Research Area: Cellular & Molecular Neuroscience

​synapses, vesicles, electrophysiology, protein complexes, signaling, small molecules, disease-linked genes, dendrites, cell death, brain disorders, neurodevelopment

Celebrating worm science

by Jennifer Michalowski |

For decades, scientists with big questions about biology have found answers in a tiny worm. That worm–a millimeter-long creature called Caenorhabditis elegans–has helped researchers uncover fundamental features of how cells and organisms work. The impact of that work is enormous: Discoveries made using C. elegans have been recognized with four Nobel prizes and have led to the development of new treatments for human disease.

Portrait of Robert Horvitz at a computer.
McGovern Investigator Robert Horvitz shared the 2002 Nobel Prize in Medicine with colleagues Sydney Brenner and John Sulston for discoveries that helped explain how genes regulate programmed cell death and organ development. Photo: AP Images/Aynsley Floyd

In a perspective piece published in the November 2025 issue of the journal PNAS, eleven biologists including Robert Horvitz, the David H. Koch (1962) Professor of Biology at MIT, celebrate Nobel Prize-winning advances made through research in C. elegans. The authors discuss how that work has led to advances for human health and highlight how a uniquely collaborative community among worm researchers has fueled the field.

MIT scientists are well represented in that community: The prominent worm biologists who coauthored the PNAS paper include former MIT graduate students Andy Fire and Paul Sternberg, now at Stanford University and the California Institute of Technology, and two past postdoctoral researchers in Horvitz’s lab, University of Massachusetts Medical School professor Victor Ambros and Massachusetts General Hospital investigator Gary Ruvkun. Ann Rougvie at the University of Minnesota is the paper’s corresponding author.

Early worm discoveries

“This tiny worm is beautiful—elegant both in its appearance and in its many contributions to our understanding of the biological universe in which we live,” says Horvitz, who in 2002 was awarded the Nobel Prize in Medicine along with colleagues Sydney Brenner and John Sulston for discoveries that helped explain how genes regulate programmed cell death and organ development. Horvitz is also a member of MIT’s McGovern Institute for Brain Research and Koch Institute for Integrative Cancer Research as well as an investigator at the Howard Hughes Medical Institute.

Those discoveries were among the early successes in C. elegans research, made by pioneering scientists who recognized the power of the microscopic roundworm. C. elegans offers many advantages for researchers: The worms are easy to grow and maintain in labs; their transparent bodies make cells and internal processes readily visible under a microscope; they are cellularly very simple (e.g., they have only 302 nerve cells, compared with about 100 billion in a human) and their genomes can be readily manipulated to study gene function.

Microscopic image of C. elegans roundworm with cells highlighted in pink and green.
Caenorhabditis elegans, a transparent roundworm only 1mm in length, has provided answers to many fundamental questions in biology. Image: Robert Horvitz

Most importantly, many of the molecules and processes that operate in C. elegans have been retained throughout evolution, meaning discoveries made using the worm can have direct relevance to other organisms, including humans. “Many aspects of biology are ancient and evolutionarily conserved,” Horvitz explains. “Such shared mechanisms can be most readily revealed by analyzing organisms that are highly tractable in the laboratory.”

In the 1960s, Brenner, a molecular biologist who was curious about how animals’ nervous systems develop and function, recognized that C. elegans offered unique opportunities to study these processes. Once he began developing the worm into a model for laboratory studies, it did not take long for other biologists to join him to take advantage of the new system.

In the 1970s, the unique features of the worm allowed Sulston to track the transformation of a fertilized egg into an adult animal, tracing the origins of each of the adult worm’s 959 cells. His studies revealed that in every developing worm, cells divide and mature in predictable ways. He also learned that some of the cells created during development do not survive into adulthood and are instead eliminated by a process termed programmed cell death.

“This tiny worm is beautiful—elegant both in its appearance and in its many contributions to our understanding of the biological universe in which we live,” says Horvitz.

By seeking mutations that perturbed the process of programmed cell death, Horvitz and his colleagues identified key regulators of that process, which is sometimes referred to as apoptosis. These regulators, which both promote and oppose apoptosis, turned out to be vital for programmed cell death across the animal kingdom.

In humans, apoptosis shapes developing organs, refines brain circuits, and optimizes other tissue structures. It also modulates our immune systems and eliminates cells that are in danger of becoming cancerous. The human version of CED-9, the anti-apoptotic regulator that Horvitz’s team discovered in worms, is BCL-2. Researchers have shown that activating apoptotic cell death by blocking BCL-2 is an effective treatment for certain blood cancers. Today, researchers are also exploring new ways of treating immune disorders and neurodegenerative disease by manipulating apoptosis pathways.

Collaborative worm community

Horvitz and his colleagues’ discoveries about apoptosis helped demonstrate that understanding C. elegans biology has direct relevance to human biology and disease. Since then, a vibrant and closely connected community of worm biologists—including many who trained in Horvitz’s lab—has continued to carry out impactful work. In their PNAS article, Horvitz and his coauthors highlight that early work, as well as the Nobel Prize-winning work of:

  • Andrew Fire and Craig Mello, whose discovery of an RNA-based system of gene silencing led to powerful new tools to manipulate gene activity. The innate process they discovered in worms, known as RNA interference, is now used as the basis of six FDA-approved therapeutics for genetic disorders, silencing faulty genes to stop their harmful effects.
  • Martin Chalfie, who used a fluorescent protein made by jellyfish to visualize and track specific cells in C. elegans, helping launch the development of a set of tools that transformed biologists’ ability to observe molecules and processes that are important for both health and disease.
  • Victor Ambros and Gary Ruvkun, who discovered a class of molecules called microRNAs that regulate gene activity not just in worms, but in all multicellular organisms. This prize-winning work was started when Ambros and Ruvkun were postdoctoral researchers in Horvitz’s lab. Humans rely on more than 1,000 microRNAs to ensure our genes are used at the right times and places. Disruptions to microRNAs have been linked to neurological disorders, cancer, cardiovascular disease, and autoimmune disease, and researchers are now exploring how these small molecules might be used for diagnosis or treatment.

Horvitz and his coauthors stress that while the worm itself made these discoveries possible, so too did a host of resources that facilitate collaboration within the worm community and enable its scientists to build upon the work of others. Scientists who study C. elegans have embraced this open, collaborative spirit since the field’s earliest days, Horvitz says, citing the Worm Breeder’s Gazette, an early newsletter where scientists shared their observations, methods, and ideas.

Today, scientists who study C. elegans—whether the organism is the centerpiece of their lab or they are looking to supplement studies of other systems—contribute to and rely on online resources like WormAtlas and WormBase, as well as the Caenorhabditis Genetics Center, to share data and genetic tools. Horvitz says these resources have been crucial to his own lab’s work; his team uses them every day.

WormAtlas provides users with numerous anatomical resources including tools to view electron microscopy slices of the same cell. Image: WormAtlas.org

Just as molecules and processes discovered in C. elegans have pointed researchers toward important pathways in human cells, the worm has also been a vital proving ground for developing methods and approaches later deployed to study more complex organisms. For example, C. elegans, with its 302 neurons, was the first animal for which neuroscientists successfully mapped all of the connections of the nervous system. The resulting wiring diagram, or connectome, has guided countless experiments exploring how neurons work together to process information and control behavior. Informed by both the power and limitations of the C. elegans’ connectome, scientists are now mapping more complex circuitry, such as the 139,000-neuron brain of the fruit fly, whose connectome was completed in 2024.

