Brain Disorder: Schizophrenia

Study reveals a universal pattern of brain wave frequencies

Anne Trafton |

Throughout the brain’s cortex, neurons are arranged in six distinctive layers, which can be readily seen with a microscope. A team of MIT and Vanderbilt University neuroscientists has now found that these layers also show distinct patterns of electrical activity, which are consistent over many brain regions and across several animal species, including humans.

The researchers found that in the topmost layers, neuron activity is dominated by rapid oscillations known as gamma waves. In the deeper layers, slower oscillations called alpha and beta waves predominate. The universality of these patterns suggests that these oscillations are likely playing an important role across the brain, the researchers say.

“When you see something that consistent and ubiquitous across cortex, it’s playing a very fundamental role in what the cortex does,” says Earl Miller, the Picower Professor of Neuroscience, a member of MIT’s Picower Institute for Learning and Memory, and one of the senior authors of the new study.

Imbalances in how these oscillations interact with each other may be involved in brain disorders such as attention deficit hyperactivity disorder, the researchers say.

“Overly synchronous neural activity is known to play a role in epilepsy, and now we suspect that different pathologies of synchrony may contribute to many brain disorders, including disorders of perception, attention, memory, and motor control. In an orchestra, one instrument played out of synchrony with the rest can disrupt the coherence of the entire piece of music,” says Robert Desimone, director of MIT’s McGovern Institute for Brain Research and one of the senior authors of the study.

André Bastos, an assistant professor of psychology at Vanderbilt University, is also a senior author of the open-access paper, which appears today in Nature Neuroscience. The lead authors of the paper are MIT research scientist Diego Mendoza-Halliday and MIT postdoc Alex Major.

Layers of activity

The human brain contains billions of neurons, each of which has its own electrical firing patterns. Together, groups of neurons with similar patterns generate oscillations of electrical activity, or brain waves, which can have different frequencies. Miller’s lab has previously shown that high-frequency gamma rhythms are associated with encoding and retrieving sensory information, while low-frequency beta rhythms act as a control mechanism that determines which information is read out from working memory.

His lab has also found that in certain parts of the prefrontal cortex, different brain layers show distinctive patterns of oscillation: faster oscillation at the surface and slower oscillation in the deep layers. One study, led by Bastos when he was a postdoc in Miller’s lab, showed that as animals performed working memory tasks, lower-frequency rhythms generated in deeper layers regulated the higher-frequency gamma rhythms generated in the superficial layers.

In addition to working memory, the brain’s cortex also is the seat of thought, planning, and high-level processing of emotion and sensory information. Throughout the regions involved in these functions, neurons are arranged in six layers, and each layer has its own distinctive combination of cell types and connections with other brain areas.

“The cortex is organized anatomically into six layers, no matter whether you look at mice or humans or any mammalian species, and this pattern is present in all cortical areas within each species,” Mendoza-Halliday says. “Unfortunately, a lot of studies of brain activity have been ignoring those layers because when you record the activity of neurons, it’s been difficult to understand where they are in the context of those layers.”

In the new paper, the researchers wanted to explore whether the layered oscillation pattern they had seen in the prefrontal cortex is more widespread, occurring across different parts of the cortex and across species.

Using a combination of data acquired in Miller’s lab, Desimone’s lab, and labs from collaborators at Vanderbilt, the Netherlands Institute for Neuroscience, and the University of Western Ontario, the researchers were able to analyze 14 different areas of the cortex, from four mammalian species. This data included recordings of electrical activity from three human patients who had electrodes inserted in the brain as part of a surgical procedure they were undergoing.

Recording from individual cortical layers has been difficult in the past, because each layer is less than a millimeter thick, so it’s hard to know which layer an electrode is recording from. For this study, electrical activity was recorded using special electrodes that record from all of the layers at once, then feed the data into a new computational algorithm the authors designed, termed FLIP (frequency-based layer identification procedure). This algorithm can determine which layer each signal came from.

“More recent technology allows recording of all layers of cortex simultaneously. This paints a broader perspective of microcircuitry and allowed us to observe this layered pattern,” Major says. “This work is exciting because it is both informative of a fundamental microcircuit pattern and provides a robust new technique for studying the brain. It doesn’t matter if the brain is performing a task or at rest and can be observed in as little as five to 10 seconds.”

Across all species, in each region studied, the researchers found the same layered activity pattern.

“We did a mass analysis of all the data to see if we could find the same pattern in all areas of the cortex, and voilà, it was everywhere. That was a real indication that what had previously been seen in a couple of areas was representing a fundamental mechanism across the cortex,” Mendoza-Halliday says.

Maintaining balance

The findings support a model that Miller’s lab has previously put forth, which proposes that the brain’s spatial organization helps it to incorporate new information, which carried by high-frequency oscillations, into existing memories and brain processes, which are maintained by low-frequency oscillations. As information passes from layer to layer, input can be incorporated as needed to help the brain perform particular tasks such as baking a new cookie recipe or remembering a phone number.

“The consequence of a laminar separation of these frequencies, as we observed, may be to allow superficial layers to represent external sensory information with faster frequencies, and for deep layers to represent internal cognitive states with slower frequencies,” Bastos says. “The high-level implication is that the cortex has multiple mechanisms involving both anatomy and oscillations to separate ‘external’ from ‘internal’ information.”

Under this theory, imbalances between high- and low-frequency oscillations can lead to either attention deficits such as ADHD, when the higher frequencies dominate and too much sensory information gets in, or delusional disorders such as schizophrenia, when the low frequency oscillations are too strong and not enough sensory information gets in.

