Research Area: Human Disease

Harnessing the moonseed plant’s chemical know-how
Eva Frederick | Whitehead Institute
April 20, 2020

In overgrown areas from Canada to China, a lush, woody vine with crescent-shaped seeds holds the secret to making a cancer-fighting chemical. Now, Whitehead Institute researchers in Member Jing-Ke Weng’s lab have discovered how the plants do it.

Plants in the family Menispermaceae, from the Greek words “mene” meaning “crescent moon,” and “sperma,” or seed, have been used in the past for a variety of medicinal purposes. Native Americans used the plants to treat skin diseases, and would ingest them as a laxative. Moonseed was also used as an ingredient in curare, a muscle relaxant used on the tips of poison arrows.

But the plants also may have a use in modern-day medicine: a compound called acutumine shown to have anti-cancer properties (although not tested specifically against cancer cells, the chemical has been shown to kill human T-cells, an important quality for leukemia and lymphoma treatments). Acutumine is a halogenated product, which means the molecule is capped on one end by a halogen atom — a group that includes fluorine, chlorine and iodine, among others. In this case, the halogen is chlorine.

Halogenated compounds like acutumine can be useful in medicinal chemistry — their unusual chemical appendages mean they react in interesting ways with other biomolecules, and drug designers can put them to use in creating compounds to complete specific tasks in the body. Today, 20% of pharmaceutical compounds are halogenated. “However, chemists’ ability to efficiently install halogen atoms to desirable positions of starting compounds has been quite limited,” Weng says.

Most natural halogenated products come from microorganisms such as algae or bacteria, and acutumine is one of the only halogenated products made by plants. Chemists finally succeeded in synthesizing the compound in 2009, although the reaction is time-consuming and expensive (10 mg of synthesized acutumine can cost around $2,000).

Colin Kim, a graduate student in the Weng lab at Whitehead Institute, wanted to know how these plants were completing this tricky reaction using only their own genetic material. “We thought, why don’t we ask how the plants make it and then upscale the reaction [to produce it more efficiently]?” Kim says.

“By understanding how living organisms such as the moonseed plant perform chemically challenging halogenation chemistry, we could devise new biochemical approaches to produce novel halogenated compounds for drug discovery,” Weng says.

Kim knew that for every halogenated molecule in an organism, there is an enzyme called a halogenase that catalyzes the reaction that sticks on that halogen. Halogenases are useful in creating pharmaceuticals – a well-placed halogen can help fine-tune the bioactivities of various drugs. So Weng, who is also an associate professor of biology at Massachusetts Institute of Technology, and Kim, who spearheaded the project, began working to identify the helper molecule responsible for creating acutumine in moonseed plants.

First, the scientists obtained three species of Menispermaceae plants. Two of them, common moonseed (Menispermum canadense) and Chinese moonseed (Sinomenium acutum), were known to produce acutumine. They also procured one plant in the same family called snake vine (Stephania japonica) which did not produce the compound.

They began their investigation by using mass spectrometry to look for acutumine in all three plants, and then find out exactly where in the plants it was located. They found the chemical all throughout the first two — and some extra in the roots of common moonseed. As expected, the third plant, snake vine, had none, and could therefore be used as a reference species, since presumably it would not ever express the gene for the halogenase enzyme that could stick on the chlorine molecule.

Next, the researchers started searching for the gene. They began by sequencing the RNA that was being expressed in the plants (RNA serves as a messenger between genomic DNA and functional proteins), and created a huge database of RNA sorted by what tissue it had been identified in.

At this point, the extra acutumine in the roots of common moonseed came in handy. The researchers had some idea of what the enzyme might look like – past research on other halogenases in bacteria suggested that one specific family of enzyme, called Fe(II)/2-oxoglutarate-dependent halogenases, or 2ODHs, for short, was capable of site-specifically adding a halogen in the same way that the moonseed’s mystery enzyme did. Although no 2ODHs had yet been found in plants, the researchers thought this lead was worth a look. So they searched specifically for transcripts similar to 2ODH sequences that were more highly expressed in the roots of common moonseed than in the leaves and stems.

After analyzing the RNA transcripts, Kim and Weng were pretty sure they had found what they were looking for: one gene in particular (which they named McDAH, short for M. canadense dechloroacutumine halogenase) was highly expressed in the roots of common moonseed. Then, in Chinese moonseed, they identified another protein that shared 99.1 percent of McDAH’s sequence, called SaDAH. No similar protein was found in snakevine, suggesting that this protein was likely the enzyme they wanted.

To be sure, the researchers tested the enzyme in the lab, and found that it was indeed the first-ever plant 2ODH, able to stick on the chlorine molecule to the alkaloid molecule dechloroacutumine to form acutumine. Interestingly, the enzyme was pretty picky; when they gave it other alkaloids like codeine and berberine to see if it would install a halogen on those as well, the enzyme ignored them, suggesting it was highly specific toward its preferred substrate, dechloroacutumine, the precursor of acutumine. They compared the enzyme’s activity to other similar enzymes, and found the key to its ability lay in the substitution of one specific amino acid in the active site– aspartic acid — for a glycine.

Now that they had identified the enzyme responsible for the moonseed’s halogenation reactions, Kim and Weng wanted to see what else it could do. A chemical capable of catalyzing such a complex reaction might be useful for chemists trying to synthesize other compounds, they hypothesized.

So they presented the enzyme with some dechloroacutumine and a whole buffet of alternative anions to see whether it might catalyze a reaction with any of these molecules in lieu of chlorine. Of the selection of anions, including bromide, azide, and nitrogen dioxide, the enzyme catalyzed a reaction only with azide, a construct of 3 nitrogen atoms.

“That is super cool, because there isn’t any other naturally occurring azidating enzyme that we know of,” Kim says. The enzyme could be used in click chemistry, a nature-inspired method to create a desired product through a series of simple, easy reactions.