C. elegans remains a mainstay of biological research, including in neuroscience. Scientists worldwide are using the worm to explore new questions about neural circuits, neurodegeneration, development, and disease. Horvitz’s lab continues to turn to C. elegans to investigate the genes that control animal development and behavior. His team is now using the worm to explore how animals develop a sense of time and transmit that information to their offspring.

Also at MIT, Steven Flavell’s team in the Department of Brain and Cognitive Sciences and the Picower Institute for Learning and Memory is using the worm to investigate how neural connectivity, activity, and modulation integrate internal states, such as hunger, with sensory information, such as the smell of food, to produce sometimes long-lasting behaviors. Flavell is Horvitz’s academic grandson, as Flavell trained with one of Horvitz’s postdoctoral trainees. As new technologies accelerate the pace of scientific discovery, Horvitz and his colleagues are confident that the humble worm will bring more unexpected insights.

 

Who discovered neurons?

by Rubina Veerakone |

A self-portrait of Santiago Ramón y Cajal looking through a microscope.
A self-portrait of Santiago Ramón y Cajal looking through a microscope. Image: CC 2.0

On this day, December 10th, nearly 120 years ago, Santiago Ramón y Cajal received a Nobel Prize for capturing and interpreting the very first images of the brain’s most essential components — neurons.

“Many scientists consider Cajal the progenitor of neuroscience because he was the first to really see the brain for what it was: a computational engine made up of individual units,” says Mark Harnett, an investigator at the McGovern Institute and an associate professor in the Department of Brain and Cognitive Sciences. His lab explores how the biophysical features of neurons enable them to perform complex computations that drive thought and behavior.

For Harnett, Cajal is one of the greatest scientific minds to have helped us understand ourselves and our place in the world. Cajal was the first to uncover what neurons look like and propose how they function — equipping the field to solve a slew of the mind’s mysteries. Scientists built on this framework to learn how these remarkable cells relay information — by zapping electrical signals to each other — so we can think, feel, move, communicate, and create.

From art to science and back again

Cajal was born on May 1, 1852, in a small village nestled in the Spanish countryside. It was there Cajal fell deeply and madly in love with … art. But his father was a physician, and urged him to trade his sketches for a scalpel. Begrudgingly, Cajal eventually did. After graduating from medical school in 1873, he worked as an army doctor, but around 1880, he turned his attention to studying the nervous system.

An illustration of a brain cell.
A Purkinje neuron from the human cerebellum. Image: Cajal Institute (CSIC), Madrid

Nineteenth-century scientists didn’t think of the brain as a network of cells but more as plumbing, like the blood vessels in the circulatory system — a series of hollow tubes through which information somehow flowed. Cajal and others were skeptical of this perspective, yet had no way of visualizing the brain at a detailed, cellular level to confirm their suspicions. Scientists at the time stained thin slices of tissue to make cells visible under a microscope, but even the most sophisticated methods stained all cells at once, leaving an indecipherable mass under the microscope’s lens.

This changed in 1887 when Cajal encountered a technique devised by Camillo Golgi that stained only some cells. “Rather than seeing all the cells simultaneously, you saw one at a time,” Harnett explains, making it easier to view a cell’s precise form (Golgi shared the 1906 Nobel Prize with Cajal for this method). If he could refine Golgi’s approach and apply it to neural tissue, Cajal thought, he might finally determine the brain’s architecture.

When he did, a remarkable landscape appeared — black bulbs with sprawling branches, each casting a stringy silhouette. The scene awakened a prior passion. While viewing brain slices under a microscope, Cajal drew what he saw, with surgical precision and an artist’s eye. He had captured — for the first time — the mind’s timberland of cells.

A new theory of the mind

Cajal’s illustrations revealed that brain cells did not form a singular plumbing network, but were distinctly separate, with small gaps between them. “This completely upended what people at the time thought about the brain,” Harnett explains. “It wasn’t made up of connected tubes, but individual cells,” which a few years later in 1891 would be called neurons. Over nearly five decades Cajal created around 2,900 drawings — a collage of neurons from humans and a menagerie of fauna: mice, pigeons, lizards, newts, and fish — spanning a host of cell types, from Purkinje cells to basket and chandelier interneurons.

“Part of Cajal’s genius was that he proposed what the incredible anatomical diversity among neurons meant. He reasoned that maybe one part of the cell could work like an antenna to take in signals, and another might be a cable to send signals out. Cajal was already thinking about input and output at neurons, and synapses as points of contact between them,” Harnett notes. “Each neuron becomes a very complex engine for computation, as opposed to tube-based things that can’t really compute.”

Cajal’s notion that the brain was a network of individual cells would come to be known as the neuron doctrine, a bedrock principle that underlies all of neuroscience today. In his autobiography, Cajal describes neurons as “the mysterious butterflies of the soul, the beating of whose wings may someday – who knows? – clarify the secret of mental life.” And in many ways, they have.

One of thousands of neuron illustrations created by Santiago Ramón y Cajal. Image: CC 2.0

One scientist’s enduring influence

Much of scientists’ current approach to studying the brain is guided by Cajal’s blueprint. This is certainly true for the Harnett lab. “As many in the field do, we share Cajal’s aspiration to apply cutting-edge imaging to reveal hidden aspects of the brain and hypothesize about their function,” Harnett says. “Thankfully, unlike Cajal, we now have the advantage of functional tests to try to validate our hypotheses.”

An ultra high resolution image of a neuron taken by the Harnett lab. Image: Mark Harnett

In a study published in 2022, the Harnett lab used a super-resolution imaging tool to find that filopodia — tiny structures that protrude from dendrites (the signal-receiving “antennas” of neurons) — were far more abundant in the brain than previously thought. Through a battery of tests, they found that these “silent synapses” can become active to facilitate new neural connections. Such pliable sites were believed to only be present very early in life, but the researchers observed filopodia in adult mice, suggesting that they support continuous learning and computational flexibility over the lifespan.

Harnett explains that Cajal’s impact extends beyond neuroscience. “Where does the power of artificial intelligence (AI) come from? It comes, originally, from Cajal.” It’s no wonder, he says, that AI uses neural networks — a mimicry of one of nature’s most powerful designs, first described by Cajal. “The idea that neurons are computational units is really critical to the power and complexity you can achieve within a network. Cajal even hypothesized that changing the strength of signaling between neurons was how learning worked, an idea that was later validated and became one of the critical insights for revolutionizing deep learning in AI.”

By unveiling what’s really happening beneath our skulls, Cajal’s work would both motivate and guide studies of the brain for over a hundred years to come. “Many of his early hypotheses have proven to be true decades and decades later,” Harnett says. “He has and continues to inspire generations of neuroscientists.”

 

 

Astrocyte diversity across space and time

by Jennifer Michalowski |

McGovern Investigator Guoping Feng. Photo: Justin Knight

When it comes to brain function, neurons get a lot of the glory. But healthy brains depend on the cooperation of many kinds of cells. The most abundant of the brain’s non-neuronal cells are astrocytes, star-shaped cells with a lot of responsibilities. Astrocytes help shape neural circuits, participate in information processing, and provide nutrient and metabolic support to neurons. Individual cells can take on new roles throughout their lifetimes, and at any given time, the astrocytes in one part of the brain will look and behave differently than the astrocytes somewhere else.

