MIT News - Cancer

Gene-controlling mechanisms play key role in cancer progression

Anne Trafton | MIT News Office — Thu, 23 Jul 2020 10:36:51 -0400

As cancer cells evolve, many of their genes become overactive while others are turned down. These genetic changes can help tumors grow out of control and become more aggressive, adapt to changing conditions, and eventually lead the tumor to metastasize and spread elsewhere in the body.

MIT and Harvard University researchers have now mapped out an additional layer of control that guides this evolution — an array of structural changes to “chromatin,” the mix of proteins, DNA, and RNA that makes up cells’ chromosomes. In a study of mouse lung tumors, the researchers identified 11 chromatin states, also called epigenomic states, that cancer cells can pass through as they become more aggressive.

“This work provides one of the first examples of using single-cell epigenomic data to comprehensively characterize genes that regulate tumor evolution in cancer,” says Lindsay LaFave, an MIT postdoc and the lead author of the study.

In addition, the researchers showed that a key molecule they found in the more aggressive tumor cell states is also linked to more advanced forms of lung cancer in humans, and could be used as a biomarker to predict patient outcomes.

Tyler Jacks, director of MIT’s Koch Institute for Integrative Cancer Research, and Jason Buenrostro, an assistant professor of stem cell and regenerative biology at Harvard University, are the senior authors of the study, which appears today in Cancer Cell.

Epigenomic control

While a cell’s genome contains all of its genetic material, the epigenome plays a critical role in determining which of these genes will be expressed. Every cell’s genome has epigenomic modifications — proteins and chemical compounds that attach to DNA but do not alter its sequence. These modifications, which vary by cell type, influence the accessibility of genes and help to make a lung cell different from a neuron, for example.

Epigenomic changes are also believed to influence cancer progression. In this study, the MIT/Harvard team set out to analyze the epigenomic changes that occur as lung tumors develop in mice. They studied a mouse model of lung adenocarcinoma, which results from two specific genetic mutations and closely recapitulates the development of human lung tumors.

Using a new technology for single-cell epigenome analysis that Buenrostro had previously developed, the researchers analyzed the epigenomic changes that occur as tumor cells evolve from early stages to later, more aggressive stages. They also examined tumor cells that had metastasized beyond the lungs.

This analysis revealed 11 different chromatin states, based on the locations of epigenomic alterations and density of the chromatin. Within a single tumor, there could be cells from all 11 of the states, suggesting that cancer cells can follow different evolutionary pathways.

For each state, the researchers also identified corresponding changes in where gene regulators called transcription factors bind to chromosomes. When transcription factors bind to the promoter region of a gene, they initiate the copying of that gene into messenger RNA, essentially controlling which genes are active. Chromatin modifications can make gene promoters more or less accessible to transcription factors.

“If the chromatin is open, a transcription factor can bind and activate a specific gene program,” LaFave says. “We were trying to understand those transcription factor networks and then what their downstream targets were.”

As the structure of tumor cells’ chromatin changed, transcription factors tended to target genes that would help the cells to lose their original identity as lung cells and become less differentiated. Eventually many of the cells also gained the ability to leave their original locations and seed new tumors.

Much of this process was controlled by a transcription factor called RUNX2. In more aggressive cancer cells, RUNX2 promotes the transcription of genes for proteins that are secreted by cells. These proteins help remodel the environment surrounding the tumor to make it easier for cancer cells to escape.

The researchers also found that these aggressive, premetastatic tumor cells were very similar to tumor cells that had already metastasized.

“That suggests that when these cells were in the primary tumor, they actually changed their chromatin state to look like a metastatic cell before they migrated out into the environment,” LaFave says. “We believe they undergo an epigenetic change in the primary tumor that allows them to become migratory and then seed in a distal location like the lymph nodes or the liver.”

A new biomarker

The researchers also compared the chromatin states they identified in mouse tumor cells to chromatin states seen in human lung tumors. They found that RUNX2 was also elevated in more aggressive human tumors, suggesting that it could serve as a biomarker for predicting patient outcomes.

“The RUNX positive state was very highly predictive of poor survival in human lung cancer patients,” LaFave says. “We’ve also shown the inverse, where we have signatures of early states, and they predict better prognosis for patients. This suggests that you can use these single-cell gene regulatory networks as predictive modules in patients.”

RUNX could also be a potential drug target, although it traditionally has been difficult to design drugs that target transcription factors because they usually lack well-defined structures that could act as drug docking sites. The researchers are also seeking other potential targets among the epigenomic changes that they identified in more aggressive tumor cell states. These targets could include proteins known as chromatin regulators, which are responsible for controlling the chemical modifications of chromatin.

“Chromatin regulators are more easily targeted because they tend to be enzymes,” LaFave says. “We’re using this framework to try to understand what are the important targets that are driving these state transitions, and then which ones are therapeutically targetable.”

The research was funded by a Damon Runyon Cancer Foundation postdoctoral fellowship, the Paul G. Allen Frontiers Group, the National Institutes of Health, and the Koch Institute Support (core) Grant from the National Cancer Institute.

How cancer drugs find their targets

Eva Frederick | Whitehead Institute — Fri, 26 Jun 2020 14:20:01 -0400

In the watery inside of a cell, complex processes take place in tiny functional compartments called organelles. Energy-producing mitochondria are organelles, as is the frilly golgi apparatus, which helps to transport cellular materials. Both of these compartments are bound by thin membranes.

But in the past few years, research at Whitehead Institute and elsewhere has shown that there are other cellular organelles held together without a membrane. These organelles, called condensates, are tiny droplets which keep certain proteins close together amidst the chaos of the cell, allowing complex functions to take place within. “We know of about 20 types of condensate in the cell so far,” says Isaac Klein, a postdoc in Richard Young’s lab at the Whitehead Institute and oncologist at the Dana-Farber Cancer Institute.

Now, in a paper published in Science on June 19, Klein and Ann Boija, another postdoc in Young’s lab, show the mechanism by which small molecules, including cancer drugs, are concentrated in these cellular droplets — a finding that could have implications for the development of new cancer therapeutics. If researchers could tailor a chemical to seek out and concentrate in one kind of droplet in particular, it might have a positive effect on the delivery efficiency of the drug. “We thought, maybe that's an avenue by which we can improve cancer treatments and discover new ones,” says Klein.

“This [research] is part of a revolutionary new way of looking at the organization within cells,” says MIT Institute Professor Phillip Sharp, a professor of biology at the Koch Institute for Integrative Cancer Research and a co-author on the study. “Cells are not little pools of soup, all mixed together. They are actually highly organized, compartmentalized units, and that organization is important in their function and in their diseases. We've just started to understand that, and this new paper is a really important step, using that insight, to understand how to potentially treat diseases differently.”

Condensates and drug delivery

To explore how different properties of condensates inside the cell’s nucleus affected the delivery of cancer drugs, Boija and Klein selected a few example condensates to study. These included splicing speckles, which store cellular materials needed for RNA splicing; nucleoli, where ribosomes are formed; and a new kind of droplet Young’s lab discovered in 2018 called a transcriptional condensate. These new condensates bring together all the different proteins needed to successfully transcribe a gene.

The researchers created their own suite of four different fluorescently-labeled condensates by adding glowing tags to marker proteins specific to each kind of droplet. For example, transcriptional condensates are marked by the droplet-forming protein MED1, splicing speckles by a protein called SRSF2, and nucleoli by FIB1 and NPM1.

Now that they could tell individual droplets apart by their cellular purpose, the team, along with the help of Nathanael Gray, a chemical biologist at Harvard University and the Dana-Farber Cancer Institute, created fluorescent versions of clinically important drugs. The tested drugs included cisplatin and mitoxantrone, two anti-tumor medicines commonly used in chemotherapy. These therapeutics were the perfect test subjects, because they both target proteins that lie within nuclear condensates.

The researchers added the cancer drugs to a mixture containing various droplets (and only droplets, none of the actual drug targets), and found that the drugs sorted themselves into specific condensates. Mitoxantrone concentrated in condensates marked by MED1, FIB1 and NPM1, selectively avoiding the others. Cisplatin, too, showed a particular affinity for droplets held together by MED1.

“The big discovery with these in vitro studies is that a drug can concentrate within transcriptional condensate independent of its target,” Boija says. “We used to think that drugs come to the right place because their targets are there, but in our in vitro system, the target is not there. That’s really informative — it shows the drug is actually being concentrated in a different way than we thought.”

To understand why some drugs were drawn into transcriptional condensates, they screened a panel of chemically-modified dyes and found that the important part of many drugs — the part that led them to concentrate in transcriptional condensates — is the molecules’ aromatic ring structure. Aromatic rings are stable, ring-shaped groupings of carbon atoms. The aromatic ring in some drugs are thought to stack with rings in MED1’s amino acids, leading the drug to concentrate in transcriptional condensates.

Being able to tailor a drug to enter a certain condensate is a powerful tool for drug developers. “We found that if we add an aromatic group to a molecule, it becomes concentrated within the transcriptional condensate,” Boija says. “It's that type of interaction that is important when we design new drugs to enter transcriptional condensates — and maybe we can improve existing drugs by modifying their structure. This will be very exciting to look into.”

Where drugs concentrate affects how well they fight cancer

In order for this tool to be practically useful in drug development, the researchers had to make sure that concentration in specific droplets would actually impact the drugs’ performance. Boija and Klein decided to test this using cisplatin, which is drawn to transcriptional condensates by MED1 and works to fight cancer by adding clunky platinum molecules to DNA strands. This damages tumor cells’ genetic material. When the researchers administered cisplatin to a mixture of different condensates, both in the test tube and in cells, the drug preferentially altered DNA that lay within transcriptional condensates.

This could explain why cisplatin and other platinum drugs are effective against so many diverse cancers, says Young, who is also a professor of biology at MIT; cancer-causing genes often carry regions of DNA called super enhancers, which are extremely active in transcription, leading to very large transcriptional condensates. “We now think the reason that drugs like cisplatin can work well in patients with diverse cancers is because they're becoming selectively concentrated at the cancer-causing genes, where these large transcriptional condensates occur,” he says. “The effect is to have the drug home in on the gene that's causing each cancer to be so deadly.”

A drug resistance mystery, solved

The new insights in condensate behavior also provided some answers to another question in cancer research: why people become immune to the breast cancer drug tamoxifen.Tamoxifen works by attaching itself to estrogen receptors in the cancer cells, preventing them from getting the hormones they need to grow and eventually slowing or stopping the formation of new cancer cells altogether. The drug is one of the most effective treatments for the disease, reducing recurrence rates for ER+ breast cancers by around 50 percent.

Unfortunately, many patients quickly develop a resistance to tamoxifen — sometimes as soon as a few months after they start taking it. This happens in a variety of ways — for example, sometimes the cancer cells will mutate to be able to kick the tamoxifen out of the cells, or simply produce fewer estrogen receptors for the drug to bind. One form of resistance was associated with an overproduction of the protein MED1, but scientists didn’t know why.

With their newfound knowledge of how a drug’s activity is affected by where it concentrates, Boija and Klein had a hypothesis: The extra MED1 might increase the size of the droplets, effectively diluting the concentration of tamoxifen and making it more difficult for the drug to bind its targets. When they tested this in the laboratory, the team found that more MED1 did indeed cause larger droplets, leading to lower concentrations of tamoxifen.

A new toolset for drug designers

The ability to better understand the behavior of drugs in cancer cells — how they concentrate, and why the cancer could become resistant to them — may provide drug developers with a new arsenal of tools to craft efficient therapeutics.

“This study suggests that we should be exploring whether we can design or isolate drugs that are concentrated in a given condensate, and to understand how existing drugs are concentrated in the cell,” says Phil Sharp. “I think this is really important for drug development — and I think [figuring it out] is going to be fun.”

Counting your antigens

Bendta Schroeder | Koch Institute — Tue, 02 Jun 2020 09:00:00 -0400

Normally, the immune system is able to differentiate between healthy and abnormal cells. Peptides, fragments created by the synthesis and breakdown of proteins inside each cell, are presented on the surface as antigens and act as signals to immune cells whether the cell should be left alone or flagged for destruction and removal.

Because cancer cells display a small number of tumor-associated antigens and antigens that result from genetic mutations, they can be targeted by the immune system. However, cancer cells can develop strategies for evading detection by the immune system. Cancer immunotherapies counteract those strategies, but only for some cancers and only in some patients. Those that do work produce powerful results.

Researchers and clinicians are exploring how to improve the success rate of immunotherapies for more cancer types and patients. In this effort, they are combining immunotherapies with targeted therapies, small molecules designed to inhibit selected protein targets in the cell. To design effective combinations, a better understanding of how targeted therapies change the immunopeptidome — the repertoire of surface-presenting peptide antigens — is needed.

A team of researchers including Koch Institute members Forest White, the Ned C. and Janet Bemis Rice Professor and member of the MIT Center for Precision Cancer Medicine, and Douglas Lauffenburger, Ford Professor of Biological Engineering, Chemical Engineering, and Biology, developed a technique for accurately quantifying changes in the immunopeptidome.

In a study led by graduate student Lauren Stopfer and appearing in Nature Communications, researchers used the platform to analyze the effect of CDK4/6 inhibitors, a class of known anticancer agents, on the immunopeptidome of melanoma cell lines. In addition to identifying potential antigen targets for drug development, their results highlighted the potential of CDK4/6 inhibitors to make an effective partner for certain kinds of immunotherapies. Ultimately, the platform could help cancer researchers design new targeted drugs and immunotherapies or clinical trials for combinations of these types of therapies.

High-quality quantification

Currently, in order to examine how a cell changes its immunopeptidome in response to exposure to a drug or other perturbation, researchers perform a technique known as mass spectrometry to quantify the foldchange, or relative change in magnitude between subsequent measurements, of the expression of peptide antigens. However, most current mass spectrometry-based methods do not provide a complete — or even reliably accurate — picture of immunopeptidome dynamics.

The process of preparing a sample for mass spectrometry analysis can result in substantial losses of antigens. In isolating the relatively small number of antigen peptides from the entire contents of cells, there can be significant variation in the proportion of peptide antigens recovered from sample to sample or from peptide to peptide. Existing methods for accounting for how many antigens are lost are laborious and have limited effectiveness.

Foldchange alone does not indicate the magnitude of a change in peptide antigen levels. For example, a three-fold increase in antigens may mean an increase from 10 to 30 antigens, or it may mean an increase of 1,000 to 3,000. Because different drugs require different antigens to be present at different quantities in order to be effective, an accurate count of the change in antigen is needed to identify drugs that elicit the optimal response in the cell. Furthermore, the measurement may be undermined by underlying “noise” in the sample — data that can cloud the relative proportion of observable “signal” produced by the antigen of interest.

“People will say that you need a certain number of a peptide antigen in order for an immunotherapy to work, but, right now, that number is typically based on anecdotal evidence,” says White. “To make truly informed decisions about immunotherapy options, there needs to be a way to quantify antigens very accurately and very reliably.”

The new platform enables the accurate quantification of peptide antigens presented at the cell surface, accounting for variation in sample processing and giving an absolute number of detectable peptides. Using a widely available ultraviolet light-based technology, the method inserts peptides loaded with heavy isotopes into genetically engineered versions of the molecules that present the antigens on the cell surface, class I major histocompatibility complexes (MHCs). The labeled peptide-MHC (pMHC) complexes are then added to samples of the contents of whole cells. When the antigen peptides are extracted, the heavy isotope labeled peptides can be used to account for how many antigens have been lost to processing.

To determine how many of a specific antigen are presented on cells, heavy isotope labeled pMHCs can be added to samples of cell contents at different concentrations. The resulting standard curve, or graph, can be used to extrapolate the number of peptide antigens.

Making antigens count

The researchers used the new platform to quantify how CDK4/6 inhibitors change the repertoire of antigens presented on the surface of melanoma cells.

Melanoma can be treated effectively with a class of immunotherapy called immune checkpoint blockade inhibitors, but as many as 40 percent of patients do not respond to these therapies. Recent studies have suggested that checkpoint blockade immunotherapies may be more effective in more patients when combined with other anticancer agents, particularly those that stimulate an immune response, such as CDK4/6 inhibitors. CDK4/6 inhibitors are thought to strengthen the immune system’s response to cancer in part by increasing expression of MHCs, thereby rendering cancer cells more visible to the immune system.

Researchers profiled peptide antigen repertoires in four cell lines of melanoma treated with the CDK4/6 inhibitor palbociclib at low and high doses, finding that low doses of the palbociclib resulted in a larger increase of MHC presentation than the higher-dose therapy. At lower doses, the immunopeptidome showed increases in tumor-associated peptide antigens derived from intracellular pathways known to be affected by the inhibition of CDK4 and CDK6. These results add to a growing body of evidence that CDK4/6 could be used together with checkpoint blockade to increase the immune system’s ability to respond to tumors, and suggest that CDK4/6 inhibitors and other treatments like them could be used to tune which peptides are presented to the immune system.

The researchers were also able to identify an antigen, a serine-phosphorylated IRS2 peptide, that occurs exclusively in malignant tumors. They found that it was expressed at high levels, demonstrating that the platform could also be used to help cancer researchers identify immunotherapy targets.

Because of its sensitivity and speed, the new platform could be used in the clinic to develop treatment strategies on a patient-specific basis. The multiplexed platform can analyze many samples in tandem, allowing for the short time scale critical to clinical trials. Its sensitivity allows it to be used on small samples, including samples from individual patients’ tumors. Analysis of peptide antigen repertoire changes could be used to optimize the order and timing of therapies for the greatest impact, in addition to calibrating cancer cells’ antigen presentation for targeting by immunotherapies.

“One of the most promising applications for this tool is to better understand how much of some of these peptide antigen targets are presented, not just on cell lines, but in real tumors,” says Stopfer. “Knowing how much antigen is present in tumor cells could inform what kind of therapies we develop and our ability to make informed decisions about immunotherapy options.”

The research was funded by the National Institutes of Health, a Melanoma Research Alliance Team Science Award, the MIT Center for Precision Cancer Medicine, the Koch Institute Frontier Research Program through the Kathy and Curt Marble Cancer Research Fund, and the Takeda Pharmaceuticals Immune Oncology Research Fund.

A boost for cancer immunotherapy

Anne Trafton | MIT News Office — Mon, 01 Jun 2020 14:59:59 -0400

One promising strategy to treat cancer is stimulating the body’s own immune system to attack tumors. However, tumors are very good at suppressing the immune system, so these types of treatments don’t work for all patients.

MIT engineers have now come up with a way to boost the effectiveness of one type of cancer immunotherapy. They showed that if they treated mice with existing drugs called checkpoint inhibitors, along with new nanoparticles that further stimulate the immune system, the therapy became more powerful than checkpoint inhibitors given alone. This approach could allow cancer immunotherapy to benefit a greater percentage of patients, the researchers say.

“These therapies work really well in a small portion of patients, and in other patients they don’t work at all. It’s not entirely understood at this point why that discrepancy exists,” says Colin Buss PhD ’20, the lead author of the new study.

The MIT team devised a way to package and deliver small pieces of DNA that crank up the immune response to tumors, creating a synergistic effect that makes the checkpoint inhibitors more effective. In studies in mice, they showed that the dual treatment halted tumor growth, and in some cases, also stopped the growth of tumors elsewhere in the body.

Sangeeta Bhatia, the John and Dorothy Wilson Professor of Health Sciences and Technology and Electrical Engineering and Computer Science, and a member of MIT’s Koch Institute for Integrative Cancer Research and the Institute for Medical Engineering and Science, is the senior author of the paper, which appears this week in the Proceedings of the National Academy of Sciences.

Removing the brakes

The human immune system is tuned to recognize and destroy abnormal cells such as cancer cells. However, many tumors secrete molecules that suppress the immune system in the environment surrounding the tumor, rendering the T cell attack useless.

The idea behind checkpoint inhibitors is that they can remove this “brake” on the immune system and restore T cells’ ability to attack tumors. Several of these inhibitors, which target checkpoint proteins such as CTLA-4, PD-1, and PD-L1, have been approved to treat a variety of cancers. These drugs work by turning off checkpoint proteins that prevent T cells from being activated.

“They work incredibly well in some patients, and they’ve given what some would call cures, for about 15 to 20 percent of patients with particular cancers,” Bhatia says. “However, there’s still a lot more to do to open up the possibility of using this approach for more patients.”

Some studies have found that combining checkpoint inhibitors with radiation therapy can make them more effective. Another approach that researchers have tried is combining them with immunostimulatory drugs. One such class of drugs is oligonucleotides — specific sequences of DNA or RNA that the immune system recognizes as foreign.

However, clinical trials of these immunostimulatory drugs have not been successful, and one possible reason is that the drugs are not reaching their intended targets. The MIT team set out to find a way to achieve more targeted delivery of these immunostimulatory drugs, allowing them to accumulate at tumor sites.

To do that, they packaged oligonucleotides into tumor-penetrating peptides that they had previously developed for delivering RNA to silence cancerous genes. These peptides can interact with proteins found on the surfaces of cancer cells, helping them to specifically target tumors. The peptides also include positively charged segments that help them penetrate cell membranes once they reach the tumor.

The oligonucleotides that Bhatia and Buss decided to use for this study contain a specific DNA sequence that often occurs in bacteria but not in human cells, so that the human immune system can recognize it and respond. These oligonucleotides specifically activate immune cell receptors called toll-like receptors, which detect microbial invaders.

“These receptors evolved to allow cells to recognize the presence of pathogens like bacteria,” Buss says. “That tells the immune system that there’s something dangerous here: Turn on and kill it.”

A synergistic effect

After creating their nanoparticles, the researchers tested them in several different mouse models of cancer. They tested the oligonucleotide nanoparticles on their own, the checkpoint inhibitors on their own, and the two treatments together. The two treatments together produced the best results, by far.

“When we combined the particles with the checkpoint inhibitor antibody, we saw a vastly improved response relative to either the particles alone or the checkpoint inhibitor alone,” Buss says. “When we treat these mice with particles and the checkpoint inhibitor, we can stop their cancer from progressing.”

The researchers also wondered whether they could stimulate the immune system to target tumors that had already spread through the body. To explore that possibility, they implanted mice with two tumors, one on each side of the body. They gave the mice the checkpoint inhibitor treatment throughout the entire body but injected the nanoparticles into only one tumor. They found that once T cells had been activated by the treatment combination, they could also attack the second tumor.

“We saw some signs that you could stimulate in one location and then get a systemic response, which was encouraging,” Bhatia says.

The researchers now plan to perform safety testing of the particles, in hopes of further developing them to treat patients whose tumors don’t respond to checkpoint inhibitor drugs on their own. To that end, they are working with Errki Ruoslahti of the Sanford Burnham Prebys Medical Discovery Institute, who originally discovered the tumor-penetrating peptides. A company that Ruoslahti founded has already taken other versions of the tumor-penetrating peptides into human clinical trials to treat pancreatic cancer.

“That makes us optimistic about the potential to scale up, manufacture them, and advance them to help patients,” Bhatia says.

The research was funded by the Koch Institute Support (core) Grant from the National Cancer Institute, a Core Center Grant from the National Institute of Environmental Health Sciences, and the Koch Institute’s Marble Center for Cancer Nanomedicine. Bhatia also has affiliations with the Ludwig Institute for Cancer Research, the Broad Institute of MIT and Harvard, the Wyss Institute for Biologically Inspired Engineering, the Howard Hughes Medical Institute, and Brigham and Women’s Hospital.

Deep learning accurately stains digital biopsy slides

Becky Ham | MIT Media Lab — Fri, 22 May 2020 15:25:01 -0400

Tissue biopsy slides stained using hematoxylin and eosin (H&E) dyes are a cornerstone of histopathology, especially for pathologists needing to diagnose and determine the stage of cancers. A research team led by MIT scientists at the Media Lab, in collaboration with clinicians at Stanford University School of Medicine and Harvard Medical School, now shows that digital scans of these biopsy slides can be stained computationally, using deep learning algorithms trained on data from physically dyed slides.

Pathologists who examined the computationally stained H&E slide images in a blind study could not tell them apart from traditionally stained slides while using them to accurately identify and grade prostate cancers. What’s more, the slides could also be computationally “de-stained” in a way that resets them to an original state for use in future studies, the researchers conclude in their May 20 study published in JAMA Network.

This process of computational digital staining and de-staining preserves small amounts of tissue biopsied from cancer patients and allows researchers and clinicians to analyze slides for multiple kinds of diagnostic and prognostic tests, without needing to extract additional tissue sections.

“Our development of a de-staining tool may allow us to vastly expand our capacity to perform research on millions of archived slides with known clinical outcome data,” says Alarice Lowe, an associate professor of pathology and director of the Circulating Tumor Cell Lab at Stanford University, who was a co-author on the paper. “The possibilities of applying this work and rigorously validating the findings are really limitless.”

The researchers also analyzed the steps by which the deep learning neural networks stained the slides, which is key for clinical translation of these deep learning systems, says Pratik Shah, MIT principal research scientist and the study’s senior author.

“The problem is tissue, the solution is an algorithm, but we also need ratification of the results generated by these learning systems,” he says. “This provides explanation and validation of randomized clinical trials of deep learning models and their findings for clinical applications.”

Other MIT contributors are joint first author and technical associate Aman Rana (now at Amazon) and MIT postdoc Akram Bayat in Shah’s lab. Pathologists at Harvard Medical School, Brigham and Women's Hospital, Boston University School of Medicine, and Veterans Affairs Boston Healthcare provided clinical validation of the findings.

Creating “sibling” slides

To create computationally dyed slides, Shah and colleagues have been training deep neural networks, which learn by comparing digital image pairs of biopsy slides before and after H&E staining. It’s a task well-suited for neural networks, Shah said, “since they are quite powerful at learning a distribution and mapping of data in a manner that humans cannot learn well.”

Shah calls the pairs “siblings,” noting that the process trains the network by showing them thousands of sibling pairs. After training, he said, the network only needs the “low-cost, and widely available easy-to-manage sibling,”— non-stained biopsy images—to generate new computationally H&E stained images, or the reverse where an H&E dye stained image is virtually de-stained.

In the current study, the researchers trained the network using 87,000 image patches (small sections of the entire digital images) scanned from biopsied prostate tissue from 38 men treated at Brigham and Women’s Hospital between 2014 and 2017. The tissues and the patients’ electronic health records were de-identified as part of the study.

When Shah and colleagues compared regular dye-stained and computationally stained images pixel by pixel, they found that the neural networks performed accurate virtual H&E staining, creating images that were 90-96 percent similar to the dyed versions. The deep learning algorithms could also reverse the process, de-staining computationally colored slides back to their original state with a similar degree of accuracy.

“This work has shown that computer algorithms are able to reliably take unstained tissue and perform histochemical staining using H&E,” says Lowe, who said the process also “lays the groundwork” for using other stains and analytical methods that pathologists use regularly.

Computationally stained slides could help automate the time-consuming process of slide staining, but Shah said the ability to de-stain and preserve images for future use is the real advantage of the deep learning techniques. “We’re not really just solving a staining problem, we’re also solving a save-the-tissue problem,” he said.

Software as a medical device

As part of the study, four board-certified and trained expert pathologists labeled 13 sets of computationally stained and traditionally stained slides to identify and grade potential tumors. In the first round, two randomly selected pathologists were provided computationally stained images while H&E dye-stained images were given to the other two pathologists. After a period of four weeks, the image sets were swapped between the pathologists, and another round of annotations were conducted. There was a 95 percent overlap in the annotations made by the pathologists on the two sets of slides. “Human readers could not tell them apart,” says Shah.

The pathologists’ assessments from the computationally stained slides also agreed with majority of the initial clinical diagnoses included in the patient’s electronic health records. In two cases, the computationally stained images overturned the original diagnoses, the researchers found.

“The fact that diagnoses with higher accuracy were able to be rendered on digitally stained images speaks to the high fidelity of the image quality,” Lowe says.

Another important part of the study involved using novel methods to visualize and explain how the neural networks assembled computationally stained and de-stained images. This was done by creating a pixel-by-pixel visualization and explanation of the process using activation maps of neural network models corresponding to tumors and other features used by clinicians for differential diagnoses.

This type of analysis helps to create a verification process that is needed when evaluating “software as a medical device,” says Shah, who is working with the U.S. Food and Drug Administration on ways to regulate and translate computational medicine for clinical applications.

“The question has been, how do we get this technology out to clinical settings for maximizing benefit to patients and physicians?” Shah says. “The process of getting this technology out involves all these steps: high quality data, computer science, model explanation and benchmarking performance, image visualization, and collaborating with clinicians for multiple rounds of evaluations.”

The JAMA Network study was supported by the Media Lab Consortium and the Department of Pathology at Brigham and Women’s Hospital.

Making an impact through chemical engineering

Anne Trafton | MIT News Office — Mon, 18 May 2020 23:59:59 -0400

As a chemical engineer, Hadley Sikes loves studying complex systems such as networks of chemical reactions. But in her work designing practical devices for diagnostics and other applications, she embraces simplicity.