In future studies, Weng and Kim hope to use what they’ve learned about the McDAH and SaDAH enzymes as a starting point to create enzymes that can be used as tools in drug development. They’re also interested in using the enzyme on other plant products to see what happens. “Plant natural products, even without chlorines, are pretty effective and bioactive, so it would be cool to see if you can take those plant natural products and then install chlorines to see what kind of changes and bioactivity it has, whether it develops new-to-nature functions or retain its original bioactivity with enhanced properties,” Kim says. “It expands the biocatalytic toolbox we have for natural product biosynthesis and its derivatization.”

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Written by Eva Frederick

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Citation: Kim, Colin Y. et al. The chloroalkaloid (−)-acutumine is biosynthesized via a Fe(II)- and 2-oxoglutarate-dependent halogenase in Menispermaceae plants. Nature Communications. April 20, 2020. DOI: 10.1038/s41467-020-15777-w

Global perspectives on microscopic pathogens

Junior Emily O’Rourke traveled to South Africa to investigate epidemics and returned with a broader outlook on her fundamental disease research.

Raleigh McElvery
March 31, 2020

Growing up in El Paso, Texas near the border of the U.S. and Mexico, Emily O’Rourke could venture across cultures in less time than it takes most people to commute to work. In fact, her dad would make this short trip each day for his job as a mechanical engineer. Watching him cross over so frequently reminded O’Rourke that “ideas and skills don’t stop at the border.” O’Rourke herself would visit Mexico to see relatives, and these experiences seeded aspirations to spearhead international scientific collaborations. Now a junior in Course 7 (Biology), O’Rourke is continuing to add stamps to her passport while exploring the global implications of disease research.

O’Rourke chose MIT because it offered a particularly wide array of study abroad programs, in addition to having top-tier research opportunities. One such study abroad program, MIT International Science and Technology Initiatives (MISTI), operates 25 regional programs, matching undergraduate and graduate students with fully-funded internship, research, and teaching opportunities in over 40 countries. The summer after her first year, O’Rourke participated in MISTI’s MIT-Italy Program in order to gain some research experience in the realm of urban planning. For six weeks, she investigated the urban effects of sea level rise while living in Venice.

When she returned to campus for her sophomore year, O’Rourke was intending to double major in physics and biology. But she ultimately opted to drop physics and pursue the life sciences once she started working in Becky Lamason’s lab in the Department of Biology.

“I started to see how biology worked on a practical level,” she says. “I get to experience a hands-on connection by running DNA on a gel and doing other experiments. During our weekly lab meetings, I witness scientific stories as they unfold.”

More recently, the duo has begun to examine how Sca4 may coopt another protein in the host cell, known as clathrin, for its own malicious means. “Sca4 is a really big protein and we still don’t know its entire structure,” O’Rourke says, “and we’re hoping to uncover some new functions.”The Lamason lab investigates how parasites hijack host cells processes in order to spread infection. O’Rourke is working with graduate student Cassandra Vondrak to probe the proteins that allow the tick-borne Rickettsia parkeri to migrate from one cell to the next. Their protein of interest, surface cell antigen 4 (Sca4), is secreted by the bacterium and binds to the host’s cell membrane, reducing the tension across the membrane and allowing Rickettsia to punch through to the neighboring cell. O’Rourke and Vondrak aim to determine how Rickettsia releases Sca4, in the hopes of piecing together a general mechanism by which pathogens propagate.

While O’Rourke was studying infectious disease on a cellular level, she heard about an opportunity to explore epidemics on a global scale. Each January, the Harvard-MIT Program in Health Sciences and Technology sponsors a two-week class in South Africa called Evolution of an Epidemic. The class, taught by Professor of the Practice Bruce Walker, covers the medical, scientific, and political responses to new diseases, focusing on the HIV/AIDS epidemic. Walker, who is also the director of the Ragon Institute of MGH, MIT and Harvard, is a world leader in the study of immune control and evasion in HIV infection. Since then, he’s developed strong connections and research partnerships in South Africa where the disease is most prevalent.

O’Rourke enrolled in Evolution of an Epidemic, and MISTI helped her to plan her trip. On January 16, she landed in Johannesburg, the first of three destinations. The cohort of students from MIT, Harvard, and the African Leadership Academy attended lectures, spoke with patients, and met medical professionals.

After Johannesburg, the class traveled to Durban where they visited traditional healers who were learning to administer HIV/AIDS tests as part of the iTeach program.

“We had the chance to ask these healers how they felt about interacting with Western medicine, and whether it clashed with their traditional values,” O’Rourke says. “They said HIV was so new that they couldn’t draw upon ancient wisdom from their ancestors to treat it. They were directing patients towards Western treatments because they’d seen the devastation the disease could cause.”

iTeach building
The iTEACH Program located in KwaZulu-Natal, South Africa.

At their third and final destination, the province of KwaZulu-Natal, O’Rourke toured the FRESH Program. Twice a week, as part of a clinical trial, healthy African women around O’Rourke’s age attend classes that address topics like self-esteem, gender-based violence, HIV prevention, career development, and computer training. Before each session, the women are tested for HIV/AIDS, so if they contract it the researchers can treat it early and learn more about the disease’s initial stages.

“I really liked going there because it helped me see a direct connection between science and social good,” O’Rourke says. “It showed the value of talking to patients and asking about their experiences, rather than just looking at study outcomes.”

After two weeks, O’Rourke returned to MIT Biology and the Lamason lab with a broader outlook on her parasite research. “I’m able to see how my works fits into a larger context,” she says, “and how it may eventually have far-reaching impacts on disease evolution and spread.”

O’Rourke still plans to pursue fundamental biological research, but intends to seek out international collaborations focused on global health as well. It’s hard to leave the MIT bubble, she says, but it’s worth it. “Traveling can really broaden your perspective as a scientist, and inform your research in unexpected ways.”

Photos courtesy of Emily O’Rourke
Posted 4.1.20
Thank you for your patients

An unusual synergy between cancer researchers, clinical centers, and industry leads to promising clinical trials for a new combination therapy for prostate cancer.