After an extensive analysis by scientists at MIT’s McGovern Institute, neuroscientists now have an atlas detailing astrocytes’ dynamic diversity. Its maps depict the regional specialization of astrocytes across the brains of both mice and marmosets—two powerful models for neuroscience research—and show how their populations shift as brains develop, mature, and age. The study, reported in the November 20 issue of the journal Neuron, was led by Guoping Feng, the James W. (1963) and Patricia T. Poitras Professor of Brain and Cognitive Sciences at MIT. This work was supported by the Hock E. Tan and K. Lisa Yang Center for Autism Research, part of the Yang Tan Collective at MIT, and the National Institutes of Health’s BRAIN Initiative.

Probing the unknown

“It’s really important for us to pay attention to non-neuronal cells’ role in health and disease,” says Feng, who is also the associate director of the McGovern Institute, the director of the Hock E. Tan and K. Lisa Yang Center for Autism Research at MIT, and a member of the Broad Institute of MIT and Harvard. And indeed, these cells—once seen as merely supporting players—have gained more of the spotlight in recent years. Astrocytes are known to play vital roles in the brain’s development and function, and their dysfunction seems to contribute to many psychiatric disorders and neurodegenerative diseases. “But compared to neurons, we know a lot less—especially during development,” Feng adds.

Feng and Margaret Schroeder, a former graduate student in his lab, thought it was important to understand astrocyte diversity across three axes: space, time, and species. They knew from earlier work in the lab, done in collaboration with Steve McCarroll’s lab at Harvard and led by Fenna Krienen in his group, that in adult animals, different parts of the brain have distinctive sets of astrocytes.

“The natural question was, how early in development do we think this regional patterning of astrocytes starts?” Schroeder says.

To find out, she and her colleagues collected brain cells from mice and marmosets at six stages of life, spanning embryonic development to old age. For each animal, they sampled cells from four different brain regions: the prefrontal cortex, the motor cortex, the striatum, and the thalamus.

Then, working with Krienen, who is now an assistant professor at Princeton University, they analyzed the molecular contents of those cells, creating a profile of genetic activity for each one. That profile was based on the mRNA copies of genes found inside the cell, which are known collectively as the cell’s transcriptome. Determining which genes a cell is using and how active those genes are gives researchers insight into a cell’s function and is one way of defining its identity.

Dynamic diversity

After assessing the transcriptomes of about 1.4 million brain cells, the group focused in on the astrocytes, analyzing and comparing their patterns of gene expression. At every life stage, from before birth to old age, the team found regional specialization: Astrocytes from different brain regions had similar patterns of gene expression, which were distinct from those of astrocytes in other brain regions.

This regional specialization was also apparent in the distinct shapes of astrocytes in different parts of the brain, which the team was able to see with expansion microscopy, a high-resolution imaging method developed by McGovern colleague Edward Boyden that reveals fine cellular features.

Notably, the astrocytes in each region changed as animals matured. “When we looked at our late embryonic time point, the astrocytes were already regionally patterned. But when we compare that to the adult profiles, they had completely shifted again,” Schroeder says. “So there’s something happening over postnatal development.” The most dramatic changes the team detected occurred between birth and early adolescence, a period during which brains rapidly rewire as animals begin to interact with the world and learn from their experiences.

Maps generated by Feng’s team depict the regional specialization of astrocytes across the brains of both mice and marmosets—two powerful models for neuroscience research—and show how their populations shift as brains develop, mature, and age.

Feng and Schroeder suspect that the changes they observed may be driven by the neural circuits that are sculpted and refined as the brain matures. “What we think they’re doing is kind of adapting to their local neuronal niche,” Schroeder says. “The types of genes that they are upregulating and changing during development points to their interaction with neurons.” Feng adds that astrocytes may change their genetic programs in response to nearby neurons, or alternatively, they might help direct the development or function of local circuits as they adopt identities best suited to support particular neurons.

Both mouse and marmoset brains exhibited regional specialization of astrocytes and changes in those populations over time. But when the researchers looked at the specific genes whose activity defined various astrocyte populations, the data from the two species diverged. Schroeder calls this a note of caution for scientists who study astrocytes in animal models, and adds that the new atlas will help researchers assess the potential relevance of findings across species.

Beyond astrocytes

With a new understanding of astrocyte diversity, Feng says his team will pay close attention to how these cells are impacted by the disease-related genes they study and how those effects change during development. He also notes that the gene expression data in the atlas can be used to predict interactions between astrocytes and neurons. “This will really guide future experiments: how these cells’ interactions can shift with changes in the neurons or changes in the astrocytes,” he says.

The Feng lab is eager for other researchers to take advantage of the massive amounts of data they generated as they produced their atlas. Schroeder points out that the team analyzed the transcriptomes of all kinds of cells in the brain regions they studied, not just astrocytes. They are sharing their findings so researchers can use them to understand when and where specific genes are used in the brain, or dig in more deeply to further to explore the brain’s cellular diversity.

 

New MIT initiative seeks to transform rare brain disorders research

by Rubina Veerakone |

More than 300 million people worldwide are living with rare disorders — many of which have a genetic cause and affect the brain and nervous system — yet the vast majority of these conditions lack an approved therapy. Because each rare disorder affects fewer than 65 out of every 100,000 people, studying these disorders and creating new treatments for them is especially challenging.

Thanks to a generous philanthropic gift from Ana Méndez ’91 and Rajeev Jayavant ’86, EE ’88, SM ’88, MIT is now poised to fill the gaps in this research landscape. By establishing the Rare Brain Disorders Nexus — or RareNet — at MIT’s McGovern Institute, the alumni aim to convene leaders in neuroscience research, clinical medicine, patient advocacy, and industry to streamline the lab-to-clinic pipeline for rare brain disorder treatments.

“Ana and Rajeev’s commitment to MIT will form crucial partnerships to propel the translation of scientific discoveries into promising therapeutics and expand the Institute’s impact on the rare brain disorders community,” says MIT President Sally Kornbluth. “We are deeply grateful for their pivotal role in advancing such critical science and bringing attention to conditions that have long been overlooked.”

Building new coalitions

Several hurdles have slowed the lab-to-clinic pipeline for rare brain disorder research. It is difficult to secure a sufficient number of patients per study, and current research efforts are fragmented since each study typically focuses on a single disorder (there are more than 7,000 known rare disorders, according to the World Health Organization). Pharmaceutical companies are often reluctant to invest in emerging treatments due to a limited market size and the high costs associated with preparing drugs for commercialization.

Méndez and Jayavant envision that RareNet will finally break down these barriers. “Our hope is that RareNet will allow leaders in the field to come together under a shared framework and ignite scientific breakthroughs across multiple conditions. A discovery for one rare brain disorder could unlock new insights that are relevant to another,” says Jayavant. “By congregating the best minds in the field, we are confident that MIT will create the right scientific climate to produce drug candidates that may benefit a spectrum of uncommon conditions.”

Guoping Feng, the James W. (1963) and Patricia T. Poitras Professor in Neuroscience and associate director of the McGovern Institute for Brain Research at MIT, will serve as RareNet’s inaugural faculty director. Feng holds a strong record of advancing studies on therapies for neurodevelopmental disorders, including autism spectrum disorders, Williams syndrome, and uncommon forms of epilepsy. His team’s gene therapy for Phelan-McDermid syndrome, a rare and profound autism spectrum disorder, has been licensed to Jaguar Gene Therapy and is currently undergoing clinical trials. “RareNet pioneers a unique model for biomedical research — one that is reimagining the role academia can play in developing therapeutics,” says Feng.

