Cancer Biology Archives - Page 9 of 13 - MIT Department of Biology

A new study linking RNA processing to DNA repair may open new avenues to cancer therapy.

Bendta Schroeder | Koch Institute

December 3, 2018

Mutations in the BRCA1 and BRCA2 genes pose a serious risk for breast and ovarian cancer because they endanger the genomic stability of a cell by interfering with homologous recombination repair (HR), a key mechanism for accurately repairing harmful double-stranded breaks in DNA. Without the ability to use HR to fix double-stranded breaks, the cell is forced to resort to more error-prone — and thus more cancer-prone — forms of DNA repair.

The BRCA1 and BRCA2 genes are not the only genes whose mutations foster tumorigenesis by causing an inability to repair DNA double strand breaks by HR. Mutations in twenty-two genes are known to disrupt HR, giving rise to tumors with what researchers call “BRCAness” characteristics. All but one of these BRCAness genes are known to be directly involved in the HR pathway.

The one exception, CDK12, is thought to facilitate a set of different processes altogether, involving how RNA transcripts are elongated, spliced and cleaved into their mature forms. While the connection between this RNA-modulating gene to DNA repair remained poorly understood, the identification of CDK12 as a BRCAness gene piqued significant clinical interest.

The researchers who pinpointed this connection, Sara Dubbury and Paul Boutz, both work in the laboratory of Phillip Sharp, Institute Professor, professor of biology, and member of the Koch Institute for Integrative Cancer Research. In a study appearing online in Nature on Nov. 28, they describe how they discovered a previously unknown mechanism by which CDK12 enables the production of full-length RNA transcripts and that this mechanism was especially critical to maintain functional expression of the other BRCAness genes.

When the researchers knocked out expression of CDK12, mouse stem cells showed many signs of accumulating DNA damage that prevented DNA replication from going forward, classic indications of a BRCAness phenotype. To identify what roles CDK12 may play in regulating gene expression, the researchers turned to RNA sequencing to determine which genes had increased or decreased their overall expression.

To their surprise, only genes activated by p53 and early differentiation (side effects of accumulating unrepaired DNA damage and BRCAness in mouse stem cells) accounted for the lion’s share of changes to RNA transcription. However, when the researchers instead focused on the types of RNAs transcribed, they found that many genes produced unusually short transcripts when CDK12 was absent.

Not every stretch of DNA in a gene makes it into the final RNA transcript. The initial RNA from a gene often includes sections, which researchers call “introns,” that are cut out of transcript, the discovery that earned Sharp the 1993 Nobel Prize in Physiology or Medicine and the remaining sections. “Exons,” are spliced together to form a mature transcript (mRNA). Alternately, an intronic polyadenylation (IPA) site may be activated to cleave away the RNA sequence that follows it preventing intron removal and generating a prematurely shortened transcript. These processes allow the same gene to produce alternate forms of messenger RNA (mRNA), and thus be translated into different protein sequences.

Surprisingly CDK12 knockout cells produced significantly more IPA-truncated transcripts genome-wide, while full-length transcripts for the same genes were reduced. These shortened mRNAs can vary greatly in their stability, their ability to be translated into protein, and their protein function. Thus, even while a gene may be actively transcribed, its translation into functional proteins can be radically altered or depleted by IPA activation.

While this observation began to illuminate CDK12’s role in regulating mRNA processing, what remained puzzling was why CDK12 loss affected the HR pathway so disproportionately. In investigating this question, Dubbury and Boutz found that BRCAness genes were overrepresented as a group among those genes that have increased IPA activity upon CDK12 loss.

Additionally, while CDK12 suppresses IPA activity genome-wide, 13 of the other 21 BRCAness genes were found to be particularly vulnerable to CDK12 loss, in part, because they possess multiple high-sensitivity IPA sites, which have a compound effect in decreasing the total amount of full-length transcripts. Moreover, because multiple CDK12-senstive BRCAness genes operate in the same HR pathway, the researchers believe that the disruption to HR repair of double-stranded DNA breaks is amplified.

CDK12 mutations are found recurrently in prostate and ovarian cancer patients, making them an attractive diagnostic and therapeutic target for cancer. However, not enough is known about CDK12 to distinguish between true loss-of-function mutations and so-called “passenger mutations” with no functional consequence.

“The ability to identify patients with true loss-of-function mutations in CDK12 would enable clinicians to label a new cohort of patients with bona fide BRCAness tumors that could benefit from certain highly effective and targeted chemotherapeutics against BRCAness, such as PARP1 inhibitors,” says Dubbury, a former David H. Koch Fellow.

Dubbury and Boutz were able to confirm that IPA sites in key BRCAness genes were also used more frequently upon CDK12 loss in human tumor cells using RNA sequencing data from prostate and ovarian tumor patients with CDK12 mutations and by treating human prostate adenocarcinoma and ovarian carcinoma cells with a CDK12 inhibitor. This result suggests that the CDK12 mechanism observed in mouse cell lines is conserved in humans and that CDK12 mutations in human ovarian and prostate tumors may promote tumorigenesis by increasing IPA activity and thus functionally attenuating HR repair.

“These results not only give us a better understanding how CDK12 contributes to BRCAness, they also may have exciting potential impact in the clinic,” Dubbury says. “Currently available diagnostic techniques could be used to probe the usage of IPA sites found in this study to rapidly screen for patients with true loss-of-function CDK12 mutations, who would respond to BRCAness-targeted treatments.”

Paul Boutz, a research scientist in the Sharp Lab, is co-first author of the study, and has plans to follow-up many of these implications for ovarian and prostate cancer his lab at the University of Rochester School of Medicine and Dentistry.

“CDK12 provides a remarkable example of how factors that control the processing of RNA molecules can function as master regulators of gene networks, and thereby profoundly affect the physiology of both normal and cancerous cells,” he says.

Phil Sharp, the senior author on the work, says “Sara’s and Paul’s surprising discovery that CDK12 suppresses intronic polyadenylation has implications for fundamental new insights into gene structure as well as for control of cancer.”

Matthew Vander Heiden seeks new cancer treatments that exploit tumor cells’ abnormal metabolism.

Anne Trafton | MIT News Office

August 28, 2018

Nearly 100 years ago, the German chemist Otto Warburg discovered that cancer cells metabolize nutrients differently than most normal cells. His discovery launched the field of cancer metabolism research, but interest in this area waned; by the 1970s most cancer scientists had shifted their focus to the genetic mutations that drive cancer development.

In the past decade or so, interest in cancer metabolism has resurged, and the first drugs that target cancer cells’ abnormal metabolism were approved to treat leukemia in 2017.

“Cancer metabolism is a very sophisticated field at this point,” says Matthew Vander Heiden, an associate professor of biology at MIT. “We have a lot better understanding of what nutrients cancer cells use and what determines how those nutrients are used. This has led to different ways to think about drugs.”

Vander Heiden, who is also a member of MIT’s Koch Institute for Integrative Cancer Research, is one of the people responsible for the recent surge in cancer metabolism research. As a graduate student and postdoc, he published some of the first studies of how cancer cells alter their metabolism, and now his lab at MIT is devoted to the topic.

“All of the time that I was in grad school and working as a postdoc, I was never working in a lab that was dedicated to studying metabolism. So my vision, if someone gave me a job, was to set up a lab that could really be built in a way that would allow us to ask questions about metabolism,” he says.

