Author: Raleigh McElvery

To be long-lived or short-lived?
Nicole Davis | Whitehead
February 20, 2020

Genes are often imagined as binary actors: on or off. Yet such a simple view ignores the fact that genes’ activities, exerted by their corresponding proteins, can run the gamut from barely perceptible to off the charts. This rheostat-like range is due in part to molecular controls that determine how long the protein-making instructions for any given gene — known as messenger RNA (mRNA) — can persist before being destroyed.

Now, in a pair of papers published online in Molecular Cell, Whitehead Institute member David Bartel and his colleagues take a deep and systematic look at the dynamics of mRNA decay across thousands of genes. Their analysis — the most extensive to date — reveals surprising variability in the rate at which the ends (or “tails”) of mRNAs are shortened. In addition, the researchers uncover a link between this rate of shortening and how quickly the short-tailed mRNAs decay.

“Ultimately, these dynamics are responsible for determining how much mRNA is present for each gene, and that, of course, is really important for determining cell identity — for example, whether a cell is cancerous or a normal, healthy cell,” says Bartel, who is also a professor of biology at the Massachusetts Institute of Technology and an investigator at the Howard Hughes Medical Institute. “There is a thousand-fold difference in how long mRNAs stick around. That has a very profound effect on the amount of protein that gets made.”

TOWARDS A GLOBAL VIEW OF MRNA DEGRADATION

The anatomy of a typical mRNA consists of three key parts: a body, which contains the protein-making instructions; at one end, a string of repeating A’s known as the poly(A) tail; and at the other end, a protective biochemical cap.

Prior to the Molecular Cell studies, the future of a mRNA was known be linked to the length of its poly(A) tail — the longer the string of A’s, the longer the mRNA tends to persist. However, the speed that tails shorten as they age, and the rate at which mRNAs decay when their tails become short was known for just a handful of mRNAs.

To gain a more global picture, Bartel and his team, most recently led by graduate student Timothy Eisen, combined a set of techniques for high-throughput analyses of mRNA. These include a method for chemically modifying mRNAs as they are being made in order to distinguish newly synthesized mRNAs from those that are older, as well as sequencing-based approaches for measuring both the length of poly(A) tails and the amount of mRNA that was recently made. In addition, Eisen used computational methods to model the data they gathered and make predictions about them.

“All of the work in these papers involves time as an axis,” says Eisen. “The power of our approach is that it allowed us to plot and visualize how things change over time — and to infer for mRNAs from thousands of genes the rate at which the tail shortens and the subsequent rate at which the mRNA is destroyed.”

THE TAIL WAGS THE MRNA

By leveraging these techniques, Bartel, Eisen and their colleagues explored the mRNA dynamics for thousands of genes. One key observation is that mRNAs enter the cytoplasm with diverse poly(A) tail lengths. That variability encompasses not only the mRNAs from different genes but even those that correspond to the same gene.

“Previously, there wasn’t any reason to think there would be any differences, so people just assumed that the initial tail lengths would be the same,” says Bartel. “But it turns out there’s quite a bit of variability there.”

The Whitehead team also uncovered a striking amount of variation in the rate at which poly(A) tails are shortened. For some mRNAs, the tail shortens at a rate of about 30 nucleotides per minute. With an average tail length of around 200 nucleotides, that translates to the tail lasting just a few minutes. Other mRNAs have much more durable tails, with shortening rates of just a nucleotide or two an hour.

“That’s a thousand-fold difference,” says Eisen. Previously, researchers had shown that tail-shortening rates could vary, but they had observed only a 60-fold difference.

Bartel and his colleagues also found some striking differences among mRNAs once their poly(A) tails became short. “If we consider just those mRNA molecules that have tails of only 20 nucleotides, the ones that come from certain genes disappear much more rapidly than those coming from other genes — again spanning a thousand-fold range,” says Bartel.

That finding challenges long-held views about mRNA stability, as it had been generally assumed that short tails equaled short lives, and that all mRNAs whose tails had been shortened decay at the same rate. But it turns out that both processes are important: the rate at which mRNA tails are shortened (a process known as deadenylation), and the rate at which mRNAs decay after this shortening. Moreover, Bartel and his colleagues find that these two processes are coupled —  the more rapidly deadenylated mRNAs also degrade more rapidly once they have short tails.

“This coupling between rate of decay of short-tailed mRNAs and the rate of deadenylation is important because it prevents a large build-up of short-tailed versions of mRNAs that had undergone rapid deadenylation,” says Bartel. “Because these short-tailed versions do not build up, the thousand-fold difference that we observe in deadenylation rates can impart a thousand-fold difference in mRNA stabilities.”

SHINING A LIGHT ON MICRORNAS

MicroRNAs are small, regulatory RNA molecules that play critical roles in human biology. Their primary job is to recruit molecular machinery that shortens the poly(A) tails of mRNAs, thereby accelerating mRNA degradation, which reduces gene activity.

But strikingly, when Eisen and his colleagues harnessed their elegant system to examine microRNA activity, it appeared that these regulatory RNAs were leaving the tails of their targets completely unaltered — despite the fact that those mRNAs were being more rapidly degraded.

“That really left us scratching our heads wondering, ‘How could this be?’” adds Eisen. “It’s been known for quite some time that microRNAs operate by influencing poly(A) tail length.”

The team decided to look at the dynamics of this process, focusing on newly generated mRNAs. In this context, they observed that microRNAs accelerate both tail-shortening of target mRNAs and the subsequent decay of those mRNAs once their tails become short. “This second aspect of microRNA activity really hadn’t been appreciated before,” says Bartel. “But it’s a critical part of the story because it helps explain why we don’t see a build-up of short-tailed mRNAs.”

These findings, as well as the other results described here, significantly enhance what is known about mRNA decay and the factors that can influence it. With this expanded knowledge, Bartel and his colleagues, together with other research teams can work to uncover the molecular components and cellular contexts that cause mRNAs to have such drastically different lifetimes.

