Author: mantulin

Revising the textbook on introns

Whitehead Institute researchers uncover a group of introns in yeast that possess surprising stability and function.

Nicole Davis | Whitehead Institute
January 16, 2019

A research team from Whitehead Institute has uncovered a surprising and previously unrecognized role for introns, the parts of genes that lack the instructions for making proteins and are typically cut away and rapidly destroyed. Through studies of baker’s yeast, the researchers identified a highly unusual group of introns that linger and accumulate, in their fully intact form, long after they have been freed from their neighboring sequences, which are called exons. Importantly, these persistent introns play a role in regulating yeast growth, particularly under stressful conditions.

The researchers, whose work appears online in the journal Nature, suggest that some introns also might accumulate and carry out functions in other organisms.

“This is the first time anyone has found a biological role for full-length, excised introns,” says senior author David Bartel, a member of the Whitehead Institute. “Our findings challenge the view of these introns as simply byproducts of gene expression, destined for rapid degradation.”

Imagine the DNA that makes up your genes as the raw footage of a movie. The exons are the scenes used in the final cut, whereas the introns are the outtakes — shots that are removed, or spliced out, and therefore not represented in the finished product.

Despite their second-class status, introns are known to play a variety of important roles. Yet these activities are primarily confined to the period prior to splicing — that is, before introns are separated from their nearby exons. After splicing, some introns can be whittled down and retained for other uses — part of a group of so-called “non-coding RNAs.” But by and large, introns have been thought to be relegated to the genome’s cutting room floor.

Bartel and his Whitehead Institute colleagues, including world-renowned yeast expert Gerald Fink, now add an astonishing new dimension to this view: Full-length introns — that is, those that have been cut out but remain otherwise intact — can persist and carry out useful biological functions. As reported in their Nature paper, the team discovered that these extraordinary introns are regulated by and function within the essential TORC1 growth signaling network, forming a previously unknown branch of this network that controls cell growth during periods of stress.

“Our initial reaction was: ‘This is really weird,’” recalls first author Jeffrey Morgan, a former graduate student in Bartel’s lab who is now a postdoc in Jared Rutter’s lab at the University of Utah. “We came across genes where the introns were much more abundant than the exons, which is the exact opposite of what you’d expect.”

The researchers identified a total of 34 of these unusually stable introns, representing 11 percent of all introns in the yeast, also known as Saccharomyces cerevisiae. Surprisingly, there are very few criteria that determine which introns will become stable introns. For example, the genetic sequences of the introns or the regions that surround them are of no significance. The only defining — and necessary — feature, the team found, is a structural one, and involves the precise shape the introns adopt as they are being excised from their neighboring exons. Excised introns typically form a lasso-shaped structure, known as a lariat. The length of the lasso’s handle appears to dictate whether an intron will be stabilized or not.

Remarkably, both yeast and introns have been studied for several decades. Yet until now, these unique introns went undetected. One reason, Bartel and his colleagues believe, is the conditions under which yeast are typically grown. Often, researchers study yeast that are growing very rapidly — so-called log-phase growth. That is because abnormalities are often easiest to detect when cells are multiplying quickly.

“Biologists have focused heavily on log-phase for very good reasons, but in the wild, yeast are very rarely in that condition, whether it’s because of limited nutrients or other stresses,” says Bartel, who is also professor of biology at MIT and a Howard Hughes Medical Institute investigator.

He and his colleagues decided to grow yeast under more stressful circumstances, and that is what ultimately led them to their discovery. Although their experiments were confined to yeast, the researchers believe it is possible other organisms may harbor this long-overlooked class of introns — and that similar approaches using less-often-studied conditions could help illuminate them.

“Right now, we can say it is happening in yeast, but we’d be surprised if this is the only organism in which it is happening,” Bartel says.

The research was supported by the National Institutes of Health and the Howard Hughes Medical Institute.

School of Science honors postdocs and research staff with 2018 Infinite Kilometer Awards

Five winners are recognized for their outstanding contributions to colleagues, the school, and the Institute.

School of Science
December 25, 2018

The MIT School of Science has announced the 2018 winners of the Infinite Kilometer Award. The Infinite Kilometer Award was established in 2012 to highlight and reward the extraordinary work of the school’s postdocs and research staff.

Recipients of the award are exceptional contributors to their research programs. In many cases, they are also deeply committed to their local or global MIT community, and are frequently involved in mentoring and advising their junior colleagues, participating in the school’s educational programs, making contributions to the MIT Postdoctoral Association, or contributing to some other facet of the MIT community.

In addition to a monetary award, the honorees and their colleagues, friends, and family are invited to a celebratory reception in the spring semester.

The 2018 Infinite Kilometer winners are:

Matthew Golder, a National Institutes of Health Postdoctoral Fellow in the Department of Chemistry, nominated by Jeremiah Johnson, an associate professor of chemistry;

Robert Grant, manager of the crystallography lab in the Department of Biology, nominated by Michael Laub, a professor of biology;

Slawomir Gras, a research scientist on the LIGO project at the MIT Kavli Institute for Astrophysics and Space Research, nominated by Nergis Mavalvala, the Curtis and Kathleen Marble Professor of Astrophysics, and Matthew Evans, an associate professor of physics;

Yeong Shin Yim, a postdoc at the McGovern Institute for Brain Research, nominated by Gloria Choi, an assistant professor of brain and cognitive sciences; and

Yong Zhao, a postdoc in the Laboratory for Nuclear Science, nominated by Iain Stewart, a professor of physics.

The School of Science is also currently accepting nominations for its Infinite Mile Awards. All School of Science employees are eligible, and nominations are due by Feb. 15, 2019. The Infinite Mile Awards will be presented with the Infinite Kilometer Awards this spring.

Real-time readouts of thinking in rats

New open-source system provides fast, accurate neural decoding and real-time readouts of where rats think they are.

David Orenstein | Picower Institute for Learning and Memory
December 19, 2018

The rat in a maze may be one of the most classic research motifs in brain science, but a new innovation described in Cell Reports by an international collaboration of scientists shows just how far such experiments are still pushing the cutting edge of technology and neuroscience alike.

In recent years, scientists have shown that by recording the electrical activity of groups of neurons in key areas of the brain they could read a rat’s thoughts of where it was, both after it actually ran the maze and also later when it would dream of running the maze in its sleep — a key process in consolidating its memory. In the new study, several of the scientists involved in pioneering such mind-reading methods now report they can read out those signals in real-time as the rat runs the maze, with a high degree of accuracy and the ability to account for the statistical relevance of the readings almost instantly after they are made.