Sikes, an associate professor who recently earned tenure in MIT’s Department of Chemical Engineering, devotes much of her lab’s effort to devising inexpensive, highly sensitive tests for diseases such as malaria, tuberculosis, and cancer. Making these tests easy to use is key to their success, she says.

“In the products that we want to widely disseminate, our idea is that if things are as simple as they can be, that might give them a better chance of being more widely used,” she says.

In recent months, she has turned her attention to developing a diagnostic test for Covid-19. Unlike most diagnostics, which look for the virus’s genetic material (RNA), the test she is working on detects viral proteins, and would yield results quickly, with no specialized instruments required.

The tests she develops in her lab, while simple in appearance and use, are based on a detailed understanding of the complicated mechanisms of reactions such as transfers of electrons between atoms (known as redox reactions), as well as the precise molecular interactions between different proteins.

“In chemical engineering, we often teach our students about reactions that are occurring in chemical reactors or in engines, but you can use that same sort of methodology to study the reactions that are going on inside a cell,” Sikes says.

Fundamental chemistry

Sikes was drawn to science starting in elementary school, and she began participating in science fairs as a middle school student in Mobile, Alabama. In one project, she did a caffeine toxicology study on sea urchin embryos in hopes of persuading her father, a professor of biology at the University of South Alabama, to cut down on his coffee consumption. (Her findings did not have the desired effect.)

At Tulane University, Sikes majored in chemistry, where she worked in a lab studying phase transitions — the transformations between states of matter such as solid to liquid. She went on to Stanford University for graduate school, where she earned a PhD in physical chemistry. For her thesis, she studied a particular aspect of redox chemistry: the properties of organic materials that could be used to move electrons as quickly as possible from the surface of an electrode to an oxidizing agent dissolved in the solution surrounding the electrode.

Following those studies in fundamental chemical phenomena, Sikes decided that she wanted to try to apply her knowledge to real-world problems. “If we can have this high-level fundamental understanding and be able to design experiments and uncover molecular mechanisms, what sorts of societal benefit could I aim that at?” she says.

As a postdoc in a chemical engineering lab at the University of Colorado, she decided to try to develop biosensors that can detect interactions between proteins and other molecules. She realized that for the work to succeed, she needed to learn more about engineering proteins, so she spent two years at Caltech working in the lab of Frances Arnold, a Nobel Prize-winning pioneer in the use of directed evolution to engineer enzymes.

When applying for faculty positions, Sikes was drawn to MIT, in particular the Department of Chemical Engineering, by its focus on doing science that can be valuable to society.

“The department was excited about the same thing that I was: the idea of using science and technology to have an impact in the world,” she says. “Since that’s what I really cared about, I liked that that was not just something you could do on your own time, after you published your papers, but that was the whole purpose here.”

Simple sensors

Sikes’ lab now divides its efforts between two main projects: diagnostic sensors for infectious diseases common in the developing world, and sensors that could be used to help cancer doctors predict the best treatment for individual patients’ tumors.

In the area of infectious disease, Sikes and her colleagues are working on paper tests that could be used to detect up to five different diseases from one patient sample, which could be blood, urine, or saliva. The goal is to make the tests easy to read and inexpensive — less than a dollar per test. They have identified markers for malaria, tuberculosis, Dengue virus, and Zika virus, and are working on developing very small antibody proteins to interact with those markers. The smaller the proteins, the higher concentration they can put on the test strip, which allows it to produce results within just a few minutes.

Much of this work is being done as part of the Singapore-MIT Alliance for Research and Technology, especially the Antimicrobial Resistance Interdisciplinary Research Group.

On the cancer side, Sikes uses her expertise in redox chemistry to study the role of oxidative stress in cancer. Some tumors exhibit high levels of this kind of stress, which is caused by altered metabolism and leads to increased levels of hydrogen peroxide, an oxidant. This is somewhat surprising, Sikes says, because tumors can be cut off from the body’s blood supply and have little oxygen available.

“There’s this mystery of where are all these oxidants coming from, if it’s not an oxygen-rich environment,” Sikes says. “There’s also an idea that oxidative stress could be targeted with therapeutics that would induce cancer cell death.”

However, there is also evidence that some tumors become more aggressive when treated with drugs that target oxidative stress, so Sikes is now working to develop ways to predict how tumor cells from different patients would respond to such drugs. These studies are based on precise measurements of different oxidation states of sulfur sites within proteins, which are common targets of oxidants, and their locations within cells. The researchers correlate this data with how the cells respond to treatment with a variety of different drugs, in hopes that they can identify markers that reveal whether a particular tumor cell will be susceptible to drugs that affect the cell’s oxidative state.

“We’re hoping to discover what to measure in a tumor biopsy to know if this tumor is going to be susceptible to a redox drug or not, and our reaction network analysis has told us what to look for,” Sikes says. “Understanding complex chemical reaction networks like these is something that is core to chemical engineering.”

New sensors could offer early detection of lung tumors

Anne Trafton | MIT News Office — Wed, 01 Apr 2020 13:59:59 -0400

People who are at high risk of developing lung cancer, such as heavy smokers, are routinely screened with computed tomography (CT), which can detect tumors in the lungs. However, this test has an extremely high rate of false positives, as it also picks up benign nodules in the lungs.

Researchers at MIT have now developed a new approach to early diagnosis of lung cancer: a urine test that can detect the presence of proteins linked to the disease. This kind of noninvasive test could reduce the number of false positives and help detect more tumors in the early stages of the disease.

Early detection is very important for lung cancer, as the five-year survival rates are at least six times higher in patients whose tumors are detected before they spread to distant locations in the body.

“If you look at the field of cancer diagnostics and therapeutics, there’s a renewed recognition of the importance of early cancer detection and prevention. We really need new technologies that are going to give us the capability to see cancer when we can intercept it and intervene early,” says Sangeeta Bhatia, who is the John and Dorothy Wilson Professor of Health Sciences and Technology and Electrical Engineering and Computer Science, and a member of MIT’s Koch Institute for Integrative Cancer Research and the Institute for Medical Engineering and Science.

Bhatia and her colleagues found that the new test, which is based on nanoparticles that can be injected or inhaled, could detect tumors as small as 2.8 cubic millimeters in mice.

Bhatia is the senior author of the study, which appears today in Science Translational Medicine. The paper’s lead authors are MIT and Harvard University graduate students Jesse Kirkpatrick and Ava Soleimany, and former MIT graduate student Andrew Warren, who is now an associate at Third Rock Ventures.

Targeting lung tumors

For several years, Bhatia’s lab has been developing nanoparticles that can detect cancer by interacting with enzymes called proteases. These enzymes help tumor cells to escape their original locations by cutting through proteins of the extracellular matrix.

To find those proteins, Bhatia created nanoparticles coated with peptides (short protein fragments) that are targeted by cancer-linked proteases. The particles accumulate at tumor sites, where the peptides are cleaved, releasing biomarkers that can then be detected in a urine sample.

Her lab has previously developed sensors for colon and ovarian cancer, and in their new study, the researchers wanted to apply the technology to lung cancer, which kills about 150,000 people in the United States every year. People who receive a CT screen and get a positive result often undergo a biopsy or other invasive test to search for lung cancer. In some cases, this procedure can cause complications, so a noninvasive follow-up test could be useful to determine which patients actually need a biopsy, Bhatia says.

“The CT scan is a good tool that can see a lot of things,” she says. “The problem with it is that 95 percent of what it finds is not cancer, and right now you have to biopsy too many patients who test positive.”

To customize their sensors for lung cancer, the researchers analyzed a database of cancer-related genes called the Cancer Genome Atlas and identified proteases that are abundant in lung cancer. They created a panel of 14 peptide-coated nanoparticles that could interact with these enzymes.

The researchers then tested the sensors in two different mouse models of cancer, both of which are engineered with genetic mutations that lead them to naturally develop lung tumors. To help prevent background noise that could come from other organs or the bloodstream, the researchers injected the particles directly into the airway.

Using these sensors, the researchers performed their diagnostic test at three time points: 5 weeks, 7.5 weeks, and 10.5 weeks after tumor growth began. To make the diagnoses more accurate, they used machine learning to train an algorithm to distinguish between data from mice that had tumors and mice that did not.

With this approach, the researchers found that they could accurately detect tumors in one of the mouse models as early as 7.5 weeks, when the tumors were only 2.8 cubic millimeters, on average. In the other strain of mice, tumors could be detected at 5 weeks. The sensors’ success rate was also comparable to or better than the success rate of CT scans performed at the same time points.

Reducing false positives

The researchers also found that the sensors have another important ability — they can distinguish between early-stage cancer and noncancerous inflammation of the lungs. Lung inflammation, common in people who smoke, is one of the reasons that CT scans produce so many false positives.

Bhatia envisions that the nanoparticle sensors could be used as a noninvasive diagnostic for people who get a positive result on a screening test, potentially eliminating the need for a biopsy. For use in humans, her team is working on a form of the particles that could be inhaled as a dry powder or through a nebulizer. Another possible application is using these sensors to monitor how well lung tumors respond to treatment, such as drugs or immunotherapies.

“A great next step would be to take this into patients who have known cancer, and are being treated, to see if they're on the right medicine,” Bhatia says.

She is also working on a version of the sensor that could be used to distinguish between viral and bacterial forms of pneumonia, which could help doctors to determine which patients need antibiotics and may even provide complementary information to nucleic acid tests like those being developed for Covid-19. Glympse Bio, a company co-founded by Bhatia, is also working on developing this approach to replace biopsy in the assessment of liver disease.

The research was funded by the Koch Institute Support (core) Grant from the National Cancer Institute, the National Institute of Environmental Health Sciences, the National Science Foundation, the Ludwig Center for Molecular Oncology at MIT, the Koch Institute’s Marble Center for Cancer Nanomedicine, the Koch Institute Frontier Research Program through a gift from Upstage Lung Cancer, and Johnson and Johnson.

Thank you for your patients

Bendta Schroeder | Koch Institute — Mon, 23 Mar 2020 15:00:01 -0400

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

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

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

Network synergy

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

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

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

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

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

Speaking Frankly

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

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

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

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

The gratitude is mutual.

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

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

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

An entrepreneur finds his way to MIT

Shafaq Patel | MIT News correspondent — Mon, 17 Feb 2020 00:00:00 -0500

Jakub Chudik went to China for the first time on his dad’s business trip. A translator communicated in English, and Chudik translated to Slovak, his father’s native language. Just a few years later, as a rising junior at MIT, Chudik was in China again — this time to pitch his own business to Chinese investors.

He was pitching the startup he co-founded: ConquerX, which aims to develop a new type of blood test for detecting early-stage cancers. As chief technology officer, Chudik has high hopes for his company, but he’s also focused on finishing his senior year and graduating with a computer science and engineering degree.

Chudik began his journey to MIT as an entrepreneurially minded high school student in a small town in Slovakia. There, he discovered the free online courses offered by MITx on the edX platform.

He had learned English at his bilingual school and was interested in helping his mother grow her small accounting business, so he completed MITx’s Entrepreneurship 101 and 102 courses. From there, he applied and was accepted to the MIT Global Entrepreneurship Bootcamp.

Through the MIT Bootcamp, a weeklong innovation and leadership program on campus for people from across the world, Chudik — who at age 18 was one of the youngest in the group — conceptualized a business idea with a couple of other participants. Among them was Chudik’s current business partner, Deborah Zanforlin, who had the idea for the technology on which ConquerX is based. After the program, he decided to apply to MIT.

“I loved how welcoming the environment at MIT was,” Chudik recalls. “I felt I could be myself and always find support and guidance. Especially being able to have a frank one-on-one discussion with a professor made a big impression on me at the time.”

Hooked by helping people

Chudik became interested in medical technology, especially related to cancer, after his younger brother, who was a toddler at the time, was diagnosed with cancer during Chudik’s first year of high school. His brother is healthy now, but that experience was an eye-opener for Chudik.

“I had never had such a bad disease so close to me before. And I realized how much disease can impact not just the person but the whole family,” he says.

He was hooked by the idea of the startup once Zanforlin told him about the technology she had been working on.

“I thought it would be really great if I could be involved in helping people. I believed that I somewhat understood what people [experiencing cancer] were going through or what our company could help save them from” by enabling early intervention, Chudik says.

Chudik says he had always assumed that only doctors could help people with health problems. “I realize now that you can be an engineer; you could come up with good technology that would maybe help even more people than if you were a doctor.”

Now, through his experience with ConquerX, Chudik has become interested in the management and investing side of business. He thinks he might want to be a chief technology officer for other startups or become a venture capitalist and help fund small businesses.

Chudik spent this past summer working on his startup and gaining more experience — instead of doing an internship, he managed interns at his own startup. But he has used MIT’s Independent Activities Period (IAP) to acquire hands-on experience working for larger companies.

During the IAP of his sophomore year, he went to Singapore and was a research intern for a biomedical institute. And for his junior year, he worked as a data science intern in Geneva for Expedia.

“I must say, though, that classes and the startup have taken the majority of my time during college,” Chudik says.

No longer strictly ballroom

Chudik’s commitment to his startup echoes the way he delved into dance when he was growing up.

His junior high and high school experiences were filled with ballroom dancing. He got swept into it when one of his friends needed a partner, and her entire family came to his house to ask him to join her.

He danced for seven years, which included five years of competitive dance. He became extremely dedicated to the art, training for 12-20 hours a week plus entire weekends at competitions. He would travel to different cities throughout Slovakia, spend hours doing his hair and makeup, and practicing the routine.

After a while, competitive dance started to take over his life and added a lot of stress and demand on his parents, so he stopped.

“I’m glad it’s over now,” he says. Chudik says that he now has more control over his life and has a better sleeping and eating schedule in college than ever before.

“During international student orientation, the sophomore and junior orientation leaders found out about my ballroom dance experience. They tried tricking me into joining and spent the whole week trying to recruit me, but no, it’s in the past now,” he says, with a laugh.

He spends his time focusing on his classes — from his major-related classes to electives like game design — and the MIT International Students Association.

He says the organization is currently not very active, but it has been a source of important friendships.

“Sometimes we would meet new people, but oftentimes we would just meet up with friends at the meetings that we haven’t seen for a long time,” Chudik says. “The international community is not so big here, so we kind of all know each other.”

When Chudik first moved to Boston, he didn’t know of anyone else from Slovakia — not even students from other universities. He says that when he studied in Slovakia, it was rare for people to apply to colleges in the United States. He had to slowly convince his family to let him study so far away. But once he got into MIT and received his financial assistance, his family was overjoyed.

Chudik grew up with a large extended family who would come over regularly for dinner. He knew he would be saying goodbye to that sense of community when he came to Boston. But Chudik received MIT’s Kate and Gordon B. Baty Scholarship, and the family responsible for the scholarship made him feel at home. The family hosts lunches two to three times a year and has a Thanksgiving dinner for all the students in the scholarship program.

“They’ve become my second family here. They’re like grandparents that I’ve never had,” he says. “They’re so great.”

Chudik has adjusted to Boston and has made this “very European-like” city his home. Because he found his way around an American university, he now mentors high school students in Slovakia and helps them navigate the college application process.

Singing for joy and service

Shafaq Patel | MIT News correspondent — Sun, 02 Feb 2020 00:00:00 -0500

Swarna Jeewajee grew up loving music — she sings in the shower and blasts music that transports her to a happy state. But until this past year, she never felt confident singing outside her bedroom.

Now, the senior chemistry and biology major spends her Saturdays singing around the greater Boston area, at hospitals, homes for the elderly, and rehabilitation centers, with the a cappella group she co-founded, Singing For Service.

Jeewajee says she would not have been able to sing in front of people without the newfound confidence that came after she had transformative ear surgery in the spring of 2018.

Jeewajee grew up in Mauritius, a small island off the east coast of Madagascar, where she loved the water and going swimming. When she was around 8 years old, she developed chronic ear infections as a result of a cholesteatoma, which caused abnormal skin growth in her middle ear.

It took five years and three surgeries for the doctors in Mauritius to diagnose what had happened to Jeewajee’s ear. She spent some of her formative years at the hospital instead of leading a normal childhood and swimming at the beach.

By the time Jeewajee was properly diagnosed and treated, she was told her hearing could not be salvaged, and she had to wear a hearing aid.

“I sort of just accepted that this was my reality,” she says. “People used to ask me what the hearing aid was like — it was like hearing from headphones. It felt unnatural. But it wasn’t super hard to get used to it. I had to adapt to it.”

Eventually, the hearing aid became a part of Jeewajee, and she thought everything was fine. During her first year at MIT, she joined Concourse, a first-year learning community which offers smaller classes to fulfill MIT’s General Institute Requirements, but during her sophomore year, she enrolled in larger lecture classes. She found that she wasn’t able to hear as well, and it was a problem.

“When I was in high school, I didn’t look at my hearing disability as a disadvantage. But coming here and being in bigger lectures, I had to acknowledge that I was missing out on information,” Jeewajee says.

Over the winter break of her sophomore year, her mother, who had been living in the U.S. while Jeewajee was raised by her grandmother in Mauritius, convinced Jeewajee to see a specialist at Massachusetts Eye and Ear Hospital. That’s when Jeewajee encountered her role model, Felipe Santos, a surgeon who specializes in her hearing disorder.

Jeewajee had sought Santos’ help to find a higher-performing hearing aid, but instead he recommended a titanium implant to restore her hearing via a minimally invasive surgery. Now, Jeewajee does not require a hearing aid at all, and she can hear equally well from both ears.

“The surgery helped me with everything. I used to not be able to balance, and now I am better at that. I had no idea that my hearing affected that,” she says.

These changes, she says, are little things. But it’s the little things that made a large impact.

“I gained a lot more confidence after the surgery. In class, I was more comfortable raising my hand. Overall, I felt like I was living better,” she says.

This feeling is what brought Jeewajee to audition for the a cappella group. She never had any formal training in singing, but in January, during MIT’s Independent Activities Period, her friend mentioned that she wanted to start an a cappella group and convinced Jeewajee to help her start Singing For Service. The group launched with the help of the Council for the Arts Grants Program, which supports student arts projects that engage with the MIT community and beyond.

Jeewajee describes Singing For Service as her “fun activity” at MIT, where she can just let loose. She is a soprano singer, and the group of nine to 12 students practices for about three hours a week before their weekly performances. They prepare three songs for each show; a typical lineup is a Disney melody, Josh Groban’s “You Raise Me Up,” and a mashup from the movie “The Greatest Showman.”

Her favorite part is when they take song requests from the audience. For example, Singing For Service recently went to a home for patients with multiple sclerosis, who requested songs from the Beatles and “Bohemian Rhapsody.” After the performance, the group mingles with the audience, which is one of Jeewajee’s favorite parts of the day.

She loves talking with patients and the elderly. Because Jeewajee was a patient for so many years growing up, she now wants to help people who are going through that type of experience. That is why she is going into the medical field and strives to earn an MD-PhD.

“When I was younger, I kind of always was at the doctor’s office. Doctors want to help you and give you a treatment and make you feel better. This aspect of medicine has always fascinated me, how someone is literally dedicating their time to helping you. They don’t know you, they’re not family, but they’re here for you. And I want to be there for someone as well,” she says.

Jeewajee says that because she grew up with a medical condition that was poorly understood, she wants to devote her career to search for answers to tough medical problems. Perhaps not surprisingly, she has gravitated toward cancer research.

She discovered her passion for this field after her first year at MIT, when she spent the summer conducting research in a cancer hospital in Lyon, through MISTI-France. There, she experienced an “epiphany” as she watched scientists and physicians come together to fight cancer, and was inspired to do the same.

She cites the hospital’s motto, “Chercher et soigner jusqu’à la guérison,” which means “Research and treat until the cure,” as an expression of what she will aspire to as a physician-scientist.

Last summer, while working at The Rockefeller University investigating mechanisms of resistance to cancer therapy, she developed a deeper appreciation for how individual patients can respond differently to a particular treatment, which is part of what makes cancer so hard to treat. Upon her return at MIT, she joined the Hemann lab at the Koch Institute for Integrative Cancer Research, where she conducts research on near-haploid leukemia, a subtype of blood cancer. Her ultimate goal is to find a vulnerability that may be exploited to develop new treatments for these patients.

The Koch Institute has become her second home on MIT’s campus. She enjoys the company of her labmates, who she says are good mentors and equally passionate about science. The walls of the lab are adorned with science-related memes and cartoons, and amusing photos of the team’s scientific adventures.

Jeewajee says her work at the Koch Institute has reaffirmed her motivation to pursue a career combining science and medicine.

“I want to be working on something that is challenging so that I can truly make a difference. Even if I am working with patients for whom we may or may not have the right treatment, I want to have the capacity to be there for them and help them understand and navigate the situation, like doctors did for me growing up,” Jeewajee says.

Screen could offer better safety tests for new chemicals

Anne Trafton | MIT News Office — Tue, 17 Dec 2019 00:00:00 -0500

It’s estimated that there are approximately 80,000 industrial chemicals currently in use, in products such as clothing, cleaning solutions, carpets, and furniture. For the vast majority of these chemicals, scientists have little or no information about their potential to cause cancer.

The detection of DNA damage in cells can predict whether cancer will develop, but tests for this kind of damage have limited sensitivity. A team of MIT biological engineers has now come up with a new screening method that they believe could make such testing much faster, easier, and more accurate.

The National Toxicology Program, a government research agency that identifies potentially hazardous substances, is now working on adopting the MIT test to evaluate new compounds.

“My hope is that they use it to identify potential carcinogens and we get them out of our environment, and prevent them from being produced in massive quantities,” says Bevin Engelward, a professor of biological engineering at MIT and the senior author of the study. “It can take decades between the time you’re exposed to a carcinogen and the time you get cancer, so we really need predictive tests. We need to prevent cancer in the first place.”

Engelward’s lab is now working on further validating the test, which makes use of human liver-like cells that metabolize chemicals very similarly to real human liver cells and produce a distinctive signal when DNA damage occurs.

Le Ngo, a former MIT graduate student and postdoc, is the lead author of the paper, which appears today in the journal Nucleic Acids Research. Other MIT authors of the paper include postdoc Norah Owiti, graduate student Yang Su, former graduate student Jing Ge, Singapore-MIT Alliance for Research and Technology graduate student Aoli Xiong, professor of electrical engineering and computer science Jongyoon Han, and professor emerita of biological engineering Leona Samson.

Carol Swartz, John Winters, and Leslie Recio of Integrated Laboratory Systems are also authors of the paper.

Detecting DNA damage

Currently, tests for the cancer-causing potential of chemicals involve exposing mice to the chemical and then waiting to see whether they develop cancer, which takes about two years.

Engelward has spent much of her career developing ways to detect DNA damage in cells, which can eventually lead to cancer. One of these devices, the CometChip, reveals DNA damage by placing the DNA in an array of microwells on a slab of polymer gel and then exposing it to an electric field. DNA strands that have been broken travel farther, producing a comet-shaped tail.

While the CometChip is good at detecting breaks in DNA, as well as DNA damage that is readily converted into breaks, it can’t pick up another type of damage known as a bulky lesion. These lesions form when chemicals stick to a strand of DNA and distort the double helix structure, interfering with gene expression and cell division. Chemicals that cause this kind of damage include aflatoxin, which is produced by fungi and can contaminate peanuts and other crops, and benzo[a]pyrene, which can form when food is cooked at high temperatures.

Engelward and her students decided to try to adapt the CometChip so that it could pick up this type of DNA damage. To do that, they took advantage of cells’ DNA repair pathways to generate strand breaks. Typically, when a cell discovers a bulky lesion, it will try to repair it by cutting out the lesion and then replacing it with a new piece of DNA.

“If there’s something glommed onto the DNA, you have to rip out that stretch of DNA and then replace it with fresh DNA. In that ripping process, you’re creating a strand break,” Engelward says.

To capture those broken strands, the researchers treated cells with two compounds that prevent them from synthesizing new DNA. This halts the repair process and generates unrepaired single-stranded DNA that the Comet test can detect.

The researchers also wanted to make sure that their test, which is called HepaCometChip, would detect chemicals that only become hazardous after being modified in the liver through a process called bioactivation.

“A lot of chemicals actually are inert until they get metabolized by the liver,” Ngo says. “In the liver you have a lot of metabolizing enzymes, which modify the chemicals so that they become more easily excreted by the body. But this process sometimes produces intermediates that can turn out to be more toxic than the original chemical.”

To detect those chemicals, the researchers had to perform their test in liver cells. Human liver cells are notoriously difficult to grow outside the body, but the MIT team was able to incorporate a type of liver-like cell called HepaRG, developed by a company in France, into the new test. These cells produce many of the same metabolic enzymes found in normal human liver cells, and like human liver cells, they can generate potentially harmful intermediates that create bulky lesions.

Enhanced sensitivity

To test their new system, the researchers first exposed the liver-like cells to UV light, which is known to produce bulky lesions. After verifying that they could detect such lesions, they tested the system with nine chemicals, seven of which are known to lead to single-stranded DNA breaks or bulky lesions, and found that the test could accurately detect all of them.

“Our new method enhances the sensitivity, because it should be able to detect any damage a normal Comet test would detect, and also adds on the layer of the bulky lesions,” Ngo says.

The whole process takes between two days and a week, offering a significantly faster turnaround than studies in mice.

The researchers are now working on further validating the test by comparing its performance with historical data from mouse carcinogenicity studies, with funding from the National Institutes of Health.

They are also working with Integrated Laboratory Systems, a company that performs toxicology testing, to potentially commercialize the technology. Engelward says the HepaCometChip could be useful not only for manufacturers of new chemical products, but also for drug companies, which are required to test new drugs for cancer-causing potential. The new test could offer a much easier and faster way to perform those screens.

“Once it’s validated, we hope it will become a recommended test by the FDA,” she says.

The research was funded by the National Institute of Environmental Health Sciences, including the NIEHS Superfund Basic Research Program, and the MIT Center for Environmental Health Sciences.

Taking a moonshot at a rare childhood cancer

Bendta Schroeder | Koch Institute — Wed, 20 Nov 2019 10:40:01 -0500

MIT Professor Angela Koehler is part of a team that has been awarded a federal grant to study one of the least-understood but most-fatal forms of childhood cancer, fusion-positive alveolar rhabdomyosarcoma (ARMS).

The $5.8 million, five-year grant is part of the Cancer Moonshot Initiative, a National Institutes of Health program dedicating $1.8 billion over seven years to accelerating the discovery of new ways to prevent, diagnose, and cure cancer. Koehler, the Samuel A. Goldblith Career Development Professor in Applied Biology and a member of MIT’s Koch Institute for Integrative Cancer Research, will be part of an international team led by researchers from the Broad Institute of MIT and Harvard, Duke University, the National Cancer Institute, and the University of Zurich.

ARMS, a cancer affecting skeletal muscle tissue, is rare, accounting for about 1 percent of all cancers among children and adolescents, and an annual incidence that is truly “one in a million.” It is also deadly: The overall survival rate for fusion-positive ARMS is 30 percent, with only a 10 percent survival rate for patients whose cancer has metastasized. Currently, there are no ARMS-specific therapies available. As a poorly understood “orphan disease,” it would be difficult for the pharmaceutical industry to undertake the costly development of new treatments for such a small pool of patients.

The new grant will enable Koehler and her team to make significant strides toward improving our understanding of the molecular underpinnings of fusion-positive ARMS and identifying compounds that could be developed into new treatments.

“Fusion oncoproteins involving transcription factors are the holy grail for drug discovery, and nearly all traditional drug discovery approaches have failed,” says Koehler. “By combining new technology approaches, we may have cracked the door open on one of these targets. This high-risk, high-reward grant will enable us to develop a current lead and develop new approaches to the wider set of oncoproteins studied by the NCI Network.”

Fusion oncoproteins — proteins that result from a complex mutation joining two genes together — drive many childhood cancers. In fusion-positive ARMS, the most common culprit is a chimera of transcription factors PAX3 and FOXO1, two proteins that are part of the molecular machinery that regulates the expression of genes.

Unlike many other oncoproteins, which may be present in both cancerous and normal cells, fusion oncoproteins like PAX3-FOXO1 are present only in cancer cells. Drugs that target PAX3-FOXO1 have the potential to attack the root cause of cancer development while leaving healthy cells undamaged.

Yet PAX3-FOXO1 is considered an “undruggable” target. Like other transcription factors, its disordered nature resists conventional methods for studying structure, such as crystallography. Without comprehensive knowledge of the structure, it is challenging to design a new compound that will interfere with its function. Furthermore, transcription factors tend to lack the small, well-defined binding pockets that serve as the “lock” for the small-molecule “key” identified in high-throughput screens that use traditional binding assays.

Koehler will co-lead a project with Beat Schaefer of the University of Zurich to screen for new agents that block PAX3-FOXO1 activity. Her lab specializes in small-molecule microarray (SMM) platforms capable of identifying small molecules with multiple modes of binding, regardless of how disordered or intractable a target may be. Koehler has had promising results from pilot SMM screens of PAX3-FOXO1 and success with the same approach applied to other supposedly undruggable targets. The team will assess how binding compounds of interest change PAX3-FOXO1 activity, and optimize them to be more effective. The most promising candidate will then be tested in cell lines and mouse models.

