Author: Raleigh McElvery

Ankur Jain and Pulin Li appointed to prestigious chairs
Whitehead Institute
July 13, 2020

Massachusetts Institute of Technology (MIT) provost Martin A. Schmidt has announced that two Whitehead Institute Members — Ankur Jain and Pulin Li — have been appointed to MIT career development professorships.

Jain has been named to the Thomas D. and Virginia W. Cabot Career Development Professorship. Li has been named the Eugene Bell Career Development Professor of Tissue Engineering. Both also continue to be assistant professors in the MIT department of Biology.

The Cabot and Bell chairs both recognize and support excellence in teaching and research by gifted faculty members who show exceptional promise in their professional careers. In addition to affirming Jain’s and Li’s status as emerging leaders in biomedical research, the appointment provides funding to advance their scientific initiatives — better enabling them to pursue new research directions and capitalize on new opportunities.

“The Biology Department and MIT are delighted to provide this support to Pulin and Ankur,” says Alan D. Grossman, professor and head of the MIT department of Biology, “and we are thrilled that they are engaged and active members of our community.”

“We are very proud to have accomplished, early-career researchers like Ankur and Pulin on our faculty,” says Whitehead Institute director Ruth Lehmann, “and pleased that MIT is recognizing their talents and promise for leadership with these prestigious professorships.”

Both appointments are for a three-year term beginning July 1, 2020.

How to Reopen? Tools Visualizing Covid-19 Data Provide Concrete Guidance
Kara Baskin | Slice of MIT
July 14, 2020

Where could another Covid-19 spike happen? During the next major hurricane, will residents have access to food and appropriate shelter?

Ellie Graeden PhD ’11 answers questions like these as founder and CEO of Talus Analytics, a Colorado-based research and consulting firm. She’s a scientific interpreter, deciphering natural-disaster and public-health data for decision makers who must act sensibly—and quickly.

Talus is currently focused on modeling the spread of Covid-19 to guide response efforts, working closely with academic and research partners and the US Centers for Disease Control and Prevention in a range of efforts, several of which are publicly available.“Often, those kinds of data aren’t communicated in a way that’s immediately useful,” she explains. “We translate the data and the modeling results to inform practical decisions that need to get made on a day-in, day-out basis.”

COVID Local is a data-driven decision framework that helps policymakers determine when and how to reopen during each phase. A dashboard uses clear metrics to determine the parameters for each threshold. It’s a joint initiative from the Global Biological Policy Program at the Nuclear Threat Initiative (NTI), the Center for Global Development, and the Georgetown University Center for Global Health Science and Security, where Graeden is an adjunct professor.

“COVID Local is focused on getting concrete guidance in place for those local decision makers so that they have a checklist that they can work through, driven by some of the best experts in global public health, who have managed outbreaks for Ebola in 2014 and elsewhere,” she says.

A second tool, Re:Public COVID Log, is a map-based platform that tracks communities visually, providing views of hazard risk, infrastructure, and population. It was developed with support from the US Department of Homeland Security and FEMA, and it’s simple enough for a nonexpert to use.

“A lot of the current tools are very expert focused. This is targeted for use by those without hazard-specific expertise—for example, by the communications office for a mayor,” she says.

In collaboration with Georgetown University, Talus has also built a large-scale database to track the effectiveness of various mitigation policies, helping to guide policymakers who might need to close for a second wave.

“We let them know what worked the first time,” she says.

All of this might seem like a leap for a microbiologist. Graeden earned her doctorate in cell biology at MIT, where she studied brain development in zebrafish under Professor Hazel L. Sive.

“I learned how to tell scientific stories visually, which is essentially what microscopy is. You’re telling stories with pictures,” she says.

She founded her 10-person firm in 2015 to do the same with global health issues: There was plenty of data, she felt, that nobody was looking at under a microscope and bringing to light. (Fellow MIT alum Trae Wallace MBA ’10 guides Talus’s development as its head of data.)

The company first made a name for itself during Hurricane Matthew in 2016, when Talus deployed to FEMA’s National Response Coordination Center to deduce how many people would be impacted by the storm’s wrath.

Her team harnessed data from the Department of Energy, looking at real-time power outages, and merged them with inland and coastal flood modeling to determine counties that would be hit. Next, they leveraged census data to capture the total number of people affected. While all the data from each source had been previously available, the questions being asked required real-time integration of the information for the response effort.

Since then, Talus has become a go-to for government and academic partners when “integrating different types of information and doing that storytelling,” Graeden says. “Flood modelers didn’t feel comfortable pulling in energy data or outage data or coastal modeling data. It was really a data analysis and storytelling problem,” she says.

Now, she tells these number stories from her perch in Colorado, where she moved in 2015 to be farther from what she calls “power-driven” Washington. It’s also closer to northern Idaho, where she grew up. Still, she looks back fondly on her time in Cambridge, where she jogged in the Arboretum and played competitive Ultimate Frisbee off campus, practicing up to 16 hours on the weekends. She also leaves a legacy of service to the school community as the founder of MIT BioREFS (Resource for Easing Friction and Stress), a peer mentorship program within the biology department, after a friend died by suicide.

