Research Area: Stem Cell and Developmental Biology

A planarian’s guide to growing a new head

Researchers at the Whitehead Institute have described a pathyway by which planarians, freshwater flatworms with spectacular regenerative capabilities, can restore large portions of their nervous system, even regenerating a new head with a fully functional brain.

Shafaq Zia | Whitehead Institute
February 6, 2025

Cut off any part of this worm’s body and it will regrow. This is the spectacular yet mysterious regenerative ability of freshwater flatworms known as planarians. The lab of Whitehead Institute Member Peter Reddien investigates the principles underlying this remarkable feat. In their latest study, published in PLOS Genetics on February 6, first author staff scientist M. Lucila Scimone, Reddien, and colleagues describe how planarians restore large portions of their nervous system—even regenerating a new head with a fully functional brain—by manipulating a signaling pathway.

This pathway, called the Delta-Notch signaling pathway, enables neurons to guide the differentiation of a class of progenitors—immature cells that will differentiate into specialized types—into glia, the non-neuronal cells that support and protect neurons. The mechanism ensures that the spatial pattern and relative numbers of neurons and glia at a given location are precisely restored following injury.

“This process allows planarians to regenerate neural circuits more efficiently because glial cells form only where needed, rather than being produced broadly within the body and later eliminated,” said Reddien, who is also a professor of biology at Massachusetts Institute of Technology and an Investigator with the Howard Hughes Medical Institute.

Coordinating regeneration

Multiple cell types work together to form a functional human brain. These include neurons and a more abundant group of cells called glial cells—astrocytes, microglia, and oligodendrocytes. Although glial cells are not the fundamental units of the nervous system, they perform critical functions in maintaining the connections between neurons, called synapses, clearing away dead cells and other debris, and regulating neurotransmitter levels, effectively holding the nervous system together like glue. A few years ago, Reddien and colleagues discovered cells in planarians that looked like glial cells and performed similar neuro-supportive functions. This led to the first characterization of glial cells in planarians in 2016.

Unlike in mammals where the same set of neural progenitors give rise to both neurons and glia, glial cells in planarians originate from a separate, specialized group of progenitors. These progenitors, called phagocytic progenitors, can not only give rise to glial cells but also pigment cells that determine the worm’s coloration, as well as other, lesser understood cell types.

Why neurons and glia in planarians originate from distinct progenitors—and what factors ultimately determine the differentiation of phagocytic progenitors into glia—are questions that still puzzled Reddien and team members. Then, a study showing that planarian neurons regenerate before glia formation led the researchers to wonder whether a signaling mechanism between neurons and phagocytic progenitors guides the specification of glia in planarians.

The first step to unravel this mystery was to look at the Notch signaling pathway, which is known to play a crucial role in the development of neurons and glia in other organisms, and determine its role in planarian glia regeneration. To do this, the researchers used RNA interference (RNAi)—a technique that decreases or completely silences the expression of genes—to turn off key genes involved in the Notch pathway and amputated the planarian’s head. It turned out Notch signaling is essential for glia regeneration and maintenance in planarians—no glial cells were found in the animal following RNAi, while the differentiation of other types of phagocytic cells was unaffected.

Of the different Notch signaling pathway components the researchers tested, turning of the genes notch-1, delta-2, and suppressor of hairless produced this phenotype. Interestingly, the signaling molecules Delta-2 was found on the surface of neurons, whereas Notch-1 was expressed in phagocytic progenitors.

With these findings in hand, the researchers hypothesized that interaction between Delta-2 on neurons and Notch-1 on phagocytic progenitors could be governing the final fate determination of glial cells in planarians.

To test the hypothesis, the researchers transplanted eyes either from planarians lacking the notch-1 gene or from planarians lacking the delta-2 gene into wild-type animals and assessed the formation of glial cells around the transplant site. They observed that glial cells still formed around the notch-1 deficient eyes, as notch-1 was still active in the glial progenitors of the host wild-type animal. However, no glial cells formed around the delta-2 deficient eyes, even with the Notch signaling pathway intact in phagocytic progenitors, confirming that delta-2 in the photoreceptor neurons is required for the differentiation of phagocytic progenitors into glia near the eye.

“This experiment really showed us that you have two faces of the same coin—one is the phagocytic progenitors expressing Notch-1, and one is the neurons expressing Delta-2—working together to guide the specification of glia in the organism,”said Scimone.

The researchers have named this phenomenon coordinated regeneration, as it allows neurons to influence the pattern and number of glia at specific locations without the need for a separate mechanism to adjust the relative numbers of neurons and glia.

The group is now interested in investigating whether the same phenomenon might also be involved in the regeneration of other tissue types.

AI model deciphers the code in proteins that tells them where to go

Whitehead Institute and CSAIL researchers created a machine-learning model to predict and generate protein localization, with implications for understanding and remedying disease.

Greta Friar | Whitehead Institute
February 13, 2025

Proteins are the workhorses that keep our cells running, and there are many thousands of types of proteins in our cells, each performing a specialized function. Researchers have long known that the structure of a protein determines what it can do. More recently, researchers are coming to appreciate that a protein’s localization is also critical for its function. Cells are full of compartments that help to organize their many denizens. Along with the well-known organelles that adorn the pages of biology textbooks, these spaces also include a variety of dynamic, membrane-less compartments that concentrate certain molecules together to perform shared functions. Knowing where a given protein localizes, and who it co-localizes with, can therefore be useful for better understanding that protein and its role in the healthy or diseased cell, but researchers have lacked a systematic way to predict this information.

Meanwhile, protein structure has been studied for over half-a-century, culminating in the artificial intelligence tool AlphaFold, which can predict protein structure from a protein’s amino acid code, the linear string of building blocks within it that folds to create its structure. AlphaFold and models like it have become widely used tools in research.

Proteins also contain regions of amino acids that do not fold into a fixed structure, but are instead important for helping proteins join dynamic compartments in the cell. MIT Professor Richard Young and colleagues wondered whether the code in those regions could be used to predict protein localization in the same way that other regions are used to predict structure. Other researchers have discovered some protein sequences that code for protein localization, and some have begun developing predictive models for protein localization. However, researchers did not know whether a protein’s localization to any dynamic compartment could be predicted based on its sequence, nor did they have a comparable tool to AlphaFold for predicting localization.