“The proper balance between the top-down control signals and the bottom-up sensory signals is important for everything the cortex does,” Miller says. “When the balance goes awry, you get a wide variety of neuropsychiatric disorders.”

The researchers are now exploring whether measuring these oscillations could help to diagnose these types of disorders. They are also investigating whether rebalancing the oscillations could alter behavior — an approach that could one day be used to treat attention deficits or other neurological disorders, the researchers say.

The researchers also hope to work with other labs to characterize the layered oscillation patterns in more detail across different brain regions.

“Our hope is that with enough of that standardized reporting, we will start to see common patterns of activity across different areas or functions that might reveal a common mechanism for computation that can be used for motor outputs, for vision, for memory and attention, et cetera,” Mendoza-Halliday says.

The research was funded by the U.S. Office of Naval Research, the U.S. National Institutes of Health, the U.S. National Eye Institute, the U.S. National Institute of Mental Health, the Picower Institute, a Simons Center for the Social Brain Postdoctoral Fellowship, and a Canadian Institutes of Health Postdoctoral Fellowship.

One scientist’s journey from the Middle East to MIT

by Thea Singer |

Smiling man holidng paper in a room.
Ubadah Sabbagh, soon after receiving his US citizenship papers, in April 2023. Photo: Ubadah Sabbagh

“I recently exhaled a breath I’ve been holding in for nearly half my life. After applying over a decade ago, I’m finally an American. This means so many things to me. Foremost, it means I can go back to the the Middle East, and see my mama and the family, for the first time in 14 years.” — McGovern Institute Postdoctoral Associate Ubadah Sabbagh, X (formerly Twitter) post, April 27, 2023

The words sit atop a photo of Ubadah Sabbagh, who joined the lab of Guoping Feng, James W. (1963) and Patricia T. Poitras Professor at MIT, as a postdoctoral associate in 2021. Sabbagh, a Syrian national, is dressed in a charcoal grey jacket, a keffiyeh loose around his neck, and holding his US citizenship papers, which he began applying for when he was 19 and an undergraduate at the University of Missouri-Kansas City (UMKC) studying biology and bioinformatics.

In the photo he is 29.

A clarity of vision

Sabbagh’s journey from the Middle East to his research position at MIT has been marked by determination and courage, a multifaceted curiosity, and a role as a scientist-writer/scientist-advocate.  He is particularly committed to the importance of humanity in science.

“For me, a scientist is a person who is not only in the lab but also has a unique perspective to contribute to society,” he says. “The scientific method is an idea, and that can be objective. But the process of doing science is a human endeavor, and like all human endeavors, it is inherently both social and political.”

At just 30 years of age, some of Sabbagh’s ideas have disrupted conventional thinking about how science is done in the United States. He believes nations should do science not primarily to compete, for example, but to be aspirational.

“It is our job to make our work accessible to the public, to educate and inform, and to help ground policy,” he says. “In our technologically advanced society, we need to raise the baseline for public scientific intuition so that people are empowered and better equipped to separate truth from myth.”

Two men sitting at a booth wearing headphones.
Ubadah Sabbagh is interviewed for Max Planck Forida’s Neurotransmissions podcast at the 2023 Society for Neuroscience conference in San Diego. Photo: Max Planck Florida

His research and advocacy work have won him accolades, including the 2023 Young Arab Pioneers Award from the Arab Youth Center and the 2020 Young Investigator Award from the American Society of Neurochemistry. He was also named to the 2021 Forbes “30 under 30” list, the first Syrian to be selected in the Science category.

A path to knowledge

Sabbagh’s path to that knowledge began when, living on his own at age 16, he attended Longview Community College, in Kansas City, often juggling multiple jobs. It continued at UMKC, where he fell in love with biology and had his first research experience with bioinformatician Gerald Wyckoff at the same time the civil war in Syria escalated, with his family still in the Middle East. “That was a rough time for me,” he says. “I had a lot of survivor’s guilt: I am here, I have all of this stability and security compared to what they have, and while they had suffocation, I had opportunity. I need to make this mean something positive, not just for me, but in as broad a way as possible for other people.”

Child smiles in front of scientific poster.
Ubadah Sabbagh, age 9, presents his first scientific poster. Photo: Ubadah Sabbagh

The war also sparked Sabbagh’s interest in human behavior—“where it originates, what motivates people to do things, but in a biological, not a psychological way,” he says. “What circuitry is engaged? What is the infrastructure of the brain that leads to X, Y, Z?”

His passion for neuroscience blossomed as a graduate student at Virginia Tech, where he earned his PhD in translational biology, medicine, and health. There, he received a six-year NIH F99/K00 Award, and under the mentorship of neuroscientist at the Fralin Biomedical Research Institute he researched the connections between the eye and the brain, specifically, mapping the architecture of the principle neurons in a region of the thalamus essential to visual processing.

“The retina, and the entire visual system, struck me as elegant, with beautiful layers of diverse cells found at every node,” says Sabbagh, his own eyes lighting up.

His research earned him a coveted spot on the Forbes “30 under 30” list, generating enormous visibility, including in the Arab world, adding visitors to his already robust X (formerly Twitter) account, which has more than 9,200 followers. “The increased visibility lets me use my voice to advocate for the things I care about,” he says.

