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Queen of hearts

Anne Trafton |

Amphibians and humans differ in many ways, but Laurie Boyer, a professor of biology and biological engineering at MIT, is particularly interested in one of those differences. Certain types of amphibians and fish can regenerate and heal their hearts after an injury. In contrast, human adults who have experienced trauma to the heart, such as in the case of a heart attack or exposure to certain medications, are unable to repair the damage. Often, the injured heart ends up with scar tissue that can lead to heart failure.

Recent research in this area now indicates that mice, and even humans, have some capacity for cardiac repair for a short period after birth. But after even just a few days of age, that ability starts to shut off. “The heart has very limited ability to repair itself in response to injury, disease, or aging,” Boyer says.

Alexander Auld, a postdoc in the Boyer Lab, studies the key cellular mechanisms that lead heart cells to mature and lose regenerative potential. Specifically, he’s interested in understanding how cardiomyocytes, the heart cells responsible for pumping blood, develop an ability to contract and relax repeatedly. Auld tests the function of proteins that serve as signals to assemble the cardiac muscle structure after birth. The assembly of these structures coincides with the loss of regenerative ability.

“I’m trying to piece together: What are the different mechanisms that push cardiomyocytes to assemble their contractile apparatus and to stop dividing?” Auld says. “Solving this puzzle may have potential to stimulate regeneration in the adult heart muscle.”

“The holy grail of regenerative biology would be to stimulate your own heart cells to replenish themselves,” says Boyer, who joined the MIT faculty in 2007. “Before this approach is possible, we need to achieve a deep understanding of the fundamental processes that drive heart development.”

Boyer’s lab studies how many different signals and genes interact to affect heart development. The work will enable a better understanding of how faulty regulation can lead to disease, and may also enable new therapies for people suffering from a variety of heart conditions.

Critical connections

Recently, Boyer’s lab has been studying heart development in people with Trisomy 21, or Down syndrome. Every year, 6,000 babies born in the United States have Down syndrome. Around half have heart defects. The most common heart defect in babies with Down syndrome is a hole in the heart’s center, called an atrioventricular septal defect. It is often repaired with surgery, but the repair can cause scar tissue and cardiovascular complications.

Somatic cells are those that compose an organism’s body; they differ from sex cells, which are used for reproduction. Most people have 46 chromosomes, arranged in 23 pairs, in their body’s somatic cells. In 95 percent of cases, Down syndrome results when a person has three copies of chromosome 21 instead of two –– a total of 47 chromosomes per cell. It’s an example of aneuploidy, when a cell has an abnormal number of chromosomes. Cellular attempts to adapt to the extra chromosome can cause stress on the body’s cells, including those of the heart.

MIT’s Alana Down Syndrome Center (ADSC) brings together biologists, neuroscientists, engineers, and other experts to increase knowledge about Down syndrome. ADSC launched in early 2019, led by Angelika Amon, professor of biology and a member of the Koch Institute for Integrative Cancer Research, along with co-director Li-Huei Tsai, Picower Professor and director of the Picower Institute for Learning and Memory. Amon died at age 53 in 2020 after a battle with ovarian cancer. At MIT, Amon had studied the effects of aneuploidy on cells.

“In my many wonderful scientific and personal discussions with Angelika, who was a beacon of inspiration to me, it became clear that studying Trisomy 21 in the context of heart development could ultimately improve the lives of these individuals,” Boyer says.

Change of heart

To conduct their research, Boyer’s group uses human induced pluripotent cells (hiPSCs), obtained through somatic cell reprogramming. The revolutionary technique was developed by Sir John B. Gurdon and Shinya Yamanaka, who in 2012 won the Nobel Prize in Physiology or Medicine for their work. Reprogramming works by converting specialized, mature somatic cells with one particular function into specialized, mature, cells with a different function.

Boyer’s lab uses hiPSCs from human adults with Down syndrome and converts them into cardiomyocytes through somatic cell reprogramming. Then, they compare those cardiomyocytes with reprogrammed cells from individuals who do not have Down syndrome. This work helps them deduce why the extra chromosome in people with Down syndrome may cause congenital heart defects.

“We can now begin to pinpoint the faulty signals and genes in Trisomy 21 cardiac cells that affect heart development,” Boyer says. “And with that same idea, we can also discover how we might actually be able to ameliorate or fix these defects.”

With this technique, the team can track how aspects of a specific patient’s cell development correlate with their clinical presentation. The ability to analyze patient-specific cells also has implications for personalized medicine, Boyer says. For instance, a patient’s skin or blood cells –– which are more easily obtained –– could be converted into a highly specialized mature cell, like a cardiac muscle cell, and tested for its response to drugs that could possibly cause damage to the heart before they reach the clinic. This process can also be used to screen for new therapies that can improve the outcome for heart failure patients.

Boyer presented the group’s research on Down syndrome at the New England Down Syndrome Symposium, co-organized in November 2020 by MIT, ADSC, Massachusetts Down Syndrome Congress, and LuMind IDSC Foundation.

Heart of the operation

Boyer’s lab employs students at the undergraduate, graduate, and postdoc levels from engineering, life sciences, and computer sciences –– each of whom, Boyer says, brings unique expertise and value to the team.

“It’s important for me to have a lab where everyone feels welcome, and that they feel that they can contribute to these fundamental discoveries,” Boyer says.

The Boyer Lab often works with scholars across disciplines at MIT. “It’s really great,” Auld says. “You can investigate a problem using multiple tools and perspectives.”

One project, in partnership with George Barbastathis, a professor in mechanical engineering, uses image-based machine learning to understand structural differences within cardiomyocytes when the proteins that signal cells to develop have been manipulated. Auld generates high-resolution images that the machine learning algorithms can analyze.

Another project, in collaboration with Ed Boyden, a professor in the Department of Biological Engineering as well as the McGovern Institute for Brain Research, involves the development of new technologies that allow high-throughput imaging of cardiac cells. The cross-pollination across departments and areas of expertise at MIT, Boyer says, often has her feeling like “a kid in a candy shop.”

