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The Mysteries of Mitochondria

There’s a lot we don’t know about the tiny engines that reside in nearly every living cell. But CALS biochemist David Pagliarini is shedding light on more of their functions and behavior— with important implications for human health.

Imagine having your car towed to the shop for unknown repairs, and watching a trusted local mechanic pop the hood and take a ponderous look inside. Minutes pass as he runs a gauntlet of software and fluid checks, and pokes around the hoses, belts and cords. He finally emerges with a strange-looking broken part in his hand.

“This might be the culprit,” he says. “But honestly, I’ve never seen a part like this before.”

Dave Pagliarini can relate to this feeling. As an associate professor of biochemistry, Pagliarini studies engines of an entirely different stripe—engines called mitochondria, which power biological life. These tiny, grain-shaped organelles reside inside virtually every plant and animal cell type, and perform the critical task of breaking down nutritional elements and converting them into energy for basic cellular function.

Pagliarini says that only two decades ago, science had all but closed the book on mitochondria, assuming all the important pathways and processes had been worked out. But lately, the field of mitochondrial research is being defined more by how little we know about their complex role in maintaining health—and their connection to literally hundreds of diseases when things go haywire.

As one measure of this great unknown, Pagliarini points to “orphan proteins”—more than 300 proteins associated with mitochondria that still have no defined function. In a mechanical sense, they are parts without a defined purpose. A big focus of Pagliarini’s research today is linking these orphan proteins to their rightful homes and understanding how their dysfunction affects disease.

But as a University of California, San Diego graduate student in the early 2000s, Pagliarini didn’t have mitochondria anywhere on his radar. He was studying a group of proteins involved in cell signaling when he made an entirely unexpected discovery: One of those proteins traced directly back to mitochondria. Later, as a postdoctoral researcher at Harvard Medical School, he produced a seminal work on identifying all mitochondrial proteins, published in the journal Cell in 2008, which has been cited more than 1,000 times.

“That set off a whole new direction for me,” Pagliarini says. “To find something that no one expected to be there made me fascinated about what else we didn’t know. And as we began to realize there was a lot we didn’t know, I just saw a lot of opportunity.

“That’s when I became a ‘mitochondriac,’” he says with a laugh.

Mitochondria consume about 95 percent of the oxygen we breathe to make a chemical substance called ATP—or adenosine triphosphate—that is the “chemical energy currency” our bodies use to power cellular processes.

But “cellular powerhouse” is only one important function of mitochondria. For example, mitochondria are recognized as key players in cellular signaling and cellular apoptosis, or programmed cell death. They also appear to play a significant but not fully understood role in certain cancers, Parkinson’s, Alzheimer’s, diabetes and autism. And their composition varies markedly across tissue types—meaning there are many places where things can go awry.

“There are many different ways to break machines like mitochondria,” he says.

The Pagliarini lab focuses on establishing a fundamental understanding of mitochondria, with the recognition that we can’t cure what we don’t understand. There is a dire need to develop therapies for people who suffer from mitochondrial disease, which occur in 1 in 4,000 people and can be fatal or have devastating health consequences.

“There are so many diseases that are rare individually, but collectively affect lots of people,” Pagliarini says. “These are heartbreaking diseases for which we can only offer palliative care. I believe that in the long term, a fundamental understanding of how the mitochon-dria work will give us an opportunity for real cures.”

Dr. Philip Yeske, the science and alliance officer of the United Mitochondrial Disease Foundation (UMDF), agrees that mitochondrial diseases pose unique medical challenges. There are about 250 mutations on both the nuclear and mitochondrial DNA that can lead to disease. And any given mutation can manifest itself in entirely different symptoms—heart-related problems for one patient and neurological disorders for another.

“The standard of care for patients affected by mitochondrial disease right now is treatment with vitamins and supplements,” Yeske says. “There are no licensed therapies available. And with the vitamin and supplement care, we don’t know enough about them to even say they are effective.”

But thanks to a rapidly growing body of research, prospects are looking more positive. A decade ago, therapeutics would have been a “pipe dream,” Yeske says, but in 2016, four companies are in active clinical trials for mitochondrial disease therapeutics, and many more are in preclinical planning.

“We’re at the beginning of an era of mitochondrial medicine, and that’s really exciting,” Yeske says.

At UW-Madison, Pagliarini’s young career has been on overdrive. Only months after arriving at CALS in 2009, his lab was jump-started by major research support from the federal economic stimulus program, which funded only the top 2 percent of proposals that year. Shortly after, he was named a Searle scholar and helped craft a major grant related to the NIH National Protein Structure Initiative, which further put his work on mitochondrial proteins in the national spotlight.

The past academic year could arguably be Pagliarini’s most exciting yet. In fall 2015, Pagliarini was named director of the Morgridge Institute for Research Metabolism Theme, which aims to establish a vibrant group of researchers focused on the basic underpinnings of metabolism. The Morgridge Institute is poised to make strategic hires and investments under Pagliarini’s direction that will help UW–Madison grow and thrive in this field.

This year, Pagliarini experienced a pinnacle of recognition as the recipient of a Presidential Early Career Award, given to top scientists and engineers in an array of fields. He and 100 national honorees visited the White House in May, touring its opulent historical meeting rooms and chatting with President Barack Obama and special guest Jeff Bezos, the CEO of Amazon.

