Research Area: Human Disease

News brief: Calo Lab

How do cells respond to disruptions in splicing?

Lillian Eden | Department of Biology
March 4, 2024

New research from the Calo Lab in the Department of Biology has identified the protein Mdm2 generating a form that activates a cascade of cellular stress responses when splicing is disrupted.

To create proteins, DNA is transcribed into RNA, and that RNA is then “translated” into protein. Between the creation of the RNA and the translation to protein is often a step called splicing. During splicing, segments called introns are removed, and the remaining pieces, called exons, are joined together to form the blueprint for translation. By splicing together different exons, the cell can create different proteins from the same section of genetic code. When splicing goes awry, it can lead to diseases and cancers. 

New research recently published in Disease Models & Mechanisms from the Calo Lab in the Department of Biology at MIT has identified the mechanism for how cells respond to disruptions in splicing, which involves activating a cellular stress response. The stress response, once activated, causes widespread effects, including changes to cell metabolism. 

Researchers have discovered cellular stress responses for other core cellular processes, such as ribosome biogenesis. However, this is the first time researchers have identified how cells respond to perturbing the splicing process.

A particular protein acts as a kind of canary in a coal mine: Mdm2, which responds to a broad range of splicing disruptions. Mdm2 does not cause a stress response by itself. Rather, Mdm2 is itself spliced differently in response to splicing disruptions. Downstream, the alternative splicing of Mdm2 leads to the activation of a protein called p53, which is known to orchestrate a cascade of responses to stress.

Researchers have long wondered why some cell types seem more sensitive to splicing disruptions than others. For example, some disorders caused by mutations in proteins that perform RNA splicing, despite affecting the whole organism, induce more noticeable changes in tissues derived from the neural crest—a collection of stem cells that contributes to the formation of the face, jaw, retinas, limbs, and heart during development. Certain splicing inhibitors have also increased the effectiveness of some cancer treatments, but the mechanism is unknown. 

One of the p53-induced stress responses includes changing the metabolism of cells and how they use sugars, which may explain why some cells are more sensitive to splicing disruptions than others. Inhibiting glycolysis, the reactions that extract energy from glucose, can affect how cells divide and migrate. 

The way cells divide and migrate is critical during development; in experiments, zebrafish treated with glycolysis inhibitors exhibited similar changes to craniofacial features as those where splicing was disrupted. Cancerous cells, too, are known to require high levels of sugar metabolism and, therefore, may be especially sensitive to treatments that induce changes in the splicing pathway. 

The researchers knocked down genes to mimic milder splicing disruptions instead of knocking them out entirely. Splicing is so essential that knocking out the splicing machinery can lead to extreme responses like cell death. In organismal models like zebrafish, those severe phenotypes don’t accurately reflect how splicing disruptions present in human diseases.

First author Jade Varineau, a graduate student in the Calo lab, was drawn to the project because it allowed her to explore what was happening at the RNA and cellular level while also observing how splicing perturbations were affecting the whole organism. 

“I think this data can help us reframe the way we think about diseases and cancers that are impacted by splicing—that a treatment that works for one may work for another because all the symptoms may stem from the same cellular response,” Varineau says. 

Although the results indicate how cells broadly respond to splicing perturbations, the mechanism for how disruptions in splicing induce the alternate splicing of Mdm2 remains unclear. Senior author Eliezer Calo says the lab is also exploring how splicing mechanisms may be altered for things like cancer. Their work, he says, opens the door for further exploration of cell-type specificity of genetic disorders and improvements in cancer treatments using splicing inhibitors. 

 “We know that the sensor is encoded in the gene Mdm2—what are the molecules that allow Mdm2 to act as a sensor, and how does the sensor malfunction for things like cancer?” Calo says. “The next step is to find out how the sensor works.”  

How early-stage cancer cells hide from the immune system

A new study finds precancerous colon cells turn on a gene called SOX17, which helps them evade detection and develop into more advanced tumors.

Anne Trafton | MIT News
February 28, 2024

One of the immune system’s primary roles is to detect and kill cells that have acquired cancerous mutations. However, some early-stage cancer cells manage to evade this surveillance and develop into more advanced tumors.

