Episode 8: Translating Disease Models (Transcript)

Dr. Bayrer 0:00 

Tastes like a dark chocolate with cayenne or capsaicin.

Peter 0:08

Perfect. That’s exactly what it was. You do research on enterochromaffin cells and a lot of the things that these enterochromaffin cells sense are irritants; the spiciness in the chocolate was used to mix up with the sweetness of the chocolate that normally is there to give that […] conflicting message to the enterochromaffin cells.

Dr. Bayrer 0:26 

Squirrels and other rodents are smart enough to sample and then avoid these hot peppers, but people were kind of dumb about it. And we’re like, we like that we’re gonna have some more. So that’s what we do.

Peter 0:41 

And that’s why we put it in our chocolate.

Hi, and welcome back to The Gastronauts Podcast. My name is Peter and I’ll be your host. Here at Gastronauts we are committed to exploring communication throughout the body with a focus on the cross-talk between gut and brain. We invite experts in this field to share both their research and their journey. So come join me as we explore the steps that going to shaping the scientist on The Gastronauts Podcast.

Today, we have Dr. James Bayrer, an assistant professor and pediatric gastroenterologist at UCSF. He completed his MD and PhDs at Case Western Reserve University School of Medicine. At Case Western, he studied specific the structure and function of proteins involved in sex determination in the laboratory of Dr. Michael Weiss. Upon finishing his PhD, he traveled out west to California for residency in pediatrics at UCSF. He stayed on to do a fellowship in gastroenterology (where he took care of children with digestive, pancreatic and liver conditions). He worked with Dr. Robert Fletterick and Dr. Holly Ingraham to study factors involved in colon cancer development and has taken advantage of organoids as a model system. These organoids are a really neat system that displays the shape and morphology of your gut, but can be studied in a culture dish! Dr. Bayrer has used organoids to study enterochromaffin, rare 5-HT secreting cells in the epithelial layer of the gut to better understand visceral (or our internal sense of pain).

So I want to start by taking a trip down memory lane with you. When you were at Case Western, what drew you to studying sex determinations in fruit flies? And how did that inform your decision to pursue a residency in pediatrics? They seem a little bit desperate to me, but I was wondering what was going through your head at the time.

Dr. Bayrer [3:03] 

Thanks for having me. So that’s an interesting question. And yeah, the sex determination and crystallography are pretty far removed from what I’ve been doing lately. But what drew me to study this was the idea that the structure of a protein can really dictate its function. And so in Drosophila, sex is determined by this gene I was studying called double sex. And I was curious as to how the structures that the female or the male specific sequences change the function that would give you such dramatically different phenotype and development. So really, it goes back to more of an interest in structure or function and protein biochemistry.

Peter 3:52 

And development as well. Did that have any influence on your decision to pursue a career in pediatrics? Or were the two separate ideas In your head at that time?

Dr. Bayrer 4:00 

The two are separate. So when I was training in the PhD phase of my work, I knew that I was going to sub-specialize into something and what that was going to be, I wasn’t entirely sure. I still had an interest in protein interactions and structural biology, which is pretty general and can be applied across all of the disciplines in medicine. And so what really convinced me to do pediatrics was actually when I went back as a third year medical student and started my clerkship rotations. I started out with pediatrics and I really fell in love with both the patient populations and working with the families and the children but also the relationships that you can develop in the long term care of these families with complex medical issues. I found that to be a very rewarding side of medicine. And the other thing that I thought was really interesting in pediatrics is that somebody could come with you with a certain set of symptoms and depending on the age of the patient, you can have a very, very different differential diagnosis. And so in many ways, it ticked those boxes of clinical thought process and puzzle solving that makes medicine a lot of fun. And it just adds that extra layer of complexity to the process.

Peter 5:18 

Yeah, that’s really neat. Do you feel like your time away from your PhD to when you started doing research again during your fellow years while you were a third and fourth year medical student and while you were pursuing your residency in pediatrics has influenced or framed how you think of research or changed how your thought process and research was?

