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New CRISPR platform expands RNA editing capabilities

by Sabbi Lall | July 11, 2019May 24, 2023

CRISPR-based tools have revolutionized our ability to target disease-linked genetic mutations. CRISPR technology comprises a growing family of tools that can manipulate genes and their expression, including by targeting DNA with the enzymes Cas9 and Cas12 and targeting RNA with the enzyme Cas13. This collection offers different strategies for tackling mutations. Targeting disease-linked mutations in RNA, which is relatively short-lived, would avoid making permanent changes to the genome. In addition, some cell types, such as neurons, are difficult to edit using CRISPR/Cas9-mediated editing, and new strategies are needed to treat devastating diseases that affect the brain.

McGovern Institute Investigator and Broad Institute of MIT and Harvard core member Feng Zhang and his team have now developed one such strategy, called RESCUE (RNA Editing for Specific C to U Exchange), described in the journal Science.

Zhang and his team, including first co-authors Omar Abudayyeh and Jonathan Gootenberg (both now McGovern Fellows), made use of a deactivated Cas13 to guide RESCUE to targeted cytosine bases on RNA transcripts, and used a novel, evolved, programmable enzyme to convert unwanted cytosine into uridine — thereby directing a change in the RNA instructions. RESCUE builds on REPAIR, a technology developed by Zhang’s team that changes adenine bases into inosine in RNA.

RESCUE significantly expands the landscape that CRISPR tools can target to include modifiable positions in proteins, such as phosphorylation sites. Such sites act as on/off switches for protein activity and are notably found in signaling molecules and cancer-linked pathways.

“To treat the diversity of genetic changes that cause disease, we need an array of precise technologies to choose from. By developing this new enzyme and combining it with the programmability and precision of CRISPR, we were able to fill a critical gap in the toolbox,” says Zhang, the James and Patricia Poitras Professor of Neuroscience at MIT. Zhang also has appointments in MIT’s departments of Brain and Cognitive Sciences and Biological Engineering.

Expanding the reach of RNA editing to new targets

The previously developed REPAIR platform used the RNA-targeting CRISPR/Cas13 to direct the active domain of an RNA editor, ADAR2, to specific RNA transcripts where it could convert the nucleotide base adenine to inosine, or letters A to I. Zhang and colleagues took the REPAIR fusion, and evolved it in the lab until it could change cytosine to uridine, or C to U.

RESCUE can be guided to any RNA of choice, then perform a C-to-U edit through the evolved ADAR2 component of the platform. The team took the new platform into human cells, showing that they could target natural RNAs in the cell as well as 24 clinically relevant mutations in synthetic RNAs. They then further optimized RESCUE to reduce off-target editing, while minimally disrupting on-target editing.

New targets in sight

Expanded targeting by RESCUE means that sites regulating activity and function of many proteins through post-translational modifications, such as phosphorylation, glycosylation, and methylation can now be more readily targeted for editing.

A major advantage of RNA editing is its reversibility, in contrast to changes made at the DNA level, which are permanent. Thus, RESCUE could be deployed transiently in situations where a modification may be desirable temporarily, but not permanently. To demonstrate this, the team showed that in human cells, RESCUE can target specific sites in the RNA encoding β-catenin, that are known to be phosphorylated on the protein product, leading to a temporary increase in β-catenin activation and cell growth. If such a change was made permanently, it could predispose cells to uncontrolled cell growth and cancer, but by using RESCUE, transient cell growth could potentially stimulate wound healing in response to acute injuries.

The researchers also targeted a pathogenic gene variant, APOE4. The APOE4 allele has consistently emerged as a genetic risk factor for the development of late-onset Alzheimer’s Disease. Isoform APOE4 differs from APOE2, which is not a risk factor, by just two differences (both C in APOE4 vs. U in APOE2). Zhang and colleagues introduced the risk-associated APOE4 RNA into cells, and showed that RESCUE can convert its signature C’s to an APOE2 sequence, essentially converting a risk to a non-risk variant.

To facilitate additional work that will push RESCUE toward the clinic as well as enable researchers to use RESCUE as a tool to better understand disease-causing mutations, the Zhang lab plans to share the RESCUE system broadly, as they have with previously developed CRISPR tools. The technology will be freely available for academic research through the non-profit plasmid repository Addgene. Additional information can be found on the Zhang lab’s webpage.

Support for the study was provided by The Phillips Family; J. and P. Poitras; the Poitras Center for Psychiatric Disorders Research; Hock E. Tan and K. Lisa Yang Center for Autism Research.; Robert Metcalfe; David Cheng; a NIH F30 NRSA 1F30-CA210382 to Omar Abudayyeh. F.Z. is a New York Stem Cell Foundation–Robertson Investigator. F.Z. is supported by NIH grants (1R01-HG009761, 1R01-222 MH110049, and 1DP1-HL141201); the Howard Hughes Medical Institute; the New York Stem Cell Foundation and G. Harold and Leila Mathers Foundations.

Artificial “muscles” achieve powerful pulling force

Anne Trafton | July 11, 2019May 24, 2023

As a cucumber plant grows, it sprouts tightly coiled tendrils that seek out supports in order to pull the plant upward. This ensures the plant receives as much sunlight exposure as possible. Now, researchers at MIT have found a way to imitate this coiling-and-pulling mechanism to produce contracting fibers that could be used as artificial muscles for robots, prosthetic limbs, or other mechanical and biomedical applications.

While many different approaches have been used for creating artificial muscles, including hydraulic systems, servo motors, shape-memory metals, and polymers that respond to stimuli, they all have limitations, including high weight or slow response times. The new fiber-based system, by contrast, is extremely lightweight and can respond very quickly, the researchers say. The findings are being reported today in the journal Science.

