Author: Julie Pryor

New technique corrects disease-causing mutations

by Jill Crittenden |

Gene editing, or purposefully changing a gene’s DNA sequence, is a powerful tool for studying how mutations cause disease, and for making changes in an individual’s DNA for therapeutic purposes. A novel method of gene editing that can be used for both purposes has now been developed by a team led by Guoping Feng, the James W. (1963) and Patricia T. Poitras Professor in Brain and Cognitive Sciences at MIT.

“This technical advance can accelerate the production of disease models in animals and, critically, opens up a brand-new methodology for correcting disease-causing mutations,” says Feng, who is also a member of the Broad Institute of Harvard and MIT and the associate director of the McGovern Institute for Brain Research at MIT. The new findings publish online May 26 and in print June 10 in the journal Cell.

Genetic models of disease

A major goal of the Feng lab is to precisely define what goes wrong in neurodevelopmental and neuropsychiatric disorders by engineering animal models that carry the gene mutations that cause these disorders in humans. New models can be generated by injecting embryos with gene editing tools, along with a piece of DNA carrying the desired mutation.

In one such method, the gene editing tool CRISPR is programmed to cut a targeted gene, thereby activating natural DNA mechanisms that “repair” the broken gene with the injected template DNA. The engineered cells are then used to generate offspring capable of passing the genetic change on to further generations, creating a stable genetic line in which the disease, and therapies, are tested.

Although CRISPR has accelerated the process of generating such disease models, the process can still take months or years. Reasons for the inefficiency are that many treated cells do not undergo the desired DNA sequence change at all, and the change only occurs on one of the two gene copies (for most genes, each cell contains two versions, one from the father and one from the mother).

In an effort to increase the efficiency of the gene editing process, the Feng lab team initially hypothesized that adding a DNA repair protein called RAD51 to a standard mixture of CRISPR gene editing tools would increase the chances that a cell (in this case a fertilized mouse egg, or one-cell embryo) would undergo the desired genetic change.

As a test case, they measured the rate at which they were able to insert (“knock-in”) a mutation in the gene Chd2 that is associated with autism.  The overall proportion of embryos that were correctly edited remained unchanged, but to their surprise, a significantly higher percentage carried the desired gene edit on both chromosomes. Tests with a different gene yielded the same unexpected outcome.

“Editing of both chromosomes simultaneously is normally very uncommon,” explains postdoctoral fellow Jonathan Wilde.  “The high rate of editing seen with RAD51 was really striking and what started as a simple attempt to make mutant Chd2 mice quickly turned into a much bigger project focused on RAD51 and its applications in genome editing,” said Wilde, who co-authored the Cell paper with research scientist Tomomi Aida.

A molecular copy machine

The Feng lab team next set out to understand the mechanism by which RAD51 enhances gene editing. They hypothesized that RAD51 engages a process called interhomolog repair (IHR), whereby a DNA break on one chromosome is repaired using the second copy of the chromosome (from the other parent) as the template.

To test this, they injected mouse embryos with RAD51 and CRISPR but left out the template DNA. They programmed CRISPR to cut only the gene sequence on one of the chromosomes, and then tested whether it was repaired to match the sequence on the uncut chromosome. For this experiment, they had to use mice in which the sequences on the maternal and paternal chromosomes were different.

They found that control embryos injected with CRISPR alone rarely showed IHR repair. However, addition of RAD51 significantly increased the number of embryos in which the CRISPR-targeted gene was edited to match the uncut chromosome.

“Previous studies of IHR found that it is incredibly inefficient in most cells,” says Wilde. “Our finding that it occurs much more readily in embryonic cells and can be enhanced by RAD51 suggest that a deeper understanding of what makes the embryo permissive to this type of DNA repair could help us design safer and more efficient gene therapies.”

A new way to correct disease-causing mutations          

Standard gene therapy strategies that rely on injecting a corrective piece of DNA to serve as a template for repairing the mutation engage a process called homology-directed repair (HDR).

“HDR-based strategies still suffer from low efficiency and carry the risk of unwanted integration of donor DNA throughout the genome,” explains Feng. “IHR has the potential to overcome these problems because it relies upon natural cellular pathways and the patient’s own normal chromosome for correction of the deleterious mutation.”

Feng’s team went on to identify additional DNA repair-associated proteins that can stimulate IHR, including several that not only promote high levels of IHR, but also repress errors in the DNA repair process. Additional experiments that allowed the team to examine the genomic features of IHR events gave deeper insight into the mechanism of IHR and suggested ways that the technique can be used to make gene therapies safer.

“While there is still a great deal to learn about this new application of IHR, our findings are the foundation for a new gene therapy approach that could help solve some of the big problems with current approaches,” says Aida.

This study was supported by the Hock E. Tan and K. Lisa Yang Center for Autism Research at MIT, the Poitras Center for Psychiatric Disorders Research at MIT, NIH/NIMH Conte Center Grant (P50 MH094271) and NIH Office of the Director (U24 OD026638).

Michale Fee appointed head of MIT’s Brain and Cognitive Sciences Department

by Tristan Davies | BCS |

McGovern Investigator Michale Fee at work in the lab with postdoc Galen Lynch. Photo: Justin Knight

Michale Fee, the Glen V. and Phyllis F. Dorflinger Professor of Brain and Cognitive Sciences, has been named as the new head of the Department of Brain and Cognitive Sciences (BCS) effective May 1, 2021.

Fee, who is an investigator in the McGovern Institute for Brain Research, succeeds James DiCarlo, the Peter de Florez Professor of Neuroscience, who announced in December that he was stepping down to become director of the MIT Quest for Intelligence.

“I want to thank Jim for his impressive work over the last nine years as head,” says Fee. “I know firsthand from my time as associate department head that BCS is in good shape and on a steady course. Jim has set a standard of transparent and collaborative leadership, which is a solid foundation for making our community stronger on all fronts.” Fee notes that his first mission is to continue the initiatives begun under DiCarlo’s leadership—in academics (especially Course 6-9), mentoring, and diversity, equity, inclusion, and justice—while maintaining the highest standards of excellence in research and education.

