- Feature Story
BCS Faculty Use State-of-the-Art Tools and Techniques to Unravel the Mysteries of the Brain in Health and in Disorder
The human brain is a vastly complex system. While advances in tools and technologies to measure, probe, and analyze brain function have helped scientists uncover many mysteries about the brain, there is a lot we still do not know about the brain in health, much less in disorder. The stakes are high—the World Health Organization estimates that globally, about a billion people are impacted by brain disorders in some way—ranging from neurological disorders (like Alzheimer’s or Parkinson’s disease), to psychiatric disorders (like bipolar disorder) to developmental disorders (like autism or ADHD).
In the Department of Brain and Cognitive Sciences at MIT, researchers develop and employ a variety of state-of-the-art tools and techniques—including functional magnetic resonance imaging (fMRI), genetically engineered animal models enabled by CRISPR, and cell type-specific transcriptional profiling, to study the brain and all of its components. The key to unlocking the mystery behind any brain disorder could be hidden on any level—from the activity patterns in the whole brain to the molecules by which brain cells communicate with each other, to the genes that are responsible for producing the proteins that run everything in the brain.
This idea has crystallized into the core mission of BCS: to reverse engineer the mechanisms of the mind. Understanding what goes awry across all levels in the brain and developing and refining computational models to emulate these processes is critical to the discovery of new treatments and development of new preventative measures for disorders of the brain and mind.
Peering into the Whole Brain
Donning blue hospital scrubs, a volunteer lays back on the table as she listens to instructions from the researcher. The table is perched on the edge of the circular opening of a 3T magnetic resonance imaging machine (MRI) in the Martinos Imaging Center, housed in the lowest floor of the McGovern Institute for Brain Research (MIBR). The scanner contains a magnet that is 300 times stronger than the ones stuck to your kitchen refrigerator – no metal, not even a hair pin is allowed into the room containing the scanner. The volunteer, laying perfectly still on the table, is slowly moved into the enormous machine, which hums to life, whirring and clicking as the study begins. On the opposite side of a glass window researchers watch as the volunteer’s entire brain unfurls in transections, pixel by pixel, on the monitor in front of them.
Prof. John Gabrieli, Photo credit Justin Knight, MIBR
fMRI is a powerful imaging technique that measures brain activity through changes in blood flow and oxygen levels. Once inside the machine, volunteers perform a variety of tasks in the scanner—often involving language, emotion and memory—which researchers use to identify brains regions and activation patterns involved in different cognitive processes. Professor John Gabrieli uses fMRI, along with various behavioral measures, to study diversity in brain function and development, including in individuals with learning disabilities like dyslexia and developmental disorders like attention deficit hyperactivity disorder (ADHD) and autism.
“As imaging became a more practical tool, I was struck by idea that we could now look at how the brain develops differentially in children, which had been impossible to look at in our current population of adults with brain injuries,” says Gabrieli, the Grover Hermann Professor of Health Sciences and Technology and Cognitive Neuroscience, an investigator in MIBR, Director of the Martinos Imaging Center and Director, MIT Integrated Learning Initiative. “The chance to look directly at a five-year-old’s brain to learn more about how it grows, how it operates and how those processes relate to doing better or worse in school, or being better or worse emotionally seemed like a really interesting opportunity for research.”
When Gabrieli was a graduate student, imaging techniques like fMRI were not widely available. Instead, researchers who wanted to understand brain differences were limited to working with adult patients with brain injuries or Alzheimer’s disease. That changed when fMRI was made accessible. Today, Gabrieli’s lab also considers the role of socioeconomic factors and environmental factors, such as early intervention and educational support, that may impact access to treatment and the presentation of developmental disorders. Taken together, Gabrieli’s goal is to combine the basic science understanding of developmental disorders and the real-world social impacts to inform and improve practices and policies in education.
The ability to peer inside a live brain in a minimally invasive way has enabled key breakthroughs in our understanding of the neurobiology of developmental disorders and how they are impacted by environmental and social factors. For example, Gabrieli uncovered key brain differences in children who struggled with reading.