The new fibers were developed by MIT postdoc Mehmet Kanik and MIT graduate student Sirma Örgüç, working with professors Polina Anikeeva, Yoel Fink, Anantha Chandrakasan, and C. Cem Taşan, and five others, using a fiber-drawing technique to combine two dissimilar polymers into a single strand of fiber.

The key to the process is mating together two materials that have very different thermal expansion coefficients — meaning they have different rates of expansion when they are heated. This is the same principle used in many thermostats, for example, using a bimetallic strip as a way of measuring temperature. As the joined material heats up, the side that wants to expand faster is held back by the other material. As a result, the bonded material curls up, bending toward the side that is expanding more slowly.

Credit: Courtesy of the researchers

Using two different polymers bonded together, a very stretchable cyclic copolymer elastomer and a much stiffer thermoplastic polyethylene, Kanik, Örgüç and colleagues produced a fiber that, when stretched out to several times its original length, naturally forms itself into a tight coil, very similar to the tendrils that cucumbers produce. But what happened next actually came as a surprise when the researchers first experienced it. “There was a lot of serendipity in this,” Anikeeva recalls.

As soon as Kanik picked up the coiled fiber for the first time, the warmth of his hand alone caused the fiber to curl up more tightly. Following up on that observation, he found that even a small increase in temperature could make the coil tighten up, producing a surprisingly strong pulling force. Then, as soon as the temperature went back down, the fiber returned to its original length. In later testing, the team showed that this process of contracting and expanding could be repeated 10,000 times “and it was still going strong,” Anikeeva says.

Credit: Courtesy of the researchers

One of the reasons for that longevity, she says, is that “everything is operating under very moderate conditions,” including low activation temperatures. Just a 1-degree Celsius increase can be enough to start the fiber contraction.

The fibers can span a wide range of sizes, from a few micrometers (millionths of a meter) to a few millimeters (thousandths of a meter) in width, and can easily be manufactured in batches up to hundreds of meters long. Tests have shown that a single fiber is capable of lifting loads of up to 650 times its own weight. For these experiments on individual fibers, Örgüç and Kanik have developed dedicated, miniaturized testing setups.

Credit: Courtesy of the researchers

The degree of tightening that occurs when the fiber is heated can be “programmed” by determining how much of an initial stretch to give the fiber. This allows the material to be tuned to exactly the amount of force needed and the amount of temperature change needed to trigger that force.

The fibers are made using a fiber-drawing system, which makes it possible to incorporate other components into the fiber itself. Fiber drawing is done by creating an oversized version of the material, called a preform, which is then heated to a specific temperature at which the material becomes viscous. It can then be pulled, much like pulling taffy, to create a fiber that retains its internal structure but is a small fraction of the width of the preform.

For testing purposes, the researchers coated the fibers with meshes of conductive nanowires. These meshes can be used as sensors to reveal the exact tension experienced or exerted by the fiber. In the future, these fibers could also include heating elements such as optical fibers or electrodes, providing a way of heating it internally without having to rely on any outside heat source to activate the contraction of the “muscle.”

Such fibers could find uses as actuators in robotic arms, legs, or grippers, and in prosthetic limbs, where their slight weight and fast response times could provide a significant advantage.

Some prosthetic limbs today can weigh as much as 30 pounds, with much of the weight coming from actuators, which are often pneumatic or hydraulic; lighter-weight actuators could thus make life much easier for those who use prosthetics. Such fibers might also find uses in tiny biomedical devices, such as a medical robot that works by going into an artery and then being activated,” Anikeeva suggests. “We have activation times on the order of tens of milliseconds to seconds,” depending on the dimensions, she says.

To provide greater strength for lifting heavier loads, the fibers can be bundled together, much as muscle fibers are bundled in the body. The team successfully tested bundles of 100 fibers. Through the fiber drawing process, sensors could also be incorporated in the fibers to provide feedback on conditions they encounter, such as in a prosthetic limb. Örgüç says bundled muscle fibers with a closed-loop feedback mechanism could find applications in robotic systems where automated and precise control are required.

Kanik says that the possibilities for materials of this type are virtually limitless, because almost any combination of two materials with different thermal expansion rates could work, leaving a vast realm of possible combinations to explore. He adds that this new finding was like opening a new window, only to see “a bunch of other windows” waiting to be opened.

“The strength of this work is coming from its simplicity,” he says.

The team also included MIT graduate student Georgios Varnavides, postdoc Jinwoo Kim, and undergraduate students Thomas Benavides, Dani Gonzalez, and Timothy Akintlio. The work was supported by the National Institute of Neurological Disorders and Stroke and the National Science Foundation.

Speaking many languages

by Sabbi Lall | June 28, 2019May 24, 2023

Press Mentions

The mystery of people who speak dozens of languages

New Yorker

The Superlinguists

BBC

Ev Fedorenko studies the cognitive processes and brain regions underlying language, a signature cognitive skill that is uniquely and universally human. She investigates both people with linguistic impairments, and those that have exceptional language skills: hyperpolyglots, or people that are fluent in over a dozen languages. Indeed, she was recently interviewed for a BBC documentary about superlinguists as well as the New Yorker, for an article covering people with exceptional language skills.

When Fedorenko, an associate investigator at the McGovern Institute and assistant professor in the Department of Brain and Cognitive Sciences at MIT, came to the field, neuroscientists were still debating whether high-level cognitive skills such as language, are processed by multi-functional or dedicated brain regions. Using fMRI, Fedorenko and colleagues compared engagement of brain regions when individuals were engaged in linguistic vs. other high level cognitive tasks, such as arithmetic or music. Their data revealed a clear distinction between language and other cognitive processes, showing that our brains have dedicated language regions.