Dr. Bayrer 5:35 

Yeah, and so the intervening time is really a time that I focused on my clinical skills and to tried to hone those to be the best clinician that I can be. And so I really focused on that. But at the same time, the farther and farther away from the basic research that I can do, the more I really did start to miss it. To be able to ask a fundamental question and to able to answer it. So what I would say is that that clinical time served to help me focus my research questions on work that is more directly applicable to the patients that I care about, that I’m treating. That’s probably the biggest takeaway that I had in terms of my clinical experience in forming the research.

Peter 6:25 

Do you mind telling me a little bit more about your current research efforts?

Dr. Bayrer 6:26 

Yeah, so our lab has mainly two projects with some overlap. One side of that is based around epithelial regeneration and differentiation. And so what programs are there that help control this normal process where the gut intestinal lining is renewed every week or so, and help control the proper distribution of the specialized sensory cells and other cells that compose the lining of the gut. So that’s one side of the lab and then the other side of the lab is a collaborative effort. With a number of really fantastic investigators looking at the signaling side and the signal integration processing. So that’s the sensory visceral pain aspect to the research. So we have one side that’s really organoid and developmental biology focused. And then another side that’s more physiology focus.

Peter 7:20

Do you see kind of the organoid and developmental biology influencing or having an impact on the clinic? What kind of diseases are there that we know of in pediatric populations where there are developmental or programming issues with our intestinal cells?

Dr. Bayrer 7:33

So there are an increasingly recognized number of genes involved in epithelium renewal as well as barrier formation that had been implicated in our very early onset IBD patient population, and IBD stands for inflammatory bowel disease. These patients are diagnosed between zero and five years of age with inflammatory bowel disease. We now have the tools to be able to try and identify genetic causes that we can intervene on specifically. And that’s one major aspect. In terms of organoids, one of the other thing that’s been really interesting is actually cystic fibrosis. We think about cystic fibrosis mainly in terms of pulmonary disease, right? Because that’s what really drives that clinical morbidity and mortality. But when you take a step back and look, you realize that the transmembrane protein that’s mutated in cystic fibrosis is expressed throughout the GI tract as well. And so there’s liver disease, pancreatic disease, as well as intestinal disease. In cystic fibrosis, there have been a number of really game changing medications that have come to market. And when you look at trying to match those drugs with particular type of mutation, going to trials, the drugs are really targeted to a particular mutation. What we don’t know from the clinical trials is if drug x is going to work with mutation y or mutation z if it’s only been studied for mutation a. And what was figured out is that if you make organoids from cystic fibrosis patients, you can stimulate those organoids with forskolin. and functioning CFTR will allow those organoids to swell due to flux of the ion channel.

Peter 9:20 

So this essentially allows a high throughput readout.

Dr. Bayrer 9:23 

That’s right. And then in even more importantly, allows you to do a personalized medicine approach. And so now you can take an organoid from a cystic fibrosis patient, you can expose it to different potential medications and find out very quickly if there particular CF mutation is going to respond to that truck. And so again, that’s really revolutionized the ability to match the right patient with the right drug, which is really that basis of precision medicine.

Peter 9:47 

And I think the field of organoids has really taken off because it is more similar to what we see in our living tissue. What drew you initially to the field of organoids? I noticed you previously kind of did a lot of structural functional relationships but what drew you to the cell culture and organoids in particular?

Dr. Bayrer 10:04 

I became really enamored with a particular nuclear receptor that was expressed in the liver and the pancreas as well as in the intestine. And began to think about that first from structural biology aspects. I was interested in potentially drugging the receptor to tune activity either up or down. And as I was going through the biochemistry of that, I started to become really interested in the underlying biology. So at that point, I realized that I needed to add some skills to my experimental tool kit in order to be able to answer some bigger questions about how the receptors function overall in the tissue- that’s what really led me to being able to do organoids.  had a collaborative research experience with [a] lab at UCSF who had at the time recently brought in the organoids and technology. That enabled me to have support from an established stem cell investigator to teach me the ropes in terms of using this technology to be able to get at those questions about cell renewal and differentiation.