***

Written by Nicole Davis

***

Citations:

Eisen T, et al. The Dynamics of Cytoplasmic mRNA Metabolism. Molecular Cell. Published online January 2, 2020.

Eisen T, et al. MicroRNAs Cause Accelerated Decay of Short-Tailed Target mRNAs. Molecular Cell. Published online January 2, 2020.

Pediatric Radiologist Looks to AI to Learn More from Scans
Alison F. Takemura | Slice of MIT
February 12, 2020

There’s a moment during a routine pregnancy ultrasound when everything can change. When the sonographer pauses—and frowns in concentration. Inside the fetus’s brain, did she see an abnormality? Were the cavities, called ventricles, larger than normal? In such moments, the skills of doctors like Sarah Sarvis Milla ’96 are needed. Milla is a pediatric radiologist who specializes in neuroradiology, using imaging to help diagnose and direct treatment for young patients with health problems, particularly those related to the brain and spinal cord.

Milla most often uses magnetic resonance imaging (MRI) to clarify what’s happening inside her patients, including those still in utero. She says the power of MRI can amaze even seasoned professionals. “Sometimes, consulting doctors will just walk by and say, ‘Oh my goodness, you can really see the fetus!’” she says. The scans are breathtakingly detailed; you can make out bone, tissue, brain, and eyes.

An MRI of the fetus helps not only the doctor but also the family to understand what’s happening. Families may not realize how severe an abnormality is just from the ultrasound, Milla says. “So we really try to show them the more detailed MRI images, talk to them about what they’re seeing, and answer their questions.”

These conversations are a privilege—and, sometimes, a sorrow, says Milla, who has two sons of her own, ages 9 and 11. “I have definitely cried with families when there’s been bad news.” Milla’s position has taught her gratitude for “the amazing things that happen for us to develop normally. I’ve basically seen every way that development can go wrong.”

AT MIT, Milla majored in biology, but she was also drawn to art and worked closely with two professors, Ritsuko Taho and Dennis Adams, then on the faculty of the MIT Program in Art, Culture, and Technology. Her interests in science and art fused when, as a medical student at Duke University, she was assigned to a group advised by a radiology professor. Holding up radiographs, CT scans, and MRIs of patients’ chests, he started describing what he saw and could infer about their medical conditions.

“From a contemporary artist’s standpoint, it kind of blew my mind,” says Milla. “You could put someone through a tube [for a CT scan] in one minute, take pictures, and be able to look at all their organs, and essentially be able to tell what was wrong with them—without surgery. For me, that was incredible. It was such a visual field. Radiology was like a slam dunk for me.”

Today, Milla is a clinician, teacher, and researcher at Emory University in Atlanta, Georgia. She teaches pediatric radiology and neuroradiology not just to medical students but to people anywhere along the medical career path: interns, fellows, and other physicians. “All physicians are lifelong learners,” she says.

Milla has travelled to Africa and South America to share her knowledge. In November, she visited Peru through a visiting professorship from the American Society of Neuroradiology to deliver lectures on her field—including research she and her colleagues published in 2013 on applying a new MRI protocol in children, who can have trouble staying still during a scan, that renders much clearer pictures than the conventional MRI protocol.

One of the persistent challenges of radiology, Milla explains, is that findings on imaging studies can be so subtle—a radiologist might have more of a feeling about an image than something she can pinpoint. “It’s like the game where there are two pictures, and you have to find five things different in one of the pictures,” says Milla. “We have to know what normal looks like, and then our eyes are trained to look for things out of the norm. When we find them, the brain has to use knowledge, deduction, and experience to figure out what the abnormality is.”

Now, Milla has teamed up with Matthew Gombolay SM ’13, PhD ’17, an assistant professor of interactive computing at Georgia Tech, to investigate what images are most helpful for training students—and machines—to identify these subtleties. In one project, they’re harnessing machine learning to find abnormalities responsible for epilepsy. Epilepsy is a common reason why MRIs are done in children, says Milla. About half a million children in the US have the condition. But it’s estimated that about 70 percent of those patients don’t show a discernible cause for their epilepsy on MRI scans.

“I’ve been wanting to do this project for years,” she says. Being able to spot what’s abnormal can enable surgery to cure the epilepsy or improve the patient’s condition.

Milla’s outlook on radiology’s future, bolstered by machine learning, is bright. “As a scientist, I’m always excited for new technologies that may help patients, and that is how I view the field of artificial intelligence,” she says. While she doesn’t believe algorithms will perform perfectly on their own, “AI will help doctors do their jobs more accurately and efficiently. And that’ll allow us to give results to families, in person, quicker, and with more certainty.”

Whitehead Institute Member David Sabatini Receives the 2020 Sjöberg Prize from the Royal Swedish Academy Of Sciences
Whitehead Institute
February 4, 2020

The Royal Swedish Academy of Sciences has announced that Whitehead Institute Member David M. Sabatini is co-recipient of the 2020 Sjöberg Prize, which promotes scientific research on cancer, health, and the environment. Sabatini, who is also a professor of biology at Massachusetts Institute of Technology (MIT) and an Investigator of the Howard Hughes Medical Institute, is being recognized for discovering the mTOR protein and its role in controlling cell metabolism and growth.

Throughout his career, Sabatini has made insightful and important discoveries, beginning when, as a graduate student, he identified the mTOR protein. In mammalian cells, mTOR—which stands for “mechanistic target of Rapamycin,” an immunosuppressant drug that inhibits cell growth—is the keystone molecule in a pathway that regulates cellular metabolic processes in response to nutrients.

Sabatini’s lab has since identified most of the components of the mTOR pathway and shown how they contribute to the function of cells and organisms. In the last 10 years, his lab has deciphered the mechanisms through which the pathway senses nutrients. These discoveries have opened avenues for identifying disease vulnerabilities and treatment targets for diverse conditions—notably including key metabolic vulnerabilities in pancreatic and ovarian cancer cells and neurodevelopmental defects. He is currently working to exploit those vulnerabilities as targets for new therapies.