Now, Young, also member of the Whitehead Institute for Biological Research; Young lab postdoc Henry Kilgore; Regina Barzilay, the School of Engineering Distinguished Professor for AI and Health at MIT’s Computer Science and Artificial Intelligence Laboratory (CSAIL); and colleagues have built such a model, which they call ProtGPS. In a paper published on Feb. 6 in the journal Science, with first authors Kilgore and Barzilay lab graduate students Itamar Chinn, Peter Mikhael, and Ilan Mitnikov, the cross-disciplinary team debuts their model. The researchers show that ProtGPS can predict to which of 12 known types of compartments a protein will localize, as well as whether a disease-associated mutation will change that localization. Additionally, the research team developed a generative algorithm that can design novel proteins to localize to specific compartments.

“My hope is that this is a first step towards a powerful platform that enables people studying proteins to do their research,” Young says, “and that it helps us understand how humans develop into the complex organisms that they are, how mutations disrupt those natural processes, and how to generate therapeutic hypotheses and design drugs to treat dysfunction in a cell.”

The researchers also validated many of the model’s predictions with experimental tests in cells.

“It really excited me to be able to go from computational design all the way to trying these things in the lab,” Barzilay says. “There are a lot of exciting papers in this area of AI, but 99.9 percent of those never get tested in real systems. Thanks to our collaboration with the Young lab, we were able to test, and really learn how well our algorithm is doing.”

Developing the model

The researchers trained and tested ProtGPS on two batches of proteins with known localizations. They found that it could correctly predict where proteins end up with high accuracy. The researchers also tested how well ProtGPS could predict changes in protein localization based on disease-associated mutations within a protein. Many mutations — changes to the sequence for a gene and its corresponding protein — have been found to contribute to or cause disease based on association studies, but the ways in which the mutations lead to disease symptoms remain unknown.

Figuring out the mechanism for how a mutation contributes to disease is important because then researchers can develop therapies to fix that mechanism, preventing or treating the disease. Young and colleagues suspected that many disease-associated mutations might contribute to disease by changing protein localization. For example, a mutation could make a protein unable to join a compartment containing essential partners.

They tested this hypothesis by feeding ProtGOS more than 200,000 proteins with disease-associated mutations, and then asking it to both predict where those mutated proteins would localize and measure how much its prediction changed for a given protein from the normal to the mutated version. A large shift in the prediction indicates a likely change in localization.

The researchers found many cases in which a disease-associated mutation appeared to change a protein’s localization. They tested 20 examples in cells, using fluorescence to compare where in the cell a normal protein and the mutated version of it ended up. The experiments confirmed ProtGPS’s predictions. Altogether, the findings support the researchers’ suspicion that mis-localization may be an underappreciated mechanism of disease, and demonstrate the value of ProtGPS as a tool for understanding disease and identifying new therapeutic avenues.

“The cell is such a complicated system, with so many components and complex networks of interactions,” Mitnikov says. “It’s super interesting to think that with this approach, we can perturb the system, see the outcome of that, and so drive discovery of mechanisms in the cell, or even develop therapeutics based on that.”

The researchers hope that others begin using ProtGPS in the same way that they use predictive structural models like AlphaFold, advancing various projects on protein function, dysfunction, and disease.

Moving beyond prediction to novel generation

The researchers were excited about the possible uses of their prediction model, but they also wanted their model to go beyond predicting localizations of existing proteins, and allow them to design completely new proteins. The goal was for the model to make up entirely new amino acid sequences that, when formed in a cell, would localize to a desired location. Generating a novel protein that can actually accomplish a function — in this case, the function of localizing to a specific cellular compartment — is incredibly difficult. In order to improve their model’s chances of success, the researchers constrained their algorithm to only design proteins like those found in nature. This is an approach commonly used in drug design, for logical reasons; nature has had billions of years to figure out which protein sequences work well and which do not.

Because of the collaboration with the Young lab, the machine learning team was able to test whether their protein generator worked. The model had good results. In one round, it generated 10 proteins intended to localize to the nucleolus. When the researchers tested these proteins in the cell, they found that four of them strongly localized to the nucleolus, and others may have had slight biases toward that location as well.

“The collaboration between our labs has been so generative for all of us,” Mikhael says. “We’ve learned how to speak each other’s languages, in our case learned a lot about how cells work, and by having the chance to experimentally test our model, we’ve been able to figure out what we need to do to actually make the model work, and then make it work better.”

Being able to generate functional proteins in this way could improve researchers’ ability to develop therapies. For example, if a drug must interact with a target that localizes within a certain compartment, then researchers could use this model to design a drug to also localize there. This should make the drug more effective and decrease side effects, since the drug will spend more time engaging with its target and less time interacting with other molecules, causing off-target effects.

The machine learning team members are enthused about the prospect of using what they have learned from this collaboration to design novel proteins with other functions beyond localization, which would expand the possibilities for therapeutic design and other applications.

“A lot of papers show they can design a protein that can be expressed in a cell, but not that the protein has a particular function,” Chinn says. “We actually had functional protein design, and a relatively huge success rate compared to other generative models. That’s really exciting to us, and something we would like to build on.”

All of the researchers involved see ProtGPS as an exciting beginning. They anticipate that their tool will be used to learn more about the roles of localization in protein function and mis-localization in disease. In addition, they are interested in expanding the model’s localization predictions to include more types of compartments, testing more therapeutic hypotheses, and designing increasingly functional proteins for therapies or other applications.

“Now that we know that this protein code for localization exists, and that machine learning models can make sense of that code and even create functional proteins using its logic, that opens up the door for so many potential studies and applications,” Kilgore says.

Cellular interactions help explain vascular complications due to COVID-19 virus infection

Whitehead Institute Founding Member Rudolf Jaenisch and colleagues have found that cellular interactions help explain how SARS-CoV-2, the virus that causes COVID-19, could have such significant vascular complications, including blood clots, heart attacks, and strokes.

Greta Friar | Whitehead Institute
December 31, 2024

COVID-19 is a respiratory disease primarily affecting the lungs. However, the SARS-CoV-2 virus that causes COVID-19 surprised doctors and scientists by triggering an unusually large percentage of patients to experience vascular complications – issues related to blood flow, such as blood clots, heart attacks, and strokes.

