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Making sense of cell fate

MIT researchers find timing and dosage of DNA-damaging drugs are key to whether a cancer cell dies or enters senescence.

Bendta Schroeder | Koch Institute
July 31, 2023

Despite the proliferation of novel therapies such as immunotherapy or targeted therapies, radiation and chemotherapy remain the frontline treatment for cancer patients. About half of all patients still receive radiation and 60-80 percent receive chemotherapy.

Both radiation and chemotherapy work by damaging DNA, taking advantage of a vulnerability specific to cancer cells. Healthy cells are more likely to survive radiation and chemotherapy since their mechanisms for identifying and repairing DNA damage are intact. In cancer cells, these repair mechanisms are compromised by mutations. When cancer cells cannot adequately respond to the DNA damage caused by radiation and chemotherapy, ideally, they undergo apoptosis or die by other means.

However, there is another fate for cells after DNA damage: senescence — a state where cells survive, but stop dividing. Senescent cells’ DNA has not been damaged enough to induce apoptosis but is too damaged to support cell division. While senescent cancer cells themselves are unable to proliferate and spread, they are bad actors in the fight against cancer because they seem to enable other cancer cells to develop more aggressively. Although a cancer cell’s fate is not apparent until a few days after treatment, the decision to survive, die, or enter senescence is made much earlier. But, precisely when and how that decision is made has not been well understood.

In an open-access study of ovarian and osteosarcoma cancer cells appearing July 19 in Cell Systems, MIT researchers show that cell signaling proteins commonly associated with cell proliferation and apoptosis instead commit cancer cells to senescence within 12 hours of treatment with low doses of certain kinds of chemotherapy.

“When it comes to treating cancer, this study underscores that it’s important not to think too linearly about cell signaling,” says Michael Yaffe, who is a David H. Koch Professor of Science at MIT, the director of the MIT Center for Precision Cancer Medicine, a member of MIT’s Koch Institute for Integrative Cancer Research, and the senior author of the study. “If you assume that a particular treatment will always affect cancer cell signaling in the same way — you may be setting yourself up for many surprises, and treating cancers with the wrong combination of drugs.”

Using a combination of experiments with cancer cells and computational modeling, the team investigated the cell signaling mechanisms that prompt cancer cells to enter senescence after treatment with a commonly used anti-cancer agent. Their efforts singled out two protein kinases and a component of the AP-1 transcription factor complex as highly associated with the induction of senescence after DNA damage, despite the well-established roles for all of these molecules in promoting cell proliferation in cancer.

The researchers treated cancer cells with low and high doses of doxorubicin, a chemotherapy that interferes with the function with topoisomerase II, an enzyme that breaks and then repairs DNA strands during replication to fix tangles and other topological problems.

By measuring the effects of DNA damage on single cells at several time points ranging from six hours to four days after the initial exposure, the team created two datasets. In one dataset, the researchers tracked cell fate over time. For the second set, researchers measured relative cell signaling activity levels across a variety of proteins associated with responses to DNA damage or cellular stress, determination of cell fate, and progress through cell growth and division.

The two datasets were used to build a computational model that identifies correlations between time, dosage, signal, and cell fate. The model identified the activities of the MAP kinases Erk and JNK, and the transcription factor c-Jun as key components of the AP-1 protein likewise understood to involved in the induction of senescence. The researchers then validated these computational findings by showing that inhibition of JNK and Erk after DNA damage successfully prevented cells from entering senescence.

The researchers leveraged JNK and Erk inhibition to pinpoint exactly when cells made the decision to enter senescence. Surprisingly, they found that the decision to enter senescence was made within 12 hours of DNA damage, even though it took days to actually see the senescent cells accumulate. The team also found that with the passage of more time, these MAP kinases took on a different function: promoting the secretion of proinflammatory proteins called cytokines that are responsible for making other cancer cells proliferate and develop resistance to chemotherapy.

“Proteins like cytokines encourage ‘bad behavior’ in neighboring tumor cells that lead to more aggressive cancer progression,” says Tatiana Netterfield, a graduate student in the Yaffe lab and the lead author of the study. “Because of this, it is thought that senescent cells that stay near the tumor for long periods of time are detrimental to treating cancer.”

This study’s findings apply to cancer cells treated with a commonly used type of chemotherapy that stalls DNA replication after repair. But more broadly, the study emphasizes that “when treating cancer, it’s extremely important to understand the molecular characteristics of cancer cells and the contextual factors such as time and dosing that determine cell fate,” explains Netterfield.

