The Bioinformatics CRO Podcast

Episode 42 with Mauro Calabrese

Mauro Calabrese, Associate Professor at UNC Chapel Hill and Director of Graduate Studies in the Department of Pharmacology, discusses the future of RNA-based therapeutics and the role of lncRNA in gene transcription.

On The Bioinformatics CRO Podcast, we sit down with scientists to discuss interesting topics across biomedical research and to explore what made them who they are today.

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Mauro is Associate Professor at UNC Chapel Hill and Director of Graduate Studies in the Department of Pharmacology. His lab studies how long noncoding RNAs control transcription in the mammalian genome.

Transcript of Episode 42: Mauro Calabrese

Grace: [00:00:00] Welcome to The Bioinformatics CRO Podcast. My name is Grace Ratley. I’ll be your host for today’s show. And today I am joined by Mauro Calabrese. Mauro is Associate Professor and Director of Graduate Studies in the Department of Pharmacology at the University of North Carolina, Chapel Hill. Welcome Mauro.

Mauro: [00:00:14] Hi, Grace. Thanks for having me on the podcast.

Grace: [00:00:17] Yeah, we’re happy to have you on. So can you tell us a little bit about your current research on long noncoding RNAs?

Mauro: [00:00:25] Yeah. So broadly speaking, we are trying to understand fundamental mechanisms through which our genome is regulated with the understanding that by defining those mechanisms, we’re going to learn a lot about the basic biology that goes on inside of our bodies. And also we’re going to learn about really important events that give rise to and sustain human disease. So what we study in my lab are these molecules called long noncoding RNAs, unlike a typical messenger RNA that encodes information for protein. These RNAs themselves are sort of the end product. Our genomes, the mammalian genome makes lots and lots of noncoding RNA, like billions of base pairs of it, actually, the majority of which we really don’t know what its function is. It may not have a function or maybe it does.

[00:01:16] And we know from a few really amazing examples, these are genes that people have discovered now upwards of 30 years ago, that at least a subset of long noncoding RNAs play really incredible roles at gene regulation. I can give you a specific example. It’s an essential gene, it’s an RNA, a piece of RNA that’s expressed from the X chromosome in all female mammals. And the function of this RNA is to turn off one X chromosome in every cell, essentially for the life of the organism. So this piece of RNA can transcriptionly silence a hundred and sixty five million base pairs of DNA for 100 years and a billion cell divisions. That’s really incredible. And we don’t fully understand how it works, which is interesting. And then beyond that, there’s this sort of universe of long, noncoding RNAs that get produced by our genome and we have no idea how they work or what they do or whether they have a function at all. And so we use genomics and genetics and cell biology and microscopy and biochemistry and a lot of computational biology to try and understand how long noncoding RNAs regulate gene expression and develop new experimental and computational approaches that will enable others to do the same.

Grace: [00:02:33] I noted that your lab also looks at these long noncoding RNAs in the context of cancer. Can you tell us a little bit about that?

Mauro: [00:02:42] Yeah, we are not so explicitly focused on cancer, but some of the RNAs that we study do play roles in cancers. But I think sort of the biggest area that we hope to impact, like in regard to human disease and cancer, is a really I don’t know if low hanging fruit is the right word, but there’s a lot of really great genomic data in cancers. We know what RNAs are expressed in different types of cancers. And so I think that area is really ripe for discovery. And the biggest roadblock in the field is we really don’t have an understanding of at the basic level, what’s the relationship between the sequence of a noncoding RNA and its function in the cell. For the listeners that know a little bit about proteins, relatively have a much more sophisticated understanding of how protein sequence relates to function to the effect that you could take a protein that’s never been studied before and compare it to all other proteins. And chances are you might find a piece of protein that was similar to a previously studied protein, and that would give you really important clues as to the mechanism of your unstudied protein. So like if a protein has a kinase domain, there’s a good chance it’s a kinase.

[00:03:58] And those types of understood relationships just don’t exist in the long noncoding RNA field. And so the effect of that is that in a disease like cancer, people have looked at this many different ways, thousands of different long noncoding RNAs that are differentially expressed that correlate with different forms of metastasis, that correlate with different cancers that appear to be, if you like, knock down these transcripts, they appear to have therapeutic effects. And I believe clinical trials started last year targeting a few long, noncoding RNAs through Ionis and possibly some other pharmaceutical companies. So these are like there’s RNAs that get expressed in cells. Some of them almost certainly are drug targets. But we have absolutely no idea how to know which ones we should be thinking about targeting and what they might do in the cell. By sort of focusing our efforts on understanding a few noncoding RNAs whose functions are well known, we’re starting to get insight into what are the building blocks that noncoding RNAs use to encode function and ultimately hoping to sort of develop a framework that will allow us to computationally predict or identify regulatory function in essentially any noncoding RNA. And I think cancer is an area that I’m really excited to move into once we have a better handle on the approaches that we’re trying to develop, because I think there’s a lot to discover in that space.

