In cells, self-destructive behavior suggests strategy for fighting cancer

SOMETIMES, TO SURVIVE, our cells destroy their own ribonucleic acid (RNA), the part of our genetic instruction code that helps turn genes into proteins. Cells do this as part of the first line of defense against pathogens and damage. New research suggests how this mechanism could form the basis of a strategy against cancer.

The mechanism is part of the body’s innate immune system, which kicks into gear minutes after infection. The innate immune system holds pathogens at bay for the critical few days needed to make antibodies.

One of the mysterious weapons in the innate immune system is an enzyme called RNase L that chops up strands of RNA, an intermediate step between genes and their final products, proteins. Because viruses lack the machinery to make copies of themselves to spread infection, they hijack a cell’s reproductive technology and force it to make viral RNA and proteins. To fight back, the body sends RNase L. (The “ase” is a common ending for enzymes, and the “L” is for latent, because RNase L lies in wait for infection or damage signals.)

RNase L chops up the viral RNA, but it also shears the body’s own RNA. This self-mutilation is necessary for good health. Mice that lack RNase L are obese, diabetic and have signs of inflammation.

“This cleavage of the cell’s own RNA has a protective function. It does not always kill the cell, but when it does it eliminates only damaged or infected cells, which repairs the tissue. It ultimately means animals survive better,” said Alexei Korennykh, an associate professor of molecular biology. His lab was the first to solve the crystal structure of human RNase L, a result they published in the journal Science March 14, 2014.

Korennykh’s research is funded by the National Institutes of Health, the Sidney Kimmel Foundation, the Burroughs Wellcome Fund and the Vallee Foundation.

With the 3-D structure in hand, Korennykh and his team turned to the question of how RNase L works. Korennykh wondered if RNase L chops up every RNA that comes along, or just certain ones. To find out, the researchers sequenced every piece of RNA made in a typical human cell and evaluated them to see which ones were susceptible to RNase L.

What they found surprised them. RNase L chops up RNA strands that govern the rapid division of cells, as well as how well cells stick to each other. These two activities — when cells proliferate and attach themselves in new locations — are two of the key steps in the spread of cancer. They published the findings Dec. 29, 2015, in the Proceedings of the National Academy of Sciences.

The link between RNase L and cancer made sense because RNase L mutations are common in individuals from families with a hereditary predisposition for prostate cancer, Korennykh said. The team is exploring how to turn this discovery into a strategy for inhibiting cancer’s spread using small drug-like molecules to boost RNase L’s activity against cell proliferation and attachment.

“We really stumbled on this approach very unexpectedly,” Korennykh said. “Often the best experiments are the ones where you didn’t get the results you expected.” –By Catherine Zandonella

BONNIE BASSLER receives Shaw Prize in life science and medicine

PHOTO BY ALENA SOBOLEVA

PHOTO BY ALENA SOBOLEVA

Bonnie Bassler, the Squibb Professor in Molecular Biology and chair of the Department of Molecular Biology, was named a 2015 Shaw Laureate in life science and medicine on June 1, 2015. Awarded by the Hong Kong-based Shaw Foundation, the Shaw Prize honors recent breakthroughs by active researchers in the fields of mathematics, astronomy, and life and medical sciences.

Bassler was recognized for her well-known work in quorum sensing, a widespread process that bacteria use for cell-to-cell communication. Understanding quorum sensing “offers innovative ways to interfere with bacterial pathogens or to modulate the microbiome for health applications,” according to the prize citation. Bassler, a Howard Hughes Medical Institute investigator, shares the $1 million prize with E. Peter Greenberg, a University of Washington professor of microbiology. The 2015 prizes were awarded during a Sept. 24 ceremony in Hong Kong.

–By Morgan Kelly

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DAVID TANK receives Brain Prize for advance in microscopy

PHOTO BY WINFRIED DENK

PHOTO BY WINFRIED DENK

David Tank, the Henry L. Hillman Professor in Molecular Biology and co-director of the Princeton Neuroscience Institute, has been named one of four winners of the Brain Prize, an honor that recognizes scientists who have made outstanding contributions to brain research.

Tank was presented the prize by His Royal Highness Crown Prince Frederik of Denmark on May 7, 2015, in Copenhagen. He shares the 1 million euro, or roughly $1,085,000, prize with Winfried Denk of the Max Planck Institute of Neurobiology in Munich; Arthur Konnerth of the Technical University of Munich; and Karel Svoboda of the Howard Hughes Medical Institute in Chevy Chase, Maryland.

The researchers were selected for the invention, development and application of two-photon microscopy, a technology that combines advanced techniques from physics and biology to allow scientists to examine the finest structures of the brain in real time.

