The
Farber Lab

Referred to as the “modern-day plague,” obesity is on the rise worldwide. It influences a host of chronic disorders, including diabetes, high blood pressure, risk of heart disease, excess fat, and high cholesterol. Clinicians and researchers refer to a constellation of these conditions under the umbrella term ‘metabolic syndrome.’

By studying the fundamental insights underlying the cell biology of lipid function, Dr. Steven Farber hopes to uncover new tools to fight metabolic syndrome.

"The globalization of the high-fat Western diet and the concurrent rise in the incidence of lipid disorders has provided an impetus to understand lipid metabolism better in the context of metabolic dysfunction," says Farber. "Although the genes involved in cholesterol and fatty acid uptake in intestinal cells have been identified, their exact mechanisms of action are largely unknown."

The zebrafish has long been established as a powerful model for the study of early development, but Farber and his team are taking advantage of the optical clarity of zebrafish embryos and larvae to visualize lipid processing in live animals, at the level of individual organs—and even cells—within organs and tissues. 

A protein called Apolipoprotein-B, or ApoB for short, attaches itself to the waxy fat and cholesterol molecules in order to help shuttle them around the circulatory system. These complexes of lipid and protein are called lipoproteins—a type of which is commonly known as “bad cholesterol.”

Sometimes these “bad cholesterol” lipoprotein compounds will embed themselves in the sides of blood vessels, forming a dangerous buildup. Called plaque, these deposits stiffen artery walls and make it more difficult for the heart to pump blood—which can eventually lead to a heart attack.

Identifying ways to lower levels of plaque-forming lipoproteins in the bloodstream would save lives, but ApoB proteins are too large to study using many traditional research techniques.

To solve this problem, Farber and former graduate student James Thierer used state-of-the-art genome engineering to develop the LipoGlo system, a live zebrafish model that tags ApoB with a glowing enzyme similar to the one that lights up a firefly's abdomen. This innovation allowed Farber and Thierer to observe lipoprotein levels, size, and distribution directly. Their approach is so sensitive, it can be used to measure lipoproteins in an exquisitely small amount of blood or tissue—opening doors to new methods to study the cell biology of lipids and to develop possible new treatments for heart disease.

Using these glowing zebrafish, the team was able to test thousands of commonly used drugs and natural products for their ability to reduce lipoproteins. Farber Lab postdocs Lishann Ingram and Dan Kelpsch and collaborators at Johns Hopkins University identified 48 compounds that lower bad cholesterol in the zebrafish—including cinnamon oil.

The team was pleasantly surprised to find published evidence that cinnamon oil yields positive metabolic results in animal models and humans. However, these papers provided little to no insight on how cinnamon oil alters cells and organs to cause this effect. Moreover, natural oils like cinnamon oil are composed of many chemicals—and this prior work did not define which of these components reduces bad cholesterol. The Farber lab is currently using the LipoGlo system to identify cinnamon oil’s specific bioactive components that produce favorable metabolic effects.

The lab has also recently started to study how the age of lipoproteins in the blood can affect our health—not just the amount. The older the lipoprotein, the more it will get "tagged" by molecular modifications that may promote a build-up that can lead to blood clots and heart attack.

To study the lifetime of lipoproteins in living zebrafish, predoctoral associate Tabea Moll modified the LipoGlo system in a novel way—swapping its light-emitting luciferase protein with Dendra2, a photoconvertible fluorescent protein. Lipoproteins tagged with Dendra2 will glow green under a fluorescent microscope. However, when Moll shines UV light on the live fish, it turns Dendra2 red. The next time Moll looks through her scope, she can tell the new lipoproteins (green) from the old (red). With this method, she can determine how fast the old lipoproteins are cleared from the circulation—thus measuring lipoprotein turnover.

This project is in its early stages. Stay tuned for updates!

Over the last several years, the Farber Lab has had great success in researching lipoprotein biogenesis by using a gene-first approach, that is, to select a gene hypothesized to play a role in making lipoproteins, disrupting that gene, then characterizing the results. This reverse genetic method has led to a better understanding of critical players in lipoprotein metabolism, including MTP, dgat2, pla2g12b, and creb3l3.