Whitehead Institute Founding Member Rudolf Jaenisch and colleagues wanted to understand how this respiratory virus could have such significant vascular effects. They used pluripotent stem cells to generate three relevant vascular and perivascular cell types—cells that surround and help maintain blood vessels—so they could closely observe the effects of SARS-CoV-2 on the cells. Instead of using existing methods to generate the cells, the researchers developed a new approach, providing them with fresh insights into the mechanisms by which the virus causes vascular problems. The researchers found that SARS-CoV-2 primarily infects perivascular cells and that signals from these infected cells are sufficient to cause dysfunction in neighboring vascular cells, even when the vascular cells are not themselves infected. In a paper published in the journal Nature Communications on December 30, Jaenisch, postdoc in his lab Alexsia Richards, Harvard University Professor and Wyss Institute for Biologically Inspired Engineering Member David Mooney, and then-postdoc in the Jaenisch and Mooney labs Andrew Khalil share their findings and present a scalable stem cell-derived model system with which to study vascular cell biology and test medical therapies.

A new problem requires a new approach

When the COVID-19 pandemic began, Richards, a virologist, quickly pivoted her focus to SARS-CoV-2. Khalil, a bioengineer, had already been working on a new approach to generate vascular cells. The researchers realized that a collaboration could provide Richards with the research tool she needed and Khalil with an important research question to which his tool could be applied.

The three cell types that Khalil’s approach generated were endothelial cells, the vascular cells that form the lining of blood vessels; and smooth muscle cells and pericytes, perivascular cells that surround blood vessels and provide them with structure and maintenance, among other functions. Khalil’s biggest innovation was to generate all three cell types in the same media—the mixture of nutrients and signaling molecules in which stem cell-derived cells are grown.

The combination of signals in the media determines the final cell type into which a stem cell will mature, so it is much easier to grow each cell type separately in specially tailored media than to find a mixture that works for all three. Typically, Richards explains, virologists will generate a desired cell type using the easiest method, which means growing each cell type and then observing the effects of viral infection on it in isolation. However, this approach can limit results in several ways. Firstly, it can make it challenging to distinguish the differences in how cell types react to a virus from the differences caused by the cells being grown in different media.

“By making these cells under identical conditions, we could see in much higher resolution the effects of the virus on these different cell populations, and that was essential in order to form a strong hypothesis of the mechanisms of vascular symptom risk and progression,” Khalil says.

Secondly, infecting isolated cell types with a virus does not accurately represent what happens in the body, where cells are in constant communication as they react to viral exposure. Indeed, Richards’ and Khalil’s work ultimately revealed that the communication between infected and uninfected cell types plays a critical role in the vascular effects of COVID-19.

“The field of virology often overlooks the importance of considering how cells influence other cells and designing models to reflect that,” Richards says. “Cells do not get infected in isolation, and the value of our model is that it allows us to observe what’s happening between cells during infection.”

Viral infection of smooth muscle cells has broader, indirect effects

When the researchers exposed their cells to SARS-CoV-2, the smooth muscle cells and pericytes became infected—the former at especially high levels, and this infection resulted in strong inflammatory gene expression—but the endothelial cells resisted infection. Endothelial cells did show some response to viral exposure, likely due to interactions with proteins on the virus’ surface. Typically, endothelial cells press tightly together to form a firm barrier that keeps blood inside of blood vessels and prevents viruses from getting out. When exposed to SARS-CoV-2, the junctions between endothelial cells appeared to weaken slightly. The cells also had increased levels of reactive oxygen species, which are damaging byproducts of certain cellular processes.

However, big changes in endothelial cells only occurred after the cells were exposed to infected smooth muscle cells. This triggered high levels of inflammatory signaling within the endothelial cells. It led to changes in the expression of many genes relevant to immune response. Some of the genes affected were involved in coagulation pathways, which thicken blood and so can cause blood clots and related vascular events. The junctions between endothelial cells experienced much more significant weakening after exposure to infected smooth muscle cells, which would lead to blood leakage and viral spread. All of these changes occurred without SARS-CoV-2 ever infecting the endothelial cells.

This work shows that viral infection of smooth muscle cells, and their resultant signaling to endothelial cells, is the lynchpin in the vascular damage caused by SARS-CoV-2. This would not have been apparent if the researchers had not been able to observe the cells interacting with each other.

Clinical relevance of stem cell results

The effects that the researchers observed were consistent with patient data. Some of the genes whose expression changed in their stem cell-derived model had been identified as markers of high risk for vascular complications in COVID-19 patients with severe infections. Additionally, the researchers found that a later strain of SARS-CoV-2, an Omicron variant, had much weaker effects on the vascular and perivascular cells than did the original viral strain. This is consistent with the reduced levels of vascular complications seen in COVID-19 patients infected with recent strains.

Having identified smooth muscle cells as the main site of SARS-Cov-2 infection in the vascular system, the researchers next used their model system to test one drug’s ability to prevent infection of smooth muscle cells. They found that the drug, N, N-Dimethyl-D-erythro-sphingosine, could reduce infection of the cell type without harming smooth muscle or endothelial cells. Although preventing vascular complications of COVID-19 is not as pressing a need with current viral strains, the researchers see this experiment as proof that their stem cell model could be used for future drug development. New coronaviruses and other pathogens are frequently evolving, and when a future virus causes vascular complications, this model could be used to quickly test drugs to find potential therapies while the need is still high. The model system could also be used to answer other questions about vascular cells, how these cells interact, and how they respond to viruses.

“By integrating bioengineering strategies into the analysis of a fundamental question in viral pathology, we addressed important practical challenges in modeling human disease in culture and gained new insights into SARS-CoV-2 infection,” Mooney says.

“Our interdisciplinary approach allowed us to develop an improved stem cell model for infection of the vasculature,” says Jaenisch, who is also a professor of biology at the Massachusetts Institute of Technology. “Our lab is already applying this model to other questions of interest, and we hope that it can be a valuable tool for other researchers.”

Cellular traffic congestion in chronic diseases suggests new therapeutic targets

Many chronic diseases have a common denominator that could be driving their dysfunction: reduced protein mobility, which in turn reduces protein function. A new paper from the Young Lab describes this pervasive mobility defect.

Greta Friar | Whitehead Institute
November 26, 2024

Chronic diseases like type 2 diabetes and inflammatory disorders have a huge impact on humanity. They are a leading cause of disease burden and deaths around the globe, are physically and economically taxing, and the number of people with such diseases is growing.