“MIT was the first place I’d ever been where the response to an idea was routinely, ‘Well, is that the right thing to do?’ Whereas prior, the response had always been, ‘Well, can it be done right?’ At MIT, it’s not ‘Can it be done?’ but ‘What is the right way to solve it?’” she says.

As for the right thing to be doing about Covid, her assessment is stark.

“In the US, we are functionally no different from where we were three months ago. We have better treatments and a better sense for what works on the treatment side, but we have no preventative measures. We have no vaccine. We have no way to prevent people from getting sick, except social distancing measures,” she warns.

She hopes for equitable distribution of an eventual vaccine, using transparent data with demographic information layered in to target vulnerable communities.

“We need to be clear-eyed about what is happening. We need to collect data with demographic details attached. Florida, for example, decided at one point not to allow its coroners to report Covid deaths, and those limitations on data release really hamstring our ability to respond in an informed way. We have to collect the data, we need to be able to analyze it, and we need to be able to integrate data so that we can make decisions on the basis of it,” she says.

Seemingly similar, two neurons show distinct styles as they interact with the same muscle partner
Picower Institute
July 7, 2020

A new study by MIT neuroscientists into how seemingly similar neuronal subtypes drive locomotion in the fruit fly revealed an unexpected diversity as the brain’s commands were relayed to muscle fibers. A sequence of experiments revealed a dramatic difference between the two nerve cells – one neuron scrambled to adjust to different changes by the other, but received no requital in response when circumstances were reversed.

The findings published in the Journal of Neuroscience suggest that these subclasses of neurons, which are also found abundantly in people and many other animals, exhibit a previously unappreciated diversity in their propensity to respond to changes, a key property known as “synaptic plasticity.” Synaptic plasticity is considered an essential mechanism of how learning and memory occur in the brain, and aberrations in of the process are likely central to disorders such as autism.

“By seeing that these two different types of motor neurons actually show very distinct types of plasticity, that’s exciting because it means it’s not just one thing happening,” said senior author Troy Littleton, a member of The Picower Institute for Learning and Memory and Menicon Professor of Neuroscience in MIT’s Departments of Biology and of Brain and Cognitive Sciences. “There’s multiple types of things that can be altered to change connectivity within the neuromuscular system.”

Tonic and phasic neurons

Both of the neurons work in the same way, by emitting the neurotransmitter glutamate onto their connections, or synapses, with the muscles. But these two neurons do so with different styles. The “tonic” neuron, which connects only to a single muscle, emits its glutamate at a constant but low rate while the muscle is active. Meanwhile, the “phasic” neuron connects to a whole group of muscles and jumps in with a strong quick pulse of activity to spring the muscles into action.

Heading into the study Littleton and lead author Nicole Aponte-Santiago were curious to explore whether these different neurons compete or cooperate to drive the muscle fibers, and if they exhibited different plasticity when their functions were altered. To get started on what ultimately became her dissertation research, Aponte-Santiago developed the means to tailor genetic alterations specifically in each of the two neurons.

“The reason we were able to answer these questions in the first place was because we produced tools to start differentially manipulating one neuron versus the other one, or label one versus the other one,” said Aponte-Santiago, who earned her PhD in Littleton’s lab earlier this spring and is now a postdoc at the University of California at San Francisco.

With genetic access to each neuron, Aponte-Santiago distinctly labeled them to watch each one grow in fly larvae as they developed. She saw that the tonic neuron reached the muscle first and that the phasic one connected to the muscle later. She also observed that unlike in mammals, the neurons did not compete to control the muscle but remained side by side, each contributing in its characteristic way to the total electrical activity needed to drive movement.

To study the neurons’ plasticity, Aponte-Santiago employed two manipulations of each neuron. She either wiped them out completely by making them express a lethal protein called “reaper” or she substantially tamped down their glutamate activity via expression of tetanus toxin.

When she wiped out the phasic neuron with reaper, the tonic neuron quickly stepped up its signaling, attempting to compensate as much as it could. But in flies where she wiped out the tonic neuron, the phasic neuron didn’t budge at all, continuing as if nothing had changed.

Similarly when Aponte-Santiago reduced the activity of the phasic neuron with the toxin, the tonic neuron increased the number of boutons and active zone structures in its synapses to respond to the loss of its partner. But when she reduced the activity of the tonic neuron the phasic neuron again didn’t appear to respond.

In all the experiments, the muscle received less overall drive from the neurons than when everything was normal. And while the phasic neuron  apparently didn’t bother to make up for any loss on the part of the tonic neuron, the tonic neuron employed different means to compensate – either increasing its signaling or by enhancing the number of its connections on the muscle – depending on how the phasic neuron was diminished.

“It was quite intriguing that Nicole found that when the phasic input wasn’t there, there was a unique form of plasticity that the tonic neuron showed,” Littleton said, “but if the phasic neuron was there and wasn’t working, the tonic neuron behaved in a very different way.”

