Welcome to our lab and please don’t mind the fish smell. The basement of this building in Baltimore houses more aquariums than you could easily count, in a variety of sizes, and there’s also a pump room—you can hear it pushing out 260 gallons of water a minute into the fish tanks. Don’t worry, you get used to the aquarium aroma. It’s strongest in the room filled with small tanks that aren’t all that different than you might have at home, but we’ve got more. There are 16 racks holding rows and rows of clear plastic tanks full of zebrafish, some 80,000 in all, in various stages of development.
And why are they here? Well, zebrafish can teach us a lot about human health and also help us understand fundamental questions about how cells function. These tiny see-through fish have a very similar genome to humans, and because the fish are optically clear, we can see right into their bodies and ask a whole range of questions not possible in other systems. By watching how zebrafish respond to fats known as lipids, we can help develop new treatments for heart disease and potentially save lives. Lipids are the fatty molecules, like cholesterol and oils, that we eat, and they are key to making up all of our cells. But before I get into how I came to investigate the contribution that dietary nutrients make to important functions that support good cardiovascular health, it might help to explain how I turned my focus to fish.
In 1994 I was reading Science magazine, trying to figure out what I was going to do as a postdoctoral researcher, when I saw an article that said, “Zebrafish hit the big time.” And I was intrigued at the thought of studying biochemistry and biochemical processes live in these fish, because I could look right through their bodies.
When thinking about human disease today, we often use the term “environmental mismatch.” And what that means is humans have evolved on this planet for a really long time, and through much of that time, they had nutrients and food sources different from our modern industrial food system. For example, not that long ago in Africa we were wandering around as hunter-gatherers, with many days before we could successfully kill some big game. Our bodies evolved ways to manage these periods of feasting and famine. Now, in just a very short evolutionary window of time, many humans all around the world constantly have all the food. So the genes that evolved to make people very thrifty and efficient with their calories can actually become liabilities in modern society.
Today, we find genetic variance in people’s susceptibility to obesity and cardiovascular disease and plenty of things we cannot explain—such as why certain parts of the genome have changes that are associated with a resistance to metabolic diseases and other genome changes are more likely to cause people problems. We also don’t fully understand the kind of diets we should be eating—there’s been a lot of contradictory advice on healthy eating given to people over the years. I think there’s just a huge knowledge gap in this healthy diet space that will require an evidence-based approach. I and many others have a sense that diet can profoundly affect human health and partially explain why cardiovascular disease happens. For example, why do people develop insulin resistance or adult-onset diabetes? Our goal is to use the zebrafish to answer some of these questions.
And we’re doing some innovative research here. It was my idea to use fish to study lipid biology. Through a microscope, we can see the valves inside the heart as it’s beating, and we can look at every single cell. That’s why this fish is premier for cell biology and the work that we do on lipid metabolism.
With modern genome engineering such as CRISPR/Cas9, we were able to cut the DNA at the right spot and insert light-emitting protein, such as the kind that makes fireflies light up, very precisely right into the protein that makes LDL, or bad cholesterol. Once we marked these bad cholesterol particles, we could see these lipoproteins in places we did not expect. And they explain some weird things that happened to people who have diseases that mess with their lipoproteins—for example, we see a lot of lipoproteins around the areas where tendons form. So we’re asking, why are these tendon areas places where these lipoproteins go?
Once we created these fish, we realized that we could test medications on them, working in collaboration with Jeff Mumm of Johns Hopkins, who has a big robotic platform. We can take something the size of a coffee mug filled with 12,000 zebrafish embryos and pour it into a vessel in the robot, which then puts a single embryo in each depression on a 96-well plate. We then use a robot to distribute every drug that’s ever been used in people to the embryos, putting a camera over the plate and measuring what lowers the bad cholesterol, and quickly ruling out things that killed the fish.
We started by testing the 3,200 compounds in the Johns Hopkins Discovery Library that our collaborators created. Out of those, we got just 22 hits of drugs that worked. Many of these drugs are already deemed to be safe. So now we can put these compounds into mice, and we may ultimately even put them into people, because they’re already FDA-approved. Our dream would be to find some drug that works on toenail fungus that could actually be amazing at lowering bad cholesterol. Given the success of the first screen, we are now about to take a deep dive and explore a library of 10,000 compounds that are not FDA-approved and are new chemical entities. With these experiments, our small 12-person lab is tackling a big problem in a new way.
Another innovative program I began is called BioEYES. It uses zebrafish in hands-on activities with children grades K through 12 across the country to foster an interest in science. The kids have to figure out whether the fish is male or female, set up a mating, collect the embryos, and watch them develop. They ultimately get to see the fish’s beating heart. Since it began in 2002 in Philadelphia, this program has reached 155,000 kids. The key to its success was its conception with a teacher, Jamie Shuda, who knew how the classroom works. When you team up the scientists with the crazy ideas with the teacher who understands the demands of a classroom and school setting, you can do some cool stuff.
I was recently giving a seminar at NYU, and one of the postdocs said something like, “Oh, yeah, I had the fish come to my classroom in Philadelphia, and it was a reason I kind of got into science.” This isn’t the first time that’s happened to me. I mean, this project is really a gift. And I try to tell my colleagues that it can be immensely rewarding to be inspiring the next generation of life science STEM leaders. STEM education is going to be at the heart of addressing a lot of problems with health, the environment, and inequity. So you either have a populace that’s trained to think critically or you don’t. And I believe science education is going to be at the heart of how well we’re going to do as a country, and as a world.
Steven Farber is a 2002 Pew biomedical scholar, a principal investigator at the Carnegie Institution for Science Department of Embryology, and an adjunct professor in the Johns Hopkins University Department of Biology in Baltimore. Hear more about his work in Pew’s podcast, “After the Fact.”
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