“Research has suggested that 60 percent of cancers have some mechanism for turning on the mTOR pathway,” Sabatini says. “I could never have imagined the implications of that first discovery. And I am grateful that, with the Sjöberg Prize, the Academy has provided us with substantial new resources for our continuing and expanding research.”

In recent weeks, Sabatini—who is also a Member of the David H. Koch Institute for Integrative Cancer Research at MIT—has been the co-recipient of the BBVA Foundation’s Frontiers of Knowledge Award in Biology and Biomedicine for discovery of the mTOR protein, and of Columbia University’s Louisa Gross Horwitz Prize for his contributions to understanding mTOR’s role in physiology and oncogenesis.

“David Sabatini’s discoveries have helped transform cellular physiology,” says Whitehead Institute director David Page, “and they have profound implications for our understanding of cancer’s development—as well as for uncovering the processes underlying neurodegenerative disease, diabetes, and aging.”

This is the fourth time the Sjöberg Prize has been awarded. One of the first winners—James P. Allison of the MD Anderson Cancer Center—was subsequently awarded the Nobel Prize in Physiology or Medicine in 2018.

The official Sjöberg Prize Lecture will be delivered by Sabatini and fellow Laureate Michael Hall at the Karolinska Institute on March 30, 2020.

Putting a finger on the switch of chronic parasite infection
Greta Friar | Whitehead Institute
January 16, 2020

Toxoplasma gondii (T. gondii) is a parasite that chronically infects up to a quarter of the world’s population, causing toxoplasmosis, a disease that can be dangerous, or even deadly, for the immunocompromised and for developing fetuses. One reason that T. gondii is so pervasive is that the parasites are tenacious occupants once they have infected a host. They can transition from an acute infection stage into a quiescent life cycle stage and effectively barricade themselves inside of their host’s cells. In this protected state, they become impossible to eliminate, leading to long term infection. Researchers used to think that a combination of genes were involved in triggering the parasite’s transition into its chronic stage, due to the complexity of the process and because a gene essential for differentiation had not been identified. However, new research from Whitehead Institute Member Sebastian Lourido, who is also an assistant professor of biology at the Massachusetts Institute of Technology (MIT), and graduate student Benjamin Waldman has identified a sole gene whose protein product is the master regulator, which is both necessary and sufficient for the parasites to make the switch. Their findings, which appear online in the journal Cell on January 16, illuminate an important aspect of the parasite’s biology and provide researchers with the tools to control whether and when T. gondii transitions, or undergoes differentiation. These tools may prove valuable for treating toxoplasmosis, since preventing the parasites from assuming their chronic form keeps them susceptible to both treatment and elimination by the immune system.

T. gondii spreads when a potential host, which can be any warm-blooded animal, ingests infected tissue from another animal—in the case of humans, by eating undercooked meat or unwashed vegetables—or when the parasite’s progeny are shed by an infected cat, T. gondii’s target host for sexual reproduction. When T. gondii parasites first invade the body, they are in a quickly replicating part of their life cycle, called the tachyzoite stage. Tachyzoites invade a cell, isolate themselves by forming a sealed compartment from the cell’s membrane, and then replicate inside of it until the cell explodes, at which point they move on to another cell to repeat the process. Although the tachyzoite stage is when the parasites do the most damage, it’s also when they are easily targetable by the immune system and medical therapies. In order for the parasites to make their stay more permanent, they must differentiate into bradyzoites, a slow-growing stage, during which they are less susceptible to drugs and have too little effect on the body to trigger the immune system. Bradyzoites construct an extra thick wall to isolate their compartment in the host cell and encyst themselves inside of it. This reservoir of parasites remains dormant and undetectable, until, under favorable conditions, they can spring back into action, attacking their host or spreading to new ones.

Although the common theory was that multiple genes collectively orchestrate the transition from tachyzoite to bradyzoite, Lourido and Waldman suspected that there was instead a single master regulator.

“Differentiation is not something a parasite wants to do halfway, which could leave them vulnerable,” Waldman says. “Multiple genes means more chances for things to go wrong, so you would want a master regulator to ensure that differentiation happens cleanly.”

To investigate this hypothesis, Waldman used CRISPR-based screens to knock out T. gondii genes, and then tested to see if the parasite could still differentiate from tachyzoite to bradyzoite. Waldman monitored whether the parasites were differentiating by developing a strain of T. gondii that fluoresces in its bradyzoite stage. The researchers also performed a first of its kind single-cell RNA sequencing of T. gondii in collaboration with members of Alex Shalek’s lab in the department of chemistry at MIT. This sequencing allowed the researchers to profile the genes’ activity at each stage in unprecedented detail, shedding light on changes in gene expression during the parasite’s cell-cycle progression and differentiation.

The experiments identified one gene, which the researchers named Bradyzoite-Formation Deficient 1 (BFD1), as the only gene both sufficient and necessary to prevent the transition from tachyzoite to bradyzoite: the master regulator. Not only was T. gondii unable to make the transition without the BFD1 protein, but Waldman found that artificially increasing its production induced the parasites to become bradyzoites, even without the usual stress triggers required to cue the switch. This means that the researchers can now control Toxoplasma differentiation in the lab.

These findings may inform research into potential therapies for toxoplasmosis, or even a vaccine.

“Toxoplasma that can’t differentiate is a good candidate for a live vaccine, because the immune system can eliminate an acute infection very effectively,” Lourido says.

The researchers’ findings also have implications for food production. T. gondii and other cyst-forming parasites that use BFD1 can infect livestock. Further research into the gene could inform the development of vaccines for farm animals as well as humans.

“Chronic infection is a huge hurdle to curing many parasitic diseases,” Lourido says. “We need to study and figure out how to manipulate the transition from the acute to chronic stages in order to eradicate these diseases.”