A new study from MIT and Dana-Farber Cancer Institute has identified one strategy that helps these precancerous cells avoid immune detection. The researchers found that early in colon cancer development, cells that turn on a gene called SOX17 can become essentially invisible to the immune system.

If scientists could find a way to block SOX17 function or the pathway that it activates, this may offer a new way to treat early-stage cancers before they grow into larger tumors, the researchers say.

“Activation of the SOX17 program in the earliest innings of colorectal cancer formation is a critical step that shields precancerous cells from the immune system. If we can inhibit the SOX17 program, we might be better able to prevent colon cancer, particularly in patients that are prone to developing colon polyps,” says Omer Yilmaz, an MIT associate professor of biology, a member of MIT’s Koch Institute for Integrative Cancer Research, and one of the senior authors of the study.

Judith Agudo, a principal investigator at Dana-Farber Cancer Institute and an assistant professor at Harvard Medical School, is also a senior author of the study, which appears today in Nature. The paper’s lead author is MIT Research Scientist Norihiro Goto. Other collaborators include Tyler Jacks, a professor of biology and a member of MIT’s Koch Institute; Peter Westcott, a former Jacks lab postdoc who is now an assistant professor at Cold Spring Harbor Laboratory; and Saori Goto, an MIT postdoc in the Yilmaz lab.

Immune evasion

Colon cancer usually arises in long-lived cells called intestinal stem cells, whose job is to continually regenerate the lining of the intestines. Over their long lifetime, these cells can accumulate cancerous mutations that lead to the formation of polyps, a type of premalignant growth that can eventually become metastatic colon cancer.

To learn more about how these precancerous growths evade the immune system, the researchers used a technique they had previously developed for growing mini colon tumors in a lab dish and then implanting them into mice. In this case, the researchers engineered the tumors to express mutated versions of cancer-linked genes Kras, p53, and APC, which are often found in human colon cancers.

Once these tumors were implanted in mice, the researchers observed a dramatic increase in the tumors’ expression of SOX17. This gene encodes a transcription factor that is normally active only during embryonic development, when it helps to control development of the intestines and the formation of blood vessels.

The researchers’ experiments revealed that when SOX17 is turned on in cancer cells, it helps the cells to create an immunosuppressive environment. Among its effects, SOX17 prevents cells from synthesizing the receptor that normally detects interferon gamma, a molecule that is one of the immune system’s primary weapons against cancer cells.

Without those interferon gamma receptors, cancerous and precancerous cells can simply ignore messages from the immune system, which would normally direct them to undergo programmed cell death.

“One of SOX17’s main roles is to turn off the interferon gamma signaling pathway in colorectal cancer cells and in precancerous adenoma cells. By turning off interferon gamma receptor signaling in the tumor cells, the tumor cells become hidden from T cells and can grow in the presence of an immune system,” Yilmaz says.

Without interferon gamma signaling, cancer cells also minimize their production of molecules called MHC proteins, which are responsible for displaying cancerous antigens to the immune system. The cells’ insensitivity to interferon gamma also prevents them from producing immune molecules called chemokines, which normally recruit T cells that would help destroy the cancerous cells.

Targeting SOX17

When the researchers generated colon tumor organoids with SOX17 knocked out, and implanted those into mice, the immune system was able to attack those tumors much more effectively. This suggests that preventing cancer cells from turning off SOX17 could offer a way to treat colon cancer in its earliest stages.

“Just by turning off SOX17 in fairly complex tumors, we were able to essentially obliterate the ability of these tumor cells to persist,” Goto says.

As part of their study, the researchers also analyzed gene expression data from patients with colon cancer and found that SOX17 tended to be highly expressed in early-stage colon cancers but dropped off as the tumors became more invasive and metastatic.

“We think this makes a lot of sense because as colorectal cancers become more invasive and metastatic, there are other mechanisms that create an immunosuppressive environment,” Yilmaz says. “As the colon cancer becomes more aggressive and activates these other mechanisms, then there’s less importance for SOX17.”

