Author: mantulin

Using plant biology to address climate change

A Climate Grand Challenges flagship project aims to reduce agriculture-driven emissions while making food crop plants heartier and more nutritious.

Merrill Meadow | Whitehead Institute
April 20, 2022

On April 11, MIT announced five multiyear flagship projects in the first-ever Climate Grand Challenges, a new initiative to tackle complex climate problems and deliver breakthrough solutions to the world as quickly as possible. This article is the fourth in a five-part series highlighting the most promising concepts to emerge from the competition and the interdisciplinary research teams behind them.

The impact of our changing climate on agriculture and food security — and how contemporary agriculture contributes to climate change — is at the forefront of MIT’s multidisciplinary project “Revolutionizing agriculture with low-emissions, resilient crops.” The project The project is one of five flagship winners in the Climate Grand Challenges competition, and brings together researchers from the departments of Biology, Biological Engineering, Chemical Engineering, and Civil and Environmental Engineering.

“Our team’s research seeks to address two connected challenges: first, the need to reduce the greenhouse gas emissions produced by agricultural fertilizer; second, the fact that the yields of many current agricultural crops will decrease, due to the effects of climate change on plant metabolism,” says the project’s faculty lead, Christopher Voigt, the Daniel I.C. Wang Professor in MIT’s Department of Biological Engineering. “We are pursuing six interdisciplinary projects that are each key to our overall goal of developing low-emissions methods for fertilizing plants that are bioengineered to be more resilient and productive in a changing climate.”

Whitehead Institute members Mary Gehring and Jing-Ke Weng, plant biologists who are also associate professors in MIT’s Department of Biology, will lead two of those projects.

Promoting crop resilience

For most of human history, climate change occurred gradually, over hundreds or thousands of years. That pace allowed plants to adapt to variations in temperature, precipitation, and atmospheric composition. However, human-driven climate change has occurred much more quickly, and crop plants have suffered: Crop yields are down in many regions, as is seed protein content in cereal crops.

“If we want to ensure an abundant supply of nutritious food for the world, we need to develop fundamental mechanisms for bioengineering a wide variety of crop plants that will be both hearty and nutritious in the face of our changing climate,” says Gehring. In her previous work, she has shown that many aspects of plant reproduction and seed development are controlled by epigenetics — that is, by information outside of the DNA sequence. She has been using that knowledge and the research methods she has developed to identify ways to create varieties of seed-producing plants that are more productive and resilient than current food crops.

But plant biology is complex, and while it is possible to develop plants that integrate robustness-enhancing traits by combining dissimilar parental strains, scientists are still learning how to ensure that the new traits are carried forward from one generation to the next. “Plants that carry the robustness-enhancing traits have ‘hybrid vigor,’ and we believe that the perpetuation of those traits is controlled by epigenetics,” Gehring explains. “Right now, some food crops, like corn, can be engineered to benefit from hybrid vigor, but those traits are not inherited. That’s why farmers growing many of today’s most productive varieties of corn must purchase and plant new batches of seeds each year. Moreover, many important food crops have not yet realized the benefits of hybrid vigor.”

The project Gehring leads, “Developing Clonal Seed Production to Fix Hybrid Vigor,” aims to enable food crop plants to create seeds that are both more robust and genetically identical to the parent — and thereby able to pass beneficial traits from generation to generation.

The process of clonal (or asexual) production of seeds that are genetically identical to the maternal parent is called apomixis. Gehring says, “Because apomixis is present in 400 flowering plant species — about 1 percent of flowering plant species — it is probable that genes and signaling pathways necessary for apomixis are already present within crop plants. Our challenge is to tweak those genes and pathways so that the plant switches reproduction from sexual to asexual.”

The project will leverage the fact that genes and pathways related to autonomous asexual development of the endosperm — a seed’s nutritive tissue — exist in the model plant Arabidopsis thaliana. In previous work on Arabidopsis, Gehring’s lab researched a specific gene that, when misregulated, drives development of an asexual endosperm-like material. “Normally, that seed would not be viable,” she notes. “But we believe that by epigenetic tuning of the expression of additional relevant genes, we will enable the plant to retain that material — and help achieve apomixis.”

If Gehring and her colleagues succeed in creating a gene-expression “formula” for introducing endosperm apomixis into a wide range of crop plants, they will have made a fundamental and important achievement. Such a method could be applied throughout agriculture to create and perpetuate new crop breeds able to withstand their changing environments while requiring less fertilizer and fewer pesticides.

Creating “self-fertilizing” crops

Roughly a quarter of greenhouse gas (GHG) emissions in the United States are a product of agriculture. Fertilizer production and use accounts for one third of those emissions and includes nitrous oxide, which has heat-trapping capacity 298-fold stronger than carbon dioxide, according to a 2018 Frontiers in Plant Science study. Most artificial fertilizer production also consumes huge quantities of natural gas and uses minerals mined from nonrenewable resources. After all that, much of the nitrogen fertilizer becomes runoff that pollutes local waterways. For those reasons, this Climate Grand Challenges flagship project aims to greatly reduce use of human-made fertilizers.

One tantalizing approach is to cultivate cereal crop plants — which account for about 75 percent of global food production — capable of drawing nitrogen from metabolic interactions with bacteria in the soil. Whitehead Institute’s Weng leads an effort to do just that: genetically bioengineer crops such as corn, rice, and wheat to, essentially, create their own fertilizer through a symbiotic relationship with nitrogen-fixing microbes.

“Legumes such as bean and pea plants can form root nodules through which they receive nitrogen from rhizobia bacteria in exchange for carbon,” Weng explains. “This metabolic exchange means that legumes release far less greenhouse gas — and require far less investment of fossil energy — than do cereal crops, which use a huge portion of the artificially produced nitrogen fertilizers employed today.

“Our goal is to develop methods for transferring legumes’ ‘self-fertilizing’ capacity to cereal crops,” Weng says. “If we can, we will revolutionize the sustainability of food production.”

The project — formally entitled “Mimicking legume-rhizobia symbiosis for fertilizer production in cereals” — will be a multistage, five-year effort. It draws on Weng’s extensive studies of metabolic evolution in plants and his identification of molecules involved in formation of the root nodules that permit exchanges between legumes and nitrogen-fixing bacteria. It also leverages his expertise in reconstituting specific signaling and metabolic pathways in plants.

Weng and his colleagues will begin by deciphering the full spectrum of small-molecule signaling processes that occur between legumes and rhizobium bacteria. Then they will genetically engineer an analogous system in nonlegume crop plants. Next, using state-of-the-art metabolomic methods, they will identify which small molecules excreted from legume roots prompt a nitrogen/carbon exchange from rhizobium bacteria. Finally, the researchers will genetically engineer the biosynthesis of those molecules in the roots of nonlegume plants and observe their effect on the rhizobium bacteria surrounding the roots.

