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Using plant biology to address climate change

A Climate Grand Challenges flagship project aims to reduce agriculture-driven emissions while making food crop plants heartier and more nutritious.

Merrill Meadow | Whitehead Institute
April 20, 2022

On April 11, MIT announced five multiyear flagship projects in the first-ever Climate Grand Challenges, a new initiative to tackle complex climate problems and deliver breakthrough solutions to the world as quickly as possible. This article is the fourth in a five-part series highlighting the most promising concepts to emerge from the competition and the interdisciplinary research teams behind them.

The impact of our changing climate on agriculture and food security — and how contemporary agriculture contributes to climate change — is at the forefront of MIT’s multidisciplinary project “Revolutionizing agriculture with low-emissions, resilient crops.” The project The project is one of five flagship winners in the Climate Grand Challenges competition, and brings together researchers from the departments of Biology, Biological Engineering, Chemical Engineering, and Civil and Environmental Engineering.

“Our team’s research seeks to address two connected challenges: first, the need to reduce the greenhouse gas emissions produced by agricultural fertilizer; second, the fact that the yields of many current agricultural crops will decrease, due to the effects of climate change on plant metabolism,” says the project’s faculty lead, Christopher Voigt, the Daniel I.C. Wang Professor in MIT’s Department of Biological Engineering. “We are pursuing six interdisciplinary projects that are each key to our overall goal of developing low-emissions methods for fertilizing plants that are bioengineered to be more resilient and productive in a changing climate.”

Whitehead Institute members Mary Gehring and Jing-Ke Weng, plant biologists who are also associate professors in MIT’s Department of Biology, will lead two of those projects.

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For most of human history, climate change occurred gradually, over hundreds or thousands of years. That pace allowed plants to adapt to variations in temperature, precipitation, and atmospheric composition. However, human-driven climate change has occurred much more quickly, and crop plants have suffered: Crop yields are down in many regions, as is seed protein content in cereal crops.

“If we want to ensure an abundant supply of nutritious food for the world, we need to develop fundamental mechanisms for bioengineering a wide variety of crop plants that will be both hearty and nutritious in the face of our changing climate,” says Gehring. In her previous work, she has shown that many aspects of plant reproduction and seed development are controlled by epigenetics — that is, by information outside of the DNA sequence. She has been using that knowledge and the research methods she has developed to identify ways to create varieties of seed-producing plants that are more productive and resilient than current food crops.

But plant biology is complex, and while it is possible to develop plants that integrate robustness-enhancing traits by combining dissimilar parental strains, scientists are still learning how to ensure that the new traits are carried forward from one generation to the next. “Plants that carry the robustness-enhancing traits have ‘hybrid vigor,’ and we believe that the perpetuation of those traits is controlled by epigenetics,” Gehring explains. “Right now, some food crops, like corn, can be engineered to benefit from hybrid vigor, but those traits are not inherited. That’s why farmers growing many of today’s most productive varieties of corn must purchase and plant new batches of seeds each year. Moreover, many important food crops have not yet realized the benefits of hybrid vigor.”

The project Gehring leads, “Developing Clonal Seed Production to Fix Hybrid Vigor,” aims to enable food crop plants to create seeds that are both more robust and genetically identical to the parent — and thereby able to pass beneficial traits from generation to generation.

The process of clonal (or asexual) production of seeds that are genetically identical to the maternal parent is called apomixis. Gehring says, “Because apomixis is present in 400 flowering plant species — about 1 percent of flowering plant species — it is probable that genes and signaling pathways necessary for apomixis are already present within crop plants. Our challenge is to tweak those genes and pathways so that the plant switches reproduction from sexual to asexual.”

The project will leverage the fact that genes and pathways related to autonomous asexual development of the endosperm — a seed’s nutritive tissue — exist in the model plant Arabidopsis thaliana. In previous work on Arabidopsis, Gehring’s lab researched a specific gene that, when misregulated, drives development of an asexual endosperm-like material. “Normally, that seed would not be viable,” she notes. “But we believe that by epigenetic tuning of the expression of additional relevant genes, we will enable the plant to retain that material — and help achieve apomixis.”

If Gehring and her colleagues succeed in creating a gene-expression “formula” for introducing endosperm apomixis into a wide range of crop plants, they will have made a fundamental and important achievement. Such a method could be applied throughout agriculture to create and perpetuate new crop breeds able to withstand their changing environments while requiring less fertilizer and fewer pesticides.

Creating “self-fertilizing” crops

Roughly a quarter of greenhouse gas (GHG) emissions in the United States are a product of agriculture. Fertilizer production and use accounts for one third of those emissions and includes nitrous oxide, which has heat-trapping capacity 298-fold stronger than carbon dioxide, according to a 2018 Frontiers in Plant Science study. Most artificial fertilizer production also consumes huge quantities of natural gas and uses minerals mined from nonrenewable resources. After all that, much of the nitrogen fertilizer becomes runoff that pollutes local waterways. For those reasons, this Climate Grand Challenges flagship project aims to greatly reduce use of human-made fertilizers.

One tantalizing approach is to cultivate cereal crop plants — which account for about 75 percent of global food production — capable of drawing nitrogen from metabolic interactions with bacteria in the soil. Whitehead Institute’s Weng leads an effort to do just that: genetically bioengineer crops such as corn, rice, and wheat to, essentially, create their own fertilizer through a symbiotic relationship with nitrogen-fixing microbes.

“Legumes such as bean and pea plants can form root nodules through which they receive nitrogen from rhizobia bacteria in exchange for carbon,” Weng explains. “This metabolic exchange means that legumes release far less greenhouse gas — and require far less investment of fossil energy — than do cereal crops, which use a huge portion of the artificially produced nitrogen fertilizers employed today.

“Our goal is to develop methods for transferring legumes’ ‘self-fertilizing’ capacity to cereal crops,” Weng says. “If we can, we will revolutionize the sustainability of food production.”

The project — formally entitled “Mimicking legume-rhizobia symbiosis for fertilizer production in cereals” — will be a multistage, five-year effort. It draws on Weng’s extensive studies of metabolic evolution in plants and his identification of molecules involved in formation of the root nodules that permit exchanges between legumes and nitrogen-fixing bacteria. It also leverages his expertise in reconstituting specific signaling and metabolic pathways in plants.

Weng and his colleagues will begin by deciphering the full spectrum of small-molecule signaling processes that occur between legumes and rhizobium bacteria. Then they will genetically engineer an analogous system in nonlegume crop plants. Next, using state-of-the-art metabolomic methods, they will identify which small molecules excreted from legume roots prompt a nitrogen/carbon exchange from rhizobium bacteria. Finally, the researchers will genetically engineer the biosynthesis of those molecules in the roots of nonlegume plants and observe their effect on the rhizobium bacteria surrounding the roots.

While the project is complex and technically challenging, its potential is staggering. “Focusing on corn alone, this could reduce the production and use of nitrogen fertilizer by 160,000 tons,” Weng notes. “And it could halve the related emissions of nitrous oxide gas.”

School of Science announces 2022 Infinite Mile Awards

Seven staff members are recognized for their dedication to the School of Science and to MIT.

School of Science
April 15, 2022

The MIT School of Science has announced the winners of the 2022 Infinite Mile Award. The selected staff members were nominated by their colleagues for going above and beyond in their roles at the Institute. Their outstanding contributions have made MIT a better place.

The following are the 2022 Infinite Mile Award winners in the School of Science:

• Christina Andujar, senior administrative assistant in the Department of Physics, was nominated by Peter Fisher, Edmund Bertschinger, and Matt Cubstead because Andujar “has gone far beyond her assigned role and duties to improve the lives of a great many students at MIT.”