“Jim has overseen significant growth in the faculty and its impact, as well as important academic initiatives to strengthen the department’s graduate and undergraduate programs,” says Nergis Mavalvala, dean of the School of Science. “His emphasis on building ties among BCS, the McGovern Institute for Brain Research, and the Picower Institute for Learning and Memory has brought innumerable new collaborations among researchers and helped solidify Building 46 and MIT as world leaders in brain science.”

Fee earned his BE in engineering physics in 1985 at the University of Michigan, and his PhD in applied physics at Stanford University in 1992, under the mentorship of Nobel laureate Stephen Chu. His doctoral work was followed by research in the Biological Computation Department at Bell Laboratories. He joined MIT and BCS as an associate professor in 2003 and was promoted to full professor in 2008.

He has served since 2012 as associate department head for education in BCS, overseeing significant evolution in the department’s academic programs, including a complete reworking of the Course 9 curriculum and the establishment in 2019 of Course 6-9, Computation and Cognition, in partnership with EECS.

In his research, Fee explores the neural mechanisms by which the brain learns complex sequential behaviors, using the learning of song by juvenile zebra finches as a model. He has brought new experimental and computational methods to bear on these questions, identifying a number of circuits used to learn, modify, time, and coordinate the development and utterance of song syllables.

“His work is emblematic of the department in that it crosses technical and disciplinary boundaries in search of the most significant discoveries,” says DiCarlo. “His research background gives Michale a deep appreciation of the importance of every sub-discipline in our community and a broad understanding of the importance of their connections with each other.”

Fee has received numerous honors and awards for his research and teaching, including the MIT Fundamental Science Investigator Award in 2017, the MIT School of Science Teaching Prize for Undergraduate Education in 2016, the BCS Award for Excellence in Undergraduate Teaching in 2015, and the Lawrence Katz Prize for Innovative Research in Neuroscience from Duke University in 2012.

Fee will be the sixth head of the department, after founding chair Hans-Lukas Teuber (1964–77), Richard Held (1977–86), Emilio Bizzi (1986–97), Mriganka Sur (1997–2012), and James DiCarlo (2012–21).

What’s happening in your brain when you’re spacing out?

by Eva Botkin-Kowacki |

This story is adapted from a News@Northeastern post.

We all do it. One second you’re fully focused on the task in front of you, a conversation with a friend, or a professor’s lecture, and the next second your mind is wandering to your dinner plans.

But how does that happen?

“We spend so much of our daily lives engaged in things that are completely unrelated to what’s in front of us,” says Aaron Kucyi, neuroscientist and principal research scientist in the department of psychology at Northeastern. “And we know very little about how it works in the brain.”

So Kucyi and colleagues at Massachusetts General Hospital, Boston University, and the McGovern Institute at MIT started scanning people’s brains using functional magnetic resonance imaging (fMRI) to get an inside look. Their results, published Friday in the journal Nature Communications, add complexity to our understanding of the wandering mind.

It turns out that spacing out might not deserve the bad reputation that it receives. Many more parts of the brain seem to be engaged in mind-wandering than previously thought, supporting the idea that it’s actually a quite dynamic and fundamental function of our psychology.

“Many of those things that we do when we’re spacing out are very adaptive and important to our lives,” says Kucyi, the paper’s first author. We might be drafting an email in our heads while in the shower, or trying to remember the host’s spouse’s name while getting dressed for a party. Moments when our minds wander can allow space for creativity and planning for the future, he says, so it makes sense that many parts of the brain would be engaged in that kind of thinking.

But mind wandering may also be detrimental, especially for those suffering from mental illness, explains the study’s senior author, Susan Whitfield-Gabrieli. “For many of us, mind wandering may be a healthy, positive and constructive experience, like reminiscing about the past, planning for the future, or engaging in creative thinking,” says Whitfield-Gabrieli, a professor of psychology at Northeastern University and a McGovern Institute research affiliate. “But for those suffering from mental illness such as depression, anxiety or psychosis, reminiscing about the past may transform into ruminating about the past, planning for the future may become obsessively worrying about the future and creative thinking may evolve into delusional thinking.”

Identifying the brain circuits associated with mind wandering, she says, may reveal new targets and better treatment options for people suffering from these disorders.

McGovern research affiliate Susan Whitfield-Gabrieli in the Martinos Imaging Center.

Inside the wandering mind

To study wandering minds, the researchers first had to set up a situation in which people were likely to lose focus. They recruited test subjects at the McGovern Institute’s Martinos Imaging Center to complete a simple, repetitive, and rather boring task. With an fMRI scanner mapping their brain activity, participants were instructed to press a button whenever an image of a city scene appeared on a screen in front of them and withhold a response when a mountain image appeared.

Throughout the experiment, the subjects were asked whether they were focused on the task at hand. If a subject said their mind was wandering, the researchers took a close look at their brain scans from right before they reported loss of focus. The data was then fed into a machine-learning algorithm to identify patterns in the neurological connections involved in mind-wandering (called “stimulus-independent, task-unrelated thought” by the scientists).

Scientists previously identified a specialized system in the brain considered to be responsible for mind-wandering. Called the “default mode network,” these parts of the brain activated when someone’s thoughts were drifting away from their immediate surroundings and deactivated when they were focused. The other parts of the brain, that theory went, were quiet when the mind was wandering, says Kucyi.

The researchers used a technique called “connectome-based predictive modeling” to identify patterns in the brain connections involved in mind-wandering. Image courtesy of the researchers.

The “default mode network” did light up in Kucyi’s data. But parts of the brain associated with other functions also appeared to activate when his subjects reported that their minds had wandered.

For example, the “default mode network” and networks in the brain related to controlling or maintaining a train of thought also seemed to be communicating with one another, perhaps helping explain the ability to go down a rabbit hole in your mind when you’re distracted from a task. There was also a noticeable lack of communication between the “default mode network” and the systems associated with sensory input, which makes sense, as the mind is wandering away from the person’s immediate environment.

“It makes sense that virtually the whole brain is involved,” Kucyi says. “Mind-wandering is a very complex operation in the brain and involves drawing from our memory, making predictions about the future, dynamically switching between topics that we’re thinking about, fluctuations in our mood, and engaging in vivid visual imagery while ignoring immediate visual input,” just to name a few functions.