Image of SHANK3 therapy correctly finding its way to dendrites. Image: Guoping Feng
An early version of a gene therapy for SHANK3 mutations — linked to a rare brain disorder called Phelan-McDermid syndrome — correctly finds its way to neurons. Image: Feng lab

RareNet plans to deploy two major initiatives: a global consortium and a therapeutic pipeline accelerator. The consortium will form an international network of researchers, clinicians, and patient groups from the outset. It seeks to connect siloed research efforts, secure more patient samples, promote data sharing, and drive a strong sense of trust and goal alignment across the RareNet community. Partnerships within the consortium will support the aim of the therapeutic pipeline accelerator: to de-risk early lab discoveries and expedite their translation to clinic. By fostering more targeted collaborations — especially between academia and industry — the accelerator will prepare potential treatments for clinical use as efficiently as possible.

MIT labs are focusing on four uncommon conditions in the first wave of RareNet projects: Rett syndrome, prion disease, disorders linked to SYNGAP1 mutations, and Sturge-Weber syndrome. The teams are working to develop novel therapies that can slow, halt, or reverse dysfunctions in the brain and nervous system.

These efforts will build new bridges to connect key stakeholders across the rare brain disorders community and disrupt conventional research approaches. “Rajeev and I are motivated to seed powerful collaborations between MIT researchers, clinicians, patients, and industry,” says Méndez. “Guoping Feng clearly understands our goal to create an environment where foundational studies can thrive and seamlessly move toward clinical impact.”

“Patient and caregiver experiences, and our foreseeable impact on their lives, will guide us and remain at the forefront of our work,” Feng adds. “For far too long the rare brain disorders community has been deprived of life-changing treatments — and, importantly, hope. RareNet gives us the opportunity to transform how we study these conditions and to do so at a moment when it’s needed more than ever.”

 

Searching for self

by Jennifer Michalowski |

This story also appears in the Fall 2025 issue of BrainScan. 

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The question of how we know ourselves might seem the subject of philosophers, but it is just as much a matter of biology. As modern neuroscientists obtain an increasingly sophisticated understanding of how the brain generates emotions, responds to the external world, and learns from experience, some researchers are returning to a central question: How do we know our experiences, emotions, and physical sensations belong to us?

Curiosity about how the brain generates our sense of self has been a driving force for the research of McGovern Investigator Fan Wang. Following that curiosity has drawn Wang into diverse studies, exploring the origins of pain and the mechanisms we use to control our movements.

“We cannot pinpoint a set of active neurons and say that’s the sense of self. That still remains a mystery,” says Wang, who is also a professor of brain and cognitive sciences and co-director of the K. Lisa Yang and Hock E. Tan Center for Molecular Therapeutics at MIT. But she and other neuroscientists are drilling down into different functions of the brain that together might generate our awareness of ourselves.

Woman wearing blue blazer smiles and gestures off camera with man in white lab coat seated next to her.
McGovern Investigator Fan Wang (right) with research scientist Vincent Prevosto, who studies brain regions implicated in whisker movement. Photo: Steph Stevens

Wang, who teaches the undergraduate course, “Neurobiology of Self,” explains that there are lots of ways to think about our sense of self, which are probably deeply integrated in the brain. Some are mostly about our physical bodies: How do we experience touch? How do we understand
where we are in space, or recognize the boundary between ourselves and rest of the world? Some consider more internal sensations, like how we experience pain or hunger. Emotion is also key to our sense of self: How do we know that anger or joy are our own, and why do these states change the way our bodies feel?

Wang can trace her initial interest in the brain’s sense of self to work she did as a graduate student in Richard Axel’s lab at Columbia University. The lab had identified receptors expressed by sensory neurons in the nose that detect odorous substances. Wang and others discovered the pathways that information about these smells takes to the brain, and how the brain distinguishes one smell from another.

Who is the “knower” of this information? “The answer,” Wang says, “is ‘I’ or ‘me.’ But understanding where I get the sense of self and how that is constructed, is what drives me to do neuroscience.”

Mechanisms of movement

In her lab at the McGovern Institute, Wang is studying how the brain controls the body’s movements, which she sees as closely tied to the awareness of our physical selves. “The reason I think I am in my body is because I can control my movement. I generate the movement. I cannot control your movement,” says Wang. “Volitional movement gives us a sense of agency, and this sense of agency resembles the sense of self.” For the mice that the group studies, one crucial type of movement comes from the whiskers, which the animals depend on as they explore their environments. Wang’s group has traced the neural circuity that controls whiskers’ rhythmic back-and-forth, which is initiated in the brainstem, where many of the body’s most vital functions are controlled. Wang describes the simple circuit as an oscillator, or a self-generated loop.

A maximum projection image showing tracked whiskers on the mouse muzzle. The right (control) side shows the back-and-forth rhythmic sweeping of the whiskers, while the experimental side where the whisking oscillator neurons are silenced, the whiskers move very little. Image: Wang Lab

Once it’s started, “the movement can go on unless some other signals stop it,” she says. The movement the circuit generates is simple but voluntary, and can be fine-tuned based on the sensory feedback the whiskers relay back to the brain. They’ve also been investigating how mice move the larynx to generate the squeaks and calls they use to communicate. These intentional movements must be coordinated with the ongoing cycles of respiration since we produce normal sounds only during expiration. Wang’s team has found neurons in the brainstem that generate vocalization-specific movements, and also discovered how respiration-controlling neural circuits can override them, ensuring that breathing is prioritized.

Wang says understanding the circuitry that controls these simple movements sets the stage for figuring out how the brain modifies activity in those circuits to create more complex, intentional movements. “That brings me closer to understanding where this volition is generated — and closer to this sense of self,” she says.

Emotional pain

Still, she knows that volitional movements — even those generated in response to perceptions of the environment — do not, on their own, define a sense of self. As a counterexample, she looks to self-driving cars: “There’s sensory information coming into the central computer, which then generates a motor output — where to drive, where to turn, where to stop. But none of us think a Waymo taxi has a sense of self.”

Wang says when she pondered the ways in which AI-powered cars lack a sense of self, she began thinking about emotions and pain. “If the self-driving Waymo crashes, it will not feel pain,” she says. “But if we hurt ourselves, we will feel pain. And we will hate that, and then we’ll learn.” So her lab is also exploring how the nervous system generates pain perception, including the emotional response that it evokes.

Ensembles of neurons in the amygdala activated by general anesthesia. Image: Fan Wang

In both humans and mice, pain causes emotional suffering that can be recognized and measured through changes in body functions like heart rate and blood pressure. With funding from the K. Lisa Yang Brain-Body Center at MIT, Wang’s lab is carefully tracking these involuntary, or autonomic, functions to gain a more complete understanding of pain’s emotional impact. This approach has helped clarify the role of pain-suppressing neurons in the brain’s amygdala — an important emotion-processing center — that Wang’s team discovered in 2020. When researchers selectively activate those cells in mice, the animals’ behavior makes it clear that the neurons are suppressing pain. Now, the group has learned that activating these neurons suppresses the autonomic response to pain.

Wang says there’s hope that modulating pain’s emotional response might be a way to treat chronic pain in patients. She explains that some patients with damage to another one of the brain’s emotional centers, the cingulate cortex, feel painful stimuli, but experience them as merely intense sensations. That suggests that it might be possible to modulate the emotional response to pain to eliminate patients’ suffering, without blocking the protective information that pain can provide.

The team has also been focusing on another set of anesthesia-activated neurons, which they have found suppress anxiety. When anxiety-suppressing neurons are activated in mice, the animals’ heart rates slow and they become more willing to explore bright, open spaces. Another anxiety-associated measure — heart rate variability — increases. Wang explains that this change is particularly significant: “If you have persistent low heart rate variability, especially in veterans, that is a very good predictor for anxiety developing into depression in the future,” she says.

