Research Area: Cell Biology

Countering mitochondrial stress

Scientists discover a pathway that monitors a protein import into mitochondria and elicits a cellular response when the process goes awry.

Raleigh McElvery | Department of Biology
April 13, 2018

If there’s one fact that most people retain from elementary biology, it’s that mitochondria are the powerhouses of the cell. As such, they break down molecules and manufacture new ones to generate the fuel necessary for life. But mitochondria rely on a stream of proteins to sustain this energy production. Nearly all their proteins are manufactured in the surrounding gel-like cytoplasm, and must be imported into the mitochondria to keep the powerhouse running.

A duo of MIT biologists has revealed what happens when a traffic jam of proteins at the surface of the mitochondria prevents proper import. They describe how the mitochondria communicate with the rest of the cell to signal a problem, and how the cell responds to protect the mitochondria. This newly-discovered molecular pathway, called mitoCPR, detects import mishaps and preserves mitochondrial function in the midst of such stress.

“This is the first mechanism identified that surveils mitochondrial protein import, and helps mitochondria when they can’t get the proteins they need,” says Angelika Amon, the Kathleen and Curtis Marble Professor of Cancer Research in the MIT Department of Biology, who is also a member of the Koch Institute for Integrative Cancer Research at MIT, a Howard Hughes Medical Institute Investigator, and senior author of the study. “Responses to mitochondrial stress have been established before, but this one specifically targets the surface of the mitochondria, clearing out the misfolded proteins that are stuck in the pores.”

Hilla Weidberg, a postdoc in Amon’s lab, is the lead author of the study, which appears in Science on April 13.

Fueling the powerhouse

Mitochondria likely began as independent entities long ago, before being engulfed by host cells. They eventually gave up control and moved most of their important genes to a different organelle, the nucleus, where the rest of the cell’s genetic blueprint is stored. The protein products from these genes are ultimately made in the cytoplasm outside the nucleus, and then guided to the mitochondria. These “precursor” proteins contain a special molecular zip code that guides them through the channels at the surface of the mitochondria to their respective homes.

The proteins must be unfolded and delicately threaded through the narrow channels in order to enter the mitochondria. This creates a precarious situation; if the demand is too high, or the proteins are folded when they shouldn’t be, a bottleneck forms that none shall pass. This can simply occur when the mitochondria expand to make more of themselves, or in diseases like deafness-dystonia syndrome and Huntington’s.

“The machinery that we’ve identified seems to evict proteins that are sitting on the surface of the mitochondria and sends them for degradation,” Amon says. “Another possibility is that this mitoCPR pathway might actually unfold these proteins, and in doing so give them a second chance to be pushed through the membrane.”

Two other pathways were recently identified in yeast that also respond to accumulated mitochondrial proteins. However, both simply clear protein refuse from the cytoplasm around the mitochondria, rather than removing the proteins collecting on the mitochondria themselves.

“We knew about various responses to mitochondrial stress, but no one had described a response to protein import defects that specifically protected the mitochondria, and that’s exactly what mitoCPR does,” Weidberg says. “We wanted to know how the cell reacts to these problems, so we set out to overload the import machinery, causing many proteins to rush into the mitochondrion at the same time and clog the pores, triggering a cellular response.”

“What makes our cells absolutely dependent on mitochondria is one of those million-dollar questions in cell biology,” says Vlad Denic, professor of molecular and cellular biology at Harvard University. “This study reveals an interesting flip-side to that question: When you make mitochondrial life artificially tough, are they programmed to say ‘help us’ so the host cell comes to their rescue? The possible ramifications of such work in terms of human development and disease could be very impressive.”

A pathway to understanding

Roughly two decades ago, researchers began to notice that the genes required to defend cells against drugs and other foreign substances — together, called the multidrug resistance (MDR) response — were also expressed in yeast mitochondrial mutants for some unknown reason. This suggested that the protein in charge of binding to the DNA and initiating the MDR response must have a dual purpose, sometimes triggering a second, separate pathway as well. But precisely how this second pathway related to mitochondria remained a mystery.

“Twenty years ago, scientists recognized mitoCPR as some kind of mechanism against mitochondrial dysfunction,” Weidberg says. “Today we’ve finally characterized it, given it a name, and identified its precise function: to help mitochondrial protein import.”