The “default mode network” still seems to be key, Kucyi says. Virtual computer analysis suggests that if you took the regions of the brain in that network out of the equation, the other brain regions would not be able to pick up the slack in mind-wandering.

Kucyi, however, didn’t just want to identify regions of the brain that lit up when someone said their mind was wandering. He also wanted to be able to use that generalized pattern of brain activity to be able to predict whether or not a subject would say that their focus had drifted away from the task in front of them.

That’s where the machine-learning analysis of the data came in. The idea, Kucyi says, is that “you could bring a new person into the scanner and not even ask them whether they were mind-wandering or not, and have a good estimate from their brain data whether they were.”

The ADHD brain

To test the patterns identified through machine learning, the researchers brought in a new set of test subjects – people diagnosed with ADHD. When the fMRI scans lit up the parts of the brain Kucyi and his colleagues had identified as engaged in mind-wandering in the first part of the study, the new test subjects reported that their thoughts had drifted from the images of cities and mountains in front of them. It worked.

Kucyi doesn’t expect fMRI scans to become a new way to diagnose ADHD, however. That wasn’t the goal. Perhaps down the road it could be used to help develop treatments, he suggests. But this study was focused on “informing the biological mechanisms behind it.”

John Gabrieli, a co-author on the study and director of the imaging center at MIT’s McGovern Institute, adds that “there is recent evidence that ADHD patients with more mind-wandering have many more everyday practical and clinical difficulties than ADHD patients with less mind-wandering. This is the first evidence about the brain basis for that important difference, and points to what neural systems ought to be the targets of intervention to help ADHD patients who struggle the most.”

For Kucyi, the study of “mind-wandering” goes beyond ADHD. And the contents of those straying thoughts may be telling, he says.

“We just asked people whether they were focused on the task or away from the task, but we have no idea what they were thinking about,” he says. “What are people thinking about? For example, are those more positive thoughts or negative thoughts?” Such answers, which he hopes to explore in future research, could help scientists better understand other pathologies such as depression and anxiety, which often involve rumination on upsetting or worrisome thoughts.

Whitfield-Gabrieli and her team are already exploring whether behavioral interventions, such as mindfulness based real-time fMRI neurofeedback, can be used to help train people suffering from mental illness to modulate their own brain networks and reduce hallucinations, ruminations, and other troubling symptoms.

“We hope that our research will have clinical implications that extend far beyond the potential for identifying treatment targets for ADHD,” she says.

Gene changes linked to severe repetitive behaviors

by Jill Crittenden |

Extreme repetitive behaviors such as hand-flapping, body-rocking, skin-picking and sniffing are common to a number of brain disorders including autism, schizophrenia, Huntington’s disease, and drug addiction. These behaviors, termed stereotypies, are also apparent in animal models of drug addiction and autism.

In a new study published in the European Journal of Neuroscience, researchers at the McGovern Institute have identified genes that are activated in the brain prior to the initiation of these severe repetitive behaviors.

“Our lab has found a small set of genes that are regulated in relation to the development of stereotypic behaviors in an animal model of drug addiction,” says MIT Institute Professor Ann Graybiel, who is the senior author of the paper. “We were surprised and interested to see that one of these genes is a susceptibility gene for schizophrenia. This finding might help to understand the biological basis of repetitive, stereotypic behaviors as seen in a range of neurologic and neuropsychiatric disorders, and in otherwise ‘typical’ people under stress.”

A shared molecular pathway

In work led by research scientist Jill Crittenden, researchers in the Graybiel lab exposed mice to amphetamine, a psychomotor stimulant that drives hyperactivity and confined stereotypies in humans and in laboratory animals and that is used to model symptoms of schizophrenia.

They found that stimulant exposure that drives the most prolonged repetitive behaviors lead to activation of genes regulated by Neuregulin 1, a signaling molecule that is important for a variety of cellular functions including neuronal development and plasticity. Neuregulin 1 gene mutations are risk factors for schizophrenia.

The new findings highlight a shared molecular and circuit pathway for stereotypies that are caused by drugs of abuse and in brain disorders, and have implications for why stimulant intoxication is a risk factor for the onset of schizophrenia.

“Experimental treatment with amphetamine has long been used in studies on rodents and other animals in tests to find better treatments for schizophrenia in humans, because there are some behavioral similarities across the two otherwise very different contexts,” explains Graybiel, who is also an investigator at the McGovern Institute and a professor of brain and cognitive sciences at MIT. “It was striking to find Neuregulin 1 — potentially one hint to shared mechanisms underlying some of these similarities.”

Drug exposure linked to repetitive behaviors

Although many studies have measured gene expression changes in animal models of drug addiction, this study is the first to evaluate genome-wide changes specifically associated with restricted repetitive behaviors.

Stereotypies are difficult to measure without labor-intensive, direct observation, because they consist of fine movements and idiosyncratic behaviors. In this study, the authors administered amphetamine (or saline control) to mice and then measured with photobeam-breaks how much they ran around. The researchers identified prolonged periods when the mice were not running around (e.g. were potentially engaged in confined stereotypies), and then they videotaped the mice during these periods to observationally score the severity of restricted repetitive behaviors (e.g. sniffing or licking stereotypies).

They gave amphetamine to each mouse once a day for 21 days and found that, on average, mice showed very little stereotypy on the first day of drug exposure but that, by the seventh day of exposure, all of the mice showed a prolonged period of stereotypy that gradually became shorter and shorter over the subsequent two weeks.

Graphical abstract
The authors compared gene expression changes in the brains of mice treated with amphetamine for one day, seven days or 21 days. By the twenty-first day of treatment, the stereotypy behaviors were less intense as was the gene upregulation – fewer genes were strongly activated, and more were repressed, relative to the other treatments.

“We were surprised to see the stereotypy diminishing after one week of treatment. We had actually planned a study based on our expectation that the repetitive behaviors would become more intense, but then we realized that this was an opportunity to look at what gene changes were unique to that day of high stereotypy,” says first author Jill Crittenden.

The authors compared gene expression changes in the brains of mice treated with amphetamine for one day, seven days or 21 days. They hypothesized that the gene changes associated specifically with high-stereotypy-associated seven days of drug treatment were the most likely to underlie extreme repetitive behaviors and could identify risk-factor genes for such symptoms in disease.

