The Battle against Microscopic Bugs

Edward Miao, MD, PhD, earns a Jefferson-Pilot Award for his groundbreaking work on the interplay between dangerous pathogens and the human immune response.

The Battle against Microscopic Bugs click to enlarge Edward Miao, MD, PhD/Photo by Max Englund, UNC Health Care


We are constantly fending off bacteria. There are bugs on doorknobs. Bugs in the bathroom. Bugs on your steering wheel. Bugs in the dirt your kids dig in. Bugs on the kitchen table. We can’t avoid them, try as we might.

Luckily for us, most of these bacteria mean us no harm. For those that do have ill intent, our immune system can usually fight off the invaders and return us to health. Edward Miao, MD, PhD, is learning precisely how the sensors in our immune system help us eradicate bacterial infections, but also how some of the most dangerous bugs avoid detection. When our sensors fail, the bugs can replicate out of control, eventually triggering a cascading inflammatory response called sepsis that winds up doing some patients much more harm than good.

For his work, Miao, an assistant professor of microbiology and immunology, received a Jefferson Pilot Award, given to exemplary UNC School of Medicine junior faculty. The four-year fellowship carries a prize of $20,000 to support research or teaching efforts.

We sat down with Dr. Miao for a Five Questions feature to learn about his foray into microbiology, how some bacteria evade our natural defenses, and what the end goal is of his foundational research on bacterial virulence and our lacking host defenses.

5q-TIEWhy did you pursue science, particularly an undergraduate degree in microbiology from the University of California at Davis, and then an MD/ PhD focused on pathogen virulence at the University of Washington?

What comes immediately to mind is when I was six or seven and I’d take apart toy Star Wars space ships. I remember really liking the process of discovering how they worked, and putting them back together. And then at some point I realized that I should probably do something useful with this instinct for investigation, and I found a concrete direction in college.

I majored in microbiology at UC Davis, not far from where I grew up in Fairfield, California. I’m not exactly sure why I got interested in microbiology. But I do remember that genetics interested me, and so did bacteria. I had this really naïve idea that it would be too hard to work with genes because they were too small. So I wanted to work with something bigger and chose bacteria.  At least you can see them in a microscope, right? That was the notion that landed me in microbiology when I was a freshman. It’s funny how a really stupid thought, years ago, can steer the trajectory of a career.

Then I got more and more interested in bacteria, and I started thinking about infectious diseases in the context of medicine. One of the aspects of this field that I find particularly intriguing was summed up recently by one of my graduate students, Jon Hagar, who noted that we constantly think about infectious disease as a narrative story, there is a protagonist – that’s us tying to live our lives. And there are antagonists – the bugs trying to take advantage of us for their own benefit. So there’s this ongoing battle, and we constantly consider who is winning the evolutionary race, which can be a challenging intellectual puzzle. 

Sometime during my junior year someone mentioned the concept of an MD/PhD program, and I thought that had to be the best way to do medically relevant research because you learn clinical medicine, but you also learn research skills. So I’d have the whole package necessary to think about medically relevant problems.

I did the joint MD/PhD program at the University of Washington because it was one of top schools in country. There’s great research there and a really good microbiology program, which is also why I came to UNC.

5q-salmonellaMost graduate students do a postdoctoral fellowship at a university. How did you wind up at the Institute for Systems Biology, a nonprofit biotech in Seattle for your postdoc and then as a research scientist?

At the end of the MD/PhD program, I decided that I had the aptitude to be a fair clinician, but the potential to be a very good scientist. So I didn’t do residency training; instead, I focused on research.

When I was a grad student I was interested in the virulence factors that allowed Salmonella to be a pathogen. When I started doing my postdoc, I got interested in how the host organism detects those same bacterial virulence factors.

Essentially, the bacterium has armament – weapons that allow it to be a pathogen – and we have sensors in our immune systems that detect that armament. So, I’ve always been interested in the interface between the pathogen and host. I spent my postdoc fellowship trying to understand how the host detects and responds to the bacterium.