This study was supported by an NIH Director’s Early Independence Award (1DP5OD017892), a grant from the Mathers Foundation, the Searle Scholars Program, the Beckman Young Investigator Program, a Sloan Fellowship in Chemistry, the NIH (1DP2GM119419, 2U19AI089992, 5U24AI118672), and the Bill and Melinda Gates Foundation.

Written by Greta Friar

***

Sebastian Lourido’s primary affiliation is with Whitehead Institute for Biomedical Research, where his laboratory is located and all his research is conducted. He is also an assistant professor of biology at the Massachusetts Institute of Technology.

***

Citation:

“Identification of a master regulator of differentiation in Toxoplasma”

Cell, online January 16, DOI: 10.1016/j.cell.2019.12.013

Benjamin S. Waldman (1,2), Dominic Schwarz (1,3), Marc H. Wadsworth II (4,5,6), Jeroen P. Saeij (7), Alex K. Shalek (4,5,6), Sebastian Lourido (1,2)

1. Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA

2. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA

3. Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany

4. Institute for Medical Engineering & Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

5. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

6. Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02319, USA

7. Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA

With these neurons, extinguishing fear is its own reward
Picower Institute
January 16, 2020

When you expect a really bad experience to happen and then it doesn’t, it’s a distinctly positive feeling. A new study of fear extinction training in mice may suggest why: The findings not only identify the exact population of brain cells that are key for learning not to feel afraid anymore, but also show these neurons are the same ones that help encode feelings of reward.

The study, published Jan. 14 in Neuron by scientists at MIT’s Picower Institute for Learning and Memory, specifically shows that fear extinction memories and feelings of reward alike are stored by neurons that express the gene Ppp1r1b in the posterior of the basolateral amygdala (pBLA), a region known to assign associations of aversive or rewarding feelings, or “valence,” with memories. The study was conducted by Xiangyu Zhang, a graduate student, Joshua Kim, a former graduate student, and Susumu Tonegawa, Professor of Biology and Neuroscience at RIKEN-MIT Laboratory of Neural Circuit Genetics at the Picower Institute for Learning and Memory at MIT and Howard Hughes Medical Institute.

“We constantly live at the balance of positive and negative emotion,” Tonegawa said. “We need to have very strong memories of dangerous circumstances in order to avoid similar circumstances to recur. But if we are constantly feeling threatened we can become depressed. You need a way to bring your emotional state back to something more positive.”

Overriding fear with reward

In a prior study, Kim showed that Ppp1r1b-expressing neurons encode rewarding valence and compete with distinct Rspo2-expressing neurons in the BLA that encode negative valence. In the new study, Zhang, Kim and Tonegawa set out to determine whether this competitive balance also underlies fear and its extinction.

In fear extinction, an original fearful memory is thought to be essentially overwritten by a new memory that is not fearful. In the study, for instance, mice were exposed to little shocks in a chamber, making them freeze due to the formation of fearful memory. But the next day, when the mice were returned to the same chamber for a longer period of time without any further little shocks, freezing gradually dissipated and hence this treatment is called fear extinction training. The fundamental question then is whether the fearful memory is lost or just suppressed by the formation of a new memory during the fear extinction training.

While the mice underwent fear extinction training the scientists watched the activity of the different neural populations in the BLA. They saw that Ppp1r1b cells were more active and Rspo2 cells were less active in mice that experienced fear extinction. They also saw that while Rspo2 cells were mostly activated by the shocks and were inhibited during fear extinction, Ppp1r1b cells were mostly active during extinction memory training and retrieval, but were inhibited during the shocks.

These and other experiments suggested to the authors that the hypothetical fear extinction memory may be formed in the Ppp1r1b neuronal population and the team went on to demonstrate this vigorously. For this, they employed the technique previously pioneered in their lab for the identification and manipulation of the neuronal population that holds specific memory information, memory “engram” cells.  Zhang labeled Ppp1r1b neurons that were activated during retrieval of fear extinction memory with the light-sensitive protein channelrhodopsin. When these neurons were activated by blue laser light during a second round of fear extinction training it enhanced and accelerated the extinction. Moreover, when the engram cells were inhibited by another optogenetic technique, fear extinction was impaired because the Ppp1r1b engram neurons could no longer suppress the Rspo2 fear neurons. That allowed the fear memory to regain primacy.

These data met the fundamental criteria for the existence of engram cells for fear extinction memory within the pBLA Ppp1r1b cell population: activation and reactivation by recall and enduring and off-line maintenance of the acquired extinction memory.

Because Kim had previously shown Ppp1r1b neurons are activated by rewards and drive appetitive behavior and memory, the team sequentially tracked Ppp1r1b cell activity in mice that eagerly received water reward followed by food reward followed by fear extinction training and fear extinction memory retrieval. The overlap of Ppp1r1b neurons activated by fear extinction vs. water reward was as high as the overlap of neurons activated by water vs. food reward. And finally, artificial optogenetic activation of Ppp1r1b extinction memory engram cells was as effective as optogenetic activation of Ppp1r1b water reward-activated neurons in driving appetitive behaviors. Reciprocally, artificial optogenetic activation of water-responding Ppp1r1b neurons enhanced fear extinction training as efficiently as optogenetic activation of fear extinction memory engram cells. These results demonstrate that fear extinction is equivalent to bona fide rewards and therefore provide the neuroscientific basis for the widely held experience in daily life: omission of expected punishment is a reward.

What next?

By establishing this intimate connection between fear extinction and reward and by identifying a genetically defined neuronal population (Ppp1r1b) that plays a crucial role in fear extinction this study provides potential therapeutic targets for treating fear disorders like PTSD and anxiety, Zhang said.

From the basic scientific point of view, Tonegawa said, how fear extinction training specifically activates Ppp1r1b neurons would be an important question to address. More imaginatively, results showing how Ppp1r1b neurons override Rspo2 neurons in fear extinction raises an intriguing question about whether a reciprocal dynamic might also occur in the brain and behavior. Investigating “joy extinction” via these mechanisms might be an interesting research topic.