A shared anatomical pathway

Previous work from the Graybiel lab has shown that stereotypy is directly correlated to circumscribed gene activation in the striatum, a forebrain region that is key for habit formation. In animals with the most intense stereotypy, most of the striatum does not show gene activation, but immediate early gene induction remains high in clusters of cells called striosomes. Striosomes have recently been shown to have powerful control over cells that release dopamine, a neuromodulator that is severely disrupted in drug addiction and in schizophrenia. Strikingly, striosomes contain high levels of Neuregulin 1.

“Our new data suggest that the upregulation of Neuregulin-responsive genes in animals with severely repetitive behaviors reflects gene changes in the striosomal neurons that control the release of dopamine,” Crittenden explains. “Dopamine can directly impact whether an animal repeats an action or explores new actions, so our study highlights a potential role for a striosomal circuit in controlling action-selection in health and in neuropsychiatric disease.”

Patterns of behavior and gene expression

Striatal gene expression levels were measured by sequencing messenger RNAs (mRNAs) in dissected brain tissue. mRNAs are read out from “active” genes to instruct protein-synthesis machinery in how to make the protein that corresponds to the gene’s sequence. Proteins are the main constituents of a cell, thereby controlling each cell’s function. The number of times a particular mRNA sequence is found reflects the frequency at which the gene was being read out at the time that the cellular material was collected.

To identify genes that were read out into mRNA before the period of prolonged stereotypy, the researchers collected brain tissue 20 minutes after amphetamine injection, which is about 30 minutes before peak stereotypy. They then identified which genes had significantly different levels of corresponding mRNAs in drug-treated mice than in mice treated with saline.

A wide variety of genes showed modest mRNA increases after the first amphetamine exposure, which induced mild hyperactivity and a range of behaviors such as walking, sniffing and rearing in the mice.

By the seventh day of treatment, all of the mice were engaged for prolonged periods in one specific repetitive behavior, such as sniffing the wall. Likewise, there were fewer genes that were activated by the seventh day relative to the first treatment day, but they were strongly activated in all mice that received the stereotypy-inducing amphetamine treatment.

By the twenty-first day of treatment, the stereotypy behaviors were less intense as was the gene upregulation – fewer genes were strongly activated, and more were repressed, relative to the other treatments. “It seemed that the mice had developed tolerance to the drug, both in terms of their behavioral response and in terms of their gene activation response,” says Crittenden.

“Trying to seek patterns of gene regulation starting with behavior is correlative work, and we did not prove ‘causality’ in this first small study,” explains Graybiel. “But we hope that the striking parallels between the scope and selectivity of the mRNA and behavioral changes that we detected will help in further work on the tremendously challenging goal of treating addiction.”

This work was funded by the National Institute of Child Health and Human Development, the Saks-Kavanaugh Foundation, the Broderick Fund for Phytocannabinoid Research at MIT, the James and Pat Poitras Research Fund, The Simons Foundation and The Stanley Center for Psychiatric Research at the Broad Institute.

Individual neurons responsible for complex social reasoning in humans identified

by MGH News and Public Affairs |

This story is adapted from a January 27, 2021 press release from Massachusetts General Hospital.

The ability to understand others’ hidden thoughts and beliefs is an essential component of human social behavior. Now, neuroscientists have for the first time identified specific neurons critical for social reasoning, a cognitive process that requires individuals to acknowledge and predict others’ hidden beliefs and thoughts.

The findings, published in Nature, open new avenues of study into disorders that affect social behavior, according to the authors.

In the study, a team of Harvard Medical School investigators based at Massachusetts General Hospital and colleagues from MIT took a rare look at how individual neurons represent the beliefs of others. They did so by recording neuron activity in patients undergoing neurosurgery to alleviate symptoms of motor disorders such as Parkinson’s disease.

Theory of mind

The researcher team, which included McGovern scientists Ev Fedorenko and Rebecca Saxe, focused on a complex social cognitive process called “theory of mind.” To illustrate this, let’s say a friend appears to be sad on her birthday. One may infer she is sad because she didn’t get a present or she is upset at growing older.

“When we interact, we must be able to form predictions about another person’s unstated intentions and thoughts,” said senior author Ziv Williams, HMS associate professor of neurosurgery at Mass General. “This ability requires us to paint a mental picture of someone’s beliefs, which involves acknowledging that those beliefs may be different from our own and assessing whether they are true or false.”

This social reasoning process develops during early childhood and is fundamental to successful social behavior. Individuals with autism, schizophrenia, bipolar affective disorder, and traumatic brain injuries are believed to have a deficit of theory-of-mind ability.

For the study, 15 patients agreed to perform brief behavioral tasks before undergoing neurosurgery for placement of deep-brain stimulation for motor disorders. Microelectrodes inserted into the dorsomedial prefrontal cortex recorded the behavior of individual neurons as patients listened to short narratives and answered questions about them.

For example, participants were presented with the following scenario to evaluate how they considered another’s belief of reality: “You and Tom see a jar on the table. After Tom leaves, you move the jar to a cabinet. Where does Tom believe the jar to be?”

Social computation

The participants had to make inferences about another’s beliefs after hearing each story. The experiment did not change the planned surgical approach or alter clinical care.

“Our study provides evidence to support theory of mind by individual neurons,” said study first author Mohsen Jamali, HMS instructor in neurosurgery at Mass General. “Until now, it wasn’t clear whether or how neurons were able to perform these social cognitive computations.”

The investigators found that some neurons are specialized and respond only when assessing another’s belief as false, for example. Other neurons encode information to distinguish one person’s beliefs from another’s. Still other neurons create a representation of a specific item, such as a cup or food item, mentioned in the story. Some neurons may multitask and aren’t dedicated solely to social reasoning.

“Each neuron is encoding different bits of information,” Jamali said. “By combining the computations of all the neurons, you get a very detailed representation of the contents of another’s beliefs and an accurate prediction of whether they are true or false.”

Now that scientists understand the basic cellular mechanism that underlies human theory of mind, they have an operational framework to begin investigating disorders in which social behavior is affected, according to Williams.