Peter 11:13

Cystic fibrosis is typically looked at as a gene mutation and pathology is typically seen kind of within the lungs are skin as well. Why use an organoid from the intestine as opposed to an organoid from the lung to test this? Is it just because of the ease of grabbing the tissue?

Dr. Bayrer 11:29

So patients with cystic fibrosis do have intestinal dysmotility and it’s thought to be primarily due to problems with secretion. And so there are a number of GI issues that we co-manage with our pediatric pulmonologist. But to directly answer your question, it’s entirely expediency. To do a rectal biopsy to obtain tissue to do an organoid can be done even without sedation is very, very quick. it’s painless procedure. Whereas to take lung tissue is much, much more involved. And so it really just became fundamentally easier and faster.

Peter 12:07 

That’s really neat. The first thing that came to my mind when you’re telling me about inflammatory bowel disease is that we tend to delineate it into two types: Crohn’s disease and ulcerative colitis. As I learned more about the two pathologies, [IBD] most likely lies among the spectrum. Do you feel like this organoid approach will help us better classify different types of inflammatory bowel disease? And do you think ultimately, there will be a treatment that is targeted to specific subsets of these?

Dr. Bayrer 12:32 

Yeah, so certainly, so my feeling is that inflammatory bowel disease is a spectrum of probably 100 or 200 different things that are essentially pheno-copies that we have somewhat artificially sorted into ulcerative colitis, Crohn’s disease, or indeterminant colitis. And it’s been clear from the sequencing approaches that there are mutations associated with disease both in the intestinal epithelium as well as within the immune system. We know also that microbiome can play a part in disease pathogenesis and propagation. I think that it’s vast oversimplification that we’ve done, but at the end of the day, if we ask: for the current treatments that are available to that simplification work now? Well, kind of you. So we, we make a big deal trying to change between Crohn’s disease and ulcerative colitis, and then we end up treating them the same about half the time. So there’s definitely a need to be able to really separate out distinct pathophysiologic mechanisms so that we can like the CF analogy, be able to really target the right medication to the right pathophysiology. I think that organoids will be a part of that, and to some extent, they already are. And so it’s really going to be figuring out where we can use the organoids, where we have to use our other systems. But at the end of the day, I think we’re going to end up with thousands and thousands of patients with IBD from sequencing and then it’s going to be figuring out how can we can separate the signal from the noise and understand what variants we’re seeing are actually disease-related, and how we’re going to address those with medications that puts the disease into remission.

Peter 14:12 

I want to segway little bit into the other aspect of your lab, the visceral sensing component of it. And by visceral sensing, we mean this internal pain that we don’t really classify as the same type of pain that we have when we have like a cut or a wound. This is so different from inflammatory bowel disease where we do have a regimented treatment plan for how we treat [it] compared to irritable bowel syndrome, which is a common syndrome associated with visceral pain. And I was wondering, your thoughts on what our research efforts are, what your research efforts are and what kind of therapeutics do you think we’ll be able to develop for IBS?

Dr. Bayrer 14:51 

So our lab has been really interested in the enterochromaffin cell which is the serotonin producing cell within the lining of the gut. These cells that they represent about 1% of the epithelial cells, but they’re responsible for about 90% of the body serotonin production. These are major neurotransmitter factories throughout the lining of the gut. And we became interested in understanding what makes them tick and how they work. And so we incorporated the organoids to be able to study enterochromaffin in as native an environment as possible, but still accessible for excitation studies and to be able to really understand what types of signals they respond to. And then the next aspect that we’re interested in is what happens to that serotonin and so is this a humoral thing is it paracrine, is it autocrine?

Peter 15:49 

And these are all different ways that serotonin is being secreted either through the blood or to nearby neurons?

Dr. Bayrer 15:54 

Yeah, exactly. We asked where the serotonin receptor expressing neuron lies in relation to the enterochromaffin cell and found that they do traverse right underneath these enterochromaffin cells. And so then that allowed us to ask whether or not these are forming a synapse like connection. And so is this really a direct talking of enterochromaffin cell to the nerve fiber itself.