The research was supported by the RIKEN Brain Science Institute, the Howard Hughes Medical Institute and the JPB Foundation funded the research.

MIT and Sierra Leone professors collaborate on education strategy
Greta Friar | Whitehead Institute
January 13, 2020

Whitehead Member Hazel Sive, also a professor of biology at the Massachusetts Institute of Technology (MIT), is passionate about sharing MIT’s educational strategy for producing skilled, innovative problem-solvers with other educators. Sive, who was born in South Africa and is the founder and faculty director of the MIT-Africa initiative, also cares deeply about strengthening MIT’s connections to Africa—a goal that MIT shares. MIT-Africa has the tagline ‘Collaborating for Impact’ and has the goal to promote mutually beneficial engagement in research, education and innovation with African countries. The university made the African continent a global priority region for its international efforts in 2017. Consequently, Sive was thrilled by the opportunities for exchange that arose when Sierra Leone’s new president, Julius Maada Bio, selected MIT alumnus Moinina David Sengeh (SM ’12, PhD ’16) as his chief innovation officer. Sengeh, who heads the country’s Directorate of Science, Technology, and Innovation, used his MIT ties to catalyze connections between leaders at MIT and in Sierra Leone, including working with MIT-Africa to do so.

Bio and Sengeh visited MIT in March 2019 to officially launch the MIT-Sierra Leone Program.  The program’s early connections with MIT include Njala University membership in the MIT Abdul Latif Jameel World Education Lab, MIT student internships and faculty visits to Sierra Leone, and an ongoing discourse on higher education strategy. Njala University also participated in the summer 2019 launch of the MIT-Africa Short Course.

MIT-Africa Short Courses are 2- to 5-day-long, collegial workshops or lecture series, on topics of interest in research or education. MIT faculty will bring the courses to African colleagues at their home institutions. Sive led the first Short Course series, a three-day program titled, “Educating with Problem-solving Approaches,” in July and August at Njala University, the Central University of Technology in South Africa, and the Dar es Salaam Institute of Technology in Tanzania.

Sive and the three African universities selected the course topic as one of great interest. MIT has a philosophy of educating students in a problem-solving framework, where students practice problem-solving not only in class, but also in their homework, research, and independent projects.

“The great thing that we give our students at MIT, in terms of employability and flexibility to respond to shifts in careers, is the ability to solve problems, a training that is applicable across every field,” Sive said.

That skillset is one that Sierra Leone’s education leaders likewise want to foster in their students.

Sive brought two MIT students with her to each iteration of the Short Course to speak about their experiences at the Institute, six in total, including Michelle Huang, Jia-Hui Lee, Alice Li, Ashwin Narayan, Keith Puthi, and Michal Reda.

When Sive and the students ran the course in Sierra Leone, it was attended by university, technical college and higher education policy leaders. Discussion ranged from exploring MIT approaches, to considering which may be useful in Sierra Leone, to big-picture higher education strategy.

Sive is excited about connections being made between MIT and Sierra Leone, and the possibilities for important projects that can be carried out together.

“It’s outstanding to make connections with colleagues in higher education across the world,” Sive said. “The frameworks of universities across the world overlap enormously, making it easy to connect and work together toward the same goals.”

Written by Greta Friar

Pushing the field of chemical biology in a new direction
Lucy Jackub
January 8, 2020

n 1996, Virginia Cornish had the idea that would define her career in synthetic biology. She had been working in chemistry labs that were trying to imitate, in test tubes, the complex chemistry that occurs in living organisms. Inside a cell, genes code for hundreds of enzymes that are produced to catalyze different chemical reactions. But what if a cell’s natural machinery could be co-opted to do new chemistry, even chemistry that doesn’t occur in nature? She saw the potential for living cells to become tools.

Stuart Schreiber, now at the Broad Institute of MIT and Harvard, discovered early in his career that a certain immunosuppressant drug worked by allowing proteins in the cell to dimerize, or link together, with proteins they wouldn’t normally interact with strongly. These new protein-protein interactions led to new reactions in the cell. He suggested that other small molecules, or “chemical dimerizers,” could be synthesized that would cause other novel protein-protein interactions, with therapeutic potential to trigger a range of biological functions in the cell, such as gene expression, protein degradation, and apoptosis. But it struck Cornish that chemical dimzerizers could instead be used to screen for specific enzymes in a cell’s genetic library, by dimerizing transcription factors so that they would only activate gene expression in the presence of a specific enzyme. Paired with molecular engineering, this could guide directed evolution in the lab. “I called this chemical complementation,” she says.

She brought the idea to professor Bob Sauer, who had just admitted her as a postdoc to his lab in MIT’s Department of Biology. Only three months after she’d begun working with him, Cornish received an unexpected invitation to interview for an assistant professorship in the Department of Chemistry at Columbia University, where she’d gotten her undergraduate degree in biochemistry. She bused down to New York with the plans for chemical complementation in her pocket. By the end of the day she’d been offered her own laboratory.

The offer was tempting, but Cornish asked Columbia if they’d wait for her to finish her postdoc, and ended up staying in the Sauer lab for two years. Those years turned out to be vital, she says. “I had a lot of biology to learn.”

A Changing Field

Cornish came to Columbia from Savannah, Georgia in 1987, and joined the lab of Ronald Breslow, who had been chair of the committee that had urged the university to begin admitting female students in 1983. Columbia was renowned for organic chemistry, and Breslow’s work in biomimetic chemistry — synthesizing molecules in round-bottomed flasks that resemble molecules found in living systems — was laying the groundwork for the nascent field of chemical biology.

After graduating from Columbia, Cornish took her rigorous training in organic chemistry West to do her PhD in the lab of Peter Schultz at the University of California, Berkeley. Schultz’s lab had just succeeded in synthesizing unnatural amino acids that could be encoded into a cell’s DNA and fed into its translational machinery to create novel proteins. This was an unconventional project for a chemistry lab, but Schultz was interested in bringing together organic chemistry and molecular biology to manipulate large molecules, even ones as large and complex as those of the ribosome.