“There was a measurable difference in children even before getting reading instruction in school,” says Gabrieli. “This was a key insight for us because it showed that we could identify children at high risk of struggling to read before they fail and initiate an intervention much earlier to provide additional support. It made us realize we were on the right path.”
Using fMRI, Gabrieli and his research team uncovered key brain differences in children who struggled with reading.
In a study using fMRI, Gabrieli and his research team discovered that in people with dyslexia, the brain has a diminished ability to acclimate to a repeated input—a trait known as neural adaptation. For example, when dyslexic students see the same word repeatedly, brain regions involved in reading do not show the same adaptation seen in typical readers. Throughout the series of experiments, Gabrieli and his team found that in people with dyslexia, brain regions devoted to interpreting words, objects, and faces, respectively, did not show neural adaptation when the same stimuli were repeated multiple times, which was surprising because people with dyslexia typically have no documented difficulty with recognizing objects and faces. This led Gabrieli to hypothesize that the impairment shows up primarily in reading because deciphering letters and mapping them to sounds is such a demanding cognitive task.
Being able to peer inside the whole brain enables Gabrieli to assemble the disparate pieces of the puzzle together, which vary greatly between individuals, in order to obtain a more complete picture of brain disorders.
Closing the Gap
Bringing new therapies from bench to bedside is a big challenge. Treatments can have promising results in lab mice but fail when tested in human patients. After attending medical school, Professor Guoping Feng, James W. (1963) and Patricia T. Poitras Professor and an MIBR investigator, initially pursued graduate school in pharmacology, where he hoped to develop treatments that would have a positive impact on the pediatric patients he saw in medical school. However, he quickly realized that huge gaps in our basic understanding of disease significantly impeded the development of new treatments.
Prof. Guoping Feng, Photo credit: Justin Knight, MIBR
“I began to realize that without understanding the basic biology of disease, we will never develop a treatment for it,” says Feng. “So I became more and more of a basic biologist and I did my PhD on nervous system development of fruit flies. I was drawn to molecular genetics because you could actually pinpoint the causes of a problem, which helps you solve it.”
To better focus on human diseases, Feng switched from studying fly models to genetic mouse models for his postdoctoral studies—at the time the mouse was the only mammalian model available for genetic engineering. Today, Feng’s research focuses on the development and function of synapses—and their disruption in neurodevelopmental and neuropsychiatric disorders. He uses molecular genetics combined with behavioral and electrophysiological methods to study the molecular components of the synapse and how disruptions in these components can lead to brain disorders.
One of Feng’s first big breakthroughs involved a mouse model with a deleted scaffolding protein, Shank3, which is critical for brain development and implicated in autism spectrum disorder (ASD). While ASD has diverse genetic causes, most of which are still unknown, about one percent of people with autism are missing the Shank3 gene. Without this gene, individuals develop intellectual disability along with autism symptoms including repetitive behavior and avoidance of social interactions. The Shank3 protein is found at synapses—the connections that allow neurons to communicate with each other, where it helps to organize the hundreds of other proteins that are necessary to coordinate a neuron’s response to incoming signals. Using CRISPR to precisely delete the gene, Feng’s group found that these mutant mice exhibit autistic-like behaviors—compulsivity, repetition of behavior and decreased social interaction, and showed that this gene produced these abnormal behaviors by interfering with communication between brain cells.
Researchers in Guoping Feng’s lab have stained neurons in the mouse brain to reveal a protein related to autism and other brain disorders. Image: Michael Wells and Guoping Feng
While these studies in mouse models provided helpful insight that can help pinpoint more targeted treatments for brain disorders, rodent brains are fundamentally different from primate brains, which limits the ability to translate discoveries into treatments for humans. CRISPR has made it possible to test human genetic mutations in non-human primates, which has enabled Feng and his research group to quantify and track the implications of Shank3 mutations in marmosets, and how it impacts more complex cognitive processes like social communication and working memory.
“One of the key differences between a rodent brain and a human brain is the expanded prefrontal cortex in the human brain, which is a major area controlling our decision-making, our emotions and our higher cognitive function. These structural differences produce vastly different behavioral outputs in the phenotypic expressions of these disorders and this may have contributed to the failures we have seen in translating this work to the clinic,” says Feng. “So far, we have seen success in generating marmoset genetic models for brain disorders, whose brain structure and behavior are more similar to that of a human. We hope these new models will bring us much closer to new strategies for treatment.”