The team’s findings, which suggest that changes in autonomic functions may themselves relieve anxiety, point toward potential new targets for anti-anxiety therapies. And by highlighting the connection between emotion and bodily responses, they offer more clues about our sense of self. “These neurons are now changing some high-level concept about anxiety,” Wang points out.

That link between emotion and body seems to Wang to be key to the sense of self. The big questions remain unanswered, but that simply stokes her curiosity. “I can be aware of my bodily responses: I am aware of ‘I am anxious’ or ‘I am in pain.’ I can see the pathways from which stimuli go into these nervous systems and come back down to the body and control the response. But I still don’t know who is the person — the knower,” she says. “I haven’t found it, so I’m going to keep looking.”

Feng Zhang elected to EMBO membership

by Julie Pryor |

The European Molecular Biology Organization (EMBO), a professional non-profit organization dedicated to promoting international research in life sciences, announced its new members today. Among the 69 new members recognized for their outstanding achievements is Feng Zhang, the James and Patricia Poitras Professor of Neuroscience at MIT and an investigator at the McGovern Institute.

Zhang, who is also a core member of the Broad Institute, a professor of brain and cognitive sciences and biological engineering at MIT, and a Howard Hughes Medical Institute investigator, is a molecular biologist focused on improving human health. He played an integral role in pioneering the use of CRISPR-Cas9 for genome editing in human cells, including working with Stuart Orkin to develop Casgevy, the first CRISPR-based therapeutic approved for clinical use. His team is currently discovering new ways to modify cellular function and activity—including the restoration of diseased, stressed, or aged cells to a more healthful state.

Zhang has been elected to EMBO as an associate member, where he joins a community of more than 2,100 international life scientists that have demonstrated research excellence in their fields.

“A major strength of EMBO lies in the excellence and dedication of its members,” says EMBO Director Fiona Watt. “Science thrives on global collaboration, and the annual election of the new EMBO members and associate members brings fresh energy and inspiration to our community. We are honoured to welcome this remarkable group of scientists to the EMBO Membership. Their ideas and contributions will enrich the organization and help advance the life sciences internationally.”

The 60 new EMBO members in 2025 are based in 18 member states of the EMBC, the intergovernmental organization that funds the main EMBO programs and activities. The nine new EMBO associate members, including Zhang, are based in six countries outside Europe. In total, 29 (42%) of the new members are women and 40 (58%) are men.

The new members will be formally welcomed at the next EMBO Members’ Meeting in Heidelberg, Germany, on 22-24 October 2025.

Ten years of bigger samples, better views

by Jennifer Michalowski |

Nearly 150 years ago, scientists began to imagine how information might flow through the brain based on the shapes of neurons they had seen under the microscopes of the time. With today’s imaging technologies, scientists can zoom in much further, seeing the tiny synapses through which neurons communicate with one another and even the molecules the cells use to relay their messages. These inside views can spark new ideas about how healthy brains work and reveal important changes that contribute to disease.

McGovern Institute Investigator Edward Boyden. Photo: Justin Knight

This sharper view of biology is not just about the advances that have made microscopes more powerful than ever before. Using methodology developed in the lab of McGovern investigator Edward Boyden, researchers around the world are imaging samples that have been swollen to as much as 20 times their original size so their finest features can be seen more clearly.

“It’s a very different way to do microscopy,” says Boyden, who is also a Howard Hughes Medical Institute investigator and a member of the Yang Tan Collective at MIT. “In contrast to the last 300 years of bioimaging, where you use a lens to magnify an image of light from an object, we physically magnify objects themselves.” Once a tissue is expanded, Boyden says, researchers can see more even with widely available, conventional microscopy hardware.

Boyden’s team introduced this approach, which they named expansion microscopy (ExM), in 2015. Since then, they have been refining the method and adding to its capabilities, while researchers at MIT and beyond deploy it to learn about life on the smallest of scales.

“It’s spreading very rapidly throughout biology and medicine,” Boyden says. “It’s being applied to kidney disease, the fruit fly brain, plant seeds, the microbiome, Alzheimer’s disease, viruses, and more.”

Origins of ExM 

To develop expansion microscopy, Boyden and his team turned to hydrogels: a material with remarkable water-absorbing properties that had already been put to practical use: it’s layered inside disposable diapers to keep babies dry. Boyden’s lab hypothesized that hydrogels could retain their structure while they absorbed hundreds of times their original weight in water, expanding the space between their chemical components as they swell.

After some experimentation, Boyden’s team settled on four key steps to enlarging tissue samples for better imaging. First, the tissue must be infused with a hydrogel. Components of the tissue, biomolecules, are anchored to the gel’s web-like matrix, linking them directly to the molecules that make up the gel. Then the tissue is chemically softened and water is added. As the hydrogel absorbs the water, it swells and the tissue expands, growing evenly so the relative positions of its components are preserved.

Boyden and graduate students Fei Chen and Paul Tillberg’s first report on expansion microscopy was published in the journal Science in 2015. In it, the team demonstrated that by spreading apart molecules that had been crowded inside cells, features that would have blurred together under a standard light microscope became separate and distinct. Light microscopes can discriminate between objects that are separated by about 300 nanometers—a limit imposed by the laws of physics. With expansion microscopy, Boyden’s group reported an effective resolution of about 70 nanometers, for a four-fold expansion.

Boyden says this is a level of clarity that biologists need. “Biology is fundamentally, in the end, a nanoscale science,” he says. “Biomolecules are nanoscale, and the interactions between biomolecules are over nanoscale distances. Many of the most important problems in biology and medicine involve nanoscale questions.” Several kinds of sophisticated microscopes, each with their own advantages and disadvantages, can bring this kind of detail to light. But those methods are costly and require specialized skills, making them inaccessible for most researchers. “Expansion microscopy democratizes nanoimaging,” Boyden says. “Now anybody can go look at the building blocks of life and how they relate to each other.”

Empowering scientists

Since Boyden’s team introduced expansion microscopy in 2015, research groups around the world have published hundreds of papers reporting on discoveries they have made using expansion microscopy. For neuroscientists, the technique has lit up the intricacies of elaborate neural circuits, exposed how particular proteins organize themselves at and across synapses to facilitate communication between neurons, and uncovered changes associated with aging and disease.

It has been equally empowering for studies beyond the brain. Sabrina Absalon uses expansion microscopy every week in her lab at Indiana University School of Medicine to study the malaria parasite, a single-celled organism packed with specialized structures that enable it to infect and live inside its hosts. The parasite is so small, most of those structures can’t be seen with ordinary light microscopy. “So as a cell biologist, I’m losing the biggest tool to infer protein function, organelle architecture, morphology, linked to function, and all those things–which is my eye,” she says. With expansion, she can not only see the organelles inside a malaria parasite, she can watch them assemble and follow what happens to them when the parasite divides. Understanding those processes, she says, could help drug developers find new ways to interfere with the parasite’s life cycle.

Longitudinally opened mosquito midguts prepared using MoTissU-ExM. Image: Sabrina Absalon

Absalon adds that the accessibility of expansion microscopy is particularly important in the field of parasitology, where a lot of research is happening in parts of the world where resources are limited. Workshops and training programs in Africa, South America, and Asia are ensuring the technology reaches scientists whose communities are directly impacted by malaria and other parasites. “Now they can get super-resolution imaging without very fancy equipment,” Absalon says.