“Thanks to these four scientists we’re now able to study the normal brain’s development and attempt to understand what goes wrong when we’re affected by destructive diseases such as Alzheimer’s and other types of dementia,” said Professor Povl Krogsgaard- Larsen, chair of the Grete Lundbeck European Brain Research Foundation, which awards the prize.

–By Michael Hotchkiss

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Energy boost: Study sheds light on mitochondrial disease

Ileana Cristea

Ileana Cristea PHOTO BY FRANK WOJCIECHOWSKI

INSIDE OUR CELLS, TINY FACTORIES convert nutrients from food into a form of energy that cells can use. Failure of these factories, known as mitochondria, can lead to metabolic disorders that are difficult to diagnose and even harder to treat.

Now researchers have identified an important regulator of cellular energy production that could aid in the diagnosis and treatment of a range of conditions. In a study published on Dec. 18, 2014, in the journal Cell, the researchers demonstrated that an enzyme known as Sirtuin 4 acts as a guardian of cellular energy production.

“The finding has broad implications in human health,” said Ileana Cristea, associate professor of molecular biology, who led the study. “Stress, nutritional deficiencies and viral infections can impact Sirtuin 4 functions and trigger dysfunction in energy metabolism,” Cristea said. “With this knowledge, we now have a new regulatory point that can be targeted in therapeutic interventions.”

Cristea’s team discovered that Sirtuin 4 turns off energy production by removing certain protein modifications, called lipoylation, from a key part of the energy-making machinery, called the pyruvate dehydrogenase complex.

The research team included former Postdoctoral Researcher Rommel Mathias and Associate Research Scholar Todd Greco in the Cristea laboratory, as well as collaborators Thomas Shenk, the James A. Elkins Jr. Professor in the Life Sciences, and Yibin Kang, the Warner-Lambert/Parke-Davis Professor of Molecular Biology.

Cristea’s research is supported by the National Institute on Drug Abuse, the National Institute of Allergy and Infectious Disease, the National Institute of General Medical Sciences, and the Eunice Kennedy Shriver National Institute of Child Health and Human Development.

–By Catherine Zandonella

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Striking resemblance: A physical law may govern very different biological activities

Starlings

FLOCKS OF BIRDS FLY ACROSS THE SKY in shifting configurations. In the retina of an eye, millions of neurons ignite in ever-changing combinations, translating light into meaningful images. Yet both of these seemingly random behaviors have an underlying order that can be described by mathematics.

Like these cells and birds, when atoms and molecules come together they can display coordinated behaviors that are more than the sum of their parts. At a critical point, such as the boundary between liquid and gas, local interactions between molecules propagate through an entire material, changing its essential properties.

Princeton biophysicist William Bialek thinks criticality may also underlie collective behaviors in living organisms, and he’s using real-world data to test this hypothesis. Recently, Bialek and his colleagues have analyzed the flocking behaviors of birds, the genetic networks of fruit fly embryos and the activation patterns of salamander neurons.

“In physics, we use the same mathematical language to describe many seemingly different behaviors,” said Bialek, the John Archibald Wheeler/Battelle Professor in Physics and the Lewis-Sigler Institute for Integrative Genomics. “So we understand that the emergence of collective behavior from all the individual interactions has a kind of universality.”

To explore the possibility that this universality might extend to living systems, Bialek made use of a large dataset on the changing positions and velocities of thousands of individual birds in a flock of starlings. A group of Italian physicists used multiple cameras to record the birds and calculate their exact locations over time in three dimensions — “a technical triumph,” according to Bialek.

The researchers, including former Princeton postdoctoral fellows Thierry Mora and Aleksandra Walczak, analyzed the deviations of each bird from the flock’s average speed and direction of movement. They found not only that these variations were correlated between nearby birds, but also that the fluctuations from the average propagated through the group over long distances. This pattern of rapid, remote signal transmission echoes the changes that occur among molecules during a phase change from solid to liquid or liquid to gas. At a critical point, this could allow information to spread swiftly through the group, enabling the whole flock to nimbly change direction.

“The model you build just by keeping track of what each bird does relative to its neighbors predicts what happens throughout the entire flock,” Bialek said. “And it does so with an accuracy that is beyond what we had any reason to expect. It’s really a very precise prediction.”

Other biological examples of criticality play out on a microscopic scale. Bialek has an ongoing collaboration with Princeton’s Squibb Professor in Molecular Biology Eric Wieschaus, a Howard Hughes Medical Institute researcher and Nobel Prize winner, who has uncovered many of the genes involved in the embryonic development of the fruit fly — a model biological system.

