Author: Raleigh McElvery

A computational approach to cancer

Toni-Ann Nelson transformed remote summer research into an opportunity to learn a new set of tools for analyzing tumors.

Raleigh McElvery
August 20, 2020

Toni-Ann Nelson has wanted to find a cure for cancer ever since she was nine years old and lost her grandfather to the disease. “I remember thinking there must be something that the doctors and scientists were missing,” she recalls. “It just couldn’t be that complicated.” Now one semester away from earning her degree in molecular biology, Nelson is realizing cancer is just that — complicated. After conducting cancer research during MIT’s Summer Research Program in Biology (MSRP-Bio), she understands much more about the intricacies of tumors and metastasis. But she’s also glimpsed just how many cellular puzzles remain to be solved.

Growing up in Jamaica, Nelson enjoyed all her science classes, but preferred biology because she knew it would provide the foundation to probe cancer. She graduated as the valedictorian of her high school class, and earned a scholarship to Alcorn State University in Mississippi, where she began in the spring of 2017.

Alcorn doesn’t have any cancer research facilities, so Nelson secured a position as an undergraduate researcher in Yan Meng’s plant tissue culture lab. For three years, Nelson aimed to improve viral disease resistance in sweet potatoes. Even though she wasn’t conducting clinical research, she mastered key molecular biology techniques like PCR, gel electrophoresis, and tissue culture.

“Fundamental research is important because many times finding a cure requires starting with the basics, and understanding what’s going on inside the cell,” she says.

When Nelson was accepted into MSRP-Bio as a Gould Fellow and assigned to work in Tyler Jacks’ lab, she was elated to get her first hands-on cancer research experience. But in April 2020 — two months before the program was slated to begin — MIT’s campus temporarily shut down due to the COVID-19 pandemic, and MSRP-Bio 2020 became a remote learning experience.

As a result, Nelson and her MSRP-Bio cohort conducted their research from home. She took on a computationally-intensive project that was conducive to remote work and required taking an online quantitative methods class. In a manner of weeks, she learned an entirely new set of skills, including programming languages like Python.

“I always thought that I wouldn’t need those types of computational tools as part of my cancer research,” she explains. “But working at MIT was enlightening, because it showed me that they are key to understanding disease. I can definitely see myself using them on my own projects in the future.”

Pink and purple histology image
Light micrograph of a lung adenocarcinoma. Credit: Vasilena Gocheva/Jacks Lab, Koch Institute

The Jacks lab studies the genetic events that contribute to cancer, and Nelson’s project centered on lung adenocarcinoma. The predominant form of non-small cell lung cancer, it begins in alveolar type II (AT2) cells. Past studies showed that, as the tumor progresses, AT2 cells change state and lose their original identity. Nelson wanted to determine which genes and proteins underlie this evolution. Her analyses showed that genetic markers characteristic of AT2 cells tend to decrease over time, while markers denoting faster-growing “high grade” tumors become more prevalent.

“The kinetics of these gene expression changes that are happening early on are still poorly understood,” she explains. “It just goes to show how complicated this pathology is, which I find even more fascinating.”

Once researchers can pinpoint the genes and proteins that drive changes in cancer cell state, they’ll be better equipped to design drugs that target and prevent metastatic processes.

Although Nelson couldn’t visit the lab in person, as on-campus research slowly began ramping up again, her graduate student mentor Amanda Cruz would show her around during their video conference calls. Cruz also helped Nelson explore the scientific literature, choose studies for the lab’s journal club, and perform computational analyses.

Given the unprecedented circumstances, Nelson says having a solid support system was key to her success. Nelson and her MSRP cohort also relied on one another for encouragement, and were each assigned a graduate student “pal” for guidance outside of lab.

“The program catered to our every need, and it’s structured to ensure that someone will always check up on you if you’re feeling alone,” Nelson says. “I never expected to get so much from this experience, especially because I’m not physically on campus. But what I learned this summer was so much more than I could ever have anticipated.”

Her time in the Jacks lab has solidified her fervor for cancer research, and she intends to apply to cancer biology PhD programs in order to continue this line of inquiry. “I’ve realized there’s still so much more to learn,” she says, “but we’re getting there.”

Top image courtesy of Toni-Ann Nelson
Posted: 8.19.20
Solving molecular mysteries

Diego Detrés spent the summer probing protein function and collaborating with MIT researchers remotely from his home in Puerto Rico.

Raleigh McElvery
August 17, 2020

When he was young, Diego Detrés wanted to become a magician in order to learn the tricks of the trade and transform enigma into fact. Now a fourth-year industrial microbiology major at University of Puerto Rico at Mayagüez, he’s on track to become a researcher while chasing a similar aim. To Detrés, the complex biological processes that continue to stump researchers are akin to acts of magic — although deciphering them is much more complicated than pulling a rabbit out of a hat. As a participant in MIT’s Summer Research Program in Biology (MSRP-Bio), he’s getting closer to parsing the mechanisms behind molecular mysteries.

After his magician phase but before developing an affinity for biology, Detrés was on track to become a professional boxer in Puerto Rico. In high school, he spent hours each night reading about nutrition to supplement his training. Before long, he found himself entranced by the intricacies of the metabolic processes that allow cells to convert food into energy.