The ability to so robustly track the rat’s spatial representations in real-time opens the door to a whole new class of experiments, the researchers said. They predict these experiments will produce new insights into learning, memory, navigation and cognition by allowing them to not only decode rat thinking as it happens, but also to instantaneously intervene and study the effects of those perturbations.

“The use of real-time decoding and closed-loop control of neural activity will fundamentally transform our studies of the brain,” says study co-author Matthew Wilson, the Sherman Fairchild Professor in Neurobiology at MIT’s Picower Institute for Learning and Memory.

The collaboration behind the new paper began in Wilson’s lab at MIT almost 10 years ago. At that time, corresponding authors Zhe (Sage) Chen, now an associate professor of psychiatry and neuroscience and physiology at New York University, and Fabian Kloosterman, now a principal investigator at Neuro-Electronics Research Flanders and a professor at KU Leuven in Belgium, were both postdocs at MIT.

After demonstrating how neural decoding can be used to read out what places are covertly replayed in the brain, the team began a series of technical innovations that progressively improved the field’s ability to accurately decode how the brain represents place both during navigation and in sleep or rest. They reached a first milestone in 2013 when the team published their novel decoding approach in a paper in the Journal of Neurophysiology. The new approach allows researchers to directly decipher hippocampal spatiotemporal patterns detected from tetrode recordings without the need for spike sorting, a computational process that is time-consuming and error prone.

In the new study, the team shows that by implementing their neural decoding software on a graphical processing unit (GPU) chip, the same kind of highly parallel processing hardware favored by video gamers, they were able to achieve unprecedented increases in decoding and analysis speed. In the study, the team shows that the GPU-based system was 20-50 times faster than ones using conventional multi-core CPU chips.

They also show that the system remains rapid and accurate even when handling more than 1,000 input channels. This is important because it extends the real-time decoding approach to new high-density brain recording devices, such as the Neuropixels probe co-developed by imec, HHMI and other institutions — think of a many electrodes recording from many hundreds of cells — that promise to measure cellular brain activity at larger scales and in more detail.

In addition, the new study reports the ability for the software to provide a rapid statistical assessment of whether a set of reactivated neural spatiotemporal activity patterns truly pertains to the task, or is perhaps unrelated.

“We are proposing an elegant solution using GPU computing to not only decode information on the fly but also to evaluate the significance of the information on the fly,” says Chen, whose graduate student, Sile Hu, is the new paper’s lead author.

Hu tested a wide range of neural recordings in brain areas such as the hippocampus, the thalamus and cortex in multiple rats as they ran a variety of mazes ranging from simple tracks to a wide-open space. In a video accompanying the paper, the system’s readout from 36 electrode channels in the hippocampus tracks the rat’s actual measured position in open space and provides real-time estimates of the decoded position from brain activity. Only occasionally and briefly do the trajectories diverge by much.

The software of the system is open source and available for fellow neuroscientists to download and use freely, Chen and Wilson say.

Prior experiments recording neural representations of place have helped to show that animals replay their spatial experiences during sleep and have allowed researchers to understand more about how animals rely on memory when making decisions about how to navigate — for instance to maximize the rewards they can find along the way. Traditionally, though, the brain readings have been analyzed offline (after the fact. More recently, scientists have begun to perform real-time analyses but these have been limited both in the detail of the content and also in the ability to understand whether the readings are statistically significant and therefore relevant.

In a recent major step forward, Kloosterman and two other co-authors of the new study, graduate students Davide Ciliberti and Frédéric Michon, published a paper in eLife on a real-time, closed-loop read-out of hippocampal memory replay as rats navigated a three-arm maze. That system used multi-core CPUs.

“The new GPU system will bring the field even closer to having a detailed, real-time and highly scalable read-out of the brain’s internal deliberations,” says Kloosterman, “That will be necessary to increase our understanding of how these replay events drive memory formation and behavior.”

By combining these capabilities with optogenetics — a technology that makes neurons controllable with flashes of light — the researchers could conduct what they call “closed-loop” studies in which they could use their instantaneous readout of spatial thinking to trigger experimental manipulations. For example, they could see what happens to navigational performance the day after they interfered with replay during sleep, or they could determine what temporarily disrupting communication between the cortex and hippocampus might do when a rat faces a key decision about which direction to go.

Hu is also affiliated with Zhejiang University in China. In addition to Hu, Wilson, Chen, Kloosterman, Ciliberti, and Michon, the paper’s other authors are Andres Grosmark of Columbia University, Daoyun Ji of Baylor College of Medicine, Hector Penagos of MIT’s Picower Institute, and György Buzsáki of NYU.

Funding for the study came from the U.S. National Institutes of Health, the National Science Foundation, MIT’s NSF-funded Center for Brains Minds and Machines, Research Foundation – Flanders (FWO), the National Science Foundation of China, and the Simons Foundation.

Engineering “capture compounds” to probe cell growth

Researchers develop a method to investigate how bacteria respond to starvation and to identify which proteins bind to what they call the “magic spot” — ppGpp.

Raleigh McElvery | Department of Biology
December 17, 2018

In 1969, scientist Michael Cashel was analyzing the compounds produced by starved bacteria when he noticed two spots appearing on his chromatogram as if by magic. Today, we know one of these “magic spots,” as researchers call them, as guanosine tetraphosphate, or ppGpp for short. We also understand that it is a signaling molecule present in virtually all bacteria, helping tune cell growth and size based on nutrient availability.

And yet, despite decades of study, precisely how ppGpp regulates bacterial growth has remained rather mysterious. Delving further requires a more comprehensive list of the molecules that ppGpp binds to exert its effects.

Now, collaborators from MIT’s departments of Biology and Chemistry have developed a method to do just that, and used their new approach to pinpoint over 50 ppGpp targets in Escherichia coli — roughly half which had not been identified previously. Many of these targets are enzymes required to produce nucleotides, the building blocks of DNA and RNA. During times when the bacteria do not have enough nutrients to grow and divide normally, the researchers propose that ppGpp prevents these enzymes from creating new nucleotides from scratch, helping cells enter a dormant state.