As the import process slows, Amon and Weidberg determined that the protein that initiates mitoCPR — the transcription factor Pdr3 — binds to DNA within the nucleus, inducing the expression of a gene known as CIS1. The resultant Cis1 protein binds to the channel at the surface of the mitochondrion, and recruits yet another protein, the AAA+ adenosine triphosphatase Msp1, to help clear unimported proteins from the mitochondrial surface and mediate their degradation. Although the MDR response pathway differs from that of mitoCPR, both rely on Pdr3 activation. In fact, mitoCPR requires it.

“Whether the two pathways interact with one another is a very interesting question,” Amon says. “The mitochondria make a lot of biosynthetic molecules, and blocking that function by messing with protein import could lead to the accumulation of intermediate metabolites. These can be toxic to the cell, so you could imagine that activating the MDR response might pump out harmful intermediates.”

The question of what activates Pdr3 to initiate mitoCPR is still unclear, but Weidberg has some ideas related to signals stemming from the build-up of toxic metabolite intermediates. It’s also yet to be determined whether an analogous pathway exists in more complex organisms, although there is some evidence that the mitochondria do communicate with the nucleus in other eukaryotes besides yeast.

“This was just such a classic study,” Amon says. “There were no sophisticated high-throughput methodologies, just traditional, simple molecular biology and cell biology assays with a few microscopes. It’s almost like something you’d see out of the 1980s. But that just goes to show — to this day — that’s how many discoveries are made.”

The research was funded by the National Institutes of Health and by the Koch Institute Support (core) Grant from the National Cancer Institute. Amon is also an investigator of the Howard Hughes Medical Institute and the Glenn Foundation for Biomedical Research. Weidberg was supported by the Jane Coffin Childs Memorial Fund, the European Molecular Biology Organization Long-Term Fellowship, and the Israel National Postdoctoral Program for Advancing Women in Science.

Study suggests perioperative NSAIDs may prevent early metastatic relapse in post-surgical breast cancer patients
Nicole Giese Rura | Whitehead Institute
April 11, 2018

Cambridge, MA – According to research conducted in mice by Whitehead Institute scientists, surgery in breast cancer patients, which while often curative, may trigger a systemic immunosuppressive response, allowing the outgrowth of dormant cancer cells at distant sites whose ability to generate tumors had previously been kept in check by the immune system. Taking a non-steroidal anti-inflammatory drug (NSAID) around the time of surgery may thwart such early metastatic relapse without impeding post-surgical wound healing.

The team’s work was published in the April 11 issue of the journal Science Translational Medicine.

“This represents the first causative evidence of surgery having this kind of systemic response,” says Jordan Krall, the first author of the paper and a former postdoctoral researcher in the lab of Whitehead Founding Member Robert Weinberg. “Surgery is essential for treating a lot of tumors, especially breast cancer. But there are some side effects of surgery, just as there are side effects to any treatment.  We’re starting to understand what appears to be one of those potential side effects, and this could lead to supportive treatment alongside of surgery that could mitigate some of those effects.”

Although the association between surgery and metastatic relapse has been documented, a causal line between the two has never been established, leading many to consider early metastatic relapse to be the natural disease progression in some patients. Previous studies of breast cancer patients have shown a marked peak in metastatic relapse 12-18 months following surgery. Although the underlying mechanism for such a spike has not been understood, a 2010 retrospective clinical trial conducted in Belgium provides a clue: Breast cancer patients taking a non-steroidal anti-inflammatory (NSAID) for pain following tumor resection had lower rates of this early type of metastatic relapse than patients taking opioids for post-surgical pain. Anti-inflammatory drugs also have previously been shown to directly inhibit tumor growth, but Krall and Weinberg thought that the NSAIDs’ effects in these studies may be independent of the mechanism responsible for the effects noted in the retrospective clinical trial.

To investigate the causes of early metastatic relapse after surgery, the team created a mouse model that seems to mirror the immunological detente keeping in check dormant, disseminated tumor cells in breast cancer patients. In this experimental model, the mice’s T cells stall the growth of tumors that are seeded by injected cancer cells. When mice harboring dormant cancer cells underwent simulated surgeries at sites distant from the tumor cells, tumor incidence and size dramatically increased. Analysis of the blood and tumors from wounded mice showed that wound healing increases levels of cells called inflammatory monocytes, which differentiate into tumor-associated macrophages.  Such macrophages, in turn, can act at distant sites to suppress the actions of T lymphocytes that previously succeeded in keeping the implanted tumors under control. Krall and Weinberg then tested the effects of the NSAID meloxicam (Mobic®), thinking that this anti-inflammatory drug might block the effects of immuno-suppressive effects of wound healing.  In fact, when mice received the NSAID after or at the time of surgery, the drug prevented a systemic inflammatory response created by the wound healing and the meloxicam-treated mice developed significantly smaller tumors than wounded, untreated mice; often these tumors completely disappeared. Notably, meloxicam did not impede the mice’s wound healing

Still, Weinberg cautions that scientists are just beginning to understand the connections between post-surgical wound healing, inflammation, and metastasis.