Another intriguing aspect of the study is the role of the muscle itself, which may be an active intermediary of the plasticity, Littleton said. The neurons may not sense when each other have been wiped out or inactivated. Instead the muscle appears to call for those changes.

“Even though a muscle has two distinct inputs, it can sort of uniquely control those two,” Littleton said. “When the muscle is getting glutamate, does it know whether it is coming from the tonic or the phasic neuron and does it care? It appears that it does care, that it really needs the tonic more than the phasic. When the phasic is gone it shifts some of the plasticity, but when the tonic is gone the phasic can’t do much about it.”

In new work, the lab is now looking at differences in gene expression between the two neurons to identify which proteins are responsible for the unique properties and plasticity of the tonic and phasic neurons. By defining the genetic underpinnings of their unique properties, the lab hopes to begin to get a handle on the molecular underpinnings of neuronal diversity in the brain.

In addition to Aponte-Santiago and Littleton, the paper’s other authors are Kiel Ormerod and Yulia Akbergenova.

The National Institutes of Health and the JPB Foundation supported the study.

Parasite research heats up
Greta Friar | Whitehead Institute
July 7, 2020

Apicomplexan parasites infect hundreds of millions of people around the world each year. Several species of apicomplexan parasites in the Plasmodium genus cause malaria, while another apicomplexan species, Toxoplasma gondii (T. gondii), causes toxoplasmosis, a disease with flu-like symptoms that can be lethal for people with weakened immune systems. In spite of their impact, the biology of these disease-causing parasites is not very well understood and treatment options for infection are limited.

One potential approach to treat infection could be drugs that disrupt the parasites’ calcium signaling, which they rely on to spread from cell to cell in their hosts. The parasites need an influx of calcium in order to burst out of an infected host cell—a process called egress—and move through the host’s body and invade other cells. In previous work, a researcher from Whitehead Institute Member Sebastian Lourido’s lab, Saima Sidik, had tested a large collection of molecules and identified one called enhancer 1 (ENH1), which perturbed the parasites’ calcium levels and prevented egress, as a promising anti-parasitic lead. However, the original experiments did not determine how ENH1 acts. In research published in the journal ACS Chemical Biology on June 29, Alice Herneisen, a graduate student in Lourido’s lab, and Lourido, who is also an assistant professor of biology at the Massachusetts Institute of Technology, used an approach called thermal proteome profiling to discover how ENH1 prevents T. gondii parasites from egress. They identified the main target of ENH1 as a calcium-dependent molecule called CDPK1 that parasites use to prepare for egress, moving between cells, and invasion of host cells. ENH1 binds to and prevents CDPK1 from functioning.

“Advances over the past few decades have made discovering a molecule’s potentially therapeutic activity much easier, but the next step of figuring out how the molecule works is often still a challenge,” Lourido says. “By applying newer expansive approaches, we are starting to build a more holistic picture of the parasites’ cell biology.”

Understanding the biology responsible for a potential drug’s observed effects is important because most drugs require modification before they are ready for human use—they may need to be made less toxic, more potent, or more amenable to the environment of the human body—and these sorts of modifications cannot be made until the molecule and its activity are understood.

Herneisen decided to use a relatively new approach in parasites, thermal proteome profiling, to discover the targets of ENH1—the molecules it binds to, leading to its therapeutic effects. The approach works by graphing how each of the proteins inside the parasite reacts to changes in heat with and without being exposed to ENH1. One advantage of this approach is that it is unbiased, meaning that instead of researchers picking likely targets up front to test, they investigate as many molecules as possible, which can lead to unexpected findings. For example, Lourido has been investigating CDPK1 in other contexts for many years, and based on his lab’s previous understanding of its role would not have expected it to be a main target of ENH1—such surprises can direct research in exciting new directions.

Although CDPK1 is ENH1’s main target, the investigations did not uncover the target that allows ENH1 to cause oscillations in the parasites’ calcium levels. Finding this missing target is one of the lab’s next goals.

“The fact that ENH1 affects multiple aspects of calcium signaling may be what makes it such an effective antiparasitic agent,” Herneisen says. “It’s messing with the parasites on several levels.”

Translation of the research for clinical testing is a long way off, but there are multiple indicators that this is a promising direction for investigation. Not only is calcium signaling key to the parasites’ life cycle and ability to spread inside of a host, but the molecules and mechanisms that the parasites use to modulate calcium levels are very different from the ones found in mammals. This means that a drug that disrupts the parasites’ calcium signaling is unlikely to interfere with calcium signaling in human patients, and so could be deadly to the parasites without harming the patients’ cells.

Written by Greta Friar

***

Sebastian Lourido’s primary affiliation is with Whitehead Institute for Biomedical Research, where his laboratory is located and all his research is conducted. He is also an assistant professor of biology at the Massachusetts Institute of Technology.

