Transcript of Episode 33: Jon Chee

Disclaimer: Transcripts may contain errors.

Grant Belgard: [00:00:00] Welcome to The Bioinformatics CRO Podcast. I’m your host, Grant Belgard and joining me today is Jon Chee, CEO and founder of Excedr. Excedr provides services to the biotech industry and more. So with that, I’ll hand it over to Jon and hear about your company, what you do. And I’d really like to hear about what you’ve learned about the industry and what you’ve learned building out your own company.

Jon Chee: [00:00:25] Thanks for having me, Grant. Really looking forward to this. So Excedr, we’re an equipment leasing company that solely focuses on the laboratory space. And what we’re really trying to do here is enable researchers to secure the equipment they need at an affordable price so they can get their research done and reach their milestones faster. And we also provide ongoing repair and maintenance coverage for the duration of the lease terms. Excedr really was founded just like scratch my own itch. In a former life, I was doing wet lab research ten years ago and really when I was in the lab and this was at UC Berkeley, I was doing research and a lot of the pain points I felt revolved around equipment usage and equipment maintenance. More often than not, I felt like I was running up the hill to the flow core to run samples every day. And I figured like there’s got to be, I guess a more efficient way to do this and efficient use of time and capital. So from there really spoke to our PIs, tried to get a feel of is it just a me problem or is this more broadly a of pain point that everyone in the on campus was feeling. What we ended up finding was that this was a very common problem. Equipment would break down. Equipment is very expensive to procure maintain.

[00:01:53] Since then, we really started off with a pilot run of what we do. So we do equipment leasing and repair and maintenance coverage for these set equipment for the broader life sciences, really trying to alleviate these kind of financial and operational pain points for those in the lab and especially for the earlier stage ventures. And yeah we started off in the academic and government laboratory space, which we can get into more that was a baptism of fire, especially as an early entrepreneur. But we participate a lot in supporting early stage ventures, biotech, pharma diagnostics and really helping them get the equipment they need to do their research and also making sure that they’re supported along the way. But yeah, that’s what we sought out to do and really have been doing it ever since then. That’s our thing.

Grant Belgard: [00:02:44] So I find it really interesting that you started with universities and government. Because in many ways they’re more difficult institutions to sell to. Can you maybe talk a bit about that decision and what challenges you faced as a new company?

Jon Chee: [00:03:00] Hindsight is 20-20. I want to say this was a calculated go to market, but it was more along the lines of that was my immediate network and community having just participated doing research in my early career in academia. And so due to just the general proximity, getting in touch with laboratories, it was much more difficult. So we were like, okay, well, this is our community. Maybe we can give this a shot and see if we can get some buy in from our neighbors and don’t know if I would recommend trying to go through the government procurement system as the initial go to market. But hopefully someone can learn from my mistakes and slam dunk it should they choose to do this. But as an early entrepreneur really I think going through the the systems procurement, we worked with Lawrence Berkeley National Labs, Lawrence Livermore and really what the procurement taught us is we had to be very airtight in making sure the contractual language was amenable to the broader system. They were gracious enough realizing that we were young entrepreneurs fresh out of the lab. They would work with us and give us feedback on where they wanted to see things go. What that really ended up doing is it helped us hone our product from both a pricing standpoint, how do we structure these contracts so they’re mutually beneficial for everyone and just really showing us how we can or what we needed to do is get buy in from numerous stakeholders. It’s not just the end user in the lab. There’s the finance department, there’s the procurement department, there’s legal. And so that really opened our eyes is not that there’s one person that you need to appeal to. There’s many, many parties and I think it was like the baptism of fire, really.

Grant Belgard: [00:04:52] But you made it.

Jon Chee: [00:04:54] Yeah, yeah, yeah. I’m very grateful that we made it. In the very beginning, there’s a lot of existential anxiety when it comes to when you’re young and trying to put up a bid and go through the procurement system. But I think those are probably the big lessons, really how to appeal and really support all stakeholders. And really it helped us fine tune our product. And obviously since then we’ve branched out outside of the academic research government research realm and that when we did decide to go into for profit, there was a lot more polish to our product. Whereas if we did it inverse and we went directly into the for profit sector first, most early stage ventures don’t have procurement departments, let alone a full time finance department legal department. And I think we would have probably been a lot sloppier in putting out the minimum viable product, whereas through this baptism of fire really honed our product and our offering.

Grant Belgard: [00:05:55] That’s interesting. What were the biggest things that changed between your first sale and how things operate now?

Jon Chee: [00:06:03] There’s a fair amount of things that have changed. The pricing strategy definitely changed. We realized one price does not fit every end user. Obviously, if you are a government institution or your UC Berkeley, you should be getting very, very different pricing than an early stage venture. And then they should also get different pricing than a large multinational. And that’s purely because of the dynamic of the entity. That’s something that we learned the hard way because we took our first stab, which was like, let’s see if this pricing works. And quite frankly, we’re green at that time. And when we went through procurement, they’re like, Hey, this is a little bit off mark but here, try again. And they were generous enough to give us that feedback. And so that really helped us fine tune how we price things appropriately for the end user based on the “risk”, because obviously we provide leases. There’s a credit risk component that we need to evaluate. So that really was honed through procurement. And then also it allowed us to put out more accurate proposals forth when we went to the for profit. So it didn’t completely seem unreasonable. We were somewhere within the ballpark. And obviously since then we’ve gotten so many repetitions of it. We’ve worked with so many labs since then that it’s a well-oiled machine now we know based on what the company is all about, what the equipment is, what is the game plan, what is the science behind it. We can very much create a bespoke solution that is appropriate for the end user.

[00:07:41] So that’s like a really big one that we’re always trying to improve, but something that we really fine tuned during our early days. And then the second component is the repair and maintenance support throughout the lease that we provide, our flavor of equipment leasing is that we don’t want to just be a financing solution to the lab where it just simply get the equipment in there and just make payments. We pride ourselves in supporting the end user throughout the term of the lease, making sure if there’s any equipment damages, we make sure that is backed, is repaired and brought back up to spec as quickly as possible. Because I know when there’s an equipment damage and you’re in the middle of a mission critical assay, it can end. A milestone is coming up, it can become a pretty tenuous situation. So we do provide support for that. This one is especially with Lawrence Berkeley. We had to figure out what was the level of support that is required to keep a high performing laboratory operational. So that was another learning experience. And obviously all of these learned lessons we carried over to the for profit sector. But yeah, I would say those two is like finding a way to create bespoke financial solutions for the end user that fits their needs and making sure that we provide the right level of operational support for the end user as well, so they can just not worry about the potential damages that might come up throughout the lease term.

Grant Belgard: [00:09:09] One risk of working with startups in a line of business like yours is startups not infrequently fail. How does that typically play out? Is it usually pretty clean? Have you ever had to call the repo man? How does that work?

Jon Chee: [00:09:23] I would say we do things differently over here. And something that is different about us is that we’re not a bank. If you’re a bank, you’re using depositors accounts to let for loans and lending products. With that comes all kinds of regulatory requirements. You know, much like if you have a mortgage on a house, the bank is going to use your house as collateral. They’re the ones who have a regulatory burden and they will definitely call the repo man in the case of non-compliance of the loan now and then. Other leasing companies have different models and won’t speak for them. But more often than not, the way that leasing companies is where do they get their capital to create these leases is they do the fund model where they would go raise investments from limited partners, whether it be family offices, institutional like endowments, pensions, you name it. Hedge funds fund the funds. So they’re using other people’s capital as well. And when they use other people’s capital, there’s also going to be a requirement that you structure your credit facility. It might really require the repo man to go in and repossess. For us, what makes us a little bit different is that we don’t use outside capital. We don’t use depositors accounts. We don’t use LPs, capital. All of the capital comes off our balance sheet.

[00:10:39] Basically, we are underwriting and funding leases to the end user. And in the case of early stage ventures, we realized this. We totally realized that it is a non-zero chance that things might not work out. And so always obviously we need to make sure that we come to an amicable solution, but we pride ourselves in being long term partners for these companies. When things are good and when things are bad, we always pride ourselves in being able to find a amicable solution to make sure that you’re taken care of and we’re taking care of. When we sense that there’s a cash crunch coming up, that we immediately send someone in and they repo the equipment, It’s more of like, Hey, let’s have a conversation. Where are things at? Are you trying to get to your next funding round? Do you need help getting to that next funding round? How can we be helpful? And we want to give the breathing room to these early stage ventures so they can get there. And that’s our goal from the very beginning is the way we approach equipment leasing the life sciences is that. There’s three components that are very, very important and critical to the success of these early stage ventures. It’s making sure you have adequate cash runway, make sure that you can keep the lights on.

[00:11:46] Second, you need the equipment to run your assays and you need your expert staff to be able to run these assays. And if you have all three, you’re in a good position to hopefully hit your milestones. And we want to help get you there. We realize that one of the components is making sure you have cash runway and we’re not going to impose our will and prevent you from getting there. We’re going to try and help you get there. And that’s our mentality around it. We take a very stakeholder approach, making sure the lab, the company is taking care of, the investors, are taking care of, the equipment manufacturers and us. We realize there’s a lot of parties involved. We take a holistic approach there, whereas it could be when if you’re using depositors accounts, it’s a very different scenario because the federal government is going to impose its will and make sure that you take care of that. The depositor accounts in a very different way, but we approach it from that angle.

Grant Belgard: [00:12:45] That’s interesting. That’s one thing I like to do at times, too. Basically, we have a network of investors who are looking for deal flow. We work with early stage companies that periodically in this industry are going to need investment. So it’s obviously not something that’s formalized or anything like that. But it’s interesting to hear you say that. I guess that’s a maybe a bit of a common practice among those who specialize in working with smaller companies. Because it makes sense for everyone. If the company is doing a good job, it’s in everyone’s best interest to make sure they’re funded adequately.

Jon Chee: [00:13:20] Yeah. And I think the way we look at it too, is that great companies even the best companies out there will have ups and downs outside of biotech. Facebook had its ups and downs. Apple was on the brink of bankruptcy. And obviously, Facebook and Apple are what they are now.

Grant Belgard: [00:13:39] They’re doing all right.

Jon Chee: [00:13:40] Yeah, they’re doing all right. We realize that. Just because there’s a little bit of volatility, we’re not spooked by that. And we want to help support you through that volatility and get you to that next place that you need to be, whether it be the next funding round, help you get to your next milestone, help you make that next hire. If you raise a seed round that’s like 2 to 6 million and you have to spend like 1.5 million on equipment, that’s 1.5 million that can no longer be allocated towards staffing. So remember, there’s those three things we focus on is having adequate cash, having the equipment that you need and staffing your company with the experts that will take you where you need to go. So we’re trying to get you there. We want you to have all three. And so that’s what we’re really seeking to do is make your dollars go farther and give you that flexibility to hire. And it’s a competitive hiring market, too. So for these entrepreneurial scientists, it can be a lot to manage. We don’t want to be a bottleneck on you and we don’t want to be an additional anxiety or stress. We want to be supportive throughout.

Grant Belgard: [00:14:41] So tell us about those early years. I mean, obviously Excedr has grown to a pretty respectable size with a pretty good portfolio now. And of course, going from 0 to 1 is always a challenge, especially you’re starting in some ways difficult market. How did you do it?

Jon Chee: [00:15:00] You’re exactly right. It was a very different time, especially for early stage life science. I think at that time what we encountered was the start up ecosystem was just beginning. Back then, a lot of the large multinationals had a very robust in-house R&D function, and that’s when we were starting. It was very difficult back then. This kind of wave hadn’t really picked up quite yet. So when it came to getting the company off the ground. We didn’t have all these tools to do normal business functions like Gusto didn’t exist yet. Email marketing was very nascent. All of these things that make the barriers to entry much lower did not exist at that time. So it was a lot of elbow grease. Well, admittedly at that time I wasn’t quite sure if the timing was wrong or did I get into an industry that was just the wrong industry to be in.

Grant Belgard: [00:15:59] I think that’s something all entrepreneurs ask themselves in the early days.

Jon Chee: [00:16:03] Yeah, very much. There was a lot of existential dread very early because like I said, the tools that enables entrepreneurs now weren’t available. So a lot of it was old fashioned, just me either making calls or going in person and trying to meet potential clients. And you can imagine it is difficult, especially for folks in the lab. There’s like, don’t want to talk. I have my own work to do in the very beginning. There’s a lot of that sweat equity that needs to go in. But then something that we think about a lot is just those early clients that were willing to give us a shot really helped us get into that rhythm. It took a little bit of time to figure out the first couple clients that would help propel us to the next level.

Grant Belgard: [00:16:48] Where did your starting capital come from?

Jon Chee: [00:16:50] So the starting capital was actually from friends and family. We don’t have outside institutional equity in our company. So our company is 100% employee owned. There’s a small sliver of friends and family that when no one was willing to make that investment, we still don’t have outside equity. But the friends and family were willing to make that bet, and then the rest are owned by the employees. And so you can imagine it compounded the stress because it’s your friends and family’s money and they’re betting on you. So that was very anxiety inducing. I will say, me personally, I’m not the serial entrepreneur type. I look back then at those early days and I was just.

Grant Belgard: [00:17:31] A nervous wreck.

Jon Chee: [00:17:32] Yeah, Sleepless nights, nervous wreck. Is this the right market? Wrong timing. What is this? But I think it always ended up going back to my experience in the lab at Berkeley, just seeing the research being done. I feel like whether it was conscious or subconscious, I was like, This is going somewhere. Seeing the research being done led me to be optimistic about the industry. And so a lot of the time it was a matter of sticking to it, making sure that we raise awareness. And when the biotech market does have its moment, we are prepared. And so I mentioned before, when we first started, the industry was very different. Multinationals had their own in-house R&D. The IPO market was not nearly as hot. Obviously M&A was not as hot because all the multinationals had their own R&D going on. And then there was this paradigm shift where the larger enterprises, they reduced the in-house R&D, realizing that from a capital allocation perspective, it might be a better investment to let the startups focus on more high risk projects.

Grant Belgard: [00:18:40] Let someone else take the risk, then buy it when it’s a bit more proven out.

Jon Chee: [00:18:43] Yeah, exactly. And that had ripple effects everywhere because once that started happening, the venture community was able to say, Hey, our investments are de-risked because at the end of the day, VCs need to have a liquidity event, an exit whether it be an IPO, merger, acquisition, whatever. And when this happened, it was like, okay, the big strategics are now looking to acquire these smaller entities who are doing more risky research. Once that happened, the capital inflows to the startup community really started coming in and we saw more and more entrepreneurial scientists take that leap because back then it was super risky. It was like, are you going to leave your job at Pfizer to start a startup that may or may not have an opportunity to IPO or get acquired? And then you look at clinical trials, you’re like, oh, my goodness, it is so expensive. We had a lot of existential dread. Is the timing wrong? Is the industry wrong? But once that shift happened, we were kind of.

Grant Belgard: [00:19:44] You’re well poised.

Jon Chee: [00:19:46] Yeah, well, poised to be supportive in that growth. There was a large component of luck. It could have gone very differently. That paradigm shift could have just not happened. But very grateful that it did. And I think it was kind of the testing grounds, like during those early days going through government research, academic research, we were just practicing honing like honing the craft, getting better. And then when that paradigm shift happened, we’re like, okay, we’re ready for the prime time. Let’s do this now. I wish I had better advice on how to get from 0 to 1, but I think if you have deep conviction on your thesis, at least in my case, it would behoove you to stick around long enough for the adoption to happen. If the thesis is like you believe to be rock solid, I would recommend sticking it out and trying to be well poised for when things really do pick up. Right now obviously the past year has been the past year and that’s another paradigm shift that’s happening. Who could see it coming? But it accelerated all kinds of trends and pulled forward things that would have taken 5, 10 years to actually come to fruition. It’s things like that. It’s just making sure you’re building for resilience and be well poised for when the opportunity presents itself to action on it.

Grant Belgard: [00:21:03] And did those inflection points correspond to major changes to the composition of your team?

Jon Chee: [00:21:09] It did. The overall product, it’s been fine tuned. But there hasn’t been seismic shifts in what we do. But when there were the paradigm shifts, it was like drinking out of a fire hose. When you’re at that stage, as they call it technical debt, you hack things together and it works for maybe when you’re like a team of two, three, you can Frankenstein together these Google sheets, Excel sheets. And it worked for a little bit. But eventually, like all debt, you eventually need to pay it down. When the paradigm shift happened, we were scaling up the sales team to make sure that we can give each of the laboratories the attention they deserve. We really need to, one, improve the processes, the tech stack, making sure that we don’t break underneath the paradigm shift. We try to be as proactive as we can about it. We want to be more proactive, less reactionary. As an entrepreneur, it is our job to see around the curve and prepare for it. You’re not going to be able to catch everything, but we try our best to do that. The first paradigm shift is really just scaling the sales function. But the next shift was just making sure that no one falls through the cracks. There’s a lot of parties that we’re managing, making sure we’re taking care of our vendors, the manufacturers, making sure all internal parties are taken care of and not losing track of those conversations. So we had again revamped the customer success function and the operations function. Not that it wasn’t working before, it’s just that when you go through these growth spurts, your existing systems are not built for that.

Grant Belgard: [00:22:45] Well, I guess one of the advantages of bootstrapping is you in some ways have time to tool up to be at the right stage for the size your company is at and to ensure other kind of managers of the company and so on can grow into their roles as opposed to the size and the structure of the division that you’re directing or something becomes qualitatively different every year. Can you maybe comment a bit on how has that been for you? Obviously Excedr has come a long way over the last decade, and I’m sure you’ve come a long way over the last decade other than school of hard knocks, how have you tooled up?

Jon Chee: [00:23:27] In the early days, there was again like I mentioned, a lot of sweat equity that went into it. But you can’t do that forever. You can’t work every single day and not have time for friends, family, loved ones, hobbies. You can’t do that forever. And it’s what you alluded to as bootstrapping this company. We have the luxury of we can take our time a little bit more, high growth companies, different kind of schema that you need to live by. You’re looking to triple, triple, double double. You don’t really have that luxury to have that balance. I’ll only speak for Excedr here, but what I’ve learned is that building in balance into your work life and I try to have our team also have this balance enables them to really come into work refreshed and to be able to do their best work and not feel completely burnt out. And especially during remote work, that becomes even more difficult when there’s not clear separation between work and personal space.

Grant Belgard: [00:24:25] Yeah, I don’t know if you saw this recent study. I thought it was fascinating. I was reporting people were working more than ever before with this shift to remote work, a couple hours more a day while at the same time becoming less productive even overall, not just productivity per hour, because so much of that extra time was soaked up by meetings and agonizing over emails and things like this.

Jon Chee: [00:24:49] Yeah, I did see that. Like we do a lot of team check ins, making sure how is the remote work panning out for you? Do you find that you’re filling that space with more unproductive work? What we ended up coming to is we definitely tried to have clear cut offs, like when work is over, please do not want to see your green bubble on. Please go grey. Go spend time away from your computer and things like that. And yes, remote work has removed the commute component. Obviously you have an hour probably more in the morning and an hour probably at the end of the day. We try not to just fill that space because we can. We try to say, hey, with those extra hours in your day, can you spend more time with your kids? Go see your friends, get exercise, go for a hike. These kind of things, they’re not directly work productive, but it’s a sustainable practice. It helps the team come back, like I said, refreshed and actually more productive. So we don’t want to just because you’ve freed up this one hour in the beginning of the day and at the end of the day, we don’t want you to go into more meetings. So we tried to keep the hours the same, but give you that extra hour to do more things that are personal priorities of yours. And that’s what we’ve found has kept the burnout at bay, especially for the remote work situation.

Grant Belgard: [00:26:07] So I see we’re coming up on time soon, so I want to make sure we have an opportunity to hear some advice you might have for others. And especially I’d be keen to hear what’s a contrarian view that you hold.

Jon Chee: [00:26:21] When it comes to advice coming from a STEM background, there’s a large, large emphasis on specializing, specializing, specializing. But before I was in the wet lab, I actually took a lot of classes on business, a lot of legal classes too, and philosophy classes.

Grant Belgard: [00:26:40] Did you have Steve Jobs calligraphy application?

Jon Chee: [00:26:44] Yeah, yeah. And not to sound cliche, but one of the most impactful classes I actually took in school was actually a philosophy class on moral ethics. And without getting into the weeds of it, it’s been a long time in the philosophers out there might catch me on this, but there’s a utilitarian philosophy where cost benefit, that calculus is hat defines a moral life or decision. And then there’s on the other end, there’s the Kantian moral philosophy where there are binary rights and wrong based on whether or not you’re treating others with dignity. And if anyone watched The Good Place, that’s one of the shows that gives a little primer on that. What I’m getting at is that taking a well-rounded, not just a STEM path course, load informed how we built Excedr and think it’s what has made us in our DNA different. Like I said, we always try to treat every single stakeholder that we work with dignity and not just focus on shareholder value on its own at the expense of others. And that’s a very utilitarian thing, is if we cost benefit, analyze, profit, maximize, that’s the right decision. If I had strictly stuck to the course load, I don’t think Excedr would be the way it is today. When it comes to a leasing company, there is a way to do it. And I think coming from a different angle with the science background, just having taken this diverse course load, really helped us build what I would like to believe is a unique organization that approaches the life science community in a different way. And we offer a product that is differentiated and beneficial to all parties. So what I would say is specializing is obviously important, but don’t feel it’s wasted time exploring different fields of study because I think it can inform where you want to go as an entrepreneur and how your company can be built differently and approach problems from different angles.

Grant Belgard: [00:28:46] What’s the worst piece of advice you’ve received on this journey?

Jon Chee: [00:28:50] One of the early pieces of advice was given to me is that if you want to secure a customer and that customer requires 100 cold calls, so how many customers do we want to secure? Do we need ten customers? We need to do ten times 100 cold calls. That kind of mentality, it’s purely a grind and grit. Basically the advice was giving me like hustle harder and I think that was one of the worst pieces of advice for me because I think you can be working smarter. And so early on that’s what I was doing. I was like, I need to cold call this many people and I need to get into laboratories that get FaceTime with this many people in order to secure X amount of customers. Yeah. So that’s probably the worst piece of advice is like hustle harder because that’s the only solution there is. But think there are more effective ways than just the status quo.

Grant Belgard: [00:29:40] That’s great advice. I think we’ve discovered similar things along the way. So thank you so much Jon for joining us. It was a lot of fun.

Jon Chee: [00:29:49] Yeah. Thank you for having me, Grant. I really appreciate you having me on.

Transcript of Episode 32: Ian Carroll

Disclaimer: Transcripts may contain errors.

Grace Ratley: [00:00:00] Welcome to The Bioinformatics CRO Podcast. My name is Grace Ratley and I’ll be your host for today’s show. Today I’m here with Dr. Ian Carroll. Ian is assistant professor of nutrition at the University of North Carolina, Chapel Hill, and his lab focuses on characterizing the microbiota in nutrition related diseases, especially anorexia nervosa. Welcome, Ian.

Ian Carroll: [00:00:19] Thank you very much, Grace.

Grace Ratley: [00:00:21] So tell me a little bit about your research. What are the goals of your research?

Ian Carroll: [00:00:25] I’m interested in how microbes in the gut influence the host. I’m extremely interested in complex microbial communities, which we tend to refer as the gut microbiota or the gut microbiome that you may have heard and how these influence the host specifically. I’m interested in how it influences adiposity. So that’s like weight, the accumulation of fat and also how it influences behavior so your levels of anxiety and depression. And right now we’re doing this under the context of eating disorders, specifically anorexia nervosa, because those patients exhibit dysregulated adiposity so they don’t put on and lose weight in the same manner as everyone else does. And also they exhibit high level of anxiety and depression. And we want to know if the intestinal microbiota within those patients influences the symptoms that are associated with their disorder.

Grace Ratley: [00:01:27] What is it like to work with the microbiota? What’s it like to study the microbiome?

Ian Carroll: [00:01:32] Well for me, the most exciting thing was, let’s say about ten years ago, maybe a little bit more now, a paper came out that, let’s see, the Godfather of intestinal microbiota research, Jeff Gordon, he published a paper based on the complex microbial communities in the gut of patients with obesity and how they changed when those people lost weight. It was only about 12 people in that study and what they used to do was use clone libraries to profile the microbiota. So basically you’re amplifying. In this case, it was the 16S gene and cloning it into a plasmid and putting it into the bacteria and then isolating it. And basically you would get 300 copies of the 16S gene per sample, which came from one patient. And that really, really fascinated me. It wasn’t just the fact that it was the intestinal microbiota and it was a disease. I wanted to know how you manage the sequences, what you did with them. And as someone who had never done something like that before, I don’t have a background in bioinformatics. I was just fascinated on how to do it. And over the years, I’ve become a little bit more knowledgeable on how to analyze those data.

[00:02:46] One of the biggest breakthroughs was Rob Knight, who created a platform called QIIME, which is quantitative insights into microbial ecology. And this was a platform for people with a very basic understanding of bioinformatics and allowed us to get ourselves into trouble I’d like to say where we would take some data and put it into this pipeline and try and work it out. And from there, I’ve had many students that have come to my lab and know a lot more about doing these bioinformatics platforms. And yeah, it was then that I started to get really excited about it and I was a basic scientist working in gastrointestinal division, so a medical division. I think it was the perfect place, the perfect time, because you have someone who is coming with a background in microbiology. There’s an emerging field of the intestinal microbiota. I’m in a division where people routinely work with samples that you can profile the microbiota with. So that’s where it all began for me.

Grace Ratley: [00:03:49] And the microbiota is what I consider to be a pop science topic. It’s very blog post-y, I guess, if you will. What is it like to work in in Popular Science? Do you get a lot of misunderstanding from people when you tell them what you work on?

Ian Carroll: [00:04:04] Absolutely, because everybody tends to know about the intestinal microbiota these days. And in fact, they always use the term microbiome. So the microbiota is the complex community of organisms or the living organisms in your gut. The microbiome is the cumulative genomes and genetic material associated with those microbes. So when someone says microbiome, are you sure you’re talking about the right thing? And in a way I guess it’s a double edged sword. It’s good because people tend to know a little bit about what you’re doing, but in another way, they tend to know very little about what you’re doing as well. To me, it wasn’t a popular science when I started, but it makes sense that the microbes that we’ve been living with for so long and are beneficial to you, that at some point they were going to become very topical. The most common thing that you would hear is, Oh yes, you work with the microbiome, tell me about the probiotics I should take. And yeah, that’s probably one of the most frequent questions I get.

[00:05:07] But for any scientist working in a very popular area, it’s good to a point because if there’s a lot of interest in it, you can get funding to do the work you want to do. But then there’s also what I refer to as microbiome fatigue, where when everybody is saying that the microbiome is associated with a disease, then it gets a little bit boring and you’re like, No, there’s no mechanism. No, you’re just saying that I’ve heard this so many times that could be detrimental to funding your research. So I think what we need to do is when we’re talking about the microbiome say, yes, okay, perhaps it’s associated with lots and lots of diseases, but we have to move forward and look at the mechanisms in which these microbes can cause disease and how they can be used as a treatment. And I guess in a way, your question is very appropriate. It’s good and it’s bad I would say.

Grace Ratley: [00:05:58] Yeah, I feel like there’s a tendency in pop science to overstate the ability of the thing that you’re studying. So people, they think, oh, if I take this probiotic, I can cure myself of irritable bowel syndrome. So what do you think about that? What can microbiota science do and what can’t it do?

Ian Carroll: [00:06:17] Let’s take a couple of seminal studies. So first of all, probiotics. There was a group in Israel that came out of the Weizmann Institute. And what they did was they were wondering about probiotic treatment after antibiotic treatment. So Grace, if you are ever discussing the fact that you took antibiotics with one of your friends, what’s the first thing they usually say?

Grace Ratley: [00:06:41] They ask if I get diarrhea?

Ian Carroll: [00:06:45] Well, that actually is one. But typically what I find is someone will say, Oh, you’re killing off your gut microbes, you need to take probiotics, right? Or you should eat lots and lots of yogurt. In that respect, this group investigated that, and what they did was they did a mouse study and a human study in parallel. They gave both the mice and the humans antibiotics a broad range of antibiotics to wipe out the intestinal microbiota. They repopulated both of them with microbiota like a fecal microbiota. They banked from one group, the others they gave a cocktail of probiotics and the other group, they let the microbiota rebound itself. The slowest group to recover their normal microbiota was the group that received the probiotics. So the probiotics were detrimental in allowing the normal microbiota to come back. The quickest of course was the colonizing yourself with what you already had, and then the middle group was letting it rebound naturally. So that’s a very interesting point about probiotics.Now, it wasn’t in the case of a disease. It wasn’t in the case of traveler’s diarrhea, which we know probiotics work for or pouchitis that we know probiotics work for. And then another seminal study that just came out again from the lab of The Godfather of the intestinal microbiota, Jeff Gordon has been studying malnutrition. I believe this study came out of Bangladesh where they had children suffering from mild acute malnutrition.

[00:08:13] And he’s been trying to develop, let’s say, a recipe for targeting the intestinal microbiota. And he’s referring to them as microbiota directed supplemental foods. Now, what you normally do in the situation of acute malnutrition is ready to use therapeutic food. One of them is termed Plumpy’Nut. It’s a very calorically dense food. And basically you give this much nutrients and calories to an undernourished individual as possible. So he took his microbiota directed food and the ready to use therapeutic food in two different groups. And refed these kids over time. The kids that received the microbiota directed food had received fewer calories. So it wasn’t as calorically dense. They got fewer calories and yet they responded better. They had better weight gain and better height for weight z-scores. So that’s telling me that you need to restore the microbial ecosystem and have a functioning gut in order to recover from something like malnutrition, which is forming the basis of my anorexia nervosa work because there’s certain overlaps there when you consider is voluntary restriction. But we’re talking about a dysfunctional gut. Targeting your microbes helps restore that gut function because what’s the point in eating all of this food if you can’t absorb it if your gut is not working properly. So there are two kind of seminal studies that I’ve liked in the last few years.

Grace Ratley: [00:09:51] So I know from working in your lab that it’s incredibly difficult to study anorexia nervosa because there’s not necessarily a good model for it in animals. So how do you get around that?

Ian Carroll: [00:10:05] You helped me get around that by working in my lab. I do it with two approaches. One is to do a human approach. One is to do a mouse approach. So as you said, with the mouse approach, you cannot fully mimic this disorder in mice. There have been attempts with the activity based anorexia mouse. I won’t go into too much detail about that, but essentially you create conditions in which a mouse will voluntarily exercise over eating. And to me, in a mouse, the only thing you can do is try to reproduce certain hallmarks of the disease that are relevant to therapy. For instance, we would use caloric restriction in mice and that calorie restriction is going to influence the microbiota and it’s going to influence the gut function. And they are relevant for therapy because as we just mentioned, we need a functioning gut in order to refeed individuals. So that’s one of the things we do. We take a specific trait associated with the disease and try and mirror that one trait in the mouse. The other option is trying to recruit as many patients as you can into a clinical trial where you can take multiple samples over the course of refeeding. We are very fortunate here at UNC because we have a center of excellence for eating disorders that was established by Dr. Cindy Bullock many, many years ago. We have eating disorders unit where we can recruit patients and get fecal samples over time as they recover.

[00:11:38] Now another approach that we use is gnotobiotics. So this is the term noto and bios, which are Greek words that mean known life. So essentially you’re looking at an animal that has their microbial environment completely controlled. So in this case, we have a mouse that’s grown in a bubble and a massive isolator. So they’ve never encountered a microbe before. What we do or what we have done is taken fecal samples from a patient with anorexia nervosa or a non eating disorder, matched control before and after clinical renourishment. Then we colonize the germ free mouse with those microbes and look at how they gain weight over time compared to the control group. And is there differences in how they gain weight at baseline and after renourishment. And also I work with another investigator called Lisa Tarantino, who we call the Mouse Whisperer, because she is able to do a battery of behavioral techniques. So we want to see if microbes from a human source can come into a mouse and then influence the anxiety and stress levels in those mice. So in that way, we’ll be able to tell whether taking microbes from a very noisy environment, which is the human and putting them into a very controlled environment, whether they have a functional influence on, let’s say, weight gain or behavior.

Grace Ratley: [00:13:06] Yeah. And I think that gets into the complexity of the microbiome because the microbiota they interact with the host and there’s a whole bunch of research on how they interact with host genetics and they interact with the foods that we eat. And there are all of these different variables that are incredibly difficult to control for. And so one problem that comes up in microbiota science is you get all these correlational studies, but it’s really difficult to pinpoint exactly what the outcome is caused by. So you see a lot of studies that link the microbiota to neuroscience or mental illness and to gastrointestinal disorders and all of these things. But how do we funnel that into cause and effect. It is really difficult.

Ian Carroll: [00:13:51] You’ve hit the nail on the head there with your comment about cause and effect. So those cross-sectional studies that you refer to, which I being transparent have been a part of, I think are important because the first step towards cause and effect, if you take a situation where you have a disease and a matched control and there’s no difference in the microbiota, do you move forward then? But if there is a difference, okay, now we can start moving forward. I mean, there would be an argument if there was no difference moving forward, but I won’t get into that. But it’s easier to say if there is compositional difference in the microbiota between those two groups, whether you can start exploring the mechanistic link between the disease and the microbes. And it is really complicated because we’re talking about numerous microbes in one system, which is your gut. That’s very different to another person, even though they may have the same disease. And each one of those has different genome, different genetic makeup, and may have a different arsenal of proteins that are producing decades influenced the host. So one thing that we do to move the science forward into mechanistic work is to try and use the platforms I’ve mentioned before, one being Novabiotics. You can transplant as I mentioned previously, but that doesn’t always work out. I published a paper recently where we took anorexia nervosa fecal samples and matched healthy controls and put them into germ free mice and we saw no influence on adiposity that is weight gain or fat mass.

[00:15:31] And we found several microbes that are associated with weight gain and fat mass. But it didn’t matter if it came from an AN patient or a healthy control. So there are certainly microbes that can influence your weight gain, but it didn’t seem to relate to the disease. There are new technologies where you can grow androids, which you take stem cells from the intestine of a human or a mouse and grow these tiny little kind of micro guts, and you can inject microbes into the middle of them. And if you have an idea like a gene from a microbe is influencing the host, you can knock out that gene in the microbe and then have a situation where you have the mutant in an android and the wild type in an android or even in a germ free mouse. The cause and effect, let’s take inflammatory bowel diseases. So in IBD you have a lot of oxidative stress in the gut. The motility of the gut is changed and you have an infiltrate a lot of immune cells. That’s certainly going to influence the any kind of microbial community. So can you really say that the change is associated with the disease or is it coming after so it’s consequence. But there has been a wealth of research done on IBD and how the microbiota, even though it could be changed by the environment, is influencing disease. So you could have a situation where it does change, but then ultimately it’s detrimental. So you can have a cyclical pattern.

Grace Ratley: [00:16:59] Yeah, it’s amazing to me how much we still don’t know about the microbiota. And not that amazing because microbiome science is so new. It’s not just new. It’s that even though we recognized that there were associations between the microbes living in us and our health, we just didn’t really have the tools to study them. And that really came with genomic technologies. So you’ve mentioned QIIME. Are there any other technologies that have enabled your research in microbiota research?

Ian Carroll: [00:17:31] Yes. So this is a really good point. Back when I told you about the story of the 316S genes per sample, it’s about $10 per sample back then to get each one of those reads so that’s 300 by $10, $3,000 for one person. It’s quite expensive. In my latest run that we used, I generated about 3 millions. So did I spend $30 million in my last experiment? No, I didn’t. And that’s because the technology has significantly changed and it’s all got to do with high throughput sequencing. And the first one came, it was the Roche 454 platform that used a technology called Pyrosequencing. It was still quite expensive when it first came out, but the main platform that’s used these days is the Illumina platform. Now there’s two ways you can go about it. You can use the 16S gene or you can do direct sequencing of a genomic preparation, and that’s whole genome sequencing. Whole genome sequencing will tell you everything that’s there, not just the 16S gene, but the types of genes it has in its repertoire. So you get a lot more functional pathways, metabolic pathways. You get all that information. With 16S, you are looking at one tiny little piece of a gene and trying to extrapolate that to the rest of the microbiome. And not only that, you’re looking at one variable region because the variable regions will tell you who is there. Both approaches give you taxonomy. So who is there and diversity measures how rich a sample is, but only the whole genome sequencing can give you the metabolic profiling, the functional genomics and all that information. The thing is with 16S, you can multiplex many samples. I do up to 300. I’ve talked to Rob Knight. He does up to 600 samples in one read which will make your sequencing costs maybe a bit $4,000.

[00:19:33] Whole genome sequencing you can multiplex. I only run about 20 samples on one run and that one run costs you $4,000. So if you’re doing many, many samples, it adds up really quickly. So traditionally, you’re going to see a lot of papers with the 16S profiling, which is really good. There are as you mentioned about technology, Rob Knight, a developer of QIIME also, I think it was him or someone from his group made PICRUSt, which is a platform where you can predict metagenomes from 16S data, which is very, very handy. And of course in certain samples where you can’t do whole genome sequencing, let’s say a biopsy from a human or a mouse where you’ve mostly mammalian DNA, if you directly sequence, you’re not going to get microbial DNA. So you’re better off doing the 16S approach. Now there are many new platforms that have arisen that at the time when QIIME came out and since then the RDP Ribosomal database project has their own mechanism for analyzing sequences. Greengenes is another platform, their data bases which are very valuable. They accrue all these 16S sequences and put them in their database so you can identify who they are. But QIIME itself, it wraps all these different programs into one easily usable platform. Many other people have contributed different programs that has been assembled into QIIME. So it’s just a dedicated platform for analyzing microbial communities. But if you’re clever, if you’re smarter than me, which is not too hard, you can use these programs independently through something or and do your own work through that and do your own analysis. And that’s becoming more and more typical these days to use your own personalized platform through.

