Taking on Tuberculosis

Graduate student Ellen Perkowski created a new tool to study how tuberculosis survives, thrives, and escapes our immune system defenses.

Ellen Perkowski/Photo by Mark Derewicz, UNC Health Care
Lung with tuberculosis. Image by Virginia Godfrey, DVM, PhD.

Tuberculosis is a big problem around the world, and we need to develop new ways to investigate the bacteria that cause infection. Ellen Perkowski, a sixth-year graduate student at UNC, has done just that. She devised a system called EXported In vivo Technology (EXIT) to conduct genome-wide scans of the proteins that tuberculosis bacteria export from their cytoplasm to our lungs.

Finding these “exported proteins” in bacteria grown in the lab is one thing. But Ellen’s method allows her to identify the proteins when the bacteria are growing in their normal environment, inside living mammals during infection. She has already found a previously unknown set of exported proteins that could be crucial for tuberculosis virulence. This is a much-needed step toward better treatments and diagnostic tools.

For this work, Ellen earned the Gordon Sharp Graduate Innovator Award, which is given to a student in the UNC School of Medicine Microbiology and Immunology Department to honor the memory of Dr. D. Gordon Sharp – a former professor at UNC who was widely recognized for his innovation in the burgeoning field of microbiology.

We sat down with Ellen to discuss her history, her research, and her future.

Name: Ellen Perkowski

Birthdate: December 18, 1986

Hometown: Rochester Hills, Michigan

Education: B.S. in cell and molecular biology / University of Michigan; PhD student / microbiology and immunology / UNC

Dissertation: To pinpoint the proteins that drive tuberculosis infection

Mentor: Miriam Braunstein, PhD

Extracurriculars: Science outreach to kids, cooking, hiking, sleeping

Why science?

“I was total nerd as a kid. My mom actually got her PhD in genetics but she didn’t continue the work. She stayed home to take care of my sister and me. But she had a microscope. We were really curious kids. In high school, I really loved math and could’ve easily gone into something like engineering. I think it was the science teachers that I really liked; they gave me opportunities to ask questions and do research projects.

“In college, I had to work to pay for school. I knew people who knew of openings in science labs. So I wound up working in several different labs studying ticks and mites, stress and neurons. I worked for anyone who would pay me to do science. I did actual research, which was awesome. It gave me a broad experience to know what I wanted to do. I realized I wanted to pursue a doctorate in microbiology.”

Why UNC?

“I got married right after college. My husband wanted to study organic chemistry, and it’s surprising but not all universities have good microbiology and chemistry programs. UNC was one of about ten different schools we applied to. What it came down to was that we both really liked the people here. And we still do. The faculty are really interested in actually mentoring students. We’re not treated like cheap hands. They’re interested in our well-being. And, frankly, I didn’t see that at every place I applied to.”

Why tuberculosis?

“I think it had to do with my rotation in Miriam Braunstein’s lab that first year as part of BBSP [UNC’s Biological and Biomedical Sciences Program]. I went home at Christmas break and talked to people about our lab’s work on tuberculosis. I realized that people in the United States don’t realize that TB is a big problem. Then when I looked into just how big of a problem it is throughout the world, it was just overwhelming. It’s a huge global health problem that’s definitely understudied and underappreciated. We’re all going to be in big trouble if we don’t deal with it. Between eight and nine million people are newly infected each year. About 1.3 million people die from TB each year. And the World Health Organization estimates that by the end of 2015 there will be about 2 million drug-resistant cases of tuberculosis.

It’s also a just very interesting bacterium, from a genetics perspective. It’s very different.

What’s your research about?

“My project is fundamentally about tool building – creating a way to identify exported proteins in tuberculosis.”

Scientists need to identify these proteins in order to develop ways to help the immune system recognize the tuberculosis bacterium and attack it.

“The bacterium has proteins in its cytoplasm and actively transports some of those proteins out of the bacterial cell, either to the bacterial cell surface or into the environment. If the bacterium is growing in your lungs, then that means the environment is your cells.” These exported proteins help Mycobacterium tuberculosis (Mtb) infect us.

“We can study these proteins in a lab to see which ones are exported, but we hypothesized that the exported proteins we see in the lab are probably different from the proteins that are actually exported when the bacteria are growing in your lungs. My project has to do with seeing if there are differences and what they are in a mouse model. It could’ve been a complete bust, but we did find some.

“We started with a beta-lactamase, a protein that’s normally exported and breaks down β-lactam antibiotics, like Amoxicillin, to provide antibiotic resistance. We then engineered this protein to be a “reporter” able to confer antibiotic resistance only when connected to an exported protein of Mtb. Next we used this reporter to ask which proteins of Mtb are exported. What was really cool is we were able to infect mice with Mtb using this reporter, treat the mice with Amoxicillin, and ask which proteins are being exported during infection.

“By using genetics technologies, I’ve forced the bacteria to tell me what proteins they’re exporting when they are inside of a mouse. We’ve identified a subset of proteins – about 38 of them – that are exported during infection that are not exported during lab experiments where the bacteria are growing in “media” or a mixture of salts, sugars, and protein.”

What are the implications of this work?

“We’re doing experiments to find out if these proteins are fundamentally important during infection. This is a year-long process. I think they’re definitely doing something important, and I do think that they contribute to virulence during infection, but it can be difficult sometimes to identify the role of an individual protein.

“TB is interesting. It has lots of systems inside a single bacterium to promote virulence. It has back up plans in case something stops it. If you stop one export protein, there are extra proteins to compensate. It’s tricky.”

What does the future hold for you?

For right now I’m continuing my education and looking for postdoctoral positions to gain further experience.

“In the future, I would like to continue working on tuberculosis. I’m still very passionate about it, and it’s still going to be a major problem. I’m particularly interested in two challenges in the TB field. First, TB is still very difficult to diagnose, especially in the third world where the newest technologies are too expensive to implement. One of the best ways to diagnose TB is to actually grow the bacterium from sputum. Unfortunately, this takes a very long time, sometimes weeks, to get a diagnosis. And if you want to know if it’s a drug-resistant strain, you have to wait even longer. So, I’d be interested in working on developing better diagnostics.

“One other major challenge is drug development. Right now, if you have active TB, you need to be treated with four different drugs for six months. If you have drug-resistant TB, you have to inject yourself with drugs every day for up to two years. Some patients have even been identified that are essentially untreatable with the currently approved drugs. So, we also need to develop new and better drugs, and soon.

“There are a lot of big fundamental problems, and I think I’d like to find a way to work on one of them.”

Media Contact: Mark Derewicz, UNC School of Medicine; 919-923-0959, mark.derewicz@unchealth.unc.edu

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