Exploring the Brain's Hidden Landscapes
Scott Soderling, PhD, is having trouble sleeping.
It’s not that he lies awake plagued by worries or woes. On the contrary, the problem is that he’s so energized by the discoveries coming out of his lab, and by the future paths those discoveries point toward, that he can’t wait to get in and start tackling the next step.
“We’re incredibly excited about the things we’ve been doing here,” says Soderling, an associate professor of cell biology and neurobiology. “And we have a lot of really cool stuff coming up ahead. The challenge is that we’ve opened up so many new areas of investigation that we’re having to retool the lab so that we have the capability to functionally test them. I have a hard time sleeping at night thinking about all the possibilities.”
Soderling studies synapses, the connections in the brain where signals pass across the tiny gaps from one neuron to the next. Neuroscientists believe that many, if not most, brain disorders are caused by genetic mutations or other damage that disrupts the proper functioning of these connections. But many of the precise details of the synapses—what they’re made of, how genetic mutations alter their functioning, why a specific malfunction leads to a particular disorder, and so on—remain unknown.
Last year, Soderling and his lab developed a novel and elegant technique for exploring some of the most poorly understood aspects of the synaptic process. That research revealed a wealth of data that dramatically increases what we know about how the brain works, and that new knowledge points the way toward exciting new hopes for thwarting some of the most devastating neurological disorders.
What’s more, the technique Soderling developed can be applied to other parts of the brain as well, which should give him and other researchers unprecedented insights into yet more neurological processes and disorders.
“It’s keeping us pretty busy,” he says. “We’re thinking up new applications for this every week.”
Traffic Signals in the Brain
Scientists have known for more than half a century that synapses come in two basic forms. One type, known as excitatory, boosts brain activity, activating the flow of information between neurons. The other, called inhibitory, dampens that activity. Soderling likens the two types of synapses to traffic signals: excitatory synapses are like green lights, allowing neural signals to proceed, and inhibitory ones are like red lights that pause that movement.
This inhibitory process is important in preventing the brain from becoming overly active. Malfunctions in these inhibitory connections can lead to excessive electrical activity in the brain, and many researchers think this causes brain disorders such as epilepsy and autism spectrum disorders.
“We all love green lights when we’re driving because they allow us to move forward, but if all the lights were green all the time, the results would be catastrophic car accidents,” Soderling says. “The red lights are absolutely essential. It’s the same in the brain: the inhibitory synapses are as necessary for proper neural function as the excitatory ones. Without them it is equally catastrophic for the brain.”
But very little is known about the molecular makeup of inhibitory synapses. Scientists have extensively studied the excitatory synapses, describing their basic molecular structure and identifying some 1,000 proteins involved in their various functions. Inhibitory synapses, by contrast, are much harder to get at; they’re much more difficult to purify and examine biochemically, and until now only a few dozen of their component proteins had ever been identified. Relative to what we know about excitatory synapses, the inhibitory ones are the dark side of the moon.
“We’ve known they exist for more than half a century, and we know they are fundamentally important, but we know very little about what they’re made of and how they work,” says Soderling. “It’s an unexplored landscape in the brain.”
“A Little Bit of a Crazy Idea”
Soderling set out to map that uncharted territory. His first few attempts, he says, “failed miserably.” Then he and postdoctoral researcher Akiyoshi Uezu, MD, PhD, came up with an innovative idea.
Biotin is a naturally occurring molecule, also called Vitamin H. It’s commonly sold in drug stores as a dietary supplement reputed to strengthen hair and nails, but for Soderling’s purposes, it also has some more useful characteristics. When activated with a bacterial protein called BirA, biotin can be induced to “tag,” or attach to, any additional nearby proteins. Further, it happens that another particular protein, called streptavidin, has an extraordinarily high affinity for binding to biotin on proteins.
Soderling and Uezu thought perhaps they could, in essence, deliver what Soderling calls “a molecular probe.” They would fuse the bacterial BirA protein with a mouse protein known to localize at inhibitory synapses and insert it back into the mouse brain. In theory, after giving the mice biotin supplements, this chimeric protein would tag all the unknown proteins in the vicinity with biotin. Then the researchers could take that brain tissue and pass it over some streptavidin, which should, like a magnet or a strip of tape, pull out all the biotin—and along with it all those proteins it had tagged.
“It was a little bit of a crazy idea,” Soderling says. “If it worked, it would mean we could identify a lot of component proteins in the brain without having to do all this very complicated biochemical analysis: we could just purify them using biotin. But we had no idea whether it would work.”
Soderling and Uezu dubbed their new procedure in vivo BioID. They ran the study and sent the data off to have it analyzed by mass spectrometry.