Bendta Schroeder | Koch Institute
March 21, 2020

As Jesse Patterson, an MIT research scientist, and Frank Lovell, a finance industry retiree with a penchant for travel, chatted in the Koch Institute auditorium after a public lecture, they realized the anomaly of the experience: Cancer patients rarely get to meet researchers working on their treatments, and cancer researchers rarely get to put a name and a face to the people they aim to help through their work.

Lovell was participating in a clinical trial for a prostate cancer therapy that combines the widely-used targeted therapy abiraterone with the Plk1 inhibitor onvansertib. Patterson, working in the laboratory of Professor Michael Yaffe, the David H. Koch Professor of Science and director of the MIT Center for Precision Cancer Medicine, played a significant role in identifying the new drug combination and its powerful potential.

While their encounter was indeed fortunate, it was not random. They never would have met if not for the human synergy showcased at that evening’s SOLUTIONS with/in/sight event, the result of collaborative relationships built between research labs, clinical centers, and industry. Patterson and Yaffe were on hand to tell the story of the science behind their new drug combination, and were joined by some of the partners who helped translate their results into a clinical trial: David Einstein, clinical oncologist at Beth Israel Deaconess Medical Center, and Mark Erlander, chief scientific officer of Trovagene Oncology, the biotech company that developed onvansertib.

Network synergy

The need for new prostate cancer therapies is acute. Prostate cancer is the leading diagnosis among men for non-skin cancer and the second-leading cancer killer among men in the United States. Abiraterone works by shutting off androgen synthesis and interfering with the androgen receptor pathway, which plays a crucial role in prostate cancer cells’ ability to survive and divide. However, cancer cells eventually evolve resistance to abiraterone. New, more powerful drug combinations are needed to circumvent or delay the development of resistance.

Patterson and his colleagues in the Yaffe lab hypothesized that by targeting both the androgen receptor and other pathways critical to cancer cell proliferation, they could produce a synergistic effect — that is, a combination effect that is much greater than the sum of each drug’s effect by itself. Plk1, a pathway critical to each stage of cell division, was of longstanding interest to the Yaffe group, and was among those Patterson strategically selected for investigation as a potential partner target for androgen receptor. In screens of prostate cancer cell lines and in xenograft tumors, the researchers found that abiraterone and Plk1 inhibitors both interfere with cell division when delivered singly, but that together, those effects are amplified and far more often lethal to cancer cells.

An unexpected phone call from Mark Erlander at Trovagene, a San Diego-based clinical-stage biotech company, was instrumental in translating the Yaffe Lab’s research results into clinical trials.

Erlander had learned that MIT held a patent for the combination of Plk1 inhibitors and anti-androgens for any cancer — the result of Yaffe Lab studies. Although he did not know Yaffe personally and lived a continent away, Erlander picked up the phone and invited Yaffe for coffee. “This was worth flying across the country,” Erlander said.

Still in scrubs, Yaffe, who is an attending surgeon at Beth Israel Deaconess Medical Center in addition to his academic roles, chatted with Erlander during his shift break at the hospital. The new collaboration was on its way.

Speaking Frankly

While Erlander had the Plk1 inhibitor and the Yaffe Lab had the science behind it, they were still missing an important component of any clinical trial: patients. Yaffe enlisted doctors David Einstein and Steven Balk, both at Beth Israel Deaconess Medical Center and Dana Farber/Harvard Cancer Center, with whom he had worked on related research supported by the Bridge Project, to bring clinical translation expertise and patient access.

By the time clinical trials began in 2019, Frank Lovell was ready for a new treatment. When his prostate cancer was first diagnosed about a decade ago, he was treated with surgery and radiation. When the cancer came back five years later, he received a hormonal treatment that stopped working within three years. He started to see Einstein, an oncologist who specialized in novel therapies, and tried yet another treatment, this one losing effectiveness after a year. Then he joined Einstein’s trial.

For Lovell, the new combination of drugs was “effective in a wonderful way.” Many of the patients in the trial — 72 percent of those who completed phase 2 — showed declining or stabilized levels of prostate-specific androgen (PSA), indicating a positive response to the treatment. Lovell’s PSA levels stabilized, too, and he reports that he experienced very few side effects.

But most importantly, noted Lovell, “I say thank you to Dr. Einstein, Dr. Patterson, and Dr. Yaffe. They brought me hope and time.”

The gratitude is mutual.

“I especially want to thank Frank and all the patients like him who have volunteered to be on these clinical trials,” says Yaffe. “Without patients like Frank, we would never know how to better treat these types of cancers.”

Lovell is no longer in the trial for now, but enjoying making his rounds from Cape Cod in the summer; to Paris and Cannes, France, and then Hawaii in the autumn; and to Naples, Florida, in the winter, on top of visiting with family and a wide circle of friends. “Illness has not stopped me from living a normal life,” Lovell said. “You wouldn’t think I was sick.”

Meanwhile, Yaffe, Patterson, and their research collaborators are still at work. They are optimizing drug delivery regimens to maximize the time on treatment and minimize toxicity, as well as finding biomarkers that help identify which patients will best respond to the combination. They are also looking to understand the mechanism behind the synergy better, which in turn may help them find more effective partners for onvansertib, and to identify other cancer types, such as ovarian cancer, for which the combination may be effective.

Bacterial enzyme could become a new target for antibiotics

Scientists discover the structure of an enzyme, found in the human gut, that breaks down a component of collagen.

Anne Trafton | MIT News Office
March 17, 2020

MIT and Harvard University chemists have discovered the structure of an unusual bacterial enzyme that can break down an amino acid found in collagen, which is the most abundant protein in the human body.

The enzyme, known as hydroxy-L-proline dehydratase (HypD), has been found in a few hundred species of bacteria that live in the human gut, including Clostridioides difficile. The enzyme performs a novel chemical reaction that dismantles hydroxy-L-proline, the molecule that gives collagen its tough, triple-helix structure.

Now that researchers know the structure of the enzyme, they can try to develop drugs that inhibit it. Such a drug could be useful in treating C. difficile infections, which are resistant to many existing antibiotics.