If the project succeeds in targeting PAX3-FOXO1, the resulting probes — which will be made freely available to the wider research community — could serve as a starting point for developing new therapies for fusion-positive ARMS, as well as a tool for studying how PAX3-FOXO1 interacts with other proteins and DNA. But applications of the project’s results could extend well beyond this one orphan disease. The approaches developed could be used to identify therapeutic targets for other fusion-positive cancers, such as Ewing’s sarcoma and acute myeloid leukemia, and inform strategies for targeting oncogenic transcription factors more broadly.

“Given the relatively small patient populations, it may be challenging for our colleagues in the pharmaceutical industry to undertake drug discovery campaigns for these targets,” says Koehler. “We can and should take that kind of risk in my lab, given the great unmet need for these pediatric patients. Hopefully, our work will uncover leads that can be developed for translation, as well as lower the barrier for pharmaceutical companies to go after these as-of-yet undrugged targets. The trainees in our lab are very excited about this challenge and hope our work can impact the lives of children with ARMS.”

New pathway for lung cancer treatment

Bendta Schroeder | Koch Institute — Wed, 06 Nov 2019 14:00:00 -0500

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

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

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

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

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

Roadblock for cell replication

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

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

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

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

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

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

Shorter pathway to the clinic

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

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

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

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

Cell stiffness may indicate whether tumors will invade

Jennifer Chu | MIT News Office — Mon, 21 Oct 2019 11:00:00 -0400

Engineers at MIT and elsewhere have tracked the evolution of individual cells within an initially benign tumor, showing how the physical properties of those cells drive the tumor to become invasive, or metastatic.

The team carried out experiments with a human breast cancer tumor that developed in the lab. As the tumor grew and amassed more cells over a period of about two weeks, the researchers observed that cells in the interior of the tumor were small and stiff, while the cells on the periphery were soft and more swollen. These softer, peripheral cells were more apt to stretch beyond the tumor body, forming “invasive tips” that eventually broke away to spread elsewhere.

The researchers found that the cells at the tumor’s edges were softer because they contained more water than those in the center. The cells in the center of a tumor are surrounded by other cells that press inward, squeezing water out of the interior cells and into those cells at the periphery, through nanometer-sized channels between them called gap junctions.

“You can think of the tumor like a sponge,” says Ming Guo, assistant professor of mechanical engineering at MIT. “When they grow, they build up compressive stresses inside the tumor, and that will squeeze the water from the core out to the cells on the outside, which will slowly swell over time and become softer as well — therefore they are more able to invade.”

When the team treated the tumor to draw water out of peripheral cells, the cells became stiffer and less likely to form invasive tips. Conversely, when they flooded the tumor with a diluted solution, the same peripheral cells swelled and quickly formed long, branchlike tips that invaded the surrounding environment.

Above, an early stage tumor is shown. Courtesy of the researchers.

Above, an late stage tumor is shown. Courtesy of the researchers.

The results, which the team reports today in the journal Nature Physics, point to a new route for cancer therapy, focused on changing the physical properties of cancer cells to delay or even prevent a tumor from spreading.

Guo’s co-authors include lead author and MIT postdoc Yu Long Han, along with Guoqiang Xu, Zichen Gu, Jiawei Sun, Yukun Hao, Staish Kumar Gupta, Yiwei Li, and Wenhui Tang, from MIT; Adrian Pegoraro and Yuan Yuan of the Harvard John A. Paulson School of Engineering and Applied Sciences; Hui Li of the Chinese Academy of Sciences; Kaifu Li, Hua Kang, and Lianghong Teng of Capital Medical University in Beijing; and Jeffrey Fredberg of the Harvard T. H. Chan School of Public Health in Boston.

Cell tweezing

Scientists suspect that cancer cells that migrate from a main tumor are able to do so in part because of their softer, more pliable nature, enabling the cells to squeeze through the body’s labrynthine vasculature and proliferate far from the initial tumor. Past experiments have shown this soft, migratory nature in individual cancer cells, but Guo’s team is the first to explore the role of cell stiffness in a whole, developing tumor.

“People have looked at single cells for a long time, but organisms are multicellular, three-dimensional systems,” Guo says. “Each cell is a physical building block, and we’re interested in how each single cell is regulating its own physical properties, as the cells develop into a tissue like a tumor or an organ.”

The researchers used recently developed techniques to grow healthy human epithelial cells in 3D and transform them into a human breast cancer tumor in the lab. Over the next week, the researchers watched as the cells multiplied and coalesced into a benign primary tumor that comprised several hundred individual cells. Several times throughout the week, the researchers infused the growing number of cells with plastic particles.

They then probed each individual cell’s stiffness with optical tweezers, a technique in which researchers direct a highly focused laser beam at a cell. In this case, the team trained a laser on a plastic particle within each cell, pinning the particle in place, then applying a slight pulse in a attempt to move the particle within the cell, much like using tweezers to pick an egg shell out from the surrounding yolk.

Guo says the degree to which researchers can move a particle gives them an idea for the stiffness of the surrounding cell: The more resistant the particle is to being moved, the stiffer a cell must be. In this way, the researchers found that the hundreds of cells within a single benign tumor exhibit a gradient of stiffness as well as size. The interior cells were smaller and stiffer, and the further the cells were from the core, the softer and larger they became. They also became more likely to stretch out from the spherical primary tumor and form branches, or invasive tips.

To see whether altering cells’ water content affects their invasive behavior, the team added low-molecular-weight polymers to the tumor solution to draw water out from cells, and found that the cells shrank, became more stiff, and were less likely to migrate away from the tumor — a measure that delayed metastasis. When they added water to dilute the tumor solution, the cells, particularly at the edges, swelled, became softer, and formed invasive tips more quickly.

As a last test, the researchers obtained a sample of a patient’s breast cancer tumor and measured the size of every cell within the tumor sample. They observed a gradient similar to what they found in their lab-derived tumor: Cells in the tumor’s core were smaller than those closer to the periphery.

“We found this doesn’t just happen in a model system — it’s real,” Guo says. “This means we may be able to develop some treatment based on the physical picture, to target cell stiffness or size to see if that helps. If you make the cells stiffer, they are less likely to migrate, and that could potentially delay invasion.”

Perhaps one day, he says, clinicians may be able to look at a tumor and, based on the size and stiffness of cells, from the inside out, be able to say with some confidence whether a tumor will metastasize or not.

“If there is an established size or stiffness gradient, you can know this will cause trouble,” Guo says. “If there’s no gradient, you can maybe safely say it’s fine.”

This research was supported, in part, by the National Cancer Institute.

Diagnosing cellular nanomechanics

Singapore-MIT Alliance for Research and Technology — Mon, 07 Oct 2019 13:00:01 -0400

Researchers at Singapore-MIT Alliance for Research and Technology (SMART) and MIT’s Laser Biomedical Research Center (LBRC) have developed a new way to study cells, paving the way for a better understanding of how cancers spread and become killers.

The new technology is explained in a paper published recently in Nature Communications. A new confocal reflectance interferometric microscope provides 1.5 microns depth resolution and better than 200 picometers height measurement sensitivity for high-speed characterization of nanometer-scale nucleic envelope and plasma membrane fluctuations in biological cells. It enables researchers to use these fluctuations to understand key biological questions, such as the role of nuclear stiffness in cancer metastasis and genetic diseases.

“Current methods for nuclear mechanics are invasive, as they either require mechanical manipulation, such as stretching, or require injecting fluorescent probes that ‘light up’ the nucleus to observe its shape. Both these approaches would undesirably change cells' intrinsic properties, limiting study of cellular mechanisms, disease diagnosis, and cell-based therapies,” say Vijay Raj Singh, SMART research scientist, and Zahid Yaqoob, LBRC principal investigator. “With the confocal reflectance interferometric microscope, we can study nuclear mechanics of biological cells without affecting their native properties.”

While the scientists can study about a hundred cells in a few minutes, they believe that the system can be upgraded in the future to improve the throughput to tens of thousands of cells.

“Today, many disease mechanisms are not fully understood because we lack a way to look at how cells’ nucleus changes when it undergoes stress,” says Peter So, SMART BioSyM principal investigator, MIT professor, and LBRC director. “For example, people often do not die from the primary cancer, but from the secondary cancers that form after the cancer cells metastasize from the primary site — and doctors do not know why cancer becomes aggressive and when it happens. Nuclear mechanics plays a vital role in cancer metastasis as the cancer cells must ‘squeeze’ through the blood vessel walls into the bloodstream, and again when they enter a new location. This is why the ability to study nuclear mechanics is so important to our understanding of cancer formation, diagnostics, and treatment.”

With the new interferometric microscope, scientists at LBRC are studying cancer cells when they undergo mechanical stress, especially during extravasation process, paving the way for new cancer treatments. Further, the scientists are also able to use the same technology to study the effect of “lamin mutations” on nuclear mechanics, which result in rare genetic diseases such as Progeria, which leads to fast aging in young children.

The confocal reflectance interferometric microscope also has applications in other sectors. For example, this technology has the potential for studying cellular mechanics within intact living tissues. With the new technology, the scientists could shed new light on biological processes within the body’s major organs such as liver, allowing safer and more accurate cell therapies. Cell therapy is a major focus area for Singapore, with the government recently announcing a S$80 million (US $58 million) boost to the manufacturing of living cells as medicine.

About BioSyM

BioSystems and Micromechanics (BioSyM) Inter-Disciplinary Research Group brings together a multidisciplinary team of faculties and researchers from MIT and the universities and research institutes of Singapore. BioSyM’s research deals with the development of new technologies to address critical medical and biological questions applicable to a variety of diseases with an aim to provide novel solutions to the health care industry and to the broader research infrastructure in Singapore. The guiding tenet of BioSyM is that accelerated progress in biology and medicine will critically depend upon the development of modern analytical methods and tools that provide a deep understanding of the interactions between mechanics and biology at multiple length scales — from molecules to cells to tissues — that impact maintenance or disruption of human health.

About Singapore-MIT Alliance for Research and Technology (SMART)

Singapore-MIT Alliance for Research and Technology (SMART) is MIT’s research enterprise in Singapore, established in partnership with the National Research Foundation of Singapore (NRF) since 2007. SMART is the first entity in the Campus for Research Excellence and Technological Enterprise (CREATE) developed by NRF. SMART serves as an intellectual and innovation hub for research interactions between MIT and Singapore. Cutting-edge research projects in areas of interest to both Singapore and MIT are undertaken at SMART. SMART currently comprises an Innovation Centre and six Interdisciplinary Research Groups: Antimicrobial Resistance, BioSystems and Micromechanics, Critical Analytics for Manufacturing Personalized-Medicine, Disruptive & Sustainable Technologies for Agricultural Precision, Future Urban Mobility, and Low Energy Electronic Systems.

SMART research is funded by the National Research Foundation Singapore under the CREATE program.

About the Laser Biomedical Research Center (LBRC)

Established in 1985, the Laser Biomedical Research Center is a National Research Resource Center supported by the National Institute of Biomedical Imaging and Bioengineering, a Biomedical Technology Resource Center of the National Institutes of Health. The LBRC’s mission is to develop the basic scientific understanding and new techniques required for advancing the clinical applications of lasers and spectroscopy. Researchers at the LBRC develop laser-based microscopy and spectroscopy techniques for medical applications, such as the spectral diagnosis of various diseases and investigation of biophysical and biochemical properties of cells and tissues. A unique feature of the LBRC is its ability to form strong clinical collaborations with outside investigators in areas of common interest that further the center’s mandated research objectives.

Delivery system can make RNA vaccines more powerful

Anne Trafton | MIT News Office — Mon, 30 Sep 2019 11:00:00 -0400

Vaccines made from RNA hold great potential as a way to treat cancer or prevent a variety of infectious diseases. Many biotech companies are now working on such vaccines, and a few have gone into clinical trials.

One of the challenges to creating RNA vaccines is making sure that the RNA gets into the right immune cells and produces enough of the encoded protein. Additionally, the vaccine must stimulate a strong enough response that the immune system can wipe out the relevant bacteria, viruses, or cancer cells when they are subsequently encountered.

MIT chemical engineers have now developed a new series of lipid nanoparticles to deliver such vaccines. They showed that the particles trigger efficient production of the protein encoded by the RNA, and they also behave like an “adjuvant,” further boosting the vaccine effectiveness. In a study of mice, they used this RNA vaccine to successfully inhibit the growth of melanoma tumors.

“One of the key discoveries of this paper is that you can build RNA delivery lipids that can also activate the immune system in important ways,” says Daniel Anderson, an associate professor in MIT’s Department of Chemical Engineering and a member of MIT’s Koch Institute for Integrative Cancer Research and Institute for Medical Engineering and Science.

Anderson is the senior author of the study, which appears in the Sept. 30 issue of Nature Biotechnology. The lead authors of the study are former postdocs Lei Miao and Linxian Li and former research associate Yuxuan Huang. Other MIT authors include Derfogail Delcassian, Jasdave Chahal, Jinsong Han, Yunhua Shi, Kaitlyn Sadtler, Wenting Gao, Jiaqi Lin, Joshua C. Doloff, and Robert Langer, the David H. Koch Institute Professor at MIT and a member of the Koch Institute.

Vaccine boost

Most traditional vaccines are made from proteins produced by infectious microbes, or from weakened forms of the microbes themselves. In recent years, scientists have explored the idea of making vaccines using DNA that encodes microbial proteins. However, these vaccines, which have not been approved for use in humans, have so far failed to produce strong enough immune responses.

RNA is an attractive alternative to DNA in vaccines because unlike DNA, which has to reach the cell nucleus to become functional, RNA can be translated into protein as soon as it gets into the cell cytoplasm. It can also be adapted to target many different diseases.

“Another advantage of these vaccines is that we can quickly change the target disease,” he says. “We can make vaccines to different diseases very quickly just by tinkering with the RNA sequence.”

For an RNA vaccine to be effective, it needs to enter a type of immune cell called an antigen-presenting cell. These cells then produce the protein encoded by the vaccine and display it on their surfaces, attracting and activating T cells and other immune cells.

Anderson’s lab has previously developed lipid nanoparticles for delivering RNA and DNA for a variety of applications. These lipid particles form tiny droplets that protect RNA molecules and carry them to their destinations. The researchers’ usual approach is to generate libraries of hundreds or thousands of candidate particles with varying chemical features, then screen them for the ones that work the best.

“In one day, we can synthesize over 1,000 lipid materials with multiple different structures,” Miao says. “Once we had that very large library, we could screen the molecules and see which type of structures help RNA get delivered to the antigen-presenting cells.”

They discovered that nanoparticles with a certain chemical feature — a cyclic structure at one end of the particle — are able to turn on an immune signaling pathway called stimulator of interferon genes (STING). Once this pathway is activated, the cells produce interferon and other cytokines that provoke T cells to leap into action.

“Broad applications”

The researchers tested the particles in two different mouse models of melanoma. First, they used mice with tumors engineered to produce ovalbumin, a protein found in egg whites. The researchers designed an RNA vaccine to target ovalbumin, which is not normally found in tumors, and showed that the vaccine stopped tumor growth and significantly prolonged survival.

Then, the researchers created a vaccine that targets a protein naturally produced by melanoma tumors, known as Trp2. This vaccine also stimulated a strong immune response that slowed tumor growth and improved survival rates in the mice.

Anderson says he plans to pursue further development of RNA cancer vaccines as well as vaccines that target infectious diseases such as HIV, malaria, or Ebola.

“We think there could be broad applications for this,” he says. “A particularly exciting area to think about is diseases where there are currently no vaccines.”

The research was funded by Translate Bio and JDRF.

Study links certain metabolites to stem cell function in the intestine

Anne Trafton | MIT News Office — Thu, 22 Aug 2019 11:02:02 -0400

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

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

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

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

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

An unexpected role

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

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

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

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

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

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

Stem cell function

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

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

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

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

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

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

A single-photon source you can make at home

Daniel Darling | Department of Biological Engineering — Fri, 09 Aug 2019 13:30:01 -0400

Quantum computing and quantum cryptography are expected to give much higher capabilities than their classical counterparts. For example, the computation power in a quantum system may grow at a double exponential rate instead of a classical linear rate due to the different nature of the basic unit, the qubit (quantum bit). Entangled particles enable the unbreakable codes for secure communications. The importance of these technologies motivated the U.S. government to legislate the National Quantum Initiative Act, which authorizes $1.2 billion over the following five years for developing quantum information science.

Single photons can be an essential qubit source for these applications. To achieve practical usage, the single photons should be in the telecom wavelengths, which range from 1,260-1,675 nanometers, and the device should be functional at room temperature. To date, only a single fluorescent quantum defect in carbon nanotubes possesses both features simultaneously. However, the precise creation of these single defects has been hampered by preparation methods that require special reactants, are difficult to control, proceed slowly, generate non-emissive defects, or are challenging to scale.

Now, research from Angela Belcher, head of the MIT Department of Biologicial Engineering, Koch Institute member, and the James Crafts Professor of Biological Engineering, and postdoc Ching-Wei Lin, published online in Nature Communications, describes a simple solution to create carbon-nanotube based single-photon emitters, which are known as fluorescent quantum defects.

“We can now quickly synthesize these fluorescent quantum defects within a minute, simply using household bleach and light,” Lin says. “And we can produce them at large scale easily.”

Belcher’s lab has demonstrated this amazingly simple method with minimum non-fluorescent defects generated. Carbon nanotubes were submerged in bleach and then irradiated with ultraviolet light for less than a minute to create the fluorescent quantum defects.

The availability of fluorescent quantum defects from this method has greatly reduced the barrier for translating fundamental studies to practical applications. Meanwhile, the nanotubes become even brighter after the creation of these fluorescent defects. In addition, the excitation/emission of these defect carbon nanotubes is shifted to the so-called shortwave infrared region (900-1,600 nm), which is an invisible optical window that has slightly longer wavelengths than the regular near-infrared. What's more, operations at longer wavelengths with brighter defect emitters allow researchers to see through the tissue more clearly and deeply for optical imaging. As a result, the defect carbon nanotube-based optical probes (usually to conjugate the targeting materials to these defect carbon nanotubes) will greatly improve the imaging performance, enabling cancer detection and treatments such as early detection and image-guided surgery.

Cancers were the second-leading cause of death in the United States in 2017. Extrapolated, this comes out to around 500,000 people who die from cancer every year. The goal in the Belcher Lab is to develop very bright probes that work at the optimal optical window for looking at very small tumors, primarily on ovarian and brain cancers. If doctors can detect the disease earlier, the survival rate can be significantly increased, according to statistics. And now the new bright fluorescent quantum defect can be the right tool to upgrade the current imaging systems, looking at even smaller tumors through the defect emission.

“We have demonstrated a clear visualization of vasculature structure and lymphatic systems using 150 times less amount of probes compared to previous generation of imaging systems,” Belcher says, “This indicates that we have moved a step forward closer to cancer early detection.”

In collaboration with contributors from Rice University, reearchers can identify for the first time the distribution of quantum defects in carbon nanotubes using a novel spectroscopy method called variance spectroscopy. This method helped the researchers monitor the quality of the quantum defect contained-carbon nanotubes and find the correct synthetic parameters easier.

Other co-authors at MIT include biological engineering graduate student Uyanga Tsedev, materials science and engineering graduate student Shengnan Huang, as well as Professor R. Bruce Weisman, Sergei Bachilo, and Zheng Yu of Rice University.

This work was supported by grants from the Marble Center for Cancer Nanomedicine, the Koch Institute Frontier Research Program, Frontier, the National Science Foundation, and the Welch Foundation.

Study furthers radically new view of gene control

Anne Trafton | MIT News Office — Thu, 08 Aug 2019 10:59:59 -0400

In recent years, MIT scientists have developed a new model for how key genes are controlled that suggests the cellular machinery that transcribes DNA into RNA forms specialized droplets called condensates. These droplets occur only at certain sites on the genome, helping to determine which genes are expressed in different types of cells.

In a new study that supports that model, researchers at MIT and the Whitehead Institute for Biomedical Research have discovered physical interactions between proteins and with DNA that help explain why these droplets, which stimulate the transcription of nearby genes, tend to cluster along specific stretches of DNA known as super enhancers. These enhancer regions do not encode proteins but instead regulate other genes.

“This study provides a fundamentally important new approach to deciphering how the ‘dark matter’ in our genome functions in gene control,” says Richard Young, an MIT professor of biology and member of the Whitehead Institute.

Young is one of the senior authors of the paper, along with Phillip Sharp, an MIT Institute Professor and member of MIT’s Koch Institute for Integrative Cancer Research; and Arup K. Chakraborty, the Robert T. Haslam Professor in Chemical Engineering, a professor of physics and chemistry, and a member of MIT’s Institute for Medical Engineering and Science and the Ragon Institute of MGH, MIT, and Harvard.

Graduate student Krishna Shrinivas and postdoc Benjamin Sabari are the lead authors of the paper, which appears in Molecular Cell on Aug. 8.

“A biochemical factory”

Every cell in an organism has an identical genome, but cells such as neurons or heart cells express different subsets of those genes, allowing them to carry out their specialized functions. Previous research has shown that many of these genes are located near super enhancers, which bind to proteins called transcription factors that stimulate the copying of nearby genes into RNA.

About three years ago, Sharp, Young, and Chakraborty joined forces to try to model the interactions that occur at enhancers. In a 2017 Cell paper, based on computational studies, they hypothesized that in these regions, transcription factors form droplets called phase-separated condensates. Similar to droplets of oil suspended in salad dressing, these condensates are collections of molecules that form distinct cellular compartments but have no membrane separating them from the rest of the cell.

In a 2018 Science paper, the researchers showed that these dynamic droplets do form at super enhancer locations. Made of clusters of transcription factors and other molecules, these droplets attract enzymes such as RNA polymerases that are needed to copy DNA into messenger RNA, keeping gene transcription active at specific sites.

“We had demonstrated that the transcription machinery forms liquid-like droplets at certain regulatory regions on our genome, however we didn't fully understand how or why these dewdrops of biological molecules only seemed to condense around specific points on our genome,” Shrinivas says.

As one possible explanation for that site specificity, the research team hypothesized that weak interactions between intrinsically disordered regions of transcription factors and other transcriptional molecules, along with specific interactions between transcription factors and particular DNA elements, might determine whether a condensate forms at a particular stretch of DNA. Biologists have traditionally focused on “lock-and-key” style interactions between rigidly structured protein segments to explain most cellular processes, but more recent evidence suggests that weak interactions between floppy protein regions also play an important role in cell activities.

In this study, computational modeling and experimentation revealed that the cumulative force of these weak interactions conspire together with transcription factor-DNA interactions to determine whether a condensate of transcription factors will form at a particular site on the genome. Different cell types produce different transcription factors, which bind to different enhancers. When many transcription factors cluster around the same enhancers, weak interactions between the proteins are more likely to occur. Once a critical threshold concentration is reached, condensates form.

“Creating these local high concentrations within the crowded environment of the cell enables the right material to be in the right place at the right time to carry out the multiple steps required to activate a gene,” Sabari says. “Our current study begins to tease apart how certain regions of the genome are capable of pulling off this trick.”

These droplets form on a timescale of seconds to minutes, and they blink in and out of existence depending on a cell’s needs.

“It’s an on-demand biochemical factory that cells can form and dissolve, as and when they need it,” Chakraborty says. “When certain signals happen at the right locus on a gene, the condensates form, which concentrates all of the transcription molecules. Transcription happens, and when the cells are done with that task, they get rid of them.”

“A functional condensate has to be more than the sum of its parts, and how the protein and DNA components work together is something we don't fully understand,” says Rohit Pappu, director of the Center for Science and Engineering of Living Systems at Washington University, who was not involved in the research. “This work gets us on the road to thinking about the interplay among protein-protein, protein-DNA, and possibly DNA-DNA interactions as determinants of the outputs of condensates.”

A new view

Weak cooperative interactions between proteins may also play an important role in evolution, the researchers proposed in a 2018 Proceedings of the National Academy of Sciences paper. The sequences of intrinsically disordered regions of transcription factors need to change only a little to evolve new types of specific functionality. In contrast, evolving new specific functions via “lock-and-key” interactions requires much more significant changes.

“If you think about how biological systems have evolved, they have been able to respond to different conditions without creating new genes. We don’t have any more genes that a fruit fly, yet we’re much more complex in many of our functions,” Sharp says. “The incremental expanding and contracting of these intrinsically disordered domains could explain a large part of how that evolution happens.”

Similar condensates appear to play a variety of other roles in biological systems, offering a new way to look at how the interior of a cell is organized. Instead of floating through the cytoplasm and randomly bumping into other molecules, proteins involved in processes such as relaying molecular signals may transiently form droplets that help them interact with the right partners.

“This is a very exciting turn in the field of cell biology,” Sharp says. “It is a whole new way of looking at biological systems that is richer and more meaningful.”

Some of the MIT researchers, led by Young, have helped form a company called Dewpoint Therapeutics to develop potential treatments for a wide variety of diseases by exploiting cellular condensates. There is emerging evidence that cancer cells use condensates to control sets of genes that promote cancer, and condensates have also been linked to neurodegenerative disorders such as amyotrophic lateral sclerosis (ALS) and Huntington’s disease.

The research was funded by the National Science Foundation, the National Institutes of Health, and the Koch Institute Support (core) Grant from the National Cancer Institute.

New material could make it easier to remove colon polyps

Anne Trafton | MIT News Office — Tue, 30 Jul 2019 05:59:59 -0400

More than 15 million colonoscopies are performed in the United States every year, and in at least 20 percent of those, gastroenterologists end up removing precancerous growths from the colon. Eliminating these early-stage lesions, known as polyps, is the best way to prevent colon cancer from developing.

To reduce the risk of tearing the colon during this procedure, doctors often inject a saline solution into the space below the lesion, forming a “cushion” that lifts the polyp so that it’s easier to remove safely. However, this cushion doesn’t last long.

MIT researchers have now devised an alternative — a solution that can be injected as a liquid but turns into a solid gel once it reaches the tissue, creating a more stable and longer-lasting cushion.

“That really makes a huge difference to the gastroenterologist who is performing the procedure, to ensure that there’s a stable area that they can then resect using endoscopic tools,” says Giovanni Traverso, an assistant professor in MIT’s Department of Mechanical Engineering and a gastroenterologist at Brigham and Women’s Hospital.

Traverso is the senior author of the study, which appears in the July 30 issue of Advanced Science. The lead authors of the study are former MIT postdocs Yan Pang and Jinyao Liu. Other authors include MIT undergraduate Zaina Moussa, technical associate Joy Collins, former technician Shane McDonnell, Division of Comparative Medicine veterinarian Alison Hayward, Brigham and Women’s Hospital gastroenterologist Kunal Jajoo, and David H. Koch Institute Professor Robert Langer.

A stable cushion

While many colon polyps are harmless, some can eventually become cancerous if not removed. Gastroenterologists often perform this procedure during a routine colonoscopy, using a lasso-like tool to snare the tissue before cutting it off.

This procedure carries some risk of tearing the lining of the colon, which is why doctors usually inject saline into the area just below the lining, called the submucosal space, to lift the polyp away from the surface of the colon.

“What that does is separate those tissue layers briefly, and it gives one a little bit of a raised area so it’s easier to snare the lesion,” Traverso says. “The challenge is that saline dissipates very quickly, so we don’t always have enough time to go in and intervene, and may need to reinject saline.”

Complex lesions can take 10 to 20 minutes to remove, or even longer, but the saline cushion only lasts for a few minutes. Researchers have tried to make the cushions longer-lived by adding thickening agents such as gelatin and cellulose, but those are very difficult to inject through the narrow needle that is used for the procedure.

To overcome that, the MIT team decided to create a shear-thinning gel. These materials are semisolid gels under normal conditions, but when force is applied to them, their viscosity decreases and they flow more easily. This means that the material can be easily injected through a narrow needle, then turn back into a solid gel once it exits into the colon tissue.

Shear-thinning gels can be made from many different types of materials. For this purpose, the researchers decided on a combination of two biocompatible materials that can form gels — Laponite, a powdery clay used in cosmetics and other products, and alginate, a polysaccharide derived from algae.

“We chose these materials because they are biocompatible and they allow us to tune the flowing behavior of the resulting gels,” Pang says.

Using these materials, the researchers created a shear-thinning gel that could be injected and form a stable cushion for more than an hour, in pigs. This would give gastroenterologists much more time to remove any polyps.

“Otherwise, you inject the saline, then you change tools, and by the time you’re ready the tissue is kind of flat again. It becomes really difficult to resect things safely,” Traverso says.

This approach could offer “an elegant solution” to the problem of keeping lesions elevated during a surgical removal, says Jay Pasricha, a professor of medicine and neuroscience at Johns Hopkins School of Medicine.

“It’s a growing unmet need,” says Pasricha, who was not involved in the research. “In the last decade, we’ve shifted toward trying to resect more complex tumors from the colon endoscopically, rather than through traditional forms of surgery. It would be great to have a material that can last throughout the duration of the procedure.”