Metabolism and cancer

Vander Heiden grew up in a small town in Wisconsin, and unlike most of his high school classmates, he headed out of state for college, to the University of Chicago. He was interested in science, so decided on a pre-med track. A work-study job in a plant biology lab led him to discover that he also enjoyed doing research.

“At that point I already had this idea I was going to go to medical school, but then the idea of MD/PhD came up, and I ended up going down that path,” Vander Heiden says.

While in the MD/PhD program at the University of Chicago Medical School, he worked in the lab of Craig Thompson, now president of Memorial Sloan Kettering Cancer Center. At that time, Thompson was studying the biochemical regulation of apoptosis, the programmed cell death pathway. For his PhD thesis, Vander Heiden investigated the function of a protein called Bcl-x, which is a regulator of apoptosis found in the membranes of mitochondria — cell organelles responsible for generating energy.

“That project really got me thinking about how the mitochondria work and how metabolism works,” Vander Heiden recalls. “At the time, I came to the realization that we don’t understand cell metabolism anywhere near as well as we thought we did, and someone should really study this.”

After finishing his degrees, he spent five years doing clinical training, then decided to pursue research in cancer metabolism.

“Altered metabolism has been known about in cancer for 100 years, but few people were studying it,” Vander Heiden says. “The challenge was finding a lab that would allow me to study metabolism and cancer, which in 2004-2005 was not such an obvious thing to do.”

He ended up going to Harvard Medical School to work with Lewis Cantley, who studies signaling pathways in cells and was receptive to the idea of exploring cancer metabolism. There, Vander Heiden began studying an enzyme called pyruvate kinase M2 (PKM2), which is involved in regulation of glycolysis, a biochemical process that cells use to break down sugar for energy.

In 2008, Vander Heiden, Cantley, and others at Harvard Medical School reported that when cells shift between normal and Warburg (cancer-associated) metabolism, they start using PKM2 instead of PKM1, the enzyme that adult cells normally use for glycolysis. Cantley and Craig Thompson have since founded a company, Agios Pharmaceuticals, that is developing potential drugs that target PKM2, as well as other molecules involved in cancer metabolism.

While at Harvard, Vander Heiden also worked on a paper that contributed to the eventual development of drugs that target cancer cells with a mutation in the IDH gene. These drugs, the first modern FDA-approved cancer drugs that target metabolism, shut off an alternative pathway used by cancer cells with the IDH mutation.

New drug targets

In 2010, Vander Heiden became one of the first new faculty members hired after the creation of MIT’s Koch Institute, where he set up a lab focused on metabolism, particularly cancer metabolism.

His research has yielded many insights into the abnormal metabolism of cancer cells. In one study, together with other MIT researchers, he found that tumor cells turn on an alternative pathway that allows them to build lipids from the amino acid glutamine instead of the glucose that healthy cells normally use. He also found that altering the behavior of PKM2 to make it act more like PKM1 could stop tumor cell growth.

Studies such as these can offer insights that may help researchers to develop drugs that starve tumor cells of the nutrients they need, offering a new way to fight cancer, Vander Heiden says.

“If one wants to develop drugs that target metabolism, one really needs to focus on the context in which it’s happening, which is the environment of the cell plus the genetics of the cell,” he says. “That is what defines the sensitivity to drugs.”

Aviv Regev helped pioneer single-cell genomics. Now she’s cochairing a massive effort to map the trillions of cells in the human body. Biology will never be the same.

Sam Apple | MIT Technology Review

August 23, 2018

Last October, Aviv Regev spoke to a gathering of international scientists at Israel’s Weizmann Institute of Science. For Regev, a computational and systems biologist at the Broad Institute of MIT and Harvard, the gathering was also a homecoming of sorts. Regev earned her PhD from nearby Tel Aviv University in 2002. Now, 15 years later, she was back to discuss one of the most ambitious projects in the history of biology.

The project, the Human Cell Atlas, aims to create a reference map that categorizes all the approximately 37 trillion cells that make up a human. The Human Cell Atlas is often compared to the Human Genome Project, the monumental scientific collaboration that gave us a complete readout of human DNA, or what might be considered the unabridged cookbook for human life. In a sense, the atlas is a continuation of that project’s work. But while the same DNA cookbook is found in every cell, each cell type reads only some of the recipes—that is, it expresses only certain genes, following their DNA instructions to produce the proteins that carry out a cell’s activities. The promise of the Human Cell Atlas is to reveal which specific genes are expressed in every cell type, and where the cells expressing those genes can be found.

Speaking to her colleagues at the meeting in Israel, Regev, who is cochairing the Human Cell Atlas Organizing Committee with Sarah Teichmann of the Wellcome Trust Sanger Institute, displayed the no-nonsense demeanor you might expect of someone at the helm of a massive scientific undertaking. The project had been under way for a year, and Regev, an MIT biology professor who is also chair of the faculty of the Broad and director of its Klarman Cell Observatory and Cell Circuits Program, was reviewing a newly published white paper detailing how the Human Cell Atlas is expected to change the way we diagnose, monitor, and treat disease.

As Regev made her way through the white paper, the possibilities began to seem almost endless. At the most basic level, as a reference map detailing the genes expressed by each different type of healthy cell, the Human Cell Atlas will make it easier to identify how gene expression and signaling go awry in the case of disease. The same map could also help drug developers avoid toxic side effects: researchers targeting a gene that’s harmful in one part of the body would know if the same gene is playing a vital role in another. And because the atlas is expected to reveal many new types of cells, it could also add much more sensitivity to a type of standard blood test, which simply counts different subsets of immune cells. Likewise, looking at individual intestinal cells might provide new insights into the specific cells responsible for inflammation and food allergies. And a better understanding of types of neurons could have far-reaching implications for brain science.

The final product, Regev says, will amount to nothing less than a “periodic table of our cells,” a tool that is designed not to answer one specific question but to make countless new discoveries possible. Eric Lander, the founding director and president of the Broad Institute and a member of the Human Cell Atlas Organizing Committee, likens it to genomics. “People thought at the beginning they might use genomics for this application or that application,” he says. “Nothing has failed to be transformed by genomics, and nothing will fail to be transformed by having a cell atlas.”

Cellular circuits

Regev’s interest in cells began at Tel Aviv University, where she was one of just 15 or so entering students in a highly selective program that gave them the freedom to take high-level courses in any subject. “You could go your first day as a freshman and decide to take a graduate class in political science,” she says.

Regev took a genetics class her first semester and got hooked on the computational challenge of finding order in the complex, interconnected networks of proteins and genes within each cell. She pursued that topic for her doctoral work, characterizing living systems in a mathematical language that had been designed to describe computer processes. As she finished her doctorate in 2002, she was accepted into a program at Harvard’s Bauer Center for Genomics Research that allowed her to start her own lab without first training as a postdoc.

Not long after, Lander, who’d begun his own career as a mathematician after studying algebraic coding theory and combinatorial mathematics at Oxford, was searching for star talent for the newly created Broad Institute, whose mission is to use genomics to study human disease and help advance its treatment. He first met Regev at a lunch at the Bauer Center during which the fellows took turns speaking about their research for five to 10 minutes. “By the time we got all the way around the table I had written down ‘Hire Aviv Regev,’” he recalls.

