To Woods Hole and beyond: A team approach to scientific discovery
How do you speed the development of a new field of science and help solve a 150-year-old biological mystery? Perhaps with an experiment in structuring collaborations.
Dr. Michael Rosen, UT Southwestern Biophysics Chair and a Howard Hughes Medical Institute (HHMI) Investigator, recently led a major international experiment over five summers (2013-2017) at the Marine Biological Laboratory (MBL) in Woods Hole, Massachusetts, which posed the question: How can scientists best structure collaborative research teams to speed discovery?
The experience helped define a new area of scientific investigation, resulting in at least a dozen journal articles from collaborations that included an unexpected one between two UT Southwestern researchers that led to findings recently published in Cell.
Dr. Rosen teamed with colleagues Dr. Ron Vale, UC San Francisco, and Dr. Jim Wilhelm, UC San Diego, as co-principal investigators for the Woods Hole project, which received nearly $4 million in funding from the HHMI’s Collaborative Innovation Awards program designed to support ideas that enable cross-disciplinary teams “to carry out potentially transformative research.”
“We knew from the outset that we wanted a mechanism that would enable scientists from diverse disciplines to get together to work on the problem of biological phase separation, since the problem inherently draws from multiple fields of inquiry. In a series of phone calls, Ron, Jim, and I discussed organizational structures that might achieve this goal,” Dr. Rosen says.
Initially, they discussed an annual two- or three-day meeting rotating among their universities featuring diverse people presenting seminars and leading discussions.
“Eventually, Ron suggested that perhaps if we were going to try to work together, we should spend enough time to actually try some real experiments, i.e., spend the summer together. Given Ron’s long history with the MBL and the MBL’s long history of fostering summer research and creative thinking, it was the obvious choice and the location became the fourth collaborator on the grant,” he says, explaining how the structure of the experiment in teamwork emerged.
“It was a terrific experience. Every summer, two or three people from my lab and the labs of my two co-principal investigators at UCSF and UCSD would go to Massachusetts, and every summer we invited three other research labs and some of their members to join us for eight weeks. It gave us all a different view about the science because it was a different mix of researchers every year. It ended up totaling about 70 scientists – from three continents – who rotated through the program over the course of five years,” he says.
Studying eukaryotic cells
The research area they investigated is so new – only about 5 years old – that it lacks an agreed-upon name. Nevertheless, it is quickly emerging as a fundamental area of science with disease-related implications.
Broadly speaking, the field investigates the organization of eukaryotic cells – a category of nonbacterial cells that includes everything from yeast to flies to humans. The cell itself and many of the well-known organelles within it have membranes to compartmentalize the activities that keep cells functioning. Membrane-bound organelles are like balloons within the balloon of the larger cell membrane, Dr. Rosen says.
“It’s been known for maybe 150 years that there are also compartments within the cell that have no membrane and yet they are still able to concentrate certain kinds of molecules and reject others,” he explains. “They’ve been mysterious for a long, long time. Over the last decade or so, mechanistic ideas are finally emerging about how these compartments form and their likely function within cells.”
That awareness created a sea change in the biological world, and also in the biophysical world, he says.
Although the structures themselves were first identified a century and a half ago, an understanding of the physical and molecular mechanisms that form them has eluded explanation until recently. As a result, the structures he and the other 70 researchers at the summer institute studied go by several names as the nascent field tries to settle on one. Those include membraneless organelles, biomolecular condensates, cellular bodies, compartments, granules, and examples of biological phase separation.
“Over the last five years, it’s become a very, very big area. We have some leaders in that field here at UT Southwestern, including Drs. Steven McKnight, Professor of Biochemistry and the Distinguished Chair in Basic Biomedical Research; Benjamin Tu, Associate Professor of Biochemistry, who holds the Martha Steiner Professorship in Medical Research and is a UT Southwestern Presidential Scholar and a W.W. Caruth, Jr. Scholar in Biomedical Research; and Jeffrey Woodruff, an Assistant Professor of Cell Biology recently recruited from the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, Germany, as an E.E. and Greer Garson Fogelson Scholar in Medical Research.
“This is an emerging area of biology and UT Southwestern is at the forefront of it,” Dr. Rosen says, adding that there are strong disease connections in neurodegeneration and other conditions.
Scientific teamwork in action
To develop the field as quickly as possible, the Woods Hole Summer Institute participants spent each academic year planning and designing a range of experiments as well as developing reagents that could be shared among groups, Dr. Rosen says. Once at Woods Hole, they did experiments by day and discussed them at breakfast, lunch, and dinner – most served cafeteria-style. They also gathered at cookouts and campfires for evenings spent devising and revising experiments in order to do as many as possible at each summer gathering, he says.
They took the best ideas back to their laboratories to continue the research through another academic year of planning for the next summer of work.