The study, however, has more immediate implications for treatments that are already in use. One class of Erk inhibitors, MEK inhibitors, are used in the clinic with the expectation that they will curb cancer growth.

“We must be cautious about administering MEK inhibitors together with chemotherapies,” says Yaffe. “The combination may have the unintended effect of driving cells into proliferation, rather than senescence.”

In future work, the team will perform studies to understand how and why individual cells choose to proliferate instead of enter senescence. Additionally, the team is employing next-generation sequencing to understand which genes c-Jun is regulating in order to push cells toward senescence.

This study was funded, in part, by the Charles and Marjorie Holloway Foundation and the MIT Center for Precision Cancer Medicine.

Brady Weissbourd named Klingenstein-Simons Fellow

Three-year fellowship will support Weissbourd’s research on how the C. hemisphaerica jellyfish survives and thrives by constantly making new neurons.

David Orenstein | The Picower Institute for Learning and Memory
July 20, 2023

The Clytia hemisphaerica jellyfish is not only a hypnotically graceful swimmer, but also an amazing neuron-manufacturing machine with a remarkable ability to expand and regenerate its nervous system.

Now, thanks to a prestigious Klingenstein-Simons Fellowship Award in Neuroscience, MIT Assistant Professor Brady Weissbourd will study how the tiny, transparent animals use this ability to build, organize, and rebuild a stable, functional, and robust nervous system throughout their lives.

“As we look more broadly across the animal kingdom it is amazing to see how similar the basic biology is of animals that look completely different — even jellyfish have neurons similar to our own that generate their behavior,” says Weissbourd, a faculty member in MIT’s Department of Biology and The Picower Institute for Learning and Memory, whose work to engineer genetic access to C. hemisphaerica in 2021 established it as a new neuroscience model organism. “At the same time, it could be just as important to examine what is different across species, particularly when it comes to some of the incredible capabilities that have evolved.”

Weissbourd is just one of 13 researchers nationally to be recognized with this fellowship, which provides $300,000 over three years. It will enable Weissbourd’s lab to tackle several questions raised by the jellyfish’s prodigious production of neurons. Where does the constant stream of newborn neurons come from, and what guides them to their eventual places in the jellyfish’s mesh-like neural network? How does the jellyfish organize these ever-changing neural populations — for instance, into functional circuits — to enable its various behaviors?

Another question hails from the surprising results of an experiment in which Weissbourd ablated the entire class of the neurons that the jellyfish uses to fold up its umbrella-shaped body — about 10 percent of the 10,000 or so neurons that it has. He found that within a week enough new neurons had taken their place that the folding behavior was restored. Weissbourd’s studies will also seek to determine how the animal can so readily bounce back from the destruction of a whole major neural network and the behavior it produces.

“We were studying the neural control of a particular behavior and stumbled across this shocking observation that the subnetwork that controls this behavior is constantly changing size and can completely regenerate,” Weissbourd says. “We want to understand the mechanisms that allow this network to be so robust, including the ability to rebuild itself from scratch. I’m very grateful to the Klingenstein Fund and the Simons Foundation for supporting our work.”

Probe expands understanding of oral cavity homeostasis

A new approach opens the door to a greater understanding of protein-microbe interactions.

Lillian Eden | Department of Biology
July 19, 2023

Your mouth is a crucial interface between the outside world and the inside of your body. Everything you breathe, chew, or drink interacts with your oral cavity — the proteins and the microbes, including microbes that can harm us. When things go awry, the result can range from the mild, like bad breath, to the serious, like tooth and gum decay, to more dire effects in the gut and other parts of the body.

Even though the oral microbiome plays a critical role as a front-line defense for human health and disease, we still know very little about the intricacies of host-microbe interactions in the complex physiological environment of the mouth; a better understanding of those interactions is key to developing treatments for human disease.

In a recent study published in PNAS, a team of scientists from MIT and elsewhere revealed that one of the most abundant proteins found in our saliva binds to the surface of select microbes found in the mouth. The findings shed light on how salivary proteins and mucus play a role in maintaining the oral cavity microbiome.

The collaboration involved members of the labs of Barbara Imperiali in the MIT Department of Biology and Laura Kiessling in the MIT Department of Chemistry, as well as the groups of Stefan Ruhl at the University at Buffalo School of Dental Medicine and Catherine Grimes at the University of Delaware.