Treating chronic disease has proven difficult because there is not one simple cause, like a single gene mutation, that a treatment could target. At least, that’s how it has appeared to scientists. However, research from Whitehead Institute Member Richard Young and colleagues, published in the journal Cell on November 27, reveals that many chronic diseases have a common denominator that could be driving their dysfunction: reduced protein mobility. What this means is that around half of all proteins active in cells slow their movement when cells are in a chronic disease state, reducing the proteins’ functions. The researchers’ findings suggest that protein mobility may be a linchpin for decreased cellular function in chronic disease, making it a promising therapeutic target.

In this paper, Young and colleagues in his lab, including postdoc Alessandra Dall’Agnese, graduate students Shannon Moreno and Ming Zheng, and research scientist Tong Ihn Lee, describe their discovery of this common mobility defect, which they call proteolethargy; explain what causes the defect and how it leads to dysfunction in cells; and propose a new therapeutic hypothesis for treating chronic diseases.

“I’m excited about what this work could mean for patients,” says Dall’Agnese. “My hope is that this will lead to a new class of drugs that restore protein mobility, which could help people with many different diseases that all have this mechanism as a common denominator.”

“This work was a collaborative, interdisciplinary effort that brought together biologists, physicists, chemists, computer scientists and physician-scientists,” Lee says. “Combining that expertise is a strength of the Young lab. Studying the problem from different viewpoints really helped us think about how this mechanism might work and how it could change our understanding of the pathology of chronic disease.”

Commuter delays cause work stoppages in the cell

How do proteins moving more slowly through a cell lead to widespread and significant cellular dysfunction? Dall’Agnese explains that every cell is like a tiny city, with proteins as the workers who keep everything running. Proteins have to commute in dense traffic in the cell, traveling from where they are created to where they work. The faster their commute, the more work they get done. Now, imagine a city that starts experiencing traffic jams along all the roads. Stores don’t open on time, groceries are stuck in transit, meetings are postponed. Essentially all operations in the city are slowed.

The slow down of operations in cells experiencing reduced protein mobility follows a similar progression. Normally, most proteins zip around the cell bumping into other molecules until they locate the molecule they work with or act on. The slower a protein moves, the fewer other molecules it will reach, and so the less likely it will be able to do its job. Young and colleagues found that such protein slow-downs lead to measurable reductions in the functional output of the proteins. When many proteins fail to get their jobs done in time, cells begin to experience a variety of problems—as they are known to do in chronic diseases.

Discovering the protein mobility problem

Young and colleagues first suspected that cells affected in chronic disease might have a protein mobility problem after observing changes in the behavior of the insulin receptor, a signaling protein that reacts to the presence of insulin and causes cells to take in sugar from blood. In people with diabetes, cells become less responsive to insulin — a state called insulin resistance — causing too much sugar to remain in the blood. In research published on insulin receptors in Nature Communications in 2022, Young and colleagues reported that insulin receptor mobility might be relevant to diabetes.

Knowing that many cellular functions are altered in diabetes, the researchers considered the possibility that altered protein mobility might somehow affect many proteins in cells. To test this hypothesis, they studied proteins involved in a broad range of cellular functions, including MED1, a protein involved in gene expression; HP1α, a protein involved in gene silencing; FIB1, a protein involved in production of ribosomes; and SRSF2, a protein involved in splicing of messenger RNA. They used single-molecule tracking and other methods to measure how each of those proteins moves in healthy cells and in cells in disease states. All but one of the proteins showed reduced mobility (about 20-35%) in the disease cells.

“I’m excited that we were able to transfer physics-based insight and methodology, which are commonly used to understand the single-molecule processes like gene transcription in normal cells, to a disease context and show that they can be used to uncover unexpected mechanisms of disease,” Zheng says. “This work shows how the random walk of proteins in cells is linked to disease pathology.”

Moreno concurs: “In school, we’re taught to consider changes in protein structure or DNA sequences when looking for causes of disease, but we’ve demonstrated that those are not the only contributing factors. If you only consider a static picture of a protein or a cell, you miss out on discovering these changes that only appear when molecules are in motion.”

 Can’t commute across the cell, I’m all tied up right now

Next, the researchers needed to determine what was causing the proteins to slow down. They suspected that the defect had to do with an increase in cells of the level of reactive oxygen species (ROS), molecules that are highly prone to interfering with other molecules and their chemical reactions. Many types of chronic-disease-associated triggers, such as higher sugar or fat levels, certain toxins, and inflammatory signals, lead to an increase in ROS, also known as an increase in oxidative stress. The researchers measured the mobility of the proteins again, in cells that had high levels of ROS and were not otherwise in a disease state, and saw comparable mobility defects, suggesting that oxidative stress was to blame for the protein mobility defect.

The final part of the puzzle was why some, but not all, proteins slow down in the presence of ROS. SRSF2 was the only one of the proteins that was unaffected in the experiments, and it had one clear difference from the others: its surface did not contain any cysteines, an amino acid building block of many proteins. Cysteines are especially susceptible to interference from ROS because it will cause them to bond to other cysteines. When this bonding occurs between two protein molecules, it slows them down because the two proteins cannot move through the cell as quickly as either protein alone.

About half of the proteins in our cells contain surface cysteines, so this single protein mobility defect can impact many different cellular pathways. This makes sense when one considers the diversity of dysfunctions that appear in cells of people with chronic diseases: dysfunctions in cell signaling, metabolic processes, gene expression and gene silencing, and more. All of these processes rely on the efficient functioning of proteins—including the diverse proteins studied by the researchers. Young and colleagues performed several experiments to confirm that decreased protein mobility does in fact decrease a protein’s function. For example, they found that when an insulin receptor experiences decreased mobility, it acts less efficiently on IRS1, a molecule to which it usually adds a phosphate group.

From understanding a mechanism to treating a disease

Discovering that decreased protein mobility in the presence of oxidative stress could be driving many of the symptoms of chronic disease provides opportunities to develop therapies to rescue protein mobility. In the course of their experiments, the researchers treated cells with an antioxidant drug—something that reduces ROS—called N-acetyl cysteine and saw that this partially restored protein mobility.

The researchers are pursuing a variety of follow ups to this work, including the search for drugs that safely and efficiently reduce ROS and restore protein mobility. They developed an assay that can be used to screen drugs to see if they restore protein mobility by comparing each drug’s effect on a simple biomarker with surface cysteines to one without. They are also looking into other diseases that may involve protein mobility, and are exploring the role of reduced protein mobility in aging.

