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Computing changes in cell fate

Meena Chakraborty ’19 has spent two years in the lab of Nobel Prize winner Philip Sharp, combining computer science and wet lab techniques to study the impact of microRNAs on gene expression.

Raleigh McElvery
May 2, 2018

When Meena Chakraborty was eleven years old, her parents took her to South Africa to show her what life was like outside her hometown of Lexington, Massachusetts. The trip was first and foremost a family vacation, but what struck Chakraborty, now a junior at MIT, was neither the sights nor safaris, but their visit to a children’s hospital. Looking back, she identifies that experience as the catalyst that spurred her current career path, centered on three years of biology research with implications for human health.

“I remember being astounded that the patients there were my age,” she says. “I had all these things in my life to look forward to, while they were fighting HIV and might not survive. That’s when I started thinking that I could do something to counter disease, and studying biology seemed like the best way to do that.”

Up until that point, she’d intended to be a writer. So when it came time to choose a college, she initially shied away from MIT, fearing it would be too “tech-focused.”

“Even though I was primarily interested in biology, I still wanted diversity in terms of the academic subjects and the people around me,” she says. “But it became clear that MIT really encourages you to step outside your major. Every undergrad has to complete a Humanities, Arts, or Social Sciences concentration, and I chose philosophy. Those classes have become a staple of my undergrad experience, and allowed me to keep in touch with my love for writing while still focusing on my science.”

Given her propensity for math, she declared Course 6-7 (Computer Science and Molecular Biology), as a means to develop analytical tools to decipher large data sets and better understand biological systems. The summer after her freshman year, she had her first chance to marry these two skills in a real-world setting: she began working in the lab of Nobel Prize winner Philip Sharp, located in the Koch Institute for Integrative Cancer Research.

This was her first foray into computational biology, but it wasn’t her first time at the Koch — she’d shadowed two graduates students in the Irvine lab for a summer as a junior in high school. This time, though, as an undergraduate, she was assigned her own project, under the guidance of postdoctoral fellow Salil Garg. Together, they’ve studied a type of RNA known as microRNA (miRNA) for the past two years.

Messenger RNA (mRNA) — perhaps the most well-known of the RNAs — constitutes the intermediate step between DNA and the final product of gene expression: the protein. In contrast, miRNAs are never translated into proteins. Instead, they bind to complementary sequences in target mRNAs, preventing those mRNAs from being turned into proteins, and blocking gene expression.

This miRNA-directed silencing is widespread and complex. In some cases, miRNAs silence single genes. In others, multiple miRNAs coordinate to turn groups of genes on and off in concert, thereby controlling entire sets of genes that interact with one another.  For example, two years ago, Chakraborty’s mentor used computational methods to pinpoint a group of poorly expressed, understudied “nonclassical” miRNAs that appear to coordinate the expression of pluripotency genes. Pluripotency gene levels dictate the behavior and fate of embryonic stem cells — non-specialized cells awaiting instructions to “differentiate” and assume a particular cell type (skin cell, blood cell, neuron, and so on).

Chakraborty then used a technique known as fluorescence-activated cell sorting (FACS) to determine how nonclassical miRNAs affect gene expression in embryonic stem cells. She used a FACS assay to detect miRNA activity, engineering special DNA and inserting it into mouse embryonic stem cells. The DNA contained two genes: one encoding a red fluorescent protein with a place for miRNAs to bind, and another that makes a blue fluorescent protein and lacks this miRNA attachment site. When the miRNA binds to the gene expressing the red fluorescing protein, it is silenced, and the cell makes fewer red proteins compared to blue ones, whose production remains unhindered.

“We know when miRNAs are active, they will reduce the expression of the red florescent protein, but not the blue one,” she says. “And that’s precisely what we’ve seen with these nonclassical miRNAs, suggesting that they are active in the cell.”

Chakraborty is excited about what this finding could mean for cancer research. A growing number of studies have shown that some cancers arise when miRNAs fail to help embryonic stem cells interconvert between cell states.

Although she spends anywhere from four to 20 hours a week in lab, Chakraborty hasn’t lost sight of her extracurriculars. As co-president of the Biology Undergraduate Student Association, she serves as a liaison between biology students and faculty, coordinating events to connect the two. As the discussion chair for the Effective Altruism Club, she promotes dialogue between student club members regarding charities — how these organizations can maximize their donations, and how the public should decide which ones to support. As a volunteer for the non-profit Help at Your Door, she inputs grocery lists from senior citizens and disabled individuals into a computer program, and then coordinates with community members to deliver the specified order.

Last summer, she was accepted into the Johnson & Johnson UROP Scholars Program, joining approximately 20 fellow undergraduate women in STEM research at MIT during the summer term. Her cohort attended faculty presentations, workshops, and networking events geared towards post-graduate careers in the sciences.

“I really appreciated that program, because I think a lot of women are afraid of science due to societal norms,” she says. “I remember originally thinking I wouldn’t be good at computer science or math, and now here I am combining both skills with wet lab techniques in my research.”

Most recently, Chakraborty was a recipient of the 2017-2018 Barry Goldwater Scholarship Award, selected from a nationwide field of candidates nominated by university faculty. She will also remain on campus this coming summer to conduct faculty-mentored research as part of the MIT Amgen Scholars Program.

After she graduates in 2019, Chakraborty intends to pursue a PhD in a biology-related discipline, perhaps computational biology. After that, the options are endless — professor, consultant, research scientist. She’s still weighing the possibilities, and doesn’t seem too concerned about selecting one just yet.