“With small molecules or metabolites like ppGpp, it’s been difficult historically to determine which proteins they bind,” says Michael Laub, a professor of biology, a Howard Hughes Medical Institute investigator, and the senior author of the study. “This has been an intractable problem that’s held the field back for some time, but our new approach allows you to nail down the likely targets in a matter of weeks.”

Postdoc Boyuan Wang is the first author of the study, which appeares in Nature Chemical Biology on Dec. 17.

Since ppGpp was discovered nearly 50 years ago, it has been shown to suppress DNA replication, transcription, translation, and various metabolic pathways. It puts the brakes on cell growth and allows bacteria to persist in the face of starvation, stress, and antibiotics. Its influence over numerous regulatory processes has remained somewhat of a mystery, however — after all, it doesn’t just modulate a single pathway but coordinates multiple operations simultaneously to orchestrate a mass shutdown of the cell.

In order to discern which proteins ppGpp binds to effect such widespread change, the researchers built what they call “capture compounds” that contain ppGpp, allowing them to fish out its targets from bacterial extracts. These compounds included a photoreactive crosslinker that latched tightly onto the proteins of interest in the presence of light, and a biotin handle that helped the scientists pull out the proteins to identify them. Most importantly, they were joined to ppGpp in such a way that they wouldn’t interfere with its ability to bind to its targets. This method is more efficient and accurate compared to more traditional means of distinguishing ppGpp targets, which are far more arduous and lack sensitivity.

“Our approach solves these problems because you’re no longer required to do such labor-intensive protocols in order to identify ppGpp targets — and it works even in bacteria beyond E. coli,” says Wang. “Although ppGpp is common among many bacterial species, it seems to exert its effects through different mechanisms, which complicates things. Our capture compounds provide a way to unravel this diversity, and in short order.”

Although the 56 ppGpp targets Wang identified in his screen control a myriad of cellular processes, he homed in on the enzyme PurF — which initiates the biosynthesis of purine nucleotides bearing adenine and guanine bases, also known as A and G.

When bacteria are stressed or starved, they enter a dormant state to survive. But simply curbing translation and transcription is not enough; nucleotides are still being generated and will build up if their synthesis is not put on pause. Cells can build nucleotides in one of two ways: either by salvaging existing materials or starting completely from scratch. PurF kicks off the first step in the latter process leading to the A and G nucleotides. However, when ppGpp binds to PurF, it causes the enzyme to change its shape, which prevents it from doing its job, thus reducing nucleotide production in the cell.

“This is the first time that an enzyme involved in that specific pathway or function has been identified as a ppGpp target,” Wang says. “If you limit the consumption of nucleotides but not their production, the nucleotide pool is going to explode, which isn’t good for the cell. So we’ve shown that ppGpp actually addresses this problem as well.”

In addition to PurF and other enzymes required for nucleotide production, the researchers noticed that ppGpp also binds to many GTPase enzymes involved in translation. This could indicate a failsafe mechanism slowing down translation by striking multiple, similar enzymes in an almost redundant manner in the face of starvation.

As Wang continues to refine his method, he aims to increase its specificity and ensure his capture compounds bind to the exact same proteins they would inside a live cell. He also hopes to screen for ppGpp binding proteins in other bacteria, including pathogens that rely on ppGpp to survive within their hosts and propagate conditions like tuberculosis.

“This is an exciting chemical approach to better understand the function of a long-studied conserved signaling molecule in bacteria,” says Jue Wang, professor of bacteriology at the University of Wisconsin at Madison, who was not involved with the study. “Their findings and techniques are highly relevant to many other bacteria, and will greatly improve knowledge of how bacteria use this critical signaling molecule to mediate everything from surviving in the human gut to causing disease.”

Adds Laub: “We are still discovering new nucleotide-based signaling molecules in bacteria even today, and every single one of them could eventually be derivatized in a similar way to identify their binding partners.”

This research was supported by a fellowship from the Jane Coffin Childs Memorial Fund for Medical Research and a grant from the National Institutes of Health.

Five MIT students named 2019 Marshall Scholars

Radha Mastandrea, Katie O’Nell, Anna Sappington, Kyle Swanson, and Crystal Winston will begin graduate studies in the UK next fall.

Julia Mongo | Office of Distinguished Fellowships
December 3, 2018

Five MIT students — Radha Mastandrea, Kathryn O’Nell, Anna Sappington, Kyle Swanson ’18, and Crystal Winston — have been awarded Marshall Scholarships to pursue graduate studies in the United Kingdom. This class represents the largest number of Marshall Scholars from the Institute in a single year, and continues MIT students’ exceptional record of achievement in this elite fellowship program.

Funded by the British government, the Marshall Scholarship provides outstanding young Americans with the opportunity to earn advanced degrees in any academic subject at any university in the United Kingdom. Scholars are chosen through a rigorous national competition that assesses academic merit, leadership, and ambassadorial potential. Up to 40 Marshall Scholarships are granted each year.

The MIT students were guided by Kimberly Benard, assistant dean of distinguished fellowships within MIT Career Advising and Professional Development, and by the Presidential Committee on Distinguished Fellowships co-chaired by professors Rebecca Saxe and Will Broadhead. “Working with students like our Marshall Scholars is one of the great pleasures and privileges of teaching at MIT,” says Saxe. “Every year I’m impressed by how hard all of the finalists work to develop and communicate their distinctive vision for the future and their place in it.”

“MIT’s five Marshall Scholars, Radha, Katie, Anna, Kyle, and Crystal, are extraordinary; they are intelligent, creative, and dedicated to making a better world,” says MIT Chancellor Cynthia Barnhart. “Together, they make up an eighth of the entire class of 2019 Marshall Scholars, a remarkable accomplishment that would not have been possible without the hard work and passion of these students; the incredible efforts of professors Broadhead and Saxe and the entire Presidential Committee for Distinguished Fellowships; and the staff who work around the clock to support all applicants through this demanding process. We are fortunate that our 2019 Marshall Scholars have such exciting opportunities to look forward to, and that they will be representing the MIT community to the world.”

Radha Mastandrea

Hailing from Westwood, Massachusetts, Mastandrea is an MIT senior double-majoring in physics and mathematics. She is headed to Cambridge, where she will study theoretical and experimental physics before returning to the U.S. to undertake a PhD in high-energy particle physics. She aims for a career in academia as a researcher and an advocate for open data.

