Satrajit Ghosh

Personalized Medicine

A fundamental problem in psychiatry is that there are no biological markers for diagnosing mental illness or for indicating how best to treat it. Treatment decisions are based entirely on symptoms, and doctors and their patients will typically try one treatment, then if it does not work, try another, and perhaps another. Satrajit Ghosh hopes to change this picture, and his research suggests that individual brain scans and speaking patterns can hold valuable information for guiding psychiatrists and patients. His research group develops novel analytic platforms that use such information to create robust, predictive models around human health. Current areas include depression, suicide, anxiety disorders, autism, Parkinson’s disease, and brain tumors.

Polina Anikeeva

Probing the Mind

Polina Anikeeva designs, synthesizes, and fabricates optoelectronic and magnetic devices to advance fundamental understanding and treatment of disorders of the nervous system. Anikeeva’s lab designs probes that are compatible with delicate neural tissue, but match the signaling complexity of neural circuits. In addition, her group develops magnetic nanoparticles for non-invasive neural stimulation. Most recently, Anikeeva is exploring the pathways connecting the brain to other body organ systems with the goal of advancing therapies and predictive diagnostics to achieve healthy minds in healthy bodies.

Ed Boyden

Engineering Matter and Mind

Ed Boyden develops new tools for probing, analyzing, and engineering brain circuits. He uses a range of approaches, including synthetic biology, nanotechnology, chemistry, electrical engineering, and optics to develop tools capable of revealing fundamental mechanisms underlying complex brain processes.

Boyden may be best known for pioneering the development of optogenetics, a powerful method that enables neuronal activity to be controlled with light. He also led the team that invented expansion microscopy, in which a specimen is embedded in a gel that swells as it absorbs water, thereby expanding nanoscale features to a size where they can be seen using conventional microscopes. He is now seeking to systematically integrate these technologies to create detailed maps and models of brain circuitry.

Virtual Tour of Boyden Lab

New sensors track dopamine in the brain for more than a year

Dopamine, a signaling molecule used throughout the brain, plays a major role in regulating our mood, as well as controlling movement. Many disorders, including Parkinson’s disease, depression, and schizophrenia, are linked to dopamine deficiencies.

MIT neuroscientists have now devised a way to measure dopamine in the brain for more than a year, which they believe will help them to learn much more about its role in both healthy and diseased brains.

“Despite all that is known about dopamine as a crucial signaling molecule in the brain, implicated in neurologic and neuropsychiatric conditions as well as our ability to learn, it has been impossible to monitor changes in the online release of dopamine over time periods long enough to relate these to clinical conditions,” says Ann Graybiel, an MIT Institute Professor, a member of MIT’s McGovern Institute for Brain Research, and one of the senior authors of the study.

Michael Cima, the David H. Koch Professor of Engineering in the Department of Materials Science and Engineering and a member of MIT’s Koch Institute for Integrative Cancer Research, and Rober Langer, the David H. Koch Institute Professor and a member of the Koch Institute, are also senior authors of the study. MIT postdoc Helen Schwerdt is the lead author of the paper, which appears in the Sept. 12 issue of Communications Biology.

Long-term sensing

Dopamine is one of many neurotransmitters that neurons in the brain use to communicate with each other. Traditional systems for measuring dopamine — carbon electrodes with a shaft diameter of about 100 microns — can only be used reliably for about a day because they produce scar tissue that interferes with the electrodes’ ability to interact with dopamine.

In 2015, the MIT team demonstrated that tiny microfabricated sensors could be used to measure dopamine levels in a part of the brain called the striatum, which contains dopamine-producing cells that are critical for habit formation and reward-reinforced learning.

Because these probes are so small (about 10 microns in diameter), the researchers could implant up to 16 of them to measure dopamine levels in different parts of the striatum. In the new study, the researchers wanted to test whether they could use these sensors for long-term dopamine tracking.

“Our fundamental goal from the very beginning was to make the sensors work over a long period of time and produce accurate readings from day to day,” Schwerdt says. “This is necessary if you want to understand how these signals mediate specific diseases or conditions.”

To develop a sensor that can be accurate over long periods of time, the researchers had to make sure that it would not provoke an immune reaction, to avoid the scar tissue that interferes with the accuracy of the readings.

The MIT team found that their tiny sensors were nearly invisible to the immune system, even over extended periods of time. After the sensors were implanted, populations of microglia (immune cells that respond to short-term damage), and astrocytes, which respond over longer periods, were the same as those in brain tissue that did not have the probes inserted.