Peter 16:22 

And these enterochromaffin cells respond to both mechanical and chemical stimuli.

Dr. Bayrer 16:26 

Yeah. And so we’ve looked at the chemical response to this, and show that if you stimulate the enterochromaffin cell, you increase nerve firing immediately and the the associated fiber can be blocked either by using agents that block enterochromaffin cell activity or agents that block the nerve fiber. The Beyder group at Mayo has looked at mechanical sensitivity and looking at Piezo2 expression within enterochromaffin cells, I guess, oversimplify you’re poking it with a stick, but they’re using a really fine technique to apply gradients of mechanical pressure to the enterochromaffin cells, either in isolation or as part of an organoid. And seeing that the mechanical pressure does also cause depolarization and releases serotonin from the cells. And so then you can say that it looks like there’s both mechanical and chemo ensory effects.

Peter 17:20 

For me, it’s easier to intuitively understand the space that mechanical sensation occupies in the sense that you can feel a certain amount of force. But the chemical space is much larger. Do we have any idea of what compounds activate enterochromaffin cells? Do we respond to all types of food [or do] they respond to the bacteria in our gut? Is there any discrimination or has


been [data] shown that enterochromaffin cells respond to all of these stimuli?

Dr. Bayrer 17:47 

So we found that there are specific receptors for specific targets in enterochromaffin cells and you can kind of lump these things into three main categories and so they respond to irritants, the real pungent substances found in garlic or wasabi triggers them, various short chain fatty acids, which we tend to think of has microbial byproducts. In particular, isovalerate was very strong activator of enterochromaffin cells. And that’s the short chain fatty acid that gives gym socks, or stinky cheese that particular odor. And then catecholamines also activated the cells quite strongly. That was done on a relatively limited survey of things that we thought could potentially be activating the cells. It’s possible that we’ve missed whole categories, but we thought that was pretty good start and when we think about the things that activate the EC cells, and these are all potentially all seem to have the same common theme of you know, maybe there’s danger in this luminal inside gut environment, and given the importance of serotonin and secretion and motility. Maybe it’s a way for the GI tract can protect itself when it senses essential luminal danger.

Peter 19:06

Really neat. And then the other aspect is these are serotonin-secreting cells. And you touched upon this earlier, whether it’s humoral, whether it’s paracrine, do you have kind of a framework or an idea of how you think the serotonin is being transmitted?

Dr. Bayrer 19:21

We’re particularly interested in serotonin release into one of these synaptic connections. You know, what we saw is when we activate the EC cells that we can elicit a mechanical hypersensitivity in the attached afferret nerve fibers. And so what that implies to us is that this may be partially a mechanism to explain increased gut pain in a patient with IBS relative to somebody without. When we think about IBS and enterochromaffin cells, there’s been some prior work looking at the number of enterochromaffin cells, [they] appear to be potentially increased in some patients with IBS suggesting that maybe they have even more of a serotonin input. And there have also been some studies that suggest that during estrous cycle that there’s changes in the amount of serotonin produced in EC cells, or maybe even a change in EC cell number themselves. And when we think about conditions like IBS, there’s a about a three fold increase in females compared to males. So there’s definitely a biological sex based difference here that is reflected in the serotonin and is also reflected in disease pathology. And so the question is, well, is this also related? And so some of the work that we’re doing now is to really try and map out these connections between the enterochromaffin cells and their associated nerve fibers as well has to engineer their activity. So to activate or deactivate enterochromaffin cells, and ask how that affects the perception of visceral pain in our rodent models.

Peter 20:57 

I’m really excited to see some of the work that comes out of your lab to study this, I want to transition a bit to your career. I was talking to a colleague here at Duke previously, and he told me that no stage in his career really prepared him for the next stage of his career. Can you tell me some more about the challenges that you hadn’t anticipated transitioning from a fellow to an assistant professor.