Always Improving

Since 2015, Boyden’s interdisciplinary lab group has found a variety of creative ways to improve expansion microscopy and use it in new ways. Their standard technique today enables better labeling, bigger expansion factors, and higher resolution imaging. Cellular features less than 20 nanometers from one another can now be separated enough to appear distinct under a light microscope.

They’ve also adapted their protocols to work with a range of important sample types, from entire roundworms (popular among neuroscientists, developmental biologists, and other researchers) to clinical samples. In the latter regard, they’ve shown that expansion can help reveal subtle signs of disease, which could enable earlier or less costly diagnoses.

Originally, the group optimized its protocol for visualizing proteins inside cells, by labeling proteins of interest and anchoring them to the hydrogel prior to expansion. With a new way of processing samples, users can now restain their expanded samples with new labels for multiple rounds of imaging, so they can pinpoint the positions of dozens of different proteins in the same tissue. That means researchers can visualize how molecules are organized with respect to one another and how they might interact, or survey large sets of proteins to see, for example, what changes with disease.

Synaptic proteins and their associations to neuronal processes in the mouse primary somatosensory cortex imaged using expansion microscopy. Image: Boyden lab

But better views of proteins were just the beginning for expansion microscopy. “We want to see everything,” Boyden says. “We’d love to see every biomolecule there is, with precision down to atomic scale.” They’re not there yet—but with new probes and modified procedures, it’s now possible to see not just proteins, but also RNA and lipids in expanded tissue samples.

Labeling lipids, including those that form the membranes surrounding cells, means researchers can now see clear outlines of cells in expanded tissues. With the enhanced resolution afforded by expansion, even the slender projections of neurons can be traced through an image. Typically, researchers have relied on electron microscopy, which generates exquisitely detailed pictures but requires expensive equipment, to map the brain’s circuitry. “Now you can get images that look a lot like electron microscopy images, but on regular old light microscopes—the kind that everybody has access to,” Boyden says.

Boyden says expansion can be powerful in combination with other cutting-edge tools. When expanded samples are used with an ultra-fast imaging method developed by Eric Betzig, an HHMI investigator at the University of California, Berkeley, called lattice light-sheet microscopy, the entire brain of a fruit fly can be imaged at high resolution in just a few days. (See HHMI video below).

And when RNA molecules are anchored within a hydrogel network and then sequenced in place, scientists can see exactly where inside cells the instructions for building specific proteins are positioned, which Boyden’s team demonstrated in a collaboration with Harvard University geneticist George Church and then-MIT-professor Aviv Regev. “Expansion basically upgrades many other technologies’ resolutions,” Boyden says. “You’re doing mass-spec imaging, X-ray imaging, or Raman imaging? Expansion just improved your instrument.”

Expanding Possibilities

Ten years past the first demonstration of expansion microscopy’s power, Boyden and his team are committed to continuing to make expansion microscopy more powerful. “We want to optimize it for different kinds of problems, and making technologies faster, better, and cheaper is always important,” he says. But the future of expansion microscopy will be propelled by innovators outside the Boyden lab, too. “Expansion is not only easy to do, it’s easy to modify—so lots of other people are improving expansion in collaboration with us, or even on their own,” Boyden says.

Boyden points to a group led by Silvio Rizzoli at the University Medical Center Göttingen in Germany that, collaborating with Boyden, has adapted the expansion protocol to discern the physical shapes of proteins. At the Korea Advanced Institute of Science and Technology, researchers led by Jae-Byum Chang, a former postdoctoral researcher in Boyden’s group, have worked out how to expand entire bodies of mouse embryos and young zebrafish, collaborating with Boyden to set the stage for examining developmental processes and long-distance neural connections with a new level of detail. And mapping connections within the brain’s dense neural circuits could become easier with light-microscopy based connectomics, an approach developed by Johann Danzl and colleagues at the Institute of Science and Technology in Austria that takes advantage of both the high resolution and molecular information that expansion microscopy can reveal.

“The beauty of expansion is that it lets you see a biological system down to its smallest building blocks,” Boyden says.

His team is intent on pushing the method to its physical limits, and anticipates new opportunities for discovery as they do. “If you can map the brain or any biological system at the level of individual molecules, you might be able to see how they all work together as a network—how life really operates,” he says.

Seeing more in expansion microscopy

by Jennifer Michalowski |

In biology, seeing can lead to understanding, and researchers in Edward Boyden’s lab at MIT’s McGovern Institute are committed to bringing life into sharper focus. With a pair of new methods, they are expanding the capabilities of expansion microscopy—a high-resolution imaging technique the group introduced in 2015—so researchers everywhere can see more when they look at cells and tissues under a light microscope.

McGovern Institute Investigator Edward Boyden. Photo: Justin Knight

“We want to see everything, so we’re always trying to improve it,” says Boyden, the Y. Eva Tan Professor in Neurotechnology at MIT.  “A snapshot of all life, down to its fundamental building blocks, is really the goal.” Boyden is also a Howard Hughes Medical Institute investigator and a member of the Yang Tan Collective at MIT.

With new ways of staining their samples and processing images, users of expansion microscopy can now see vivid outlines of the shapes of cells in their images and pinpoint the locations of many different proteins inside a single tissue sample with resolution that far exceeds that of conventional light microscopy. These advances, both reported in the journal Nature Communications, enable new ways of tracing the slender projections of neurons and visualizing spatial relationships between molecules that contribute to health and disease.

Expansion microscopy uses a water-absorbing hydrogel to physically expand biological tissues. After a tissue sample has been permeated by the hydrogel, it is hydrated. The hydrogel swells as it absorbs water, preserving the relative locations of molecules in the tissue as it gently pulls them away from one another. As a result, crowded cellular components appear separate and distinct when the expanded tissue is viewed under a light microscope. The approach, which can be performed using standard laboratory equipment, has made super-resolution imaging accessible to most research teams.

Since first developing expansion microscopy, Boyden and his team have continued to enhance the method—increasing its resolution, simplifying the procedure, devising new features, and integrating it with other tools.

Visualizing cell membranes

One of the team’s latest advances is a method called ultrastructural membrane expansion microscopy (umExM), which they described in the February 12 issue of Nature Communications. With it, biologists can use expansion microscopy to visualize the thin membranes that form the boundaries of cells and enclose the organelles inside them. These membranes, built mostly of molecules called lipids, have been notoriously difficult to densely label in intact tissues for imaging with light microscopy. Now, researchers can use umExM to study cellular ultrastructure and organization within tissues.

Tay Shin, a former graduate student in Boyden’s lab and a J. Douglas Tan Fellow in the Tan-Yang Center for Autism Research at MIT, led the development of umExM. “Our goal was very simple at first: Let’s label membranes in intact tissue, much like how an electron microscope uses osmium tetroxide to label membranes to visualize the membranes in tissue,” he says. “It turns out that it’s extremely hard to achieve this.”

The team first needed to design a label that would make the membranes in tissue samples visible under a light microscope. “We almost had to start from scratch,” Shin says. “We really had to think about the fundamental characteristics of the probe that is going to label the plasma membrane, and then think about how to incorporate them into expansion microscopy.” That meant engineering a molecule that would associate with the lipids that make up the membrane and link it to both the hydrogel used to expand the tissue sample and a fluorescent molecule for visibility.

After optimizing the expansion microscopy protocol for membrane visualization and extensively testing and improving potential probes, Shin found success one late night in the lab. He placed an expanded tissue sample on a microscope and saw sharp outlines of cells.