Controlling viscosity

By varying the composition of the gel components, the researchers can control features such as the viscosity, which influences how long the cushion remains stable. If made to last longer, this kind of injectable gel could be useful for applications such as narrowing the GI tract, which could be used to prevent acid reflux or to help with weight loss by making people feel full. It could also potentially be used to deliver drugs to the intestinal tract, Traverso says.

The researchers also found that the material had no harmful side effects in pigs, and they hope to begin trials in human patients within the next three to five years.

“This is something we think can get into patients fairly quickly,” Traverso says. “We’re really excited about moving it forward.”

The research was funded by the National Institutes of Health, the Alexander von Humboldt Foundation, the Division of Gastroenterology at Brigham and Women’s Hospital and the MIT Department of Mechanical Engineering.

MIT “Russian Doll” tech lands $7.9M international award to fight brain tumors

Koch Institute — Fri, 26 Jul 2019 13:30:01 -0400

Cancer Research UK awarded $7.9 million to MIT researchers as part of an international team to identify combinations of drugs that could effectively tackle glioblastoma — the most aggressive and deadly type of brain tumor. The team will then use tiny “Russian doll-like” particles — a technology developed at MIT — to deliver those combinations to brain tumors.

The MIT team, based at the Koch Institute for Integrative Cancer Research, includes Paula Hammond, the David H. Koch Professor of Engineering and head of the Department of Chemical Engineering; Michael Yaffe, the David H. Koch Professor of Science and director of the MIT Center for Precision Cancer Medicine; and Forest White, the Ned C. and Janet Bemis Rice Professor of Biological Engineering.

Brain tumors represent one of the hardest types of cancer to treat. There are just a few drugs approved to treat glioblastoma, but none of them are curative. Just last year, around 24,200 people in the United States were diagnosed with brain tumors, with around 17,500 deaths from brain tumors in the same year. Patients diagnosed with disease have a median life expectancy of less than 15 months.

Treating glioblastoma is challenging in part because, like many other cancers, it can quickly develop resistance to cancer drugs. Some drug combinations deliver a powerful one-two punch that can overcome cancer cells’ ability to adapt to treatment.

The international team aims to find potential drug combinations and targets using high-throughput small molecules and CRISPRi-based screens, mass spectrometry proteomic analysis, and computational modeling platforms for systems pharmacology developed at MIT for predicting the development and reversal of drug resistance in glioblastomas. The team will then test the effectiveness of newly-identified drug combinations in cell and mouse models, including two promising combinations already identified by researchers at the Koch Institute and the University of Edinburgh.

Drugs that have already been approved, as well as experimental drugs that have passed initial safety testing in people, will be prioritized. Because of this, if an effective drug combination is found, the team won’t have to navigate the initial regulatory hurdles needed to get them into clinical testing, which could help get promising treatments to patients faster.

But glioblastoma presents an additional obstacle to treatment: Even if the researchers find potential new treatments, the drugs must cross the blood-brain barrier, a structure that keeps a tight check on anything trying to get into the brain, drugs included. The team will deploy nanoparticles developed by Hammond at MIT to ferry new drug treatments across this barrier. The nanoparticles — one-thousandth the width of a human hair — are coated in a protein called transferrin, which helps them cross the blood-brain barrier.

Not only are the nanoparticles able to access hard-to-reach areas of the brain, they have also been designed to carry multiple cancer drugs at once by holding them inside layers, similarly to the way Russian dolls fit inside one another.

To make the nanoparticles even more effective, they will carry signals on their surface so that they are preferentially taken up by brain tumor cells. This means that healthy cells should be left untouched, which will minimize the side effects of treatment.

Early research by the Hammond and Yaffe labs has already shown that nanoparticles loaded with two different drugs were able to shrink glioblastomas in mice.

“Glioblastoma is particularly challenging because we want to get highly effective but toxic drug combinations safely across the blood-brain barrier, but also want our nanoparticles to avoid healthy brain cells and only target the cancer cells," Hammond says. "We are very excited about this alliance between the MIT Koch Institute and our colleagues at Edinburgh and Oxford to address these critical challenges.”

The MIT group and their collaborators in the UK are one of three international teams to have been given Cancer Research UK Brain Tumor Awards — in partnership with The Brain Tumour Charity — receiving $7.9 million of funding. The awards are designed to accelerate the pace of brain tumor research. Altogether, teams were awarded a total of $23 million.

“The Cancer Research UK Brain Tumor Award provides us with a unique opportunity to unite perspectives in biology and engineering to create better options for patients with glioblastoma,” says Yaffe. “Each member of this international team brings a deep well of expertise— in the biology of brain tumors, signaling proteomics, high-throughput screening, drug combinations and systems pharmacology, and drug delivery technologies — that will be vital to overcoming the challenges of developing effective therapies for glioblastoma.”

This article has been updated to reflect additional specificity regarding the project and its collaborators.

Unmasking mutant cancer cells

Bendta Schroeder | Koch Institute — Wed, 17 Jul 2019 09:35:01 -0400

As cancer cells progress, they accumulate hundreds and even thousands of genetic and epigenetic changes, resulting in protein expression profiles that are radically different from that of healthy cells. But despite their heavily mutated proteome, cancer cells can evade recognition and attack by the immune system.

Immunotherapies, particularly checkpoint inhibitors that reinvigorate exhausted T cells, have revolutionized the treatment of certain forms of cancer. These breakthrough therapies have resulted in unprecedented response rates for some patients. Unfortunately, most cancers fail to respond to immunotherapies and new strategies are therefore needed to realize their full potential.

A team of cancer biologists including members of the laboratories of David H. Koch Professor of Biology Tyler Jacks, director of the Koch Institute for Integrative Cancer Research at MIT, and fellow Koch Institute member Forest White, the Ned C. and Janet Bemis Rice Professor and member of the MIT Center for Precision Cancer Medicine, took a complementary approach to boosting the immune system.

Although cancer cells are rife with mutant proteins, few of those proteins appear on a cell’s surface, where they can be recognized by immune cells. The researchers repurposed a well-studied class of anti-cancer drugs, heat shock protein 90 (HSP90) inhibitors, that make cancer cells easier to recognize by revealing their mutant proteomes.

Many HSP90 inhibitors have been studied extensively for the past several decades as potential cancer treatments. HSP90 protects the folded structure of a number of proteins when cells undergo stress, and in cancer cells plays an important role in stabilizing protein structure undermined by pervasive mutations. However, despite promising preclinical evidence, HSP90 inhibitors have produced discouraging outcomes in clinical trials, and none have achieved FDA approval.

In a study appearing in Clinical Cancer Research, the researchers identified a potential reason behind those disappointing results. HSP90 inhibitors have only been clinically tested at bolus doses — intermittent, large doses — that often result in unwanted side effects in patients.

RNA profiling of human clinical samples and cultured cancer cell lines revealed that this bolus-dosing schedule results in the profound suppression of immune activity as well as the activation of heat shock factor 1 protein (HSF1). Not only does HSF1 activate the cell’s heat shock response, which counteracts the effect of the HSP90 inhibitor, but it is known to be a powerful enabler of cancer cell malignancy.

In striking contrast, the researchers used cancer mouse models with intact immune systems to show that sustained, low-level dosing of HSP90 inhibitors avoids triggering both the heat shock response and the immunosuppression associated with high doses.

Using a method devised by the White lab that combines mass spectrometry-based proteomics and computational modeling, the researchers discovered that the new dosing regimen increased the number and diversity of peptides (protein fragments) on the cell surface. These peptides, which the team found to be released by HSP90 during sustained low-level inhibition, were then free to be taken up by the cell’s antigen-presenting machinery and used to flag patrolling immune cells.

“These results connect a fundamental aspect of cell biology — protein folding — to anti-tumor immune responses” says lead author Alex Jaeger, a postdoc in the Jacks lab and a former member of the laboratory of the late MIT biologist Professor Susan Lindquist, whose work inspired the study’s HSP90 dosing scheuled. “Hopefully, our findings can reinvigorate interest in HSP90 inhibition as a complementary approach for immunotherapy.”

Using the new dosing regimen, the researchers were able to clear tumors in mouse models at drug concentrations that are 25-50 times lower than those used in clinical trials, significantly reducing the risk for toxic side effects in patients. Importantly, because several forms of HSP90 inhibitors have already undergone extensive clinical testing, the new dosing regimen can be tested in patients quickly.

This work was supported in part by the Damon Runyon Cancer Research Foundation, the Takeda Pharmaceuticals Immune Oncology Research Fund, and an MIT Training Grant in Environmental Science; foundational work on HSF1 was supported by the Koch Institute Frontier Research Program.

New vaccine strategy boosts T-cell therapy

Anne Trafton | MIT News Office — Thu, 11 Jul 2019 14:00:00 -0400

A promising new way to treat some types of cancer is to program the patient’s own T cells to destroy the cancerous cells. This approach, termed CAR-T cell therapy, is now used to combat some types of leukemia, but so far it has not worked well against solid tumors such as lung or breast tumors.

MIT researchers have now devised a way to super-charge this therapy so that it could be used as a weapon against nearly any type of cancer. The research team developed a vaccine that dramatically boosts the antitumor T cell population and allows the cells to vigorously invade solid tumors.

In a study of mice, the researchers found that they could completely eliminate solid tumors in 60 percent of the animals that were given T-cell therapy along with the booster vaccination. Engineered T cells on their own had almost no effect.

“By adding the vaccine, a CAR-T cell treatment which had no impact on survival can be amplified to give a complete response in more than half of the animals,” says Darrell Irvine, who is the Underwood-Prescott Professor with appointments in Biological Engineering and Materials Science and Engineering, an associate director of MIT’s Koch Institute for Integrative Cancer Research, a member of the Ragon Institute of MGH, MIT, and Harvard, and the senior author of the study.

Leyuan Ma, an MIT postdoc, is the lead author of the study, which appears in the July 11 online edition of Science.

Targeting tumors

So far, the FDA has approved two types of CAR-T cell therapy, both used to treat leukemia. In those cases, T cells removed from the patient’s blood are programmed to target a protein, or antigen, found on the surface of B cells. (The “CAR” in CAR-T cell therapy is for “chimeric antigen receptor.”)

Scientists believe one reason this approach hasn’t worked well for solid tumors is that tumors usually generate an immunosuppressive environment that disarms the T cells before they can reach their target. The MIT team decided to try to overcome this by giving a vaccine that would go to the lymph nodes, which host huge populations of immune cells, and stimulate the CAR-T cells there.

“Our hypothesis was that if you boosted those T cells through their CAR receptor in the lymph node, they would receive the right set of priming cues to make them more functional so they’d be resistant to shutdown and would still function when they got into the tumor,” Irvine says.

To create such a vaccine, the MIT team used a trick they had discovered several years ago. They found that they could deliver vaccines more effectively to the lymph nodes by linking them to a fatty molecule called a lipid tail. This lipid tail binds to albumin, a protein found in the bloodstream, allowing the vaccine to hitch a ride directly to the lymph nodes.

In addition to the lipid tail, the vaccine contains an antigen that stimulates the CAR-T cells once they reach the lymph nodes. This antigen could be either the same tumor antigen targeted by the T cells, or an arbitrary molecule chosen by the researchers. For the latter case, the CAR-T cells have to be re-engineered so that they can be activated by both the tumor antigen and the arbitrary antigen.

In tests in mice, the researchers showed that either of these vaccines dramatically enhanced the T-cell response. When mice were given about 50,000 CAR-T cells but no vaccine, the CAR-T cells were nearly undetectable in the animals’ bloodstream. In contrast, when the booster vaccine was given the day after the T-cell infusion, and again a week later, CAR-T cells expanded until they made up 65 percent of the animals’ total T cell population, two weeks after treatment.

This huge boost in the CAR-T cell population translated to complete elimination of glioblastoma, breast, and melanoma tumors in many of the mice. CAR-T cells given without the vaccine had no effect on tumors, while CAR-T cells given with the vaccine eliminated tumors in 60 percent of the mice.

Long-term memory

This technique also holds promise for preventing tumor recurrence, Irvine says. About 75 days after the initial treatment, the researchers injected tumor cells identical to those that formed the original tumor, and these cells were cleared by the immune system. About 50 days after that, the researchers injected slightly different tumor cells, which did not express the antigen that the original CAR-T cells targeted; the mice could also eliminate those tumor cells.

This suggests that once the CAR-T cells begin destroying tumors, the immune system is able to detect additional tumor antigens and generate populations of “memory” T cells that also target those proteins.

“If we take the animals that appear to be cured and we rechallenge them with tumor cells, they will reject all of them,” Irvine says. “That is another exciting aspect of this strategy. You need to have T cells attacking many different antigens to succeed, because if you have a CAR-T cell that sees only one antigen, then the tumor only has to mutate that one antigen to escape immune attack. If the therapy induces new T-cell priming, this kind of escape mechanism becomes much more difficult.”

While most of the study was done in mice, the researchers showed that human cells coated with CAR antigens also stimulated human CAR-T cells, suggesting that the same approach could work in human patients. The technology has been licensed to a company called Elicio Therapeutics, which is seeking to test it with CAR-T cell therapies that are already in development.

“There’s really no barrier to doing this in patients pretty soon, because if we take a CAR-T cell and make an arbitrary peptide ligand for it, then we don’t have to change the CAR-T cells,” Irvine says. “I’m hopeful that one way or another this can get tested in patients in the next one to two years.”

The research was funded by the National Institutes of Health, the Marble Center for Cancer Nanomedicine, Johnson and Johnson, and the National Institute of General Medical Sciences.

Cancer biologists identify new drug combo

Anne Trafton | MIT News Office — Wed, 10 Jul 2019 10:59:59 -0400

When it comes to killing cancer cells, two drugs are often better than one. Some drug combinations offer a one-two punch that kills cells more effectively, requires lower doses of each drug, and can help to prevent drug resistance.

MIT biologists have now found that by combining two existing classes of drugs, both of which target cancer cells’ ability to divide, they can dramatically boost the drugs’ killing power. This drug combination also appears to largely spare normal cells, because cancer cells divide differently than healthy cells, the researchers say. They hope a clinical trial of this combination can be started within a year or two.

“This is a combination of one class of drugs that a lot of people are already using, with another type of drug that multiple companies have been developing,” says Michael Yaffe, a David H. Koch Professor of Science and the director of the MIT Center for Precision Cancer Medicine. “I think this opens up the possibility of rapid translation of these findings in patients.”

The discovery was enabled by a new software program the researchers developed, which revealed that one of the drugs had a previously unknown mechanism of action that strongly enhances the effect of the other drug.

Yaffe, who is also a member of the Koch Institute for Integrative Cancer Research, is the senior author of the study, which appears in the July 10 issue of Cell Systems. Koch Institute research scientists Jesse Patterson and Brian Joughin are the first authors of the paper.

Unexpected synergy

Yaffe’s lab has a longstanding interest in analyzing cellular pathways that are active in cancer cells, to find how these pathways work together in signaling networks to create disease-specific vulnerabilities that can be targeted with multiple drugs. When the researchers began this study, they were looking for a drug that would amplify the effects of a type of drug known as a PLK1 inhibitor. Several PLK1 inhibitors, which interfere with cell division, have been developed, and some are now in phase 2 clinical trials.

Based on their previous work, the researchers knew that PLK1 inhibitors also produce a type of DNA and protein damage known as oxidation. They hypothesized that pairing PLK1 inhibitors with a drug that prevents cells from repairing oxidative damage could make them work even better.

To explore that possibility, the researchers tested a PLK1 inhibitor along with a drug called TH588, which blocks MTH1, an enzyme that helps cells counteract oxidative damage. This combination worked extremely well against many types of human cancer cells. In some cases, the researchers could use one-tenth of the original doses of each drug, given together, and achieve the same rates of cell death of either drug given on its own.

“It’s really striking,” Joughin says. “It’s more synergy than you generally see from a rationally designed combination.”

However, they soon realized that this synergy had nothing to do with oxidative damage. When the researchers treated cancer cells missing the gene for MTH1, which they thought was TH588’s target, they found that the drug combination still killed cancer cells at the same high rates.

“Then we were really stuck, because we had a good combination, but we didn’t know why it worked,” Yaffe says.

To solve the mystery, they developed a new software program that allowed them to identify the cellular networks most affected by the drugs. The researchers tested the drug combination in 29 different types of human cancer cells, then fed the data into the software, which compared the results to gene expression data for those cell lines. This allowed them to discover patterns of gene expression that were linked with higher or lower levels of synergy between the two drugs.

This analysis suggested that both drugs were targeting the mitotic spindle, a structure that forms when chromosomes align in the center of a cell as it prepares to divide. Experiments in the lab confirmed that this was correct. The researchers had already known that PLK1 inhibitors target the mitotic spindle, but they were surprised to see that TH588 affected the same structure.

“This combination that we found was very nonobvious,” Yaffe says. “I would never have given two drugs that both targeted the same process and expected anything better than just additive effects.”

“This is an exciting paper for two reasons,” says David Pellman, associate director for basic science at Dana-Farber/Harvard Cancer Center, who was not involved in the study. “First, Yaffe and colleagues make an important advance for the rational design of drug therapy combinations. Second, if you like scientific mysteries, this is a riveting example of molecular sleuthing. A drug that was thought to act in one way is unmasked to work through an entirely different mechanism.”

Disrupting mitosis

The researchers found that while both of the drugs they tested disrupt mitosis, they appear to do so in different ways. TH588 binds to microtubules, which form the mitotic spindle, and slows their assembly. Many similar microtubule inhibitors are already used clinically to treat cancer. The researchers showed that some of those microtubule inhibitors also synergize with PLK1 inhibitors, and they believe those would likely be more readily available for rapid use in patients than TH588, the drug they originally tested.

While the PLK1 protein is involved in multiple aspects of cell division and spindle formation, it’s not known exactly how PLK1 inhibitors interfere with the mitotic spindle to produce this synergy. Yaffe said he suspects they may block a motor protein that is necessary for chromosomes to travel along the spindle.

One potential benefit of this drug combination is that the synergistic effects appear to specifically target cancer cell division and not normal cell division. The researchers believe this could be because cancer cells are forced to rely on alternative strategies for cell division because they often have too many or too few chromosomes, a state known as aneuploidy.

“Based on the work we have done, we propose that this drug combination targets something fundamentally different about the way cancer cells divide, such as altered cell division checkpoints, chromosome number and structure, or other structural differences in cancer cells,” Patterson says.

The researchers are now working on identifying biomarkers that could help them to predict which patients would respond best to this drug combination. They are also trying to determine the exact function of PLK1 that is responsible for this synergy, in hopes of finding additional drugs that would block that interaction.

The research was funded by the National Institutes of Health, the Charles and Marjorie Holloway Foundation, the Ovarian Cancer Research Fund, the MIT Center for Precision Cancer Medicine, the Koch Institute Dana Farber/Harvard Cancer Center Bridge Project, an American Cancer Society Postdoctoral Fellowship, the Koch Institute Support (core) Grant from the National Cancer Institute, and the Center for Environmental Health Support Grant.

Confining cell-killing treatments to tumors

Helen Knight | MIT News correspondent — Wed, 26 Jun 2019 13:59:59 -0400

Cytokines, small proteins released by immune cells to communicate with each other, have for some time been investigated as a potential cancer treatment.

However, despite their known potency and potential for use alongside other immunotherapies, cytokines have yet to be successfully developed into an effective cancer therapy.

That is because the proteins are highly toxic to both healthy tissue and tumors alike, making them unsuitable for use in treatments administered to the entire body.

Injecting the cytokine treatment directly into the tumor itself could provide a method of confining its benefits to the tumor and sparing healthy tissue, but previous attempts to do this have resulted in the proteins leaking out of the cancerous tissue and into the body’s circulation within minutes.

Now researchers at the Koch Institute for Integrative Cancer Research at MIT have developed a technique to prevent cytokines escaping once they have been injected into the tumor, by adding a Velcro-like protein that attaches itself to the tissue.

In this way the researchers, led by Dane Wittrup, the Carbon P. Dubbs Professor in Chemical Engineering and Biological Engineering and a member of the Koch Institute, hope to limit the harm caused to healthy tissue, while prolonging the treatment’s ability to attack the tumor.

To develop their technique, which they describe in a paper published today in the journal Science Translational Medicine, the researchers first investigated the different proteins found in tumors, to find one that could be used as a target for the cytokine treatment. They chose collagen, which is expressed abundantly in solid tumors.

They then undertook an extensive literature search to find proteins that bind effectively to collagen. They discovered a collagen-binding protein called lumican, which they then attached to the cytokines.

“When we inject (a collagen-anchoring cytokine treatment) intratumorally, we don’t have to worry about collagen found elsewhere in the body; we just have to make sure we have a protein that binds to collagen very tightly,” says lead author Noor Momin, a graduate student in the Wittrup Lab at MIT.

To test the treatment, the researchers used two cytokines known to stimulate and expand immune cell responses. The cytokines, interleukin-2 (IL-2) and interleukin-12 (IL-12), are also known to combine well with other immunotherapies.

Although IL-2 already has FDA approval, its severe side-effects have so far prevented its clinical use. Meanwhile IL-12 therapies have not yet reached phase 3 clinical trials due to their severe toxicity.

The researchers tested the treatment by injecting the two different cytokines into tumors in mice. To make the test more challenging, they chose a type of melanoma that contains relatively low amounts of collagen, compared to other tumor types.

They then compared the effects of administering the cytokines alone and of injecting cytokines attached to the collagen-binding lumican.

“In addition, all of the cytokine therapies were given alongside a form of systemic therapy, such as a tumor-targeting antibody, a vaccine, a checkpoint blockade, or chimeric antigen receptor (CAR)-T cell therapy, as we wanted to show the potential of combining cytokines with many different immunotherapy modalities,” Momin says.

They found that when any of the treatments were administered individually, the mice did not survive. Combining the treatments improved survival rates slightly, but when the cytokine was administered with the lumican to bind to the collagen, the researchers found that over 90 percent of the mice survived with some combinations.

“So we were able to show that these combinations are synergistic, they work really well together, and that cytokines attached to lumican really helped reap the full benefits of the combination,” Momin says.

What’s more, attaching the lumican eliminated the problem of toxicity associated with cytokine treatments alone.

The paper attempts to address a major obstacle in the oncology field, that of how to target potent therapeutics to the tumor microenvironment to enable their local action, according to Shannon Turley, a staff scientist and specialist in cancer immunology at Genentech, who was not involved in the research.

“This is important because many of the most promising cancer drugs can have unwanted side effects in tissues beyond the tumor,” Turley says. “The team’s approach relies on two principles that together make for a novel approach: injection of the drug directly into the tumor site, and engineering of the drug to contain a ‘Velcro’ that attaches the drug to the tumor to keep it from leaking into circulation and acting all over the body.”

The researchers now plan to carry out further work to improve the technique, and to explore other treatments that could benefit from being combined with collagen-binding lumican, Momin says.

Ultimately, they hope the work will encourage other researchers to consider the use of collagen binding for cancer treatments, Momin says.

“We’re hoping the paper seeds the idea that collagen anchoring could be really advantageous for a lot of different therapies across all solid tumors.”

Drug makes tumors more susceptible to chemo

Anne Trafton | MIT News Office — Thu, 06 Jun 2019 10:59:59 -0400

Many chemotherapy drugs kill cancer cells by severely damaging their DNA. However, some tumors can withstand this damage by relying on a DNA repair pathway that not only allows them to survive, but also introduces mutations that helps cells become resistant to future treatment.

Researchers at MIT and Duke University have now discovered a potential drug compound that can block this repair pathway. “This compound increased cell killing with cisplatin and prevented mutagenesis, which is was what we expected from blocking this pathway,” says Graham Walker, the American Cancer Society Research Professor of Biology at MIT, a Howard Hughes Medical Institute Professor, and one of the senior authors of the study.

When they treated mice with this compound along with cisplatin, a DNA-damaging drug, tumors shrank much more than those treated with cisplatin alone. Tumors treated with this combination would be expected not to develop new mutations that could make them drug-resistant.

Cisplatin, which is used as the first treatment option for at least a dozen types of cancer, often successfully destroys tumors, but they frequently grow back following treatment. Drugs that target the mutagenic DNA repair pathway that contributes to this recurrence could help to improve the long-term effectiveness of not only cisplatin but also other chemotherapy drugs that damage DNA, the researchers say.

“We’re trying to make the therapy work better, and we also want to make the tumor recurrently sensitive to therapy upon repeated doses,” says Michael Hemann, an associate professor of biology, a member of MIT’s Koch Institute for Integrative Cancer Research, and a senior author of the study.

Pei Zhou, a professor of biochemistry at Duke University, and Jiyong Hong, a professor of chemistry at Duke, are also senior authors of the paper, which appears in the June 6 issue of Cell. The lead authors of the paper are former Duke graduate student Jessica Wojtaszek, MIT postdoc Nimrat Chatterjee, and Duke research assistant Javaria Najeeb.

Overcoming resistance

Healthy cells have several repair pathways that can accurately remove DNA damage from cells. As cells become cancerous, they sometimes lose one of these accurate DNA repair systems, so they rely heavily on an alternative coping strategy known as translesion synthesis (TLS).

This process, which Walker has been studying in a variety of organisms for many years, relies on specialized TLS DNA polymerases. Unlike the normal DNA polymerases used to replicate DNA, these TLS DNA polymerases can essentially copy over damaged DNA, but the copying they perform is not very accurate. This enables cancer cells to survive treatment with a DNA-damaging agent such as cisplatin, and it leads them to acquire many additional mutations that can make them resistant to further treatment.

“Because these TLS DNA polymerases are really error-prone, they are accountable for nearly all of the mutation that is induced by drugs like cisplatin,” Hemann says. “It’s very well-established that with these frontline chemotherapies that we use, if they don’t cure you, they make you worse.”

One of the key TLS DNA polymerases required for translesion synthesis is Rev1, and its primary function is to recruit a second TLS DNA polymerase that consists of a complex of the Rev3 and Rev7 proteins. Walker and Hemann have been searching for ways to disrupt this interaction, in hopes of derailing the repair process.

In a pair of studies published in 2010, the researchers showed that if they used RNA interference to reduce the expression of Rev1, cisplatin treatment became much more effective against lymphoma and lung cancer in mice. While some of the tumors grew back, the new tumors were not resistant to cisplatin and could be killed again with a new round of treatment.

After showing that interfering with translesion synthesis could be beneficial, the researchers set out to find a small-molecule drug that could have the same effect. Led by Zhou, the researchers performed a screen of about 10,000 potential drug compounds and identified one that binds tightly to Rev1, preventing it from interacting with Rev3/Rev7 complex.

The interaction of Rev1 with the Rev7 component of the second TLS DNA polymerase had been considered “undruggable” because it occurs in a very shallow pocket of Rev1, with few features that would be easy for a drug to latch onto. However, to the researchers’ surprise, they found a molecule that actually binds to two molecules of Rev1, one at each end, and brings them together to form a complex called a dimer. This dimerized form of Rev1 cannot bind to the Rev3/Rev7 TLS DNA polymerase, so translesion synthesis cannot occur.

Chatterjee tested the compound along with cisplatin in several types of human cancer cells and found that the combination killed many more cells than cisplatin on its own. And, the cells that survived had a greatly reduced ability to generate new mutations.

“Because this novel translesion synthesis inhibitor targets the mutagenic ability of cancer cells to resist therapy, it can potentially address the issue of cancer relapse, where cancers continue to evolve from new mutations and together pose a major challenge in cancer treatment,” Chatterjee says.

A powerful combination

Chatterjee then tested the drug combination in mice with human melanoma tumors and found that the tumors shrank much more than tumors treated with cisplatin alone. They now hope that their findings will lead to further research on compounds that could act as translesion synthesis inhibitors to enhance the killing effects of existing chemotherapy drugs.

Zhou’s lab at Duke is working on developing variants of the compound that could be developed for possible testing in human patients. Meanwhile, Walker and Hemann are further investigating how the drug compound works, which they believe could help to determine the best way to use it.

“That’s a future major objective, to identify in which context this combination therapy is going to work particularly well,” Hemann says. “We would hope that our understanding of how these are working and when they’re working will coincide with the clinical development of these compounds, so by the time they’re used, we’ll understand which patients they should be given to.”

The research was funded, in part, by an Outstanding Investigator Award from the National Institute of Environmental Health Sciences to Walker, and by grants from the National Cancer Institute, the Stewart Trust, and the Center for Precision Cancer Medicine at MIT.

Measuring chromosome imbalance could clarify cancer prognosis

Anne Trafton | MIT News Office — Mon, 13 May 2019 14:59:59 -0400

Most human cells have 23 pairs of chromosomes. Any deviation from this number can be fatal for cells, and several genetic disorders, such as Down syndrome, are caused by abnormal numbers of chromosomes.

For decades, biologists have also known that cancer cells often have too few or too many copies of some chromosomes, a state known as aneuploidy. In a new study of prostate cancer, researchers have found that higher levels of aneuploidy lead to much greater lethality risk among patients.