Here is my basic question. How do I get a thought from my mind into yours?

In the time since this key study, Fedorenko has continued to unpack language in the brain. How does the brain process the overarching rules and structure of language (syntax), as opposed to meanings of words? How do we construct complex meanings? What might underlie communicative difficulties in individuals diagnosed with autism? How does the aphasic brain recover language? Intriguingly, in contrast to individuals with linguistic difficulties, there are also individuals that stand out as being able to master many languages, so-called hyperpolyglots.

In 2013, she came across a young adult that had mastered over 30 languages, a prodigy in languages. To facilitate her analysis of processing of different languages Fedorenko has collected dozens of translations of Alice in Wonderland, for her ‘Alice in the language localizer Wonderland‘ project. She has already found that hyperpolyglots tend to show less activity in linguistic processing regions when reading in, or listening to, their native language, compared to carefully matched controls, perhaps indexing more efficient processing mechanisms. Fedorenko continues to study hyperpolyglots, along with other exciting new avenues of research. Stay tuned for upcoming advances in our understanding of the brain and language.

Bridging the gap between research and the classroom

by Stefanie Koperniak | June 27, 2019May 24, 2023

In a moment more reminiscent of a Comic-Con event than a typical MIT symposium, Shawn Robinson, senior research associate at the University of Wisconsin at Madison, helped kick off the first-ever MIT Science of Reading event dressed in full superhero attire as Doctor Dyslexia Dude — the star of a graphic novel series he co-created to engage and encourage young readers, rooted in his own experiences as a student with dyslexia.

The event, co-sponsored by the MIT Integrated Learning Initiative (MITili) and the McGovern Institute for Brain Research at MIT, took place earlier this month and brought together researchers, educators, administrators, parents, and students to explore how scientific research can better inform educational practices and policies — equipping teachers with scientifically-based strategies that may lead to better outcomes for students.

Professor John Gabrieli, MITili director, explained the great need to focus the collective efforts of educators and researchers on literacy.

“Reading is critical to all learning and all areas of knowledge. It is the first great educational experience for all children, and can shape a child’s first sense of self,” he said. “If reading is a challenge or a burden, it affects children’s social and emotional core.”

A great divide

Reading is also a particularly important area to address because so many American students struggle with this fundamental skill. More than six out of every 10 fourth graders in the United States are not proficient readers, and changes in reading scores for fourth and eighth graders have increased only slightly since 1992, according to the National Assessment of Education Progress.

Gabrieli explained that, just as with biomedical research, where there can be a “valley of death” between basic research and clinical application, the same seems to apply to education. Although there is substantial current research aiming to better understand why students might have difficulty reading in the ways they are currently taught, the research often does not necessarily shape the practices of teachers — or how the teachers themselves are trained to teach.

This divide between the research and practical applications in the classroom might stem from a variety of factors. One issue might be the inaccessibility of research publications that are available for free to all — as well as the general need for scientific findings to be communicated in a clear, accessible, engaging way that can lead to actual implementation. Another challenge is the stark difference in pacing between scientific research and classroom teaching. While research can take years to complete and publish, teachers have classrooms full of students — all with different strengths and challenges — who urgently need to learn in real time.

Natalie Wexler, author of “The Knowledge Gap,” described some of the obstacles to getting the findings of cognitive science integrated into the classroom as matters of “head, heart, and habit.” Teacher education programs tend to focus more on some of the outdated psychological models, like Piaget’s theory of cognitive development, and less on recent cognitive science research. Teachers also have to face the emotional realities of working with their students, and might be concerned that a new approach would cause students to feel bored or frustrated. In terms of habit, some new, evidence-based approaches may be, in a practical sense, difficult for teachers to incorporate into the classroom.

“Teaching is an incredibly complex activity,” noted Wexler.

From labs to classrooms

Throughout the day, speakers and panelists highlighted some key insights gained from literacy research, along with some of the implications these might have on education.

Mark Seidenberg, professor of psychology at the University of Wisconsin at Madison and author of “Language at the Speed of Sight,” discussed studies indicating the strong connection between spoken and printed language.

“Reading depends on speech,” said Seidenberg. “Writing systems are codes for expressing spoken language … Spoken language deficits have an enormous impact on children’s reading.”

The integration of speech and reading in the brain increases with reading skill. For skilled readers, the patterns of brain activity (measured using functional magnetic resonance imaging) while comprehending spoken and written language are very similar. Becoming literate affects the neural representation of speech, and knowledge of speech affects the representation of print — thus the two become deeply intertwined.

In addition, researchers have found that the language of books, even for young children, include words and expressions that are rarely encountered in speech to children. Therefore, reading aloud to children exposes them to a broader range of linguistic expressions — including more complex ones that are usually only taught much later. Thus reading to children can be especially important, as research indicates that better knowledge of spoken language facilitates learning to read.

Although behavior and performance on tests are often used as indicators of how well a student can read, neuroscience data can now provide additional information. Neuroimaging of children and young adults identifies brain regions that are critical for integrating speech and print, and can spot differences in the brain activity of a child who might be especially at-risk for reading difficulties. Brain imaging can also show how readers’ brains respond to certain reading and comprehension tasks, and how they adapt to different circumstances and challenges.

“Brain measures can be more sensitive than behavioral measures in identifying true risk,” said Ola Ozernov-Palchik, a postdoc at the McGovern Institute.

Ozernov-Palchik hopes to apply what her team is learning in their current studies to predict reading outcomes for other children, as well as continue to investigate individual differences in dyslexia and dyslexia-risk using behavior and neuroimaging methods.

