Author: mantulin

Toxic proteins and type 2 diabetes

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

Nicole Davis | Whitehead Institute
March 8, 2018

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

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

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

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

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

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

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

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

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

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

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

New study solves an arthritis drug mystery

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

Anne Trafton | MIT News Office
March 6, 2018

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

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

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

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

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

A promising target

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

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

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

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

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

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

Environment matters

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

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

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

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

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

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

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

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

Scientists deliver high-resolution glimpse of enzyme structure

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

Anne Trafton | MIT News Office
February 20, 2018

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

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

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

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

An unusual enzyme

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

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

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

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

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

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

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

Designing drugs

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

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

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

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

The research was funded by the National Institutes of Health.

Study: Fragile X syndrome neurons can be restored

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

Nicole Giese Rura | Whitehead Institute
February 15, 2018

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

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

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

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

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

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

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

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

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

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

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

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

Fine-tuning cancer medicine

New cancer research initiative eyes individualized treatment for patients.

Koch Institute
February 1, 2018

Details matter — perhaps most noticeably in the fight against cancer. Some patients respond to a given anticancer therapy, and some do not. A new initiative at MIT takes aim at those details, and the name of the game is precision.

The recently launched MIT Center for Precision Cancer Medicine (CPCM) is housed within MIT’s Koch Institute for Integrative Cancer Research and headed by physician-scientist Michael B. Yaffe, the David H. Koch Professor of Science and professor of biology and biological engineering. The center brings together leading Institute faculty members to focus on key research themes to accelerate the clinical translation of novel cancer discoveries, treatments, and technologies.

Engineering approaches to the clinic

While other institutions have begun efforts in precision medicine as well, the MIT Center for Precision Cancer Medicine stands out for using engineering approaches to solve complex clinical challenges in cancer treatment that are rooted in biology. In particular, the CPCM combines understandings of biological circuitry — along with engineering, computational, and mathematical techniques (as well as genomic ones) — to focus on signaling networks and pathways that are aberrantly regulated in cancer cells. This strategy is supported by the fact that most state-of-the-art molecularly targeted cancer therapies are focused on these key pathways.

At its core, the CPCM is driven by both internal and external collaboration, and is devoted to translational research to help the substantial number of patients who do not respond well to traditional cancer therapies — for example, those with triple-negative breast cancer, ovarian cancer, non-small cell lung cancer, or advanced prostate cancer.

To improve outcomes for these patients, CPCM investigators are focused on four key areas of research. First among these is identifying and targeting the processes, signals, and mechanisms that determine an individual patient’s response to chemotherapy. Recent discoveries by CPCM researchers include mechanisms that cancer cells use to repair chemotherapy damage that should have killed them, to hide from drugs in protected “niches” in the body, or to grow when and where they should not.

CPCM members are also working on a second research pillar, which involves finding ways to use existing FDA-approved cancer drugs more effectively, particularly in carefully designed combinations. Combination therapies are currently used in the clinic to treat some cancers, yet the discovery process for these has been largely empirical. By contrast, CPCM investigators are integrating their knowledge of cancer biology, understandings of drugs’ mechanisms of action, and sophisticated analytical techniques, to identify or design specific combinations that work synergistically to disarm and then destroy cancer cells.

“We believe we can significantly alter cancer patients’ outcomes by determining the right combination of therapies and the right sequence of drugs for the right patients,” says Yaffe. “We’re also concentrating on innovative ways to give these drugs, like time-staggered dosages and nanoparticle delivery.” He notes that, as part of their analyses of drugs and combination regimens currently administered in the clinic, CPCM members expect to identify combinations of drugs that are not as efficacious when given simultaneously as when given sequentially, at specific intervals. Yaffe stresses that these will be important findings that could help reduce the toxicity of treatment by not exposing people to multiple drug toxicities at the same time.