As an undergraduate researcher with Professor Jesse Thaler at the MIT Center for Theoretical Physics, Mastandrea has been using machine learning to analyze a trove of open data from the CERN Large Hadron Collider to gain insight on quarks and gluons. Mastandrea has also conducted research on galaxy spectral emission data with Professor Michael McDonald at the MIT Kavli Institute for Astrophysics and Space Research, and neutrinoless double beta decays with Professor Lindley Winslow at the MIT Laboratory for Nuclear Science. During a summer internship at Caltech, she researched black holes with the Laser Interferometer Gravitational-wave Observatory (LIGO) Scientific Collaboration.

Mastandrea is committed to championing women in physics. As president of MIT’s Undergraduate Women in Physics, she has established connections between undergraduates and older role models to showcase women’s accomplishments in the physics field. She has mentored local high school girls by leading physics exploration days on the MIT campus, and she helped write the MIT physics department’s first community values statement to foster a culture of respect and support. Mastandrea is also co-captain of MIT Bhangra and has taught bhangra dance classes to members of the local community.

Kathryn “Katie” O’Nell

O’Nell, from San Diego, California, is an MIT senior majoring in brain and cognitive sciences. At Oxford University, she will pursue an MS in the Department of Experimental Psychology. She will then return to the U.S. to embark on doctoral studies in computational neuroscience with the goal of becoming a professor and researcher.

O’Nell is currently conducting studies on facial perception in the laboratories of Professor Rebecca Saxe in MIT’s Department of Brain and Cognitive Sciences and Professor Stefano Anzellotti of Boston College. O’Nell has also been examining the connection between gestures and speech with the MIT Speech Communication Group, and she has created calcium imaging processing pipelines in the laboratory of Professor Ann Graybiel at the McGovern Institute for Brain Research at MIT. O’Nell spent two summers interning at the J. Craig Venter Institute, which conducts genomic and bioinformatics research.

On campus, O’Nell is an associate advisor to first-year students and a member of the associate advisor steering committee. She is active with the MIT Model UN Conference for high school students and serves as special political and decolonization committee chair. She also mentors high school students as a Splash instructor for the MIT Educational Studies Program and as president of the MIT Academic Teaching Initiative. As campus engagement chair for the MIT Addir Interfaith Program, O’Nell plans and promotes campus-wide events, including an upcoming interfaith hackathon. O’Nell originated and oversees the popular murder mystery-themed puzzle hunt for her residence hall, MacGregor House.

Anna Sappington

A native of Riva, Maryland, Sappington will graduate this spring with a BS in computer science and molecular biology. She will earn master’s degrees in machine learning at University College London and medical sciences in oncology at the Cambridge University. She will then pursue an interdisciplinary career as a physician-scientist using computer science to improve precision medicine.

As an undergraduate researcher at the laboratory of Professor Aviv Regev in MIT’s Department of Biology and the Broad Institute of MIT and Harvard, Sappington has been developing machine-learning techniques to improve cell type classification for the Human Cell Atlas Initiative. She has also conducted research on hepatitis B virus infection in the laboratory of Professor Sangeeta Bhatia in the Department of Electrical Engineering and Computer Science and the Koch Institute for Integrative Cancer Research. Sappington has held summer research internships at the National Institutes of Health in Bethesda, Maryland, and as an Amgen Scholar at Kyoto University, Japan. In 2018, she was named a national Barry M. Goldwater Scholar and an MIT Burchard Scholar.

Sappington served as the Director of TechX, which hosts world-renowned events such as HackMIT. She is co-president of the MIT Biology Undergraduate Student Association, a teaching assistant for the biology department, and a peer health counselor and former residential director for MIT MedLinks. A talented dancer, Sappington has performed with MIT DanceTroupe and the MIT Asian Dance Team. For the past two years, she has volunteered for the Massachusetts General Hospital department of radiation oncology.

Kyle Swanson

Hailing from Bronxville, New York, Swanson graduated from MIT in 2018 with a BS in computer science and engineering, a BS in mathematics, and a minor in music. He will receive his MEng in computer science and engineering this spring. As a Marshall Scholar, Swanson will study mathematics and computer science at Cambridge. He intends to pursue a PhD in computer science to research applications of machine learning to the diagnosis and treatment of cancer.

As an undergraduate, Swanson worked with Professor Regina Barzilay in MIT’s Computer Science and Artificial Intelligence Laboratory (CSAIL) and Constance Lehman in the Breast Imaging Division of Massachusetts General Hospital on machine learning to improve breast cancer detection in mammography, and recently co-authored a paper published in Radiology.

Swanson’s master’s research with Barzilay focuses on machine learning for chemistry. He is currently developing machine-learning algorithms to predict molecular properties such as toxicity or solubility, with the hope of developing a property-prediction tool that can accelerate drug discovery. Swanson previously conducted research on cybersecurity at CSAIL. He has interned at Microsoft and other companies and taught machine learning to university students in Kazakhstan.

An accomplished musician, Swanson plays flute and piccolo with the MIT Symphony Orchestra where he has served as president. He is active with the music service club Ribotones, which performs concerts at nursing homes, and he has played with MIT’s Chamber Music Society and Wind Ensemble. Swanson has received multiple MIT awards recognizing his musical talent and scholarship.

Crystal Winston

Winston, from Charlotte, North Carolina, is an MIT senior majoring in mechanical engineering. At Imperial College, Winston will embark on a PhD in aerospace materials and structures to further develop her skills in redesigning transportation systems. Her goal is to start a company that transforms transportation technology.

As a sophomore, Winston co-invented a remote-controlled four-wheeled robot that converts into a flying drone, which won first place in a campus project exhibition. She has continued to refine this project and hopes it can eventually be used to reduce traffic congestion by transporting people on ground or through the air.

Winston has conducted research on a robot for detecting and repairing pipe leaks, at the MIT Mechatronics Research Laboratory. As a mechanical engineering intern at Google, she designed and programmed systems for the cameras on Google Maps Streetview cars, and at the NASA Jet Propulsion Laboratory she designed and prototyped an animal-inspired foot for the Europa Lander. She has been a mechanical team member for the MIT Solar Electric Vehicle Team, and helped design and manufacture an electric solar car for the 2017 Formula Sun Grand Prix.

Winston is dedicated to her work with the National Society of Black Engineers (NSBE) where she has held several executive positions. As an engineering immersion program mentor with NSBE, she helps local underrepresented minority high school students prepare for STEM careers. Winston is a member of the Tau Beta Pi and Pi Tau Sigma engineering honors societies.