Grace: [00:05:24] Yeah. Cancer, I think is a really great place to start because you have such amazing databases of genetic information and gene expression and all of those sorts of things. And I was going to ask how you ended up in the Department of Pharmacology, because from what it sounds like, a lot of the work you do is in genetics. So can you tell us a little bit about that?

Mauro: [00:05:44] Yeah. Great question. People ask me that all the time. You know, science is so interdisciplinary these days. I think our work certainly fits within pharmacology, and I’ll tell you why in a second. But easily, we could be in a genetics department or a cell biology department or even a biochemistry department. So everything is just cross disciplinary.

But I didn’t necessarily apply specifically to pharmacology departments when I was trying to get a faculty position, but there was a position that was open in this department. And the former chair of the department, who was Gary Johnson at the time, I think sort of recognized the potential that the things that I was just talking about in regards to cancer, like there are these really tantalizing examples of like, OK, we know there’s a few noncoding RNAs that appear to be drivers of metastasis and probably can be targeted with antisense analogues or even small molecules targeting structure of RNAs.

You know, there’s sort of a next wave of therapeutics that are going to involve RNA. And this was true in 2014 when I started the job, which is I think why I got brought into this department. But of course, everyone can appreciate it now, the power of RNA delivery through these nanoparticles that has saved, hundreds of thousands of lives through vaccines. So RNA is not something that historically has been drugged or a drug. But I believe in the future, the next 10 to 20 years, we’re going to see more and more RNA based therapeutics. And so that’s how our research fits into pharmacology.

Grace: [00:07:17] Yeah. Yeah, it’s so fascinating. And I’m excited to see how the technology that is the basis of the mRNA vaccine for COVID-19 is going to influence a lot of science, because, I mean, like you said, historically, it just wasn’t possible because RNA is so unstable.

Mauro: [00:07:33] It’s unstable, it’s big. And I mean, although I guess the technology that Moderna and and Pfizer are taking advantage of, the idea that you could deliver messenger RNA as a therapeutic even in the 80’s. It just has, I think for reasons that you just said, taken some time to take off. But, yeah, it seems like there’s just a lot of new possibilities. And I also am excited to see what happens.

Grace: [00:08:02] Yeah. And there’s also that kind of awareness piece of it. You know, it’s like I know it existed before, but I wasn’t familiar with it. I guess I can’t say that I’m an RNA biologist, though.

Mauro: [00:08:14] Well, yeah. I mean, I’ve been studying RNA for a long time, and I wasn’t familiar with it either. So that doesn’t mean that, maybe I should have been familiar with it, but anyway, like the awareness is a big deal. And now we’re all aware.

Grace: [00:08:28] Yeah, exactly. How was your lab affected by the pandemic when it started?

Mauro: [00:08:33] Yeah, I think it was brutal for us and brutal for many industries, and it continues to be brutal for many industries. But it’s a lot better for us now than it was. I remember it well, I’m sure I’ll always remember it. Like you heard about this virus and it was in China and then you heard like, oh, my gosh, they’re like shutting down essentially all of China with pop up hospitals at Wuhan. And then and it was like getting closer. Then in the beginning of March, it was like, oh, maybe it’s going to come here. A week later, it was like, okay, it’s here.

There were a few days where a UNC hadn’t shut down, but we knew it was coming because everything else had shut down. So my lab shut down like a day earlier and we’re just like, we can’t handle this. It’s definitely happening. We’re just going to close everything. And so, yeah, we just stopped research, just pulled the plug on it. And we were out of the lab for three months. But UNC opened up in June of 2020 with masks at 50 percent capacity, and that enabled us to at least get back into the lab.

But it was just a mentally extremely challenging year. People that I know, they lost loved ones. Many people experienced extreme forms of mental stress, and we weren’t spared from that in the lab. So as a father of two young kids and my wife also has a job, we had zero child care. So how do you do that? Like not very well. You know, it was like really hard on everybody, it was very hard on my family because our kids got pulled out of school and my son is like six months old and my daughter is three and a half and somebody needs to pay attention to them because they’re kids and they need that. So it was a wreck.