Transcription factors such as SOX17 are considered difficult to target using drugs, in part because of their disorganized structure, so the researchers now plan to identify other proteins that SOX17 interacts with, in hopes that it might be easier to block some of those interactions.

The researchers also plan to investigate what triggers SOX17 to turn on in precancerous cells.

The research was funded by the MIT Stem Cell Initiative via Fondation MIT, the National Institutes of Health/National Cancer Institute, and a Koch Institute-Dana Farber Harvard Cancer Center Bridge Project grant.

What can super-healing species teach us about regeneration?

Albert Almada PhD ’13 studies the mechanics of how stem cells rebuild tissues. “Digging deep into the science is what MIT taught me,” he says.

Lillian Eden | Department of Biology
February 21, 2024

When Albert E. Almada PhD ’13 embarks on a new project, he always considers two criteria instilled in him during his time as a graduate student in the Department of Biology at MIT.

“If you want to make a big discovery, you have to approach it from a unique perspective — a unique angle,” Almada says. “You also have to be willing to dive into the unknown and go to the leading edge of your field.”

This is not without its challenges — but with an innovative spirit, Almada says, one can find ways to apply technologies and approaches to a new area of research where a roadmap doesn’t yet exist.

Now an assistant professor of orthopedic surgery and stem cell biology and regenerative medicine at the Keck School of Medicine of the University of Southern California (USC), Almada studies the mechanics of how stem cells rebuild tissues after trauma and how stem cell principles are dysregulated and drive conditions like degenerative disease and aging, exploring these topics through an evolutionary lens.

He’s also trying to solve a mystery that has intrigued scientists for centuries: Why can some vertebrate species like fish, salamanders, and lizards regenerate entire body parts, but mammals cannot? Almada’s laboratory at USC tackles these critical questions in the musculoskeletal system.

Almada’s fascination with muscle development and regeneration can be traced back to growing up in southern California. Almada’s brother had a degenerative muscle disease called Duchenne muscular dystrophy — and, while Almada grew stronger and stronger, his brother grew weaker and weaker. Last summer, Almada’s brother, unfortunately, lost his battle with his disorder at the age of 41.

“Watching his disease progress in those early years is what inspired me to become a scientist,” Almada recalls. “Sometimes science can be personal.”

Almada went to the University of California at Irvine for his undergraduate degree, majoring in biological sciences. During his summers, he participated in the Undergraduate Research Program (URP) at the Cold Spring Harbor Laboratory and the MIT Summer Research Program-Bio (now the Bernard S. and Sophie G. Gould MIT Summer Research Program in Biology, BSG-MSRP-Bio), where he saw the passion, rigor, and drive that solidified his desire to pursue a PhD.

Despite his interest in clinical applications, skeletal muscle, and regenerative biology, Almada was drawn to the Department of Biology at MIT, which is focused on basic fundamental research.

“I was willing to bet that it all came down to understanding basic cellular processes and things going wrong with the cell and how it interacts with its environment,” he says. “The MIT biology program really helped me define an identity for myself and gave me a template for how to tackle clinical problems from a molecular perspective.”

Almada’s PhD thesis work was based on a curious finding that Phillip Sharp, Institute Professor emeritus, professor emeritus of biology, and intramural faculty at the Koch Institute for Integrative Cancer Research, had made in 2007 — that transcription, the process of copying DNA into a messenger molecule called RNA, can occur in both directions at gene promoters. In one direction, it was long understood that fully formed mRNA is transcribed and can be used as a blueprint to make a protein. The transcription Sharp observed, in the opposite direction, results in a very short RNA that is not used as a gene product blueprint.

Almada’s project dug into what those short RNA molecules are — their structure and sequence, and why they’re not produced the same way that coding messenger RNA is. In two papers published in PNAS and Nature, Almada and colleagues discovered that a balance between splicing and transcription termination signals controls the length of an RNA. This finding has wider implications because toxic RNAs are produced and can build up in several degenerative diseases; being able to splice out or shorten RNAs to remove the harmful segments could be a potential therapeutic treatment.

“That experience convinced me that if I want to make big discoveries, I have to focus on basic science,” he says. “It also gave me the confidence that if I can succeed at MIT, I can succeed just about anywhere and in any field of biology.”