The long and short of CDK12

A new study linking RNA processing to DNA repair may open new avenues to cancer therapy.

Bendta Schroeder | Koch Institute
December 3, 2018

Mutations in the BRCA1 and BRCA2 genes pose a serious risk for breast and ovarian cancer because they endanger the genomic stability of a cell by interfering with homologous recombination repair (HR), a key mechanism for accurately repairing harmful double-stranded breaks in DNA. Without the ability to use HR to fix double-stranded breaks, the cell is forced to resort to more error-prone — and thus more cancer-prone — forms of DNA repair.

The BRCA1 and BRCA2 genes are not the only genes whose mutations foster tumorigenesis by causing an inability to repair DNA double strand breaks by HR. Mutations in twenty-two genes are known to disrupt HR, giving rise to tumors with what researchers call “BRCAness” characteristics. All but one of these BRCAness genes are known to be directly involved in the HR pathway.

The one exception, CDK12, is thought to facilitate a set of different processes altogether, involving how RNA transcripts are elongated, spliced and cleaved into their mature forms. While the connection between this RNA-modulating gene to DNA repair remained poorly understood, the identification of CDK12 as a BRCAness gene piqued significant clinical interest.

The researchers who pinpointed this connection, Sara Dubbury and Paul Boutz, both work in the laboratory of Phillip Sharp, Institute Professor, professor of biology, and member of the Koch Institute for Integrative Cancer Research. In a study appearing online in Nature on Nov. 28, they describe how they discovered a previously unknown mechanism by which CDK12 enables the production of full-length RNA transcripts and that this mechanism was especially critical to maintain functional expression of the other BRCAness genes.

When the researchers knocked out expression of CDK12, mouse stem cells showed many signs of accumulating DNA damage that prevented DNA replication from going forward, classic indications of a BRCAness phenotype. To identify what roles CDK12 may play in regulating gene expression, the researchers turned to RNA sequencing to determine which genes had increased or decreased their overall expression.

To their surprise, only genes activated by p53 and early differentiation (side effects of accumulating unrepaired DNA damage and BRCAness in mouse stem cells) accounted for the lion’s share of changes to RNA transcription. However, when the researchers instead focused on the types of RNAs transcribed, they found that many genes produced unusually short transcripts when CDK12 was absent.

Not every stretch of DNA in a gene makes it into the final RNA transcript. The initial RNA from a gene often includes sections, which researchers call “introns,” that are cut out of transcript, the discovery that earned Sharp the 1993 Nobel Prize in Physiology or Medicine and the remaining sections. “Exons,” are spliced together to form a mature transcript (mRNA). Alternately, an intronic polyadenylation (IPA) site may be activated to cleave away the RNA sequence that follows it preventing intron removal and generating a prematurely shortened transcript. These processes allow the same gene to produce alternate forms of messenger RNA (mRNA), and thus be translated into different protein sequences.

Surprisingly CDK12 knockout cells produced significantly more IPA-truncated transcripts genome-wide, while full-length transcripts for the same genes were reduced. These shortened mRNAs can vary greatly in their stability, their ability to be translated into protein, and their protein function. Thus, even while a gene may be actively transcribed, its translation into functional proteins can be radically altered or depleted by IPA activation.

While this observation began to illuminate CDK12’s role in regulating mRNA processing, what remained puzzling was why CDK12 loss affected the HR pathway so disproportionately. In investigating this question, Dubbury and Boutz found that BRCAness genes were overrepresented as a group among those genes that have increased IPA activity upon CDK12 loss.

Additionally, while CDK12 suppresses IPA activity genome-wide, 13 of the other 21 BRCAness genes were found to be particularly vulnerable to CDK12 loss, in part, because they possess multiple high-sensitivity IPA sites, which have a compound effect in decreasing the total amount of full-length transcripts. Moreover, because multiple CDK12-senstive BRCAness genes operate in the same HR pathway, the researchers believe that the disruption to HR repair of double-stranded DNA breaks is amplified.

CDK12 mutations are found recurrently in prostate and ovarian cancer patients, making them an attractive diagnostic and therapeutic target for cancer. However, not enough is known about CDK12 to distinguish between true loss-of-function mutations and so-called “passenger mutations” with no functional consequence.

“The ability to identify patients with true loss-of-function mutations in CDK12 would enable clinicians to label a new cohort of patients with bona fide BRCAness tumors that could benefit from certain highly effective and targeted chemotherapeutics against BRCAness, such as PARP1 inhibitors,” says Dubbury, a former David H. Koch Fellow.

Dubbury and Boutz were able to confirm that IPA sites in key BRCAness genes were also used more frequently upon CDK12 loss in human tumor cells using RNA sequencing data from prostate and ovarian tumor patients with CDK12 mutations and by treating human prostate adenocarcinoma and ovarian carcinoma cells with a CDK12 inhibitor. This result suggests that the CDK12 mechanism observed in mouse cell lines is conserved in humans and that CDK12 mutations in human ovarian and prostate tumors may promote tumorigenesis by increasing IPA activity and thus functionally attenuating HR repair.

“These results not only give us a better understanding how CDK12 contributes to BRCAness, they also may have exciting potential impact in the clinic,” Dubbury says. “Currently available diagnostic techniques could be used to probe the usage of IPA sites found in this study to rapidly screen for patients with true loss-of-function CDK12 mutations, who would respond to BRCAness-targeted treatments.”

Paul Boutz, a research scientist in the Sharp Lab, is co-first author of the study, and has plans to follow-up many of these implications for ovarian and prostate cancer his lab at the University of Rochester School of Medicine and Dentistry.

“CDK12 provides a remarkable example of how factors that control the processing of RNA molecules can function as master regulators of gene networks, and thereby profoundly affect the physiology of both normal and cancerous cells,” he says.

Phil Sharp, the senior author on the work, says “Sara’s and Paul’s surprising discovery that CDK12 suppresses intronic polyadenylation has implications for fundamental new insights into gene structure as well as for control of cancer.”

Angelika Amon wins 2019 Breakthrough Prize in Life Sciences

Four other MIT researchers to receive New Horizons Prizes in math and physics; two alumni win Breakthrough Prize in Fundamental Physics.

Anne Trafton | MIT News Office
October 17, 2018

Angelika Amon, an MIT professor of biology, is one of five scientists who will receive a 2019 Breakthrough Prize in Life Sciences, given for transformative advances toward understanding living systems and extending human life.