At the University of Puerto Rico at Mayagüez, he wanted to continue exploring biology and focus on medicine. “My plan was to become a doctor, because I thought that’s what you do with a biology degree,” he says. “It also seemed like the best way to make an impact on people’s lives.”

But Detrés’ first semester was cut short when hurricane Maria tore through Puerto Rico in September 2017. His spring classes were canceled as the island reeled in the aftermath, so he joined a relief project headed by his university to bring help and legal aid to local communities. “It wasn’t scientific research, but it did show me that understanding a problem is critical to finding an effective solution,” he recalls. “It also allowed me to explore other ways in which I could impact other people.”

Group photo
Detrés (third from left) and his undergraduate research mentor, Carlos Ríos Velázquez (fourth from left)

Detrés’ first lab experience came the next summer at the University of Minnesota, where he studied the genetics of maize. That internship affirmed his interest in biology but shifted his gaze away from medicine and towards fundamental research.

“I really liked being at the bench,” he says. “I fell in love with working in lab and basic science. It’s fundamental knowledge that’s important for the building blocks of science; you might discover something today that will help a lot of people later on.”

When he returned home to the University of Puerto Rico at Mayagüez that August, Detrés was accepted into the Maximizing Access to Research Careers (MARC) Program, which is sponsored by the National Institute of General Medical Sciences and provides research-related opportunities and a special science curriculum. He joined the lab of Carlos Ríos Velázquez, investigating novel antibiotic resistance genes within the gut microbiome of the Caracolus marginella snail, and helping Ríos Velázquez teach biology workshops to high school students.

“He gave me a background in science when I didn’t have one, and I want to do the same for other people,” Detrés says. “I hope to teach eventually.”

In January 2020, Detrés was invited to come to MIT for the annual Quantitative Methods Workshop, a seven-day boot camp that introduces students to tools for analyzing experimental data. He enjoyed the “feel” of campus, and decided to apply to MSRP-Bio in hopes of returning in June.

Although the Covid-19 pandemic prevented the Institute from hosting in-person summer programs, Detrés has been gleaning the MIT experience from his apartment in Puerto Rico. His days are filled with Zoom meetings featuring faculty and graduate student talks, group hangouts, informal exercise sessions, musical jams, and cooking classes. He was also named a 2020 MSRP-Bio Gould Fellow. “Even remotely, I’ve gotten to know the MSRP cohort really well, and the faculty have been very interactive,” he says.

He’s been conducting research in Eliezer Calo’s lab for the past two months, running literature searches and bioinformatic analyses. Like Detrés, Calo grew up in Puerto Rico and attended MSRP-Bio. Now, Calo is a professor in MIT’s Department of Biology. His lab investigates RNA metabolism to inform developmental disorders and cancer research.

Detrés is focusing on a family of RNA helicases called DEAD-box ATPases, or “DDXs,” which are involved in every step of RNA metabolism. These proteins are conserved across many species, and contain a core amino acid sequence that helps catalyze reactions with other molecules in the cell.

However, the Calo lab suspects that the less-conserved sequences near the ends of the proteins may be more critical for specialized function. Detrés is investigating what it is about these terminal sequences that determines DDXs’ specific roles in RNA metabolism.

Student with Bunsen burner
Detrés in the Ríos Velázquez lab at the University of Puerto Rico at Mayagüez

This summer, he showed that DDX proteins are more likely to lack a stable structure near one end, known as the C-terminus, compared to other closely-related helicases. These findings will help the Calo lab better understand the relationship between DDX’s functional specificity and its intrinsically disordered regions like the C-terminus.

“Most of these proteins are essential for life, and yet we don’t really know how they’re involved in so many dynamic processes,” Detrés says. “It’s been interesting to analyze already-existing data in ways that allow us to investigate novel possibilities.”

Working from home has been challenging to say the least. Not having the in-person support from his labmates has been difficult. On the other hand, spending so much time with his family has been enjoyable.

“I had to make a routine for myself that allowed me to work effectively from home, as well as maintain my physical and mental well-being,” he says. “Program activities also gave us the chance to be physically active and to interact with other students”.

Detrés aims to return for a second summer of MSRP next year, hopefully in person.

“Since starting MSRP, I’ve noticed a lot of changes in myself,” he says. “The more I get into research, even remote research, the more I realize it’s what I want to do. Science is not about being really smart; it’s about being really curious.”

As Detrés continues to follow his curiosity, the inner workings of the cell are becoming more comprehensible — but no less mesmerizing.

Photos courtesy of Diego Detrés
Posted: 8.18.20
New gene regulation model provides insight into brain development

A well-known protein family binds to many more RNA sequences than previously thought to help neurons grow.

Raleigh McElvery
August 17, 2020

In every cell, RNA-binding proteins (RBPs) help tune gene expression and control biological processes by binding to RNA sequences. Researchers often assume that individual RBPs latch tightly to just one RNA sequence. For instance, an essential family of RBPs, the Rbfox family, was thought to bind one particular RNA sequence alone. However, it’s becoming increasingly clear that this idea greatly oversimplifies Rbfox’s vital role in development.