While the project is complex and technically challenging, its potential is staggering. “Focusing on corn alone, this could reduce the production and use of nitrogen fertilizer by 160,000 tons,” Weng notes. “And it could halve the related emissions of nitrous oxide gas.”

School of Science announces 2022 Infinite Mile Awards

Seven staff members are recognized for their dedication to the School of Science and to MIT.

School of Science
April 15, 2022

The MIT School of Science has announced the winners of the 2022 Infinite Mile Award. The selected staff members were nominated by their colleagues for going above and beyond in their roles at the Institute. Their outstanding contributions have made MIT a better place.

The following are the 2022 Infinite Mile Award winners in the School of Science:

• Christina Andujar, senior administrative assistant in the Department of Physics, was nominated by Peter Fisher, Edmund Bertschinger, and Matt Cubstead because Andujar “has gone far beyond her assigned role and duties to improve the lives of a great many students at MIT.”

• Monika Avello, an instructor in the Department of Biology, was nominated by Barbara Imperiali, Cathy Drennan, Graham Walker, Adam Martin, Lenny Guarente, David Des Marais, Seychelle Vos, and Jing-Ke Weng because Avello “was always meticulous in attention to detail and never hesitated when we threw out crazy ideas that might make the students gain something unique from the class — even if it gave her ever more things to do.”

• David Orenstein, director of communications in The Picower Institute for Learning and Memory, was nominated by Li-Huei Tsai, Mriganka Sur, Earl Miller, Gloria Choi, William Lawson, Asha Bhakar, Julie Pryor, Raleigh McElvery, and Julia Keller because Orenstein is “always willing to help out in whatever way is needed, whether as a part of a brainstorming session about any given topic, or lending a helping hand for an event or something else going on with the Institute. His dedication to the mission of the Picower Institute is unquestionable and it is evident in everything he does.”

• Dennis Porche, assistant to the department head in the Department of Mathematics, was nominated by Michel Goemans, Gigliola Staffilani, Michael Sipser, and Amanda Kuhl because Porche “has been amazingly dedicated to the well-being of the mathematics department at MIT, and cares tremendously about everything that goes on in the department. He will spend many hours making sure everything is perfect, nothing or no one is omitted, everyone is properly acknowledged, and everything goes smoothly.”

• Joshua Stone, administrative assistant in the Department of Biology, was nominated by Michael Laub, Hallie Dowling-Huppert, Alex Pike, Rebecca Chamberlain, and Janice Chang because Stone “has driven a movement to create an inclusive environment for staff within the biology department, implementing programs for welcoming new staff and establishing peer mentoring to increase the sense of inclusion within the department. These efforts are essential to shifting the culture and integrating pillars of DEI into the everyday operations of the biology department.”

• Sierra Vallin, academic administrator in the Department of Brain and Cognitive Sciences, was nominated by Michale Fee, Laura Schulz, Rebecca Saxe, Joshua McDermott, Mehrdad Jazayeri, Mark Harnett, Kate White, Laura Frawley, Kian Caplan, Di Kang, Halie Olson, Tobias Kaiser, and Julianne Ormerod because Vallin is “truly incredible” and “goes way above and beyond the call of duty to help students and other staff,” and for her “willingness to stand up for staff throughout our building, and to support our ongoing diversity efforts.”

• Shannon Wagner, senior administrative assistant in the Department of Chemistry, was nominated by Troy Van Voorhis, Stephen Buchwald, Jeremiah Johnson, Rick Danheiser, Richard Wilk, and Jennifer Weisman because Wagner “is someone who goes far above and beyond her usual call of duty. Her work has positively impacted many in the department including our students. She demonstrates an exceptional commitment to every aspect of her work and the staff with whom she works. Our department is a far better place with her in it.”

How molecular biology could reduce global food insecurity

Mary Gehring is using her background in plant epigenetics to grow climate-resilient crops.

Summer Weidman | Abdul Latif Jameel Water and Food Systems Lab
March 30, 2022

Staple crops like rice, maize, and wheat feed over half of the global population, but they are increasingly vulnerable to severe environmental risks. The effects of climate change, including changing temperatures, rainfall variability, shifting patterns of agricultural pests and diseases, and saltwater intrusion from sea-level rise, all contribute to decreased crop yields. As these effects continue to worsen, there will be less food available for a rapidly growing population.

Mary Gehring, associate professor of biology and a member of the Whitehead Institute for Biomedical Research, is growing increasingly concerned about the potentially catastrophic impacts of climate change and has resolved to do something about it.

The Gehring Lab’s primary research focus is plant epigenetics, which refers to the heritable information that influences plant cellular function but is not encoded in the DNA sequence itself. This research is adding to our fundamental understanding of plant biology and could have agricultural applications in the future. “I’ve been working with seeds for many years,” says Gehring. “Understanding how seeds work is going to be critical to agriculture and food security,” she explains.

Laying the foundation

Gehring is using her expertise to help crops develop climate resilience through a 2021 seed grant from MIT’s Abdul Latif Jameel Water and Food Systems Lab (J-WAFS). Her research is aimed at discovering how we can accelerate the production of genetic diversity to generate plant populations that are better suited to challenging environmental conditions.

Genetic variation gives rise to phenotypic variations that can help plants adapt to a wider range of climates. Traits such as flood resistance and salt tolerance will become more important as the effects of climate change are realized. However, many important plant species do not appear to have much standing genetic variation, which could become an issue if farmers need to breed their crops quickly to adapt to a changing climate.

In researching a nutritious crop that has little genetic variation, Gehring came across the pigeon pea, a species she had never worked with before. Pigeon peas are a legume eaten in Asia, Africa, and Latin America. They have some of the highest levels of protein in a seed, so eating more pigeon peas could decrease our dependence on meat, which has numerous negative environmental impacts. Pigeon peas also have a positive impact on the environment; as perennial plants, they live for three to five years and sequester carbon for longer periods of time. They can also help with soil restoration. “Legumes are very interesting because they’re nitrogen-fixers, so they create symbioses with microbes in the soil and fix nitrogen, which can renew soils,” says Gehring. Furthermore, pigeon peas are known to be drought-resistant, so they will likely become more attractive as many farmers transition away from water-intensive crops.

Developing a strategy

Using the pigeon pea plant, Gehring began to explore a universal technology that would increase the amount of genetic diversity in plants. One method her research group chose is to enhance transposable element proliferation. Genomes are made up of genes that make proteins, but large fractions are also made up of transposable elements. In fact, about 45 percent of the human genome is made up of transposable elements, Gehring notes. The primary function of transposable elements is to make more copies of themselves. Since our bodies do not need an infinite number of these copies, there are systems in place to “silence” them from copying.