NetBet sport• Monika Avello, an instructor in the Department of Biology, was nominated by Barbara Imperiali, Cathy Drennan, Graham Walker, Adam Martin, Lenny Guarente, David Des Marais, Seychelle Vos, and Jing-Ke Weng because Avello “was always meticulous in attention to detail and never hesitated when we threw out crazy ideas that might make the students gain something unique from the class — even if it gave her ever more things to do.”

• David Orenstein, director of communications in The Picower Institute for Learning and Memory, was nominated by Li-Huei Tsai, Mriganka Sur, Earl Miller, Gloria Choi, William Lawson, Asha Bhakar, Julie Pryor, Raleigh McElvery, and Julia Keller because Orenstein is “always willing to help out in whatever way is needed, whether as a part of a brainstorming session about any given topic, or lending a helping hand for an event or something else going on with the Institute. His dedication to the mission of the Picower Institute is unquestionable and it is evident in everything he does.”

• Dennis Porche, assistant to the department head in the Department of Mathematics, was nominated by Michel Goemans, Gigliola Staffilani, Michael Sipser, and Amanda Kuhl because Porche “has been amazingly dedicated to the well-being of the mathematics department at MIT, and cares tremendously about everything that goes on in the department. He will spend many hours making sure everything is perfect, nothing or no one is omitted, everyone is properly acknowledged, and everything goes smoothly.”

• Joshua Stone, administrative assistant in the Department of Biology, was nominated by Michael Laub, Hallie Dowling-Huppert, Alex Pike, Rebecca Chamberlain, and Janice Chang because Stone “has driven a movement to create an inclusive environment for staff within the biology department, implementing programs for welcoming new staff and establishing peer mentoring to increase the sense of inclusion within the department. These efforts are essential to shifting the culture and integrating pillars of DEI into the everyday operations of the biology department.”

• Sierra Vallin, academic administrator in the Department of Brain and Cognitive Sciences, was nominated by Michale Fee, Laura Schulz, Rebecca Saxe, Joshua McDermott, Mehrdad Jazayeri, Mark Harnett, Kate White, Laura Frawley, Kian Caplan, Di Kang, Halie Olson, Tobias Kaiser, and Julianne Ormerod because Vallin is “truly incredible” and “goes way above and beyond the call of duty to help students and other staff,” and for her “willingness to stand up for staff throughout our building, and to support our ongoing diversity efforts.”

• Shannon Wagner, senior administrative assistant in the Department of Chemistry, was nominated by Troy Van Voorhis, Stephen Buchwald, Jeremiah Johnson, Rick Danheiser, Richard Wilk, and Jennifer Weisman because Wagner “is someone who goes far above and beyond her usual call of duty. Her work has positively impacted many in the department including our students. She demonstrates an exceptional commitment to every aspect of her work and the staff with whom she works. Our department is a far better place with her in it.”

A single memory is stored across many connected brain regions

Innovative brain-wide mapping study shows that “engrams,” the ensembles of neurons encoding a memory, are widely distributed, including among regions not previously realize

Picower Institute
April 12, 2022

A new study by scientists at The Picower Institute for Learning and Memory at MIT provides the most comprehensive and rigorous evidence yet that the mammalian brain stores a single memory across a widely distributed, functionally connected complex spanning many brain regions, rather than in just one or even a few places.

Memory pioneer Richard Semon had predicted such a “unified engram complex” more than a century ago, but achieving the new study’s affirmation of his hypothesis required the application of several technologies developed only recently. In the study, the team identified and ranked dozens of areas that were not previously known to be involved in memory and showed that memory recall becomes more behaviorally powerful when multiple memory-storing regions are reactivated, rather than just one.

“When talking about memory storage we all usually talk about the hippocampus or the cortex,” said co-lead and co-corresponding author Dheeraj Roy. He began the research while a graduate student in the RIKEN-MIT Laboratory for Neural Circuit Genetics at The Picower Institute led by senior author Susumu Tonegawa, Picower Professor in the Departments of Biology and Brain and Cognitive Sciences. “This study reflects the most comprehensive description of memory encoding cells, or memory ‘engrams,’ distributed across the brain, not just in the well-known memory regions. It basically provides the first rank-ordered list for high-probability engram regions. This list should lead to many future studies, which we are excited about, both in our labs and by other groups.”

In addition to Roy, who is now a McGovern Fellow in the Broad Institute of MIT and Harvard and the lab of MIT neuroscience Professor Guoping Feng, the study’s other lead authors are Young-Gyun Park, Minyoung Kim, Ying Zhang and Sachie Ogawa.

Mapping Memory

The team was able to map regions participating in an engram complex by conducting an unbiased analysis of more than 247 brain regions in mice who were taken from their home cage to another cage where they felt a small but memorable electrical zap. In one group of mice their neurons were engineered to become fluorescent when they expressed a gene required for memory encoding. In another group, cells activated by naturally recalling the zap memory (e.g. when the mice returned to the scene of the zap) were fluorescently labeled instead. Cells that were activated by memory encoding or by recall could therefore readily be seen under a microscope after the brains were preserved and optically cleared using a technology called SHIELD, developed by co-corresponding author Kwanghun Chung, Associate Professor in The Picower Institute, the Institute for Medical Engineering & Science and the Department of Chemical Engineering. By using a computer to count fluorescing cells in each sample, the team produced brain-wide maps of regions with apparently significant memory encoding or recall activity.

The maps highlighted many regions expected to participate in memory but also many that were not. To help factor out regions that might have been activated by activity unrelated to the zap memory, the team compared what they saw in zap-encoding or zap-recalling mice to what they saw in the brains of controls who were simply left in their home cage. This allowed them to calculate an “engram index” to rank order 117 brain regions with a significant likelihood of being involved in the memory engram complex. They deepened the analysis by engineering new mice in which neurons involved in both memory encoding and in recall could be doubly labeled, thereby revealing which cells exhibited overlap of those activities.

To really be an engram cell, the authors noted, a neuron should be activated both in encoding and recall.

“These experiments not only revealed significant engram reactivation in known hippocampal and amygdala regions, but also showed reactivation in many thalamic, cortical, midbrain and brainstem structures,” the authors wrote. “Importantly when we compared the brain regions identified by the engram index analysis with these reactivated regions, we observed that ~60 percent of the regions were consistent between analyses.”

Memory manipulations

Having ranked regions significantly likely to be involved in the engram complex, the team engaged in several manipulations to directly test their predictions and to determine how engram complex regions might work together.

For instance, they engineered mice such that cells activated by memory encoding would also become controllable with flashes of light (a technique called “optogenetics”). The researchers then applied light flashes to select brain regions from their engram index list to see if stimulating those would artificially reproduce the fear memory behavior of freezing in place, even when mice were placed in a “neutral” cage where the zap had not occurred.

“Strikingly, all these brain regions induced robust memory recall when they were optogenetically stimulated,” the researchers observed. Moreover, stimulating areas that their analysis suggested were insignificant to zap memory indeed produced no freezing behavior.

The team then demonstrated how different regions within an engram complex connect. They chose two well-known memory regions, CA1 of the hippocampus and the basolateral amygdala (BLA), and optogenetically activated engram cells there to induce memory recall behavior in a neutral cage. They found that stimulating those regions produced memory recall activity in specific “downstream” areas identified as being probable members of the engram complex. Meanwhile, optogenetically inhibiting natural zap memory recall in CA1 or the BLA (i.e. when mice were placed back in the cage where they experienced the zap) led to reduced activity in downstream engram complex areas compared to what they measured in mice with unhindered natural recall.