[00:10:13] We were exceedingly careful in the lab and we managed to make some progress during the year, but it was really limited relative to what we would have expected. And things began to come online once we all got vaccinated. But it’s still a challenge. I mean, I think we need to be wearing masks at work. I’m in a private office, so I’m not wearing a mask right now. But everyone that’s in the lab wears masks all day. So I think people do more work at home than they would otherwise, which I think is fair. You know, your face gets hot. So it’s a fact.

So we’re still like kind of a little fragmented as a lab because we’re doing more remote work than we were used to. The remoteness of Zoom is enabling on one level, but it’s also stifling. And I think it limits the creativity that we get from being all together for a full eight hours a day. And so we still haven’t gotten that back. And I don’t know whether maybe in a year or two, when we stop having to wear masks at work, we’re making discoveries, we’re making good progress. We’re figuring things out that are interesting and important. But I don’t think we’re operating at the same level that we were before. But we’re close.

Grace: [00:11:31] It’s good to hear that you guys are rebounding a little bit now, although it does make me worried, looking at a lot of the numbers, especially around North Carolina. I have a lot of friends going back to school and everything is increasing again. And it does make you a little nervous.

Mauro: [00:11:47] It does. You know, I think I totally agree. I guess the flip side is that UNC research operations did a pretty good job last year. Of course, the Delta variant is different than it was: it’s far more contagious. But I don’t think there was like a single case where they could say there was workplace transmission at UNC at all last year. Like in all the school of medicine, people are wearing masks, they’re adhering to it. And over the last year, I think objectively it was a very safe place to work.

And so even though the Delta variant is like 10 times as contagious as the original coronavirus, I think it still remains like a pretty safe place to work. For now, fortunately, most of us are being vaccinated. And so I’m not immune to getting COVID, but it’s less likely that it’ll be severe. And so this time, even though cases are similarly high now and probably will be higher than they were in January of last year soon, I don’t think a lot of that is happening at work at UNC or even in classes. I think it’s the personal spaces where people are relaxing and interacting closely where the bulk of the transmission is.

Grace: [00:12:58] Yeah. Yeah, very true. Very true. Those darn college students partying. Yeah, it’s been a hard year, hard year and a half. It’s been interesting to see how the pandemic has sped up science in some ways, but also how it’s slowed science down in other ways. It’ll be interesting to see how it works out going forward.

Mauro: [00:13:22] Yeah, but I think I’ve always enjoyed what I do, and I don’t necessarily do it for the benefit of public health. I just I think I’m interested in it. But I do firmly believe that there’s a strong benefit to humankind, as well as an economic benefit to research. And I think the pandemic on one level is inspiring for what you just said/ Being able to develop these vaccines in a record amount of time, and they’re safe and they’re highly effective. And all the amazing research that’s going on in regard to the coronavirus, I think is really underscored the necessity for science and its power.

Grace: [00:14:00] It’s been great to see all of the collaborative efforts, industry and government and universities working all together. And it’s kind of like a world war. You know, it’s like everyone, all the industries, all the people are coming together to fight, not an enemy, but a virus.

Mauro: [00:14:17] Yeah, I think that’s when we’re at our best, when we come together.

Grace: [00:14:21] Yeah. So tell me a little bit about how you got into RNA biology and how you became interested in these long noncoding RNAs.

Mauro: [00:14:31] Happy to do so. It’s a little bit by chance. You know, you make these decisions over the course of your life and then the next decision follows. So I guess I was interested in gene regulation in college, like I found it to be like just really interesting. There’s like all this DNA and it gets read in different ways in different cells at different times. And that was like really interesting to me. And then I went to graduate school at MIT and when you’re first year of graduate student, you rotate in different labs and pretty much by dumb luck I rotated in Phil Sharp’s lab.

Phil Sharp won the Nobel Prize in 1991 for the discovery of splicing and has just made all these really incredible contributions to our understanding of biology and RNA. And I knew I was interested in mammalian gene regulation. So I rotated in Phil’s lab and it was really great. So I ended up joining that lab. And so that sort of left me cultivate my interest in RNA. And when I was in Phil’s lab, we were studying micro RNAs, which are short, twenty one to twenty three nucleotides long, but they’re like genes. Some of them are extremely conserved, incredibly, even though they’re teeny, tiny and short. And they do amazing things like RNA tends to do.