“This is very exciting because this enzyme doesn’t exist in humans, so it could be a potential target,” says Catherine Drennan, an MIT professor of chemistry and biology and a Howard Hughes Medical Institute Investigator. “If you could potentially inhibit that enzyme, that could be a unique antibiotic.”

Drennan and Emily Balskus, a professor of chemistry and chemical biology at Harvard University, are the senior authors of the study, which appears today in the journal eLife. MIT graduate student Lindsey Backman and former Harvard graduate student Yolanda Huang are the lead authors of the study.

A difficult reaction

The HypD enzyme is part of a large family of proteins called glycyl radical enzymes. These enzymes work in an unusual way, by converting a molecule of glycine, the simplest amino acid, into a radical — a molecule that has one unpaired electron. Because radicals are very unstable and reactive, they can be used as cofactors, which are molecules that help drive a chemical reaction that would otherwise be difficult to perform.

These enzymes work best in environments that don’t have a lot of oxygen, such as the human gut. The Human Microbiome Project, which has sequenced thousands of bacterial genes from species found in the human gut, has yielded several different types of glycyl radical enzymes, including HypD.

In a previous study, Balskus and researchers at the Broad Institute of MIT and Harvard discovered that HypD can break down hydroxy-L-proline into a precursor of proline, one of the essential amino acids, by removing the hydroxy modification as a molecule of water. These bacteria can ultimately use proline to generate ATP, a molecule that cells use to store energy, through a process called amino acid fermentation.

HypD has been found in about 360 species of bacteria that live in the human gut, and in this study, Drennan and her colleagues used X-ray crystallography to analyze the structure of the version of HypD found in C. difficile. In 2011, this species of bacteria was responsible for about half a million infections and 29,000 deaths in the United States.

The researchers were able to determine which region of the protein forms the enzyme’s “active site,” which is where the reaction occurs. Once hydroxy-L-proline binds to the active site, a nearby glycine molecule forms a glycyl radical that can pass that radical onto the hydroxy-L-proline, leading to the elimination of the hydroxy group.

Removing a hydroxy group is usually a difficult reaction that requires a large input of energy.

“By transferring a radical to hydroxy-L-proline, it lowers the energetic barrier and allows for that reaction to occur pretty rapidly,” Backman says. “There’s no other known enzyme that can perform this kind of chemistry.”

New drug target

It appears that once bacteria perform this reaction, they divert proline into their own metabolic pathways to help them grow. Therefore, blocking this enzyme could slow down the bacteria’s growth. This could be an advantage in controlling C. difficile, which often exists in small numbers in the human gut but can cause illness if the population becomes too large. This sometimes occurs after antibiotic treatment that wipes out other species and allows C. difficile to proliferate.

“C. difficile can be in your gut without causing problems — it’s when you have too much of it compared to other bacteria that it becomes more problematic,” Drennan says. “So, the idea is that by targeting this enzyme, you could limit the resources of C. difficile, without necessarily killing it.”

The researchers now hope to begin designing drug candidates that could inhibit HypD, by targeting the elements of the protein structure that appear to be the most important in carrying out its function.

The research was funded by the National Institutes of Health, a National Science Foundation Graduate Research Fellowship, Harvard University, a Packard Fellowship for Science and Engineering, the NSERC Postgraduate Scholarship-Doctoral Program, an Arnold O. Beckman Postdoctoral Fellowship, a Dow Fellowship, and a Gilliam Fellowship from the Howard Hughes Medical Institute.

Chimeras offer a new way to study childhood cancer in mice
Eva Frederick | Whitehead Institute
March 5, 2020

In a new paper published March 5 in the journal Cell Stem Cell, researchers in Whitehead Institute Member Rudolf Jaenisch’s lab introduce a new way to model human neuroblastoma tumors in mice using chimeras — in this case, mice that have been modified to have human cells in parts of their nervous systems. “This may serve as a unique model that you can use to study the dynamic of immune cells within human tumors,” says Malkiel Cohen, a postdoc in Jaenisch’s lab and the first author of the paper.

Neuroblastoma is a rare and unpredictable form of childhood cancer that affects around 800 young children in the US each year. Neuroblastoma tumors often occur in parts of the sympathetic nervous system, which includes the nerves that run parallel to the spinal cord and the adrenal medulla, part of the glands that produce hormones such as adrenaline. Neuroblastoma is notoriously hard to study primarily because of its disparate behavior: the tumors often shrink spontaneously in infants, while in toddlers they are highly aggressive and often fatal. “The seeds for the cancer are sown during fetal life,” says Rani George, MD, PhD, an associate professor of pediatrics at Harvard Medical School and a neuroblastoma researcher and physician at Dana-Farber Cancer Institute and Boston Children’s Hospital, and a co-senior author on the paper. “For obvious reasons, you can’t really study the development of these tumors in humans.”

Until now, researchers didn’t have many realistic ways to study these tumors in animal models, either. They could create transgenic mice with cancer-causing genes, but the resulting tumors were mouse tumors, not human ones, and had some key differences. Another method involved taking human tumor cells and implanting them in a mouse — a process called xenotransplantation — but that only worked in mice with compromised immune systems, and didn’t allow researchers to study how the tumors formed in the first place or how they interacted with a fully functioning immune system. “This is where we think the new model is a perfect fit,” said Stefani Spranger, PhD, an assistant professor of Biology at the Massachusetts Institute of Technology (MIT) and the Koch Institute for Integrative Cancer Research at MIT and a co-senior author on the paper.

Human-mouse chimeras have been used in the past to study Alzheimer’s disease and brain development. Jaenisch, who is also a professor of biology at MIT, and his lab had been working for years to create chimeric mice with human cells in the neural crest — the group of developing cells that go on to form parts of the sympathetic nervous system — and published their findings in 2016. “In this study, we hoped to use these mice with human neural crest cells to study how neuroblastoma tumors form and respond to immune system attacks,” Jaenisch says.