“This is an important first step in exploring the potential importance of this mechanism in oncology,” says Weinberg, who is also a professor of biology at Massachusetts Institute of Technology (MIT) and director of the MIT/Ludwig Center for Molecular Oncology.

This work was supported by the Advanced Medical Research Foundation, the Transcend Program (a partnership between the Koch Institute and Janssen Pharmaceuticals Inc.), the Breast Cancer Research Foundation, the Ludwig Center for Molecular Oncology at MIT, and the Samuel Waxman Cancer Research Foundation, the American Cancer Society, Hope Funds for Cancer Research, the Charles A. King Trust, the National Health and Medical Research Council of Australia (NHMRC APP1071853), the National Institutes of Health (NIH/NCI 1K99CA201574-01A1), the American Cancer Society Ellison Foundation (PF-15-131-01-CSM), and the U.S. Department of Defense (W81XWH-10-1-0647).

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Robert Weinberg’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 director of the MIT/Ludwig Center for Molecular Oncology.
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Full Citation:
“The systemic response to surgery triggers the outgrowth of distant immune-controlled tumors in mouse models of dormancy”
Science Translational Medicine, April 11, 2018.
 Jordan A. Krall (1), Ferenc Reinhardt (1), Oblaise A. Mercury (1), Diwakar R. Pattabiraman (1), Mary W. Brooks (1), Michael Dougan (1,2), Arthur W. Lambert (1), Brian Bierie (1), Hidde L. Ploegh (1,3 *) Stephanie K. Dougan (1,4), Robert A. Weinberg (1,3,5).
1. Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
2. Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA.
3. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
4. Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
5. Ludwig Center for Molecular Oncology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
*Present address: Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA.
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.

Novel human/mouse model could boost type 1 diabetes research
Nicole Giese Rura | Whitehead Institute
March 27, 2018

Cambridge, MA – About 1.5 million people in the United States have type 1 diabetes, according to the Centers for Disease Control and Prevention (CDC), and yet doctors know very little about what triggers the disease. Now researchers at Whitehead Institute have developed a novel platform with human beta cells that could allow scientists to better understand the mechanisms underlying this disease and what provokes it.

In Type 1 diabetes, an autoimmune disease also called juvenile or insulin-dependent diabetes, the immune system destroys beta cells—the cells in the pancreas that produce insulin. Insulin is required for glucose to enter the body’s cells, so people with type 1 diabetes must closely monitor their glucose levels and take insulin daily. Type 1 diabetes is usually diagnosed during childhood or young adulthood, and possible causes of the disease that are being actively researched include genetics, viral infection, other environmental factors, or some combination of these.

Currently, scientists studying the disease may use animal models, such as non-obese diabetic (NOD) mice that do not include human cells, or mouse and rat models with beta cells derived from human induced pluripotent stem cells (iPSCs)—cells that have been pushed to a pluripotent state—implanted into the animals’ kidney capsules. These models hint at clinical applications that may control glucose levels in type 1 diabetes patients, but because the beta cells do not reside in the pancreas, the models do not reflect the cell-tissue interactions that are likely intrinsic in the development of type 1 diabetes.

To address these shortcomings, a team of researchers led by Haiting Ma, a postdoctoral researcher in Whitehead Founding Member Rudolf Jaenisch’s lab, implanted beta cells derived from iPSCs into the pancreas of neonatal mice. As the mice grow, the human beta cells become integrated into the mice’s pancreases, respond to increased glucose levels, and secrete insulin into the mouse’s bloodstream for several months following implantation. The team’s work is described online in the journal PNAS this week.

Using mice with human beta cells successfully engrafted into their pancreases, scientists will be able to study how beta cells function in normal and disease conditions, and perhaps help identify the causes of type 1 diabetes. Such insights may lead to new approaches to treat this autoimmune disease.

This work was supported by Liliana and Hillel Bachrach, the National Institutes of Health (NIH RO1-CA084198, 5R01-MH104610-16, R37-HD045022, R01-GM114864, RF1-AG048029, U19-AI3115135, and 1R01-1NS088538-01), the Harvard Stem Cell Institute, the JBP Foundation, and Howard Hughes Medical Institute. Jaenisch is co-founder advisor of Fate Therapeutics, Fulcrum Therapeutics, and Omega Therapeutics, and Doug Melton is the founder of Semma Therapeutics.