Gehring is trying to reverse that silencing so that the transposable elements can move freely throughout the genome, which could create genetic variation by creating mutations or altering the promoter of a gene — that is, what controls a certain gene’s expression. Scientists have traditionally initiated mutagenesis by using a chemical that changes single base pairs in DNA, or by using X-rays, which can cause very large chromosome breaks. Gehring’s research team is attempting to induce transposable element proliferation by treatment with a suite of chemicals that inhibit transposable element silencing. The goal is to impact multiple sites in the genome simultaneously. “This is unexplored territory where you’re changing 50 genes at a time, or 100, rather than just one,” she explains. “It’s a fairly risky project, but sometimes you have to be ambitious and take risks.”

Looking forward

Less than one year after receiving the J-WAFS seed grant, the research project is still in its early stages. Despite various restrictions due to the ongoing pandemic, the Gehring Lab is now generating data on the Arabidopsis plant that will be applied to pigeon pea plants. However, Gehring expects it will take a good amount of time to complete this research phase, considering the pigeon pea plants can take upward of 100 days just to flower. While it might take time, this technology could help crops withstand the effects of climate change, ultimately contributing to J-WAFS’ goal of finding solutions to food system challenges.

“Climate change is not something any of us can ignore. … If one of us has the ability to address it, even in a very small way, that’s important to try to pursue,” Gehring remarks. “It’s part of our responsibility as scientists to take what knowledge we have and try to apply it to these sorts of problems.”

An early diagnosis sparks a lifelong interest in science and medicine

Senior Isha Mehrotra works to discover more about autoimmune diseases, aiming for a future in which patients can be treated effectively or avoid the conditions altogether.

Alli Armijo | MIT News correspondent
March 25, 2022

“Five second rule!” her classmates shouted as they rushed to pick up some food they had dropped on the ground. At that moment, 10-year-old Isha Mehrotra knew what she wanted to do for the annual science fair.

After scouring the internet with her father, Mehrotra learned how to culture bacteria from home, first tossing food on the floor of her kitchen and swabbing samples onto agar plates — her very first microbiology project. She remembers presenting the data to her peers, watching their faces fall as they realized how much bacteria was on the food even after just five seconds. The experience kindled Mehrotra’s love of learning about the natural world, and more importantly, sharing that knowledge with others.

Now a senior studying biology, Mehrotra enjoys the investigative quality of science above all else.

“The more you study science, the more you realize what you don’t know about it,” she says.

MIT has also been a place for Mehrotra to learn more about herself. In the spring of her sophomore year, she worked in the lab of Alessio Fasano with Maureen Leonard at Massachusetts General Hospital’s Mucosal Immunology and Biology Research Center, investigating the blood microbiome of pediatric patients with an autoimmune condition called celiac disease — which Mehrotra herself was diagnosed with when she was a child.

Her diagnosis sparked an early interest in science and medicine. Today, she works to discover more about celiac, its causes, and effects on the individuals who have it, aiming for a future in which patients can be treated effectively or avoid getting the disease altogether.

Through her research experience, which has included publishing her work as a first author in the journal Current Research in Microbial Sciences, Mehrotra has learned that when presenting her findings, having faith in her work is half the battle, especially when challenging canonical scientific beliefs. “At the end of the day, you know, your data is your data. And presenting that with conviction and confidence is something that I’ve learned how to balance. I try to do that even when I’m acknowledging that there are various aspects of the work that have yet to be understood or validated,” she says.

Mehrotra also serves as a member on the Board of Directors at Boston Children’s Hospital Celiac Kids Connection, where she works to build a safe space for children with celiac. She she understands firsthand the physical and emotional toll celiac disease can have, and values the opportunity to learn more about how to support people and navigate these challenges. For instance, she recognized the connection of food insecurity to celiac early on, as celiac is treated with a gluten-free diet. One of her most fulfilling projects, funded through the PKG Center at MIT, has been helping reduce gluten-free food insecurity exacerbated by the pandemic, working with a team at Children’s to research and mitigate these food access issues.

“It comes back to looking at things in different ways. How can I have a great impact in one area if I don’t consider all the various facets of it?” she asks.

In her classes, Mehrotra has also been drawn to complex public health topics with multiple perspectives, developing an anthropology background via her HASS coursework (for which she was named a Burchard Scholar) and an entrepreneurial framework by participating in MIT Sandbox. In January 2020, she took HST.434 (Evolution of an Epidemic), travelling to South Africa to study the evolution of the HIV/AIDS epidemic in the area. The experience was eye-opening for Mehrotra; she saw firsthand the variety of factors — social, political, biological — needed to approach a singular issue.

In June of last year, Mehrotra participated in the MIT Washington Summer Internship Program, where she worked for Gryphon Scientific, studying data to see how pandemics emerge and evolve at the biological level and what can be done at the policy level to prevent them. The experience allowed Mehrotra to see how different players can influence a singular problem.

“Social processes that underlie science and medicine are really important to me to continue studying,” she says.

On campus, Mehrotra has also been working as a mentor in her dormitory, Maseeh Hall, and peer tutor. During her first year she joined dynaMIT, a STEM outreach program for middle school students in Boston through which she taught biology in ways that made it more fun and accessible. She has also found ways to bring MIT biology students together as co-president of the Biology Undergraduate Sudent Assocation and to provide funding for on-campus initiatives as a board member of the Harvard-MIT Cooperative. Mehrotra also taught chemistry and biology to students in Wales through the Global Teaching Labs program and was a teaching assistant for the biology lab course 7.002 (Fundamentals of Experimental Molecular Biology) and for 7.012 (Introduction to Biology). While she understands that not all students are excited to take a required class such as 7.012, Mehrotra enjoys helping them engage with the content in meaningful ways.

“I just don’t see a better use of gaining knowledge than spreading it to other people,” she says.

Mehrotra is also a member of MIT’s women’s lightweight crew team. As the coxswain, she steers the boat and directs the other rowers both technically and motivationally during practices and races. She says the position has helped her develop her teamwork and leadership skills and allowed her to learn something new that she had never done before MIT. “It has been a great exercise in learning to be a leader and learning what I can do to support people even if I’m not experiencing exactly what they are, which is something I will have to do long term in my career as well,” she says.

Mehrotra will attend Stanford Medical School in the fall, with the goal of becoming a physician-scientist, dedicated to sharing knowledge, doing science, and interfacing with humanistic issues. Mehrotra wants to work directly with patients and researchers to solve medical issues, discovering new information and working with people who bring diverse perspectives. In the long run, she would like to start her own multidisciplinary research practice, where she envisions being able to see and treat patients some days a week, while also running a lab with different types of researchers, such as technical and social scientists.

For now, she is savoring the last few months of her time at MIT. “I’m happiest when I’m going around doing different things. It’s a shame I have to graduate now because there’s so much more to be done!” she says.