Further experiments showed that optogenetic reactivations of engram complex neurons followed similar patterns as those observed in natural memory recall. So having established that natural memory encoding and recall appears to occur across a wide engram complex, the team decided to test whether reactivating multiple regions would improve memory recall compared to reactivating just one. After all, prior experiments have shown that activating just one engram area does not produce recall as vividly as natural recall. This time the team used a chemical means to stimulate different engram complex regions and when they did, they found that indeed stimulating up to three involved regions simultaneously produced more robust freezing behavior than stimulating just one or two.

Meaning of distributed storage

Roy said that by storing a single memory across such a widespread complex the brain might be making memory more efficient and resilient.

“Different memory engrams may allow us to recreate memories more efficiently when we are trying to remember a previous event (and similarly for the initial encoding where different engrams may contribute different information from the original experience),” he said. “Secondly, in disease states, if a few regions are impaired, distributed memories would allow us to remember previous events and in some ways be more robust against regional damages.”

In the long term that second idea might suggest a clinical strategy for dealing with memory impairment: “If some memory impairments are because of hippocampal or cortical dysfunction, could we target understudied engram cells in other regions and could such a manipulation restore some memory functions?”

That’s just one of many new questions researchers can ask now that the study has revealed a listing of where to look for at least one kind of memory in the mammalian brain.

The paper’s other authors are Nicholas DiNapoli, Xinyi Gu, Jae Cho, Heejin Choi, Lee Kamentsky, Jared Martin, Olivia Mosto and Tomomi Aida.

Funding sources included the JPB Foundation, the RIKEN Center for Brain Science, the Howard Hughes Medical Institute, a Warren Alpert Distinguished Scholar Award, the National Institutes of Health, the Burroughs Wellcome Fund, the Searle netbet sports bettingScholars Program, a Packard Award in Science and Engineering, a NARSAD Young Investigator Award, the McKnight Foundation Technology Award, the NCSOFT Cultural Foundation, and the Institute for Basic Science.

A spectrum of cancer cells
Greta Friar | Whitehead Institute
April 11, 2022

Cancer is at its most deadly when it spreads and forms tumors in new tissues. This process, called metastasis, is responsible for the vast majority of cancer deaths, and yet there is still a lot that researchers do not know about how and when it happens. Whitehead Institute Founding Member Robert Weinberg, also the Daniel K. Ludwig Professor for Cancer Research at the Massachusetts Institute of Technology, studies the mechanisms behind metastasis. One such mechanism is a process called the epithelial-mesenchymal transition (EMT), which causes epithelial cells, which normally stick tightly together, to lose their cohesion, enabling them to move around and even invade nearby tissue. This EMT program also operates during embryonic development. Cancer cells can co-opt this process and use it travel from their original tumor site to distant tissues throughout the body. Some of the cancer cells that spread are able, on rare occasions, to form new tumors in these tissues—metastases—while the great majority of these cells remain dormant after entering the distant tissues.

New research from Weinberg and postdoc Yun Zhang shows that cells change in diverse ways through the actions of the EMT, which can influence whether cells are able to form new tumors after they spread. The work, published in Nature Cell Biology on April 11, 2022, also identifies two regulators of the EMT and shows that loss of each regulator leads to a different metastatic risk profile.

“Using triple negative breast cancer as a model, we are trying to go a bit deeper into understanding the molecular mechanisms that regulate the EMT, how cells enter into different EMT intermediate states, and which of these states contribute to metastasis,” Zhang says.

The EMT was originally imagined as a sort of binary switch, in which cells start out epithelial and become mesenchymal, much like a light switch being flicked from off to on. However, researchers are learning that the EMT works more like a dimmer switch that can be shifted along a spectrum of brightness. Cells that undergo the EMT usually end up in hybrid states between the epithelial and mesenchymal extremes. These cells in the middle of the spectrum, which have some characteristics of each extreme, are called “quasi-mesenchymal” cells, and it turns out that they–rather than cells that become fully mesenchymal–are the most capable of metastasizing and forming new tumors throughout the body.

Protected versus plastic cells

Weinberg and Zhang set out to better understand the EMT spectrum and what controls cells’ movement along it. First, they compared epithelial cells to each other and found that some were more plastic or prone to transitioning along the EMT spectrum than others. They also used the CRISPR gene editing tool to screen for genes that might be regulating the cells’ plasticity. If researchers can learn what makes a cell become quasi-mesenchymal—posing a high risk for metastasis—they might be able use this information, at some time in the future, to develop strategies to prevent cells from entering this high-risk state.

The CRISPR gene screen turned up a number of molecules that seemed to influence cells’ epithelial-mesenchymal plasticity. Two groups of these molecules had especially strong effects: PRC2, a complex that operates in chromosomes to silence or inactivate genes, and KMT2D-COMPASS, a complex that helps activate genes. Both complexes help to keep cells in a stable epithelial state. Loss of either complex makes cells more prone to moving along the EMT spectrum.

The researchers then determined how the loss of either complex enables the EMT. PRC2 normally silences several key EMT-related genes. When PRC2 is lost, those genes activate, which in turn sensitizes the cell to a signal that can trigger the EMT. The loss of KMT2D-COMPASS affects how well PRC2 can bind its targets, leading to the same signal sensitivity. In spite of the similar mechanisms at play, the loss of PRC2 versus KMT2D-COMPASS leads cells to transition to end up in different EMT states, an exciting finding for the researchers. Cells without KMT2D-COMPASS became fully mesenchymal, while cells without PRC2 became hybrid or quasi-mesenchymal. Consequently, cells without PRC2 were much more capable of metastasis than cells without KMT2D-COMPASS (or cells in which both complexes were active) in mouse models. When the researchers looked at historical data from breast cancer patients, they observed the same pattern: people with faulty PRC2 component genes had worse outcomes. These findings provide further evidence that cells in the middle of the EMT spectrum are most likely to metastasize.

This work supports the understanding of the EMT as a spectrum rather than a simple switch, and shows that different EMT regulators can program cells to transition to different parts of the EMT spectrum. Additionally, the finding that loss of PRC2 is linked to metastasis has implications for cancer drugs currently in development that work by inactivating PRC2. Benefits of the drugs may outweigh risks for patients with certain types of cancer for which PRC2 is an effective target. However, Weinberg and Zhang caution that researchers leading clinical trials of PRC2-targeting drugs should be careful about selecting patients and monitoring outcomes. In the types of cancer cells that the researchers looked at, even temporary PRC2 inactivation, such as from a therapy trial, was sufficient to trigger cells to become EMT hybrids with increased metastatic capacity.

Weinberg and Zhang intend to continue exploring the genes identified in their CRISPR screen to see if they can identify other hybrid states along the EMT spectrum, in which cells have different combinations of epithelial and mesenchymal features. They hope that by deepening their understanding of the gene expression profiles of cancer cells associated with different EMT trajectories, they can contribute to the development of therapies for people with potentially metastatic cancers.

“Understanding when and how cancer cells become able to form life-threatening metastases is crucial in order to help the many patients for whom this is a risk,” Weinberg says. “This work provides new insights into the mechanisms that enable cells to metastasize and the roles that different EMT programs can play.”

Two proteins found to induce cell death through incomplete base excision repair

Depletion of either the DapB or Dxr proteins causes oxidative stress and cell death in bacteria, which could aid the development of more effective antibiotics.