***

Herneisen, Alice L. et al. “Identifying the target of an antiparasitic compound in Toxoplasma using thermal proteome profiling.” ACS Chemical Biology, June 29, 2020. https://doi.org/10.1021/acschembio.0c00369

LEAH Knox Scholars Program celebrates fourth summer with kick-off event

The science program for local high school students will be remote this year, as MIT instructors create at-home lab experiences.

Raleigh McElvery
July 2, 2020

A kick-off event on June 24 commenced a summer of science for local high school students. Established in 2017 as a biomedical research track within the Leaders through Education, Action, and Hope (LEAH) Project, the LEAH Knox Scholars Program is a collaboration between MIT and Health Resources in Action (HRiA), providing mentorship and hands-on lab experience in the field of biology.

Each summer, 24 rising juniors and seniors from disadvantaged and underrepresented backgrounds enrolled in Boston, Cambridge, and Everett public schools attend a five-week lab course at MIT. They receive a stipend, learn basic laboratory and quantitative techniques, and attend workshops to develop other professional skills. The next summer, they join research groups throughout the Boston area to complete a six-week internship.

The kick-off event was held via Zoom, and brought together over 63 current and former students, donors, partners, parents, and instructors.

“The LEAH Project has a concept called ‘FamiLEAH,’ and so the kick-off event is all about welcoming everyone into that community,” says Lisa Aslan, director of HRiA’s LEAH Project.

Ryan Elbashir, LEAH Knox teaching assistant and incoming first-year Biology graduate student, says she knew when she was applying to MIT that she wanted to interact with the greater Boston community.

“Programs like LEAH Knox inspire other students from under-represented groups to get excited about science and form meaningful connections with higher education institutions like MIT,” she adds. “My impression from the kick-off event was that this program aims to not only provide students with an educational experience, but also a support network and source of mentorship for the remainder of their academic careers.”

Participants split into breakout rooms for icebreaker activities, and then reconvened for a live Q&A with Lynn Porter. A pediatrician and advisor to the program, Porter is the granddaughter of the man who inspired the LEAH Knox Program: William J. Knox.

Knox was the grandson of slaves, and went on to earn degrees from Harvard and MIT, contributed to the Manhattan Project, and had a fruitful career at the technology company Eastman Kodak. Despite his many accomplishments, he faced adversity simply because of the color of his skin. For instance, as a student at Harvard he was forced to sleep in the kitchen because Black men were not allowed in the dorms.

Porter recounted her grandfather’s life and discussed why it’s crucial for people of color to pursue science degrees. She encouraged the LEAH Knox Scholars to work hard, form lasting relationships with mentors, and never give up on their dreams.

Following Porter’s Q&A, the keynote speech was delivered by Nancy Kanwisher, the Walter A. Rosenblith Professor of Cognitive Neuroscience in MIT’s Department of Brain and Cognitive Sciences, and a founding member of the McGovern Institute. She shared her love of research, and explained her work studying the functional organization of the human brain. The LEAH Knox Scholars had the chance to ask Kanwisher questions, before a brief orientation for their families.

Rothsaida Sylvaince, a former LEAH Knox Scholar, says the program introduced her to another world where she transformed into a scientist. As she entered her second year, she realized “that I could be a scientist not only within MIT’s lab, but anywhere. It gave me the confidence and support network to pursue science with all of my energy.”

Person in lab teaching to iPhone
Vanessa Cheung teaches lab techniques remotely

This year, due to the Covid-19 pandemic, students will not be conducting lab work on MIT’s campus. Instead, Director of Outreach Mandana Sassanfar and Technical Instructor Vanessa Cheung partnered with MIT’s Edgerton Center to enable participants to bring their research home. Sassanfar and Cheung created “Bags of Science” containing specialized DNA and protein modeling kits, as well as tubes, pipettes, and other lab equipment. These tools, Cheung says, will help students participate in hands-on activities — like extracting DNA from fruit and running an agarose gel — from the comfort of their own kitchens.

“The hope is that even though the students can’t physically be in the lab this summer, they will still get a chance to practice some basic lab techniques and gain a better appreciation for molecular biology research,” she adds.

HRiA will be providing their college and career readiness programing for all students virtually, and second-years will complete their research internships remotely. Eight have been placed in labs at MIT, and started their six-week internships on June 29.

Sassanfar says that, despite the current circumstances, it was very important to offer second-year students the opportunity to work on remote research projects.

“The eight students placed at MIT will gain very valuable coding skills,” she adds. “It was even more important to offer a virtual lab course to the first-years this summer, so they can apply for internships next summer. The LEAH Knox Scholars Program is all about teaching students underrepresented in the STEM fields how to do research, and to prepare them for a career in STEM.”

Don Pinkerton, a biology teacher at Revere High School and LEAH Knox intern supervisor, says he admires the program’s mission to bring STEM (science, technology, engineering, and math) opportunities to low-income students of color.

“Even though we won’t be in the lab this summer,” he says, “our students will be able to conduct real science through the exploration of data. In addition to reading and discussing papers and other media, I hope to bring in engaging guest speakers and possibly run some at-home experiments.”