“The complex biology of chronic diseases has made it challenging to come up with effective therapeutic hypotheses,” says Young, who is also a professor of biology at the Massachusetts Institute of Technology. “The discovery that diverse disease-associated stimuli all induce a common feature, proteolethargy, and that this feature could contribute to much of the dysregulation that we see in chronic disease, is something that I hope will be a real game changer for developing drugs that work across the spectrum of chronic diseases.”

A cell protector collaborates with a killer

New research from the Horvitz Lab reveals what it takes for a protein that is best known for protecting cells against death to take on the opposite role.

Jennifer Michalowski | McGovern Institute
November 1, 2024

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.

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.

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.

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.

Bat cells possess a unique antiviral mechanism, preventing the SARS-CoV-2 virus from taking control

Bats have the amazing ability to coexist with viruses that are deadly to humans. New work from the Jaenisch Lab uncovers an antiviral mechanism that allows viruses to enter bat cells but prevents them from replicating.

Shafaq Zia | Whitehead Institute
October 14, 2024

Viruses are masters of stealth. From the moment a virus enters the host’s body, it begins hijacking its cells. First, the virus binds to a specific protein on the cell’s surface through a lock-and-key mechanism. This protein, known as a receptor, facilitates the entry of the virus’s genetic material into the cell. Once inside, this genetic code takes over the cell’s machinery, directing it to produce copies of the virus and assemble new viral particles, which can go on to infect other cells. Upon detecting the invasion, the host’s immune system responds by attacking infected cells in hopes of curbing the virus’s spread.

But in bats, this process unfolds differently. Despite carrying several viruses — Marburg, Ebola, Nipah, among others — bats rarely get sick from these infections. It seems their immune systems are highly specialized, allowing them to live with viruses that would typically be deadly in humans, without any clinical symptoms.

Since the onset of the COVID-19 pandemic, the lab of Whitehead Institute Founding Member Rudolf Jaenisch has been investigating the molecular basis of bats’ extraordinary resilience to viruses like SARS-CoV-2. In their latest study, published in the journal PNAS on Oct. 14 , Jaenisch lab postdoc Punam Bisht and colleagues have uncovered an antiviral mechanism in bat cells that allows viruses to enter the cells but prevents them from replicating their genome and completing the hijacking process.

“These cells have elevated expressions of antiviral genes that act immediately, neutralizing the virus before it can spread,” says Jaenisch, a professor of biology at the Massachusetts Institute of Technology. “What’s particularly interesting is that many of these antiviral genes have counterparts, or orthologs in humans.”

Striking a delicate balance

The innate immune system is the body’s first line of defense against foreign invaders like the SARS-CoV-2 virus. This built-in security system is always on alert, responding swiftly — within minutes to hours — to perceived threats.

Upon detecting danger, immune cells rush to the site of infection, where they target the virus with little precision in attempts to slow it down and buy time for the more specialized adaptive immune system to take over. During this process, these cells release small signaling proteins called cytokines, which coordinate the immune response by recruiting additional immune cells and directing them to the battleground.

If the innate immune response alone isn’t sufficient to defeat the virus, it signals the adaptive immune system for support. The adaptive immune system tailors its attacks to the exact pathogen it is fighting and can even keep records of past infections to launch a faster, more aggressive attack the next time it encounters the same pathogen.

But in some infections, the innate immune response can quickly spiral out of control before the adaptive immune response is activated. This phenomenon, called a cytokine storm, is a life-threatening condition characterized by the overproduction of cytokines. These proteins continue to signal the innate immune system for backup even when it’s not necessary, leading to a flood of immune cells at the site of infection, where they inadvertently begin damaging organs and healthy tissues.

Bats, on the other hand, are uniquely equipped to manage viral infections without triggering an overwhelming immune response or allowing the virus to take control. To understand how their innate immune system achieves this delicate balance, Bisht and her colleagues turned their attention to bat cells.

In this study, researchers compared how the SARS-CoV-2 virus replicates in human and bat stem cells and fibroblasts — a type of cell involved in the formation of connective tissue. While fibroblasts are not immune cells, they can secrete cytokines and guide immune response, particularly to help with tissue repair.

After exposing these cells to the SARS-CoV-2 virus for 48 hours, the researchers used a Green Fluorescent Protein (GFP) tag to track the virus’s activity. GFP is a fluorescent protein whose genetic code can be added as a tag to a gene of interest. This causes the products of that gene to glow, providing researchers with a visual marker of where and when the gene is expressed.

They observed that over 80% of control cells — derived from the kidneys of African green monkeys and known to be highly susceptible to SARS-CoV-2 — showed evidence of the virus replicating. In contrast, they did not detect any viral activity in human and bat stem cells or fibroblasts.

In fact, even after introducing the human ACE2 receptor — which SARS-CoV-2 uses to bind and enter cells — into bat cells, the infected bat fibroblasts were able to replicate viral RNA and produce viral proteins, but at much lower levels compared to infected human fibroblasts.

These bat fibroblasts, however, could not assemble these viral proteins into fully infectious virus particles, suggesting an abortive infection, where the virus is able to initiate replication but fails to complete the process and produce progeny viruses.

Using electron microscopy to look inside bat and human cells, they began to understand why: in human cells, SARS-CoV-2 had created special structures called double-membrane vesicles (DMV). These vesicles acted like a bubble, shielding the viral genome from detection and providing it safe space to replicate more effectively. However, these “viral replication factories” were absent in bat fibroblasts.

When the researchers examined the gene expression profiles of these bat fibroblasts and compared them those of infected human cells, they found that although both human and bat cells have genes regulating the release of a type of cytokine called interferons, these genes are already turned on in bat fibroblasts — unlike in human cells — even before virus infection occurs.

These findings suggest that bat cells are in a constant state of vigilance. This allows their innate immune system to stop the SARS-CoV-2 virus in its tracks early on in the replication process before it can entirely hijack cellular machinery.

Surprisingly, this antiviral mechanism does not protect bat cells against all viruses. When the researchers infected bat fibroblasts with Zika virus, the virus was able to replicate and produce new viral particles.

“This means there are still many questions unanswered about how bat cells resist infection,” says Bisht. “COVID-19 continues to circulate, and the virus is evolving quickly. Filling in these gaps in our knowledge will help us develop better vaccines and antiviral strategies.”
The researchers are now focused on identifying the specific genes involved in this antiviral mechanism, and exploring how they interact with the virus during infection.

Growing to greatness: Professor Mary Gehring on plant epigenetics and becoming an HHMI Investigator

From the intricacies of plant reproduction to genome-wide analyses, Gehring’s lab delves deep into the epigenetic mechanisms shaping plant biology.