Grace van Deelen
April 7, 2022

How do bacteria die? It’s an important question, especially since these single-celled organisms seem to be outpacing the development of new antibiotics. However, any one bacterial cell will often die from a number of separate but related pathways acting simultaneously, making understanding bacterial death difficult. Determining how to induce those pathways — and the role each pathway plays in a cell’s death — is key to creating effective antibiotics, especially after bacteria evolve to resist some drugs. But new research from Graham Walker’s lab in the MIT Department of Biology suggests that one historically under-appreciated cause of bacterial death, called oxidative stress, could help scientists develop antibiotics that kill bacteria more effectively.

Many antibiotics target the bacteria’s cell wall or replication process. However, some antibiotics can additionally cause changes in a cell’s ­metabolism that lead to a phenomenon called oxidative stress. Reactive oxygen-containing molecules float around freely inside the cell, sometimes bumping into other molecules, reacting with them, and stealing their unpaired electrons in a process called oxidation. For example, a guanine molecule — the DNA nucleotide commonly abbreviated to “G” — may become an oxidized guanine called 8-oxo-dG, a transformation that causes mutations in a cell’s genetic code. The harmful effects of oxidation are usually managed by the cell, but the disruption caused by these antibiotics can also become fatal to the cell.

In the case of 8-oxo-dG, the cell responds to this oxidative stress by attempting to cut the oxidized guanine out of the genome and repair it with a regular nucleotide during a process called base excision repair (BER). However, during BER, every completed step produces intermediate substances, including other forms of damaged DNA, which then must be cleared by another enzyme or protein. However, sometimes the cell is unable to complete BER because these intermediate substances build up. When there is an imbalance of intermediate substances, the cell pauses the repair, leaving breaks in the strands of DNA that cause cell death.

Because incomplete BER is just one of many contributing causes of cell death, the total contribution of incomplete BER to cell death remained unclear. As a result, scientists in the Walker lab were interested in determining other stressors, besides known antibiotics, that might cause incomplete BER of 8-oxo-dG. “If this mechanism of 8-oxo-dG getting into DNA causes bacteria to die, there’s probably some other stressor that isn’t an antibiotic that would cause cells to die by the same way,” says Walker.

In the paper, published on February 8 in mBio, the researchers determined two additional stressors that also induce cell death via incomplete BER of 8-oxo-dG. They found that the depletion of proteins DapB and Dxr also induced oxidative stress and incomplete BER of 8-oxo-dG. Scientists have known of these proteins — both of which are involved in bacterial metabolism — for some time, but had never associated them with incomplete BER.

“Incomplete base excision repair is probably one of more underappreciated ways a cell can die,” Walker says. “So we wanted to explore that pathway further.”

Charley Gruber, a postdoc in the Walker lab and lead author on the paper, identified DapB and Dxr by screening a library of 238 proteins essential for Escherichia coli growth. He determined that, in the absence of these two proteins, the cell overproduced the reactive oxygen-containing molecules that contribute to oxidative stress. As a result, the oxidized nucleotide 8-oxo-dG was incorporated into the genome, leading to cell death through incomplete BER. Researchers don’t know for sure why depletion of DapB and Dxr increases the amount of reactive oxygen-containing molecules inside the cell, but oxidative stress is a common reaction to many disruptions that bacterial cells may face.

To Walker and Gruber’s surprise, their results also showed that the total contribution of incomplete BER to cell death was different between the two proteins — Dxr-depleted cells died faster than DapB-depleted cells, suggesting that a lack of Dxr played a larger role in cell death. Because the responses to protein depletion were so different between DapB and Dxr, the researchers concluded that there is no singular pathway that causes oxidative stress; rather, it is probably a common consequence of many possible disruptions to bacterial cell physiology.

“If there’s one important thing I think we need to realize about cell death,” Gruber says, “it’s that a lot is happening to a stressed cell. And netbet online sports bettingwhat is actually lethal might differ between two cells.”

This study adds to a body of research by Gruber, Walker, and others about the role of incomplete BER in the process of cell death. In 2012, the Walker lab published a paper in Science — building on earlier work from MIT’s Termeer Professor of Bioengineering, Jim Collins — which showed for the first time that some commonly-used antibiotics kill by way of oxidative stress and the 8-oxo-dG pathway of incomplete BER. The idea was not immediately accepted by the scientific community, and a debate ensued: Shortly after Walker’s paper, Northeastern University biologist Kim Lewis and University of Illinois biologist Jim Imlay each published separate papers suggesting that bactericidal antibiotics had nothing to do with oxidative stress. Since then, the Walker and Collins labs have continued to research the topic, producing more supporting data for their argument that oxidative stress and incomplete BER are, in fact, an important pathway of cell death.

“This new work provides a strong genetic foundation for the role of incomplete BER in bacterial cell death,” Collins says . “Oxidative stress and BER should be targeted as a means to potentiate existing antibiotics and enhance our antibiotic arsenal.”

Scientific debates like the one surrounding the contribution of incomplete BER to bacterial death are crucial to the creation of effective antibiotics. Most antibiotics work by breaking the cell wall and causing cell death that way. However, the lab’s findings offer a possibility for antibiotic assistance: the common practice of using secondary antibiotics to aid in cell death thorough a different pathway. For example, administering a secondary antibiotic that triggers the 8-oxo-dG pathway along with the primary antibiotic that is lethal to bacteria through cell wall destruction could be more effective than one antibiotic on its own, Gruber suggests.

“Many of our antibiotics are not working, or we’ve overused them in some cases, so we’re really running out of drugs,” he says. “So an antibiotic that induces oxidative stress could be another way to help existing drugs work better.”


Top image: E. coli cells with either DapB (left) or Dxr (right) depleted. Living cells are stained green while dead cells are stained red. Credit: Charley Gruber

Citation:
“Degradation of the Escherichia coli Essential Proteins DapB and Dxr Results in Oxidative Stress, which Contributes to Lethality through Incomplete Base Excision Repair”
mBio, online February 8, 2022, DOI: 10.1128/mbio.03756-21
Charley C. Gruber, Vignesh M. P. Babu, Kamren Livingston, Heer Joisher, and Graham C. Walker

Navigating new worlds in biology and at MIT

Institute Professor Sallie “Penny” Chisholm is best known for her role in discovering the tiny bacteria called Prochlorococcus — the world’s most abundant photosynthetic organism. But she has also played a pivotal role in pioneering and advocating for women’s rights at MIT and beyond.

Celina Zhao
March 31, 2022

Without the ancestors of the ocean microbe that Sallie “Penny” Watson Chisholm discovered in 1986, humans may not have ever evolved on Earth. The tiny microbe is called Prochlorococcus, and it’s full of superlatives. One hundred of them can fit on the width of a single strand of human hair, making them the smallest photosynthetic organisms on the planet. At the same time, they’re also the most abundant, comprising an integral piece of the oceans’ “invisible forest.” In fact, you can thank them for the oxygen you breathe in every twentieth breath you take.

With their population, which numbers in the billion billion billions and weighs a collective 220 million Volkswagen Beetles, you might expect Prochlorococcus to be easy to find. But they were not uncovered until the 1980s — and by accident, at that. Since that fateful discovery, Chisholm has dedicated her life and career to studying these intriguing little cells. They have earned her a National Medal of Science from former President Barack Obama, led her to a debate with the Dalai Lama, and even sparked a meeting with the Wu-Tang Clan’s GZA, a rapper interested in featuring the bacterium in his album.