In this study, the researchers implanted three to five sensors per animal, about 5 millimeters deep, in the striatum. They took readings every few weeks, after stimulating dopamine release from the brainstem, which travels to the striatum. They found that the measurements remained consistent for up to 393 days.

“This is the first time that anyone’s shown that these sensors work for more than a few months. That gives us a lot of confidence that these kinds of sensors might be feasible for human use someday,” Schwerdt says.

Paul Glimcher, a professor of physiology and neuroscience at New York University, says the new sensors should enable more researchers to perform long-term studies of dopamine, which is essential for studying phenomena such as learning, which occurs over long time periods.

“This is a really solid engineering accomplishment that moves the field forward,” says Glimcher, who was not involved in the research. “This dramatically improves the technology in a way that makes it accessible to a lot of labs.”

Monitoring Parkinson’s

If developed for use in humans, these sensors could be useful for monitoring Parkinson’s patients who receive deep brain stimulation, the researchers say. This treatment involves implanting an electrode that delivers electrical impulses to a structure deep within the brain. Using a sensor to monitor dopamine levels could help doctors deliver the stimulation more selectively, only when it is needed.

The researchers are now looking into adapting the sensors to measure other neurotransmitters in the brain, and to measure electrical signals, which can also be disrupted in Parkinson’s and other diseases.

“Understanding those relationships between chemical and electrical activity will be really important to understanding all of the issues that you see in Parkinson’s,” Schwerdt says.

The research was funded by the National Institute of Biomedical Imaging and Bioengineering, the National Institute of Neurological Disorders and Stroke, the Army Research Office, the Saks Kavanaugh Foundation, the Nancy Lurie Marks Family Foundation, and Dr. Tenley Albright.

Ultrathin needle can deliver drugs directly to the brain

MIT researchers have devised a miniaturized system that can deliver tiny quantities of medicine to brain regions as small as 1 cubic millimeter. This type of targeted dosing could make it possible to treat diseases that affect very specific brain circuits, without interfering with the normal function of the rest of the brain, the researchers say.

Using this device, which consists of several tubes contained within a needle about as thin as a human hair, the researchers can deliver one or more drugs deep within the brain, with very precise control over how much drug is given and where it goes. In a study of rats, they found that they could deliver targeted doses of a drug that affects the animals’ motor function.

“We can infuse very small amounts of multiple drugs compared to what we can do intravenously or orally, and also manipulate behavioral changes through drug infusion,” says Canan Dagdeviren, the LG Electronics Career Development Assistant Professor of Media Arts and Sciences and the lead author of the paper, which appears in the Jan. 24 issue of Science Translational Medicine.

“We believe this tiny microfabricated device could have tremendous impact in understanding brain diseases, as well as providing new ways of delivering biopharmaceuticals and performing biosensing in the brain,” says Robert Langer, the David H. Koch Institute Professor at MIT and one of the paper’s senior authors.

Michael Cima, the David H. Koch Professor of Engineering in the Department of Materials Science and Engineering and a member of MIT’s Koch Institute for Integrative Cancer Research, is also a senior author of the paper.

Targeted action

Drugs used to treat brain disorders often interact with brain chemicals called neurotransmitters or the cell receptors that interact with neurotransmitters. Examples include l-dopa, a dopamine precursor used to treat Parkinson’s disease, and Prozac, used to boost serotonin levels in patients with depression. However, these drugs can have side effects because they act throughout the brain.

“One of the problems with central nervous system drugs is that they’re not specific, and if you’re taking them orally they go everywhere. The only way we can limit the exposure is to just deliver to a cubic millimeter of the brain, and in order to do that, you have to have extremely small cannulas,” Cima says.

The MIT team set out to develop a miniaturized cannula (a thin tube used to deliver medicine) that could target very small areas. Using microfabrication techniques, the researchers constructed tubes with diameters of about 30 micrometers and lengths up to 10 centimeters. These tubes are contained within a stainless steel needle with a diameter of about 150 microns. “The device is very stable and robust, and you can place it anywhere that you are interested,” Dagdeviren says.

The researchers connected the cannulas to small pumps that can be implanted under the skin. Using these pumps, the researchers showed that they could deliver tiny doses (hundreds of nanoliters) into the brains of rats. In one experiment, they delivered a drug called muscimol to a brain region called the substantia nigra, which is located deep within the brain and helps to control movement.