Members of the Rbfox family are among the best-studied RBPs and have been implicated in mammalian brain, heart, and muscle development since their discovery 25 years ago. They influence how RNA transcripts are “spliced” together to form a final RNA product, and have been associated with disorders like autism and epilepsy. But this family of RBPs is compelling for another reason as well: until recently, it was considered a classic example of predictable binding.

More often than not, it seemed, Rbfox proteins bound to a very specific sequence, or motif, of nucleotide bases, “GCAUG.” Occasionally, binding analyses hinted that Rbfox proteins might attach to other RNA sequences as well, but these findings were usually discarded. Now, a team of biologists from MIT has found that Rbfox proteins actually bind less tightly — but no less frequently — to a handful of other RNA nucleotide sequences besides GCAUG. These so-called “secondary motifs” could be key to normal brain development, and help neurons grow and assume specific roles.

“Previously, possible binding of Rbfox proteins to atypical sites had been largely ignored,” says Christopher Burge, professor of biology and the study’s senior author. “But we’ve helped demonstrate that these secondary motifs form their own separate class of binding sites with important physiological functions.”

Graduate student Bridget Begg is the first author of the study, published on August 17 in Nature Structural & Molecular Biology.

“Two-wave” regulation

After the discovery that GCAUG was the primary RNA binding site for mammalian Rbfox proteins, researchers characterized its binding in living cells using a technique called CLIP (crosslinking-immunoprecipitation). However, CLIP has several limitations. For example, it can indicate where a protein is bound, but not how much protein is bound there. It’s also hampered by some technical biases, including substantial false-negative and false-positive results.

To address these shortcomings, the Burge lab developed two complementary techniques to better quantify protein binding, this time in a test tube: RBNS (RNA Bind-n-Seq), and later, nsRBNS (RNA Bind-n-Seq with natural sequences), both of which incubate an RBP of interest with a synthetic RNA library. First author Begg performed nsRBNS with naturally-occurring mammalian RNA sequences, and identified a variety of intermediate-affinity secondary motifs that were bound in the absence of GCAUG. She then compared her own data with publicly-available CLIP results to examine the “aberrant” binding that had often been discarded, demonstrating that signals for these motifs existed across many CLIP datasets.

To probe the biological role of these motifs, Begg performed reporter assays to show that the motifs could regulate Rbfox’s RNA splicing behavior. Subsequently, computational analyses by Begg and co-author Marvin Jens using mouse neuronal data established a handful of secondary motifs that appeared to be involved in neuronal differentiation and cellular diversification.

Based on analyses of these key secondary motifs, Begg and colleagues devised a “two-wave” model. Early in development, they believe, Rbfox proteins bind predominantly to high-affinity RNA sequences like GCAUG, in order to tune gene expression. Later on, as the Rbfox concentration increases, those primary motifs become fully occupied and Rbfox additionally binds to the secondary motifs. This results in a second wave of Rbfox-regulated RNA splicing with a different set of genes.

Begg theorizes that the first wave of Rbfox proteins binds GCAUG sequences early in development, and she showed that they regulate genes involved in nerve growth, like cytoskeleton and membrane organization. The second wave appears to help neurons establish electrical and chemical signaling. In other cases, secondary motifs might help neurons specialize into different subtypes with different jobs.

John Conboy, a molecular biologist at Lawrence Berkeley National Lab and an expert in Rbfox binding, says the Burge lab’s two-wave model clearly shows how a single RBP can bind different RNA sequences — regulating splicing of distinct gene sets and influencing key processes during brain development. “This quantitative analysis of RNA-protein interactions, in a field that is often semi-quantitative at best, contributes fascinating new insights into the role of RNA splicing in cell type specification,” he says.

A binding spectrum

The researchers suspect that this two-wave model is not unique to Rbfox. “This is probably happening with many different RBPs that regulate development and other dynamic processes,” Burge says. “In the future, considering secondary motifs will help us to better understand developmental disorders and diseases, which can occur when RBPs are over- or under-expressed.”

Begg adds that secondary motifs should be incorporated into computer models that predict gene expression, in order to probe cellular behavior. “I think it’s very exciting that these more finely-tuned developmental processes, like neuronal differentiation, could be regulated by secondary motifs,” she says.

Both Begg and Burge agree it’s time to consider the entire spectrum of Rbfox binding, which are highly influenced by factors like protein concentration, binding strength, and timing. According to Begg, “Rbfox regulation is actually more complex than we sometimes give it credit for.”

Citation:
“Concentration-dependent splicing is enabled by Rbfox motifs of intermediate affinity”
Nature Structural & Molecular Biology, online August 17, 2020, DOI: 10.1038/s41594-020-0475-8
Bridget E. Begg, Marvin Jens, Peter Y. Wang, Christine M. Minor, and Christopher B. Burge

Top illustration: Some RNA-binding proteins like Rbfox (gold ellipses) help tune gene expression and control biological processes by latching onto more RNA sequences (black and gold lines) as their concentration increases (teal shading). Credit: Bridget Begg
Posted: 8.17.20
Iain Cheeseman earns a Global Consortium for Reproductive Longevity & Equality (GCRLE) Scholar Award
Buck Institute
August 10, 2020

The Global Consortium for Reproductive Longevity and Equality (GCRLE) at the Buck Institute for Research on Aging, made possible by the Bia-Echo Foundation, announces its inaugural recipients of its GCRLE Scholar Awards. The 22 recipients comprise a global group who share a vision of advancing research to better understand the underlying causes of female reproductive aging. Grantees were selected by a Scientific Advisory Council composed of leaders in the fields of Aging and Reproductive Biology. Grantees range from early career scientists to established scholars in the field.