Identifying certain differences early on can be tremendously helpful in providing much-needed early interventions and tailored solutions. Many speakers noted the problem with the current “wait-to-fail” model of noticing that a child has a difficult time reading in second or third grade, and then intervening. Research suggests that earlier intervention could help the child succeed much more than later intervention.

Speakers and panelists spoke about current efforts, including Reach Every Reader (a collaboration between MITili, the Harvard Graduate School of Education, and the Florida Center for Reading Research), that seek to provide support to students by bringing together education practitioners and scientists.

“We have a lot of information, but we have the challenge of how to enact it in the real world,” said Gabrieli, noting that he is optimistic about the potential for the additional conversations and collaborations that might grow out of the discussions of the Science of Reading event. “We know a lot of things can be better and will require partnerships, but there is a path forward.”

Mark Harnett receives a 2019 McKnight Scholar Award

Anne Trafton | June 24, 2019May 24, 2023

McGovern Institute investigator Mark Harnett is one of six young researchers selected to receive a prestigious 2019 McKnight Scholar Award. The award supports his research “studying how dendrites, the antenna-like input structures of neurons, contribute to computation in neural networks.”

Harnett examines the biophysical properties of single neurons, ultimately aiming to understand how these relate to the complex computations that underlie behavior. His lab was the first to examine the biophysical properties of human dendrites. The Harnett lab found that human neurons have distinct properties, including increased dendritic compartmentalization that could allow more complex computations within single neurons. His lab recently discovered that such dendritic computations are not rare, or confined to specific behaviors, but are a widespread and general feature of neuronal activity.

“As a young investigator, it is hard to prioritize so many exciting directions and ideas,” explains Harnett. “I really want to thank the McKnight Foundation, both for the support, but also for the hard work the award committee puts into carefully thinking about and giving feedback on proposals. It means a lot to get this type of endorsement from a seriously committed and distinguished committee, and their support gives even stronger impetus to pursue this research direction.”

The McKnight Foundation has supported neuroscience research since 1977, and provides three prominent awards, with the Scholar award aimed at supporting young scientists, and drawing applications from the strongest young neuroscience faculty across the US. William L. McKnight (1887-1979) was an early leader of the 3M Company and had a personal interest in memory and brain diseases. The McKnight Foundation was established with this focus in mind, and the Scholar Award provides $75,000 per year for three years to support cutting edge neuroscience research.

A chemical approach to imaging cells from the inside

by Karen Zusi | June 20, 2019June 8, 2023

Press Mentions

A new ‘DNA microscope’ peers deep inside living cells

STAT News

DNA Microscope Sees ‘Through the Eyes of the Cell’

The New York Times

A team of researchers at the McGovern Institute and Broad Institute of MIT and Harvard have developed a new technique for mapping cells. The approach, called DNA microscopy, shows how biomolecules such as DNA and RNA are organized in cells and tissues, revealing spatial and molecular information that is not easily accessible through other microscopy methods. DNA microscopy also does not require specialized equipment, enabling large numbers of samples to be processed simultaneously.

“DNA microscopy is an entirely new way of visualizing cells that captures both spatial and genetic information simultaneously from a single specimen,” says first author Joshua Weinstein, a postdoctoral associate at the Broad Institute. “It will allow us to see how genetically unique cells — those comprising the immune system, cancer, or the gut, for instance — interact with one another and give rise to complex multicellular life.”

The new technique is described in Cell. Aviv Regev, core institute member and director of the Klarman Cell Observatory at the Broad Institute and professor of biology at MIT, and Feng Zhang, core institute member of the Broad Institute, investigator at the McGovern Institute for Brain Research at MIT, and the James and Patricia Poitras Professor of Neuroscience at MIT, are co-authors. Regev and Zhang are also Howard Hughes Medical Institute Investigators.

The evolution of biological imaging

In recent decades, researchers have developed tools to collect molecular information from tissue samples, data that cannot be captured by either light or electron microscopes. However, attempts to couple this molecular information with spatial data — to see how it is naturally arranged in a sample — are often machinery-intensive, with limited scalability.

DNA microscopy takes a new approach to combining molecular information with spatial data, using DNA itself as a tool.

To visualize a tissue sample, researchers first add small synthetic DNA tags, which latch on to molecules of genetic material inside cells. The tags are then replicated, diffusing in “clouds” across cells and chemically reacting with each other, further combining and creating more unique DNA labels. The labeled biomolecules are collected, sequenced, and computationally decoded to reconstruct their relative positions and a physical image of the sample.

The interactions between these DNA tags enable researchers to calculate the locations of the different molecules — somewhat analogous to cell phone towers triangulating the locations of different cell phones in their vicinity. Because the process only requires standard lab tools, it is efficient and scalable.

In this study, the authors demonstrate the ability to molecularly map the locations of individual human cancer cells in a sample by tagging RNA molecules. DNA microscopy could be used to map any group of molecules that will interact with the synthetic DNA tags, including cellular genomes, RNA, or proteins with DNA-labeled antibodies, according to the team.

“DNA microscopy gives us microscopic information without a microscope-defined coordinate system,” says Weinstein. “We’ve used DNA in a way that’s mathematically similar to photons in light microscopy. This allows us to visualize biology as cells see it and not as the human eye does. We’re excited to use this tool in expanding our understanding of genetic and molecular complexity.”

Funding for this study was provided by the Simons Foundation, Klarman Cell Observatory, NIH (R01HG009276, 1R01- HG009761, 1R01- MH110049, and 1DP1-HL141201), New York Stem Cell Foundation, Simons Foundation, Paul G. Allen Family Foundation, Vallee Foundation, the Poitras Center for Affective Disorders Research at MIT, the Hock E. Tan and K. Lisa Yang Center for Autism Research at MIT, J. and P. Poitras, and R. Metcalfe.