The work is focused on an abundant oral cavity protein called zymogen granule protein 16 homolog B (ZG16B). Finding ZG16B’s interaction partners and gaining insight into its function were the overarching goals of the project. To accomplish this, Soumi Ghosh, a postdoc in the Imperiali lab, and colleagues engineered ZG16B to add reporter tags such as fluorophores. They called these modified proteins “microbial glycan analysis probes (mGAPs)” because they allowed them to identify ZG16B binding partners using complementary methods. They applied the probes to samples of healthy oral microbiomes to identify target microbes and binding partners.

The results excited them.

“ZG16B didn’t just bind to random bacteria. It was very focused on certain species, including a commensal bacteria called Streptococcus vestibularis,” says Ghosh, who is first author on the paper.

Commensal bacteria are found in a normal healthy microbiome and do not cause disease.

Using the mGAPs, the team showed that ZG16B binds to cell wall polysaccharides of the bacteria, which indicates that ZG16B is a lectin, a carbohydrate-binding protein. In general, lectins are responsible for cell-cell interactions, signaling pathways, and some innate immune responses against pathogens. “This is the first time that it has been proven experimentally that ZG16B acts as a lectin because it binds to the carbohydrates on the cell surface or cell wall of the bacteria,” Ghosh highlights.

ZG16B was also shown to recruit Mucin 7 (MUC7), a salivary glycoprotein in the oral cavity, and together the results suggest that ZG16B may help maintain a healthy balance in the oral microbiome by forming a complex with MUC7 and certain bacteria. The results indicate that ZG16B regulates the bacteria’s abundance by preventing overgrowth through agglutination when the bacteria exceed a certain level of growth.

“ZG16B, therefore, seems to function as a missing link in the system; it binds to different types of glycans — the microbial glycans and the mucin glycans — and ultimately, maintains a healthy balance in our oral cavity,” Ghosh says.

Further work with this probe and samples of oral microbiome from healthy and diseased subjects could also reveal the lectin’s importance for oral health and disease.

Current attention is focused on developing and applying additional mGAPs based on other human lectins, such as those found in serum, liver, and intestine to reveal their binding specificities and their roles in host-microbe interactions.

“The research carried out in this collaboration exemplifies the kind of synergy that made me excited to move to MIT five years ago,” says Kiessling. “I’ve been able to work with outstanding scientists who share my interest in the chemistry and the biology of carbohydrates.”

Kiessling and Imperiali, both senior authors of the paper, came up with the term for the probes they’re creating: “mGAPS to fill in the gaps” in our understanding of the role of lectins in the human microbiome, according to Ghosh.

“If we want to develop therapeutics against bacterial infection, we need a better understanding of host-microbe interactions,” Ghosh says. “The significance of our study is to prove that we can make very good probes for microbial glycans, find out their importance in the front-line defense of the immune system, and, ultimately, come up with a therapeutic approach to disease.”

This research was supported by the National Institute of Health.

It takes three to tango: transcription factors bind DNA, protein, and RNA
Greta Friar | Whitehead Institute
July 7, 2023

Transcription factors could be the Swiss Army knives of gene regulation; they are versatile proteins containing multiple specialized regions. On one end they have a region that can bind to DNA. On the other end they have a region that can bind to proteins. Transcription factors help to regulate gene expression—turning genes on or off and dialing up or down their level of activity—often in partnership with the proteins that they bind. They anchor themselves and their partner proteins to DNA at binding sites in genetic regulatory sequences, bringing together the components that are needed to make gene expression happen.

Transcription factors are a well-known family of proteins, but new research from Whitehead Institute Member Richard Young and colleagues shows that the picture we have had of them is incomplete. In a paper published in Molecular Cell on July 3, Young and postdocs Ozgur Oksuz and Jonathan Henninger reveal that along with DNA and protein, many transcription factors can also bind RNA. The researchers found that RNA binding keeps transcription factors near their DNA binding sites for longer, helping to fine tune gene expression. This rethinking of how transcription factors work may lead to a better understanding of gene regulation, and may provide new targets for RNA-based therapeutics.

“It’s as if, after carrying around a Swiss Army knife all your life for its blade and scissors, you suddenly realize that the odd, small piece in the back of the knife is a screwdriver,” Young says. “It’s been staring you in the face this whole time, and now that you finally see it, it becomes clear how many more uses there are for the knife than you had realized.”