“I am incredibly excited by the potential impact for the GCRLE. The ability to convene a diverse community from across institutions will positively and constructively impact this field and move science forward in a way that simply would not be possible otherwise,” says GCRLE Pilot Award recipient Iain Cheeseman, PhD, of the Whitehead Institute for Biomedical Research at MIT. GCRLE Junior Scholar Award recipient Lynae Brayboy, MD of Charité-Universitätsmedizin, Berlin adds, “I think reproductive scientists can often exist in isolation and don’t have the unique experience GCRLE is fostering…I think it also very challenging for physician scientists to find support in the field of reproductive aging and reproductive biology in general.”

The mission of the GCRLE is to support breakthrough research on reproductive aging through funding, training, infrastructure, programs to support women in science, and a collaborative intellectual network. The GCRLE network will enable grantees and all consortium members to pursue support and collaboration across multidisciplinary approaches and institutions, thereby establishing a foundation on which to grow a diverse and sustainable research ecosystem.

Grants totaling $7.4 million will be awarded over 2 years, with flexibility in budgeting for maximum creativity and non-traditional support such as childcare. “We are thrilled to welcome these promising researchers as our very first grant recipients.” says Jennifer Garrison, PhD, GCRLE Faculty Director and Assistant Professor at the Buck Institute for Research on Aging. “The GCRLE unites two disciplines – reproductive science and geroscience – in an unprecedented way to investigate an area of biology that has tangible societal and clinical implications. Our goal is to foster truly bold, innovative scientists with the potential to transform the field. Beyond funding, we are building an infrastructure to grow a vibrant community and developing creative programs to break down gender barriers in scientific research careers. This is the beginning of something big!”

The GCRLE is anchored at the Buck’s Center for Female Reproductive Longevity and Equality which was established in 2018 with a gift from attorney and entrepreneur Nicole Shanahan. The Center is the first research facility in the world focused solely on reproductive equality and ovarian aging, a key determinant not only of fertility but of overall health and longevity. The GCRLE was established in 2019 with a gift from Shanahan’s Bia-Echo Foundation to build the global ecosystem for this new and exciting field of research.

2020 Inaugural GCRLE Scholars

The Senior Scholar Award supports established investigators who are thought leaders in their fields and are recognized for substantial contributions of creative and productive research.

2020 Senior Scholar Award Recipients:

Holly Ingraham, Ph.D.
University of California, San Francisco
“Identifying Novel Drivers in Central Control of Female Reproduction”

Coleen Murphy, Ph.D.
Princeton University
“Defining a “Clock” for Female Reproductive Decline”

Mary Zelinski, Ph.D.
Oregon Health & Science University
“Interventions for Ovarian Aging”

The Junior Scholar Award supports newly independent investigators with outstanding promise as they are establishing their own labs.

2020 Junior Scholar Award Recipients:

Bérénice Benayoun, Ph.D.
University of Southern California
“Establishing new age-relevant mouse models of menopause”

Lynae Brayboy, M.D.
Charité – Universitätsmedizin, Berlin
“Dysfunctional MDR-1 disrupts mitochondrial homeostasis in the oocyte”

Ingrid Fetter-Pruneda, Ph.D.
Universidad Nacional Autónoma de México
“The molecular and cellular basis of high fecundity in social insects”

Amanda Kallen, M.D.
Yale University
“Ovarian Senescence as a Novel Driver of Female Reproductive Aging”

The Pilot Award is designed to foster innovative collaborative or novel research projects that have the potential for high impact and high reward at an accelerated rate.

Pilot Award Recipients:

Ivana Celic, Ph.D.
Tulane University
“LINE1 Retrotransposons in Female Reproductive Aging”

Iain Cheeseman, Ph.D.
Whitehead Institute/MIT
“Analyzing centromere rejuvenation during female reproductive aging”

Marco Conti, M.D.
University of California, San Francisco
“mRNA translation program and oocyte aging”

Arjumand Ghazi, Ph.D.
University of Pittsburgh
“Genetic & Chemical Modulation of Splicing to Combat Reproductive Senescence”

Polina Lishko, Ph.D.
University of California, Berkeley
“Endocannabinoid signaling in the mammalian ovary and reproductive longevity”

Zita Santos, Ph.D., Carlos Ribeiro, Ph.D.
Champalimaud Foundation, Portugal
“Metabolic reprogramming, dietary nutrients and food cravings in ovary aging”

Yousin Suh, Ph.D.
Columbia University
“Genetic Control of Ovarian Aging in Humans”

The Postdoctoral Scholar Award supports training imaginative junior scientists who will lead the next generation of reproductive aging researchers.