The authors have applied for a patent on this technology.

McGovern neuroscientists develop a new model for autism

Anne Trafton | June 12, 2019May 24, 2023

Using the genome-editing system CRISPR, researchers at MIT and in China have engineered macaque monkeys to express a gene mutation linked to autism and other neurodevelopmental disorders in humans. These monkeys show some behavioral traits and brain connectivity patterns similar to those seen in humans with these conditions.

Mouse studies of autism and other neurodevelopmental disorders have yielded drug candidates that have been tested in clinical trials, but none of them have succeeded. Many pharmaceutical companies have given up on testing such drugs because of the poor track record so far.

The new type of model, however, could help scientists to develop better treatment options for some neurodevelopmental disorders, says Guoping Feng, who is the James W. and Patricia Poitras Professor of Neuroscience, a member of MIT’s McGovern Institute for Brain Research, and one of the senior authors of the study.

“Our goal is to generate a model to help us better understand the neural biological mechanism of autism, and ultimately to discover treatment options that will be much more translatable to humans,” says Feng, who is also an institute member of the Broad Institute of MIT and Harvard and a senior scientist in the Broad’s Stanley Center for Psychiatric Research.

“We urgently need new treatment options for autism spectrum disorder, and treatments developed in mice have so far been disappointing. While the mouse research remains very important, we believe that primate genetic models will help us to develop better medicines and possibly even gene therapies for some severe forms of autism,” says Robert Desimone, the director of MIT’s McGovern Institute for Brain Research, the Doris and Don Berkey Professor of Neuroscience, and an author of the paper.

Huihui Zhou of the Shenzhen Institutes of Advanced Technology, Andy Peng Xiang of Sun Yat-Sen University, and Shihua Yang of South China Agricultural University are also senior authors of the study, which appears in the June 12 online edition of Nature. The paper’s lead authors are former MIT postdoc Yang Zhou, MIT research scientist Jitendra Sharma, Broad Institute group leader Rogier Landman, and Qiong Ke of Sun Yat-Sen University. The research team also includes Mriganka Sur, the Paul and Lilah E. Newton Professor in the Department of Brain and Cognitive Sciences and a member of MIT’s Picower Institute for Learning and Memory.

Gene variants

Scientists have identified hundreds of genetic variants associated with autism spectrum disorder, many of which individually confer only a small degree of risk. In this study, the researchers focused on one gene with a strong association, known as SHANK3. In addition to its link with autism, mutations or deletions of SHANK3 can also cause a related rare disorder called Phelan-McDermid Syndrome, whose most common characteristics include intellectual disability, impaired speech and sleep, and repetitive behaviors. The majority of these individuals are also diagnosed with autism spectrum disorder, as many of the symptoms overlap.

The protein encoded by SHANK3 is found in synapses — the junctions between brain cells that allow them to communicate with each other. It is particularly active in a part of the brain called the striatum, which is involved in motor planning, motivation, and habitual behavior. Feng and his colleagues have previously studied mice with Shank3 mutations and found that they show some of the traits associated with autism, including avoidance of social interaction and obsessive, repetitive behavior.

Although mouse studies can provide a great deal of information on the molecular underpinnings of disease, there are drawbacks to using them to study neurodevelopmental disorders, Feng says. In particular, mice lack the highly developed prefrontal cortex that is the seat of many uniquely primate traits, such as making decisions, sustaining focused attention, and interpreting social cues, which are often affected by brain disorders.

The recent development of the CRISPR genome-editing technique offered a way to engineer gene variants into macaque monkeys, which has previously been very difficult to do. CRISPR consists of a DNA-cutting enzyme called Cas9 and a short RNA sequence that guides the enzyme to a specific area of the genome. It can be used to disrupt genes or to introduce new genetic sequences at a particular location.

Members of the research team based in China, where primate reproductive technology is much more advanced than in the United States, injected the CRISPR components into fertilized macaque eggs, producing embryos that carried the Shank3 mutation.

Researchers at MIT, where much of the data was analyzed, found that the macaques with Shank3 mutations showed behavioral patterns similar to those seen in humans with the mutated gene. They tended to wake up frequently during the night, and they showed repetitive behaviors. They also engaged in fewer social interactions than other macaques.

Magnetic resonance imaging (MRI) scans also revealed similar patterns to humans with autism spectrum disorder. Neurons showed reduced functional connectivity in the striatum as well as the thalamus, which relays sensory and motor signals and is also involved in sleep regulation. Meanwhile, connectivity was strengthened in other regions, including the sensory cortex.

Michael Platt, a professor of neuroscience and psychology at the University of Pennsylvania, says the macaque models should help to overcome some of the limitations of studying neurological disorders in mice, whose behavioral symptoms and underlying neurobiology are often different from those seen in humans.

“Because the macaque model shows a much more complete recapitulation of the human behavioral phenotype, I think we should stand a much greater chance of identifying the degree to which any particular therapy, whether it’s a drug or any other intervention, addresses the core symptoms,” says Platt, who was not involved in the study.

Drug development

Within the next year, the researchers hope to begin testing treatments that may affect autism-related symptoms. They also hope to identify biomarkers, such as the distinctive functional brain connectivity patterns seen in MRI scans, that would help them to evaluate whether drug treatments are having an effect.

A similar approach could also be useful for studying other types of neurological disorders caused by well-characterized genetic mutations, such as Rett Syndrome and Fragile X Syndrome. Fragile X is the most common inherited form of intellectual disability in the world, affecting about 1 in 4,000 males and 1 in 8,000 females. Rett Syndrome, which is more rare and almost exclusively affects girls, produces severe impairments in language and motor skills and can also cause seizures and breathing problems.