To create these chimeric mice, Cohen and coauthors at MIT’s Koch Institute and the Dana-Farber Cancer Institute first engineered human pluripotent stem cells to express two genes known to be abnormal in neuroblastoma, MYCN and mutated ALK, and modified them so they became neural crest cells, from which human neuroblastomas are derived. The genes could be turned on and off with the addition of doxycycline, an antibiotic. They also inserted the gene for eGFP, a brightly glowing fluorescent protein originally isolated from jellyfish. This would allow the team to tell whether the cells were spreading correctly through the bodies of the mice, and would cause any tumors originating from these human cells to be luminous under fluorescent light.

The researchers injected mouse embryos with these cells, and watched over the course of embryonic development as the cells proliferated and human tissues crept into the developing peripheral nervous systems of the tiny mice. To activate the two cancer-causing genes, researchers spiked the pregnant mice’ water with doxycycline, and over the next few days in utero — and in the weeks and months after the pups were born — the researchers inspected the chimeras to see whether tumors would appear.

Over the course of the next 15 months, 14% of the mice developed tumors — 29 mice out of 198 total. The tumors mostly appeared in the space behind the abdominal cavity close to the nerves along the spinal cord, although one mouse developed a tumor in its adrenal gland. Both locations are common places for human children to develop neuroblastoma. The researchers took samples of the tumors and found that they contained the glowing protein eGFP, which confirmed that they were of human origin.

When the team examined the growth patterns of the cancerous cells, they found that the tumors were remarkably similar to human neuroblastomas: they contained cell markers typical of human tumors, and some grew in characteristic rosette shapes — features that did not often appear in tumors implanted in immunocompromised mice through xenotransplantation.

Having successfully induced neuroblastoma tumors in the chimeric mice, the researchers took the opportunity to examine the communication between immune cells and tumors — and specifically, how the tumors evaded destruction by anti-cancer immune cells called T cells. One factor that makes human neuroblastomas and many other cancers dangerous is their sophisticated strategy for avoiding being destroyed by T cells. “The cancer tricks the immune system,” Cohen says.  By activating chemical signals that exhaust the T cells, the tumors effectively weaken their attack. The tumors in the chimeric mice, Cohen found, use a similar method to human neuroblastomas to evade immune responses.

Cohen and others plan to test the new system’s potential for modeling other cancers such as melanoma, and to use it to investigate potential treatments for neuroblastoma patients. “The obvious next step is to study how treatment of these tumors will allow these chimeric mice to be cured,” he says. “This is a model that will allow us to approach not only how to get rid of the tumor, but also to fix the immune system and recover those exhausted T cells, allowing them to fight back and deplete the tumor.”

This research was funded by the National Institutes of Health, as well as grants from the Emerald Foundation, the LEO Foundation, the Melanoma Research Foundation, and the St. Baldrick’s Foundation.

Citation: Cohen, M., et al. Formation of Human Neuroblastoma in Mouse-Human Neural Crest Chimeras. Cell Stem Cell. March 5, 2020. DOI: https://doi.org/10.1016/j.stem.2020.02.001

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Written by Eva Frederick

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A force for health equity

Through on-site projects in developing countries and internships in the business world, Kendyll Hicks explores the political and economic drivers of global health.

Becky Ham | MIT News Office
March 1, 2020

After spending three weeks in Kenya working on water issues with Maasai women, Kendyll Hicks was ready to declare it her favorite among the international projects she’s participated in through MIT.

As a volunteer with the nonprofit Mama Maji, Hicks spoke about clean water, menstrual hygiene, and reproductive health with local women, sharing information that would enable them to become community leaders. “In rural Kenya, women are disproportionately affected by water issues,” she explains. “This is one way to give them a voice in societies that traditionally will silence them.”

The team also planned to build a rainwater harvesting tank, but climate change has transformed Kenya’s dry season into a rainy one, and it was too wet to break ground for the project. During her stay, Hicks lived in the home of the first female chief of the Masaai, Beatrice Kosiom, whom Hicks describes as “simultaneously a political animal and the most down-to-earth-person.” It was this close contact with the community that made the project especially fulfilling.

During MIT’s Independent Activities Period, Hicks also has traveled to South Africa to learn more about the cultural and biological determinants of that country’s HIV/AIDS epidemic, and to Colombia to lead an entrepreneurial initiative among small-scale coffee farmers. Hicks joined the Kenya trip after taking an MIT D-Lab class on water, sanitation, and hygiene. Each experience has been successively more hands-on, she says.

“I’ve been drawn to these experiences mainly because I love school, and I love the classroom experience,” Hicks says. “But it just can’t compare to living with people and understanding their way of life and the issues they face every day.”

Hicks, a senior majoring in computer science and molecular biology, says she has shifted her focus during her time at MIT from more incremental technical discoveries to addressing larger forces that affect how those discoveries contribute — or fail to contribute — to global health.

Her love of biology began with animals and zoology, later expanding into an interest in medicine. “Humans are these amazing machines that have been crafted by nature and evolution, and we have all these intricacies and mechanisms that I knew I wanted to study further,” Hicks says.

At the same time, she says, “I’ve always been interested in health care and medicine, and the main impetus behind that is the fact that when someone you love is sick, or if you’re sick, you’ll do whatever you can.”

As a first-year student she worked in the Lippard Lab at MIT, helping to synthesize and test anticancer compounds, but she soon decided that lab work wasn’t the right path for her. “I made the realization that health care and medicine are extremely political,” she recalls. “Health policy, health economics, law — those can be the drivers of real large-scale change.”

To learn more about those drivers, Hicks has worked two summers at the management consulting firm McKinsey and Company, and will take a full-time position with the company after graduation.

“As someone immersed in the world of science and math and tech, I had this lingering insecurity that I didn’t know that much about this entirely different but super-important area,” she says. “I thought it would be important to understand what motivates business and the private sector, since that can have a huge effect on health care and helping communities that are often disenfranchised.”

Hicks wants to steer her work at McKinsey toward their health care and hospital sector, as well as their growing global health sector. Over the long term, she is also interested in continuing fieldwork that involves science, poverty eradication, and international development.