Grace Ratley: [00:21:27] Yeah. So with the advent of all of these technologies and the decreasing costs, it’s put microbiota science in the hands of so many scientists, including people who want to commercialize it. I personally don’t believe that we’re really at the point of, since there’s so much that we don’t know about the microbiota, I’m not convinced that we can really commercialize it yet. I don’t think really anything demonstrates that more than the uBiome scandal that happened a couple of years ago. I don’t know if you have any thoughts on that.

Ian Carroll: [00:21:58] I had a collaboration with them and I would consider it the 23andMe of the microbiome. Basically they were giving us lots of 16S data. The collaboration was mutual. They were going to, when they sent out the kits, ask about eating disorder tendencies. And that would have been so useful for the scientific community. And we were about to receive all the data when something went wrong. And next thing you know, the FBI took all of their computers, so we didn’t even get those data. I have two stories that may answer this question for you. So as you know, I also work in a GI division, so at least the 23andMe can tell you if you’re prone to baldness or Alzheimer’s disease or maybe certain cancers. But that’s not there yet with the microbiome. And I know some GI physicians who would have patients come in and show them their uBiome report and say, my Bacteroidetes are low, what am I going to do? And this is nothing. I mean, what does it mean? They thought this would be the be all and end all of everything. So it’s not really there and just profiling something with specifically 16S just taxonomically. I don’t think it tells you that much. You can argue with me that it does. I’m happy to listen to other arguments about it, but what the Human Microbiome Project has shown is that even though we’re differing based on the types of microbes you have, the genes in those microbes are very similar.

[00:23:31] So I think it’s more important to have that kind of information. But you have to know the mechanism of how the disease works to bring that to the next level. And again, this is another commercial company. It’s called DE2.com. And this again was coming from the Weismann Institute. It was based on a study they did where they took a lot of people and they took a lot of clinical measures, blood, BMI, all those things. But one of the things they did was glycemic index, which is related to diabetes, and they did several types of analyses to work out what could predict the glycemic index in people. And it turned out it was an individual based combination of a few things, notably being a combination of certain components of the intestinal microbiota could predict your glycemic response to foods so they can tell you can eat ice cream and have a low glycemic index, whereas if I ate it, it could be quite high. I’m not saying that it’s real, but it’s there and it does something a little more useful than just profiling your microbiota, but telling you something biologically about yourself is a lot more promising than just you need to increase your Bacteroidetes. These technologies, I find them very exciting. I find them very interesting, but you have to be very careful with them as well as you move forward.

Grace Ratley: [00:25:03] Yeah, I totally agree. So let’s talk a little bit about you and how you got to where you are and at UNC and studying the microbiome and anorexia. So take us back to when you first became interested in science.

Ian Carroll: [00:25:18] I did my bachelors in Dublin City University DCU about a million years ago. I can’t remember now, but in Ireland what you do is when you’re in your final year, you work in someone’s lab, you have to. Back then I was working on a project that didn’t go anywhere, absolutely nowhere. But it didn’t matter because I isolated DNA. I made agarose gels. I ran DNA on those gels and I was like, Whoa this is DNA. This is brilliant. I was really excited by it, even though, again, it didn’t go anywhere. But the techniques and being in the lab and having the possibility of working on a bench as your job was just really, really exciting to me. So I went away for a summer and this is relevant. I went to South Carolina, so I finished my BSC and I went to South Carolina based on my girlfriend at the time’s recommendation. And I sold Frozen custard for the entire summer. While I was there, my wife and I, well, she’s my wife now. I got talking to someone and they said, Did you know about North Carolina? It’s the same kind of weather. It’s a nice place to be. And it has this research triangle park and you guys seem to want to be scientists. So this was really, really cool. And funnily enough, a hurricane came through at the time where we had to evacuate to North Carolina. So we got to see a little bit of it.

[00:26:43] So after that summer we had applied for PhDs, and it turns out my wife [Marie], got into Trinity College Dublin, and so did I. And we started our PhDs at the same time. A few years later, we graduated and were thinking about where we wanted to go. I had done my PhD in the Moyne Institute for Preventative Medicine under the stewardship of Professor Cyril Smyth, who is Scottish, and I was working on an organism called Helicobacter pylori. And when we’re talking about causes or consequences, this story kind of jumped into my mind because the person who discovered Helicobacter pylori was Barry Marshall and his supervisor was Dr. Warren, and they’re Australian. And no one would believe this guy that there is a microbe growing in your stomach. It’s too acidic, blah, blah, blah. Nothing, nothing, nothing. And he was convinced it was there. In the past, you had Koch’s postulates. Well not in the past, still today, but Koch’s postulates was a series of criteria you needed to fulfil to see if an organism, particularly a microorganism causes disease. And he grew Helicobacter pylori in a culture and he drank it. It colonized the stomach and caused gastritis. He isolated it from his stomach and he grew it, shows the same strain. And then he got rid of it with antibiotics and got rid of his gastritis fulfilling Koch’s postulates. And ultimately years later, he got a Nobel Prize. So that’s a very radical thing to do.

[00:28:13] But there you have your cause of consequence. But it’s not as easy as that with a complex microbial community. Anyway, I digress a little bit. So that’s what I was working on. And during that time we found that not we, but the community found that Helicobacter pylori has this injection system and it injects an antigen into the host cell which changes its shape. So Helicobacter can tuck itself nicely into the epithelium and avoid the harsh environment of the stomach. I was like, Whoa, that’s brilliant. And so I wanted to further investigate host microbe interactions. If we jump a few years back to when we were in South Carolina and we heard about North Carolina, myself and my wife, we sent CVS over to UNC Duke and I got an interview at UNC, and Marie got an interview with Duke, which was great. We came over and we got postdocs, and so we started here. I was working with a husband and wife team, David Threadgill and Debbie Threadgill, and Debbie Threadgill was my direct mentor because she was the microbiologist. And we basically worked on a microbe called Lactobacillus gasseri. So that’s a kind of a probiotic microbe, and we genetically altered it to produce a superoxide dismutase, which is an antioxidant with the idea that this probiotic, if in an environment with a lot of oxidative stress, it’s going to be able to neutralize it. And in IBDm, there’s a lot of oxidative stress.

[00:29:42] So we use the mouse model of inflammatory bowel diseases. This was a mouse model of colonic inflammation, the IL-10 deficient mouse, and we gave the wild type probiotic to one group and the mutant probiotic to the other group. And lo and behold, it had a greater effect on inflammation. And I was like, Wow, this is brilliant. And then at that time, when my postdoc was ending, I moved into the gastrointestinal division in UNC, and that’s when Jeff Gordon’s work started to emerge, and that’s when I hit it. Now, to get to where I am, it’s not just good enough to have these good ideas and have a passion for it because everybody has a passion and interest. But I feel that I benefited from a lot of mentorship and really good guidance. So there were people who I would say put their neck out for me, maybe thought they saw some potential in me. The first being was Robert Sandler, who was the head of the GI Division at the time, and then Balfour Sartor, who was my direct mentor. And basically what we did was we put a training grant together and I got this award that allowed me to become independent and work as a scientist under the guidance of Balfour Sartor. And then I met Cindy Bullock later on in life where we got interested in microbes and eating disorders, and here I am.

Grace Ratley: [00:31:11] How did your training as a traditional microbiologist color your experience as a microbiome scientist?

Ian Carroll: [00:31:19] It’s kind of a tough question to answer because when I was training as a traditional microbiologist. It’s very basic, you’re looking at, let’s say, a gene or a pathway or something in a pathogen. There’s a lot of work that goes into pathogens or antimicrobials is another hot area in microbiology at the moment. But basically you’re working at the molecular level to understand the machinery within that cell that leads to it being a pathogen or something else. And although I found that really fascinating, I kept thinking about what’s the clinical relevance of looking at this? What does it mean? And yes, I continued, and that basic foundation of my microbiology knowledge, although a lot of it is disappeared right now and how to do in vitro mutagenesis and transposon mutagenesis and try and find out which genes are associated with, let’s say, colonization of an animal. I really like but right now and I’m much more interested in the machinery, what does it mean to the human? What does it mean to a population? What does it mean to the influence of that microbe on the human? It gave me the understanding to be able to do the molecular techniques that gave me this stepping stone towards working in a clinical environment.

Ian Carroll: [00:32:42] And that meant working with human feces, knowing how to store it properly, knowing what to do if I wanted to transplant those samples into mice. So it was a perfect foundation. But traditionally most people would go down the basic science route of microbiology, whereas I was lucky to be able to chase what I wanted to do into the more translational aspect. And I guess my interest flourished being in the division of GI and Hepatology because I got to interact with physicians and they have a completely different way of looking at things than basic scientists. Although they are basic scientists in their own right, they’ve been doing basic science, learning their techniques, their thinking mostly about the disease outcome ultimately. And this kind of thinking is very much in line with the NIH mission. So if you’re looking for funding and you have your idea, if it’s in line with a clinically relevant idea, then you’re more likely to get that funding.

Grace Ratley: [00:33:49] So to younger scientists or scientists who are interested in going into microbiota science, what advice would you give these people?

Ian Carroll: [00:34:00] There’s just two routes because you don’t need to know the basic science if you want to get involved in in this field. There’s an emerging area where you’re epidemiology, nutrition and microbiome and that is quite exciting because you don’t even have to get into a lab. It’s the way that human genetics moved. Genetics started out on the benchtop, but now it’s all about statistics. Genome wide association studies like someone else can collect the samples. All you need to know is the data and you need to know how to put it together. And that’s one way that the microbiota is heading. Now, if you’re more interested in mechanism, then you’re going to have to get in on the bench and start working on it like that. But I would recommend is if you’re starting a postdoc or you’re at a stage where you’re ready for independence, I’d find a good mentor who has a good track record and has time for you. And they should be helping you develop your independent research niche. And to do that, they have to be willing to spend time with you to help develop it, but also maybe share some of their equipment, share their resources, and maybe their preliminary data and help you write a K award.

Ian Carroll: [00:35:21] So the K award is something that I had. It’s a mentored award for young scientists. It’s important to get into an environment that is collaborative rather than competitive. Competition just quells your interest in science I find. If you’re in an area where you can walk into a neighboring lab and talk to someone openly about what they do and there’s no secrets and they’re willing to share protocols with you, it’s just wonderful. Your choice of mentor is very, very important. I would also say I think it’s important for who you are to be represented in a mentor. So I’m not saying if you’re a white male, you need a white male mentor, okay? It’s the type of person you are. If you get into a, let’s say, a very well known college and they’re like, okay off you go, sink or swim. You could sink very easily. You need some support. And I think it’s good to be thinking about that when you’re moving forward.

Grace Ratley: [00:36:19] Outside of science, what do you enjoy doing?

Ian Carroll: [00:36:22] I have two children. One is 11 and one is 4, and they take up 95% of my time when I’m not in work. That’s another thing about work life balance. I’m the type of person who is not going to stay until midnight and not see my family. I don’t know anybody who would want to do that, even if you’re really busy. Okay, there are certain times where grants are due, but I always try and make time for being with my family, playing Transformers with the little guy, reading Harry Potter with the older girl. So what I really like doing personally and I don’t have a huge amount of time for it these days. But I used to devour science fiction. I would have hundreds of science fiction books read before the onset of Kindles and stuff like that. When I was walking around, I would always have a coat and I’d have a sci fi novel hanging out of my coat, so that was me. It’s also important to try and I think, stay fit. I don’t have as much time for as usual, but I have a trail right out behind my back garden and I can go out and do a bit of running and that keeps me a little bit sharper. Make time for yourself. Make time for your family. The ambition is there. But if it’s up to me, if I wanted to be the provost of the chair or something really big, I’m more happy doing really interesting science and spending more time with my family than doing anything like that.

Grace Ratley: [00:37:48] It’s really refreshing to hear scientists working on that work life balance.

Ian Carroll: [00:37:53] But once you’ve done your grad work, you should try and get your balance together and more and more people are having children while they do their grad work. When you have children, it’s really hard to do those long nights and not be there. I still see those people who do nothing but talk about science, nothing that dream about science and work all the time. And I’m like, okay, that’s fine, That’s fine for you. But I think it’s more important for young people nowadays to know that that’s not the model. I swear, sometimes I’ve spent those whole nights and absolutely done nothing. It hasn’t benefited me whatsoever, but being more focused and having better time to really, really work hard with a more disciplined mind is better.

Grace Ratley: [00:38:39] I couldn’t agree more. Thank you so much for coming on the podcast Ian. It was wonderful to talk to you. I loved hearing your perspective about microbiome science and about your journey becoming a scientist.

Ian Carroll: [00:38:48] It was great talking to you as well Grace.

Transcript of Episode 31: Mark Kotter

Disclaimer: Transcripts may contain errors.

Grant Belgard: [00:00:00] Welcome to The Bioinformatics CRO Podcast. I’m Grant Belgard. And joining me today is Mark Kotter, founder and CEO of bit.bio.

Mark Kotter: [00:00:07] Hi, Grant. Thank you so much for inviting me to that podcast.

Grant Belgard: [00:00:11] I didn’t want to insert myself into your introduction, but I guess as a matter of conflict of interest disclosure, of course, I’m head of bioinformatics at bit.bio, so I’m not an impartial party here.

Mark Kotter: [00:00:24] I’m so excited about what your team is building and how it’s contributing to the bio. It’s the bit bio. So thank you.

Grant Belgard: [00:00:34] The pleasure is all mine. I just stay out of the way and let them do their work.

Mark Kotter: [00:00:38] That’s a good position.

Grant Belgard: [00:00:41] Can you tell us about bit.bio?

Mark Kotter: [00:00:42] Yeah, of course. So bit.bio is a synthetic biology company and we’re focused on human cells. And what you can do with these cells is you can either use them for your research purposes or to create new drugs, or you can also use this technology for cell therapies.

Grant Belgard: [00:00:59] What’s so special about the technology?

Mark Kotter: [00:01:01] It’s really the approach plus the technology that differentiates us from other companies that also are creating human cells. The way that we differentiate ourselves is that we really look at cells like hardware, like their computers. So for us, the cell has a nucleus that contains the DNA, and the DNA is a bit like the hard drive. So all the information is stored. It’s actually read only memory and then within a cell, only part of that operating system, part of these programs that are stored on the DNA level are actually active. And this is structured in what’s called gene regulatory networks. Then these are the sub programs in the cell. The genes that control these programs are called transcription factors. So what we do is we activate these transcription factors to instruct the cells and obtain certain functions. And what you can do is you can take this approach and you can literally program a stem cell to become the cell type that you’re interested in. And this is ten times faster and we can do it with extreme precision and it’s very, very scalable.

Grant Belgard: [00:02:11] So what’s the big advancement over where the field has been previously?

Mark Kotter: [00:02:16] I mean, stem cell biology and the concept of embryology has really gone and made huge advances over the last 20, 30 years. We’ve identified at the beginning of this field that the stem cell that’s responsible for generating an entire embryo, all the organ systems, all the cells in a growing organism. And the idea was that if we could replicate this somehow, if we could use the tools of biology to recapitulate this development, we could get to every cell type and we would have a source of cells that we could use for research, obviously, but also for regenerative medicine. And there’s been some huge advances in this field and some early applications. But if we’re honest, we really didn’t move this very far. I mean, it got stuck somehow in the process. At this point in time, you don’t have stem cell derived products in the clinic. And the reason why is because it’s very, very difficult to get the stem cells to do what you want them to do. And then another area opened up, which I would call synthetic biology. And that really goes back to the 1980s when Winetraub and Davis, in the heydays of molecular biology, discovered a gene that they named and they called it MyoD. And their observation was, if you activate this gene in a cell, it turns into muscle like magic. And of course, nobody expected that. And that a single gene could turn on a new cell type. But then in 2006 and 2007, something really even bigger happened. Shinya Yamanaka discovered that you can use four transcription factors, and if you activate them, then you can take pretty much any cell of your body back into a stem cell stage. So it gives you essentially everyone a source of stem cells.

[00:04:18] And what that means is access to in principle to all the cells in your body, in the culture dish. And that was the second time around that someone showed that gene combinations dictate the identity of a cell. And then, of course, others like Marius Wernig, took up this idea and they showed that this is probably a generalizable principle. It’s amazing things like taking a skin cell and turning them into brain cells. He also took a liver cell and turned into a brain cell. I’m not sure how useful this is, but it really shook the foundation of what we knew about cell biology, the identity, what makes a cell a cell and stem cell biology. So this is cell reprogramming and this is synthetic biology. And so we’re very excited to bring this into a company setting and an industrial process. But we were able to do is create a technology that allows you to very precisely control these transcription factors. What we can do with that is we can instruct cells so they have no alternative. And of course, if you have that level of control, then you have the foundation of an industrial process that is very scalable and it can open up hopefully all these things that people were dreaming of, better cells to understand biology, cells that allow you to actually study human disease and create better drugs or make it easier for drugs to be developed and actually be successful, which is a big bottleneck, as you know. And of course, the new generation of drugs are cells by themselves, and they’re so powerful because they can react to the environment. And we’re very excited about that.

Grant Belgard: [00:06:07] So it’s amazing to be able to differentiate cells that are very much like what we ordinarily have in the body. How excited are you about cells that may have characteristics from different types, cells that may have synthetic circuits engineered in them and so on. How far do you think that that thing can take us?

Mark Kotter: [00:06:28] So this brings us back to the question what is actually how is the cell defined? And there’s maybe two theoretical concepts. You could say, okay, within our DNA, a cell is defined as the whole package and you can’t do anything about it. It’s what it is. It’s like a blueprint. This is one cell type, a neuron, and the other cell type has a completely different information content. Or the alternative hypothesis is that a cell is really not much more than the parts. The individual sub programs that are active in any given time. Actually Weintraub and Lassar already in the 1980s looked at this a bit and said, can we combine traits of different cells? So they showed that they can create cells that have a bit of a muscle phenotype that behave like muscles. They also bit like neurons, like brain cells. And they also did that in melanocytes and combined these are the pigment cells of your skin and also create some hybrid cells there. And I also had a very talented PhD student in my lab who did some experiments combining macrophages with brain cells. And she showed that that’s also possible. You can create cells that have this dual identity.

[00:07:44] And so what we’ve learned from that is really, again, we have to refine the concept of what makes a cell. And we really think I’m at the point where I’m really thinking it’s just the information program that’s active and you can puzzle it together and you can combine it and certain combinations aren’t possible or not. And then of course, you can think about cells that have combination of functions that you may want for a therapeutic application that don’t really exist in the human body. And I think that’s very exciting. It’s very science fiction, but it’s very exciting. You could go even further. As you said, you could create logic gates. You can gate their function in constraints. And I think that might be very interesting and helpful. And potentially you can even import functions that don’t exist in human cells. So I think there’s a lot we can discover. It’s just like endless opportunities of engineering. But let’s be realistic. Right now, I think we have huge amount to do to actually recreate some of the cells that actually exist in our human body, and that’s really the focus right now.

Grant Belgard: [00:08:51] What areas do you think will be impacted first by this technology?

Mark Kotter: [00:08:55] So speaking from our own experience in bit.bio, there’s always this huge ambition of creating software and we’re working on it. But it’s also think about the regulatory hurdles, the quality of the cells that you have to have for clinical and preclinical studies, etcetera. That’s of course a huge endeavor. In bit.bio, we decided to look at another alternative application initially, which is really providing these cells for drug discovery. If you think about Alzheimer drugs, they have been very successful, let’s say, in the past. So drug companies are extremely good at creating a drug to a specific biological problem. But really the biology is the thing that they need to get right so that the process actually is running and providing the output, the drug that you desire. And here’s the meta, mice don’t get Alzheimer’s. So what people do is they create something in the mouse that looks a bit like Alzheimer’s, which it isn’t. It’s a different thing. It’s something that humans created. It has certain features, and then they use this model and then create drugs to treat this model. But because the thing that they’ve created in mouse isn’t real Alzheimer, the drug then fails in the clinical trial. And there’s other reasons as well. Sometimes it’s just toxic. Mice can tolerate other things than humans do.

Grant Belgard: [00:10:21] This is a bit of a recurring theme on this podcast. There’s an industry wide reluctance to move forward without rodent data, even when it’s so widely recognized that the translate ability is nil.

Mark Kotter: [00:10:35] There are some papers that make very strong statements about the correlation of animal models, but I don’t want to at all argue against the animal models. At some point, you probably need to understand how biology works in the context of an entire organism. But in order to fix that translation gap, I think you need to start with the actual condition, in the actual cell that is actually sort of human. And I think that’s what we’re really excited about, being able to create these cells for big pharma companies that have ambitious programs to develop a next generation of medicines and enable them to do this in a real human cell in the right, real human cells. I think it’s extremely exciting.

Grant Belgard: [00:11:21] So bit.bio didn’t start out as bit.bio. Can you tell us about the origins and what prompted you to start? What was to become bit?

Mark Kotter: [00:11:29] So that brings me back to a personal experience. I’m a lost mathematician. Let’s start at the beginning. I did a year of Maths and then had crisis units that had to do something that’s somehow contributes to something in this world. And I was not aware how great mathematics can contribute. So I decided to go into medicine and then of course, drawn to the how and research in medicine. This led to some very early encounters. So before I decided to go to medicine, I tried it out. I became a healthcare assistant for six month period and I worked with people with spinal cord injuries. And I just saw how that condition changed their lives. And I just thought something has to be done. One needs to push this forward. This is really something that needs to change. It turns out this is extremely difficult problem. And I think we’re not very close to a cure. We are much easier problems to solve. But that set me up and really defined my career, not consciously. So I didn’t have this picture in my mind, but I ended up as a neurosurgeon that looks after spinal cord injury patients who went to research and discover regenerative processes in the brain and the spinal cord hit those limitations of stem cell biology that we discussed before, try to find another way, follow the footsteps of giants. And that had this extreme luck to identify a technology that allows you to really exert, I would say, supreme control over cells. It’s like a control system or an antibody to the operating system of a cell. And that then sparked and it became first a hopeful project. So we called the company after the Greek goddess of Hope, Elpis. And then when it got legs, when we saw that actually it’s not only fanciful, but actually real, we decided to call it what it is, really the merger of data science and biology, and this is how it came about.

Grant Belgard: [00:13:40] What are you long term ambitions with bit.bio?

Mark Kotter: [00:13:42] So if you think what human cells can do fundamentally change medicine in the form of cell therapies, and we already saw this, I always say that the right flight in cell therapy were CAR T’s. So they were really products that were extremely expensive, not very scalable, very I would say crude at the beginning, often with a lot of side effects. But what they taught us is that cancers that had no hope of surviving suddenly were cured. Nobody expected this. This is a real revolution. Why is this the case? Because cells are not drugs like small molecules or biologics, and they interact with the environment and then they instruct other cells to do certain things and they can mount an immune response and they wipe out the cancer. And if you think a bit further, think about Parkinson’s, think about other conditions, diabetes, where cells are lost. And the only way to really fix this is to really somehow replace these cells. Then you can see how powerful this is. And as a medic, seeing that hope, seeing that glimpse, seeing actually this progress is just a huge driver of ambition. And then that hopefully has translated into bit.bio. Everyone in bit.bio is really excited about the opportunity ahead, enabling something that hasn’t been there before, but not only our own progress in cell therapies, but also as we discussed the application of cells to enable better research and better drug discovery.

Grant Belgard: [00:15:24] What do you think are the biggest challenges that the field has to overcome?

Mark Kotter: [00:15:28] The biggest challenges in cell therapy is really manufacturing scale with precision and high product definition. And this is really what was the biggest bottleneck for the application of stem cell biology. And it’s a huge task. I do think that the approach that we have provides a real unique opportunity to overcome some of these challenges, and we were able to demonstrate this. So, for example, our two products that we have released into the market, one of them is a human brain cell glutamatergic neuron, and the other one is the human muscle cell. And then of course, more to come. But these are the first products that are consistent and scalable enough for high throughput screening, which is the process that drug companies use to create new drugs. And that’s a major step. So we’re very excited and hope that we can translate this into a clinical product as well.

Grant Belgard: [00:16:22] Going way back maybe to childhood, what do you think influenced you and shaped you, what made you Mark Kotter?

Mark Kotter: [00:16:32] I think one thing that you already glanced from my accent is that I don’t think I have a locality. I was born in Canada and I was raised in Austria and Germany. I had the pleasure to live in Australia and my parents tried to make me comfortable with speaking foreign languages. And I think that’s one aspect I would say that has shaped my thinking. And the necessity to move around places and adapt, I think was the other thing that really influenced me. So new cultures, new locations mean people act differently, they think differently, and I had to reinvent myself a few times. And another reason I think is because I have a certain handicap. I think you would now call it dyslexia. And this is like someone throws a huge spanner to your brain and it means that you have to deal with things that others don’t even encounter. And it’s hard and you have to iterate around it. You have to figure out how you think around this problem. So I started to, I think, program my mind away from languages, more into Maths. Music and Maths, I think these are probably my biggest talents or were my biggest talents, they’re not now. So I was then entered national selection of Maths special programs in Germany and I really really enjoyed this. But then came the stage where I felt, what am I doing with this? And I didn’t really realize at that point in time how powerful Maths can be. And I had this idea of I love what I’m doing, I love all these problems, but I don’t see a reason why I should pursue this.

[00:18:21] And that made me go into the thing that really would be the last on my list, which was medicine. But it made sense to me because I thought this is something all goes to pot. That’s something that makes sense, helping others, serving others. I can live with that. But what it also meant was I had to learn a complete new language. So medicine to a large extent is a language. It’s words that you use to describe biology and disease. And it was fabulously difficult for me to memorize stuff because I inherently was programmed to think in causal relationships and cause effect relationships and not natural to synthesize information. And I managed over time, got better there. And then I had this battle between medicine and music. I sort of end up doing music. So I studied music medicine in parallel. And I guess looking back at this just means that I probably had to keep my head plastic, I had to reinvent myself. And I think that’s really given me a slightly eccentric perspective on problems, which then allowed us to do things that other people might have not done, being very persistent to generate this object of knowledge. That was a real huge risk for me. I nearly lost my credibility in my academic lab, my funding because people said [it was] crazy. I’ve had people saying this is not stem cell biology. You shouldn’t be part of the Stem Cell Institute, but you get a bit feisty over time and then you start pushing through walls. Even just combining neurosurgical training with academic work was extremely rare. And I still got accepted in Cambridge and I had the opportunity to push through these walls.

Grant Belgard: [00:20:15] How do you manage it all?

Mark Kotter: [00:20:18] Now I think my life’s become a lot simpler. I have this incredible opportunity to help facilitate other people to work on an interesting problem. I think scientifically it’s super fundamental. What makes a cell? A cell identity. And the moment you crack it, we have a system that allows you to actually use it for research or other applications. And so my job now is really much more to give other people the opportunity to do what they enjoy doing and what aligns with that purpose. And it means, of course, I’m a bit busy. But at the same time, it’s really amazing to see how things come together. So I really enjoy that and the creativity.

Grant Belgard: [00:21:01] What preparation would you say you found useful in that transition, going from doing yourself to creating an environment in a structure where others execute on this vision in an orchestrated way?

Mark Kotter: [00:21:16] A certain amount of self-awareness is really helpful. Knowing yourself, I think, and getting to grips with the good things and not so good things, and then the impact that you have on others I think is really, really critical for any person that assumes any kind of leadership. And I don’t mean management or I don’t mean power. It’s more about leading and enticing others, stimulating others to join the path that you’re on. And the other thing is having experience in different environments. So I know I had a lot of things that I saw different hospitals, different universities, even different companies. And you experience the culture and you experience how people interact, and then you have a vision of how you don’t want to have what you don’t want to happen and then what you would like to happen. But the reality in a startup is that things are moving so rapid, so that you create a culture that’s right for one moment in time and then you transition to a bigger stage. And then you have to recreate the culture because it what happened and what worked in a 30, 40 person company is no longer applicable in a company that is 100 people because information doesn’t just flow easily, people don’t see each other and they’re not in sync. So suddenly you have to think about structures and responsibilities and roles and responsibilities. And that’s a transition that’s been talked about before. And it’s hard because people have to give up things that they like to do at the beginning, and some people don’t like it and others thrive on this.

Grant Belgard: [00:23:02] And in COVID probably hasn’t helped.

Mark Kotter: [00:23:05] Oh yeah, I think COVID has been, everyone was locked up in the Zoom box. We started out with this idea, we have this technology, what can we do? So how do we use it? It was one research question. The second question was, okay, is this really transferable to other cell types? And then how can we create new cell types? And and we figured out components in bioinformatics, how important it is screening. But the areas that little bit remained, let’s say artisanal for a longer time period. It’s only recently, only this year that we have identified structures and patterns that allow you to really create a cell with high efficiency. And I never thought that we could really process this part because I think that’s the bit of biology that can’t be structured. But I was taught wrong. We’ve got this incredibly talented scientists who essentially showed us a way of actually how to do this efficiently and allowed us to design processes.

Grant Belgard: [00:24:15] What advice would you have for other biotech entrepreneurs?

Mark Kotter: [00:24:19] So the first thing that you need to do is come to a clear visualization, I would say, of what it is that you want to create, and that’s extremely hard and then find a way to communicate. And I still struggle with that. It’s extremely difficult. So how can I make people understand that having a human cell is really impactful, creates opportunities that you haven’t had before. Often it’s a bit like sculpture and you start with a stone and changing create structure and you basically discover structure. The second thing that you acquire, I think is really that self-consciousness. And I was the least self-conscious person when I was in my space. I thought I was extremely clever and everyone else wasn’t and turned out to be wrong. Of course, if you have this distorted view of life, learn more about who you are or how others perceive you. I really do think that having a strong moral compass is also very helpful. I think it’s very fundamental. And then once you know what you want to do, you will have so many people telling you that you can’t do it and you just connect with what you think is right. More often than not you’ll be right, but you still make some massive mistakes. And then you have to be not shy to acknowledge that you’ve made a mistake and change and pivot. I think that’s the other thing. You don’t learn when things go right. You learn when things go wrong. It’s painful if things go wrong. I mean, it feels awful. And then you just have to pick yourself up and say, hey, I did this, I own this, This was wrong. What can I learn from it? And more often than not, you’ll end up at a higher level of understanding. You become better at what you do, the ability to rethink yourself, rethink your approach, rethink your context is really important as well.

Grant Belgard: [00:26:24] One thing I’ve noticed is I think you do a really good job of bringing in a team players. How do you do that? How do you attract really good people to your vision?

Mark Kotter: [00:26:35] I think it starts a bit with a vision. I think it’s easier to attract someone to a problem like, Hey, it’s great new medicines and more efficient trading platform. And the other thing that I do is I try and just be myself and honest. I’m going to be very frank with things that I didn’t do well, and I try to just be naming the things as they are and then give other people the opportunity to contribute and shape and change the trajectory of the journey that you go on. And I think if people sense that you are well meaning honest and trustworthy and that you connect them or enable them to pursue something that’s close at their heart and you don’t shy away from saying, hey, I’ve done something stupid here, let’s get together and correct it. I think most of the time they forgive your mistakes and will follow you. And I think that’s what we’ve been able to do in bit.bio, incredibly smart people. The scientists are much better scientists than I was. And my job now is really just to try and connect things, getting people to work together.

Grant Belgard: [00:27:48] What’s something about which you’ve changed your mind over the last few years?

Mark Kotter: [00:27:53] There’s so many things that I don’t even know where to start. I can tell you one thing that I haven’t changed my mind about, although I have been pushed to change my mind about very often, is this idea of either doing only a therapeutic play, only self therapy, or having cells for tools. And for me it always seemed a bit weird because the only difference is the market and the data package that we wrap around the cell. But the process fundamentally is very similar. Of course, clinical manufacturing is dimensions more difficult than others, and so that’s something I held. But in the science, one thing that really changed where I was wrong was this concept. There’s errors that can’t be captured where you just need scientific intuition and you’re going from a known transcription factor to a combination or unknown to [actual] cell that you can grow and produce. I always thought that’s probably the heart, that’s where you need intuition. It’s more like exploration. And again, I think I’ve learned that you can actually process this. This is something where the approach and the mentality is more important than the skill set, which is extraordinary. And for me, I’ve never expected this. A very young scientist was able to teach us how to take a cell from a concept to a tool for yourself.

[00:29:21] There’s another young scientist and she was working on a particular cell type and it looked fine. But after 18 months, she said, I haven’t made any progress and I just want to step up and say, Hey, this project has failed. And she did this in town hall and she said, I’ve done this and this and that. And I went down the rabbit hole and I just want to show you and I want to tell you guys that this has happened to me. It wasn’t good. It was painful. And then the credibility and being honest and stepping up and saying, hey, this project didn’t go well. And then she started to talk about the learnings and it’s like a miracle this year as a side project, she just cracked it. She changed her approach and within a few weeks, a few months, something that was stuck suddenly turned into something that worked. And of course, it has to do with technical innovation, etcetera. But it is that resilience not giving up, knowing when you go wrong, acknowledging that you go wrong, that something has to change fundamentally and resetting and being open and honest about it. I really think that’s incredibly important and powerful at all levels.

Grant Belgard: [00:30:38] What do you think is the worst piece of advice you’ve received since starting bit.bio?

Mark Kotter: [00:30:45] And the advice that was totally wrong at the beginning turns out to be extremely valuable at the stage of the company that you are now. So the advice that I’m referring to, if someone said you need to create role profiles, but at the beginning, when you have a four people band, you don’t have any roles and you have no idea what you’re doing and how you get to where you need to be and you think, Oh, this person could be this role. And it turns out that’s absolutely not their skill set. But first of all, you can’t recruit anyone else that has that specific because you’re not in a position to make an offer to a person who has. And because you don’t know what you need. And so at that point in time, that piece of advice wasn’t a good piece of advice. But a couple of years later, now it’s an incredibly important piece of advice because it helps people to understand their role within a larger organization. And now like any company, we’re working on definition of these roles. I guess what I’m saying I don’t think I received any bad advice.

Grant Belgard: [00:31:52] It’s all a matter of timing.

Mark Kotter: [00:31:53] Yeah, exactly. It doesn’t match the circumstances, but I often think about this advice.

Grant Belgard: [00:32:00] It’s interesting. Yeah. I guess as an insider, you’ll always have more information on the company and the stage things are at and so on than outside advisors who may have a much larger breadth of experience, but may not have as much insight into the applicability of that advice in terms of the stage the company is at.

Mark Kotter: [00:32:21] Yeah. And the amazing thing about bit.bio, we’re recreating something completely new, something that hasn’t been there. I mean, the team that we’ve got is incredible. The people are incredibly skilled. The personalities that we have in bit.bio, really handpicked individuals that are fundamentally collaborative, kind, purposeful, ambitious in the right sense and empirical. And I think it’s the biggest and strongest team that I’ve ever seen. And what they were able to do is really to do something that’s never been there before. I mean, we have more cells in our company than any other company. I know of more different cell types, more cell types than the entire Stem cell Institute in Cambridge, which have been working on this for 20 years, plus the speed at which we can innovate the complexity of biology and approaches is second to no other institution I know. I think the commercial capabilities, the interest that we were able to spark at that very early point in time is extraordinary. So I think when things come together in the right way, you can create such a powerful team and such an incredible force that I think that’s the most exciting thing at the moment for me, to be honest, seeing how this thing is crystallizing and it’s actually creating cells that are really valuable. We know, for example, that the first screens are going to take place very soon with our cells, and I can’t wait to hear some of the results. So this would be very large. Billions of cells going into screening systems, etcetera. So these are major feats. And knowing that we’re probably maybe the only company that can deliver this, this is incredibly exciting and also exciting to see the investors that we have, the backing that we have received to facilitate our growth, etcetera. It’s thrilling.

Grant Belgard: [00:34:17] It’s really interesting because in a way it feels like we’re looping back to music because you change a few words in there and you could be talking about improvisation.

Mark Kotter: [00:34:25] I guess an orchestra is very similar, isn’t it? It has to listen to what other people do and be synchronized. It’s better if they have the same score sheet. It’s better when they play the same tune. I mean, when human beings come together and come together in the right way with the right purpose, I think magic can happen. I certainly see a lot of magic in.

Grant Belgard: [00:34:49] Well, thank you so much. It was a lot of fun.

Mark Kotter: [00:34:51] Thanks, Grant.

Transcript of Episode 30: Matthias Gromeier

Disclaimer: Transcripts may contain errors.

Grace Ratley: [00:00:00] Welcome to The Bioinformatics CRO Podcast. My name is Grace Ratley and I’m your host for today’s show. And today I’m joined by Dr. Matthias Gromeier from Duke University. Matthias is a professor of neurosurgery and molecular genetics and microbiology at Duke. His lab studies viral cancer immunotherapies. Welcome, Matthias.

Matthias Gromeier: [00:00:19] Hello. Grateful to join you.

Grace Ratley: [00:00:21] We’re excited to have you on here. So let’s go ahead and talk a little bit about your science, because this is something that’s really cutting edge, really exciting. It has been featured on 60 Minutes two times, I believe, and it was awarded a breakthrough designation. Correct?

Matthias Gromeier: [00:00:37] Yeah. So FDA administrative action for cancer therapies, most commonly for therapies against devastating disease that show extraordinary promise.

Grace Ratley: [00:00:45] So tell us a little bit about what you’ve created.

