Engineering Bacteria to Monitor and Treat Disease with Arthur Prindle, PhD

“We hope to not only understand bacterial community biology, including the microbiome, but then even potentially re-engineer it or change it in a beneficial way to mitigate human disease or environmental pollution or toxin production.” 

-Arthur Prindle, PhD 

• Assistant Professor of Biochemistry and Molecular Genetics, McCormick School of Engineering   
• Assistant Professor Microbiology-Immunology

Through investigative work into biofilm communities, the Prindle Lab at Northwestern is researching the potential of engineered probiotics to detect inflammation in those with Inflammatory Bowel Disease (IBD). It is possible that similar technology could one day deliver therapeutics to these sites of inflammation, and even detect the presence of tumors, as IBD patients are at higher risk for colorectal cancer.  

• Communities of bacteria that live together are often termed biofilms. They exhibit altered behavior compared to free living bacteria, including possible changes in gene expression, metabolism, in the proteins they produce, or the signals they communicate. 
• One of the main biomedical challenges for biofilms is their high degree of antibiotic resistance, a topic of Prindle’s research. His team is also investigating the prospect of engineering probiotic bacteria to sense biomarkers of disease in the human microbiome. 
• IBD is marked by the production of the protein calprotectin, a primary clinical biomarker of IBD. An engineered probiotic could potentially sense the presence of calprotectin as a way of monitoring IBD flares, rather than current clinical procedures which are complex and time-consuming.  
• In current animal models, administered probiotics are monitored by luminescence (where bacteria produce enzymes that emit light). This will likely not work in humans, and instead, would require the use of MRI or ultrasound, which Prindle is investigating.  
• Prindle is also investigating the possibility that, in addition to detecting the presence of inflammation in IBD, could probiotics – already at the site of the flare – also deliver therapeutics.  
• IBD is associated with an increased risk of colorectal cancer. It is possible that probiotics could be engineered to survey for tumor DNA as well.  
• Now approaching the 15 to 20 year anniversary of the start of the field, synthetic biology is thriving at Northwestern, a field enabled by a combination of technologies and a variety of fields not limited to biology alone.  

 Recorded on November 9, 2023. 

Additional Reading 

• Explore Prindle’s lab 
• Read about Prindle’s paper published in the Proceedings of the National Academy of Sciences about an engineered probiotic capable of detecting inflammatory bowel disease. 
• Find out more about Prindle’s Faculty Early Career Development Program award from the National Science Foundation. 

Target Audience

Academic/Research, Multiple specialties

Learning Objectives

At the conclusion of this activity, participants will be able to:

1. Identify the research interests and initiatives of Feinberg faculty.
2. Discuss new updates in clinical and translational research.

Accreditation Statement

The Northwestern University Feinberg School of Medicine is accredited by the Accreditation Council for Continuing Medical Education (ACCME) to provide continuing medical education for physicians.

Credit Designation Statement

The Northwestern University Feinberg School of Medicine designates this Enduring Material for a maximum of 0.50 AMA PRA Category 1 Credit(s)™. Physicians should claim only the credit commensurate with the extent of their participation in the activity.

American Board of Surgery Continuous Certification Program

Successful completion of this CME activity enables the learner to earn credit toward the CME requirement(s) of the American Board of Surgery’s Continuous Certification program. It is the CME activity provider's responsibility to submit learner completion information to ACCME for the purpose of granting ABS credit.

All the relevant financial relationships for these individuals have been mitigated.

Disclosure Statement

Arthur Prindle, PhD, has nothing to disclose. Course director, Robert Rosa, MD, has nothing to disclose. Planning committee member, Erin Spain, has nothing to disclose. FSM’s CME Leadership, Review Committee, and Staff have no relevant financial relationships with ineligible companies to disclose.

[00:00:00] Erin Spain, MS: This is Breakthroughs, a podcast from Northwestern University Feinberg School of Medicine. I'm Erin Spain, host of the show. The human body is full of bacterial species, collectively called the microbiome. A healthy microbiome not only supports digestion and strengthens the immune system, it can also reduce the risk of obesity, heart disease, diabetes, and even cancer. New advances in synthetic biology at Northwestern are paving the way for an even deeper understanding of these bacteria. Dr. Arthur Prindle and a team of investigators are developing ways to actually engineer bacterial communities in order to both monitor and treat disease. Dr. Prindle is an assistant professor of biochemistry and molecular genetics and of chemical and biological engineering at Northwestern University. He joins me to discuss his latest research, including a study on an engineered probiotic capable of detecting inflammatory bowel disease. Welcome to the show, Dr. Prindle. 