In parallel with their efforts to use existing drugs more effectively, CPCM investigators are also working to identify compounds, materials, and approaches that can engage key “undruggable” genetic and molecular targets and disrupt processes driving drug resistance. The “undruggable” label often refers to the fact that a target protein or molecule lacks a site to which drugs can bind, and thus is not considered a good drug target by the pharmaceutical industry. However, using novel chemistry approaches, CPCM researchers have made early inroads against several such high-value cancer targets, including specific transcription factors and RNA-binding proteins. The center will continue and expand these efforts as the third part of its research platform, including collaborations with industry.

Finally, the fourth component of the CPCM’s efforts will be harnessing MIT’s particular expertise in big data analysis and tools to begin new and expedite existing cancer research efforts. For example, the researchers plan to use data analytics to identify selective panels of biomarkers that can be used to prioritize which of their drug combinations, treatment protocols, and formulations are best suited to a particular patient’s tumor.

Getting discoveries out the door

“Patients will be the ultimate beneficiaries of the work of the new MIT Center for Precision Cancer Medicine,” says Tyler Jacks, director of the Koch Institute and the David H. Koch Professor of Biology. “This research is, by its nature, imminently and rapidly translatable. By concentrating efforts on which patients will benefit from particular existing drugs or combinations of drugs, there is a relatively small step from laboratory to a treatment that is benefitting a cancer patient.”

While work on combinations of approved therapies, like that at the CPCM, may be more rapidly translatable than other cancer research, it can be challenging for industry to pursue, particularly when those drugs hail from multiple companies. Overcoming this disjuncture is one of the goals behind the establishment of the MIT Center for Precision Cancer Medicine, which was made possible by a generous gift from an anonymous donor.

Yaffe and his CPCM colleagues are committed to finding viable routes to move their cancer research into the clinic, particularly through collaborations between CPCM members, hospitals, and industry. Logistically, this means more work for the center’s research groups, including advanced laboratory and preclinical studies, safety and scale-up studies, and clinical-grade manufacturing, as well as staff to carry it out. Woven into these efforts, CPCM investigators will tap into MIT’s celebrated tradition of entrepreneurship and, even more so, the Institute’s expanding network of clinical collaborators. The philanthropic investment behind the center will provide stable financial support for the researchers’ endeavors.

The new hub in town

In addition to supporting the research of member investigators, the CPCM offers a robust training ground for young engineers and scientists interested in precision medicine. Moreover, it will serve as the hub of precision cancer medicine research at MIT and beyond, connecting with researchers across the MIT campus and partnering with clinical investigators in Greater Boston’s noted health care centers and around the country.

Five outstanding cancer researchers make up the center’s founding faculty:

  • Michael B. Yaffe, MD, PhD, director, MIT Center for Precision Cancer Medicine; David H. Koch Professor of Science, professor of biology and biological engineering
  • Michael Hemann, PhD, associate professor of biology
  • Angela Koehler, PhD, Karl Van Tassel (1925) Career Development Associate Professor, assistant professor of biological engineering
  • Matthew Vander Heiden, MD, PhD, associate professor of biology, associate director, Koch Institute for Integrative Cancer Research
  • Forest M. White, PhD, professor of biological engineering

Efforts are currently underway to recruit an assistant director and a scientific advisory board.

As part of its charge, and key to spurring the new collaborations in precision cancer medicine that are its focus, the MIT Center for Precision Cancer Medicine will also convene lectures, events, and scientific exchanges and symposia, the first of which is slated for the fall.

Reading and writing DNA

Department of Biology kicks off IAP seminar series with a lecture by synthetic-biology visionary George Church.

Raleigh McElvery | Department of Biology
January 31, 2018

Thanks to the invention of genome sequencing technology more than three decades ago, we can now read the genetic blueprint of virtually any organism. After the ability to read came the ability to edit — adding, subtracting, and eventually altering DNA wherever we saw fit. And yet, for George Church, a professor at Harvard Medical School, associate member of the Broad Institute, and founding core faculty and lead for synthetic biology at the Wyss Institute — who co-pioneered direct genome sequencing in 1984 — the ultimate goal is not just to read and edit, but also to write.

What if you could engineer a cell resistant to all viruses, even the ones it hadn’t yet encountered? What if you could grow your own liver in a pig to replace the faulty one you were born with? What if you could grow an entire brain in a dish? In his lecture on Jan. 24 — which opened the Department of Biology’s Independent Activities Period (IAP) seminar series, Biology at Transformative Frontiers — Church promised all this and more.