“Understanding social reasoning is also important to many different fields, such as child development, economics, and sociology, and could help in the development of more effective treatments for conditions such as autism spectrum disorder,” Williams said.

Previous research on the cognitive processes that underlie theory of mind has involved functional MRI studies, where scientists watch which parts of the brain are active as volunteers perform cognitive tasks.

But the imaging studies capture the activity of many thousands of neurons all at once. In contrast, Williams and colleagues recorded the computations of individual neurons. This provided a detailed picture of how neurons encode social information.

“Individual neurons, even within a small area of the brain, are doing very different things, not all of which are involved in social reasoning,” Williams said. “Without delving into the computations of single cells, it’s very hard to build an understanding of the complex cognitive processes underlying human social behavior and how they go awry in mental disorders.”

Adapted from a Mass General news release.

The pursuit of reward

by Jennifer Michalowski |

View the interactive version of this story in our Spring 2021 issue of BrainScan.

The brain circuits that influence our decisions, cognitive functions, and ultimately, our actions are intimately connected with the circuits that give rise to our motivations. By exploring these relationships, scientists at McGovern are seeking knowledge that might suggest new strategies for changing our habits or treating motivation-disrupting conditions such as depression and addiction.

Risky decisions

MIT Institute Professor Ann Graybiel. Photo: Justin Knight

In Ann Graybiel’s lab, researchers have been examining how the brain makes choices that carry both positive and negative consequences — deciding to take on a higher-paying but more demanding job, for example. Psychologists call these dilemmas approach-avoidance conflicts, and resolving them not only requires weighing the good versus the bad, but also motivation to engage with the decision.

Emily Hueske, a research scientist in the Graybiel lab, explains that everyone has their own risk tolerance when it comes to such decisions, and certain psychiatric conditions, including depression and anxiety disorders, can shift the tipping point at which a person chooses to “approach” or “avoid.”

Studies have shown that neurons in the striatum (see image below), a region deep in the brain involved in both motivation and movement, activate as we grapple with these decisions. Graybiel traced this activity even further, to tiny compartments within the striatum called striosomes.

(She discovered striosomes many years ago and has been studying their function for decades.)

A motivational switch

In 2015, Graybiel’s team manipulated striosome signaling within genetically engineered mice and changed the way animals behave in approach-avoidance conflict situations. Taking cues from an assessment used to evaluate approach-avoidance behavior in patients, they presented mice with opportunities to obtain chocolate while experiencing unwelcome exposure in a brightly lit area.

Experimentally activating neurons in striosomes had a dramatic effect, causing mice to venture into brightly lit areas that they would normally avoid. With striosomal circuits switched on, “this animal all of a sudden is like a different creature,” Graybiel says.

Two years later, they found that chronic stress and other factors can also disrupt this signaling and change the choices animals make.

An image of the mouse striatum showing clusters of striosomes (red and yellow). Image: Graybiel lab

Age of ennui

This November, Alexander Friedman, who worked as a research scientist in the Graybiel lab, and Hueske reported in Cell that they found an age-related decline in motivation-modulated learning in mice and rats. Neurons within striosomes became more active than the cells that surround them as animals learned to assign positive and negative values to potential choices. And older mice were less engaged than their younger counterparts in the type of learning required to make these cost-benefit analyses. A similar lack of motivation was observed in a mouse model of Huntington’s disease, a neurodegenerative disorder that is often associated with mood
disturbances in patients.

“This coincides with our previous findings that striosomes are critically important for decisions that involve a conflict.”

“This coincides with our previous findings that striosomes are critically important for decisions that involve a conflict,” says Friedman, who is now an assistant professor at the University of Texas at El Paso.

Graybiel’s team is continuing to investigate these uniquely positioned compartments in the brain, expecting to shed light on the mechanisms that underlie both learning and motivation.

“There’s no learning without motivation, and in fact, motivation can be influenced by learning,” Hueske says. “The more you learn, the more excited you might be to engage in the task. So the two are intertwined.”

The aging brain

Researchers in John Gabrieli’s lab are also seeking to understand the circuits that link motivation to learning, and recently, his team reported that they, too, had found an age-related decline in motivation-modulated learning.

Studies in young adults have shown that memory improves when the brain circuits that process motivation and memory interact. Gabrieli and neurologist Maiya Geddes, who worked in Gabrieli’s lab as a postdoctoral fellow, wondered whether this holds true in older adults, particularly as memory declines.

To find out, the team recruited 40 people to participate in a brain imaging study. About half of the participants were between the ages of 18 and 30, while the others were between the ages of 49 and 84. While inside an fMRI scanner, each participant was asked to commit certain words to memory and told their success would determine how much money they received for participating in the experiment.

Diminished drive

MRI scan
Younger adults show greater activation in the reward-related regions of the brain during incentivized memory tasks compared to older adults. Image: Maiya Geddes

Not surprisingly, when participants were asked 24 hours later to recall the words, the younger group performed better overall than the older group. In young people, incentivized memory tasks triggered activity in parts of the brain involved in both memory and motivation. But in older adults, while these two parts of the brain could be activated independently, they did not seem to be communicating with one another.

“It seemed that the older adults, at least in terms of their brain response, did care about the kind of incentives that we were offering,” says Geddes, who is now an assistant professor at McGill University. “But for whatever reason, that wasn’t allowing them to benefit in terms of improved memory performance.”

Since the study indicates the brain still can anticipate potential rewards, Geddes is now exploring whether other sources of motivation, such as social rewards, might more effectively increase healthful decisions and behaviors in older adults.

Circuit control

Understanding how the brain generates and responds to motivation is not only important for improving learning strategies. Lifestyle choices such as exercise and social engagement can help people preserve cognitive function and improve their quality of life as they age, and Gabrieli says activating the right motivational circuits could help encourage people to implement healthy changes.

By pinpointing these motivational circuits in mice, Graybiel hopes that her research will lead to better treatment strategies for people struggling with motivational challenges, including Parkinson’s disease. Her team is now exploring whether striosomes serve as part of a value-sensitive switch, linking our intentions to dopamine-containing neurons in the midbrain that can modulate our actions.

“Perhaps this motivation is critical for the conflict resolution, and striosomes combine two worlds, dopaminergic motivation and cortical knowledge, resulting in motivation to learn,” Friedman says.