This extraordinary journey, however, was not a straight path — in part because being a pioneering female researcher was no easy feat.

Early life and education

Chisholm was born on November 5, 1947 in Marquette, Michigan, a small town located on the shores of Lake Superior. While growing up, her passion was not science, but skiing, and when it came time to apply for college, she had little ambition and few dreams in higher education.

Her parents, however, intervened. Chisholm’s mother, a traditional 1950s housewife, hated not having her own job or income. In particular, she stressed to her daughter the importance of being able to get an education and career. So, Chisholm traveled east to Saratoga Springs, New York, enrolling at Skidmore College — then a private liberal arts women’s college.

Chisholm on the RV Ellen B. Scripps during her postdoctoral years at the Scripps Institute of Oceanography. Credit: David Karl, University of Hawaii

Living at Skidmore, where she studied biology and chemistry, was a formative experience. “It unconsciously builds a confidence,” Chisholm says of the absence of men competing for attention and resources. In her senior year, she participated in her first fieldwork expedition, studying the prevalence of the mineral manganese in a local lake. Noticing her interest and potential in research, her advisor suggested she attend graduate school. Though the idea had never occurred to her before, it sounded much more interesting than entering the workforce, and so she agreed.

After a year as a graduate student at Cornell University, Chisholm transferred to the State University of New York (SUNY) to study freshwater plankton. With her PhD in hand — the first PhD in her entire extended family — she moved to the sunny beaches of La Jolla, California for her postdoctoral studies. At the University of California San Diego’s Scripps Institute of Oceanography, she began studying the massive system to which she’d dedicate the rest of her career: the ocean.

Just a few months after arriving at Scripps, Chisholm sailed around the Gulf of California on her first research cruise, the R/V Alpha Helix. She stood out from most of the members of the ship in a prominent way — she was one of only a few women aboard. Women were only just starting to be allowed on research vessels in the 1970s, an imbalance that would persist on Chisholm’s other cruises at Scripps.

And, though she loved her time at Scripps, by 1976 it was time to move on. She had three options: a small marine lab in Maine, an oceanography department in Canada, or the Civil and Environmental Engineering Department at MIT. In the case of the latter, she would not simply be the only biologist; she would be the only woman. Should she choose a comfortable route, or should she choose the challenge? Then, one of her mentors at Scripps told her, “Penny, you don’t turn down MIT.” It was a once-in-a-lifetime opportunity, so she decided to give it a shot.

Settling into MIT

In 1976, Chisholm arrived at MIT to continue studying the physiology of various phytoplankton species. One of the instruments she used was a flow cytometer. Though traditionally only used in medical settings, she’d discovered that flow cytometers — with their ability to move individual cells in single file past a laser for a convenient close-up view — were also excellent for her research. In addition, she’d noticed that the unique pigments of phytoplankton fluoresced distinctive colors in the laser’s presence. For example, the green chlorophyll found in phytoplankton would emit red light when struck by a blue laser. Accessory pigments in some would emit orange light.

One day, she and her team came to a game-changing idea: “Wouldn’t it be cool if we could take an instrument like this out on a ship and just squirt sea water through it to see what the diversity of phytoplankton look like?” she mused. This idea immediately opened a whole new set of doors for possible research.

At the start of Chisholm’s career, scientists had a highly restricted picture of microbes in the ocean. This was largely due to limitations in microscope technology: phytoplankton smaller than 5 microns were extremely difficult to see using standard microscopy of the day. In 1979, however, John Waterbury of the Woods Hole Oceanographic Institution, using a technique known as epifluorescence microscopy, discovered tiny photosynthetic cyanobacteria only about 2 microns in diameter, which glowed orange. He named the bacterium Synechococcus. Chisholm was intrigued, and her team set off to the Caribbean in 1985 with their flow cytometer to study them.

While studying images of Synechococcus, they started seeing extremely tiny red signals on their instrument. They didn’t think much of it at first — assuming it was probably just electronic noise. But, as these signals kept showing up, they began to wonder: Could these signals be coming from something that was alive?

The Department of Civil and Environmental Engineering faculty picture from 1978 shows that Chisholm (middle, second row from the back) was the only female faculty member.

It was an intriguing possibility, with evidence in its favor. She and her team noticed that the signals varied depending on the depth and temperature of the water sample being analyzed. There was no reason for electronic noise to increase with depth. But there was good reason for cells to have more chlorophyll (hence the red color under the blue laser of the flow cytometer) the deeper they were under the surface of the water, in order to help with photosynthesis.

Over the next few years, collaborators discovered the same little cells in other seas across the globe. In 1988, Chisholm and her team published their findings in the journal Nature. In the paper, the researchers referred to them as a “new group of pico-plankters,” but members of the lab affectionally called them “little greens” because they contained chlorophyll b, which is a characteristic of green plant chloroplasts. For its formal name, they eventually chose “Prochlorococcus,” meaning “little round progenitors of chloroplasts,” or more colloquially “primitive green berries.”

Chisholm ultimately refocused her entire lab on Prochlorococcus, which revealed itself to be a fascinating subject. She had been looking for a phytoplankton species that could be both easily studied in the lab and easily found in the oceans. Prochlorococcus seemed like a promising model system through which she and her lab could begin understanding how the ocean works.

It turns out that Prochlorococcus wasn’t just one uniform organism, but a collective, composed of more than 30 clusters of strains called “ecotypes” with their own unique survival tactics. This collective has adapted to various environments, dividing up vast swaths of the oceans with various light, temperature, and nutrient combinations. Each ecotype is the “most efficient photosynthetic machine” at its particular conditions — and added together produce 10% of the oxygen in the atmosphere.

To Chisholm, this was an unmistakable sign that there was something truly remarkable about Prochlorococcus. But it would take a few more years for technology to develop far enough to uncover more.

flow cytometery and light microscopy image side-by-side showing red dots
The intriguing new cells glowed red under the flow cytometer (left), but appeared like mere specks of dust or electronic NetBet sportnoise under the commonly-used light microscopes (right). Credit: Rob Olson, Woods Hole Oceanographic Institute


Taking a stance on women’s rights at MIT

Deep in the thralls of Procholorococcus research, Chisholm worked early mornings and stayed late into the night. She was in her late forties, and her life revolved around her job. In 1994, during one of those typical long days in her office, she received a phone call that dramatically changed the way she viewed her career.

It was from Nancy Hopkins, a fellow MIT professor whom she casually knew. Hopkins was rallying the support of the 17 other senior female faculty at MIT for a purpose: She believed MIT was discriminating against all of them in multiple areas, including lab space, pay, and support. Hopkins asked Chisholm if she would be willing to come to a meeting and discuss these issues.

Chisholm didn’t know what would come of the meeting, nor did she expect much change to happen. In fact, she had never really thought about what it meant for her to be among the few female faculty at MIT. “I was just doing my work,” she says, “and I liked being one of the guys. I wasn’t plugged into feminist issues or anything.”

But she agreed to attend, and in a few days, found herself in a discreet location on campus. The room was small. Some women sat on chairs, while others sprawled on the floor.

It was awkward at first. “We didn’t know each other that well, so nobody wanted to speak out. We didn’t want to be that one woman faculty member to complain because that meant you couldn’t cut it,” she recalls. But soon everyone started shedding their protective shells. Hours went by as they all found common ground.

Chisholm came to a realization, which she later articulated in her Killian Award acceptance speech: “There’s always a general sense of not being part of the club. It’s like there’s a playbook for this whole enterprise we’re involved in, and it was written by men. As a woman, you’re just constantly trying to figure out what the game is and what the playbook is.”