Jayashabari Shankar and Alex Tang | The Tech
September 5, 2024

Dr. Mary Gehring is a professor of biology at MIT and a core member of the Whitehead Institute for Biomedical Research. Her research focuses on how epigenetic mechanisms like DNA methylation influence gene regulation during plant reproduction and seed development in the model organism Arabidopsis thaliana. In the classroom, she teaches genetics (7.03), a required course for biology and biological engineering majors.

With her recent appointment as an Howard Hughes Medical Institute (HHMI) investigator, Gehring joins an elite legion of HHMI investigators at the Institute. New cohorts of investigators are only announced once every three years, and they receive $11 million in funding over a seven year term (which can be renewed). Three other MIT faculty received HHMI appointments this year: Gene-Wei Li, associate professor of biology, and brain and cognitive sciences professors Mehrdad Jazayeri and Steven Flavell.

Here, she shares her lab’s research, journey into plant biology, and what she values in undergraduate researchers.

TT: What does your lab conduct research in, and how has being named an HHMI investigator changed your plans, if at all?

My lab focuses on plant biology, particularly on how epigenetic mechanisms like DNA methylation affect gene regulation in plants, especially during reproduction and seed development. We mostly work with Arabidopsis thaliana, a model plant, but we’re also exploring other plant systems.

A typical day in the lab can vary, but it often starts with checking on our plants in the greenhouse. Depending on the day, we might pollinate plants for genetic crosses or genotyping them by isolating DNA and performing PCR. We’re particularly focused on understanding gene expression within seeds: we isolate different seed tissues, sort nuclei based on their properties, and then perform RNA sequencing. We also do a lot of chromatin profiling, histone modifications and DNA methylation analyses across the genome. Since much of our work is genome-wide, bioinformatics plays a big role in our research, with a significant amount of time spent on analyzing data.

It’s still sinking in, but being named an HHMI investigator certainly provides a new level of freedom. It allows us to pursue ideas without the constraints of specific grant funding, which is incredibly liberating. We’re considering expanding our research into new areas beyond epigenetics, like genome structure and chromosome dosage changes, while sticking with plant biology. This recognition has encouraged us to think bigger and explore new directions in our work.

TT: How far back do these interests extend for you?

My interest in plant biology started during my undergraduate years. I majored in biology and was eager to get involved in research. My real fascination with plants began when a new professor, with a background in plant biology, came to my school. I took her course on plant growth and development, which I found incredibly exciting. I was drawn to how plants communicate within their tissues and with each other. This led me to work on a research project for two years, culminating in a senior thesis on root development. After college, I took a year off to work in environmental consulting before heading to graduate school in Plant Biology at UC Berkeley.

TT: What perspectives and characteristics do you appreciate in undergraduate researchers?

Whether it’s undergraduates or postdocs, I value curiosity and dedication. For undergraduates, especially those in UROPs, it’s crucial that they are genuinely interested in the research and willing to ask questions when they don’t understand something. Balancing research with coursework and extracurriculars at MIT is challenging, so I also look for students who can manage their time well. It’s about being curious, dedicated, and communicative.

I hope there are students at MIT who are excited about plant research. It’s a vital area of biology, especially with the growing focus on climate change. While there isn’t a large presence of plant biology at MIT yet, I’m hopeful that it will expand in the coming years, and I’d love to see more students getting involved in this important field.

Brain cell types are affected differently by Rett Syndrome mutation

New research from Jaenisch Lab postdoc Danielle Tomasello focuses on an understudied question: how Rett Syndrome affects cell types in the human brain other than neurons.

Greta Friar | Whitehead Institute
September 6, 2024

Rett Syndrome is a X-chromosome-linked neurodevelopmental disorder; it can lead to loss of coordination, mobility, ability to speak, and use of the hands, among other symptoms. The syndrome is typically caused by mutations within the gene MECP2. Researchers in Whitehead Institute Founding Member Rudolf Jaenisch’s lab have studied Rett Syndrome for many years in order to understand the biological mechanisms that cause disease symptoms, and to identify possible avenues for treatments or a cure. Jaenisch and colleagues have gained many insights into the biology of Rett syndrome and developed tools that can rescue neurons from Rett syndrome symptoms in lab models.

However, much about the biology of Rett Syndrome remains unknown. New research from Jaenisch and postdoc in his lab Danielle Tomasello focuses on an understudied question: how Rett Syndrome affects cell types in the human brain other than neurons. Specifically, Tomasello investigated the effects of Rett Syndrome on astrocytes, a type of brain cell that supports and provides energy for neurons. The work, shared in the journal Scientific Reports on September 6, details changes that occur in Rett syndrome astrocytes, in particular in relation to their mitochondria, and shows how these changes directly impact neurons. The findings provide a new framework for thinking about Rett Syndrome and possible new avenues for therapies.

“By considering Rett Syndrome from a different perspective, this project expands our understanding of a multifaceted and thus far incurable disease,” says Jaenisch, who is also a professor of biology at the Massachusetts Institute of Technology.

Energy metabolism in Rett Syndrome

Mitochondria are organelles that generate energy, which cells use to carry out their functions, and mitochondrial dysfunction was known to occur in Rett Syndrome. Jaenisch and Tomasello found that mitochondria in astrocytes are particularly affected, even more so than mitochondria in neurons. Tomasello grew human stem-cell-derived astrocytes in 2D cultures and also grew 3D organoids: mini brain-like tissues that contain multiple cell types growing in a structure that resembles actual brain anatomy. This approach allowed Tomasello to use human cells, rather than an animal model, and to study how cells behave within a brain-like environment.

When the researchers observed Rett astrocytes grown in these conditions, they found that the mitochondria were misshapen: short, small circles instead of large, long ovals. Additional studies showed evidence of the mitochondria experiencing stress and not being able to generate enough energy through their usual processes. The mitochondria did not have enough of the typical proteins they use to make energy, and so began to break down the cell’s supply of the building blocks of proteins, amino acids, for parts to make up for the missing material. Additionally, the researchers observed an increase in reactive oxygen species, byproducts of mitochondrial metabolism that are toxic to the cell.

Further experiments suggested that the cells try to compensate for this mitochondrial stress by increasing transcription of mitochondrial genes. For example, Tomasello found that regions of DNA called promoters that can increase expression of key mitochondrial genes were more open for the cell to use in Rett astrocytes. Altogether, these findings paint a picture of severe mitochondrial dysfunction in Rett astrocytes.