“We began by dividing the Biology IAP events into two tracks: one related to careers in academia and another equivalent track for industry,” says Jing-Ke Weng, assistant professor and IAP faculty coordinator for the department. “But then it became clear that George Church, Patrick Brown, and other speakers we hoped to invite blurred the boundaries between those two tracks. The Biology at Transformative Frontiers seminar series became about the interface of these trajectories, and how transferring technologies from lab bench to market is altering society as we know it.”

The seminar series is a staple in the Department of Biology’s IAP program, but during the past several years it has been oriented more toward quantitative biology. Weng recalls these talks as being relegated to the academic sphere, and wanted to show students that the lines between academia, industry, and scientific communication are actually quite porous.

“We chose George Church to kick off the series because he’s been in synthetic biology for a long time, and continues to have a successful academic career even while starting so many companies,” says Weng.

Church’s genomic sequencing methods inspired the Human Genome Project in 1984 and resulted in the first commercial genome sequence (the bacterium Helicobacter pylori) 10 years later. He also serves as the director of the Personal Genome Project, the “Wikipedia” of open-access human genomic data. Beyond these ventures, he’s known for his work on barcoding, DNA assembly from chips, genome editing, and stem cell engineering.

He’s also the same George Church who converted the book he co-authored with Ed Regis, “Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves,” into a four-letter code based on the four DNA nucleotides (A, T, C, and G), subsisted on nutrient broth from a lab vendor for an entire year, and dreams of eventually resurrecting woolly mammoths. He’s being featured in an upcoming Netflix Original documentary, so when he arrived at the Stata Center to give his lecture last week he was trailed by a camera crew.

According to Church, the transformative technologies that initially allowed us to read and edit DNA have grown exponentially in recent years with the invention of molecular multiplexing and CRISPR-Cas9 (think Moore’s Law but even more exaggerated). But there’s always room for improvement.

“There’s been a little obsession with CRISPR-Cas9s and other CRISPRs,” said Church. “Everybody is saying how great it is, but it’s important to say what’s wrong with it as well, because that tells us where we’re going next and how to improve on it.”

He outlined several of his own collaborations, including those aimed at devising more precise methods of genome editing, one resulting in 321 changes to the Escherichia coli genome — the largest change in any genome yet — rendering the bacterium resistant to all viruses, even those it had not yet come into contact with. The next step? Making similarly widespread changes in plants, animals, and eventually perhaps even human tissue. In fact, Church and his team have set their sights on combatting the global transplantation crisis with humanlike organs grown in animals.

“Since the dawn of transplantation as a medical practice, we’ve had to use either identical twins or rare matches that are very compatible immunologically, because we couldn’t engineer the donor or the recipient,” said Church.

Since it’s clearly unethical to engineer human donors, Church reasoned, why not engineer animals with compatible organs instead? Pigs, to be exact, since most of their organs are comparable in size and function to our own.

“This is an old dream; I didn’t originate it,” said Church. “It started about 20 years ago, and the pioneers of this field worked on it for a while, but dropped it largely because the number of changes to the genome were daunting, and there was a concern that the viruses all pigs make — retroviruses — would be released and infect the immunocompromised organ recipient.”

Church and his team successfully disrupted 62 of these retroviruses in pig cells back in 2015, and in 2017 they used these cells to generate living, healthy pigs. Today, the pigs are thriving and rearing piglets of their own. Church is also considering the prospect of growing augmented organs in pigs for human transplantation, perhaps designing pathogen-, cancer-, and age-resistant organs suitable for cryopreservation.

“Hopefully we’ll be doing nonhuman primate trials within a couple of years, and then almost immediately after that human trials,” he said.

Another possibility, rather than cultivating organs in animals for transplant, is to generate them in a dish. A subset of Church’s team is working on growing from scratch what is arguably the most complicated organ of all, the brain.

This requires differentiating multiple types of cells in the same dish so they can interact with each other to form the complex systems of communication characteristic of the human brain.