“Being at MIT, it’s like this hub of tech, trying to venture further into novel breakthroughs and innovations, and I think it’s amazing,” Hicks says. “But as I have started to garner more of an interest in politics and economics and the highly socialized aspects of science, I would say it’s important to take a pause before venturing further and deeper into that realm, to make sure that you truly understand the downstream effects of what you are developing.”

“Those effects can be negative,” she adds, “and they oftentimes impact communities that already are systematically and institutionally oppressed.”

Hicks joined MIT’s Black Students Union as a first-year student and now serves as the BSU Social and Cultural Co-Chair. In the role, she is responsible for planning the annual Ebony Affair fly-in program, which brings more than 30 black high school students to campus each year to participate in workshops, tour labs, and join a gala celebration with BSU students, faculty, and staff. “We’re doing our best as a community to convince young bright black minds to come to a place like MIT,” she says.

It worked for Hicks: She participated in Ebony Affair as a high schooler, and the experience cemented her decision to attend. “When I saw everyone showing out and having such pride in being black and being at MIT, I was like, ‘OK, I want to be a part of that,’” she recalls.

Last year, Hicks planned BSU’s first Black Homecoming event, a barbecue that brought together current and former black MIT students — some who attended the school 50 years ago. The event was a celebration of support and a way to strengthen the BSU network. “You have to do what you can to cultivate communities wherever you are, and that’s what I’ve tried to do here at MIT,” she says.

Hicks also served as the Black Women’s Alliance alumni relations chair and GlobeMed’s campaigns co-director, and was on the Undergraduate Association Diversity and Inclusion Committee. She has discovered a love of event organizing and leadership at MIT, although it has been a change of pace from her former shy, “hyper-bookworm” self, she says.

“I have realized that in my career that I really want to do a lot of good and affect a lot of change in people’s lives, and in order to do that, you kind of have to be this way.”

New pathway for lung cancer treatment

MIT researchers identify pyrimidine biosynthesis as a target for the treatment of small cell lung cancer.

Bendta Schroeder | Koch Institute
November 11, 2019

MIT cancer biologists have identified a new therapeutic target for small cell lung cancer, an especially aggressive form of lung cancer with limited options for treatment.

Lung cancer is the leading cause of cancer-associated mortality in the United States and worldwide, with a five-year survival rate of less than 20 percent. But of the two major sub-types of lung cancer, small cell and non-small cell, small cell is more aggressive and has a much poorer prognosis. Small cell lung cancer tumors grow quickly and metastasize early, resulting in a five-year survival rate of about 6 percent.

“Unfortunately, we haven’t seen the same kinds of new treatments for small cell lung cancer as we have for other lung tumors,” says Tyler Jacks, director of the Koch Institute for Integrative Cancer Research at MIT. “In fact, patients are treated today more or less the same way they were treated 40 or 50 years ago, so clearly there is a great need for the development of new treatments.”

A study appearing in the Nov. 6 issue of Science Translational Medicine shows that small cell lung cancer cells are especially reliant on the pyrimidine biosynthesis pathway and that an enzyme inhibitor called brequinar is effective against the disease in cell lines and mouse models.

Jacks is the senior author of this study. Other MIT researchers include Associate Professor of Biology and Koch Institute member Matthew Vander Heiden, and co-lead authors postdoc researcher Leanne Li and graduate student Sheng Rong Ng.

Roadblock for cell replication

Researchers in the Jacks lab used CRISPR to screen small cell lung cancer cell lines for genes that already have drugs targeting them, or that are likely to be druggable, in order to find therapeutic targets that can be tested more quickly and easily in a clinical setting.

The group found that small cell lung cancer tumors are particularly sensitive to the loss of a gene encoding dihydroorotate dehydrogenase (DHODH), a key enzyme in the de novo pyrimidine biosynthesis pathway. Upon discovering that the sensitivity involved a metabolic pathway, the researchers sought the collaboration of the Vander Heiden lab, experts in normal and cancer cell metabolism who were already conducting studies on the role of pyrimidine metabolism and DHODH inhibitors in other cancers.

Pyrimidine is one of the major building blocks of DNA and RNA. Unlike healthy cells, cancer cells are constantly dividing and need to synthesize new DNA and RNA to support the production of new cells. The investigators found that small cell lung cancer cells have an unexpected vulnerability: Despite their dependence on the availability of pyrimidine, this synthesis pathway is much less active in small cell lung cancer cells than in other types of cancer cells examined in the study. Through inhibiting DHODH, they found that small cell lung cancer cells were not able to produce enough pyrimidine to keep up with demand.

When researchers treated a genetically engineered mouse model of small cell lung cancer tumors with the DHODH inhibitor brequinar, tumor progression slowed down and the mice survived longer than untreated mice. Similar results were observed for small cell lung cancer tumors in the liver, a frequent site of metastasis in patients.

In addition to mouse model studies, the researchers tested four patient-derived small cell lung cancer tumor models and found that brequinar worked well for two of these models — one of which does not respond to the standard platinum-etoposide regimen for this disease.

“These findings are noteworthy because second-line treatment options are very limited for patients whose cancers no longer respond to the initial treatment, and we think that this could potentially represent a new option for these patients,” says Ng.

Shorter pathway to the clinic

Brequinar has already been approved for use in patients as an immunosuppressant, and there has been some preclinical research showing that brequinar and other DHODH inhibitors may be effective for other types of cancers.

“We’re excited because our findings could provide a new way to help small cell lung cancer patients in the future,” says Li. “While we still have a lot of work to do before brequinar can be tested in the clinic as a therapy for small cell lung cancer, we’re hopeful that this might happen more quickly now that we’re starting with a drug that is known to be safe in humans.”

Next steps for the researchers include optimizing the therapeutic efficacy of DHODH inhibitors and combining them with other currently available treatment options for small cell lung cancer, such as chemotherapy and immunotherapy. To help clinicians tailor treatments to individual patients, researchers will also work to identify biomarkers for tumors that are susceptible to this therapy, and investigate resistance mechanisms in tumors that do not respond to this treatment.