The findings suggest a possible way to more accurately predict patients’ prognosis, and could be used to alert doctors which patients might need to be treated more aggressively, says Angelika Amon, the Kathleen and Curtis Marble Professor in Cancer Research in the Department of Biology and a member of the Koch Institute for Integrative Cancer Research.

“To me, the exciting opportunity here is the ability to inform treatment, because prostate cancer is such a prevalent cancer,” says Amon, who co-led this study with Lorelei Mucci, an associate professor of epidemiology at the Harvard T.H. Chan School of Public Health.

Konrad Stopsack, a research associate at Memorial Sloan Kettering Cancer Center, is the lead author of the paper, which appears in the Proceedings of the National Academy of Sciences the week of May 13. Charles Whittaker, a Koch Institute research scientist; Travis Gerke, a member of the Moffitt Cancer Center; Massimo Loda, chair of pathology and laboratory medicine at New York Presbyterian/Weill Cornell Medicine; and Philip Kantoff, chair of medicine at Memorial Sloan Kettering; are also authors of the study.

Better predictions

Aneuploidy occurs when cells make errors sorting their chromosomes during cell division. When aneuploidy occurs in embryonic cells, it is almost always fatal to the organism. For human embryos, extra copies of any chromosome are lethal, with the exceptions of chromosome 21, which produces Down syndrome; chromosomes 13 and 18, which lead to developmental disorders known as Patau and Edwards syndromes; and the X and Y sex chromosomes. Extra copies of the sex chromosomes can cause various disorders but are not usually lethal.

Most cancers also show very high prevalence of aneuploidy, which poses a paradox: Why does aneuploidy impair normal cells’ ability to survive, while aneuploid tumor cells are able to grow uncontrollably? There is evidence that aneuploidy makes cancer cells more aggressive, but it has been difficult to definitively demonstrate that link because in most types of cancer nearly all tumors are aneuploid, making it difficult to perform comparisons.

Prostate cancer is an ideal model to explore the link between aneuploidy and cancer aggressiveness, Amon says, because, unlike most other solid tumors, many prostate cancers (25 percent) are not aneuploid or have only a few altered chromosomes. This allows researchers to more easily assess the impact of aneuploidy on cancer progression.

What made the study possible was a collection of prostate tumor samples from the Health Professionals Follow-up Study and Physicians’ Health Study, run by the Harvard T.H. Chan School of Public Health over the course of more than 30 years. The researchers had genetic sequencing information for these samples, as well as data on whether and when their prostate cancer had spread to other organs and whether they had died from the disease.

Led by Stopsack, the researchers came up with a way to calculate the degree of aneuploidy of each sample, by comparing the genetic sequences of those samples with aneuploidy data from prostate genomes in The Cancer Genome Atlas. They could then correlate aneuploidy with patient outcomes, and they found that patients with a higher degree of aneuploidy were five times more likely to die from the disease. This was true even after accounting for differences in Gleason score, a measure of how much the patient’s cells resemble cancer cells or normal cells under a microscope, which is currently used by doctors to determine severity of disease.

The findings suggest that measuring aneuploidy could offer additional information for doctors who are deciding how to treat patients with prostate cancer, Amon says.

“Prostate cancer is terribly overdiagnosed and terribly overtreated,” she says. “So many people have radical prostatectomies, which has significant impact on people’s lives. On the other hand, thousands of men die from prostate cancer every year. Assessing aneuploidy could be an additional way of helping to inform risk stratification and treatment, especially among people who have tumors with high Gleason scores and are therefore at higher risk of dying from their cancer.”

“When you’re looking for prognostic factors, you want to find something that goes beyond known factors like Gleason score and PSA [prostate-specific antigen],” says Bruce Trock, a professor of urology at Johns Hopkins School of Medicine, who was not involved in the research. “If this kind of test could be done right after a prostatectomy, it could give physicians information to help them decide what might be the best treatment course.”

Amon is now working with researchers from the Harvard T.H. Chan School of Public Health to explore whether aneuploidy can be reliably measured from small biopsy samples.

Aneuploidy and cancer aggressiveness

The researchers found that the chromosomes that are most commonly aneuploid in prostate tumors are chromosomes 7 and 8. They are now trying to identify specific genes located on those chromosomes that might help cancer cells to survive and spread, and they are also studying why some prostate cancers have higher levels of aneuploidy than others.

“This research highlights the strengths of interdisciplinary, team science approaches to tackle outstanding questions in prostate cancer,” Mucci says. “We plan to translate these findings clinically in prostate biopsy specimens and experimentally to understand why aneuploidy occurs in prostate tumors.”

Another type of cancer where most patients have low levels of aneuploidy is thyroid cancer, so Amon now hopes to study whether thyroid cancer patients with higher levels of aneuploidy also have higher death rates.

“A very small proportion of thyroid tumors is highly aggressive and lethal, and I’m starting to wonder whether those are the ones that have some aneuploidy,” she says.

The research was funded by the Koch Institute Dana Farber/Harvard Cancer Center Bridge Project and by the National Institutes of Health, including the Koch Institute Support (core) Grant.

Using AI to predict breast cancer and personalize care

Adam Conner-Simons and Rachel Gordon | CSAIL — Tue, 07 May 2019 10:00:01 -0400

Despite major advances in genetics and modern imaging, the diagnosis catches most breast cancer patients by surprise. For some, it comes too late. Later diagnosis means aggressive treatments, uncertain outcomes, and more medical expenses. As a result, identifying patients has been a central pillar of breast cancer research and effective early detection.

With that in mind, a team from MIT’s Computer Science and Artificial Intelligence Laboratory (CSAIL) and Massachusetts General Hospital (MGH) has created a new deep-learning model that can predict from a mammogram if a patient is likely to develop breast cancer as much as five years in the future. Trained on mammograms and known outcomes from over 60,000 MGH patients, the model learned the subtle patterns in breast tissue that are precursors to malignant tumors.

MIT Professor Regina Barzilay, herself a breast cancer survivor, says that the hope is for systems like these to enable doctors to customize screening and prevention programs at the individual level, making late diagnosis a relic of the past.

Although mammography has been shown to reduce breast cancer mortality, there is continued debate on how often to screen and when to start. While the American Cancer Society recommends annual screening starting at age 45, the U.S. Preventative Task Force recommends screening every two years starting at age 50.

“Rather than taking a one-size-fits-all approach, we can personalize screening around a woman’s risk of developing cancer,” says Barzilay, senior author of a new paper about the project out today in Radiology. “For example, a doctor might recommend that one group of women get a mammogram every other year, while another higher-risk group might get supplemental MRI screening.” Barzilay is the Delta Electronics Professor at CSAIL and the Department of Electrical Engineering and Computer Science at MIT and a member of the Koch Institute for Integrative Cancer Research at MIT.

The team’s model was significantly better at predicting risk than existing approaches: It accurately placed 31 percent of all cancer patients in its highest-risk category, compared to only 18 percent for traditional models.

Harvard Professor Constance Lehman says that there’s previously been minimal support in the medical community for screening strategies that are risk-based rather than age-based.

“This is because before we did not have accurate risk assessment tools that worked for individual women,” says Lehman, a professor of radiology at Harvard Medical School and division chief of breast imaging at MGH. “Our work is the first to show that it’s possible.”

Barzilay and Lehman co-wrote the paper with lead author Adam Yala, a CSAIL PhD student. Other MIT co-authors include PhD student Tal Schuster and former master’s student Tally Portnoi.

How it works

Since the first breast-cancer risk model from 1989, development has largely been driven by human knowledge and intuition of what major risk factors might be, such as age, family history of breast and ovarian cancer, hormonal and reproductive factors, and breast density.

However, most of these markers are only weakly correlated with breast cancer. As a result, such models still aren’t very accurate at the individual level, and many organizations continue to feel risk-based screening programs are not possible, given those limitations.

Rather than manually identifying the patterns in a mammogram that drive future cancer, the MIT/MGH team trained a deep-learning model to deduce the patterns directly from the data. Using information from more than 90,000 mammograms, the model detected patterns too subtle for the human eye to detect.

“Since the 1960s radiologists have noticed that women have unique and widely variable patterns of breast tissue visible on the mammogram,” says Lehman. “These patterns can represent the influence of genetics, hormones, pregnancy, lactation, diet, weight loss, and weight gain. We can now leverage this detailed information to be more precise in our risk assessment at the individual level.”

Making cancer detection more equitable

The project also aims to make risk assessment more accurate for racial minorities, in particular. Many early models were developed on white populations, and were much less accurate for other races. The MIT/MGH model, meanwhile, is equally accurate for white and black women. This is especially important given that black women have been shown to be 42 percent more likely to die from breast cancer due to a wide range of factors that may include differences in detection and access to health care.

“It’s particularly striking that the model performs equally as well for white and black people, which has not been the case with prior tools,” says Allison Kurian, an associate professor of medicine and health research/policy at Stanford University School of Medicine. “If validated and made available for widespread use, this could really improve on our current strategies to estimate risk.”

Barzilay says their system could also one day enable doctors to use mammograms to see if patients are at a greater risk for other health problems, like cardiovascular disease or other cancers. The researchers are eager to apply the models to other diseases and ailments, and especially those with less effective risk models, like pancreatic cancer.

“Our goal is to make these advancements a part of the standard of care,” says Yala. “By predicting who will develop cancer in the future, we can hopefully save lives and catch cancer before symptoms ever arise.”

3Q: Susan Hockfield on a new age of living machines

Bendta Schroeder | Koch Institute — Tue, 07 May 2019 10:00:00 -0400

What if viruses could build batteries with almost no toxic waste? What if a protein common to almost every organism on Earth could purify drinking water at a large scale? What if a nanoparticle-based urine test could detect the early signals of cancer? What if machine learning and other advanced computing methods could engineer higher crop yields? Such biotechnologies may sound like the province of science fiction, but are in fact just over the scientific horizon.

In "The Age of Living Machines," a book published this week by W.W. Norton and Co., MIT President Emerita Susan Hockfield offers a glimpse into a possible future driven by a new convergence of biology and engineering. She describes how researchers from many disciplines, at MIT and elsewhere, are transforming elements of the natural world, such as proteins, viruses, and biological signaling pathways, into “living” solutions for some of the most important — and challenging — needs of the 21st century.

Q. What are living machines?

A: Thanks to the emergence and expansion of the fields of molecular biology and genetics, we are amassing an ever-growing understanding of nature’s genius — the exquisitely adapted molecular and genetic machinery cells use to accomplish a multitude of purposes. I believe we are on the brink of a convergence revolution, where engineers and physical scientists are recognizing how we can use this biological “parts list” to adapt these natural machines to our own uses.

We can already see this revolution at work. In the late 1980s, Peter Agre, a physician-scientist at the Johns Hopkins University Medical Center, found an unknown protein that contaminated his every attempt to isolate the Rh protein from red blood cells. Intrigued by this mysterious interloper, he persevered until he revealed its function and structure. The protein, which he named “aquaporin,” turned out to be an essential piece of the cell’s apparatus for maintaining the right balance of water inside and outside of the cell. Its structure is superbly adapted to let water molecules — and only water molecules — pass through in large number with remarkable efficiently and speed.

The discovery of aquaporin transformed our understanding of the fundamental biology of cells, and thanks to the insight of Agre’s biophysicist colleagues, it may also transform our ability to purify drinking water at a large scale. With the launch of the company Aquaporin A/S in 2005, engineers, chemists, and biologists are translating this molecular machine into working water purification systems, now in people’s sinks and even, in 2015, in space, recycling drinking water for Danish astronauts.

Q: Why do we need living machines?

A: We are facing an existential crisis. The anticipated global population of more than 9.7 billion by 2050 poses daunting challenges for providing sufficient energy, food, and water, as well as health care, more accurately and at lower cost. These challenges are enormous in scale and complexity, and we will need to take equally enormous leaps in our imagination to meet them successfully.

But I am optimistic. Innovations like those inspired by the structure of aquaporin or the viruses that MIT materials scientist and biological engineer Angela Belcher is adapting to build more powerful, smaller batteries with cleaner, more efficient energy storage, demonstrate just how bold we can be. And yet I think the true promise of living machines lies in what we haven’t imagined yet.

In 1937, MIT President Karl Taylor Compton wrote a delightful essay called “The Electron: Its Intellectual and Social Significance” to celebrate the 40th anniversary of the discovery of the electron. Compton wrote that the electron was “the most versatile tool ever utilized,” having already resulted in seemingly magical technologies, such as radio, long-distance telephone calls, and soundtracks for movies. But Compton also recognized — accurately — that we had not even begun to realize the impact of its discovery.

In the coming decades, the atomic parts list discovered by physicists sparked a first convergence revolution, bringing us radar, television, computers, and the internet, just to start. Neither Compton nor anyone else could fully imagine the breadth of innovations to come or how radically our conception of what is possible would be altered. We can’t predict the transformations that “Convergence 2.0” will bring any more than Compton could predict the internet in 1937. But we can see clearly from the first convergence revolution that if we’re willing to throw open the doors of innovation, world-changing ideas will walk through.

Q: How do we ensure that these doors remain open?

A: The convergence revolution is happening all around us, but its success is not inevitable. For it to succeed at the maximum pace with maximum impact, biologists and engineers, along with clinicians, physicists, computational scientists, and others, need to be able to move across disciplines with shared ambition. This will require us to reorganize our thinking and our funding.

The organization of universities into departments serves us well in a number of ways, but it sometimes leads to disciplinary boundaries that can be quite difficult to cross. Interdisciplinary labs and centers can serve as reaction vessels that catalyze new approaches to research. Models for this abound at MIT. For example, soon after chemical engineer Paula Hammond joined MIT’s Koch Institute for Integrative Cancer Research, she found a new use for the layer-by-layer fabrication of nanomaterials she pioneered for energy storage devices. With the expertise of physician and molecular biologist Michael Yaffe, Hammond used that same layering method to produce nanoparticles that deliver a one-two punch of different anti-cancer drugs carefully timed to increase their effectiveness.

Our biggest sources of funding likewise constrain cross-disciplinary efforts, with the National Institutes of Health, the National Science Foundation, and the departments of Energy and Defense all investing in research along disciplinary lines. Increased experimentation with cross-disciplinary and cross-agency funding initiatives could help break down those barriers. We have already seen what such funding models can do. The Human Genome Project — which brought together biologists, computer scientists, chemists, and technologists with funding primarily from U.S.- and U.K.-based agencies — did not just give us the first map of the human genome, but paved the way for tools that allow us to study cells and diseases at entirely new scales of depth and breadth.

But ultimately, we need to renew a shared national commitment to developing new ideas. This July, we will celebrate the 50th anniversary of the Apollo 11 lunar landing. While some might argue that it offered no real benefit, it produced enormous technological gains. We should recall that the technological feat of putting men on the moon and returning them to Earth was accomplished during a time of profound social disruption. Besides providing a focus for our shared ambitions and hopes, the drive to put astronauts on the moon also led to an amazing acceleration of technology in numerous areas including computing, nanotechnology, transportation, aeronautics, and health care. History shows us we need to be willing to make these great leaps, without necessarily knowing where they will take us. Convergence 2.0, the convergence of biology with engineering and the physical sciences, offers a new model for invention, for collaboration, and for shared ambition to solve some of the most pressing problems of this century.

A new approach to targeting tumors and tracking their spread

Helen Knight | MIT News correspondent — Mon, 06 May 2019 14:59:59 -0400

The spread of malignant cells from an original tumor to other parts of the body, known as metastasis, is the main cause of cancer deaths worldwide.

Early detection of tumors and metastases could significantly improve cancer survival rates. However, predicting exactly when cancer cells will break away from the original tumor, and where in the body they will form new lesions, is extremely challenging.

There is therefore an urgent need to develop new methods to image, diagnose, and treat tumors, particularly early lesions and metastases.

In a paper published today in the Proceedings of the National Academy of Sciences, researchers at the Koch Institute for Integrative Cancer Research at MIT describe a new approach to targeting tumors and metastases.

Previous attempts to focus on the tumor cells themselves have typically proven unsuccessful, as the tendency of cancerous cells to mutate makes them unreliable targets.

Instead, the researchers decided to target structures surrounding the cells known as the extracellular matrix (ECM), according to Richard Hynes, the Daniel K. Ludwig Professor for Cancer Research at MIT. The research team also included lead author Noor Jailkhani, a postdoc in the Hynes Lab at the Koch Institute for Integrative Cancer Research.

The extracellular matrix, a meshwork of proteins surrounding both normal and cancer cells, is an important part of the microenvironment of tumor cells. By providing signals for their growth and survival, the matrix plays a significant role in tumor growth and progression.

When the researchers studied this microenvironment, they found certain proteins that are abundant in regions surrounding tumors and other disease sites, but absent from healthy tissues.

What’s more, unlike the tumor cells themselves, these ECM proteins do not mutate as the cancer progresses, Hynes says. “Targeting the ECM offers a better way to attack metastases than trying to prevent the tumor cells themselves from spreading in the first place, because they have usually already done that by the time the patient comes into the clinic,” Hynes says.

The researchers began developing a library of immune reagents designed to specifically target these ECM proteins, based on relatively tiny antibodies, or “nanobodies,” derived from alpacas. The idea was that if these nanobodies could be deployed in a cancer patient, they could potentially be imaged to reveal tumor cells’ locations, or even deliver payloads of drugs.

The researchers used nanobodies from alpacas because they are smaller than conventional antibodies. Specifically, unlike the antibodies produced by the immune systems of humans and other animals, which consist of two “heavy protein chains” and two “light chains,” antibodies from camelids such as alpacas contain just two copies of a single heavy chain.

Nanobodies derived from these heavy-chain-only antibodies comprise a single binding domain much smaller than conventional antibodies, Hynes says.

In this way nanobodies are able to penetrate more deeply into human tissue than conventional antibodies, and can be much more quickly cleared from the circulation following treatment.

To develop the nanobodies, the team first immunized alpacas with either a cocktail of ECM proteins, or ECM-enriched preparations from human patient samples of colorectal or breast cancer metastases.

They then extracted RNA from the alpacas’ blood cells, amplified the coding sequences of the nanobodies, and generated libraries from which they isolated specific anti-ECM nanobodies.

They demonstrated the effectiveness of the technique using a nanobody that targets a protein fragment called EIIIB, which is prevalent in many tumor ECMs.

When they injected nanobodies attached to radioisotopes into mice with cancer, and scanned the mice using noninvasive PET/CT imaging, a standard technique used clinically, they found that the tumors and metastases were clearly visible. In this way the nanobodies could be used to help image both tumors and metastases.

But the same technique could also be used to deliver therapeutic treatments to the tumor or metastasis, Hynes says. “We can couple almost anything we want to the nanobodies, including drugs, toxins or higher energy isotopes,” he says. “So, imaging is a proof of concept, and it is very useful, but more important is what it leads to, which is the ability to target tumors with therapeutics.”

The ECM also undergoes similar protein changes as a result of other diseases, including cardiovascular, inflammatory, and fibrotic disorders. As a result, the same technique could also be used to treat people with these diseases.

In a recent collaborative paper, also published in Proceedings of the National Academy of Sciences, the researchers demonstrated the effectiveness of the technique by using it to develop nanobody-based chimeric antigen receptor (CAR) T cells, designed to target solid tumors.

CAR T cell therapy has already proven successful in treating cancers of the blood, but it has been less effective in treating solid tumors.

By targeting the ECM of tumor cells, nanobody-based CAR T cells became concentrated in the microenvironment of tumors and successfully reduced their growth.

The ECM has been recognized to play crucial roles in cancer progression, but few diagnostic or therapeutic methods have been developed based on the special characteristics of cancer ECM, says Yibin Kang, a professor of molecular biology at Princeton University, who was not involved in the research.

“The work by Hynes and colleagues has broken new ground in this area and elegantly demonstrates the high sensitivity and specificity of a nanobody targeting a particular isoform of an ECM protein in cancer,” Kang says. “This discovery opens up the possibility for early detection of cancer and metastasis, sensitive monitoring of therapeutic response, and specific delivery of anticancer drugs to tumors.”

This work was supported by a Mazumdar-Shaw International Oncology Fellowship, fellowships for the Ludwig Center for Molecular Oncology Research at MIT, the Howard Hughes Medical Institute and a grant from the Department of Defence Breast Cancer Research Program, and imaged on instrumentation purchased with a gift from John S. ’61 and Cindy Reed.

The researchers are now planning to carry out further work to develop the nanobody technique for treating tumors and metastases.

Department of Biology hosts second annual Science Slam

Raleigh McElvery | Department of Biology — Mon, 29 Apr 2019 16:10:01 -0400

Trainees recently took over the Tuesday Biology Colloquium for the second annual Science Slam, hosted by MIT’s Department of Biology. Topics ranged from the science behind cancer metastasis to parasites, hangovers, and, notably, poop.

A science slam features a series of short presentations where researchers explain their work in a compelling manner, and — as the name suggests — make an impact. These presentations aren’t just talks, they’re performances geared towards a science-literate but non-specialized public audience. In this case, competitors were each given one slide and three minutes to tell their scientific tales and earn votes from audience members and judges.

The latter included Mary Carmichael, founder and CEO of the strategic communications consultancy Quark 4; John Pham, editor-in-chief of Cell; and Ari Daniel, an independent science reporter who crafts digital videos for PBS NOVA and co-produces the Boston branch of Story Collider.

Among the competitors were six graduate students and two postdocs who hailed from labs scattered throughout Building 68, the Whitehead Institute, and the Koch Institute for Integrative Cancer Research at MIT. In order of appearance:

Rebecca Silberman, from Angelika Amon’s lab, who spoke about how there is something special about cancer cells that allows them to thrive with the wrong number of chromosomes;
Tyler Smith, from Sebastian Lourido’s lab, who spoke about his organism of choice, Toxoplasma gondii, and how these parasites provide insights into fundamental biology that classic “model” organisms do not;
Jasmin Imran Alsous, from Adam Martin’s lab, who spoke about the coordinated cellular interactions required for fruit fly egg development;
Darren Parker, from Gene-Wei Li’s lab, who spoke about the ratio of ingredients needed to concoct nature’s winning recipe for the perfect cell;
Sophia Xu, from Jing-Ke Weng’s lab, who spoke about the molecules responsible for the kudzu flower’s capacity to alleviate hangovers;
Jay Thangappan, from Silvi Rouskin’s lab, who spoke about the importance of RNA structure in splicing and its consequences for many important biological processes;
Lindsey Backman, from Catherine Drennan’s lab, who spoke about the biochemical processes carried out by gut bacteria that make poop smell bad; and
Arish Shah, from Eliezer Calo’s lab, who spoke about how developing zebrafish clear maternally-contributed molecules and replace them with their own, thus becoming “independent from mom.”

The event was moderated by former Slammers, postdoc Monika Avello and graduate student Emma Kowal. The duo joined forces with the Building 68 communications team and Biology Graduate Student Council to publicize the event and host two pre-slam workshops and a practice session.

Kowal, last year’s winner, was motivated to mentor this year’s cohort because, as she puts it, most scientists either don't recognize the importance of clear communication or don't recognize the challenge of doing it well.

“It is rare to see graduate programs devote training time to this,” she says, “but I believe it's worth the effort. Taking the time to distill what excites and motivates us in our research not only inspires people to value science and even become scientists, but also helps us connect with each other — and remember why we love doing science in the first place.”

Avello recalls signing up for last year’s slam at the last minute, and “loving the experience.”

“I wanted to facilitate the experience of thinking hard about science communication in a fun and inclusive way for other graduate students and postdocs,” she says. “I really enjoyed watching everyone wrestle with the challenge of presenting their science in such a tight, condensed format, and ultimately developing their own unique story and style.”

There were two prizes, one awarded by the three judges and another awarded by the audience. Silberman, a fifth-year graduate student whose talk was titled “Does Chromosome Imbalance Cause Cancer?,” took home the Judges’ Prize, while third-year graduate student Sophia Xu claimed the Audience Prize with her talk, “Plant Natural Products and Human Ethanol Metabolism.”

Silberman said her favorite part was watching her fellow participants’ talks develop over time during the consecutive practice sessions. “Getting the opportunity to workshop my ideas and get input from Emma, Moni, and the other participants made the final presentation much less terrifying than it would have been otherwise, and made my talk much better,” she says.

Xu saw the Slam as an opportunity to practice presenting her research in an engaging way, and take a small step toward conquering her fear of public speaking. “I was overwhelmed by the support I received, not only from the organizers, but also from the other speakers,” she says. “It felt much like what I imagine a collaborative, friendly British cooking show would be like.”

Silberman encourages Department of Biology trainees considering participating in next year’s slam to “go for it.” She adds: “As grad students, we often aren’t challenged to distill our research down to its simplest terms. It was both harder and more fun than I expected.”

Nanoparticles take a fantastic, magnetic voyage

Anne Trafton | MIT News Office — Fri, 26 Apr 2019 13:59:59 -0400

MIT engineers have designed tiny robots that can help drug-delivery nanoparticles push their way out of the bloodstream and into a tumor or another disease site. Like crafts in “Fantastic Voyage” — a 1960s science fiction film in which a submarine crew shrinks in size and roams a body to repair damaged cells — the robots swim through the bloodstream, creating a current that drags nanoparticles along with them.

The magnetic microrobots, inspired by bacterial propulsion, could help to overcome one of the biggest obstacles to delivering drugs with nanoparticles: getting the particles to exit blood vessels and accumulate in the right place.

“When you put nanomaterials in the bloodstream and target them to diseased tissue, the biggest barrier to that kind of payload getting into the tissue is the lining of the blood vessel,” says Sangeeta Bhatia, the John and Dorothy Wilson Professor of Health Sciences and Technology and Electrical Engineering and Computer Science, a member of MIT’s Koch Institute for Integrative Cancer Research and the Institute for Medical Engineering and Science, and the senior author of the study.

“Our idea was to see if you can use magnetism to create fluid forces that push nanoparticles into the tissue,” adds Simone Schuerle, a former MIT postdoc and lead author of the paper, which appears in the April 26 issue of Science Advances.

In the same study, the researchers also showed that they could achieve a similar effect using swarms of living bacteria that are naturally magnetic. Each of these approaches could be suited for different types of drug delivery, the researchers say.

Tiny robots

Schuerle, who is now an assistant professor at the Swiss Federal Institute of Technology (ETH Zurich), first began working on tiny magnetic robots as a graduate student in Brad Nelson’s Multiscale Robotics Lab at ETH Zurich. When she came to Bhatia’s lab as a postdoc in 2014, she began investigating whether this kind of bot could help to make nanoparticle drug delivery more efficient.

In most cases, researchers target their nanoparticles to disease sites that are surrounded by “leaky” blood vessels, such as tumors. This makes it easier for the particles to get into the tissue, but the delivery process is still not as effective as it needs to be.

The MIT team decided to explore whether the forces generated by magnetic robots might offer a better way to push the particles out of the bloodstream and into the target site.

The robots that Schuerle used in this study are 35 hundredths of a millimeter long, similar in size to a single cell, and can be controlled by applying an external magnetic field. This bioinspired robot, which the researchers call an “artificial bacterial flagellum,” consists of a tiny helix that resembles the flagella that many bacteria use to propel themselves. These robots are 3-D-printed with a high-resolution 3-D printer and then coated with nickel, which makes them magnetic.

To test a single robot’s ability to control nearby nanoparticles, the researchers created a microfluidic system that mimics the blood vessels that surround tumors. The channel in their system, between 50 and 200 microns wide, is lined with a gel that has holes to simulate the broken blood vessels seen near tumors.

Using external magnets, the researchers applied magnetic fields to the robot, which makes the helix rotate and swim through the channel. Because fluid flows through the channel in the opposite direction, the robot remains stationary and creates a convection current, which pushes 200-nanometer polystyrene particles into the model tissue. These particles penetrated twice as far into the tissue as nanoparticles delivered without the aid of the magnetic robot.

This type of system could potentially be incorporated into stents, which are stationary and would be easy to target with an externally applied magnetic field. Such an approach could be useful for delivering drugs to help reduce inflammation at the site of the stent, Bhatia says.

Bacterial swarms

The researchers also developed a variant of this approach that relies on swarms of naturally magnetotactic bacteria instead of microrobots. Bhatia has previously developed bacteria that can be used to deliver cancer-fighting drugs and to diagnose cancer, exploiting bacteria’s natural tendency to accumulate at disease sites.

For this study, the researchers used a type of bacteria called Magnetospirillum magneticum, which naturally produces chains of iron oxide. These magnetic particles, known as magnetosomes, help bacteria orient themselves and find their preferred environments.

The researchers discovered that when they put these bacteria into the microfluidic system and applied rotating magnetic fields in certain orientations, the bacteria began to rotate in synchrony and move in the same direction, pulling along any nanoparticles that were nearby. In this case, the researchers found that nanoparticles were pushed into the model tissue three times faster than when the nanoparticles were delivered without any magnetic assistance.

This bacterial approach could be better suited for drug delivery in situations such as a tumor, where the swarm, controlled externally without the need for visual feedback, could generate fluidic forces in vessels throughout the tumor.

The particles that the researchers used in this study are big enough to carry large payloads, including the components required for the CRISPR genome-editing system, Bhatia says. She now plans to collaborate with Schuerle to further develop both of these magnetic approaches for testing in animal models.

