Author: mantulin

Meenakshi Chakraborty and Anna Sappington named 2017-2018 Goldwater Scholars

Two MIT computer science and molecular biology majors honored for their academic achievements.

Bendta Schroeder | School of Science
April 11, 2018

MIT students Meenakshi Chakraborty and Anna Sappington have been named recipients of the Barry Goldwater Scholarship Awards for 2017-2018. They were selected on the basis of academic merit from a field of candidates nominated by university faculty nationwide.

Chakraborty, a junior majoring in computer science and molecular biology, made an early start on biological research at MIT, having reached out to Institute Professor and professor of biology Phillip Sharp for mentorship on a high school report on circular RNA. The quality of her report earned her a place in the Sharp Lab as a Undergraduate Research Opportunities Program researcher during her first year at MIT. Now in her third year, Chakraborty works with mentor Salil Garg to test a theory about how microRNAs regulate embryonic stem cells (ESCs). Garg, Chakraborty, and Sharp propose that a certain understudied set of miRNAs coordinates the expression of key pluripotency genes, whose levels determine ESC behavior and fate.

In the future, Chakraborty plans to continue to pursue her combined interests in computation and molecular biology in doctoral studies, where she hopes to address a fundamental problem pertinent to human health. One faculty advisor wrote that he has “no doubt that she will continue in science at the highest level after her [undergraduate] degree,” describing her as “an extraordinary person; bright and modest, with an ambition to be the best.”

Sappington, a senior majoring in computer science and molecular biology, has worked on three major computational genomics projects in as many years at MIT. The first, now completed, she describes as a “robust computational pipeline for translating genome-wide association studies into real biological insights.” Initially applied to polygenic myocardial infarction and coronary heart disease risks, the methodology can now be applied to a range of high-impact disorders such as schizophrenia, Type 2 diabetes, autism, and cancer. In her current work, Sappington is using neural networks to help build a comprehensive catalog of retinal cell types for the Human Cell Atlas in the lab of professor of biology and Broad Institute investigator Aviv Regev. In a 2016 National Institutes of Health summer internship at the National Human Genomic Research Institute, Sappington conducted a third research project in which she demonstrated a fast, alignment-free computational method for identifying orthologs — similar genes from species that are related by descent from a common ancestor.

In the future, Sappington says she hopes to become a physician-scientist with the goal of improving the lives of patients through more personalized medicine. One faculty advisor wrote that she “has that rare combination of intelligence, drive, compassion and interpersonal skills needed to excel at the highest levels,” adding that it is clear she may one day be “a leader in the new field of personalized medicine.”

In addition to MIT’s Goldwater Scholarship recipients, two seniors, physics major Zachary Bogorad and chemical engineering major Janice Ong, were given honorable mentions.

The Barry Goldwater Scholarship and Excellence in Education Program was established by Congress in 1986 to honor Senator Barry Goldwater, who served for 30 years in the U.S. Senate. The program is designed to encourage outstanding students to pursue careers in math, the natural sciences, and engineering. Recipients receive stipends of $7,500 per year toward covering the cost of tuition, fees, books, and room and board.

School of Science announces Infinite Mile Awards for 2018

Seven staff members honored for their outstanding contributions to the MIT community.

School of Science
April 4, 2018

The MIT School of Science has announced seven winners of the Infinite Mile Award for 2018. The award will be presented at a luncheon this May in recognition of staff members whose accomplishments and contributions to their departments, laboratories, and centers far exceed expectations.

The 2018 Infinite Mile Award winners are:

Hristina Dineva, Department of Biology;

Theresa Cummings, Department of Mathematics;

Mary Gallagher, Department of Biology;

Jack McGlashing, Laboratory for Nuclear Science;

Sydney Miller, Department of Physics;

Miroslava Parsons, Department of Earth, Atmospheric and Planetary Sciences; and

Alexandra Sokhina, Simons Center for the Social Brain.

The awards luncheon will also honor winners of last fall’s Infinite Kilometer Award, which was established to highlight and reward the extraordinary — but often underrecognized — work of the school’s research staff and postdoctoral researchers.

The 2017 Infinite Kilometer winners are:

Rodrigo Garcia, McGovern Institute for Brain Research;

Lydia Herzel, Department of Biology;

Yutaro Iiyama, Laboratory for Nuclear Science;

Kendrick Jones, Picower Institute for Learning and Memory;

Matthew Musgrave, Laboratory for Nuclear Science;

Cody Siciliano, Picower Institute for Learning and Memory;

Peter Sudmant, Department of Biology; and

Ashley Watson, Picower Institute for Learning and Memory.

Scientists find different cell types contain the same enzyme ratios

New discovery suggests that all life may share a common design principle.

Justin Chen | Department of Biology
March 29, 2018

By studying bacteria and yeast, researchers at MIT have discovered that vastly different types of cells still share fundamental similarities, conserved across species and refined over time. More specifically, these cells contain the same proportion of specialized proteins, known as enzymes, which coordinate chemical reactions within the cell.

To grow and divide, cells rely on a unique mixture of enzymes that perform millions of chemical reactions per second. Many enzymes, working in relay, perform a linked series of chemical reactions called a “pathway,” where the products of one chemical reaction are the starting materials for the next. By making many incremental changes to molecules, enzymes in a pathway perform vital functions such as turning nutrients into energy or duplicating DNA.