Convinced by Lander to join the Broad after “many cups of tea” at Cafe Algiers in Harvard Square, Regev continued to apply computational approaches to study the mind-bogglingly complicated machinery of the cell. A single cell is made up of millions of molecules that are in constant conversation as they work together to do all the things cells need to do: divide, grow, repair internal damage, and, in the case of immune cells, signal other cells about threats. Inside the nucleus, the DNA is transcribed into RNA. That in turn gives rise to proteins, the molecules that do the work inside a cell. Meanwhile, proteins on the surface of the cell are constantly receiving molecular messages from outside—glucose is available, an invader has arrived. These must be relayed back to proteins in the nucleus, which will respond by transcribing other DNA, giving rise to new proteins and still more signaling networks.

“It’s like a complex computer that is made of these many, many different parts that are interacting with each other and telling each other what to do,” says Regev. The protein signaling networks are like “circuits”—and you can think about the cell “almost like a wiring diagram,” she says. But using computational approaches to understand their activity first requires gathering an enormous amount of data, which Regev has long done through RNA sequencing. Unlike DNA sequencing, she says, it can tell her which genes are actually being expressed, so it offers a far more dynamic picture of a cell in action. But simply sequencing the RNA of the cells she’s studying can tell her only so much. To understand how the circuits change under different circumstances, Regev subjects cells to different stimuli, such as hormones or pathogens, to see how the resulting protein signals change.

Next comes what she calls “the modeling step”—creating algorithms that try to decipher the most likely sequence of molecular events following a stimulus. And just as someone might study a computer by cutting out circuits and seeing how that changes the machine’s operation, Regev tests her model by seeing if it can predict what will happen when she silences specific genes and then exposes the cells to the same stimulus.

In a 2009 study, Regev and her team examined how exposure to molecular components of pathogens like bacteria, viruses, or fungi affected the circuitry of the immune system’s dendritic cells. She turned to a technique known as RNA interference (she now uses CRISPR), which allowed her to systematically shut genes down. Then she looked at which genes were expressed to determine how the cells’ response changed in each case. Her team singled out 100 different genes that were involved in regulating the response to the pathogens—some of which weren’t previously known to be involved in immune function. The study, published in Science, generated headlines. But according to longtime colleague Dana Pe’er, now chair of computational and systems biology at the Sloan Kettering Institute at the Memorial Sloan Kettering Cancer Center and a member of the Human Cell Atlas Organizing Committee, what really sets Regev apart is the elegance of her work. Regev, says Pe’er, “has a rare, innate ability of seeing complex biology and simplifying it and formalizing it into beautiful, abstract, describable principles.”

From smoothies to fruit salad

There are lots of empty coffee mugs in Regev’s office at the Broad Institute, but very little in the way of decoration. She approaches her science with a businesslike efficiency. “There are many brilliant people,” says Lander. “She’s a brilliant person who can get things done.”

In the fast-changing arena of genomics (“2015 in my field is considered ancient history,” she says), she is known for making the most of the latest innovations—and for helping to spur the next ones. For years, she and others in the field struggled with a dirty secret of RNA sequencing: though its promise has always been precision—the power of knowing the exact code—the techniques produced results that were unspecific. Every cell has only a minuscule amount of RNA. For sequencing purposes, the RNA from millions of cells had to be pooled together. Bulk RNA sequencing left researchers with what she likens to a smoothie. Once it’s blended together, there’s no way to distinguish all the fruits—or in this case, the RNA from individual cells—that went into it. What researchers needed was something more like a fruit salad, a way to separate all the blueberries, raspberries, and blackberries.

In 2011, working with Broad Institute colleague Joshua Levin, PhD ’92, and postdocs Alex Shalek, now at MIT’s Institute for Medical Engineering and Science, and Rahul Satija, now at the New York Genome Center, Regev managed to obtain enough RNA from a single cell to sequence it. To test the method, they sequenced 18 individual dendritic cells from the bone marrow of a mouse. The cells were all obtained in the same way and were expected to be the same type. But to the researchers’ amazement, they were expressing different genes and could be classified into two distinct subtypes. It was like finding out the smoothie you’d been drinking for years had ingredients you’d never known about.

Regev and her colleagues weren’t the only ones figuring out how to sequence a single cell with such sensitivity, nor were they the very first to succeed. Other labs were making similar advances at approximately the same time, each using its own technology and algorithms. And they all faced the same problem: isolating and extracting enough RNA from individual cells was time consuming and expensive. Regev and her colleagues had spent many thousands of dollars to sequence only 18 cells. If the body was full of rare, undiscovered cells, it was going to take an extraordinarily long time to find them.

Skip ahead seven years and the cost of single-cell RNA sequencing is down to only pennies per cell. A critical breakthrough was Drop-Seq, a new technology developed by researchers at Harvard and the Broad Institute, including Regev and members of her lab. The device embeds individual cells into distinct oil droplets with a tiny “bar-coded” bead. When the cell is broken apart for sequencing, some of its RNA attaches to the bead in its droplet. This allows researchers to analyze thousands at once without getting their genetic material mixed up.

Cell theory 2.0

When cell theory was first proposed by German scientists some 180 years ago, it was hard to fathom that our tissues are built from “individual elementary units,” as Theodor Schwann, one of the two scientists credited with the theory, described cells. But it soon became a central tenet of biology, and over the decades and centuries, cells began to give up their secrets. Microscopes improved; new staining and sorting techniques became available. With each advance, new distinctions became possible. Muscle cells could be distinguished from neurons, and then categorized again as smooth or skeletal muscle cells. Cells, it became clear, were all fundamentally similar but came in different forms that had different properties.

By the 21st century, 200 to 300 major cell types had been identified. And while biologists have long recognized that the true number of cell types must be higher, the extent of their diversity is only now coming into full focus, thanks in large part to single-cell RNA sequencing. Regev says that the immune system alone can now be divided into more than 200 cell types and that even our retinas have 100 or more distinct types of neurons. She and her colleagues have discovered several of them.

The idea that knowing so much more about our cells could lead to medical breakthroughs is no longer hypothetical. By sequencing the RNA of individual cancer cells in recent years—“Every cell is an experiment now,” she says—she has found remarkable differences between the cells of a single tumor, even when they have the same mutations. (Last year that work led to Memorial Sloan Kettering’s Paul Marks Prize for Cancer Research.) She found that while some cancers are thought to develop resistance to therapy, a subset of melanoma cells were resistant from the start. And she discovered that two types of brain cancer, oligodendroglioma and astrocytoma, harbor the same cancer stem cells, which could have important implications for how they’re treated.

The excitement in the field has become tangible as more new cell types have been found. And yet Regev realized that if the aim was comprehensive knowledge, the approach needed to be coordinated. If each lab were to rely on its own techniques, it would be hard to standardize the computational tools and the resulting data. The new studies were producing “very nice glimmers of light,” Regev says—“a thing here, a thing there.” But she wanted to make sure those findings could be connected.Regev has also been busily mapping cells from the immune system, brain, gut, and elsewhere. She is not alone. Other labs have started their own mapping projects, each tackling a different part of the body. Last year researchers at the University of Washington attempted to classify every cell type in the microscopic worm C. elegans. “Every single field in biology is saying, ‘Of course we have to look at single-cell resolution,’” says Lander. “How did we ever imagine we were going to solve a problem without single-cell resolution?”