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Rudolf Jaenisch’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.
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Full Citation:
“Establishment of human pluripotent stem cell derived pancreatic β-like cells in the mouse pancreas”
PNAS, online March 26, 2018.
Haiting Ma (1), Katherine Wert (1), Dmitry Shvartsman (2), Douglas Melton (2), and Rudolf Jaenisch (1,3).
1. Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
2. Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
3. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
A Vision for Science

Clare Harding's microscope image of Toxoplasma gondii parasites is one of this year's winners at the Koch Institute Image Awards

Nicole Giese Rura
March 9, 2018

Scientists use a variety of approaches to unravel the functions of organisms, cells, and even molecules, and some of these approaches produce images that are as stunning as they are informative.  Since 2011, the annual Koch Institute Image Awards, conducted by The Koch Institute for Integrative Cancer Research at MIT, has honored outstanding images created by life science and biomedical researchers in the MIT community.

This year, one of the winning pictures was created by Clare Harding, a postdoctoral researcher in the lab of Whitehead Institute Member and MIT assistant professor of biology, Sebastian Lourido. Harding and the other winners were lauded last night at a gala opening of the exhibit on the Koch building’s ground floor where the winning images will be on display for the coming year.

Whitehead has participated in this contest since its inception, with winning images by Gianluca De Rienzo (postdoctoral researcher in Whitehead Member Hazel Sive’s lab) in 2011, Rob Mathis (graduate student in Whitehead Member Piyush Gupta’s lab) in 2013, Daphne Superville (undergraduate student in Gupta’s lab) in 2015, Dexter Jin (graduate student in Gupta’s lab) in 2016, and Samuel A. LoCascio and Kutay Deniz Atabay (graduate students in Whitehead Member Peter Reddien’s lab) in 2017.

In Harding’s striking entry this year, each white and blue “petal” of the rosettes is a single-celled Toxoplasma gondii, the parasite that causes toxoplasmosis infection. This image was taken moments before the individual parasites comprising the daisy-like clusters would have triggered a massive, coordinated “egress”, which would destroy the host cell they had called home. The host’s nucleus is the large blue oblong jutting in from the upper left (host and parasite DNA are marked blue), and the red dapple marks a molecule in the host cell’s internal skeleton, called tubulin.

Toxoplasmosis infects about 25% of the world’s population and can cause serious disease in pregnant women, infants, and immunocompromised people. Not only is the Lourido lab’s work on T. gondii revealing important clues about this disease, but their research can also shed light on T. gondii’s close cousins on the evolutionary tree: Plasmodium spp., which cause malaria and contribute to more than a million deaths each year; and Cryptosporidium spp., which cause cryptosporidiosis, a gastrointestinal illness that can be fatal in those with a compromised immune system.

Harding’s research in the Lourido lab is focused on GAPM1a, a structural protein that forms a layer directly under T. gondii’s outer membrane and plays a similar architectural role in Plasmodium. This protein scaffold (marked as white in the image) is so vital that it is one of the first things established within daughter cells, which appear in the image as two small white spheres within some of the larger parasites. Parasites lacking the GAPM1a scaffold degrade into amorphous blobs that are unable to infect new host cells—a visual testament of how important this protein is to the parasites.

Light microscopy images like Harding’s are created by passing or reflecting light off of a sample and using one or more lenses to magnify the resulting representation. According to Wendy Salmon, the light microscopy specialist at Whitehead’s W.M. Keck Biological Imaging Facility and a two-time Koch Image Awards judge, all microscopy-based images are imperfect representations of the samples that they depict, because light microscopy is limited by the physics of the light shined on the sample and the glass that comprises the lenses. To push beyond the boundaries of physics and reveal the otherwise invisible, Harding employed two techniques: fluorescent markers and structured illumination microscopy.

Using a light microscope alone, the GAPM1a protein is indiscernible within T. gondii parasites.  But by genetically modifying the parasite to produce the GAPM1a protein fused to a green fluorescent protein, Harding could shine a particular wavelength of light onto the sample and cause the fluorescent protein to glow, thereby illuminating GAPM1a’s presence.