Cornish’s thesis used Schultz’s method of unnatural amino acid mutagenesis to introduce a chemical group called a ketone, rather than an amino acid, into the cell. The ketone could then be tagged with a fluorescent label, and serve as a biosensor for certain chemicals. This was early work in what would later become the field of bio-orthogonal chemistry.

Excited by the molecular engineering she’d learned in the Schultz lab, Cornish wanted to explore it further in living cells. That meant joining a biology laboratory. She’d heard that MIT’s Department of Biology was a great place to be a postdoc, and was drawn to the molecular engineering Bob Sauer’s lab was doing with bacteria. Then the idea for chemical complementation came to her as she was getting coffee with a friend from the Schreiber lab, and she knew exactly what she wanted to do with her postdoc.

“The main thing I remember about Virginia is that she was just fearless,” Sauer recalls. Cornish’s project, to synthesize a small molecule that could be easily adapted to dimerize a large variety of proteins, was a problem the Sauer lab had never taken on before. “As biochemists, we were interested in protein-protein interactions, and how those mediated networks of genetic regulation, because a lot of the proteins that bind DNA specifically do so as dimers or tetramers,” says Sauer. “She took it to a different level by thinking about how you can use chemical biology to actually dimerize things.”

Cornish remembers the “intellectually vibrant environment” at MIT and the cross-fertilization between labs in the department, and learned as much from other postdocs as from faculty. Petra Levin, a postdoc in professor Alan Grossman’s lab, spent hours patiently teaching her genetics. At that time, Sauer’s lab held joint group meetings to discuss their research in protein folding and transcription with two other labs in the department at that time, headed by Peter Kim and Carl Pabo. It was the genesis of a larger collaboration, informally known as “the structural biology supergroup.”

“I still remember the first time I presented my idea of chemical complementation to this group,” Cornish says. “Peter Kim grilled me for a good fifteen to twenty minutes, going so far as to ask me what my transcription factor was.”

Sauer’s lab works with Escherichia coli, but Cornish decided that her model organism of choice chemical complementation wasn’t a bacterium. It was a yeast, Saccharomyces cerevisiae. Researchers at Johns Hopkins had just found a method for chemically dimerizing proteins in yeast, and it had “all the right parts and pieces” that Cornish needed for her own experiment. She began spending more and more time in Chris Kaiser’s lab next door, borrowing their media to culture yeast. She was introduced to a postdoc in Gerald Fink’s lab, Hiten Madhani, who taught her the fundamentals of yeast genetics. She still has the pieces of paper from their meetings, where Madhani sketched out the yeast plasmids and genetic markers.

“She was down the hall learning stuff from the Kaiser lab, over in the Chemistry Department learning stuff from them,” says Sauer. “I provided a bench for her.”

Synthetic Solutions

When Cornish finished her postdoc and finally took her position at Columbia in 1999, chemical complementation became the foundation for the research in her lab. Working in yeast distinguished Cornish from other scientists who came out of MIT and were doing similar experiments in bacteria in the early 2000s, synthesizing molecules to work together in living cells — the first forays in what is now known as synthetic biology.

Cornish is now the Helena Rubinstein Professor in the departments of Chemistry and Systems Biology at Columbia. She has become a leader in her field, serving on the executive committee of Genome Project-Write, a group of synthetic biologists that has come together to establish ethical standards and self-regulation of new technologies to edit and synthesize genetic information.

She stays focused on how synthetic biology can advance medicine and make products that solve real problems. In 2017, the Cornish Group engineered baker’s yeast to detect fungal pathogens and react by turning red, creating a cheap biosensor with the potential to save lives in regions without medical access. Synthetic biologists have, up until now, focused on engineering individual cells, but Cornish’s next project is to engineer entire communities of yeast cells to work together, like our microbiome does, by taking advantage of the complex communication networks between them. Cornish says that in the lab, “the most exciting moment really is when you’re doing something that you can’t quite articulate.”

She credits her mentors — Breslow, Schultz, and Sauer — with instilling that creative drive in her. All of them were “pushing the field in a new direction,” as she puts it. She pays that mentorship forward to her students. “Sometimes there’s a sense that great science and mentorship are at odds with one another,” she says, but she’s found that the opposite is true. “I think the best way to do great science is just to enable your students to be everything that they can be. And then it really becomes an exciting collaboration.”

Images courtesy of Virginia Cornish
Human-human and protein-protein interactions.

A change in fields and a two-body problem ultimately led Biology and BE Professor Amy Keating to MIT to study coiled-coils and other protein interactions.

J. Carota | CSB Grad Office
December 17, 2019

About 330 miles west of Cambridge lies the small academic town of Ithaca, New York: the location of Cornell University and the hometown of Professor Amy Keating. Surrounded by academics (her father is a professor of computer science at Cornell), Keating was eager to continue her education after high school—just not in Ithaca.

“I could have stayed at Cornell, which is obviously an extremely good school in my hometown, but my family and I agreed that it was important that I go away,” recounts Keating. The scholar/athlete set her sights on Harvard University based on the excellent rowing team and outstanding academics. Physics particularly appealed to her, because it involved using math to explain mechanical and electrical phenomena, and she chose this as her major. She likes to tell people that she also “attempted pure math but failed miserably.” Keating admits that she was not very good at the abstract subject material, and tackling it side-by-side with math whizzes was a harsh awakening after performing well throughout high school. She switched to studying applied math, which was easier for her to manage and also more useful for a physics major.

With an intense rowing schedule, Keating often found herself working late into the night, struggling to solve problems alone. It took a year or two and a serious injury for her to realize that that most of the physics majors were working together in the library many afternoons while she was on the river. “That was very eye-opening. Now I’m a strong advocate of students teaching each other and learning from each other,” explains Keating.