How transcription factors’ RNA binding went overlooked

A few papers, including one from Young’s lab, had previously identified individual transcription factors as being able to bind RNA, but researchers thought that this was a quirk of the specific transcription factors. Instead, Young, Oksuz, Henninger and collaborators have shown that RNA-binding is in fact a common feature present in at least half of transcription factors.

“We show that RNA binding by transcription factors is a general phenomenon,” Oksuz says. “Individual examples in the past were thought to be exceptions to the rule. Other studies dismissed signs of RNA binding in transcription factors as an artifact—an accident of the experiment rather than a real finding. The clues have been there all along, but I think earlier work was so focused on the DNA and protein interactions that they didn’t consider RNA.”

The reason that researchers had not recognized transcription factors’ RNA binding region as such is because it is not a typical RNA binding domain. Typical RNA binding domains form stable structures that researchers can detect or predict with current technologies. Transcription factors do not contain such structures, and so standard searches for RNA binding domains had not identified them in transcription factors.

“We show that RNA binding by transcription factors is a general phenomenon,” Oksuz says.

Young, Oksuz and Henninger got their biggest clue that researchers might be overlooking something from the human immunodeficiency virus (HIV), which produces a transcription factor-like protein called Tat. Tat increases the transcription of HIV’s RNA genome by binding to the virus’ RNA and then recruiting cellular machinery to it. However, Tat does not contain a structured RNA binding site; instead, it binds RNA from a region called an arginine-rich motif (ARM) that is unstructured but has a high affinity for RNA. When the ARM binds to HIV RNA, the two molecules form a more stable structure together.

The researchers wondered if Tat might be more similar to human transcription factors than anyone had realized. They went through the list of transcription factors, and instead of looking for structured RNA binding domains, they looked for ARMs. They found them in abundance; the majority of human transcription factors contain an ARM-like region between their DNA and protein binding regions, and these sequences were conserved across animal species. Further testing confirmed that many transcription factors do in fact use their ARMs to bind RNA.

RNA binding fine tunes gene expression

Next, the researchers tested to see if RNA binding affected the transcription factors’ function. When transcription factors had their ARMs mutated so they couldn’t bind RNA, those transcription factors were less effective in finding their target sites, remaining at those sites and regulating genes. The mutations did not prevent transcription factors from functioning altogether, suggesting that RNA binding contributes to fine-tuning of gene regulation.

Further experiments confirmed the importance of RNA binding to transcription factor function. The researchers mutated the ARM of a transcription factor important to embryonic development, and found that this led to developmental defects in zebrafish. Additionally, they looked through a list of genetic mutations known to contribute to cancer and heritable diseases, and found that a number of these occur in the RNA binding regions of transcription factors. All of these findings point to RNA binding playing an important role in transcription factors’ regulation of gene expression.

They may also provide therapeutic opportunities. The transcription factors studied by the researchers were found to bind RNA molecules that are produced in the regulatory regions of the genome where the transcription factors bind DNA. This set of transcription factors includes factors that can increase or decrease gene expression. “With evidence that RNAs can tune gene expression through their interaction with positive and negative transcription factors,” says Henninger, “we can envision using existing RNA-based technologies to target RNA molecules, potentially increasing or decreasing expression of specific genes in disease settings.”

Notes

Ozgur Oksuz, Jonathan E. Henninger, Robert Warneford-Thomson, Ming M. Zheng, Hailey Erb, Adrienne Vancura, Kalon J. Overholt, Susana Wilson Hawken, Salman F. Banani, Richard Lauman, Lauren N. Reich, Anne L. Robertson, Nancy M. Hannett, Tong I. Lee, Leonard I. Zon, Roberto Bonasio, Richard A. Young. “Transcription factors interact with RNA to regulate genes.” Molecular Cell, July 3, 2023. https://doi.org/10.1016/j.molcel.2023.06.012.

Department of Biology opens its doors for Community College outreach

15 from Bunker Hill Community College visited campus as part of an outreach initiative to build stronger ties with local institutions that serve diverse, nontraditional learners.

Lillian Eden | Department of Biology
July 6, 2023

Although many undergraduates may be home for the summer, the halls and labs of MIT are still teeming with activity. On a sunny Thursday in June, 15 students from Bunker Hill Community College (BHCC) got to peek behind the curtain of research at MIT. 