“I know I’m going in the right direction, because it hits me every time I finish a challenging assignment or whenever I figure out a new approach in the lab,” she says. “When I complete a task like that with the help of friends and mentors, there’s this sense of pride and a feeling that I can’t believe how much I’ve learned in just once semester. The way my brain considers problems and finds solutions is just so different from the way it was three years ago when I first started out as a freshman.”

Photo credit: Raleigh McElvery
Single-cell database to propel biological studies

Whitehead team analyzes transcriptomes for roughly 70,000 cells in planarians, creates publicly available database to drive further research.

Nicole Davis | Whitehead Institute
April 20, 2018

A team at Whitehead Institute and MIT has harnessed single-cell technologies to analyze over 65,000 cells from the regenerative planarian flatworm, Schmidtea mediterranea, revealing the complete suite of actives genes (or “transcriptome”) for practically every type of cell in a complete organism. This transcriptome atlas represents a treasure trove of biological information on planarians, which is the subject of intense study in part because of its unique ability to regrow lost or damaged body parts. As described in the April 19 advance online issue of the journal Science, this new, publicly available resource has already fueled important discoveries, including the identification of novel planarian cell types, the characterization of key transition states as cells mature from one type to another, and the identity of new genes that could impart positional cues from muscles cells — a critical component of tissue regeneration.

“We’re really at the beginning of an amazing era,” says senior author Peter Reddien, a member of Whitehead Institute, professor of biology at MIT, and investigator with the Howard Hughes Medical Institute. “Just as genome sequences became indispensable resources for studying the biology of countless organisms, analyzing the transcriptomes of every cell type will become another fundamental tool — not just for planarians, but for many different organisms.”

The ability to systematically reveal which genes in the genome are active within an individual cell flows from a critical technology known as single-cell RNA sequencing. Recent advances in the technique have dramatically reduced the per-cell cost, making it feasible for a single laboratory to analyze a suitably large number of cells to capture the cell type diversity present in complex, multi-cellular organisms.

Reddien has maintained a careful eye on the technology from its earliest days because he believed it offered an ideal way to unravel planarian biology. “Planarians are relatively simple, so it would be theoretically possible for us to capture every cell type. Yet they still have a sufficiently large number of cells — including types we know little or even nothing about,” he explains. “And because of the unusual aspects of planarian biology — essentially, adults maintain developmental information and progenitor cells that in other organisms might be present transiently only in embryos — we could capture information about mature cells, progenitor cells, and information guiding cell decisions by sampling just one stage, the adult.”

Two and a half years ago, Reddien and his colleagues — led by first author Christopher Fincher, a graduate student in Reddien’s laboratory — set out to apply single-cell RNA sequencing systematically to planarians. The group isolated individual cells from five regions of the animal and gathered data from a total of 66,783 cells. The results include transcriptomes for rare cell types, such as those that comprise on the order of 10 cells out of an adult animal that consists of roughly 500,000 to 1 million cells.

In addition, the researchers uncovered some cell types that have yet to be described in planarians, as well cell types common to many organisms, making the atlas a valuable tool across the scientific community. “We identified many cells that were present widely throughout the animal, but had not been previously identified. This surprising finding highlights the great value of this approach in identifying new cells, a method that could be applied widely to many understudied organisms,” Fincher says.

“One main important aspect of our transcriptome atlas is its utility for the scientific community,” Reddien says. “Because many of the cell types present in planarians emerged long ago in evolution, similar cells still exist today in various organisms across the planet. That means these cell types and the genes active within them can be studied using this resource.”

The Whitehead team also conducted some preliminary analyses of their atlas, which they’ve dubbed “Planarian Digiworm.” For example, they were able to discern in the transcriptome data a variety of transition states that reflect the progression of stem cells into more specialized, differentiated cell types. Some of these cellular transition states have been previously analyzed in painstaking detail, thereby providing an important validation of the team’s approach.

In addition, Reddien and his colleagues knew from their own prior, extensive research that there is positional information encoded in adult planarian muscle — information that is required not only for the general maintenance of adult tissues but also for the regeneration of lost or damaged tissue. Based on the activity pattern of known genes, they could determine roughly which positions the cells had occupied in the intact animal, and then sort through those cells’ transcriptomes to identify new genes that are candidates for transmitting positional information.

“There are an unlimited number of directions that can now be taken with these data,” Reddien says. “We plan to extend our initial work, using further single-cell analyses, and also to mine the transcriptome atlas for addressing important questions in regenerative biology. We hope many other investigators find this to be a very valuable resource, too.”

This work was supported by the National Institutes of Health, the Howard Hughes Medical Institute, and the Eleanor Schwartz Charitable Foundation.

Study suggests perioperative NSAIDs may prevent early metastatic relapse in post-surgical breast cancer patients
Nicole Giese Rura | Whitehead Institute
April 11, 2018

Cambridge, MA – According to research conducted in mice by Whitehead Institute scientists, surgery in breast cancer patients, which while often curative, may trigger a systemic immunosuppressive response, allowing the outgrowth of dormant cancer cells at distant sites whose ability to generate tumors had previously been kept in check by the immune system. Taking a non-steroidal anti-inflammatory drug (NSAID) around the time of surgery may thwart such early metastatic relapse without impeding post-surgical wound healing.

The team’s work was published in the April 11 issue of the journal Science Translational Medicine.