“That our work could ultimately impact human health is very fulfilling for me, and the ability to use our scientific discoveries to improve medical outcomes is an important direction of my lab,” Boyer says. “Given the enormous talent at MIT and the excitement and willingness of everyone here to work together, we have an unprecedented opportunity to solve important problems that can make a difference in people’s lives.”

Exploring the unknown

by Jennifer Michalowski |

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

 

McGovern Investigator Ed Boyden.

McGovern Investigator Ed Boyden says his lab’s vision is clear.

“We want to understand how our brains take our sensory inputs, generate emotions and memories and decisions, and ultimately result in motor outputs. We want to be able to see the building blocks of life, and how they go into disarray in brain diseases. We want to be able to control the signals of the brain, so we can repair it,” Boyden says.

To get there, he and his team are exploring the brain’s complexity at every scale, from the function and architecture of its neural networks to the molecules that work together to process information.

And when they don’t have the tools to take them where they want to go, they create them, opening new frontiers for neuroscientists everywhere.

Open to discovery

Boyden’s team is highly interdisciplinary and collaborative. Its specialty, Boyden says, is problem solving. Creativity, adaptability, and deep curiosity are essential, because while many of neuroscience’s challenges are clear, the best way to address them is not. In its search for answers, Boyden’s lab is betting that an important path to discovery begins with finding new ways to explore.

They’ve made that possible with an innovative imaging approach called expansion microscopy (ExM). ExM physically enlarges biological samples so that minute details become visible under a standard laboratory microscope, enabling researchers everywhere to peer into spaces that once went unseen (see video below).

To use the technique, researchers permeate a biological sample with an absorbent gel, then add water, causing the components of the gel to spread apart and the tissue to expand.

This year, postdoctoral researcher Ruixuan Gao and graduate student Chih-Chieh (Jay) Yu made the method more precise, with a new material that anchors a sample’s molecules within a crystal-like lattice, better preserving structure during expansion than the irregular mesh-like composition of the original gel. The advance is an important step toward being able to image expanded samples with single-molecule precision, Gao says.

A revealing look

By opening space within the brain, ExM has let Boyden’s team venture into those spaces in new ways.

Areas of research and brain disorders page
Graduate student Oz Wassie examines expanded brain tissue. Photo: Justin Knight

In work led by Deblina Sarkar (who is now an assistant professor at MIT’s Media Lab), Jinyoung Kang, and Asmamaw (Oz) Wassie, they showed that they can pull apart proteins in densely packed regions like synapses so that it is easier to introduce fluorescent labels, illuminating proteins that were once too crowded to see. The process, called expansion revealing, has made it possible to visualize in intact brain tissue important structures such as ion channels that help transmit signals and fine-scale amyloid clusters in Alzheimer’s model mice.

Another reaction the lab has adapted to the expanded-brain context is RNA sequencing—an important tool for understanding cellular diversity. “Typically, the first thing you do in a sequencing project is you grind up the tissue, and you lose the spatial dimension,” explains Daniel Goodwin, a graduate student in Boyden’s lab. But when sequencing reactions are performed inside cells instead, new information is revealed.

Confocal image showing targeted ExSeq of a 34-panel gene set across a slice of mouse hippocampus. Green indicates YFP, magenta indicates reads identified with ExSeq, and white indicates reads localized within YFP-expressing cells. Image courtesy of the researchers.

Goodwin and fellow Boyden lab members Shahar Alon, Anubhav Sinha, Oz Wassie, and Fei Chen developed expansion sequencing (ExSeq), which copies RNA molecules, nucleotide by nucleotide, directly inside expanded tissue, using fluorescent labels that spell out the molecules’ codes just as they would in a sequencer.

The approach shows researchers which genes are turned on in which cells, as well as where those RNA molecules are—revealing, for example, which genes are active in the neuronal projections that carry out the brain’s communications. A next step, Sinha says, is to integrate expansion sequencing with other technologies to obtain even deeper insights.

That might include combining information revealed with ExSeq with a topographical map of the same cells’ genomes, using a method Boyden’s lab and collaborators Chen (who is now a core member of the Broad Institute) and Jason Buenrostro at Harvard have developed for DNA sequencing. That information is important because the shape of the genome varies across cells and circumstances, and that has consequences for how the genetic code is used.

Using similar techniques to those that make ExSeq possible, graduate students Andrew Payne, Zachary Chiang, and Paul Reginato figured out how to recreate the steps of commercial DNA sequencing within the genome’s natural environment.

By pinpointing the location of specific DNA sequences inside cells, the new method, called in situ genome sequencing (IGS) allows researchers to watch a genome reorganize itself in a developing embryo.

They haven’t yet performed this analysis inside expanded tissue, but Payne says integrating in situ genome sequencing (IGS) with ExM should open up new opportunities to study genomes’ structure.

Signaling clusters

Alongside these efforts, Boyden’s team is working to give researchers better tools to explore how molecules move, change, and interact, including a modular system that lets users assemble sets of sensors into clusters to simultaneously monitor multiple cellular activities.

Molecular sensors use fluorescence to report on certain changes inside cells, such as the calcium that surges into a neuron after it fires. But they come in a limited palette, so in most experiments only one or two things can be seen at once.

Graduate student Shannon Johnson and postdoctoral fellow Changyang Linghu solved this problem by putting different sensors at different points throughout a cell so they can report on different signals. Their technique, called spatial multiplexing, links sensors to molecular scaffolds designed to cling to their own kind. Sensors built on the same scaffold form islands inside cells, so when they light up their signals are distinct from those produced by other sensor islands.

Eventually, as new sensors and scaffolds become available, Johnson says the technique might be used to simultaneously follow dozens of molecular signals in living cells. The more precise information they can help people uncover, the better, Boyden says.