In addition to being able to identify the protein she is studying in a sample, Harding has the additional challenge that the parasites are so tiny—5 micrometers in length, or about 1/16th the width of a human hair—that they are beyond the resolution of light microscopy. In order to visualize the GAPM1a scaffold, Harding used a technique called structured illumination microscopy, which takes advantage of the properties of light in order to see things half the size of what is visible with a conventional light microscope. In this technique, the microscope casts a grid of light onto the specimen and takes images as the grid rotates. The resulting data from the images are processed using an algorithm that reconstructs the specimen’s appearance, enhancing its resolution.

Harding has been working with T. gondii for more than three years and microscopy has always played a major role in her work, but her appreciation for the science and art of microscopy has recently flourished.

“I like microscopy partly because it’s beautiful and partly because with a lot of other techniques, you need to interpret the data. With microscopy, you know what you’re looking at is right there,” says Harding, who is thrilled to have her work featured in the Koch Institute Public Galleries. “I definitely fell in love with microscopy right away. The first time I did it, I realized how much there is to a cell. Even just staining the DNA in a cell, suddenly you can see stars.”

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.

The Man Who Uncovered a New (Old) Way to Fight Cancer

Matthew Vander Heiden helped revive the forgotten— but critical—study of cancer metabolism.

Sam Apple | MIT Technology Review
February 21, 2018

Person in plaid shirt by windowOne day last October, MIT biology professor Matthew Vander Heiden showed up in one of his trademark plaid shirts to teach his undergraduate course on cancer biology. As usual, he peppered his lecture with questions, filling six sliding chalkboards with arrows mapping cellular pathways; he had to erase the boards halfway through class to make room for more notations. But what might have seemed like an ordinary lecture was far from ordinary in one respect: although Vander Heiden was explaining some of the most fundamental aspects of how tumors grow, most of what he was teaching his students would have been absent from nearly every introductory course on cancer biology a decade ago. The science Vander Heiden discussed that afternoon amounted to a once-lost but recently rediscovered chapter in the history of cancer research.

What he didn’t mention in class is that he’d played as large a role as anyone in bringing it back.

That lost chapter focuses on metabolism, and how cancers use nutrients for energy and as building blocks for new cancer cells. It began with a discovery in the early 1920s that most cancers stuff themselves with glucose and then use it in an unusual way. Whereas normal cells typically break down glucose by burning it with oxygen, cancer cells extract much of its energy through fermentation—essentially the same process microorganisms use to make yogurt, beer, and other foods. Indeed, early-20th-century researchers noticed that cancer cells seemed to behave more like yeast than the cells of an animal. But though it would briefly become a major school of cancer research, metabolism fell by the wayside in the 1960s as researchers turned their attention to how cancer-causing genes signal cells to divide.

Cancer metabolism research appeared to be dead, until Vander Heiden helped launch its revival around two decades ago. Today it’s among the hottest areas of the field, spawning conferences, journals, and promising new therapies. And it has fundamentally changed the way many researchers understand cancer and its origins.

Modest revolutionary

Metabolism’s downfall as a research area in the late 20th century was largely a reflection of the faddish nature of science. It didn’t help that Otto Warburg, the German scientist who discovered the unusual metabolism of cancer cells, was so arrogant that much of the scientific community disliked him. So it’s probably a good thing that Vander Heiden, a down-to-earth type who’s been known to downplay his own role on research papers to give his students and postdocs first-author billing, has been so central to the metabolism revival.

Vander Heiden, 45, grew up in Port Washington, Wisconsin, a small town on Lake Michigan once known for its lawnmower factories, and he lives up to every stereotype of his background. “He carries his Midwestern sensibilities with him everywhere he goes,” says his wife, Brooke Bevis, a biologist and the operations manager for Vander Heiden’s lab at MIT’s Koch Institute for Integrative Cancer Research. “I finally made him give up my old 1995 Honda Civic just a few years ago.”

When Vander Heiden enrolled at the University of Chicago in 1990, medicine was already on his mind. His younger brother had suffered from a rare blood disorder as a child, and Vander Heiden spent much of his own childhood hanging around children’s hospitals. But he had little thought of becoming an academic scientist until he began a work-study job washing out equipment in a University of Chicago biology lab. The work was not glamorous but came with a perk: the graduate students in the lab would let Vander Heiden make solutions for them and show him how they did their experiments.

After graduating, he enrolled in Chicago’s MD-PhD program and landed in the lab of Craig B. Thompson. Today Thompson is the president and CEO of the Memorial Sloan Kettering Cancer Center, but at the time he was studying immunology, looking at how the body eliminated huge numbers of immune cells once they were no longer needed.