Yukiko Yamashita, unraveler of stem cells’ secrets

The MIT biologist’s research has shed light on the immortality of germline cells and the function of “junk DNA.”

Anne Trafton | MIT News Office
March 22, 2022

When cells divide, they usually generate two identical daughter cells. However, there are some important exceptions to this rule: When stem cells divide, they often produce one differentiated cell along with another stem cell, to maintain the pool of stem cells.

Yukiko Yamashita has spent much of her career exploring how these “asymmetrical” cell divisions occur. These processes are critically important not only for cells to develop into different types of tissue, but also for germline cells such as eggs and sperm to maintain their viability from generation to generation.

“We came from our parents’ germ cells, who used to be also single cells who came from the germ cells of their parents, who used to be single cells that came from their parents, and so on. That means our existence can be tracked through the history of multicellular life,” Yamashita says. “How germ cells manage to not go extinct, while our somatic cells cannot last that long, is a fascinating question.”

Yamashita, who began her faculty career at the University of Michigan, joined MIT and the Whitehead Institute in 2020, as the inaugural holder of the Susan Lindquist Chair for Women in Science and a professor in the Department of Biology. She was drawn to MIT, she says, by the eagerness to explore new ideas that she found among other scientists.

“When I visited MIT, I really enjoyed talking to people here,” she says. “They are very curious, and they are very open to unconventional ideas. I realized I would have a lot of fun if I came here.”

Exploring paradoxes

Before she even knew what a scientist was, Yamashita knew that she wanted to be one.

“My father was an admirer of Albert Einstein, so because of that, I grew up thinking that the pursuit of the truth is the best thing you could do with your life,” she recalls. “At the age of 2 or 3, I didn’t know there was such a thing as a professor, or such a thing as a scientist, but I thought doing science was probably the coolest thing I could do.”

Yamashita majored in biology at Kyoto University and then stayed to pursue her PhD, studying how cells make exact copies of themselves when they divide. As a postdoc at Stanford University, she became interested in the exceptions to that carefully orchestrated process, and began to study how cells undergo divisions that produce daughter cells that are not identical. This kind of asymmetric division is critical for multicellular organisms, which begin life as a single cell that eventually differentiates into many types of tissue.

Those studies led to a discovery that helped to overturn previous theories about the role of so-called junk DNA. These sequences, which make up most of the genome, were thought to be essentially useless because they don’t code for any proteins. To Yamashita, it seemed paradoxical that cells would carry so much DNA that wasn’t serving any purpose.

“I couldn’t really believe that huge amount of our DNA is junk, because every time a cell divides, it still has the burden of replicating that junk,” she says. “So, my lab started studying the function of that junk, and then we realized it is a really important part of the chromosome.”

In human cells, the genome is stored on 23 pairs of chromosomes. Keeping all of those chromosomes together is critical to cells’ ability to copy genes when they are needed. Over several years, Yamashita and her colleagues at the University of Michigan, and then at MIT, discovered that stretches of junk DNA act like bar codes, labeling each chromosome and helping them bind to proteins that bundle chromosomes together within the cell nucleus.

Without those barcodes, chromosomes scatter and start to leak out of the cell’s nucleus. Another intriguing observation regarding these stretches of junk DNA was that they have much greater variability between different species than protein-coding regions of DNA. By crossing two different species of fruit flies, Yamashita showed that in cells of the hybrid offspring flies, chromosomes leak out just as they would if they lost their barcodes, suggesting that the codes are specific to each species.

“We think that might be one of the big reasons why different species become incompatible, because they don’t have the right information to bundle all of their chromosomes together into one place,” Yamashita says.

Stem cell longevity

Yamashita’s interest in stem cells also led her to study how germline cells (the cells that give rise to eggs and sperm cells) maintain their viability so much longer than regular body cells across generations. In typical animal cells, one factor that contributes to age-related decline is loss of genetic sequences that encode genes that cells use continuously, such as genes for ribosomal RNAs.

A typical human cell may have hundreds of copies of these critical genes, but as cells age, they lose some of them. For germline cells, this can be detrimental because if the numbers get too low, the cells can no longer form viable daughter cells.

Yamashita and her colleagues found that germline cells overcome this by tearing sections of DNA out of one daughter cell during cell division and transferring them to the other daughter cell. That way, one daughter cell has the full complement of those genes restored, while the other cell is sacrificed.

That wasteful strategy would likely be too extravagant to work for all cells in the body, but for the small population of germline cells, the tradeoff is worthwhile, Yamashita says.

“If skin cells did that kind of thing, where every time you make one cell, you are essentially trashing the other one, you couldn’t afford it. You would be wasting too many resources,” she says. “Germ cells are not critical for viability of an organism. You have the luxury to put many resources into them but then let only half of the cells recover.”

From bench to biotech

Life sciences class brings biotech industry experience into the classroom with part-time internships for graduate students.

Leah Campbell | School of Science
March 9, 2022

Kendall Square has been called the most innovative square mile in the United States, in part due to the high density of biotechnology and biopharmaceutical companies in the MIT-adjacent neighborhood of Cambridge, Massachusetts — but more so thanks to the generations of MIT-trained doctoral students who have pursued careers in these local companies after graduation. Yet, that innovation ecosystem remains a mystery for many current students.

“Many, or even most, graduate students have no substantive experience with the biopharma industry despite the likelihood that they will pursue careers in this realm,” says Doug Lauffenburger, the Ford Professor of Biological Engineering, Chemical Engineering, and Biology. For the last several years, the departments of Biology and Biological Engineering have tried to better inform and prepare their students for that possibility with 7.930/20.930 (Research Experience in Biopharma), a for-credit class providing late-stage doctoral students with hands-on experience in industry.

“It’s really designed to demystify doing research in industry,” says Amy Keating, a professor of biology and biological engineering. “The feedback we get suggests it’s quite eye-opening in terms of changing some assumptions about what that life is like.”

The class has been offered annually since Spring 2016. Most recently offered this past fall, it’s co-taught by Keating and Sean Clarke, a communications instructor and manager of biotech outreach within the Department of Biological Engineering. Participants spend most of their time at part-time internships with local biotech and biopharma companies working on semester-long projects.

“The emphasis really is more on the experience than the particular project or hitting some milestone,” says Clarke. He explains that industry partners offer up potential projects, and students are matched “so that they’re close enough in expertise and interest, but not directly overlapping with thesis work or so outrageous that they can’t be contributors.”

Most students are based in the departments of Biology and Biological Engineering, but others have come from Chemistry, Mechanical Engineering, Brain and Cognitive Sciences, and the Harvard-MIT Program in Health Sciences and Technology. Clarke and Keating say that almost all participants have gone on to pursue industry careers, sometimes at the companies that hosted them during the class.