Traceability of umExM. 3D rendering of 20 manually traced and reconstructed myelinated axons in the corpus callosum. Image: Ed Boyden

Because of the high resolution enabled by expansion, the method allowed Boyden’s team to identify even the tiny dendrites that protrude from neurons and clearly see the long extensions of their slender axons. That kind of clarity could help researchers follow individual neurons’ paths within the densely interconnected networks of the brain, the researchers say.

Boyden calls tracing these neural processes “a top priority of our time in brain science.” Such tracing has traditionally relied heavily on electron microscopy, which requires specialized skills and expensive equipment. Shin says that because expansion microscopy uses a standard light microscope, it is far more accessible to laboratories worldwide.

Shin and Boyden point out that users of expansion microscopy can learn even more about their samples when they pair the new ability to reveal lipid membranes with fluorescent labels that show where specific proteins are located. “That’s important, because proteins do a lot of the work of the cell, but you want to know where they are with respect to the cell’s structure,” Boyden says.

One sample, many proteins

To that end, researchers no longer have to choose just a few proteins to see when they use expansion microscopy. With a new method called multiplexed expansion revealing (multiExR), users can now label and see more than 20 different proteins in a single sample. Biologists can use the method to visualize sets of proteins, see how they are organized with respect to one another, and generate new hypotheses about how they might interact.

A key to the new method, reported November 9, 2024, in Nature Communications, is the ability to repeatedly link fluorescently labeled antibodies to specific proteins in an expanded tissue sample, image them, then strip these away and use a new set of antibodies to reveal a new set of proteins. Postdoctoral fellow Jinyoung Kang fine-tuned each step of this process, assuring tissue samples stayed intact and the labeled proteins produced bright signals in each round of imaging.

After capturing many images of a single sample, Boyden’s team faced another challenge: how to ensure those images were in perfect alignment so they could be overlaid with one another, producing a final picture that showed the precise positions of all of the proteins that had been labeled and visualized one by one.

Expansion microscopy lets biologists visualize some of cells’ tiniest features—but to find the same features over and over again during multiple rounds of imaging, Boyden’s team first needed to home in on a larger structure. “These fields of view are really tiny, and you’re trying to find this really tiny field of view in a gel that’s actually become quite large once you’ve expanded it,” explains Margaret Schroeder, a graduate student in Boyden’s lab who, with Kang, led the development of multiExR.

“Here’s one of the most famous receptors in all of neuroscience, hiding out in one of the most famous molecular hallmarks of pathology in neuroscience.” – Ed Boyden

To navigate to the right spot every time, the team decided to label the blood vessels that pass through each tissue sample and use these as a guide. To enable precise alignment, certain fine details also needed to consistently appear in every image; for this, the team labeled several structural proteins. With these reference points and customized imaging processing software, the team was able to integrate all of their images of a sample into one, revealing how proteins that had been visualized separately were arranged relative to one another.

The team used multiExR to look at amyloid plaques—the aberrant protein clusters that notoriously develop in brains affected by Alzheimer’s disease. “We could look inside those amyloid plaques and ask, what’s inside of them? And because we can stain for many different proteins, we could do a high throughput exploration,” Boyden says. The team chose 23 different proteins to view in their images. The approach revealed some surprises, such as the presence of certain neurotransmitter receptors (AMPARs). “Here’s one of the most famous receptors in all of neuroscience, and there it is, hiding out in one of the most famous molecular hallmarks of pathology in neuroscience,” says Boyden. It’s unclear what role, if any, the receptors play in Alzheimer’s disease—but the finding illustrates how the ability to see more inside cells can expose unexpected aspects of biology and raise new questions for research.

Funding for this work came from MIT, Lisa Yang and Y. Eva Tan, John Doerr, the Open Philanthropy Project, the Howard Hughes Medical Institute, the US Army, Cancer Research UK, the New York Stem Cell Foundation, the National Institutes of Health, Lore McGovern, Good Ventures, Schmidt Futures. Samsung, MathWorks, the Collamore-Rogers Fellowship, the National Science Foundation, Alana Foundation USA, the Halis Family Foundation, Lester A. Gimpelson, Donald and Glenda Mattes, David B. Emmes, Thomas A. Stocky, Avni U. Shah, Kathleen Octavio, Good Ventures/Open Philanthropy, and the European Union’s Horizon 2020 program.

A cell protector collaborates with a killer

by Jennifer Michalowski |

From early development to old age, cell death is a part of life. Without enough of a critical type of cell death known as apoptosis, animals wind up with too many cells, which can set the stage for cancer or autoimmune disease. But careful control is essential, because when apoptosis eliminates the wrong cells, the effects can be just as dire, helping to drive many kinds of neurodegenerative disease.

Portrait of a scientist
McGovern Investigator Robert Horvitz poses for a photo in his laboratory. Photo: AP Images/Aynsley Floyd

By studying the microscopic roundworm Caenorhabditis elegans—which was honored with its fourth Nobel Prize last month—scientists at MIT’s McGovern Institute have begun to unravel a longstanding mystery about the factors that control apoptosis: how a protein capable of preventing programmed cell death can also promote it. Their study, led by McGovern Investigator Robert Horvitz and reported October 9, 2024, in the journal Science Advances, sheds light on the process of cell death in both health and disease.

“These findings, by graduate student Nolan Tucker and former graduate student, now MIT faculty colleague, Peter Reddien, have revealed that a protein interaction long thought to block apoptosis in C. elegans, likely instead has the opposite effect,” says Horvitz, who shared the 2002 Nobel Prize for discovering and characterizing the genes controlling cell death in C. elegans.

Mechanisms of cell death

Horvitz, Tucker, Reddien and colleagues have provided foundational insights in the field of apoptosis by using C. elegans to analyze the mechanisms that drive apoptosis as well as the mechanisms that determine how cells ensure apoptosis happens when and where it should. Unlike humans and other mammals, which depend on dozens of proteins to control apoptosis, these worms use just a few. And when things go awry, it’s easy to tell: When there’s not enough apoptosis, researchers can see that there are too many cells inside the worms’ translucent bodies. And when there’s too much, the worms lack certain biological functions or, in more extreme cases, can’t reproduce or die during embryonic development.

black and white microscopic image of worms
The nematode worm Caenorhabditis elegans has provided answers to many fundamental questions in biology. Image: Robert Horvitz

Work in the Horvitz lab defined the roles of many of the genes and proteins that control apoptosis in worms. These regulators proved to have counterparts in human cells, and for that reason studies of worms have helped reveal how human cells govern cell death and pointed toward potential targets for treating disease.

A protein’s dual role

Three of C. elegans’ primary regulators of apoptosis actively promote cell death, whereas just one, CED-9, reins in the apoptosis-promoting proteins to keep cells alive. As early as the 1990s, however, Horvitz and colleagues recognized that CED-9 was not exclusively a protector of cells. Their experiments indicated that the protector protein also plays a role in promoting cell death. But while researchers thought they knew how CED-9 protected against apoptosis, its pro-apoptotic role was more puzzling.

CED-9’s dual role means that mutations in the gene that encode it can impact apoptosis in multiple ways. Most ced-9 mutations interfere with the protein’s ability to protect against cell death and result in excess cell death. Conversely, mutations that abnormally activate ced-9 cause too little cell death, just like mutations that inactivate any of the three killer genes.

An atypical ced-9 mutation, identified by Reddien when he was a PhD student in Horvitz’s lab, hinted at how CED-9 promotes cell death. That mutation altered the part of the CED-9 protein that interacts with the protein CED-4, which is proapoptotic. Since the mutation specifically leads to a reduction in apoptosis, this suggested that CED-9 might need to interact with CED-4 to promote cell death.