“I need to make this mean something positive, not just for me, but in as broad a way as possible for other people.” — Ubadah Sabbagh

Those causes range from promoting equity and inclusion in science to transforming the American system of doing science for the betterment of science and the scientists themselves. He cofounded the nonprofit Black in Neuro to celebrate and empower Black scholars in neuroscience, and he continues to serve on the board. He is the chair of an advisory committee for the Society for Neuroscience (SfN), recommending ways SfN can better address the needs of its young members, and a member of the Advisory Committee to the National Institutes of Health (NIH) Director working group charged with re-envisioning postdoctoral training. He serves on the advisory board of Community for Rigor, a new NIH initiative that aims to teach scientific rigor at national scale and, in his spare time, he writes articles about the relationship of science and policy for publications including Scientific American and the Washington Post.

Still, there have been obstacles. The same year Sabbagh received the NIH F99/K00 Award, he faced major setbacks in his application to become a citizen. He would not try again until 2021, when he had his PhD in hand and had joined the McGovern Institute.

An MIT postdoc and citizenship

Sabbagh dove into his research in Guoping Feng’s lab with the same vigor and outside-the-box thinking that characterized his previous work. He continues to investigate the thalamus, but in a region that is less involved in processing pure sensory signals, such as light and sound, and more focused on cognitive functions of the brain. He aims to understand how thalamic brain areas orchestrate complex functions we carry out every day, including working memory and cognitive flexibility.

“This is important to understand because when this orchestra goes out of tune it can lead to a range of neurological disorders, including autism spectrum disorder and schizophrenia,” he says. He is also developing new tools for studying the brain using genome editing and viral engineering to expand the toolkit available to neuroscientists.

Microscopic image of mouse brain
Neurons in a transgenic mouse brain labeled by Sabbagh using genome editing technology in the Feng lab. Image: Ubadah Sabbagh

The environment at the McGovern Institute is also a source of inspiration for Sabbagh’s research. “The scale and scope of work being done at McGovern is remarkable. It’s an exciting place for me to be as a neuroscientist,” said Sabbagh. “Besides being intellectually enriching, I’ve found great community here – something that’s important to me wherever I work.”

Returning to the Middle East

Profile of scientist Ubadah Sabbagh speaking at a table.
McGovern postdoc Ubadah Sabbagh at the 2023 Young Arab Pioneers Award ceremony in Abu Dhabi. Photo: Arab Youth Center

While at an advisory meeting at the NIH, Sabbagh learned he had been selected as a Young Arab Pioneer by the Arab Youth Center and was flown the next day to Abu Dhabi for a ceremony overseen by Her Excellency Shamma Al Mazrui, Cabinet Member and Minister of Community Development in the United Arab Emirates. The ceremony recognized 20 Arab youth from around the world in sectors ranging from scientific research to entrepreneurship and community development. Sabbagh’s research “presented a unique portrayal of creative Arab youth and an admirable representation of the values of youth beyond the Arab world,” said Sadeq Jarrar, executive director of the center.

“There I was, among other young Arab leaders, learning firsthand about their efforts, aspirations, and their outlook for the future,” says Sabbagh, who was deeply inspired by the experience.

Just a month earlier, his passport finally secured, Sabbagh had reunited with his family in the Middle East after more than a decade in the United States. “I had been away for so long,” he said, describing the experience as a “cultural reawakening.”

Woman hands man an award on stage.
Ubadah Sabbagh receives a Young Arab Pioneer Award by Her Excellency Shamma Al Mazrui, Cabinet Member and Minister of Community Development in the United Arab Emirates. Photo: Arab Youth Center

Sabbagh saw a gaping need he had not been aware of when he left 14 years earlier, as a teen. “The Middle East had such a glorious intellectual past,” he says. “But for years people have been leaving to get their advanced scientific training, and there is no adequate infrastructure to support them if they want to go back.” He wondered: What if there were a scientific renaissance in the region? How would we build infrastructure to cultivate local minds and local talent? What if the next chapter of the Middle East included being a new nexus of global scientific advancements?

“I felt so inspired,” he says. “I have a longing, someday, to meaningfully give back.”

Unpacking auditory hallucinations

by Thea Singer |

Tamar Regev, the 2022–2024 Poitras Center Postdoctoral Fellow, has identified a new neural system that may shed light on the auditory hallucinations experienced by patients diagnosed with schizophrenia.

Scientist portrait
Tamar Regev is the 2022–2024 Poitras Center Postdoctoral
Fellow in Ev Fedorenko’s lab at the McGovern Institute. Photo: Steph Stevens

“The system appears integral to prosody processing,”says Regev. “‘Prosody’ can be described as the melody of speech — auditory gestures that we use when we’re speaking to signal linguistic, emotional, and social information.” The prosody processing system Regev has uncovered is distinct from the lower-level auditory speech processing system as well as the higher-level language processing system. Regev aims to understand how the prosody system, along with the speech and language processing systems, may be impaired in neuropsychiatric disorders such as schizophrenia, especially when experienced with auditory hallucinations in the form of speech.

“Knowing which neural systems are affected by schizophrenia can lay the groundwork for future research into interventions that target the mechanisms underlying symptoms such as hallucinations,” says Regev. Passionate about bridging gaps between disciplines, she is collaborating with Ann Shinn, MD, MPH, of McLean Hospital’s Schizophrenia and Bipolar Disorder Research Program.

Regev’s graduate work at the Hebrew University of Jerusalem focused on exploring the auditory system with electroencephalography (EEG), which measures electrical activity in the brain using small electrodes attached to the scalp. She came to MIT to study under Evelina Fedorenko, a world leader in researching the cognitive and neural mechanisms underlying language processing. With Fedorenko she has learned to use functional magnetic resonance imaging (fMRI), which reveals the brain’s functional anatomy by measuring small changes in blood flow that occur with brain activity.