Student ideas for student opportunities

Lauffenburger, Keating, and Clarke all stress that the driving force behind the class in its early days was students. In particular, they highlight the contributions of Raven Reddy PhD ’17 and Nathan Stebbins PhD ’17, two former biological engineering doctoral students.

“It’s a good example of identifying an excellent idea that came from students themselves and simply putting departmental support, attention, and resources behind it,” says Lauffenburger.

Reddy and Stebbins were two of the early leaders of the MIT Biotechnology Group, a student-led organization designed precisely to expose students to the world of industry. In brainstorming with members how best to explore potential careers path, “part-time internships were far and away one of the most popular things that people said would be a really enriching experience,” says Reddy, now vice president of science operations at BridgeBio Pharma in Palo Alto, California.

The industry representatives they approached were thrilled by the opportunity to host MIT PhD students; so, Reddy and Stebbins sought out a way to make part-time internships possible. Given time constraints on students and their advisors — and legal constraints for companies — they landed on a class as the best possible arrangement.

Formatting the experience as a class was a “win-win scenario on all sides that decreased the barrier to entry for every party,” says Stebbins, now a principal at Flagship Pioneering, a life sciences investment group in Cambridge.

Stebbins and Reddy were listed as co-teachers that first semester. It’s been taught every year since, with Lauffenburger, Keating, and Clarke keeping the momentum going after Stebbins and Reddy graduated and began their own careers in the private sector.

Outside perspective

While the focus of the Research Experience in Biopharma class is on the internship, students spend one hour per week in the classroom together to hear from guest lecturers, make contacts in industry, and build professional development skills.

This past fall, one such guest speaker was Becky Kusko ’09, one of the first undergraduates in the Department of Biological Engineering. After getting her PhD in genetics and genomics at Boston University in 2014, she now works for Immuneering Corporation, a local company that uses bioinformatics technology to streamline drug development.

In October 2021, Kusko spoke to students in the class to describe her own transition from academia to the private sector and provide a “behind-the-scenes” look at day-to-day life in biotech. She says she’s envious that students have this opportunity to explore their options now. Personally, she says, she had “zero interest” in — or understanding of — the private sector until a series of happy accidents took her to Immuneering as she wrapped up her dissertation.

“I had my list of 72 reasons why I was perfectly cut out for academia,” she says, “but then I realized all of those things I could do in an industry career.” During her time at Immuneering, she says, she’s published in peer-review journals, mentored students, and presented at conferences — all things she assumed were limited to the academic track. Her take-home message for the students was simply to be open-minded to different opportunities.

Ongoing benefits

Kusko’s lecture was a highlight of the class for Allen Sanderlin, a fifth-year graduate student in biology, who says he’s always been interested in the industry route and enrolled in the class to explore that possibility further. The fact that it’s a for-credit class, he says, means it’s more “regimented” than a speaker series or seminar, and so it felt easier to fit into his schedule and more reflective of the actual experience of working at a company.

During his internship this past fall, Sanderlin worked with the functional genomics team at Pfizer, helping to identify target genes and determine if certain equipment and techniques are worth investing in. “We’re at the very start of the drug pipeline,” he says. “It’s like nothing I’ve done before.”

That’s not to say that there haven’t been parallels between his internship and his doctoral work in the lab of Becky Lamason, the Robert A. Swanson Career Development Professor of Biology. “Fundamentally, they’re very different things, but at the same time, the skills and techniques I’ve learned in the lab, like tissue culturing, have helped,” he says. Similarly, what he’s learned at Pfizer about managing huge numbers of samples and automating processes has inspired him to find ways to be more efficient in his own work.

Anna Yeh is another fifth-year student in biology. Like Sanderlin, Yeh was always interested in industry but wasn’t sure of what that life entailed.

“Before this, I’ve just been purely in an academic setting,” Yeh says. “This seemed like a nice contained, low-bar way to be exposed to the industry career path.”

Like Sanderlin, Yeh was based at Pfizer for her internship, in the internal medicine unit, doing research totally unlike her doctoral work in the lab of Adam Martin, an associate professor of biology. At MIT, she uses flies to study how organisms come together into a coherent shape in the early stages of development. In contrast, at Pfizer, she worked with mice to see how increasing fructose in their diet affects liver health.

Yet, Yeh sees clear ways that her own research in molecular biology has helped her during her time at Pfizer, as well as how to incorporate skills from her internship into her own work going forward.

“The knowledge is definitely helpful,” she says, “just in terms of trying new things and using techniques I’ve only read about in papers.”

After taking the class, both Sanderlin and Yeh are more confident than ever about pursuing careers in industry. Their mentors at Pfizer, they say, have been invaluable helping them network, looking over their resumes, and discussing career options with them. Both also recommend the course wholeheartedly for future students.

“If anyone is unsure of whether they’d like to go into industry, this is a great class to get a taste of it,” says Yeh. “I think everyone should be aware of it as an option.”

Mentorship and medicine

MIT senior Daniel Zhang aims to provide hope for young patients and support to young students.

Celina Zhao | Department of Biology
February 24, 2022

During the virtual spring 2020 semester, Daniel Zhang, a senior majoring in biology, put his time at home to good use. In the garage of his home in San Diego, California, Zhang helped his 13-year-old brother build a lab to study dry eye disease.

This combination of mentorship and medicine feels like second nature to Zhang. When his parents opened a family-run optometry clinic, Zhang was their first patient and then their receptionist. And after a close family member passed away from leukemia, he remembers thinking, “Humans are susceptible to so many diseases — why don’t we have better cures?”

That question propelled him to spend his high school summers studying biomarkers for the early detection of leukemia at the University of California at San Diego. He was invited to present his research at the London International Youth Science Forum, where he spoke to scientists from almost 70 countries. Afterward, he was hooked on the idea of scientific research as a career.

“Research is like standing on the shoulders of giants,” he says. “My experience at the forum was when I knew I loved science and wanted to continue using it to find common ground with others from completely different cultures and backgrounds.”

Exploring the forefront of cancer research

As soon as he arrived at MIT as a first-year undergraduate, Zhang began working under the guidance of postdoc Peter Westcott in professor Tyler Jacks’ lab. The lab focuses on developing better mouse and organoid models to study cancer progression — in Zhang’s case, metastatic colorectal cancer.

One of the ways to model colorectal cancer is by injecting an engineered virus directly into the colons of mice. The viruses, called lentiviral agents, “knock out” tumor suppressor genes and activate the so-called oncogenes that drive cancer forward. However, the imprecise nature of this injection also unintentionally transforms many “off-target” cells into cancer cells, producing a cancer that’s far too widespread and aggressive. Additionally, rare tumors called sarcomas are often initiated rather than adenocarcinomas, the type of tumor found in 95 percent of human cases. As a result, these mouse models are limited in their ability to accurately model colorectal cancer.