“Now we know that these challenges have a biological basis, and that there are neural circuits that can promote or reduce our feeling of motivational energy,” explains Graybiel. “This realization in itself is a major step toward learning how we can control these circuits both behaviorally and by highly selective therapeutic targeting.”

Two MIT Brain and Cognitive Sciences faculty members earn funding from the G. Harold and Leila Y. Mathers Foundation

by David Orenstein |

Two MIT neuroscientists have received grants from the G. Harold and Leila Y. Mathers Foundation to screen for genes that could help brain cells withstand Parkinson’s disease and to map how gene expression changes in the brain in response to drugs of abuse.

Myriam Heiman, an associate professor in MIT’s Department of Brain and Cognitive Sciences and a core member of the Picower Institute for Learning and Memory and the Broad Institute of MIT and Harvard, and Alan Jasanoff, who is also a professor in biological engineering, brain and cognitive sciences, nuclear science and engineering and an associate investigator at the McGovern Institute for Brain Research, each received three-year awards that formally begin January 1, 2021.

Jasanoff, who also directs MIT’s Center for Neurobiological Engineering, is known for developing sensors that monitor molecular hallmarks of neural activity in the living brain, in real time, via noninvasive MRI brain scanning. One of the MRI-detectable sensors that he has developed is for dopamine, a neuromodulator that is key to learning what behaviors and contexts lead to reward. Addictive drugs artificially drive dopamine release, thereby hijacking the brain’s reward prediction system. Studies have shown that dopamine and drugs of abuse activate gene transcription in specific brain regions, and that this gene expression changes as animals are repeatedly exposed to drugs. Despite the important implications of these neuroplastic changes for the process of addiction, in which drug-seeking behaviors become compulsive, there are no effective tools available to measure gene expression across the brain in real time.

Cerebral vasculature in mouse brain. The Jasanoff lab hopes to develop a method for mapping gene expression the brain with related labeling characteristics .
Image: Alan Jasanoff

With the new Mathers funding, Jasanoff is developing new MRI-detectable sensors for gene expression. With these cutting-edge tools, Jasanoff proposes to make an activity atlas of how the brain responds to drugs of abuse, both upon initial exposure and over repeated doses that simulate the experiences of drug addicted individuals.

“Our studies will relate drug-induced brain activity to longer term changes that reshape the brain in addiction,” says Jasanoff. “We hope these studies will suggest new biomarkers or treatments.”

Dopamine-producing neurons in a brain region called the substantia nigra are known to be especially vulnerable to dying in Parkinson’s disease, leading to the severe motor difficulties experienced during the progression of the incurable, chronic neurodegenerative disorder. The field knows little about what puts specific cells at such dire risk, or what molecular mechanisms might help them resist the disease. In her research on Huntington’s disease, another incurable neurodegenerative disorder in which a specific neuron population in the striatum is especially vulnerable, Heiman has been able to use an innovative method her lab pioneered to discover genes whose expression promotes neuron survival, yielding potential new drug targets. The technique involves conducting an unbiased screen in which her lab knocks out each of the 22,000 genes expressed in the mouse brain one by one in neurons in disease model mice and healthy controls. The technique allows her to determine which genes, when missing, contribute to neuron death amid disease and therefore which genes are particularly needed for survival. The products of those genes can then be evaluated as drug targets. With the new Mathers award, Heiman plans to apply the method to study Parkinson’s disease.

An immunofluorescence image taken in a brain region called the substantia nigra (SN) highlights tyrosine hydroxylase, a protein expressed by dopamine neurons. This type of neuron in the SN is especially vulnerable to neurodegeneration in Parkinson’s disease. Image: Preston Ge/Heiman Lab

“There is currently no molecular explanation for the brain cell loss seen in Parkinson’s disease or a cure for this devastating disease,” Heiman said. “This award will allow us to perform unbiased, genome-wide genetic screens in the brains of mouse models of Parkinson’s disease, probing for genes that allow brain cells to survive the effects of cellular perturbations associated with Parkinson’s disease. I’m extremely grateful for this generous support and recognition of our work from the Mathers Foundation, and hope that our study will elucidate new therapeutic targets for the treatment and even prevention of Parkinson’s disease.”

Sequencing inside cells

by Jennifer Michalowski |

By bringing DNA sequencing out of the sequencer and directly to cells, MIT scientists have revealed an entirely new view of the genome. With a new method for in situ genome sequencing reported December 31, 2020, in the journal Science, researchers can, for the first time, see exactly how DNA sequences are organized and packed inside cells.

The approach, whose development was led by Ed Boyden, the Y. Eva Tan Professor in Neurotechnology at MIT, and Harvard University Stem Cell and Regenerative Biology faculty members Jason Buenrostro and Fei Chen, integrates DNA sequencing technology with microscopy to pinpoint exactly where specific DNA sequences are located inside intact cells.

While alternative methods allow scientists to reconstruct structural information about the genome, this is the first sequencing technology to give scientists a direct look.

The technology creates new opportunities to investigate a broad range of biology, from fundamental questions about how DNA’s three-dimensional organization affects its function to the structural changes and chromosomal rearrangements associated with aging, cancer, brain disorders, and other diseases.

Seeing is believing

“How structure yields function is one of the core themes of biology,” says Boyden, who is also an investigator at the McGovern Institute and the Howard Hughes Medical Institute.“And the history of biology tells us that when you can actually see something, you can make lots of advances.” Seeing how an organism’s genome is packed inside its cells could help explain how different cell types in the brain interpret the genetic code, or reveal structural patterns that mean the difference between health and disease, he says. Additionally, the researchers note, the technique also makes it possible to directly see how proteins and other factors interact with specific parts of the genome.

The new method builds on work underway in Boyden and Chen’s laboratories focused on sequencing RNA inside cells. Buenrostro collaborated with Boyden and Chen, who is also a core member of the Broad Institute, to adapt the technique for use with DNA. “It was clear the technology they had developed would be an extraordinary opportunity to have a new perspective on cells’ genomes,” Boyden says.