The research was funded, in part, by the MIT Center for Precision Cancer Medicine and the Ludwig Center for Molecular Oncology at MIT.

Researchers discover new source of drug resistance in pancreatic cancer
Lucy Jackub
October 17, 2019

The best available treatments for pancreatic cancer are highly toxic, and, as chemotherapies go, not very effective. The drug gemcitabine has been used for decades to extend the life of patients, but very high doses are required to combat the tumor, which grows in the pancreas surrounded by stiff, fibrous, noncancerous tissue called stroma. This hallmark of pancreatic cancer makes it unusually difficult to treat: the more stromal tissue accumulates, the less the drug works, while patients still endure brutal side effects. Only 8.5 percent of pancreatic cancer patients survive five years beyond their diagnosis, so there’s an urgent need to figure out why existing treatments are failing.

Scientists have known for a long time that gemcitabine fights cancer by killing cells during replication, though why it works for pancreatic cancer in particular is a bit of a mystery. The drug is a small molecule that masquerades as the nucleoside deoxycytidine, one unit in the nucleic acids that make up DNA. Once gemcitabine is integrated into a replicating strand of DNA, additional nucleosides can’t be joined to it. The new DNA strand can’t be completed, and the cell dies. Now, researchers from MIT have discovered that non-cancer cells in the pancreatic stromal tissue secrete astonishing quantities of deoxycytidine. They found that competition with deoxycytidine makes its imposter, gemcitabine, less effective, explaining why higher doses of the drug are needed as more stromal tissue grows around the tumor.

“That was an answer we were looking for — what is making pancreatic tumors resistant to gemcitabine?” says Michael Hemann, associate professor of biology, a member of MIT’s Koch Institute for Integrative Cancer Research, and co-senior author of the study. “Understanding the basic mechanisms of these drugs allows us to return to the clinic with improved strategies to treat patients with cancer.”

Douglas Lauffenburger, a professor of biological engineering, is also a co-senior author of the study, which represents a collaboration between the Hemann lab, the Lauffenburger lab, and the Vander Heiden lab, and appeared online in Cancer Research on September 4. Hemann lab graduate student Simona Dalin is the lead author.

The mystery ingredient

For years, researchers at MIT have been investigating different sources of chemotherapy resistance in stromal tissue. When Dalin took up the study two years ago, she was building on the findings of a former postdoc in the Hemann lab, Emanuel Kreidl. Kreidl had found that stellate cells, one type of cell in the pancreatic stromal tissue surrounding the tumor, were releasing something into the microenvironment of the pancreas that disrupted the function of gemcitabine.

Cells secrete all sorts of things — micro RNAs, fatty acids, proteins — that may be taken up and used by neighboring cells. Biologists call these ambient materials around the cell its “media.”  Kreidl had tried boiling, digesting, and filtering the stellate cell media, but nothing he did made gemcitabine any more effective against the cancer cells. The usual suspects commonly implicated in drug resistance caused by neighboring cells, like proteins, would break down under such tests. “That’s when we knew there was something new here,” says Dalin. Her challenge was to figure out what that mystery ingredient was.

Mark Sullivan PhD ‘19, then a graduate student and biochemist in Vander Heiden lab, was enlisted to help separate the stellate cell media into its molecular components and identify them. After doing so, Dalin says, “it was fairly obvious that deoxycytidine was the thing that we were looking for.” Because gemcitabine works by taking deoxycytidine’s place in DNA replication, it made sense that the presence of a lot of deoxycytidine could make it difficult for gemcitabine to fulfill its function.

Molecules pass in and out of cells through gates in the cell membrane, called transporters. Using a drug that blocks certain transporters, Dalin was able to shut the gate in the stellate cells through which deoxycytidine is released. With less deoxycytidine around, the gemcitabine was effective at lower doses, confirming her hypothesis. Now, the researchers just needed to figure out how and where deoxycytidine was getting in the way of the drug.

Once inside the cell, a nucleoside must have one or more phosphate groups added to it by several enzymes in order to become a nucleotide that can be used to build DNA. Gemcitabine goes through the same process. The researchers determined that gemcitabine was competing with deoxycytidine for the first of those enzymes, deoxycytidine kinase. When they flooded the cell with that enzyme, gemcitabine didn’t have to wait in line for its phosphate groups — and could get into the DNA to work its fatal subterfuge.

Upending Assumptions

Going forward, the Hemann lab aims to identify drugs that could inhibit the production of deoxycytidine and restore the tumor’s sensitivity to gemcitabine. Senthil Muthuswamy, an associate professor of medicine at Beth Israel Deaconess Medical Center who was not involved in the research, says this study provides “new and important insights” into how and why tumors develop resistance to gemcitabine. The findings, he adds, are “likely to have important implications for developing ways to overcome gemcitabine resistance in pancreatic cancer.”

The study’s findings may shed light on other cancer treatments that work similarly to gemcitabine. For every nucleoside, there are look-alike molecules, or analogs, that are used in cancer therapies. For example, the purine analog fludarabine is used to treat acute myeloid leukemia, another tenacious carcinoma. These generic drugs have been adopted through trial and error in the clinic, but scientists don’t fully understand why they are effective at the molecular level.

In theory, nucleoside analog drugs should work interchangeably; every nucleoside is necessary in either the replication of DNA or RNA. In practice, though, these drugs are only effective for certain cancers. The MIT researchers speculate that the sheer amount of deoxycytidine being produced in the pancreas could suggest that pancreatic cells have a particular need for deoxycytidine that also makes them more responsive to its analogs — perhaps explaining why gemcitabine targets pancreatic cancer cells effectively.

“Understanding more about nucleoside biology, and more about which organs have high levels of which nucleosides, might help us understand when to use which chemotherapies,” Dalin says.

This study leaves the researchers with many questions about how and why nucleosides are produced in the body, a realm of basic biology that is still poorly understood. It’s generally assumed that cells only make nucleosides for their own internal use in DNA replication. But pancreatic stellate cells produce a lot of deoxycytidine, far more than they need for themselves, suggesting the excess nucleosides may serve some unknown purpose in neighboring cells. Although more experiments are needed to determine this mysterious purpose, the MIT researchers have some ideas.