I chose the Institute for Systems Biology because that’s where Alan Aderem was studying innate immune sensors, and that’s what I was interested in. Had his lab been at a large research university, then that’s where I would’ve gone.

I was there for a long time, from 2004 to 2011, first as a postdoc then as a research scientist. It was a very large lab with about 15 postdocs and one graduate student. I was chosen – or volunteered – to co-mentor the grad student. Then I wound up working with an infectious disease fellow and two research technicians. I managed to mentor this small group within the lab working on a specific group of immune sensors that the larger lab wasn’t working on. I sort of had this semi-independent pre-assistant professor experience. I must have done a pretty good job working with this team, because one of the technicians, Dat Mao, made the trek across the country with me to start up the lab here at UNC, and he’s still with me as my lab manager.

Another reason I stayed as long as I did at ISB was that my wife, Cheryl Carlson, was in Seattle doing her hematology and oncology residency and then fellowship at Washington.

5q-northcarolinablueWas it always your plan to start an independent academic lab, and why did you choose to establish your lab at UNC?

Yes. When my wife was finishing up her fellowship, I started looking for jobs. I applied here because it has one of the best microbiology and immunology programs in the county. Also, the density of research at UNC is amazing; there’s just a really vibrant research community here, particularly in the fields of microbiology and immunology. Then add Duke, NC State, NIEHS, and the Research Triangle Park, and there’s just a massive amount of collaboration and expertise in this area. 

After I applied here, my wife got a position here, as well. She’s now an attending physician in GI oncology.

5q-explodingcellYou still work on Salmonella typhimurium. Why is Salmonella so often associated with food contamination, and what has your research revealed about this bacterium and the human immune response, in general?

I think the reason it’s so prevalent in our food supply is the very compressed conditions in which we house our livestock, particularly chickens and cattle. This increases transmission between the animals, which can harbor the Salmonella without becoming overtly sick. Now, pair this with a greater centralization of food processing and distribution. One particularly horrible example in 2008-9 was a peanut processing plant where horrible conditions somehow allowed Salmonella to get into the machinery. The peanut products were shipped across the country, making 714 people sick in 46 states, and killing nine of them. In this case, the owner of the processing plant received felony conspiracy and fraud convictions for knowingly shipping the tainted peanut products. At any rate, you can see how a single source spread the infections far and wide.

In my lab, we’ve used Salmonella as a tool to ask: what can the innate immune system detect? This led us to learn about sensors for virulence factors. One main factor a lot of bacteria use is a type-3 secretion system, which is essentially a little syringe that bacteria use to inject their proteins into our cells to change the physiology of our cells. Obviously, that’s bad. We learned that we have inflammasome sensors that will detect that injection event when some bacteria do this.

Then we learned that Salmonella is doing a good job getting away from our sensors.

So we’re probably getting a benefit from these sensors, but there’s this constant battle going on between sensors and bacteria. Some bacteria are winning this battle.

5q-eggsIn 2013, your lab published two papers in Science, showing how the immune system distinguishes between suspicious activity and real threats, such as virulent bacteria. What precisely did you find and what is the significance of this work?

Part of our immune system is like an alarm system for a house. This really is how I think about it. There are sensors that know there is activity outside the cell, and there are sensors that really strike the alarm when that suspicious activity enters the cell. It’s kind of like the difference between a suspicious character in your front yard and someone in your living room. The latter is much more frightening!  I think of the comparison as the difference between a yellow alert and a red alert.

In the late 1990s, scientists discovered a cell sensor called TLR4. This sensor identifies a piece of the bacterial cell wall called LPS. But this TLR4 sensor can’t tell the difference between the harmless bacteria that we all have living inside of us right now and, say, Burkholderia pseudomallei, which is an extremely dangerous bacterium and a potential bioweapon.

These harmless and virulent bacteria look the same to the TLR4 sensor because TLR4 is just watching for bacteria in the extracellular space outside of cells.

The sensor that we found – called caspase-11 – identifies the same LPS molecule when the bacterium is inside a human cell. Caspase-11 seems to be especially expressed in a type of white blood cell called the macrophage, which is essentially a sentinel for the immune system, watching out for invaders.