Their approach begins by fixing cells onto a glass surface to preserve their structure. Then, after inserting small DNA adapters into the genome, thousands of short segments of DNA—about 20 letters of code apiece—are amplified and sequenced in their original locations inside the cells. Finally, the samples are ground up and put into a sequencer, which sequences all of the cells’ DNA about 300 letters at a time. By finding the location-identified short sequences within those longer segments, the method pinpoints each one’s position within the three-dimensional structure of the cell.

Sequencing inside the cells is done more or less the same way DNA is sequenced inside a standard next-generation sequencer, Boyden explains, by watching under a microscope as a DNA strand is copied using fluorescently labeled building blocks. As in a traditional sequencer, each of DNA’s four building blocks, or nucleotides, is tagged with a different color so that they can be visually identified as they are added to a growing DNA strand.

A collaborative effort

Boyden, Buenrostro, and Chen, who began their collaboration several years ago, say the new technology represents a heroic effort on the part of MIT and Harvard graduate students Andrew Payne, Zachary Chiang, and Paul Reginato, who took the lead in developing and integrating its many technical steps and computational analyses. That involved both recapitulating the methods used in commercial sequencers and introducing several key innovations. “Some advances on the technology side have taken this from impossible to do to being possible,” Chen says.

The team has already used the method to visualize a genome as it reorganizes itself during the earliest moments of life. Brightly colored representations of DNA that they sequenced inside a mouse embryo show how genetic information inherited from each parent remains distinct and compartmentalized immediately after fertilization, then gradually intertwines as development progresses. Their sequencing also reveals how patterns of genome organization, which very early in life vary from cell to cell, are passed on as cells divide, generating a memory of each cell’s developmental origins. Being able to watch these processes unfold across entire cells instead of piecing them together through less direct means offered a dramatic new view of development, the researchers say.

While the team continues to improve the spatial resolution of the technique and adapt it to a broader range of cell types, they have made their method and associated software freely available to other labs. The researchers hope this new approach to DNA sequencing will change the way people think about studying the structure of the genome and will help illuminate patterns and consequences of genome organization across a variety of contexts.

Powered by viruses

by Jennifer Michalowski |

View the interactive version of this story in our Winter 2021 issue of Brain Scan.

Viruses are notoriously adept invaders. The efficiency with which these unseen threats infiltrate tissues, evade immune systems, and occupy the cells of their hosts can be alarming — but it’s exactly why most McGovern neuroscientists keep a stash of viruses in the freezer.

In the hands of neuroscientists, viruses become vital tools for delivering cargo to cells.

With a bit of genetic manipulation, they can instruct neurons to produce proteins that illuminate complex circuitry, report on activity, or place certain cells under scientists’ control. They can even deliver therapies designed to correct genetic defects in patients.

“We rely on the virus to deliver whatever we want,” says McGovern Investigator Guoping Feng. “This is one of the most important technologies in neuroscience.”

Tracing connections

In Ian Wickersham’s lab, researchers are adapting a virus that, in its natural form, is devastating to the mammalian nervous system. Once it gains access to a neuron, the rabies virus spreads to connected cells, killing them within weeks. “That makes it a very dangerous pathogen, but also a very powerful tool for neuroscience,” says Wickersham, a Principal Research Scientist at the Institute.

Taking advantage of its pernicious spread, neuroscientists use a modified version of the rabies virus to introduce a fluorescent protein to infected cells and visualize their connections (above). As a graduate student in Edward Callaway’s lab at the Salk Institute for Biological Studies, Wickersham figured out how to limit the virus’s passage through the nervous system, allowing it to access cells that are directly connected to the neuron it initially infects, but go no further. Rabies virus travels across synapses in the opposite direction of neuronal signals, so researchers can deliver it to a single cell or set of cells, then see exactly where those cells’ inputs are coming from.

Labs around the world use Wickersham’s modified rabies virus to trace neuronal anatomy in the brains of mice. While his team tinkers to make the virus even more powerful, his collaborators have deployed it to map a variety of essential connections, offering clues into how the brain controls movement, detects odors, and retrieves memories.

With the newest tracing tool from the Wickersham lab, moving from anatomical studies to experiments that reveal circuit function is seamless, because the lab has further modified their virus so that it cannot kill cells. Researchers can label connected cells, then proceed to monitor their signals or manipulate their activity in the same animals.

Researchers usually conduct these experiments in genetically modified mice to control the subset of cells that activate the tracing system. It’s the same approach used to restrict most virally-delivered tools to specific neurons, which is crucial, Feng says. When introducing a fluorescent protein for imaging, for example, “we don’t want the gene we deliver to be activated everywhere, otherwise the whole brain will be lighting up,” he says.

Selective targets

In Feng’s lab, research scientist Martin Wienisch is working to make it easier to control this aspect of delivery. Rather than relying on the genetic makeup of an entire animal to determine where a virally-transported gene is switched on, instructions can be programmed directly into the virus, borrowing regulatory sequences that cells already know how to interpret.

Wienisch is scouring the genomes of individual neurons to identify short segments of regulatory DNA called enhancers. He’s focused on those that selectively activate gene expression in just one of hundreds of different neuron types, particularly in animal models that are not very amenable to genetic engineering. “In the real brain, many elements interact to drive cell specific expression. But amazingly sometimes a single enhancer is all we need to get the same effect,” he says.

Researchers are already using enhancers to confine viral tools to select groups of cells, but Wienisch, who is collaborating with Fenna Krienen in Steve McCarroll’s lab at Harvard University, aims to create a comprehensive library. The enhancers they identify will be paired with a variety of genetically-encoded tools and packaged into adeno-associated viruses (AAV), the most widely used vectors in neuroscience. The Feng lab plans to use these tools to better understand the striatum, a part of the primate brain involved in motivation and behavioral choices. “Ideally, we would have a set of AAVs with enhancers that would give us selective access to all the different cell types in the striatum,” Wienisch says.

Enhancers will also be useful for delivering potential gene therapies to patients, Wienisch says. For many years, the Feng lab has been studying how a missing copy of a gene called Shank3 impairs neurons’ ability to communicate, leading to autism and intellectual disability. Now, they are investigating whether they can overcome these deficits by delivering a functional copy of Shank3 to the brain cells that need it. Widespread activation of the therapeutic gene might do more harm than good, but incorporating the right enhancer could ensure it is delivered to the appropriate cells at the right dose, Wienisch says.