In her office in 1988, Chisholm holds an image of Prochlorococcus. Credit: Donna Coveney

Armed with a letter calling for investigation, they marched into Dean Robert J. Birgeneau’s office. One of the women even put on a skirt for the first time. They had no idea how he’d react, but preliminary evidence seemed to be on their side. Not only were there 194 tenured male professors compared to only 15 tenured women faculty in the School of Science, the percentage of female faculty hadn’t budged from 8% in 20 years.

Seeing their determination and the evidence, Birgeneau agreed to help. Together with MIT President Charles Vest, he established the MIT Committee on Women Faculty in the MIT School of Science. Birgeneau and Vest charged the committee “to study the status of women in science at MIT and, among other things, to determine the reasons for [MIT’s] failure in the School of Science to hire and promote significant numbers of women faculty.”

The committee’s findings over a two year period were published in a report in 1999. The report made headlines in nearly every major newspaper when President Vest admitted to and apologized for the gender discrimination.

“It was a shot heard around the world,” Chisholm says. And it was true — the MIT administration acted quickly and decisively to right its wrongs. Salaries were adjusted, space and equipment allocation were corrected, retirement packages were increased, among many other changes. Importantly, several other higher education institutions followed MIT’s lead.

As a result of their shared experience, the group of women faculty grew close. Chisholm says, “In my mind, that was one of the best outcomes — on top of all the positive changes by the administration — in terms of my quality of life at MIT: having a community of women that I could talk to.”

Increasing recognition for Prochlorococcus and legacy at MIT

Parallel to the push for equity for women faculty at MIT was the development of one of the most ambitious science expeditions to date — sequencing the human genome.  After the Human Genome Project released the sequence of all 20,000 human genes in 2003, there was an abundance of DNA sequencing machines available for other projects. Chisholm leapt at the chance to learn more about her “little greens.” A strain of Prochlorococcus called MED4 became the second microbial genome to be sequenced.

The sequencing “completely opened up the black box,” Chisholm says. With only 1,700 genes, that strain of cyanobacteria is one of the simplest self-sustaining organisms known. Chisholm wrote in a chapter of “Microbes and Evolution: The World that Darwin Never Saw”, “This cell is truly the ‘essence’ of life. As a photosynthesizer, it can do what humans cannot, even with all of our technology: It can split water using sunlight and make hydrogen and oxygen — all with only 1,700 genes.”

The cyanobacterium Prochlorococcus was Chisholm’s muse throughout the majority of her career. Credit: Luke Thompson and Nicki Watson

Together, Chisholm and her lab eventually learned that though each Prochlorococcus strain contains fewer than 2,000 genes, the collective as a whole contains more than 80,000 — four times the size of the human genome. There is a core set of genes (about 1,200) that all Prochlorococcus share, and a few hundred more that are shared only by a subset of strains. In addition, each individual strain has an additional 80-200 genes that are completely unique to it. That incredible diversity allows Prochlorococcus to thrive in all sorts of environmental conditions, from 40 degrees north to 40 degrees south latitudes to almost 200 meters under the ocean where there’s less than 1% light penetration. As the environment shifts, so does the ecotype composition, stabilizing the total population of the species.

Additionally, it turns out that Prochlorococcus is also integral to its local environment. The 5 billion tons of living biomass it produces though photosynthesis each year is eaten by small microorganisms, then zooplankton, then fish. Ultimately, Prochlorococcus feeds 10% of all the creatures in the sea.

Over the years, Chisholm has led the charge in uncovering more about these intriguing cyanobacteria, including how they interact with other things in their environment like viruses or different microorganisms, as well as the unusual molecules Prochlorococcus produce. This persistent dedication has earned her many awards and honors. In 2011, former President Barack Obama presented her with the National Medal of Science, the White House’s highest honor for American scientists. In 2014, she won the MIT James R. Killian Faculty Award, and in 2015 she was named an MIT Institute Professor — the highest title that MIT bestows, and one that only 13 faculty presently hold. In 2019, she was awarded the Crafoord Prize in Biological Sciences by the Swedish Academy of Sciences, the equivalent of a Nobel Prize for biosciences.

As she was gaining worldwide recognition for her research, Chisholm also served as teacher and mentor to many classes of students at MIT. In 1993, she joined the Department of Biology to teach 7.014 (Introductory Biology). Her class was the only introductory biology class to feature ecology. In her lab, she advises undergraduate and graduate students with varying backgrounds, from biology, to chemistry, to oceanography, to civil and environmental engineering.

Her advocacy for women faculty’s rights at MIT has also paid off over the years, with statistics slowly but surely improving to more equal footing. As of June 2019, 250 of the approximately 1,050 faculty members are women, and within the Schools of Science and Engineering, women comprise 22% of the faculty.

And, nearly four decades later, Prochlorococcus still remains an irresistible siren to her. “I should probably be thinking about retiring, but I’m not because Prochlorococcus is too darn interesting,” Chisholm says. “I’m really very grateful to have this organism in my life.”

Posted: 3.31.22
How molecular biology could reduce global food insecurity

Mary Gehring is using her background in plant epigenetics to grow climate-resilient crops.

Summer Weidman | Abdul Latif Jameel Water and Food Systems Lab
March 30, 2022

Staple crops like rice, maize, and wheat feed over half of the global population, but they are increasingly vulnerable to severe environmental risks. The effects of climate change, including changing temperatures, rainfall variability, shifting patterns of agricultural pests and diseases, and saltwater intrusion from sea-level rise, all contribute to decreased crop yields. As these effects continue to worsen, there will be less food available for a rapidly growing population.

Mary Gehring, associate professor of biology and a member of the Whitehead Institute for Biomedical Research, is growing increasingly concerned about the potentially catastrophic impacts of climate change and has resolved to do something about it.

The Gehring Lab’s primary research focus is plant epigenetics, which refers to the heritable information that influences plant cellular function but is not encoded in the DNA sequence itself. This research is adding to our fundamental understanding of plant biology and could have agricultural applications in the future. “I’ve been working with seeds for many years,” says Gehring. “Understanding how seeds work is going to be critical to agriculture and food security,” she explains.

Laying the foundation

Gehring is using her expertise to help crops develop climate resilience through a 2021 seed grant from MIT’s Abdul Latif Jameel Water and Food Systems Lab (J-WAFS). Her research is aimed at discovering how we can accelerate the production of genetic diversity to generate plant populations that are better suited to challenging environmental conditions.

Genetic variation gives rise to phenotypic variations that can help plants adapt to a wider range of climates. Traits such as flood resistance and salt tolerance will become more important as the effects of climate change are realized. However, many important plant species do not appear to have much standing genetic variation, which could become an issue if farmers need to breed their crops quickly to adapt to a changing climate.

In researching a nutritious crop that has little genetic variation, Gehring came across the pigeon pea, a species she had never worked with before. Pigeon peas are a legume eaten in Asia, Africa, and Latin America. They have some of the highest levels of protein in a seed, so eating more pigeon peas could decrease our dependence on meat, which has numerous negative environmental impacts. Pigeon peas also have a positive impact on the environment; as perennial plants, they live for three to five years and sequester carbon for longer periods of time. They can also help with soil restoration. “Legumes are very interesting because they’re nitrogen-fixers, so they create symbioses with microbes in the soil and fix nitrogen, which can renew soils,” says Gehring. Furthermore, pigeon peas are known to be drought-resistant, so they will likely become more attractive as many farmers transition away from water-intensive crops.