At the time Almada was in graduate school, there was a lot of excitement about transcription factor reprogramming. Transcription factors are the proteins responsible for turning on essential genes that tell a cell what to be and how to behave; a subset of them can even theoretically turn one cell type into another.

Almada began to wonder whether a specialized set of transcription factors instructs stem cells to rebuild tissues after trauma. After MIT, Almada moved on to a postdoctoral position in the lab of Amy Wagers, a leader in muscle stem cell biology at Harvard University, to immerse himself in this problem.

In many tissues in our bodies, a population of stem cells typically exists in an inactive, non-dividing state called quiescence. Once activated, these stem cells interact with their environment, sense damage signals, and turn on programs of proliferation and differentiation, as well as self-renewal, which is critical to maintaining a pool of stem cells in the tissue.

One of the biggest mysteries in the field of regenerative biology is how stem cells transition from dormancy into that activated, highly regenerative state. The body’s ability to turn on stem cells, including those in the skeletal muscle system, declines as we age and is often dysregulated in degenerative diseases — diseases like the one Almada’s brother suffered from.

In a study Almada published in Cell Reports several years ago, he identified a family of transcription factors that work together to turn on a critical regenerative gene program within hours of muscle trauma. This program drives muscle stem cells out of quiescence and speeds up healing.

“Now my lab is studying this regenerative program and its potential dysregulation in aging and degenerative muscle diseases using mouse and human models,” Almada says. “We’re also drawing parallels with super-healing species like salamanders and lizards.”

Recently, Almada has been working on characterizing the molecular and functional properties of stem cells in lizards, attempting to understand how the genes and pathways differ from mammalian stem cells. Lizards can regenerate massive amounts of skeletal muscle from scratch — imagine if human muscle tissue could be regrown as seamlessly as a lizard’s tail can. He is also exploring whether the tail is unique, or if stem cells in other tissues in lizards can regenerate faster and better than the tail, by comparing analogous injuries in a mouse model.

“This is a good example of approaching a problem from a new perspective: We believe we’re going to discover new biology in lizards that we can use to enhance skeletal muscle growth in vulnerable human populations, including those that suffer from deadly muscle disorders,” Almada says.

In just three years of starting his faculty position at USC, his work and approach have already received recognition in academia, with junior faculty awards from the Baxter Foundation and the Glenn Foundation/American Federation of Aging Research. He also received his first RO1 award from the National Institutes of Health with nearly $3 million in funding. Almada and his first graduate student, Alma Zuniga Munoz, were also awarded the HHMI Gilliam Fellowship last summer. Zuniga Munoz is the first to be recognized with this award at USC; fellowship recipients, student and advisor pairs, are selected with the goal of preparing students from underrepresented groups for leadership roles in science.

Almada himself is a second-generation Mexican American and has been involved in mentoring and training throughout his academic career. He was a graduate resident tutor for Spanish House at MIT and currently serves as the chair of the Diversity, Equity, and Inclusion Committee in the Department of Stem Cell Biology and Regenerative Medicine at USC; more than half of his lab members identify as members of the Hispanic community.

“The focus has to be on developing good scientists,” Almada says. “I learned from my past research mentors the importance of putting the needs of your students first and providing a supportive environment for everyone to excel, no matter where they start.”

As a mentor and researcher, Almada knows that no question and no challenge is off limits — foundations he built in Cambridge, where his graduate studies focused on teaching him to think, not just do.

“Digging deep into the science is what MIT taught me,” he says. “I’m now taking all of my knowledge in molecular biology and applying it to translationally oriented questions that I hope will benefit human health and longevity.”

Protein production glitches in Huntington’s disease revealed

Research from the Jain Lab finds that, in Huntington's disease, repeats of certain nucleotides too many times in a row interferes with splicing.

January 30, 2024
Sex chromosomes responsible for much more than determining sex

Genes expressed from the X and Y chromosomes impact cells throughout the body—not just in the reproductive system—by dialing up or down the expression of thousands of genes found on other chromosomes.