Matthias Gromeier: [00:00:50] Yes. So even for me, it’s sometimes hard to realize just how long I’ve been doing this. So the agent we’re working with, it’s a very interesting form of the poliovirus vaccine. If you’re older than 20, that’s the very poliovirus vaccine we got as children. And I made this. This was part of a really nerdy lab experiment, very basic, just we wanted to see if it can be done in 1994. And so ever since I’ve been working on making this into a form of cancer immunotherapy. Because I’ve been doing this so long, this strategy has morphed into something completely different than what I thought it was at the beginning and actually something much better that I thought it was at the beginning. And it doesn’t have so much to do with myself, but with what’s happened outside. So there were some major breakthroughs in immunology and virology and cancer research and cancer immunotherapy research, and it all came together. It’s the purpose of my life, I could say, to make this happen. We are a very exciting stage and it was quite a journey to get to this point.

Grace Ratley: [00:01:56] Yeah. So the agent you’re working with is a polio vaccine and it’s called PVS-RIPO, if our listeners want to look into it and it’s very interesting. So it’s the poliovirus. And then you edited out some of the infectious RNA and you replaced it with a rhinovirus. So what exactly does this virus target in the body?

Matthias Gromeier: [00:02:19] Yeah. So what this recombinant is so you described it correctly. So it has the genome of what we call the oral poliovirus vaccine that was used until roughly the year 2000 in the US, is still being used in many parts of the world. So the family of viruses, that poliovirus belongs to the picornaviruses, they use a very, very sophisticated and really genial strategy to do their replication strategy, and they use a particular important genetic element that sits in their genome called Internal Ribosome Entry Site or IRES. I call it the transmission of the virus. So this is really what makes the virus succeed. And what we did, we gave the poliovirus vaccine the corresponding portion of a rhinovirus. These are related viruses. They both have these elements. They use them in the same way. But these viruses function very differently. And so we basically have now a polio vaccine with a rhinovirus transmission. The really beautiful part of this is that the virus doesn’t mind. It’s very difficult when you’re so polarized is an RNA virus just like coronaviruses is. And what we’re experiencing right now, these viruses like to mutate a lot. So whenever you design a recombinant RNA virus for a therapy purpose, you have to worry about what this virus will become. They like to change and adapt and this virus doesn’t. It’s perfectly happy with what it is. And that’s really interesting because what it has become is a truly remarkable type of virus that’s very different from what poliovirus naturally is.

[00:03:54] It’s actually more something what a rhinovirus would do. So when I started out, poliovirus was, it is a very well studied virus. However, there are some very important gaps in our knowledge and they have been filled in gradually in the last few decades. And what we realized the biggest change in my career scientifically was when we realized that poliovirus doesn’t actually target the type of cell we thought it did. So much of the research on poliovirus has focused on the brain or on the central nervous system because that’s what the disease polio causes, paralytic poliomyelitis. That’s a disease in the spinal cord. So people looked in the spinal cord to study polio. And that’s unfortunate because this is not the primary playground, if you want, of the virus. This is more an accidental site of the infection. So the virus really lives in the gastrointestinal system. And there was a very beautiful, very, very well done study published in monkeys where people for the first time looked where the virus actually goes to, in the gastrointestinal system. Nobody else had done this before. And I saw this paper. I stumbled over this and I literally fell out of the chair in my office because what we saw was that the virus targets a type of cell with very high priority that we were not really aware of.

[00:05:16] And those are cells, myeloid cells, antigen presenting cells, macrophages and dendritic cells. This is not such a rare thing with viruses, but for poliovirus was completely unknown how important this was in a living being. And it has really shaped my view of the virus. I think it should make everybody think again when they look at these types of viruses. So for our cancer immunotherapy strategy, this changed everything because before that we had primarily regarded the virus as an agent that would infect cancerous cells. But now we realized that probably the main target we should look at are actually myeloid cells, antigen presenting cells. So these are macrophages, dendritic cells and microglia in the brain because these are the cells the virus obviously prefers to grow in. And for immunotherapy, this is a very, very momentous finding because these are the very cells, antigen presenting cells as the name say, that you need to engage for cancer immunotherapy. So this was really a turning point in my career. After this, I have become an immunologist, which I’m still not, but I’m moving in that direction. And again, so it’s remarkable how this was completely out of my work. There was the work of others. If they hadn’t done this primate study, we would never have known. So it was truly remarkable that the study done by others has turned view of our work completely upside down.

Grace Ratley: [00:06:48] It’s amazing how collaborative science can be and how serendipitous as well. Yeah. So let’s talk a little bit about how this virus is used as a cancer therapeutic. Can you tell us a little bit about the cancers that it targets and how it goes about killing these cancers.

Matthias Gromeier: [00:07:05] In cancer research, it’s probably easy to imagine why most people are obsessed with targeting the cancer cells themselves. They are the problem and we need to know how they are behaving. What are they doing? What are they like? Let’s hit them. Let’s somehow target the neoplastic cells because they are the problem. And if you work in cancer research, you intuitively lean towards this view. And here at Duke, we had a visitor James Allison, I think 2018 Nobel Prize laureate for the discovery of immune checkpoint blockade and cancer immunotherapy in general. And he gave a lecture here, and I will never forget this. The first sentence in his talk was I transformed cancer care forever and my drug doesn’t even target the cancer. So it’s true. And I just told you how we realized the past 6 or 7 years that maybe our virus really targets myeloid cells more than cancer cells themselves. And in a way, this is the breakthrough to success. So once you stop obsessing about the cancer cells themselves and open yourself up to the bigger picture, I think you are up to something promising. So most people regard cancer as an accumulation of cancerous cells or bad cells that sit in a big lump. That’s very far from the truth. So in many cancers, the cancer I’m mostly interested in glioblastoma is the case, the neoplastic cells. So the malignant cells are actually in the minority. So much of what the tumor is composed of are cells other than malignant cells.

[00:08:43] So you have blood vessel cells, fibroblasts and different things. And the number one cell, at least for glioblastoma and a very important cells for all cancers are myeloid cells. So macrophages mostly, and various shapes of antigen presenting cells that sit in the tumor and the important part is that the tumor cannot live without these non cancerous parts inside it. So it needs a supportive nest of non cancer cells. And these are cells that live in our body and they are being corrupted by the tumor to do its bidding. They’re recruited into the tumor site and they begin under the influence of the cancer to act and the cancer’s interest, if you want, for the most part. And so these cells they often referred to as stroma or tumor microenvironment. So the entirety of the stuff inside a tumor that’s not cancerous. And this is much more in terms of mass or number of cells. This is much more important than the cancerous cells themselves. So it follows that why not target this comfortable nest? These tumors build themselves rather than the cancerous cells themselves. And this has many advantages because the biggest problem in cancer, especially my research targets these horrible killer cancers where nothing works. So these cancers are known to be so heterogeneous, meaning that virtually every cancer cell has its own private genetic code. They have very specific biochemical anomalies. So it’s like a snowflake situation where you have this terrible, heterogeneous population of cancer cells. So in this situation, it’s very difficult to decide what to even target because if every cancer cell is different, how can you know what you should go after? So in that sense, it’s much more simple in a way to think about the non cancerous parts, because these are for the most part, cells that behave pretty normally.

[00:10:47] They’re not malignant, so it’s not an easy target, but they’re more well behaved if you want. So we learned that through our work spanning all these years that the tumor microenvironment really is what our virus targets. Now, PVS-RIPO does infect, malignant cells, too. It can replicate in these malignant cells. It can kill them. And we believe that infection of the cancerous cells and damage of cancerous cells and possibly also killing is part of our strategy. But it’s just one component that contributes to a much bigger series of events. But killing the cancer cells with the virus itself is not the objective of our therapy. So the more important mechanisms that what our virus does and we know this from important animal studies that were recently published and some that are coming out soon hopefully, that it’s the inflammatory wave that is created when the virus infects the non cancerous cells and the tumor. And based on our study, the number one cell by far that’s targeted by the virus are the macrophages inside the tumor, which makes sense because we know from this monkey gastrointestinal work that it is those cells that the virus naturally prefers. So it makes sense that in the tumor it would do the same thing.

Grace Ratley: [00:12:16] Yeah. This concept of activating the immune system in order to generate anticancer effects. I mean, it’s not necessarily a new idea. Observations even back in like the 1800s where people had cancers and they had some sort of infection like influenza infection, where their immune system was stimulated in such a way that it ended up killing the cancers within their bodies. Can you maybe speak a little bit to other forms of immunostimulatory anticancer drugs?

Matthias Gromeier: [00:12:46] Yes. What you’re saying is true. So there have been all kinds of usually anecdotal observations where people had infections, sometimes coincidentally, and this helped them fight off their cancer. Let me draw a very important distinction in the way we approach this phenomenon compared to a lot what you see out there. So that is true. Sometimes my colleagues tell me this is completely anecdotal. This is not a scientific study, but it is an unfortunate complication of brain surgery that sometimes a patient develops a brain abscess. And I’ve heard some of our colleagues tell that such patients do better when they have a brain tumor just because the infection creates some antitumor effect. We don’t want people to have brain abscess, but there’s a lot of these coincidental observations that suggest that having an inflammatory process helps. That’s true. However, attempts to leverage this in a more systematic fashion so to make this a safe kind of intervention that you can give to many patients in a way that it has a therapy effect and a clinical study, that has been very difficult. So while there are these anecdotal observations of inflammatory processes, having anticancer properties, that’s one thing. But turning this into a real drug that performs in a trial has been very difficult and there have been so many attempts in this direction. There are too many to really list. Some of them terrible, some of them really unsafe. And this has never quite really worked.

[00:14:28] What is necessary and this is what we are pursuing because we have made so much progress in immunology that we now know what may be behind these antitumor effects mechanistically, what it is about an infectious process that could turn into an antitumor effect, that we can begin to devise cancer therapies that are both safe and that have more of a reliable antitumor effect in a clinical trial. So the mainstay of cancer immunotherapy, we know this now is something called the CD8 T cells. So these are cytotoxic T lymphocytes. And they are so important in cancer immunotherapy because they are the obvious part of the immune system capable of recognizing, attacking and killing cancer cells. Ultimately, you’re going to have to kill some cancer cells to fight the tumor. And it is the CD8 T cells that can do it. So for our approach with the recombinant poliovirus, we do not think that the poliovirus itself kills off significant amount of cancer cells. It is the immunologic reaction, the CD8 T cell response against the tumor that does this job. So how do you get a CD8 T-cell response against the tumor? How do you make that happen? And here comes the idea of the infectious agent. So our immune system is not primarily an anti cancer system. It is mostly that has to do with evolution. It has mostly an antimicrobial type of machine. So the immune system is really designed and geared to fight viral and bacterial infection and other infectious challenges.

[00:16:11] And the CD8 T cell response, so the very response that we want to have to fight the tumor really is an antiviral function. Because CD8 T cells, their natural job in an immunology sense is to fight viruses that sit inside of cells. So CD8 T cells kill cells that have a virus in them. And typically it’s an RNA virus like poliovirus. And you see where I’m going with this, use a virus that can provide the signals and the stimuli to get CD8 T cells going, to turn that against the cancer. And so in that sense, what started as a primitive idea to infect cancers with God knows what, things are often very unsafe things. Can we maybe have a sophisticated strategy to design infectious agents so we get the good part of the immune response? And so that’s where we are now, I think, in the field. And that’s very much where my research is going. So we are trying to understand when our PVS-RIPO virus infects the macrophages inside a tumor and it generates a very, very substantial inflammatory program, how does this program contribute to making anti-tumor CD8 T cell response? We now know how it can work. We know the mechanism, and we have to figure out how to best get there. So that’s where we are currently. But you’re absolutely right. There’s this long history of infectious agents being lobbed against cancers.

Grace Ratley: [00:17:46] Yeah, but despite this long history of viruses potentially being used against cancers, there was still a lot of pushback to your study for good reasons, but it did slow down the research process for you. Can you speak a little bit to that?

Matthias Gromeier: [00:18:02] Yes. So the long delay, 1994 to 2021, this is mostly because of what you mentioned. And that’s not a bad thing. People sometimes think these regulatory processes are bad because they prevent progress. I don’t see it this way, and I’m probably one of the most regulated scientists around because we inject people with live poliovirus into their brain. Research is so far ahead in the US, partly because we have regulatory agencies that have the knowledge, the experience and they’re equipped to provide regulatory insight. So I know from some of my colleagues who don’t have an FDA in their home countries. They can’t even do the type of research I do because there’s nobody there who can certify that what they’re proposing is safe. So regulation is a very necessary part. Of course it’s challenging. You’re being pushed and the demands are extremely high. And I’ve dealt with this forever. I still do and always will. And it’s just part of what we do. And if we didn’t have this, we would see horrible, unsafe things move to the clinic. And I don’t think there’s a better system than that what we have in the US. So I have a very positive experience working with the FDA. It took a very long time. It was very demanding, but that’s good. We want to be safe. We have to be. And I had very positive interaction with them. It really helped me also to make our strategy better. Yeah, there was a lot of pushback of course. You have to work yourself through the regulatory concerns. So one concern for us was does your virus change when it replicates? And this is something we will always deal with and you have to answer this through science. This is why we carry out research to make sure what we’re doing is safe. And also is it efficacious? This is a very, very big part of my career, my life to answer the regulatory agencies. And I think I found a very good way of working constructively through this. There’s no other option, really. So I’ve seen how productive this can be to engage in these regulatory interactions.

Grace Ratley: [00:20:08] Yeah, but despite all of the hoops you had to jump through, it’s been incredibly successful. PVS-RIPO was in late phase two for clinical trials in glioblastoma and it’s being applied to melanoma as well. To what extent do you think PVS-RIPO could be applied to other cancers?

Matthias Gromeier: [00:20:27] Yeah, the longest program we have going on is in brain tumors is a recurrent glioblastoma. So these are brain tumors that have failed standard of care. Standard of care is surgery. It is a form of chemotherapy and radiation therapy that all patients get when they’re first diagnosed. Unfortunately, this treatment is not effective. So virtually everybody recurs. So the tumor returns, and at that point, patients become eligible for our trial that’s currently ongoing with PVS-RIPO. This is a horrible disease. It’s invariably lethal and it’s very problematic for somebody who’s interested in immunotherapy like myself, because chemotherapy and radiation more or less destroys the type of immune cancer relationships we require for the virus to do its job. So it’s a very, very tough challenge. We have to make progress in this area. So the mission of my life is to get rid of chemotherapy and radiation and replace it with something safer and more efficacious. That’s very difficult to do because you have to design trials that are acceptable to the establishment. So you can’t just stop chemo. So we have to work through this and we are in the process. So glioblastoma, that’s my scientific home, a very big focus for us and we’re very excited about the future there however slow it is. Melanoma is an easier tumor if you’re an immuno therapist because there’s very little use of chemo and radiation in that disease. So in general, dealing with patients who have a better immune status and melanoma is in the skin or close to the skin, there’s metastatic lesions often, but there’s usually tumor you can treat with an intratumoral inoculation where you don’t need surgery to administer your drug. So it’s a little bit easier. They’re not as many safety issues with the tumor growing where melanoma grows.

[00:22:23] We published our first very exciting clinical results just in March, I believe, and there’s a very exciting trial ongoing in multiple hospitals in the US now. We are in the preparation for a trial in bladder cancer that may enroll its first subject this summer, if I’m not mistaken. So these are again, patients who have failed everything else. And it’s a new protocol that I’m very excited about because of how the virus is being used to give patients a shot at immunotherapy where they otherwise wouldn’t have any options. There’s other trials in preparation. We are talking to many physicians who are head and neck carcinoma experts. There is discussions about colorectal cancer and then further down the line, ovarian cancer, hepatocellular cancer and various other diseases. We can’t treat any cancer with this, not blood cancers. So leukemias, that’s not an option as long as there’s a tumor we can inject. And so here you see the attraction. If you don’t target the cancer cells themselves so much, but it’s more about the macrophages and antigen presenting cells. So they sit in every tumor. It doesn’t really matter what kind of cancer this is, because these immunologic processes are the same, at least in principle are the same regardless of the tumor of origin. This is a very lengthy process to find out which cancers can be injected because they have to be physicians that are willing to do this. They don’t do what I say. So there has to be an interest in the clinical community and what we have to offer and you have to design a trial for patients that are suitable subjects for this kind of treatment. That takes some time. But we are very, very aggressively moving forward towards other types of cancers.

Grace Ratley: [00:24:12] Where do you think this technology is is going to go? I know I’ve read mention of it potentially being used as a cancer vaccine. Can you maybe speak a little to that as well?

Matthias Gromeier: [00:24:22] Yeah. So cancer vaccine, that’s a kind of dirty word. So when you say cancer vaccine, typically that means conventionally just like an antiviral vaccine. You pick out a feature in a particular cancer that is an antigen and you make an immune response against that antigen. And this largely has been unsuccessful. And the main reason is this terrible heterogeneity that I already mentioned. So there’s just not a whole lot of antigens that are common to many cancers, let alone to all the cells inside a cancer. So it’s extremely challenging to come up with a vaccine idea. So the way you could describe a virus is what we call an in-situ vaccine. What that means is rather than picking out something, deciding what to target, you throw the virus into the tumor and you let the virus basically reveal whatever is in this particular patient’s tumor with all the heterogeneity. So anything that’s present in a one particular patient gets presented to the immune system as an antigen. So the idea is rather than you picking what should be targeted, it’s the in situ situation that reveals what’s there. So in that sense, you could call this a vaccine, although I don’t like this word because it gets associated with these other failed ideas. Mainly what we need to learn is how to use it properly. And it sounds silly, but you wouldn’t believe how many questions there are. So we are combining the virus with another drug that’s approved for cancer therapy called anti-PD-1. This is a very logical combination for us. So certainly there’s a lot to be learned from that. So the trials that I described that are ongoing are in combination with that drug. There’s a large number of similar drugs we could combine the virus with.

[00:26:20] So we need to figure out which is the ideal combination. Generally in cancer, you don’t see a lot of drugs that are used alone. It’s too hard. So almost everything we do is some kind of combination. We need to figure out dosing. The advice I get from many of my immunologist colleagues is please give repeat treatments because that’s how our immune system works. We call this a boost. That’s how we give vaccines. You get your Covid shot twice. That’s how you stimulate the immune system. So this is something we have to fully learn. There’s all kinds of ideas about where to inject it, what kind of tumor, in what organ and what sequence, how many times. So there’s all these questions to be answered. But ultimately, where we want to be, of course, is that we want to give as many cancer patients that chance of immunotherapy so that they do mount and enter tumors once, I think we can. It is amazing to see, for example, in the melanoma space, basically it’s all immunotherapy or mostly. So cancer therapy has moved on from these horrible cytotoxic regimen to something that I think is a much better choice. And I think that we can reach this for many cancers. That will require a lot of clinical trials, a lot of work, but that’s where we want to be. That’s my mission. So my own mother passed away from gastric cancer a long time ago, and she she got standard of care chemotherapy. And she told me that the chemotherapy was worse than the cancer. It’s just this sticks with you. And if you have an opportunity like I do now, this is where I think I need to invest my energy.

Grace Ratley: [00:28:01] You’d be hard pressed to find a person whose life hasn’t been affected by cancer, whether it is them themselves or a family member or a friend. And it’s really unfortunate that we have so many incredible advances in the biomedical space, and yet we still face this monster of a disease with so few treatments.

Matthias Gromeier: [00:28:22] Yeah, well, these things just take a long time. Whether this is good or bad, I don’t know. It just does. I’ve made peace with this, and I’m glad we came as long as we did. But you have to think in decades. So when you hear these people talk about how they are going to make a big change in the year or two and all these fast track, quick, forget that. That usually doesn’t bode well. So you have to have a long horizon with these things. And this is how you make progress. It is this long, steady learning that gets you to places, not this quick action.

Grace Ratley: [00:29:00] Do you hope to see, I hate to say, a cure for cancer because as you’ve mentioned, cancer is extremely heterogeneous. But do you see it at least dropping off of our top ten killers in the world in our life?

Matthias Gromeier: [00:29:14] Hard to say. It’s more like a chipping away at it at the edges for now. I think it may remain this way, but if you just look at breast cancer. So my experience back in the 80s, it’s completely different now. There’s so many good treatment options and patients live very long times and many times they remain cancer free. And it came gradually, but it did achieve amazing things. This is more how it’s going to happen, this gradual improvement, and it’s never just one thing. So most of these breast cancer things are. It’s not one solution for everyone, but there’s just a lot of options. So whatever problem that’s presented, there is another option available to deal with it. So it’s not one thing, but a whole lot of complementary system. And I think this is what should happen in most cancers just to have a better choice for the physician. So in brain tumors, it’s depressing. It’s almost nothing. And so I think immunotherapy could provide great options there because there are some good openings provided that it’s done correctly. But it’s going to be a slow chipping away at it and improving things. And I think it has been shown for breast cancer and that was a horrible disease and it’s much less so now because of all the options that have become available. So that’s how I see it.

Grace Ratley: [00:30:36] So I want to get into what inspired you to study this virus and what inspired you to go into cancer. So maybe you can tell us a little bit about your path to science.

Matthias Gromeier: [00:30:46] Sure. So I’m German. I was born in Germany, and when I was born, you had to go to the army. You could either do that so train with weapons or you could work in a civil sector. That’s what I did. So for 20 months I worked in a hospital in a big university center for women’s cancer, and I was very young. I was 18. We were very lowly, so low in the hierarchy. So we were abused. I say so for all kinds of really low jobs. So I was an assistant in the O.R. and the anesthesia division there. I had a lot of contact with patients. Most of the patients there were breast cancer patients and ovarian cancer patients. And this was around 1984, 1985, 1986. So it’s a long time ago. And back in those days, cancer care was very different from now. It was very doctor focused, so nobody cared what patients felt or what they thought. They had to do what they were told. The treatment was completely inadequate. It was awful. Breast cancer then was a more or less a death sentence.

[00:31:54] And so my overall experience was I was quite depressed about this because it was this doctor centric world where people use these completely ineffective, very toxic treatments that really didn’t help patients. And there was just this feeling of authority that patients had to swallow this and just deal with it because that’s how it was. So I was really turned off by that. And while I was fascinated with this medical apparatus, I wasn’t really excited about what it meant for the people working there. I finished there. I had very good grades from high school. I didn’t know what I wanted to do. And my father without asking me enrolled me in the equivalent of MCAT in Germany. So I went there. I didn’t want to go to med school. I didn’t prepare for it or anything and I did amazing, probably because I didn’t really want to go. So everybody was very nervous. I was completely relaxed. So I got a really high score and I got into med school and I said, Why not? So I went and I was immediately drawn to research because of my earlier experience of the inadequacy of the medical establishment. I went to med school with the intent to not do what I experienced there. So research was my way out of this. And in Germany, to get an MD degree, you have to do a thesis which is not a PhD type, but more like a master’s, maybe a body of work. And I wanted to work with viruses. I can’t tell you why. They fascinated me. And this was around 1989. So back then it was all HIV. So I was looking for a virus lab that would take me and nobody would from the HIV side. But I found a guy who was a polio guy who said, I’ll take you. And I had absolutely zero interest in polio, but I went because that was the only guy who would take me. And he was a very nice man. And I did an interesting project. That’s how I got to polio. So my advice just go with the flow. And sometimes what you don’t expect works out really amazingly well. So this is not what I had planned, but I immediately caught the interest. I was very, very excited to be in the lab. It just worked out right from the beginning and it was the right thing to do. And after I finished there, then instead of becoming a doctor, I did get an MD degree. I came to United States and embarked on a research career. So I joined the laboratory of a very famous polio researcher, and that’s where I started this cancer work.

Grace Ratley: [00:34:41] And why did you choose the United States?

Matthias Gromeier: [00:34:43] In Germany, you either go to the US, it’s like 90% of the UK, about 10%. Back then I had a fellowship to come to the US that paid for three years of postdoctoral support in the US and then go back to Germany, which I never did. Research is just much better organized, better funded. There’s a better structure here than anywhere else in the world, in my opinion. It’s just you can’t beat this. And especially for the type of work I do, this type of research really is not possible anywhere else, I would say, at least not easily. The FDA actually is a big part of this. The Europeans are trying to copy something similar just to create an infrastructure where you can do clinical trials of innovative approaches better. But for now it’s unmatched in the US.

Grace Ratley: [00:35:36] So you mentioned that you developed this poliovirus while you were working as a postdoc. So what was that like? Why were you making chimeric poliovirus and rhinovirus?

Matthias Gromeier: [00:35:48] For no reason. That had something to do with the structure of this element we were studying. It’s a very complicated RNA element that’s hard to study because you can’t do a whole lot of things to it without destroying it. So we just thought maybe we should flip it out. This was actually somebody else’s project. So I got involved in it because I had an idea of how to clone this. Cloning was more complicated than. It’s a joke now, but back then it was more of an effort. And I had a good idea how to make it. This is actually the virus we’re using now. This is how I got to this. You see, it’s all coincidences and serendipity.

Grace Ratley: [00:36:27] Go with the flow, it is.

Matthias Gromeier: [00:36:30] This is how I teach my students. This idea that you can make a plan and this is not how it works.

Grace Ratley: [00:36:36] So after your post-doc, when did you know that this technology was going to be really important and useful in cancer?

Matthias Gromeier: [00:36:44] About two years ago. It takes a long time, because what we’re doing is so different from anything else. I know there’s other viruses studying being studied for cancer immunotherapy. Ours is very different from the others. And there comes this moment when you really know. We had some hopeful signs when we began our first clinical trial in brain tumor patients. There were some very hopeful signs, but we just didn’t have enough mechanistic information about the immune effects of what we were doing. Our research hadn’t caught up yet, but now I know. So I’d say in the last few years we really got the certainty that we’re on the right track. We are nowhere near to where we need to be with cancer, you never are. That’s not one of these things you can finish. It’s a constant challenge, but it took an extremely long time. And this is healthy. You never want to be too sure of yourself because that leads to dangerous developments. It’s good to have doubts. And of course, we had that. Research just takes time. And then there’s these events that are outside your control what I just told you about these studies going on elsewhere. There was a lot of work in the immunotherapy field with which we couldn’t have done what we are doing now. So it’s never one person charting the course. It’s a very complicated story where a lot of different influences flow together to make something happen. And I think we’re on the more exciting edge of that. But it took a long time to get there.

Grace Ratley: [00:38:20] I would say very exciting, definitely. So your work has been used in the biotechnology space, a company called Istari. So why did you end up staying in academia to continue this research?

Matthias Gromeier: [00:38:33] Yeah. So full disclosure, I’m a co-founder of Istari. I own equity in them. I’m a paid consultant to them. So in the type of work I do and the very first clinical trials we put up where what we call academic clinical trials, and that’s very difficult to put up because clinical trials are expensive. They are very involved. There’s a lot of red tape. Moving forward, these trials that are currently ongoing, it would be impossible to make this happen through an academic setting. So this has to be done in the commercial space because they have completely different resources and means to do this. So this is the natural way it happens. PVS-RIPO is still in a developmental phase, so we still are learning a tremendous amount of information about its mechanisms. So my objective is to make it a success for patients. That’s why I work on it. I want to make sure it can reach the most patients in the best way possible. And right now, the best way to make sure is for me to continue my basic research. Of course, I absolutely want these trials to succeed. And I’ll do anything to make this happen in the interest of everybody involved, especially the patients. But you have to decide for yourself where your best places and where you most need it because it has so many activities, infects cancer cells. It infects antigen presenting cells. It does really interesting things in them in terms of inflammation, the way it engages T cells. This is what makes it attractive. But this is also makes it very complicated from a research perspective. So as long as we must learn about its mechanism, then there is a need to maintain a basic research effort on it.

Grace Ratley: [00:40:23] So to aspiring scientists or people who are interested in going into oncology or virology, what advice would you give to these people as they go about their journey?

Matthias Gromeier: [00:40:35] From my own experience, be open to the unforeseen. Don’t be too strict with your plan. Have a little bit more creativity and freedom about your career. You never know where something really interesting may come from. What is very important and something like not just cancer, but in these big challenges like Alzheimer’s. And there was so much discussion about this controversial drug being approved. A career doesn’t mean to get other people to agree with you or to please the leadership or the establishment. You have to challenge existing paradigms and move to the unknown territory. That’s very risky. I can’t tell you how many times I got very close to complete elimination of my career, but that’s part of the story. You can’t change paradigms without risk. Somebody has to take this risk. There was the biggest fun in hindsight. It wasn’t so much fun going through it, but in hindsight just to challenge existing norms and existing lazy thought. So that’s what I’m trying to do and I think we need more of that. That’s what being a scientist means. It means not being satisfied with the status quo. That would be my advice.

Grace Ratley: [00:41:53] Well, thank you so much Matthias for coming on. You were really an inspiring scientist and it’s been a pleasure to talk to you about your career in the science.

Matthias Gromeier: [00:41:59] Thank you for having me.

Transcript of Episode 29: Carolyn Coyne

Disclaimer: Transcripts may contain errors.

Grace Ratley: [00:00:00] Welcome to The Bioinformatics CRO Podcast. My name is Grace Ratley. I’m the editor and occasional host of The Bioinformatics CRO Podcast. And today I’m joined by Carolyn Coyne. Carolyn just recently joined the faculty of Duke University as Professor of Molecular Genetics and Microbiology in April of this past year. Previously, her lab was located at the University of Pittsburgh and her lab studies cellular barriers to pathogens in the gut and the placenta. Welcome, Carolyn.

Carolyn Coyne: [00:00:27] Thank you for having me Grace.

Grace Ratley: [00:00:28] Yeah. So tell us a little bit about the research that you’re doing in your lab.

Carolyn Coyne: [00:00:33] Sure. I always like to describe our research as barriers, as you mentioned and this dates back to interests I had even as a graduate student. I really always have been fascinated by this idea of how at least initially viruses cross what I refer to as cellular barriers. And so what these are, the cells in our body that are supposed to keep us from being infected or exposed to pollutants and things like that. And so when you think about those things, of course, probably nowadays the first one that comes to mind is the airway, is the respiratory epithelium. And that’s actually how I started a lot of my earlier studies. I was kind of initially trying to understand the airway as a barrier to respiratory pathogens, let’s say. So again, in the midst of a pandemic, of course this is now very timely. At that time, I certainly never thought that we would be living under the current situation. And so my interest in the airway then kind of started to broaden. So I did work in the airway as a graduate student. And at that time, we were actually thinking about things like gene therapy, like how would you deliver actually a virus to the respiratory epithelium as a therapeutic approach.

[00:01:37] But again, the kind of topics or things that we were thinking about were very similar to this concept of why can’t then a therapeutic virus cross the epithelium? How does that barrier work? And then the counter of that is then how do viruses that naturally make us sick through the respiratory epithelium, influenza virus, now coronaviruses that we know very well, how does that happen? And then we really started to broaden our interest from there as I got through a little bit more training. So as a postdoctoral fellow, I actually went to the Children’s Hospital of Philadelphia and I worked on enteric viruses. And so these are viruses that naturally, of course cross the gut, another important barrier that exists to keep things out. And these are again natural viruses that are very common. They’re one of the most common viruses that infect humans. And so what that tells someone like me who is interested in barriers is that these viruses are really smart and they’re really good at bypassing barriers. And so the work we continue to do in the lab is really centered at least on that part of the lab on the gut as a barrier, understanding how the barrier forms, modeling the barrier. And then secondary to that, how do viruses that naturally cross that barrier figure out a way to do that? And so then, maybe it’s not surprising that that the other half of my lab studies the placenta, which is also a really important barrier.

[00:02:54] But just an interesting point, and I’ve probably told this this story too many times now, but it really wasn’t until I was pregnant with my son that this idea of a placental barrier dawned on me. I’d studied barriers a long time. You’d think I would have thought of the placenta. But as most people do, we overlook that as a barrier. And so I became pregnant with my son, who just turned 12. So it was a long time ago now. And that was when I literally had a light bulb moment where I thought, Ah, the placenta is a barrier. And so now my lab also studies the placenta. And from that side of the lab again, the topic is still the same, which is how does the placenta actually protect the fetus from most infections? And we know that it does a very, very good job of that. If it didn’t, we wouldn’t be able to populate the world to the levels that we have. And so we know the placenta is a good barrier.

[00:03:38] And then again, our secondary questions are how do then pathogens and on that side of the lab, we’re not just virus focused. We study parasites, we study bacteria. And what we study is actually a family of viruses that are called TORCH pathogens. And these designate microorganisms that are known to be what’s called teratogenic, so damaging to the fetus if they’re infected in utero. And the TORCH acronym stands for Toxoplasma gondii, which is a parasite other, which is sort of a dumping ground for many things bacteria, viruses and of course, rubella, cytomegalovirus and herpes viruses. And so on that side of the lab, we then try to understand how does this kind of class of very diverse, unrelated microorganisms bypass this placental barrier, which I think the overarching goal then is to then think a little bit more therapeutically, which we don’t really do per se in the lab. But you could imagine that the more we know and understand about that process, the more you can target that process to stop it from happening. And so that really is, I would say, the central kind of themes of the lab. But beyond the gut and the placenta, we’re usually interested in pretty much all barriers we can get our hands on. But those are the two main ones that we study.

Grace Ratley: [00:04:46] That is so fascinating. I am very much interested in the gut barrier, but I know that your lab is focused more on the placenta.

Carolyn Coyne: [00:04:54] Folks sometimes forget that we also work on the gut, which is, you know, actually by a per person basis in the lab, sometimes more skewed on the gut side than the placenta side at any time. So we’re usually pretty evenly split down the middle. I think our placenta work is certainly unique in the sense that it’s a very, I would say, small field overall particularly when you think about like microorganisms and doing the more infectious diseases aspect of the placenta.

Grace Ratley: [00:05:19] So what do you think are some of the biggest unanswered questions in your field?

Carolyn Coyne: [00:05:26] Oh, well, I think on both sides, there are many I would say. The placental kind of side is easier in the sense that it’s a barrier and a tissue and organ that is really difficult to study. And so inherent to that then is a lot of limitations just on what you can do, what kind of questions you can ask, and so certainly from the standpoint of infectious diseases, there are a lot of unanswered questions. Some are very basic. How and why is the placenta such a good barrier? How did it evolve to be such a good barrier? What’s interesting about that tissue and the cells that comprise that tissue is that they’ve almost co-opted the strengths of things like epithelial cells and more immune cells to become the barrier. And so how and why has that happened? Just basic questions. And then certainly I’d say what we focus on more are the questions just related to, we know it’s a great barrier. I mean, I hate to focus on the pandemic too much, but what we’ve learned from this, of course, it’s a very large human biology study.

[00:06:25] What we’ve learned from this is that pregnant women can be infected with Corona SARS-2, and they can develop COVID-19 and they can certainly go on to have complications of pregnancy. But there’s actually all of the data would suggest that that the virus is not transmitted in utero to the fetus. And so, again, what that tells us is that the placenta is acting as a very, very good barrier. And so then I’d say the number one question that drives most of what we do is how then does the placenta form a barrier to something like a coronavirus or influenza virus, but not form a barrier to something like Zika virus. And so I think dissecting that is probably, at least in my own very biased mind, the biggest question we have. Figuring out how and why it’s a barrier to virus or pathogen A and not a pathogen or virus B. So that’s kind of the biggest question I would say on that side.

Grace Ratley: [00:07:14] And do you have any ideas of how that might happen or is it?

Carolyn Coyne: [00:07:18] Well, I think we certainly have experimental data that are based on human things that we can do ex vivo in the lab, taking cells or tissue, obviously animal work that has been done by others. What’s very clear is that as good of a barrier as the placenta is, barriers are not without breaches. And that’s just the nature of what barriers are. And that happens in, of course in the lung and in the gut and all different barriers. And so it could be as simple as there are breaches in the barrier that occur. And unfortunately, at that very time, there’s a circulating viral particle that figures out, makes it seem like the virus is trying when in actuality it’s very passive participant in this process. But nonetheless that a virus would cross. And maybe the difference then is that it’s not so much then the difference between crossing the barrier is that it’s the end point that’s different. So for example, we know that Zika virus, for example really targets the neuronal progenitor cells in the developing fetal brain.

[00:08:18] So these are the cells in a developing, especially first trimester human fetus that is forming our brain. We know that Zika will target those cells. We know that Zika will replicate in those cells and we know that Zika will damage those cells, whereas other viruses then may not have that ability. And so it’s a little bit of, I hate to use this analogy, but it is a little bit of a chicken or an egg type thing. And that we don’t really know that because let’s say coronaviruses are not inducing fetal disease, that they don’t actually reach the fetus, but maybe they just don’t damage the fetus. So it depends on your end points. So I think the questions are, are they targeting different cells that allow them to bypass, which is one I would say hypothesis or is that what’s really different is their end points being that one virus, for example can induce disease and the other one can’t. And if that is your end point, then you would never know that both of them crossed, if that makes sense.

Grace Ratley: [00:09:10] Yeah, that makes sense. So it must be pretty difficult to study the placenta. I know that it’s kind of a hyper politicized kind of field.

Carolyn Coyne: [00:09:21] It is.

Grace Ratley: [00:09:22] Especially with getting samples. And I know that you wrote a really wonderful article in the Washington Post a couple of years ago when the Trump administration instituted a policy that heavily restricted the use of human fetal tissues in research. Can you talk a little bit about how that affected your research?