[00:01:17] Arthur Prindle, PhD: Oh, thanks so much. Happy to be here. 

[00:01:19] Erin Spain, MS: Let's talk a little bit about microbiome communities in your research. These are called biofilms in your research. How do they fit in with the larger context of the microbiome and disease? 

[00:01:31] Arthur Prindle, PhD: So bacteria are one of the oldest model organisms studied in biology. And we know that they exist all over planet earth and many different environmental niches, such as soil, water, like rivers and streams. And more recently, we've appreciated that bacteria exist within the human body, and that's termed the human microbiome. And while these bacteria, of course, are single celled organisms, as distinguished from a multicellular organism, you know, like a person or an animal, much more commonly in those different niches in the environment, they exist in the context of many other species of bacteria or many copies of bacteria living together. So communities of bacteria that live together are often termed biofilms, and those biofilm communities exhibit altered behavior, compared to free living bacteria, and that can mean that their gene expression has changed, their metabolism has changed, and the proteins they produce and the signals they communicate with are all changed when the bacteria are growing and living together. And so the hope is to better understand how bacteria live. We need to study how they live in communities. And by doing that,   to not only understand bacterial community biology, including the microbiome, but then even potentially re-engineer it or change it in a beneficial way to mitigate, you know, human disease or environmental pollution or toxin production. 

[00:03:02] Erin Spain, MS: How is it that you got involved with this work? 

[00:03:05] Arthur Prindle, PhD: So back in undergraduate, I was a chemical engineer. I always wanted to be an engineer and build things, sort of, in my DNA. And I didn't envision myself at that time of being a biologist or even a research scientist until I had a really excellent undergraduate research experience as a junior, where I discovered the field of synthetic biology. And the concept there, which is really sounded like a sci-fi kind of concept at the time, was reprogramming cells. So we know about building machines, we know about programming computers, but the cell, it always seemed, you know, too mysterious, too much of a black box. We don't know enough about it that we could actually reprogram a cell, but as an undergrad, I heard that people were trying, and I wanted to be one of those people. So I kind of jumped all in and I started with bacteria because there are some of the simplest cells that you could work with. So if we're going to be able to reprogram a cell, we'd probably start with bacteria. 

[00:04:02] Erin Spain, MS: You've actually said and you've been quoted saying if we understand the cell as a machine, we can seek to rearrange the parts of the cell to do a new function. So that's what you mean by this actually reprogramming of a cell? 

[00:04:15] Arthur Prindle, PhD: Exactly. So the cell, you know, as a living machine, it has parts, it has enzymes, it has proteins, it has DNA. Those are parts that are all working together to serve the function of a cell, which is usually to grow and survive. If we as a synthetic biologist or a research scientist can understand those parts well enough, we can envision new ways of rearranging those parts to do functions that are beyond survival for the cell. So we can have them produce a reporter molecule of interest that would signal the presence of a pollutant or a biomarker of a disease. We could have them produce a new enzyme from a different organism that could actually break down that pollutant, or it could actually potentially produce a therapeutic molecule in response to a disease. And so those are all functions that exist in different organisms in biology. They're not all found in the same cell. And so we can look around in different cells that people have studied and then bring those parts together to produce a new function. And we like to do that in bacteria because they're very simple or comparatively simple compared to higher organisms. But then bacteria are found, as we mentioned earlier, everywhere on planet earth. And so why can't we co-opt where those bacteria are naturally living to sense disease or pollution and then mitigate those effects. 

[00:05:36] Erin Spain, MS: So tell me about some of the diseases that you've been focused on, especially looking for therapeutics, finding a way to kind of solve some of these problems through biomedical engineering. 

[00:05:47] Arthur Prindle, PhD: So one of the main biomedical challenges related to biofilms is their high degree of antibiotic resistance. And so it's known that when these communities grow together, they produce structural changes like an extracellular matrix that can prevent antibiotics from getting to cells. But they can also have ways of keeping large numbers of bacteria alive in a nondividing state. It's sort of a mystery how this happens, but what it means is that many of the antibiotics we've developed that are effective on actively growing bacteria are now ineffective on these non-growing cells in biofilms. And so by doing sort of basic science studies of biofilms to answer the question of how do they keep these non-dividing cells alive, even though they're far away from nutrients being delivered to the biofilm. If we can answer that, it might give us new approaches to overcome that antibiotic resistance. Beyond antibiotic resistance in biofilms, we're also doing applied work in the microbiome where we're trying to re-engineer probiotic bacteria to sense biomarkers of disease in the human microbiome. And so there are a few examples that you could focus on, but one that we've had a recent study on is called inflammatory bowel disease, which is sort of a disease where you get recurrent patterns of gut inflammation, where this inflammation is manageable if detected and monitored, but it's often difficult to measure that biomarker in a timely manner, in a non invasive manner. And so the idea here is, if bacteria are already living in the environment where the disease is occurring, like the human gut, why can't we co-opt those bacteria to sense those biomarkers and then report that information out to us in a potentially less invasive and less, technically challenging manner than current methods? 