For decades, scientists wondered whether the relative amounts of enzymes in a pathway were tightly controlled in order to better coordinate their chemical reactions. Now, researchers have demonstrated that cells not only produce precise amounts of enzymes, but that evolutionary pressure selects for a preferred ratio of enzymes. In this way, enzymes behave like ingredients of a cake that must be combined in the correct proportions and all life may share the same enzyme recipe.

“We still don’t know why this combination of enzymes is ideal,” says Gene-Wei Li, assistant professor of biology at MIT, “but this question opens up an entirely new field of biology that we’re calling systems level optimization of pathways. In this discipline, researchers would study how different enzymes and pathways behave within the complex environment of the cell.”

Li is the senior author of the study, which appears online in the journal Cell on March 29, and in print on April 19. The paper’s lead author, Jean-Benoît Lalanne, is a graduate student in the MIT Department of Physics.

An unexpected observation

For more than 100 years, biologists have studied enzymes by watching them catalyze chemical reactions in test tubes, and — more recently — using X-rays to observe their molecular structure.

And yet, despite years of work describing individual proteins in great detail, scientists still don’t understand many of the basic properties of enzymes within the cell. For example, it is not yet possible to predict the optimal amount of enzyme a cell should make to maximize its chance of survival.

The calculation is tricky because the answer depends not only on the specific function of the enzyme, but also how its actions may have a ripple effect on other chemical reactions and enzymes within the cell.

“Even if we know exactly what an enzyme does,” Li says, “we still don’t have a sense for how much of that protein the cell will make. Thinking about biochemical pathways is even more complicated. If we gave biochemists three enzymes in a pathway that, for example, break down sugar into energy, they would probably not know how to mix the proteins at the proper ratios to optimize the reaction.”

The study of the relative amounts of substances — including proteins — is known as “stoichiometry.” To investigate the stoichiometry of enzymes in different types of cells, Li and his colleagues analyzed three different species of bacteria — Escherichia coli, Bacillus subtilis, and Vibrio natriegens — as well as the budding yeast Saccharomyces cerevisiae. Among these cells, scientists compared the amount of enzymes in 21 pathways responsible for a variety of tasks including repairing DNA, constructing fatty acids, and converting sugar to energy. Because these species of yeast and bacteria have evolved to live in different environments and have different cellular structures, such as the presence or lack of a nucleus, researchers were surprised to find that all four cells types had nearly identical enzyme stoichiometry in all pathways examined.

Li’s team followed up their unexpected results by detailing how bacteria achieve a consistent enzyme stoichiometry. Cells control enzyme production by regulating two processes. The first, transcription, converts the information contained in a strand of DNA into many copies of messenger RNA (mRNA). The second, translation, occurs as ribosomes decode the mRNAs to construct proteins. By analyzing transcription across all three bacterial species, Li’s team discovered that the different bacteria produced varying amounts of mRNA encoding for enzymes in a pathway.

Different amounts of mRNA theoretically lead to differences in protein production, but the researchers found instead that the cells adjusted their rates of translation to compensate for changes in transcription. Cells that produced more mRNA slowed their rates of protein synthesis, while cells that produced less mRNA increased the speed of protein synthesis. Thanks to this compensation, the stoichiometry of enzymes remained constant across the different bacteria.

“It is remarkable that E. coli and B. subtilis need the same relative amount of the corresponding proteins, as seen by the compensatory variations in transcription and translation efficiencies,” says Johan Elf, professor of physical biology at Uppsala University in Sweden. “These results raise interesting questions about how enzyme production in different cells have evolved.”

“Examining bacterial gene clusters was really striking,” lead author Lalanne says. “Over a long evolutionary history, these genes have shifted positions, mutated into different sequences, and been bombarded by mobile pieces of DNA that randomly insert themselves into the genome. Despite all this, the bacteria have compensated for these changes by adjusting translation to maintain the stoichiometry of their enzymes. This suggests that evolutionary forces, which we don’t yet understand, have shaped cells to have the same enzyme stoichiometry.”

Searching for the stoichiometry regulating human health

In the future, Li and his colleagues will test whether their findings in bacteria and yeast extend to humans. Because unicellular and multicellular organisms manage energy and nutrients differently, and experience different selection pressures, researchers are not sure what they will discover.

“Perhaps there will be enzymes whose stoichiometry varies, and a smaller subset of enzymes whose levels are more conserved,” Li says. “This would indicate that the human body is sensitive to changes in specific enzymes that could make good drug targets. But we won’t know until we look.”

Beyond the human body, Li and his team believe that it is possible to find simplicity underlying the complex bustle of molecules within all cells. Like other mathematical patterns in nature, such as the the spiral of seashells or the branching pattern of trees, the stoichiometry of enzymes may be a widespread design principle of life.

The research was funded by the National Institutes of Health, Pew Biomedical Scholars Program, Sloan Research Fellowship, Searle Scholars Program, National Sciences and Engineering Research Council of Canada, Howard Hughes Medical Institute, National Science Foundation, Helen Hay Whitney Foundation, Jane Coffin Childs Memorial Fund, and the Smith Family Foundation.

Structure of key growth regulator revealed

Researchers identify the molecular structure of the GATOR1 protein complex, which regulates growth signals in human cells, using cryo-electron microscopy.