The Power of Connection
Throughout life the brain can constantly adapt to a changing environment and in response to new experiences. This phenomenon called plasticity is implemented at the level of individual connections between brain cells (neurons). Neurons communicate with each other via neurotransmitter molecules released at connection points called synapses. Synapses can form and change strength during growth and development, but also prompted by a variety of factors including environment, injury, and activities like learning and reading. Professor Elly Nedivi (PILM), William R. (1964) & Linda R. Young Professor of Neuroscience and PILM investigator, studies the cellular mechanisms that underlie activity-dependent plasticity in the developing and adult brain.
Prof. Elly Nedivi, Photo credit: Josh Sariñana
“We are interested in plasticity, or the ability of the brain to adapt. The concept is similar to working out at the gym to make your muscles stronger or practicing something over and over so you can remember it better,” says Nedivi. “You can take the same idea and apply it to individual connections in your brain. When we say these connections get stronger when they're used, what does that actually mean? How are the properties of the connections actually changing?”
By employing molecular and genetic techniques to study the dynamics of neuronal structure and identify the participating genes and the proteins they encode, what started as a question about the biology of this phenomenon led to new and exciting insights that could impact the way we understand and treat patients with bipolar disorder (BPD), an inheritable mood disorder characterized by recurrent episodes of high and low moods, or mania and depression. Left untreated, BPD worsens in patients, and researchers estimate that between 25 to 60 percent of BPD patients will attempt suicide at least once in their lives.
While conducting studies on the fundamental properties of synaptic plasticity, Nedivi discovered CPG2, a protein expressed in response to neural activity, that helps regulate the number of receptors for a key neurotransmitter, glutamate, at excitatory synapses. Regulation of glutamate receptor numbers is a key mechanism for modulating the strength of connections in brain circuits. When genetic studies identified SYNE1, the gene encoding CPG2, as a risk gene specific to bipolar disorder, Nedivi and her research team saw an opportunity to understand how a set of genetic differences in patients with bipolar disorder can lead to specific dysfunction of synapses in the brain.
Some variants of the SYNE1 gene, such as V551A top right, reduced the ability of the protein CPG2, shown here as bright spots, to locate in protruding spines of dendrites that house excitatory synapses in the neurons of rats. Image credit: Nedivi Lab/Picower Institute
“The levels of glutamate in the synapse contribute to the strength of the synapse itself, and pushing receptors for glutamate in and out of the synapse is a highly regulated process because it changes the sensitivity of the synapse to the transmitter,” says Nedivi. The researchers are suggesting that the CPG2-related variations in SYNE1 likely contribute to susceptibility to bipolar disorder. Notably, they found that some human genetic variants found in bipolar patients, and in particular combinations of variants, could results in diminished CPG2 levels, and synaptic dysfunction.
“Our results align with the heritability of the disease where we know that there is a genetic element to a lot of neuropsychiatric disorders, and the genetic environment also impacts how different alleles get combined, which affects whether or not BPD emerges,” says Nedivi, “In the lab, we can actually knock down the mouse or rat gene and replace it with the human gene and the model acts like it’s at home, so it’s a really helpful model for testing the impact of human mutations in vivo.”
For BPD patients, drug treatment requires a lot of trial and error and as a result, is often unsuccessful. In many cases, full recovery between episodes is not achieved in all patients. Models of BPD, like the ones developed in Nedivi’s lab, not only shed light onto the mechanistic details of disease-related genetic mutations, but also offer an opportunity to study ways to prevent, manage, or even reverse the disease.
From Cells and Molecules
The brain is comprised of many different cell types including neurons, astrocytes, microglia, and oligodendrocytes, and many variations in the types of neurons and glia. Different disorders are not only specific to particular brain regions, but often to specific cell types. However, it has been difficult to characterize the function of cellular subtypes and pinpoint the mechanisms of dysfunction that underlie disorders.