[00:07:45] Erin Spain, MS: And you mentioned this study with inflammatory bowel disease, which does affect roughly 3 million Americans. And you recently published results in the Proceedings of the National Academy of Sciences. Tell me a little bit about the results of this study and what you were able to prove. 

[00:08:02] Arthur Prindle, PhD: So, inflammatory bowel disease, or IBD, is a disease in humans that's characterized by recurrent gut inflammation. These inflammatory flares that come and go are intermittent, but whenever they arise, they are always associated with the production of calprotectin. Calprotectin is a protein produced by the human host that is the current clinical gold standard biomarker of IBD. And so, if we were going into the hospital today to get a send out lab test for IBD, that is what would be measured is calprotectin. Calprotectin itself has different functions that have been proposed. Some of them involve potentially mitigating unwanted bacteria that might be growing in the gut. But one of those functions that we took advantage of is that calprotectin can chelate or bind up metal ions, including zinc. And so we wondered whether we could find a very strong transcriptional response to that zinc binding activity of calprotectin that would allow us to engineer the probiotics to report out when they're encountering calprotectin. And so the idea would be, as a way of accurately monitoring calprotectin flares, we engineer the probiotic bacteria to sense calprotectin and then convert that to a luminescent or fluorescent output from the bacteria. 

[00:09:25] Erin Spain, MS: And this approach could be so different than what the current gold standard is right now, which involves a lot of time consuming and invasive monitoring. Can you tell me about that? 

[00:09:36] Arthur Prindle, PhD: Yeah, so current approaches to monitoring IBD, they all range in effectiveness. There's sort of trade-offs. The absolute gold standard diagnosis method for IBD would be an endoscopy or colonoscopy, which would accurately report what's going on, but it's of course invasive. There are non-invasive biomarkers that are either in blood. CRP is one. However, it's not very specific to IBD. So you would probably, if you saw a CRP up, you would then follow it up with an endoscopy or some other assay to confirm. There's a stool biomarker of IBD, which is calprotectin. So that's what we're trying to measure here with the bacteria. But the current method for measuring calprotectin is a send out lab test, which is a sort of an ELISA based lab test. So you'd go in, you'd be having symptoms, talk to the doctor. They would order that test. So, you'd provide the sample, it'd be sent off to another lab, and then, you know, seven to ten days, you'd get the result back. But the doctor needs to decide how to proceed at that time without those results. So, they usually kind of take their best guess. They might ask you to report your symptoms. How are you feeling today? How are you feeling last week? So, they will use a combination of patient reported symptoms together with the send out lab test. The send out lab test takes time and has a cost, and then the patient reported symptoms are going to be subjective, and you might not remember accurately. So what we're hoping to achieve here is something that's potentially faster and cheaper, but still highly accurate, and less invasive than the endoscopy approach. 

[00:11:13] Erin Spain, MS: So how would you be tracking? You would be using imaging? 

[00:11:16] Arthur Prindle, PhD: Yeah, so in our current study, which is a proof of principle, so we're clear this is sort of the first step towards, you know, developing this technology in humans. We show in animal models that when we orally deliver the probiotics to mice that have inflammation, that's sort of a model of IBD. We see those probiotics lighting up within the gut as they pass through the gut following oral administration. We don't see them lighting up when the mouse is healthy. And, of course, we don't see them lighting up when we just deliver probiotics that lack the engineered detection for calprotectin. That lighting up, I mean, it's called luminescence. So the bacteria are producing enzymes that emit light and then we detect the light using a camera. That works fine in mice, that likely will not work in humans. Mice, there's less tissue in the way basically to get the light out from the bacteria. To modify our diagnostic to work in humans for imaging, there are a few options that we're looking into. These would be things like MRI or ultrasound. So there are currently bacteria that can produce basically contrast agents or reporter molecules that show up in both MRI and ultrasound. So it would be the same gene expression response to calprotectin that we have in our current study, but instead of producing the luminescent output, they'd produce an MRI or an ultrasound reporter. Currently what we do have in the study is ex vivo samples. So the stool sample from the patient where they're measuring calprotectin. We test our probiotic on those same samples, and we show that we're able to get a signal that correlates very well with the lab test results for calprotectin. So the healthy patients that have low calprotectin, according to the sendout lab test, they also have low signal with our probiotic. Those patients in remission that have a low to an intermediate level, they have a still low signal, but slightly higher. And then patients with active IBD that are undergoing an inflammatory flare that had high calprotectin measurements also were very bright in our probiotic diagnostic. So, you know, it's sort of projecting forward a little bit, but if I combine in the animal, I can get in vivo bacteria lighting up as they pass through the gut. And then on the human patient samples ex vivo, my signal correlates with the calprotectin measurement. So the hope then would be that if you could try this in a person, maybe the bacteria would be able to produce a reporter molecule. That involves a lot more work, clinical trials, you know, that would be done together with, you know, a physician, appropriate study design. But a few people here have emailed me after the study came out and are interested in doing those kinds of phase one safety trials to start with. 