December 13, 2023
Study explains why certain immunotherapies don’t always work as predicted

The findings could help doctors identify cancer patients who would benefit the most from drugs called checkpoint blockade inhibitors.

Anne Trafton | MIT News
September 14, 2023

Cancer drugs known as checkpoint blockade inhibitors have proven effective for some cancer patients. These drugs work by taking the brakes off the body’s T cell response, stimulating those immune cells to destroy tumors.

Some studies have shown that these drugs work better in patients whose tumors have a very large number of mutated proteins, which scientists believe is because those proteins offer plentiful targets for T cells to attack. However, for at least 50 percent of patients whose tumors show a high mutational burden, checkpoint blockade inhibitors don’t work at all.

A new study from MIT reveals a possible explanation for why that is. In a study of mice, the researchers found that measuring the diversity of mutations within a tumor generated much more accurate predictions of whether the treatment would succeed than measuring the overall number of mutations.

If validated in clinical trials, this information could help doctors to better determine which patients will benefit from checkpoint blockade inhibitors.

“While very powerful in the right settings, immune checkpoint therapies are not effective for all cancer patients. This work makes clear the role of genetic heterogeneity in cancer in determining the effectiveness of these treatments,” says Tyler Jacks, the David H. Koch Professor of Biology and a member of MIT’s Koch Institute for Cancer Research.

Jacks; Peter Westcott, a former MIT postdoc in the Jacks lab who is now an assistant professor at Cold Spring Harbor Laboratory; and Isidro Cortes-Ciriano, a research group leader at EMBL’s European Bioinformatics Institute (EMBL-EBI), are the senior authors of the paper, which appears today in Nature Genetics.

A diversity of mutations

Across all types of cancer, a small percentage of tumors have what is called a high tumor mutational burden (TMB), meaning they have a very large number of mutations in each cell. A subset of these tumors has defects related to DNA repair, most commonly in a repair system known as DNA mismatch repair.

Because these tumors have so many mutated proteins, they are believed to be good candidates for immunotherapy treatment, as they offer a plethora of potential targets for T cells to attack. Over the past few years, the FDA has approved a checkpoint blockade inhibitor called pembrolizumab, which activates T cells by blocking a protein called PD-1, to treat several types of tumors that have a high TMB.

However, subsequent studies of patients who received this drug found that more than half of them did not respond well or only showed short-lived responses, even though their tumors had a high mutational burden. The MIT team set out to explore why some patients respond better than others, by designing mouse models that closely mimic the progression of tumors with high TMB.

These mouse models carry mutations in genes that drive cancer development in the colon and lung, as well as a mutation that shuts down the DNA mismatch repair system in these tumors as they begin to develop. This causes the tumors to generate many additional mutations. When the researchers treated these mice with checkpoint blockade inhibitors, they were surprised to find that none of them responded well to the treatment.

“We verified that we were very efficiently inactivating the DNA repair pathway, resulting in lots of mutations. The tumors looked just like they look in human cancers, but they were not more infiltrated by T cells, and they were not responding to immunotherapy,” Westcott says.

The researchers discovered that this lack of response appears to be the result of a phenomenon known as intratumoral heterogeneity. This means that, while the tumors have many mutations, each cell in the tumor tends to have different mutations than most of the other cells. As a result, each individual cancer mutation is “subclonal,” meaning that it is expressed in a minority of cells. (A “clonal” mutation is one that is expressed in all of the cells.)

In further experiments, the researchers explored what happened as they changed the heterogeneity of lung tumors in mice. They found that in tumors with clonal mutations, checkpoint blockade inhibitors were very effective. However, as they increased the heterogeneity by mixing tumor cells with different mutations, they found that the treatment became less effective.

“That shows us that intratumoral heterogeneity is actually confounding the immune response, and you really only get the strong immune checkpoint blockade responses when you have a clonal tumor,” Westcott says.

Failure to activate

It appears that this weak T cell response occurs because the T cells simply don’t see enough of any particular cancerous protein, or antigen, to become activated, the researchers say. When the researchers implanted mice with tumors that contained subclonal levels of proteins that normally induce a strong immune response, the T cells failed to become powerful enough to attack the tumor.