“I hope my research will lead to a better understanding of the neural architectures that underlie these disorders—and eventually help us as a society to better understand and accept special populations.”- Tamar Regev

“EEG has very good temporal resolution but poor spatial resolution, while fMRI provides a map of the brain showing where neural signals are coming from,” says Regev. “With fMRI I can connect my work on the auditory system with that on the language system.”

Regev developed a unique fMRI paradigm to do that. While her human subjects are in the scanner, she is comparing brain responses to speech with expressive prosody versus flat prosody to find the role of the prosody system among the auditory, speech, and language regions. She plans to apply her findings to analyze a rich data set drawn from fMRI studies that Fedorenko and Shinn began a few years ago while investigating the neural basis of auditory hallucinations in patients with schizophrenia and bipolar disorder. Regev is exploring how the neural architecture may differ between control subjects and those with and without auditory hallucinations as well as those with schizophrenia and bipolar disorder.

“This is the first time these questions are being asked using the individual-subject approach developed in the Fedorenko lab,” says Regev. The approach provides superior sensitivity, functional resolution, interpretability, and versatility compared with the group analyses of the past. “I hope my research will lead to a better understanding of the neural architectures that underlie these disorders,” says Regev, “and eventually help us as a society to better understand and accept special populations.”

Dealing with uncertainty

by Jennifer Michalowski |

As we interact with the world, we are constantly presented with information that is unreliable or incomplete – from jumbled voices in a crowded room to solicitous strangers with unknown motivations. Fortunately, our brains are well equipped to evaluate the quality of the evidence we use to make decisions, usually allowing us to act deliberately, without jumping to conclusions.

Now, neuroscientists at MIT’s McGovern Institute have homed in on key brain circuits that help guide decision-making under conditions of uncertainty. By studying how mice interpret ambiguous sensory cues, they’ve found neurons that stop the brain from using unreliable information.

“One area cares about the content of the message—that’s the prefrontal cortex—and the thalamus seems to care about how certain the input is.” – Michael Halassa

The findings, published October 6, 2021, in the journal Nature, could help researchers develop treatments for schizophrenia and related conditions, whose symptoms may be at least partly due to affected individuals’ inability to effectively gauge uncertainty.

Decoding ambiguity

“A lot of cognition is really about handling different types of uncertainty,” says McGovern Associate Investigator Michael Halassa, explaining that we all must use ambiguous information to make inferences about what’s happening in the world. Part of dealing with this ambiguity involves recognizing how confident we can be in our conclusions. And when this process fails, it can dramatically skew our interpretation of the world around us.

“In my mind, schizophrenia spectrum disorders are really disorders of appropriately inferring the causes of events in the world and what other people think,” says Halassa, who is a practicing psychiatrist. Patients with these disorders often develop strong beliefs based on events or signals most people would dismiss as meaningless or irrelevant, he says. They may assume hidden messages are embedded in a garbled audio recording, or worry that laughing strangers are plotting against them. Such things are not impossible—but delusions arise when patients fail to recognize that they are highly unlikely.

Halassa and postdoctoral researcher Arghya Mukherjee wanted to know how healthy brains handle uncertainty, and recent research from other labs provided some clues. Functional brain imaging had shown that when people are asked to study a scene but they aren’t sure what to pay attention to, a part of the brain called the mediodorsal thalamus becomes active. The less guidance people are given for this task, the harder the mediodorsal thalamus works.

The thalamus is a sort of crossroads within the brain, made up of cells that connect distant brain regions to one another. Its mediodorsal region sends signals to the prefrontal cortex, where sensory information is integrated with our goals, desires, and knowledge to guide behavior. Previous work in the Halassa lab showed that the mediodorsal thalamus helps the prefrontal cortex tune in to the right signals during decision-making, adjusting signaling as needed when circumstances change. Intriguingly, this brain region has been found to be less active in people with schizophrenia than it is in others.

group photo of study authors
Study authors (from left to right) Michael Halassa, Arghya Mukherjee, Norman Lam and Ralf Wimmer.

Working with postdoctoral researcher Norman Lam and research scientist Ralf Wimmer, Halassa and Mukherjee designed a set of animal experiments to examine the mediodorsal thalamus’s role in handling uncertainty. Mice were trained to respond to sensory signals according to audio cues that alerted them whether to focus on either light or sound. When the animals were given conflicting cues, it was up to them animal to figure out which one was represented most prominently and act accordingly. The experimenters varied the uncertainty of this task by manipulating the numbers and ratio of the cues.

Division of labor

By manipulating and recording activity in the animals’ brains, the researchers found that the prefrontal cortex got involved every time mice completed this task, but the mediodorsal thalamus was only needed when the animals were given signals that left them uncertain how to behave. There was a simple division of labor within the brain, Halassa says. “One area cares about the content of the message—that’s the prefrontal cortex—and the thalamus seems to care about how certain the input is.”

Within the mediodorsal thalamus, Halassa and Mukherjee found a subset of cells that were especially active when the animals were presented with conflicting sound cues. These neurons, which connect directly to the prefrontal cortex, are inhibitory neurons, capable of dampening downstream signaling. So when they fire, Halassa says, they effectively stop the brain from acting on unreliable information. Cells of a different type were focused on the uncertainty that arises when signaling is sparse. “There’s a dedicated circuitry to integrate evidence across time to extract meaning out of this kind of assessment,” Mukherjee explains.