Dr. Bayrer 21:22 

I was really blessed with a very supportive division and supportive mentors. So I think that actually was really nice about my environment, particular where I trained. I think probably one of the biggest difficulties is figuring out how to manage your time. You’re working on your independence for both your research career, but at the same time, now you’re an attending physician and you’re responsible for an awful lot of patient care. It’s trying to being able to balance those two worlds, so that you’re providing optimal care to your patients. And you’re not letting people down. But at the same time, you’re really jealously guarding your time, so that you can be productive in the lab and prepare yourself for the next stage after that, which is the independent investigator stage.

Peter 22:13 

Being a physician is a full-time job being a professor as a full time job as well. And how do you manage to put both of those? Are there some things that you have to compromise on? Or do you feel like, there are some things that you’ve given away a little bit?

Dr. Bayrer 22:26 

Yeah, and so I’ve certainly pulled back from the number of patients that I see, you know, if I’m out traveling, I feel it’s not entirely fair to my patients, for them to not be able to find an appointment for me for like five months; that’s not so good. And so, moving towards systems of working within the pediatric fellowship training program to work in teaching clinic situations, and to have patient care there but also be working with a larger team of physicians. So that if I’m not around somebody else who knows the patient and is involved in the cares around, and so we can always make sure that we’re delivering the care to the patient that we need. That’s probably been the biggest change and the biggest pullback that I’ve had from my regular fellowship years to where I am now.

Peter 23:18 

It’s a dependence on a team. It’s a team effort. And that’s something you’ve reiterated before and something that you continue to impress. You are also the assistant fellowship director at UCSF. What do you feel this role has taught you about yourself and what are you hoping to instill in your trainees or your fellows at this point?

Dr. Bayrer 23:36 

In terms of what is taught about myself, I really reiterated that I very much enjoy teaching and I enjoy working with learners in a complicated academic environment where we can really sit and think about problems, think about solutions for patients if I’m in the patient setting. Or challenging hypotheses or research plans in the basic science setting. That’s been actually been lot of fun working with our fellows as they go through this really intensive period of training. You know, they come in on one side has graduating pediatric residents, and then leave three or four years later as gastroenterology specialists and academicians. And that’s been a very fulfilling part of my job.

Peter 24:31 

And when you are training some of these fellows, do you feel like there are some common mistakes or challenges, or growth opportunities that you notice and I don’t know- when you reflect on your own time as a fellow, are these things that you have also recognized?

Dr. Bayrer 24:44 

I think the biggest thing is just how quickly time goes by and how much of a compressed timeline you’re on has a fellow and especially if you’re interested in developing an academic research career there, if you don’t have as much of a baseline background and doing science, it takes a good effort to really get up to speed. And so it’s really stopping and in thinking coming back, even at the end of your first year, say, all right, so by x many months, we need to be kind of this far along so that you can have an application because that NIH application isn’t going to be renewed or be reviewed for like four months after you put it in and then anticipate another submission. And so all of a sudden, you’re building in a year and a half time before you would know if you’re going to get a grant or not, as a junior faculty. And so the timing is I think one of the biggest surprises in the for fellows.

Peter 25:52 

And do you feel like there is a pressure kind of with regards to time as you’re starting up your own lab. Do you feel this similar time crunch? Or not so much?

Dr. Bayrer 26:04 

Yeah, I think that it’s, it’s fair, I think everybody feels kind of that pressure. There’s always that pressure. Again, I’ve been lucky in that the environment that I’ve been in has been very supportive. And, you know, working with, with David and Holly and Stu on this collaborative environment has also given me access to additional resources that, you know, I didn’t foresee myself having even a few years ago as I was looking more in staying more on the affiliate side of things. So I think that that’s been a real leg up.

Peter 26:42 

Sounds like you’ve had some really great mentors. And I was wondering, as you’re looking to build your team, what are you looking for in mentees?