“These extra nucleosides introduce a possibility that perhaps making deoxycytidine is a normal function of stellate cells in the pancreas, in order to provide building blocks for the cells around them,” says Hemann. “And that’s a real surprise.”

This work was funded in part by a David H. Koch Fellowship and the MIT Center for Precision Cancer Medicine.

Image: Deoxycytidine and gemcitabine, its look-alike molecule, enter a cancer cell through the same gate in the cell membrane and are altered by the same enzyme (dCK) before they are integrated into DNA. Credit: Courtesy of the researchers.

Citation:
“Deoxycytidine Release from Pancreatic Stellate Cells Promotes Gemcitabine Resistance.”
Cancer Research, online Sept. 4, 2019, DOI: 10.1158/0008-5472.CAN-19-0960.
Dalin, S., Sullivan, M.R., Lau, A.N., Grauman-Boss, B., Mueller, H.S., Kreidl, E., Fenoglio, S., Luengo, A., Lees, J.A., Vander Heiden, M.G. and Lauffenburger, D.A.

Study links certain metabolites to stem cell function in the intestine

Molecules called ketone bodies may improve stem cells’ ability to regenerate new intestinal tissue.

Anne Trafton | MIT News Office
August 22, 2019

MIT biologists have discovered an unexpected effect of a ketogenic, or fat-rich, diet: They showed that high levels of ketone bodies, molecules produced by the breakdown of fat, help the intestine to maintain a large pool of adult stem cells, which are crucial for keeping the intestinal lining healthy.

The researchers also found that intestinal stem cells produce unusually high levels of ketone bodies even in the absence of a high-fat diet. These ketone bodies activate a well-known signaling pathway called Notch, which has previously been shown to help regulate stem cell differentiation.

“Ketone bodies are one of the first examples of how a metabolite instructs stem cell fate in the intestine,” says Omer Yilmaz, the Eisen and Chang Career Development Associate Professor of Biology and a member of MIT’s Koch Institute for Integrative Cancer Research. “These ketone bodies, which are normally thought to play a critical role in energy maintenance during times of nutritional stress, engage the Notch pathway to enhance stem cell function. Changes in ketone body levels in different nutritional states or diets enable stem cells to adapt to different physiologies.”

In a study of mice, the researchers found that a ketogenic diet gave intestinal stem cells a regenerative boost that made them better able to recover from damage to the intestinal lining, compared to the stem cells of mice on a regular diet.

Yilmaz is the senior author of the study, which appears in the Aug. 22 issue of Cell. MIT postdoc Chia-Wei Cheng is the paper’s lead author.

An unexpected role

Adult stem cells, which can differentiate into many different cell types, are found in tissues throughout the body. These stem cells are particularly important in the intestine because the intestinal lining is replaced every few days. Yilmaz’ lab has previously shown that fasting enhances stem cell function in aged mice, and that a high-fat diet can stimulate rapid growth of stem cell populations in the intestine.

In this study, the research team wanted to study the possible role of metabolism in the function of intestinal stem cells. By analyzing gene expression data, Cheng discovered that several enzymes involved in the production of ketone bodies are more abundant in intestinal stem cells than in other types of cells.

When a very high-fat diet is consumed, cells use these enzymes to break down fat into ketone bodies, which the body can use for fuel in the absence of carbohydrates. However, because these enzymes are so active in intestinal stem cells, these cells have unusually high ketone body levels even when a normal diet is consumed.

To their surprise, the researchers found that the ketones stimulate the Notch signaling pathway, which is known to be critical for regulating stem cell functions such as regenerating damaged tissue.

“Intestinal stem cells can generate ketone bodies by themselves, and use them to sustain their own stemness through fine-tuning a hardwired developmental pathway that controls cell lineage and fate,” Cheng says.

In mice, the researchers showed that a ketogenic diet enhanced this effect, and mice on such a diet were better able to regenerate new intestinal tissue. When the researchers fed the mice a high-sugar diet, they saw the opposite effect: Ketone production and stem cell function both declined.

Stem cell function

The study helps to answer some questions raised by Yilmaz’ previous work showing that both fasting and high-fat diets enhance intestinal stem cell function. The new findings suggest that stimulating ketogenesis through any kind of diet that limits carbohydrate intake helps promote stem cell proliferation.

“Ketone bodies become highly induced in the intestine during periods of food deprivation and play an important role in the process of preserving and enhancing stem cell activity,” Yilmaz says. “When food isn’t readily available, it might be that the intestine needs to preserve stem cell function so that when nutrients become replete, you have a pool of very active stem cells that can go on to repopulate the cells of the intestine.”

The findings suggest that a ketogenic diet, which would drive ketone body production in the intestine, might be helpful for repairing damage to the intestinal lining, which can occur in cancer patients receiving radiation or chemotherapy treatments, Yilmaz says.

The researchers now plan to study whether adult stem cells in other types of tissue use ketone bodies to regulate their function. Another key question is whether ketone-induced stem cell activity could be linked to cancer development, because there is evidence that some tumors in the intestines and other tissues arise from stem cells.

“If an intervention drives stem cell proliferation, a population of cells that serve as the origin of some tumors, could such an intervention possibly elevate cancer risk? That’s something we want to understand,” Yilmaz says. “What role do these ketone bodies play in the early steps of tumor formation, and can driving this pathway too much, either through diet or small molecule mimetics, impact cancer formation? We just don’t know the answer to those questions.”

The research was funded by the National Institutes of Health, a V Foundation V Scholar Award, a Sidney Kimmel Scholar Award, a Pew-Stewart Trust Scholar Award, the MIT Stem Cell Initiative, the Koch Institute Frontier Research Program through the Kathy and Curt Marble Cancer Research Fund, the Koch Institute Dana Farber/Harvard Cancer Center Bridge Project, and the American Federation of Aging Research.