[00:14:04] Erin Spain, MS: I am curious, you know, you're talking about a probiotic. We think about yogurt. We think about how people consume probiotics. Would you potentially deliver this probiotic through a spoonful of yogurt, or would it be a pill? 

[00:14:17] Arthur Prindle, PhD: Exactly. Yeah. We eat food that has bacteria in it all the time, as you mentioned yogurt. This probiotic that we use, it's currently over the counter in the United States, generally regarded as safe by the FDA. You can buy it on Amazon. I believe you can buy it in Whole Foods. You know, we started with something that's totally innocuous and has proven safety in human trials. So this could be delivered either through a pill or yogurt. And then maybe, you know, wait an hour, wait 30 minutes and then go get the imaging done. There are things like this done today, not cell based as much. But that's sort of the vision there. 

[00:14:55] Erin Spain, MS: So you've mentioned you've already had some interest from clinicians who are interested in doing clinical trials. Where do you see this going? What could be next? 

[00:15:04] Arthur Prindle, PhD: So we're very excited to show safety and proof of principle in human patients. That's potentially a longer term goal that would be done with a GI physician here in sort of a phase one trial. Even before that, we're still working on improving our diagnostic in the lab. So I mentioned the different imaging readouts, such as MRI and ultrasound, that'd be one. Another capability that I always am asked about is can you not only detect the inflammatory flare, but can you actually produce and deliver a therapeutic molecule in response to that flare? You already have those probiotics at the site of disease. They can already respond to the flare. Couldn't they then secrete or release a therapeutic molecule directly in response. So we're pursuing what are called anti TNF antibodies or nanobodies. So these are molecules that are used today as therapeutics for IBD. They're usually administered in blood, I believe, although they're being developed now for oral delivery as well. And some of these are produced commercially in bacteria today. And so we have a belief that our bacteria will be able to produce them as well. And so the idea there would be that these probiotics have internal therapeutics that they're producing as they're growing in the gut. Then when they sense that inflammatory flare, they induce secretion or release of those molecules into the gut in that neighboring environment. 

[00:16:36] Erin Spain, MS: And of course, in this study, we're talking about inflammatory bowel disease, but there are many other conditions that could also be helped with this approach. Just tell me about some of those and maybe even diseases such as cancer or diabetes. Could there be a way to not only detect but deliver therapeutics? 

[00:16:54] Arthur Prindle, PhD: So we're very interested in a number of those other diseases that you mentioned. So, IBD in particular has been associated with an increased risk for colorectal cancer if left untreated. So, of course, one benefit of our diagnostic as it is today is that if IBD symptoms can be better detected and managed, that would decrease the longer term risk of colorectal cancer. But beyond that, you know, we have the goal of detecting other diseases as well. So, it's possible that you could have probiotics engineered to survey for tumor DNA in the environment. So if you had a colorectal cancer or a tumor growing, that would potentially be releasing mutant DNA, like KRAS, to the local environment, could our probiotics be collecting that DNA, and then they'd report out the presence of a mutant DNA versus an unmodified DNA. There's definitely some technical challenges there, but I think it's possible in principle. We know that bacteria can take up DNA. We know that they can incorporate that DNA into their genome, but they can also, in a sequence specific manner, using CRISPR or other things like that, look for different versions of DNA that would potentially allow a different response between healthy and tumor sequences for a given gene. So we would have our probiotics always collecting small fragments of DNA from the environment. And then in the event that they encounter a mutant DNA, like a KRAS, we'd have them produce an output that would tell us.  

[00:18:29] Erin Spain, MS: I mean, that does sound like science fiction, but so exciting.  