Amon, the Kathleen and Curtis Marble Professor in Cancer Research and a member of MIT’s Koch Institute for Integrative Cancer Research, was honored for her work in determining the consequences of aneuploidy, an abnormal chromosome number that results from mis-segregation of chromosomes during cell division.

The award, announced this morning, comes with a $3 million prize.

“Angelika Amon is an outstanding choice to receive the Breakthrough Prize,” says Tyler Jacks, director of the Koch Institute and the David H. Koch Professor of Biology. “Her work on understanding how cells control the decisions to divide and the effects of imbalances in chromosome number has helped shape how we think about normal development and disease. Angelika is a fearless investigator and a true scientist’s scientist. All of us in the Koch Institute and across MIT are thrilled by this news.”

Two MIT alumni, Charles Kane PhD ’89 and Eugene Mele PhD ’78, both professors at the University of Pennsylvania, will share a Breakthrough Prize in Fundamental Physics. Kane and Mele are being recognized for their new ideas about topology and symmetry in physics, leading to the prediction of a new class of materials that conduct electricity only on their surface.

New Horizons winners

Also announced today, three MIT physics researchers will receive the $100,000 New Horizons in Physics Prize, awarded to promising junior researchers who have already produced important work.

Lisa Barsotti, a principal research scientist at MIT’s Kavli Institute, and Matthew Evans, an MIT associate professor of physics, will share the prize with Rana Adhikari of Caltech for their work on ground-based detectors of gravitational waves. Daniel Harlow, an MIT assistant professor of physics, will share the prize with Daniel Jafferis of Harvard University and Aron Wall of Stanford University for their work generating fundamental insights about quantum information, quantum field theory, and gravity.

Additionally, Chenyang Xu, an MIT professor of mathematics, will receive a 2019 New Horizons in Mathematics Prize for his work in the minimal model program and applications to the moduli of algebraic varieties.

“On behalf of the School of Science, I congratulate Angelika Amon for this extraordinary honor, in recognition of her brilliant work that expands our understanding of cellular mechanisms that may lead to cancer,” says Michael Sipser, dean of the MIT School of Science and the Donner Professor of Mathematics. “We celebrate all recipients of these prestigious awards, including MIT’s four researchers whose impressive early-career achievements in physics and mathematics are being recognized today. Our scientists pursue fundamental research that advances human knowledge, which in turn leads to a better world.”

Chromosome imbalance

Most living cells have a defined number of chromosomes. Human cells, for example, have 23 pairs of chromosomes. However, as cells divide, they can make errors that lead to a gain or loss of chromosomes.

Amon has spent much of her career studying how this condition affects cells. When aneuploidy occurs in embryonic cells, it is almost always fatal to the organism. For human embryos, extra copies of any chromosome are lethal, with the exceptions of chromosome 21, which produces Down syndrome; chromosomes 13 and 18, which lead to developmental disorders known as Patau and Edwards syndromes; and the X and Y sex chromosomes, extra copies of which may sometimes cause various disorders but are not usually lethal.

In recent years, Amon’s lab has been exploring an apparent paradox of aneuploidy: When normal adult cells become aneuploid, it impairs their ability to survive and proliferate; however, cancer cells, which are nearly all aneuploid, can grow uncontrollably. Amon has shown that aneuploidy disrupts cells’ usual error-repair systems, allowing genetic mutations to quickly accumulate.

A better understanding of the consequences of aneuploidy could shed light on how cancer cells evolve and help to identify new therapeutic targets for cancer. Last year, Amon discovered a mechanism that the immune system uses to eliminate aneuploid cells from the body, raising the possibility of harnessing this system, which relies on natural killer cells, to destroy cancer cells.

Amon, who was informed of the prize several weeks ago, was sworn to secrecy until today’s announcement.

“When I received the phone call, I was driving in the car with my daughter, and it was really hard to not be too excited and thereby spill the beans,” she says. “Of course I am thrilled that our work is recognized in this manner.”

Scientists Frank Bennett of Ionis Pharmaceuticals, Adrian Krainer of Cold Spring Harbor Laboratory, Xiaowei Zhuang of Harvard University, and Zhijian Chen of the University of Texas Southwestern Medical Center will also receive Breakthrough Prizes in Life Sciences.

The 2019 Breakthrough Prize and New Horizon Prize recipients will be recognized at the seventh annual Breakthrough Prize ceremony, hosted by actor, producer and philanthropist Pierce Brosnan, on Sunday, Nov. 4, at NASA Ames Research Center in Mountain View, California, and broadcast live on National Geographic.

Joining the resolution revolution

Department of Biology hosts a symposium to celebrate the launch of MIT.nano and its new Cryogenic Electron Microscopy Facility.

Raleigh McElvery | Department of Biology
October 16, 2018

It’s a time of small marvels and big ideas. Welcome to the Nano Age.

MIT’s preparations for this new era are in full swing, including the recent launch of MIT.nano, the Institute’s center for nanoscience and nanotechnology. And on the day after MIT.nano’s opening ceremonies, the Department of Biology hosted its Cryogenic Electron Microscopy (Cryo-EM) Symposium, which was co-organized by biology professor Thomas Schwartz and the director of the new facility, Edward Brignole.

“We organized the symposium to raise awareness of this new research capacity, and to celebrate the many people who worked to fund these instruments, design the space, build the suites, and set up the microscopes,” Brignole said of the Oct. 5 event. “We also wanted to bring together the various groups across MIT working on diverse technologies to improve Cryo-EM, from mathematicians, computer scientists, and electrical engineers to biologists, chemists, and biological engineers.”

The event featured pioneers leveraging Cryo-EM for various interdisciplinary applications both on campus and outside of MIT — from biology and machine learning to quantum mechanics.

The program included Ed Egelman from the University of Virginia, Mark Bathe from the MIT Department of Biological Engineering, Katya Heldwein from Tufts University’s School of Medicine, and Karl Berggren from the Department of Electrical Engineering and Computer Science. Also giving talks were computational and systems biology graduate student Tristan Bepler from MIT’s Computer Science and Artificial Intelligence Laboratory, Luke Chao from Harvard Medical School and Massachusetts General Hospital, postdoc Kuang Shen from the Whitehead Institute at MIT, and graduate student Jonathan Weed from the MIT Department of Mathematics. The talks were followed by a reception in Building 68 and guided tours of the Cryo-EM Facility.