Regev began to advocate creating something more unified: a map that would allow researchers to chart gene expression and cell types across the entire body. Sarah Teichmann had been thinking along the same lines. When she reached out to Regev in late 2015 about the possibility of joining forces, Regev immediately said yes.

A Google Maps for our cells

The Human Cell Atlas is a collaboration among hundreds of biologists, technologists, and software engineers across the globe. Results from single-cell RNA sequencing will be combined with other data points to provide a comprehensive catalogue of all human cells.

But the many researchers involved won’t simply be compiling spreadsheets listing different cell types. The atlas will also reveal where the cells are located in the body, how many there are, what forms they can take, even the developmental history of different cell types as they differentiated from stem cells. And all of this will be made accessible through a data coordination platform and a rich visual interface that Regev compares to Google Maps. It will allow users to zoom in to the molecular level of our cells, but zooming out to the level of tissues and organs will be important too. As a 2017 overview of the Human Cell Atlas by the project’s organizing committee noted, an atlas “is a map that aims to show the relationships among its elements.” Just as corresponding coastlines seen in an atlas of Earth offer visual evidence of continental drift, compiling all the data about our cells in one place could reveal relationships among cells, tissues, and organs, including some that are entirely unexpected. And just as the periodic table made it possible to predict the existence of elements yet to be observed, the Human Cell Atlas, Regev says, could help us predict the existence of cells that haven’t been found.

The plan is not to sequence all 37 trillion cells but to sample from every part of the body. As Regev talks about the project, her enthusiasm evident, she digs up a slide to demonstrate how effective sampling can be. The slide, first only an empty frame of white, begins to fill in, pixel by pixel, with specks of blue and yellow. Soon, even though many of the pixels haven’t yet been filled, the image on the screen is unmistakable: it is Van Gogh’s Starry Night. Likewise, Regev explains, the Human Cell Atlas can give a complete picture even if not every single cell has been sequenced.

To do the sequencing, Regev and Teichmann have welcomed and recruited experts in each different tissue type. Though expected to take years, the project is moving ahead rapidly with such backers as NIH, the EU, the Wellcome Trust, the Manton Foundation, and the Chan Zuckerberg Initiative, which pledged to spend $3 billion to battle disease over the next decade; this year alone it will fund 85 Human Cell Atlas grants. Early results are already pouring in. In March, Swedish researchers working on cells related to human development announced they had sequenced 250,000 individual cells. In May, a team at the Broad made a data set of more than 500,000 immune cells available on a preview site. The goal, Regev says, is for researchers everywhere to be able to use the open-source platform of the Human Cell Atlas to perform joint analyses.

Plenty of challenges remain before the atlas can become a reality. New visualization software must be developed. Sequencing and computational approaches will need to be standardized across a huge number of labs. Conceptual issues, such as what distinguishes one cell type from another, have to be worked through. But the community behind the Human Cell Atlas—including more than 800 individuals as of June—has no shortage of motivation.

One of Regev’s own recent studies, published in August in Nature, is perhaps the best example of how the project could change biology. In mapping cells of the lungs, Regev and Jay Rajagopal’s lab at Massachusetts General Hospital found a new, very rare cell type that primarily expresses a gene linked to cystic fibrosis. Regev now thinks that these rare cells probably play a key role in the disease. More surprising yet, researchers had previously thought that a different cell type was expressing the gene.

“Imagine if somebody wanted to do gene therapy,” Regev says. “You have to fix the gene, but you have to fix it in the right cell.” The Human Cell Atlas could help researchers identify the right cell and understand how the gene in question is regulated by that cell’s extraordinarily complicated molecular networks.

For Regev, the importance of the Human Cell Atlas goes beyond its promise to revolutionize biology and medicine. As she once put it, without an atlas of our cells, “we don’t really know what we’re made of.”

Study suggests glaucoma may be an autoimmune disease

Unexpected findings show that the body’s own immune system destroys retinal cells.

Anne Trafton | MIT News Office

August 11, 2018

Glaucoma, a disease that afflicts nearly 70 million people worldwide, is something of a mystery despite its prevalence. Little is known about the origins of the disease, which damages the retina and optic nerve and can lead to blindness.

A new study from MIT and Massachusetts Eye and Ear has found that glaucoma may in fact be an autoimmune disorder. In a study of mice, the researchers showed that the body’s own T cells are responsible for the progressive retinal degeneration seen in glaucoma. Furthermore, these T cells appear to be primed to attack retinal neurons as the result of previous interactions with bacteria that normally live in our body.

The discovery suggests that it could be possible to develop new treatments for glaucoma by blocking this autoimmune activity, the researchers say.

“This opens a new approach to prevent and treat glaucoma,” says Jianzhu Chen, an MIT professor of biology, a member of MIT’s Koch Institute for Integrative Cancer Research, and one of the senior authors of the study, which appears in Nature Communications on Aug. 10.

Dong Feng Chen, an associate professor of ophthalmology at Harvard Medical School and the Schepens Eye Research Institute of Massachusetts Eye and Ear, is also a senior author of the study. The paper’s lead authors are Massachusetts Eye and Ear researchers Huihui Chen, Kin-Sang Cho, and T.H. Khanh Vu.

Genesis of glaucoma

One of the biggest risk factors for glaucoma is elevated pressure in the eye, which often occurs as people age and the ducts that allow fluid to drain from the eye become blocked. The disease often goes undetected at first; patients may not realize they have the disease until half of their retinal ganglion cells have been lost.

Most treatments focus on lowering pressure in the eye (also known as intraocular pressure). However, in many patients, the disease worsens even after intraocular pressure returns to normal. In studies in mice, Dong Feng Chen found the same effect.

“That led us to the thought that this pressure change must be triggering something progressive, and the first thing that came to mind is that it has to be an immune response,” she says.

To test that hypothesis, the researchers looked for immune cells in the retinas of these mice and found that indeed, T cells were there. This is unusual because T cells are normally blocked from entering the retina, by a tight layer of cells called the blood-retina barrier, to suppress inflammation of the eye. The researchers found that when intraocular pressure goes up, T cells are somehow able to get through this barrier and into the retina.

The Mass Eye and Ear team then enlisted Jianzhu Chen, an immunologist, to further investigate what role these T cells might be playing in glaucoma. The researchers generated high intraocular pressure in mice that lack T cells and found that while this pressure induced only a small amount of damage to the retina, the disease did not progress any further after eye pressure returned to normal.

Further studies revealed that the glaucoma-linked T cells target proteins called heat shock proteins, which help cells respond to stress or injury. Normally, T cells should not target proteins produced by the host, but the researchers suspected that these T cells had been previously exposed to bacterial heat shock proteins. Because heat shock proteins from different species are very similar, the resulting T cells can cross-react with mouse and human heat shock proteins.

To test this hypothesis, the team brought in James Fox, a professor in MIT’s Department of Biological Engineering and Division of Comparative Medicine, whose team maintains mice with no bacteria. The researchers found that when they tried to induce glaucoma in these germ-free mice, the mice did not develop the disease.