Posted: 7.2.20
The story behind the science: How discovery develops
Picower Institute
June 29, 2020

Scientific discoveries can sometimes seem like products on a store shelf. Packaged neatly in the wrapping of a journal article or maybe a news story, there remain few hints of what they really took to produce – the struggle and surprises, the ingenuity and serendipity, the toil and triumph. Perhaps it’s no wonder that many members of the public (7 in 10, by one National Science Foundation measure) feel at least somewhat unclear about how scientists know what they know or do what they do.

To deconstruct and perhaps demystify discovery, let’s unwrap the inside story of a paper published by the lab of Troy Littleton, Menicon Professor of Neuroscience in the Departments of Biology and Brain and Cognitive Sciences. The study reported important findings both about a possible mechanism of seizures in epilepsy, which affects 60 million people worldwide, and also the underappreciated relationship between neurons and the brain cells called glia that help them function. Through four years of work led by former postdoc Shirley Weiss, Littleton’s team thoroughly unraveled the complex breakdown that makes fruit flies with a genetic mutation prone to seizures and showed multiple ways to intervene, including with human medicines. Published in April 2019 in eLife, a far-reaching “open access” journal that is free for all to read, the paper has since been viewed thousands of times.

Figuring out the puzzle of exactly how the mutation made glial cells fail to prevent seizures was a source of particular excitement for Weiss. Littleton adds that the discovery could open up new strategies for developing drugs to address epilepsy in humans, which the flies model well.

“One of the long-term motivations for the field in general, not just our lab, is there might be pharmacological access to glial cells that might have less side effects than would happen if you target neurons directly,” he said.

Too much excitement

First, a little biological background. Neurons are electrical. Their participation in the brain circuits that guide behavior, emotion, reasoning and memory depends on how they build up or dissipate electrical charge by taking in or ejecting ions of calcium, potassium and sodium. If they remain too electrically charged up because of an imbalance of these ions, they can become hyperactive and, in groups, produce seizures. In this study, it turned out that a certain kind of glial cells were responsible for regulating the balance of potassium ions around their neuronal neighbors to help govern their electrical charge and activity. The mutation, Weiss discovered, caused the glia to leave too much potassium outside the neurons, making it harder for the neurons to get rid of the potassium they had built up inside when they were electrically active. Without the ability to get their potassium out, the neurons stayed too excited, producing seizures.

The lab first discovered the mutation, which the Louisianan Littleton named “zydeco,” in 2005 when a team led by Zhuo  Guan used genetic screening techniques Littleton learned when he was a postdoc in the 1990s at the University of Wisconsin. The team’s broader goal was to learn about how neurons communicate with each other, so they looked for flies with mutations that either shut the process down, leading to a readily observable symptom of paralysis, or amped it way up, leading to seizures. Zydeco fell into that second category, making fruit flies seize dramatically when stressed by heat or by getting jostled around.

“It was so striking, it was hard to ignore,” Littleton said. “Whatever this gene was, it was doing something very important in the brain.”

When Weiss joined the Littleton lab after earning her PhD at Hebrew University in Jerusalem in 2013, the lab had just  published a new paper about zydeco. It was a long-awaited follow-up. Zydeco disrupted a gene on the fly’s X chromosome which at the time was poorly understood. Led by former graduate student Jan Melom, the lab finally was able to clone the gene that was mutated in Zydeco and showed that it specifically affected “cortex glial” cells and that it caused them to retain too much calcium. But what remained completely unclear was how this made the neurons that those glia contact so susceptible to seizures.

Though Weiss had a research specialty in studying calcium in brain cells, at first she worked on a few other ideas. But because Melom had left the lab, Weiss soon picked up the zydeco baton. In so doing, she was taking on what would become an especially extensive effort involving scores of experiments and a vast array of techniques, some of which she would have to learn along the way.

No hypothesis needed or heeded

Based on the 2013 findings, Littleton had formulated a working hypothesis about what might be going on to cause the seizures. He figured the excess of calcium in the cortex glia probably caused them to emit too much of some kind of signal to the neurons, in turn causing them to remain too active.

That turned out to be wrong, Littleton acknowledges with a smile.

“What Shirley did was to disprove my very strong impression of what was actually happening,” Littleton said. “Sometimes that’s very difficult to do. Once you have an idea of how you think the biology is working, that can reinforce the sorts of experiments you do and affects how you think about the project. It was very exciting in the end that Shirley was able to get past my pre-conceived notions and figure out what was really happening.”

The team didn’t fall into that trap because the experimental approach they chose didn’t depend on what they thought. Weiss’s key initial inquiries were based on a wide-open, free-ranging manipulation of the zydeco flies’ genes. Her strategy was to “knock down” or interfere with the cell’s ability to make use of 847 different genes covering a wide variety of potentially relevant glial cell functions. If knocking down any particular gene stopped the seizures, that would give them a huge clue about how the seizures happen. And whatever worked, if anything, would work regardless of anyone’s guesses up front.