“The brain is so full of surprises, we don’t know where the next big discovery will come from,” he says. With new support from the recently established K. Lisa Yang and Hock E. Tan Center for Molecular Therapeutics in Neuroscience, the Boyden lab is positioned to make these big discoveries.

“My dream would be to image the signaling dynamics of the brain, and then perturb the dynamics, and then use expansion methods to make a map of the brain. If we can get those three data sets—the dynamics, the causality, and the molecular organization—I think stitching those together could potentially yield deep insights into how the brain works, and how we can repair it in disease states.”

Abnormal brain connectivity may precede schizophrenia onset

by Jill Crittenden |

The cerebellum is named “little brain” for its distinctive structure. Although the cerebellum was long considered only for its role in maintaining the balance and timing of movements, it has become evident that it is also important for balanced thoughts and emotions, belying the diversity of functions that “little brain” implies.

In a new study published in Schizophrenia Bulletin, McGovern Research Affiliate and Northeastern University Professor of Psychiatry Susan Whitfield-Gabrieli shows for the first time that cerebellar dysfunction actually precedes the onset of psychosis in schizophrenia, a brain disorder characterized by severe thought and emotional imbalances.

“This study exemplifies the concept of “neuroprediction,” the discovery of brain-based biomarkers that allow early detection and therefore early intervention for mental disorders,” says Whitfield-Gabrieli.

Cerebellar connectivity and schizophrenia

Early evidence that the cerebellum is involved in more than movement came from numerous reports that people with brain damage originating in the cerebellum can have severely disordered thought processes. Now cerebellar abnormalities have been identified in numerous neurodevelopmental and neuropsychiatric conditions including autism, attention-deficit hyperactivity disorder (ADHD), Alzheimer’s disease, and schizophrenia.

Whitfield-Gabrieli has focused on how symptoms in these disorders correlate with how well the cerebellum is connected to other brain regions, including regions of the cerebral cortex, the characteristically-folded, outer part of the brain. Active connections in the brain of people who are resting or who are engaged in a mental task can be found by functional magnetic resonance imaging (fMRI), a brain scanning technique that detects when and where oxygen is being used by cells. If oxygen usage in two brain regions consistently peaks at the same time while someone is in the scanner, they are considered to be functionally connected.

Connectivity differences prior to psychosis

In her new study, Whitfield-Gabrieli explored whether brain scans could reveal cerebellar abnormalities in people at-risk for schizophrenia.

To do this, she and her colleagues compared cerebellar connectivity among at-risk adolescents and young adults who went on to develop psychosis within the following year versus those that remained stable or improved. The at-risk participants were identified in an international collaboration called the Shanghai At Risk for Psychosis (SHARP) program that recruited people who were seeking help at China’s largest outpatient mental health center. Of the 144 adolescents and young adults at-risk for schizophrenia at the outset of the study, 23 went on to develop the disorder. Notably, this group showed fMRI patterns of cerebellar dysfunction at the outset of the study, before they developed psychosis.

Abnormal brain architecture

All of the brain scans were evaluated to determine the degree to which three specific cerebellar regions were connected to the cerebral cortex, a brain region that does not finish development until young adulthood. The cerebellar regions of interest to Whitfield-Gabrieli are part of the “dentate nuclei,” so named because they look like a set of jagged teeth. Neurons in the dentate nuclei serve to integrate inputs from the rest of the cerebellum and send the compiled information out to the rest of the brain. Whitfield-Gabrieli and colleagues divided the dentate nuclei into three zones according to what parts of the cerebral cortex they are functionally connected to while people are relaxing, doing visual tasks, or engaging in a motor task or receiving some sort of stimulation.

The team found abnormal connectivity for all three zones of the dentate nuclei in the individuals who later went on to develop schizophrenia. Since the connectivity patterns varied across regions within the three zones, with some regions over-connected and others under-connected to the cerebral cortex in the group that developed psychosis, separated high-resolution analyses of the different connections was key.

Previous work established that cerebellar abnormalities are associated with schizophrenia but this study is the first to show that functional connections between the deep cerebellar nuclei and the cerebral cortex might precede disease onset.  “Treatments for mental disorders are inherently reactive to suffering and incapacity. A proactive approach by which abnormal brain architecture is identified prior to clinical diagnosis has the potential to prevent suffering by helping people before they become ill, one of my ultimate goals” said Whitfield-Gabrieli.

This study was supported by the Poitras Center for Psychiatric Disorders Research at MIT), US National Institute of Mental Health (R21 MH 093294, R01 MH 101052, R01 MH 111448, and R01 MH 64023), Ministry of Science and Technology of China (2016 YFC 1306803), European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 749201 and by a VA Merit Award.

New technique corrects disease-causing mutations

by Jill Crittenden |

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

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

Genetic models of disease

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

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

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

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

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

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

A molecular copy machine

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

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

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

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

A new way to correct disease-causing mutations          

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

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

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

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

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

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

by Tristan Davies | BCS |

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

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

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

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

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

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

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

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

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

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

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

Biologists discover a trigger for cell extrusion

Anne Trafton |

For all animals, eliminating some cells is a necessary part of embryonic development. Living cells are also naturally sloughed off in mature tissues; for example, the lining of the intestine turns over every few days.

One way that organisms get rid of unneeded cells is through a process called extrusion, which allows cells to be squeezed out of a layer of tissue without disrupting the layer of cells left behind. MIT biologists have now discovered that this process is triggered when cells are unable to replicate their DNA during cell division.

The researchers discovered this mechanism in the worm C. elegans, and they showed that the same process can be driven by mammalian cells; they believe extrusion may serve as a way for the body to eliminate cancerous or precancerous cells.

“Cell extrusion is a mechanism of cell elimination used by organisms as diverse as sponges, insects, and humans,” says H. Robert Horvitz, the David H. Koch Professor of Biology at MIT, a member of the McGovern Institute for Brain Research and the Koch Institute for Integrative Cancer Research, a Howard Hughes Medical Institute investigator, and the senior author of the study. “The discovery that extrusion is driven by a failure in DNA replication was unexpected and offers a new way to think about and possibly intervene in certain diseases, particularly cancer.”