Nicole Davis | Whitehead Institute
March 28, 2018

A team of researchers from Whitehead Institute and the Howard Hughes Medical Institute has revealed the structure of a key protein complex in humans that transmits signals about nutrient levels, enabling cells to align their growth with the supply of materials needed to support that growth. This complex, called GATOR1, acts as a kind of on-off switch for the “grow” (or “don’t grow”) signals that flow through a critical cellular growth pathway known as mTORC1.

Despite its importance, GATOR1 bears little similarity to known proteins, leaving major gaps in scientists’ understanding of its molecular structure and function. Now, as described online on March 28 in the journal Nature, Whitehead scientists and their colleagues have generated the first detailed molecular picture of GATOR1, revealing a highly ordered group of proteins and an extremely unusual interaction with its partner, the Rag GTPase.

“If you know something about a protein’s three-dimensional structure, then you can make some informed guesses about how it might work. But GATOR1 has basically been a black box,” says senior author David Sabatini, a member of Whitehead Institute, a professor of biology at MIT, and investigator with the Howard Hughes Medical Institute (HHMI). “Now, for the first time, we have generated high-resolution images of GATOR1 and can begin to dissect how this critical protein complex works.”

GATOR1 was first identified about five years ago. It consists of three protein subunits (Depdc5, Nprl2, and Nprl3), and mutations in these subunits have been associated with human diseases, including cancers and neurological conditions such as epilepsy. However, because of the lack of similarity to other proteins, the majority of the GATOR1 complex is a molecular mystery. “GATOR1 has no well-defined protein domains,” explains Whitehead researcher Kuang Shen, one of the study’s first authors. “So, this complex is really quite special and also very challenging to study.”

Because of the complex’s large size and relative flexibility, GATOR1 cannot be readily crystallized — a necessary step for resolving protein structure through standard, X-ray crystallographic methods. As a result, Shen and Sabatini turned to HHMI’s Zhiheng Yu. Yu and his team specialize in cryo-electron microscopy (cryo-EM), an emerging technique that holds promise for visualizing the molecular structures of large proteins and protein complexes. Importantly, it does not utilize protein crystals. Instead, proteins are rapidly frozen in a thin layer of vitrified ice and then imaged by a beam of fast electrons inside an electron microscope column.

“There have been some major advances in cryo-EM technology over the last decade, and now, it is possible to achieve atomic or near atomic resolution for a variety of proteins,” explains Yu, a senior author of the paper and director of HHMI’s shared, state-of-the-art cryo-EM facility at Janelia Research Campus. Last year’s Nobel Prize in chemistry was awarded to three scientists for their pioneering efforts to develop cryo-EM.

GATOR1 proved to be a tricky subject, even for cryo-EM, and required some trial-and-error on the part of Yu, Shen, and their colleagues to prepare samples that could yield robust structural information. Moreover, the team’s work was made even more difficult by the complex’s unique form. With no inklings of GATOR1’s potential structure, Shen and his colleagues, including co-author Edward Brignole of MIT, had to derive it completely from scratch.

Nevertheless, the Whitehead-HHMI team was able to resolve near-complete structures for GATOR1 as well as for GATOR1 bound to its partner proteins, the Rag GTPases. (Two regions of the subunit Depdc5 are highly flexible and therefore could not be resolved.) From this wealth of new information as well as from the team’s subsequent biochemical analyses, some surprising findings emerged.

First is the remarkable level of organization of GATOR1. The protein is extremely well organized, which is quite unusual for proteins that have no predicted structures. (Such proteins are usually quite disorganized.) In addition, the researchers identified four protein domains that have never before been visualized. These novel motifs — named NTD, SABA, SHEN, and CTD — could provide crucial insights into the inner workings of the GATOR1 complex.

Shen, Sabatini, and their colleagues uncovered another surprise. Unlike other proteins that bind to Rag GTPases, GATOR1 contacts these proteins at at least two distinct sites. Moreover, one of the binding sites serves to inhibit — rather than stimulate — the activity of the Rag GTPase. “This kind of dual binding has never been observed — it is highly unusual,” Shen says. The researchers hypothesize that this feature is one reason why GATOR1 is so large — because it must hold its Rag GTPase at multiple sites, rather than one, as most other proteins of this type do.

Despite these surprises, the researchers acknowledge that their analyses have only begun to scratch the surface of GATOR1 and the mechanisms through which it regulates the mTOR signaling pathway.

“There is much left to discover in this protein,” Sabatini says.

This work was supported by the National Institutes of Health, Department of Defense, National Science Foundation, the Life Sciences Research Foundation, and the Howard Hughes Medical Institute.

Study suggests method for boosting growth of blood vessels and muscle

Activating proteins linked to longevity may help to increase endurance and combat frailty in the elderly.

Anne Trafton | MIT News Office
March 22, 2018

As we get older, our endurance declines, in part because our blood vessels lose some of their capacity to deliver oxygen and nutrients to muscle tissue. An MIT-led research team has now found that it can reverse this age-related endurance loss in mice by treating them with a compound that promotes new blood vessel growth.

The study found that the compound, which re-activates longevity-linked proteins called sirtuins, promotes the growth of blood vessels and muscle, boosting the endurance of elderly mice by up to 80 percent.

If the findings translate to humans, this restoration of muscle mass could help to combat some of the effects of age-related frailty, which often lead to osteoporosis and other debilitating conditions.