Like most gene therapies in development, the therapeutic Shank3, which is currently being tested in animal models, is packaged into an AAV. AAVs safely and efficiently infect human cells, and by selecting the right type, therapies can be directed to specific cells. But AAVs are small viruses, capable of carrying only small genes. Xian Gao, a postdoctoral researcher in the Feng lab, has pared Shank3 down to its most essential components, creating a “minigene” that can be packaged inside the virus, but some things are difficult to fit inside an AAV. Therapies that aim to correct mutations using the CRISPR gene editing system, for example, often exceed the carrying capacity of an AAV.

Expanding options

“There’s been a lot of really phenomenal advances in our gene editing toolkit,” says Victoria Madigan, a postdoctoral researcher in McGovern Investigator Feng Zhang’s lab, where researchers are developing enzymes to more precisely modify DNA. “One of the main limitations of employing these enzymes clinically has been their delivery.”

To open up new options for gene therapy, Zhang and Madigan are working with a group of viruses called densoviruses. Densoviruses and AAVs belong to the same family, but about 50 percent more DNA can be packed inside the outer shell of some densoviruses.

A molecular model of Galleria mellonella densovirus. Image: Victoria Madigan / Zhang Lab

They are an esoteric group of viruses, Madigan says, infecting only insects and crustaceans and perhaps best known for certain members’ ability to devastate shrimp farms. While densoviruses haven’t received a lot of attention from scientists, their similarities to AAV have given the team clues about how to alter their outer capsids to enable them to enter human cells, and even direct them to particular cell types. The fact that they don’t naturally infect people also makes densoviruses promising candidates for clinical use, Madigan says, because patients’ immune systems are unlikely to be primed to reject them. AAV infections, in contrast, are so common that patients are often excluded from clinical trials for AAV-based therapies due to the presence of neutralizing antibodies against the vector.

Ultimately, densoviruses could enable major advances in gene therapy, making it possible to safely deliver sophisticated gene editing systems to patients’ cells, Madigan says — and that’s good reason for scientists to continue exploring the vast diversity in the viral world. “There’s something to be said for looking into viruses that are understudied as new tools,” she says. “There’s a lot of interesting stuff out there — a lot of diversity and thousands of years of evolution.”

New clues to brain changes in Huntington’s disease

by Jill Crittenden |

Huntington’s disease is a fatal inherited disorder that strikes most often in middle age with mood disturbances, uncontrollable limb movements, and cognitive decline. Years before symptom onset, brain imaging shows degeneration of the striatum, a brain region important for the rapid selection of behavioral actions. As the striatal neurons degenerate, their “identity” proteins, the building blocks that give particular cell types their unique function, are gradually turned off.

A new study from the lab of Institute Professor Ann Graybiel has found a surprising exception to this rule. The researchers discovered that in mouse models of Huntington’s disease, the cell identity protein MOR1, named as the Mu type Opioid Receptor, actually becomes more abundant as the striatal neurons degenerate.

“This is one of the most striking immunohistochemical change that I have ever seen in the literature of Huntington’s disease model animals,” says Ryoma Morigaki, a research scientist in the Graybiel laboratory and lead author of the report, who worked with Tomoko Yoshida and others in the Graybiel lab.

Immunohistochemical stainings using anti-mu-opioid receptor antibody. Wild type mouse striatum (left) and Q175 Huntington’s disease model mouse striatum (right) at 19 months old. Image: Ryoma Morigaki

More opioid receptors

MOR1 is a receptor on the surface of neurons that binds to opioids that are produced by the body or those taken for pain relief, such as morphine. The natural opioid in the brain is a small molecule called enkephalin, and it is normally produced by the same striatal neurons that degenerate in the earliest stages of Huntington’s disease.

The research team speculates that the striatum increases the quantity of MOR1 receptors in Huntington’s disease models to compensate for plummeting levels of enkephalin, but they also believe this upregulation may play a role in the perception of reward.

Previous work suggests that MOR1 has distinct signaling mechanisms related to its function in pain perception and its function in drug-seeking. These distinct mechanisms might be related to the fact that MOR1 is produced as multiple “isoforms,” slight variations of a protein that can be read out from the same gene. The MOR1 isoform that is found in the striatum is thought to be more important for drug-seeking behaviors than for pain perception. This in turn means that MOR1 might play a role in a key striatal function, which is to learn what actions are most likely to lead to reward.

“It is now recognized that mood disturbances can pre-date the overt motor abnormalities of Huntington’s patients by many years. These can even be the most disturbing symptoms for patients and their families. The finding that this receptor for opioids becomes so elevated in mood-related sites of the striatum, at least in a mouse model of the disorder, may give a hint to the underlying circuit dysfunction leading to these problems,” says Ann Graybiel.

Clues for treatment

MOR1 is used as a standard to identify subsets of neurons that are located within small clusters of neurons in the striatum that were previously discovered by Ann Graybiel and named striosomes.

“The most exciting point for me is the involvement of striatal compartments [striosomes] in the pathogenesis of Huntington’s disease,” says Morigaki, who has now moved to the University of Fukoshima in Japan and is a practicing neurosurgeon who treats movement disorders.

MOR1-positive striosomal neurons are of high interest in part because they have direct connections to the same dopamine-producing neurons that are thought to degenerate in Parkinson’s disease. Whereas Parkinson’s disease is characterized by a loss of dopamine and loss of movement, Huntington’s disease is characterized by ups and downs in dopamine and excessive movements. In fact, the only drugs that are FDA-approved to treat Huntington’s disease are drugs that minimize dopamine release, thereby working to dampen the abnormal movements. But these treatments come with potentially severe side-effects such as depression and suicide.

This latest discovery might provide mechanistic clues to dopamine fluctuations in Huntington’s disease and provide avenues for more specific treatments.

This research was funded by the CHDI Foundation (A-5552), Broderick Fund for Phytocannabinoid Research at MIT, NIH/NIMH R01 MH060379, the Saks Kavanaugh Foundation, JSPS KAKENHI Grants #16KK0182, 17K10899 and 20K17932 , Dr. Tenley Albright, Kathleen Huber, and Dr. Stephan and Mrs. Anne Kott.