“You can have these potently immunogenic tumor cells that otherwise should lead to a profound T cell response, but at this low clonal fraction, they completely go stealth, and the immune system fails to recognize them,” Westcott says. “There’s not enough of the antigen that the T cells recognize, so they’re insufficiently primed and don’t acquire the ability to kill tumor cells.”

To see if these findings might extend to human patients, the researchers analyzed data from two small clinical trials of people who had been treated with checkpoint blockade inhibitors for either colorectal or stomach cancer. After analyzing the sequences of the patients’ tumors, they found that patients’ whose tumors were more homogeneous responded better to the treatment.

“Our understanding of cancer is improving all the time, and this translates into better patient outcomes,” Cortes-Ciriano says. “Survival rates following a cancer diagnosis have significantly improved in the past 20 years, thanks to advanced research and clinical studies. We know that each patient’s cancer is different and will require a tailored approach. Personalized medicine must take into account new research that is helping us understand why cancer treatments work for some patients but not all.”

The findings also suggest that treating patients with drugs that block the DNA mismatch repair pathway, in hopes of generating more mutations that T cells could target, may not help and could be harmful, the researchers say. One such drug is now in clinical trials.

“If you try to mutate an existing cancer, where you already have many cancer cells at the primary site and others that may have disseminated throughout the body, you’re going to create a super heterogeneous collection of cancer genomes. And what we showed is that with this high intratumoral heterogeneity, the T cell response is confused and there is absolutely no response to immune checkpoint therapy,” Westcott says.

The research was funded by the Koch Institute Support (core) Grant from the U.S. National Cancer Institute, the Howard Hughes Medical Institute, and a Damon Runyon Fellowship Award.

SARS-Cov-2, the virus behind Covid-19, can infect sensory neurons

New research from the Jaenisch lab shows that SARS-CoV-2 can infect sensory neurons, leading to changes in the cells' gene expression. These findings may help to explain how the virus causes symptoms in the peripheral nervous system

Greta Friar | Whitehead Institute
September 5, 2023
Without a key extracellular protein, neuronal axons break and synaptic connections fall apart
David Orenstein | The Picower Institute for Learning and Memory
June 23, 2023

Perhaps the most obvious feature of a neuron is the long branch called an axon that ventures far from the cell body to connect with other neurons or muscles. If that long, thin projection ever seems like it could be vulnerable, a new MIT study shows that its structural integrity may indeed require the support of a surrounding protein called perlecan. Without that protein in Drosophila fruit flies, researchers at The Picower Institute for Learning and Memory found axonal segments can break apart during development and the connections, or synapses, that they form end up dying away.

Perlecan helps make the extracellular matrix, the proteins and other molecules that surround cells, stable and flexible so that cells can develop and function in an environment that is supportive without being rigid.

“What we found was that the extracellular matrix around nerves was being altered and essentially causing the nerves to break completely. Broken nerves eventually led to the synapses retracting,” says study senior author Troy Littleton, the Menicon Professor in MIT’s departments of Biology and Brain and Cognitive Sciences.

Humans need at least some perlecan to survive after birth. Mutations that reduce, but don’t eliminate, perlecan can cause Schwartz-Jampel syndrome, in which patients experience neuromuscular problems and skeletal abnormalities. The new study may help explain how neurons are affected in the condition, Littleton says, and also deepen scientists’ understanding of how the extracellular matrix supports axon and neural circuit development.

Ellen Guss PhD ’23, who recently defended her doctoral thesis on the work, led the research published June 8 in eLife.

At first she and Littleton didn’t expect the study to yield a new discovery about the durability of developing axons. Instead, they were investigating a hypothesis that perlecan might help organize some of the protein components in synapses that fly nerves develop to connect with muscles. But when they knocked out the gene called “trol” that encodes perlecan in flies, they saw that the neurons appeared to “retract” many synapses at a late stage of larval development. Proteins on the muscle side of the synaptic connection remained, but the neuron side of the connection withered away. That suggested that perlecan had a bigger role than they first thought.