These genes all cause the yolk sac to become opaque, a phenomenon the lab refers to as "dark yolk." With this in mind, postdoctoral researcher McKenna Feltes has designed a phenotype-first genetic approach to identify additional genes linked to lipoprotein biogenesis. By starting with a search through mutated zebrafish for "dark yolk," she hopes to uncover surprising and unanticipated genes that regulate lipoprotein biology.

The intestine produces lipoproteins based on what it takes in from the diet, and zebrafish have a digestive system very similar to humans. For these reasons, many of the Farber Lab's experiments hone in on intestinal lipoproteins.

But lipoproteins are produced by both the intestine and the liver, and if you measure lipoproteins in the blood, it's difficult to pinpoint their place of origin.

So, the lab uses a superfusion system built in the Carnegie Embryology machine shop to maintain tiny, thinly-sliced samples of zebrafish intestine—kept alive in small plastic chambers bathed in a solution of salts, sugars, and oxygen. The resulting fluid from this perfusion system is collected to quantify the levels of secreted intestinal lipoproteins.

With heart disease as the leading cause of death in the United States, it is imperative to understand how the gut microbiome—the vast communities of microorganisms that live within the digestive system—influences our response to diet.

In a collaborative study, graduate student Josh Derrick is working with both zebrafish in the Farber Lab, and fruit flies in the Ludington Lab to understand the relationship between a high-fat diet, the microbiome, and health.

The fruit fly's microbiome is small and easy to manipulate, which allows researchers to systematically test combinations of microbes and to interrogate the roles of each. In terms of the cell biology and physiology involved in the digestion and storage of dietary fat, the fly is surprisingly similar to both humans and zebrafish; anything that Derrick finds—a signaling molecule or a receptor, for example—could be directly applicable to vertebrates like humans. Moreover, Josh hopes to define the rules that govern how microbes can live inside animals to promote health.

Another biological process that the Farber Lab seeks to understand is the liver's contribution to mitochondrial disease—a set of long-term, genetic disorders in which mitochondria fail to produce the energy that cells need to function.

Mitochondrial disease affects the parts of the body that demand the most energy—the brain, heart, digestive system, and muscle. Since the liver is the hub of carbohydrate, lipid, and protein metabolism, liver mitochondria have the unique job of regulating the flux of metabolic molecules within cells. Inability to properly carry out this essential function results in devastating effects on the entire body.

In collaboration with Steve Ekker’s lab at the Mayo Clinic, the Farber Lab has developed a zebrafish model with the hallmark characteristics of the deadly mitochondrial disorder Leigh Syndrome, French-Canadian variant (LSFC)—including a shortened lifespan, and muscle and liver defects. Since LSFC patients have defects in dietary lipid metabolism, the lab asked whether these disease-model zebrafish metabolize their food differently.

Using methods developed by previous lab member Vanessa Quinlivan, research scientist Jen Anderson found that half a day after ingesting a high-fat meal, the diseased zebrafish have twice as much fat in their bodies than their normal siblings.

The lab applies a genetic method in which the broken liver mitochondria are fully rescued (while mitochondria in other tissues remain broken). This study allowed the team to figure out how the liver contributes to the overall manifestation of disease. Intriguingly, they found that whole animal lipid metabolism and lifespan returned to normal by restoring liver mitochondrial function.

The Farber Lab’s research bays and facilities are always buzzing with energy—about half of the lab is made up of graduate and undergraduate students—and their friendship and hunger for collaboration are palpable. Several of the projects are also supported by high school students.

For Steven Farber, this is by design. He believes scientific pursuit is more than just the search for results. It’s about mentorship, community, and sparking curiosity in the natural world.

Farber has a tremendous amount of enthusiasm for getting young kids turned on to science. In 2002, he partnered with educator Jamie Shuda to create BioEYES, a K–12 science outreach and teacher training program that uses zebrafish to teach children developmental biology, genetics, and experimental design.

With a dozen centers in the U.S., Australia, and China—including in Farber's lab in Baltimore—over 155,000 students and 1,000 teachers have participated in BioEYES so far.