Carolyn Coyne: [00:09:39] Yeah. I think that whole process, looking back on my career now, certainly that was one of the most I would say stressful points of my career in a way that honestly I think it shows what a either a vacuum or different kind of land we lived in and that I really never again when I started working in this in this field. And I think for most people this is true. You don’t really think about that. And part of it is it just seems so natural that, oh, of course we can do our research. And so when that happened, which I will say once the election had happened and there was a shift in leadership in the White House, I knew that there would be changes. I mean, I think all of us that worked in this realm in terms of using fetal tissue knew that there were going to be policy changes. I mean, that was not at all a surprise to me. The only thing honestly that surprised me is that it didn’t happen earlier. I remember coming into the lab the day after the election and saying, we need to think about other model because this is going to change and it’s going to change soon.

[00:10:40] And so I think the effects of that are much more broad and really devastating than I would say most people recognize, even folks that don’t work in this domain. And so in my view, there are kind of different levels of the ramifications. And I would say ripple effect of these policy changes. One of course was just scientific. One was that we were all somewhat paralyzed in having to pivot and think about ways that we could ask our questions. And again, staying true to the biology. We do this not because we want to model it the best way possible because we think it’s more true to the biology. And so we’re driven, of course by the scientific question. And so if this tissue allows us to ask those questions in the best way, in the most rigorous way, that of course is the driving force for using the tissue. And it really is true. And with the placenta and in pregnancy is that the placenta is a very unique organ compared to anything else probably in the human body in that it really changes very dramatically across gestation. And so a full term post-delivery placenta is quite different than an earlier gestation placenta.

[00:11:48] And so it really does become, especially when thinking in the context of infectious diseases to model throughout pregnancy. And so one of I would say the ramifications and after effects was just on science. So basically all of us being somewhat paralyzed in obtaining tissue, of course, being funded to do tissue. But in some ways as stressful as that was, and let me tell you, it was, we were affected in a number of ways. What I personally think is probably the more upsetting or most upsetting aftereffect of this is the impact it has on an entire generation of scientists. And I mean younger scientists, scientists that haven’t entered this field. The field of maternal fetal medicine, the field of pregnancy in general is already I would say a field that is understudied, certainly underfunded through the the NIH at least. And I think that for me at least the most devastating effect is that I think what’s happened then is you have a whole generation of younger scientists who are in training, maybe haven’t started their training, and they’re looking at entering this field and they’re saying to themselves, and who could blame them? Why would I want to enter in this field when this is such a highly politicized thing, when there have been so many horrible devastating things that have happened even to the scientists that work in this realm? Why would I do that? I don’t want to subject myself to that.

[00:13:06] And so what I’m going to do is work in a different field. And so I think for me, that is the most upsetting aspect of it. There’s of course the personal somewhat more self-centered view of it, which is the impact of my own research. But really that although it was an acute, very stressful situation, what I find the absolutely most upsetting aspect of it is that this is going to then affect an entire generation. I think this will live in the minds of people for a long time. I think we are going to see people not wanting to work in this domain. I mean, certainly in the United States. I’m really focusing much more in the US because they’re nervous. And again, who could blame them. If I were a postdoc picking a lab to go to thinking about I want to go into an academic career that requires me to be funded or mostly requires me to be funded through the NIH, would I want to go to into a field, into a lab that may work in this domain and may make my life very complicated?

[00:14:02] And the answer to that is probably no in many cases. And again, naturally. So I don’t blame those people. I think that was really the most devastating aspect. I think we will feel that for a very long time to come. I think it holds back science in the United States. I think it holds back the field of maternal fetal medicine, I mean which is again already an area that I think is not focused on enough, not funded enough. And so I think at the time this happened, I felt like it didn’t get as much attention as I think it should have. Because I think people were focused a little bit more on the stories of how this was going to impact our science, which again is very important. And I feel like what was left on the cutting room floor so to speak was more of the impact on this on trainees. And then also the impact of this on just the field in general, which just as a human let alone a woman, I find that to be really upsetting.

Grace Ratley: [00:14:56] How can we change the public perspective on this, to let them know that it’s important work?

Carolyn Coyne: [00:15:03] Unfortunately, I think it’s almost impossible. And I hate to say that, usually I like to be an optimist. But the problem is this is that the narrative has been so politicized in that it is become, at least from my view again very biased view, very difficult to disentangle the more political, pro-life, pro-choice movement kind of just differences in opinion. Untangling that from the idea of using fetal tissue for research is something that, at least from my perspective that I’ve seen is very difficult to do. And so, unfortunately while I think the folks that are very much anti use of human fetal tissue in research and I hate to generalize. And so I mean it probably doesn’t apply to everyone, but at least certainly from what I’ve seen, I think that often this goes back to just abortion period. And I think there’s this, I would say incorrect notion that somehow the use of human fetal tissue in research promotes abortion, that a woman going in to get an abortion would somehow, and again I think that does a huge disservice to those women, a huge disservice. And I find it actually rather offensive, but anyway. And so I think it’s really difficult because at least the narrative that I’ve seen is often people saying who are very much opposed to the use of fetal tissue, the narrative that is most commonly I would say, kind of brought up is well, what are the cures that have happened using fetal tissue? And when your bar is curing something that would then relegate all science to being unimportant if you use that as the bar.

[00:16:36] But nonetheless, that’s the bar that’s set. And so if that’s the bar, it’s almost impossible to show. I mean of course, because often within the comeback of the opposing party would say, well back in the day, the polio virus vaccine, they were using human embryonic kidney cells again from a from a fetus, from an elective termination. So clearly, that led to the ability to to make the vaccine, which is fact. That is truth. But again, that’s still not enough. That doesn’t, for them, meet the bar. And so I think that for me is the disappointing thing about this, is that unfortunately, I think the political parties in this country on both sides have certainly then made this into a political issue. And I think until it is not a political issue, it’s going to be impossible to convince people, it’s justified. Unfortunately, I think that’s just the nature of what’s happened.

Grace Ratley: [00:17:25] So what are some of the workarounds to that? Can you use things like stem cells?

Carolyn Coyne: [00:17:32] It’s a great question. I think it’s something that we’ve really as a lab focused on, I would say the most in the last few years, which was brought on. And so maybe trying to look on the bright sides, the silver lining of this was that it did make us decide what are we going to then focus on? And so about, I think just two years ago now, there was a really phenomenal outstanding paper from a group in the UK in Cambridge making organoids from stem cells that they at least isolated from first trimester placentas, where there’s a lot more stem cells. And you can imagine that this is when the placenta is really developing so what we decided to do is, well, we obviously can’t access first trimester tissue for a variety of reasons that what we will then do is really focus on trying to make these organoids from stem cells that we isolate later in gestation from either natural preterm deliveries, which I suppose that’s never natural. But certainly preterm delivery is not elective terminations that occur, let’s say in the second trimester all the way to term. And that’s really what we’ve been able to do. And again, there are pros and cons to any model in science. I think that’s certainly something that I preach often. And so there are pros and cons to that model. But the huge pro in my mind is that we can isolate these organoids and they essentially you can propagate them so they can be expanded, you can split them, you can freeze them.

[00:18:45] And so what we’re really hoping to do in the next few years is to have a very large what I would say, biobank in our freezer essentially of stem cells that we’ve obtained or organoids rather, that we’ve obtained from a bunch of different placentas that we can really then use to model this. And for us, that’s probably the system that we’re going to be focusing on in the nearest term. And really what we’re trying to do now then is to just establish that model because it’s a little different, of course than the previous model using first trimester tissue validated. And then compare it to what we’ve seen from things like the tissue that we used to use from elective terminations. And again if we see things that are very similar, then we know that that’s a model that can recapitulate at least some of that. So that’s really, I think what we’ve focused on. We tend to focus very much on human models, and that’s simply because the placenta is so different amongst different organisms. So that’s really, I’d say the only I hate to say anything positive came from that. But truly for us, at least personally the positive thing was that we really worked very, very hard to focus on that. And so far I’ve been successful.

Grace Ratley: [00:19:48] I’m glad to hear that there are some workarounds because I do think this field is very important. Well, let’s go ahead and transition then into a little bit about you as a scientist. Tell us a little bit about your path to science. I know you weren’t always super interested in science growing up.

Carolyn Coyne: [00:20:06] The thing I always say is, I was never someone that thought I would go into science again. I don’t know how or why I did, but nonetheless, I’m here. And so the journey for me was a really, I would say slow one. And I’m not sure that there was ever a moment where the light bulb switch was flipped, so to speak. So I went to undergraduate. I was an undergraduate at Florida State because I’m a Floridian. And really at that time I was convinced I was going to go to law school. And that’s always what I said. Through high school, we would have debates and things. I just for some reason always was drawn to that. I’m so thankful now I didn’t do it. But at the time, and so my path was not a straight one. So I started majoring in things like psychology and criminology, and I’m going to be a prosecutor. I mean, all of these things that I just had built in my head. And the transition for me started when I was probably a sophomore maybe in college. I was a psychology major at that point. I decided that I was interested in neuropsychology. And so that is basically the real more scientific study of the brain and how that then influences psychological outputs. And so what that required me to do was to start taking some science classes.

[00:21:13] And so this is when I enrolled and I think biology, biochemistry. And to be honest, I was not a fan of the biological sciences at that point. I was a biochemistry then major. So then I switched my major to biochemistry. And it’s crazy, at least for most people. But you know what I really fell in love with was organic chemistry and analytical chemistry. And it was organic that I found. I just loved organic chemistry, the solving and figuring out I mean, I just I remember just loving that and taking that class was really when I said, okay, I’m going to switch to being a chemistry major. And then I was a biochemistry major. But even if you look at my grades from an undergraduate, I did much better in chemistry than I ever did in the biological. And so that was when the transition started. But even then, I don’t know that I had a game plan. I just was knew that I was interested. And then the other I would say life experience that influenced me was that I had a pretty near full time job as an undergraduate. I worked at Target and I started in the checkout lanes of Target. And then I started working as a pharmacy tech. And so for about, I don’t know, 2 or 3 years of my undergraduate, I worked as a pharmacy tech at Target.

[00:22:23] And I would work maybe 30 to 40 hours a week. And I spent a lot of time talking to the pharmacist and what I found myself drawn to. And so by this point, I was a biochemistry major. I started to be a little bit more science leaning or science interested. I again at that time thought I was going to get a PhD in organic chemistry or medicinal chemistry and these kinds of things. And I would talk to the pharmacist and what we would talk about was the drugs and how the drugs worked. And I would want to know if I’m giving this person this drug, what is this? How does it work? What’s the pathway? And that was when I think it was around the time I was probably nearing maybe my senior year. And then I got interested in pharmacology, pharmaceutical sciences. And again, it was more and I knew I didn’t want to go to pharmacy school after that experience, but that was ultimately what led me to look for a PhD in pharmacology was that I liked this idea of at least at the time, what I thought was getting a PhD in how drugs worked. And then in those days, which maybe dates me a little bit, there were less of these umbrella graduate programs where you could go in and then pick a track. Back then, you really applied more specifically.

[00:23:26] And so I went to get a PhD in pharmacology, and that was when my PhD project then was in the airway, more gene therapy. And then that of course led to everything subsequent to that. I think the other thing to note just in this kind of conversation is and I always tell this to trainees that I talk about the other thing about me that I don’t know if it’s unique or maybe just weird is that as a postdoc, I was also never the postdoc that wanted an academic job. Even now I always say that there are many things about science I really enjoy. Some of this is even science communication. Like these sorts of things I actually find really important. And so I’ve always had the kind of mindset that as much as I like academic science and I do, I love bench work. I mean, I still work at the bench. I don’t ever want to leave the bench. I think there are many other fun things that I could do. And so I think when I was a postdoc, the opportunity presented itself and I took it. But I was also never a postdoc or certainly a PhD student that had a clear, I want to be faculty, I want to work in an academic medical center. It really was probably the opposite of that. But there are many things about the job that obviously drew me to it.

Grace Ratley: [00:24:27] It definitely is interesting hearing your path to science going from law to.

Carolyn Coyne: [00:24:32] Great pivot.

Grace Ratley: [00:24:33] Yeah, a great pivot. So did you have any mentors who really influenced your path to where you are now?

Carolyn Coyne: [00:24:41] In various ways, Yes. I don’t think I ever had a faculty mentor that was my guiding light, so to speak. Like I’ll see this on social media and I didn’t have that. It’s not to say I didn’t have great mentors. That’s not at all meant to be disparaging, but I don’t think they were the ones that were guiding my career path. What I found to be 100% the most valuable thing that I’ve done, which again I’ve done not because I had any intention of doing it. Things just kind of wind up working out, it was finding almost more of like peer mentoring. And I have one very, very close friend of mine. Her name is Sarah Cherry. She’s at the University of Pennsylvania. And she’s my closest friend and she’s like a sister. And I met her when I was towards the last year or two of my postdoc. And she had come to Penn as a new faculty member. And she and I just became very close friends. And so if anyone helped me guide towards an academic position, even helped me now. We talk all the time now. It was really probably her as much as anyone. And then of course, there were others who played a role. But for me, developing a network of peer mentors who are usually your friends as well, I think is so valuable. I know people say this, but you know what? At least I’ve found the most valuable is I very much appreciate direct, honest advice even if the advice may not be what I want to hear.

[00:26:02] And so I think I’ve always gravitated to people who are just honest and direct. That’s probably been just even still to this day what influences me most from a mentoring perspective. And then there are other senior people over the years that have influenced me. I will say many of them tend to be women. When I was at the University of Pittsburgh, JoAnne Flynn is there and she’s a bacteriologist and an immunologist and she’s just phenomenal and she’s everything you want to be as a young faculty member. She was also someone I looked to as advice when I was starting. And so for me, I think I’ve had just a couple of people and sometimes they don’t even know that I view them so much as like my mentors. Like so for JoAnne, for example, I’ve known her for a long time. But she may not even have known what an influence she had on me. And that’s also something I try to remember for myself and that I even tell junior faculty is that even if we don’t know it, we’re influencing positive or negative a lot of people. And so you kind of have to always act accordingly, if that makes sense. Yeah, I’ve had various mentors in different ways, but maybe not the classic mentors.

Grace Ratley: [00:27:03] Yeah, In my personal opinion, I’ve found it a lot easier to connect with people who are closer to me and more peer mentors because faculty tend to be very busy.

Carolyn Coyne: [00:27:14] Now, of course. And the challenges are each generation of scientists, I feel especially in academic science, I mean in science in general, but certainly academic has a completely different life experience. And those are based upon things like funding paylines, things like fetal tissue. I mean, all of us have a different perspective and or influence. And so even if I talk to someone who’s more senior or more junior for me, we’re having completely different experiences just based upon the way life works.

Grace Ratley: [00:27:40] Right. Yeah. What brought you from the University of Pittsburgh over to Duke?

Carolyn Coyne: [00:27:46] Yeah. I had been at Pitt very comfortably and quite happily, really for about 14 years. I think it’s natural over the years when you’re at an institution for a long time to think about other options. And there had been other options that had presented themselves. And so it’s one of these things that I think happens commonly where you’re approached or you talk to people, but it’s just not enough to push it over the edge. What I’d always said to my husband is that for me to move which requires of course uprooting not just the lab, not just professional life, but as much if not more importantly so personal life that I would have to be able to look him in the eye very honestly and tell him it was going to be transformative, which is again a very high bar. And I could really never do that before. So even if other opportunities presented themselves, I would come home and I would say, Oh, this is great. It’s certainly a great place. There are great people. But is it going to be transformative? No. And that was always my bar. That’s a really go through this process, which is a very painful process in many different ways. I would have to know that.

[00:28:50] And so the path started somewhat innocently. I was at a conference at the NIH and I was sitting next to someone named Bart Haynes, who’s the head of the Duke Human Vaccine Institute, right across the way from me now, having coffee kind of in the morning. And he mentioned he was at Duke. I obviously was a UNCW student and said, Oh, I really love the area. And he mentioned, Oh, why don’t you come and check out Duke? And again, I entered in very innocently, and I remember even after that first visit, coming home and saying to my husband, like, I think this could really be transformative. And so why is that? So what was so special? Part of it is just the infrastructure, things that that when I was a junior faculty, you were looking for a position to be junior faculty. You think about cores, but you don’t really think about the nitty gritty of cores. You don’t think about things like administration administrators, things that really impact you more on an everyday basis. And so for me, I came and recognized that there are really I mean truly outstanding scientists here and that the scientists are right across the walkway. I mean, literally I’m looking over at DHVI right now. One of the best, I would say vaccine centers in the world, certainly in the country if not the world. And so being in such close proximity to really phenomenal scientists and researchers.

[00:30:01] And so I was very fortunate that I’m now in the MGM department here, which is molecular genetics and microbiology, and there are outstanding people here. I think you’ve interviewed Bryan Cullen, Micah Luftig. Stacy Horner is here and Nick Keaton, The list could go on. Really phenomenal people. And I just thought, wow, this is really going to elevate our research. The analogy I use is that I used to play tennis in high school and I wasn’t a great tennis player, but nonetheless I played tennis. I was in Florida. It’s what you did. And when I practiced, you always wanted to practice against people that were as good of you, even better if they’re better than you, because it elevates your game. It makes you better. And so I felt like I was going to have a lot of really solid opponents here. That would really kind of challenge us and elevate us. And again, it’s not to say that the University of Pittsburgh didn’t have that because they certainly did. But when you play with the same opponents for 14 years, you need some new opponents. And so that was really I think the motivation. I was just really feeling like it was going to elevate and transform our science.

Grace Ratley: [00:30:57] Yeah, that’s an excellent analogy. And was it difficult to move during a pandemic?

Carolyn Coyne: [00:31:05] I’ve talked to a lot of people about this. I think it’s always hard to move the disentangling, especially after 14 years, is not an easy one. There were certainly challenges that I do think were pandemic specific. Probably the biggest one we’re struggling with is just equipment. Everything is backordered. It takes a very long time to get things. I think that is probably unique in the pandemic. I think moves are always hard. I think to move, you have to really think it’s transformative because it is a hard process and it’s a very stressful process. Again that is the probably most stressful thing I’ve ever done, different ways than the fetal tissue issues. But that’s probably the biggest thing that’s pandemic specific. So we just moved, what two months ago in the beginning of April. And that is, I will say, when things were starting, nothing is normal of course. But things were starting to get a little bit more normal in terms of vaccination. All of us were vaccinated by then. I think most of the people here at Duke had been vaccinated. So in some ways, at least things I think got a little bit less intense than in the real lockdown with like you couldn’t leave your house. But yeah, I think the biggest challenge has just been stocking the lab with equipment, replacing equipment that we left behind. And just the time it takes to get that. We’re certainly hiring. When you move, the sad thing is leaving behind people that unfortunately can’t move with you. And that happened. And so absolutely, very much looking forward to recruiting new people, postdocs, graduate students. I’ve always liked having trainees in the lab. I’ve always been really fortunate also to have a lot of graduate students in the lab. And so certainly coming into the program here, I’m excited to kind of meet the students, have students come to the lab. So planning and in the process of hiring. So if you’re interested in barriers, check us out.

Grace Ratley: [00:32:40] All right. And I’ll just ask one more question before we wrap up. For trainees or for people interested in science or going into science, what is one piece of advice that you would give to people interested?

Carolyn Coyne: [00:32:52] I really try. I used to have a little and I actually gave it to someone else to help them through a hard time, a little kind of plaque I would put on my desk that said, Just keep swimming, the Dory quote from Finding Nemo. And when I was going through a lot of this fetal tissue stuff, truly it became a focal point for me on days that were really tough. And I would just look over to that and I would remind myself. Just keep going. Just keep going. And so that’s advice in the sense that it’s wrapped in, I’d say really what is my number one advice, which is I think sometimes scientists have a tendency to take this a little too seriously. I think especially in academic science, I think this is a great job. I think there are many pros, there are certainly cons, but there are many pros. But some of it is that I think we have to really realize that we shouldn’t take it that seriously. That this is a great job. I think for trainees this is probably more tailored towards trainees is that there are many things to do in science that are important and fun and make an impact. And whether that’s at the bench or not at the bench is totally fine. And so I think part of it is to the advice I guess is just not to take it too seriously. And what I mean by that is to just not feel like there’s only one path to success in science. There are many. And then when, not if, when you reach the hard times in that path. Because there are always hard times in any path, but is to just keep swimming. I feel like that was my mantra. It’s something even though I gifted my little plaque to a friend of mine who was kind of struggling and I said to her, look at it every day. I did. I think that’s probably my maybe top advice.

Grace Ratley: [00:34:24] Well, thank you so much for coming on, Carolyn. It was so wonderful to hear your perspective and to hear about your science. I really appreciate it.

Carolyn Coyne: [00:34:32] Thank you for having me.

Transcript of Episode 28: Bryan Cullen

Disclaimer: Transcripts may contain errors.

Grace Ratley: [00:00:00] Welcome to The Bioinformatics CRO Podcast. My name is Grace Ratley. I am the editor of the podcast and your host for today’s show. Today I’m joined by Professor Bryan Cullen, who is the James B. Duke Professor of molecular genetics and microbiology at Duke University Medical Center and the founding director of the Duke University Center for Virology. Welcome, Bryan.

Bryan Cullen: [00:00:21] Nice to be here.

Grace Ratley: [00:00:22] Perhaps we can start with talking a little bit about your research on viral epitranscriptomics and epigenomics, for which you recently published a review article. So can you explain maybe the difference between epitranscriptomics and epigenomics?

Bryan Cullen: [00:00:35] Epigenetics has been around for some time so that as you will understand, genetics is the process by which different genes are passed down from parent to a child, and the differences in the sequences can have ramifications such as hair color or skin color or eye color, or how tall you are or how fat you get those kinds of things. Now it became clear some time ago that things are inherited that are actually not in the DNA, and the word that was coined was epigenetics. And it turns out that there are modifications to the DNA or modifications more generally to chromatin, which is the DNA with histones wrapped around it, which can also be inherited. The biggest things that arise in epigenetics are changes of the methylation status for example of histone molecules, so that there are certain residues on histones that if they’re methylated, it silences the gene that’s underlying the histones and certain methylations which occur on the same histone that actually activate the gene underlying the histones on the chromatin and those can be inherited. And then there are also most important modification of DNA in this regard is the methylation of C residues in the context of the dinucleotide CPG, and that can be inherited across time. Obviously CG is GC. It seem to be on the opposite strand as well, and there is a mechanism in cells so that if one C is methylated and the DNA is replicated, then the C that comes in opposite it is also going to be methylated.

[00:02:05] And that’s a way of silencing genes long term. If you sequence the DNA, you don’t see it. You don’t see these changes in the histones. You don’t see these changes at the C residues. And nevertheless, they can have major ramifications and can be inherited from cell to cell during cell division, but also from parent to child. And there are some evidence that they can even be learned, which gets back to this idea that people can actually change their genetics during their lifetime and hand them on to their children. That has been reported for lower organisms at least. So that’s epigenetics. Epitranscriptomics is the same thing for RNA. So there are methylations of A residues, methylations of C residues, acetylations of C residues that are put on by different enzymes in the cell, and they can strongly affect the fate of the RNA after the modification has been added. So that methylation of C residues, as we showed recently increases their translation methylation of adenosine residues increases RNA stability in some settings and decreases it in others. It’s actually not understood why that would be. But regardless, these are then again changes that you can’t see in the sequence of the RNA that nevertheless affect the functionality of that RNA.

Grace Ratley: [00:03:16] And how do viruses use these two different methods to regulate their own biology?

Bryan Cullen: [00:03:22] Yeah, well, that’s complicated. So let’s talk about epigenetics first. So epigenetics can either activate expression or silence expression. And what we actually see is that cells have evolved the ability to use epigenetics to silence incoming DNA viruses. Now, viruses aren’t going to let that happen, of course. And so they’ve developed ways to either prevent the silencing or they take advantage of the silencing in order to enter a latent state from which they can reactivate at a later point. And so if they’re latent, which is to say they’re not producing any proteins, then they’re invisible to the immune system. And so they can actually subvert what really is a defense mechanism on the part of the cell to actually then remain invisible and remain able to reactivate a lytic replication cycle. Nevertheless, there are some settings in which this silencing works very well and does silence viruses. The example that we and others in particular Steve Gough at Columbia have worked on is with retroviruses, which are a kind of virus, which is an RNA virus that then gives rise to a DNA intermediate when it enters the cell. And that DNA intermediate is integrated or inserted into the genome of the host cell. And it turns out that if you block that integration, then the unintegrated DNA is epigenetically silenced and eventually destroyed.

[00:04:41] So in this case, the defense mechanism actually works. Now unfortunately the viruses have figured out that if they integrate, they avoid this mechanism because this mechanism is based on identifying small pieces of viral DNA that are not part of the genome of the host cell. So by becoming part of the genome of the host cell, you become invisible to the defense mechanism. That’s the case with retroviruses. Other related viruses that go through reverse transcription and make a DNA copy of an RNA template include hepatitis B virus. And hepatitis B virus actually encodes a protein that destroys the factors that silence the DNA. So the viruses have come to completely different ways of avoiding this defense mechanism. Herpes viruses however actually take advantage, as I alluded to earlier and can become latent. So as anybody with mouth sores will tell you, the virus lies doggo for months at a time and then reappears, causes an ulcer which releases infectious virus for a few days. And then the whole thing goes silent again. So there we have an example of a virus that’s using this defense mechanisms. Epigenetic defense mechanism actually facilitate its own spread.

[00:05:49] Epitranscriptomic, these are modifications that are added to the RNA as we discussed. It turns out that if you look at RNA viruses such as retroviruses, they have a lot more epitranscriptomic marks on the viral RNA than is typical of a cellular RNA. And that tells you right away that the viruses love it. They think it’s great because the viruses would not have it if they didn’t like it. They evolve extremely rapidly and under extreme selective pressure at all times. And so it turns out that a number of different epitranscriptomic marks can actually firstly increase the functionality of the RNA that the virus has, but then also they can disguise the RNA so that it’s not detected by innate immune factors in the cell. Now that turns out to be very advantageous to humans because that led to the discovery, that modification of RNA using epitranscriptomic marks makes it safe to give as a vaccine. And in fact the Moderna vaccine and the BioNTech-Pfizer vaccine are based on this finding that epitranscriptomic marks prevent this innate immune activation, which, you know, actually you might think would be a good thing in a vaccine, but it turns out to be quite deleterious and really makes it impossible to use.

Grace Ratley: [00:07:02] Can you maybe expand a little bit more on how we can take advantage of how viruses use these modifications to create antivirals and vaccines?

Bryan Cullen: [00:07:13] Right. Because the viruses are very dependent on epitranscriptomic marks, particularly methylations of adenosine and cytosine in RNA, that gives you the opportunity to selectively target viruses by interfering with methylation of RNA. Now, cellular mRNAs are also methylated. So this is going to have some issues in terms of messing with cellular gene expression. But in fact, there are a couple of drugs that have been developed. One is called 5 adenosine that inhibit the ability of the cell to make the substrate that’s used to methylate RNA. Without going into any details, this of course would globally inhibit RNA methylation. But it turns out that in acute diseases such as Ebola virus, for example or influenza virus, you can treat animals for a week with a drug that inhibits the methylation of RNA, and you selectively reduce the replication of these highly pathogenic viruses. There was an interesting study published where they looked at Ebola virus in mice, and when they gave this drug, they had 80% survival. And if they gave no drug, they had 0% survival. Now obviously because cellular mRNAs are also methylated, you couldn’t give this drug for months and months because that would accumulate deleterious effects. But given the high dependency of the virus on methylation of RNA for maximal gene expression, it’s possible to use something that inhibits that step for a short period of time to allow the immune system to get its act in gear and mount an adaptive immune response.

 

[00:08:50] And by reducing the peak load of the virus, you can actually then hopefully allow the animal or human to get rid of the virus completely and survive the infection. Personally, I’ve been proselytizing for this idea for a while. I don’t know that anybody has really run with it because I think people are concerned about the fact that you really wanting to target something that happens to both cellular RNAs and viral RNAs, but essentially that’s how cancer drugs work, I mean almost all cancer drugs. Chemotherapy is notorious for causing nasty side effects. And that’s because it affects normal cells as well as transformed cancerous cells. So I think the key question with these kinds of drugs that act on host targets is you need to use them for limited amounts of time during an acute phase of the disease. To go into the second part of your question, I actually just proposed the two inventors of this strategy of modifying RNA so that it’s not doesn’t activate the innate immune system, nominated them for an award. I think the work is extremely important. So the people who actually did this work are Katalin Kariko, who is now head of Research at BioNTech, which is one of the companies that developed the vaccine. And then there’s a guy called Drew Weissman, and they work together at Penn to discover that RNA modifications make RNA much more readily tolerated.

[00:10:12] So if you inject a regular RNA into a mouse, just send it off the shelf looks like a regular mRNA, nothing special about it. You get a very strong, innate immune response, high levels of interferon in the blood. The mice get really sick from their own immune system. By modifying it, you then make it invisible to the innate immune system. But it still works really well as an mRNA pumps out proteins which are then presented to the adaptive immune system. And so you get really good antibody and T-cell responses. And so I think that’s one of the most important discoveries of the last 20 years. They started working on it in 2005 and it really took off when the emergency hit with COVID. But think about it, this allows you to use RNA as a vaccine for anything. All you have to do is reprogram the little computer that’s synthesizing the RNA. And you could do flu, you could do anything you like. And not only that because the RNA is injected into cells, it’s actually presented at the cell surface, which means it’s presented in the way that a viral protein would be presented. So it should activate both the humoral and cellular arms of the immune system much more effectively than simply injecting proteins into the blood, which generally gives you a good humoral response, but not a very good cell mediated response.

Grace Ratley: [00:11:25] Yeah, I know there’s been a lot of discussion for how mRNA vaccine technology could be used to generate vaccines for a lot of these pathogens, which we haven’t been able to to treat before. So let’s move into your other research. I know one of the things that you have worked on that has been very successful is micro RNAs. Can you tell us a little bit about that?

Bryan Cullen: [00:11:48] So RNA interference was discovered, I guess it was in the late 1990s by Fire and Mello looking at C elegans nematodes and they discovered that if you injected nematodes with double stranded RNA, what resulted is the gene from which the double stranded RNA derived would be silenced. And so it took a little while to figure out what’s going on. And probably a guy called Tom Tuthill, who’s at Rockefeller, probably has more responsibility for figuring it out than anybody else. But what he figured out was that that in nematodes, there’s a mechanism in place whereby double stranded RNA is cleaved into 21 nucleotide double stranded pieces. And then one strand of that double stranded RNA is inserted into a protein complex and then acts as a guide to bring the protein complex to a complementary RNA. And so the idea is you get the antisense strand from the duplex is incorporated into this protein complex and then the complex sees the RNA. When it sees the RNA and that complementary is complete, it cleaves it. So there’s an endonuclease cleavage event which results in the RNA being degraded. Now Tom Tuthill and a couple of other guys, but initially Tom Tuthill were very interested in characterizing these small RNAs that were arising from these double stranded RNAs that they were making and introducing into cells. And so he figured out a way to sequence small RNAs, 21 nucleotides long, which nobody had ever been interested in before. I mean, why would who could care about 21 nucleotide RNAs? And when he did that, he found that he not only saw the 21 nucleotide RNAs from the double stranded RNA that he put into the cells, but he also found lots and lots of 21 nucleotide RNA that were already there.

 

[00:13:31] But it wasn’t just random pieces of 21 nucleotide RNA. They were specific pieces of RNA derived from specific locations in the genome of the cell, and there were only maybe 400 or 500 different small RNAs in the cell. So it was actually my lab that was one of the two that figured out how these microRNAs are made. So they’re actually derived by the cleavage of a stem loop structure that forms part of an RNA polymerase to capped polyadenylated mRNA like product, which is now referred to as a primary micro RNA. So that was interesting. We figured out how to make microRNA and that was actually extremely helpful because we were able to patent the process of micro RNA synthesis that has been extensively licensed by Duke to lots of people and was very nice for me and very nice for my lab in terms of generating income. But once I was doing this, I thought well these small RNAs can turn off our target, an RNA that is made by a virus or a host cell, and there are only 21 nucleotides long, so they don’t take up much room. So would viruses have come up with this idea? Would the use small RNAs like microRNAs to target host cell factors that are involved in repressing virus replication? When I thought about that, I thought what virus would be the most likely to do this?

[00:14:57] Now the thing about microRNAs is they downregulate mRNAs. They don’t touch the protein that’s made from that mRNA. Most proteins have a half life of 12, 24 hours, and most lytic viruses, poliovirus COVID-19, for example go through their entire replication cycle in about a day. And so that means that even if the virus produced a microRNA that completely destroyed an mRNA population, the protein from that mRNA population would only have gone down by maybe twofold at the end of the replication cycle. So I thought well, probably not an RNA virus then, but what viruses hang around forever and a day. And the obvious answer is herpes viruses, not just herpes simplex, but also Kaposi sarcoma virus, Epstein-Barr virus. And so I contacted scientists called Blossom Damania at Duke and asked her for some of these cell lines that she had that were duly infected with Kaposi sarcoma herpes virus, which is a virus that causes cancers in immunodeficient people and was originally only discovered as a function of HIV because fully immunocompetent individuals basically very, very rarely have Kaposi sarcoma. But if you don’t have an immune system, then it’s quite probable that you’ll get one. And then it turns out that a lot of these cells are duly infected with Epstein-Barr virus, which causes infectious mononucleosis.

[00:16:18] So I thought well this gives me two bang for my buck. So if I sequence the small RNAs in these cells, if the Kaposi sarcoma virus or Epstein-Barr virus make small RNAs, then we’ll identify them. Now I was scooped on this, so we actually came second. We were the first to report microRNAs made by Kaposi sarcoma virus. But Churchill Laboratory had been interested in looking at microRNAs that were characteristic of different tissue types. So he was looking in liver cells. He was looking in neural cells. He also looked in B cells, and B cells are what Epstein-Barr virus infects. And so he actually ended up looking I think by chance at a B cell that was infected by Epstein-Barr virus. And so he identified five Epstein-Barr virus microRNAs. And then we came in a couple of months later and we identified ten Kaposi sarcoma virus ones. But it turned out that the cell line that Tuchel’s group had sequenced small RNAs in was infected with an Epstein-Barr virus mutant that has a huge deletion, whereas the ones that we did was infected with a wild type Epstein-Barr virus. That is the one that makes people sick. And it turned out that the big deletion took out almost all the microRNAs of the virus. So we actually discovered over 20 Epstein-Barr virus microRNAs. So that was really interesting. And we initially tried to figure out what they were doing. We had some luck at the beginning.

[00:17:39] One of the really interesting things that turned out was that if you look at Epstein-Barr virus, when it infects B cells, it actually turns on several cellular microRNAs to very high levels. And one of the ones it turns on over 100 fold to make it the most highly expressed RNA in the cell. It’s called MiR-155. So Epstein-Barr virus induces B cells to grow rapidly. Kaposi sarcoma Herpesvirus also induces B cells to grow rapidly, but it doesn’t induce MiR-155. Instead, it encodes Mir-155. It has its own MiR-155. And so the two viruses that are both herpes viruses that want the cells to grow fast and to make B cells grow fast, you have to have MiR-155. One of them decided to figure out a way to turn on the cellular microRNA by over 100 fold, and the other one decided to make its own. And so that was a really interesting discovery. It was actually followed up by another group in the UK who worked on a disease of chickens. It’s actually a herpes virus that causes cancers in chickens called Marek’s disease virus. And it turns out that Marek’s disease virus which is a herpes virus, also encodes a MiR-155. And they did a very cute experiment where they knocked out the MiR-155, and the virus was still able to grow perfectly well, but it couldn’t make tumors anymore. So this MiR-155, has been around since dinosaurs. It’s only 21 nucleotides long, but it’s exactly the same since T-Rex was wandering around the earth.

[00:19:08] They took the one from the chicken and put it into the Marek’s disease virus, and it regained the ability to cause tumors. Very clean demonstration that it is in fact, the micro RNA that allows the virus to become carcinogenic. But that was one of the few instances I think, where we really could figure out what the microRNA did. So we banged our head against the wall for multiple years trying to figure out what these microorganisms were doing. And the problem is that they downregulate 200 mRNAs each. And so the question is, all right what are those 200 are important. Is one important or 5 important or 17 important? I’m certainly not all of them, because these are with exception of the MiR-155, almost all the viral microRNAs are completely different from cellular microRNAs. And the cell hasn’t conveniently sprinkled around targets for that microRNA at all. Its antiviral genes. So what the virus is probably doing is turning off 90 things that it doesn’t care about one way or the other in order to get ten things that he does care about. Trying to separate the wheat from the chaff was just very frustrating. And in fact, I would say that most of the literature out there on viral microRNAs is wrong. They haven’t really identified the targets. They’re oversimplifying. It’s all artifacts based on overexpression and things like that.

Grace Ratley: [00:20:22] What sort of methods do you think could be used to correct the wrongs of the RNA papers that have been published?

Bryan Cullen: [00:20:31] Well, what people do is you have a microRNA that you happen to be interested in for whatever reason. So we know from that microRNAs downregulate any mRNA that has a perfect complement to nucleotides 2 through 9 of the microRNA, which is called the seed sequence. Now the problem is that eight nucleotide sequences occur a lot. I mean this is every 50,000 bases you’re going to get one. And so that means something like 10% of all the RNAs in the cell have a seed sequence that could be targeted by microRNA. So what people do is they have the microRNA and they see an interesting phenotype associated with it for some reason or whatever it is. They see it overexpressed in cancer cells like MiR-155 and then you say, okay, well what is MiR-155 complementary to. And you can do that using a computer program and it will pick out all the mRNAs in the cell, which have an eight nucleotide complementarity and you’ll probably get 1000 or 800 or something like that. And you have no way to tell which ones are important. And so what you do is you do what’s I’ve heard called the shiny pebble syndrome, where you if you look in a big bucket of pebbles and one of them is really shiny, you’re going to pick that one. Because that’s that’s a cool looking pebble.