Previous studies have shown that muscimol induces symptoms similar to those seen in Parkinson’s disease. The researchers were able to generate those effects, which include stimulating the rats to continually turn in a clockwise direction, using their miniaturized delivery needle. They also showed that they could halt the Parkinsonian behavior by delivering a dose of saline through a different channel, to wash the drug away.

“Since the device can be customizable, in the future we can have different channels for different chemicals, or for light, to target tumors or neurological disorders such as Parkinson’s disease or Alzheimer’s,” Dagdeviren says.

This device could also make it easier to deliver potential new treatments for behavioral neurological disorders such as addiction or obsessive compulsive disorder, which may be caused by specific disruptions in how different parts of the brain communicate with each other.

“Even if scientists and clinicians can identify a therapeutic molecule to treat neural disorders, there remains the formidable problem of how to delivery the therapy to the right cells — those most affected in the disorder. Because the brain is so structurally complex, new accurate ways to deliver drugs or related therapeutic agents locally are urgently needed,” says Ann Graybiel, an MIT Institute Professor and a member of MIT’s McGovern Institute for Brain Research, who is also an author of the paper.

Measuring drug response

The researchers also showed that they could incorporate an electrode into the tip of the cannula, which can be used to monitor how neurons’ electrical activity changes after drug treatment. They are now working on adapting the device so it can also be used to measure chemical or mechanical changes that occur in the brain following drug treatment.

The cannulas can be fabricated in nearly any length or thickness, making it possible to adapt them for use in brains of different sizes, including the human brain, the researchers say.

“This study provides proof-of-concept experiments, in large animal models, that a small, miniaturized device can be safely implanted in the brain and provide miniaturized control of the electrical activity and function of single neurons or small groups of neurons. The impact of this could be significant in focal diseases of the brain, such as Parkinson’s disease,” says Antonio Chiocca, neurosurgeon-in-chief and chairman of the Department of Neurosurgery at Brigham and Women’s Hospital, who was not involved in the research.

The research was funded by the National Institutes of Health and the National Institute of Biomedical Imaging and Bioengineering.

Robotic system monitors specific neurons

Recording electrical signals from inside a neuron in the living brain can reveal a great deal of information about that neuron’s function and how it coordinates with other cells in the brain. However, performing this kind of recording is extremely difficult, so only a handful of neuroscience labs around the world do it.

To make this technique more widely available, MIT engineers have now devised a way to automate the process, using a computer algorithm that analyzes microscope images and guides a robotic arm to the target cell.

This technology could allow more scientists to study single neurons and learn how they interact with other cells to enable cognition, sensory perception, and other brain functions. Researchers could also use it to learn more about how neural circuits are affected by brain disorders.

“Knowing how neurons communicate is fundamental to basic and clinical neuroscience. Our hope is this technology will allow you to look at what’s happening inside a cell, in terms of neural computation, or in a disease state,” says Ed Boyden, an associate professor of biological engineering and brain and cognitive sciences at MIT, and a member of MIT’s Media Lab and McGovern Institute for Brain Research.

Boyden is the senior author of the paper, which appears in the Aug. 30 issue of Neuron. The paper’s lead author is MIT graduate student Ho-Jun Suk.

Precision guidance

For more than 30 years, neuroscientists have been using a technique known as patch clamping to record the electrical activity of cells. This method, which involves bringing a tiny, hollow glass pipette in contact with the cell membrane of a neuron, then opening up a small pore in the membrane, usually takes a graduate student or postdoc several months to learn. Learning to perform this on neurons in the living mammalian brain is even more difficult.

There are two types of patch clamping: a “blind” (not image-guided) method, which is limited because researchers cannot see where the cells are and can only record from whatever cell the pipette encounters first, and an image-guided version that allows a specific cell to be targeted.

Five years ago, Boyden and colleagues at MIT and Georgia Tech, including co-author Craig Forest, devised a way to automate the blind version of patch clamping. They created a computer algorithm that could guide the pipette to a cell based on measurements of a property called electrical impedance — which reflects how difficult it is for electricity to flow out of the pipette. If there are no cells around, electricity flows and impedance is low. When the tip hits a cell, electricity can’t flow as well and impedance goes up.