The research was funded by the Swiss National Science Foundation, the Branco Weiss Fellowship, the National Institutes of Health, the National Science Foundation, and the Howard Hughes Medical Institute.

Imaging system helps surgeons remove tiny ovarian tumors

Anne Trafton | MIT News Office — Tue, 23 Apr 2019 23:59:59 -0400

Ovarian cancer is usually diagnosed only after it has reached an advanced stage, with many tumors spread throughout the abdomen. Most patients undergo surgery to remove as many of these tumors as possible, but because some are so small and widespread, it is difficult to eradicate all of them.

Researchers at MIT, working with surgeons and oncologists at Massachusetts General Hospital (MGH), have now developed a way to improve the accuracy of this surgery, called debulking. Using a novel fluorescence imaging system, they were able to find and remove tumors as small as 0.3 millimeters — smaller than a poppy seed — during surgery in mice. Mice that underwent this type of image-guided surgery survived 40 percent longer than those who had tumors removed without the guided system.

“What’s nice about this system is that it allows for real-time information about the size, depth, and distribution of tumors,” says Angela Belcher, the James Mason Crafts Professor of Biological Engineering and Materials Science at MIT, a member of the Koch Institute for Integrative Cancer Research, and the recently appointed head of MIT’s Department of Biological Engineering.

The researchers are now seeking FDA approval for a phase 1 clinical trial to test the imaging system in human patients. In the future, they hope to adapt the system for monitoring patients at risk for tumor recurrence, and eventually for early diagnosis of ovarian cancer, which is easier to treat if it is caught earlier.

Belcher and Michael Birrer, formerly the director of medical gynecologic oncology at MGH and now the director of the O’Neal Comprehensive Cancer Center at the University of Alabama at Birmingham, are the senior authors of the study, published online in the journal ACS Nano on April 22.

Neelkanth Bardhan, a Mazumdar-Shaw International Oncology Fellow at the Koch Institute, and Lorenzo Ceppi, a researcher at MGH, are the lead authors of the paper. Other authors include MGH researcher YoungJeong Na, MIT Lincoln Laboratory technical staff members Andrew Siegel and Nandini Rajan, Robert Fruscio of the University of Milan-Bicocca, and Marcela del Carmen, a gynecologic oncologist at MGH and chief medical officer of the Massachusetts General Physicians Organization.

Glowing tumors

Because there is no good way to detect early-stage ovarian cancer, it is one of the most difficult types of cancer to treat. Of 250,000 new cases diagnosed each year worldwide, 75 percent are in an advanced stage. In the United States, the five-year combined survival rate for all stages of ovarian cancer is 47 percent, only a slight improvement from 38 percent three decades ago, despite the advent of chemotherapeutic drugs such as cisplatin, approved by the FDA in 1978 for ovarian cancer treatment. In contrast, the five-year combined survival rate for all stages of breast cancer has steadily improved, from around 75 percent in the 1970s to over 90 percent now.

“We desperately need better upfront therapies, including surgery, for these (ovarian cancer) patients,” Birrer says.

Belcher and Birrer joined forces to work on this problem through the Bridge Project, a collaboration between the Koch Institute and Dana-Farber/Harvard Cancer Center. Belcher’s lab has been developing a novel type of medical imaging based on light in the near-infrared (NIR) spectrum. In a paper published in March, she reported that this imaging system could achieve an unprecedented combination of resolution and penetration-depth in living tissue.

In the new study, Belcher, Birrer, and their colleagues worked with researchers at MIT Lincoln Laboratory to adapt NIR imaging to help surgeons locate tumors during ovarian cancer surgery, by providing continuous, real-time imaging of the abdomen, with tumors highlighted by fluorescence. Previous analyses have shown that survival rates are strongly inversely correlated with the amount of residual tumor mass left behind in the patient during debulking surgery, but many ovarian tumors are so small or hidden that surgeons can’t find them.

To make the tumors visible, the researchers designed chemical probes using single-walled carbon nanotubes that emit fluorescent light when illuminated by a laser. They coated these nanotubes with a peptide that binds to SPARC, a protein that is overexpressed by highly invasive ovarian cancer cells. This probe binds to the tumors and makes them fluoresce at NIR wavelengths, allowing surgeons to more easily find them with fluorescence imaging.

The researchers tested the image-guided system in mice that had ovarian tumors implanted in a region of the abdominal cavity known as the intraperitoneal space, and showed that surgeons were able to locate and remove tumors as small as 0.3 millimeters. Ten days after surgery, these mice had no detectable tumors, while mice that had undergone the traditional, non-image-guided surgery, had many residual tumors missed by the surgeon.

By three weeks after the surgery, many of the tumors had grown back in the mice that underwent image-guided surgery, but those mice still had a median survival rate that was 40 percent longer than that of mice that underwent traditional surgery.

No other imaging system would be able to locate tumors that small during a surgical procedure, the researchers say.

“You can’t have a patient in a CT machine or an MRI machine and have the surgeon perform this surgical debulking procedure at the same time, and you can’t expose the patient to X-ray radiation for multiple hours of the long surgery. This optics-based imaging system allows us to do that in a safe manner,” Bardhan says.

Alessandro Santin, a professor of obstetrics and gynecology and clinical research program leader at the Yale University School of Medicine, described the results as “intriguing.”

“These data support the potential use of this novel imaging system in the intraoperative setting for the optical detection of residual malignant tissue at the time of surgical staging, and/or cytoreductive surgery in ovarian cancer patients,” says Santin, who was not involved in the study.

Monitoring patients

For most ovarian cancer patients, tumor debulking surgery is followed by chemotherapy, so the researchers now plan to do another study where they treat the mice with chemotherapy after image-guided surgery, in hopes of preventing the remaining tiny tumors from spreading.

“We know that the amount of tumor removed at the time of surgery for patients with advanced-stage ovarian cancer is directly correlated with their outcome,” Birrer says. “This imaging device will now allow the surgeon to go beyond the limits of resecting tumors visible to the naked eye, and should usher in a new age of effective debulking surgery.”

Now that they have demonstrated that this concept can be successfully applied to imaging during surgery, the researchers hope to begin adapting the system for use in human patients.

“In principle, it’s quite doable,” Siegel says. “It’s purely the mechanics and the funding at this point, because this mouse experiment serves as the proof of principle and may actually have been more challenging than building a human-scale system.”

The researchers also hope to deploy this type of imaging to monitor patients after surgery, and eventually to develop it as a diagnostic tool for screening women at high risk for developing ovarian cancer.

“A major focus for us right now is developing the technology to be able diagnose ovarian cancer early, in stage 1 or stage 2, before the disease becomes disseminated,” Belcher says. “That could have a huge impact on survival rates, because survival is related to the stage of detection.”

The research was funded, in part, by the Bridge Project and the Koch Institute Support (core) Grant from the National Cancer Institute, with previous support for the development of the system from the Koch Institute Frontier Research Program and the Kathy and Curt Marble Cancer Research Fund.

The fluid that feeds tumor cells

Anne Trafton | MIT News Office — Tue, 16 Apr 2019 00:00:00 -0400

Before being tested in animals or humans, most cancer drugs are evaluated in tumor cells grown in a lab dish. However, in recent years, there has been a growing realization that the environment in which these cells are grown does not accurately mimic the natural environment of a tumor, and that this discrepancy could produce inaccurate results.

In a new study, MIT biologists analyzed the composition of the interstitial fluid that normally surrounds pancreatic tumors, and found that its nutrient composition is different from that of the culture medium normally used to grow cancer cells. It also differs from blood, which feeds the interstitial fluid and removes waste products.

The findings suggest that growing cancer cells in a culture medium more similar to this fluid could help researchers better predict how experimental drugs will affect cancer cells, says Matthew Vander Heiden, an associate professor of biology at MIT and a member of the Koch Institute for Integrative Cancer Research.

“It’s kind of an obvious statement that the tumor environment is important, but I think in cancer research the pendulum had swung so far toward genes, people tended to forget that,” says Vander Heiden, one of the senior authors of the study.

Alex Muir, a former Koch Institute postdoc who is now an assistant professor at the University of Chicago, is also a senior author of the paper, which appears in the April 16 edition of the journal eLife. The lead author of the study is Mark Sullivan, an MIT graduate student.

Environment matters

Scientists have long known that cancer cells metabolize nutrients differently than most other cells. This alternative strategy helps them to generate the building blocks they need to continue growing and dividing, forming new cancer cells. In recent years, scientists have sought to develop drugs that interfere with these metabolic processes, and one such drug was approved to treat leukemia in 2017.

An important step in developing such drugs is to test them in cancer cells grown in a lab dish. The growth medium typically used to grow these cells includes carbon sources (such as glucose), nitrogen, and other nutrients. However, in the past few years, Vander Heiden’s lab has found that cancer cells grown in this medium respond differently to drugs than they do in mouse models of cancer.

David Sabatini, a member of the Whitehead Institute and professor of biology at MIT, has also found that drugs affect cancer cells differently if they are grown in a medium that resembles the nutrient composition of human plasma, instead of the traditional growth medium.

“That work, and similar results from a couple of other groups around the world, suggested that environment matters a lot,” Vander Heiden says. “It really was a wake up call for us that to really know how to find the dependencies of cancer, we have to get the environment right.”

To that end, the MIT team decided to investigate the composition of interstitial fluid, which bathes the tissue and carries nutrients that diffuse from blood flowing through the capillaries. Its composition is not identical to that of blood, and in tumors, it can be very different because tumors often have poor connections to the blood supply.

The researchers chose to focus on pancreatic cancer in part because it is known to be particularly nutrient-deprived. After isolating interstitial fluid from pancreatic tumors in mice, the researchers used mass spectrometry to measure the concentrations of more than 100 different nutrients, and discovered that the composition of the interstitial fluid is different from that of blood (and from that of the culture medium normally used to grow cells). Several of the nutrients that the researchers found to be depleted in tumor interstitial fluid are amino acids that are important for immune cell function, including arginine, tryptophan, and cystine.

Not all nutrients were depleted in the interstitial fluid — some were more plentiful, including the amino acids glycine and glutamate, which are known to be produced by some cancer cells.

Location, location, location

The researchers also compared tumors growing in the pancreas and the lungs and found that the composition of the interstitial fluid can vary based on tumors’ location in the body and at the site where the tumor originated. They also found slight differences between the fluid surrounding tumors that grew in the same location but had different genetic makeup; however, the genetic factors tested did not have as big an impact as the tumor location.

“That probably says that what determines what nutrients are in the environment is heavily driven by interactions between cancer cells and noncancer cells within the tumor,” Vander Heiden says.

Scientists have previously discovered that those noncancer cells, including supportive stromal cells and immune cells, can be recruited by cancer cells to help remake the environment around the tumor to promote cancer survival and spread.

Vander Heiden’s lab and other research groups are now working on developing a culture medium that would more closely mimic the composition of tumor interstitial fluid, so they can explore whether tumor cells grown in this environment could be used to generate more accurate predictions of how cancer drugs will affect cells in the body.

The research was funded by the National Institutes of Health, the Lustgarten Foundation, the MIT Center for Precision Cancer Medicine, Stand Up to Cancer, the Howard Hughes Medical Institute, and the Ludwig Center at MIT.

Academic institutions grant commercial license for CRISPR-based SHERLOCK diagnostic technology in developed world

Broad Institute — Thu, 21 Mar 2019 09:43:31 -0400

The following press release was issued today by the Broad Institute of MIT and Harvard.

A group of academic institutions has granted a license for SHERLOCK™, the highly-sensitive, low-cost CRISPR-based diagnostic, for commercial uses in the developed world, while reserving rights to enable its broad use by organizations to serve developing nations as well as unmet public health needs in the developed world.

First unveiled in 2017, SHERLOCK lifts a barrier to rapid deployment of diagnostics in outbreak zones. The system (which stands for Specific High-sensitivity Enzymatic Reporter unLOCKing), allows clinicians to quickly and inexpensively diagnose disease and track epidemics, such as Ebola and Zika, without the need for extensive specialized equipment. SHERLOCK can detect the presence of viruses with an unmatched degree of sensitivity in clinical samples like blood or saliva.

Under an agreement announced today, the institutions — Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Harvard University, Massachusetts General Hospital (MGH), Rutgers, The State University of New Jersey, Skolkovo Institute of Science and Technology (Skoltech), Wageningen, and University of Tokyo — have granted a license to Sherlock Biosciences Inc., a biotechnology company.

The license provides a limited exclusive right, under the Broad Institute’s inclusive innovation model, to deploy SHERLOCK diagnostic tools for commercial applications in the developed world.

“Because SHERLOCK is simple and inexpensive, it holds impressive potential for transforming how we detect disease,” said Issi Rozen, chief business officer at the Broad Institute. “It is therefore important to ensure creative commercial innovation while at the same time protecting access to new diagnostic tools in the developing world, and for public health applications in the developed world, where they are desperately needed. We designed our licensing strategy to accomplish this.” (Rozen will serve as an academic representative on the board of directors of Sherlock Biosciences, but will receive no personal compensation.)

The licensing agreement announced today does not cover SHERLOCK’s use in the developing world. In addition, the license is not exclusive for certain public health applications in the developed world — for example, the licensing structure is designed to make SHERLOCK available to help health care professionals quickly diagnose a host of circulating bacterial and viral infections such as malaria, tuberculosis, Zika, and rotavirus, among others. For such purposes, the academic coalition will ensure SHERLOCK is made widely available. In addition, SHERLOCK tools, knowledge, and methods will continue to be made freely available for academic research worldwide.

The technology was developed by a team of scientists from the Broad Institute, the McGovern Institute for Brain Research at MIT, the Institute for Medical Engineering & Science at MIT, the Wyss Institute for Biologically Inspired Engineering at Harvard University, MGH, Rutgers, and Skolkovo Institute of Science and Technology. It is a rapid, inexpensive, highly sensitive diagnostic tool with the potential for a transformative effect on research and global public health.

“Skoltech is proud to be working with Broad Institute and the international academic community to address important medical challenges facing humanity, save lives and improve health and well-being for the world’s citizens,” said Professor Alexander Kuleshov, President of Skoltech, and Member of the Russian National Academy of Sciences.

Broad Institute of MIT and Harvard was launched in 2004 to empower this generation of creative scientists to transform medicine. The Broad Institute seeks to describe all the molecular components of life and their connections; discover the molecular basis of major human diseases; develop effective new approaches to diagnostics and therapeutics; and disseminate discoveries, tools, methods, and data openly to the entire scientific community.

Founded by MIT, Harvard, Harvard-affiliated hospitals, and the visionary Los Angeles philanthropists Eli and Edythe L. Broad, the Broad Institute includes faculty, professional staff, and students from throughout the MIT and Harvard biomedical research communities and beyond, with collaborations spanning over a hundred private and public institutions in more than 40 countries worldwide. For further information about the Broad Institute, go to http://www.broadinstitute.org.

How tumors behave on acid

Anne Trafton | MIT News Office — Wed, 20 Mar 2019 00:00:00 -0400

Scientists have long known that tumors have many pockets of high acidity, usually found deep within the tumor where little oxygen is available. However, a new study from MIT researchers has found that tumor surfaces are also highly acidic, and that this acidity helps tumors to become more invasive and metastatic.

The study found that the acidic environment helps tumor cells to produce proteins that make them more aggressive. The researchers also showed that they could reverse this process in mice by making the tumor environment less acidic.

“Our findings reinforce the view that tumor acidification is an important driver of aggressive tumor phenotypes, and it indicates that methods that target this acidity could be of value therapeutically,” says Frank Gertler, an MIT professor of biology, a member of MIT’s Koch Institute for Integrative Cancer Research, and the senior author of the study.

Former MIT postdoc Nazanin Rohani is the lead author of the study, which appears in the journal Cancer Research.

Mapping acidity

Scientists usually attribute a tumor’s high acidity to the lack of oxygen, or hypoxia, that often occurs in tumors because they don’t have an adequate blood supply. However, until now, it has been difficult to precisely map tumor acidity and determine whether it overlaps with hypoxic regions.

In this study, the MIT team used a probe called pH (Low) Insertion Peptide (pHLIP), originally developed by researchers at the University of Rhode Island, to map the acidic regions of breast tumors in mice. This peptide is floppy at normal pH but becomes more stable at low, acidic pH. When this happens, the peptide can insert itself into cell membranes. This allows the researchers to determine which cells have been exposed to acidic conditions, by identifying cells that have been tagged with the peptide.

To their surprise, the researchers found that not only were cells in the oxygen-deprived interior of the tumor acidic, there were also acidic regions at the boundary of the tumor and the structural tissue that surrounds it, known as the stroma.

“There was a great deal of tumor tissue that did not have any hallmarks of hypoxia that was quite clearly exposed to acidosis,” Gertler says. “We started looking at that, and we realized hypoxia probably wouldn’t explain the majority of regions of the tumor that were acidic.”

Further investigation revealed that many of the cells at the tumor surface had shifted to a type of cell metabolism known as aerobic glycolysis. This process generates lactic acid as a byproduct, which could account for the high acidity, Gertler says. The researchers also discovered that in these acidic regions, cells had turned on gene expression programs associated with invasion and metastasis. Nearly 3,000 genes showed pH-dependent changes in activity, and close to 300 displayed changes in how the genes are assembled, or spliced.

“Tumor acidosis gives rise to the expression of molecules involved in cell invasion and migration. This reprogramming, which is an intracellular response to a drop in extracellular pH, gives the cancer cells the ability to survive under low-pH conditions and proliferate,” Rohani says.

Those activated genes include Mena, which codes for a protein that normally plays a key role in embryonic development. Gertler’s lab had previously discovered that in some tumors, Mena is spliced differently, producing an alternative form of the protein known as Mena^INV (invasive). This protein helps cells to migrate into blood vessels and spread though the body.

Another key protein that undergoes alternative splicing in acidic conditions is CD44, which also helps tumor cells to become more aggressive and break through the extracellular tissues that normally surround them. This study marks the first time that acidity has been shown to trigger alternative splicing for these two genes.

Reducing acidity

The researchers then decided to study how these genes would respond to decreasing the acidity of the tumor microenvironment. To do that, they added sodium bicarbonate to the mice’s drinking water. This treatment reduced tumor acidity and shifted gene expression closer to the normal state. In other studies, sodium bicarbonate has also been shown to reduce metastasis in mouse models.

Sodium bicarbonate would not be a feasible cancer treatment because it is not well-tolerated by humans, but other approaches that lower acidity could be worth exploring, Gertler says. The expression of new alternative splicing genes in response to the acidic microenvironment of the tumor helps cells survive, so this phenomenon could be exploited to reverse those programs and perturb tumor growth and potentially metastasis.

“Other methods that would more focally target acidification could be of great value,” he says.

The research was funded by the Koch Institute Support (core) Grant from the National Cancer Institute, the Howard Hughes Medical Institute, the National Institutes of Health, the KI Quinquennial Cancer Research Fellowship, and MIT’s Undergraduate Research Opportunities Program.

Other authors of the paper include Liangliang Hao, a former MIT postdoc; Maria Alexis and Konstantin Krismer, MIT graduate students; Brian Joughin, a lead research modeler at the Koch Institute; Mira Moufarrej, a recent graduate of MIT; Anthony Soltis, a recent MIT PhD recipient; Douglas Lauffenburger, head of MIT’s Department of Biological Engineering; Michael Yaffe, a David H. Koch Professor of Science; Christopher Burge, an MIT professor of biology; and Sangeeta Bhatia, the John and Dorothy Wilson Professor of Health Sciences and Technology and Electrical Engineering and Computer Science.

Using machine learning for medical solutions

Gina Vitale | MIT News correspondent — Tue, 19 Mar 2019 00:00:00 -0400

Pharmaceutical companies spend a lot of time testing potential drugs, and they end up wasting much of that effort on candidates that don’t pan out. Kyle Swanson wants to change that.

A master’s student in computer science and engineering, Swanson is working on a project that involves feeding a computer information about chemical compounds that have or have not worked as drugs in the past. From this input, the machine “learns” to predict which kinds of new compounds have the most promise as drug candidates, potentially saving money and time otherwise spent on testing. Several prominent companies have already adopted the software as their new model.

“Our model is never going to be perfect … but the hope is that by doing this prediction phase first, the molecules that they actually test in the lab have a much higher chance of being viable drugs,” says Swanson, who graduated from MIT in 2018 with a BS in computer science and engineering, a BS in mathematics, and a minor in music.

Swanson’s overall aim is to use his skills in computer science and machine learning for real-world science applications. He’ll work toward that goal as a Marshall Scholar for the next two years, attending Cambridge University to pursue a pair of master’s degrees, one in mathematical statistics and the other in computational biology.

“I think the ultimate goal is to do something very similar to what I’m doing right now,” he says. “I feel like it’s a great mix of doing interesting computer science research and pushing the field of machine learning forward, while also having practical applications in the sciences.”

Researcher and survivor

Swanson’s first experience researching medical applications for machine learning was as an undergraduate in the lab of Regina Barzilay, the Delta Electronics Professor in the Computer Science and Artificial Intelligence Laboratory and the Department of Electrical Engineering and Computer Science. Swanson worked on a system designed to identify the presence of breast cancer from mammogram images. While the original goal of cancer detection proved to be difficult, the tool was successful at a related task. The algorithm is still used to analyze mammogram images, but rather than identifying cancer, it identifies whether patients are at greater risk for cancer, depending on the density of their breast tissue.

While he was already interested in machine learning, Swanson entered cancer research for a very personal reason. One day, he noticed he had a little cough, which he attributed to catching a cold from his roommate. But while his roommate’s cough subsided, Swanson’s didn’t. Walking home one night a few weeks later, he found a lump above his collarbone. It turned out to be Hodgkin’s lymphoma.

“My approach is to try and laugh it off as much as possible. I feel like if I were to take it seriously, it would just be so awful I wouldn’t be able to handle it,” Swanson says. “I mean, obviously there were times when I actually was very distraught about the whole thing. … The way I’ve tried to handle it is just to be as positive as possible.”

He asked to join Barzilay’s lab not only because he found her research important, but also because she’d been through a similar scare with breast cancer. He felt that she understood what he was going through. Even now, as he’s working on that pharmaceutical machine learning project, she is still his advisor.

“She’s been a role model for the kind of person I want to be both professionally and personally, and I hope that one day I can be in a similar position, making a real difference in the lives of others through my research,” he says.

After several rounds of treatment, Swanson’s most recent PET scans indicate that he’s now cancer free.

A symphony for all seasons

Swanson first went to music school in Scarsdale, New York, when he was 2 years old. He picked up the flute in third grade, and later the piccolo. With many hours of practice, he became a skilled classical musician. He’s been in the MIT Symphony Orchestra for five straight years, and he’s played in a number of other ensembles as well.

“The great thing about MIT is that I’ve been able to continue that interest. …The music program here is really excellent,” Swanson says. “I’ve enjoyed all the classes I’ve taken, and the ensembles are great as well.”

His favorite experience in the music department is one to be rivaled. His first-year roommate, Bertrand Stone, also a mathematics major and musician, is a very talented composer. Before the summer of 2016, Swanson joked that Stone should use some of his free time outside of class to write a flute piece for him. When he returned in the fall, Stone handed him a 135-page, fully composed 20-minute flute concerto. Stone had already shown the piece to the MIT symphony conductor for input during the composition process, and Swanson was asked to perform it with the orchestra.

“That was my favorite by far,” Swanson says.

Music still takes up most of Swanson’s free time. But when he’s not practicing on some sort of woodwind, he enjoys pounding the pavement with MIT’s Running Club and spending time with friends. His undergraduate fraternity, Alpha Epsilon Pi, is still a big part of his life. He met many of his closest friends there, including one of his current roommates, and they played a key supportive role for him when he was wrestling with cancer.

“They’re just some of the smartest and nicest people I know on campus,” Swanson says.

A master of degrees

By the time Swanson leaves Cambridge, he’ll have three master’s degrees. “Really, I want to just have a better understanding of the fields that I’m going to be applying machine learning to,” he says.

As for his future after that, he’s not exactly sure. He will most likely go back to school for a PhD, and then he’ll decide if he wants to enter industry or academia. The important thing for him is that he’s applying his knowledge of machine learning to science that has a real impact on human lives.

“If I were to keep doing what I’m doing right now, I think I would be very happy. I love machine learning and I love the way it can do such amazing things,” he says. “But I also specifically like seeing the difference that I’m making in the world.”

A new approach to drugging a difficult cancer target

Anne Trafton | MIT News Office — Thu, 14 Mar 2019 11:00:00 -0400

One of the most common cancer-promoting genes, known as Myc, is also one of the most difficult to target with drugs. Scientists have long tried to develop drugs that block the Myc protein, but so far their efforts have not been successful.

Now, using an alternative strategy, MIT researchers have discovered a compound that can reduce Myc activity by tying up the protein that is Myc’s usual binding partner, leaving Myc partnerless and unable to perform its usual functions.

The research team, led by Angela Koehler, an assistant professor of biological engineering and a member of MIT’s Koch Institute for Integrative Cancer Research, found that the compound they developed could suppress tumor growth in mice with certain types of cancer. The compound has been licensed by an MIT spinout that is now seeking to develop more powerful versions that could potentially be tested in human patients.

Koehler is the senior author of the study, which appears online in the journal Cell Chemical Biology on March 14. MIT postdoc Nicholas Struntz and graduate student Andrew Chen are the lead authors of the study, and the research team also includes authors from the Broad Institute of MIT and Harvard, Stanford University, Baylor College of Medicine, Brigham and Women’s Hospital, and Dana-Farber Cancer Institute.

A new approach

For decades, cancer researchers have been trying to find ways to shut off Myc, which is a transcription factor — a protein that controls the expression of other genes. Known as a “master regulator,” Myc controls many genes involved in basic cellular functions such as growth and metabolism. When it becomes overexpressed, as it does in about 70 percent of cancers, it drives uncontrolled cell growth and proliferation.

Myc usually forms a structure known as a heterodimer with the Max protein, and these proteins together bind to DNA to turn on gene transcription. Drug development efforts have traditionally focused on disrupting the interaction of Myc and Max, which has proven difficult. Most of the compounds that researchers have tested have proven too weak, or not specific enough to the Myc-Max interaction.

Koehler encountered similar difficulties, but several years ago, she decided to pursue a different strategy, based on the Max protein. The idea was to try to find compounds that would interact with Max, and then see if they had any effect on Myc’s ability to drive cell growth.

Using a technology developed by Koehler known as a microarray binding assay, the researchers screened a library of about 20,000 compounds, including both natural products and a collection of compounds synthesized by the Broad Institute, as possible drug candidates. The top six hits, in terms of ability to bind to Max and inhibit Myc transcriptional activity in another assay, all came from the Broad Institute collection.

The researchers tested the compounds in several different cancer cell lines and identified one that appeared to be most effective at halting cell growth.

At first, the researchers were unsure how this compound was blocking Myc activity, but experiments revealed that it was stabilizing a structure in which two molecules of Max bind together, forming a structure called a homodimer. This reduces the formation of the Myc-Max heterodimer and leads to a decrease in Myc levels, which the researchers believe may be the result of the unpartnered protein being broken down within cells.

Shrinking tumors

The researchers found that the compound slowed cell growth in a variety of Myc-dependent human cancer cells, including models for hepatocellular carcinoma, T-cell acute lymphoblastic leukemia, and Burkitt’s lymphoma.

They also tested the compound in mice, and found that even though the compound they originally identified was not optimized for maximum potency, it could slow tumor progression in mouse models of hepatocellular carcinoma and T-cell acute lymphoblastic leukemia.

“The discovery and detailed validation of a small molecule targeting Max homodimers represents a significant advance over previous attempts to directly inhibit either Myc itself or Myc-Max dimerization,” says Robert Eisenman, a principal investigator at the Fred Hutchinson Cancer Research Center, who was not involved in the study. “It not only provides new insight into how Myc functions but reveals what is likely to be an important exploitable vulnerability in Myc-driven cancers.”

Kronos Bio, the company that has licensed the rights to the compound described in this paper, is now working to optimize it to be more potent and more efficient. Koehler’s lab is also working on learning more about how this compound works, as well as determining the structure of the complex that it forms with the Max homodimer, in hopes of potentially developing better versions.

“This particular compound isn’t going to be a drug — it’s really just a tool to clarify the relevance of stabilizing Max homodimers as a strategy to perturb Myc function,” Koehler says. “That can guide people in the pharmaceutical industry who are thinking about trying to drug Myc, to maybe think about other ways to find Max homodimer stabilizers.”

Her lab is also pursuing other ways to target Myc, such as finding ways to stabilize a homodimer of two Myc molecules, which would likely end up being degraded within the cell.

“There may be different ways to stabilize biomolecular interactions within the Myc-Max network that could lead to different ways of perturbing Myc function,” she says.

The research was funded, in part, by the National Cancer Institute, including the Koch Institute Support (core) Grant, the National Institutes of Health, the Leukemia and Lymphoma Society, the Ono Pharma Foundation, the MIT Deshpande Center for Technological Innovation, the MIT Center for Precision Cancer Medicine, the AACR-Bayer Innovation and Discovery Grant, and the Merkin Institute Fellows Program at the Broad Institute.