[00:21:48] And so what you do is you get this list of mRNAs that have complementarity to the microRNA and you go through a B7 62, I’d never heard of that. A6 543, never heard of that. And then you get, oh tumor suppressor. That’s got to be it. And so now what they do is they take the sequence of that that is complementary and they stick it into an indicator construct behind an indicator gene. But of course, that’s a circular argument. It’s an eight nucleotide homology, of course it’s going to be a target at some level. And so what they do is they make a massive amount of the microRNA by overexpressing it. They throw in this indicator and it goes down by four fold and they say, Oh, so you can down regulate. But that doesn’t show you that the actual mRNA is down regulated by the microRNA when the microRNA is expressed at physiological levels. Because the microRNA is able to bind to hundreds of different mRNAs. And so which of those can it actually down regulate to a sufficient degree? That’s basically what they do. And they never actually demonstrate that the physiological level of that microRNA in the relevant cell, which cancer cell is actually down regulating the whatever tumor suppressor or whatever. And if you got rid of the microRNA or you increase the expression of the tumor suppressor, that you would actually reverse the phenotype. They almost never see that, almost never see that.

Grace Ratley: [00:23:07] So what is your approach then?

Bryan Cullen: [00:23:08] We gave up on microRNAs. One of the things that you have as a professor is you have people come through your lab all the time. And I’ve tended to have a lot more postdocs than graduate students, although I’ve had some really good graduate students as well that are professors at universities now. But what happens is the postdocs come into your lab and they spend 4 or 5 years there and they’re working on problem X. And then they go off to another university. And what are they going to work on? Well, they want to work on problem X because that’s what they’ve been working on for the last 4 or 5 years. That’s what they know how to do. And so that puts you as an established investigator into a difficult situation because you don’t really want to directly compete with your own offspring, so to speak. And so what I’ve done over the years is that I basically change everything I work on about every ten years. And so we only started working on epitranscriptomics in 2018 and we’ve only been working on epigenetics since 2019.

[00:24:03] And so the other stuff that we were doing before that has gone away with people. I’m going to be retiring in 2 or 3 years and that will solve the problem in a permanent sense. But I’m not going to worry about epigenetics and transcriptomics being a problem, but it’s an issue that everybody faces and some PIs are really nasty about it. They’ll bring a postdoc into their lab and give them a project to work on, and then when they’re going to leave, they won’t even let them take their own reagents with them. They say, No, those reagents are made in my lab. They belong with me, and you don’t even get to take them, which I think is extraordinarily reprehensible. I mean, I don’t know how anybody gets a postdoc done that once or twice, but I’ve always felt that it was important to let people take things along. So there are several postdocs of mine out there working on viral microarrays with greater or lesser success.

Grace Ratley: [00:24:51] Well speaking of postdocs, I know that you did not complete your postdoc. So let’s talk a little bit about your training as a scientist. So I guess we’ll start from the beginning. What got you into science when you were a kid?

Bryan Cullen: [00:25:05] I was interested in a lot of things, but I was interested in things that were black and white more than I were in things that were gray. I liked my answers to be yes or no, not well, maybe and twice on Wednesdays or something. But I was very interested in things like archeology, astronomy. And like a lot of kids, I was thinking that would be really cool being an astronaut. And then as you get older and you start reading the fine print, you realize, well, that’s not such a good job actually. You spend your entire life and you maybe go to the moon once. I mean, that’s not fun. So I always did really well at science. I graduated top of my class in high school and I grew up in industrial northern England in a town called Bradford, which was rapidly declining as the industries which had supported it were being lost. So I was not totally aware of all the possibilities that existed. The school I went to was actually quite good, but the concept of giving people advice on their career had not penetrated through to the British educational system at that point. So nobody in my family had ever been to university, but I thought, Well, I definitely want to go.

[00:26:11] And I actually got a full scholarship to Warwick University, which has gone on since then to become one of the top universities in the UK. It’s ranked like number five or something like that now. And at the time it had a I thought a very forward looking department called Biological Sciences, which really wasn’t so much a biology department or a biochemistry department, which a lot of them were in those days. But actually it was really interested in what was going to become molecular genetics. And they were very interested in pathogens. And so I became interested in that. And then when finishing my third year in in England, a bachelor’s degree only takes three years. My parents told me that they were going to emigrate to the United States, to New York specifically. So what I ended up doing was I went to graduate school at University of Birmingham in England, at the medical school there. And the reason I went there was because they had a Department of Virology, which is really unusual and I wanted to do virology. But I didn’t end up staying there to do a PhD. I ended up deciding to take a master’s degree after a year and moved to the United States. Because I don’t know whether this is still true, but at that time if you were less than 22 years old, you could emigrate to the United States as a dependent child, which meant that I had to leave within a year of going to Birmingham. Otherwise, I wouldn’t have been able to go to the United States at all.

[00:27:30] So the concept was really to go to the United States, work there as a tech for a couple of years. And then move back to England, which I felt very happy as a Briton. And I liked the UK and do my PhD and unfortunately I didn’t do much research on this. So I got to the United States and I got a really great job as a tech in a research institute called the Roche Institute of Molecular Biology, which actually had a Nobel Prize winner on the staff and three National Academy members and some really good virologists. And I got a job there and learned vast amounts actually working there. And then after a few years, I got married to an American woman, but she was okay with the idea of going back to the UK. So I applied back to the UK. At that point, I was a British citizen. And they said, Well, yes you’re a British citizen, but in fact we can’t give you a scholarship because you’re not a resident. And I was like, Well nobody told me this before. So an opportunity came up, in fact, at Hoffmann-La Roche, where the Roche Institute was, because they were setting up a Department of Biotechnology and I had become an expert at cloning and was considered a cloning whiz in those days before PCR.

[00:28:39] And there were a lot of tricks that you had to do. You had restriction enzymes and that was about all you had. And all you had was pBR322, which is a low copy number plasmids, so much lower amounts of DNA than you get these days. Every plasmid had to be isolated through caesium gradient centrifugation. So it was extremely hard work, but I was good at it. And they decided to set up a Department of Biotechnology at Hoffmann-La Roche. And they asked me if I’d like to come on board. And I said, Well I mean, what’s in it for me? And they said, tell you what, we will sponsor you for a PhD. And when you finish the PhD, we guarantee you your own lab here at Roche. So I said, Well, that’s good, I’ll work with that. So they said, Well, go find a university that’s not too far away. That’ll take you because we need you here 40 hours a week to do your regular job. So you’ll have to do your PhD basically in your spare time. So eventually what was then the University of Medicine and Dentistry of New Jersey is now part of Rutgers University in Newark, said they would take me on and they would allow me to use my work at Roche as my project.

[00:29:42] So there was a lot of commuting involved because I had to go to attend all the classes, of course in Newark. So I was driving back and forth between Nutley and Newark two or three times a day to go to class. And then we also had to demonstrate stuff for the medical students and so forth and teach them lab. But that was the hardest I’ve ever worked in my life. And I managed to get my PhD in two and a half years and it wasn’t a cheap PhD. I actually got seven first author papers out of it, including a nature article that then was my PhD and they gave me a job that they promised me and they asked me to work on something called Interleukin-2. There are lots and lots of interleukins now, but in the old days it started with one and two and three. Now there’s like 40 of them. I don’t know. But interleukin-2 is one that was discovered by Bob Gallo, and it’s required in culture to make T cells grow. And so the idea was that I was going to generate cell lines that produced large levels of interleukin-2 that then might be a drug.

[00:30:39] They said, well you can work on that, but you can also work on another project that might interest you. And my PhD project had actually been on avian retroviruses, particularly avian leukosis virus. And at that point HIV was discovered. So I got my PhD in 87. HIV was sequenced in 88, and I said, Well, I know how to work with retroviruses. I’ve been working with retroviruses for years when I work on HIV. So I started working on HIV. It was an odd thing because I was doing it in my spare time sort of thing. My lab was very small. I had a technician initially and that was it. Later on I got a postdoc, but I was working on this one issue, which was this protein called Tat that HIV one makes. And it had been proposed that it regulated the translation of HIV RNAs. And when I did some work on it, I discovered it was actually a transcription factor. And so in 1986, I submitted a paper to cell, which was very unusual and that I was the only author. So I’d done every single experiment in the manuscript and written it, put it all together, sent it off. And I remember I was on vacation with my wife, so we went on vacation right after I submitted it. In those days, we didn’t have computers. And so I got a fax from Hoffmann-La Roche that had originally come from Sal saying that they were going to accept the paper for publication. So I knew at that point that that was going to really kick start my career.

[00:32:03] So the next thing that happened was somebody from Duke approached me. Actually, I was approached by several people at several different places. But one of the people at Duke approached me and they said, well, we have a Howard Hughes investigator position available. In those days, universities were assigned Howard Hughes investigators, and they could then recruit somebody. That doesn’t work that way anymore. But in those days they did. And so how would you investigate? A position came with about $800,000 a year in research funds. And so I looked at that. I’d never been to North Carolina before in my life and came down and thought, Well, this looks nice. I took the job. And within a year we had actually figured out how the RF protein of HIV worked. So we published two nature and two cell papers on that. I was very lucky because I brought the postdoc with me from Duke, a guy called Yogi Huber, a German guy. And then I recruited a really talented English postdoc called Michael Milam. In 1990, the three of us plus one tech, we had 19 papers out of the lab when I was an assistant professor. It was actually funny because I got a phone call from from Sal and they wanted me to be an editor on Sal, and I wasn’t even tenured yet. So I was put on the editorial board of Sal. Turned out to be a really bad idea actually because I was one of only two people on the editorial board of Sal, who was a virologist. And so only 10% of the manuscripts that go to Sal are accepted. And they all assumed that I was responsible for the rejection. I got me a lot of really negative vibes from a lot of colleagues who were more senior than me out there in the field. So it was good for the ego, but it really didn’t help my career, although it certainly impressed Duke and they moved my tenure along real quick after that. And since then I’ve been at Duke. I’ve looked at a number of jobs elsewhere. There was one at Rockefeller a few years ago that was tempting, but my wife said that she would absolutely refuse to move to New York City.

[00:33:54] So that kind of went out the window. What’s interesting is that most of the top universities around the country are either in the middle of nasty areas in cities like Johns Hopkins, for example, which historically was in a not very nice area. And that was also true of Yale, although it’s gotten a lot better. It was also true of Penn and Chicago. Generally, what you have to do is live way out of town and have this big long commute. But then secondarily, most of the top universities around the country are in really expensive places. They’re in places like San Diego or San Francisco or Boston or whatever. I remember one offer from a California school, and they basically couldn’t give me much more money than I was making at Duke because it’s a state position. And so they have strict rules about how much they can pay you. So they would have given me maybe $20,000 more to move there, but I would have had to take on an extra million dollar of mortgage for a house that would be about half the size of the one I had. I thought, well, does this really make any sense? So here I am still and say getting ready to retire. But yeah, it’s been interesting watching this area grow and change over the years, especially Durham. Nobody went to downtown Durham when I got here in 1986, and now it’s sort of this vibrant hub and everybody wants to live there, which is curious.

Grace Ratley: [00:35:13] Yeah, I’m a huge fan of North Carolina, having done my undergrad over at UNCW. I totally respect your decision to stay there, but I am curious what your plans are for after you retire. Are you thinking of maybe moving back to England or staying in the Durham area, being a professor emeritus?

Bryan Cullen: [00:35:34] We actually built a house about five years ago in Chapel Hill. We used to live in Durham before that. It’s on a four acre lot in the forest, so it’s only six miles from Duke. It’s a single floor house, very appropriate for our life going forward as we get older. And really a beautiful place. I love it. We spent so much time on planning it and working with the architect and the builder to make it just perfect. I can’t imagine leaving this place any other way, but in a big box I do quite a few other things than just work for Duke. I do quite a lot of consulting and expert witness work, so right at this moment in time, I’m an expert witness on three different patent litigation lawsuits. That actually keeps me busy some of the time and is very interesting. I mean, they’ve all been very quiet recently because all the courts are shut. But that will resume in the relatively near future. I like working with these really high quality lawyers. They’re people who are from the very top law schools that have clerked on the Supreme Court. And they’re really, really bright, but they’re bright in a different way than scientists are bright. Their minds work in a somewhat obtuse way, but it’s really entertaining to watch. And I actually really enjoy being cross-examined by really bright lawyers from the other side. It’s a real game of intellectual cut and thrust.

[00:36:55] When you’re up there on the witness stand for eight hours or whatever, with three lawyers going after you. It’s quite an entertaining. I do like to travel and I do serve on several advisory boards for universities and things like that. So that’ll presumably keep going when I’m emeritus. I mean, part of the problem for me has been it’s become much more difficult to get funding. I lost my Howard Hughes investigator position a few years ago, so that made life a lot more difficult. Then I had to get all my money I had to come from NIH. And so you spend a lot of your time writing grants and actually getting postdocs and graduate students. Graduate students, not so much, but postdocs is a challenge in North Carolina. Most European postdocs, for example, want to go to the big cities. They want to go to San Francisco or Boston or New York or what have you. You can get some people from universities in the South or the Midwest, who think Durham is a cool place, really like basketball or whatever. Those individuals will come. But not so many people from the Northeast or the West I think. You’re only as good as the people in your lab. If you don’t have good people, then you’re not going to make any progress, that’s for sure.

Grace Ratley: [00:38:03] So as we wrap up here, I just wanted to ask one more question. From your many years working in science, what is the most important piece of advice that you could give to young scientists, early career scientists, or students who are interested in entering the field of science?

Bryan Cullen: [00:38:23] Stay nimble on your feet. I mean, I think there’s a tendency for people to keep doing what they’ve been doing. And eventually you just run into the ground if you do that. So there are labs out there that are still working on Lambda Phage or whatever because that’s what they did when they were 25 and they’re still doing it at 55. Try to move with what’s out there. So when something like CRISPR-CAS comes along, jump on it immediately and something like epitranscriptomics comes along, jump on it immediately and something like RNA comes along, jump on it immediately. You’ve got to go with what’s hot. That doesn’t mean that you have to work on Ebolavirus because Ebolavirus was important for a year. And I don’t think it necessarily means you have to work on COVID at this point in time. But for these incrementally game changing technologies like CRISPR-Cas and RNA and epitranscriptomics. I think there is a lot of potential for high profile, high citation work. That in the end is going to allow you to move forward and become successful.

[00:39:23] The other thing I would say is think about patents. I mean, I’ve probably made almost as much money from patents as I have from being paid by the university. That’s because I was very aware of things that could be patented. Obviously if you’re working on fruit flies, the chances of you getting a patent that’s going to be of use to anybody, a relatively low. So if you can think in terms of working in areas that have applied potential and after all, that is about human health, which is something important as well. That’s an area that you might want to consider taking into account. Because if you can, it doesn’t have to be a drug. It can be a process or a method or something. If you do discover something important like that, then that can make a big difference to your long term financial welfare, which if you’re just living off a faculty salary, isn’t necessarily going to be that great, especially if you’re in an expensive area like San Francisco or something.

Grace Ratley: [00:40:16] Well, thank you for that advice and thank you for coming on our podcast. I have really enjoyed talking with you. You have such a wonderful, varied experience working in science and a lot of awesome insight into emerging technologies. Yeah, thank you for coming on.

Transcript of Episode 27: Micah Luftig

Disclaimer: Transcripts may contain errors.

Grace Ratley: [00:00:00] Welcome to The Bioinformatics CRO Podcast. My name is Grace Ratley and I am the editor of the podcast and today I’m joined by Micah Luftig. Micah is an Associate Professor and vice chair of Molecular Genetics and Microbiology at Duke University. Welcome, Micah.

Micah Luftig: [00:00:16] Thanks for having me.

Grace Ratley: [00:00:17] No problem. So let’s start off with a little bit of the work that you’re doing now. So you work with Epstein-Barr virus, which is one of the nine herpes viruses to infect humans. So what is your research focused on?

Micah Luftig: [00:00:30] Sure. We’ve been studying EBV here at Duke for the last 14 years, and I actually did my PhD studying EBV so I’ve got a long history with this virus. For the most part, what we study is understanding how the virus takes over cells. We’re really a cell biology and cancer biology lab using the virus as a tool to guide our understanding of cell biology. EBV is a common pathogen. Actually, it’s virtually all adults worldwide have been infected and are latently infected with the virus, like 95% of us and in most people doesn’t cause much disease. But that’s because you’re infected when you’re really young and it doesn’t cause much disease. You make a really strong immune response to the virus. It goes latent. And then there’s a balance for your lifetime of a little bit of reactivation of the virus. And then the immune system deals with it and then the virus stays latent in your blood cells if you’re infected when you’re older. So in the second decade of life that actually most primary infections can lead to infectious mononucleosis. So that’s what causes mono. And a lot of folks don’t know that and don’t think about that too much. But EBV, not really through the infection process, but more the immune response is a little more exuberant in adolescence and post adolescent individuals. And so that causes the fatigue and other symptoms of mono usually resolves over weeks, sometimes months.

Micah Luftig: [00:02:00] But any event, then you wind up like the rest of us. And, well, I didn’t have mono, but many people did. Usually when I ask in a classroom how many folks have either had mono or know somebody who has, everybody raises their hand. In any event, when you’re past that phase, the virus latently infecting your B cells just like an asymptomatic carrier. But where the virus really becomes a problem is in the immune suppressed. So either transplant patients or HIV infected individuals, or even as we age in our immune system weakens, EBV actually can cause lymphomas in those patients at really high levels. So you have about 100 fold increase risk of an EBV lymphoma in the setting of HIV co-infection, for example. So the path that EBV uses to cause cancer in those settings is something that you can actually recreate in the lab. And so when you infect primary human B cells, the lymphocytes that EBV finds itself in, in vivo in the lab, EBV will immortalize the B cells and they become these lymphoblastoid cell lines or LCLs that mimic the initiation process of lymphomagenesis in these immune suppressed patients because you don’t have an immune system in the tissue culture dish in the lab to prevent those cells from growing out so many labs in the field. We have as well used this model to study the virus host interaction. And so it turns out to be super interesting.

[00:03:29] The virus expresses 8 or 9, depending on how you count them, latency, proteins and also actually about 44 microRNAs and some other non-coding RNAs. And together all of these gene products really take over the cell. So they infect a resting B cell, which is out of the blood otherwise would just sit there and then over a couple of days would die. The virus infects these cells and then within about 2 or 3 days, once you start making all of those viral proteins, the virus turns on the cell cycle. The cells get going and proliferating, and they’re constitutively activated through a number of pathways that the viral proteins mimic in terms of what those cells would normally see in the body. And they just keep going indefinitely. And so we and others study how that process works. So what the viral proteins are, what they do, how they interface with cellular proteins, how they regulate transcription, how they regulate cell survival, proliferation, metabolism, the immune system, you name it. That’s the bulk of what we do. And there are obviously more details beyond that. But in recent years expanded to studying other aspects of EBV biology. So the virus also infects epithelial cells. So what I didn’t mention earlier is that the virus spreads by saliva. So that’s why mono is often called kissing disease. The virus is always spread by saliva, whether it’s your mom or dad kissing you when you’re a kid or however saliva is exchange when you’re younger.

[00:05:00] That’s how the virus moves. And so what we know is that actually epithelial cells in the oral mucosa are a site of high level lytic replication, like the amplification of the virus. And that’s the reservoir for transmission. This biphasic life cycle between B cells and epithelial cells is really interesting. And the virus that comes out of a B cell is better at infecting an epithelial cell and the virus comes out of an epithelial cell is better than infecting a B cell because of the glycoproteins that put on the surface of the virus. And moreover, the ability to infect an epithelial cells increases about a thousand fold 100 to 1000 fold when a B cell is physically touching an epithelial cell. So it’s thought that these latently infected B cells get reactivated when they’re interfacing with an epithelial cell and transfer virus directly that way, rather than just virus that’s floating around in the saliva or something infecting new epithelial cells. So that’s super cool biology, which we study a little bit of. But it turns out the consequences of epithelial infection, while is normally just virus replication different from B cells where it goes latent typically as a default mechanism. When that goes awry for one reason or another, the virus can’t replicate and it has to go latent.

[00:06:20] So you can envision cells that have an amplified antiviral sensing mechanism or are not fully differentiated and don’t provide the proper milieu of cellular factors to allow virus replication. So something keeps the virus from replicating or maybe there’s a deletion in the viral genome. That could lead to a latent infection of epithelial cells and turns out again, the virus is really good at persisting and keeping cells alive. And so that can cause epithelial cancers. So EBV is associated with Nasopharyngeal carcinoma and also about 10% of gastric cancer, stomach cancer. So we have a couple of projects in the lab looking at how EBV causes stomach cancer and de novo infection models and corroborating that with clinical specimens from our collaborators in Singapore at Duke-NUS, where they’re studying changes in tumor cells that are infected or not with EBV in vivo. And we’re doing that in vitro and trying to understand mechanistically how that works. Part of that collaboration and thinking a little bit more translationally has opened up other translational projects in the lab also. So we have a couple of collaborations now where we study new antivirals that are being developed for EBV with small biotech companies that are starting up and interested in understanding more mechanistically about how they work and also what clinical correlates they might use to predict outcomes in patients that have these EBV lymphomas or carcinomas. So that’s what we do.

Grace Ratley: [00:07:54] Yeah, that is some really fascinating biology. So when are people who have Epstein-Barr virus infectious? Can you be infectious when you’re latent?

Micah Luftig: [00:08:03] Yeah, you’re basically always shedding virus. So yeah, there have been a couple of studies looking at this in people in this guy’s lab where they sampled saliva and everybody sheds a different amount of virus and it’s stable over time. It’s kind of fascinating, but it oscillates. It’s like the set point is stable. Like you’re kind of a high shedder or your medium shed or what have you. But like at different times during the days, over the course of weeks, you might be shedding more or less. So it’s really fascinating and it makes sense given how successful EBV is in transmitting across the world. It’s interesting when you think about things from that perspective where if a goal, let’s say, clinically, was to prevent infectious mononucleosis, what would be the best way to get there? Would it be a vaccine against EBV that prevents infection or that prevents symptoms somehow or would it be just getting infected naturally earlier? And how would you do that? It makes you think of chickenpox parties that happened in the maybe 70s and 80s. And to make sure all the kids get infected, which is another herpes virus. And maybe not the smartest approach, but gets the job done. I mean, it’s nuanced. In any event, there are vaccines now obviously for that virus. There are vaccines in development for EBV as well.

Grace Ratley: [00:09:31] Yeah. And how does it EBV differ from most of these other herpes viruses?

Micah Luftig: [00:09:36] Sort of what I alluded to earlier about the tropism, the cells that it infects. So the dogma in the herpes virus field is based on the genetics of these viruses. So you mentioned nine, which I appreciate because there’s 1, 2, 3, 4, 5, 6A and 6B, which the aficionado’s say are two different viruses, 7 and 8. So they branch out phylogenetically. Their genetics tell us that there are alpha, beta and gamma. So these three distinct groups of viruses and the dogma in the field, which is I think true, is that the alpha herpes viruses tend to have a broader tropism so they can infect more cell types and they can infect more different organisms. So a virus like herpes simplex virus that causes cold sores or genital herpes, herpes simplex 1 and 2 can infect lots of different cell types, certainly in the lab and I think also in vivo, it’s found in a number of cell types and also again in the lab you can infect mice or rabbits or monkey cells or what have you. And then the thought is that as you go towards beta and gamma herpes viruses, so beta an example is cytomegalovirus, Gammas are EBV and another oncogenic herpes virus KSHV associated with Kaposi sarcoma. The gamma is tend to be more narrow in terms of their tropism, so they infect less cell types. So for example, EBV primarily B cells and epithelial cells, although there are always exceptions to the rule and also much more narrow in terms of host range. So EBV cannot infect mice or rabbits or other organisms, so humans and then some nonhuman primates can be infected by EBV. Those would be what make EBV distinct from these other viruses.

Grace Ratley: [00:11:21] Yeah, it sounds like that might make EBV pretty difficult to study. Are there other model organisms?

Micah Luftig: [00:11:27] Yeah. So the way to address that is twofold. So one is what we do basically is use human cells. So we infect primarily human B cells for all of our work. Recently, in the last decade or so, humanized mice have been developed where in an immune deficient background you can reconstitute a human immune system by providing hematopoietic stem cells that then differentiate into lymphocytes and other cell types in the blood that allow you to do infections with EBV. It turns out those models often favor B cells. You have more B cells in the blood than you would normally in a human. If anything, it helps things out. They’re really great for studying early infection and B cell expansion and replication of the virus and tumorigenesis. There is some immune response. There is a bona fide immune response to the virus. It’s not quite as broad and complex as the immune response that humans have, but it is restrictive. And so if you eliminate T cells or natural killer cells in that humanized mice model, EBV can cause tumors 100% of the time on infection. So it’s a pretty good model for studying viral genetics and signaling pathways and the kinds of things that we have studied in vitro.

Micah Luftig: [00:12:47] There are other ways of approaching this. Very expensive way is to use the rhesus lymphocryptovirus, which is very similar to EBV in lots of ways. A couple of labs have developed that model and shown that you can recapitulate a lot of human EBV biology in the rhesus macaque. But again, they’re super expensive to work with. And then the other way that folks go and I think is good to understand basic viral host interactions, but may not tell us a lot about EBV, but is to use mouse viruses like MHV68, is a virus that phylogenetically looks a little bit more like KSHV, but it’s definitely a gamma herpes virus and can recapitulate various aspects of B cell latency and reactivation and has some of the same signaling proteins that EBV and KSHV has. But I think has been a really great model for understanding gammaherpesvirus pathogenesis. But it may not be as specific to the unique biology of EBV as, for example, the rhesus lymphocryptovirus as an animal model.

Grace Ratley: [00:13:55] Now I’d really like to get back to talking a little bit about how viruses can cause cancer in people. I was wondering if you could give us a sense of how common that is or maybe give some other examples of viruses that can cause cancers in humans.

Micah Luftig: [00:14:12] At present, the viruses that we understand are associated with or cause cancer, it’s about 20% of all human cancers. And I say at present, because one of the major components of that is human papillomavirus, which I think most people know causes cervical cancer and also causes a range of other cancers, including anal cancer, penile cancer and some head and neck cancers. And there are also papillomavirus is associated with certain skin cancers, but human papillomavirus. Now there’s a vaccine against to prevent cervical cancer. And it’s amazing. It was an amazing breakthrough by Doug Lowy and John Schiller at the NIH for developing those papillomavirus like particles to immunize and acquire what became sterilizing immunity to prevent infection with these viruses. And so it prevents those cancers. I think most teenagers get this vaccine. The problem is it has been vaccine uptake. And so the reason I say at present is that it’s hopefully we’ll reach a point where the vaccine uptake is much higher. And cervical cancer, for example, is a thing of the past, or at least viral associated, which is the vast majority of it. And these other cancers that I mentioned. But there are about 8 or 9 depending on how you call them, human rather oncogenic viruses. We classify those as direct and indirect. So the direct cancer causing viruses would be papillomavirus and EBV, KSHV, where there are viral oncoproteins that are expressed in the tumors that are driving the process, and that if you were to eradicate the virus, you would treat the cancer or prevent the cancer. And then there are others which are more what we would call indirect oncogenic viruses, and that includes viruses like HIV and hepatitis C virus and hepatitis B virus, although there are certainly direct oncoproteins there.

[00:16:09] But HCV is an example where the constant infection and the inflammation in the liver that’s induced by HCV is thought to drive the oncogenic process. But it’s not necessarily that the virus is in every tumor cell driving the liver cancer. Those are some examples of oncogenic viruses in humans and how we think about dealing with them. And so vaccines is obviously a great approach if one can develop those. There are also now T cell based therapies. So the idea would be that and this has been demonstrated in EBV for many years in the setting of transplant, that if you develop specific and potent T cells against the viral antigens and it’s been done as an autologous process, which means you take the patient’s T cells out and you expand them against the viral antigens and then you re-infuse them. That has been shown to cure EBV lymphomas in the setting of stem cell transplant associated lymphoma. But really it’s not boutique, but only certain centers have the ability to do that. And so now with the advent of cellular therapies for cancer much more broadly, CAR T cells and so forth, the logic of simply developing viral specific T cells and expanding them and whether they’re autologous or allogeneic, I think is a super exciting area of research and development that’s ongoing certainly for the transplant population and also for some of these other viral associated cancers.

Grace Ratley: [00:17:45] Do you have any other technologies that you’re really excited about that maybe make your job studying the virus a lot easier? I know that you recently used single cell sequencing, which is something we do a lot here.

Micah Luftig: [00:17:57] That’s what I was going to bring up, if that’s okay. Yeah, I think single cell biology is really taking over a lot of the way. Most folks think about their experimental systems. I mean, certainly in virology, the idea of what the heterogeneity of a response to viral infection looks like is something we think about all the time. And now we can see it. And whether it’s single cell RNA seek guiding the way or some of these new beautiful spatial transcriptomic approaches to see what that looks like in tissue. It’s definitely a revolution that I think a number of folks are embracing. And we’ve gotten our start with some single cell RNA seek on EBV infected cells in the context of latent infection. We published that recently, and then now we’re doing that also in the context of lytic infection. So it’s really cool because we can basically see cells that are infected but do not replicate the virus and we can ask, Well, why is that? What’s their gene expression program that’s potentially preventing that from happening? And likewise, they may get started along the way and then stuck. They don’t make it all the way to full virus replication. Well, who’s expressed in those cells and what might be responsible for that? So it’s a beautiful hypothesis generating tool to then allow us to go back in and say, well, if we now knock out or overexpress these genes, how does that influence the outcome of infection? And you can imagine directly identifying therapeutic targets for EBV in our case, but certainly any virus by using an approach like that and I know a number of investigators have been doing that for their favorite virus, basically.

Grace Ratley: [00:19:37] Yeah, just reading all of the single cell papers that have come out in the last few years feel so lucky to be entering science at this point in time because I feel like there’s so much going on and so many places to apply these new things. So viruses are very popular right now. I feel a lot of people have taken up interest in virology and as a result of the pandemic, having a virologist on the show, I’m obligated to ask you questions about COVID-19. So how has COVID-19 affected your research overall, how you conduct it, and whether you’ve made any transition to helping out COVID-19 research efforts?

Micah Luftig: [00:20:19] That’s a great question. I think like most of us, the pandemic obviously shut things down for a while. There was quite a bit of uncertainty in March, mid-March, and Duke shut down pretty readily. We had about a two week runway before we had to essentially evacuate the lab. So everybody had to get their lab shut down, protocols in place and approved and then just do it. And for us, it was not too bad because we don’t have mice and we don’t have. Primarily we have a lot of primary cultures, but things that we can viably freeze. So for us, we took advantage of the shutdown in some ways by knowing we’d be out for a little while, by basically finding as many RNA samples as we had in the lab to do a massive RNA-Seq experiment so that people could analyze it over the break, not knowing how long the break would be. So we ended up sending 96 samples to Novogen for sequencing. And I was in the lab. We had evacuated and I was the last man standing. And I was literally pipetting from everybody’s tubes into the samples, packaging the box and sending it out while everything was shutting down around us. And we managed to get it out. And it was pretty chaotic on their end, too.

[00:21:37] They kept things open, but it was like, we’re going to ship it to the West Coast. No, we might ship it to China to sequence. No, we can’t ship it to China now so it was crazy. So we shut everything down and everybody went home and we got into this mode of learning computational biology. So I think a lot of folks probably did that, but luckily I’d recruited a computational postdoc to come to the lab. I think he started in March, February or March, it was right around then. And so he was brilliant in teaching everybody Python and basic programming and then some of the computational tools that he knew and helped us to analyze the data that we were getting back three or four weeks after that. So it was a lot of uncertainty, obviously, across the board for the first month or two there. And then by about, jeez, I can’t remember May, June, July time frame, we started to get the indication that we could come back. So we didn’t do any COVID research directly or indirectly. And so we weren’t prioritized in the labs, but a number of colleagues here did. And it was actually pretty exciting to see the Vaccine Institute dive in. And Duke is lucky to have a BSL-3 facility.

[00:22:46] So we had the ability to work with the virus in a number of those suites right off the bat, and everything from testing on campus developed by some of the folks in the Vaccine Institute to a colleague of mine upstairs, Nick Keaton, who works on flu, had a big contract from DARPA that they basically said, we want you to shift some of this to COVID. And all of a sudden, he generated all the tools and reagents to shift to do some screening and developing assays for COVID infection in cells and in animals. And there were a couple of other labs in our department and on campus that I think, again, either diagnostics and screening or really doing some biology very early on. And so a lot of that work has come to fruition and been published, a lot of really exciting studies at all those levels actually. We were one of the earliest places to start doing pool testing of COVID samples and so on campus for undergraduates and ultimately the research staff, whoever was going to be on campus, they found they could pool actually up to ten, but I think they ended up with five samples per and really reduced cost and kept sensitivity and specificity high. So there was a lot of efforts on that front. And then a lot of the the research that was ongoing while all of us were at home on our computers, there was quite a bit being done still at Duke.

[00:24:07] And so then over the summer time, they open up the research labs with distancing and masking and started at 15 foot distances. And not long after that I think got to six. And so we were lucky we had pretty decent sized lab space and so we were able to accommodate most folks back in the lab full time. But tissue culture was a little tight. A lot of labs struggled with density and so they had to have shifts for their scientists coming back in. So that really, I think, compromised a lot of the return to the lab for folks. But like I said, we were lucky in that regard, just space wise. So things other than the fact that everyone’s wearing masks and distancing and there’s a lot of uncertainty for the next 6 to 8 months, things were basically back to normal. We were able to ramp up and get our experiments going again. I think the other big hiccup has been just ordering, just getting supplies in. Because lab supplies have been in high demand, obviously, over the course of the pandemic. And so right early on, we donated our gloves and our masks and everything that we had to the hospital to help them keep up with the PPE needs.

[00:25:23] So then there’s this phase of the vaccine. We just watch the data come rolling in. And there were trials here and things were approved and like, next thing you know, the whole lab is vaccinated and it’s just like, wow, here we are. Like, we’re in this pseudo post-pandemic world. We’re still masking in the lab, obviously. So there’s that and distancing is the same. But everyone feels a bit more comfortable with being together in the lab. So everyone’s basically back on the same routine. And we’ve had a couple outdoor lab meetings together and everybody’s really looking forward to getting off a zoom. And that’s the upshot is like the day that we can have in-person lab meeting again and then ultimately seminar speakers and folks on campus. I mean, everybody’s really looking forward to that. In April of last year when we were shut down, Duke really had a number of investigators and a number of different fields coming together to work on COVID, ranging from the testing to vaccine development and testing to developing animal models and screening in cell lines. So this whole enterprise of COVID research just manifested over literally weeks or maybe a couple of months.

[00:26:45] Once the sequence came out, everybody knew what we were dealing with. And so even if you weren’t a card carrying corona virologist, you knew what a polymerase looked like and you knew what a spike protein looked like and you knew what the length of the RNA was and the structures of the RNAs. And so the whole Duke Research enterprise really took a serious look at this virus and started to make some headway. And so we organized a symposium about mid-April that brought together all of these folks, everything from Coronavirus 101 basics for everyone to therapeutic ideas to vaccine approaches. And it was just Duke investigators. And we had over 1000 people on the Zoom call on campus. It was restricted to Duke. I mean, it was astounding. An all day symposium on this new virus. I have goosebumps thinking about it like it was such a well attended event. And it just was organized, great discussions. It was fantastic. And it spearheaded a lot of the efforts on campus to study this virus. And so that’s been maintained. They have a, I think, biweekly colloquia on COVID research and again coming from all these different fields. And so it’s cool to see what’s happened on campus research wise and screening wise for COVID.

Grace Ratley: [00:28:10] Yeah, that is incredible. I just find all the collaboration that has come out of COVID to be so exciting. Obviously within a university like collaboration between departments. And then there’s been a lot of collaboration between biotech and academia to develop the vaccines and a lot of collaboration internationally. Now that we have all of this infrastructure in place to really communicate long distance from home. And to me, it’s really exciting and I hope that the collaborative atmosphere is something that is maintained even after we go back to doing things in person.

Micah Luftig: [00:28:45] One of the things that I hope it showed the public is just how collaborative globally science really is. I mean, we were lucky to have Zoom and Skype and everything else in place to be able to do it, but we’ve been collaborating with people around the world the whole time. And so this idea that a virus that’s identified in China, that the sequence is posted and researchers in Germany and Cambridge and everywhere else around the world can just immediately start working on it and sharing information and sharing reagents that the community would come together, really rallying around this common enemy. I think it’s great for science. I actually think that despite all of the challenges that we have in this country, at least with regard to science as truth or not, I think it showed those that are willing to listen that there’s actually a lot of really great collaborative work that’s been done where there was an infrastructure there and then new pathogen inserted. And then here you go. We can all work together for this common enemy. But for the first three or four months, six months, maybe, my wife who’s not a scientist was listening to Twib every week. This week in virology and like, really getting into the details of mutations and Spike and the T-cell responses and what’s the neutralizing antibody and all this stuff. And The New York Times and all of these news media outlets have just educated the public broadly about how viruses work, how the immune system works. And so it’s really cool to have this collective education happening in real time on this pandemic. I hope that we can retain that level of engagement with the public in terms of communicating how these pathogens work and how scientists work and all of that stuff.