MIT postdoc Vivek Dwivedi is the lead author of the paper, which appears today in Nature. Other authors of the paper are King’s College London research fellow Carlos Pardo-Pastor, MIT research specialist Rita Droste, MIT postdoc Ji Na Kong, MIT graduate student Nolan Tucker, Novartis scientist and former MIT postdoc Daniel Denning, and King’s College London professor of biology Jody Rosenblatt.

Stuck in the cell cycle

In the 1980s, Horvitz was one of the first scientists to analyze a type of programmed cell suicide called apoptosis, which organisms use to eliminate cells that are no longer needed. He made his discoveries using C. elegans, a tiny nematode that contains exactly 959 cells. The developmental lineage of each cell is known, and embryonic development follows the same pattern every time. Throughout this developmental process, 1,090 cells are generated, and 131 cells undergo programmed cell suicide by apoptosis.

Horvitz’s lab later showed that if the worms were genetically mutated so that they could not eliminate cells by apoptosis, a few of those 131 cells would instead be eliminated by cell extrusion, which appears to be able to serve as a backup mechanism to apoptosis. How this extrusion process gets triggered, however, remained a mystery.

To unravel this mystery, Dwivedi performed a large-scale screen of more than 11,000 C. elegans genes. One by one, he and his colleagues knocked down the expression of each gene in worms that could not perform apoptosis. This screen allowed them to identify genes that are critical for turning on cell extrusion during development.

To the researchers’ surprise, many of the genes that turned up as necessary for extrusion were involved in the cell division cycle. These genes were primarily active during first steps of the cell cycle, which involve initiating the cell division cycle and copying the cell’s DNA.

Further experiments revealed that cells that are eventually extruded do initially enter the cell cycle and begin to replicate their DNA. However, they appear to get stuck in this phase, leading them to be extruded.

Most of the cells that end up getting extruded are unusually small, and are produced from an unequal cell division that results in one large daughter cell and one much smaller one. The researchers showed that if they interfered with the genes that control this process, so that the two daughter cells were closer to the same size, the cells that normally would have been extruded were able to successfully complete the cell cycle and were not extruded.

The researchers also showed that the failure of the very small cells to complete the cell cycle stems from a shortage of the proteins and DNA building blocks needed to copy DNA. Among other key proteins, the cells likely don’t have enough of an enzyme called LRR-1, which is critical for DNA replication. When DNA replication stalls, proteins that are responsible for detecting replication stress quickly halt cell division by inactivating a protein called CDK1. CDK1 also controls cell adhesion, so the researchers hypothesize that when CDK1 is turned off, cells lose their stickiness and detach, leading to extrusion.

Cancer protection

Horvitz’s lab then teamed up with researchers at King’s College London, led by Rosenblatt, to investigate whether the same mechanism might be used by mammalian cells. In mammals, cell extrusion plays an important role in replacing the lining of the intestines, lungs, and other organs.

The researchers used a chemical called hydroxyurea to induce DNA replication stress in canine kidney cells grown in cell culture. The treatment quadrupled the rate of extrusion, and the researchers found that the extruded cells made it into the phase of the cell cycle where DNA is replicated before being extruded. They also showed that in mammalian cells, the well-known cancer suppressor p53 is involved in initiating extrusion of cells experiencing replication stress.

That suggests that in addition to its other cancer-protective roles, p53 may help to eliminate cancerous or precancerous cells by forcing them to extrude, Dwivedi says.

“Replication stress is one of the characteristic features of cells that are precancerous or cancerous. And what this finding suggests is that the extrusion of cells that are experiencing replication stress is potentially a tumor suppressor mechanism,” he says.

The fact that cell extrusion is seen in so many animals, from sponges to mammals, led the researchers to hypothesize that it may have evolved as a very early form of cell elimination that was later supplanted by programmed cell suicide involving apoptosis.

“This cell elimination mechanism depends only on the cell cycle,” Dwivedi says. “It doesn’t require any specialized machinery like that needed for apoptosis to eliminate these cells, so what we’ve proposed is that this could be a primordial form of cell elimination. This means it may have been one of the first ways of cell elimination to come into existence, because it depends on the same process that an organism uses to generate many more cells.”

Dwivedi, who earned his PhD at MIT, was a Khorana scholar before entering MIT for graduate school. This research was supported by the Howard Hughes Medical Institute and the National Institutes of Health.

Josh McDermott seeks to replicate the human auditory system

Anne Trafton |

The human auditory system is a marvel of biology. It can follow a conversation in a noisy restaurant, learn to recognize words from languages we’ve never heard before, and identify a familiar colleague by their footsteps as they walk by our office.

So far, even the most sophisticated computational models cannot perform such tasks as well as the human auditory system, but MIT neuroscientist Josh McDermott hopes to change that. Achieving this goal would be a major step toward developing new ways to help people with hearing loss, says McDermott, who recently earned tenure in MIT’s Department of Brain and Cognitive Sciences.

“Our long-term goal is to build good predictive models of the auditory system,” McDermott says.

“If we were successful in that goal, then it would really transform our ability to make people hear better, because we could design a computer program to figure out what to do to incoming sound to make it easier to recognize what somebody said or where a sound is coming from.”

McDermott’s lab also explores how exposure to different types of music affects people’s music preferences and even how they perceive music. Such studies can help to reveal elements of sound perception that are “hardwired” into our brains, and other elements that are influenced by exposure to different kinds of sounds.

“We have found that there is cross-cultural variation in things that people had widely supposed were universal and possibly even innate,” McDermott says.

Sound perception

As an undergraduate at Harvard University, McDermott originally planned to study math and physics, but “I was very quickly seduced by the brain,” he says. At the time, Harvard did not offer a major in neuroscience, so McDermott created his own, with a focus on vision.