Human connection

The researchers then turned to human patients with glaucoma and found that these patients had five times the normal level of T cells specific to heat shock proteins, suggesting that the same phenomenon may also contribute to the disease in humans. The researchers’ studies thus far suggest that the effect is not specific to a particular strain of bacteria; rather, exposure to a combination of bacteria can generate T cells that target heat shock proteins.

One question the researchers plan to study further is whether other components of the immune system may be involved in the autoimmune process that gives rise to glaucoma. They are also investigating the possibility that this phenomenon may underlie other neurodegenerative disorders, and looking for ways to treat such disorders by blocking the autoimmune response.

“What we learn from the eye can be applied to the brain diseases, and may eventually help develop new methods of treatment and diagnosis,” Dong Feng Chen says.

The research was funded by the National Institutes of Health, the Lion’s Foundation, the Miriam and Sheldon Adelson Medical Research Foundation, the National Nature Science Foundation of China, the Ivan R. Cottrell Professorship and Research Fund, the Koch Institute Support (core) Grant from the National Cancer Institute, and the National Eye Institute Core Grant for Vision Research.

Sharpening the edges of cancer chemotherapy

Nicole Davis | Whitehead Institute

July 11, 2018

Cambridge, MA — Tackling unsolved problems is a cornerstone of scientific research, propelled by the power and promise of new technologies. Indeed, one of the shiniest tools in the biomedical toolkit these days is the genome editing system known as CRISPR/Cas9. Whitehead Institute Member David Sabatini and his colleagues pioneered the use of this tool as a foundation for large-scale genetic screens in human cells, turning up a treasure trove of new insights into cellular metabolism, in both normal cells and cancer cells.

When Naama Kanarek, a postdoc in Sabatini’s laboratory, pondered how to apply these state-of-the-art CRISPR/Cas9 screens to her own research, her thoughts turned to a classic cancer chemotherapy drug, methotrexate, which has been in clinical use for nearly seven decades. Often used to treat a form of pediatric leukemia, known as acute lymphoblastic leukemia (ALL), the drug, when deployed as part of a multifaceted treatment plan, can be highly effective. But its power comes at a cost. Because methotrexate can damage not only cancer cells but also healthy tissues, it must be administered with great care. For children who receive high doses of the drug, a mainstay of ALL treatment, that can mean several days spent in the hospital with rigorous clinical monitoring.

In other forms of cancer, methotrexate’s efficacy is more uncertain. For example, in pediatric osteosarcoma, only 65 percent of patients respond. Unfortunately, there is currently no way for doctors to pinpoint who will and who will not.

“From a scientific standpoint, methotrexate is quite special because it was the first metabolic drug to be developed, but much of its biology remains to be discovered — particularly what drives these different responses in patients,” Kanarek says. “So, this is really one of these old, classic questions that has been lingering in the field for some time. We thought we could learn something new.”

And they did. In the July 11 online issue of the journal Nature, Kanarek, Sabatini, and their colleagues report the findings of a CRISPR/Cas9 screen for factors involved in methotrexate sensitivity. The team’s work yielded a surprising set of discoveries that point to the breakdown of histidine — one of several amino acids used by the body to construct proteins — as a critical gatekeeper of cancer cells’ vulnerability to methotrexate. The researchers’ findings not only help illuminate the biology of a well-known cancer chemotherapy, but also suggest a simple dietary supplement that could help broaden its therapeutic window and reduce its toxicity.

“This study is an example of the power of modern genomic tools to shine a bright light on longstanding questions in human biology,” says senior author David Sabatini, a Member of Whitehead Institute, a professor of biology at Massachusetts Institute of Technology and investigator with the Howard Hughes Medical Institute (HHMI). “While cancer chemotherapies can be quite effective, their biological effects are often poorly understood. By laying bare their biology, we may be able to devise ways to utilize them more wisely.”

ATTACK THE CANCER, NOT THE PATIENT

The history of methotrexate stretches back to the 1940s, a time when strikingly little was known about the origins of cancer much less how best to treat it. The birth of methotrexate as a chemotherapeutic agent was sparked by the astute observations of Sidney Farber, a pediatric pathologist at Boston Children’s Hospital who cared for children with a variety of maladies, including ALL. In the course of caring for patients with ALL, Farber recognized that cancer cells depended on the nutrient folic acid for their own proliferation. That gave him the idea of using folate antagonists to treat ALL. Methotrexate was developed in 1949 precisely for this purpose and was subsequently shown to induce remission in children with ALL. Fast forward to today, and the drug has evolved into a significant tool in oncologists’ toolkit.

“Methotrexate is a major part of the backbone of chemotherapy treatment across many human cancers,” says Loren Walensky, a pediatric hematologist/oncologist at the Dana-Farber Cancer Institute who is not a study co-author but served as an early adviser on the project and will also play a deeper role in planning future follow-up studies. “It is also used outside of the cancer field for the treatment of several autoimmune diseases.”

He added, “But as with all chemotherapy, the critical issue is how to best use it to inflict maximal damage on the cancer without irreparably harming the patient.”

Kanarek explains how new genetic tools are allowing insights into the sensitivity of cancer cells to methotrexate.

The basic mechanics of methotrexate are fairly well known. The drug inhibits dihydrofolate reductase (DHFR), an enzyme that generates the functional form of folate, known as tetrahydrofolate (THF). THF is essential for preparing the raw materials needed to make nucleic acids, such as DNA, which carries cells’ genetic information, and RNA, a close chemical relative involved in making proteins. “Proliferating cells must duplicate their DNA, so they need a lot of THF,” Kanarek explains. “But even cells that are not dividing need to make RNA, and that requires THF, too.”

The results of Kanarek’s CRISPR/Cas9 screen now bring greater clarity to this molecular picture. She and her colleagues uncovered another enzyme, called FTCD, which is involved in the breakdown of histidine. Interestingly, FTCD also requires THF for its function — though not nearly as much as the main target of methotrexate, DHFR. Despite the differential demands of the two enzymes, they both draw from the same, shared pool of THF.

“Under normal conditions, this pool is sufficiently full, so there is no competition for resources, even in rapidly dividing cells,” Kanarek says.

But when the amount of THF becomes limiting — as it does in cells that are treated with methotrexate — the story is quite different, the Whitehead Institute team discovered. In that case, the activity of FTCD poses serious problems, because there isn’t enough THF in the pool to support both cell proliferation and histidine breakdown. When that happens, the cells die.

That got Kanarek thinking more about histidine: Could the nutrient provide a way to tinker with FTCD activity and, by virtue of the cancer cells’ own metabolism, make them more vulnerable to methotrexate?

To explore this question, the researchers used mouse models of leukemia, engineered by transplanting human leukemia cells under the skin of immunocompromised mice. A subset of the mice received injections of methotrexate together with histidine. This one-two punch, Kanarek hypothesized, should ramp up the function of FTCD and more rapidly drain the THF pool, thereby making the cells more sensitive to the cancer-killing effects of methotrexate.

That is precisely what the team observed. Notably, these experiments involved lower than normal doses of methotrexate, suggesting the cells had indeed been made more sensitive to the cancer drug. Moreover, the studies included a human leukemia cell line, called SEM, which harbors a specific genetic mutation that is associated with a particularly poor prognosis in patients — further underscoring the power of the histidine degradation pathway to weaken cells’ defenses.