[00:18:33] Arthur Prindle, PhD: It is, you know, yeah, I should be honest. This is a forward looking goal. So, you know, there's many challenges here. A lot of the probiotics people take today, one of the knocks on those is they usually just pass through. They don't colonize. There's already bacteria in the microbiome. There's no room, so it's actually not that easy to get probiotics to colonize and remain persistent in the gut. But there's approaches where you could maybe re-engineer native bacteria rather than a sort of foreign probiotic. You don't always want them to colonize either, just from a safety perspective. Sometimes knowing the dynamics of when you deliver to when they're cleared is actually important. And so there's different applications you can envision. Just on the other diseases too looking for things like C. diff. So if you have pathogens or problematic bacteria that might be growing in the gut, many of those bacteria, they're always there, but they're not in a problematic or virulent state all the time. So being able to distinguish between active virulent bacteria and just sort of benign is important and can't be done just by sequencing the bacteria themselves. So you know, today, if you get a stool sample, you sequence to look for which bacteria are present. You will often find a range of bacteria, some of which could cause problems, they might not. So what you really want are activity based measurements where you say not just who's there in the microbiome, but what is their metabolic activity? Are they producing virulence genes? Are they producing toxins? So, you know, you might want to adapt this probiotic to sense C. diff toxin or sort of other pathogenic toxins that you could then report the presence of. 

[00:20:18] Erin Spain, MS: As you've mentioned, this field it is relatively young, synthetic biology, but it's thriving here at Northwestern and as a research priority. You're part of the Center for Synthetic Biology here, which has been expanding. So tell me what it's like right now at Northwestern doing this type of research here. 

[00:20:37] Arthur Prindle, PhD: Yes, synthetic biology at Northwestern is absolutely exploding right now. It's a really exciting time to be working in the field. So we have a relatively recently established Center for Synthetic Biology here. We have faculty on both the Evanston and the Chicago campuses of Northwestern. And this brings together faculty that are working to engineer and reprogram cells in all different contexts. So there are a few of us working on bacteria. There are a few working on mammalian cells, you know, engineering things like CAR-T and immunotherapy. And then there's people trying to engineer cell free systems. So it's taking the enzymes and the DNA from cells that we know and love, but now removing the cell so I can just use the parts themselves. There's, you know, faculty from engineering, from biomedical engineering, pharmacology, biochemistry, where my home department is, cell and developmental biology. And so we're all in different home departments, but we have these research themes in common. And so it's a really sort of interesting way of doing interdisciplinary research and doing new and innovative work in synthetic biology. It's a relatively young field. You know, I think we're probably approaching maybe the 15 to 20 year mark here. But it's really a field that's enabled by a combination of technologies. So we have the ability to synthesize DNA, the ability to sequence DNA. And then those led to a lot of people coming into biology that weren't maybe traditionally trained as biologists. But I, what I think they all share is this fascination with the idea of the cell as a machine, you know, can we use engineering methods that we've developed and used for machines and computers, but is it really time to apply those to biology? It's hard. The cell has its own goals and there's a lot we don't know about the cell, but I think it's still sort of a good source of inspiration and very motivating and exciting. 

[00:22:40] Erin Spain, MS: And you have actually received a number of awards, most recently the National Science Foundation Award, which specifically supports early career development of individuals who exemplify the role of teacher scholar. Just tell me, how do you see your role as an educator in this breakthrough science of synthetic biology? 

[00:23:00] Arthur Prindle, PhD: So the NSF Career Award is very exciting. I was very honored to receive that. That award is focused on developing sort of a systems biology or a quantitative understanding of these microbial communities. So we're doing experimental measurements of bacteria, so imaging, sort of growth, metabolism, gene expression, but then also making mathematical models of how those bacteria are interacting. So, it's a very good opportunity for training students. It's also a good way of making sure our experimental work is rigorous, using these models to make new predictions that we can then test experimentally. But then get the students excited about biology, you know, maybe that hadn't been thinking about biology as a career, like I was as a chemical engineering student. If I think back to, you know, what was the initial inspiration there, it was seeing a cell, but then imagining using equations, using engineering to describe how it's behaving and modify how it's behaving. So I hope to give that opportunity to new engineering undergraduate students here at Northwestern. 

[00:24:08] Erin Spain, MS: Thank you so much, Dr. Prindle, for coming on the show and talking about your recent work and all the exciting things ahead. We appreciate your time today. 

[00:24:16] Arthur Prindle, PhD: Thanks a lot. It was a lot of fun. 

[00:24:18] Erin Spain, MS: You can listen to shows from the Northwestern Medicine Podcast Network to hear more about the latest developments in medical research, health care, and medical education. Leaders from across specialties speak to topics ranging from basic science to global health to simulation education. Learn more at feinberg. northwestern. edu slash podcasts.