After earning a master’s degree from University College London, he came to MIT to do a PhD in brain and cognitive sciences. His focus was still on vision, which he studied with Ted Adelson, the John and Dorothy Wilson Professor of Vision Science, but he found himself increasingly interested in audition. He had always loved music, and around this time, he started working as a radio and club DJ. “I was spending a lot of time thinking about sound and why things sound the way they do,” he recalls.

To pursue his new interest, he served as a postdoc at the University of Minnesota, where he worked in a lab devoted to psychoacoustics — the study of how humans perceive sound. There, he studied auditory phenomena such as the “cocktail party effect,” or the ability to focus on a particular person’s voice while tuning out background noise. During another postdoc at New York University, he started working on computational models of the auditory system. That interest in computation is part of what drew him back to MIT as a faculty member, in 2013.

“The culture here surrounding brain and cognitive science really prioritizes and values computation, and that was a perspective that was important to me,” says McDermott, who is also a member of MIT’s McGovern Institute for Brain Research and the Center for Brains, Minds and Machines. “I knew that was the kind of work I really wanted to do in my lab, so it just felt like a natural environment for doing that work.”

One aspect of audition that McDermott’s lab focuses on is “auditory scene analysis,” which includes tasks such as inferring what events in the environment caused a particular sound, and determining where a particular sound came from. This requires the ability to disentangle sounds produced by different events or objects, and the ability to tease out the effects of the environment. For instance, a basketball bouncing on a hardwood floor in a gym makes a different sound than a basketball bouncing on an outdoor paved court.

“Sounds in the world have very particular properties, due to physics and the way that the world works,” McDermott says. “We believe that the brain internalizes those regularities, and you have models in your head of the way that sound is generated. When you hear something, you are performing an inference in that model to figure out what is likely to have happened that caused the sound.”

A better understanding of how the brain does this may eventually lead to new strategies to enhance human hearing, McDermott says.

“Hearing impairment is the most common sensory disorder. It affects almost everybody as they get older, and the treatments are OK, but they’re not great,” he says. “We’re eventually going to all have personalized hearing aids that we walk around with, and we just need to develop the right algorithms in order to tell them what to do. That’s something we’re actively working on.”

Music in the brain

About 10 years ago, when McDermott was a postdoc, he started working on cross-cultural studies of how the human brain perceives music. Richard Godoy, an anthropologist at Brandeis University, asked McDermott to join him for some studies of the Tsimane’ people, who live in the Amazon rainforest. Since then, McDermott and some of his students have gone to Bolivia most summers to study sound perception among the Tsimane’. The Tsimane’ have had very little exposure to Western music, making them ideal subjects to study how listening to certain kinds of music influences human sound perception.

These studies have revealed both differences and similarities between Westerners and the Tsimane’ people. McDermott, who counts soul, disco, and jazz-funk among his favorite types of music, has found that Westerners and the Tsimane’ differ in their perceptions of dissonance. To Western ears, for example, the chord of C and F# sounds very unpleasant, but not to the Tsimane’.

He has also shown that that people in Western society perceive sounds that are separated by an octave to be similar, but the Tsimane’ do not. However, there are also some similarities between the two groups. For example, the upper limit of frequencies that can be perceived appears to be the same regardless of music exposure.

“We’re finding both striking variation in some perceptual traits that many people presumed were common across cultures and listeners, and striking similarities in others,” McDermott says. “The similarities and differences across cultures dissociate aspects of perception that are tightly coupled in Westerners, helping us to parcellate perceptual systems into their underlying components.”

Investigating the embattled brain

by Laura Carter | School of Science + Julie Pryor | McGovern Institute |

Omar Rutledge served as a US Army infantryman in the 1st Armored and 25th Infantry Divisions. He was deployed in support of Operation Iraqi Freedom from March 2003 to July 2004. Photo: Omar Rutledge

As an Iraq war veteran, Omar Rutledge is deeply familiar with post-traumatic stress – recurring thoughts and memories that persist long after a danger has passed – and he knows that a brain altered by trauma is not easily fixed. But as a graduate student in the Department of Brain and Cognitive Sciences, Rutledge is determined to change that. He wants to understand exactly how trauma alters the brain – and whether the tools of neuroscience can be used to help fellow veterans with post-traumatic stress disorder (PTSD) heal from their experiences.

“In the world of PTSD research, I look to my left and to my right, and I don’t see other veterans, certainly not former infantrymen,” says Rutledge, who served in the US Army and was deployed to Iraq from March 2003 to July 2004. “If there are so few of us in this space, I feel like I have an obligation to make a difference for all who suffer from the traumatic experiences of war.”

Rutledge is uniquely positioned to make such a difference in the lab of McGovern Investigator John Gabrieli, where researchers use technologies like magnetic resonance imaging (MRI), electroencephalography (EEG), and magnetoencephalography (MEG) to peer into the human brain and explore how it powers our thoughts, memories, and emotions. Rutledge is studying how PTSD weakens the connection between the amygdala, which is responsible for emotions like fear, and the prefrontal cortex, which regulates or controls these emotional responses. He hopes these studies will eventually lead to the development of wearable technologies that can retrain the brain to be less responsive to triggering events.

“I feel like it has been a mission of mine to do this kind of work.”

Though Covid-19 has unexpectedly paused some aspects of his research, Rutledge is pursuing another line of research inspired both by the mandatory social distancing protocols imposed during the lockdown and his own experiences with social isolation. Does chronic social isolation cause physical or chemical changes in the brain similar to those seen in PTSD? And does loneliness exacerbate symptoms of PTSD?

“There’s this hypervigilance that occurs in loneliness, and there’s also something very similar that occurs in PTSD — a heightened awareness of potential threats,” says Rutledge, who is the recipient of Michael Ferrara Graduate Fellowship provided by the Poitras Center, a fellowship made possible by the many friends and family of Michael Ferrara. “The combination of the two may lead to more adverse reactions in people with PTSD.”