Early attempts at fashioning brain organoids often lacked capillaries to distribute oxygen and nutrients (roughly one capillary for each of the 86 billion neurons in the human brain). However, thanks to their new human transcription factor library, Church and colleagues have begun to generate the cell types necessary to create such capillaries, plus the scaffolding needed to promote the three-dimensional organization of these and additional brain structures. Church and his team have not only successfully integrated the structures with one another, but have also created an algorithm that spits out the list of molecular ingredients required to generate each cell type.

Church noted these de novo organoids are extremely useful in determining which genetic variants are responsible for certain diseases. For instance, you could sequence a patient’s genome and then create an entire organoid with the mutation in question to test whether it was the root cause of the condition.

“I’m still stunned by the breadth of projects and approaches that he’s running simultaneously,” says Emma Kowal, a second-year graduate student, member of Weng’s planning committee, and a former researcher in Church’s lab. “The seminar series is called Biology at Transformative Frontiers, and George is very much a visionary, so we thought it would be a great way to start things off.”

The four-part series also features Melissa Moore, chief scientific officer of the Moderna Therapeutics mRNA Research Platform, Jay Bradner, president of the Novartis Institutes for BioMedical Research, and Patrick Brown, CEO and founder of Impossible Foods.

How some facial malformations arise

Study explains why mutations that would seemingly affect all cells lead to face-specific birth defects.

Anne Trafton | MIT News Office
January 24, 2018

About 1 in 750 babies born in the United States has some kind of craniofacial malformation, accounting for about one-third of all birth defects.

Many of these craniofacial disorders arise from mutations of “housekeeping” genes, so called because they are required for basic functions such as building proteins or copying DNA. All cells in the body require these housekeeping genes, so scientists have long wondered why these mutations would produce defects specifically in facial tissues.

Researchers at MIT and Stanford University have now discovered how one such mutation leads to the facial malformations seen in Treacher-Collins Syndrome, a disorder that affects between 1 in 25,000 and 1 in 50,000 babies and produces underdeveloped facial bones, especially in the jaw and cheek.

The team found that embryonic cells that form the face are more sensitive to the mutation because they more readily activate a pathway that induces cell death in response to stress. This pathway is mediated by a protein called p53. The new findings mark the first time that scientists have determined how mutations in housekeeping genes can have tissue-specific effects during embryonic development.

“We were able to narrow down, at the molecular level, how issues with general regulators that are used to make ribosomes in all cells lead to defects in specific cell types,” says Eliezer Calo, an MIT assistant professor of biology and the lead author of the study.

Joanna Wysocka, a professor of chemical and systems biology at Stanford University, is the senior author of the study, which appears in the Jan. 24 online edition of Nature.

From mutation to disease

Treacher-Collins Syndrome is caused by mutations in genes that code for proteins required for the assembly and function of polymerases. These proteins, known as TCOF1, POLR1C, and POLR1D, are responsible for transcribing genes that make up cell organelles called ribosomes. Ribosomes are critical to all cells.

“The question we were trying to understand is, how is it that when all cells in the body need ribosomes to function, mutations in components that are required for making the ribosomes lead to craniofacial disorders? In these conditions, you would expect that all the cell types of the body would be equally affected, but that’s not the case,” Calo says.

During embryonic development, these mutations specifically affect a type of embryonic cells known as cranial neural crest cells, which form the face. The researchers already knew that the mutations disrupt the formation of ribosomes, but they didn’t know exactly how this happens. To investigate that process, the researchers engineered larvae of zebrafish and of an aquatic frog known as Xenopus to express proteins harboring those mutations.

Their experiments revealed that the mutations lead to impairment in the function of an enzyme called DDX21. When DDX21 dissociates from DNA, the genes that encode ribosomal proteins do not get transcribed, so ribosomes are missing key components and can’t function normally. However, this DDX21 loss only appears to happen in cells that are highly sensitive to p53 activation, including cranial neural crest cells. These cells then undergo programmed cell death, which leads to the facial malformations seen in Treacher-Collins Syndrome, Calo says.