“This represents the first causative evidence of surgery having this kind of systemic response,” says Jordan Krall, the first author of the paper and a former postdoctoral researcher in the lab of Whitehead Founding Member Robert Weinberg. “Surgery is essential for treating a lot of tumors, especially breast cancer. But there are some side effects of surgery, just as there are side effects to any treatment.  We’re starting to understand what appears to be one of those potential side effects, and this could lead to supportive treatment alongside of surgery that could mitigate some of those effects.”

Although the association between surgery and metastatic relapse has been documented, a causal line between the two has never been established, leading many to consider early metastatic relapse to be the natural disease progression in some patients. Previous studies of breast cancer patients have shown a marked peak in metastatic relapse 12-18 months following surgery. Although the underlying mechanism for such a spike has not been understood, a 2010 retrospective clinical trial conducted in Belgium provides a clue: Breast cancer patients taking a non-steroidal anti-inflammatory (NSAID) for pain following tumor resection had lower rates of this early type of metastatic relapse than patients taking opioids for post-surgical pain. Anti-inflammatory drugs also have previously been shown to directly inhibit tumor growth, but Krall and Weinberg thought that the NSAIDs’ effects in these studies may be independent of the mechanism responsible for the effects noted in the retrospective clinical trial.

To investigate the causes of early metastatic relapse after surgery, the team created a mouse model that seems to mirror the immunological detente keeping in check dormant, disseminated tumor cells in breast cancer patients. In this experimental model, the mice’s T cells stall the growth of tumors that are seeded by injected cancer cells. When mice harboring dormant cancer cells underwent simulated surgeries at sites distant from the tumor cells, tumor incidence and size dramatically increased. Analysis of the blood and tumors from wounded mice showed that wound healing increases levels of cells called inflammatory monocytes, which differentiate into tumor-associated macrophages.  Such macrophages, in turn, can act at distant sites to suppress the actions of T lymphocytes that previously succeeded in keeping the implanted tumors under control. Krall and Weinberg then tested the effects of the NSAID meloxicam (Mobic®), thinking that this anti-inflammatory drug might block the effects of immuno-suppressive effects of wound healing.  In fact, when mice received the NSAID after or at the time of surgery, the drug prevented a systemic inflammatory response created by the wound healing and the meloxicam-treated mice developed significantly smaller tumors than wounded, untreated mice; often these tumors completely disappeared. Notably, meloxicam did not impede the mice’s wound healing

Still, Weinberg cautions that scientists are just beginning to understand the connections between post-surgical wound healing, inflammation, and metastasis.

“This is an important first step in exploring the potential importance of this mechanism in oncology,” says Weinberg, who is also a professor of biology at Massachusetts Institute of Technology (MIT) and director of the MIT/Ludwig Center for Molecular Oncology.

This work was supported by the Advanced Medical Research Foundation, the Transcend Program (a partnership between the Koch Institute and Janssen Pharmaceuticals Inc.), the Breast Cancer Research Foundation, the Ludwig Center for Molecular Oncology at MIT, and the Samuel Waxman Cancer Research Foundation, the American Cancer Society, Hope Funds for Cancer Research, the Charles A. King Trust, the National Health and Medical Research Council of Australia (NHMRC APP1071853), the National Institutes of Health (NIH/NCI 1K99CA201574-01A1), the American Cancer Society Ellison Foundation (PF-15-131-01-CSM), and the U.S. Department of Defense (W81XWH-10-1-0647).

* * *
Robert Weinberg’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 and director of the MIT/Ludwig Center for Molecular Oncology.
* * *
Full Citation:
“The systemic response to surgery triggers the outgrowth of distant immune-controlled tumors in mouse models of dormancy”
Science Translational Medicine, April 11, 2018.
 Jordan A. Krall (1), Ferenc Reinhardt (1), Oblaise A. Mercury (1), Diwakar R. Pattabiraman (1), Mary W. Brooks (1), Michael Dougan (1,2), Arthur W. Lambert (1), Brian Bierie (1), Hidde L. Ploegh (1,3 *) Stephanie K. Dougan (1,4), Robert A. Weinberg (1,3,5).
1. Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
2. Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA.
3. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
4. Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
5. Ludwig Center for Molecular Oncology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
*Present address: Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA.
AACR Announces Special Recognition Awards
American Association for Cancer Research
April 2, 2018

PHILADELPHIA — The American Association for Cancer Research (AACR) will present Special Recognition Awards to four individuals whose work has made extraordinary contributions to the AACR’s mission to accelerate the prevention and cure of all cancers through research, education, communication, and collaboration.

Anna D. Barker, PhD; C. Kent Osborne, MD; Phillip A. Sharp, PhD; and Col. James E. Williams will receive the awards at the AACR Annual Meeting 2018, which is being held from Saturday, April 14, through Wednesday, April 18, at McCormick Place in Chicago.

These AACR Awards recognize groundbreaking, innovative work across the entire cancer community, and they reflect a wide range of contributions to cancer science and medicine. This year’s award recipients represent meritorious work in research, patient care, policymaking, and advocacy.

“It is our great personal honor to present these Special Recognition Awards,” said AACR Chief Executive Officer Margaret Foti, PhD, MD (hc). “This year’s award recipients have made such tremendous contributions to the cancer field. Their extraordinary accomplishments, whether in the lab, the clinic, the halls of Congress, or in their very own community, have truly changed the lives of cancer patients and their loved ones. We are so grateful for their enduring commitments to the cause.”

This year’s winners:

Anna D. Barker, PhD, will receive the 2018 AACR Distinguished Award for Exceptional Leadership in Cancer Science Policy and Advocacy.