Grace Ratley: [00:30:47] Certainly I’m sure that it’ll inspire a new generation of young scientists, especially those interested in virology and biology at large. Speaking of inspiration, I figure this is a good time to try and transition to what led you to become a scientist. So I guess you probably didn’t have a global pandemic to really spark your interest in Epstein-Barr virus. But tell us a little bit about what got you into science.

Micah Luftig: [00:31:16] Sure. This one’s actually easy. It’s a dirty little secret. My dad’s a virologist, so that’s what got me started. My dad studied viruses since the 60s. He worked on phage in graduate school and his postdoc, and he used the electron microscope to study the structure of viruses and moved to retroviruses in the 70s and 80s and discovered the retroviral proteases that are important for maturation of retroviruses including HIV, and also worked a little bit on adenovirus structure and function. And so when I grew up in Louisiana, he was the chair of microbiology at LSU Medical School in New Orleans and had started to already wind his research lab down and was doing more mentorship and administrative work, but really was someone who inspired me to think about viruses and challenging biological questions. So when I was a kid, I would go to American Society for Virology meetings in college campuses in the summers, met virologists there and started to go to talks when I was about 14 or 15 and started asking questions when I was about 16 or 17, and they would say little Luftig in the back. What’s your question? And so, yeah, I just loved it. I really thought viruses were such fascinating little machines. I guess what I wanted to do, though, as I went through high school and college and started thinking about really what I wanted to study was I was always interested in Math pretty heavily. So quantitative biology was an interest. And then I have always been really interested in cancer. It’s just one of those great challenges. And so my dad didn’t work on cancer viruses, although I did say HIV was an indirect one, but he didn’t work on any of these oncogenic viruses. And I wanted to do something different. And I had worked in a herpes simplex virus lab when I was in college at LSU, and then I had an opportunity to go to the CDC when I was between my junior and senior year in college, and we were working on this new virus that had been discovered called KSHV Kaposi sarcoma associated herpesvirus. So I guess there was my own little pandemic or at least viral discovery moment. And so we were characterizing glycoproteins of KSHV, and I went to the CDC and worked in the herpes virus section there, and I learned a ton of basic virology and biochemistry and viral characterization. And that was on an oncogenic herpes virus. So I thought this is pretty cool. But it wasn’t clear that any of the tools were really in place to study this virus yet. And so I wasn’t quite ready to jump into that for graduate school. But in talking with my mentors about my interest in oncogenic viruses and being in a great environment and just the challenges of these complex viruses, I landed on EBV as the one to go after it was discovered in 1964, and we knew all about the genome structure and the RNAs that are expressed and all these crazy latencies and the B cell immortalization and all this stuff. And so I basically wrote to a handful of EBV Labs and said, I’d like to work with you. And then I applied to those schools and wound up going to Harvard and working with Elliott Kieff, who is one of the real pioneers in EBV molecular virology. So that was the backstory of how I got interested in viruses.

Grace Ratley: [00:34:56] Yeah. And then after your PhD, you did your postdoc in Italy. Tell us a little bit about that. How did you wind up there?

Micah Luftig: [00:35:03] Yeah, that was a pretty non-traditional decision. So when I was a graduate student, we were required to do two rotations, not three. And I really knew I wanted to work with Elliott Kieff, so I had to do another rotation. So I met with folks and I really enjoyed meeting Don Wiley, who is a crystallographer, who had solved the structure of the influenza haemagglutinin protein and also MHC Class 1 to show what the peptide presentation looked like. Really preeminent structural biologist and virologist. And I met with him and I was telling him about our work on glycoproteins of herpes viruses, and he said we were given these herpes virus glycoproteins to solve. And I don’t know anything about herpes viruses, but it sounds like you do. So he said, Well, why don’t you come work in the lab as a rotation student and you work with this postdoc I have named Andrea Carfi. He’s a great crystallographer, but he doesn’t really know anything about viruses either. So why don’t you guys work together? And I think you’d be good for him and you’d learn some things from him. And I thought, Wow, Don Wiley thinks I’d be good at anything. That’s cool, Let’s do it. And it was just a really amazing, amazing experience. So Don Wiley and Steve Harrison, who was one of the first to crystallize the structure of whole viruses. They had shared a joint lab since the 70s at Harvard, and they actually had one lab in Cambridge, one in Boston at the medical school.

[00:36:33] And so I rotated with Don technically or with Andrea, this postdoc in the lab in Boston. And I went in the summer before graduate school because they had an opportunity for us to do that and spent three months full time, knee deep or head deep whatever, into studying or really into learning biochemistry and crystallography at a very basic level. And it was awesome. I mean, it was beautiful. We purified proteins that we expressed in baculovirus. I was challenged constantly. It was the kind of thing where all of the basic knowledge I had from undergrad, which I thought was pretty good, I had purified viruses and run gels and done all kinds of techniques and I would be challenged. Andrea would say, Well, how does this work? Well, how do you think these proteins actually fold or how do you think this? I just didn’t really know. And I had to do this exploratory sort of self, not totally self driven, he was making me do it. But I had to learn all this stuff. Not just practical stuff about how you purify proteins, but why do you do it this way then that way. And it was just a transformative experience being in Don’s lab and with Andrea and the folks that were in that lab at the time and have always been are now world leaders in virology and infectious disease biology. It’s amazing that I had that opportunity.

[00:38:02] So I spent about almost a year in Don’s lab rotating, crystallize the herpes simplex virus gD glycoprotein D bound to its entry receptor nectin-1, went on many trips to synchrotrons to collect diffraction data on crystals almost. But didn’t quite get to solve the structure. We didn’t have high enough resolution data. You’re probably wondering at this point, what does this have to do with Italy? Except you did hear an Italian name along the way. So I moved to Elliot’s lab and started my thesis work. I actually came back to Don’s lab to do some stuff on some other glycoproteins that he had acquired from a collaborator. And so I still have my feet in the structural biology world a little bit. I really loved it. And then sadly, actually, Don passed away in 2001, and I was in Elliot’s lab a couple of years at that point and just really sad situation. And so Andrea, the postdoc I was working with had been applying for jobs and he was recruited to be the head of structural biology at a Merck research lab site in Rome. And it was this really beautiful opportunity for him because the place was actually a hybrid institute where they had students and postdocs, but they also had Merck funding and Merck pharmacology and chemistry and drug development and everything else. And he was recruited to publish well and to do Merck work. It was kind of a hybrid situation.

[00:39:35] So he goes there and then I wrapping up my PhD, I had a short list of folks I wanted to do a postdoc with more in cancer biology. I did my PhD with Elliott mostly on NF-kappa B signaling from this viral protein, LMP1 and EBV. And that was really exciting. But I wanted to also do broader cancer biology signaling and so forth. But I don’t know exactly what it was. My wife and I went to Italy for the last year of graduate school and just really fell in love with it. We backpacked around for about a month and saw Andrea, spent some time with him and connecting and when it came down to deciding what to do, we were in touch. And I said, What if I came to work with you? And he said, Why would you come work with me? You could go anywhere in the world with your credentials. And I said, Well, because I know you and I know our relationship and I think we could do amazing things. We could really solve some cool structures. And I said maybe what I’ll do is I’ll come there, we’ll solve some cool structures, and then I’ll go do a postdoc in cancer biology and David Baltimore’s lab or something at Caltech, if David’s ever listening to this now he knows that story.

[00:40:46] Anyhow, I convinced him that that was a good idea. He would be happy to have me. So he wrote up. We wrote up an Italian fellowship. I got it. And we packed our bags. And my wife, who was five months pregnant, we got on a plane and we went to Rome and moved into an apartment provided by the institute initially. And I started working. I was thinking I would do when I got there was to solve the structures of HDAC histone deacetylases, which had not been solved at that point. And there was a big biochemistry effort there and there was a lot of enthusiasm around HDAC inhibitor called SAHA that had been developed and Merck was in the process of acquiring that company and getting into stocks and a lot of biochemistry and chemistry and cool stuff was going on at that site. But I knew that they were also doing viral stuff. They were working on Hepatitis C virus, they were working on HIV, and Andrea had brought some of the herpes projects with him from Don’s lab. So I get there and rather than HDAC as the project, they say, Well, we just identified this new neutralizing antibody against HIV. And this was a time where in the field there were less than a handful of what are called broadly neutralizing antibodies, which was thought to be the holy grail for HIV vaccine design. And frankly, it’s still the holy grail for HIV vaccine design if you could elicit these.

[00:42:11] And so they said, we have this new antibody that we discovered. We’ve got the heavy and light chain plasmids. You want to make this thing and see if you can express it and crystallize it with Gp41, which is one of the HIV fusion proteins. I said, okay my dad worked on HIV, so I really don’t want to do this for a living. But I’ll give it a go here if this is new and exciting. And really, I wanted to cut my teeth with an exciting crystallography project more than anything. Things just worked. Things just went really quickly. Like we made the antibody, I purified it. Marco Mattu made the Gp41. I made the complex. I purified it. I crystallized it and in a total of four months, I had a 1.9 angstrom structure of this complex. And it was amazing. It was beautiful. Like it actually told us something unexpected. But also that corroborated some of the genetics that the other groups were doing. They hadn’t even published the identification of this antibody yet before we had the structure. So obviously I made a lot of friends on the Merck research video conferences, both in Rome, but in New Jersey and West Point where they were calling in from. And so we had a really great time developing that story and our understanding of HIV neutralization from that work. And I followed up a little bit on that, trying to make the antibody even better at neutralizing by predicting mutations that one could make to improve the structural interface and whatnot.

[00:43:41] But really what I had an amazing opportunity to do though, was to switch gears and I actually won an EMBO fellowship. So that’s given to postdocs that are moving from one country to another, probably the only one maybe ever that went from the US to Italy to do it. But nevertheless, I was a part of this cohort, which is a really cool group of, it’s probably 100 or 200 every year or something, but mostly Europeans either going to the US or other countries. But then you get together at meetings and stuff like that. And so I had this EMBO fellowship so they weren’t paying for me. And like I said, it’s an institute where there are students and postdocs and it’s a really cool environment. And I just started to think about what I wanted to do next. What I thought I wanted to do was cancer still. But I wanted to bring the structural biology background that I had been developing to a problem in cancer biology. And so just around this time since about 2004 or 2005, there was a paper published in Nature reviews cancer called the Census of Cancer Genes so the first shot at cataloging all the genes that were mutated in cancer. And there was something like 200 genes, and it had the functions of the proteins and where the mutations were and what cancers they were in and all this stuff.

Micah Luftig: [00:45:06] And I just spent weeks studying this census thinking about which gene am I going to land on and couple the genetics and signaling and cancer biology with structural biology. And it’s going to be beautiful. We’re going to understand how cancer works, at least for this one, protein or one system. And I landed on a gene called ATM, which is a DNA damage response kinase, many mutations in cancer, breast cancers, lymphomas, lots of different cancers and ataxia telangiectasia where the gene comes from is actually a cancer predisposing syndrome. And so there was a lot of cool stuff to do and there was really great signaling work that had been done on how ATM works. And so I started writing to people and asking for constructs and developing, the tools to study the signaling and start doing structural biology on my own. I had the blessing of Andre and the Institute director, and I thought it was like a brilliant project that I had written up and started applying to jobs, academic jobs in the United States at top notch places with this set of ideas and some preliminary data in mind. And it was fairly naive frankly of me to think that I would be competitive for those jobs or ambitious, maybe you could say.

[00:46:29] And so I started getting feedback from some colleagues that were in the field and they said, this is all great, but you’re not working in this field. You’re not pedigreed in cancer biology right now or in ATM signaling. It’s great you have some new data, but that’s not how it works. And so the advice I got was interesting, which was go back to the virus. You’re not that far out of your PhD, go back to your virus that you started with your cancer virus. What are the most exciting and interesting questions there that haven’t been answered around the same time? As I tell the story, I realize how serendipitous it is. But around that time, Antonio Lanzavecchia comes to our institute, who’s a famous immunologist who studies B cell, T cell interactions, and he was really interested in identifying neutralizing antibodies to SARS 1. At the beginning of his talk, he said, I wanted to use EBV immortalization of memory B cells to expand them to identify neutralizing antibodies. But it turns out it’s really inefficient like only 1% of the infected cells grow out and so we can’t screen anything. So he said, but we found a trick to get EBV to immortalized 100% of the cells. And the trick he used was to add an agonist of the toll like receptor 9. And together with EBV, he actually got a much more robust outgrowth that then allowed him to identify neutralizing antibodies to SARS.

[00:48:04] And I thought I’d never heard anybody say EBV immortalization wasn’t efficient. And so I look back at the literature and it turns out two papers, 1977 Journal of Virology, the efficiency of EBV transformation is about 1% of infected cells. And I thought, Well, jeez, that sounds like a problem. What’s going on in 99% of the cells? And how does that work? To cut a long story short, at the same time in 2005, there were a series of papers in nature showing, of all things, the DNA damage response, ATM-Chk2 and ATR-Chk1 were responsible for sensing the earliest events in oncogenic stress. So when an oncogene is activated, induces replicative stress. The DNA damage response gets activated and that prevents the cells from continuing to grow, either by causing apoptosis or cell cycle arrest. And so if you eliminate those pathways genetically or however, you get growth of tumors more robustly, and that also reconciles the cancer predisposing nature of an ATM. And so all this stuff was coming together and I thought, geez, I wonder if EBV is inducing the DNA damage response early in infection. And that’s why most of the cells don’t grow out. The answer is yes. We started scratching the surface of that, but I wrote the Proposal for Jobs on this idea of EBV and the DNA damage response that I then ultimately got an interview at Duke and a couple other places and landed here in Durham and started my lab.

[00:49:46] And over the next maybe two or three years, we worked it out in primary B cells. That was our first big paper in 2010 we published to show the DNA damage response was indeed a barrier or a repressor of transformation. Probably 5 to 10 fold of that 100 fold restriction, the DNA damage response is responsible for that. The cool twist is that that actually collaborates with TLR9 agonists and can make efficiency even better. And so you can imagine there’s a practical application, which is if you want to identify antibodies to SARS 2 or HIV or flu or anything else, you take memory B cells from some convalescent patient, put them in culture with EBV. But now not only do you activate TLR9, but you inhibit the DNA damage response and you get a much more robust outgrowth and you can screen many more wells for possible antibodies that are being made. And so now, I would guess most vaccine institutes and companies use this approach. I know that our Vaccine Institute does. I know that James Crowe at Vanderbilt does. I know lots of other people, because when we made that discovery, we published it and we shared that information with all those folks. And so it really helped improve the efficiency of that process and help to identify antibodies for lots of different pathogens.

Grace Ratley: [00:51:10] Wow. Well, we have made it full circle. And what an amazing story. It’s been wonderful talking with you today Micah. Thank you so much for coming on the podcast. I learned so much and it was just really awesome to get to talk to you today.

Micah Luftig: [00:51:22] Thank you for having me. It has been a lot of fun too.

Transcript of Episode 26: Jim Ray

Disclaimer: Transcripts may contain errors.

Grant Belgard: [00:00:00] Welcome to The Bioinformatics CRO Podcast. I’m Grant Belgard. And joining me today is Jim Ray. Jim is the executive director of the Neurodegeneration Consortium at MD Anderson. Welcome, Jim.

Jim Ray: [00:00:10] Hi, Grant. Thanks for having me. It’s great to be here.

Grant Belgard: [00:00:13] It’s great to have you. So can you tell us about your work at the Neurodegeneration Consortium?

Jim Ray: [00:00:18] Sure. So I’m at MD Anderson Cancer Center, which is part of the University of Texas system. And it’s the number one cancer hospital in the United States. So it’s a place where patient care is of utmost importance, but it also is a very strong research institute and one of the investments MD Anderson has made is in drug discovery. We have an entire division committed to discovering novel therapeutics, and not surprisingly, most of it is focused on oncology. Being that it’s a cancer center, but my group is actually focused on neurodegenerative diseases. Alzheimer’s is the primary focus of our mission, but in the process of studying the pathways that lead to Alzheimer’s disease, we feel like we can also impact other neurodegenerative conditions like Parkinson’s and multiple sclerosis, ALS, as well as provide therapies hopefully one day for cancer patients receiving therapies that damage the nervous system. I think one interesting opportunity that’s come out of this being at a cancer center as a neuroscientist working on neurodegeneration is understanding how devastating cancer therapy is to the nervous system, whether it’s whole brain radiation or whether it’s chemotherapy. And many of those same pathways that are activated to cause this damage are the ones that are important for Alzheimer’s disease. So that’s the space we live in, is looking at the intersection between neurotoxicity and neurodegenerative processes.

Grant Belgard: [00:01:42] And how long is MD Anderson had a big presence in neuroscience?

Jim Ray: [00:01:45] We have a lot of neuroscientists there that have an oncology angle to brain metastases are a critically important area of research, so there’s a lot of people who are interested in that as well as these neurotoxicities. Cancer causes depression and fatigue. Cancer therapy causes neuropathy and cognitive impairment. So I was actually pleasantly surprised to find a relatively robust neuroscience community here when I came. However, we don’t have much of an emphasis on neurodegenerative disease historically, so for that reason, we actually teamed up with our partners at MIT, where Dr. Li-Huei Tsai is the principal investigator there participating in the NDC and at Mount Sinai School of Medicine, Dr. Alison Goate, who’s the director of the Alzheimer’s Center there and is an Alzheimer’s geneticist, is part of our consortium as well. And then we have a number of academic collaborators at other institutions, and that really beefs up our ability to explore novel areas of biology outside of the walls of MD Anderson.

Grant Belgard: [00:02:46] You went to MD Anderson from Takeda, right?

Jim Ray: [00:02:49] That’s right, yes.

Grant Belgard: [00:02:50] Can you tell us about that move? And I guess also moving from San Diego to Houston?

Jim Ray: [00:02:56] Yeah, well, my career has been entirely in biopharma. I’ve spent 11 years at Merck, and then I left to help start a company called Envoy Therapeutics, which was based in Jupiter, Florida. We were acquired by Takeda, so left from Jupiter, which is an incredibly beautiful place to live, to San Diego, which is an incredibly beautiful place to live. So I could be part of the Takeda experience after the acquisition and it was fantastic, loved it. It’s a great company, but my wife is from Texas. At least half my family’s from Texas, and MD Anderson had this amazing opportunity to do something very different, and there was quite a bit of philanthropy that had been raised to entice MD Anderson to dedicate some of their resources to Alzheimer’s disease. They just needed somebody who knew drug discovery to come in and try to lead it and thought it was an exciting adventure and get a chance to live close to family. And why not? Moving from Jupiter to San Diego to Houston wasn’t sounding so great from a location point of view, but actually, Houston is a very exciting place to live. We have the largest medical center in the world here. There are just thousands of faculty in the area. There’s like 10 million patient visits here a year. So the access to the science is amazing. So I really have enjoyed my time here.

Grant Belgard: [00:04:13] Yeah, I was an undergrad across the street at RICE, so I’m a big Houston fan.

Jim Ray: [00:04:17] Oh, is that right? I didn’t know that.

Grant Belgard: [00:04:19] So how do you think all your time in BioPharma has impacted the decisions you’ve made as head of the consortium? And do you think there are maybe ways that you approach decision making and so on in a different way than maybe you would if you had come up through the professorial path?

Jim Ray: [00:04:38] Oh, it’s tremendously impactful. Like I said, I started at Merck and spent over a decade there. So at the time I joined, Merck was the largest pharmaceutical company in the world, then later acquired Schering-Plough make it even bigger. So I got to be trained by the best. These were some legendary figures in medicinal chemistry and drug metabolism. And the power of a large organization like Merck or GSK or Pfizer is unbelievable. It was fantastic education in terms of learning drug discovery, but not only drug discovery, but how to think strategically about the entire process of making therapeutics. And it’s so much more to it than the science. It has to be commercially viable. It has to have a strong patent position. It has to have a clinical path. You have to be able to distribute it. You have to be able to educate physicians on how to deliver it. That entire chain of events exist in large pharma. So it’s I think everyone who’s interested in drug discovery should experience it to get the entire picture. Then going from there to a small startup, I think was employee number six.

Grant Belgard: [00:05:41] You need everyone to be a generalist to some extent, right?

Jim Ray: [00:05:44] Yes, exactly. Now you learn everything yourself. It’s you can’t call somebody and ask them what to do. And that was also a great experience to tap into that entrepreneurial spirit and that innovation that pharma relies on to feed their pipelines, it was great. And then Takeda was a mid-size pharma, so sampling all three of those environments was extremely helpful in terms of building up the skill set to actually do drug discovery from end to end.

Grant Belgard: [00:06:12] And so how do you accomplish that through the neurodegeneration consortium, I mean, it sounds like you work with a bunch of academic groups, you work with some companies. How does that look?

Jim Ray: [00:06:20] Although we’re located within a research hospital, we’re actually very similar to a biotech company. We are not faculty. We’re administrative staff hired by the institution to produce therapeutics, and we work in project teams across disciplines. We have medicinal chemists, we have antibody specialists, cell therapy specialists, manufacturing for cell therapy. We have drug metabolism. All the disciplines that you see in a mid-sized biotech company are available to us either internally or through our contract research network. So it’s partially a hybrid model, but it basically we have all the capabilities necessary to take drugs from idea stage all the way into phase one. On the oncology side, you could continue in clinical trials at MD Anderson, but for the Alzheimer’s and neurodegeneration side, we would partner with people who have those capabilities. We don’t have a clinical operation to do those studies, but we can take drugs from one of our collaborators has an idea. We can screen for inhibitors or activators of the pathway and then optimize compounds and prepare them for clinical trials.

Grant Belgard: [00:07:24] And what impacts have you seen from COVID and how do you think those impacts might be different with the model you have versus a fully integrated pharmaceutical company versus a biotech startup?

Jim Ray: [00:07:35] Being in a cancer hospital where we have immunocompromised patients, extraordinary caution had to be taken. We actually shut down the labs for an extended period of time. And during that time, we have a relatively small team, full time dedicated on the neuro side. We didn’t have a lab to go to, so we spent 3 or 4 months just thinking about the disease. And that was really exciting, actually, a period that I was really worried about that people would lose engagement or not know how to contribute if they were primarily working at the bench. But it turns out that everyone really contributed to thinking about new pathways and disease mechanisms, and we came out of that period invigorated and ready to get back in the lab and try some of these ideas. So it was an extremely disruptive not only for us, our partners in other countries, in Italy and the UK and Germany and so forth were being shut down as well. But I think at the end of the day, learning to work remotely, learning to tap into talents that we didn’t know were there, these have all been benefits of having to rethink the model in which we work.

Grant Belgard: [00:08:43] And if you can talk about it, what mechanisms are you most excited about?

Jim Ray: [00:08:47] Well, I think we’re in an extremely exciting moment for Alzheimer’s research right now. When I was a postdoc, it was the first big breakthrough in the field, and that’s when two genes, the amyloid precursor protein and presenilins, presenilin 1 and 2 had been found to be causative in familial Alzheimer’s disease. And they were linked together mechanistically, as it turns out for those of you who know the story, the villains are actually enzymes that cleave APP to release the a-beta fragment which forms the plaques and Alzheimer’s disease. I think we’re at that same type of moment again, and that’s due to the power of human genetics studies that have been published over the last 5 to 7 years. We now have at last count, I think, around 75 genetic risk factors for Alzheimer’s disease, many of which map to the myeloid cells of the brain, which are the microglia. The most powerful known risk factors for Alzheimer’s are microglial expressed genes. They’re not expressed in the neurons at high levels, and that caused the entire field to pause and rethink the disease mechanism. So we’re very interested in finding pathways in microglia that can be modulated by small molecule therapies. So that we can promote a disease protective phenotype in these cells or to prevent them from aggravating the disease because they seem to be the gatekeepers in terms of whether you progress to a disease state or simply accumulate a little amyloid with age as most people do.

Grant Belgard: [00:10:15] Do you care to comment on the amyloid hypothesis and biogen’s drug?

Jim Ray: [00:10:20] Sure. I think the amyloid hypothesis has been extremely important for the field, and you have to think back to where Alzheimer’s was before the amyloid hypothesis. Most people who weren’t scientists in the field thought of senility as something that happens to some people as you age. Maybe it’s inevitable. You just kind of get that point. And it was the amyloid hypothesis that gave a molecular underpinning to a disease process that actually could be stopped and the field changed dramatically. As a result, people started making a-beta in the lab and aggregating it and giving it to neurons and seeing what happens. And the clinical trials, of course, have been disappointing. We as a field been able to remove amyloid from the brain or inhibit the production with BACE inhibitors and seen no real clinical benefit, with the exception now of a couple of antibodies, one from Biogen, the Aducanumab, and then Lilly’s antibody have both shown some hints of, I think most people would describe as modest activity. So a lot of people would like to say that the amyloid hypothesis has been disproven or I think that’s a little harsh. It may be that you need to intervene way earlier in the process, that once you get accumulated amyloid, a second phase of the disease has been triggered and it’s no longer relevant to remove the amyloid. If you get early enough, you can see some hints of activity. But regardless, we’re learning a tremendous amount from this experience. I mean, you don’t know until you do the experiment what the answer is. We did the experiment and we’re starting to learn the answer. I think the current hypothesis around tau spreading like a prion and microglia contributing to this process may be where the new wave of therapeutics are going to come from, and those may wind up being more effective in people with the disease.

Grant Belgard: [00:12:09] And what do you think about these reported associations between gum disease and Alzheimer’s and Gingivalis antibodies and so on?

Jim Ray: [00:12:17] It’s really interesting. And you can expand that to herpes infections and other forms of viral infection or fungal infection or spirochaetes. There’s actually a fungal infection. There’s a long list of systemic infections that people have linked to Alzheimer’s with varying degrees of validation of the data. I think actually the dental health angle with the gingivalis infection is a strong link. The Cortexyme is going after that aggressively with their phase two trial. I think it makes sense that if you’re chronically inflamed due to some low level infection, that it could influence the priming of your microglia, which in turn could change the way in which they are addressing other age related problems in the brain. So I think it’s an interesting hypothesis that deserves some investigation. Absolutely.

Grant Belgard: [00:13:12] It’s quite interesting, isn’t it right, that the genetics for Alzheimer’s is pretty convincingly pointing towards towards microglia, but that’s certainly not the case for a number of other neurodegenerative disorders. What’s your working model of how different neurodegenerative conditions are related to one another? Like if you were to cluster them into a few buckets, which ones would be put together and why?

Jim Ray: [00:13:34] A interesting question. So the way I personally look at it is that all of these diseases are ultimately driven by protein misfolding and not the most novel thought I’ve ever offered. But a lot of people think of it the same way and then how exactly it manifests differs by disease. So the genetics of Parkinson’s are quite different than Alzheimer’s, but ultimately you do have alpha synuclein aggregation. Just like in Alzheimer’s, you have tau and amyloid, same with TDP-43 or 12 and tauopathies, etcetera, or even in Huntington’s disease. So these protein misfolding accumulation seems to be central, but seems also to be caused by a number of different upstream factors and the genetic forms of the disease, it can be overproduction of the protein or a mutation in the protein that makes it more likely to aggregate. But in the sporadic, much more common forms of the disease, I think that’s an open question why age related neurodegenerative diseases manifest in one person as ALS and in another person as FTD, frontotemporal dementia. And that’s the best example because in many cases, the risk factors for those two very different clinical diseases are the same.

Grant Belgard: [00:14:45] It’s wild.

Jim Ray: [00:14:46] Yeah, it is. It is. There’s a lesson in there somewhere. I’m not sure we totally understand why those pathways differ in people to drive them in one direction versus the other.

Grant Belgard: [00:14:59] Most of these diseases we’re talking about, the biggest risk factor is age. How do you think about aging?

Jim Ray: [00:15:05] Absolutely. So our brain is a unique organ. It’s protected behind the blood brain barrier that presents, of course, a necessary element to its function. And protection against infection, which I’m sure evolutionarily speaking, was very, very important. But it also presents some challenges. You don’t have access to the same level of clearance mechanisms you would in, let’s say, your liver or other organs. So you have to have special clearance mechanisms, the ones that appear to be really important in the brain include autophagy, the Glymphatic system and microglial mediated phagocytosis and clearance of debris and so forth. All three of these are compromised during aging. So whether your, for example, the Glymphatic system is triggered by sleep in part. So as your age, your sleep gets disrupted, deep sleep particularly in which you might expect the clearance of misfolded proteins and other toxins to be at its peak is reduced with age. The ability of mitochondria to supply energy to highly energy demanding processes like autophagy or like phagocytosis is diminished. And so I think aging is particularly impactful to the brain environment because of its unique physiology and because of its protected behind the blood brain barrier. Those elements conspire to make the brain a place where proteins can aggregate and then eventually trigger inflammation in the disease.

Grant Belgard: [00:16:34] So speaking of the Glymphatic system, I mean, this may be a bit of a detour, but do you think there will be any other huge anatomical surprises like that to be found?

Jim Ray: [00:16:44] Wow, yeah. That the Glymphatic system is one of those that as soon as it was discovered, you had this V8 moment, if you remember those commercials where you’re like, Oh yeah, that of course that’s there, right? I should have known that, should have predicted that which is how something’s a great discovery when it’s obvious the minute you hear about it. So I think there’s still a lot to learn. I’ve been a little bit interested, for example, in these little tiny connections between neurons. People have seen these tunneling nanotubes.

Grant Belgard: [00:17:13] Yeah, there was just a report out about exchanging mitochondria, right?

Jim Ray: [00:17:17] Yeah, exactly. The idea that these cells in the brain are exchanging subcellular compartments through exosomes or shuttling mitochondria between each other through tunneling. I think that cell interaction part, we’re just scratching the surface.

Grant Belgard: [00:17:34] Yeah. I really wonder about what would drive that in case of neurons have these single post-mitotic cells that need to survive for decades. And of course, their mitochondria may not make it. I don’t know if they’re like sharing mitochondria to maybe replenish that pool. Like I don’t know.

Jim Ray: [00:17:51] I think the reason why you would want this exchange is unknown as far as I know. There’s probably some good ideas, but certainly I haven’t seen an explanation myself. Of course there’s other ways to the cells are exchanging all kinds of material and then just the complexity of the synapse itself as a protein machine is beginning to be understood. I’ve seen some really cool papers where people have done reconstruction of the synapse from proteomics studies and ultra high resolution microscopy. So that element of the brain, I think we’re starting to really understand at a deep level. But all these other connections between brain cells are going to be needing the same level of attention.

Grant Belgard: [00:18:33] And how do you think about sleep? Like what’s always amazed me is the huge variation person to person in certainly how much sleep they need to feel rested. I don’t really know how well that corresponds to neurodegeneration risk, right? Like if you’re just naturally a short sleeper and you feel fine, is your risk not elevated even though you’re sleeping six hours a night?

Jim Ray: [00:19:00] Oh, that’s a good question. I suspect there’s research on that question that I’m not aware of. But definitely we know that disrupted sleep is coincident with Alzheimer’s. And if you interrupt sleep intentionally, you get all kinds of bad things that happen to you from a biomarker standpoint, including for Alzheimer’s biomarkers. It seems very likely to me that sleep is an important active process. And when disrupted, as David Holtzman and others have shown, you accumulate toxic proteins in the brain. So it seems like it probably is on the pathway there. But whether someone who needs four hours sleep only needs four hours sleep because they’re have a super souped-up clearance mechanism in their brain and everything’s clear in four hours and that’s all they needed. Or they’re actually feel okay, but they’re not. They’re actually sleep deprived in some ways, even though they feel fine. I think that’s a great question, Grant. I don’t know the answer.

Grant Belgard: [00:19:55] So let’s talk about your own path. When did you decide you wanted to be a scientist?

Jim Ray: [00:20:00] Oh, well, I wanted to be a neurosurgeon from the time I was 5 or 6 years old. I thought that was the coolest thing I’d ever heard, that you could actually operate on the brain. And I spent my entire life working towards the day I become a neurosurgeon, working in hospitals, worked in the OR, worked in the ICU for my summer jobs and premed path. And then one day I walked into this class called Molecular Mechanisms of Development which was an intro to molecular biology and the very first lecture I was blown away, changed my mind. I’m going to be a molecular biologist. I loved it ever since. I just couldn’t believe that you could clone genes. And it seems so obvious now.

Grant Belgard: [00:20:44] It is pretty cool. Right?

Jim Ray: [00:20:45] Right. This was 1988, 89. It was a long time ago. So now this stuff gets taught in high schools. But for me, biology had been memorizing anatomy, doing comparative evolution, learning the Krebs cycle, that kind of stuff. And but here, you could actually snip out a gene and study it in isolation and figure out what it does. And back then we thought we had 100,000 genes. I was like, Well, I just discovered one of those, that would be awesome. And I was particularly interested in differential gene expression. How come some genes are expressed in one cell type or in one situation, but not in others? How does that happen? How does that work?

Grant Belgard: [00:21:30] Well, it’s interesting that that’s still a huge question, right? Like you look at any kind of cell type marker patterning or something and you come up with different ribosomal protein subunits in different cell types and so on. You have this enormous specificity of genes that people often think of as more or less interchangeable, but it seems like they’re probably not.

Jim Ray: [00:21:51] Yeah, it’s amazing, isn’t it? I mean, going back to the discussion we were having a moment ago when people were isolating microglia from the mouse models for Alzheimer’s disease and sequencing them for the first time. The number of gene expression differences in those disease associated microglia is amazing. There’s thousands. It’s almost like a completely different cell type. If you were blinded to the experiment and someone just showed you the gene expression differences and you’re used to looking at gene expression data, you may think that someone was showing you two different cells, like a liver versus intestine cell or something. And the idea that those cells can switch their molecular phenotype so vigorously in response to an insult is amazing. And I don’t believe we understand that mechanism yet.

Grant Belgard: [00:22:40] How conserved do you expect those Microglial states to be among mammals?

Jim Ray: [00:22:47] Probably have a minority view on this one. I think ultimately we’ll find out they’re well conserved. I think that the original few publications that really concern the field oh my gosh, maybe the mice are responding so differently. It’s irrelevant to the human. May have had some technical challenges to those data and may have made the situation look more dire than it actually is. And one reason I think that is because one of the risk factors for Alzheimer’s is TREM-2 and the TREM-2 knockout mouse phenocopies in terms of microglial response to plaques, the human loss of function. So I think that the responding to, in this case amyloid plaques in a similar way, there will be significant species differences. But ultimately whether the exact genes are exactly the same repertoire, unlikely, but probably the net direction of the functional changes is going to wind up being similar.

Grant Belgard: [00:23:44] How do you think about definitions of cell type versus cell state? Like every single cell conference, people are always arguing about this.

Jim Ray: [00:23:52] Yeah, right. Well, I mean they’re useful. It’s useful to have markers for cells to be able to generate hypotheses, to be able to measure response to an intervention or a genetic manipulation. And to quantify your data. It’s all important to be able to do that. But I think during development, that’s an important concept because you can have irretrievable differentiation from one lineage to the X, and the cells then become very, very clearly different. But when you’re talking about the difference between a monocyte and a macrophage, it’s probably a gradient. There’s probably hundreds of variants of those two extremes.

Grant Belgard: [00:24:32] And it’s interesting. Even in the same organ, it seems like different cell types can be either discrete or fuzzy in different ways. So for neurons, oftentimes you see large differences relative to say astrocytes, where it often seems you have several axes of variation that are real and reproducible and so on, but that are more continuous than having discrete attractor states.

Jim Ray: [00:24:53] I agree with that. When I was at Envoy, the purpose of our company was to study cell type specificity in the brain, and this was using Nat Hines’s technology back trap, a ribo trap. What we learned is there are clearly distinct cell type states among neurons, but there’s also a tremendous amount of overlap and gradation between states. And I think the single cell sequencing data is going to eventually show that not every GABAergic positive neuron in the hippocampus is the same, that they’re probably intentionally somewhat different from each other. And we need to learn what those differences are and understand why they’re important.

Grant Belgard: [00:25:32] Yeah. Even in one of the early large scale single cell papers from the Allen Institute, they were showing these cells in these cross-over states.

Jim Ray: [00:25:42] Is that right, yeah.

Grant Belgard: [00:25:43] Cool. So can you talk maybe a little bit about the acquisition of Envoy and how things changed? And did you immediately move out to San Diego or did you stay in Jupiter for a while and then your role changed? How does the medium sized pharma acquisition of a small biotech look?

Jim Ray: [00:26:00] I think there was a huge lesson in that. I left the conference security of Merck where even though it’s not true in Big Pharma, you feel like that you could retire from there. Now there’s a lot of churn in the industry, a lot of turnover, but in terms of the spectrum of stability in our field, Big Pharma is on the more stable end. To leave that and go to a tiny little startup is a bit scary. So what you do is think about should I buy a house and should I make friends? What if we go bankrupt? What if we run out of money? What are we going to do? What if we don’t succeed? And Big Pharma if you don’t hit your objective for your I&D that year, you may take a hit at bonus time, but you don’t get fired. Usually in a small company, if you don’t hit that, you may not get your next tranche, you may not get any investors to step up. And so it could be disconcerting in terms of planning. And that’s fun because now you get to control your own destiny. It’s not up to someone else whether or not your drug is developed, it’s up to you. What I didn’t expect was that it could actually succeed. I was worried about what if it fails? What if this doesn’t work out? I never prepared for the possibility that we could have tremendous success and that be recognized by pharma and we be acquired that’s quickly.