When Vander Heiden arrived in Thompson’s lab in 1996, part of the explanation was already understood. Those cells would simply commit suicide, a process known as apoptosis. It was also known that a family of proteins named Bcl-2 could stop a cell from committing suicide—and that they appeared to do so through their impact on mitochondria, tiny organelles known as the powerhouses of the cell for their role in energy production.

Vander Heiden had just joined a cutting–edge immunology lab interested in protein signaling. Yet he had been asked to investigate how Bcl-2 proteins affect mitochondria, a relic of the old, outdated metabolism research. When it became clear that no one in the lab knew much about metabolism, Vander Heiden reread the relevant sections of his undergraduate biochemistry textbook. He also teamed up with Navdeep Chandel, a metabolism researcher at Northwestern University who was then a graduate student in a University of Chicago cellular physiology lab.

When another lab showed that proteins released from the mitochondria could trigger apoptosis, Vander Heiden and -Chandel got an important clue: the decision to commit suicide could now be traced directly to the mitochondria. And yet the deeper question of what was happening inside them remained mysterious until the two researchers arrived at an answer, thanks to a series of elegant experiments designed by Vander Heiden (whom Chandel calls “a world-class experimentalist”) to study how molecules moved through the mitochondrial membrane. They discovered that the release of the mitochondrial proteins was a sign of a failing powerhouse, a notice to the cell that a brownout was under way so it was time to abort. But brownouts weren’t inevitable; the Bcl-2 proteins, like emergency workers called to the scene of an imminent disaster, could resuscitate the metabolic function of the mitochondria and keep things from getting to that point. The suicide signal, in turn, would never be released.

Person pipets in lab hood
Daniel Schmidt, a postdoc in Vander Heiden’s lab, prepares cells to study how metabolism affects cancer cell proliferation. Credit: BUCK SQUIBB
Daniel Schmidt, a postdoc in Vander Heiden’s lab, prepares cells to study how metabolism affects cancer cell proliferation.

BUCK SQUIBB

For Vander Heiden, this was a “watershed moment.” Among other things, it meant that metabolic enzymes weren’t merely supplying energy from food. Metabolism was governing the most fundamental decision a cell has to make—whether to live or die. That meant it had to be interwoven into the signaling cascades that molecular biologists studied. His feeling at the time, he recalls, was “Oh my goodness. We don’t really understand metabolism.”

Vander Heiden might not have envisioned himself delving into research areas that had been discarded decades earlier, but what was more surprising was how little research was then being done in an area that was “as fundamental as you get in terms of how biology works,” he says. “I looked around and no one was studying it.”

Thompson, recognizing the opportunity, shifted the focus of his lab to metabolism. Vander Heiden, meanwhile, continued to pursue Thompson’s broader question of how the body eliminates unwanted immune cells. He already knew that growth factors, messages sent from one cell to the next, kept cells from committing suicide, but how the signals delivered their survival message remained unclear. What he discovered in a series of studies carried out in the late ’90s followed perfectly from his previous research. Growth factors kept cells alive by giving them permission to eat. Without that permission, a cell soon faced an energy crisis, and the mitochondria released their death signals.

The takeaway was clear: our bodies eliminate unwanted cells by starving them to death.

Solving the metabolism mystery

As Vander Heiden’s MD-PhD program was coming to an end, he hadn’t yet begun to focus on cancer, but its possible links with his research on cell suicide were intriguing. Cancer cells were the other side of the coin—cells that were resistant to suicide, that no longer cared about instructions from other cells. So in 2004, after completing a residency in oncology at Brigham and Women’s Hospital in Boston, he was anxious to investigate cancer metabolism for his postdoc research.

Finding the right lab wasn’t easy. At the time, telling leading researchers he wanted to study how cancer cells consumed glucose was like approaching a high-tech manufacturer and announcing you wanted to study the trucks that brought fuel to the factory. It sounded, Vander Heiden says, “like a really ridiculous thing.”

Vander Heiden eventually found a home in the Harvard lab of Lewis Cantley, who now directs the Meyer Cancer Center at Weil Cornell. His research in Cantley’s lab would help solve one of the central riddles of cancer metabolism: why cancer cells are so ravenous for glucose. Researchers had once assumed that cancer cells were turning to fermentation because they’d lost the ability to use oxygen properly and needed some other way to produce energy. But Vander Heiden’s research on a mutated form of the enzyme pyruvate kinase showed something else. Rather than being used for energy, much of the glucose was being shunted into pathways used to build new molecules. What a growing cancer needs most of all from its food, the research suggested, is more spare parts—raw materials for making new DNA, membranes, and proteins.