Barker is the director of the National Biomarker Development Alliance; the director of Transformative Healthcare Knowledge Networks; co-director, Complex Adaptive Systems; and a professor in the School of Life Sciences at Arizona State University.

Barker has been chairperson of the AACR Scientist↔Survivor Program since she conceptualized the program more than two decades ago. She also provided outstanding leadership in cancer science policy and advocacy for the AACR through her work as Chair of the AACR’s Public Education Committee (now the Science Policy and Government Affairs Committee) from 1993-2002. She continues to serve on this committee, lending her considerable expertise to its initiatives. In addition, she served on the AACR Board of Directors from 1995-1996 and 1998-2001. She was Deputy Director of the National Cancer Institute from 2002-2010.

“Dr. Barker’s innovative leadership in cancer advocacy has driven the success of her brainchild, the AACR Scientist↔Survivor Program, for it brings together cancer scientists and physicians along with cancer advocates at our scientifically vibrant Annual Meeting and at the Science of Cancer Health Disparities Meeting,” Foti said. “This unique program has had an indelible, positive effect on the professional and personal lives of both cancer researchers and advocates, and it has been hailed around the world as the most important initiative of its type.”

C. Kent Osborne, MD, will receive the 2018 AACR Distinguished Award for Extraordinary Scientific Achievement and Leadership in Breast Cancer Research.

Osborne is the director of the Dan L Duncan Comprehensive Cancer Center at Baylor College of Medicine, where he is also a professor and the Dudley and Tina Sharp Chair for Cancer Research. Since 1992, he has been a codirector of the San Antonio Breast Cancer Symposium (SABCS), the world’s largest and most prestigious conference devoted to breast cancer.
Osborne’s own research has focused on improving the effectiveness of endocrine and HER-2 targeted therapies in patients with breast cancer.

“Dr. Osborne has made extraordinary contributions to breast cancer research during his spectacular career as a physician-scientist, producing significant new insights and providing important data that have improved the clinical outcomes of breast cancer patients,” Foti said. “In addition, this award recognizes his exceptional, selfless stewardship of SABCS, which has grown and thrived under his capable leadership. The AACR is proud to be a partner in SABCS, along with UT Health and Baylor College of Medicine, and we look forward to a long and fruitful relationship with Dr. Osborne.”

Phillip A. Sharp, PhD, FAACR, will receive the 2018 AACR Distinguished Award for Extraordinary Scientific Innovation and Exceptional Leadership in Cancer Research and Biomedical Science.

Sharp is an Institute professor and faculty member at Massachusetts Institute of Technology’s David H. Koch Institute for Integrative Cancer Research. A world leader in molecular biology and biochemistry, he won the 1993 Nobel Prize in Physiology or Medicine for his co-discovery of RNA splicing. He was elected as an inaugural Fellow of the AACR Academy in 2013.

Dr. Sharp has been Chair of the Stand Up To Cancer (SU2C) Scientific Advisory Committee over the past decade, leading the selection of 23 “Dream Teams” of top researchers and other SU2C research groups. He served as program chair of the AACR’s Inaugural Special Conference in 1988. That conference, “Gene Regulation and Oncogenes,” has been characterized as a watershed meeting in stimulating novel, transformative thinking about the molecular biology of cancer. In October 2018, he will lead the 30th Anniversary Special Conference on “Convergence: Artificial Intelligence, Big Data, and Prediction in Cancer.”

“During his illustrious career, Dr. Sharp has consistently manifested extraordinary dedication to the AACR and its mission,” Foti said. “He has provided sage advice and counsel to the AACR on numerous important issues, and his loyalty to our organization continues to this day.

“As the Scientific Partner of Stand Up To Cancer, the AACR has had a spectacular vantage point to witness how Dr. Sharp embraces the urgent need for collaboration in cancer research. He has translated his considerable scientific expertise into a dynamic leadership role in cancer science that stimulates innovation and encourages other scientists to bring their best original work to the goal of defeating cancer in all its forms,” Foti said.

Col. James E. Williams will receive the AACR 2018 Distinguished Public Service Award for Exceptional Leadership in Cancer Advocacy.

Williams, a retired Army colonel who served in the Vietnam War, was diagnosed with prostate cancer in 1991. After he beat the disease, he embarked on a passionate effort to educate men about the disease. His advocacy efforts include serving as a member of the Editorial Advisory Board of the AACR’s Cancer Today magazine; serving as Chairman of the Board of The Intercultural Cancer Council (ICC); serving as Chairman of the Pennsylvania Prostate Cancer Coalition; participating on the Patient Advocacy Committee of the Alliance for Clinical Trials in Oncology; and serving as a Board member of the Alliance for Prostate Cancer Prevention.

“Jim Williams is an inspiration and a role model not only to other cancer survivors, but also to the scientific community at large,” Foti said.  “We are indebted to him for his steadfast passion to advocate for increased funding and research dedicated to men’s health issues, with an emphasis on prostate cancer. His selfless efforts are also instrumental in improving outcomes for racial and ethnic minorities and the medically underserved.”

Scientists find different cell types contain the same enzyme ratios

New discovery suggests that all life may share a common design principle.

Justin Chen | Department of Biology
March 29, 2018

By studying bacteria and yeast, researchers at MIT have discovered that vastly different types of cells still share fundamental similarities, conserved across species and refined over time. More specifically, these cells contain the same proportion of specialized proteins, known as enzymes, which coordinate chemical reactions within the cell.