In the future, Rutledge hopes to explore whether chronic loneliness impairs reasoning and logic skills and has a deeper impact on veterans who have PTSD.

Although his research tends to resurface painful memories of his own combat experiences, Rutledge says if it can help other veterans heal, it’s worth it.  “In the process, it makes me a little bit stronger as well,” he adds.

Nine MIT students awarded 2021 Paul and Daisy Soros Fellowships for New Americans

by Julia Mongo | Office of Distinguished Fellowships |

An MIT senior and eight MIT graduate students are among the 30 recipients of this year’s P.D. Soros Fellowships for New Americans. In addition to senior Fiona Chen, MIT’s newest Soros winners include graduate students Aziza Almanakly, Alaleh Azhir, Brian Y. Chang PhD ’18, James Diao, Charlie ChangWon Lee, Archana Podury, Ashwin Sah ’20, and Enrique Toloza. Six of the recipients are enrolled at the Harvard-MIT Program in Health Sciences and Technology.

P.D. Soros Fellows receive up to $90,000 to fund their graduate studies and join a lifelong community of new Americans from different backgrounds and fields. The 2021 class was selected from a pool of 2,445 applicants, marking the most competitive year in the fellowship’s history.

The Paul & Daisy Soros Fellowships for New Americans program honors the contributions of immigrants and children of immigrants to the United States. As Fiona Chen says, “Being a new American has required consistent confrontation with the struggles that immigrants and racial minorities face in the U.S. today. It has meant frequent difficulties with finding security and comfort in new contexts. But it has also meant continual growth in learning to love the parts of myself — the way I look; the things that my family and I value — that have marked me as different, or as an outsider.”

Students interested in applying to the P.D. Soros fellowship should contact Kim Benard, assistant dean of distinguished fellowships in Career Advising and Professional Development.

Aziza Almanakly

Aziza Almanakly, a PhD student in electrical engineering and computer science, researches microwave quantum optics with superconducting qubits for quantum communication under Professor William Oliver in the Department of Physics. Almanakly’s career goal is to engineer multi-qubit systems that push boundaries in quantum technology.

Born and raised in northern New Jersey, Almanakly is the daughter of Syrian immigrants who came to the United States in the early 1990s in pursuit of academic opportunities. As the civil war in Syria grew dire, more of her relatives sought asylum in the U.S. Almanakly grew up around extended family who built a new version of their Syrian home in New Jersey.

Following in the footsteps of her mathematically minded father, Almanakly studied electrical engineering at The Cooper Union for the Advancement of Science and Art. She also pursued research opportunities in experimental quantum computing at Princeton University, the City University of New York, New York University, and Caltech.

Almanakly recognizes the importance of strong mentorship in diversifying engineering. She uses her unique experience as a New American and female engineer to encourage students from underrepresented backgrounds to enter STEM fields.

Alaleh Azhir

Alaleh Azhir grew up in Iran, where she pursued her passion for mathematics. She immigrated with her mother to the United States at age 14. Determined to overcome strict gender roles she had witnessed for women, Azhir is dedicated to improving health care for them.

Azhir graduated from Johns Hopkins University in 2019 with a perfect GPA as a triple major in biomedical engineering, computer science, and applied mathematics and statistics. A Rhodes and Barry Goldwater Scholar, she has developed many novel tools for visualization and analysis of genomics data at Johns Hopkins University, Harvard University, MIT, the National Institutes of Health, and laboratories in Switzerland.

After completing a master’s in statistical science at Oxford University, Azhir began her MD studies in the Harvard-MIT Program in Health Sciences and Technology. Her thesis focuses on the role of X and Y sex chromosomes on disease manifestations. Through medical training, she aims to build further computational tools specifically for preventive care for women. She has also founded and directs the nonprofit organization, Frappa, aimed at mentoring women living in Iran and helping them to immigrate abroad through the graduate school application process.

Brian Y. Chang PhD ’18

Born in Johnson City, New York, Brian Y. Chang PhD ’18 is the son of immigrants from the Shanghai municipality and Shandong Province in China. He pursued undergraduate and master’s degrees in mechanical engineering at Carnegie Mellon University, graduating in a combined four years with honors.

In 2018, Chang completed a PhD in medical engineering at MIT. Under the mentorship of Professor Elazer Edelman, Chang developed methods that make advanced cardiac technologies more accessible. The resulting approaches are used in hospitals around the world. Chang has published extensively and holds five patents.

With the goal of harnessing the power of engineering to improve patient care, Chang co-founded X-COR Therapeutics, a seed-funded medical device startup developing a more accessible treatment for lung failure with the potential to support patients with severe Covid-19 and chronic obstructive pulmonary disease.

After spending time in the hospital connecting with patients and teaching cardiovascular pathophysiology to medical students, Chang decided to attend medical school. He is currently a medical student in the Harvard-MIT Program in Health Sciences and Technology. Chang hopes to advance health care through medical device innovation and education as a future physician-scientist, entrepreneur, and educator.

Fiona Chen

MIT senior Fiona Chen was born in Cedar Park, Texas, the daughter of immigrants from China. Witnessing how her own and many other immigrant families faced significant difficulties finding work and financial stability sparked her interest in learning about poverty and economic inequality.

At MIT, Chen has pursued degrees in economics and mathematics. Her economics research projects have examined important policy issues — social isolation among students, global development and poverty, universal health-care systems, and the role of technology in shaping the labor market.

An active member of the MIT community, Chen has served as the officer on governance and officer on policy of the Undergraduate Association, MIT’s student government; the opinion editor of The Tech student newspaper; the undergraduate representative of several Institute-wide committees, including MIT’s Corporation Joint Advisory Committee; and one of the founding members of MIT Students Against War. In each of these roles, she has worked to advocate for policies to support underrepresented groups at MIT.