“We’ll have to see if this plays out in people, but you may actually be able to rescue muscle mass in an aging population by this kind of intervention,” says Leonard Guarente, the Novartis Professor of Biology at MIT and one of the senior authors of the study. “There’s a lot of crosstalk between muscle and bone, so losing muscle mass ultimately can lead to loss of bone, osteoporosis, and frailty, which is a major problem in aging.”

The first author of the paper, which appears in Cell on March 22, is Abhirup Das, a former postdoc in Guarente’s lab who is now at the University of New South Wales in Australia. Other senior authors of the paper are David Sinclair, a professor at Harvard Medical School and the University of New South Wales, and Zolt Arany, a professor at the University of Pennsylvania.

Race against time

In the early 1990s, Guarente discovered that sirtuins, a class of proteins found in nearly all animals, protect against the effects of aging in yeast. Since then, similar effects have been seen in many other organisms.

In their latest study, Guarente and his colleagues decided to explore the role of sirtuins in endothelial cells, which line the inside of blood vessels. To do that, they deleted the gene for SIRT1, which encodes the major mammalian sirtuin, in endothelial cells of mice. They found that at 6 months of age, these mice had reduced capillary density and could run only half as far as normal 6-month-old mice.

The researchers then decided to see what would happen if they boosted sirtuin levels in normal mice as they aged. They treated the mice with a compound called NMN, which is a precursor to NAD, a coenzyme that activates SIRT1. NAD levels normally drop as animals age, which is believed to be caused by a combination of reduced NAD production and faster NAD degradation.

After 18-month-old mice were treated with NMN for two months, their capillary density was restored to levels typically seen in young mice, and they experienced a 56 to 80 percent improvement in endurance. Beneficial effects were also seen in mice up to 32 months of age (comparable to humans in their 80s).

“In normal aging, the number of blood vessels goes down, so you lose the capacity to deliver nutrients and oxygen to tissues like muscle, and that contributes to decline,” Guarente says. “The effect of the precursors that boost NAD is to counteract the decline that occurs with normal aging, to reactivate SIRT1, and to restore function in endothelial cells to give rise to more blood vessels.”

These effects were enhanced when the researchers treated the mice with both NMN and hydrogen sulfide, another sirtuin activator.

Vittorio Sartorelli, a principal investigator at the National Institute of Allergy and Infectious Diseases who was not involved in the research, described the experiments as “elegant and compelling.” He added that “it will be of interest and of clinical relevance to evaluate the effect of NMN and hydrogen sulfide on the vascularization of other organs such as the heart and brain, which are often damaged by acutely or chronically reduced blood flow.”

Benefits of exercise

The researchers also found that SIRT1 activity in endothelial cells is critical for the beneficial effects of exercise in young mice. In mice, exercise generally stimulates growth of new blood vessels and boosts muscle mass. However, when the researchers knocked out SIRT1 in endothelial cells of 10-month-old mice, then put them on a four-week treadmill running program, they found that the exercise did not produce the same gains seen in normal 10-month-old mice on the same training plan.

If validated in humans, the findings would suggest that boosting sirtuin levels may help older people retain their muscle mass with exercise, Guarente says. Studies in humans have shown that age-related muscle loss can be partially staved off with exercise, especially weight training.

“What this paper would suggest is that you may actually be able to rescue muscle mass in an aging population by this kind of intervention with an NAD precursor,” Guarente says.

In 2014, Guarente started a company called Elysium Health, which sells a dietary supplement containing a different precursor of NAD, known as NR, as well as a compound called pterostilbene, which is an activator of SIRT1.

The research was funded by the Glenn Foundation for Medical Research, the Sinclair Gift Fund, a gift from Edward Schulak, and the National Institutes of Health.

A blueprint for regeneration

Whitehead Institute researchers uncover framework for how stem cells determine where to form replacement structures.

Lisa Girard | Whitehead Institute
March 15, 2018

Researchers at Whitehead Institute have uncovered a framework for regeneration that may explain and predict how stem cells in adult, regenerating tissue determine where to form replacement structures.

In a paper that appeared online March 15 in the journal Science, the researchers describe a model for planarian (flatworm) eye regeneration that is governed by three principles acting in concert, which inform how progenitor cells behave in regeneration. The model invokes positional cues that create a scalable map; self-organization that attracts progenitors to existing structures; and progenitor cells that originate in a diffuse spatial zone, rather than a precise location, allowing flexibility in their path. These principles appear to dictate how progenitor cells decide where to go during regeneration to recreate form and function, and they bring us closer to a systems-level understanding of the process.

From previous work, the researchers knew that stem cells are likely reading out instructions from neighboring tissues to guide their path, and it became clear that the process faces some serious challenges in regeneration. “We realized that positional information has to move; it needs to change during regeneration in order to specify the new missing parts to be regenerated. This revised information can then guide progenitor cells that are choosing to make new structures to differentiate into the correct anatomy at the correct locations,” says the paper’s senior author Peter Reddien, a Whitehead Institute researcher, an MIT professor of biology, and a Howard Hughes Medical Institute (HHMI) investigator. “There is a puzzle that emerges, however. Since positional information shifts after injury during regeneration, there is a mismatch between the positional information pattern and the remaining anatomy pattern. Realizing this mismatch exists was a trigger for our study. We wanted to understand how stem cells making particular tissues decide where to go and differentiate. Is it based on anatomy, or is it based on positional information? And when those two things are not aligned, how do they decide?”