[00:15:51] So we were studying microRNAs and then I became aware of some of the work that was done by researchers, in at that point, the nascent, long noncoding RNA field. So this RNA, I’m not sure I mentioned it by name, but I referenced it very loosely at the beginning of our conversation called Xist. The function of this RNA is to turn off the whole X chromosome. There were a lot of really interesting breakthrough studies on this Xist long noncoding RNA when I was a graduate student, and those were pretty cool to me. There were also independently some breakthrough studies on a different long noncoding RNA that has a function that’s analogous to Xist. All these RNAs have weird names. They’re just gene names. But this is called Air. Actually, we study it in my lab now. It is this amazingly strange RNA. It’s huge. It’s ninety thousand nucleotides long, which is like crazy. It’s un-spliced, highly unstable. But the function is to silence gene expression over about one third of mouse chromosome 17. And it’s not even conserved outside of rodents. And so it’s got this incredible biological activity that has appeared to have evolved very recently in evolution.

[00:17:04] Anyway, some really amazing work from a researcher in Austria who has unfortunately since passed away, Denise Barlowe. But I remember reading some of her papers, as well as these papers from the Xist field, while I was a graduate student at Phil’s lab they piqued my interest. And ultimately I decided to pursue that area of research for postdoc, I thought it was really interesting. And so I did that. I was a postdoc here at UNC and Terry Magnuson’s lab in the genetics department. I wasn’t necessarily set on starting my own lab, but I was just doing what I thought was the next best thing, which was to pursue a postdoc in an area that I found to be interesting. And I still found it to be interesting at the end of my postdoc. And I had enough success to convince the pharmacology department to hire me. And so that sort of brings us to the present day, I guess is an abridged version.

Grace: [00:17:55] Yeah. In your lab, you have such a variety of approaches and computational biology, microscopy. How did all of that come together?

Mauro: [00:18:05] Yeah. I think you just sort of do what needs to be done and get into it a little bit at a time. I was a graduate student right at the inflection point of the sequencing revolution. When I started graduate school we were sequencing micro RNAs by hand. We would like take these little bacterial colonies and after like three weeks of work, you would get three hundred sequences back. And then all of a sudden there was this instrument that came online from a company that was bought by Roche and then I think has gone under. But all of a sudden, instead of for three weeks of work, instead of getting three hundred sequences, you would get ten thousand sequences, 300 times more. And then like a few months later, instead of ten thousand sequences, you could easily get 10 million sequences. So like in the span of nine months, it was like the genome revolution. And so I learned computational biology for that.

Then I was a postdoc in a genetics lab. And questions arise and you want to figure out what are the most important questions to answer and what are the things I need to understand to answer these questions? And if they’re interesting enough and if they’re within your capacity, then you learn the skills necessary to answer them. Like I’m not a math person. So structural biology is probably something I would never be able to pick up myself. But you just sort of over time, I think, figure stuff out.

Grace: [00:19:25] Yeah, certainly. So we work a lot with biotech companies and generally, people who have such varied experience and who have a lot of random skills tend to do very well in biotech companies. Have you ever considered joining a biotech or starting biotech?

Mauro: [00:19:42] Yeah, I have considered it. The benefit of working in an academic lab as long as you can convince somebody that it’s important, they should fund your research. You can do what you find to be the most interesting. And I think we’ve sort of like fallen into this path. I think, the computational objectives that we have, like we’ve started to make some insight into how we can computationally predict the function of a noncoding RNA. And I don’t think we’ve really finished that work yet.

So I’d like us to get there. And I think when we get there, it’s going to be pretty exciting. But I’m not sure that anything that we have done so far or maybe that we will do is–what’s the word–is like IP-able, you know, like it’s information. We’re trying to figure out how to figure things out. And when we figure that out, we’re going to publish it and make it public.

So I think some people’s research, especially in pharmacology is good for biotech. Like we have this protein that we study with a mutation and we’re developing a small molecule to fit in this pocket. And you can then spin off that molecule in IP. We haven’t quite done that work, but I think about it, many of my friends actually from graduate school went into industry, and now they’re like doing all these amazing things at high levels in these biotech companies. And I’m like, wow, that would have been cool. But this was my path. And it’s been great so far. But I’m not averse to doing work in the biotech sphere as well.

Grace: [00:21:04] Yeah. Your path hasn’t ended yet, so you’ve still got time. And if IP-able isn’t a word that’s used in biotech, I think they should add it to the biotech dictionary. What skills do you think are most important for scientists today?

Mauro: [00:21:23] You know, I think a lot of them are skills that are transferable to everything: you know, focus. This is maybe a weird thing to say, but we live in a very distracted time, especially during the pandemic. I mean, the news cycle is like from one crisis to next. And there’s all these things that take our focus away, like text messages and email and different forms of social media. And I think to really do excellent work, somehow you need to put your blinders on and think deeply about stuff, especially if you’re trying to make discoveries. To figure out things that we don’t know yet really takes a lot of ruminating and deep thoughts. So an ability to focus, a strong interest in the work that you do, because that’s going to give you those insights. You’re going to be thinking about your work and you’re going to have the insights, but if you don’t find it so interesting, then you’re not really going to be thinking about it that much. And that’s fine. But it’s not great for research.