As Halassa and Mukherjee investigate these circuits more deeply, a priority will be determining whether they are disrupted in people with schizophrenia. To that end, they are now exploring the circuitry in animal models of the disorder. The hope, Mukherjee says, is to eventually target dysfunctional circuits in patients, using noninvasive, focused drug delivery methods currently under development. “We have the genetic identity of these circuits. We know they express specific types of receptors, so we can find drugs that target these receptors,” he says. “Then you can specifically release these drugs in the mediodorsal thalamus to modulate the circuits as a potential therapeutic strategy.”

This work was funded by grants from the National Institute of Mental Health (R01MH107680-05 and R01MH120118-02).

Single gene linked to repetitive behaviors, drug addiction

by Jill Crittenden |

Making and breaking habits is a prime function of the striatum, a large forebrain region that underlies the cerebral cortex. McGovern researchers have identified a particular gene that controls striatal function as well as repetitive behaviors that are linked to drug addiction vulnerability.

To identify genes involved specifically in striatal functions, MIT Institute Professor Ann Graybiel previously identified genes that are preferentially expressed in striatal neurons. One identified gene encodes CalDAG-GEFI (CDGI), a signaling molecule that effects changes inside of cells in response to extracellular signals that are received by receptors on the cell surface. In a paper to be published in the October issue of Neurobiology of Disease and now available online, Graybiel, along with former Research Scientist Jill Crittenden and collaborators James Surmeier and Shenyu Zhai at the Feinman School of Medicine at Northwestern University, show that CDGI is key for controlling behavioral responses to drugs of abuse and underlying neuronal plasticity (cellular changes induced by experience) in the striatum.

“This paper represents years of intensive research, which paid off in the end by identifying a specific cellular signaling cascade for controlling repetitive behaviors and neuronal plasticity,” says Graybiel, who is also an investigator at the McGovern Institute and a professor of brain and cognitive sciences at MIT.

McGovern Investigator Ann Graybiel (right) with former Research Scientist Jill Crittenden. Photo: Justin Knight

Surprise discovery

To understand the essential roles of CDGI, Crittenden first engineered “knockout” mice that lack the gene encoding CDGI. Then the Graybiel team began looking for abnormalities in the CDGI knockout mice that could be tied to the loss of CDGI’s function.

Initially, they noticed that the rodent ear-tag IDs often fell off in the knockout mice, an observation that ultimately led to the surprise discovery by the Graybiel team and others that CDGI is expressed in blood platelets and is responsible for a bleeding disorder in humans, dogs, and other animals. The CDGI knockout mice were otherwise healthy and seemed just like their “wildtype” brothers and sisters, which did not carry the gene mutation. To figure out the role of CDGI in the brain, the Graybiel team would have to scrutinize the mice more closely.

Challenging the striatum

Both the CDGI knockout and wildtype mice were given an extensive set of behavioral and neurological tests and the CDGI mice showed deficits in two tests designed to challenge the striatum.

In one test, mice must find their way through a maze by relying on egocentric (i.e. self-referential) cues, such as their turning right or turning left, and not competing allocentric (i.e. external) cues, such as going toward a bright poster on the wall. Egocentric cues are thought to be processed by the striatum whereas allocentric cues are thought to rely on the hippocampus.

In a second test of striatal function, mice learned various gait patterns to match different patterns of rungs on their running wheel, a task designed to test the mouse’s ability to learn and remember a motor sequence.

The CDGI mice learned both of these striatal tasks more slowly than their wildtype siblings, suggesting that the CDGI mice might perform normally in general tests of behavior because they are able to compensate for striatal deficits by using other brain regions such as the hippocampus to solve standard tasks.

The team then decided to give the mice a completely different type of test that relies on the striatum. Because the striatum is strongly activated by drugs of abuse, which elevate dopamine and drive motor habits, Crittenden and collaborator Morgane Thomsen (now at the University of Copenhagen) looked to see whether the CDGI knockout mice respond normally to amphetamine and cocaine.

Psychomotor stimulants like cocaine and amphetamine normally induce a mixture of hyperactive behaviors such as pacing and focused repetitive behaviors like skin-picking (also called stereotypy or punding in humans). The researchers found however, that the drug-induced behaviors in the CDGI knockout mice were less varied than the normal mice and consisted of abnormally prolonged stereotypy, as though the mice were unable to switch between behaviors. The researchers were able to map the abnormal behavior to CDGI function in the striatum by showing that the same vulnerability to drug-induced stereotypy was observed in mice that were engineered to delete CDGI in the striatum after birth (“conditional knockouts”), but to otherwise have normal CDGI throughout the body.

Controlling cravings

In addition to exhibiting prolonged, repetitive behaviors, the CDGI knockout mice had a vulnerability to self-administer drugs. Although previous research had shown that treatments that activate the M1 acetylcholine receptor can block cocaine self-administration, the team found that this therapy was ineffective in CDGI knockout mice. Knockouts continued to self-administer cocaine (suggesting increased craving for the drug) at the same rate before and after M1 receptor activation treatment, even though the treatment succeeded with their sibling control mice. The researchers concluded that CDGI is critically important for controlling repetitive behaviors and the ability to stop self-administration of addictive stimulants.

mouse brain images
Brain sections from control mice (left) and mice engineered for deletion of the CDGI gene after birth. The expression of CDGI in the striatum (arrows) grows stronger as mice grow from pups to adulthood in control mice, but is gradually lost in the CDGI engineered mice (“conditional knockouts”). Image courtesy of the researchers

To better understand how CDGI is linked to the M1 receptor at the cellular level, the team turned to slice physiologists, scientists who record the electrical activity of neurons in brain slices. Their recordings showed that striatal neurons from CDGI knockouts fail to undergo the normal, expected electrophysiological changes after receiving treatments that target the M1 receptor. In particular, the neurons of the striatum that function broadly to stop ongoing behaviors, did not integrate cellular signals properly and failed to undergo “long-term potentiation,” a type of neuronal plasticity thought to underlie learning.