Reddien and his lab have spent over a decade unraveling the mysteries of regeneration using a small flatworm, called the planarian. If a planarian’s head is amputated, or its side is removed, each piece will regenerate an entire animal. In order to understand how progenitors decide where to go in the noisy environment of animal regeneration, the researchers used the planarian eye, a visible organ that is small enough to be removed without serious injury and has the added advantage of having defined progenitor cell molecular markers.

The researchers devised a simple experiment to resolve the question of how the progenitors decide where to go: amputate the animal’s head, then after three days remove one of the eyes from the head piece. What they found was that progenitor cells would nucleate a new eye in a position anterior (closer to the tip) to the remaining eye, rather than in the “correct” position specified by the anatomy, symmetrical with the current eye. However, if the same experiment is done, except with one of the eyes removed from the head piece earlier — the same day as the amputation, rather than three days later — there is a different result: The new eye is nucleated at a position symmetrical to the remaining eye, at the “correct” position according to the anatomy, suggesting that when the choices are conflicting, anatomical self-organizing dynamics win.

These simple rules guide the system to successful regeneration and also yield surprising outcomes when the system is pushed to its limits, producing alternative stable anatomical states with three-, four-, and five-eyed animals. Resecting both the side of an animal and amputating the head can place progenitors far enough from existing, self-organizing attractors that they miss them, allowing them to nucleate a new attractor — a third eye — in the head fragments. “If the migrating progenitors are too close to the attractor that is the existing eye, it will suck them in, just like a black hole; if they are far enough, they can escape,” says Kutay Deniz Atabay, first author on the paper and a graduate student in the Reddien lab.

When the researchers did the same surgery on a three-eyed animal, the progenitors miss the attraction of existing eyes and form a five-eyed animal. In each of these cases, all of the eyes are functionally integrated into the brain and exhibit the same light-avoidance response of the planarian eye. The researchers also observed that these alternative anatomical states endure, revealing rules for maintenance of existing and alternative anatomical structures. “This recipe helps provide an explanation for a fundamental problem of animal regeneration, which is how migratory progenitors make choices that lead the system to regenerate and maintain organs,” Atabay says.

“These studies contribute to a proposed framework for regeneration in which competing forces, self-organization, and extrinsic cues, are the guideposts impacting the choice of progenitor targeting in regeneration; and those two forces together determine the outcome,” Reddien says.

This work was supported by the National Institutes of Health (NIH) and the HHMI. Additional funding was provided by the MIT Presidential Fellowship Program and a National Defense Science and Engineering Graduate Fellowship.

Toxic proteins and type 2 diabetes

Whitehead Institute study in yeast illuminates the role of a molecular de-clogger in disease biology.

Nicole Davis | Whitehead Institute
March 8, 2018

Nearly half a billion people worldwide live with type 2 diabetes. Yet despite the disease’s sizeable and increasing impact, its precise causes remain murky. Current scientific thinking points to two key processes: insulin resistance, wherein cells develop ways of tuning out insulin’s signals, and the breakdown of beta cells, the specialized cells in the pancreas that produce insulin. The molecular bases for these activities, however, are largely unknown.

Now, a team of researchers based at Whitehead Institute is casting new light on the theory that abnormal protein deposits — similar to ones that emerge in neurodegenerative disorders such as Alzheimer’s disease — accumulate in and around beta cells and derail their normal function. The team’s findings, which appear in today’s advance online edition of the journal Cell, illuminate the function of a key protein, called Ste24, which unclogs the cellular machinery that helps shuttle proteins into compartments within the cell. The researchers believe that this unclogging action could be an important way to minimize or even prevent the protein deposits that damage precious beta cells in type 2 diabetes.

“We’ve created a new platform for identifying potential genetic and pharmaceutical targets that can help neutralize the toxic proteins that build up in patients with the disease,” says lead author Can Kayatekin. “In initial studies with this platform, we unveiled a very interesting target, Ste24, which has opened an important window on the biology of proteotoxicity in type 2 diabetes.”

Alongside the glucose-lowering hormone insulin, beta cells produce another protein, called IAPP (short for human islet amyloid polypeptide). As these two proteins mature inside the cells, they are bundled together and released within the same miniature packets, or vesicles. However, as its name suggests, IAPP is very amyloidogenic — that is, prone to forming large aggregates, which can pile up both within and outside of cells.

“What happens is that as demand for insulin increases, you get more and more IAPP production, and the more you make, the more likely it is to aggregate,” Kayatekin says. “So, the idea is that as you make more IAPP, it starts poisoning the very cells that are producing it.”

To further explore the molecular mechanisms of IAPP production and aggregation, Kayatekin harnessed a powerful paradigm established by his late mentor and supervisor Susan Lindquist, a Whitehead Institute member, MIT professor of biology, and HHMI Investigator who passed away in 2016. Her pioneering approach leverages the baker’s yeast Saccharomyces cerevisiae to create models of toxic proteins in order to probe, perturb, and expose their underlying biology.

Kayatekin and the study’s co-authors generated a yeast model that carries six tandem copies of IAPP. “In most of the neurodegenerative and protein aggregation diseases, the research has trended towards these kinds of smaller oligomers, which seem to be more capable of diffusing in the cell and are therefore likely to be more toxic,” he explains.