To grow and divide, cells rely on a unique mixture of enzymes that perform millions of chemical reactions per second. Many enzymes, working in relay, perform a linked series of chemical reactions called a “pathway,” where the products of one chemical reaction are the starting materials for the next. By making many incremental changes to molecules, enzymes in a pathway perform vital functions such as turning nutrients into energy or duplicating DNA.

For decades, scientists wondered whether the relative amounts of enzymes in a pathway were tightly controlled in order to better coordinate their chemical reactions. Now, researchers have demonstrated that cells not only produce precise amounts of enzymes, but that evolutionary pressure selects for a preferred ratio of enzymes. In this way, enzymes behave like ingredients of a cake that must be combined in the correct proportions and all life may share the same enzyme recipe.

“We still don’t know why this combination of enzymes is ideal,” says Gene-Wei Li, assistant professor of biology at MIT, “but this question opens up an entirely new field of biology that we’re calling systems level optimization of pathways. In this discipline, researchers would study how different enzymes and pathways behave within the complex environment of the cell.”

Li is the senior author of the study, which appears online in the journal Cell on March 29, and in print on April 19. The paper’s lead author, Jean-Benoît Lalanne, is a graduate student in the MIT Department of Physics.

An unexpected observation

For more than 100 years, biologists have studied enzymes by watching them catalyze chemical reactions in test tubes, and — more recently — using X-rays to observe their molecular structure.

And yet, despite years of work describing individual proteins in great detail, scientists still don’t understand many of the basic properties of enzymes within the cell. For example, it is not yet possible to predict the optimal amount of enzyme a cell should make to maximize its chance of survival.

The calculation is tricky because the answer depends not only on the specific function of the enzyme, but also how its actions may have a ripple effect on other chemical reactions and enzymes within the cell.

“Even if we know exactly what an enzyme does,” Li says, “we still don’t have a sense for how much of that protein the cell will make. Thinking about biochemical pathways is even more complicated. If we gave biochemists three enzymes in a pathway that, for example, break down sugar into energy, they would probably not know how to mix the proteins at the proper ratios to optimize the reaction.”

The study of the relative amounts of substances — including proteins — is known as “stoichiometry.” To investigate the stoichiometry of enzymes in different types of cells, Li and his colleagues analyzed three different species of bacteria — Escherichia coli, Bacillus subtilis, and Vibrio natriegens — as well as the budding yeast Saccharomyces cerevisiae. Among these cells, scientists compared the amount of enzymes in 21 pathways responsible for a variety of tasks including repairing DNA, constructing fatty acids, and converting sugar to energy. Because these species of yeast and bacteria have evolved to live in different environments and have different cellular structures, such as the presence or lack of a nucleus, researchers were surprised to find that all four cells types had nearly identical enzyme stoichiometry in all pathways examined.

Li’s team followed up their unexpected results by detailing how bacteria achieve a consistent enzyme stoichiometry. Cells control enzyme production by regulating two processes. The first, transcription, converts the information contained in a strand of DNA into many copies of messenger RNA (mRNA). The second, translation, occurs as ribosomes decode the mRNAs to construct proteins. By analyzing transcription across all three bacterial species, Li’s team discovered that the different bacteria produced varying amounts of mRNA encoding for enzymes in a pathway.

Different amounts of mRNA theoretically lead to differences in protein production, but the researchers found instead that the cells adjusted their rates of translation to compensate for changes in transcription. Cells that produced more mRNA slowed their rates of protein synthesis, while cells that produced less mRNA increased the speed of protein synthesis. Thanks to this compensation, the stoichiometry of enzymes remained constant across the different bacteria.

“It is remarkable that E. coli and B. subtilis need the same relative amount of the corresponding proteins, as seen by the compensatory variations in transcription and translation efficiencies,” says Johan Elf, professor of physical biology at Uppsala University in Sweden. “These results raise interesting questions about how enzyme production in different cells have evolved.”

“Examining bacterial gene clusters was really striking,” lead author Lalanne says. “Over a long evolutionary history, these genes have shifted positions, mutated into different sequences, and been bombarded by mobile pieces of DNA that randomly insert themselves into the genome. Despite all this, the bacteria have compensated for these changes by adjusting translation to maintain the stoichiometry of their enzymes. This suggests that evolutionary forces, which we don’t yet understand, have shaped cells to have the same enzyme stoichiometry.”

Searching for the stoichiometry regulating human health

In the future, Li and his colleagues will test whether their findings in bacteria and yeast extend to humans. Because unicellular and multicellular organisms manage energy and nutrients differently, and experience different selection pressures, researchers are not sure what they will discover.

“Perhaps there will be enzymes whose stoichiometry varies, and a smaller subset of enzymes whose levels are more conserved,” Li says. “This would indicate that the human body is sensitive to changes in specific enzymes that could make good drug targets. But we won’t know until we look.”

Beyond the human body, Li and his team believe that it is possible to find simplicity underlying the complex bustle of molecules within all cells. Like other mathematical patterns in nature, such as the the spiral of seashells or the branching pattern of trees, the stoichiometry of enzymes may be a widespread design principle of life.

The research was funded by the National Institutes of Health, Pew Biomedical Scholars Program, Sloan Research Fellowship, Searle Scholars Program, National Sciences and Engineering Research Council of Canada, Howard Hughes Medical Institute, National Science Foundation, Helen Hay Whitney Foundation, Jane Coffin Childs Memorial Fund, and the Smith Family Foundation.

Structure of key growth regulator revealed

Researchers identify the molecular structure of the GATOR1 protein complex, which regulates growth signals in human cells, using cryo-electron microscopy.