Other embryonic cells, including other types of neural crest cells, which form nerves and other parts of the body such as connective tissue, are not affected by the loss of DDX21.

Role of DNA damage

The researchers also found that mutations of POLR1C and POLR1D also cause damage to stretches of DNA that encode some of the RNA molecules that make up ribosomes. The amount of DNA damage correlated closely with the severity of malformations seen in individual larvae, and mutations in POLR1C led to far more DNA damage than mutations in POLR1D. The researchers believe these differences in DNA damage may explain why the severity of Treacher-Collins Syndrome can vary widely among individuals.

Calo’s lab is now studying why affected cells experience greater levels of DNA damage in those particular sequences. The researchers are also looking for compounds that could potentially prevent craniofacial defects by making the cranial neural crest cells more resistant to p53-induced cell death. Such interventions could have a big impact but would have to be targeted very early in embryonic development, as the cranial neural crest cells begin forming the tissue layers that will become the face at about three weeks of development in human embryos.

The research was funded by the National Institutes of Health, Howard Hughes Medical Institute, and March of Dimes Foundation.

Twelve School of Science faculty members appointed to named professorships
School of Science
January 19, 2018

The School of Science has appointed 12 faculty members to named professorships.

The new appointments are:

Stephen Bell, the Uncas (1923) and Helen Whitaker Professor in the Department of Biology: Bell is a leader in the field of DNA replication, specifically in the mechanisms controlling initiation of chromosome duplication in eukaryotic cells. Combining genetics, genomics, biochemistry, and single-molecule approaches, Bell has provided a mechanistic picture of the assembly of the bidirectional DNA replication machine at replication origins.

Timothy Cronin, the Kerr-McGee Career Development Professor in the Department of Earth, Atmospheric and Planetary Sciences: Cronin is a climate physicist interested in problems relating to radiative‐convective equilibrium, atmospheric moist convection and clouds, and the physics of the coupled land‐atmosphere system.

Nikta Fakhri, the Thomas D. and Virginia W. Cabot Professor in the Department of Physics: Combining approaches from physics, biology, and engineering, Fakhri seeks to understand the principles of active matter and aims to develop novel probes, such as single-walled carbon nanotubes, to map the organization and dynamics of nonequilibrium heterogeneous materials.

Robert Griffin, the Arthur Amos Noyes Professor in the Department of Chemistry: Griffin develops new magnetic resonance techniques to study molecular structure and dynamics and applies them to interesting chemical, biophysical, and physical problems such as the structure of large enzyme/inhibitor complexes, membrane proteins, and amyloid peptides and proteins.

Jacqueline Hewitt, the Julius A. Stratton Professor in Electrical Engineering and Physics in the Department of Physics: Hewitt applies the techniques of radio astronomy, interferometry, and image processing to basic research in astrophysics and cosmology. Current topics of interest are observational signatures of the epoch of reionization and the detection of transient astronomical radio sources, as well as the development of new instrumentation and techniques for radio astronomy.

William Minicozzi, the Singer Professor of Mathematics in the Department of Mathematics: Minicozzi is a geometric analyst who, with colleague Tobias Colding, has resolved a number of major results in the field, among them: proof of a longstanding S.T. Yau conjecture on the function theory on Riemannian manifolds, a finite-time extinction condition of the Ricci flow, and recent work on the mean curvature flow.

Aaron Pixton, the Class of 1957 Career Development Professor in the Department of Mathematics: Pixton works on various topics in enumerative algebraic geometry, including the tautological ring of the moduli space of algebraic curves, moduli spaces of sheaves on 3-folds, and Gromov-Witten theory.

Gabriela Schlau-Cohen, the Thomas D. and Virginia W. Cabot Professor in the Department of Chemistry: Schlau-Cohen’s research employs single-molecule and ultrafast spectroscopies to explore the energetic and structural dynamics of biological systems. She develops new methodology to measure ultrafast dynamics on single proteins to study systems with both sub-nanosecond and second dynamics. In other research, she merges optical spectroscopy with model membrane systems to provide a novel probe of how biological processes extend beyond the nanometer scale of individual proteins.