We think of it like this: first, it really does take a unique type of bacterium to find one of your cells, attack the cell, get inside the cytosol of the cell – the intercellular space in a cell – and then replicate inside the cell. This takes several virulence traits; the bacteria must have genes that allow it to do this.

Francisella, for instance, invades the cytosol. Burkholdedaria does, as well.

We found that caspase-11 senses many kinds of bacteria when they get into the cytosol. Caspase-11 is the sensor that triggers a red alert, and when that happens, the cell explodes because killing itself is the best thing a cell can do to get rid of a bacterium. When you think about this using the house analogy, it’s like blowing up your house to prevent a burglar from hiding in there. It’s an extreme, but very effective, response.

The trouble with evolution is that bacteria evolve faster than we do. Some pathogens actually know about this caspase-11 sensor and have evolved ways to get around it. Francisella, for instance, is a horribly virulent pathogen probably because it completely evades this sensor. We showed this in our second paper. Francisella has an LPS with a different structure that caspase-11 cannot detect.

You might ask, “why bother having these sensors if the pathogens just evade them?” Well, we think of it like this: Burkholderia pseudomallei is a very virulent microorganism and potentially a bioweapon, and may also be getting around this sensor to some extent. But it has a cousin called Burkholderia thailandensis, which can also invade the cytosol of our cells but it’s not infectious. It doesn’t cause disease.

This cousin bacterium lives in the dirt; it hasn’t evolved in people. So it hasn’t created ways to get around our sensors. When our cells detect it, we clear it efficiently and don’t get sick. We’re completely immune because of this caspase-11 sensor. We showed this in mouse studies in which normal mice were completely immune to this bug. But mice that lack this caspase-11 were incredibly sensitive to this infection; the Burkholderia thailandensis replicated out of control.

The new idea that I’m advancing is that there’s a world of dangerous bacteria out there but we have these sensors inside our cells watching for their ill intent. And if we don’t detect them, then we’re in big trouble. In terms of the narrative aspect: “who is winning?” We think that we humans are using caspase-11 to win against bacteria like Burkholderia thailandensis, but we are losing against Francisella, which evades this sensor. 

One potential impact of this work has to do with septic shock. Bacteria have lots of LPS. And we have sensors that detect it. We think that when someone has a bad infection and they become septic – when their bodies produce an overwhelming inflammation response – what’s actually happening is that the body is accidentally activating this caspase-11 sensor in a way that isn’t normal; it starts sounding a false alarm.

Normally, the caspase-11 sensors should only detect the bacteria that enter cells. But in sepsis, we suspect that there’s so much LPS everywhere that some of it starts to leak into cells, our sensors trip incorrectly, and macrophages explode willy-nilly throughout the body.

So we suspect – based on our animal studies – that when you have too many of these macrophages exploding all over your body, this contributes to the pathology of sepsis.

Macrophages are important to fight off infection. But when they explode, all of their insides come out and this rings more alarm bells, causing further inflammation.

One of the biggest problems with sepsis is that we have very few treatments.

If it’s a bacterial infection, we can use antibiotics. Other than that, we use supporting care – fluids and maintaining the person’s blood pressure – and just hope the patient can get through it. No directed treatment to go after the inflammatory response, which is really what’s killing them.

This is what happens with Ebola, for instance, or with the flu. We generally think that all infections that get out of control lead to too many inflammatory mediators, and these mediators are what actually kills the patient.

Of course, if you didn’t have those mediators, then you’d have been dead a long time ago because you would’ve failed to fight the infection in the first place.

But for patients who get to sepsis, hopefully – down the road – the knowledge that we are gaining about these inflammasome sensors will let us create some new directed therapeutics so we’ll be able to inhibit the inflammatory response without immunosuppressing the person too much.

Right now, I view our research as laying the foundation of knowledge so that we can start to build treatments for septic shock, or inspire new ideas about how to treat people who have sepsis.

Dr. Miao is also a member of the UNC Lineberger Comprehensive Cancer Center and the UNC Center for Gastrointestinal Biology and Disease.

Media contact: Mark Derewicz, science communications manager,

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