Unlike other popular techniques for determining 3-D macromolecular structures, Cryo-EM permits researchers to visualize more diverse and complex molecular assemblies in multiple conformations. Cryo-EM is housed in precisely climate-controlled rooms in the basement of MIT.nano, built atop a 5 million pound slab of concrete to minimize vibrations. Two multimillion-dollar instruments are being installed that will enable scientists to analyze cellular machinery in near-atomic detail; the microscopes are the first instruments to be installed in MIT.nano.

As Schwartz explained to an audience of more than 100 people during his opening remarks, he and his colleagues realized they needed to bring this technology to the MIT community. Like many of the center’s other tools, they would be too costly to purchase and too onerous to maintain for a single researcher or lab.

“Microscopes are very special and expensive tools, so this endeavor turned out to be much more involved than anything else I have done during my 14 years at MIT,” he said. “But this was not an effort of one or two people, it really took a whole community. We have many people to thank today.”

Establishing the Cryogenic Electron Microscopy Facility at MIT has been a long-time dream for Catherine Drennan, a professor of chemistry and biology and a Howard Hughes Medical Institute investigator. At the symposium, Drennan spoke about her work using the microscopes to capture snapshots of enzymes in action.

She remembers it was a “happy coincidence” that the plans for MIT.nano and the Cryo-EM Facility unfolded around the same time and then merged together to become one multi-disciplinary effort. Drennan, Schwartz, and others worked closely with MIT.nano Founding Director Vladimir Bulović and Vice President for Research Maria Zuber to gain institutional support and jumpstart the project. It took six years to design and construct MIT.nano, and four to implement the Cryo-EM Facility.

“We had this vision that the Cryo-EM Facility would be a shared space that people from all around MIT would use,” Drennan said.

An anonymous donor offered $5 million to fund the first microscope, the Titan Krios, while the Arnold and Mabel Beckman Foundation contributed $2.5 million to purchase the second, the Talos Arctica.

“The Beckman Foundation is really pleased to be supporting this kind of technology,” said Anne Hultgren, the foundation’s executive director, who attended the symposium. “It was a win-win in terms of the timing and the need in the community. We are excited to be part of this effort, and to drive forward new innovations and experiments.”

The Beckman Foundation has made similar instrumentation grants to Johns Hopkins University School of Medicine, University of Pennsylvania’s Perelman School of Medicine, the University of Utah, and the University of Washington School of Medicine.

Drennan said that as the revolution in resolution continues to build, she hopes MIT’s new microscopes will bolster the resurging Cryo-EM community that’s slowly growing in and around Boston.

“Thanks to facilities like this, the Boston area went from being way behind the curve to right in front of it,” she said. “It’s an incredibly exciting time, and I can’t wait to see how we learn and grow as a research community.”

In pursuit of the elusive stem cell

New MIT initiative delves into the biology of stem cells and cancer stem cells, seeks ways to identify, purify, and propagate them.

Koch Institute
October 16, 2018

How does the body renew itself? How do cancer cells use the same or similar processes to form tumors and spread throughout the body? How might we use those processes to heal injuries or fight cancer?

A new research program at MIT is tackling fundamental biological questions about normal adult stem cells and their malignant counterparts, cancer stem cells. Launched last spring with support from Fondation MIT, the MIT Stem Cell Initiative is headed by Jacqueline Lees, the Virginia and D.K. Ludwig Professor of Cancer Research, professor of biology, and associate director of the Koch Institute for Integrative Cancer Research. Other founding members of the initiative are Robert Weinberg, a professor of biology, Whitehead Institute member, and director of the Ludwig Center at MIT; and Omer Yilmaz, an assistant professor of biology.

Rare power

Normal adult stem cells have been defined for more than a half-century. Relatively rare, they are undifferentiated cells within a tissue that divide to produce two daughter cells. One remains in the stem cell state to maintain the stem cell population, a process called self-renewal. The second daughter cell adopts a partially differentiated state, then goes on to divide and differentiate further to yield multiple cell types that form that tissue. In many fully formed adult tissues, normal stem cells divide periodically to replenish or repair the tissue. Importantly, this division is a carefully controlled process to ensure that tissues are restricted to the appropriate size and cell content.

Cancer stem cells are also of long-standing interest and share many similarities with normal adult stem cells. They perform the same division but, rather than differentiating, the additional cells produced by the second daughter cell amass to form the bulk of the tumor. Following surgery or treatment, cancer stem cells can regrow the tumor — and are frequently resistant to chemotherapy — making them especially dangerous. This unique ability of normal and cancer stem cells to both self-renew and form a tissue or tumor is referred to by researchers as “stemness,” and has important implications for biomedical applications.

Because of the key role they play in tissue maintenance and regeneration, normal stem cells hold great promise for use in repairing damaged tissues. Cancer stem cells, correspondingly, are the lifeblood of tumors. Although relatively rare within tumors, they are particularly important because they possess the ability to create tumors and are also chemotherapy-resistant. As a result, cancer stem cells are thought to be responsible for tumor recurrence after remission, and also for the formation of metastases, which account for the majority of cancer-associated deaths. Accordingly, an anti-cancer stem cell therapy that can target and kill cancer stem cells is one of the holy grails of cancer treatment — a means to suppress both tumor recurrence and metastatic disease.

Hiding in plain sight

One of the fundamental challenges to studying normal and cancer stem cells, and to ultimately harnessing that knowledge, is developing the ability to identify, purify, and propagate these cells. This has often proved tricky, as another key similarity between normal and cancer stem cells is that neither is visibly different from other cells in a tissue or tumor. Thus, a major goal in stem cell and cancer stem cell research is finding ways to distinguish these rare specimens from other cells, ideally by identifying unique surface markers that can be used to purify stem cell and cancer stem cell populations and enable their study.

The MIT Stem Cell Initiative is applying new technologies and approaches in pursuit of this goal. More specifically, the program aims to:

  • identify the stem cells and cancer stem cells in various tissues and tumor types;
  • determine how these cells change during aging (in the case of normal stem cells) or with disease progression (in the case of degenerative conditions and cancer); and
  • determine the similarities and differences between normal and cancer stem cells, with the goal of finding vulnerabilities in cancer stem cells that can be viable and specific targets for treatment.