Once the pipette detects a cell, it can stop moving instantly, preventing it from poking through the membrane. A vacuum pump then applies suction to form a seal with the cell’s membrane. Then, the electrode can break through the membrane to record the cell’s internal electrical activity.

The researchers achieved very high accuracy using this technique, but it still could not be used to target a specific cell. For most studies, neuroscientists have a particular cell type they would like to learn about, Boyden says.

“It might be a cell that is compromised in autism, or is altered in schizophrenia, or a cell that is active when a memory is stored. That’s the cell that you want to know about,” he says. “You don’t want to patch a thousand cells until you find the one that is interesting.”

To enable this kind of precise targeting, the researchers set out to automate image-guided patch clamping. This technique is difficult to perform manually because, although the scientist can see the target neuron and the pipette through a microscope, he or she must compensate for the fact that nearby cells will move as the pipette enters the brain.

“It’s almost like trying to hit a moving target inside the brain, which is a delicate tissue,” Suk says. “For machines it’s easier because they can keep track of where the cell is, they can automatically move the focus of the microscope, and they can automatically move the pipette.”

By combining several imaging processing techniques, the researchers came up with an algorithm that guides the pipette to within about 25 microns of the target cell. At that point, the system begins to rely on a combination of imagery and impedance, which is more accurate at detecting contact between the pipette and the target cell than either signal alone.

The researchers imaged the cells with two-photon microscopy, a commonly used technique that uses a pulsed laser to send infrared light into the brain, lighting up cells that have been engineered to express a fluorescent protein.

Using this automated approach, the researchers were able to successfully target and record from two types of cells — a class of interneurons, which relay messages between other neurons, and a set of excitatory neurons known as pyramidal cells. They achieved a success rate of about 20 percent, which is comparable to the performance of highly trained scientists performing the process manually.

Unraveling circuits

This technology paves the way for in-depth studies of the behavior of specific neurons, which could shed light on both their normal functions and how they go awry in diseases such as Alzheimer’s or schizophrenia. For example, the interneurons that the researchers studied in this paper have been previously linked with Alzheimer’s. In a recent study of mice, led by Li-Huei Tsai, director of MIT’s Picower Institute for Learning and Memory, and conducted in collaboration with Boyden, it was reported that inducing a specific frequency of brain wave oscillation in interneurons in the hippocampus could help to clear amyloid plaques similar to those found in Alzheimer’s patients.

“You really would love to know what’s happening in those cells,” Boyden says. “Are they signaling to specific downstream cells, which then contribute to the therapeutic result? The brain is a circuit, and to understand how a circuit works, you have to be able to monitor the components of the circuit while they are in action.”

This technique could also enable studies of fundamental questions in neuroscience, such as how individual neurons interact with each other as the brain makes a decision or recalls a memory.

Bernardo Sabatini, a professor of neurobiology at Harvard Medical School, says he is interested in adapting this technique to use in his lab, where students spend a great deal of time recording electrical activity from neurons growing in a lab dish.

“It’s silly to have amazingly intelligent students doing tedious tasks that could be done by robots,” says Sabatini, who was not involved in this study. “I would be happy to have robots do more of the experimentation so we can focus on the design and interpretation of the experiments.”

To help other labs adopt the new technology, the researchers plan to put the details of their approach on their web site, autopatcher.org.

Other co-authors include Ingrid van Welie, Suhasa Kodandaramaiah, and Brian Allen. The research was funded by Jeremy and Joyce Wertheimer, the National Institutes of Health (including the NIH Single Cell Initiative and the NIH Director’s Pioneer Award), the HHMI-Simons Faculty Scholars Program, and the New York Stem Cell Foundation-Robertson Award.

New way to turn genes on

Using a gene-editing system originally developed to delete specific genes, MIT researchers have now shown that they can reliably turn on any gene of their choosing in living cells.

This new application for the CRISPR/Cas9 gene-editing system should allow scientists to more easily determine the function of individual genes, according to Feng Zhang, the W.M. Keck Career Development Professor in Biomedical Engineering in MIT’s Departments of Brain and Cognitive Sciences and Biological Engineering, and a member of the Broad Institute and MIT’s McGovern Institute for Brain Research.

This approach also enables rapid functional screens of the entire genome, allowing scientists to identify genes involved in particular diseases. In a study published in the Dec. 10 online edition of Nature, Zhang and colleagues identified several genes that help melanoma cells become resistant to a cancer drug.