With their model of IAPP toxicity in hand, the researchers then turned to genetic techniques to identify yeast proteins that either enhance or ameliorate the effects of IAPP aggregation. Kayatekin and his team identified several intriguing finds, perhaps the most interesting one being a protease called Ste24. According to a 2016 study published in Cell by Maya Schuldiner’s laboratory, Ste24 can cleave proteins that clog translocons — the channels through which secreted proteins, including IAPP, must pass before they can be released. Much like liquid drain cleaners can clear household pipes of hair balls and other muck, Ste24 can remove proteins that get stuck as they venture through the cell’s inner straits. Indeed, Kayatekin finds that overexpressing Ste24 in his yeast model can help rescue some of the effects of IAPP deposits.

Notably, Ste24 is highly conserved through evolution — so much so that the human version, ZMPSTE24, can stand in for its yeast counterpart, the researchers found. This remarkable feature allowed the team to begin functionally dissecting how natural variation in the human protein might impact its unclogging function. By scouring different genetic variants in ZMPSTE24 identified with the help of the AMP T2D-GENES Consortium, they discovered versions whose function was impaired. Initial data suggests that some of these loss-of-function mutants may be more common in type 2 diabetes patients than those without the disease — suggesting that a less-than-robust declogger could possibly contribute to type 2 diabetes progression.

More work is needed to fully decipher the biology of Ste24, IAPP toxicity, and type 2 diabetes. Nevertheless, Kayatekin hopes that his innovative yeast model will prove to be as powerful a tool for illuminating the molecular underpinnings of disease as the ones that preceded it.

Funding for this work was provided by Whitehead Institute, the Picower Institute at MIT, the University of Texas, M.D. Anderson Center, the Howard Hughes Medical Institute, the Glenn Foundation for Medical Research, the Eleanor Schwartz Charitable Foundation, the Edward N. and Della L. Thome Foundation, the JPB Foundation, the Robert A. and Renee E. Belfer Foundation, the National Institutes of Health, the Canadian Institute of Health Research, and the U.S. Department of Defense. The researchers received additional support from the American Italian Cancer Foundation, the American Parkinson’s Disease Foundation, and the Helen Hay Whitney Foundation.

New study solves an arthritis drug mystery

MIT biological engineers discover why a promising drug failed in clinical trials.

Anne Trafton | MIT News Office
March 6, 2018

Pharmaceutical companies once considered a protein called p38 a very attractive target for treating rheumatoid arthritis. Arthritis patients usually have elevated activity of this inflammation-producing protein, and in lab studies p38 inhibitors appeared to soothe inflammation. However, these drugs failed in several clinical trials.

A new study from MIT sheds light on just why these drugs did not work for arthritis. By untangling the complex interactions between different cell pathways involved in inflammation, the researchers discovered that shutting off p38 triggers other inflammatory pathways.

The findings demonstrate the importance of studying a potential drug’s impact on complex cellular systems, says Doug Lauffenburger, head of MIT’s Department of Biological Engineering and the senior author of the study. It’s also important to do these studies under environmental conditions that match those found in diseased tissue, he adds.

“You’ve got to make sure you understand the complexity of the intracellular networks, and beyond that, you need to think about the environment you put the cells in,” Lauffenburger says. “It’s easy to get different results in different contexts, so you need to study them under many different conditions.”

Former MIT postdoc Doug Jones is the lead author of the paper, which appears in the March 6 issue of Science Signaling.

A promising target

Rheumatoid arthritis, which afflicts more than 1 million Americans, is an autoimmune disorder that produces swollen and painful joints, primarily affecting the wrists and hands. This pain results from inflammation in the lining of the joints. Cells called synovial fibroblasts, which typically provide structural support for the joint lining, promote the inflammation and swelling in arthritic conditions.

Several years ago, scientists seeking new treatments for arthritis discovered that synovial fibroblasts from arthritis patients had very high levels of p38, and many pharmaceutical companies began working on p38 inhibitors. “The activity of this pathway was so strong that people tended to think that it was the best one to inhibit,” Lauffenburger says.

Despite their promise, p38 inhibitors failed in phase II clinical trials run by at least eight pharmaceutical companies. One of those companies, Boehringer Ingelheim, asked Lauffenburger to help them figure out why. Lauffenburger’s lab focuses on systems biology, a field that involves measuring the interactions of many cell components and then performing computational modeling of those measurements to predict cell behavior.

The researchers’ analysis revealed that the inflammatory pathway controlled by p38 interacts with several other pathways that can cause inflammation. These pathways, known collectively as stress pathways, produce inflammatory cytokines in response to events such as infection or injury.

The MIT team found that when p38 is extremely elevated, it suppresses the activity of these other inflammatory pathways. Therefore, when it gets turned off, the brake on the other pathways is released. Under these circumstances, inflammation remains high — the difference is that now it is controlled by other stress pathways.

“This is an insightful paper on redundancy in signaling and the need to understand compensatory mechanisms before spending billions on drug development. In that sense, it is a far more important insight than ‘just’ p38 inhibitors, and it makes clear again that animal efficacy models have severe limitations as tools to predict human efficacy,” says David De Graaf, CEO and president of Syntimmune, who was not involved in the research. “This paper outlines one very thoughtful and generic approach to answer complex questions about efficacy in ex vivo human model systems.”