As a Soros fellow, Chen will pursue a PhD in economics to deepen her understanding of economic policy. Her ultimate goal is to become a professor who researches poverty and economic inequality, and applies her findings to craft policy solutions.

James Diao

James Diao graduated from Yale University with degrees in statistics and biochemistry and is currently a medical student at the Harvard-MIT Program in Health Sciences and Technology. He aspires to give voice to patient perspectives in the development and evaluation of health-care technology.

Diao grew up in Houston’s Chinatown, and spent summers with his extended family in Jiangxian. Diao’s family later moved to Fort Bend, Texas, where he found a pediatric oncologist mentor who introduced him to the wonders of modern molecular biology.

Diao’s interests include the responsible development of technology. At Apple, he led projects to validate wearable health features in diverse populations; at PathAI, he built deep learning models to broaden access to pathologist services; at Yale, where he worked on standardizing analyses of exRNA biomarkers; and at Harvard, he studied the impacts of clinical guidelines on marginalized groups.

Diao’s lead author research in the New England Journal of Medicine and JAMA systematically compared race-based and race-free equations for kidney function, and demonstrated that up to 1 million Black Americans may receive unequal kidney care due to their race. He has also published articles on machine learning and precision medicine.

Charlie ChangWon Lee

Born in Seoul, South Korea, Charlie ChangWon Lee was 10 when his family immigrated to the United States and settled in Palisades Park, New Jersey. The stress of his parents’ lack of health coverage ignited Lee’s determination to study the reasons for the high cost of health care in the U.S. and learn how to care for uninsured families like his own.

Lee graduated summa cum laude in integrative biology from Harvard College, winning the Hoopes Prize for his thesis on the therapeutic potential of human gut microbes. Lee’s research on novel therapies led him to question how newly approved, and expensive, medications could reach more patients.

At the Program on Regulation, Therapeutics, and Law (PORTAL) at Brigham and Women’s Hospital, Lee studied policy issues involving pharmaceutical drug pricing, drug development, and medication use and safety. His articles have appeared in JAMA, Health Affairs, and Mayo Clinic Proceedings.

As a first-year medical student at the Harvard-MIT Health Sciences and Technology program, Lee is investigating policies to incentivize vaccine and biosimilar drug development. He hopes to find avenues to bridge science and policy and translate medical innovations into accessible, affordable therapies.

Archana Podury

The daughter of Indian immigrants, Archana Podury was born in Mountain View, California. As an undergraduate at Cornell University, she studied the neural circuits underlying motor learning. Her growing interest in whole-brain dynamics led her to the Princeton Neuroscience Institute and Neuralink, where she discovered how brain-machine interfaces could be used to understand diffuse networks in the brain.

While studying neural circuits, Podury worked at a syringe exchange in Ithaca, New York, where she witnessed firsthand the mechanics of court-based drug rehabilitation. Now, as an MD student in the Harvard-MIT Health Sciences and Technology program, Podury is interested in combining computational and social approaches to neuropsychiatric disease.

In the Boyden Lab at the MIT McGovern Institute for Brain Research, Podury is developing human brain organoid models to better characterize circuit dysfunction in neurodevelopmental disorders. Concurrently, her work in the Dhand Lab at Brigham and Women’s Hospital applies network science tools to understand how patients’ social environments influence their health outcomes following acute neurological injury.

Podury hopes that focusing on both neural and social networks can lead toward a more comprehensive, and compassionate, approach to health and disease.

Ashwin Sah ’20

Ashwin Sah ’20 was born and raised in Portland, Oregon, the son of Indian immigrants. He developed a passion for mathematics research as an undergraduate at MIT, where he conducted research under Professor Yufei Zhao, as well as at the Duluth and Emory REU (Research Experience for Undergraduates) programs.

Sah has given talks on his work at multiple professional venues. His undergraduate research in varied areas of combinatorics and discrete mathematics culminated in the Barry Goldwater Scholarship and the Frank and Brennie Morgan Prize for Outstanding Research in Mathematics by an Undergraduate Student. Additionally, his work on diagonal Ramsey numbers was recently featured in Quanta Magazine.

Beyond research, Sah has pursued opportunities to give back to the math community, helping to organize or grade competitions such as the Harvard-MIT Mathematics Tournament and the USA Mathematical Olympiad. He has also been a grader at the Mathematical Olympiad Program, a camp for talented high-school students in the United States, and an instructor for the Monsoon Math Camp, a virtual program aimed at teaching higher mathematics to high school students in India.

Sah is currently a PhD student in mathematics at MIT, where he continues to work with Zhao.

Enrique Toloza

Enrique Toloza was born in Los Angeles, California, the child of two immigrants: one from Colombia who came to the United States for a PhD and the other from the Philippines who grew up in California and went on to medical school. Their literal marriage of science and medicine inspired Toloza to become a physician-scientist.

Toloza majored in physics and Spanish literature at the University of North Carolina at Chapel Hill. He eventually settled on an interest in theoretical neuroscience after a summer research internship at MIT and completing an honors thesis on noninvasive brain stimulation.

After college, Toloza joined Professor Mark Harnett’s laboratory at MIT for a year. He went on to enroll in the Harvard-MIT MD/PhD program, studying within the Health Sciences and Technology MD curriculum at Harvard and the PhD program at MIT. For his PhD, Toloza rejoined Harnett to conduct research on the biophysics of dendritic integration and the contribution of dendrites to cortical computations in the brain.

Toloza is passionate about expanding health care access to immigrant populations. In college, he led the interpreting team at the University of North Carolina at Chapel Hill’s student-run health clinic; at Harvard Medical School, he has worked with Spanish-speaking patients as a student clinician.

Method offers inexpensive imaging at the scale of virus particles

Anne Trafton |

Using an ordinary light microscope, MIT engineers have devised a technique for imaging biological samples with accuracy at the scale of 10 nanometers — which should enable them to image viruses and potentially even single biomolecules, the researchers say.