Now, Kanarek and her colleagues are working to extend these initial findings with additional preclinical studies and, together with Walensky, determine how to best evaluate the potential benefits of histidine supplementation in cancer patients. Their ultimate goal: to pursue clinical trials that will assess histidine’s ability to improve the effectiveness of methotrexate in humans.

In addition to making cancer cells more vulnerable to methotrexate, the Whitehead Institute team’s research also holds promise for another therapeutic challenge: identifying which patients will or will not respond to the drug.

Two other enzymes cooperate with FTCD in breaking down histidine. The levels of one of the enzymes, known as HAL, appears to correlate with cells’ sensitivity to methotrexate: That is, cancer cells with high levels of HAL tend to be more sensitive to the drug. More work is needed to determine whether this correlation extends to a broader swath of patient samples and if it has predictive value in the clinic. Nevertheless, Kanarek and her colleagues are already beginning work on this front. Together with Abner Louissaint, Jr., a hematopathologist at Massachusetts General Hospital who also served as an early adviser on the Nature study, the Whitehead Institute team will launch a second clinical study to examine whether HAL levels can predict methotrexate response in patients with lymphoma.

“Being able to understand who is going to respond to methotrexate and who is not, and how to achieve a therapeutic benefit while mitigating the drug’s potential side effects, could have a profound impact on patient care,” Walensky says. “The insights from this study bring an entirely new dimension to our understanding of a decades-old and critically important cancer medicine. And as a physician and a scientist, that’s truly exciting.”

Written by Nicole Davis

* * *

David Sabatini’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 Howard Hughes Medical Institute investigator and a professor of biology at Massachusetts Institute of Technology.

* * *

Full citation:

“Histidine catabolism is a major determinant of methotrexate sensitivity”

Nature, online on July 11, 2018.

Naama Kanarek (1,2,3,4), Heather R. Keys (1), Jason R. Cantor (1,2,3,4), Caroline A. Lewis (1), Sze Ham Chan (1), Tenzin Kunchok (1), Monther Abu-Remaileh (1,2,3,4), Elizaveta Freinkman (1), Lawrence D. Schweitzer (4), and David M. Sabatini (1,2,3,4).

Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 455 main Street, Cambridge, Massachusetts 02142, USA
Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Koch Institute for Integrative Cancer Research and Massachusetts Institute of Technology, Department of Biology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
Broad Institute of Harvard and Massachusetts Institute of Technology, 415 main Street, Cambridge, Massachusetts 02142, USA

Restricting a key cellular nutrient could slow tumor growth

Researchers identify the amino acid aspartate as a metabolic limitation in certain cancers.

Raleigh McElvery | Department of Biology

June 29, 2018

Remove tumor cells from a living organism and place them in a dish, and they will multiply even faster than before. The mystery of why this is has long stumped cancer researchers, though many have simply focused on the mutations and chains of molecular reactions that could prompt such a disparity. Now, a group of MIT researchers suggests that the growth limitations in live organisms may stem from a different source: the cell’s environment. More specifically, they found that the amino acid aspartate serves as a key nutrient needed for the “proliferation” or rapid duplication of cancer cells when oxygen is not freely available.

The biologists took cancer cells from various tissue types and engineered them to convert another, more abundant substrate into aspartate using the gene encoding an enzyme from guinea pigs. This had no effect on the cells sitting in a dish, but the same cells implanted into mice engendered tumors that grew faster than ever before. The researchers had increased the cells’ aspartate supply, and in doing so successfully sped up proliferation in a living entity.

“There hasn’t been a lot of thought into what slows tumor growth in terms of the cellular environment, including the sort of food cancer cells need,” says Matthew Vander Heiden, associate professor of biology, associate director of the Koch Institute for Integrative Cancer Research, and senior author of the study. “For instance, if you’re trying to get to a given destination and I want to slow you down, my best bet is to set up a roadblock at a place on your route where you’d experience a slow-down anyways, like a long traffic light. That’s essentially what we’re interested in here — understanding what nutrients the cell is already lacking that put the brakes on proliferation, and then further limiting those nutrients to inhibit growth even more.”

Lucas Sullivan, a postdoc in Vander Heiden’s lab, is the lead author of the study, which appeared in Nature Cell Biology on June 25.

Building the case for aspartate

Isolating a single factor that could impact tumor growth within an organism is tricky business. One potential candidate came to Sullivan via a paper he co-authored with graduate student Dan Gui in 2015, which asked a somewhat controversial question: Why is it that cells need to consume oxygen through cellular respiration in order to proliferate?

It’s a rather counter-intuitive question, because some scientific literature suggests just the opposite: Cancer cells in an organism (“in vivo”) do not enjoy the same access to oxygen as they would in a dish, and therefore don’t depend on oxygen to produce enough energy to divide. Instead, they switch to a different process, fermentation, that doesn’t require oxygen. But Sullivan and Gui noted that cancer cells do rely on oxygen for another reason: to produce aspartate as a byproduct.

Aspartate, they soon confirmed, does, in fact, play a crucial role in controlling the rate of cancer cell proliferation. In another study one year later, Sullivan and Gui noted that the antidiabetic drug metformin, known to inhibit mitochondria, slowed tumor growth and decreased aspartate levels in cells in vivo. Since mitochondria are key to cellular respiration, Sullivan reasoned that blocking their function in an already oxygen-constrained environment (the tumor) might make cancer cells vulnerable to further suppression of respiration — and aspartate — explaining why metformin seems to have such a strong effect on tumor growth.

Despite being potentially required for certain amino acids and the synthesis of all four DNA nucleotides, aspartate is already hard to come by, even in oxygen-rich environments. It’s among the lowest concentration amino acids in our blood, and has no way to enter our cells unless a rare protein transporter is present. Precisely why aspartate import is so inefficient remains an evolutionary mystery; one possibility is that its scarcity serves as a “failsafe,” preventing cells from multiplying until they have all the resources to properly do so.

Regardless, the easiest way for cells to get aspartate is not to import it from outside, but rather to make it directly inside, breaking down another amino acid called asparagine to generate it. However, there are very few known mammals that have an enzyme capable of producing aspartate from asparagine — among them, the guinea pig.

Channeling the guinea pig

In the 1950s, a researcher named John Kidd made an accidental discovery. He injected cancer-ridden rats with sera from various animals — rabbits, horses, guinea pigs, and the like — and discovered that guinea pig serum alone shrunk the rats’ tumors. It wasn’t until years later that scientists learned it was an enzyme in the guinea pig blood called guinea pig asparaginase 1 (gpASNase1) that was responsible for this antitumorigenic effect. Today, we know about a host of simpler organisms with similar enzymes, including bacteria and zebrafish. In fact, bacterial asparaginase is approved as a medicine to treat acute lymphocytic leukemia.

Because guinea pigs are mammals and thus have similar metabolisms to our own, the MIT researchers decided to use gpASNase1 to increase aspartate levels in tumors in four different tumor types and ask whether the tumors would grow faster. This was the case for three of the four types: The colon cancer cells, osteosarcoma cells, and mouse pancreatic cancer cells divided more rapidly than before, but the human pancreatic cancer cells continued to proliferate at their normal pace.

“This is a relatively small sample, but you could take this to mean that not every cell in the body is as sensitive to loss of aspartate production as others,” Sullivan says. “Acquiring aspartate may be a metabolic limitation for only a subset of cancers, since aspartate can be produced via a number of different pathways, not just through asparagine conversion.”