Graduate study gridlock

As she approached the end of her senior year, she had no doubt that she would pursue a PhD, but she did face a crisis about what to study. Initially, she thought she would go to graduate school for physics and applied to and visited many schools. However, she was troubled by the fact that she had tried out a number of areas of physics but never found one that truly captured her interest. In addition to this, Keating began dating a young man, now her husband, who was majoring in chemistry and not set to graduate for another year. “I learned a lot of organic chemistry from him and got very interested in the subject.”

With the decision made to stay in Cambridge for an additional year, she picked up part time work at a Harvard student residence hall cooking, baking, and cleaning in exchange for room and board. Keating also took a few chemistry courses for credit, coached adult rowing, and spent the rest of her time working in the lab of Harvard Physics Professor Mara Prentiss. By the end of that year, she had developed a keen interest in the field of computational chemistry. Having faced difficult decisions about her own post-college plans, she has “a lot of empathy for students who are twenty-one and trying to decide what they want to do in the world.”

Keating and her future husband applied to the same chemistry PhD program at UCLA, where they were both admitted and joined separate labs. She looks back at the interview weekend at UCLA and remembers one faculty interviewer who pointed out the lack of chemistry in her background. “We were talking about cooking, and I told him I like to cook and had been cooking for a job. He said ‘if you can cook, you can do chemistry’, and there is some truth to that, of course.”  Keating acknowledges that the first few months of graduate school were traumatic. “I had exactly two undergrad chemistry classes under my belt. I didn’t really know much chemistry and then I was thrown into this PhD program with chemistry majors. And I was taking graduate level courses with my husband, who is a brilliant chemist. But I caught up and managed to learn a lot in a short time.”

Graduate life smoothed out when Keating joined the lab of Ken Houk, a leader in computational physical organic chemistry. Later in her doctoral studies, she added co-advisor Miguel Garcia-Garibay, an expert in experimental photochemistry. Having the two advisors worked out well and led to several joint publications over Keating’s graduate school career. After her husband’s advisor left UCLA for a company, the couple “had to decide what to do. So, we decided we should graduate quickly.” Now married, Keating and her husband earned their PhDs in under five years, but they would continue to be challenged by the “two-body problem” as they formulated a plan for after graduation.

Further afield

The couple knew they both wanted to find postdoc positions, so they looked in cities like San Diego, San Francisco, and Boston, where positions were abundant. Of that time, Keating says: “I was thinking about different problems or fields where my background might apply. I was reading a lot, just to find out what was out there.” This also marks the first time that she started thinking about problems in biology. “I was actually interested in two areas: material science, and biochemistry, both of which are exciting and rapidly growing areas where chemical principles are centrally important.” Keating’s hard work landed her a position back in Cambridge, where she was again co-advised, this time by former MIT Biology Professor Peter Kim at the Whitehead Institute and MIT Professor of Chemistry  Bruce Tidor(who was later the founding director of the CSB PhD Program).

The postdoc transition was another time in Keating’s life that she good-naturedly describes as “traumatic,” as she once again had to work to understand all-new vocabulary and experimental methods. Her postdoc provided Keating with her first exposure to large molecules; it was also when she first started working on protein interactions, which would become the crux of her future research.  It was in the Kim Lab that she was introduced to coiled-coil proteins. With her background in physics and chemistry, the simplified repeating interactions in these molecules appealed to her. A principle the Keating Lab continues to follow to this day is that they try not to study the most complicated interactions in biology, but rather simpler interactions that they seek to understand in fine detail.

More two-body problems

After four years, Keating hit the academic job market, but she wasn’t sure if she would be accepted as a biochemist because of her change in fields as a postdoc . Her concerns were short-lived as she ended up with a number of exciting offers, including one from MIT. Keating’s husband decided he would go into industry in Boston and with this decision she accepted MIT’s offer to join the Biology faculty in 2002. Later, she added a joint appointment in Biological Engineering.

Keating offers advice to students who are dealing with the two-body problem as she once did.“I think something that helped me and my husband is that we stayed in sync. So, we never had one person make a decision without knowing how that would impact the options of the other person. Of course, that’s not possible for everybody. But that did make our trajectory easier. We would collect our options, put them on the table, look for overlap, and then try to figure out what decision would work best for both of us. And we were very fortunate that we had good options. People have to be flexible to make this work out.” She also recommends looking in cities where there is a high density of opportunities.

The general interest of the Keating lab is in protein-protein interactions, how they work in nature, and how they can be re-engineered using computational and experimental methods. Her group studies proteins that regulate critical processes but are also relatively simple. For example, a system the Keating lab is attracted to is the Bcl-2 family of proteins that control cell death. They have developed a variety of methods that can be used to reprogram the interaction between proteins, and applying these methods to Bcl-2 proteins has generated short peptide molecules that inhibit processes that keep cancer cells alive. Recently the lab has been investigating other types of interactions in cells that are structurally different from the Bcl-2 family. Switching protein families challenges them to develop new methods and allows them to continue to change and evolve their research.

Students and postdocs from the Keating lab have gone on a wide variety of jobs where they study proteins and their interactions in both academia and industry. Keating is happy that young scientists today have so many options. She reflects: “When I was finishing my postdoc, the range of jobs in industry was nothing like it is today. It has been fun to watch my trainees apply their skills to antibody engineering, cancer biology, immuno-oncology and even to start their own companies.” She marvels at how many paths are open to young biologists and likes to tell them that they can’t possibly forsee where they will end up, given the myriad exciting possibilities. Certainly, as a young rower and physics student at Harvard, she had no idea she would end up as a Professor of Biology at MIT.