Indeed, the authors found that the perlecan wasn’t particularly enriched around synapses. Where it was pronounced was in a structure called the neural lamella, which surrounds axon bundles and acts a bit like the rubbery cladding around a TV cable to keep the structure intact. That suggested that a lack of perlecan might not be a problem at the synapse, but instead causes trouble along axons due to its absence in the extracellular matrix surrounding nerve bundles.

Littleton’s lab had developed a technique for daily imaging of fly neural development called serial intravital imaging. They applied it to watch what happened to the fly axons and synapses over a four-day span. They observed that while fly axons and synapses developed normally at first, not only synapses but also whole segments of axons faded away.

They also saw that the farther an axon segment was from the fly’s brain, the more likely it was to break apart, suggesting that the axon segments became more vulnerable the further out they extended. Looking segment by segment, they found that where axons were breaking down, synapse loss would soon follow, suggesting that axon breakage was the cause of the synapse retraction.

“The breakages were happening in a segment-wide manner,” Littleton says. “In some segments the nerves would break and in some they wouldn’t. Whenever there was a breakage event, you would see all the neuromuscular junctions (synapses) across all the muscles in that segment retract.”

When they compared the structure of the lamella in mutant versus healthy flies, they found that the lamella was thinner and defective in the mutants. Moreover, where the lamella was weakened, axons were prone to break and the microtubule structures that run the length of the axon would become misdirected, protruding outward and becoming tangled up in dramatic bundles at sites of severed axons.

In one other key finding, the team showed that perlecan’s critical role depended on its secretion from many cells, not just neurons. Blocking the protein in just one cell type or another did not cause the problems that total knockdown did, and enhancing secretion from just neurons was not enough to overcome its deficiency from other sources.

Altogether, the evidence pointed to a scenario where lack of perlecan secretion caused the neural lamella to be thin and defective, with the extracellular matrix becoming too rigid. The further from the brain nerve bundles extended, the more likely movement stresses would cause the axons to break where the lamella had broken down. The microtubule structure within the axons then became disorganized. That ultimately led to synapses downstream of those breakages dying away because the disruption of the microtubules means the cells could no longer support the synapses.

“When you don’t have that flexibility, although the extracellular matrix is still there, it becomes very rigid and tight and that basically leads to this breakage as the animal moves and pulls on those nerves over time,” Littleton says. “It argues that the extracellular matrix is functional early on and can support development, but doesn’t have the right properties to sustain some key functions over time as the animal begins to move and navigate around. The loss of flexibility becomes really critical.”

In addition to Littleton and Guss, the paper’s other authors are Yulia Akbergenova and Karen Cunningham.

Support for the study came from the National Institutes of Health. The Littleton Lab is also supported by The Picower Institute for Learning and Memory and The JPB Foundation.

MIT alum filling in the gaps in urology research

Now an assistant professor at UT Dallas, Nicole De Nisco draws on love of problem solving and interdisciplinary skills honed as an undergraduate and graduate student at MIT

Lillian Eden | Department of Biology
June 12, 2023

There were early signs that Nicole De Nisco, SB ‘07, PhD ‘13, might become a scientist. She ran out of science classes to take in high school and fondly remembers the teacher that encouraged her to pursue science instead of the humanities. But she ended up at MIT, in part, out of spite. 

“I applied because my guidance counselor told me I wouldn’t get in,” she said. The rest, as they say, is history for the first-generation college student from Los Angeles. 

Now, she’s an assistant professor of biological sciences at UT Dallas studying urinary tract infections (UTIs) and the urinary microbiome in postmenopausal women. 

De Nisco has already made some important advancements in the field: she developed a new technique for visualizing bacteria in the bladder and used it to demonstrate that bacteria form reservoirs in human bladder tissue, leading to chronic or recurrent UTIs. 

It was known that in mice, bacteria are able to create communities within the bladder tissue, forming reservoirs and staying there long term—but no one had shown that occurring in human tissue before. 

People in lab coats looking at something Nicole De Nisco is holding in her hand.
De Nisco says MIT prepared her well for the type of interdisciplinary work she does every day at UT Dallas, where all research buildings are fully integrated. She works closely with mathematicians, chemists, and engineers. Photo provided by The University of Texas at Dallas

De Nisco found that reservoirs of tissue-resident bacteria exist in human patients with recurring UTIs, a condition which may ultimately lead to women needing to have their bladder removed. De Nisco now mostly works with postmenopausal women who have been suffering from decades of recurring UTIs. 