To address this problem, Zhang and Westcott designed a method using CRISPR/Cas9 to target a special stem cell called LGR5+, which researchers believe are the types of cells that, when mutated, grow into colorectal cancer. His technique modifies only the LGR5+ cells, which would allow researchers to control the rate at which adenocarcinomas grow. Therefore, it generates a model that is not only much more similar to human colorectal cancer than other models, but also allows researchers to quickly test for other potential cancer driver genes with CRISPR/Cas9. Designing an accurate model is crucial for developing and testing effective new therapies for patients, Zhang says.

During MIT’s virtual spring and fall semesters of 2020, Zhang shifted his focus from benchwork in the lab to computational biology. Using patient data from the Cancer Genome Atlas, Zhang analyzed mutation rates and discovered three genes potentially involved in colorectal cancer tumor suppression. He plans to test their function in his new mouse model to further validate how the dysfunction of these genes drives colorectal cancer progression.

For his work on organoid modeling of colorectal cancer, a third project he’s worked on during his time at the Jacks lab, he also won recognition from the American Association for Cancer Research (AACR). As one of 10 winners of the Undergraduate Scholar Award, he had the opportunity to present his research at the virtual AACR conference in 2021 and again at the next AACR Conference in New Orleans in April 2022.

He credits MIT’s “mens et manus” philosophy, encouraging the hands-on application of knowledge, as a large part of his early success in research.

“I’ve found that, at MIT, a lot of people are pursuing projects and asking questions that have never been thought of before,” Zhang says. “No one has ever been able to develop a late-stage model for colorectal cancer that’s amenable to gene editing. As far as I know, other than us, no one in the world is even working on this.”

Inspiring future generations to pursue STEM

Outside of the lab, Zhang devotes a substantial amount of time to sharing the science he’s so passionate about. Not only has he been awarded the Gene Brown Prize for undergraduate teaching for his time as a teaching assistant for the lab class 7.002 (Fundamentals of Experimental Molecular Biology), but he’s also taken on leadership roles in science outreach activities.

During the 2020-21 academic year, he served as co-director of DynaMIT, an outreach program that organizes a two-week STEM program over the summer for underserved sixth to ninth graders in the greater Boston area. Although the program is traditionally held in-person, in summer 2021 it was held virtually. But Zhang and the rest of the board didn’t let the virtual format deter them from maximizing the fun and interactive nature of the program. They packed and shipped nearly 120 science kits focused on five major topics — astronomy, biology, chemistry, mechanical engineering, and math — allowing the students to explore everything from paper rockets to catapults and trebuchets to homemade ice cream.

“At first, we were worried that most of the students wouldn’t turn on their cameras, since we saw that trend all over MIT classes during the semester,” Zhang says. “But almost everyone had their cameras on the entire time. It was really gratifying to see students come in on Monday really shy, but by Friday be actively participating, making jokes with the mentors, and being really excited about STEM.”

To investigate the long-term impacts of the program, he also helped kick-start a project that followed up with DynaMIT alumni, some of whom have already graduated from college. Zhang says: “We were happy to see that 80-90 percent of DynaMIT alumni enjoyed the program, rating it four or five out of five, and close to 70 percent of them said that DynaMIT had a really positive impact on their trajectory toward a career in STEM.”

Zhang has also served as president of the MIT Pre-medical Society, with the goals of fostering an encouraging environment for premed undergraduates, and providing guidance and resources to first- and second-year students still undecided about the premed path. To achieve these objectives, he pioneered an MIT-hosted mixer with the premedical societies of other Boston colleges, including Wellesley College, Boston University, Tufts University, and Harvard University. At the mixer, students were able to network with each other and listen to guest speakers from the different universities talk about their experiences in medicine. He also started a “big/little” initiative that paired third- and fourth-year mentors with first- and second-year students.

Providing new opportunity and hope

The wealth of activities Zhang has participated in at MIT has inspired his choices for the future. After graduation, he plans to take a gap year and work as a research technician in pediatric oncology before applying to MD/PhD programs.

On the mentorship side, he’s currently working to establish a nonprofit organization called Future African Scientist with his former Ugandan roommate, Martin Lubowa, whom he met at a study abroad program during MIT’s Independent Activities Period in 2020. The organization will teach high schoolers in Africa professional skills and expose them to different STEM topics — a project Zhang plans to work on post-MIT and into the long term.

Ultimately, he hopes to lead his own lab at the intersection of CRISPR-Cas9 technology and cancer biology, and to serve as a mentor to future generations of researchers and physicians.

As he puts it: “All of the experiences I’ve had so far have solidified my goal of conducting research that impacts patients, especially young ones. Being able to provide new opportunity and hope to patients suffering from late-stage metastatic diseases with no current cures is what inspires me every day.”

Alan Grossman to step down as head of the Department of Biology

Grossman led the biology community for eight years, increasing faculty diversity, support for outreach programs and graduate students.

School of Science
February 23, 2022

Alan D. Grossman, the Praecis Professor of Biology at MIT, has announced he will step down as the head of the Department of Biology before the start of the next academic year. He will continue to lead the department until the new head is selected. A search committee will convene later this spring to recommend candidates for Grossman’s successor.

“Alan Grossman is an outstanding biologist who is, and has been, deeply committed to the research and educational missions of the biology department,” says Nergis Mavalvala, the Curtis and Kathleen Marble Professor of Astrophysics and the dean of the MIT School of Science. “He has time and again established MIT biology as a leader in the life sciences at the Institute, in Kendall Square, and beyond.”

“It has been a privilege to lead this department and its talented members — faculty, staff, and students — for the past eight years,” says Grossman. “With the dedication and drive of this community, we have accomplished so much together and set new and ambitious goals for the future of life sciences research and education.”

Grossman was instrumental in securing a $50 million gift from Professor Emeritus Paul Schimmel PhD ’66 and his family to support life sciences across the Institute. Schimmel’s initial gift of $25 million established the Schimmel Family Program for Life Sciences that matched $25 million secured from other sources in support of the Department of Biology. The remaining $25 million from the Schimmel family will support the Schimmel Family Program in the form of matching funds.

“This transformative gift provides students with the resources they need to be successful in their education, research, and careers,” says Institute Professor Phillip A. Sharp, who also contributed to the matching gift. “Alan’s leadership and vision provided the framework to make this gift a reality for graduate students who perform life sciences research across the Institute, not just in biology.”

For many years, Grossman was deeply involved in graduate education. He served on the committees that oversee the graduate program in biology and the interdepartmental graduate program in computational and systems biology. For seven years, Grossman was director or co-director of the biology graduate program. He helped establish the interdepartmental graduate program in microbiology in 2007 and served as its founding director until 2012.