Prof. Myriam Heiman, Photo credit: Josh Sariñana
Professor Myriam Heiman, Latham Career Development Chair and member of PILM, came to MIT armed with an expertise in cellular and molecular biology and a unique methodology she devised during her postdoctoral studies. TRAP or “Translating Ribosome Affinity Purification”, enables cell type-specific transcriptional profiling to identify the pattern of protein production ongoing in a particular cell type. Heiman uses a combination of TRAP and genetic screening methods to study the underlying mechanisms of degenerative diseases in the central nervous system, which includes Huntington’s disease and Parkinson’s disease.
“Though these diseases have distinct clinical presentations, they are both caused by dysfunction of the basal ganglia in the brain, which is a group of subcortical areas that are important in many developmental and degenerative diseases,” says Heiman. “Our approach is first to understand how these neurons work in the normal developmental situation, and then to understand how they dysfunction in disease states.”
Huntington’s disease is a genetic, progressive, neurodegenerative disorder characterized by gradual, involuntary muscle movements and progressive deterioration of cognitive processes and memory (i.e. dementia). In Huntington’s disease, a specific subtype of neuron, striatal spiny projection neurons (SPNs), are especially vulnerable to the genetic defect underlying the disease, and this enhanced vulnerability is also seen in animal models of the disease. Heiman utilized her TRAP method to understand the mechanisms behind this vulnerability. One of her first key findings with the enhanced resolution that TRAP offers is that the genetic defect in HD caused an alteration to transcription in SPNs during very early stages of the disease model. Previously, it hadn’t been known whether this transcriptional dysregulation was a cause or consequence of the disease taking hold, but it was a clear indication from the early timing that this represented a first step involved in the eventual death of these particular neurons.
This finding led to Myriam identifying a particular gene, Foxp2, an important gene in the basal ganglia that is connected to producing and comprehending speech. Heiman noticed that Foxp2 has a section of its gene encoding many glutamine amino acids in a row, a region called a polyglutamine domain. Other researchers had previously found that the mutant HD gene also has an expanded polyglutamine domain in the disease state, and it can cause other polyglutamine-containing proteins to lose function. Seeing the parallel in the Foxp2 made Heiman question whether there was a connection between the two.
The above image compares the control mouse striatal tissue (top row) with striatal tissue from a transgenic mouse with an HD gene mutation (bottom row) that mimics features of HD. The first column shows the Foxp2 protein, the second column shows the mutant Huntingtin protein, and the third column shows both Foxp2 and mutant Huntingtin together. The R6/2 merge (bottom right) shows Foxp2 and mutant Huntingtin are co-localized in the striatal tissue, supporting the hypothesis that the interaction between the two may be implicated in Huntington's disease. Image courtesy of the researchers
“From pioneering work by Ann Graybiel and others, we know that Foxp2 also has a more primitive role, in regulating how the cortex communicates with the striatum. We became interested in Foxp2, because in Huntington's disease, these communication points between the cortex and the striatum are thought to be among the first part of the neurons that dysfunction in HD,” says Heiman. “It is likely that Foxp2 is also important in the maintenance of these communication points, or synapses, after they form. Further, we noticed that Foxp2 has a polyglutamine domain, a stretch of many glutamine amino acids in a row, similar to the polyglutamine domain that is expanded in the Huntingtin gene in HD. Could it be that the mutated gene is basically sticking onto Foxp2 and preventing it from doing its job and impeding proper neural communication?”
To test this idea, Heiman first decreased levels of Foxp2 in mouse models and observed HD-associated changes in behavior relevant to HD. When Heiman added the protein back into two of the HD mouse models for the second part of the experiment, she observed a surprising phenomenon: the HD-associated deficits in the mice from removing Foxp2 decreased.
“From our findings, we think that Foxp2 protein interacts with the HD gene protein through their polyglutamine domains. Our paper concluded that given these two proteins are in the same place physically in the cell, we think part of the early deficits seen in HD may be attributable to the lack of proper Foxp2 function,” says Heiman. “Because transcription factors control many genes, they are incredibly difficult to work with in human gene therapy, but it certainly presents an opportunity to see if we can restore the effects of Foxp2 function in potential future therapies.”
Stories by Anne Trafton and David Orenstein contributed to this report.