[00:27:19] So that was a shock. And for anyone else who’s thinking about taking the plunge and going into a startup, I would suggest that you plan for success as well as failure, because obviously both can happen. Going back to Big pharma or mid-sized pharma after being in a small company, took a period of adjustment because you’re so used to being able to do whatever makes sense. So if we wanted to do a high throughput screen on a target that came out of one of our experiments, we could talk about it at lunch and then call a CRO that afternoon and get a PO generated before we went home that day. In pharma you have to go to the high throughput screening people, talk to them, then you got to go to the Target evaluation committee, talk to them. Then you got to write up the target CV and have that approved by another committee. And then you got to present to your department. It’s like completely different. So going back from this incredibly agile environment to a structured environment, it wasn’t bad. It was just a big difference in a period of readjustment.

Grant Belgard: [00:28:23] I guess in your case, you’re going back though, somewhat to something you were familiar with as opposed to I don’t know if there were others in the company where they had only been in small companies before.

Jim Ray: [00:28:33] Yeah, there were. And I think it was a shock for them. It was a shock to have governance, that it was a shock to have a bunch of meetings, to have to worry about your outlook calendar. So much in a startup, you just grab people and talk. In pharma, you need to schedule a meeting. It’s like two weeks from now we’ll get together for 30 minutes, just walking, sticking your head in the the CEO’s door to ask a question is something that doesn’t happen in a big company, but it can happen in a biotech company no matter who you are. There’s only 20 of you, maybe.

Grant Belgard: [00:29:09] And what advice would you have for people looking at drug discovery that maybe you see frequently violated?

Jim Ray: [00:29:18] Right. You have to be willing to take risk. Drug discovery is not for the faint of heart. I like to say this to people who are thinking about going into drug discovery. Let’s say there’s 50 science nature papers published a week and there may be 20 drugs approved all year, and about 15 of those are probably for oncology. There hasn’t been an Alzheimer’s drug approved since Namenda back in 2003. This is a field in which you are expected to fail at a very high rate. And if you play it safe and don’t take risk, it’s unlikely you’ll ever break out of that. It’s important that you’re comfortable taking risk and people who aren’t comfortable with that probably are going to have a hard time enjoying drug discovery. Another piece of advice is just based on my own experience. I would see drug discovery from a number of different angles. If that’s your field, if you’re an academic who’s done, who’s doing drug discovery and you’ve never been in pharma, I think you would learn a lot from it and vice versa. I think industry scientists tend to think that they know best, which I certainly felt that way when I was at Merck, because Merck was great and we felt we knew drug discovery better than anyone else. And in many ways that was true. But it turned out there was a lot to learn from going to a small company or going into an academic environment where the rules are different. Your risk tolerance is different, your decision-making is different. What’s exciting is different. Commercial considerations are different. And just to see the world in a different way is, I think, very helpful.

Grant Belgard: [00:30:53] What do you think from all your own experiences, from your own academic training, from your time at Merck, from your time at Envoy, Takeda, from each of those buckets of experience, what do you think is the most useful thing you learned from each of them?

Jim Ray: [00:31:09] One of the most useful things I learned at Merck was the art of being a manager. I think big companies do a great job of training scientists to be managers, and being a great scientist has no relationship to being a good manager. In fact, it may be somewhat anti-correlated.

Grant Belgard: [00:31:25] Very true.

Jim Ray: [00:31:26] Right. So learning how to lead a professional scientific staff is a skill set that postdocs just don’t have yet, generally speaking, and learning to do that really well and get the most out of people is a lifelong journey. Everyone can get better, but it’s just a great place to learn those skills. Going to a small company is where you learn the whole process because you’re everything from changing the toner and the printer to meeting with the search and evaluation director of neuroscience from a major company could be on your agenda that morning. Then getting back in the lab and doing experiments yourself and then writing a presentation for the board of directors. I mean everything, you see everything. So that’s a great learning experience. Being back in a more academic environment after being in biopharma for a number of years was also tremendously valuable and educational. I forgot where science comes from. I forgot about the trainees, the people who actually generate the figures and the papers you read, what their motivations are, what they’re like, what they care about, what kind of techniques they think are new and exciting. What motivates your typical professor? We all know this, but it’s recognition, it’s grants, it’s publication. That’s what their careers depend on. And after more than a decade discovering drugs, you forget at an emotional level what they’re going through. And just to be reconnected with the font of all of our knowledge, the scientists themselves in the academic institutions has been a tremendous experience.

Grant Belgard: [00:33:11] What do you think is the worst common advice you hear in this industry?

Jim Ray: [00:33:20] The worst advice, one piece of advice that I think is not particularly great is when bright young scientists are urged to go into industry too soon. If you’re interested in drug discovery and you’re getting your PhD, I would recommend in most cases, doing your postdoc before you go into industry. Establish yourself as a scientist. Get some papers on your CV. You’ll go in at a higher level with more influence. You will be given more opportunity. Generally speaking, there are exceptions, but I hate to see people who were maybe 2 or 3 years of coming in at a more senior scientist level with more opportunities and influence come in more like the guy who runs the binding assay because they pulled the trigger too soon on making the transition. Thus you hear less of this now. But people like this used to like to say that it’s very difficult to go from drug discovery to academics, and once you go there, you’ll never come back. Maybe others have heard that, too. I think that’s less true now than it’s ever been. You see a lot of people moving back from industry into academic environment and doing very, very well. So I think people shouldn’t think that if they decide to spend some time doing therapeutic discovery, that it’s the end of their academic career. It may actually be a boost to it.

Grant Belgard: [00:34:44] That’s interesting. Certainly do hear that a lot. But then I think there are a lot of cases examples of people like you. You’re in an academic institution after spending years in companies of all sizes. Great. Well, thank you so much for joining us today, Jim. It was really nice.

Jim Ray: [00:34:59] I really enjoyed our time together Grant and thank you for the opportunity. It was a great discussion.

Transcript of Episode 25: Fernando Martinez

Disclaimer: Transcripts may contain errors.

Grant Belgard: [00:00:00] Welcome to The Bioinformatics CRO Podcast. I’m Grant Belgard. And joining me today is Fernando Martinez. Fernando did his AB in physics at Princeton, followed by an MSC in biophysics at Stanford and a PhD in biomedical sciences at UCSD. He’s now a senior scientist at Fountain Therapeutics. Welcome, Fernando.

Fernando Martinez: [00:00:16] Thanks, Grant. Thanks for having me. I really appreciate the opportunity.

Grant Belgard: [00:00:20] Yeah, I really appreciate you coming on. So can you tell us about what you’re doing in Fountain?

Fernando Martinez: [00:00:24] Yeah, I’d be happy to. I’m just coming up on my two year anniversary on Fountain. I think it was maybe yesterday. We’re a company that’s interested in longevity and anti-aging technology. It was founded by a couple of people. But one person who’s involved is Tom Rando from Stanford, and he’s quite famous for his mouse Parabiosis experiments where he showed that blood from a young mouse could actually rejuvenate an aged mouse. So we have a modern spin on that where we harvest primary cells from young and aged mice, and then we put them in culture and we train various computer vision algorithms to estimate the age of images of the cells. So we can obviously train it because we know what the age of the mouse was ahead of time. Once we have a model that can estimate the age of cells basically from microscopy images, we screen drugs and then ask the same model to basically estimate the age of cells that have been treated with drugs. And we’re searching for compounds that might be able to rejuvenate or reverse some of the signs of aging. And so far, it’s gone really well. It’s really promising. I think everybody who’s involved has been really impressed. So as to my role, I joined Fountain like I said, about two years ago and it was a pretty small operation at that time. It was still small, but maybe there’s only like, I don’t know, I think five of us. And we’re just in a temporary space, an incubator space with a bunch of other small companies. I’ve been doing a whole a whole hodgepodge of different things. My boss, Joe Rogers, he actually calls me the utility infielder for Fountain Therapeutics because I just need to play whatever position the team needs at that time.

Grant Belgard: [00:02:20] Sounds like a startup.

Fernando Martinez: [00:02:22] Yeah. So far, I’ve been happy to do it. The main things that I did during my my first two years was trying to figure out how to automate and standardize the assay that we were doing. So mostly involved buying and setting up a couple pieces of automation equipment that let us increase our throughput pretty dramatically. So when I first started, we were maybe working with only a handful of 96 well plates and now we’re processing up to 6384 well plates per week, screening a whole bunch of different compounds. So that came about through optimization of our assays, but also finding the right equipment and configuring it to work for us. The other thing that I’ve been involved in, and I got roped into this just by chance, is we had someone leave that was spearheading a lot of the computational work, especially the image pre-processing. So there’s quite a bit of pre-processing involved in getting the microscopy images ready to go into a classification network, let’s say, for machine learning. So I took over a lot of that work, improving the performance and just adding features, I guess to our pre-processing pipeline. And I’ve been working on that with a software engineer that we hired and that’s been great. So yeah, it’s actually very different from the work that I’ve done previously in my career, but I’m happy with it so far. Like I said, I get the opportunity to be a utility infielder and do something different.

Grant Belgard: [00:03:56] That’s really interesting. So of course there are a lot of hypotheses floating around about aging. Which of those do you think are amenable to being rescued in cellular models and which do you think are not?

Fernando Martinez: [00:04:12] That’s a good question, and it’s interesting that you should bring that up because Fountain doesn’t actually use a hypothesis of aging. We do unbiased screening, but there are other people that have tried to select libraries, small molecules or large molecules according to a hypothesis. So in terms of which hypotheses are amenable and which are not, I think is still an open question, to be honest. I wouldn’t say that there is a drug on the market right now that anybody says is really like a rejuvenating agent or anti aging. But I can’t give you probably my best example and that would be arthritis. I guess the hypothesis there is inflammation. If you look at drugs, that interfere with the TNF Alpha pathway and Remicade and Humira are the biggest ones. That’s definitely hypothesis driven and there’s definitely something to it because those drugs have had a huge impact on how people treat arthritis. There’s cases where someone was in a wheelchair before they had access to one of these drugs and now they can play golf. There’s actually cases like that. We also know that they’re some of the best selling drugs on the planet that have made billions of dollars for the companies that made them. So I definitely think there’s something to the inflammation hypothesis if that’s where people want to look. There’s other things like senescent cells, that hasn’t worked out for anybody yet. But, who’s to say that that it won’t.

Grant Belgard: [00:05:46] What do you think are the strongest hypotheses in aging right now?

Fernando Martinez: [00:05:51] I think inflammation is a pretty important component. It seems like there’s definitely something in the immune system that’s not the same in a young patient versus an aged patient. We can see this with COVID. I think there could be some interesting things having to do with extracellular matrix proteins, for example. If you look at things like osteoporosis or fibrosis, where all of a sudden it’s much more common in an aged patient and a young patient, inflammation could certainly be involved there. But there might be something that’s separate from that, just having to do with the deposition of extracellular matrix proteins. That’s certainly interesting. The other thing that I would say is probably pretty promising would be some hormones or growth factors that are declining in age. I mean, that’s certainly the implication from Tom Rando’s work that I mentioned earlier. I think the trouble is that nobody’s really found like 1 or 2 molecules that are rejuvenating. But that’s not to say that we won’t. And to be honest, there are, I would say, evidence of some large molecules and hormones. I mean, certainly some people advocate for hormone replacement therapy for men with low testosterone, for instance or there’s cases where people will give human growth hormone to a burn victim or something, let’s say, because it does seem to increase the rate at which the injury heals. So I think there’s something to that. But you then you get into the question of whether or not it was worth the side effects. And I think that’s really the rub with taking any any kind of hormone, is that it usually does lots of other things that you didn’t really intend.

Grant Belgard: [00:07:34] So speaking of COVID, it’s interesting because the odds ratios for age are just so much higher than for it seems pretty much anything else. What are your thoughts on that? How do you think the kind of COVID risk that’s age related fits in with mechanisms of aging?

Fernando Martinez: [00:07:52] I’m not super well versed on it, but from the bit that I’ve reading that I’ve done, it seems like there’s a pretty substantial inflammation component. I’m not sure that there’s controlled studies available yet. There may be, but it seems anecdotally and observationally, once they started treating patients that were getting severe disease with things like dexamethasone, that seemed to have a pretty big impact on the outcome of those patients, at least that’s my understanding from the doctors doing it. So yeah, I think there is some inflammation component there and I think that’s consistent with just how sick some people get after they get severe disease. Some people stay extremely ill for months. Some of the patients who have died are or even not died have spent a couple of months in the hospital or the ICU. And this is way after the virus is gone, probably a couple of weeks after infection that you can’t test for the virus anymore. And yet these people are still on a ventilator, fluid on their lungs or whatever. So I think that’s indicative of something going on in their own bodies that’s separate from the virus.

Grant Belgard: [00:09:00] Do you think there might be any intersection between the work you’re doing at Fountain and COVID Therapeutics?

Fernando Martinez: [00:09:06] We have done some work with lung epithelial cells. It’s too early for me to really comment too much on that, but it’s definitely an area of interest for us.

Grant Belgard: [00:09:16] Cool. So can you maybe take us back to the beginning? Tell us about young Fernando growing up and what led you to do what you did and how did you ultimately end up where you are now?

Fernando Martinez: [00:09:30] Yeah, I’d be happy to. So I grew up in New Jersey. It’s South Jersey. It’s a town called Mount Laurel. It’s actually a suburb of Philadelphia. So that’s the thing that’s interesting, is that we tend to affiliate much more with Philadelphia, Philly sports teams and that sort of thing. It’s different from what you would expect from someone from New Jersey. But yeah, South Jersey is its own little region, even though it’s inside of a very small state. So yeah, I grew up in this medium sized town. I would say is pretty typical suburban childhood, moved around a couple times. So we’re always in these same small towns in South Jersey. I went to public school for most of my young life and I got started in swimming relatively early. I actually started when I was six and I continued doing it throughout high school and college. High school was relatively uneventful, small town growing up, playing sports and all that. But I got interested in physics even when I was in high school. I had one teacher who was really, really good. His name was Mr. Hessler, and he just did a great job of getting everybody really excited about physics, even taking the class outside at night with telescopes to look at Saturn and the moon and all that kind of thing. So at the time to apply to college, it’s looking around. And I knew that Princeton had a pretty good physics program. It’s right there in New Jersey. I figured why not give it a shot? So I actually applied early and I was fortunate enough to get in. This is 15 years ago. So the odds are a lot lower now.

Grant Belgard: [00:11:05] Which they seem to tout. Like there’s always a press release every admission cycle, it seems.

Fernando Martinez: [00:11:10] Yeah. I mean that the odds of admission keep going down. I don’t know. I guess that’s a good thing to the admissions office. Not sure how I feel about that, but once I got there, I had an advisor that told me that my interest in physics might have been important for me being accepted because there is a big push by the department actually to get more students in that were interested in physics. The department is very small there. It’s usually only like 25 undergraduates or something like that, that choose to major in physics. The thing about physics is a pretty vast area of research. You can have nuclear or particle and theoretical and experimental disciplines, all these different things. So it’s up to the student to decide what they want because you obviously can’t know everything. But I started to get interested in biophysics and that’s from meeting a couple professors that were pretty interesting and influential also just because it’s still a relatively small area of research, I guess. Not that it’s not important, but there’s a lot of questions in biophysics that can be addressed with relatively small experiments or just some creative theories that it hasn’t evolved to the point of something like high energy physics where it’s not really possible to do a very impactful experiment in high energy physics, unless you have access to a huge staff and a particle accelerator and all these kind of things, that’s just how things have evolved.

[00:12:41] So I’d say that biophysics is still at an earlier stage where it’s still possible to do thought experiments or benchtop experiments that still have a very high impact. The two professors at Princeton that were really important for my decision to continue studying biophysics were David Tank and Bob Austin. So David Tank is a pretty distinguished neuroscientist. He worked at Bell Labs back in the 90s, and he contributed both experimentally and theoretically to what we know about neuroscience, especially neural networks, and also these high tech recording techniques that let people probe individual neurons and neural circuits and try to figure out what’s going on. The other scientist, Bob Austin, he’s a condensed matter physicist who’s interested in biological materials. So he’s got a wide ranging research like looking at devices and things like that that can be used to analyze or sort biomolecules development of fluorescent probes and things like that. So yeah, that was college, I guess.

Grant Belgard: [00:13:48] I assume you’re also a party animal.

Fernando Martinez: [00:13:50] Yeah, I was a bit of a party animal.

Grant Belgard: [00:13:54] I was not expecting that response.

Fernando Martinez: [00:13:57] It’s important to be social when you’re young.

Grant Belgard: [00:13:59] Well, for physics majors usually aren’t.

Fernando Martinez: [00:14:02] It’s tough, right? There’s a lot to manage there. If you have 3 or 4 pretty complicated physics classes. And then I was swimming about 20 hours a week, like the maximum that the NCAA would allow, pretty much. So I had to juggle my homework, my classes and that kind of thing. So every now and then you just need to go out with your friends and have a good time and not worry about that stuff.

Grant Belgard: [00:14:25] Were you in an eating club?

Fernando Martinez: [00:14:27] I was in an eating club. I don’t know maybe I should say something about that. I guess that people might not be familiar. But Princeton, we do have fraternities, but it’s not a very big scene in terms of the social life the university has. It’s 11 clubs now. They’re quite old, a lot of them. The history goes back at least a century. Probably about two thirds of the upperclassmen, juniors and seniors will join one of these clubs. And it’s really just number one, a place to eat. So instead of the university dining hall, most people take their meals there. Number two, it’s a place to socialize and meet people. So for the most part, they’ll host parties and other events a couple of times a week. You can hang out with your friends and meet new people, that sort of thing. I was in an eating club called the Cloister Inn. We just call it Cloister, but it had a reputation for having a lot of swimmers and rowers, so we probably had about half the swim team and half the rowing team in Cloister and a bunch of other people from the university as well.

Grant Belgard: [00:15:30] So your masters was still in biophysics so it sounds like it was a slow transition from physics to bench biology. Can you tell us about that? And I know you did some things in the intervening periods.

Fernando Martinez: [00:15:42] So yeah after undergrad, I decided I would apply to grad school. I didn’t consider too much what else I would do. I applied and I got into Stanford into their biophysics program, which was a very small program. I think it still is. There’s typically only like, I don’t know, six or so students per year that they accept. So I moved all the way across the country. Until that point, I had grown up and lived in New Jersey. I think it was the first time I’d been in California, other than my interviews at Stanford and Cal and a few other places, and I started in the biophysics program there. So I actually started in a PhD program. I left early. That’s why I have the Master’s. So I’ll touch on that in a second. But the lab that I joined was pretty hardcore electrophysiology, so I was doing single cell recordings from slices and in Vivo Mouse Brain, really classic like patch clamping that people have done for a lot of years. So that was a pretty interesting experience. I’m pretty happy that I did that actually, because that’s a pretty unique skill that is not that common anymore in traditional biology as everything has shifted towards cellular and molecular. So I mentioned that I started a PhD program there and I actually left after three years, I think. So what happened was I actually injured myself pretty severely.

[00:17:07] I was rock climbing and I had a pretty bad knee injury in my second year of grad school. I ended up having five surgeries on it and I spent six months, maybe more on crutches. So there’s a pretty complicated injury. And the doctors just didn’t know what to do. And I just had one surgery after another and hundreds of physical therapy appointments by the end of it. It really put me in a tough spot and cut into what I was able to do. I ended up leaving after three years with my masters, and I joined a company at the time. It was called Hyperion. Hyperion was a pretty interesting company. It was founded, I think, about 2007ish, like right after Shinya Yamanaka published his famous induced pluripotent stem cell work. So the whole point of Hyperion was to get IPS cells from patients and differentiate them into various kinds of neural tissue. At the time, we were mostly working with motor neurons, but we moved to astrocytes and also cortical neurons. So the idea was to differentiate these neurons from patients that are affected with various neurodegenerative diseases and screened drugs against them to see if there was something we could find that would reverse this disease phenotype. So I spent two and a half years at Hyperion, which was a pretty interesting experience. We actually had five different CEOs in the two and a half years that I was there.

Grant Belgard: [00:18:41] How large was the company at the time?

Fernando Martinez: [00:18:43] At the time I joined, the company was about 15 people, and the biggest that we got was 50 people towards the end of my tenure there. But it was a pretty volatile place in a lot of ways. So the rapid turnover of senior staff that I mentioned, it was also at the time Hyperion was a pretty hot topic. It was funded by Kleiner Perkins, while the firm was still in their heyday. There’s a lot of money and a lot of expectations that came with it. So while I was there, I worked on their ALS and their SMA program, and that was my first opportunity to learn about high throughput screening and small molecule screening, because that was so important to the company. There were a lot of people there that were extremely expert in that you had having come from Lake Merck, ultra-high-throughput screening labs. So that’s my first introduction to robotics, compound handling and high throughput screening.

Grant Belgard: [00:19:40] And they’re ultimately acquired by BMS, right?

Fernando Martinez: [00:19:43] Yeah, that’s right. So Hyperion was acquired by BMS. Let’s see, I left in 2011, wrapped up my work and we submitted a paper. Then I went back to grad school at UCSD, and then a couple of years later, Hyperion was acquired by Bristol-Myers Squibb. It was acquired based on some work that we had done on an Anti-tau antibody that was intended for some rare familial tauopathies and an Alzheimer’s disease. I forget what the dollar value of the acquisition was. It was pretty significant at the time, $600 million or something like that, including the milestone payments. And then the thing that’s interesting is that Bristol-Myers Squibb then sold the company a couple of years later. After wrapping up a phase one trial, they sold the company to Biogen because they decided they didn’t want to work on neuroscience anymore. Biogen actually still has the asset, the antibody from Hyperion. It’s in a couple clinical trials. One of them flunked, unfortunately, maybe a year or two ago, but they still have it going in at least one more that I know of. So yeah, I’m still rooting for them and hoping for the best at Biogen.

Grant Belgard: [00:20:57] Do you consider those assets your babies jointly?

Fernando Martinez: [00:20:59] Yeah me and hundreds of other people that I’ve worked on it since then. I think that most people that were there are very proud of it. But it goes to show you how long some of these things can take, right? Because I left the company in 2011 and Biogen is still working on it now. In 2021, there’s hundreds of people and hundreds of millions of dollars that have gone into that since then. So as I mentioned, I left the company in 2011 to go back to grad school.

Grant Belgard: [00:21:33] Why did you decide to do that? Because you went like full on biologist at that point, right?

Fernando Martinez: [00:21:38] Yeah. That’s a good point. I kind of over the years moved away from physics. I haven’t used an oscilloscope or something in probably longer than I can remember. I wouldn’t say there’s really a conscious decision to continue to to move in that way. I think it’s just easy for me to transition to different spots in my career, I guess, by doing that. And the other thing is I really did like the work that I was doing at Hyperion because I felt like we really had a chance to help someone, not that a physicist can’t help someone. But it was pretty rewarding to work on something that could be a medicine one day that someone would actually take and it might improve their life. For those reasons, I was comfortable moving more and more towards biology. So yeah, I guess as to the question of why decided to go and do my PhD, I wanted to do that for a while. I felt like I had been dealt an unlucky hand, I guess, and that I should take an opportunity to correct that, I guess, if I could. The only thing that really cost me was time. There’s a few years spent working on a master’s degree, that’s not that important for my career anymore, I guess. But you still learn something during that time.

[00:22:57] I certainly don’t regret the time that I spent at Hyperion. I certainly learned a lot there. Having thought all of this through, I got to like an inflection point at Hyperion where I had wrapped up a project and we had put packaged everything into a paper. This is actually the first small molecule screen that I know of where we screened maybe 20,000 compounds in IPS derived motor neurons from ALS patients. So we put that together into a paper and it was just a pretty good place. If I were ever going to leave the company for me to move on because it’s had achieved a major milestone. So I took that opportunity to apply to a bunch of other schools in California. California had become home for me, I guess at that time. I’d been there for so many years. So I got accepted to UCSD and I went there and met a few professors that I actually still am in contact with now. I really liked them in the work that they were doing. The main people that influenced me were Larry Goldstein, Gene Yau and Bruce Hamilton. So there are three pretty distinguished full professors there. I was just so impressed with their work and the conversations that we had that I accepted the offer from UCSD and moved down to San Diego.

Grant Belgard: [00:24:17] This is a bit of a diversion. But speaking of California, has your attitude on that changed at all over the years?

Fernando Martinez: [00:24:23] Yeah. There’s a lot of things that have happened, I guess over the intervening years. So let’s think, I got to California in 2006 and I’ve lived in Palo Alto, San Diego, and various other places in the Bay Area. So there’s still a lot of things that I like about California. I mean, it’s full of wide open spaces.

Grant Belgard: [00:24:45] It is beautiful.

Fernando Martinez: [00:24:46] Yeah, exactly. There’s a lot there. There’s the mountains, the desert, and a huge and very beautiful coastline. So I was fortunate to be close to there when I was in San Diego and in the Bay Area as well. But there’s a couple things that I’m not too crazy about. Just to give you an idea, when I was working at Hyperion, I was renting a pretty old apartment that wasn’t the best in Burlingame, and I was renting it for about $1,000 a month. This is kind of like 2008 to 2011. And the landlord actually only gave me a month to month lease because they told me that the building was in such a state of disrepair that they were considering demolishing the entire building and building something else. So if you fast forward to 2017, when I was moving from San Diego back to the Bay Area, it’s looking around for apartments. And I came across the exact same apartment that I had rented in 2011, and it hasn’t been demolished. And to my knowledge, there hasn’t been any significant improvement to the building. But instead of renting for $1,000 a month, which at the time was extremely expensive, it now rents for $2,200 a month. So I would say that that’s pretty typical story for most of the populated areas in San Diego where the commercial development over the time that I’ve been there has just exploded. And for various reasons, the residential development has not kept up.

[00:26:20] And it’s put people into a pretty tough spot including myself. I mean, the proposition of paying someone $25,000 a year for a property that they were previously considering demolishing. That’s kind of an interesting thing. But yeah, I would say that’s something that’s not terribly positive about California. It’s only gotten worse in the time that I’ve been there. 2011 moved from Bay Area to San Diego to start school at UCSD. So I joined the Biomedical Sciences program, which is pretty vanilla bread and butter, a biology program. I rotated through a couple of the labs that I interviewed with when I was there visiting Larry Goldstein’s lab, Gene Yau’s Lab and Human Genetics Lab, Joe Gleason’s lab. I had a pretty good time everywhere that I rotated in. But I decided to join Gene Yau’s lab, which was a risk at the time because at that time, Gene was still an assistant professor as opposed to Larry and Joe that were like full professor in HHMI. But I decided to join Gene’s lab for a couple of different reasons. One was Gene was and still is really focused on RNA biology and an RNA binding proteins. And of course, when I was at Hyperion, one of the proteins that we were interested in when we were working on ALS was TDP-43, which is a pretty famous RNA binding protein. So I knew that Gene was interested in TDP-43, and I knew that I could get opportunity to look at the protein in more detail and the mechanisms of disease.

[00:27:57] I guess in ALS, which we were less concerned about at Hyperion because we were busy screening small molecules and all that. The other thing was that Gene, he was and he still is a really enthusiastic guy. He’s always excited about science. It doesn’t matter too much what it is. He’s always excited and he’s able to recruit and get a lot of people into the lab that were also really enthusiastic and really excited. Sometimes you’ll come across an academic lab where a lot of the postdocs don’t really want to be there, like people are just looking for the exit whatever they need to do to get their next thing. And somehow Gene’s lab didn’t have so much of that. Most of the postdocs that were there were really stoked about the work that they were doing and they were still engaged. So that’s why I decided to do that. And he ended up being my advisor for the five years that it took me to finish my PhD. We’re still friends, we still talk. He actually had his ten year anniversary of the founding of his lab when he got his assistant professor position and he invited myself and a lot of other alumni back to San Diego and we had a great time. So it’s become a community of people that that still talk and look out for each other even years later.

Grant Belgard: [00:29:14] And then you went into biotech.

Fernando Martinez: [00:29:16] That’s right. So then I went back to biotech. After I finished my PhD, I wasn’t sure what I wanted to do. I was doing a bunch of different things. I was interviewing for all kinds of different jobs, biotech companies. I was interviewing with venture capital firms. I interviewed with some management consulting, even investment banks like sell-side equity research, just all kinds of things. I probably took maybe 60 job interviews or something like that, and I still hadn’t really decided what I wanted to do. So I needed some way to pay the bills. And that’s how I got started working with Verge Genomics. Verge actually hired me as a consultant because the company was so small and early stage at that point. They hired me as a consultant to work on some of their early programs on ALS and a couple other things. That worked for me because I was working remotely and helping this small company to grow and plan their next experiment. But at the same time, I could still take plenty of time to go around and talk to people trying to figure out what I would do next, I guess.

Grant Belgard: [00:30:22] Cool. And so been going through your education and dipping in and out of biotech and going back and all this, what would you say are the most impactful things you’ve learned?

Fernando Martinez: [00:30:31] I would say probably the most important thing that I’ve learned is that your relationships matter, maybe even more so than what milestones or what your salary was or whatever at any particular place, because biotech is still a relatively small community. It’s obviously growing, but where I am here in the Bay Area, a lot of people know each other, either directly or by association and work together for a lot of years. So your reputation and your relationships, that’s really important. I can’t stress that enough. Be nice to everybody. You never know where you’re going to run into these people again. And they they may be able to help you or you may have the opportunity to help them.

Grant Belgard: [00:31:15] Was there anything that surprised you? I guess in your case, you had already worked at a biotech before doing your PhD, so maybe you weren’t as influenced by misperceptions as some other students might be.

Fernando Martinez: [00:31:30] Yeah, I think I was fortunate about that. I would say that and maybe this goes into another piece of advice, I think it behooves people to think pretty carefully about where they decide to work. One thing that you see with students who know that they want out of academia and they want to go to a biotech is they think that basically any biotech job is going to be better than whatever their alternative is. That’s just not the case. Just because you land a job at a biotech, doesn’t mean that it could be a very unpleasant place to work in general, or it could be the wrong place for you to work. That’s one thing when I talk to students, I try to tell them to do some due diligence on these places that they’re considering working. A lot of small biotech companies are founded on the promise of some new technology. And a lot of times that it’s untested. So one thing that I tell students is to look at whatever technology this biotech company is pitching and ask yourself if you really believe it yourself or not, because everybody sees the seminars or a paper that has a ton of things in there that nobody really believes. And if that’s the cornerstone for a new company, then you should not go. Probably be preferable to stay in an academic postdoc or hold out for something else than to jump on a bandwagon that’s not really there, I guess.

Grant Belgard: [00:32:59] Are there any other pieces of advice you have for students looking for their first biotech job?

Fernando Martinez: [00:33:05] Networking and talking to everyone that you can either formally or informally is critical. A lot of people send out applications for a job cold and that can work. Plenty of people have gotten jobs that way. Plenty of people hire that way. But I think if you can engage with someone in a conversation. This could be someone that you connect to through LinkedIn, through an alumni network, through a professor that has contacts somewhere. If you can speak to someone, you can make a case for yourself and be considered for a job where you might not ordinarily write for. For example, if you’re just submitting applications cold and you don’t have like every single checkbox, there could be somebody there that’s just going to put it into the trash can or a low priority pile, whatever it might be, and turn to the next one. But if you can actually speak to a person and say, look, I’m a little bit underqualified for this, but over here I did like X, Y and Z, and it was great. Then you have opportunity to make a case for yourself and be considered for something where you ordinarily wouldn’t be.

Grant Belgard: [00:34:14] I think that’s a great point, having written up a number of job specs now. I think very often what’s written may not be entirely the perfect depiction of what they really need. There may be certain requirements that are a lot more important than others, even though on a page they’re given equal weight.

Fernando Martinez: [00:34:33] Yep. Makes sense.

Grant Belgard: [00:34:34] The classic Peter Thiel question, what’s something you believe to be true that most others don’t?

Fernando Martinez: [00:34:40] I’ll give you something. Maybe it’s a little bit controversial, but I think that people don’t want to be told what to do. A lot of people might not agree with this. I wouldn’t say that it’s a truth that I find self-evident, that nobody does. But I think a lot of people think that other people want to be told what to do or need to be told what to do, or that they will make other people’s lives much better by telling people what to do. And it’s my belief that most people want to do their own thing, whether it’s in life or their career, whatever it may be. And they want to figure out things on their own, draw their own conclusions, make their own observations, and then pursue whatever goal or desire it is that they have as opposed to buying into some kind of centralized goal or necessarily getting a lot of input from someone who’s in authority. So that I would say is my truth, that I believe that many other people don’t.

Grant Belgard: [00:35:44] And how do you think founders of biotech startups can take advantage of that?

Fernando Martinez: [00:35:50] I think the key is to give your employees the latitude and the independence that they need to pursue goals that are important for the company in their own way. So I would say that a lot of founders, they certainly have a vision for the company and they have goals and then they will hire people. And for the most part, those people if they’re going to a company that’s small like that, a lot of times they’re also excited by the vision and the prospects of the company. Founders could do a lot more to just trust the motivations of the people that they have hired without trying to impose tons of external culture influences, for example, or micromanaging or ad nauseam like goal setting where every single activity is monitored and tracked. I think there’s some founders, mostly because they’re so passionate about their own vision. They want to impose a lot of a lot of strict rules about how people should pursue that vision. I think they could be a lot more productive by just trusting that their employees vision and their own is aligned and that the employee will actually figure out how to get things done, maybe more efficiently than someone who’s at a very high level handing out mandates, I guess.

Grant Belgard: [00:37:14] Do you have any closing words of wisdom for our listeners?

Fernando Martinez: [00:37:17] You guys should keep an eye on The Bioinformatics CRO Podcast. I listened to a couple of these podcasts and honored to have the opportunity to be here and I’ll certainly listen to more in the future and advise all the other listeners to tune in when you have time as well.

Grant Belgard: [00:37:36] Well, it’s our privilege to have you. Thanks so much for joining us Fernando.

Fernando Martinez: [00:37:38] Thanks Grant.

Transcript of Episode 24: Jeremy Kamil

Disclaimer: Transcripts may contain errors.

Razib Khan: [00:00:00] Hey everybody, this is Razib Khan. It is not Dr. Grant Belgard. I am hosting this for now. Some of you may know from my previous appearance on Grant’s show on the CRO Podcast. I am a geneticist who works in the domain of ancestry population genetics. I also have a quite large mouth. You can find me on Twitter at Razib Khan and you can find all of my stuff at razib.com. I talk mostly about ancestry, history, those sorts of things, but I am really, really super interested in genomics. And over the last year, I have gotten super interested in COVID-19 or should I say COVID-19 has gotten super interested in me. Through this process, I have met some people on Twitter which a lot of people denigrate the site and I do too. But I have to say that COVID-19 brought out the best in humanity, even though it was a difficult circumstance. And I got my first shot recently. So hopefully I’m going to put this behind myself personally, although as a culture and as a society will be grappling with the consequences for a while. And so I wanted to have a friend, Dr. Jeremy Kamil at LSU Shreveport, who I have met over the past year through social media and other forums, because he’s a virologist who’s also interested in genomics. Obviously, he’s gotten to be a deal because of the circumstances we find ourselves in. I think Jeremy will probably tell us, like every virologist now, is in much hotter demand than they were in previous years. Jeremy, can you introduce yourself to the audience.

Jeremy Kamil: [00:01:36] Yeah. My name is Jeremy Kamil. I’m at LSU Health Science Center, Shreveport. Not to be confused with Shreveport, the undergrad campus in town, but we’re like a medical school and I’ve been here about a decade. I am now an associate professor. I came here from a finishing a postdoc at Harvard Medical School studying a virus called cytomegalovirus, which I still work on. And until the beginning of the pandemic was basically the exclusive domain of my research. So yeah, I mean, viruses and virus genes are not foreign to me at all. I’m not a genomics whiz next gen sequencing, as they call it, or Illumina sequencing or nanopore sequencing, all that stuff is pretty new to me, although I grasp all the concepts. But yeah, I’ve worked on viruses for a long time, deleting genes, putting jellyfish genes into viruses to watch, what organelle the protein goes to that kind of stuff. Pretty nerdy stuff, outside the realm of what the general public cares about at all. So it’s usually like Battle of the Geeks trying to get some federal dollars to do your research and then battle of the geeks again to publish your research again you know in some journal but then yeah when COVID-19 hit, I started just because I was mostly forced to. They shut our campus down and told us all of our normal virology research had to stop and the only thing we were allowed to help out with was COVID-19.

[00:02:57] And to me that was less research and more just public health work. So it was really my first encounter, like doing public health work, which usually people think that’s utilitarian or maybe even a little bit drowsy. But I found during a pandemic, it’s pretty exciting. The moment we’re in with regard to sequencing the SARS-CoV-2 virus, which of course is the virus that causes COVID-19, that has never been done. No virus, arguably since HIV has been sequenced so much and i think this far eclipses what have been done with HIV. So the amount of sequencing to watch a virus evolve in real time I think been is a colossal achievement for humanity. And it’s been just a stroke of luck that I’ve had pretty close to a front row seat. I won’t say I have a front row seat, but I’ve had pretty close to a front row seat in the auditorium watching this viral observatory or whatever you want to call it. Actually, there’s a lot of politics, of course, that’s always behind the scenes in anything, not just science, but who gets the funding to do stuff? What is the data look like? Who gets to do the work? Who controls the data? All these things have a lot more to do with politics than they do with pure science.

[00:04:06] And I think it’s just really, really fascinating to see a battle of the geeks and the battle of the rarified monkeys that we are fighting over, things that we do. And as you mentioned, it’s a very collaborative moment in humanity, like we all are getting together to solve this problem and come up with vaccines and watch out for new variants and try to understand them. So there’s a lot of people who are genuinely trying to do the right thing and do good. Even if you can consider people who work at a grocery store or still willing to go to work and change a tire and do you know what they do every day? I mean, there’s a heroism when you’re putting your life on the line to do that kind of work that I think also is going unrecognized. It’s not just the scientists who are doing important stuff. It’s like anyone willing to show up to their job takes on an added importance when there’s like a giant spike of cases in your area. So I think we all deserve a pat on the back. There are things to be cynical about at the same time. There’s a lot of funny stuff going on. It’s been interesting just crashing into it at a whole bunch of different levels over the last year.