Before assuming the role as department head, Grossman also served the department as associate head and had served MIT on several committees, including as a member of the Committee on Curriculum and the Faculty Advisory Committee for the Office of Minority Education. Through the work of the department’s academic officers, student leaders, and advisors, Grossman oversaw the development of the most recent interdisciplinary undergraduate biology major, Course 5-7 (Chemistry and Biology).

Within his department, Grossman raised funds to endow support for students in the MIT Summer Research Program in Biology (MSRP-Biology). He worked with others to expand the diversity of the graduate program, the applicant pool for biology faculty positions, and the scientific workforce through a variety of outreach programs and endeavors.

Recently, Grossman raised additional funds to endow MSRP-Biology. Michael Gould and Sara Moss supplemented their initial gift in 2015 with an additional donation to further support, endow and rename MSRP-Biology to the Bernard S. and Sophie G. Gould MIT Summer Research Program in Biology to honor Gould’s parents.

“Sara and I are grateful for Alan’s nurturing of the program,” said Gould. “Without Alan, we never would have supported this wonderful program; and with Alan at the helm and Mandana Sassanfar as the director of outreach, we knew that many talented individuals would benefit from the research opportunities at MIT.”

Grossman’s tenure also saw the establishment of a cryo-electron microscopy (cryo-EM) facility at MIT. An anonymous donation of $5 million and a $2.5 million gift from the Arnold and Mabel Beckman Foundation supported the purchase of two cryo-electron microscopes that are housed in MIT.nano. These microscopes are used by life science researchers from many departments across MIT and throughout the Boston area.

“The existence of this facility has made it possible for MIT to recruit outstanding junior faculty members focused on using cryo-EM to address fundamental biological problems,” says associate department head Professor Jacqueline Lees. “At a more general level, Alan has been remarkably successful at junior faculty recruitment and in increasing the diversity of our faculty.”

During Grossman’s tenure as department head and in collaboration with the MIT-affiliated life sciences institutes and the hard work of search committees, the department has hired more than 20 faculty members, over than half of whom are women and/or from groups underrepresented in STEM. This faculty renewal involved forging a relationship with the Ragon Institute of MGH, MIT, and Harvard and includes three new faculty members located at the Ragon Institute. With the influx of new faculty members, the department’s senior faculty instituted a robust plan for mentoring junior faculty, supplementing programs that are offered at the school and Institute levels.

In his own research, Grossman combines a range of approaches — genetic, molecular, physiological, biochemical, cell-biological, and genomic — to study fundamental biological processes in bacteria. His current work is focused mechanisms controlling horizontal gene transfer, the process by which bacteria move genes from one organism to another, the primary means by which antibiotic resistances are spread among bacteria.

Grossman received a BA in biochemistry from Brown University in 1979, and a PhD in molecular biology from the University of Wisconsin at Madison in 1984. After a postdoctoral fellowship in the Department of Cellular and Developmental Biology at Harvard University, Grossman joined MIT’s Department of Biology in 1988. He is a fellow of the American Academy of Arts and Sciences, the American Academy of Microbiology, and is a member of the National Academy of Sciences. He received a life-saving heart transplant in 2006.

Seven new faculty join the MIT School of Science

Departments of Biology and Brain and Cognitive Sciences welcome new professors.

School of Science
February 16, 2022

This winter, seven new faculty members join the MIT School of Science in the departments of Biology and Brain and Cognitive Sciences.

Siniša Hrvatin studies how animals initiate, regulate, and survive states of stasis, such as torpor and hibernation. To survive extreme environments, many animals have evolved the ability to decrease metabolic rate and body temperature and enter dormant states. His long-term goal is to harness the potential of these biological adaptations to advance medicine. Previously, he identified the neurons that regulate mouse torpor and established a platform for the development of cell-type-specific viral drivers.

Hrvatin earned his bachelor’s degree in biochemical sciences in 2007 and his PhD in stem cell and regenerative medicine in 2013, both from Harvard University. He was then a postdoc in bioengineering at MIT and a postdoc in neurobiology at Harvard Medical School. Hrvatin returns to MIT as an assistant professor of biology and a member of the Whitehead Institute for Biomedical Research.

Sara Prescott investigates how sensory inputs from within the body control mammalian physiology and behavior. Specifically, she uses mammalian airways as a model system to explore how the cells that line the surface of the body communicate with parts of the nervous system. For example, what mechanisms elicit a reflexive cough? Prescott’s research considers the critical questions of how airway insults are detected, encoded, and adapted to mammalian airways with the ultimate goal of providing new ways to treat autonomic dysfunction.

Prescott earned her bachelor’s degree in molecular biology from Princeton University in 2008 followed by her PhD in developmental biology from Stanford University in 2016. Prior to joining MIT, she was a postdoc at Harvard Medical School and Howard Hughes Medical Institute. The Department of Biology welcomes Prescott as an assistant professor.

Alison Ringel is a T-cell immunologist with a background in biochemistry, biophysics, and structural biology. She investigates how environmental factors such as aging, metabolism, and diet impact tumor progress and the immune responses that cause tumor control. By mapping the environment around a tumor on a cellular level, she seeks to gain a molecular understanding of cancer risk factors.

Ringel received a bachelor’s degree in molecular biology, biochemistry, and physics from Wesleyan University, then a PhD in molecular biophysics from John Hopkins University School of Medicine. Previously, Ringel was a postdoc in the Department of Cell Biology at Harvard Medical School. She joins MIT as an assistant professor in the Department of Biology and a core member of the Ragon Institute of MGH, MIT and Harvard.

Francisco J. Sánchez-Rivera PhD ’16 investigates genetic variation with a focus on cancer. He integrates genome engineering technologies, genetically-engineered mouse models (GEMMs), and single cell lineage tracing and omics approaches in order to understand the mechanics of cancer development and evolution. With state-of-the-art technologies — including a CRISPR-based genome editing system he developed as a graduate student at MIT — he hopes to make discoveries in cancer genetics that will shed light on disease progression and pave the way for better therapeutic treatments.

Sánchez-Rivera received his bachelor’s degree in microbiology from the University of Puerto Rico at Mayagüez followed by a PhD in biology from MIT. He then pursued postdoctoral studies at Memorial Sloan Kettering Cancer Center supported by a HHMI Hanna Gray Fellowship. Sánchez-Rivera returns to MIT as an assistant professor in the Department of Biology and a member of the Koch Institute for Integrative Cancer Research at MIT.

Nidhi Seethapathi builds predictive models to help understand human movement with a combination of theory, computational modeling, and experiments. Her research focuses on understanding the objectives that govern movement decisions, the strategies used to execute movement, and how new movements are learned. By studying movement in real-world contexts using creative approaches, Seethapathi aims to make discoveries and develop tools that could improve neuromotor rehabilitation.