Environment matters

Why was the MIT team able to see this phenomenon when others had not? Lauffenburger says one key is the environment in which the synovial fibroblast cells were studied.

Normally, cells studied in the lab are grown in a culture medium that offers them nutrients and molecules called growth factors, which keep the cells alive and proliferating. However, the MIT team found that under these conditions, a pro-growth pathway called MEK actually keeps p38 levels lower than in cells under stress. Because p38 is not as high, it doesn’t inhibit the other stress pathways as strongly, so when the cells are exposed to p38 inhibitors, the other pathways don’t soar into action and overall inflammation goes down.

“It looks like p38 inhibitors work well, if cells are in these growth factor environments,” Lauffenburger says.

However, the MIT team found that synovial fluid from arthritis patients is not a pro-growth environment but is full of inflammatory cytokines. They then decided to expose synovial fibroblasts taken from patients with arthritis and from healthy individuals to this inflammatory environment. In both healthy and diseased cells, p38 levels skyrocketed, producing more inflammation and shutting off other stress pathways.

One question still to be answered is whether p38 inhibitors could work against other diseases such as cancer, in which the cells targeted would likely be in a pro-growth environment. They are also being considered as potential treatments for other inflammatory diseases such as multiple sclerosis and Alzheimer’s. Lauffenburger says that their success will likely depend on what kind of environment the affected cells are in.

“A p38 inhibitor could work; you just have to know what the context is that the target cells are in. If you have the same kind of inflammatory cytokines there, then you might encounter the same problem” seen in arthritis, he says.

It’s also possible that p38 inhibitors could work against arthritis or other drugs if given along with drugs that shut off other stress pathways, but more research would be needed to investigate that possibility, Lauffenburger says.

The research was funded by the National Institutes of Health, the Army Research Office, and Boehringer Ingelheim Inc. The project was undertaken in collaboration with Professor Peter Sorger at Harvard Medical School; Brian Joughin at MIT and Anne Jenney at Harvard were also significantly involved in the work.

Scientists deliver high-resolution glimpse of enzyme structure

New finding suggests differences in how humans and bacteria control production of DNA’s building blocks.

Anne Trafton | MIT News Office
February 20, 2018

Using a state-of-the-art type of electron microscopy, an MIT-led team has discovered the structure of an enzyme that is crucial for maintaining an adequate supply of DNA building blocks in human cells.

Their new structure also reveals the likely mechanism for how cells regulate the enzyme, known as ribonucleotide reductase (RNR). Significantly, the mechanism appears to differ from that of the bacterial version of the enzyme, suggesting that it could be possible to design antibiotics that selectively block the bacterial enzyme.

“People have been trying to figure out whether there is something different enough that you could inhibit bacterial enzymes and not the human version,” says Catherine Drennan, an MIT professor of chemistry and biology and a Howard Hughes Medical Institute Investigator. “By considering these key enzymes and figuring out what are the differences and similarities, we can see if there’s anything in the bacterial enzyme that could be targeted with small-molecule drugs.”

Drennan is one of the senior authors of the study, which appears in the Feb. 20 issue of the journal eLife. JoAnne Stubbe, the Novartis Professor of Chemistry Emerita at MIT, and Francisco Asturias, an associate professor of biochemistry at the University of Colorado School of Medicine, are also senior authors. The paper’s lead authors are MIT research scientist Edward Brignole and former Scripps Research Institute postdoc Kuang-Lei Tsai, who is now an assistant professor at the University of Texas Houston Medical Center.

An unusual enzyme

The RNR enzyme, which is found in all living cells, converts ribonucleotides (the building blocks of RNA) to deoxyribonucleotides (the building blocks of DNA). Cells must keep a sufficient stockpile of these building blocks, but when they accumulate too many, RNR is shut off by a deoxynucleotide molecule known as dATP. When more deoxynucleotides are needed, a related molecule called ATP binds to RNR and turns it back on.

An unusual feature of RNR is that it can catalyze the production of four different products: the nucleotide bases often abbreviated as A, G, C, and T. In 2016, Drennan discovered that the enzyme achieves this by changing its shape in response to regulatory molecules.

Most of the researchers’ previous work on RNR structure has focused on the version found in E. coli. For those studies, they used X-ray crystallography, a technique that can reveal the atomic and molecular structure of a protein after it has been crystallized.

In the new study, Drennan and her colleagues set out to examine the human version of RNR. This protein’s structure, which turned out to be very different from the bacterial version, proved elusive using X-ray crystallography, which doesn’t work well for proteins that don’t readily crystallize. Instead, the researchers turned to an advanced form of microscopy known as cryo-electron microscopy (cryo-EM).

Until recently, cryo-EM typically offered resolution of about 10 to 20 angstroms, which might reveal the overall shape of a protein but no detail about the position and shape of smaller structural units within it. However, in the past few years, technological advances have led to an explosion in the number of structures achieving resolutions of about 3 angstroms. That is high enough to trace individual protein chains within the larger molecule, as well as internal structures such as helices and even side chains of amino acids.