2020 Postdoctoral Scholar Award Recipients:

Cristina Quesada Candela, Ph.D.
University of Pittsburg​
“Proteasomal Targets Driving Meiotic Failure During Reproductive Aging”

Ana Milunovic Jevtic, Ph.D., D.V.M.
University of California, Berkeley
“The role of endocannabinoid hydrolase ABHD2 in the ovarian aging”

Gul Bikem Soygur Kaya, Ph.D.
University of California, San Francisco
“How duration of meiotic prophase affects development and aging of oocytes”

Min Hoo Kim, Ph.D.
University of Southern California
“Elucidating causal effects of the microbiome on reproductive aging”

Seungsoo Kim, Ph.D.
Columbia University Medical Center
“Integrative bioinformatic analysis of human ovarian aging and healthspan”

Olfat Malak, Ph.D.
Buck Institute for Research on Aging
“Role of sympathetic transmission in the regulation of ovarian aging”

Farners Amargant i Riera, Ph.D.
Northwestern University
“Targeting fibrosis and inflammation to extend reproductive longevity”

Zijing Zhang, Ph.D.
University of Arkansas for Medical Sciences
“The impact of ovarian macrophage population on mouse ovarian aging”

About the Global Consortium for Reproductive Longevity and Equality

The Buck Institute, through the generous support of the Bia Echo Foundation, has launched a novel, global collaborative Consortium dedicated to facilitating and accelerating research on female reproductive longevity and equality. The end of fertility sets off a cascade of negative health effects in a woman’s body. As a society, every aspect of a woman’s life is influenced by the fact that reproductive capacity is limited — overall health, family planning, career decisions. The downstream consequences are clear, but why women undergo a precipitous decline in fertility at midlife and what sets it in motion are a mystery. Despite its profound impact on health and well-being, female reproductive aging is an understudied topic.

The Global Consortium for Reproductive Longevity and Equality (GCRLE) is advancing research to better understand the underlying causes of female reproductive aging. This has implications for everyone – we think that understanding the limits on reproductive capacity will provide important clues about aging in other tissues.  Through funding, collaboration, and innovation, we hope to accelerate the pace of discovery and inform the path to intervention. We believe we can profoundly alter the societal balance toward equality for women by defining what leads to menopause and developing interventions to slow or reverse it. Our goal is to build the field to understand the basic biological mechanisms that trigger female reproductive senescence, from the earliest stages through to menopause, and ultimately leverage this understanding to intervene and balance the scales.  Contact info@gcrle.org for more information and to find out how to join the GCRLE today! https://buckinstitute.org/gcrle/

About the Buck Institute for Research on Aging

Our success will ultimately change healthcare. At the Buck, we aim to end the threat of age-related diseases for this and future generations by bringing together the most capable and passionate scientists from a broad range of disciplines to identify and impede the ways in which we age. An independent, nonprofit institution, our goal is to increase human health span, or the healthy years of life. Globally recognized as the pioneer and leader in efforts to target aging, the number one risk factor serious diseases including Alzheimer’s, Parkinson’s, cancer, macular degeneration, heart disease, and diabetes, the Buck wants to help people live better longer.  Learn more at: https://buckinstitute.org

About the Bia-Echo Foundation

Bia-Echo Foundation is a private foundation, founded by Nicole Shanahan that aims to accelerate social change in order to establish a fair and equitable society for future generations to thrive. We invest in changemakers at the forefront of innovation who are tackling some of the world’s greatest challenges within our core areas of equality-based investment:  Reproductive Longevity & Equality, Criminal Justice Reform and Healthy and Livable Ecosystems. https://www.biaecho.org

To distinguish contexts, animals think probabilistically, study suggests
Picower Institute
August 3, 2020

Among the many things rodents have taught neuroscientists is that in a region called the hippocampus, the brain creates a new map for every unique spatial context – for instance, a different room or maze. But scientists have so far struggled to learn how animals decide when a context is novel enough to merit creating, or at least revising, these mental maps. In a study in eLife, MIT and Harvard researchers propose a new understanding: The process of “remapping” can be mathematically modeled as a feat of probabilistic reasoning by the rodents.

The approach offers scientists a new way to interpret many experiments that depend on measuring remapping to investigate learning and memory. Remapping is integral to that pursuit, because animals (and people) associate learning closely with context, and hippocampal maps indicate which context an animal believes itself to be in.

“People have previously asked ‘What changes in the environment cause the hippocampus to create a new map?’ but there haven’t been any clear answers,” said lead author Honi Sanders. “It depends on all sorts of factors, which means that how the animals define context has been shrouded in mystery.”

Sanders is a postdoc in the lab of co-author Matthew Wilson, Sherman Fairchild Professor in The Picower Institute for Learning and Memory and the departments of Biology and Brain and Cognitive Sciences at MIT.  He is also a member of the Center for Brains, Minds and Machines. The pair collaborated with Samuel Gershman, a professor of psychology at Harvard on the study.

Fundamentally a problem with remapping that has frequently led labs to report conflicting, confusing, or surprising results, is that scientists cannot simply assure their rats that they have moved from experimental Context A to Context B, or that they are still in Context A, even if some ambient condition, like temperature or odor, has inadvertently changed. It is up to the rat to explore and infer that conditions like the maze shape, or smell, or lighting, or the position of obstacles, and rewards, or the task they must perform, have or have not changed enough to trigger a full or partial remapping.