“The great thing about using forward genetics is you don’t have to have a very strong hypothesis,” Weiss said. “You can let the genetics lead the way. I tried to be hypothesis free and to be as unbiased as I could be.”

The knockdown screening yielded about 50 genes where interference totally or partially alleviated the seizures. One in particular squared well with what Melom had observed about a specific cellular process (scientists call it a “pathway”)that related to handling calcium.

Around that time, though, life outside the lab intervened. In February 2015 Weiss and her husband Kfir Sharabi, also a postdoc, and their then four-and-a-half year old daughter, Amit, welcomed their second daughter, Ma’ayan, to the world. With two young kids and the rest of her family in Israel, Weiss came back from maternity leave and got back to investigating the most promising hits of the knockdown screen.

A calcium conundrum

The particular hit related to calcium that caught Weiss’s eye was a gene was called CanB2. Zydeco flies with that gene knocked down experienced no more seizure troubles at all. Moreover, she found that it was specifically helpful to knock it down in cortex glia and that knocking it down in healthy flies didn’t do any discernable harm.

So what does CanB2 do? In general the gene, along with two others, make a protein called calcineurin. No one had ever characterized what calcineurin does in glia. If Weiss could become the first to figure that out, she could whatever problems the zydeco mutation causes.

By manipulating all three calcineurin genes, Weiss was able to confirm that calcineurin activity was indeed crucial for zydeco seizures. She engineered cortex glia so that a glowing green protein would start to be expressed when calcineurin was active. She could see the protein light up under the microscope. This told her there was a lot more calcineurin activity in zydeco mutant brains than in normal fly brains. Apparently, the excess calcium in the cortex glia correlated with increased calcineurin activity.

There are human medicines that ratchet back calcineurin activity. They are typically used to suppress the immune system after a transplant. Weiss wanted to see whether they could reduce seizures in the zydeco flies. When she fed them the drugs the seizures did subside, providing a clear demonstration that intervening in this glial pathway could hold promise for drug development.

Any such effort, to be truly well targeted, would require more than just an association between calcineurin and seizures. Weiss was determined to discover the mechanism that linked the two.

Figuring out what that mechanism was and how it led to seizures, would turn out to be the heart of the discovery and the most challenging phase of her four year endeavor.

A potassium epiphany

Weiss needed to find out what process this excess calcineurin activity might be putting into overdrive. She went back to genetics. She performed a screen to knock down direct targets of calcineurin. It didn’t appear to yield anything helpful. She did another screen of pathways where calcineurin was implicated. In that case, a process called “endocytosis” came up and sure enough, Weiss found that by inhibiting the process in the cortex glia she could again stop seizures in the zydeco flies. Endocytosis is how cells ingest material from their surroundings, including regulating the content of their cell surface membrane proteins. The process can therefore affect the proteins they employ on the membrane to interact with the environment outside the cell. Excess endocytosis could mean that the way by which cortex glia interact with their environment is altered in zydeco, perhaps affecting the neurons they support. But how might that matter in this case?

Weiss struggled with this question for months. She received feedback and advice in meetings with Littleton and in lab meetings where the members discuss, challenge and refine ideas. The discussions were helpful, but it turns out that the key breakthrough came from Weiss attending a conference in Cold Spring Harbor, N.Y. in July, 2018.

Among Weiss’s genetic screen results of calcineurin targets was a gene called “SAND” that makes a protein in flies called “sandman” (the human version is called TRESK). Sandman, when deployed to the cell membrane, forms a channel (picture a portal though the cell’s surface) that allows a cell to bring in potassium ions from outside. At first this result didn’t strike Weiss as all that notable, but at the conference, potassium channels kept coming up as a topic in talks. An idea started to percolate as she took notes. Then at the conference posters she started talking with a scientist who said that problems with potassium channels in glial cells have been linked to epilepsy. Potassium channels apparently merited another look.

“I already had the result,” Weiss said. “I just didn’t connect the two dots.”

One of her screens indeed showed that knocking down SAND in healthy flies caused seizures just like the ones seen in zydeco mutants. Further genetic manipulations confirmed that SAND knockdown and zydeco affected the same pathway in cortex glia cells.

By September 2018, a new hypothesis was emerging: Elevated calcium in cortex glia triggered excess calcineurin activity, which spurred increased endocytosis that hindered sandman’s intake of potassium. This came at a good time as Weiss was nearing the point where she had to start thinking of wrapping up her postdoctoral appointment at MIT. The hypothesis, and the evidence she’d built up, seemed enough to submit a paper to a journal.

Always mindful that a paper was the goal, Weiss had been writing as she went and developing the key figures. When she had a draft done, Littleton then set to polishing it and giving her feedback. eLife wasn’t the first journal they submitted the paper to, but the editors received it enthusiastically. All three of the scientists who reviewed the manuscript for eLife, however, said the same thing: If endocytosis was pulling sandman back from the membrane of the cortex glia, thereby disrupting its ability to take in potassium ions, they wanted to see it happening. Weiss and Littleton not only agreed with that critique, they had even anticipated it.