When the researchers tried to slow tumor growth using the antidiabetic metformin, the cells expressing gpASNase1 remained unaffected — confirming Sullivan’s prior suspicion that metformin slows tumor growth specifically by impeding cellular respiration and suppressing aspartate production.

“Our initial finding connecting metformin and proliferation was very serendipitous,” he says, “but these most recent results are a clear proof of concept. They show that decreasing aspartate levels also decreases tumor growth, at least in some tumors. The next step is to determine if there are other ways to more intentionally target aspartate synthesis in certain tissues and improve our current therapeutic approaches.”

Although the efficacy of using metformin to treat cancer remains controversial, these findings indicate that one means to target tumors would be to prevent them from accessing or producing nutrients like aspartate to make new cells.

“Although there are many limitations to cancer cell proliferation, which metabolites become limiting for tumor growth has been poorly understood,” says Kivanc Birsoy, the Chapman-Perelman Assistant Professor at Rockefeller University. “This study identifies aspartate as one such limiting metabolite, and suggests that its availability could be targeted for anti-cancer therapies.”

Birsoy is a former postdoc in professor of biology David Sabatini’s lab, who authored a paper published in the same issue of Nature Cell Biology, identifying aspartate as a major growth limitation in oxygen-deprived tumors.

“These companion papers demonstrate that some tumors in vivo are really limited by the chemical processes that require oxygen to get the aspartate they need to grow, which can affect their sensitivity to drugs like metformin,” Vander Heiden says. “We’re beginning to realize that understanding which cancer patients will respond to which treatments may be determined by factors besides genetic mutations. To really get the full picture, we need to take into account where the tumor is located, its nutrient availability, and the environment in which it lives.”

The research was funded by an NIH Pathway to Independence Award, the American Cancer Society, Ludwig Center for Molecular Oncology Fund, the National Science Foundation, a National Institutes of Health Ruth Kirschstein Fellowship, Alex’s Lemonade Stand Undergraduate Research Fellowship, Damon Runyon Cancer Research Foundation, Howard Hughes Medical Institute Faculty Scholar Award, Stand Up to Cancer, Lustgarten Foundation, Ludwig Center at MIT, the National Institutes of Health, and the Koch Institute’s Center for Precision Cancer Medicine.

Fasting boosts stem cells’ regenerative capacity

A drug treatment that mimics fasting can also provide the same benefit, study finds.

Anne Trafton | MIT News Office

May 1, 2018

As people age, their intestinal stem cells begin to lose their ability to regenerate. These stem cells are the source for all new intestinal cells, so this decline can make it more difficult to recover from gastrointestinal infections or other conditions that affect the intestine.

This age-related loss of stem cell function can be reversed by a 24-hour fast, according to a new study from MIT biologists. The researchers found that fasting dramatically improves stem cells’ ability to regenerate, in both aged and young mice.

In fasting mice, cells begin breaking down fatty acids instead of glucose, a change that stimulates the stem cells to become more regenerative. The researchers found that they could also boost regeneration with a molecule that activates the same metabolic switch. Such an intervention could potentially help older people recovering from GI infections or cancer patients undergoing chemotherapy, the researchers say.

“Fasting has many effects in the intestine, which include boosting regeneration as well as potential uses in any type of ailment that impinges on the intestine, such as infections or cancers,” says Omer Yilmaz, an MIT assistant professor of biology, a member of the Koch Institute for Integrative Cancer Research, and one of the senior authors of the study. “Understanding how fasting improves overall health, including the role of adult stem cells in intestinal regeneration, in repair, and in aging, is a fundamental interest of my laboratory.”

David Sabatini, an MIT professor of biology and member of the Whitehead Institute for Biomedical Research and the Koch Institute, is also a senior author of the paper, which appears in the May 3 issue of Cell Stem Cell.

“This study provided evidence that fasting induces a metabolic switch in the intestinal stem cells, from utilizing carbohydrates to burning fat,” Sabatini says. “Interestingly, switching these cells to fatty acid oxidation enhanced their function significantly. Pharmacological targeting of this pathway may provide a therapeutic opportunity to improve tissue homeostasis in age-associated pathologies.”

The paper’s lead authors are Whitehead Institute postdoc Maria Mihaylova and Koch Institute postdoc Chia-Wei Cheng.

Boosting regeneration

For many decades, scientists have known that low caloric intake is linked with enhanced longevity in humans and other organisms. Yilmaz and his colleagues were interested in exploring how fasting exerts its effects at the molecular level, specifically in the intestine.

Intestinal stem cells are responsible for maintaining the lining of the intestine, which typically renews itself every five days. When an injury or infection occurs, stem cells are key to repairing any damage. As people age, the regenerative abilities of these intestinal stem cells decline, so it takes longer for the intestine to recover.

“Intestinal stem cells are the workhorses of the intestine that give rise to more stem cells and to all of the various differentiated cell types of the intestine. Notably, during aging, intestinal stem function declines, which impairs the ability of the intestine to repair itself after damage,” Yilmaz says. “In this line of investigation, we focused on understanding how a 24-hour fast enhances the function of young and old intestinal stem cells.”

After mice fasted for 24 hours, the researchers removed intestinal stem cells and grew them in a culture dish, allowing them to determine whether the cells can give rise to “mini-intestines” known as organoids.

The researchers found that stem cells from the fasting mice doubled their regenerative capacity.

“It was very obvious that fasting had this really immense effect on the ability of intestinal crypts to form more organoids, which is stem-cell-driven,” Mihaylova says. “This was something that we saw in both the young mice and the aged mice, and we really wanted to understand the molecular mechanisms driving this.”

Metabolic switch

Further studies, including sequencing the messenger RNA of stem cells from the mice that fasted, revealed that fasting induces cells to switch from their usual metabolism, which burns carbohydrates such as sugars, to metabolizing fatty acids. This switch occurs through the activation of transcription factors called PPARs, which turn on many genes that are involved in metabolizing fatty acids.

The researchers found that if they turned off this pathway, fasting could no longer boost regeneration. They now plan to study how this metabolic switch provokes stem cells to enhance their regenerative abilities.

They also found that they could reproduce the beneficial effects of fasting by treating mice with a molecule that mimics the effects of PPARs. “That was also very surprising,” Cheng says. “Just activating one metabolic pathway is sufficient to reverse certain age phenotypes.”

Jared Rutter, a professor of biochemistry at the University of Utah School of Medicine, described the findings as “interesting and important.”

“This paper shows that fasting causes a metabolic change in the stem cells that reside in this organ and thereby changes their behavior to promote more cell division. In a beautiful set of experiments, the authors subvert the system by causing those metabolic changes without fasting and see similar effects,” says Rutter, who was not involved in the research. “This work fits into a rapidly growing field that is demonstrating that nutrition and metabolism has profound effects on the behavior of cells and this can predispose for human disease.”

The findings suggest that drug treatment could stimulate regeneration without requiring patients to fast, which is difficult for most people. One group that could benefit from such treatment is cancer patients who are receiving chemotherapy, which often harms intestinal cells. It could also benefit older people who experience intestinal infections or other gastrointestinal disorders that can damage the lining of the intestine.