The new findings suggest that excessive repetitive movements are controlled by M1 receptor signaling through CDGI in indirect pathway neurons of the striatum, a neuronal subtype that degenerates in Huntington’s disease and is affected by dopamine loss and l-DOPA replacement therapy in Parkinson’s disease.

“The M1 acetylcholine receptor is a target for therapeutic drug development in treating cognitive and behavioral problems in multiple disorders, but progress has been severely hampered by off-target side-effects related to the wide-spread expression of the M1 receptor,” Graybiel explains. “Our findings suggest that CDGI offers the possibility for forebrain-specific targeting of M1 receptor signaling cascades that are of interest for blocking pathologically repetitive and unwanted behaviors that are common to numerous brain disorders including Huntington’s disease, drug addiction, autism, and schizophrenia as well as drug-induced dyskinesias. We hope that this work can help therapeutic development for these major health problems.”

This work was funded by the James W. (1963) and Patricia T. Poitras Fund, the William N. & Bernice E. Bumpus Foundation, the Saks Kavanaugh Foundation, the Simons Foundation, and the National Institute of Health.

Some brain disorders exhibit similar circuit malfunctions

Anne Trafton |

Many neurodevelopmental disorders share similar symptoms, such as learning disabilities or attention deficits. A new study from MIT has uncovered a common neural mechanism for a type of cognitive impairment seen in some people with autism and schizophrenia, even though the genetic variations that produce the impairments are different for each condition.

In a study of mice, the researchers found that certain genes that are mutated or missing in some people with those disorders cause similar dysfunctions in a neural circuit in the thalamus. If scientists could develop drugs that target this circuit, they could be used to treat people who have different disorders with common behavioral symptoms, the researchers say.

“This study reveals a new circuit mechanism for cognitive impairment and points to a future direction for developing new therapeutics, by dividing patients into specific groups not by their behavioral profile, but by the underlying neurobiological mechanisms,” says Guoping Feng, the James W. and Patricia T. Poitras Professor in Brain and Cognitive Sciences at MIT, a member of the Broad Institute of Harvard and MIT, the associate director of the McGovern Institute for Brain Research at MIT, and the senior author of the new study.

Dheeraj Roy, a Warren Alpert Distinguished Scholar and a McGovern Fellow at the Broad Institute, and Ying Zhang, a postdoc at the McGovern Institute, are the lead authors of the paper, which appears today in Neuron.

Thalamic connections

The thalamus plays a key role in cognitive tasks such as memory formation and learning. Previous studies have shown that many of the gene variants linked to brain disorders such as autism and schizophrenia are highly expressed in the thalamus, suggesting that it may play a role in those disorders.

One such gene is called Ptchd1, which Feng has studied extensively. In boys, loss of this gene, which is carried on the X chromosome, can lead to attention deficits, hyperactivity, aggression, intellectual disability, and autism spectrum disorders.

In a study published in 2016, Feng and his colleagues showed that Ptchd1 exerts many of its effects in a part of the thalamus called the thalamic reticular nucleus (TRN). When the gene is knocked out in the TRN of mice, the mice show attention deficits and hyperactivity. However, that study did not find any role for the TRN in the learning disabilities also seen in people with mutations in Ptchd1.

In the new study, the researchers decided to look elsewhere in the thalamus to try to figure out how Ptchd1 loss might affect learning and memory. Another area they identified that highly expresses Ptchd1 is called the anterodorsal (AD) thalamus, a tiny region that is involved in spatial learning and communicates closely with the hippocampus.

Using novel techniques that allowed them to trace the connections between the AD thalamus and another brain region called the retrosplenial cortex (RSC), the researchers determined a key function of this circuit. They found that in mice, the AD-to-RSC circuit is essential for encoding fearful memories of a chamber in which they received a mild foot shock. It is also necessary for working memory, such as creating mental maps of physical spaces to help in decision-making.

The researchers found that a nearby part of the thalamus called the anteroventral (AV) thalamus also plays a role in this memory formation process: AV-to-RSC communication regulates the specificity of the encoded memory, which helps us distinguish this memory from others of similar nature.

“These experiments showed that two neighboring subdivisions in the thalamus contribute differentially to memory formation, which is not what we expected,” Roy says.

Circuit malfunction

Once the researchers discovered the roles of the AV and AD thalamic regions in memory formation, they began to investigate how this circuit is affected by loss of Ptchd1. When they knocked down expression of Ptchd1 in neurons of the AD thalamus, they found a striking deficit in memory encoding, for both fearful memories and working memory.

The researchers then did the same experiments with a series of four other genes — one that is linked with autism and three linked with schizophrenia. In all of these mice, they found that knocking down gene expression produced the same memory impairments. They also found that each of these knockdowns produced hyperexcitability in neurons of the AD thalamus.

These results are consistent with existing theories that learning occurs through the strengthening of synapses that occurs as a memory is formed, the researchers say.

“The dominant theory in the field is that when an animal is learning, these neurons have to fire more, and that increase correlates with how well you learn,” Zhang says. “Our simple idea was if a neuron fires too high at baseline, you may lack a learning-induced increase.”