“It was pretty special,” Pagliarini says. “What really stood out about it was how optimistic and forward-looking it was. You hear so much in science now about problems with funding or rising competition from other countries. This was very much about celebrating what we can do with U.S.-driven scientific research.”

Brad Schwartz, CEO of the Morgridge Institute, started getting indications early that Pagliarini was the right person to lead the campus-wide initiative. While meeting with potential recruits in 2014 from leading research universities, Schwartz was struck by how frequently Pagliarini’s name came up in conversations.

“After a very thorough national search, it only reinforced that Dave had the innovative thinking and creativity we were looking for,” Schwartz says. “He has all the personal characteristics needed to help build stronger community around as many as 500 scientists working on some aspect of metabolism in Madison.”

The Pagliarini lab is focused on a grand question: How do we define the unknown parts that contribute to the fully functioning engine of mitochondria? Pagliarini teamed with chemistry professor Josh Coon to win an award from a UW–Madison and Wisconsin Alumni Research Foundation (WARF) initiative called UW 2020—supporting projects that could change the direction of a field.

The goal will be to develop a “genetic knockout” strategy for a wide range of human cell lines. By analyzing all of the cellular changes that occur in each “knockout”—cells with a single gene removed—the researchers will be able to define molecular signatures that show an association between orphan proteins and established ones.

The team already has demonstrated great success by applying the same process to yeast, a model organism that is simple and fast growing, and employs cellular processes similar to those in humans. The yeast project, recently published in Nature Biotechnology, completed 174 individual gene deletions that helped predict the function of many orphan proteins. Replicating this process with human cells will require CRISPR gene editing technology as well as a private sector partner to create these knockout cell lines in an industrial process, so that the scientists can focus on growing and analyzing the lines.

Another research theme focuses on an important component of the energy chemical ATP production process called coenzyme Q. This lipid was discovered at the UW–Madison Enzyme Institute in the 1950s and was recognized as a key missing piece in the electron transport chain that mitochondria use for ATP synthesis. It is a complex molecule that needs to be made by mitochondria and is not supplied in the human diet.

Coenzyme Q deficiency causes a wide array of problems, from minor muscle disorders to severe disabilities and death. The research challenge is a familiar one: several steps in the coenzyme Q pathway are accomplished by proteins that have yet to be identified and defined. If the lab can identify the different steps of biosynthesis the body uses to make this important molecule, Pagliarini says, it could lead to breakthrough therapeutics to replace its loss. Some of the precursors for making coenzyme Q follow the same pathways as cholesterol, and statin-based drugs that block cholesterol may provide important insights.

Pagliarini and his 18-member research team now make their home on the second floor of the Discovery Building, which is dedicated to collaborative science that cuts across disciplines. The team includes postdoctorates, graduate students, senior staff researchers and a healthy mix of undergraduates.

They can even claim a bit of celebrity: PhD student Zachary Kemmerer is a former college wrestler and premier athlete who competes on the hit TV competition “American Ninja Warrior,” and is known as the “Science Ninja.” Kemmerer contributes to Discovery science outreach programs, helping kids get pumped up about the possibilities of science. His motto: “Powered by Mitochondria.”

Assistant scientist Jarred Rensvold PhD’15 first joined the Pagliarini lab as a graduate student at its inception in 2009 and has been there ever since. In one afternoon just before graduate school began, a parade of biochemistry professors offered “elevator pitches” of their work to new graduate students, hoping to generate recruits. “Dave gave a really energetic talk and I could see he was really excited about starting up his lab,” Rensvold says. “He seemed like he would be an excellent mentor. Even with all of his expanded responsibilities today, he makes time to give to each individual and each project in his lab, which is remarkable, I think.”

Postdoctoral research associate Natalie Niemi’s introduction to mitochondria was remarkably similar to Pagliarini’s, having “stumbled” on a connection in graduate school while doing unrelated protein studies. Today she studies an important process called phosphorylation, which is the turning on or off of enzymes that control energy metabolism. She has funding from the UMDF on this topic, and she gives back by helping organize a Wisconsin “Energy for Life” fundraiser to support UMDF causes.

“I think the potential to have an impact on the future matters,” Niemi says. “We’re working quite a few steps back from clinical trials, but trying to project how your research could have an impact on human health is rewarding. It’s also rewarding to make discoveries and be the first person to know something.”

The future for Pagliarini is brimming with opportunity. If you think of metabolism research as a living cell within UW–Madison, the Morgridge Metabolism Initiative provides a nucleus—or, perhaps, a mitochondrion!—for the first time. The effort already has produced a monthly symposia series and a major investment in mass spectrometry tools—a gold standard technology for conducting metabolism research.

Part of the challenge is building a sense of community within a very diverse group of researchers, where one finds pockets of metabolism-related work in the medical school, in countless bioscience labs, in chemical engineering, computer science and bioinformatics. The potential for new ideas and collaborations is only beginning.

“We’re in the era of collaborative science, so as our interactions build and gain success, they are bound to attract more people,” says Brian Fox, professor and chair of biochemistry. “Dave’s got a great eye for a problem, he’s very articulate in describing that problem, and he’s an excellent collaborator. That’s the kind of style that will help drive a campus-level project like the metabolism initiative.”