Developing a strategy

Using the pigeon pea plant, Gehring began to explore a universal technology that would increase the amount of genetic diversity in plants. One method her research group chose is to enhance transposable element proliferation. Genomes are made up of genes that make proteins, netbet sports bettingbut large fractions are also made up of transposable elements. In fact, about 45 percent of the human genome is made up of transposable elements, Gehring notes. The primary function of transposable elements is to make more copies of themselves. Since our bodies do not need an infinite number of these copies, there are systems in place to “silence” them from copying.

Gehring is trying to reverse that silencing so that the transposable elements can move freely throughout the genome, which could create genetic variation by creating mutations or altering the promoter of a gene — that is, what controls a certain gene’s expression. Scientists have traditionally initiated mutagenesis by using a chemical that changes single base pairs in DNA, or by using X-rays, which can cause very large chromosome breaks. Gehring’s research team is attempting to induce transposable element proliferation by treatment with a suite of chemicals that inhibit transposable element silencing. The goal is to impact multiple sites in the genome simultaneously. “This is unexplored territory where you’re changing 50 genes at a time, or 100, rather than just one,” she explains. “It’s a fairly risky project, but sometimes you have to be ambitious and take risks.”

Looking forward

Less than one year after receiving the J-WAFS seed grant, the research project is still in its early stages. Despite various restrictions due to the ongoing pandemic, the Gehring Lab is now generating data on the Arabidopsis plant that will be applied to pigeon pea plants. However, Gehring expects it will take a good amount of time to complete this research phase, considering the pigeon pea plants can take upward of 100 days just to flower. While it might take time, this technology could help crops withstand the effects of climate change, ultimately contributing to J-WAFS’ goal of finding solutions to food system challenges.

“Climate change is not something any of us can ignore. … If one of us has the ability to address it, even in a very small way, that’s important to try to pursue,” Gehring remarks. “It’s part of our responsibility as scientists to take what knowledge we have and try to apply it to these sorts of problems.”

Ragon Institute Women Make a Difference: Alison Ringel
Emily Makowski | Ragon Institue
March 25, 2022

Dr. Alison Ringel didn’t set out to exclusively choose female mentors when she started out in scientific research, but by following her research interests, that’s what happened. “I have been mentored by what I call a dream team of women faculty,” she says.

Ringel joined the Ragon in January 2022 as one of three faculty recently hired in newly created joint appointment positions between the Ragon Institute and the Department of Biology at Massachusetts Institute of Technology. She currently studies how T cells — white blood cells that help protect against infection and can help fight cancer — survive in stressful environments. Originally from Wilton, CT, Ringel’s first research experience was in yeast genetics as an undergrad at Wesleyan University. “I was really given a lot of freedom to pursue my own ideas … having that very early exposure and freedom to manipulate systems experimentally, make hypotheses, make mistakes, really solidified my interest,” she says.

Ringel graduated with two bachelor’s degrees — one in molecular biology and biochemistry, and one in physics — and completed a molecular biophysics PhD at Johns Hopkins University School of Medicine in the lab of structural biologist Cynthia Wolberger. She studied how chromatin-modifying enzymes — enzymes that modify the material that our chromosomes are made of, affecting gene expression — choose which proteins to modify. The experience was a very positive one. “Not only was that an incredibly rich environment, but she was also a very supportive mentor, and still is a supportive person in my life,” Ringel says.

As Ringel was finishing up her PhD, she became more interested in the small molecule cofactors that catalyze reactions involving these enzymes. She started to look into labs studying immunology and metabolism, and she met cell biologist Marcia Haigis, who became Ringel’s postdoctoral mentor at Harvard Medical School (HMS). Ringel, Haigis and their collaborators identified a single gene change in cancerous tumor cells that prevented T cells from functioning properly in obese mice, suggesting that obesity can have an impact on the immune system’s ability to recognize and clear a tumor.

Ringel also became a close collaborator with Arlene Sharpe, chair of the Immunology Department at HMS. Seeing how both Haigis and Sharpe were able to balance success in science with fulfilling personal lives has been a great inspiration to Ringel, who has two young sons. “Working for women who had done the whole thing — they had been amazing scientists, they had made significant discoveries that advanced their field, they all had families, they all had navigated tenure processes at really big, impactful research institutions — has been enormously helpful and inspiring to me throughout my career trajectory,” she says. Her advice for women in STEM and STEM-related fields? “Don’t be dissuaded by the challenges. Understand them and use them for your forward momentum.”

Ringel has been enjoying starting her own lab in her dual-appointment role and is currently looking at how T cells can restrict the growth of tumors. “I’m particularly excited about this connection between MIT Biology and the Ragon Institute,” she says. “I was so excited to land here because the Ragon Institute is a real powerhouse in everything immunology, and MIT Bio has the immense depth and breadth of scientific interest. This position was really unique in having both of those arms represented.”

Helping drugs play nice in the human body
Whitehead Institute
March 25, 2022

For the hundreds of thousands of people diagnosed with breast cancer each year, surgery to remove the cancerous tissue is often the best option — but this relatively simple procedure comes with some drawbacks. In more than a few cases, the surgical removal of a tumor can lead to an increased risk of the cancer reemerging in other locations in the body.

In a 2018 study, a postdoc in the lab of Whitehead Institute Member Bob Weinberg discovered that, at least in mice, this phenomenon was due to a bodily butterfly effect: the creation of a wound site in one place in the body, which necessitated subsequent wound healing, caused immune system changes affecting distant parts of the body.

These changes occurred as bone marrow cells responded to the wounding with a flood of inflammatory cells that entered into the wound site and, at the same time,  scattered throughout the body. These dispersed inflammatory cells weakened the ability of the immune system to control the outgrowth of a distantly located metastatic tumor.  Without this immune control, which otherwise could keep the metastasis at a very small size,  the metastasis would grow out aggressively.

Hence, wounding in one part of the body provoked metastasis outgrowth at a distant site. This suggested, among other things, that the outgrowth of metastatic tumors, which is often seen in women who have recently undergone a mastectomy,  might be actively provoked by the post-surgical wound-healing process.

Weinberg’s work also presented a way to potentially avoid this effect, using a preventative measure that’s probably sitting in your bathroom cabinet right now: the cheap and common class of drugs known as NSAIDS, which includes ibuprofen and aspirin. When mice were given NSAIDS before and after tumor removal surgeries, they experienced a fivefold lower rate of cancer recurrence at the site of metastasis than a control group given opioids. These NSAIDs could therefore be used in place of the opioids, which are often used to treat post-surgical pain.

The human body is full of undiscovered connections like this one and adding in foreign substances further complicates matters. While a treatment might work well in a Petri dish, researchers describe whole -body metabolism as “a whole different kettle of fish.”

The way drugs move through the body and interact with internal systems is called pharmacokinetics. When a person is given a medicine — either orally, through a chemotherapy method, or via injection — that drug must be able to find its way to its target in a high enough concentration to have an effect, and then when its purpose is served, it must be able to leave the body safely and not build up to a harmful amount.

Much like Weinberg’s work on NSAIDS in breast cancer, Whitehead Institute’s basic research has led to other surprising discoveries about drug activities in the human body. Read on to learn about research that is changing the way new drugs are designed, making existing treatments less toxic, and more.

Concentration is key

When it comes to the action of drugs in the human body, concentration is key. Just ask Rick Young, a Whitehead Institute Member and professor of biology at MIT. In 2018, Young’s lab, which had previously studied the regulatory circuitry involved in transcription (the copying of DNA into RNA), shifted its focus after discovering tiny droplets within cells that concentrate the molecular materials needed to transcribe the DNA.