“You sort of know your own holes in the story,” Littleton said. “This is what we were planning to do next anyway.”

Since sending in the paper, Weiss had already produced those smoking gun images, showing that in zydeco cortex glia, sandman was much less abundant on the membranes than in the non-mutant flies. This cemented the argument, neatly wrapped up in the paper, that neurons become more susceptible to seizing when zydeco cortex glia, saddled with too much calcium and resulting calcineurin activity, overdo the endocytosis of sandman potassium channels, leaving too much potassium outside of neurons, causing increased excitability and the onset of seizures.

Since publication, the paper has garnered some mentions in the scientific press. It has also earned a new National Institutes of Health grant for Littleton’s lab, where they are following in Melom’s and Weiss’ footsteps to study how calcium levels in glia affect the flux of membrane proteins, not just in disease, but as a matter of course in healthy cells. And for Weiss, the paper impressed funders in Israel, providing her with the money to support her new position where she continues studying glia, calcium and seizures.

It was a hard-earned success. Though their end product is knowledge, scientists spend the vast majority of their time with the unknown. Between the lines of most every paper are years of effort in which scientists persistently asked open questions with open minds so that the evidence could lead them to a discovery they could share with the world.

Mary Gehring and Iain Cheeseman appointed to endowed professorships
Whitehead Institute
June 26, 2020

At the heart of Whitehead Institute are its Members, a group of world-class investigators who propel science forward through their research discoveries and technical advances. Recently, Whitehead Institute singled out two Members for special recognition: appointment to endowed professorships, which provide financial support for their research programs and serve as an endorsement of their scientific visions.

Whitehead Institute Member Mary Gehring, who is also an associate professor of Biology at Massachusetts Institute of Technology (MIT), has been appointed to the Landon T. Clay Career Development Chair. “Mary is an emerging superstar in plant biology and a respected leader within the Whitehead Institute community,” says Institute director David C. Page. “I know that Landon held her in high regard, and I think he would be very pleased that Mary is this chair’s first incumbent.”

Gehring recalls, “I met Landon on my very first day at Whitehead Institute. His curiosity, insight, and wide-ranging knowledge made that initial conversation absorbing — as was every subsequent discussion we had. His impact as an Institute board member was formidable, and I will hold the Clay Career Development Chair with pride.”

Gehring’s research focuses on plant epigenetics — the heritable information that influences cellular function but is not encoded in the DNA sequence itself. Primarily using the model plant Arabidopsis thaliana, Gehring has determined that altering the methylation state of a single gene is sufficient to cause changes in seed weight and in the timing of certain aspects of seed development. Methylation patterns can be passed from one cell generation to the next and from one plant to its offspring. By studying the epigenetic difference between multiple generations of plants, Gehring seeks to learn if epigenetic responses to environmental factors can ultimately lead to evolutionary changes. Her work has tremendous implications for addressing food security in a period of significant climate change.

Institute Member Iain Cheeseman has been appointed to the Margaret and Herman Sokol Chair in Biomedical Research. He succeeds Member and former director Gerald Fink, who held the chair since it was established in 2006. “Iain is an extraordinary scientist, a dedicated teacher, and a wonderful colleague,” says Page. “He is, therefore, the perfect person to succeed Gerry in the Sokol Chair.”

“This is a great honor,” says Cheeseman, who is also a professor of Biology at MIT. “I am humbled to hold a chair named for Margaret and Herman Sokol, who were among Whitehead Institute’s earliest and most ardent supporters; and a chair that has so long been associated with Gerry Fink.”

Cheeseman’s research focuses on the kinetochore — a central player in directing chromosome segregation — which comprises more than 100 different proteins. Although the kinetochore’s importance has long been appreciated, the molecular basis for its many activities remains poorly understood. His lab has helped identify dozens of the kinetochore’s molecular components and their specific roles, and is defining how the attachments between kinetochores and spindle microtubules are regulated throughout cell division. Because many cancers may be driven by errors in chromosome segregation, Cheeseman’s studies may inform cancer research — and may contribute to development of more effective treatments for leukemia and other diseases.

Earlier this spring, Whitehead Institute announced appointments to two other endowed chairs.

Cell biologist Jonathan Weissman, who recently became a Member, is the inaugural incumbent of the Landon T. Clay Chair of Biology at Whitehead Institute. And in September 2020, developmental biologist Yukiko Yamashita will join the Institute and become the inaugural incumbent of the Susan Lindquist Chair for Women in Science at Whitehead Institute.

These muscle cells are guideposts to help regenerative flatworms grow back their eyes
Eva Frederick | Whitehead Institute
June 25, 2020

If anything happens to the eyes of the tiny, freshwater-dwelling planarian Schmidtea mediterranea, they can grow them back within just a few days. How they do this is a scientific conundrum — one that Peter Reddien’s lab at Whitehead Institute has been studying for years.

The lab’s latest project offers some insight: in a paper published in Science June 25, researchers in Reddien’s lab have identified a new type of cell that likely serves as a guidepost to help route axons from the eyes to the brain as the worms complete the difficult task of regrowing their neural circuitry.