Razib Khan: [00:05:09] Yeah. So I guess one thing I want to make it clear to the listener is there’s genomics and there’s genomics. So the human genome has about 3 billion base pairs. That’s about the same size as most mammals. I think there are some birds are a little smaller, but that’s the range. So viruses, they’re small, right? Like, can you give us an intuition of how genomics on a viral scale is different?

Jeremy Kamil: [00:05:35] Yeah. I mean, a virus is like a footnote to a footnote to a footnote compared to the human genome. I mean, these are even. Well, there are some new viruses out there like Mimiviruses that are ginormous and have genomes the size of bacterial genomes. But those are really the exception that proves the rule. I had a lecturer at UC Davis where I got my PhD named Martin Privalsky, and he trained with Bishop and Varmus, who won the Nobel Prize for discovering Oncogenes at UCSF. And he I remember to this day his colorful analogy from like some virology class he gave to us. There’s a good size range of genomes for viruses. You have little tiny ones like Circoviruses, and then things like HIV that are about nine kilobases. So that’s 9000 chemical units long, like APGC or AUGC and RNA. So it’s like 9000 letters long, which is obviously a lot smaller than 3 billion base pairs. And his analogy was like, Well, that’s the dude who gets on an international flight with his toothbrush and a handkerchief. And that’s all that person needs to go traveling. And then on the other end of the scale, you have pox viruses and herpes viruses, which are more like 300,000 base pairs in length and they’re double stranded DNA genome. So I can say base pair instead of bases and length. That’s like the virus that pulls up with an RV to the cell. It literally brings the kitchen sink with it, doesn’t trust the cell to do all that much for it, especially a pox virus. Poxvirus encodes its own RNA polymerase, so it doesn’t let the cell do very much for it. It’s still a parasite of the cell, but relative to HIV, it’s a pack rat. There’s nice range there.

Razib Khan: [00:07:09] So actually while you were talking, I decided to be rude and Google SARS-CoV-2. It seems like it’s in the middle of that range. It’s 30,000, which is a good number because, you could just divide it by 3 billion. So I think that’s like, what? Like, like 100,000th or something of a human genome. And so it’s small on an individual scale, but there’s a lot of viral particles out there to sequence. And so this is one of the issues that is going on. So going off memory, I think the original SARS, didn’t it take like two months to sequence it? Like, can you do you remember off the top of your head?

Jeremy Kamil: [00:07:48] I don’t. So that was long before I worked on SARS. So that was around 2003. People in the field called OG SARS and SARS stands for Severe Acute Respiratory Syndrome coronavirus. And yeah, I think gene sequencing then probably was a little slower.

Razib Khan: [00:08:04] I’m looking at the Wikipedia. They isolated it on March 21st. They finished mapping on April 12th, 2003. I think the publication was a little bit later. So yeah, it’s on the order of a couple of weeks to a month or so. And this is just for a single, the consensus sequence of the virus, I’m assuming. Whereas today, can you give us an intuition of how fast the sequencing is happening with the numbers?

Jeremy Kamil: [00:08:32] Well, the sequencing usually happens way slower than it needs to. But if you wanted to go right from a clinical sample to a complete sequence of a nanopore, you could probably get it done in about 12 hours. Mostly what we do is amplicon sequencing now because it’s cheaper, but a lot of our first sequences were all done using hybridization enrichment capture, where basically the same technology used to sequence like DNA from Neanderthal bones and caves. You have a bunch of biotinylated probes that are tiled along the whole genome of the organism you’re interested in. And in the case of Neanderthal cave bones, that’s the entire human genome. And you’re trying to enrich for human genome fragments from cave dust, basically. And there’s a bunch of bacterial garbage around and you don’t want that. So they’re able to enrich for human reads on their NGS preparations. But with SARS-CoV-2, it’s a similar problem in that when you take a swab from someone’s nose, there’s a bunch of other junk in there, a lot of human ribosomal RNA, probably a bunch of metagenomic bacterial stuff. The virus might be fragmented and not super high quality, so it is important to be able to enrich for that. It’s usually cheaper to make amplicons so they have amplicon protocols. But in the beginning, we were using that hybridization capture enrichment and I think that those approaches, some of those would have been possible in 2003, definitely Amplicon sequencing would have been. I don’t think NGS protocols were anywhere near the maturity that they are now. I don’t know when the Illumina first came out with their version zero, but think it must have been around then.

Razib Khan: [00:10:04] I thought the Illumina technology did it too, like 2007 or 2008. But I did actually look at the publication date. The publication date of the sequence was May 1st, so they isolated it on March 21st and they claimed that they had the sequence on April 13th. So it was still pretty fast. So interesting, this is partly a technology issue. So would you say that you’ve been having to deal with this two track parallel issue where there’s the whole science, there’s the virology, which is what you were trained in, and then you had to

learn this genomics stuff and communicate it to the public. Like there’s just two issues the technology and the science.

Jeremy Kamil: [00:10:44] Yeah. And I think you hit the nail on the head that there’s a lot of smoke and mirrors around that, too when people get political with how the work is distributed, how the funding is distributed. The people who want to play games with where the funding goes and who gets to keep ownership of the data, you’ll notice that they always want to talk about metadata standards and they want to keep talking about bioinformatics because what they don’t want to talk about is the fact that these virus samples that are of interest all come from people. And a lot of people don’t have health insurance. A lot of people don’t have access to medical care. There’s this buzzword now about genomic surveillance. And Rick Bright’s leading a really good initiative from the Rockefeller Foundation to amplify the message that we need constant decentralized sequencing of the things that make us sick to make our world more secure. But I would add to that that you can also make the world more fair and more equal by using genomic surveillance. And that may sound rather abstract, but the rich do care about the viruses that are making the poor sick because they can make the rich sick, too. And how are you going to get a stream of data on the viruses that are making people sick in a South African ghetto if you don’t educate those people about what a virus is and you don’t give them medical care. So the poor have an immensely valuable bargaining chip in genomic epidemiology, in viral surveillance.

[00:12:08] But here almost no one talking about this issue. To me, it’s a great opportunity for humanity to give health care to marginalized people, and in exchange, they would provide samples that could be sequenced for viruses or bacteria that are making them sick. And I don’t think that it stops at a transaction. I think you have to give these people, not just the education to understand that they have diamonds under their front lawn, so to speak, but that they should have a connection to those samples forever, like an anonymous code that, hey, you provided this sample. If we get a sequence from it, here’s a code. You can put this into a computer or into your smartphone and see what science has done with your data. And no one’s talking about that and I think it’s a big global opportunity to make the whole world a lot more secure from the next COVID 2024 or whether it’s a really gnarly flu that’s going to come at us in a couple of years. But also to make the world more fair.

Razib Khan: [00:13:03] Yeah. And want to loop back to the politics policy stuff. You’ve kind of gotten involved, I mean arguably involuntarily, because you’re a virologist, you’re a scientist. But I want to loop back to that. But actually first, I want to take a step back because you talked about being trained as a virologist. You were at Davos a little earlier than me, but you were in the microbiology group, I believe. And so you’re a biologist, you’re a legit biologist. I was in the genomics group, so I’m not really a biologist, in terms of I start with the genomics and I go to the organisms. So tell me about what a virus is actually for the listener, because I think SARS-CoV-2 is part of our world. And yet there are still people out there who don’t know what a virus is, what a bacteria is. Can you talk a little bit about the biology and the structure?

Jeremy Kamil: [00:13:47] Yeah, sure. First, I would tell you that I think any biologist would say someone who studies genomics is a biologist of one sort or another. So I would consider you a biologist Razib whether you like that or not.

Razib Khan: [00:13:59] I’ll take it. I’ll take it Jeremy.

Jeremy Kamil: [00:14:00] And so as far as what a virus is like, something around 8% of our genome is like fossil viruses. So viruses are really ancient things. And there’s still a debate out there about what the RNA world was like, the primordial soup that life first came from. So unless you’re a creationist, it’s still not a resolved question in most people’s mind, like what the first life forms were. But viruses probably came pretty darn early. Virus, just by definition, is an obligate intracellular parasite. It’s something that infects a cell, and most viruses are what we call cytolytic, which means they eventually kill the cell even if they go through a latency or something. When they replicate, they turn the cell into a virus factory and it’s basically like harnessing all of its metabolic might into the assembly of de novo virus particles. So all the macromolecular synthesis machinery of the cell to make protein, to make nucleic acid polymers starts to just shift to make polymers that are virally encoded polypeptides or proteins, if you want to call them that. Of course, viral RNAs and depending on what the viral genome is, the viral genome might be a double stranded DNA virus or it might be an RNA virus, but the virus is going to usually encode a replicase or a replication enzyme to copy its own genetic material. There are, of course, viruses like Papilloma or Polyomaviruses that use our own cellular DNA polymerase to copy their DNA genomes.

[00:15:26] So there’s something called the Baltimore Classification Scheme named after David Baltimore, who discovered reverse transcriptase and also NF Kappab. He’s done some pretty important things in science, but one of his contributions was to classify viruses by, I think, seven different groups as to what type of genome they have and what their replication strategy is. So you can get lost in the weeds pretty quick, even trying to transmit the big picture. But a virus is essentially a rogue, self-replicating, selfish gene that takes over your cell and makes copies of itself. Someone called it like a gene wrapped in bad news or whatever. It’s usually got a little lipid envelope or a way of entering your cell. So it’s a really efficient transfection reagent. If you’re a biologist out there like molecular biologists are often interested in putting foreign genes into cells to study them, and viruses are almost like they’re their own transfection reagent too. I mean, they are really good at getting into cells. That’s one of the things that in biotechnology they’re exploited for. We call them viral vectors, like some of the coronavirus vaccines indeed use Adenoviruses. It’s actually an adenovirus vector. It’s like a gutted adenovirus that can’t really replicate and they put a foreign gene in it, in this case, the SARS-CoV-2 spike to send that gene into your cell. So you make spike and then you can mount an immune response against it.

Razib Khan: [00:16:40] You actually anticipated some of the things that I was going to say back to you. So it’s like a selfish gene. So I think a virus holds your cellular machinery hostage. And it does what it needs to do. And a lot of the negative consequences are due to the fact that it just co-opts things and all it cares about its own replication. It doesn’t care about you. Like if you die, whatever it’s going to like go all over the place.

This is what’s happening with SARS coronavirus too. But then we have some viruses I think like MERS have much higher fatality rates, whereas others, I don’t know, there are coronaviruses I believe that cause the common cold. So I think this is called virulence. Is that the technical term?

Jeremy Kamil: [00:17:21] Virulence? Yeah. That’s a very good term.

Razib Khan: [00:17:24] And so it’s basically how harsh it is cause fatality and morbidity. Can you explain how virulence emerges and evolves? Is it just like a random act of God or is there like a logic to this?

Jeremy Kamil: [00:17:39] There’s definitely a logic to it. A lot of the nastiest viruses and infections and I wouldn’t confine myself to viruses here are things called zoonoses, which just means a virus or a bacteria or even a protozoan parasite that ordinary lives in an animal infection cycle. It could have multiple hosts, for instance, like parasites. But when it spills over into a human being, you get problems. So, I mean, there’s a protozoan parasite that’s found in kitty litter called Toxoplasma Gondii and in immune suppressed people, it can get into their brain. I even had a friend I didn’t know he was HIV positive. I met him in Oregon doing forest activism years ago and I found out and I think 2006 that he died of toxoplasmosis and really brilliant, wonderful person. But in a way that’s a zoonotic infection because that parasite, it lives in a rodent cat cycle. And when it gets into people, it causes problems. If you are immunocompetent, you don’t get very ill from it. But if you’re immune suppressed, you have problems. Flu each year in essence is semi zoonotic because that virus evolves in birds and pigs, mainly in birds, and it’s tropism, almost like the coronavirus is determined by its entry glycoproteins and it reliably spills into humans each year and then transmit between humans, sometimes the nastiest. They call them bird flus don’t transmit well between people. They spill from a bird into a human and the human dies. But the virus is not able to transmit from human to human. They like to sequence those. There’s a lot of different perspectives on virulence, and I’m just giving you more of an evolutionary one and not a mechanistic one. But I’d like the evolutionary perspective because it explains a lot. A zoonosis, it has no responsibility to the host, like a really, really super virulent virus, like Ebola.

[00:19:28] It’s easy for that to burn out because if it kills the host very fast and very efficiently, even if it’s rather infectious, people notice when there’s blood coming out your eyes and you’re collapsing on the ground. You don’t get a chance to infect too many people other than the people trying to clean your body or take care of you in the hospital. It’s hard for an Ebola patient to hop on a plane to a different country, walk around, shake lots of people’s hands, go to a bar, do lots of stuff before the disease kicks in. So the original SARS virus wasn’t like Ebola, but the people who were the most ill were the most infectious. So it actually wasn’t until you were hospitalized that you became super infectious with the OG SARS back in 2003, even though it used the same ACE2 receptor and a lot of ways was a similar looking virus, it didn’t have this presymptomatic transmission phase. And so that’s why Tony Fauci got up in the Rose Garden or whatever it was. He gave a warning speech back, I think March a year ago, and he got it wrong. They thought that only people who had fevers or were sick needed to wear a mask. They should have known better by then. How do you think this virus got all over the place so efficiently if there’s not a presymptomatic transmission? But hindsight’s 2020 and in science dogma is the most stubborn and awful force is the arrogance of, Oh, well, we’ve already seen this before, guys. We had a coronavirus looks almost identical from 2003. And so you have all these public health authorities thinking they knew exactly what this meant, but they didn’t.

Razib Khan: [00:21:02] Yeah, yeah. I guess one thing that people have said is that in some ways, SARS-CoV-2 operates in a Goldilocks zone for spread. Its infectiousness is quite high more than the flu. Its virulence is not horrible, but it’s also not great. And then it has this pre-symptomatic spread stage. And so it seems it’s a combination of a lot of different things to make it bad. Now, it’s not like the bubonic plague where one third of Europeans died. So I don’t want to exaggerate how people get mad at me, but case fatality rate, what are we thinking? Like around 1% or so? Like a little higher, a little lower, depending on public health infrastructure? Is it something that is optimized in the modern world? I mean, obviously not consciously. I’m not conspiracy theorist here to just cause havoc because a lot of people aren’t going to take it seriously because you’re not bleeding out your eyes, but you are going to spread it around to people who are going to die.

Jeremy Kamil: [00:22:05] Yeah, that’s I think correct. It does live in the Goldilocks zone for transmissibility. And I think the IFR and the CFR are two different things. So a case fatality rate is when you’ve actually had an encounter with the medical system, the bureaucracy, and you get diagnosed, that’s a case. So it’s a documented case. This person tested positive for SARS-CoV-2, the COVID-19 virus are you going to call it? And what percentage of those people die? And then there’s something called the infection fatality ratio, which is going to be a lot smaller. It’s the number of actual infections that occur in the world, whether or not they are documented by the medical bureaucracy and what’s the rate of death. And I don’t have those numbers off the top of my head. I should look them up. But I think the case fatality rate is somewhere between 0.5 and 1% on average. But if you get up into people who are in their 80s and late 70s, you can have easily 10% of them dying depending on where in the world you are and whether they have access to medical oxygen and steroid treatments and stuff like that. Especially early in the pandemic when physicians didn’t really know how to treat it, it was a higher case fatality rate in those elderly patients. And of course, different populations have different age segmentation. So if a population is full of a lot of younger people and there aren’t a lot of elderly, the infection or case fatality rates are going to be a little bit lower.

Razib Khan: [00:23:30] The next question is, we talk right now and I want to go back to the genomics and the sequencing. We talk about the British variant, the South African variant and all of this stuff, what was it like before sequencing? Like how did people figure out different variants? There are older techniques, whatnot, but how fast was it like, has genomics really transformed our understanding of how these viruses are mutating and diversifying into different lineages in a way that’s actionable and actually is helping us fight the pandemic?

Jeremy Kamil: [00:24:05] Well, that’s a really good question. I think it’s clear that we haven’t realized or harnessed the ability of genomic epidemiology to protect ourselves from the virus or to take public health action. I think that a lot of the stuff about variants is to some degree more of an exhilarating intellectual curiosity than it is something that’s going to protect the average person in India from coronavirus. I mean, quite arguably, and I’m entirely convinced of this, you don’t need to know about new variants to know that if people in India had not been convinced by reading inaccurate information from news organizations that, hey, maybe Indian people are immune naturally to the coronavirus because of their heritage or the spicy food they eat or something, because we expected to see far more deaths earlier and we didn’t see them. I’m guessing people were pretty worried and probably followed precautions early on or something, because I don’t think there’s some magical difference about the variants there that are driving the huge spike in case rates. I’m pretty much assuming that it’s mostly because people stopped being careful. And you there is undoubtedly some role for the increased transmissibility of variants like B117, which clearly is better at spreading. But most of all, it’s people crowding together.

[00:25:31] And once the virus gets into enough people, it’s really hard to stop it. Like it’s exponential growth. That’s something that someone like you can understand really quickly. But a lot of the average public haven’t had enough experience watching a bacterial culture grow and taking the OD and seeing what exponential growth looks like because it is an awesome thing and it’s a scary awesome thing when it’s not an investment making money or something positive that you want. It’s death and fevers and more spread. India has such a high population and also in the urban areas a really high population density. So that’s a recipe for disaster. Back to what you were saying about phylogenetic trees or strains and variants, I think it’s absolutely amazing that we can watch that happen. And it’s crazy to see one spillover event from a bat or some strange animal in a jungle in China or Vietnam or wherever this emerged from turned into basically a family tree. And I like the biblical example of like, Cain and Abel and all this because it’s almost like it was one species. But now that one strain became a tree and now the branches of the tree are competing with each other and you have like B117, like outrunning everyone else, replicating more.

[00:26:51] But there’s also some other rogue variants just trying to eke out a living or to still exist. And so it’s funny because it was one and then it became many and then many are competing with each other. In the past with viruses like dengue, we know there’s different stereotypes and I think before the advent of genomic sequencing and became so inexpensive to deduce the entire genetic code of a virus. And we mostly used serology which is like antibodies to detect a different strain or a different serotype. Because when viruses evolve or change or are different from each other, some proteins won’t change very much and others will. And so the antibodies from a patient from like 1984 that you had in your freezer, they might not recognize all the same proteins that the 1994 variant had, but it’ll still recognize some. And so you’re like, oh, this is a serotype A, because it has this pattern of detection. And then of course when you sequence, you can figure out, Oh, well, these are the genetic sequences that encode these epitopes on these proteins that the antibodies are recognizing.

Razib Khan: [00:27:53] Yeah. That’s one of the interesting things. You bring all these different sciences or scientific disciplines together that have different histories or genomics, which is almost no history comparatively. It’s pretty fascinating. I see this stuff in the media now sometimes, like the California variant, the British variant. Can you tell the listener, I think most listeners are going to be American what the current state of variants in the United States is. I heard Michigan had a massive spike that seems to be declining now. But I heard someone say, well, it could be its own variant. I don’t know, like, what do you know about this stuff? What’s going on right now?

Jeremy Kamil: [00:28:29] I haven’t geeked out over the latest data, but I’ve been looking at it pretty regularly over the pandemic. There’s certainly a ton of B117 here which emerged in Kent and England probably around November, and the first sequences really were collected in October. But the scientific literature says November. So it came out late last year and it’s thought that that came from prolonged infection of like an immunosuppressed person. They don’t have proof of the exact patient who was patient zero for B117. But it’s really thought that infecting immunocompromised people where the virus can live in one host for a long time, allows the virus to adapt to antibodies that the patient comes up with. So an immunosuppressed person usually doesn’t have zero immune system. They just have a weaker one. So it pushes the virus into a corner but leaves the virus enough room to navigate and comes up with some mutant that escapes a major neutralizing response and then it grows a little bit better. And so it accumulates a series of changes within one patient. And that’s really thought theoretically by the people who really understand the mathematics to study viral evolution. They’ve got some pretty compelling models that show one of the key disproportionate drivers of viral evolution for SARS-CoV-2 is infection of immunosuppressed people. And then of course, there is some baseline change in normal infections as well. But when you have an out-of-control pandemic, you end up finding some people who are in immunosuppressed.

[00:29:57] And if you’re in a country like South Africa or sub-Saharan Africa, where there’s a lot of HIV that’s unmedicated and untreated, you have a lot more people who are immunosuppressed who can be infected. And now, as far as the other variants you’re talking about, like the California variant, which has a couple different names depending on what clade system or nomenclature you’re using. I like the Pango lineages, which call it B.1.427 or 429 after that first B.1. And that has some interesting mutations on the spike that are now shown to slightly escape certain neutralizing antibodies. When people say it’s escaping neutralization, it’s hardly ever a complete escape. I think the most concerning one is the one they call the South African variant, which is B.1.351. I’ve seen it in our own data where we collaborated with a guy named Ben Hurley, who’s a professor at Mount Sinai School of Medicine in New York City. And that one really does in our hands. We got some serum from people who are fully immunized using the Sputnik vaccine, the Russian Sputnik vaccine from Argentina. We got their ben-hur’s collaborator in Argentina, Claudia Pedernales. I think that’s how you pronounce her name. Sent us some serum from people who are fully vaccinated. And we saw that that serum really neutralized B117 just fine, but it could not neutralize B.1.351 at all.

Razib Khan: [00:31:21] Jeremy, you’re really reassuring me right now.

Jeremy Kamil: [00:31:24] Yeah, but that’s just neutralization. That’s not T-cells. Like you still have many layers of your immune response. So I think most people should take heart that these vaccines are outstanding. They’re phenomenal vaccines and just being able to be infected is not the same thing as having severe disease. And the most severe disease we know is having bilateral pneumonia, where you end up in the hospital with a risk of dying. And I think these vaccines nearly 100% prevent that outcome even when you talk about infection with variants. And that’s even before we’ve updated the vaccines to incorporate, say, the spike protein of B1351. There’s a guy named Tulio de Oliveira, who’s a Brazilian man who works in South Africa at a place called KRISP. I forget what it stands for, but they’ve discovered B1351, and he has data showing that a patient who recovered from B1351, their serum neutralizes B1351 and neutralizes all the earlier variants. That was an N equals one, but it suggests that we will easily be able to update vaccines to crush this virus. It’s just what does crush the virus really mean? I don’t know if it means driving the virus extinct. I think it means crushing the pandemic in terms of hospitalizations and deaths from COVID-19, very little doubt that we’re going to control the disease. I don’t think it’s going to turn to zero. Even the vaccines are not 100% effective, they’re close to that. But what will happen probably is we have a new pandemic. I hate the word common cold coronavirus because I think that trivializes what all these previous coronavirus that we now call common cold coronaviruses. There is no such thing as the common cold. That is bogus because I took a lot of virology classes. I went to reasonably good schools and I was trained that the common cold is caused by a rhinovirus which looks a little bit like a polio virus, but it can only grow in the upper respiratory tract or the nasal passages because its optimal growth temperature is a little bit below body temperature. So it’s confined to your upper respiratory tract. It can cause you to sneeze and be a little bit uncomfortable. Lots of mucus, lots of keeping the Kleenex company in business, but it’s not that bad. And then someone’s like, Oh, there’s all these common cold coronaviruses, too. I’m like, What are those? No one told me about those before. I mean, unless you really were a coronavirus geek. Even virologists, most of them don’t know about that. So I guess RNA virus, people who study respiratory viruses probably know about them, but I never knew. And those things probably are all the products of previous pandemics, previous coronaviruses that spilled over from nature. And there’s a bunch of veterinary ones and it is a trip, this coronavirus that we get sick with SARS-CoV-2 can also infect mink and cats. It’s obviously has a broad host range. It seems like once you’ve been exposed probably as a child to these common cold coronaviruses, you have a dedicated army of T cells and B cells literally for life.

[00:34:27] They talk about the antibody, the antibodies waning. But that’s, I don’t want to sound too overconfident, but from what I’ve learned about the immune system and I’m not an immunologist, you have memory B cells. They aren’t called memory B cells for nothing. It’s their job to go hide out. Their numbers decrease, but they hide out and they circulate. And then if you get re-infected, dendritic cells, sample antigen from out in tissues and they bring it to the dendritic cell, it’s almost like the station or the station or the cop station, whatever you want to call it, of your body. And then they’re like, they show mug shots of whatever they find to the immune cells. And when one of the memory B cells is like, Oh, I know that dude, that guy got a six, 12 years ago and that that cell just goes, okay, cool. I found my enemy. It’s almost like the Matrix. They make like 4000 copies of themselves. They divide like crazy and then they differentiate into plasma blasts and make antibody that matches that target. Or if it’s a T cell, it clones out and makes a lot of cytotoxic T cells against a specific epitope of a virus. So I have a huge amount, like even if I’m not an immunologist, but what little I’ve learned of immunology from just being a virologist gives me a huge amount of faith in what our body can do to fight a virus.

[00:35:49] And you got to imagine these common cold coronaviruses that kids catch and that adults catch. We probably get infected multiple times in our life by them. And so it keeps a boot camp for our body and it keeps our memory trained on the pathogen. And so that limits the disease. And because the immune system is so dynamic, the immune system generates a response in proportion to the threat. That’s a beautiful thing about it. It doesn’t waste a lot of time making T cells against the virus that’s having an easy time containing. So if there’s a very small amount of disease, you generate a decent response. But it’s not like dominating your pool of memory. So yeah, you can be re-infected a couple of years later, but your immune system ramps up and controls it. So by the time someone’s an elderly person, they probably have a really good trained immune system against all the common cold coronaviruses. And a guy named Steven Goldstein, who trained with a famous coronavirus, just one of the very first ones in the world named Susan Weiss, who’s at University of Pennsylvania. He was saying on Twitter that like, no one really knows how nasty these common cold coronaviruses would be if you were a naive to them, if you grew up on an island and never got infected with one and then got moved into an old folks home and got infected for the first time in your life with one of these, “common cold coronaviruses”. Maybe you’d have pneumonia and die from it, because a lot of what might be keeping us safe from the “common cold viruses” is the fact we have preexisting immunity.

[00:37:14] And if you look at children, they have the least bad infections from this virus. Now, I don’t want to trivialize things like multisystem inflammatory or I forget what it’s called MIS-C. Like there are some really nasty outcomes in a small number of children from this coronavirus. So I don’t recommend people being like, Oh, don’t worry about it at all because kids don’t get sick. I mean, this is a pretty nasty little virus, but I don’t think it’s so, so, so different from viruses that we’ve seen before. Like the measles virus is freaking scary. I mean without a vaccination, you lose 1 in 1000 people and often children, they end up dying of bacterial pneumonia. So that’s a pretty nasty virus and it’s very, very infectious. So people I don’t like the alarmism about this virus.

Razib Khan: [00:38:01] You were going in a positive direction and then you’re talking about people die of measles, at least just in the past.

Jeremy Kamil: [00:38:08] We have a vaccine. That’s a difference, right? Oh, the really scary thing with measles is the brain disease. There’s something called, um.

Razib Khan: [00:38:16] Okay. Jeremy, Jeremy. Talking to a virologist, it’s like Dr. Jekyll and Mr. Hyde. Like, we got these vaccines. We’re super bad all of our technology. And then, like, all of a sudden, it’s like, you want to know a scary disease? No, I don’t want to know a scary disease.

Jeremy Kamil: [00:38:32] Yes, you do. Because it helps people take vaccines. Because I think the scariest thing about coronavirus is that some people think that, oh, I’m going to be fine with no vaccine or vaccines don’t matter. There’s a lot of misinformation out there. And the measles thing is called subacute sclerosing panencephalitis. It’s when measles gets in your brain and it can be like 7 to 10 years after you recover from measles. You have a degenerate brain disease because the virus has evolved inside your body to infect brain cells and not need a receptor anymore. It’s like spike protein, if you will. It’s called F, and it starts to it learns how to enter cells without needing a receptor. Just super scary stuff. And so without the measles vaccine, we’d have a lot more of that. And it’s rare, but it happens. So I think it is important to freak people out a little bit and be like, Look, there’s a bunch of freaky stuff that’s already around. Don’t freak out about it. Like, this is not our first rodeo so to speak. We’re battling, scary things all the time. You just don’t have a powerful enough microscope to watch the horror show. It’s just part of life.

Razib Khan: [00:39:35] Yeah. Yeah, it is part of life. I guess the last question, you’ve been geeking out on science. That’s great. But I do have a question more like policy, politics, communication, which you’ve inadvertently been drafted into over the last year. What do you think about the pause on the J&J vaccine? Like my cards on the table is I understand why they did it to be cautious. But I think part of the issue over the last year is making people conscious of the fact that this is a big deal and there are always trade offs in life, but we need to be a little less cautious because we have something in front of our face right now with the CFRs and the IFRs is that you’re talking about. I felt like the AstraZeneca decision in Europe and the J&J decision indicates a pre COVID-19 mode of thinking. It really confuses people and makes them suspicious because on the one hand, this is horrible and it is horrible even if it’s not the bubonic plague. And we’re trying to convince people of this like this is not just the flu. And then on the other hand, there’s some blood clotting issues. People died. Not a trivial problem. But when you look at the numbers, they were really small. And I’ve told this story before and I’ll tell it again. My best friend from middle school died of a brain bleed due to the anthrax vaccine when he was inducted into the Marines.

Jeremy Kamil: [00:41:01] Wow.

Razib Khan: [00:41:01] This happens every year like he died within an hour.

Jeremy Kamil: [00:41:04] Wow.

Razib Khan: [00:41:05] Why don’t you hear about it? Well, because that’s the risk you take. Like you got to be inoculated against the anthrax vaccine and that happens to some people and they understand that the risks. And so I just think that in terms of cost versus benefit, it was a bad call. And now I’m seeing stuff about how the vaccine uptake drops just on the day of the pause. And other people are saying, well there’s other factors, blah, blah, blah. And I’m just like, okay, but it’s really suspicious that it’s exactly on the day that they announce the pause that the vaccine uptake has dropped. And I recently got the Moderna vaccine, and I was shocked at one how many people were working there compared to how many people were actually getting vaccinated. It just seems that there’s a lot fewer people all of a sudden and other people have said the same thing. They went for their second shot a month later and they’re just like, Wait, what happened? Like, they’re just like, way fewer people. Okay. So a lot of people are immunized. You got the low hanging fruit. But I also think that this was a communication error and it’s part of a general problem of calibrating how our society and our public health communicates.

[00:42:10] What I said recently on Twitter was we have the biotechnology. But one thing we found out is we don’t have the social technology, a place like Taiwan, South Korea, to some extent, Japan, they’ve done really well. And mostly it’s just they were really early and aggressive about certain things like crush and contain. They were not denialists about asymptomatic spread and super spreading events like all of this stuff. They were ahead of the curve. And so I think it really showed some inadequacies in terms of our just social cohesion, social mobilization. And I think the J&J decision is just part of that in terms of after all this years of warning people that you have to take it seriously. All of a sudden some of these downside effects are making the administrators and the regulators be super cautious, which is fine. But now people are just like, well, if you’re going to be cautious, why shouldn’t I be cautious? Why should I take the risk? I don’t know about this mRNA technology. You know what I read on Facebook, which I don’t personally know, but I hear the weirdest things and I’m sure you’ve heard the weirdest things because I’m like, I don’t even know how to respond to this because I have no idea what you’re talking about. But you read it on Facebook. Great.

Jeremy Kamil: [00:43:22] Yeah. They call it an infodemic. It’s like a pandemic of misinformation. And you can almost see like how Russia and countries that are trying to compete with us or they’re not really superpowers anymore, they can use asymmetrical warfare because you can divide Americans against themselves so easily because frankly, our education system sucks. Our public education system is not harmonized well across 50 states. And that’s a really unfair thing. So it’s just like it highlights all these disparities and flaws, some of the virtues of our country, like the independence and freedom we have, are also in some ways weaknesses and some of these countries like Japan or South Korea or Vietnam, there’s a little bit more command and control from the central government to harmonize the message really strictly. I mean, maybe it’s not as totalitarian as place like North Korea, where Kim Jong-il says probably goes.

Razib Khan: [00:44:24] I’ve heard North Korea has no code, never had COVID-19.

Jeremy Kamil: [00:44:27] Yeah, right.

Razib Khan: [00:44:28] That’s what they say.

Jeremy Kamil: [00:44:30] Exactly. Tanzania, too, until the dictator died of it. Right. But what you said about J&J and I think that’s tricky because these things aren’t done on a completely ad hoc basis. I think they did update a lot of policies to fast track the vaccine development and approval to things. But at the same time, the FDA has, I think, preserved its credibility quite well compared to the CBC during this whole pandemic. And they do have guidelines that they put in place ahead of time before they they gave an EUA, the organization. And I don’t work at the FDA, but the sense I have is that they have things that trigger an event and the event is we’re going to have a meeting and we have to gather the data and figure out just how big this problem is because they have a lot of credibility that they don’t want to waste. And if they’re okay, we’re seeing fatal blood clots in women in a certain age group and we don’t know exactly how many of these events that there have been, but we’ve detected this many. We need to stop for just a week or two and figure out what this means and then we’ll issue new guidance. And undoubtedly there probably are people, I went to the post office and it was an older black woman who was the postal clerk and was like, oh, we’re talking. I was like, Are you vaccinated? She’s like, Oh, I was going to get that J&J, but now I don’t know.

[00:45:53] I’m like, Oh, well, you can go to Walmart and get the Moderna or something. And she’s like, Yeah, I probably will. But yeah, I think it did drive hesitancy and probably that hesitancy will no doubt translate to some hospitalizations and probably some deaths. But at the same time, you have to have some kind of a policy for how you’re going to approve vaccines, especially on an emergency basis. I mean, this is like a miracle how quickly these vaccines went from design to first round production to pre-clinical stuff. But if you’re going to commit to that fast tracking, you also have to commit to some safety standards. And if you’re the FDA, you can’t move the goalposts that you agreed to when you decided to emergency authorize this. It was always like, hey, we’re going to emergency authorize this. But the minute we see something weird, we do have to have this meeting and have like a bunch of people who by necessity, are going to be cautious. They’re going to be cautious. And I would argue that, yes, be nice if you could, know the future in advance, but you don’t. And if they knew that it was more than 6 million cases that it was, and it’s limited to women of a certain age and they can just put a black box warning in there and say, hey, if you’re a woman between the ages of 34 and 50, you might want to consider a different vaccine.

[00:47:14] But hindsight is 2020. It’s really easy to criticize them. I think they’ve done a better job than a lot of other parts of the federal government during this thing. But yeah, it’s easy to be Nate Silver on Twitter with your 2 million followers and be like, Oh my gosh, this is such a mistake. Yeah, Like, well, yeah, it’s easy to pontificate and tell people what a mistake is, but it’s their ass that’s on the line when you know someone dies. And if you’re the FDA administrator who just ignores, if it’s someone’s sister who died of a blood clot and it’s clearly thrombocytopenia that looks like it’s related to the vaccine, you’re going to tell her that, oh, no, we’re not going to pause the vaccine for a second because we’re absolutely sure that there is no bigger problem here. We don’t even need to stop. And look, we’re just confident. There’s probably good reasons why they did what they did. And I’m not in a position to second guess them. There’s plenty of other parts of the federal government where I’m happy to second guess how that and even more than that to tell you very clearly that they’re screwing up and they’re screwing you with your own tax dollars in terms of like what they’re doing.

Razib Khan: [00:48:19] So we’ve touched on most of the topics I wanted to talk about. It was a really great conversation. Your infectious enthusiasm for viruses shows through. It’s not virulent at all, just highly infectious. And so I think hopefully the listeners will get that and understand that there’s a reason we got these vaccines, like there’s this huge scientific establishment that pivoted and did this in a year. And it is a miracle. I talked to people last spring who were not as hooked in, but they had worked in the immune system space and immune genetics, and they’re like, oh, this is going to take years. It’s going to take a long time. McNeil was saying, the fastest turnaround had been, what like five years maybe for the mumps vaccine. And so people were freaking out. And so here we are a year later. You’ve been vaccinated for a while. I think a lot of listeners have been vaccinated. I’m still waiting on my second shot, but soon. And so that is the definite positive for all the downsides. It’s a good place to be in to have these gripes.

[00:49:20] And so I don’t want to end on a negative note. I was going to ask about the mRNA technology, but I think we take a lot of your time and listeners can look that up. It’s fascinating. There’s the adenovirus technology, which is kind of older, but there’s new mRNA technology, which I think on the horizon. And maybe someone will do a podcast on this in the future. They’re using it in malaria and other things. So it’s a very, very, very positive development and maybe coronavirus and the pandemic accelerated that, trying to make lemonade out of a lemon here. Finally, I do want to say I didn’t mention your Twitter handle, macrolitter and macro is a macrobiotic, Jeremy Kamil. Dr. Jeremy Kamil, it has been great to have you on. I really enjoy talking to you as always. You’re really good at what you do and I hope people get to hear from you more because you’re clear, you’re concise and you have a definite passion for science. And that’s what I really love.

Jeremy Kamil: [00:50:14] Thank you Razib. I always enjoy hearing you speak as well. You’ve I think much more depth of knowledge than I have about viruses, about human evolution and people and how genes work so admiration is mutual.

Razib Khan: [00:50:25] You are too kind sir.