“Given the limitations of mouse models, patients really need this kind of advance to bring them hope,” Feng says. “We don’t know whether this will succeed in developing treatments, but we will see in the next few years how this can help us to translate some of the findings from the lab to the clinic.”

The research was funded, in part, by the Shenzhen Overseas Innovation Team Project, the Guangdong Innovative and Entrepreneurial Research Team Program, the National Key R&D Program of China, the External Cooperation Program of the Chinese Academy of Sciences, the Patrick J. McGovern Foundation, the National Natural Science Foundation of China, the Shenzhen Science, Technology Commission, the James and Patricia Poitras Center for Psychiatric Disorders Research at the McGovern Institute at MIT, the Stanley Center for Psychiatric Research at the Broad Institute of MIT and Harvard, and the Hock E. Tan and K. Lisa Yang Center for Autism Research at the McGovern Institute at MIT. The research facilities in China where the primate work was conducted are accredited by AAALAC International, a private, nonprofit organization that promotes the humane treatment of animals in science through voluntary accreditation and assessment programs.

How we tune out distractions

Anne Trafton | June 12, 2019May 24, 2023

Imagine trying to focus on a friend’s voice at a noisy party, or blocking out the phone conversation of the person sitting next to you on the bus while you try to read. Both of these tasks require your brain to somehow suppress the distracting signal so you can focus on your chosen input.

MIT neuroscientists have now identified a brain circuit that helps us to do just that. The circuit they identified, which is controlled by the prefrontal cortex, filters out unwanted background noise or other distracting sensory stimuli. When this circuit is engaged, the prefrontal cortex selectively suppresses sensory input as it flows into the thalamus, the site where most sensory information enters the brain.

“This is a fundamental operation that cleans up all the signals that come in, in a goal-directed way,” says Michael Halassa, an assistant professor of brain and cognitive sciences, a member of MIT’s McGovern Institute for Brain Research, and the senior author of the study.

The researchers are now exploring whether impairments of this circuit may be involved in the hypersensitivity to noise and other stimuli that is often seen in people with autism.

Miho Nakajima, an MIT postdoc, is the lead author of the paper, which appears in the June 12 issue of Neuron. Research scientist L. Ian Schmitt is also an author of the paper.

Shifting attention

Our brains are constantly bombarded with sensory information, and we are able to tune out much of it automatically, without even realizing it. Other distractions that are more intrusive, such as your seatmate’s phone conversation, require a conscious effort to suppress.

In a 2015 paper, Halassa and his colleagues explored how attention can be consciously shifted between different types of sensory input, by training mice to switch their focus between a visual and auditory cue. They found that during this task, mice suppress the competing sensory input, allowing them to focus on the cue that will earn them a reward.

This process appeared to originate in the prefrontal cortex (PFC), which is critical for complex cognitive behavior such as planning and decision-making. The researchers also found that a part of the thalamus that processes vision was inhibited when the animals were focusing on sound cues. However, there are no direct physical connections from the prefrontal cortex to the sensory thalamus, so it was unclear exactly how the PFC was exerting this control, Halassa says.

In the new study, the researchers again trained mice to switch their attention between visual and auditory stimuli, then mapped the brain connections that were involved. They first examined the outputs of the PFC that were essential for this task, by systematically inhibiting PFC projection terminals in every target. This allowed them to discover that the PFC connection to a brain region known as the striatum is necessary to suppress visual input when the animals are paying attention to the auditory cue.

Further mapping revealed that the striatum then sends input to a region called the globus pallidus, which is part of the basal ganglia. The basal ganglia then suppress activity in the part of the thalamus that processes visual information.

Using a similar experimental setup, the researchers also identified a parallel circuit that suppresses auditory input when animals pay attention to the visual cue. In that case, the circuit travels through parts of the striatum and thalamus that are associated with processing sound, rather than vision.

The findings offer some of the first evidence that the basal ganglia, which are known to be critical for planning movement, also play a role in controlling attention, Halassa says.

“What we realized here is that the connection between PFC and sensory processing at this level is mediated through the basal ganglia, and in that sense, the basal ganglia influence control of sensory processing,” he says. “We now have a very clear idea of how the basal ganglia can be involved in purely attentional processes that have nothing to do with motor preparation.”

Noise sensitivity

The researchers also found that the same circuits are employed not only for switching between different types of sensory input such as visual and auditory stimuli, but also for suppressing distracting input within the same sense — for example, blocking out background noise while focusing on one person’s voice.

The team also showed that when the animals are alerted that the task is going to be noisy, their performance actually improves, as they use this circuit to focus their attention.

“This study uses a dazzling array of techniques for neural circuit dissection to identify a distributed pathway, linking the prefrontal cortex to the basal ganglia to the thalamic reticular nucleus, that allows the mouse brain to enhance relevant sensory features and suppress distractors at opportune moments,” says Daniel Polley, an associate professor of otolaryngology at Harvard Medical School, who was not involved in the research. “By paring down the complexities of the sensory stimulus only to its core relevant features in the thalamus — before it reaches the cortex — our cortex can more efficiently encode just the essential features of the sensory world.”

Halassa’s lab is now doing similar experiments in mice that are genetically engineered to develop symptoms similar to those of people with autism. One common feature of autism spectrum disorder is hypersensitivity to noise, which could be caused by impairments of this brain circuit, Halassa says. He is now studying whether boosting the activity of this circuit might reduce sensitivity to noise.

“Controlling noise is something that patients with autism have trouble with all the time,” he says. “Now there are multiple nodes in the pathway that we can start looking at to try to understand this.”