Nicole Davis | Whitehead Institute
March 28, 2018

A team of researchers from Whitehead Institute and the Howard Hughes Medical Institute has revealed the structure of a key protein complex in humans that transmits signals about nutrient levels, enabling cells to align their growth with the supply of materials needed to support that growth. This complex, called GATOR1, acts as a kind of on-off switch for the “grow” (or “don’t grow”) signals that flow through a critical cellular growth pathway known as mTORC1.

Despite its importance, GATOR1 bears little similarity to known proteins, leaving major gaps in scientists’ understanding of its molecular structure and function. Now, as described online on March 28 in the journal Nature, Whitehead scientists and their colleagues have generated the first detailed molecular picture of GATOR1, revealing a highly ordered group of proteins and an extremely unusual interaction with its partner, the Rag GTPase.

“If you know something about a protein’s three-dimensional structure, then you can make some informed guesses about how it might work. But GATOR1 has basically been a black box,” says senior author David Sabatini, a member of Whitehead Institute, a professor of biology at MIT, and investigator with the Howard Hughes Medical Institute (HHMI). “Now, for the first time, we have generated high-resolution images of GATOR1 and can begin to dissect how this critical protein complex works.”

GATOR1 was first identified about five years ago. It consists of three protein subunits (Depdc5, Nprl2, and Nprl3), and mutations in these subunits have been associated with human diseases, including cancers and neurological conditions such as epilepsy. However, because of the lack of similarity to other proteins, the majority of the GATOR1 complex is a molecular mystery. “GATOR1 has no well-defined protein domains,” explains Whitehead researcher Kuang Shen, one of the study’s first authors. “So, this complex is really quite special and also very challenging to study.”

Because of the complex’s large size and relative flexibility, GATOR1 cannot be readily crystallized — a necessary step for resolving protein structure through standard, X-ray crystallographic methods. As a result, Shen and Sabatini turned to HHMI’s Zhiheng Yu. Yu and his team specialize in cryo-electron microscopy (cryo-EM), an emerging technique that holds promise for visualizing the molecular structures of large proteins and protein complexes. Importantly, it does not utilize protein crystals. Instead, proteins are rapidly frozen in a thin layer of vitrified ice and then imaged by a beam of fast electrons inside an electron microscope column.

“There have been some major advances in cryo-EM technology over the last decade, and now, it is possible to achieve atomic or near atomic resolution for a variety of proteins,” explains Yu, a senior author of the paper and director of HHMI’s shared, state-of-the-art cryo-EM facility at Janelia Research Campus. Last year’s Nobel Prize in chemistry was awarded to three scientists for their pioneering efforts to develop cryo-EM.

GATOR1 proved to be a tricky subject, even for cryo-EM, and required some trial-and-error on the part of Yu, Shen, and their colleagues to prepare samples that could yield robust structural information. Moreover, the team’s work was made even more difficult by the complex’s unique form. With no inklings of GATOR1’s potential structure, Shen and his colleagues, including co-author Edward Brignole of MIT, had to derive it completely from scratch.

Nevertheless, the Whitehead-HHMI team was able to resolve near-complete structures for GATOR1 as well as for GATOR1 bound to its partner proteins, the Rag GTPases. (Two regions of the subunit Depdc5 are highly flexible and therefore could not be resolved.) From this wealth of new information as well as from the team’s subsequent biochemical analyses, some surprising findings emerged.

First is the remarkable level of organization of GATOR1. The protein is extremely well organized, which is quite unusual for proteins that have no predicted structures. (Such proteins are usually quite disorganized.) In addition, the researchers identified four protein domains that have never before been visualized. These novel motifs — named NTD, SABA, SHEN, and CTD — could provide crucial insights into the inner workings of the GATOR1 complex.

Shen, Sabatini, and their colleagues uncovered another surprise. Unlike other proteins that bind to Rag GTPases, GATOR1 contacts these proteins at at least two distinct sites. Moreover, one of the binding sites serves to inhibit — rather than stimulate — the activity of the Rag GTPase. “This kind of dual binding has never been observed — it is highly unusual,” Shen says. The researchers hypothesize that this feature is one reason why GATOR1 is so large — because it must hold its Rag GTPase at multiple sites, rather than one, as most other proteins of this type do.

Despite these surprises, the researchers acknowledge that their analyses have only begun to scratch the surface of GATOR1 and the mechanisms through which it regulates the mTOR signaling pathway.

“There is much left to discover in this protein,” Sabatini says.

This work was supported by the National Institutes of Health, Department of Defense, National Science Foundation, the Life Sciences Research Foundation, and the Howard Hughes Medical Institute.

Novel human/mouse model could boost type 1 diabetes research
Nicole Giese Rura | Whitehead Institute
March 27, 2018

Cambridge, MA – About 1.5 million people in the United States have type 1 diabetes, according to the Centers for Disease Control and Prevention (CDC), and yet doctors know very little about what triggers the disease. Now researchers at Whitehead Institute have developed a novel platform with human beta cells that could allow scientists to better understand the mechanisms underlying this disease and what provokes it.

In Type 1 diabetes, an autoimmune disease also called juvenile or insulin-dependent diabetes, the immune system destroys beta cells—the cells in the pancreas that produce insulin. Insulin is required for glucose to enter the body’s cells, so people with type 1 diabetes must closely monitor their glucose levels and take insulin daily. Type 1 diabetes is usually diagnosed during childhood or young adulthood, and possible causes of the disease that are being actively researched include genetics, viral infection, other environmental factors, or some combination of these.