New optical imaging system could be deployed to find tiny tumors

Anne Trafton | MIT News Office — Thu, 07 Mar 2019 04:59:59 -0500

Many types of cancer could be more easily treated if they were detected at an earlier stage. MIT researchers have now developed an imaging system, named “DOLPHIN,” which could enable them to find tiny tumors, as small as a couple of hundred cells, deep within the body.

In a new study, the researchers used their imaging system, which relies on near-infrared light, to track a 0.1-millimeter fluorescent probe through the digestive tract of a living mouse. They also showed that they can detect a signal to a tissue depth of 8 centimeters, far deeper than any existing biomedical optical imaging technique.

The researchers hope to adapt their imaging technology for early diagnosis of ovarian and other cancers that are currently difficult to detect until late stages.

“We want to be able to find cancer much earlier,” says Angela Belcher, the James Mason Crafts Professor of Biological Engineering and Materials Science at MIT and a member of the Koch Institute for Integrative Cancer Research, and the newly-appointed head of MIT’s Department of Biological Engineering. “Our goal is to find tiny tumors, and do so in a noninvasive way.”

Belcher is the senior author of the study, which appears in the March 7 issue of Scientific Reports. Xiangnan Dang, a former MIT postdoc, and Neelkanth Bardhan, a Mazumdar-Shaw International Oncology Fellow, are the lead authors of the study. Other authors include research scientists Jifa Qi and Ngozi Eze, former postdoc Li Gu, postdoc Ching-Wei Lin, graduate student Swati Kataria, and Paula Hammond, the David H. Koch Professor of Engineering, head of MIT’s Department of Chemical Engineering, and a member of the Koch Institute.

Deeper imaging

Existing methods for imaging tumors all have limitations that prevent them from being useful for early cancer diagnosis. Most have a tradeoff between resolution and depth of imaging, and none of the optical imaging techniques can image deeper than about 3 centimeters into tissue. Commonly used scans such as X-ray computed tomography (CT) and magnetic resonance imaging (MRI) can image through the whole body; however, they can’t reliably identify tumors until they reach about 1 centimeter in size.

Belcher’s lab set out to develop new optical methods for cancer imaging several years ago, when they joined the Koch Institute. They wanted to develop technology that could image very small groups of cells deep within tissue and do so without any kind of radioactive labeling.

Near-infrared light, which has wavelengths from 900 to 1700 nanometers, is well-suited to tissue imaging because light with longer wavelengths doesn’t scatter as much as when it strikes objects, which allows the light to penetrate deeper into the tissue. To take advantage of this, the researchers used an approach known as hyperspectral imaging, which enables simultaneous imaging in multiple wavelengths of light.

The researchers tested their system with a variety of near-infrared fluorescent light-emitting probes, mainly sodium yttrium fluoride nanoparticles that have rare earth elements such as erbium, holmium, or praseodymium added through a process called doping. Depending on the choice of the doping element, each of these particles emits near-infrared fluorescent light of different wavelengths.

Using algorithms that they developed, the researchers can analyze the data from the hyperspectral scan to identify the sources of fluorescent light of different wavelengths, which allows them to determine the location of a particular probe. By further analyzing light from narrower wavelength bands within the entire near-IR spectrum, the researchers can also determine the depth at which a probe is located. The researchers call their system “DOLPHIN”, which stands for “Detection of Optically Luminescent Probes using Hyperspectral and diffuse Imaging in Near-infrared.”

To demonstrate the potential usefulness of this system, the researchers tracked a 0.1-millimeter-sized cluster of fluorescent nanoparticles that was swallowed and then traveled through the digestive tract of a living mouse. These probes could be modified so that they target and fluorescently label specific cancer cells.

“In terms of practical applications, this technique would allow us to non-invasively track a 0.1-millimeter-sized fluorescently-labeled tumor, which is a cluster of about a few hundred cells. To our knowledge, no one has been able to do this previously using optical imaging techniques,” Bardhan says.

Earlier detection

The researchers also demonstrated that they could inject fluorescent particles into the body of a mouse or a rat and then image through the entire animal, which requires imaging to a depth of about 4 centimeters, to determine where the particles ended up. And in tests with human tissue-mimics and animal tissue, they were able to locate the probes to a depth of up to 8 centimeters, depending on the type of tissue.

Guosong Hong, an assistant professor of materials science and engineering at Stanford University, described the new method as “game-changing.”

“This is really amazing work,” says Hong, who was not involved in the research. “For the first time, fluorescent imaging has approached the penetration depth of CT and MRI, while preserving its naturally high resolution, making it suitable to scan the entire human body.”

This kind of system could be used with any fluorescent probe that emits light in the near-infrared spectrum, including some that are already FDA-approved, the researchers say. The researchers are also working on adapting the imaging system so that it could reveal intrinsic differences in tissue contrast, including signatures of tumor cells, without any kind of fluorescent label.

In ongoing work, they are using a related version of this imaging system to try to detect ovarian tumors at an early stage. Ovarian cancer is usually diagnosed very late because there is no easy way to detect it when the tumors are still small.

“Ovarian cancer is a terrible disease, and it gets diagnosed so late because the symptoms are so nondescript,” Belcher says. “We want a way to follow recurrence of the tumors, and eventually a way to find and follow early tumors when they first go down the path to cancer or metastasis. This is one of the first steps along the way in terms of developing this technology.”

The researchers have also begun working on adapting this type of imaging to detect other types of cancer such as pancreatic cancer, brain cancer, and melanoma.

The research was funded by the Koch Institute Frontier Research Program, the Marble Center for Cancer Nanomedicine, the Koch Institute Support (core) Grant from the National Cancer Institute, the NCI Center for Center for Cancer Nanotechnology Excellence, and the Bridge Project.

Predicting sequence from structure

Raleigh McElvery | Department of Biology — Fri, 15 Feb 2019 11:00:00 -0500

One way to probe intricate biological systems is to block their components from interacting and see what happens. This method allows researchers to better understand cellular processes and functions, augmenting everyday laboratory experiments, diagnostic assays, and therapeutic interventions. As a result, reagents that impede interactions between proteins are in high demand. But before scientists can rapidly generate their own custom molecules capable of doing so, they must first parse the complicated relationship between sequence and structure.

Small molecules can enter cells easily, but the interface where two proteins bind to one another is often too large or lacks the tiny cavities required for these molecules to target. Antibodies and nanobodies bind to longer stretches of protein, which makes them better suited to hinder protein-protein interactions, but their large size and complex structure render them difficult to deliver and unstable in the cytoplasm. By contrast, short stretches of amino acids, known as peptides, are large enough to bind long stretches of protein while still being small enough to enter cells.

The Keating lab at the MIT Department of Biology is hard at work developing ways to quickly design peptides that can disrupt protein-protein interactions involving Bcl-2 proteins, which promote cancer growth. Their most recent approach utilizes a computer program called dTERMen, developed by Keating lab alumnus, Gevorg Grigoryan PhD ’07, currently an associate professor of computer science and adjunct associate professor of biological sciences and chemistry at Dartmouth College. Researchers simply feed the program their desired structures, and it spits out amino acid sequences for peptides capable of disrupting specific protein-protein interactions.

“It’s such a simple approach to use,” says Keating, an MIT professor of biology and senior author on the study. “In theory, you could put in any structure and solve for a sequence. In our study, the program came up with new sequence combinations that aren’t like anything found in nature — it deduced a completely unique way to solve the problem. It’s exciting to be uncovering new territories of the sequence universe.”

Former postdoc Vincent Frappier and Justin Jenson PhD ’18 are co-first authors on the study, which appears in the latest issue of Structure.

Same problem, different approach

Jenson, for his part, has tackled the challenge of designing peptides that bind to Bcl-2 proteins using three distinct approaches. The dTERMen-based method, he says, is by far the most efficient and general one he’s tried yet.

Standard approaches for discovering peptide inhibitors often involve modeling entire molecules down to the physics and chemistry behind individual atoms and their forces. Other methods require time-consuming screens for the best binding candidates. In both cases, the process is arduous and the success rate is low.

dTERMen, by contrast, necessitates neither physics nor experimental screening, and leverages common units of known protein structures, like alpha helices and beta strands — called tertiary structural motifs or “TERMs” — which are compiled in collections like the Protein Data Bank. dTERMen extracts these structural elements from the data bank and uses them to calculate which amino acid sequences can adopt a structure capable of binding to and interrupting specific protein-protein interactions. It takes a single day to build the model, and mere seconds to evaluate a thousand sequences or design a new peptide.

“dTERMen allows us to find sequences that are likely to have the binding properties we're looking for, in a robust, efficient, and general manner with a high rate of success,” Jenson says. “Past approaches have taken years. But using dTERMen, we went from structures to validated designs in a matter of weeks.”

Of the 17 peptides they built using the designed sequences, 15 bound with native-like affinity, disrupting Bcl-2 protein-protein interactions that are notoriously difficult to target. In some cases, their designs were surprisingly selective and bound to a single Bcl-2 family member over the others. The designed sequences deviated from known sequences found in nature, which greatly increases the number of possible peptides.

“This method permits a certain level of flexibility,” Frappier says. “dTERMen is more robust to structural change, which allows us to explore new types of structures and diversify our portfolio of potential binding candidates.”

Probing the sequence universe

Given the therapeutic benefits of inhibiting Bcl-2 function and slowing tumor growth, the Keating lab has already begun extending their design calculations to other members of the Bcl-2 family. They intend to eventually develop new proteins that adopt structures that have never been seen before.

“We have now seen enough examples of various local protein structures that computational models of sequence-structure relationships can be inferred directly from structural data, rather than having to be rediscovered each time from atomistic interaction principles,” says Grigoryan, dTERMen’s creator. “It’s immensely exciting that such structure-based inference works and is accurate enough to enable robust protein design. It provides a fundamentally different tool to help tackle the key problems of structural biology — from protein design to structure prediction.”

Frappier hopes one day to be able to screen the entire human proteome computationally, using methods like dTERMen to generate candidate binding peptides. Jenson suggests that using dTERMen in combination with more traditional approaches to sequence redesign could amplify an already powerful tool, empowering researchers to produce these targeted peptides. Ideally, he says, one day developing peptides that bind and inhibit your favorite protein could be as easy as running a computer program, or as routine as designing a DNA primer.

According to Keating, although that time is still in the future, “our study is the first step towards demonstrating this capacity on a problem of modest scope.”

This research was funded the National Institute of General Medical Sciences, National Science Foundation, Koch Institute for Integrative Cancer Research, Natural Sciences and Engineering Research Council of Canada, and Fonds de Recherche du Québec.

Why too much DNA repair can injure tissue

Anne Trafton | MIT News Office — Tue, 12 Feb 2019 14:00:00 -0500

DNA-repair enzymes help cells survive damage to their genomes, which arises as a normal byproduct of cell activity and can also be caused by environmental toxins. However, in certain situations, DNA repair can become harmful to cells, provoking an inflammatory response that produces severe tissue damage.

MIT Professor Leona Samson has now determined that inflammation is a key component of the way this damage occurs in photoreceptor cells in the retinas of mice. About 10 years ago, she and her colleagues discovered that overactive initiation of DNA-repair systems can lead to retinal damage and blindness in mice. The key enzyme in this process, known as Aag glycosylase, can also cause harm in other tissues when it becomes hyperactive.

“It’s another case where despite the fact that inflammation is there to protect you, in some circumstances it can actually be harmful, when it’s overactive,” says Samson, a professor emerita of biology and biological engineering and the senior author of the study.

Aag glycosylase helps to repair DNA damage caused by a class of drugs known as alkylating agents, which are commonly used as chemotherapy drugs and are also found in pollutants such as tobacco smoke and fuel exhaust. Retinal damage from these drugs has not been seen in human patients, but alkylating agents may produce similar damage in other human tissues, Samson says. The new study, which reveals how Aag overactivity leads to cell death, suggest possible targets for drugs that could prevent such damage.

Mariacarmela Allocca, a former MIT postdoc, is the lead author of the study, which appears in the Feb. 12 issue of Science Signaling. MIT technical assistant Joshua Corrigan, former postdoc Aprotim Mazumder, and former technical assistant Kimberly Fake are also authors of the paper.

A vicious cycle

In a 2009 study, Samson and her colleagues found that a relatively low level of exposure to an alkylating agent led to very high rates of retinal damage in mice. Alkylating agents produce specific types of DNA damage, and Aag glycosylase normally initiates repair of such damage. However, in certain types of cells that have higher levels of Aag, such as mouse photoreceptors, the enzyme’s overactivity sets off a chain of events that eventually leads to cell death.

In the new study, the researchers wanted to find exactly out how this happens. They knew that Aag was overactive in the affected cells, but they didn’t know exactly how it was leading to cell death or what type of cell death was occurring. The researchers initially suspected it was apoptosis, a type of programmed cell death in which a dying cell is gradually broken down and absorbed by other cells.

However, they soon found evidence that another type of cell death called necrosis accounts for most of the damage. When Aag begins trying to repair the DNA damage caused by the alkylating agent, it cuts out so many damaged DNA bases that it hyperactivates an enzyme called PARP, which induces necrosis. During this type of cell death, cells break apart and spill out their contents, which alerts the immune system that something is wrong.

One of the proteins secreted by the dying cells, known as HMGB1, stimulates production of chemicals that attract immune cells called macrophages, which specifically penetrate the photoreceptor layer of the retina. These macrophages produce highly reactive oxygen species — molecules that create more damage and make the environment even more inflammatory. This in turn causes more DNA damage, which is recognized by Aag.

“That makes the situation worse, because the Aag glycosylase will act on the lesions produced from the inflammation, so you get a vicious cycle, and the DNA repair drives more and more degeneration and necrosis in the photoreceptor layer,” Samson says.

None of this happens in mice that lack Aag or PARP, and it does not occur in other cells of the eye or in most other body tissues.

“It amazes me how segmented this is. The other cells in the retina are not affected at all, and they must experience the same amount of DNA damage. So, one possibility is maybe they don’t express Aag, while the photoreceptor cells do,” Samson says.

“These molecular studies are exciting, as they have helped define the underlying pathophysiology associated with retinal damage,” says Ben Van Houten, a professor of pharmacology and chemical biology at the University of Pittsburgh, who was not involved in the study. “DNA repair is essential for the faithful inheritance of a cell’s genetic material. However, the very action of some DNA repair enzymes can result in the production of toxic intermediates that exacerbate exposures to genotoxic agents.”

Varying effects

The researchers also found that retinal inflammation and necrosis were more severe in male mice than in female mice. They suspect that estrogen, which can interfere with PARP activity, may help to suppress the pathway that leads to inflammation and cell death.

Samson’s lab has previously found that Aag activity can also exacerbate damage to the brain during a stroke, in mice. The same study revealed that Aag activity also worsens inflammation and tissue damage in the liver and kidney following oxygen deprivation. Aag-driven cell death has also been seen in the mouse cerebellum and some pancreatic and bone marrow cells.

The effects of Aag overactivity have been little studied in humans, but there is evidence that healthy individuals have widely varying levels of the enzyme, suggesting that it could have different effects in different people.

“Presumably there are some cell types in the human body that would respond the same way as the mouse photoreceptors,” Samson says. “They may just not be the same set of cells.”

The research was funded by the National Institutes of Health.

A better way to measure cell survival

Anne Trafton | MIT News Office — Tue, 05 Feb 2019 11:00:00 -0500

Measuring the toxic effects of chemical compounds on different types of cells is critical for developing cancer drugs, which must be able to kill their target cells. Analyzing cell survival is also an important task in fields such as environmental regulation, to test industrial and agricultural chemicals for possible harmful effects on healthy cells.

MIT biological engineers have now devised a new toxicity test that can measure chemical effects on cell survival with much greater sensitivity than some of the most popular tests used today. It is also much faster than the gold-standard test, which is not widely used because it takes two to three weeks to yield results. The new test could thus help drug companies and academic researchers identify and evaluate new drugs more rapidly.

“Cytotoxicity assays are one of the most commonly used assays in life sciences,” says Bevin Engelward, a professor of biological engineering at MIT and the senior author of the study.

Le Ngo, a former MIT graduate student and postdoc, is the lead author of the paper, which appears in the Feb. 5 issue of Cell Reports. Other authors include Tze Khee Chan, a former graduate student at the Singapore-MIT Alliance for Research and Technology (SMART); Jing Ge, a former MIT graduate student; and Leona Samson, Ngo’s co-advisor and an MIT professor emerita of biological engineering.

Measuring survival

The traditional test for measuring cell survival, known as the colony formation assay, involves growing cell colonies in tissue culture dishes for two to three weeks after exposing the cells to a chemical compound or another harmful agent such as radiation. A researcher then counts the number of colonies to determine how the treatment affected the cells’ survival.

Part of Engelward’s motivation for this study was the memory of the long hours she spent counting such colonies as a graduate student.

“The counting is really laborious and painfully difficult because you have to constantly make judgement calls as to what is a colony versus debris,” she says. “Few people use the colony formation assay anymore because it’s difficult, way too slow, and requires huge amounts of cell growth media, so you need a lot of the compound being tested.”

In recent years, scientists have begun using other methods that are faster but not as accurate and sensitive as the colony formation assay. These tests do not measure cell growth directly but instead analyze mitochondrial function.

Engelward and colleagues set out to develop a test that could generate results in just a few days while still matching the accuracy and sensitivity of the colony formation assay. The system they invented, which they call the MicroColonyChip, consists of tiny wells on a plate. Treated and untreated cells are placed into these wells and begin to form very small colonies in a grid pattern. Within just a few days, before the colonies become visible to the naked eye, the researchers can use a microscope to image the cells’ DNA, which is fluorescently labeled.

By modifying code originally developed by former MIT postdoc David Wood and MIT Professor Sangeeta Bhatia, the researchers created a software program that measures the amount of fluorescent DNA in each well and then calculates how much cell growth occurred. By comparing the growth of treated and untreated cells, the researchers can determine the toxicity of whatever compound they are studying.

“We have an automatic scanning system to do the fluorescent imaging, and afterward, the image analysis is completely automated,” Ngo says.

The researchers compared their new test to the gold-standard colony formation assay and found that the results were indistinguishable. They were also able to precisely reproduce data on the effects of gamma radiation on human lymphoblastoid cells, collected 20 years ago using the colony formation assay. Using the MicroColonyChip, the researchers obtained their data in three days, instead of three weeks.

“We were able reproduce radiation studies from 20 years ago, using a process much easier than what they did,” Engelward says.

Greater sensitivity

The researchers also compared their new test to the two toxicity tests that are most commonly used by researchers and pharmaceutical companies, known as XTT and CellTiter-Glo (CTG). Both of these tests are indirect measures of cell viability: XTT measures cells’ ability to break down tetrazolium, a key step in cellular metabolism, and CTG measures intracellular levels of ATP, molecules that cells use to store energy.

“The MicroColonyChip is much more sensitive than the XTT assay, so it really gives you the ability to see subtle changes in cell survival, and it is as sensitive as the CTG assay while being more robust to artifacts,” Engelward says.

Using the new test, the researchers examined the effects of two DNA-damaging drugs used for chemotherapy and found that they could accurately reproduce the results obtained using the traditional colony formation assay. “We now plan to expand those studies in hopes of demonstrating that the test works for many more types of drugs and cells,” Ngo says.

In addition to being useful for drug development, this test could also be helpful for environmental regulatory agencies responsible for testing chemical compounds for potential harmful effects, Engelward says. Another possible application is in personalized medicine, where it could be used to test a variety of drugs on a patient’s cells before a treatment is chosen.

The researchers have filed for a patent on their technology. The research was funded by the National Institute of Environmental Health Sciences, including the NIEHS Superfund Basic Research Program, and the National Institutes of Health.

Bacteria promote lung tumor development, study suggests

Anne Trafton | MIT News Office — Thu, 31 Jan 2019 11:00:00 -0500

MIT cancer biologists have discovered a new mechanism that lung tumors exploit to promote their own survival: These tumors alter bacterial populations within the lung, provoking the immune system to create an inflammatory environment that in turn helps the tumor cells to thrive.

In mice that were genetically programmed to develop lung cancer, those raised in a bacteria-free environment developed much smaller tumors than mice raised under normal conditions, the researchers found. Furthermore, the researchers were able to greatly reduce the number and size of the lung tumors by treating the mice with antibiotics or blocking the immune cells stimulated by the bacteria.

The findings suggest several possible strategies for developing new lung cancer treatments, the researchers say.

“This research directly links bacterial burden in the lung to lung cancer development and opens up multiple potential avenues toward lung cancer interception and treatment,” says Tyler Jacks, director of MIT’s Koch Institute for Integrative Cancer Research and the senior author of the paper.

Chengcheng Jin, a Koch Institute postdoc, is the lead author of the study, which appears in the Jan. 31 online edition of Cell.

Linking bacteria and cancer

Lung cancer, the leading cause of cancer-related deaths, kills more than 1 million people worldwide per year. Up to 70 percent of lung cancer patients also suffer complications from bacterial infections of the lung. In this study, the MIT team wanted to see whether there was any link between the bacterial populations found in the lungs and the development of lung tumors.

To explore this potential link, the researchers studied genetically engineered mice that express the oncogene Kras and lack the tumor suppressor gene p53. These mice usually develop a type of lung cancer called adenocarcinoma within several weeks.

Mice (and humans) typically have many harmless bacteria growing in their lungs. However, the MIT team found that in the mice engineered to develop lung tumors, the bacterial populations in their lungs changed dramatically. The overall population grew significantly, but the number of different bacterial species went down. The researchers are not sure exactly how the lung cancers bring about these changes, but they suspect one possibility is that tumors may obstruct the airway and prevent bacteria from being cleared from the lungs.

This bacterial population expansion induced immune cells called gamma delta T cells to proliferate and begin secreting inflammatory molecules called cytokines. These molecules, especially IL-17 and IL-22, create a progrowth, prosurvival environment for the tumor cells. They also stimulate activation of neutrophils, another kind of immune cell that releases proinflammatory chemicals, further enhancing the favorable environment for the tumors.

“You can think of it as a feed-forward loop that forms a vicious cycle to further promote tumor growth,” Jin says. “The developing tumors hijack existing immune cells in the lungs, using them to their own advantage through a mechanism that’s dependent on local bacteria.”

However, in mice that were born and raised in a germ-free environment, this immune reaction did not occur and the tumors the mice developed were much smaller.

Blocking tumor growth

The researchers found that when they treated the mice with antibiotics either two or seven weeks after the tumors began to grow, the tumors shrank by about 50 percent. The tumors also shrank if the researchers gave the mice drugs that block gamma delta T cells or that block IL-17.

The researchers believe that such drugs may be worth testing in humans, because when they analyzed human lung tumors, they found altered bacterial signals similar to those seen in the mice that developed cancer. The human lung tumor samples also had unusually high numbers of gamma delta T cells.

“If we can come up with ways to selectively block the bacteria that are causing all of these effects, or if we can block the cytokines that activate the gamma delta T cells or neutralize their downstream pathogenic factors, these could all be potential new ways to treat lung cancer,” Jin says.

Many such drugs already exist, and the researchers are testing some of them in their mouse model in hopes of eventually testing them in humans. The researchers are also working on determining which strains of bacteria are elevated in lung tumors, so they can try to find antibiotics that would selectively kill those bacteria.

The research was funded, in part, by a Lung Cancer Concept Award from the Department of Defense, a Cancer Center Support (core) grant from the National Cancer Institute, the Howard Hughes Medical Institute, and a Margaret A. Cunningham Immune Mechanisms in Cancer Research Fellowship Award.

From microfluidics to metastasis

Bendta Schroeder | Koch Institute — Mon, 21 Jan 2019 15:00:00 -0500

Circulating tumor cells (CTCs) — an intermediate form of cancer cell between a primary and metastatic tumor cell — carry a treasure trove of information that is critical to treating cancer. Numerous engineering advancements over the years have made it possible to extract cells via liquid biopsy and analyze them to monitor an individual patient’s response to treatment and predict relapse.

Thanks to significant progress toward creating genetically engineered mouse models, liquid biopsies hold great promise for the lab as well. These mouse models mimic many aspects of human tumor development and have enabled informative studies that cannot be performed in patients. For example, these models can be used to trace the evolution of cells from initial mutation to eventual metastasis, a process in which CTCs play a critical role. But since it has not been possible to monitor CTCs over time in mice, scientists’ ability to study important features of metastasis has been limited.

The challenge lies in capturing enough cells to conduct such longitudinal studies. Although primary tumors shed CTCs constantly, the density of CTCs in blood is very low — fewer than 100 CTCs per milliliter. For human patients undergoing liquid biopsy, this does not present a problem. Clinicians can withdraw enough blood to guarantee a sufficient sample of CTCs, just a few milliliters out of five or so liters on average, with minimal impact to the patient.

A mouse, on the other hand, only has about 1.5 milliliters of blood in total. If researchers want to study CTCs over time, they may safely withdraw no more than a few microliters of blood from a mouse each day — nowhere near enough to ensure that many (or any) CTCs are collected.

But with a new approach developed by researchers at the Koch Institute for Integrative Cancer Research, it is now possible to collect CTCs from mice over days and even weeks, and analyze them as the disease progresses. The system, described in the Proceedings of the National Academy of Sciences the week of Jan. 21, diverts blood to a microfluidic cell-sorting chip that extracts individual CTCs before returning the blood back to an awake mouse.

A menu of sorts

The inspiration for the project was cooked up, not in the lab, but during a chance encounter in the Koch Café between Tyler Jacks, director of the Koch Institute and the David H. Koch Professor of Biology, and Scott Manalis, the Andrew and Erna Viterbi Professor in the departments of Biological Engineering and Mechanical Engineering and a member of the Koch Institute.

As luck and lunch lines would have it, the pair would discuss thesis work being done by then-graduate student Shawn Davidson, who was using a dialysis-like system to track metabolites in the bloodstream of mice in the laboratory of Matthew Vander Heiden, an associate professor of biology. Jacks and Manalis were inspired: Could a similar approach could be used to study rare CTCs in real time?

Along with their Koch Institute colleague Alex K. Shalek, the Pfizer-Laubach Career Development Assistant Professor of Chemistry and a core member of the Institute for Medical Engineering and Science (IMES) at MIT, it would take Jacks and Manalis more than five years to put all the pieces of the system together, drawing from different areas of expertise around the Koch Institute. The Jacks lab supplied its fluorescent small cell lung cancer model, the Manalis lab developed the real-time CTC isolation platform, and the Shalek lab provided genomic profiles of the collected CTCs using single-cell RNA sequencing.

“This is a project that could not have succeeded without a sustained effort from several labs with very different sets of expertise. For my lab, which primarily consists of engineers, the opportunity to participate in this type of research has been incredibly exciting and is the reason why we are in the Koch Institute,” Manalis says.

The CTC sorter uses laser excitation to identify tumor cells expressing a fluorescent marker that is incorporated in the mouse model. The system draws blood from the mouse and passes it through a microfluidic chip to detect and extract the fluorescing CTCs before returning the blood back to the mouse. A minute amount of blood — approximately 100 nanoliters — is diverted with every detected CTC into a collection tube, which then is purified further to extract individual CTCs from the thousands of other blood cells.

“The real-time detection of CTCs happens at a flow rate of approximately 2 milliliters per hour which allows us to scan nearly the entire blood volume of an awake and moving mouse within an hour,” says Bashar Hamza, a graduate student in the Manalis lab and one of the lead authors on the paper.

Biology in their blood

With the development of a real-time cell sorter, the researchers could now, for the first time, longitudinally collect CTCs from the same mouse.

Previously, the low blood volume of mice and the rarity of CTCs meant that groups of mice had to be sacrificed at successive times so that their CTCs could be pooled. However, CTCs from different mice often have significantly different gene expression profiles that can obscure subtle changes that occur from the evolution of the tumor or a perturbation such as a drug.

To demonstrate that their cell-sorter could capture these differences, the researchers treated mice with a compound called JQ1, which is known to inhibit the proliferation of cancer cells and perturb gene expression. CTCs were collected and profiled with single-cell RNA sequencing for two hours prior to the treatment, and then every 24 hours after the initial treatment for four days.

When the researchers pooled data for all mice that had been treated with JQ1, they found that the data clustered based on individual mice, offering no confirmation that the drug affects CTC gene expression over time. However, when the researchers analyzed single-mouse data, they observed gene expression shift with time.

“What’s so exciting about this platform and our approach is that we finally have the opportunity to comprehensively study longitudinal CTC responses without worrying about the potentially confounding effects of mouse-to-mouse variability. I, for one, can’t wait to see what we will be able to learn as we profile more CTCs, and their matched primary and metastatic tumors,” says Shalek.

Researchers believe their approach, which they intend to use in additional cancer types including non-small cell lung, pancreatic, and breast cancer, could open new avenues of inquiry in the study of CTCs, such as studying long-term drug responses, characterizing their relationship to metastatic tumors, and measuring their rate of production in short timeframes — and the entire metastatic cascade. In future work, researchers also plan to use their approach for profiling rare immune cells and monitoring cells in dynamic contexts such as wound healing and tumor formation.