The research was funded by the National Institutes of Mental Health, the National Institute of Neurological Disorders and Stroke, the Simons Foundation, the Alfred P. Sloan Foundation, the Esther A. and Joseph Klingenstein Fund, and the Human Frontier Science Program.

McGovern Institute postcard collection

by Julie Pryor | June 12, 2019December 18, 2023

A collection of 13 postcards arranged in columns. — The McGovern Institute postcard collection, 2023.

The McGovern Institute may be best known for its scientific breakthroughs, but a captivating series of brain-themed postcards developed by McGovern researchers and staff now reveals the institute’s artistic side.

What began in 2017 with a series of brain anatomy postcards inspired by the U.S. Works Projects Administration’s iconic national parks posters, has grown into a collection of twelve different prints, each featuring a unique fusion of neuroscience and art.

More information about each series in the McGovern Institute postcard collection, including the color-your-own mindfulness postcards, can be found below.

Mindfulness Postcard Series, 2023

In winter 2023, the institute released its mindfulness postcard series, a collection of four different neuroscience-themed illustrations that can be colored in with pencils, markers, or paint. The postcard series was inspired by research conducted in John Gabrieli’s lab, which found that practicing mindfulness reduced children’s stress levels and negative emotions during the pandemic. These findings contribute to a growing body of evidence that practicing mindfulness — focusing awareness on the present, typically through meditation, but also through coloring — can change patterns of brain activity associated with emotions and mental health.

Download and color your own postcards.

Genes

The McGovern Institute is at the cutting edge of applications based on CRISPR, a genome editing tool pioneered by McGovern Investigator Feng Zhang. Hidden within this DNA-themed postcard is a clam, virus, bacteriophage, snail, and the word CRISPR. Click the links to learn how these hidden elements relate to genetic engineering research at the McGovern Institute.

The McGovern Institute’s “mindfulness” postcard series includes this DNA-themed illustration containing five hidden design elements related to McGovern research. Image: Joseph Laney

Neurons

McGovern researchers probe the nanoscale and cellular processes that are critical to brain function, including the complex computations conducted in neurons, to the synapses and neurotransmitters that facilitate messaging between cells. Find the mouse, worm, and microscope — three critical elements related to cellular and molecular neuroscience research at the McGovern Institute — in the postcard below.

The McGovern Institute’s “mindfulness” postcard series includes this neuron-themed illustration containing three hidden design elements related to McGovern research. Image: Joseph Laney

Human Brain

Cognitive neuroscientists at the McGovern Institute examine the brain processes that come together to inform our thoughts and understanding of the world. Find the musical note, speech bubbles, and human face in this postcard and click on the links to learn more about how these hidden elements relate to brain research at the McGovern Institute.

The McGovern Institute’s “mindfulness” postcard series includes this brain-themed illustration containing three hidden design elements related to McGovern research. Image: Joseph Laney

Artificial Intelligence

McGovern researchers develop machine learning systems that mimic human processing of visual and auditory cues and construct algorithms to help us understand the complex computations made by the brain. Find the speech bubbles, DNA, and cochlea (spiral) in this postcard and click on the links to learn more about how these hidden elements relate to computational neuroscience research at the McGovern Institute.

The McGovern Institute’s “mindfulness” postcard series includes this AI-themed illustration containing three hidden design elements related to McGovern research. Image: Joseph Laney

Neuron Postcard Series, 2019

In 2019, the McGovern Institute released a second series of postcards based on the anatomy of a neuron. Each postcard includes text on the back side that describes McGovern research related to that specific part of the neuron. The descriptive text for each postcard is shown beloSynapse

Synapse

Signals flow through the nervous system from one neuron to the next across synapses.

Synapses are exquisitely organized molecular machines that control the transmission of information.

McGovern researchers are studying how disruptions in synapse function can lead to brain disorders like autism.

Image: Joseph Laney

Axon

The axon is the long, thin neural cable that carries electrical impulses called action potentials from the soma to synaptic terminals at downstream neurons.

Researchers at the McGovern Institute are developing and using tracers that label axons to reveal the elaborate circuit architecture of the brain.

Image: Joseph Laney

Soma

The soma, or cell body, is the control center of the neuron, where the nucleus is located.

It connects the dendrites to the axon, which sends information to other neurons.

At the McGovern Institute, neuroscientists are targeting the soma with proteins that can activate single neurons and map connections in the brain.

Image: Joseph Laney

Dendrites

Long branching neuronal processes called dendrites receive synaptic inputs from thousands of other neurons and carry those signals to the cell body.

McGovern neuroscientists have discovered that human dendrites have different electrical properties from those of other species, which may contribute to the enhanced computing power of the human brain.

Image: Joseph Laney

Brain Anatomy Postcard Series, 2017

The original brain anatomy-themed postcard series, developed in 2017, was inspired by the U.S. Works Projects Administration’s iconic national parks posters created in the 1930s and 1940s. Each postcard includes text on the back side that describes McGovern research related to that specific part of the neuron. The descriptive text for each postcard is shown below.

Sylvian Fissure

Illustration of explorer in cave labeled with temporal and parietal letters — The Sylvian fissure is a prominent groove on the right side of the brain that separates the frontal and parietal lobes from the temporal lobe. McGovern researchers are studying a region near the right Sylvian fissure, called the rTPJ, which is involved in thinking about what another person is thinking.

Hippocampus

Basal Ganglia

The arcuate fasciculus is a bundle of axons in the brain that connects Broca’s area, involved in speech production, and Wernicke’s area, involved in understanding language. McGovern researchers have found a correlation between the size of this structure and the risk of dyslexia in children.

Order and Share

To order your own McGovern brain postcards, contact our colleagues at the MIT Museum, where proceeds will support current and future exhibitions at the growing museum.