Rethinking chemotherapy

Vander Heiden’s research with Cantley would also lead to his involvement with Agios Pharmaceuticals, the company behind one of the most promising new drugs to emerge from the metabolism revival. (Cantley says he played a major role in building the company’s science in its early days.) The drug, AG-221, treats acute myelogenous leukemia, a cancer of the blood and bone marrow. It works by blocking the product of a mutated form of the mitochondrial enzyme IDH-2. Approved by the US Food and Drug Administration in August, it has been hailed as the first real advance for the disease in 30 years.

The approval of AG-221 isn’t the only thing generating excitement in the cancer world. Unlike almost all other cancer drugs, AG-221 doesn’t kill the cancer cells but, rather, allows them to develop out of their deranged state into noncancerous, mature, functioning cells. That a single metabolic enzyme could have such profound effects on which genes are expressed in a cell is now one of the many signs that changes in metabolism are not just a response to the needs of a growing cancer. Often, they may actually be causing the cancer itself. It represents a major shift in thought: many cancer-causing genes long known for their ability to signal cells to keep dividing have now been shown to have additional roles in signaling cells to keep eating. Some researchers now believe the overeating typically comes first, driving the transformations that follow.

Since his arrival at MIT and the opening of his lab at the Koch Institute in 2009, Vander Heiden has treated cancer patients and continued to search for better therapies. In recent years he has focused on improving understanding of chemotherapy. Though typically thought of as general poisons, most chemotherapy drugs work because they disrupt metabolic functions. That much has long been known, but less clear is why a particular drug works for some cancers and not for others, even when two cancers carry the same mutations.

It was while explaining to his undergrad cancer biology students how targeted drugs work that Vander Heiden first thought of an answer. As a cancer doctor, he knew that chemotherapies are often chosen on the basis of where in the body a tumor first arose, but what was it about this location that made the difference?

Vander Heiden’s research in mice now suggests that the answer may lie in which foods are available to the cancer as it forms. Melanoma and colon cancer, for example, often have the same mutations, and yet, as he explains, because the two cancers “grow in very different places in the body,” they likely “have access to different nutrients.” He adds, “It has nothing to do with the genetics.” If he turns out to be right, it could lead to a fundamental change in how oncologists think about which drugs to give their patients.

As Vander Heiden turns his attention to old chemotherapy drugs, rethinking why and how they work, he is once again looking to the past for new insights on cancer. It might be more than a coincidence. As Bevis, his wife, says, the outdated Honda Civic isn’t the only item he has struggled to let go of. “The list goes on and on,” she says. “He hates waste and will use items long after someone else would have replaced them with a newer, shinier model.”

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.

Probing a critical player in cancer growth

Alissandra Hillis ’18 has spent all four years at MIT in the same cancer metabolism lab, deciphering the basic science behind pancreatic cancer.

Raleigh McElvery
February 19, 2018

Senior Alissandra Hillis attributes her appetite for the basic sciences to her craving for fundamental knowledge. She’s spent her four years at MIT in the same lab, committed to unraveling the molecular mechanics of pancreatic cancer — the fourth leading cause of cancer death for both men and women, given that symptoms do not often appear until the disease is quite advanced.

“I was always very curious growing up,” she says. “I taught myself how to read at a very young age, just because I wanted to know about things and how they worked. But I didn’t become interested in biology and chemistry specifically until I came to MIT and started taking my General Institute Requirements.”

In doing so, Hillis became enthralled by the prospect of breaking down life into its most fundamental, biological units to decipher cellular function and disease. Originally a Course 7 major with a chemistry minor, she declared Course 5-7 (Chemistry and Biology) as soon as it became available in the fall of 2017 — applying her study of biochemistry and cell metabolism to cancer research.

“When I was quite young, my grandfather was diagnosed with stomach cancer, and ended up having almost three quarters of his stomach removed,” she says. “I was too little to really understand the severity of the situation, but as soon as I came to MIT I started to wonder what was going on at a cellular level. Most people today know someone who is fighting cancer, and yet we’re still lacking effective treatments for its most severe forms.”

Hillis joined Matthew Vander Heiden’s cancer metabolism lab the first semester of her freshman year, and has been there ever since.

“Professor Vander Heiden does an excellent job of tailoring the research project to the individual, and there is no hierarchy among lab members,” she says. “I really liked it from the onset, so I stayed.”