The droplets, called transcriptional condensates, were the newest in a slew of recent discoveries of other such groupings of cellular components. Some of these aggregations facilitate RNA splicing while others help to form ribosomes.

For Young, the discovery of transcription-related condensates sparked an interest in how these droplets were affecting the action of drugs. Previous theories held that transcription was able to take place in cells because there was a sufficient concentration of necessary proteins, such as RNA polymerase and other accessory proteins. As the Young lab showed,  these collaborating cellular players were actually being concentrated in the condensates,

In 2020, Young and Ann Boija and Isaac Klein, two postdocs in his lab, took their investigation a step further, analyzing the mechanism by which several cancer drugs are concentrated in cellular condensates, and how that concentration could affect their action in individual cells and thus in the body. They found that cancer drugs sort themselves into specific types of condensates, independently of their targets, which can allow them to build up into high concentrations in these localized areas within cells.

“This could have enormous implications for the way we discover and develop drugs,” said Rick Young.  “If drugs had properties that had them partitioning into a condensate where their target lives, then they would enjoy two properties of condensates: they would be compartmentalized, and they would be at much higher concentrations than if they diffuse through the cell.”

Young’s work on condensates led him to co-create a pharmaceutical company called Dewpoint Therapeutics, with the goal of reformulating treatments for cancer or neurological conditions such as amyotrophic lateral sclerosis by targeting biomolecular condensates. Whitehead Institute Founding Member Rudolf Jaenisch serves as a scientific advisor.

Trouble in parasites

While researchers in Young’s lab investigate how drugs could be more efficiently targeted, Sebastian Lourido’s lab is taking a different tack — why do some drugs stop working as time progresses?

The malaria drug artemisinin was developed in China netbet online sports bettingin the 1970s, and completely changed the way the world treated malaria. In the following decades, however, the parasites that cause malaria, several species within the genus Plasmodium, have slowly grown less susceptible to the drug.

In a paper published in September of 2020, Whitehead Institute Member Lourido and collaborators identified two parasite genes that were negatively impacting the actions of the drug in the parasite’s cells.

Researchers liken artemisinin to a “ticking time bomb,” which needs another molecule, called heme, to light its fuse. Heme, a small molecule that is one component of hemoglobin, helps transport electrons and deliver oxygen to tissues. When heme encounters artemisinin, it activates the drug, allowing the creation of small, toxic chemical radicals. These proceed to react with the parasites proteins, fats, and metabolites, eventually leading to its death.

In order to understand how some parasites were becoming less vulnerable to the drug, Lourido, along with researchers Clare Harding, Boryana Petrova and Saima Sidik, ran a genetic screen on a related parasite, Toxoplasma gondii. The screen allowed them to assess which mutations in the parasites’ genomes were beneficial for their survival and which ones were harmful.

The screen revealed two genes that affected how susceptible the parasites were to treatment with artemisinin. One, called Tmem14c, seemed to be protecting the parasites. The gene is analogous to a gene that transports heme out of mitochondria where it is generated. Lourido hypothesized that when the  Tmem14c protein is working properly, it helps the cells shuttle heme and its building blocks and get them where they need to go in the cell. When this gene is knocked out or mutated, heme can build up in the parasite cells, making them more likely to activate the artemisinin “bomb.”

Another gene, when mutated, made the parasites less sensitive to artemisinin. The gene, called DegP2, encodes a protein that plays a role in heme metabolism, so when it was mutated, less heme was available in the cells to activate the drug.

This knowledge provides useful insights for treatment methods, said Lourido. For example, healthcare providers should take into consideration the fact that heme is key in artemisinin’s action, and avoid combining the drug with other treatments that might lower the amount of heme in parasite cells. “Understanding how different pathways within the cell participate to render parasites susceptible to these antiparasitic drugs helps us better pair them with other compounds that are going to be synergistic and not work against our own goal of defeating parasites,” Lourido said.

Taking the edge off toxic treatments 

Another application of fundamental pharmacokinetics research involves mitigating the harmful effects of drugs. Consider the chemotherapy drug methotrexate. Methotrexate was the very first targeted drug ever made. Developed more than 60 years ago by Dr. Sidney Farber, the drug acts by inhibiting a key molecule in the metabolic process that builds DNA and RNA, thereby interfering with basic functions of the cell and with DNA synthesis, repair and replication, helping to destroy cancerous cells in the body.

Methotrexate is still a widely used component of chemotherapy cocktails, especially for pediatric leukemia. In the human body, though, methotrexate is like a bull in a china shop. It is very effective at knocking back cancer, but the drug’s life-threatening side effects, including gut, liver, kidney and brain damage, often lead doctors to terminate their patients’ treatment early, or seriously compromise the survivors’ quality of life.

The drug was much-studied in the 70s, but research trailed off in the subsequent decades due to limits on the existing technologies. Nearly fifty years later, Naama Kanarek, then a postdoctoral researcher in the lab of former Whitehead Institute Member David Sabatini, decided to take  a fundamental research approach to studying the effects of methotrexate, in hopes that she might discover some way to make the drug less toxic.

“We now have access to genetic tools that allow us to address long standing questions in a way that was not possible before,” said Kanarek, who now runs her own lab at Boston Children’s Hospital. “We can use a CRISPR screen, and instead of focusing on what is known, we can ask what is unknown about the drug. We can find new genes that are involved in the response of cells to the drug that were not found before simply because the tools were not there.”

The screen revealed one gene in particular that seemed to be playing a role in how sensitive cancer cells were to methotrexate, the researchers reported in Nature in July of 2018. The cells’ sensitivity is important, Kanarek said, because if the cells can be made more vulnerable to methotrexate, the duration of treatment or required dose could be reduced. “If we can reduce dose because we can improve efficacy, then we can reduce toxicity without compromising on the cure rates and that is good news to the patients,” Kanarek said.

The gene in question, called FTCD, encodes an enzyme involved in the breakdown of the amino acid histidine. When the gene was knocked out, cancer cells were less sensitive to methotrexate. When the pathway was boosted with the addition of extra histidine, cells became more sensitive.

Former Whitehead Institute Director Susan Lindquist, who passed away 2016, performed similar work on the natural product amphotericin B, a drug which is used to treat some fungal infections. The drug is especially useful because fungi have not yet developed a resistance to it, as they have with so many other treatments. But amphotericin B also has some serious drawbacks; it can cause kidney damage, heart failure, and other serious and even fatal side effects.

These side effects mostly happened because amphotericin B works by binding to a chemical group called a sterol. In fungi, it binds to molecules called ergosterols in the cell wall, destabilizing the cells. Unfortunately humans also have a prevalent sterol: cholesterol. When amphotericin B binds to cholesterol in human cell membranes, it can damage human cells.

Using chemical synthesis methods, Lindquist and colleagues at Whitehead Institute and elsewhere were able to tweak the structure of the drug to bind only to ergosterol molecules and not cholesterol, bypassing most of the harmful side effects.

Why fundamental research 

Drug development is often an extremely targeted pursuit, but for Whitehead Institute scientists, their advances have mostly come from a simple curiosity about the cellular mechanisms. For example, Rick Young didn’t set out to study condensates, but an inquiry into the fundamentals of transcription led him in this entirely new direction.

Such fundamental research has the potential to branch in any number of different ways. “Fundamental science can lead in directions that you would not foresee,” said the Institute’s Associate Director of Intellectual Property Shoji Takahashi. Basic research into drug behavior is essential and can contribute to life-changing therapies down the line.