The researchers demonstrated that each of the genes they studied affects different ion channels that influence neurons’ firing rates. The overall effect of each mutation is an increase in neuron excitability, which leads to the same circuit-level dysfunction and behavioral symptoms.

The researchers also showed that they could restore normal cognitive function in mice with these genetic mutations by artificially turning down hyperactivity in neurons of the AD thalamus. The approach they used, chemogenetics, is not yet approved for use in humans. However, it may be possible to target this circuit in other ways, the researchers say.

The findings lend support to the idea that grouping diseases by the circuit malfunctions that underlie them may help to identify potential drug targets that could help many patients, Feng says.

“There are so many genetic factors and environmental factors that can contribute to a particular disease, but in the end, it has to cause some type of neuronal change that affects a circuit or a few circuits involved in this behavior,” he says. “From a therapeutic point of view, in such cases you may not want to go after individual molecules because they may be unique to a very small percentage of patients, but at a higher level, at the cellular or circuit level, patients may have more commonalities.”

The research was funded by the Stanley Center at the Broad Institute, the Hock E. Tan and K. Lisa Yang Center for Autism Research at MIT, the James and Patricia Poitras Center for Psychiatric Disorders Research at MIT, and the National Institutes of Health BRAIN Initiative.

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.

New neuron type discovered only in primate brains

by Stephanie M. McPherson |

Neuropsychiatric illnesses like schizophrenia and autism are a complex interplay of brain chemicals, environment, and genetics that requires careful study to understand the root causes. Scientists have traditionally relied on samples taken from mice and non-human primates to study how these diseases develop. But the question has lingered: are the brains of these subjects similar enough to humans to yield useful insights?

Now work from the Broad Institute of MIT and Harvard and the McGovern Institute for Brain Research is pointing towards an answer. In a study published in Nature, researchers from the Broad’s Stanley Center for Psychiatric Research report several key differences in the brains of ferrets, mice, nonhuman primates, and humans, all focused on a type of neuron called interneurons. Most surprisingly, the team found a new type of interneuron only in primates, located in a part of the brain called the striatum, which is associated with Huntington’s disease and potentially schizophrenia.

The findings could help accelerate research into causes of and treatments for neuropsychiatric illnesses, by helping scientists choose the lab model that best mimics features of the human brain that may be involved in these diseases.

“The data from this work will inform the study of human brain disorders because it helps us think about which features of the human brain can be studied in mice, which features require higher organisms such as marmosets, and why mouse models often don’t reflect the effects of the corresponding mutations in human,” said Steven McCarroll, senior author of the study, director of genetics at the Stanley Center, and a professor of genetics at Harvard Medical School.

“Dysfunctions of interneurons have been strongly linked to several brain disorders including autism spectrum disorder and schizophrenia,” said Guoping Feng, co-author of the study, director of model systems and neurobiology at the Stanley Center, and professor of neuroscience at MIT’s McGovern Institute for Brain Research. “These data further demonstrate the unique importance of non-human primate models in understanding neurobiological mechanisms of brain disorders and in developing and testing therapeutic approaches.”

Enter the interneuron

Interneurons form key nodes within neural circuitry in the brain, and help regulate neuronal activity by releasing the neurotransmitter GABA, which inhibits the firing of other neurons.

Fenna Krienen, a postdoctoral fellow in the McCarroll Lab and first author on the Nature paper, and her colleagues wanted to track the natural history of interneurons.

“We wanted to gain an understanding of the evolutionary trajectory of the cell types that make up the brain,” said Krienen. “And then we went about acquiring samples from species that could inform this understanding of evolutionary divergence between humans and the models that so often stand in for humans in neuroscience studies.”

One of the tools the researchers used was Drop-seq, a high-throughput single nucleus RNA sequencing technique developed by McCarroll’s lab, to classify the roles and locations of more than 184,000 telencephalic interneurons in the brains of ferrets, humans, macaques, marmosets, and mice. Using tissue from frozen samples, the team isolated the nuclei of interneurons from the cortex, the hippocampus, and the striatum, and profiled the RNA from the cells.

The researchers thought that because interneurons are found in all vertebrates, the cells would be relatively static from species to species.

“But with these sensitive measurements and a lot of data from the various species, we got a different picture about how lively interneurons are, in terms of the ways that evolution has tweaked their programs or their populations from one species to the next,” said Krienen.

She and her collaborators identified four main differences in interneurons between the species they studied: the cells change their proportions across brain regions, alter the programs they use to link up with other neurons, and can migrate to different regions of the brain.

But most strikingly, the scientists discovered that primates have a novel interneuron not found in other species. The interneuron is located in the striatum—the brain structure responsible for cognition, reward, and coordinated movements that has existed as far back on the evolutionary tree as ancient primitive fish. The researchers were amazed to find the new neuron type made up a third of all interneurons in the striatum.

“Although we expected the big innovations in human and primate brains to be in the cerebral cortex, which we tend to associate with human intelligence, it was in fact in the venerable striatum that Fenna uncovered the most dramatic cellular innovation in the primate brain,” said McCarroll. “This cell type had never been discovered before, because mice have nothing like it.”

“The question of what provides the “human advantage” in cognitive abilities is one of the fundamental issues neurobiologists have endeavored to answer,” said Gordon Fishell, group leader at the Stanley Center, a professor of neurobiology at Harvard Medical School, and a collaborator on the study. “These findings turn on end the question of ‘how do we build better brains?’. It seems at least part of the answer stems from creating a new list of parts.”