The Community College Partnership builds ties with two local community colleges that serve diverse, nontraditional students. The program was first conceived in 2020 as part of the biology department’s participation in #ShutDownSTEM, a day to consider equity and inclusion for marginalized communities and to educate and take action against injustice. 

The visit is part of a larger effort to encourage students to pursue research opportunities and careers in research at and beyond MIT; other initiatives include virtual career panels and workshops for students at BHCC and Roxbury Community College. In addition, two community college students perform research as part of MRSP-Bio each summer, thanks to funding from the Packard Foundation acquired by Ankur Jain, Assistant Professor of Biology and Core Member of the Whitehead Institute. 

BHCC students toured the MIT Cryo-EM facility with director Sarah Sterling. Photo Credit: Mandana Sassanfar

Sarah Sterling, Director of the Cryo-EM facility, loves giving tours because students ask such great questions, and the BHCC students were no exception: they were curious and inquisitive at every stop of their tour. Sterling explained that she chose her position, in part, because she enjoys “facilitating science”—helping researchers use cutting-edge equipment to find answers to their questions. 

The students also visited labs in Building 68, Whitehead Institute, and the Picower Institute for Learning and Memory. 

 Reddien Lab postdoc Thomas Cooke described exploring mechanisms of regeneration in planarians, and Professor Laurie Boyer described the core questions underlying her research on heart development. 

“The process of forming tissues and organs works sufficiently well that we’re all here, and we’re all relatively healthy,” Boyer says. “To me, that is remarkable.” 

What isn’t well understood, she explains, is how faulty regulation can lead to disease and congenital malformations, and research using model systems can provide answers. For example, creating a model system in a dish can lead to a better understanding of the formation of circuits and molecular players. That, in turn, can lead to therapies or early diagnosis. The lab also works on tools to visualize what is occurring inside cells because “seeing is believing.”

“As scientists, we are not only trying to plan the best experiments possible, but we are also trying to develop new tools that push the boundaries of what we can discover,” she says. “Keeping an eye on the big picture is important because you’re never studying a problem in isolation. You’re studying a biological mechanism that has implications for many different things.” 

It was “really eye-opening” to see what’s happening in some of the labs, according to BHCC student Robinson Le. Le is a dancer turned Biology major but had only ever come to campus for breakdancing practice—a skill they showed off to cheering BHCC students during lunch. 

BHCC students with Department of Biology Faculty Laurie Boyer. Photo Credit: Mandana Sassanfar

Badara Mbengue, another BHCC student, was excited to learn “what everyday life is like in the department.” 

“It makes me very happy to see how much this has grown and continues to grow,” says Sheena Vasquez, PhD ‘23, who helped spearhead the initiative. 

BHCC alums at MIT also showed students around the labs they are working in and shared their experiences at MIT, including as MSRP-Bio students, Quantitative Methods Workshop students, and as an undergraduate transfer student. 

Libby Dunphy, a professor at BHCC, helped arrange the visit. She says the trip was an excellent opportunity for her students, who don’t get much exposure to real research.

“Seeing actual researchers, seeing that they’re real people, and that they’re nice, can help students imagine themselves in this place,” Dunphy says. “The Bunker Hill motto is ‘imagine the possibilities.’ And it’s cheesy, but we’re imagining the possibilities here.” 

Boyer also offered advice for pursuing research at this stage in the students’ careers. 

“The opportunities are unlimited, and so many people would be happy to support you—but sometimes, you have to ask,” Boyer advises. “Stay ambitious. You should be so proud of yourselves for embarking on this journey.” 

Andrea Lo ’21 draws on ecological lessons for life, work, and education

With a minor in literature and environmental sustainability, the biology alumna considers perspectives from Charles Darwin to Annie Dillard.

Lillian Eden | Department of Biology
July 6, 2023

Growing up in Los Angeles about 10 minutes away from the Ballona Wetlands, Andrea Lo ’21 has long been interested in ecology. She witnessed, in real-time, the effects of urbanization and the impacts that development had on the wetlands.

“In hindsight, it really helped shape my need for a career — and a life — where I can help improve my community and the environment,” she says.

Lo, who majored in biology at MIT, says a recurring theme in her life has been the pursuit of balance, valuing both extracurricular and curricular activities. She always felt an equal pull toward STEM and the humanities, toward wet lab work and field work, and toward doing research and helping her community.

“One of the most important things I learned in 7.30[J] (Fundamentals of Ecology) was that there are always going to be trade-offs. That’s just the way of life,” she says. “The biology major at MIT is really flexible. I got a lot of room to explore what I was interested in and get a good balance overall, with humanities classes along with technical classes.”