So rather than trying to understand remapping measurements based on what the experimental design is supposed to induce, Sanders, Wilson and Gershman argue that scientists should predict remapping by mathematically accounting for the rat’s reasoning using Bayesian statistics, which quantify the process of starting with an uncertain assumption and then updating it as new information emerges.

“You never experience exactly the same situation twice. The second time is always slightly different,” Sanders said. “You need to answer the question: ‘Is this difference just the result of normal variation in this context or is this difference actually a different context?’ The first time you experience the difference you can’t be sure, but after you’ve experienced the context many times and get a sense of what variation is normal and what variation is not, you can pick up immediately when something is out of line.”

The trio call their approach “hidden state inference” because to the animal, the possible change of context is a hidden state that must be inferred.

In the study the authors describe several cases in which hidden state inference can help explain the remapping, or the lack of it, observed in prior studies.

For instance, in many studies it’s been difficult to predict how changing some of cues that a rodent navigates by in a maze (e.g. a light or a buzzer) will influence whether it makes a completely new map or partially remaps the current one and by how much. Mostly the data has showed there isn’t an obvious “one-to-one” relationship of cue change and remapping. But the new model predicts how as more cues change, a rodent can transition from becoming uncertain about whether an environment is novel (and therefore partially remapping) to becoming sure enough of that to fully remap.

In another, the model offers a new prediction to resolve a remapping ambiguity that has arisen when scientists have incrementally “morphed” the shape of rodent enclosures. Multiple labs, for instance, found different results when they familiarized rats with square and round environments and then tried to measure how and whether they remap when placed in intermediate shapes, such as an octagon. Some labs saw complete remapping while others observed only partial remapping. The new model predicts how that could be true: rats exposed to the intermediate environment after longer training would be more likely to fully remap than those exposed to the intermediate shape earlier in training, because with more experience they would be more sure of their original environments and therefore more certain that the intermediate one was a real change.

The math of the model even includes a variable that can account for differences between individual animals. Sanders is looking at whether rethinking old results in this way could allow researchers to understand why different rodents respond so variably to similar experiments.

Ultimately, Sanders said, he hopes the study will help fellow remapping researchers adopt a new way of thinking about surprising results – by considering the challenge their experiments pose to their subjects.

“Animals are not given direct access to context identities, but have to infer them,” he said. “Probabilistic approaches capture the way that uncertainty plays a role when inference occurs. If we correctly characterize the problem the animal is facing, we can make sense of differing results in different situations because the differences should stem from a common cause: the way that hidden state inference works.”

The National Science Foundation funded the research.

This molecule helps sweet-toothed protein complex sense sugar
Eva Frederick | Whitehead Institute
July 28, 2020

In order to grow and thrive, cells need sugar. A repertoire of cellular mechanisms turn unwieldy molecules of glucose and fructose into versatile building blocks for making useful molecules such as lipids, and energy to fuel necessary processes in the cell. But for any of these things to happen, the cells need to sense when sugars are present in the first place — and scientists are still unraveling how they do it.

Now, in a new paper online July 27 in Nature Metabolism, researchers in the lab of Whitehead Institute Member David Sabatini, identify a key molecule that signals to the cell’s growth-triggering complex mTORC1 when there is sugar to be had, leading to a metabolic response. “This discovery puts us another step closer to understanding the biology of mTORC1 and its effects on cellular growth and metabolism,” said Sabatini, who is also a professor of biology at Massachusetts Institute of Technology and investigator with the Howard Hughes Medical Institute.

mTORC1 — short for “mechanistic target of rapamycin complex 1” — is a complex of proteins involved in regulating cell growth and metabolism. Jose Orozco, a fifth-year M.D./Ph.D student in Sabatini’s lab, describes mTORC1 as a sort of cellular licensing board. In order for other parts of the cell to grow and create new products, they must first be “approved” by mTORC1. If there are enough building blocks in the cell to create a certain product, mTORC1 will add a phosphate group to the appropriate “builders” — a signal that allows the building to begin.

“The builders in this case are metabolic pathways responsible for the creation of proteins, the regulation of nucleotides, regulation of glycolysis, regulation of fatty acid synthesis,” he says. “None of these builders can sense everything. But mTORC1 can, and it makes this sort of unified decision for the cell, ‘Yes, we have everything we need to grow.’”

One essential component for cellular building is glucose. That means mTORC1 has a sweet tooth by necessity: the complex is only active when there is enough glucose in the cell. When there’s glucose to go around, mTORC1 is “on” and binds to a lysosome, a structure that serves as the cell’s “digestive system”, where it perches to perform its phosphorylation duties. When a cell is starved for glucose, the complex falls off the lysosome, inactive.

Since the early 2010s, scientists have known one way that mTOR proteins sense glucose: when there is no glucose available, the cell inhibits the action of mTORC1 through a pathway involving the protein AMPK. But another study suggested that even without AMPK, mTORC1 can still sense an absence of glucose. “I think a lot of people had written it off as ‘Oh, [the signal] must just be AMPK,’” Orozco says. “But when we tested that hypothesis, we showed that even cells that didn’t have any AMPK were still able to sense glucose availability. That was the observation that started this project.”