A better understanding of how these inhibitory neurons vary between humans and lab models will provide researchers with new tools for investigating various brain disorders. Next, the researchers will build on this work to determine the specific functions of each type of interneuron.

“In studying neurodevelopmental disorders, you would like to be convinced that your model is an appropriate one for really complex social behaviors,” Krienen said. “And the major overarching theme of the study was that primates in general seem to be very similar to one another in all of those interneuron innovations.”

Support for this work was provided in part by the Broad Institute’s Stanley Center for Psychiatric Research and the NIH Brain Initiative, the Dean’s Innovation Award (Harvard Medical School), the Hock E. Tan and K. Lisa Yang Center for Autism Research at MIT, the Poitras Center for Psychiatric Disorders Research at MIT, the McGovern Institute for Brain Research at MIT, and the National Institute of Neurological Disorders and Stroke.

Optogenetics with SOUL

by Sabbi Lall |

Optogenetics has revolutionized neurobiology, allowing researchers to use light to activate or deactivate neurons that are genetically modified to express a light-sensitive channel. This ability to manipulate neuron activity has allowed causal testing of the function of specific neurons, and also has therapeutic potential to reduce symptoms in brain disorders. However, activating neurons deep within a given brain, especially a large primate brain but even a small mouse brain, is challenging and currently requires implanting fibers that could cause damage or inflammation.

McGovern Investigator Guoping Feng and colleagues have now overcome this challenge, developing optogenetic tools that allow non-invasive stimulation of neurons in the deep brain.

“Neuroscientists have dreamed of methods to turn neurons on and off, to understand the function of different neurons, but also to repair brain malfunctions that lead to psychiatric disorders, and optogenetics made this possible” explained Feng, the James W. (1963) and Patricia T. Poitras Professor in Brain and Cognitive Sciences. “We were trying to improve the light sensitivity of optogenetic tools to broaden applications.”

Engineering with light

In order to stimulate neurons with minimal invasiveness, Feng and colleagues engineered a new type of opsin. The original breakthrough optogenetics protocol used channelrhodopsin, a light-sensitive channel discovered in algae. By expressing this channel in neurons, light of the right wavelength can be used to activate the neuron in a dish or in vivo. However, in vivo application requires the implantation of optical fibers to deliver the light close to the specific brain region being stimulated, especially if the target region is in the deep brain. In addition, if the neuron being targeted is in the deep brain, it is hard for light to reach the region in the absence of invasive tools that can damage tissue and impact the behavior of the animal.

Our study creates a method that can activate any mouse brain region, independent of its location, non-invasively.

“Prior to our study, a few studies have contributed in various ways to the development of optogenetic stimulation methods that would be minimally invasive to the brain. However, all of these studies had various limitations in the extent of brain regions they could activate,” said co-senior study author Robert Desimone, director of the McGovern Institute and the Doris and Don Berkey Professor of Neuroscience at MIT.

Probing the brain with SOUL

Feng and colleagues turned instead to new opsins, in particular SOUL, a new type of opsin that is very sensitive to even low-level light. The Feng group engineered this opsin, based on SSFO a second generation optogenetics tool, to have increased light sensitivity, and took advantage of a second property: that SOUL is activated in multiple steps, and once activated, it stays active for longer than other commonly used opsins. This means that a burst of a few seconds of low-level light can cause neurons to stay active for 10-30 minutes.

In order to put SOUL through its paces, the Feng lab expressed this channel in the lateral hypothalamus of the mouse brain. This is a deep region, challenging to reach with light, but with neurons that have clear functions that will lead to changes in behavior. Feng’s group was able to turn on this region non-invasively with light from outside the skull, and cause changes in feeding behavior.

“We were really surprised that SOUL was able to activate one of the deepest areas in the mouse brain, the lateral hypothalamus, which is 6 mm deep,” explains Feng.

But there were more surprises. When the authors activated a region of the primate brain using SOUL, they saw oscillations, waves of synchronized neuronal activity coming together like a choir. Such waves are believed to be important for many brain functions, and this result suggests that the new opsin can manipulate these brain waves, allowing scientists to study their role in the brain.

The authors are planning to move the study in several directions, studying models of brain disorders to identify circuits that may be suitable targets for therapy, as well as moving the methodology so that it can be used beyond the superficial cortex in larger animals. While it is too early to discuss applying the system to humans, the research brings us one step closer to future treatment of neurological disorders.

CRISPR makes several Discovery of the Decade lists

by Sabbi Lall |

As we reach milestones in time, it’s common to look back and review what we learned. A number of media outlets, including National Geographic, NPR, The Hill, Popular Mechanics, Smithsonian Magazine, Nature, Mental Floss, CNBC, and others, recognized the profound impact of genome editing, adding CRISPR to their discovery of the decade lists.

“In 2013, [CRISPR] was used for genome editing in a eukaryotic cell, forever altering the course of biotechnology and, ultimately our relationship with our DNA.”
— Popular Mechanics

It’s rare for a molecular system to become a household name, but in less than a decade, CRISPR has done just that. McGovern Investigator Feng Zhang played a key role in leveraging CRISPR, an immune system found originally in prokaryotic – bacterial and archaeal – cells, into a broadly customizable toolbox for genomic manipulation in eukaryotic (animal and plant) cells. CRISPR allows scientists to easily and quickly make changes to genomes, has revolutionized the biomedical sciences, and has major implications for control of infectious disease, agriculture, and treatment of genetic disorders.