Currently, scientists studying the disease may use animal models, such as non-obese diabetic (NOD) mice that do not include human cells, or mouse and rat models with beta cells derived from human induced pluripotent stem cells (iPSCs)—cells that have been pushed to a pluripotent state—implanted into the animals’ kidney capsules. These models hint at clinical applications that may control glucose levels in type 1 diabetes patients, but because the beta cells do not reside in the pancreas, the models do not reflect the cell-tissue interactions that are likely intrinsic in the development of type 1 diabetes.

To address these shortcomings, a team of researchers led by Haiting Ma, a postdoctoral researcher in Whitehead Founding Member Rudolf Jaenisch’s lab, implanted beta cells derived from iPSCs into the pancreas of neonatal mice. As the mice grow, the human beta cells become integrated into the mice’s pancreases, respond to increased glucose levels, and secrete insulin into the mouse’s bloodstream for several months following implantation. The team’s work is described online in the journal PNAS this week.

Using mice with human beta cells successfully engrafted into their pancreases, scientists will be able to study how beta cells function in normal and disease conditions, and perhaps help identify the causes of type 1 diabetes. Such insights may lead to new approaches to treat this autoimmune disease.

This work was supported by Liliana and Hillel Bachrach, the National Institutes of Health (NIH RO1-CA084198, 5R01-MH104610-16, R37-HD045022, R01-GM114864, RF1-AG048029, U19-AI3115135, and 1R01-1NS088538-01), the Harvard Stem Cell Institute, the JBP Foundation, and Howard Hughes Medical Institute. Jaenisch is co-founder advisor of Fate Therapeutics, Fulcrum Therapeutics, and Omega Therapeutics, and Doug Melton is the founder of Semma Therapeutics.

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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.
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Full Citation:
“Establishment of human pluripotent stem cell derived pancreatic β-like cells in the mouse pancreas”
PNAS, online March 26, 2018.
Haiting Ma (1), Katherine Wert (1), Dmitry Shvartsman (2), Douglas Melton (2), and Rudolf Jaenisch (1,3).
1. Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
2. Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
3. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
Study suggests method for boosting growth of blood vessels and muscle

Activating proteins linked to longevity may help to increase endurance and combat frailty in the elderly.

Anne Trafton | MIT News Office
March 22, 2018

As we get older, our endurance declines, in part because our blood vessels lose some of their capacity to deliver oxygen and nutrients to muscle tissue. An MIT-led research team has now found that it can reverse this age-related endurance loss in mice by treating them with a compound that promotes new blood vessel growth.

The study found that the compound, which re-activates longevity-linked proteins called sirtuins, promotes the growth of blood vessels and muscle, boosting the endurance of elderly mice by up to 80 percent.

If the findings translate to humans, this restoration of muscle mass could help to combat some of the effects of age-related frailty, which often lead to osteoporosis and other debilitating conditions.

“We’ll have to see if this plays out in people, but you may actually be able to rescue muscle mass in an aging population by this kind of intervention,” says Leonard Guarente, the Novartis Professor of Biology at MIT and one of the senior authors of the study. “There’s a lot of crosstalk between muscle and bone, so losing muscle mass ultimately can lead to loss of bone, osteoporosis, and frailty, which is a major problem in aging.”

The first author of the paper, which appears in Cell on March 22, is Abhirup Das, a former postdoc in Guarente’s lab who is now at the University of New South Wales in Australia. Other senior authors of the paper are David Sinclair, a professor at Harvard Medical School and the University of New South Wales, and Zolt Arany, a professor at the University of Pennsylvania.

Race against time

In the early 1990s, Guarente discovered that sirtuins, a class of proteins found in nearly all animals, protect against the effects of aging in yeast. Since then, similar effects have been seen in many other organisms.

In their latest study, Guarente and his colleagues decided to explore the role of sirtuins in endothelial cells, which line the inside of blood vessels. To do that, they deleted the gene for SIRT1, which encodes the major mammalian sirtuin, in endothelial cells of mice. They found that at 6 months of age, these mice had reduced capillary density and could run only half as far as normal 6-month-old mice.

The researchers then decided to see what would happen if they boosted sirtuin levels in normal mice as they aged. They treated the mice with a compound called NMN, which is a precursor to NAD, a coenzyme that activates SIRT1. NAD levels normally drop as animals age, which is believed to be caused by a combination of reduced NAD production and faster NAD degradation.

After 18-month-old mice were treated with NMN for two months, their capillary density was restored to levels typically seen in young mice, and they experienced a 56 to 80 percent improvement in endurance. Beneficial effects were also seen in mice up to 32 months of age (comparable to humans in their 80s).

“In normal aging, the number of blood vessels goes down, so you lose the capacity to deliver nutrients and oxygen to tissues like muscle, and that contributes to decline,” Guarente says. “The effect of the precursors that boost NAD is to counteract the decline that occurs with normal aging, to reactivate SIRT1, and to restore function in endothelial cells to give rise to more blood vessels.”

These effects were enhanced when the researchers treated the mice with both NMN and hydrogen sulfide, another sirtuin activator.

Vittorio Sartorelli, a principal investigator at the National Institute of Allergy and Infectious Diseases who was not involved in the research, described the experiments as “elegant and compelling.” He added that “it will be of interest and of clinical relevance to evaluate the effect of NMN and hydrogen sulfide on the vascularization of other organs such as the heart and brain, which are often damaged by acutely or chronically reduced blood flow.”