“The ability to study CTCs as well other rare cells in the blood longitudinally gives us a powerful view into cancer development. This sorter represents a real breakthrough for the field and it is a great example of the Koch Institute in action,” says Jacks.

The paper’s other co-lead authors are graduate students Sheng Rong Ng from the Jacks lab and Sanjay Prakadan from the Shalek lab. The research is supported, in part, by the Ludwig Center at MIT, the National Cancer Institute, the National Institutes of Health and the Searle Scholars Program.

To guide cancer therapy, device quickly tests drugs on tumor tissue

Rob Matheson | MIT News Office — Wed, 12 Dec 2018 00:00:00 -0500

MIT and Draper researchers have 3-D printed a novel microfluidic device that simulates cancer treatments on biopsied tumor tissue, so clinicians can better examine how individual patients will respond to different therapeutics — before administering a single dose.

Testing cancer treatments today relies mostly on trial and error; patients may undergo multiple time-consuming and hard-to-tolerate therapies in pursuit of one that works. Recent innovations in pharmaceutical development involve growing artificial tumors to test drugs on specific cancer types. But these models take weeks to grow and don’t account for an individual patient’s biological makeup, which can affect treatment efficacy.

The researchers’ device, which can be printed in about one hour, is a chip slightly larger than a quarter, with three cylindrical “chimneys” rising from the surface. These are ports used to input and drain fluids, as well as remove unwanted air bubbles. Biopsied tumor fragments are placed in a chamber connected to a network of channels that deliver fluids — containing, for instance, immunotherapy agents or immune cells — to the tissue. Clinicians can then use various imaging techniques to see how the tissue responds to the drugs.

A key feature was using a new biocompatible resin — traditionally used for dental applications — that can support long-term survival of biopsied tissue. Although previous 3-D-printed microfluidics have held promise for drug testing, chemicals in their resin usually kill cells quickly. The researchers captured fluorescence microscopy images that show their device, called a tumor analysis platform (TAP), kept more than 90 percent of the tumor tissue alive for at least 72 hours, and potentially much longer.

Because the 3-D printed device is easy and cheap to fabricate, it could be rapidly implemented into clinical settings, the researchers say. Doctors could, for instance, print out a multiplexed device that could support multiple tumor samples in parallel, to enable modeling of the interactions between tumor fragments and many different drugs, simultaneously, for a single patient.

“People anywhere in the world could print our design. You can envision a future where your doctor will have a 3-D printer and can print out the devices as needed,” says Luis Fernando Velásquez-García, a researcher in the Microsystems Technology Laboratories and co-author on a paper describing the device, which appears in the December issue of the Journal of Microelectromechanical Systems. “If someone has cancer, you can take a bit of tissue in our device, and keep the tumor alive, to run multiple tests in parallel and figure out what would work best with the patient’s biological makeup. And then implement that treatment in the patient.”

A promising application is testing immunotherapy, a new treatment method using certain drugs to rev up a patient’s immune system to help it fight cancer. (This year’s Nobel Prize in physiology or medicine was awarded to two immunotherapy researchers who designed drugs that block certain proteins from preventing the immune system from attacking cancer cells.) The researchers’ device could help doctors better identify treatments to which an individual is likely to respond.

“Immunotherapy treatments have been specifically developed to target molecular markers found on the surface of cancer cells. This helps to ensure that the treatment elicits an attack on the cancer directly while limiting negative impacts on healthy tissue. However, every individual’s cancer expresses a unique array of surface molecules — as such, it can be difficult to predict who will respond to which treatment. Our device uses the actual tissue of the person, so is a perfect fit for immunotherapy,” says first author Ashley Beckwith SM ’18, a graduate researcher in Velásquez-García’s research group.

Co-author on the paper is Jeffrey T. Borenstein, a researcher at Draper, where he leads its program in immuno-oncology. “A key challenge in cancer research has been the development of tumor microenvironments that simulate mechanisms of cancer progression and the tumor-killing effects of novel therapeutics,” Borenstein says. “Through this collaboration with Luis and the MTL, we are able to benefit from their great expertise in additive manufacturing technologies and materials science for extremely rapid design cycles in building and testing these systems.”

Supporting cells

Microfluidics devices are traditionally manufactured via micromolding, using a rubberlike material called polydimethylsiloxane (PDMS). This technique, however, was not suitable for creating the three-dimensional network of features — such as carefully sized fluid channels — that mimic cancer treatments on living cells. Instead, the researchers turned to 3-D printing to craft a fine-featured device “monolithically” — meaning printing an object all in one go, without the need to assemble separate parts.

The heart of the device is its resin. After experimenting with numerous resins over several months, the researchers landed finally on Pro3dure GR-10, which is primarily used to make mouthguards that protect against teeth grinding. The material is nearly as transparent as glass, has barely any surface defects, and can be printed in very high resolution. And, importantly, as the researchers determined, it does not negatively impact cell survival.

The team subjected the resin to a 96-hour cytotoxicity test, an assay that exposes cells to the printed material and measures how toxic that material is to the cells. After the 96 hours, the cells in the material were still kicking. “When you print some of these other resin materials, they emit chemicals that mess with cells and kill them. But this doesn’t do that,” Velasquez-Garcia says. “To the best of my knowledge, there’s no other printable material that comes close to this degree of inertness. It’s as if the material isn’t there.”

Setting traps

Two other key innovations on the device are the “bubble trap” and a “tumor trap.” Flowing fluids into such a device creates bubbles that can disrupt the experiment or burst, releasing air that destroys tumor tissue.

To fix that, the researchers created a bubble trap, a stout “chimney” rising from the fluid channel into a threaded port through which air escapes. Fluid — including various media, fluorescent markers, or lymphocytes — gets injected into an inlet port adjacent to the trap. The fluid enters through the inlet port and flows past the trap, where any bubbles in the fluid rise up through the threaded port and out of the device. Fluid is then routed around a small U-turn into the tumor’s chamber, where it flows through and around the tumor fragment.

This tumor-trapping chamber sits at the intersection of the larger inlet channel and four smaller outlet channels. Tumor fragments, less than 1 millimeter across, are injected into the inlet channel via the bubble trap, which helps remove bubbles introduced when loading. As fluid flows through the device from the inlet port, the tumor is guided downstream to the tumor trap, where the fragment gets caught. The fluid continues traveling along the outlet channels, which are too small for the tumor to fit inside, and drains out of the device. A continuous flow of fluids keeps the tumor fragment in place and constantly replenishes nutrients for the cells.

“Because our device is 3-D printed, we were able to make the geometries we wanted, in the materials we wanted, to achieve the performance we wanted, instead of compromising between what was designed and what could be implemented — which typically happens when using standard microfabrication,” Velásquez-García says. He adds that 3-D printing may soon become the mainstream manufacturing technique for microfluidics and other microsystems that require complex designs.

In this experiment, the researchers showed they could keep a tumor fragment alive and monitor the tissue viability in real-time with fluorescent markers that make the tissue glow. Next, the researchers aim to test how the tumor fragments respond to real therapeutics.

“The traditional PDMS can’t make the structures you need for this in vitro environment that can keep tumor fragments alive for a considerable period of time,” says Roger Howe, a professor of electrical engineering at Stanford University, who was not involved in the research. “That you can now make very complex fluidic chambers that will allow more realistic environments for testing out various drugs on tumors quickly, and potentially in clinical settings, is a major contribution.”

Howe also praised the researchers for doing the legwork in finding the right resin and design for others to build on. “They should be credited for putting that information out there … because [previously] there wasn’t the knowledge of whether you had the materials or printing technology to make this possible,” he says. Now “it’s a democratized technology.”

New drug combination could be more effective against melanoma

Anne Trafton | MIT News Office — Mon, 03 Dec 2018 10:34:38 -0500

A class of cancer drugs called protein kinase inhibitors is one of the most effective treatments for melanoma. However, in many cases, tumors eventually become resistant to the drugs and cause a relapse in the patient.

A new study from MIT suggests that combining kinase inhibitors with experimental drugs known as ribonucleases could lead to better results. In tests with human cancer cells, the researchers found that the two drugs given together kill cells much more effectively than either drug does on its own. The combination could also help to prevent tumors from developing drug resistance, says Ronald Raines, the Firmenich Professor of Chemistry at MIT.

“We discovered that this ribonuclease drug could be paired favorably with other cancer chemotherapeutic agents, and not only that, the pairing made logical sense in terms of the underlying biochemistry,” Raines says.

Raines is the senior author of the study, which appears in the Dec. 3 issue of Molecular Cancer Therapeutics and was posted in the journal’s “online first” section on Nov. 20. Trish Hoang, a former graduate student at the University of Wisconsin at Madison, is the lead author of the study.

Unexpected link

Ribonucleases are enzymes produced by all human cells that break down RNA molecules. They degrade cellular RNA that is no longer needed, and they help to defend against viral RNA. Because of ribonucleases’ ability to kill cells by damaging their RNA, Raines has been working on developing these enzymes as cancer drugs for about two decades.

His lab has also been studying the protein that has evolved to help cells defend against ribonucleases, which can be very destructive if unchecked. This protein, called ribonuclease inhibitor, binds to ribonucleases with a half-life of at least three months — the strongest naturally occurring protein-binding interaction ever recorded. “That means that should ribonuclease invade cells, there is an unbelievable defense system,” Raines says.

To create a ribonuclease drug for testing, the researchers modified it so that ribonuclease inhibitors don’t bind as tightly — the half-life for the interaction is only a few seconds. One version of this drug is now in a phase 1 clinical trial, where it has stabilized the disease in about 20 percent of patients.

In the new study, the researchers found an unexpected link between ribonucleases and enzymes called protein kinases (the targets of protein kinase inhibitors), which led them to discover that the two drugs can kill cancer cells much better when used together than either one can alone.

The discovery came about when Hoang decided to try to produce the ribonuclease inhibitor protein in human cells instead of in E. coli, which Raines’ lab normally uses to produce the protein. She found that the human-cell-produced version, though identical in amino acid sequence to the protein produced by bacteria, bound to ribonucleases 100 times more strongly. This boosted the half-life of the interaction from months to decades — a protein-binding strength previously unheard of.

The researchers hypothesized that human cells were somehow modifying the inhibitor in a way that made it bind more tightly. Their studies revealed that, indeed, the inhibitor produced by human cells had phosphate groups added to it. This “phosphorylation” made the inhibitor bind much more strongly than anyone had previously suspected.

The researchers also discovered that phosphorylation was being carried out by protein kinases that are part of a cell signaling pathway called ERK. This pathway, which controls how cells respond to growth factors, is often overactive in cancer cells. The protein kinase inhibitors trametinib and dabrafenib, used to treat melanoma, can shut off the ERK pathway.

“This was a fortuitous intersection of two different strategies, because we reasoned that if we could use these drugs to deter the phosphorylation of ribonuclease inhibitor, then we could make the ribonucleases more potent at killing cancer cells,” Raines says.

Combating resistance

Tests of human melanoma cells supported this idea. The combination of a kinase inhibitor plus a ribonuclease was much deadlier to cancer cells, and the drugs were effective at lower concentrations. The kinase inhibitor prevented the ribonuclease inhibitor from being phosphorylated, making it weaker and allowing the ribonuclease more freedom to perform its function and destroy RNA.

If the same holds true in human patients, this approach could lead to reduced side effects and a lower chance of tumor cells becoming drug-resistant, Raines says. The researchers now hope to test this drug combination in mice, as a step toward testing the combination in clinical trials.

“We’re hoping that we can explore relationships with some of the many pharmaceutical companies that develop ERK pathway inhibitors, to team up and use our ribonuclease drug in concert with kinase inhibitors,” Raines says.

The researchers have also engineered mice that do not produce ribonucleases, which they plan to use to further study the biological functions of these enzymes.

The research was funded by the National Institutes of Health.

The long and short of CDK12

Bendta Schroeder | Koch Institute — Fri, 30 Nov 2018 16:00:00 -0500

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. 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 at 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.”

Measuring cancer cell “fitness” reveals drug susceptibility

Anne Trafton | MIT News Office — Thu, 29 Nov 2018 11:06:39 -0500

By studying both the physical and genomic features of cancer cells, MIT researchers have come up with a new way to investigate why some cancer cells survive drug treatment while others succumb.

Their new approach, which combines measurements of cell mass and growth rate with analysis of a cell’s gene expression, could be used to reveal new drug targets that would make cancer treatment more effective. Exploiting these targets could help knock out the defenses that cells use to overcome the original drug treatment, the researchers say.

In a paper appearing in the Nov. 28 issue of the journal Genome Biology, the researchers identified a growth signaling pathway that is active in glioblastoma cells that are resistant to an experimental type of drug known as an MDM2 inhibitor.

“By measuring a cell's mass and growth rate immediately prior to single-cell RNA-sequencing, we can now use a cell’s ‘fitness’ to classify it as responsive or nonresponsive to a drug, and to relate this to underlying molecular pathways,” says Alex K. Shalek, the Pfizer-Laubach Career Development Assistant Professor of Chemistry, a member of MIT’s Institute for Medical Engineering and Science (IMES), an extramural member of the Koch Institute for Integrative Cancer Research, and an associate member of the Ragon and Broad Institutes.

Shalek and Scott Manalis, the Andrew and Erna Viterbi Professor in the MIT departments of Biological Engineering and Mechanical Engineering and a member of the Koch Institute, are the senior authors of the study. The paper’s lead author is Robert Kimmerling, a recent MIT PhD recipient.

Cancer cell analysis

About a decade ago, Manalis’ lab invented a technology that allows researchers to measure the mass of single cells. In recent years, they have adapted the device, which measures cells’ masses as they flow through tiny channels, so that it can also measure cell growth rates by repeatedly weighing the cells over short periods of time.

Last year, working with researchers at Dana-Farber Cancer Institute (DFCI), Manalis and his colleagues used this approach to test drug responses of tumor cells from patients with multiple myeloma, a type of blood cancer. After treating the cells with three different drugs, the researchers measured the cells’ growth rates and found they were correlated with the cells’ susceptibility to the treatment.

“Single-cell biophysical properties such as mass and growth rate provide early indicators of drug response, thereby offering the potential to delineate sensitive cells from resistant cells while they are still viable,” Manalis says.

In their new study, the researchers wanted to add a genomic component, which they hoped could help reveal why only certain cells are susceptible to a particular drug. “We wanted to be able to take those measurements and add on some of the biological context for why a cell is growing a certain way or behaving a certain way,” Kimmerling says.

To accomplish this, Kimmerling and Manalis teamed up with Shalek, who has extensive experience in sequencing the messenger RNA (mRNA) of individual cells. This information can provide a snapshot of which genes are being expressed in a single cell at a particular moment.

The researchers modified the cell-weighing system so that cells would be spaced evenly as they flowed through, making it easier to collect them one at a time when they exit the system. The cells are weighed several times over the course of 20 minutes to determine growth rate, and as soon as they reach the end of the channel, they are immediately captured and ruptured to release their RNA for analysis. Shalek’s lab then sequenced the RNA of each of the cells. This approach enabled the mass and growth rate of each cell to be directly linked to its gene expression.

Once they had the system working, the researchers collaborated with Keith Ligon and his lab at DFCI to analyze cancer cells derived from a patient with glioblastoma, an aggressive type of brain cancer. The researchers treated the cells with an MDM2 inhibitor, a type of drug that helps to boost the function of p53, a protein that helps cells stop tumor formation. Such drugs are now in clinical trials to treat glioblastoma. In animal studies, this drug has been effective against tumors, but the tumors often grow back later.

In this study, the researchers hoped to find out why some glioblastoma cells survive MDM2 treatment. They treated the cells, measured their growth rates about 16 hours after the treatment, and then sequenced their RNA. “Before the cells have lost viability, we can measure their mass and their growth rate to reveal drug response heterogeneity to that treatment, and then link that with their gene expression,” Kimmerling says.

Importantly, the researchers found subpopulations of cells that were not responsive to the drug. RNA sequencing revealed that in cells that were responsive, genes required for programmed cell death were turned on. Meanwhile, in cells that did not seem to be vulnerable to the drug, genes involved in mTOR, a signaling pathway involved in growth and survival, were turned up.

“What we’re excited about here is we now have this list of biological targets to look into,” Kimmerling says. “We can start to generate testable hypotheses from these gene expression signatures that are more highly expressed in the cells that continue to grow after drug treatment.”

Possible drug targets

The researchers now plan to explore the possibility of targeting some of the genes that were turned up on the nonresponding cells, in hopes of developing drugs that could be used together with the original MDM2 inhibitor. They also hope to adapt this approach for other types of cancers. Some, such as blood cancers, are easier to study than solid tumors, which are more difficult to separate into single cells.

“The hope is that we’ll be able to apply this technology to any sample that can be dissociated into a single-cell population,” Kimmerling says.

Another possible application of the cell-growth measurement technology is studying tumor cells from individual patients to try to predict how they will respond to a particular drug. Kimmerling, Manalis, and others have founded a company called Travera, which has licensed the technology and hopes to develop it for patient use. The company is currently not working on the RNA sequencing aspect of the technology, but that element could also be valuable to incorporate in the future, Kimmerling says.

The research was funded by the Cancer Systems Biology Consortium U54 Research Center and the Cancer Center Support (core) Grant from the National Cancer Institute; the Searle Scholars Program; the Beckman Young Investigator Program; the National Institutes of Health, including an NIH New Innovator Award; the Pew-Stewart Scholars; and a Sloan Fellowship in Chemistry.

Exploring unknowns in cancer, the human brain, and the road ahead

Brittany Flaherty | School of Science — Sun, 18 Nov 2018 00:00:00 -0500

Looking up at the sun-filled atrium of the Brain and Cognitive Sciences Complex, MIT senior Kerrie Greene smiles. “I love this building,” she says about the place that houses the lab where she first became interested in the inner workings of the human brain.

Greene juggles many roles on campus and in her personal life — vice president of her dorm, neuroscientist, bioengineer, volleyball player, older sister — and she doesn’t plan to slow down any time soon. With her medical school applications complete, Greene is currently interviewing at prospective programs. She says she enjoys being involved and working hard, but it hasn’t exactly been easy.

“I’m just happy to have made it to senior year,” Greene says with a laugh. “And I’m very excited for the future.”

Finding direction

Raised in Atlanta, Greene arrived on campus the summer before her first year, as a participant in Interphase EDGE, a program administered through the MIT Office of Minority Education that allows students to acclimate and transition to life at MIT.

“I’m very fortunate to have done Interphase,” Greene says. “Starting out my freshman year, I was very confident in terms of living in Boston and already having a great friend group. Students from the program are still some of my best friends.”

Greene says one of her goals in coming to MIT was to study drug design, a topic that incorporates her interests in both medicine and engineering. For Greene, drug design offers a chance to increase the efficiency and accessibility of new drugs, and ultimately maximize their impact and reach. She found the ideal first major in bioengineering.

Then, as a sophomore, Greene read a description of the social cognition research led by Rebecca Saxe, a professor of cognitive neuroscience, and began working in the Saxe lab through the Undergraduate Research Opportunities Program (UROP). Greene was instantly hooked.

“The more involved I was in the lab, the more I wanted to learn about the brain,” Greene explains. “I knew I had to take classes in brain and cognitive sciences.”

Inspired by Saxe’s research, she added brain and cognitive sciences as a second major her junior year. For Greene, the intense coursework is outweighed by her passion for both fields. “It’s been great,” she says. “I’ve really enjoyed getting to know students in both schools. Whichever class I’m in is the major I like more.”

Infant brain development

Greene’s work in the Saxe lab explores an area with many unknowns: infant and early childhood cognition, learning, and brain development. Working with postdoc Lindsey Powell, Greene is studying how 7- and 8-month-old babies evaluate and respond to imitation.

In the observation room where she conducts these studies, Greene describes how the team sets up a monitor to record infants’ reactions as they sit on their parents’ laps and watch various stimuli and animations. One animation, for example, depicts a “nonimitative” social interaction (one person performs a gesture and the other performs a different gesture) and then shows an “imitative” social interaction (one person performs a gesture and the other person performs the same gesture). Greene and her collaborators watch the recording to observe the infants’ reactions, including how long various animations hold their attention. The team then compares these findings to brain measurements they take using infrared spectroscopy.

“Infrared spectroscopy uses the same type of light you’ll see in a pulse oximeter,” Greene explains. “We put this little cap around the baby’s head to measure blood-oxygen level changes, which we can correlate to brain activity.”

Greene says the team aims to create a fun and welcoming environment for the families involved in their studies. “My favorite aspect of working in the lab is meeting the families and babies,” she says. “It’s absolutely fantastic, and I feel like I’ve grown so much as a scientist through the lab.”

Advancing cancer therapies

Beyond the Saxe lab, Greene spent the past two summers conducting bioengineering research at the Mayo Clinic — “a life-changing experience, honestly,” she says.

She worked with Maryam Raeeszadeh-Sarmazdeh, a senior research fellow, in the laboratory of Evette Radisky, a professor of cancer biology. Radisky’s team uncovers strategies to target natural interactions between enzymes and inhibitors that have been linked to cancer. Greene’s work focused on a group of enzymes called matrix metalloproteinases (MMPs). Responsible for breaking down proteins, these enzymes can also promote the development and progression of cancer. Since previous MMP inhibitors were ineffective and lacked selectivity, Greene worked with a team striving to develop drugs that specifically inhibit MMPs’ tumor-driving activity.

“There are natural inhibitors of this proteinase called tissue inhibitors of metalloproteinases, or TIMPs,” she says. “We were able to engineer TIMPs to bind with a higher affinity and specificity.”

Greene and the team at the Mayo Clinic will soon publish a paper highlighting their results and progress in these efforts. Greene also helped present their work this past September at the Bioengineering and Translational Medicine Conference in Boston.

Building community on campus

Outside of the lab, Greene is the vice president and treasurer of her dorm, McCormick Hall. The only all-women residence hall on campus, McCormick has been Greene’s home through all four years at MIT.

“I’ve made a great group of friends there,” says Greene. “I also love being able to go back to my dorm, have my own space, and clear my head — and it’s clean!” Greene laughs.

Greene also found community on MIT’s volleyball team during her first and second years. “There aren’t many other sports where you have such a high concentration of people in such a small square — 30 by 30 feet,” she says. “Communication is super key and it’s just a good way to release energy and have fun. It was a great part of my MIT experience.”

With two majors and graduate school applications looming, Greene decided to focus on her academic commitments in her junior and senior years. She continues to join the club team occasionally to relieve stress, and always makes time to play volleyball with someone special to her whenever she visits home: her younger sister, Kalissa.

“She’s 15 and she’s really everything to me,” Greene says, her face lighting up at mention of her sister. “She’s killing it in school, she’s killing it in sports; she’s already taking her AP computer science classes. I think she would thrive at a place like MIT.”

Looking ahead

In addition to close ties with her family, Greene says she’s received crucial support from her faculty advisors and mentors at MIT, particularly Rebecca Saxe; Doug Lauffenburger, a professor of bioengineering; and Emery Brown, a professor of medical engineering and computational neuroscience. Greene says she’s also grateful to have friends who applied to medical school and can relate to the challenges it presents.

Still passionate about both bioengineering and neuroscience, she notes that her exact focus in graduate school will be shaped by the program she selects.

“I’ve been working really hard for the past three years, going on four,” Greene says. “I’m just excited to continue working hard. I get to start my next chapter.”

Helping blood cells regenerate after radiation therapy

Anne Trafton | MIT News Office — Wed, 24 Oct 2018 05:00:00 -0400

Patients with blood cancers such as leukemia and lymphoma are often treated by irradiating their bone marrow to destroy the diseased cells. After the treatment, patients are vulnerable to infection and fatigue until new blood cells grow back.

MIT researchers have now devised a way to help blood cells regenerate faster. Their method involves stimulating a particular type of stem cell to secrete growth factors that help precursor cells differentiate into mature blood cells.

Using a technique known as mechanopriming, the researchers grew mesenchymal stem cells (MSCs) on a surface whose mechanical properties are very similar to that of bone marrow. This induced the cells to produce special factors that help hematopoietic stem and progenitor cells (HSPCs) differentiate into red and white blood cells, as well as platelets and other blood cells.

“You can think about it like you’re trying to grow a plant,” says Krystyn Van Vliet, the Michael and Sonja Koerner Professor of Materials Science and Engineering, a professor of biological engineering, and associate provost. “The MSCs are coming in and improving the soil so that the progenitor cells can start proliferating and differentiating into the blood cell lineages that you need to survive.”

In a study of mice, the researchers showed that the specially grown MSCs helped the animals to recover much more quickly from bone marrow irradiation.

Van Vliet is the senior author of the study, which appears in the Oct. 24 issue of the journal Stem Cell Research and Therapy. The paper’s lead author is recent MIT PhD recipient Frances Liu. Other authors are Singapore-MIT Alliance for Research and Technology (SMART) postdoc Kimberley Tam, recent MIT PhD recipient Novalia Pishesha, and former SMART postdoc Zhiyong Poon, now at Singapore General Hospital.

Cellular drug factories

MSCs are produced throughout the body and can differentiate into a variety of tissues, including bone, cartilage, muscle, and fat. They can also secrete proteins that help other types of stem cells differentiate into mature cells.

“They act like drug factories,” Van Vliet says. “They can become tissue lineage cells, but they also pump out a lot of factors that change the environment that the hematopoietic stem cells are operating in.”

When cancer patients receive a stem cell transplant, they usually receive only HPSCs, which can become blood cells. Van Vliet’s team has shown previously that when mice are also given MSCs, they recover faster. However, in a given population of MSCs, usually only about 20 percent produce the factors that are needed to stimulate blood cell growth and bone marrow recovery.

“Left to their own devices in the current state-of-the-art culture environments, MSCs become heterogeneous and they all express a variety of factors,” Van Vliet says.

In an earlier study, Van Vliet and her SMART colleagues showed that she could sort MSCs with a special microfluidic device that can identify the 20 percent that promote blood cell growth. However, she and her students wanted to improve on that by finding a way to stimulate an entire population of MSCs to produce the necessary factors.

To do that, they first had to discover which factors were the most important. They showed that while many factors contribute to blood cell differentiation, secretion of a protein called osteopontin was most highly correlated with better survival rates in mice treated with MSCs.

The researchers then explored the idea of “mechanopriming” the cells so that they would produce more of the necessary factors. Over the past decade, Van Vliet and other researchers have shown that varying the mechanical properties of surfaces on which stem cells are grown can affect their differentiation into mature cell types. However, in this study, for the first time, she showed that mechanical properties can also affect the factors that stem cells secrete before committing to a specific tissue cell lineage.

Usually, stem cells removed from the body are grown on a flat sheet of glass or stiff plastic. The MIT team decided to try growing the cells on a polymer called PDMS and to vary its mechanical properties to see how that would affect the cells. They designed materials that varied in both their stiffness and their viscosity, which is a measure of how quickly the material stretches when stress is applied.

The researchers found that MSCs grown on materials with mechanical properties most similar that of bone marrow produced the greatest number of the factors necessary to induce HPSPCs to differentiate into mature blood cells.

Better recovery

The researchers then tested their specially grown MSCs by implanting them into mice that had had their bone marrow irradiated. Even though they did not implant any HSPCs, this treatment quickly repopulated the animals’ blood cells and helped them to recover more quickly than mice treated with MSCs grown on traditional glass surfaces. They also recovered faster than mice treated with the factor-producing MSCs that were selected by the microfluidic sorting device.

“The mouse studies were models of radiation therapy commonly used to kill cancer cells in the clinic. However, these therapies are highly destructive and also destroy healthy cells as well,” Liu says. “Our mechanoprimed MSCs can help to better support and regenerate those healthy bone marrow cells faster in these mouse models, and we hope the same results would translate to humans.”

“Illustrating how mechanopriming of mesenchymal stem cells can be exploited to improve on hematopoietic recovery is of huge medical significance,” says Viola Vogel, chair of the Department of Health Science at Technology at ETH Zurich, who was not involved in the research. “It also sheds light onto how to utilize their approach to perhaps take advantage of other cell subpopulations for therapeutic applications in the future.”

Van Vliet’s lab is now performing more animal studies in hopes of developing a combination treatment of MSCs and HSPCs that could be tested in humans.

“You can’t survive with a low blood cell count for very long,” she says. “If you’re able to get your complete blood cell count up to normal levels faster, you have a much better prognosis for speed of recovery.”

The researchers also hope to study whether mechanopriming can induce MSCs to produce different factors that would stimulate the development of additional cell types that could be useful for treating other diseases.

“You could imagine that by changing their culture environment, including their mechanical environment, MSCs could be used for administration to target several other diseases,” such as Parkinson’s disease, rheumatoid arthritis, and others, Van Vliet says.

The research was funded by the BioSystems and Micromechanics Interdisciplinary Research Group of the Singapore-MIT Alliance for Research and Technology (SMART), through the Singapore National Research Foundation, and the National Institutes of Health.