“When the results came back, Akiyoshi came in with the computer printout showing this list of proteins,” says Soderling. “I looked at it, and I almost fell out of my chair. I was so excited I could hardly breathe.”
Opening the Safe
The printout included all of the few dozen proteins already known to be present at inhibitory synapses. But the list went on to show additional proteins—a lot of them. Using the in vivo BioID method, Soderling and Uezu identified some 140 proteins that had never before been known to exist at inhibitory synapse sites.
“It’s as if these proteins had been locked away in a safe for 50 years, and we believe that our study has cracked open the safe,” says Soderling. “And there are a lot of gems in there.”
More than two dozen of the newly revealed proteins have known links to brain disorders including inherited epilepsies, intellectual disabilities, and autism spectrum disorder.
The newly discovered presence of these proteins at inhibitory synaptic sites leads to a tantalizing hypothesis: that these proteins are necessary for the inhibitory mechanism to work properly, and that in some cases mutations in the genes encoding those proteins disrupt that functioning. And then you have a traffic grid with no red lights.
“When you lose that inhibitory mechanism, the excitatory input goes unopposed, and that leads to over-excitation in the brain: epilepsy,” says Soderling. “And many children with autism spectrum disorders also have seizures, and it’s long been thought that an imbalance between the excitatory and inhibitory mechanisms may be an underlying cause there too. So this may help explain that too.”
If the newly revealed proteins are indeed complicit in causing these disorders, then those proteins may offer new targets for therapies. Soderling and his lab are now engaged in follow-up research to try to determine exactly what role the recently revealed inhibitory proteins play in these diseases.
“We think this is going to lead to new insights into the etiology of these types of disorders,” Soderling says. “So we’re very excited about where that might lead.”
Scratching the Surface
Beyond the immediate work of further exploring the newly discovered inhibitory synaptic proteins, Soderling and his lab are beginning to apply the in vivo BioID technique to other little-known parts of the brain. And there are many of those.
“This was a good example of a fundamental part of the brain that we’ve known existed for half a century but that we didn’t have a good working parts list for,” Soderling says. “And it turns out there are a lot more of those. There’s a huge landscape within the brain that, at a molecular level, we have a very poor grasp of. This new technique opens up a huge potential for uncovering the molecular basis for how the brain works in many other regions.”
One of those involves the other kind of synapses, the excitatory ones. In patients with developmental brain disorders, the normal growth and development of those synapses in the young, developing brain appears to be disrupted. A graduate student in the Soderling lab, Erin Spence, has now used the in vivo BioID method to identify a host of novel proteins that play a role in the development of those synapses: when these proteins are knocked out in mouse neurons, development is dramatically disrupted.
“This is an example of how, using this new molecular tool, we can go in and precisely pick out the internal components of a variety of different brain structures,” Soderling says. “My guess is that as we identify these component proteins in different regions, we’re also going to identify genes implicated in many different disorders. Paired with the wealth of human genetic data, we can now start to explain the underpinnings of these disorders. There’s so much potential here. We’ve only just scratched the surface.”
The First Step
Soderling didn’t set out to be a neuroscientist. He did his doctoral work in pharmacology at the University of Washington and followed that up with research as a Howard Hughes Medical Institute postdoctoral investigator. In the course of that research, he identified a novel protein in which mutations cause a rare and severe form of intellectual disabilities in children.
“That was my first ‘aha!’ moment,” Soderling says. “That’s when it really hit me that the molecular mechanisms we were studying have huge impact on human health.”
He came to Duke in late 2005. It was the perfect environment for the kind of research he wanted to pursue.
“The research environment here is special,” he says. “We have world-class facilities and resources, but beyond that the atmosphere is one that gives you the ability to grow in new directions, which is especially important when you’re just starting out. My colleagues are fantastic. There’s a lot of collaboration, a lot of sharing of ideas and approaches, and it was clear to me that Duke was one of those places that had that special combination of factors.”
The research he and Uezu did in uncovering the inhibitory proteins garnered a lot of attention, and it has led to exciting new avenues of inquiry. New therapeutic approaches surely remain a long way off—but by illuminating previously dark corners of the brain, Soderling’s research helps light the way for those kinds of advances in the future.
“If your car is broken, you want to take it to a mechanic who understands how cars work,” Soderling says. “It’s the same with the brain. Unfortunately, we have a very poor understanding of how the brain works. If we can gain a better understanding of that, that will lead to better treatments. When it’s broken, we’ll understand exactly why it’s broken. And that is the first step to learning how to fix it.”
By Dave Hart
September 5, 2018
"When it’s broken, we’ll understand exactly why it’s broken. And that is the first step to learning how to fix it.”