Scientists already knew that RNR consists of two protein subunits known as alpha and beta. Using cryo-EM, the MIT team found that the human version of the enzyme forms a ring made from six of the alpha subunits. When ATP, which activates RNR, is bound to the enzyme, the ring is unstable and can be easily opened up, allowing the beta subunit to make its way into the ring. This joining of alpha and beta allows the enzyme’s active site, located in the beta subunit, to perform the chemical reactions necessary to produce deoxynucleotides.

However, when the inhibitor dATP is present, the ring becomes much more rigid and does not allow the beta subunit to enter. This prevents the enzyme from catalyzing the production of deoxynucleotides.

Designing drugs

Several cancer drugs now in use or in development target the human version of RNR, interfering with cancer cells’ ability to reproduce by limiting their supply of DNA building blocks. The MIT team has found evidence that at least one of these drugs, clofarabine diphosphate, works by inducing the formation of rigid 6-unit alpha rings.

This 6-unit ring is not found in the bacterial form of RNR, which instead assembles into a distinct ring containing four alpha subunits and four beta subunits. This means it could be possible to design antibiotics that target the bacterial version but not the human version, Drennan says.

She now plans to investigate the structures of other protein molecules that are difficult to study with X-ray crystallography, including proteins with iron sulfur clusters, which are found in many metabolic pathways. The microscopy work in this study was performed at the Scripps Research Institute, but when MIT’s new MIT.nano building opens, it will house two cryo-EM microscopes that will be available to the MIT community as well as other potential users in industry and academia.

“The technological advances that have allowed cryo-EM to get to such high resolution are really exciting,” Drennan says. “It’s really starting to revolutionize the study of biology.”

The research was funded by the National Institutes of Health.

Study: Fragile X syndrome neurons can be restored

Whitehead Institute researchers are using a modified CRISPR/Cas9-guided activation strategy to investigate the most frequent cause of intellectual disability in males.

Nicole Giese Rura | Whitehead Institute
February 15, 2018

Fragile X syndrome is the most frequent cause of intellectual disability in males, affecting one out of every 3,600 boys born. The syndrome can also cause autistic traits, such as social and communication deficits, as well as attention problems and hyperactivity. Currently, there is no cure for this disorder.

Fragile X syndrome is caused by mutations in the FMR1 gene on the X chromosome, which prevent the gene’s expression. This absence of the FMR1-encoded protein during brain development has been shown to cause the overexcitability in neurons associated with the syndrome. Now, for the first time, researchers at Whitehead Institute have restored activity to the fragile X syndrome gene in affected neurons using a modified CRISPR/Cas9 system they developed that removes the methylation — the molecular tags that keep the mutant gene shut off — suggesting that this method may prove to be a useful paradigm for targeting diseases caused by abnormal methylation.

Research by the lab of Whitehead Institute for Biomedical Research Founding Member Rudolf Jaenisch, which is described online this week in the journal Cell, is the first direct evidence that removing the methylation from a specific segment within the FMR1 locus can reactivate the gene and rescue fragile X syndrome neurons.

The FMR1 gene sequence includes a series of three nucleotide (CGG) repeats, and the length of these repeats determines whether or not a person will develop fragile X syndrome: A normal version of the gene contains anywhere from 5 to 55 CGG repeats, versions with 56 to 200 repeats are considered to be at a higher risk of generating some of the syndrome’s symptoms, and those versions with more than 200 repeats will produce fragile X syndrome.

Until now, the mechanism linking the excessive repeats in FMR1 to fragile X syndrome was not well-understood. But Shawn Liu, a postdoc in Jaenisch’s lab and first author of the Cell study, and others thought that the methylation blanketing those nucleotide repeats might play an important role in shutting down the gene’s expression.

In order to test this hypothesis, Liu removed the methylation tags from the FMR1 repeats using a CRISPR/Cas9-based technique he recently developed with Hao Wu, a postdoc in the Jaenisch lab. This technique can either add or delete methylation tags from specific stretches of DNA. Removal of the tags revived the FMR1 gene’s expression to the level of the normal gene.

“These results are quite surprising — this work produced almost a full restoration of wild type expression levels of the FMR1 gene,” says Jaenisch, whose primary affiliation is with Whitehead Institute, where his laboratory is located and his research is conducted. He is also a professor of biology at MIT. “Often when scientists test therapeutic interventions, they only achieve partial restoration, so these results are substantial,” he says.

The reactivated FMR1 gene rescues neurons derived from fragile X syndrome induced pluripotent stem (iPS) cells, reversing the abnormal electrical activity associated with the syndrome. When rescued neurons were engrafted into the brains of mice, the FMR1 gene remained active in the neurons for at least three months, suggesting that the corrected methylation may be sustainable in the animal.

“We showed that this disorder is reversible at the neuron level,” says Liu. “When we removed methylation of CGG repeats in the neurons derived from fragile X syndrome iPS cells, we achieved full activation of FMR1.”

The CRISPR/Cas-9-based technique may also prove useful for other diseases caused by abnormal methylation including facioscapulohumeral muscular dystrophy and imprinting diseases.

“This work validates the approach of targeting the methylation on genes, and it will be a paradigm for scientists to follow this approach for other diseases,” says Jaenisch.

This work was supported by the National Institutes of Health, the Damon Runyon Cancer Foundation, the Rett Syndrome Research Trust, the Brain and Behavior Research Foundation, and the Helen Hay Whitney Foundation. Jaenisch is co-founder of Fate Therapeutics, Fulcrum Therapeutics, and Omega Therapeutics.