are emerging from genome studies at the Broad Institute and elsewhere.

“I’m optimistic that we’re going to see dramatic advances in our understanding of neuropsychiatric disease over the next few years.” — Bob Desimone

Confirming these associations will require a “big data” approach, in which results from multiple labs are consolidated into large repositories and analyzed for significant associations. Resting state imaging lends itself to this approach, says Gabrieli. “To find the links between brain function and genetics, big data is the direction we need to go to be successful.”

How soon might this happen? “It won’t happen overnight,” cautions Desimone. “There are a lot of dots that need to be connected. But we’ve seen in the case of genome research how fast things can move once the right technologies are in place. I’m optimistic that we’re going to see equally dramatic advances in our understanding of neuropsychiatric disease over the next few years.”

Compulsive no more

Anne Trafton |

By activating a brain circuit that controls compulsive behavior, McGovern neuroscientists have shown that they can block a compulsive behavior in mice — a result that could help researchers develop new treatments for diseases such as obsessive-compulsive disorder (OCD) and Tourette’s syndrome.

About 1 percent of U.S. adults suffer from OCD, and patients usually receive antianxiety drugs or antidepressants, behavioral therapy, or a combination of therapy and medication. For those who do not respond to those treatments, a new alternative is deep brain stimulation, which delivers electrical impulses via a pacemaker implanted in the brain.

For this study, the MIT team used optogenetics to control neuron activity with light. This technique is not yet ready for use in human patients, but studies such as this one could help researchers identify brain activity patterns that signal the onset of compulsive behavior, allowing them to more precisely time the delivery of deep brain stimulation.

“You don’t have to stimulate all the time. You can do it in a very nuanced way,” says Ann Graybiel, an Institute Professor at MIT, a member of MIT’s McGovern Institute for Brain Research and the senior author of a Science paper describing the study.

The paper’s lead author is Eric Burguière, a former postdoc in Graybiel’s lab who is now at the Brain and Spine Institute in Paris. Other authors are Patricia Monteiro, a research affiliate at the McGovern Institute, and Guoping Feng, the James W. and Patricia T. Poitras Professor of Brain and Cognitive Sciences and a member of the McGovern Institute.

Controlling compulsion

In earlier studies, Graybiel has focused on how to break normal habits; in the current work, she turned to a mouse model developed by Feng to try to block a compulsive behavior. The model mice lack a particular gene, known as Sapap3, that codes for a protein found in the synapses of neurons in the striatum — a part of the brain related to addiction and repetitive behavioral problems, as well as normal functions such as decision-making, planning and response to reward.

For this study, the researchers trained mice whose Sapap3 gene was knocked out to groom compulsively at a specific time, allowing the researchers to try to interrupt the compulsion. To do this, they used a Pavlovian conditioning strategy in which a neutral event (a tone) is paired with a stimulus that provokes the desired behavior — in this case, a drop of water on the mouse’s nose, which triggers the mouse to groom. This strategy was based on therapeutic work with OCD patients, which uses this kind of conditioning.

After several hundred trials, both normal and knockout mice became conditioned to groom upon hearing the tone, which always occurred just over a second before the water drop fell. However, after a certain point their behaviors diverged: The normal mice began waiting until just before the water drop fell to begin grooming. This type of behavior is known as optimization, because it prevents the mice from wasting unnecessary effort.

This behavior optimization never appeared in the knockout mice, which continued to groom as soon as they heard the tone, suggesting that their ability to suppress compulsive behavior was impaired.

The researchers suspected that failed communication between the striatum, which is related to habits, and the neocortex, the seat of higher functions that can override simpler behaviors, might be to blame for the mice’s compulsive behavior. To test this idea, they used optogenetics, which allows them to control cell activity with light by engineering cells to express light-sensitive proteins.

When the researchers stimulated light-sensitive cortical cells that send messages to the striatum at the same time that the tone went off, the knockout mice stopped their compulsive grooming almost totally, yet they could still groom when the water drop came. The researchers suggest that this cure resulted from signals sent from the cortical neurons to a very small group of inhibitory neurons in the striatum, which silence the activity of neighboring striatal cells and cut off the compulsive behavior.

“Through the activation of this pathway, we could elicit behavior inhibition, which appears to be dysfunctional in our animals,” Burguière says.