Dr. Bayrer 26:49 

So I think the biggest thing that I want the that I look for is curiosity and a drive to answer questions. And so to have people that are excited to come in and to think about a problem and to think big about a problem, not being afraid to fail at it. As long as you know, you’re learning a lesson from the work in the process. So that’s one of the big things that I look for. And then the other thing is somebody that works well in a collaborative team environment. In many ways, what I’m looking for in somebody coming into the lab is the same thing that I’m looking for in somebody coming into our fellowship program. We’ve got a lot of folks that we’ve had real success with in training in an active research environment, and with wide, wide variety of backgrounds. Again, I think that those key qualities are ones that they don’t necessarily show up on a research pedigree of you know, I went to Harvard, Yale, Duke, wherever but rather, that they really come across and how that person approaches science.

Peter  27:59 

Do you feel that a lot of the skills to be successful in medicine are the same as the skills that are necessary to be successful in research?

Dr. Bayrer 28:07 

I think so. So a large part of medicine is really about pattern recognition, being able to separate that signal from the noise. And so when you’ve got a panel of lab tests coming back, and somebody who has a whole bunch of different somatic complaints, but figuring out like, what’s really the heart of the matter. That pattern recognition also plays a role in science, right? When you’re looking through your data, and sometimes you just have noise in there. And sometimes you have a real signal to being able to identify that that signal and go with it. And so I think that those are two there are things that are very, very similar. I think, certainly curiosity is important in medicine, and so particularly at large academic centers where people coming in are not necessarily coming in with their garden variety problems to really be able to think like, all right, well, what else is going on in here? And what tests do I need to do? Or what what history questions do I need to ask that will really allow me to get to the to the heart of what’s bothering this patient? Yeah, there’s an awful lot of overlap. At the same time. There’s also a real distinction in the time course of decision making. If you’re thinking about your lab experiment, and you’re trying to get the best controls, because you know, you’re going to send out this $30,000 single cell RNA sequencing data set adventure and like, boy, you better make sure you got everything absolutely correct on that. You know, you’ve got some luxury of time where you can sit and you can think about that for a week or so. You don’t always have that luxury so the PhD year you can gather a lot more information and really feel like you’re making informed decision. In medicine, sometimes you’re operating on imperfect data and you just have to acknowledge all right, this is imperfect data. And I may be wrong, but I have to go with the best guess because we don’t really have a lot of extra time to figure this out.

Peter 30:30 

Speaking of the concept of time, I was wondering, where would you like to see the field of gastroenterology in 10 years?

Dr. Bayrer  30:38 

You know, I think right now we’re really at a golden age of a nexus between being able to have epithelial biology, neuronal, microbiome and immune response systems all coming together and having the tools to be able to dissect and try and understand what the what the inputs and the outputs from each of these systems are and how they work with each other. So in 10 years, you know, I’d like to know that we’ve been able to map out some of the sensory systems and getting a handle on the pathways that are involved in the problems that really affect activities of daily life for people with chronic pain issues. So can we figure out what those with some of these pathways [affected] are so that we can target some treatments. In 10 years, I’d like to be able to say that yeah, we finally have a medication that can help or a therapy plan that can that can really benefit somebody with really severe IBS and get them so that they can pursue the things that they want to do. Really neat.

Peter 31:41 

Well, thank you so much for your time.

Dr. Bayrer 31:43 

Of course. Thank you.

Peter 31:55 

Dr. Bayrer, took us from bench to bedside and really focused on how he sees intestinal organoid models being incorporated in the diagnosis of disease. He underscored the importance of improving our time management during each phase of our career. And that’s something I hope we all take the time to think about. How can we make sure we’re being both rigorous and efficient? I’ll leave you with that. I want to thank you all so much for listening, and we’ll see you on the next episode. If you like what you’ve heard, we’d love it if you could leave us a review. For more of our content, you can follow us on Twitter @Gutbrains or visit our website at thinkgastronauts com. The Gastronauts Podcast would be impossible without the incredible team that we have here. Meredith Schmehl is our producer and theme music composer. And special thanks to the founders of Gastronauts, Dr. Diego Bohórquez, and the Bohórquez laboratory