Lo was drawn to MIT because of the focus on hands-on work — but many of the activities Lo was hoping to do, both extracurricular and curricular, were cut short because of the pandemic, including her lab-based Undergraduate Research Opportunities Program (UROP) project.

Instead, she pursued a UROP with MIT Sea Grant, working on a project in partnership with Northeastern University and the Charles River Conservancy with funding support from the MIT Community Service fund as part of STEAM Saturday.

She was involved in creating Floating Wetland kits, an educational activity directed at students in grades 4 to 6 to help students understand ecological concepts,the challenges the Charles River faces due to urbanization, and how floating wetlands improve the ecosystem.

“Our hope was to educate future generations of local students in Cambridge in order for them to understand the ecology surrounding where they live,” she says.

In recent years, many bodies of water in Massachusetts have become unusable during the warmer months due to the process of eutrophication: stormwater runoff picks up everything — from fertilizer and silt to animal excrement — and deposits it at the lowest point, which is often a body of water. This leads to an excess of nutrients in the body of water and, when combined with warm temperatures, can lead to harmful algal blooms, making the water sludgy, bright green, and dangerously toxic.

The wetland kits Lo worked with were mini ecosystems, replicating a full-sized floating wetland. One such floating wetland can be seen from the Longfellow Bridge at one end of MIT’s campus — the Charles River floating wetland is a patch of grass attached to a buoy like a boat, which is often visited by birds and inhabited by much smaller critters that cannot be seen from the shore.

The Charles River floating wetland has a variety of flora, but the kits Lo helped present use only wheat grass because it is easy to grow and has long, dangling roots that could penetrate the watery medium below. A water tray beneath the grass — the Charles river of the mini ecosystem — contains spirulina powder for replicating algae growth and daphnia, which are small, planktonic crustaceans that help keep freshwater clean and usable.

“This work was really fulfilling, but it’s also really important, because environmental sustainability relies on future generations to carry on the work that past generations have been doing,” she says. “MIT’s motto is ‘mens et manus’ — education for practical application, and applying theoretical knowledge to what we do in our daily lives. I think this project really helped reinforce that.”

Since 2021, Lo has been working in Denmark in a position she learned about through the MIT-Denmark program.

She chose Denmark because of its reputation for environmental and sustainability issues and because she didn’t know much about it except for it being one of the happiest countries in the world, often thought of synonymously with the word “hygge,” which has no direct translation but encapsulates coziness and comfort from the small joys in life.

“At MIT, we have a very strong work-hard, play-hard culture. I think we can learn a lot from the work-life balance that Denmark has a reputation for,” she says. “I really wanted to take the opportunity in between graduation and whatever came after to explore beyond my bubble. For me, it was important to step back, out of my comfort zone, step into a different environment — and just live.”

Currently, her personal project is comparing the conditions of two lagoons on the island of Fyn in Denmark. Both are naturally occurring, but in different states of environmental health.

She’s been doing a mix of field work and lab work. She collects sediment and fauna samples using a steel corer, or “butter stick” in her lab’s slang. In the same way that one can use a metal tube-shaped tool to remove the core of an apple, she punches the steel corer into the ground, removing a plug of sample. She then sifts the sample through 1 millimeter mesh, preserves the filtered sample in formalin, and takes everything back to the lab.

Once there, she looks through the sample to find macrofauna — mollusks, barnacles, and polychaetes, a bristly-looking segmented worm, for example. Collected over time, sediment characteristics like organic matter content, sediment grain size, and the size and abundance of macrofauna, can reveal trends that can help determine the health of the ecosystem.

Lo doesn’t have any concrete results yet, but her data could help researchers project the recovery of a lagoon that was rehabilitated using a technique called managed realignment, where water is allowed to reclaim areas where it was once found. She says she’s glad she gets a mix of field work and lab work, even on Denmark’s stormiest days.

“Sometimes there are really cold days where it’s windy and I wish I was in the lab, but, at the same time, it’s nice to have a balance where I can be outside and really be hands-on with my work,” she says.

Reflecting her dual interests in the technical and the innovative, she will be back in the Greater Boston area in the fall, pursuing a master of science in innovation and management and an MS in civil and environmental engineering at the Tufts Gordon Institute.