Schmidtea mediterranea’s eyes are composed of light-capturing photoreceptor neurons connected to the brain with long, spindly processes called axons. They use their eyes to respond to light to help navigate their environment.

The worms, which are popular models for research into regeneration, can regrow pretty much any part of their body; eyes are an interesting part to study because regenerating the visual system requires the worms rewire their neurons to connect them to the brain.

When neural systems develop in embryos, the first nerve fibers, called pioneer axons, snake their way through tissue to form the circuitry needed to perceive and interpret external stimuli. The axons are helped along their way by specialized cells called guidepost cells. These special cells are positioned at choice points — places where the axon’s path could fork in different directions.

In many organisms, these guidepost cells aren’t a priority anymore once development is finished, and typically are not renewed through adulthood. That’s one reason why, when humans experience brain or nerve damage, the injury is usually permanent.

“This is a fundamental mystery of regeneration that we hadn’t even been thinking about,” says Reddien, the senior author of the paper who is also a professor of biology at Massachusetts Institute of Technology and an investigator with the Howard Hughes Medical Institute. “How can an adult animal regenerate a functional nervous system when the original development of the nervous system typically involves a number of cues that are thought to be transient?”

Then, in 2018, Reddien Lab scientist Lucila Scimone found something surprising in adult planarians: groups of mysterious cells that looked like they might play a role in guiding growing axons. She’d noticed this group of cells because they co-expressed two genes not often seen together and some were conspicuously close to the eyes.

“I was captivated by these cells,” she says. They appeared in very small numbers (a normal worm might have around 5; a large one might have up to 10) in every planarian she examined. They were divided into two distinct groups: some around the flatworms’ eyes, and others spaced out along the path to the brain center. When she traced the path of existing axons leading from the planarians’ eyes to their brain, they coincided with the positions of these cells without exception.

When the researchers characterized the cells, they found that they did not express any of the genes that are hallmarks of photoreceptor neurons; instead, they had markers often found in muscle tissue. “That was very striking, because muscle cells — that’s not what they do in most animals,” Scimone says.

In other organisms, guidepost cells are often neurons or glia. It would be unusual for muscle cells to serve as guideposts; but past work in the Reddien Lab had shown that planarian muscle cells played other special roles, such as secreting the extracellular matrix. The researchers now wondered whether they could add the role of guidepost to the long list of planarian muscle cell functions.

To test their hypothesis, the researchers designed a series of experiments. “We developed an eye transplantation method where you can take an eye from an animal and transplant it into another animal,” says Reddien Lab postdoc Kutay Deniz Atabay. “When you do this, the axonal projections from that eye will basically, if positioned appropriately, correctly wire themselves into the brain, producing a functional state.”

The researchers also created genetically engineered planarians that had the muscle cells, but no eyes, and then transplanted eyes onto their eyeless heads. Sure enough, the neurons grew as normal, snaking towards the cells and then adjusting their trajectories after encountering them.

Without the cells, it was a different story. When the researchers transplanted eyes to distant parts of planarians’ bodies without a population of these muscle cells, the photoreceptor neurons did not connect to the brain center. Likewise, when they transplanted eyes into planarians that had been modified to not have these muscle cells, their photoreceptor neurons still grew — but they did not wire properly to reach the brain.

These findings combined suggested that the cells were fully independent of the visual system — they did not form because of eyes or photoreceptor neurons, but likely established themselves before the neurons grew — which provided more evidence for the guidepost role.

The guidepost-like activity of these cells then begged the question: how do the cells themselves know where to be? “We found that there’s a pattern of signaling molecules in muscle that is setting where these cells should be,” Reddien says. “If we perturb the global positional information of the system, these cells get placed in the wrong positions, and then axons go to the wrong positions — so we think there’s a positional information framework that places the cells during regeneration, and that allows them to work as guideposts in the correct locations.”

At this point, the researchers don’t know exactly how the cells are able to communicate with growing axons to serve as guideposts. They could be releasing some sort of signaling molecule that attracts the axons, or they could be communicating by using trans-membrane proteins.

“That will be an exciting direction for the future,” Reddien says. “We have now identified the transcriptome for the cells, which means we know all the genes that these cells express. That provides us with an intriguing list of genes that can be probed functionally, to try to see which ones are mediating the functions of these cells.”

This study is a step forward in a body of work that aims to expand the capabilities of regenerative medicine. “Imagine a scenario where someone experiences a spinal cord injury or an eye injury or stroke that leads to the loss of a neural circuit,” says Atabay. “The reason we can’t fully cure these cases today is that we lack fundamental information regarding how these systems can regenerate. Looking at regenerative organisms provides a lot of insights. From this case, we see that regenerating the lost system may not be enough; you may also need to regenerate systems that are properly patterning that system.”

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Written by Eva Frederick

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Scimone, M. L. et al. “Muscle and neuronal guidepost-like cells facilitate planarian visual system regeneration.” Science, June 25, 2020.