For nearly two years, Hillis has been investigating the role of one enzyme, pyruvate kinase muscle isozyme M2 (PKM2), in pancreatic cancer. PKM2 is responsible for catalyzing the final step in glycolysis, which is required to create the energy that fuels cells. Glycolysis is also important in tumor metastasis and growth, since cancer cells demand energy in order to proliferate.

Cancer cells often preferentially express PKM2 over other types of pyruvate kinases such as PKM1. This spurred William Israelsen PhD ’14, a former graduate student in the Vander Heiden lab working in breast cancer models, to delete the PKM2 gene and see what happened. Since PKM2 is critical for glycolysis, and cancer cells require energy to proliferate, he anticipated that removing PKM2 would hinder energy production and thus disrupt tumor development. To his surprise, he found the opposite: deleting PKM2 actually accelerated tumor formation and promoted liver metastasis in mice.

In his 2014 paper, Israelsen concluded that PKM2 might permit cancer cells to maintain their “plasticity,” shifting from one specialized role to another even after they’ve fully matured. In the absence of PKM2, he proposed PKM1 might take over PKM2’s influential role.

Hillis wondered if she could replicate Israelsen’s breast cancer results in a model for pancreatic cancer, especially given the conflicting findings in human data regarding PKM2 expression in the latter. Some studies suggest that high PKM2 expression correlates with accelerated disease, whiles others indicate just the opposite: that high PKM2 expression is associated with better survival rates.

“Going into the project, we were expecting similar effects in both pancreatic and breast cancer models because both cancers preferentially express PKM2, and we were using the same method of PKM2 deletion, just bred into a different cancer model,” Hillis explains. “We anticipated that PKM2 deletion would accelerate pancreatic tumor size and tumor genesis, and decrease the mouse’s lifespan. But we’ve noticed that these effects — if they exist — are very much attenuated in the pancreatic cancer model; there is only a slight decrease in lifespan and increase in tumor size without PKM2.”

Right now, her working hypothesis holds that PKM2’s influence varies depending on the tissue in question. This might explain why her own results don’t exactly parallel what Israelsen found in his breast cancer model. For instance, the method they were using to delete PKM2 is quite effective in the breast and pancreatic cells themselves, but less so in the dense scar-like tissue characteristic of pancreatic tumors in particular. It’s possible, she thinks, that this fibrous tissue may still express some PKM2 even post-knockout, perhaps hindering both a drastic decrease in lifespan and increase in tumor size.

Hillis hopes piecing together PKM2’s mechanism of action will help us better diagnose — and eventually treat — certain cancers. Her most recent results were published in the November 2017 issue Cancer & Metabolism.

Although Hillis enjoys tackling the more fundamental questions concerning cancer, she’s also interested in translating this work from bench to bedside. That’s why she decided to intern with David Ting at the Massachusetts General Hospital Cancer Center this past summer.

“I wanted to try a different type of research before applying to graduate school,” she says. “The Department of Biology frequently sends out emails about job opportunities, and there was one advertising that the Ting lab was looking for a research technician.”

Although she was still a junior at the time, she contacted Ting — an MIT alumnus with a dual degree in 7A and 10 — and together they fashioned a summer position just for her, studying the role of miniscule, fluid-filled transportation structures called exosomes in cancer development and diagnosis.

“That was the first time I’d worked with samples from actual patients,” she says. “Many of the assays were the same, but I felt closer to a clinical application than I ever had before. I really enjoy doing the foundational work to identify the basic problem, but there’s definitely something to be said for experiencing research targeted at creating a diagnostic tool. I can see the pros and cons of both approaches.”

As Hillis begins her final semester at MIT, she’s continuing her work in the Vander Heiden lab, while also finishing up the requirements for her HASS concentration in legal studies. She’s still set on pursuing a PhD in cancer biology, but the propensity to ask tough questions that drew her to science in the first place has led her to realize that the questions she raises in her own research have ramifications far beyond her lab bench. Taking policy-oriented classes in addition to her science-related ones has inspired her to pursue a law degree in conjunction with her PhD — weaving together her love for science with a newfound interest in the rules and regulations that govern how science is funded, performed, shared, applied, and monetized.

“I really enjoy doing research, and that’s something I probably will continue to do,” she says, “but I also want to influence science-related regulations, which is something I couldn’t possibly do without a law degree. I would still be heavily immersed in science, while applying the subjects I love in new and exciting ways.”

Photo credit: Raleigh McElvery