The researchers plan to explore the potential effectiveness of such treatments, and they also hope to study whether fasting affects regenerative abilities in stem cells in other types of tissue.

The research was funded by the National Institutes of Health, the V Foundation, a Sidney Kimmel Scholar Award, a Pew-Stewart Trust Scholar Award, the Kathy and Curt Marble Cancer Research Fund, the MIT Stem Cell Initiative through Fondation MIT, the Koch Institute Frontier Research Program through the Kathy and Curt Marble Cancer Research Fund, the American Federation of Aging Research, the Damon Runyon Cancer Research Foundation, the Robert Black Charitable Foundation, a Koch Institute Ludwig Postdoctoral Fellowship, a Glenn/AFAR Breakthroughs in Gerontology Award, and the Howard Hughes Medical Institute.

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).

* * *

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.

* * *

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.

Elizabeth Li ’18 has worked in three cancer-related labs over the past six years, and one day intends to start her own.

Raleigh McElvery

March 6, 2018

Senior Elizabeth Li recreates miniature organs — lungs and intestines — outside the body. She does so in order to study cancer progression in both environments, and over the past six years has worked in three separate cancer-focused labs: two at MIT and another beginning her junior year of high school. One day, she aims to run her own.

“I’ve been into math and science ever since I was little,” she explains, “but in third grade I met a friend who was pretty important to me. She was diagnosed with a very malignant form of brain cancer and ended up dying from it. From that point on — even though I was still very young — I knew I wanted to do cancer research.”

In 9^th grade, Li began at the School for Science and Math at Vanderbilt, a joint program between the university and Metro Nashville Public Schools. “I got to skip school once a week to learn research techniques, and had the opportunity to join Andries Zijlstra’s lab my junior year,” she recalls. “I’m actually still part of that group, and I’ve been working on the same project related to cancer metastasis for six years now.”

When it came time to select a university, Li was torn between Vanderbilt — where she was already performing research — and MIT, which she describes as “the place of opportunity.” She was ultimately swayed by MIT’s vast array of research areas, and fully sold after an overnight to preview the undergraduate culture.

Li opted for Course 7 in order to continue doing cancer research, and joined Omer Yilmaz’s lab in 2015 to investigate intestinal tumorigenesis. Here, she spent most of her time doing organoid work, studying the progression of colorectal cancer in miniaturized and simplified versions of the intestine. Li removed individual intestinal stem cells — or sometimes the entire “crypts” in which they reside — and grew them inside a 3D gel. This environment allowed the cells to differentiate and interact as they would in the colon, rather than growing on a flat, plastic dish.

Li and other members of the Yilmaz lab watched these cells multiply, observing their shape and the regeneration process. Li’s method of assessment varied depending on the research question: on some days, she stained the cells for proliferation markers, and on others she exposed them to different metabolites or drugs to see how the cells responded.

“On a typical day, I would come in during the morning between classes, and again in the afternoons and evenings,” she says. “The experiments differed, but we tended to do a lot of genetic manipulation. We’d make plasmids, CRISPR-Cas9 knockouts, or test for gene and protein expression using qPCR and Western blots.”

After two years, Li’s primary mentor finished her postdoctoral training, and Li transitioned to Jackie Lees’ lab at the beginning of her senior year. Li is now working with a fellow undergraduate on an independent project, centered on the enzyme protein arginine methyltransferase 5 (PRMT5).

PRMT5 catalyzes the transfer of methyl groups to the amino acid arginine in certain proteins, modifying their function. The enzyme also plays a key role in regulating gene splicing, the process by which segments of pre-mRNA are removed — changing the genetic code so that multiple genes can be encoded by the same initial transcript.

The Lees lab is interested in PRMT5 because it affects glioblastoma formation, the most common form of adult brain malignancy. As Li explains, when PRMT5 expression increases, so does tumor formation. Since there are still relatively few therapeutic options to treat glioblastomas, she’s hoping to use small molecules to inhibit PRMT5 expression and thus impede tumor initiation and progression.

“We’re considering using nanoparticles to deliver them,” she says, “and in doing so, hoping to gain a better understanding of how PRMT5 inhibition might impact cancer progression and tumorigenesis.”

Li is testing one small molecule PRMT5 inhibitor in lung organoids and several 2D cell lines — determining how sensitive the cells are and if the organoids will form, to gauge whether a tumor would still develop in the presence of the drug. “Depending on when you add the drug, you can test different aspects of tumorigenesis,” she explains.

She’s also split the past four years between the Biology Undergraduate Student Association (of which she was faculty liaison, outreach chair, and then co-president), the MIT Pre-Medical Society, MIT Lion Dance, Asian Dance Team, Wind Ensemble, and Improv-a-Do! She’s also heavily involved in DynaMIT, which organizes an annual, week-long science program for economically disadvantaged middle school students.

“There are a lot of extracurriculars to do,” Li admits. “But it’s pretty easy to get involved in the MIT community and still stay on top of your coursework, if you keep it to four or five classes per semester. It’s worked out for me so far — I’m still alive and happy and have time for eating, sleeping, and friends.”

As Li applies to MD-PhD programs, she hopes one day to practice medicine (perhaps pediatric oncology) while running her own lab.

“My advice for incoming MIT undergrads would be to remember to have fun,” she says. “You only have four years, so take advantage of your time here: hang out with your friends, take the classes you want to take, and do things that you enjoy. Hopefully most of those activities will be one and the same.”

Photo credit: Raleigh McElvery

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

One 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

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.”

Faculty

Staff

Current Faculty

In Memoriam

Biochemistry, Biophysics, and Structural Biology

Cancer Biology

Cell Biology

Computational Biology

Genetics

Human Disease

Immunology

Microbiology

Neurobiology

Stem Cell and Developmental Biology

Undergraduate Testimonials

General Institute Requirement

Advanced Standing Exam

Transfer Credit

Subject Offerings

Research Opportunities

Biology Undergraduate Student Association

Career Development

Tutoring

Diversity in the Graduate Program

NIH Training Grant

Career Outcomes

Graduate Testimonials

Application Process

Interdisciplinary and Joint Degree Programs

Funding

Living in Cambridge

Subject Offerings

Graduate Manual: Key Program Info

Graduate Teaching

Career Development Resources

Biology Graduate Student Council

BioPals Program

Postdoc Associations

Postdoc Testimonials

Workshops for MIT Biology Postdocs Entering the Academic Job Market

Bernard S. and Sophie G. Gould MIT Summer Research Program in Biology (BSG-MSRP-Bio)

Quantitative Methods Workshop

Summer Workshop for Teachers

MIT Field Trips

LEAH Knox Scholars Program

Additional Resources

Resources for MD/PhD Students

Preliminary Exam Guidelines

Thesis Committee Meetings

Guidelines for Graduating

Contact Us

Directory

Faculty

Staff

Community

2026 MIT Biology Catalyst Symposium

Get Help

Honors and Awards

Employment Opportunities

Support Biology

Faculty

Current Faculty

In Memoriam

Areas of Research

Biochemistry, Biophysics, and Structural Biology

Cancer Biology

Cell Biology

Computational Biology

Genetics

Human Disease

Immunology

Microbiology

Neurobiology

Stem Cell and Developmental Biology

Locations

Core Facilities

Video Gallery

Faculty Resources

Why Biology?

Undergraduate Testimonials