Silvana Konermann, a graduate student in Zhang’s lab, and Mark Brigham, a McGovern Institute postdoc, are the paper’s lead authors.

A new function for CRISPR

The CRISPR system relies on cellular machinery that bacteria use to defend themselves from viral infection. Researchers have previously harnessed this cellular system to create gene-editing complexes that include a DNA-cutting enzyme called Cas9 bound to a short RNA guide strand that is programmed to bind to a specific genome sequence, telling Cas9 where to make its cut.

In the past two years, scientists have developed Cas9 as a tool for turning genes off or replacing them with a different version. In the new study, Zhang and colleagues engineered the Cas9 system to turn genes on, rather than knock them out. Scientists have tried to do this before using proteins that are individually engineered to target DNA at specific sites. However, these proteins are  difficult to work with. “If you use the older generation of tools, getting the technology to do what you actually want is a project on its own,” Konermann says. “It takes a lot of time and is also quite expensive.”

There have also been attempts to use CRISPR to turn on genes by inactivating the part of the Cas9 enzyme that cuts DNA and linking Cas9 to pieces of proteins called activation domains. These domains recruit the cellular machinery necessary to begin reading copying RNA from DNA, a process known as transcription.

However, these efforts have been unable to consistently turn on gene transcription. Zhang and his colleagues, Osamu Nureki and Hiroshi Nishimasu at the University of Tokyo, decided to overhaul the CRISPR-Cas9 system based on an analysis they published earlier this year of the structure formed when Cas9 binds to the guide RNA and its target DNA. “Based on knowing its 3-D shape, we can think about how to rationally improve the system,” Zhang says.

In previous efforts, scientists had tried to attach the activation domains to either end of the Cas9 protein, with limited success. From their structural studies, the MIT team realized that two small loops of the RNA guide poke out from the Cas9 complex and could be better points of attachment because they allow the activation domains to have more flexibility in recruiting transcription machinery.

Using their revamped system, the researchers activated about a dozen genes that had proven difficult or impossible to turn on using the previous generation of Cas9 activators. Each gene showed at least a twofold boost in transcription, and for many genes, the researchers found multiple orders of magnitude increase in activation.

Genome-scale activation screening

Once the researchers had shown that the system was effective at activating genes, they created a library of 70,290 guide RNAs targeting all of the more than 20,000 genes in the human genome.

They screened this library to identify genes that confer resistance to a melanoma drug called PLX-4720. Drugs of this type work well in patients whose melanoma cells have a mutation in the BRAF gene, but cancer cells that survive the treatment can grow into new tumors, allowing the cancer to recur.

To discover the genes that help cells become resistant, the researchers delivered CRISPR components to a large population of melanoma cells grown in the lab, with each cell receiving a different guide RNA targeting a different gene. After treating the cells with PLX-4720, they identified several genes that helped the cells to survive — some previously known to be involved in drug resistance, as well as several novel targets.
Studies like this could help researchers discover new cancer drugs that prevent tumors from becoming resistant.

“You could start with a drug that targets the mutated BRAF along with combination therapy that targets genes that allow the cell to survive. If you target both of them at the same time, you could likely prevent the cells from developing resistance mechanisms that enable further growth despite drug treatment,” Konermann says.

Scientists have tried to do large-scale screens like this by delivering single genes carried by viruses, but that does not work with all genes.

“This new technique could allow you to sample a larger spectrum of genes that might be playing a role,” says Levi Garraway, an associate professor of medicine at Dana-Farber Cancer Institute who was not involved in the research. “This is really a technology development paper, but the tantalizing results from the drug resistance screen speak to the rich biological possibilities of this approach.”

Zhang’s lab also plans to use this technique to screen for genes that, when activated, could correct the effects of autism or neurodegenerative diseases such as Alzheimer’s. He also plans to make the necessary reagents available to academic labs that want to use them, through the Addgene repository.

The research was funded by the National Institute of Mental Health; the National Institute of Neurological Disorders and Stroke; the Keck, Searle Scholars, Klingenstein, Vallee, and Simons foundations; and Bob Metcalfe.

Genome Editing with CRISPR – Cas9

This animation depicts the CRISPR-Cas9 method for genome editing – a powerful new technology with many applications in biomedical research, including the potential to treat human genetic disease. Feng Zhang, a leader in the development of this technology, is a faculty member at MIT, an investigator at the McGovern Institute for Brain Research, and a core member of the Broad Institute.