Seethapathi earned her bachelor’s degree in mechanical engineering from the Veermata Jijabai Technological Institute followed by her PhD in mechanical engineering from Ohio State University. In 2018, she continued to the University of Pennsylvania where she was a postdoc. She joins MIT as an assistant professor in the Department of Brain and Cognitive Sciences with a shared appointment in the Department of Electrical Engineering and Computer Science at the MIT Schwarzman College of Computing.

Hernandez Moura Silva researches how the immune system supports tissue physiology. Silva focuses on macrophages, a type of immune cell involved in tissue homeostasis. He plans to establish new strategies to explore the effects and mechanisms of such immune-related pathways, his research ultimately leading to the development of therapeutic approaches to treat human diseases.

Silva earned a bachelor’s degree in biological sciences and a master’s degree in molecular biology from the University of Brasilia. He continued to complete a PhD in immunology at the University of São Paulo School of Medicine: Heart Institute. Most recently, he acted as the Bernard Levine Postdoctoral Fellow in immunology and immuno-metabolism at the New York University School of Medicine: Skirball Institute of Biomolecular Medicine. Silva joins MIT as an assistant professor in the Department of Biology and a core member of the Ragon Institute.

Yadira Soto-Feliciano PhD ’16 studies chromatin — the complex of DNA and proteins that make up chromosomes. She combines cancer biology and epigenetics to understand how certain proteins affect gene expression and, in turn, how they impact the development of cancer and other diseases. In decoding the chemical language of chromatin, Soto-Feliciano pursues a basic understanding of gene regulation that could improve the clinical management of diseases associated with their dysfunction.

Soto-Feliciano received her bachelor’s degree in chemistry from the University of Puerto Rico at Mayagüez followed by a PhD in biology from MIT, where she was also a research fellow with the Koch Institute. Most recently, she was the Damon Runyon-Sohn Pediatric Cancer Postdoctoral Fellow at The Rockefeller University. Soto-Feliciano returns to MIT as an assistant professor in the Department of Biology and a member of the Koch Institute.

Probing how proteins pair up inside cells

MIT biologists drilled down into how proteins recognize and bind to one another, informing drug treatments for cancer.

Raleigh McElvery | Department of Biology
February 3, 2022

Despite its minute size, a single cell contains billions of molecules that bustle around and bind to one another, carrying out vital functions. The human genome encodes about 20,000 proteins, most of which interact with partner proteins to mediate upwards of 400,000 distinct interactions. These partners don’t just latch onto one another haphazardly; they only bind to very specific companions that they must recognize inside the crowded cell. If they create the wrong pairings — or even the right pairings at the wrong place or wrong time — cancer or other diseases can ensue. Scientists are hard at work investigating these protein-protein relationships, in order to understand how they work, and potentially create drugs that disrupt or mimic them to treat disease.

The average human protein is composed of approximately 400 building blocks called amino acids, which are strung together and folded into a complex 3D structure. Within this long string of building blocks, some proteins contain stretches of four to six amino acids called short linear motifs (SLiMs), which mediate protein-protein interactions. Despite their simplicity and small size, SLiMs and their binding partners facilitate key cellular processes. However, it’s been historically difficult to devise experiments to probe how SLiMs recognize their specific binding partners.

To address this problem, a group led by Theresa Hwang PhD ’21 designed a screening method to understand how SLiMs selectively bind to certain proteins, and even distinguish between those with similar structures. Using the detailed information they gleaned from studying these interactions, the researchers created their own synthetic molecule capable of binding extremely tightly to a protein called ENAH, which is implicated in cancer metastasis. The team shared their findings in a pair of eLife studies, one published on Dec. 2, 2021, and the other published Jan. 25.

“The ability to test hundreds of thousands of potential SLiMs for binding provides a powerful tool to explore why proteins prefer specific SLiM partners over others,” says Amy Keating, professor of biology and biological engineering and the senior author on both studies. “As we gain an understanding of the tricks that a protein uses to select its partners, we can apply these in protein design to make our own binders to modulate protein function for research or therapeutic purposes.”

Most existing screens for SLiMs simply select for short, tight binders, while neglecting SLiMs that don’t grip their partner proteins quite as strongly. To survey SLiMs with a wide range of binding affinities, Keating, Hwang, and their colleagues developed their own screen called MassTitr.

The researchers also suspected that the amino acids on either side of the SLiM’s core four-to-six amino acid sequence might play an underappreciated role in binding. To test their theory, they used MassTitr to screen the human proteome in longer chunks comprised of 36 amino acids, in order to see which “extended” SLiMs would associate with the protein ENAH.

ENAH, sometimes referred to as Mena, helps cells to move. This ability to migrate is critical for healthy cells, but cancer cells can co-opt it to spread. Scientists have found that reducing the amount of ENAH decreases the cancer cell’s ability to invade other tissues — suggesting that formulating drugs to disrupt this protein and its interactions could treat cancer.

Thanks to MassTitr, the team identified 33 SLiM-containing proteins that bound to ENAH — 19 of which are potentially novel binding partners. They also discovered three distinct patterns of amino acids flanking core SLiM sequences that helped the SLiMs bind even tighter to ENAH. Of these extended SLiMs, one found in a protein called PCARE bound to ENAH with the highest known affinity of any SLiM to date.

Next, the researchers combined a computer program called dTERMen with X-ray crystallography in order understand how and why PCARE binds to ENAH over ENAH’s two nearly identical sister proteins (VASP and EVL). Hwang and her colleagues saw that the amino acids flanking PCARE’s core SliM caused ENAH to change shape slightly when the two made contact, allowing the binding sites to latch onto one another. VASP and EVL, by contrast, could not undergo this structural change, so the PCARE SliM did not bind to either of them as tightly.

Inspired by this unique interaction, Hwang designed her own protein that bound to ENAH with unprecedented affinity and specificity. “It was exciting that we were able to come up with such a specific binder,” she says. “This work lays the foundation for designing synthetic molecules with the potential to disrupt protein-protein interactions that cause disease — or to help scientists learn more about ENAH and other SLiM-binding proteins.”

Ylva Ivarsson, a professor of biochemistry at Uppsala University who was not involved with the study, says that understanding how proteins find their binding partners is a question of fundamental importance to cell function and regulation. The two eLife studies, she explains, show that extended SLiMs play an underappreciated role in determining the affinity and specificity of these binding interactions.

“The studies shed light on the idea that context matters, and provide a screening strategy for a variety of context-dependent binding interactions,” she says. “Hwang and co-authors have created valuable tools for dissecting the cellular function of proteins and their binding partners. Their approach could even inspire ENAH-specific inhibitors for therapeutic purposes.”

Hwang’s biggest takeaway from the project is that things are not always as they seem: even short, simple protein segments can play complex roles in the cell. As she puts it: “We should really appreciate SLiMs more.”