Benefits of exercise

The researchers also found that SIRT1 activity in endothelial cells is critical for the beneficial effects of exercise in young mice. In mice, exercise generally stimulates growth of new blood vessels and boosts muscle mass. However, when the researchers knocked out SIRT1 in endothelial cells of 10-month-old mice, then put them on a four-week treadmill running program, they found that the exercise did not produce the same gains seen in normal 10-month-old mice on the same training plan.

If validated in humans, the findings would suggest that boosting sirtuin levels may help older people retain their muscle mass with exercise, Guarente says. Studies in humans have shown that age-related muscle loss can be partially staved off with exercise, especially weight training.

“What this paper would suggest is that you may actually be able to rescue muscle mass in an aging population by this kind of intervention with an NAD precursor,” Guarente says.

In 2014, Guarente started a company called Elysium Health, which sells a dietary supplement containing a different precursor of NAD, known as NR, as well as a compound called pterostilbene, which is an activator of SIRT1.

The research was funded by the Glenn Foundation for Medical Research, the Sinclair Gift Fund, a gift from Edward Schulak, and the National Institutes of Health.

A blueprint for regeneration

Whitehead Institute researchers uncover framework for how stem cells determine where to form replacement structures.

Lisa Girard | Whitehead Institute
March 15, 2018

Researchers at Whitehead Institute have uncovered a framework for regeneration that may explain and predict how stem cells in adult, regenerating tissue determine where to form replacement structures.

In a paper that appeared online March 15 in the journal Science, the researchers describe a model for planarian (flatworm) eye regeneration that is governed by three principles acting in concert, which inform how progenitor cells behave in regeneration. The model invokes positional cues that create a scalable map; self-organization that attracts progenitors to existing structures; and progenitor cells that originate in a diffuse spatial zone, rather than a precise location, allowing flexibility in their path. These principles appear to dictate how progenitor cells decide where to go during regeneration to recreate form and function, and they bring us closer to a systems-level understanding of the process.

From previous work, the researchers knew that stem cells are likely reading out instructions from neighboring tissues to guide their path, and it became clear that the process faces some serious challenges in regeneration. “We realized that positional information has to move; it needs to change during regeneration in order to specify the new missing parts to be regenerated. This revised information can then guide progenitor cells that are choosing to make new structures to differentiate into the correct anatomy at the correct locations,” says the paper’s senior author Peter Reddien, a Whitehead Institute researcher, an MIT professor of biology, and a Howard Hughes Medical Institute (HHMI) investigator. “There is a puzzle that emerges, however. Since positional information shifts after injury during regeneration, there is a mismatch between the positional information pattern and the remaining anatomy pattern. Realizing this mismatch exists was a trigger for our study. We wanted to understand how stem cells making particular tissues decide where to go and differentiate. Is it based on anatomy, or is it based on positional information? And when those two things are not aligned, how do they decide?”

Reddien and his lab have spent over a decade unraveling the mysteries of regeneration using a small flatworm, called the planarian. If a planarian’s head is amputated, or its side is removed, each piece will regenerate an entire animal. In order to understand how progenitors decide where to go in the noisy environment of animal regeneration, the researchers used the planarian eye, a visible organ that is small enough to be removed without serious injury and has the added advantage of having defined progenitor cell molecular markers.

The researchers devised a simple experiment to resolve the question of how the progenitors decide where to go: amputate the animal’s head, then after three days remove one of the eyes from the head piece. What they found was that progenitor cells would nucleate a new eye in a position anterior (closer to the tip) to the remaining eye, rather than in the “correct” position specified by the anatomy, symmetrical with the current eye. However, if the same experiment is done, except with one of the eyes removed from the head piece earlier — the same day as the amputation, rather than three days later — there is a different result: The new eye is nucleated at a position symmetrical to the remaining eye, at the “correct” position according to the anatomy, suggesting that when the choices are conflicting, anatomical self-organizing dynamics win.

These simple rules guide the system to successful regeneration and also yield surprising outcomes when the system is pushed to its limits, producing alternative stable anatomical states with three-, four-, and five-eyed animals. Resecting both the side of an animal and amputating the head can place progenitors far enough from existing, self-organizing attractors that they miss them, allowing them to nucleate a new attractor — a third eye — in the head fragments. “If the migrating progenitors are too close to the attractor that is the existing eye, it will suck them in, just like a black hole; if they are far enough, they can escape,” says Kutay Deniz Atabay, first author on the paper and a graduate student in the Reddien lab.

When the researchers did the same surgery on a three-eyed animal, the progenitors miss the attraction of existing eyes and form a five-eyed animal. In each of these cases, all of the eyes are functionally integrated into the brain and exhibit the same light-avoidance response of the planarian eye. The researchers also observed that these alternative anatomical states endure, revealing rules for maintenance of existing and alternative anatomical structures. “This recipe helps provide an explanation for a fundamental problem of animal regeneration, which is how migratory progenitors make choices that lead the system to regenerate and maintain organs,” Atabay says.

“These studies contribute to a proposed framework for regeneration in which competing forces, self-organization, and extrinsic cues, are the guideposts impacting the choice of progenitor targeting in regeneration; and those two forces together determine the outcome,” Reddien says.

This work was supported by the National Institutes of Health (NIH) and the HHMI. Additional funding was provided by the MIT Presidential Fellowship Program and a National Defense Science and Engineering Graduate Fellowship.

Toxic proteins and type 2 diabetes

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

Nicole Davis | Whitehead Institute
March 8, 2018

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

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

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

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

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

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

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

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

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

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

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