The idea was particularly intriguing because researchers had long thought that CED-9’s interaction with CED-4 had exactly the opposite effect: In the canonical model, CED-9 anchors CED-4 to cells’ mitochondria, sequestering the CED-4 killer protein and preventing it from associating with and activating another key killer, the CED-3 protein —thereby preventing apoptosis.

To test the hypothesis that CED-9’s interactions with the killer CED-4 protein enhance apoptosis, the team needed more evidence. So graduate student Nolan Tucker used CRISPR gene editing tools to create more worms with mutations in CED-9, each one targeting a different spot in the CED-4-binding region. Then he examined the worms. “What I saw with this particular class of mutations was extra cells and viability,” he says—clear signs that the altered CED-9 was still protecting against cell death, but could no longer promote it. “Those observations strongly supported the hypothesis that the ability to bind CED-4 is needed for the pro-apoptotic function of CED-9,” Tucker explains. Their observations also suggested that, contrary to earlier thinking, CED-9 doesn’t need to bind with CED-4 to protect against apoptosis.

When he looked inside the cells of the mutant worms, Tucker found additional evidence that these mutations prevented CED-9’s ability to interact with CED-4. When both CED-9 and CED-4 are intact, CED-4 appears associated with cells’ mitochondria. But in the presence of these mutations, CED-4 was instead at the edge of the cell nucleus. CED-9’s ability to bind CED-4 to mitochondria appeared to be necessary to promote apoptosis, not to protect against it.

In wild-type worms CED-4 is localized to mitochondria. However, the introduction of CED-9-CED-4 binding mutations such as ced-4(n6703) or ced-9(n6704), causes CED-4 protein to localize to the outer edge of the nucleus. Image: Nolan Tucker, Robert Horvitz

Looking ahead

While the team’s findings begin to explain a long-unanswered question about one of the primary regulators of apoptosis, they raise new ones, as well. “I think that this main pathway of apoptosis has been seen by a lot of people as more or less settled science. Our findings should change that view,” Tucker says.

The researchers see important parallels between their findings from this study of worms and what’s known about cell death pathways in mammals. The mammalian counterpart to CED-9 is a protein called BCL-2, mutations in which can lead to cancer.  BCL-2, like CED-9, can both promote and protect against apoptosis. As with CED-9, the pro-apoptotic function of BCL-2 has been mysterious. In mammals, too, mitochondria play a key role in activating apoptosis. The Horvitz lab’s discovery opens opportunities to better understand how apoptosis is regulated not only in worms but also in humans, and how dysregulation of apoptosis in humans can lead to such disorders as cancer, autoimmune disease and neurodegeneration.

Brain pathways that control dopamine release may influence motor control

Anne Trafton |

Within the human brain, movement is coordinated by a brain region called the striatum, which sends instructions to motor neurons in the brain. Those instructions are conveyed by two pathways, one that initiates movement (“go”) and one that suppresses it (“no-go”).

In a new study, MIT researchers have discovered an additional two pathways that arise in the striatum and appear to modulate the effects of the go and no-go pathways. These newly discovered pathways connect to dopamine-producing neurons in the brain — one stimulates dopamine release and the other inhibits it.

By controlling the amount of dopamine in the brain via clusters of neurons known as striosomes, these pathways appear to modify the instructions given by the go and no-go pathways. They may be especially involved in influencing decisions that have a strong emotional component, the researchers say.

“Among all the regions of the striatum, the striosomes alone turned out to be able to project to the dopamine-containing neurons, which we think has something to do with motivation, mood, and controlling movement,” says Ann Graybiel, an MIT Institute Professor, a member of MIT’s McGovern Institute for Brain Research, and the senior author of the new study.

Iakovos Lazaridis, a research scientist at the McGovern Institute, is the lead author of the paper, which appears today in the journal Current Biology.

New pathways

Graybiel has spent much of her career studying the striatum, a structure located deep within the brain that is involved in learning and decision-making, as well as control of movement.

Within the striatum, neurons are arranged in a labyrinth-like structure that includes striosomes, which Graybiel discovered in the 1970s. The classical go and no-go pathways arise from neurons that surround the striosomes, which are known collectively as the matrix. The matrix cells that give rise to these pathways receive input from sensory processing regions such as the visual cortex and auditory cortex. Then, they send go or no-go commands to neurons in the motor cortex.

However, the function of the striosomes, which are not part of those pathways, remained unknown. For many years, researchers in Graybiel’s lab have been trying to solve that mystery.

Their previous work revealed that striosomes receive much of their input from parts of the brain that process emotion. Within striosomes, there are two major types of neurons, classified as D1 and D2. In a 2015 study, Graybiel found that one of these cell types, D1, sends input to the substantia nigra, which is the brain’s major dopamine-producing center.

It took much longer to trace the output of the other set, D2 neurons. In the new Current Biology study, the researchers discovered that those neurons also eventually project to the substantia nigra, but first they connect to a set of neurons in the globus palladus, which inhibits dopamine output. This pathway, an indirect connection to the substantia nigra, reduces the brain’s dopamine output and inhibits movement.

The researchers also confirmed their earlier finding that the pathway arising from D1 striosomes connects directly to the substantia nigra, stimulating dopamine release and initiating movement.

“In the striosomes, we’ve found what is probably a mimic of the classical go/no-go pathways,” Graybiel says. “They’re like classic motor go/no-go pathways, but they don’t go to the motor output neurons of the basal ganglia. Instead, they go to the dopamine cells, which are so important to movement and motivation.”

Emotional decisions

The findings suggest that the classical model of how the striatum controls movement needs to be modified to include the role of these newly identified pathways. The researchers now hope to test their hypothesis that input related to motivation and emotion, which enters the striosomes from the cortex and the limbic system, influences dopamine levels in a way that can encourage or discourage action.

That dopamine release may be especially relevant for actions that induce anxiety or stress. In their 2015 study, Graybiel’s lab found that striosomes play a key role in making decisions that provoke high levels of anxiety; in particular, those that are high risk but may also have a big payoff.

“Ann Graybiel and colleagues have earlier found that the striosome is concerned with inhibiting dopamine neurons. Now they show unexpectedly that another type of striosomal neuron exerts the opposite effect and can signal reward. The striosomes can thus both up- or down-regulate dopamine activity, a very important discovery. Clearly, the regulation of dopamine activity is critical in our everyday life with regard to both movements and mood, to which the striosomes contribute,” says Sten Grillner, a professor of neuroscience at the Karolinska Institute in Sweden, who was not involved in the research.

Another possibility the researchers plan to explore is whether striosomes and matrix cells are arranged in modules that affect motor control of specific parts of the body.

“The next step is trying to isolate some of these modules, and by simultaneously working with cells that belong to the same module, whether they are in the matrix or striosomes, try to pinpoint how the striosomes modulate the underlying function of each of these modules,” Lazaridis says.

They also hope to explore how the striosomal circuits, which project to the same region of the brain that is ravaged by Parkinson’s disease, may influence that disorder.

The research was funded by the National Institutes of Health, the Saks-Kavanaugh Foundation, the William N. and Bernice E. Bumpus Foundation, Jim and Joan Schattinger, the Hock E. Tan and K. Lisa Yang Center for Autism Research, Robert Buxton, the Simons Foundation, the CHDI Foundation, and an Ellen Schapiro and Gerald Axelbaum Investigator BBRF Young Investigator Grant.