Please share a photo of yourself in your own lab (or natural habitat) with one of our cards on social media. Tell us what you’re studying and don’t forget to tag us @mcgovernmit using the hashtag #McGovernPostcards.

New gene-editing system precisely inserts large DNA sequences into cellular DNA

by Karen Zusi, Broad Institute | June 11, 2019May 24, 2023

A team led by researchers from Broad Institute of MIT and Harvard, and the McGovern Institute for Brain Research at MIT, has characterized and engineered a new gene-editing system that can precisely and efficiently insert large DNA sequences into a genome. The system, harnessed from cyanobacteria and called CRISPR-associated transposase (CAST), allows efficient introduction of DNA while reducing the potential error-prone steps in the process — adding key capabilities to gene-editing technology and addressing a long-sought goal for precision gene editing.

Precise insertion of DNA has the potential to treat a large swath of genetic diseases by integrating new DNA into the genome while disabling the disease-related sequence. To accomplish this in cells, researchers have typically used CRISPR enzymes to cut the genome at the site of the deleterious sequence, and then relied on the cell’s own repair machinery to stitch the old and new DNA elements together. However, this approach has many limitations.

Using Escherichia coli bacteria, the researchers have now demonstrated that CAST can be programmed to efficiently insert new DNA at a designated site, with minimal editing errors and without relying on the cell’s own repair machinery. The system holds potential for much more efficient gene insertion compared to previous technologies, according to the team.

The researchers are working to apply this editing platform in eukaryotic organisms, including plant and animal cells, for precision research and therapeutic applications.

The team molecularly characterized and harnessed CAST from two cyanobacteria, Scytonema hofmanni and Anabaena cylindrica, and additionally revealed a new way that some CRISPR systems perform in nature: not to protect bacteria from viruses, but to facilitate the spread of transposon DNA.

The work, appearing in Science, was led by first author Jonathan Strecker, a postdoctoral fellow at the Broad Institute; graduate student Alim Ladha at MIT; and senior author Feng Zhang, a core institute member at the Broad Institute, investigator at the McGovern Institute for Brain Research at MIT, the James and Patricia Poitras Professor of Neuroscience at MIT, and an associate professor at MIT, with joint appointments in the departments of Brain and Cognitive Sciences and Biological Engineering. Collaborators include Eugene Koonin at the National Institutes of Health.

A New Role for a CRISPR-Associated System

“One of the long-sought-after applications for molecular biology is the ability to introduce new DNA into the genome precisely, efficiently, and safely,” explains Zhang. “We have worked on many bacterial proteins in the past to harness them for editing in human cells, and we’re excited to further develop CAST and open up these new capabilities for manipulating the genome.”

To expand the gene-editing toolbox, the team turned to transposons. Transposons (sometimes called “jumping genes”) are DNA sequences with associated proteins — transposases — that allow the DNA to be cut-and-pasted into other places.

Most transposons appear to jump randomly throughout the cellular genome and out to viruses or plasmids that may also be inhabiting a cell. However, some transposon subtypes in cyanobacteria have been computationally associated with CRISPR systems, suggesting that these transposons may naturally be guided towards more-specific genetic targets. This theorized function would be a new role for CRISPR systems; most known CRISPR elements are instead part of a bacterial immune system, in which Cas enzymes and their guide RNA will target and destroy viruses or plasmids.

In this paper, the research team identified the mechanisms at work and determined that some CRISPR-associated transposases have hijacked an enzyme called Cas12k and its guide to insert DNA at specific targets, rather than just cutting the target for defensive purposes.

“We dove deeply into this system in cyanobacteria, began taking CAST apart to understand all of its components, and discovered this novel biological function,” says Strecker, a postdoctoral fellow in Zhang’s lab at the Broad Institute. “CRISPR-based tools are often DNA-cutting tools, and they’re very efficient at disrupting genes. In contrast, CAST is naturally set up to integrate genes. To our knowledge, it’s the first system of this kind that has been characterized and manipulated.”

Harnessing CAST for Genome Editing

Once all the elements and molecular requirements of the CAST system were laid bare, the team focused on programming CAST to insert DNA at desired sites in E. coli.

“We reconstituted the system in E. coli and co-opted this mechanism in a way that was useful,” says Strecker. “We reprogrammed the system to introduce new DNA, up to 10 kilobase pairs long, into specific locations in the genome.”

The team envisions basic research, agricultural, or therapeutic applications based on this platform, such as introducing new genes to replace DNA that has mutated in a harmful way — for example, in sickle cell disease. Systems developed with CAST could potentially be used to integrate a healthy version of a gene into a cell’s genome, disabling or overriding the DNA causing problems.

Alternatively, rather than inserting DNA with the purpose of fixing a deleterious version of a gene, CAST may be used to augment healthy cells with elements that are therapeutically beneficial, according to the team. For example, in immunotherapy, a researcher may want to introduce a “chimeric antigen receptor” (CAR) into a specific spot in the genome of a T cell — enabling the T cell to recognize and destroy cancer cells.

“For any situation where people want to insert DNA, CAST could be a much more attractive approach,” says Zhang. “This just underscores how diverse nature can be and how many unexpected features we have yet to find.”

Support for this study was provided in part by the Human Frontier Science Program, New York Stem Cell Foundation, Mathers Foundation, NIH (1R01-HG009761, 1R01-MH110049, and 1DP1-HL141201), Howard Hughes Medical Institute, Poitras Center for Psychiatric Disorders Research, J. and P. Poitras, and Hock E. Tan and K. Lisa Yang Center for Autism Research.

J.S. and F.Z. are co-inventors on US provisional patent application no. 62/780,658 filed by the Broad Institute, relating to CRISPR-associated transposases.

Expression plasmids are available from Addgene.