The researchers also tested the optogenetic intervention in mice as they groomed in their cages, with no conditioning cues. During three-minute periods of light stimulation, the knockout mice groomed much less than they did without the stimulation.

Scott Rauch, president and psychiatrist-in-chief of McLean Hospital in Belmont, Mass., says the MIT study “opens the door to a universe of new possibilities by identifying a cellular and circuitry target for future interventions.”

“This represents a major leap forward, both in terms of delineating the brain basis of pathological compulsive behavior and in offering potential avenues for new treatment approaches,” adds Rauch, who was not involved in this study.

Graybiel and Burguière are now seeking markers of brain activity that could reveal when a compulsive behavior is about to start, to help guide the further development of deep brain stimulation treatments for OCD patients.

The research was funded by the Simons Initiative on Autism and the Brain at MIT, the National Institute of Child Health and Human Development, the National Institute of Mental Health, and the Simons Foundation Autism Research Initiative.

Calcium reveals connections between neurons

Anne Trafton |

A team led by MIT neuroscientists has developed a way to monitor how brain cells coordinate with each other to control specific behaviors, such as initiating movement or detecting an odor.

The researchers’ new imaging technique, based on the detection of calcium ions in neurons, could help them map the brain circuits that perform such functions. It could also provide new insights into the origins of autism, obsessive-compulsive disorder and other psychiatric diseases, says Guoping Feng, senior author of a paper appearing in the Oct. 18 issue of the journal Neuron.

“To understand psychiatric disorders we need to study animal models, and to find out what’s happening in the brain when the animal is behaving abnormally,” says Feng, the James W. and Patricia Poitras Professor of Neuroscience and a member of the McGovern Institute for Brain Research at MIT. “This is a very powerful tool that will really help us understand animal models of these diseases and study how the brain functions normally and in a diseased state.”

The lead author of the Neuron paper is McGovern Institute postdoc Qian Chen.

Performing any kind of brain function requires many neurons in different parts of the brain to communicate with each other. They achieve this communication by sending electrical signals, triggering an influx of calcium ions into active cells. Using dyes that bind to calcium, researchers have imaged neural activity in neurons. However, the brain contains thousands of cell types, each with distinct functions, and the dye is taken up nonselectively by all cells, making it impossible to pinpoint calcium in specific cell types with this approach.

To overcome this, the MIT-led team created a calcium-imaging system that can be targeted to specific cell types, using a type of green fluorescent protein (GFP). Junichi Nakai of Saitama University in Japan first developed a GFP that is activated when it binds to calcium, and one of the Neuron paper authors, Loren Looger of the Howard Hughes Medical Institute, modified the protein so its signal is strong enough to use in living animals.

The MIT researchers then genetically engineered mice to express this protein in a type of neuron known as pyramidal cells, by pairing the gene with a regulatory DNA sequence that is only active in those cells. Using two-photon microscopy to image the cells at high speed and high resolution, the researchers can identify pyramidal cells that are active when the brain is performing a specific task or responding to a certain stimulus.

In this study, the team was able to pinpoint cells in the somatosensory cortex that are activated when a mouse’s whiskers are touched, and olfactory cells that respond to certain aromas.

This system could be used to study brain activity during many types of behavior, including long-term phenomena such as learning, says Matt Wachowiak, an associate professor of physiology at the University of Utah. “These mouse lines should be really useful to many different research groups who want to measure activity in different parts of the brain,” says Wachowiak, who was not involved in this research.

The researchers are now developing mice that express the calcium-sensitive proteins and also exhibit symptoms of autistic behavior and obsessive-compulsive disorder. Using these mice, the researchers plan to look for neuron firing patterns that differ from those of normal mice. This could help identify exactly what goes wrong at the cellular level, offering mechanistic insights into those diseases.

“Right now, we only know that defects in neuron-neuron communications play a key role in psychiatric disorders. We do not know the exact nature of the defects and the specific cell types involved,” Feng says. “If we knew what cell types are abnormal, we could find ways to correct abnormal firing patterns.”

The researchers also plan to combine their imaging technology with optogenetics, which enables them to use light to turn specific classes of neurons on or off. By activating specific cells and then observing the response in target cells, they will be able to precisely map brain circuits.

The research was funded by the Poitras Center for Affective Disorders Research, the National Institutes of Health and the McNair Foundation