The new technique builds on expansion microscopy, an approach that involves embedding biological samples in a hydrogel and then expanding them before imaging them with a microscope. For the latest version of the technique, the researchers developed a new type of hydrogel that maintains a more uniform configuration, allowing for greater accuracy in imaging tiny structures.

This degree of accuracy could open the door to studying the basic molecular interactions that make life possible, says Edward Boyden, the Y. Eva Tan Professor in Neurotechnology, a professor of biological engineering and brain and cognitive sciences at MIT, and a member of MIT’s McGovern Institute for Brain Research and Koch Institute for Integrative Cancer Research.

“If you could see individual molecules and identify what kind they are, with single-digit-nanometer accuracy, then you might be able to actually look at the structure of life.”

“And structure, as a century of modern biology has told us, governs function,” says Boyden, who is the senior author of the new study.

The lead authors of the paper, which appears today in Nature Nanotechnology, are MIT Research Scientist Ruixuan Gao and Chih-Chieh “Jay” Yu PhD ’20. Other authors include Linyi Gao PhD ’20; former MIT postdoc Kiryl Piatkevich; Rachael Neve, director of the Gene Technology Core at Massachusetts General Hospital; James Munro, an associate professor of microbiology and physiological systems at University of Massachusetts Medical School; and Srigokul Upadhyayula, a former assistant professor of pediatrics at Harvard Medical School and an assistant professor in residence of cell and developmental biology at the University of California at Berkeley.

Low cost, high resolution

Many labs around the world have begun using expansion microscopy since Boyden’s lab first introduced it in 2015. With this technique, researchers physically enlarge their samples about fourfold in linear dimension before imaging them, allowing them to generate high-resolution images without expensive equipment. Boyden’s lab has also developed methods for labeling proteins, RNA, and other molecules in a sample so that they can be imaged after expansion.

“Hundreds of groups are doing expansion microscopy. There’s clearly pent-up demand for an easy, inexpensive method of nanoimaging,” Boyden says. “Now the question is, how good can we get? Can we get down to single-molecule accuracy? Because in the end, you want to reach a resolution that gets down to the fundamental building blocks of life.”

Other techniques such as electron microscopy and super-resolution imaging offer high resolution, but the equipment required is expensive and not widely accessible. Expansion microscopy, however, enables high-resolution imaging with an ordinary light microscope.

In a 2017 paper, Boyden’s lab demonstrated resolution of around 20 nanometers, using a process in which samples were expanded twice before imaging. This approach, as well as the earlier versions of expansion microscopy, relies on an absorbent polymer made from sodium polyacrylate, assembled using a method called free radical synthesis. These gels swell when exposed to water; however, one limitation of these gels is that they are not completely uniform in structure or density. This irregularity leads to small distortions in the shape of the sample when it’s expanded, limiting the accuracy that can be achieved.

To overcome this, the researchers developed a new gel called tetra-gel, which forms a more predictable structure. By combining tetrahedral PEG molecules with tetrahedral sodium polyacrylates, the researchers were able to create a lattice-like structure that is much more uniform than the free-radical synthesized sodium polyacrylate hydrogels they previously used.

Three-dimensional (3D) rendered movie of envelope proteins of an herpes simplex virus type 1 (HSV-1) virion expanded by tetra-gel (TG)-based three-round iterative expansion. The deconvolved puncta (white), the overlay of the deconvolved puncta (white) and the fitted centroids (red), and the extracted centroids (red) are shown from left to right. Expansion factor, 38.3×. Scale bars, 100 nm.
Credit: Ruixuan Gao and Boyden Lab

The researchers demonstrated the accuracy of this approach by using it to expand particles of herpes simplex virus type 1 (HSV-1), which have a distinctive spherical shape. After expanding the virus particles, the researchers compared the shapes to the shapes obtained by electron microscopy and found that the distortion was lower than that seen with previous versions of expansion microscopy, allowing them to achieve an accuracy of about 10 nanometers.

“We can look at how the arrangements of these proteins change as they are expanded and evaluate how close they are to the spherical shape. That’s how we validated it and determined how faithfully we can preserve the nanostructure of the shapes and the relative spatial arrangements of these molecules,” Ruixuan Gao says.

Single molecules

The researchers also used their new hydrogel to expand cells, including human kidney cells and mouse brain cells. They are now working on ways to improve the accuracy to the point where they can image individual molecules within such cells. One limitation on this degree of accuracy is the size of the antibodies used to label molecules in the cell, which are about 10 to 20 nanometers long. To image individual molecules, the researchers would likely need to create smaller labels or to add the labels after expansion was complete.

Left, HeLa cell with two-color labeling of clathrin-coated pits/vesicles and microtubules, expanded by TG-based two-round iterative expansion. Expansion factor, 15.6×. Scale bar, 10 μm (156 μm). Right, magnified view of the boxed region for each color channel. Scale bars, 1 μm (15.6 μm). Image: Boyden Lab

They are also exploring whether other types of polymers, or modified versions of the tetra-gel polymer, could help them realize greater accuracy.

If they can achieve accuracy down to single molecules, many new frontiers could be explored, Boyden says. For example, scientists could glimpse how different molecules interact with each other, which could shed light on cell signaling pathways, immune response activation, synaptic communication, drug-target interactions, and many other biological phenomena.

“We’d love to look at regions of a cell, like the synapse between two neurons, or other molecules involved in cell-cell signaling, and to figure out how all the parts talk to each other,” he says. “How do they work together and how do they go wrong in diseases?”

The research was funded by Lisa Yang, John Doerr, Open Philanthropy, the National Institutes of Health, the Howard Hughes Medical Institute Simons Faculty Scholars Program, the Intelligence Advanced Research Projects Activity, the U.S. Army Research Laboratory, the US-Israel Binational Science Foundation, the National Science Foundation, the Friends of the McGovern Fellowship, and the Fellows program of the Image and Data Analysis Core at Harvard Medical School.