“So much has happened and changed due to the pandemic that it’s easy to dwell on what could’ve been, but I tell myself to be optimistic and take the positive aspects that have come out of the circumstances,” Lo says. “My opportunities with the Sea Grant, MISTI, and Tufts definitely wouldn’t have happened if the pandemic hadn’t happened.”

Facundo Batista

Education

  • Graduate: PhD, 1995, International School of Advanced Studies
  • Undergraduate: BSc, 1991, University of Buenos Aires

Research Summary

B lymphocytes are the fulcrum of our immunological memory, the source of antibodies, and the focus of vaccine development. My lab has investigated how, where, and when B cell responses take shape. In recent years, my group has expanded into preclinical vaccinology, developing cutting-edge humanized mouse models for diseases including malaria, HIV, and SARS-CoV-2.

Awards

  •      Fellow, Ministero degli Affari Esteri of Italy, 1991-1992
  •      Fellow, UNIDO-International Centre for Genetic Engineering and Biotechnology, 1993-1995
  •      Fellow, Cancer Research Institute, 1995
  •      Long Term Postdoctoral Fellowship, European Molecular Biology Organization, 1996-1997
  •      Project Grant, Arthritis Research Campaign, 1999
  •      Young Investigator Award, European Molecular Biology Organization, 2004
  •      The Royal Society Wolfson Research Merit Award, The Royal Society/The Wolfson Foundation, 2009
  •      Faculty of 1000, 2009
  •      EMBO Member, European Molecular Biology Organization, 2009
  •      Fellow, British Academy of Medical Sciences, 2013
  •      Fellow, American Academy of Microbiology, 2017
  •      Member, Academia de Ciencias de América Latina (ACAL), 2022
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.

Focus on function helps identify the changes that made us human

It can be difficult to tell which of the many small genetic differences between us and chimps have been significant to our evolution. New research from Jonathan Weissman and colleagues narrowed in on the key differences in how humans and chimps rely on certain genes, including how humans became able to grow comparatively large brains.

Greta Friar | Whitehead Institute
June 22, 2023

Humans split away from our closest animal relatives, chimpanzees, and formed our own branch on the evolutionary tree about seven million years ago. In the time since—brief, from an evolutionary perspective—our ancestors evolved the traits that make us human, including a much bigger brain than chimpanzees and bodies that are better suited to walking on two feet. These physical differences are underpinned by subtle changes at the level of our DNA. However, it can be hard to tell which of the many small genetic differences between us and chimps have been significant to our evolution.

New research from Whitehead Institute Member Jonathan Weissman; University of California, San Francisco Assistant Professor Alex Pollen; Weissman lab postdoc Richard She; Pollen lab graduate student Tyler Fair; and colleagues uses cutting edge tools developed in the Weissman lab to narrow in on the key differences in how humans and chimps rely on certain genes. Their findings, published in the journal Cell on June 20, may provide unique clues into how humans and chimps have evolved, including how humans became able to grow comparatively large brains.

Studying function rather than genetic code

Only a handful of genes are fundamentally different between humans and chimps; the rest of the two species’ genes are typically nearly identical. Differences between the species often come down to when and how cells use those nearly identical genes. However, only some of the many differences in gene use between the two species underlie big changes in physical traits. The researchers developed an approach to narrow in on these impactful differences.

Their approach, using stem cells derived from human and chimp skin samples, relies on a tool called CRISPR interference (CRISPRi) that Weissman’s lab developed. CRISPRi uses a modified version of the CRISPR/Cas9 gene editing system to effectively turn off individual genes. The researchers used CRISPRi to turn off each gene one at a time in a group of human stem cells and a group of chimp stem cells. Then they looked to see whether or not the cells multiplied at their normal rate. If the cells stopped multiplying as quickly or stopped altogether, then the gene that had been turned off was considered essential: a gene that the cells need to be active–producing a protein product–in order to thrive. The researchers looked for instances in which a gene was essential in one species but not the other as a way of exploring if and how there were fundamental differences in the basic ways that human and chimp cells function.

By looking for differences in how cells function with particular genes disabled, rather than looking at differences in the DNA sequence or expression of genes, the approach ignores differences that do not appear to impact cells. If a difference in gene use between species has a large, measurable effect at the level of the cell, this likely reflects a meaningful difference between the species at a larger physical scale, and so the genes identified in this way are likely to be relevant to the distinguishing features that have emerged over human and chimp evolution.