Bialek has found signatures of criticality in gene activation patterns during the first few hours of fly embryo development. The synchronized actions of “gap genes” establish the fly’s 14-segment body plan. Mutations in these genes lead to gaps between segments, whose effects are reflected in the names of the genes: two examples are “hunchback” and “giant.”

Recently, Thomas Gregor, an assistant professor of physics and also a member of the Lewis-Sigler Institute, has developed experimental tools to precisely measure the activity of many gap genes at once, all along the halfmillimeter length of the fly embryo. These measurements allowed Bialek and physics graduate student Dmitry Krotov to test whether the patterns of gene activity across the embryo fit a model of criticality. Indeed, using data from 24 embryos, they found that fluctuations from the average level of gene activity at each point along the embryo were correlated between certain pairs of gap genes, which regulate one another’s activity like on/off switches. They mapped the locations of these switch points, which appear to act like signals that spread over long distances, just as changes in velocity are correlated in a flock of birds.

Bialek has also looked for signatures of criticality among the activation patterns in a patch of 160 nerve cells from a salamander retina, a model system for studying this light-sensing layer of the eye. In collaboration with Michael Berry, an associate professor of molecular biology and the Princeton Neuroscience Institute, Bialek and his colleagues showed how the coordinated activity of the neurons could be tuned to a critical state.

Bialek thinks critical systems may be common features of life that have repeatedly evolved in different organisms and at different levels — both molecular and behavioral. This could explain why, though systems of cells or groups of organisms could be organized in any number of possible ways, networks with similar properties continue to emerge.

“Is there anything special about the way nature has organized things in living systems?” Bialek wondered. He said much more work is necessary to claim criticality as a general biological principle. “But I do think we’re seeing in the data, somehow, signs of that specialness — things that it seems you can only get if the system has been set up in particular ways and not in others,” he said. “That I find very appealing.”

This work was supported in part by the National Science Foundation, the National Institutes of Health, the Howard Hughes Medical Institute, the W.M. Keck Foundation and the Swartz Foundation.

–By Molly Sharlach

Math and music spark student’s research interests

Alexander Iriza

Alexander Iriza. Photo by Denise Applewhite

WHILE PRINCETON SENIOR Alexander Iriza, of Astoria, New York, credits his parents for sparking his interest in math — his mother gave him math workbooks when he was a toddler — that was merely “a nudge” in the right direction.

For his senior thesis, required of all Princeton undergraduates, Iriza worked with Yannis Kevrekidis, the Pomeroy and Betty Perry Smith Professor in Engineering, to examine specific data analysis techniques.

“The idea is to start with a dynamical system of many particles that interact with each other on the microscopic level,” Iriza explained. “It’s believed that many animal species in the wild operate in this way, with each organism having its own personal preferences but also reacting to the individuals in its vicinity. Then we seek to understand the often beautiful and complex behavior that emerges at the macroscopic level of the entire flock.”

Iriza was also a violinist in the University orchestra. His exceptional scholarship led to his being named salutatorian for the Class of 2014, delivering a speech in Latin at Commencement. Comparing the maturity and depth of Iriza’s work to that of a strong graduate student, or even a postdoc or colleague, Kevrekidis said: “His intellectual strength, his work ethic, his joy in discovery and thinking, [and] his own vision about research directions single him out among the wonderful students I have had the good fortune to work with in my 28 years in Princeton. I truly look forward to finding out what he will accomplish in his research life.”

–By Jamie Saxon

How to train your worm to explore the circuits involved in learning

Angelina Sylvain

Angelina Sylvain, a graduate student in the Princeton Neuroscience Institute, trains C. elegans roundworms to associate food with the smell of butterscotch for her studies of the neural circuits involved in learning and memory. (Photo by Molly Sharlach)

AS AN UNDERGRADUATE, Angelina Sylvain was fascinated to learn that devastating declines in cognition and muscle coordination could be caused by changes in a single gene — the cause of Huntington’s disease. She was intrigued by the fact that brain surgery on an epileptic patient cured him of seizures, but wiped out his ability to form short-term memories.

These remarkable discoveries first drew Sylvain to the field of neuroscience, though she never imagined that her own efforts to understand the human brain would involve training tiny worms.

A fourth-year graduate student in the Princeton Neuroscience Institute, Sylvain seeks to understand how the activities of neurons in the brain lead to particular behaviors and memories.

“The problem with studying the human brain is that we have 86 billion neurons,” she said. “But worms have only 302. And they’re transparent, so you can use imaging techniques to indirectly observe the activities of neurons.”