To find the mysterious second sugar-sensing process, Orozco and colleagues created cells in which the known signalling protein AMPK was out of the picture. Using these modified cells, they began looking for specific traits of the glucose molecule that might be triggering the response. The team found that sugars that could be broken down by the cell, such as mannose, glucosamine and fructose, were able to activate mTORC1. Non-metabolizable sugars had no effect.

This suggested that the signaling molecule was not glucose itself, but something produced when glucose is taken apart during glycolysis — the biochemical process that breaks down the sugar into usable building blocks. With this in mind, the researchers next combed step by step through glycolysis products to see which ones could be the signal molecule.

The team identified a step of glycolysis that seemed to be key, zeroing  in on a glycolysis product called dihydroxyacetone phosphate, or DHAP. Even in the complete absence of glucose, the researchers could turn on mTORC1 by adding DHAP.

It is difficult to prove exactly why the cell relies on DHAP as a signal, but Orozco has some ideas. For one thing, DHAP later goes on to serve as the backbone of lipids, which are built by a process controlled by mTORC1 — so it would make sense that mTORC1 would respond to its presence or absence. Also, DHAP levels are extremely sensitive to changes in the amount of cellular glucose, more so than any other glycolysis intermediary. Also, DHAP is a product of both glucose and fructose, which are both important sugars in the human diet.

In the future, the team hopes to understand more. “We don’t know the biochemical details of how DHAP [conveys its message],” Orozco says. “We don’t know the sensor, we don’t know what proteins bind it, and we don’t know if that causes conformational changes in [associated proteins]. That we sort of leave as the enticing next question that we want to tackle.”

At the moment, studying the glucose sensing pathway is purely foundational research. But while there are no clear applications yet, surprises could lurk just around the corner. “Targeting nutrient sensing in mTOR has shown some promise in, of all things, regulating depression and mood,” Orozco says. “That’s interesting, and we don’t really understand why that is the case. How is glucose targeting going to be important? We don’t know yet. But we think it has a lot of potential.”

***

Written by Eva Frederick

Citation:

Orozco, J.M., Krawczyk, P.A., Scaria, S.M. et al. Dihydroxyacetone phosphate signals glucose availability to mTORC1. Nat Metab (2020). https://doi.org/10.1038/s42255-020-0250-5

A recipe for cell fitness

Researchers determine how much of an enzyme is ‘just enough’ to keep a cell healthy and growing.

Raleigh McElvery
July 28, 2020

What ratio of ingredients makes a healthy cell? Researchers know which components are required for proper function, but they’re still working to understand what happens when there’s too much of one protein or not enough of another. As a graduate student in Gene-Wei Li’s lab, Darren Parker PhD ’20 spent years tweaking the recipe for a bacterial cell, adding more or less of one enzyme, aminoacyl-tRNA synthetase (aaRS). He wanted to know: How much aaRS is “just right” for bacterial cells? His findings were published in Cell Systems on July 28.

tRNAs, or transfer RNAs, carry amino acids to the ribosome to help produce proteins. But first, aaRSs must “charge” the tRNAs by attaching an amino acid to them. In doing so, aaRSs not only help the cell make proteins and grow; they also ensure the levels of “uncharged” tRNAs lacking amino acids don’t rise too high, as too many of them can trigger stress responses that slow cell growth. Parker and his collaborators predicted that tinkering with aaRS levels would uncover one of two possible scenarios. Perhaps cells tune their aaRS production to minimize the amount of uncharged tRNAs present. Alternatively, aaRS production could be dictated by the rate of protein synthesis necessary for cell growth — even if that means accumulating uncharged tRNAs.

The researchers determined the latter was true: cells make “just enough” aaRSs to optimize protein production and cell growth. This delicate balance was easily upset when too few aaRSs were produced, cueing the stress responses to kick in and slow growth. Although excess aaRSs reduced the amount of uncharged tRNA, it also hindered cell growth. The researchers determined that the cellular circuits in charge of controlling and sensing tRNA charging are collectively tuned to optimize bacterial growth.

“These results demonstrate that cells have delicately balanced the costs and benefits of producing their proteins,” Parker says. “Understanding the driving forces behind protein production is important for better understanding disease processes, and engineering cells to perform new functions.”

Proteins and labs come together to prevent Rett syndrome
Greta Friar | Whitehead Institute
July 22, 2020

New discoveries about the disruption of condensates in the neurodevelopmental disorder Rett syndrome provide insights into how cells compartmentalize chromosomes as well as new potential paths for therapies.

Scientists have, for many years, conceptualized the cell as a relatively free-flowing space, where–apart from the organization provided by specific cellular structures–molecules float freely, somehow ultimately ending up in the right place at the right time. In recent years, however, scientists have discovered that cells have much more spatial organization than previously thought thanks to a mechanism called phase separation, which occurs in cells when certain molecules form large droplet-like structures that separate what’s inside of the droplet from the rest of the cell. The droplets, called condensates, help sequester and concentrate molecules in specific locations, and appear to increase the efficiency of certain cellular functions.