The surprising individuality of miRNAs
Greta Friar | Whitehead Institute
December 5, 2019

In order for the instructions contained within a gene to ultimately execute some function in the body, the nucleotides, or letters, that make up the gene’s DNA sequence must be “read” and used to produce a messenger RNA (mRNA). This mRNA must then be translated into a functional protein. A number of different pathways within the cell influence this essential biological process, informing whether, when, and to what extent a gene is expressed. A major class of such regulators are microRNAs (miRNAs). These minute RNAs—they are, on average, 22 nucleotides long—join with a protein called Argonaute to cause certain mRNAs to be degraded, which in turn decreases the amount of translation of those mRNAs into their functional protein forms. Scientists have identified hundreds of miRNAs that are common amongst mammals and other vertebrate animals, and most mammalian mRNAs are targeted by at least one of these miRNAs—an indication of their pervasive importance to our biology. Accurately predicting how any particular miRNA will affect gene expression in a cell is important for understanding our own biology, and might facilitate the design of therapeutic drugs that affect or utilize miRNAs, but the complexity of the miRNA pathway makes this sort of prediction difficult.

The success rate with which a miRNA is able to repress a specific gene (by degrading its mRNA) is called its targeting efficacy, and researchers have used a variety of models to calculate it, with mixed results. In the past, researchers have treated miRNAs as a group and looked at average behavior in order to make predictions, because there simply wasn’t enough data specific to individual miRNAs available to do otherwise. However, Whitehead Institute Member David Bartel, who is also a professor of biology at the Massachusetts Institute of Technology and a Howard Hughes Medical Institute investigator, graduate student Sean McGeary, and former graduate student Kathy Lin collected a massive amount of data on six miRNAs, and from that foundation developed an improved predictive model for all individual miRNAs. Their findings, published online in Science on December 5, provide unprecedented accuracy and granularity in miRNA targeting prediction.

“We used to focus our attention on microRNA targeting patterns that were consistent, because that consistency gave us confidence in what we were seeing,” Bartel says, “but with the robust results of this research, we can now pay attention to differences between individual miRNAs.”

Bartel and the Whitehead Institute Bioinformatics and Research Computing group operate one of the go-to resources for prediction of miRNAs’ targets and target efficacy, known as TargetScan. This latest research will be used to update TargetScan, giving scientists around the world an even more useful reference tool for research involving miRNA-mediated regulation of gene expression.

To understand miRNA targeting, researchers need to identify the particular sites within an mRNA sequence where the miRNA can bind, and they additionally need to know how strong the interaction will be at each site—the binding affinity. In general, a miRNA will bind to an mRNA when there is a match between at least six of the first eight nucleotides of the miRNA and a complementary sequence of nucleotides somewhere on the mRNA. The two sequences are like rows of puzzle pieces being pushed together: if each puzzle piece slots into the corresponding piece, the rows combine into one locked puzzle—the miRNA binds its target. If the pieces don’t fit together, the rows can’t connect. These sorts of binding sites, perfect matches within the first eight nucleotides of the miRNA, are called canonical site types, and researchers used to think that there was a clear hierarchy between them, with each individual site type conferring a similar amount of repression regardless of the miRNA identity. But that’s not what McGeary observed.

McGeary looked at six miRNAs and developed a method to measure, for each miRNA, relative binding affinities to a massive collection of RNA sequences.

“I performed experiments that provide vast numbers of measurements, which collectively inform us on how well a miRNA will bind to an mRNA,” McGeary says.

These measurements, as well as further calculations that McGeary made from them, formed a novel, rich pool of data with which to improve miRNA targeting prediction. From their experiments, the researchers found that the expected targeting hierarchy of canonical sites did not apply to all miRNAs. An individual miRNA might actually have a stronger affinity to one of the canonical sites lower in the expected hierarchy than another. Furthermore, the group discovered that the miRNAs each had unique noncanonical binding sites, some of which were sites that contained at least one mismatch but were still able to bind miRNA. The researchers found many instances in which a miRNA bound more strongly to one of its noncanonical sites than to some of its canonical sites, despite the imperfect or unusual pairing of the noncanonical sites.

“As humans, we like to classify things into discrete buckets with discrete characteristics,” Lin says. “But to build a model that is quantitative, you have to recognize that each miRNA and target interaction is different.”

Factors in a target site’s environment contribute to the individuality of target interactions, as they can affect the structural accessibility of the site for binding. In particular, the researchers found that the four nucleotides closest to a target site could have a huge, even 100-fold combined impact on affinity.

With their high-resolution data, the researchers were able to rigorously verify a supposition within the miRNA research community: that the strength with which a miRNA binds to a target site is the major determinant for how effective that miRNA will be at degrading that mRNA. This striking correlation between site affinity and targeting efficacy also allowed them to create a biochemical model of miRNA targeting that used the vast collection of affinity measurements to predict the efficacy of repression of every mRNA in cell, significantly out-performing all existing models of miRNA targeting. They then used machine learning, in the form of a convolutional neural network developed by Lin, to extend the improved predictions to all miRNAs without the need to generate additional data.

Altogether, these findings paint a much richer picture of miRNA-mediated gene repression. The new level of specificity in miRNA targeting prediction will provide all researchers working on the subject with better information about the impact of a given miRNA in a cell.

This work was supported by the NIH and Howard Hughes Medical Institute.

Written by Greta Friar

***

David Bartel’s primary affiliation is with Whitehead Institute for Biomedical Research, where his laboratory is located and all his research is conducted. He is also a professor of biology at Massachusetts Institute of Technology and investigator with the Howard Hughes Medical Institute.

***

Citation:

“The biochemical basis of microRNA targeting efficacy”

Science, online December 5, 2019, DOI: 10.1126/science.aav1741

Sean E. McGeary (1,2,3†), Kathy S. Lin (1,2,3,4†), Charlie Y. Shi (1,2,3), Thy Pham (1,2,3), Namita Bisaria (1,2,3), Gina M. Kelley (1,2,3), and David P. Bartel (1,2,3,4)

  1. Howard Hughes Medical Institute, Cambridge, MA, 02142, USA
  2. Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
  3. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
  4. Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA

†These authors contributed equally to this work.