Although mitochondria in Rett neurons did not have such severe defects, astrocytes and neurons have a close relationship. Not only do neurons rely on astrocytes to supply them with energy, they even accept mitochondria from astrocytes to use for themselves. Jaenisch and Tomasello found that neurons take up dysfunctional mitochondria from Rett astrocytes at a higher rate than they take up mitochondria from unaffected astrocytes. This means that the effects of Rett syndrome on astrocytes have a direct effect on neurons: the dysfunctional mitochondria from the astrocytes end up in the neurons, where they cause damage. Tomasello took mitochondria from Rett astrocytes and placed them on both healthy and Rett neurons. In either case, the neurons took up the dysfunctional mitochondria in large numbers and then experienced significant problems. The neurons entered a hyperexcitable state that is ultimately toxic to the brain. The neurons also contained higher levels of reactive oxygen species, the toxic byproducts of mitochondrial metabolism, which can cause widespread damage. These effects occurred even in otherwise healthy neurons that did not themselves contain a Rett-causing MECP2 mutation.

“This shows that in order to understand Rett Syndrome, we need to look beyond what’s happening in neurons to other cell types,” Tomasello says.

Learning about the role that astrocytes play in Rett Syndrome could provide new avenues for therapies. The researchers found that supplying affected astrocytes with healthy mitochondria helped them to recover normal mitochondrial function. This suggests to Tomasello that one possibility for future Rett Syndrome therapies could be something that either targets mitochondria, or supplies additional mitochondria through the bloodstream.

Together, these insights and their possible medical implications demonstrate the importance of taking a broader look at the foundational biology underlying a disease.

Whitehead Institute researchers uncover a new clue toward understanding the molecular basis of Parkinson’s disease

In Parkinson's disease, a mutation that causes protein misfolding can also turn the brain’s immune cells from friends to foes, possibly accelerating the progression of the disease. New Research from the Jaenisch Lab aims to uncover mechanisms that go awry in the brain, which may inform the development of new therapies that can halt or even reverse the progression of neurological conditions such as Parkinson's.

Shafaq Zia | Whitehead Institute
August 29, 2024

Dopamine is more than the “rush molecule”. This chemical messenger, produced by neurons in the midbrain, acts as a traffic controller that regulates the flow of electrical signals between neurons, assisting with brain functions like cognition, attention, movement, and behavior. But, in instances of Parkinson’s disease (PD), a progressive brain disorder, dopamine-producing neurons begin to die at an unprecedented rate, leading to dwindling levels of this vital chemical and impaired neural communication.

The lab of Whitehead Institute’s Founding Member Rudolf Jaenisch studies genetic and epigenetic factors — changes in gene expression that control which genes are turned on and off, and to what extent, without altering the DNA sequence itself — underlying neurological disorders like PD, Alzheimer’s disease, and Rett Syndrome. Their work aims to uncover the mechanisms that go awry in the brain, which may inform the development of new therapies that can halt or even reverse the progression of these conditions.

In their latest work, Jaenisch and former postdoctoral associate Marine Krzisch examine how a mutation in the gene that encodes for alpha-synuclein, a protein regulating the release of dopamine, affects the resident immune cells of the brain called microglia. The researchers’ detailed findings, published in the journal Biological Psychiatry on August 29, reveal that the mutation renders microglia extremely sensitive, worsening the problem of inflammation in the brain and potentially exacerbating damage to neurons in Parkinson’s disease.

“In fact, even when these mutant microglia are transplanted into a healthy, young brain, they have heightened activation upon stimulation, and low levels of the protective antioxidant catalase,” Krzisch says. “This tells us that in Familial Parkinson’s disease, which is due to genetic mutations, these microglia may be playing an important role in neuron degeneration.”

When nature’s origami falters

The human body is home to tens of thousands of unique proteins, each essential for processes sustaining life. These proteins are composed of linear chains of smaller building blocks called amino acids that are linked together in a specific sequence. For the proteins to perform their functions, the amino acid chains must crumple, rotate, and twist into stable three-dimensional structures. The stakes are high — just as precise folds and creases are crucial to the art of origami, even minor errors in the protein folding process can result in dysfunctional proteins that contribute to disease.

To date, scientists have identified over 20 causative genes in which mutations can result in Familial Parkinson’s disease, a rare, genetically inherited form of PD affecting individuals under or around the age of 50. Among them is SNCA, which encodes for alpha-synuclein, a small protein abundant in dopamine-producing neurons.

The A53T mutation in SNCA promotes the formation of dysfunctional alpha-synuclein proteins that clump together — almost like a ball of yarn — within dopamine-producing neurons. The accumulation of these protein clumps, also known as Lewy bodies, triggers inflammatory signaling in the brain, eventually killing the affected neurons. However, prior research has also shown that the A53T mutation accelerates the progression of PD, or the rate at which neurons die, although the full molecular mechanisms underlying this process are not yet fully understood.

To uncover pathways involved in this progression, researchers in the Jaenisch Lab turned their attention to star-shaped patrollers called microglia that protect the brain from foreign invaders and respond to injuries, including protein aggregates within neurons. This immune response includes activated microglia trying to clear out Lewy bodies by digesting them, recruiting additional immune cells to the site of neurons with protein aggregates, and even killing off diseased neurons to limit damage to the brain.

But these friends can quickly turn to foes. Over-activated microglia can also degrade healthy neurons in the brain, prompting Jaenisch, Krzisch, and colleagues to investigate if excessive microglia activation is one pathway that contributes to progression in PD.

Microglia go rogue

To explore how the A53T mutation in the SNCA gene affects microglia function in PD, scientists at the Jaenisch Lab began by growing human myeloid precursors — the cells that eventually develop into microglia — in lab culture and transplanting them into the brains of immune-deprived mice.

Given the complexity of the brain, it’s common for researchers to study brain cells in the Petri dish. “But in cell cultures, microglia do not have the same morphology [form] as in the brain, show signs of chronic activation, and they don’t survive for a very long time,” says Krzisch. “When we transplant them in mice, the precursors differentiate into microglia that look and function like those in the human brain, and survive for the mouse’s lifespan.”

Using this method, the researchers compared the gene expression profiles of A53T-mutant microglia with those that did not carry the mutation, revealing differences in pathways linked to inflammation, microglia activation, and DNA repair. Additionally, when A53T-mutant microglia were exposed to an immune activator called lipopolysaccharide, they exhibited a heightened inflammatory response compared to non-mutant microglia.