[00:22:29] And then I think an ability to communicate. So it’s not enough. It’s never enough, I think, to work in a silos. Our best advances as humankind have come from collaborative efforts. And I think it’s probably always been true, but it’s definitely true today. Especially the more complex a project is, the more likely it is that you’ll need to rely on multiple people to achieve an objective. And at The Bioinformatics CRO–I’m sure you understand this–you have computational biologists and you have biologists who don’t understand computational and communication is really key. Like if you have people that communicate well, then the speed of the project is like orders of magnitude, greater than two people that are not communicating well. So I find that to be extremely true with our work as well. Those are the big ones, I think focus, interest, and an ability to communicate. If you can do those three things, you can pretty much do anything.

Grace: [00:23:30] So the things that you’ve mentioned are traditionally very difficult to learn. So the communication, like team management, that’s very difficult and focus I mean, it’s impossible. I mean, really. So what are some ways that people can cultivate these skills?

Mauro: [00:23:45] Yeah, and I think that’s a great question. And I do think we all need to cultivate them. They’re not necessarily taught in class and they’re not really taught in society either. The way that the news communicates to us is not really the way that we should communicate to each other. The way that like Facebook inundates us with distractions is not healthy. So you really have to like steel your mind against the forces of the world that we live in. To varying success, I have been able to do this. I mean, I think there’s times, especially last year during the election where I was unable to focus. Actually, much of last year, I was unable to focus for a lot of reasons, and I wasn’t alone.

But I think dedicating a time to shut off external communication via text message, take your Apple watch off, don’t listen to music, turn off Slack. Setting aside time to make sure that you do that, I think that’s what I do. Whether or not that’s a transferable skill, I don’t know. But I find that to be very helpful. The times when I’m able to not check my email every five seconds and not look at the news every five seconds. Like those are the days that I feel the best about the work that I’ve done. And those are the days that I’ve accomplished the most.

[00:24:59] I think, similarly in terms of communication, that’s something that I’ve learned. Writing in particular in my job is essential, and it’s not anything that I was formally trained in. I took like an English class in high school, and I learned that a paragraph has a topic sentence and three sentences after that support the topic, which is true sometimes, but that’s not actually the best way to write most of the time. But there is a structure and understanding what people expect and how to include it in a document and how to write words that are going to give you the highest probability of success communicating to your audience. That’s something I’ve read about, I mean, by necessity. If I can’t write, I don’t have money to fund my research. So like anything, essentially, you have to sort of set a goal and work towards it in practice and seek out resources that can help you. And in terms of communication, if you’re a natural communicator, then you have a leg up. But if it’s something that you want to improve, there’s leadership courses, there’s books that people would recommend, I think, in practice and engage and self evaluate. And over time, you will improve.

Grace: [00:26:11] So as we wrap up this episode, I always like to ask our guests what advice they have for early career scientists or graduate student postdocs who are looking to go into a similar path that you’re following. What are some of the lessons that you’ve learned and words of wisdom that you might share with younger scientists?

Mauro: [00:26:33] Yeah. You know, the thing I tell many of the graduate students I interact with and I would share here, is to do your best to figure out what it is that you are interested in. And if you’re going to join a lab or do a postdoc or pick a research project or join a company that you find interesting and that you believe in the mission. Like this work is interesting to me and I believe that it’s worthwhile. And I feel like that’s like the number one thing.

I couldn’t tell you why I’m interested in the work that I do. I just find it interesting and I don’t think I need to justify it. It’s interesting to me, and I can tell you why it’s important. And so I think that’s true. I suspect for other people, like you don’t have to justify it to anybody. It’s meaningful to you and just tap into that feeling, like don’t overthink it. But if you find yourself feeling like, it’s a slog–it’s bound to happen–just sort of reflect on that. And when it comes time to make another career decision, think about the things that you’ve done and what you enjoyed and what you didn’t enjoy. I think follow your interests as best as you can and that’s going to get you really far because it’s the more interested you are, the more excited you are, the better work you’re going to do, the harder you’re going to work and the greater successes that you’ll have.

Grace: [00:27:53] Excellent advice. So thank you so much Mauro for coming on the podcast and sharing your wisdom and your experiences. I had a really great time talking with you today.

Mauro: [00:28:02] Yeah, Grace. It was really fun.