There was a big gap in the field, De Nisco explained, so entering the field of urology was also an opportunity to make new discoveries and find new ways to treat those recurring infections.  

De Nisco said she’s in the minority, both as a woman studying urology and as someone studying diseases that affect female patients. Most researchers in the urology field are men, and most focus on the prostate. 

But things are changing. 

“I think there are a lot of women in the field who are now pushing back, and I actually collaborate with a lot of other female investigators in the field. We’re trying to support each other so that we can survive and, hopefully, actually advance the science—instead of it being in the same place it was 15 years ago,” De Nisco says.

De Nisco first fell in love with biomedical research as an undergrad doing a UROP in Catherine Drennan’s lab, back when Drennan was still located in the chemistry building. 

“Cathy herself was incredibly encouraging, and is probably the main reason I decided to pursue a career in science—or felt that I could,” De Nisco said. 

De Nisco became fascinated with the dialogue between a microbe and a host organism during an undergraduate course in microbial physiology with Graham Walker, which led to De Nisco’s decision to remain at MIT for her PhD work and to perform her doctoral research in rhizobia legume symbiosis in Walker’s lab. 

De Nisco said during her time at MIT, Drennan and Walker gave her a lot of encouragement and “room to do my own thing,” fostering a love of discovery and problem solving. It’s a mentoring style she’s using now with her own graduate students; she currently has eight working in her lab. 

“Every student is different: some just want a project and they want to know what they’re doing, and some want to explore,” she said. “I was the type that wanted to do my own thing and so they gave me the room and the patience to be able to explore and find something new that I was interested in and excited about.” 

As a low-income student sending financial help home, she also pursued teaching opportunities outside of her usual duties; Walker was very supportive of pursuing other teaching opportunities. De Nisco was a graduate student tutor for Next House watching over 40 undergrads, served as a teaching fellow with the Harvard Extension School, and worked with Eric Lander to help launch the course 7.00x Introduction to Biology – The Secret of Life for EdX, one of the most highly rated MOOCs of all time.  

She said MIT definitely prepared her for a life as a professor, teacher, and mentor; the most important thing about graduate school isn’t choosing “the most cutting-edge research project,” but making sure you have a good training experience and an advisor who can provide that. 

“You don’t need to start building your name in the field when you’re a grad student. The lab environment is much more important than the topic. It’s easy to get burned out or to be turned off to a career in academia altogether if you have the wrong advisor,” she said. “You need to learn how to be a scientist, and you have plenty of time later in your career to follow whatever path you want to follow.”

She knows this from experience: her current research is somewhat parallel but unrelated to her previous research experience. 

“I think my motivation for being a scientist is rooted in my desire to help people doing something I enjoy,” she said. “I was not doing this kind of research as a graduate student, and that doesn’t mean that I wasn’t able to end up at this point in my career where I’m doing research that is focused on improving the lives of women, specifically.”

She did her postdoctoral work at UT Southwestern Medical Center studying Vibrio parahaemolyticus, a human pathogen that causes gastroenteritis. The work was a marriage of her interests in biochemistry and host-microbiome interactions.

She said MIT prepared her well for the type of interdisciplinary work that she does every day: At UT Dallas, all the research buildings are fully integrated, with engineers, chemists, physicists, and biologists sharing lab spaces in the same building. Her closest collaborators are mathematicians, chemists, and engineers. 

Although she may not be fully literate, she has a common language with the people she works with thanks to MIT’s undergraduate course requirements in many different topics and MIT’s focus on interdisciplinary research, which is “how real advancement is made.” 

Ultimately, De Nisco said she is glad to this day that she attended MIT. 

“Getting that acceptance letter to attend MIT probably changed the trajectory of my life,” she said. “You never know, on paper, what someone is going to achieve eventually, and what kind of force they’re going to be. I’m always grateful to whoever was on the admissions committees that made the decision to accept me—twice.”