Ultimately, the ability to identify, purify, and establish various populations of stem cells and cancer stem cells could help researchers better understand the biology of these cells, and learn how to utilize them more effectively in regenerative medicine applications and target them in cancer.

When biology meets technology

MIT Stem Cell Initiative studies focus on normal and cancer stem cells of epithelial tissues. Epithelia are one of four general tissue types in the body; they line most organs and are where the vast majority of cancers arise. Epithelial cells from different organs share some biological properties, but also have distinct differences reflecting the organ’s specific role and/or environment. In particular, the MIT Stem Cell Initiative has focused on the breast and colon, as these tissues are quite different from each other, yet each constitutes a major portion of cancer incidence.

New technologies are enabling the researchers to make significant headway in these investigations, progress that was not feasible just a few years ago. Specifically, they are using a combination of specially cultured cells, sophisticated and highly controllable mouse models of cancer, and single-cell RNA sequencing and computational analysis techniques that are uniquely suited to extracting a great deal of information from the relatively small number of stem cells.

While breast and colon work is ongoing, MIT Stem Cell Initiative members are planning studies of additional tissues and recruiting collaborators for pilot projects. The results of the researchers’ studies will advance understandings of stem cell regulation and may ultimately lead to advances in tissue regeneration and/or cancer analysis and treatment.

Progress against pancreatic cancer

Lustgarten Foundation names MIT laboratory to improve understanding and treatment of a deadly disease

Erika Reinfeld | Koch Institute
October 12, 2018

Genetically complex and hard to detect in its early stages, pancreatic cancer is the fourth leading cause of cancer mortality in the U.S. It is also a long-standing staple of the MIT cancer research portfolio, with multiple active projects at the Koch Institute and beyond seeking to transform the way the disease is studied and treated.

On Sept. 21, the Lustgarten Foundation, the nation’s largest private funder of pancreatic cancer research, honored MIT’s commitment to pancreatic cancer research with the naming of the Lustgarten Laboratory for Pancreatic Cancer Research at MIT. The Lustgarten Laboratory is headed by Tyler Jacks, director of the Koch Institute and the David H. Koch Professor of Biology.

The Lustgarten Foundation’s investment will support postdocs, graduate students, technicians and a senior scientist for its duration. The Lustgarten Lab’s goals are to better understand the immunological conditions and genetic events that contribute to the development of pancreatic cancer, to study the disease on a single-cell level in both humans and mouse models, and to develop novel high throughput tools for culture and drug testing using mini-organs known as organoids.

The Jacks lab is ideally suited for this massive undertaking, thanks to its solid portfolio of pancreatic cancer research, developed with the support of the Lustgarten Foundation and others, and its deep connections with both biology and engineering laboratories at the Koch Institute and across the MIT campus.

At the dedication ceremony, David Tuveson, the chief scientist of the Lustgarten Foundation, praised the Jacks lab’s “collective skills and talents” and its “highly collaborative approach” as the driving force behind many advances in pancreatic cancer research over the last two decades, a legacy of which Tuveson is part.

Of mice and mentorship

Jacks is widely considered a pioneer in the development of engineered mouse models of human cancers. It was in his laboratory, then a part of MIT’s Center for Cancer Research, the predecessor to the Koch Institute, that Tuveson began work on what would become the KPC mouse model of pancreatic ductal adenocarcinoma (PDAC). The model, which centers around the exploitation of commonly mutated genes Kras (a cancer driver) and p53 (a tumor suppressor) is now the gold standard for pre-clinical studies of the disease. With it, scientists can trace the development of tumors inside a living pancreas from a single mutated cell to metastatic invasion of distant organs.

In a way, the model presents a microcosm of the robust training environment within the Jacks Lab. Current postdoctoral researcher and designated Lustgarten Lab lead scientist Will Freed-Pastor praises his mentor’s willingness to step back and give his mentees space to make their own marks on the world. “Training future leaders,” he says, “is one of Tyler’s most valuable contributions to the field.”

With the new resources from Lustgarten, Jacks looks forward to bringing even more researchers into field and applying knowledge gained from his lab’s work in lung cancer, immunology, and gene editing to the unique challenges of pancreatic tumors.

“We have a formidable team and it is only going to get stronger,” Jacks says. “We are grateful for the Lustgarten Foundation’s investment in our work as it allows us to recruit new investigators from across MIT who have never worked in pancreatic cancer before but whose tools and approaches will help us develop new treatment paradigms for early diagnosis and intervention.”

A signature investment

The naming of the Lustgarten Laboratory for Pancreatic Cancer Research at MIT is happening side-by-side with that of Brian Wolpin’s lab across the river at Dana-Farber Cancer Institute. In addition to serving as the Jacks lab’s clinical liaison, Wolpin has collaborated on pancreatic cancer research with Matthew Vander Heiden, professor of biology and associate director of the Koch Institute.

The dual investment represents a milestone for the Lustgarten Foundation — the second and third lab spaces dedicated to pancreatic cancer research — in its 20th anniversary year. Tuveson heads the first, Cold Spring Harbor Laboratory, where he is now a professor and the director of the Cancer Center.

“We are so excited to usher in a new era of pancreatic cancer research,” says Kerri Kaplan, president and chief executive officer of the Lustgarten Foundation. “Twenty years ago, this was truly an ‘orphan’ disease, but thanks to the commitment and innovative approaches of these researchers at MIT and beyond, we are rapidly expanding our knowledge and ability to improve patient outcomes.”

As a researcher himself and the shepherd of MIT’s transition from the Center for Cancer Research to the Koch Institute, Jacks has long sought to balance basic science research with clinical applications. Pancreatic cancer was among the first disease areas identified as a priority for the Bridge Project, the Koch Institute’s signature collaboration between MIT and Dana-Farber/Harvard Cancer Center. The Lustgarten Foundation was among the primary supporters of the Bridge Project in its inaugural year. Even with these resources, however, pancreatic cancer continues to be a difficult disease to approach.

Jacks and his colleagues describe the Lustgarten investment as high-risk, high-reward — an innovation fund to move beyond incremental improvements at both the bench and the bedside.

“This gives us the freedom to ask very challenging questions about cancer cells themselves and the immune system,” Freed-Pastor says.

Jacks agrees. “This is exactly the right time for this work,” he says. “We understand so much more about this disease than we did two decades ago, and we now have the teams and technologies to transform that knowledge into actionable solutions for patients. We are honored by the Lustgarten Foundation’s trust in that endeavor.”