Whitehead Institute Member Richard Young, also a professor of biology at Massachusetts Institute of Technology (MIT), has been exploring the previously unknown role that condensates play in gathering the molecules needed for gene transcription–the process by which DNA is read into RNA. In order to better understand when and how cells use phase separation, Charles Li, a graduate student in Young’s lab, set out to identify more proteins that can form condensates. That search led him to MeCP2, a protein associated with the severe neurodevelopmental disorder Rett syndrome, studied by Young’s colleague at Whitehead Institute, Founding Member Rudolf Jaenisch, who is also a professor of biology at MIT. No cure for Rett syndrome currently exists, and Jaenisch’s lab has been investigating the biology of the disorder in the hopes of discovering a medical therapy that can rescue neurons affected by Rett syndrome.

With the discovery of MeCP2’s condensate forming ability, Young and Jaenisch saw the opportunity for a promising collaboration between their labs. Led by co-first authors Li and Eliot Coffey, another graduate student in Young’s lab, the two labs investigated MeCP2 and whether the disruption of its condensate-forming ability contributes to Rett syndrome. During these investigations, the researchers also uncovered how cells may use condensates to help organize the active and inactive parts of chromosomes. Their findings, published in the journal Nature on June 22, report on these insights and suggest new paths for developing therapies for Rett syndrome.

PHASE SEPARATION AND RETT SYNDROME

Proteins that form condensates often contain intrinsically disordered regions (IDRs), long spaghetti-like strands that transiently stick together to form a dynamic mesh. Research has historically focused on the structured regions of proteins, which bind very specifically to other molecules, while IDRs have largely been overlooked. In this case, MeCP2’s large IDRs were exactly what drew Li to it.

“What was striking to me was that this protein has been studied for decades, and so much function has been ascribed to the protein as a whole, yet it only has one structured domain with a recognized function, the DNA binding domain. Beyond that, the entire protein is disordered, and how its parts function was largely unknown,” Li says.

The researchers found that MeCP2 used its IDRs to glom together and form condensates. Then they tested many of the mutations in the MECP2 gene that are associated with Rett syndrome and found that they all disrupt MeCP2’s ability to form condensates. Their findings suggest that therapies targeting condensates associated with the protein, rather than the protein itself, may be promising in the hunt for a Rett syndrome treatment.

“MeCP2 and Rett syndrome have been studied intensely for many years in many labs and yet not a single therapy has been developed. When the project began, I was immediately fascinated by the idea that we might find a new disease mechanism that could help us finally understand how Rett syndrome arises and how it could be treated,” Coffey says.

“Rick [Young] has shown that condensates play key roles in maintaining normal cellular function, and our latest collaboration illuminates how their disruption may drive diseases such as Rett syndrome,” Jaenisch says. “I hope the insights we have gained will prove useful both in our continued search for a treatment for Rett syndrome and more broadly in research on condensates and disease.”

COMPARTMENTALIZING CHROMOSOMES

The researchers’ investigation into MeCP2’s condensate forming behavior also shed light on how chromosomes are organized into regions of active and inactive genes. When MeCP2 is functioning normally, it helps to maintain heterochromatin, the roughly half of our chromosomes where genes are “turned off,” unable to be read into RNA or further processed to make proteins. MeCP2 binds to sequences of DNA marked with a certain type of regulatory tag that is typically found in heterochromatin. This helps crowd MeCP2 to the threshold concentration needed to form heterochromatin condensates. These condensates, in turn, help to sequester the molecules needed to maintain it apart from euchromatin, the half of our chromosomes filled with active genes. Different proteins form condensates near euchromatin, concentrating the molecular machinery needed to transcribe active genes there.

Since condensates form when proteins with large spaghetti-like IDRs stick together, one might expect that any protein containing IDRs could interact with any other IDR-containing protein to form droplets, and that is what the researchers have often seen. However, what they observed with MeCP2, which is associated with heterochromatin, is that key condensate-forming proteins associated with euchromatin refused to mix.

It’s important for the health of the cell that the genes in heterochromatin not be inadvertently turned on. The researchers reason that discrete euchromatin and heterochromatin condensates may play a key role in ensuring that transcriptional machinery localizes to euchromatin only, while repressive machinery–like MeCP2–localizes to heterochromatin. The researchers are excited to turn their attention to how proteins are able to join condensates selectively, and when and where else in the cell they do so.

“There’s a chemical grammar waiting to be deciphered that explains this difference in the ability of some proteins to move into one condensate versus another,” Young says. “Discovering that grammar can help us understand how cells maintain the crucial balance between the active and silent halves of our genome, and it could help us understand how to treat disorders such as Rett syndrome.”

***

Written by Greta Friar

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

Rudolf Jaenisch’s primary affiliation is with Whitehead Institute for Biomedical Research, where his laboratory is located and all his research is conducted. He is also a professor of biology at Massachusetts Institute of Technology.

Li, C.H., Coffey, E., et al. (2020). MeCP2 links heterochromatin condensates and neurodevelopmental disease. Nature. DOI: 10.1038/s41586-020-2574-4