Alexander Shalek, the Pfizer Inc.-Gerald Laubach Career Development Professor in the Department of Chemistry: Shalek studies how our individual cells work together to perform systems-level functions in both health and disease. Using the immune system as his primary model, Shalek leverages advances in nanotechnology and chemical biology to develop broadly applicable platforms for manipulating and profiling many interacting single cells in order to examine ensemble cellular behaviors from the bottom up.

Scott Sheffield, the Leighton Family Professor in the Department of Mathematics: Sheffield is a probability theorist, working on geometrical questions that arise in such areas as statistical physics, game theory and metric spaces, as well as long-standing problems in percolation theory.

Susan Solomon, the Lee and Geraldine Martin Professor in Environmental Studies in the Department of Earth, Atmospheric and Planetary Sciences: Solomon focuses on issues relating to both atmospheric climate chemistry and climate change, and is well-recognized for her insights in explaining the cause of the Antarctic ozone “hole” as well as her research on the irreversibility of global warming linked to anthropogenic carbon dioxide emissions and on the influence of the ozone hole on the climate of the southern hemisphere.

Stefani Spranger, the Howard S. (1953) and Linda B. Stern Career Development Professor in the Department of Biology: Spranger studies the interactions between cancer and the immune system with the goal of improving existing immunotherapies or developing novel therapeutic approaches. Spranger seeks to understand how CD8 T cells, otherwise known as killer T cells, are excluded from the tumor microenvironment, with a focus on lung and pancreatic cancers.

School of Science Infinite Kilometer Awards for 2017

Eight research staffers and postdocs are recognized for their extraordinary contributions and dedication to programs, colleagues, and the Institute.

School of Science
January 16, 2018

The MIT School of Science has announced the 2017 winners of the Infinite Kilometer Award. The Infinite Kilometer Award was established in 2012 to highlight and reward the extraordinary — but often underrecognized — work of the school’s research staff and postdocs.

Recipients of the award are exceptional contributors to their research programs. In many cases, they are also deeply committed to their local or global MIT community, and are frequently involved in mentoring and advising their junior colleagues, participating in the school’s educational programs, making contributions to the MIT Postdoctoral Association, or contributing to some other facet of the MIT community.

In addition to a monetary award, honorees and their colleagues, friends, and family are invited to a celebratory lunch in May.

The 2017 Infinite Kilometer winners are:

Rodrigo Garcia, McGovern Institute for Brain Research;

Lydia Herzel, Department of Biology;

Yutaro Iiyama, Laboratory for Nuclear Science;

Kendrick Jones, Picower Institute for Learning and Memory;

Matthew Musgrave, Laboratory for Nuclear Science;

Cody Siciliano, Picower Institute for Learning and Memory;

Peter Sudmant, Department of Biology;

Ashley Watson, Picower Institute for Learning and Memory;

The School of Science is also currently accepting nominations for its Infinite Mile Awards. Nominations are due by Feb. 16 and all School of Science employees are eligible. Infinite Mile Awards will be presented with the Infinite Kilometer Awards this spring.

Biologists’ new peptide could fight many cancers

Drug that targets a key cancer protein could combat leukemia and other types of cancer.

Anne Trafton | MIT News Office
January 15, 2018

MIT biologists have designed a new peptide that can disrupt a key protein that many types of cancers, including some forms of lymphoma, leukemia, and breast cancer, need to survive.

The new peptide targets a protein called Mcl-1, which helps cancer cells avoid the cellular suicide that is usually induced by DNA damage. By blocking Mcl-1, the peptide can force cancer cells to undergo programmed cell death.

“Some cancer cells are very dependent on Mcl-1, which is the last line of defense keeping the cell from dying. It’s a very attractive target,” says Amy Keating, an MIT professor of biology and one of the senior authors of the study.

Peptides, or small protein fragments, are often too unstable to use as drugs, but in this study, the researchers also developed a way to stabilize the molecules and help them get into target cells.