The millimeter-long roundworms, known by the scientific name Caenorhabditis elegans, can be found squirming underfoot in temperate environments. In the lab, they swim in petri dishes and feast on E. coli bacteria. Working with Coleen Murphy, an associate professor of molecular biology and the Lewis-Sigler Institute for Integrative Genomics, Sylvain teaches the worms to associate food with the scent of butanone, a chemical that smells like butterscotch.

During the training process, Sylvain tracks the activation of individual neurons as the worms learn to identify and move toward the alluring odor. She uses specially engineered worms in which specific neurons glow green in response to calcium ions, hallmarks of neuron activation. At first, only a sensory neuron lights up when the worms smell butanone. But after the worms learn to associate butanone with a meal, Sylvain can detect the activation of an entire neural circuit — a sensory neuron, an interneuron and a motor neuron. The motor neuron leads the worm to swim toward the scent.

By training the worms, Sylvain hopes to answer basic questions about how long-term memories are formed. She plans to examine the numbers and combinations of neurons required to establish memories, as well as the adaptability of memory-forming pathways. By eliminating specific neurons, she can test whether the worms can still form memories, and how the circuits change.

Sylvain relishes both the challenges and the rewards of academic research. “Academia offers a fantastic combination of the ability to teach and mentor, and also to ask awesome research questions,” she said. “It’s always a struggle when experiments fail. But when things finally work out, there’s a great sense of satisfaction that you’ve uncovered something nobody else knows.”

Coleen Murphy’s research group is funded by the National Institute on Aging of the National Institutes of Health.

–By Molly Sharlach

Captured on video: Virus-sized particle trying to enter cell

Virus video

Researchers captured video of a virus-like particle trying to enter a cell (Image courtesy of Kevin Welsher)

RESEARCHERS AT PRINCETON UNIVERSITY achieved an unprecedented look at a virus-like particle as it tries to break into and infect a cell. The video reveals the particle zipping around in a rapid, erratic manner until it encounters a cell, bounces and skids along the surface, and either lifts off again or, in much less time than it takes to blink an eye, slips into the cell’s interior. The work, conducted by Professor of Chemistry Haw Yang and postdoctoral researcher Kevin Welsher, was supported by the U.S. Department of Energy and published in the Feb. 23, 2014, issue of Nature Nanotechnology.

–By Catherine Zandonella

Small RNAs fight cancer’s spread

Tumor cells spread toward bone

Breast cancer cells (right) spread toward the hindlimb bone (left), using natural bone-destroying cells (osteoclasts) to continue their advance. (Image courtesy of Yibin Kang)

Cancer patients may benefit from a dual strategy for tackling their disease in a class of molecules called microRNAs. Molecular biology graduate student Brian Ell has revealed that microRNAs — small bits of genetic material capable of repressing the expression of certain genes — may serve as both therapeutic targets and predictors of metastasis, or a cancer’s spread from its initial site to other parts of the body.

MicroRNAs are specifically useful for tackling bone metastasis, which occurs in about 70 percent of late-stage cancer patients. During bone metastasis, tumors invade the tightly regulated bone environment and take over the osteoclasts, cells that break down bone material. These cells then go into overdrive and dissolve the bone far more quickly than they would during normal bone turnover, leading to bone lesions and ultimately pathological conditions such as fracture, nerve compression and extreme pain.

“The tumor uses the osteoclasts as forced labor,” explained cancer metastasis expert in the Department of Molecular Biology Yibin Kang, who is Ell’s adviser. Their research is supported by the National Institutes of Health, the Department of Defense, the Susan G. Komen for the Cure Foundation, the Brewster Foundation and the Champalimaud Foundation.

MicroRNAs can reduce that forced labor by inhibiting osteoclast proteins and thus limiting the number of osteoclasts present, as Kang’s lab observed when mice with bone metastasis injected with microRNAs developed significantly fewer bone lesions. Their findings suggest that microRNAs could be effective treatment targets for tackling bone metastasis. And that’s not all: microRNAs may also help doctors detect the cancer’s spread to the bone, with trials in human patients demonstrating a strong correlation between elevated levels of another group of microRNAs and the occurrence of bone metastasis.

Kang, the Warner-Lambert/Parke- Davis Professor of Molecular Biology, said he ultimately hopes to extend mice experimentation to clinical trials. “In the end, we want to help the patients,” he said.

–By Tara Thean

Princeton role in federal BRAIN initiative

Princeton neuroscientists are poised to play a leading role in revolutionizing our understanding of the human brain as outlined in President Barack Obama’s BRAIN Initiative, announced in April 2013. David Tank, co-director of the Princeton Neuroscience Institute (PNI) and the Henry L. Hillman Professor in Molecular Biology, was named a member of the steering committee appointed to lay out the scientific strategy for the project.

–By Catherine Zandonella