The experiment in creating investigational teams paid off. Several projects arose from the collaboration including one that led to a Cell paper on which Dr. Yuh Min Chook and Dr. Rosen, her husband, are corresponding authors. Dr. Chook is a Professor of Pharmacology and Biophysics and, a Eugene McDermott Scholar in Medical Research, who holds the Alfred and Mabel Gilman Chair in Molecular Pharmacology.
The research that grew out of the Woods Hole project marks their first substantive collaboration since they met in the Harvard library during their Ph.D. training. They always excelled in very different areas of biophysics – hers closer to pharmacology, his more abstract – thus their scientific convergence was unexpected.
“We began collaborating there and did many of the experiments with our own two pairs of hands over three summers at Woods Hole. We then continued the collaboration with people in our labs back in Dallas on nuclear magnetic resonance [NMR] spectroscopy studies using equipment in the Biophysics Department,” Dr. Chook says.
Their study may someday lead to a better understanding of and improved treatments for Lou Gehrig’s disease and other neurodegenerative conditions.
Binding and transport
The UT Southwestern study identifies details in how molecules bind – or fail to bind – to each other for transport into the nucleus of nerve cells in the brain and spinal cord. Proper binding and transport appear essential for the protein FUS (fused in sarcoma).
Normally, FUS binds to one of a class of nuclear transport receptors, in this case, the importin molecule called karyopherin-β2 (Kapβ2), which transports proteins into the nucleus. Proper binding of FUS to Kapβ2 is necessary to take FUS into the nucleus. FUS that cannot be transported into the nucleus remains in the gel-like cytoplasm of the cell and tends to self-associate (stick to itself) and form droplets of FUS suspended in the cytoplasm that look like the drops that form after a flask of oil and vinegar dressing is shaken, i.e., phase separation.
Mutations in this transport system are blamed for a genetic neurodegenerative disease called familial amyotrophic lateral sclerosis (fALS), also known as hereditary Lou Gehrig’s disease.
The National Institutes of Health (NIH) describes ALS as a progressive neurodegenerative disease that kills nerve cells that control muscle movement. Death usually occurs within 10 years after symptom onset. An estimated 90 to 95 percent of ALS cases occur sporadically in people with no apparent family history. Several genes have been identified for the familial form of the disease (fALS), which accounts for an estimated 5 to 10 percent of all ALS cases.
In 2006, Dr. Chook identified a family of nuclear localization signals, dubbed the PY-NLS, which acts like a ZIP code for delivery of FUS protein molecules into the cell’s nucleus. In 2012 she showed how the importin Kapβ2 recognizes the PY-NLS on the FUS protein and delivers it to the nucleus when the system works properly. When the transport system fails, droplets of FUS protein clump together in the cytoplasm, perhaps eventually becoming solid and toxic in the motor neurons of ALS patients.
“We knew from the outset that we wanted a mechanism that would enable scientists from diverse disciplines to get together to work on the problem of biological phase separation, since the problem inherently draws from multiple fields of inquiry.”
The NLS she identified became recognized as central to the development of fALS.
Her discoveries allowed neuroscientists to figure out how FUS mutations lead to the aggregation of the FUS protein in the cytoplasm, but many questions remained. “The mutant FUS forms little liquid droplets within 10 minutes and these become less liquid and more solid over time, forming fibrils if the sample is left for 24 hours,” Dr. Chook says.
“My laboratory had been working on phase separation, and Yuh Min’s laboratory has done all this work on the FUS protein transport system. We wondered if the FUS droplets that we and others had observed would be affected by importin binding,” says Dr. Rosen, who holds the Mar Nell and F. Andrew Bell Distinguished Chair in Biochemistry.
In studies using purified FUS and Kapβ2 proteins, they found that the Kapβ2 blocks phase separation of FUS and that the importin’s ability to block phase separation depends on its ability to read the ZIP code of the PY-NLS nuclear localization signal.
Using UT Southwestern's NMR spectroscopy technology, the researchers next studied how the Kapβ2 importin binds to the FUS protein. The in-depth article can be found in our Newsroom.
“Binding at the right time, in the right place, in the right way is really important,” Dr. Chook says. “Those droplets are probably the initial stages of the aggregates that are a hallmark of familial ALS. If we could find a way to keep the droplets from forming, perhaps someday we could change the course of that neurodegenerative disease.”
During the teamwork experiment’s final summer, Dr. Rosen and his colleagues did something unique that aimed to pay their experience forward. Working with Dr. Lisa Dennison, also recruited to UT Southwestern from Max Planck and known internationally for her Science Sketches two-minute videos, the team created a series of animations explaining the project and, equally importantly, the lessons their enterprise taught them about collaboration. Dr. Dennison is now Director of Research Development Communications and an Assistant Professor of Cell Biology at UTSW.
Not a bad way to spend five summers.