Loren Walensky, a professor of pediatrics at Harvard Medical School and a physician at Dana-Farber Cancer Institute, is also a senior author of the study, which appears in the Proceedings of the National Academy of Sciences the week of Jan. 15. Researchers in the lab of Anthony Letai, an associate professor of medicine at Harvard Medical School and Dana-Farber, were also involved in the study, and the paper’s lead author is MIT postdoc Raheleh Rezaei Araghi.

A promising target

Mcl-1 belongs to a family of five proteins that play roles in controlling programmed cell death, or apoptosis. Each of these proteins has been found to be overactive in different types of cancer. These proteins form what is called an “apoptotic blockade,” meaning that cells cannot undergo apoptosis, even when they experience DNA damage that would normally trigger cell death. This allows cancer cells to survive and proliferate unchecked, and appears to be an important way that cells become resistant to chemotherapy drugs that damage DNA.

“Cancer cells have many strategies to stay alive, and Mcl-1 is an important factor for a lot of acute myeloid leukemias and lymphomas and some solid tissue cancers like breast cancers. Expression of Mcl-1 is upregulated in many cancers, and it was seen to be upregulated as a resistance factor to chemotherapies,” Keating says.

Many pharmaceutical companies have tried to develop drugs that target Mcl-1, but this has been difficult because the interaction between Mcl-1 and its target protein occurs in a long stretch of 20 to 25 amino acids, which is difficult to block with the small molecules typically used as drugs.

Peptide drugs, on the other hand, can be designed to bind tightly with Mcl-1, preventing it from interacting with its natural binding partner in the cell. Keating’s lab spent many years designing peptides that would bind to the section of Mcl-1 involved in this interaction — but not to other members of the protein family.

Once they came up with some promising candidates, they encountered another obstacle, which is the difficulty of getting peptides to enter cells.

“We were exploring ways of developing peptides that bind selectively, and we were very successful at that, but then we confronted the problem that our short, 23-residue peptides are not promising therapeutic candidates primarily because they cannot get into cells,” Keating says.

To try to overcome this, she teamed up with Walensky’s lab, which had previously shown that “stapling” these small peptides can make them more stable and help them get into cells. These staples, which consist of hydrocarbons that form crosslinks within the peptides, can induce normally floppy proteins to assume a more stable helical structure.

Keating and colleagues created about 40 variants of their Mcl-1-blocking peptides, with staples in different positions. By testing all of these, they identified one location in the peptide where putting a staple not only improves the molecule’s stability and helps it get into cells, but also makes it bind even more tightly to Mcl-1.

“The original goal of the staple was to get the peptide into the cell, but it turns out the staple can also enhance the binding and enhance the specificity,” Keating says. “We weren’t expecting that.”

Killing cancer cells

The researchers tested their top two Mcl-1 inhibitors in cancer cells that are dependent on Mcl-1 for survival. They found that the inhibitors were able to kill these cancer cells on their own, without any additional drugs. They also found that the Mcl-1 inhibitors were very selective and did not kill cells that rely on other members of the protein family.

Keating says that more testing is needed to determine how effective the drugs might be in combating specific cancers, whether the drugs would be most effective in combination with others or on their own, and whether they should be used as first-line drugs or when cancers become resistant to other drugs.

“Our goal has been to do enough proof-of-principle that people will accept that stapled peptides can get into cells and act on important targets. The question now is whether there might be any animal studies done with our peptide that would provide further validation,” she says.

Joshua Kritzer, an associate professor of chemistry at Tufts University, says the study offers evidence that the stapled peptide approach is worth pursuing and could lead to new drugs that interfere with specific protein interactions.

“There have been a lot of biologists and biochemists studying essential interactions of proteins, with the justification that with more understanding of them, we would be able to develop drugs that inhibit them. This work now shows a direct line from biochemical and biophysical understanding of protein interactions to an inhibitor,” says Kritzer, who was not involved in the research.

Keating’s lab is also designing peptides that could interfere with other relatives of Mcl-1, including one called Bfl-1, which has been less studied than the other members of the family but is also involved in blocking apoptosis.

The research was funded by the Koch Institute Dana-Farber Bridge Project and the National Institutes of Health.