In fact, even in non-inflammatory conditions, A53T-mutant microglia had decreased expression of catalase, an enzyme that helps break down harmful reactive oxygen species produced in response to protein aggregates in PD.

Understanding the molecular basis of progression in PD is challenging, which explains why there are currently no drugs to alter the disease’s course. With these findings in hand, researchers at the Jaenisch Lab are now eager to explore how factors like aging also influence microglia function and contribute to an increased rate of progression in PD.

“Overactivation of microglia isn’t the only cause of neuron death in Parkinson’s,” says Jaenisch. “But if we can decrease their activation, it will help us get to the point where we can slow down or actually stop the disease.”

 

Study reveals the benefits and downside of fasting

Fasting helps intestinal stem cells regenerate and heal injuries but also leads to a higher risk of cancer in mice, MIT researchers report.

Anne Trafton | MIT News
August 21, 2024

Low-calorie diets and intermittent fasting have been shown to have numerous health benefits: They can delay the onset of some age-related diseases and lengthen lifespan, not only in humans but many other organisms.

Many complex mechanisms underlie this phenomenon. Previous work from MIT has shown that one way fasting exerts its beneficial effects is by boosting the regenerative abilities of intestinal stem cells, which helps the intestine recover from injuries or inflammation.

In a study of mice, MIT researchers have now identified the pathway that enables this enhanced regeneration, which is activated once the mice begin “refeeding” after the fast. They also found a downside to this regeneration: When cancerous mutations occurred during the regenerative period, the mice were more likely to develop early-stage intestinal tumors.

“Having more stem cell activity is good for regeneration, but too much of a good thing over time can have less favorable consequences,” says Omer Yilmaz, an MIT associate professor of biology, a member of MIT’s Koch Institute for Integrative Cancer Research, and the senior author of the new study.

Yilmaz adds that further studies are needed before forming any conclusion as to whether fasting has a similar effect in humans.

“We still have a lot to learn, but it is interesting that being in either the state of fasting or refeeding when exposure to mutagen occurs can have a profound impact on the likelihood of developing a cancer in these well-defined mouse models,” he says.

MIT postdocs Shinya Imada and Saleh Khawaled are the lead authors of the paper, which appears today in Nature.

Driving regeneration

For several years, Yilmaz’s lab has been investigating how fasting and low-calorie diets affect intestinal health. In a 2018 study, his team reported that during a fast, intestinal stem cells begin to use lipids as an energy source, instead of carbohydrates. They also showed that fasting led to a significant boost in stem cells’ regenerative ability.

However, unanswered questions remained: How does fasting trigger this boost in regenerative ability, and when does the regeneration begin?

“Since that paper, we’ve really been focused on understanding what is it about fasting that drives regeneration,” Yilmaz says. “Is it fasting itself that’s driving regeneration, or eating after the fast?”

In their new study, the researchers found that stem cell regeneration is suppressed during fasting but then surges during the refeeding period. The researchers followed three groups of mice — one that fasted for 24 hours, another one that fasted for 24 hours and then was allowed to eat whatever they wanted during a 24-hour refeeding period, and a control group that ate whatever they wanted throughout the experiment.

The researchers analyzed intestinal stem cells’ ability to proliferate at different time points and found that the stem cells showed the highest levels of proliferation at the end of the 24-hour refeeding period. These cells were also more proliferative than intestinal stem cells from mice that had not fasted at all.

“We think that fasting and refeeding represent two distinct states,” Imada says. “In the fasted state, the ability of cells to use lipids and fatty acids as an energy source enables them to survive when nutrients are low. And then it’s the postfast refeeding state that really drives the regeneration. When nutrients become available, these stem cells and progenitor cells activate programs that enable them to build cellular mass and repopulate the intestinal lining.”

Further studies revealed that these cells activate a cellular signaling pathway known as mTOR, which is involved in cell growth and metabolism. One of mTOR’s roles is to regulate the translation of messenger RNA into protein, so when it’s activated, cells produce more protein. This protein synthesis is essential for stem cells to proliferate.

The researchers showed that mTOR activation in these stem cells also led to production of large quantities of polyamines — small molecules that help cells to grow and divide.

“In the refed state, you’ve got more proliferation, and you need to build cellular mass. That requires more protein, to build new cells, and those stem cells go on to build more differentiated cells or specialized intestinal cell types that line the intestine,” Khawaled says.

Too much of a good thing

The researchers also found that when stem cells are in this highly regenerative state, they are more prone to become cancerous. Intestinal stem cells are among the most actively dividing cells in the body, as they help the lining of the intestine completely turn over every five to 10 days. Because they divide so frequently, these stem cells are the most common source of precancerous cells in the intestine.

In this study, the researchers discovered that if they turned on a cancer-causing gene in the mice during the refeeding stage, they were much more likely to develop precancerous polyps than if the gene was turned on during the fasting state. Cancer-linked mutations that occurred during the refeeding state were also much more likely to produce polyps than mutations that occurred in mice that did not undergo the cycle of fasting and refeeding.

“I want to emphasize that this was all done in mice, using very well-defined cancer mutations. In humans it’s going to be a much more complex state,” Yilmaz says. “But it does lead us to the following notion: Fasting is very healthy, but if you’re unlucky and you’re refeeding after a fasting, and you get exposed to a mutagen, like a charred steak or something, you might actually be increasing your chances of developing a lesion that can go on to give rise to cancer.”

Yilmaz also noted that the regenerative benefits of fasting could be significant for people who undergo radiation treatment, which can damage the intestinal lining, or other types of intestinal injury. His lab is now studying whether polyamine supplements could help to stimulate this kind of regeneration, without the need to fast.

“This fascinating study provides insights into the complex interplay between food consumption, stem cell biology, and cancer risk,” says Ophir Klein, a professor of medicine at the University of California at San Francisco and Cedars-Sinai Medical Center, who was not involved in the study. “Their work lays a foundation for testing polyamines as compounds that may augment intestinal repair after injuries, and it suggests that careful consideration is needed when planning diet-based strategies for regeneration to avoid increasing cancer risk.”

The research was funded, in part, by a Pew-Stewart Trust Scholar award, the Marble Center for Cancer Nanomedicine, the Koch Institute-Dana Farber/Harvard Cancer Center Bridge Project, and the MIT Stem Cell Initiative.