“The problem with looking at expression changes or changes in DNA sequences is that there are many of them and their functional importance is unclear,” says Weissman, who is also a professor of biology at the Massachusetts Institute of Technology and an Investigator with the Howard Hughes Medical Institute. “This approach looks at changes in how genes interact to perform key biological processes, and what we see by doing that is that, even on the short timescale of human evolution, there has been fundamental rewiring of cells.”

After the CRISPRi experiments were completed, She compiled a list of the genes that appeared to be essential in one species but not the other. Then he looked for patterns. Many of the 75 genes identified by the experiments clustered together in the same pathways, meaning the clusters were involved in the same biological processes. This is what the researchers hoped to see. Individual small changes in gene use may not have much of an effect, but when those changes accumulate in the same biological pathway or process, collectively they can cause a substantive change in the species. When the researchers’ approach identified genes that cluster in the same processes, this suggested to them that their approach had worked and that the genes were likely involved in human and chimp evolution.

“Isolating the genetic changes that made us human has been compared to searching for needles in a haystack because there are millions of genetic differences, and most are likely to have negligible effects on traits,” Pollen says. “However, we know that there are lots of small effect mutations that in aggregate may account for many species differences. This new approach allows us to study these aggregate effects, enabling us to weigh the impact of the haystack on cellular functions.”

Researchers think bigger brains may rely on genes regulating how quickly cells divide

One cluster on the list stood out to the researchers: a group of genes essential to chimps, but not to humans, that help to control the cell cycle, which regulates when and how cells decide to divide. Cell cycle regulation has long been hypothesized to play a role in the evolution of humans’ large brains. The hypothesis goes like this: Neural progenitors are the cells that will become neurons and other brain cells. Before becoming mature brain cells, neural progenitors divide multiple times to make more of themselves. The more divisions that the neural progenitors undergo, the more cells the brain will ultimately contain—and so, the bigger it will be. Researchers think that something changed during human evolution to allow neural progenitors to spend less time in a non-dividing phase of the cell cycle and transition more quickly towards division. This simple difference would lead to additional divisions, each of which could essentially double the final number of brain cells.

Consistent with the popular hypothesis that human neural progenitors may undergo more divisions, resulting in a larger brain, the researchers found that several genes that help cells to transition more quickly through the cell cycle are essential in chimp neural progenitor cells but not in human cells. When chimp neural progenitor cells lose these genes, they linger in a non-dividing phase, but when human cells lose them, they keep cycling and dividing. These findings suggest that human neural progenitors may be better able to withstand stresses—such as the loss of cell cycle genes—that would limit the number of divisions the cells undergo, enabling humans to produce enough cells to build a larger brain.

“This hypothesis has been around for a long time, and I think our study is among the first to show that there is in fact a species difference in how the cell cycle is regulated in neural progenitors,” She says. “We had no idea going in which genes our approach would highlight, and it was really exciting when we saw that one of our strongest findings matched and expanded on this existing hypothesis.”

More subjects lead to more robust results

Research comparing chimps to humans often uses samples from only one or two individuals from each species, but this study used samples from six humans and six chimps. By making sure that the patterns they observed were consistent across multiple individuals of each species, the researchers could avoid mistaking the naturally occurring genetic variation between individuals as representative of the whole species. This allowed them to be confident that the differences they identified were truly differences between species.

The researchers also compared their findings for chimps and humans to orangutans, which split from the other species earlier in our shared evolutionary history. This allowed them to figure out where on the evolutionary tree a change in gene use most likely occurred. If a gene is essential in both chimps and orangutans, then it was likely essential in the shared ancestor of all three species; it’s more likely for a particular difference to have evolved once, in a common ancestor, than to have evolved independently multiple times. If the same gene is no longer essential in humans, then its role most likely shifted after humans split from chimps. Using this system, the researchers showed that the changes in cell cycle regulation occurred during human evolution, consistent with the proposal that they contributed to the expansion of the brain in humans.

The researchers hope that their work not only improves our understanding of human and chimp evolution, but also demonstrates the strength of the CRISPRi approach for studying human evolution and other areas of human biology. Researchers in the Weissman and Pollen labs are now using the approach to better understand human diseases—looking for the subtle differences in gene use that may underlie important traits such as whether someone is at risk of developing a disease, or how they will respond to a medication. The researchers anticipate that their approach will enable them to sort through many small genetic differences between people to narrow in on impactful ones underlying traits in health and disease, just as the approach enabled them to narrow in on the evolutionary changes that helped make us human.