Seventeen Minutes of Science: Using C. elegans in Rare Disease Research

Transcript

Ben Jussila (Host): [00:00:10] Good morning, good afternoon, good evening, everybody, and welcome to this week’s edition of 17 Minutes of Science. My name is Ben Jussila and I am a scientist with InVivo Biosystems. It is my pleasure to introduce our guest today, Dr. Oliver Blacque. He is an Associate Professor at the University College of Dublin at the School of Biomolecular and Biomedical Sciences. He heads a human disease research group there, and as for the focus of today’s talk, [he] makes use of the model system Caenorhabditis elegans in rare disease research focusing on primary cilia biology and the diseases associated with that. So thank you for joining us today, Oliver. And I’ll let you provide any additional background you’d like there.

 Dr. Oliver Blacque (Guest) : [00:01:02] No that was great, yeah it’s a real pleasure to be here. Thanks for having me, I’m very excited to do this.

Ben Jussila (Host): [00:01:08] Yeah, we’re we’re always happy to have our C. elegans folks join us here. And rare disease research and model organism biology is very near and dear to me. So. And so, it turns out, is primary ciliary search. So it is a double pleasure to have you with us today. And I’m going to go ahead and kick things off with our 17 minute timer and I will dive right in. And as I’ve ever maybe hinted at this a little too much, but why don’t you tell us a little bit about what your lab primarily focuses on for your research goals?

 Dr. Oliver Blacque (Guest) : [00:01:44] Yes. So, yeah, sure. So so I mean, my lab is interested in a class of human disease called ciliopathies that you basically mentioned, briefly. So maybe I’ll tell you a little bit about those. So these are genetically inherited disorders. Found, in fact, to affect the development, and even the maintenance, of many tissues and organs. In fact, most body tissues and organs are probably affected across the disease class. So you see things like blindness, assisted kidneys, obesity, organs pattern on the wrong side, malformation bones, things like infertility. And there’s about 20 different types of ciliopathies, actually. And about 200 genes linked to this disease class. So it’s pretty big in terms of this gene variation. Many of these diseases are syndromic, so patients actually have lots of these symptoms. Some of them are non syndromic, so they may just have one symptom. Some of these diseases are very severe, like Meckel-Gruber syndrome, is one that can be lethal, and some are milder. But yeah, so still pretty debilitating. Now, they’re rare, in fact about one in 100000 people – most of them. Some of them like autosomal recessive polycystic kidney disease is actually very common. So in fact, that’s probably the most common genetic disorder. The thing they all have in common is a defect in cilia. So, you know, my lab is interested in ciliopathies. But of course, we’re interested in this little tiny structure on the surface of cells. We try and understand what these cilia do, and we try and understand what the ciliopathies genes do in cilia.

Ben Jussila (Host): [00:03:18] Yeah. Awesome, thank you for for that overview, and yeah, that’s I mean, that’s my, my understanding and my experience – is that there’s,  the more that you look, the more it seems, especially over the last, I don’t know, five to 10 years. It seems like we’re uncovering more and more, ‘Oh, it’s actually involved in this. Oh, these tissues are ciliated. We find that this thing localizes to the primary cilia.’ So it’s, it seems to kind of have its hands, so to speak, in just about everything that you can find, either directly or indirectly.

 Dr. Oliver Blacque (Guest) : [00:03:54] Yeah.

Ben Jussila (Host): [00:03:55] Can you tell us, I guess, a little bit more about cilia and why they are linked in so many of these, these human disorders, human diseases and disorders and these polygenic disorders?

 Dr. Oliver Blacque (Guest) : [00:04:08] Sure. Well, maybe I’ll reiterate, that they’re very tiny. That’s the first thing. They’re about a micron long, or maybe up to 10 microns. So pretty small and they can be motile. Most people would know about the beating flagella that moves the sperm cell around. Or the motile cilia in the upper epithelium tract, pushing mucus out of the lungs. But actually, most of us have a non-motile version of cilia. These are called Primary Cilia, because there is about one per cell. And these little primary cilia, they act as little sensory devices for cells, they’re like a little GPA sensor for the cell. So good examples of that would be in the sensory systems, for example, sensing taste, compounds and lights and odorants. And these are on sensory neurons in our nose and our taste buds. But all of the primary cilia internally, in our internal organs – you know, they do things too. For a long time, we actually thought these cilia were some kind of appendix of the cell, some kind of vestigial remnants of where maybe all cells were beating around in fluids. But actually, we know most of these primary cilia do things too. And they sense very important internal molecules that cells use to communicate with each other. So cells must communicate with each other during development in tissue homeostasis to build a proper kind of structure, cells have to regulate their division. They have to regulate their differentiation properties. And the only way they can coordinate this is by sending signals to one another. So one cell might release a signal sensed by neighboring cells. Well, you probably guessed what sense sends that signal: so the cilium is a primary part of the surface of cells that actually senses those signals because they have lost the channels that are important in the sensing mechanism. And when the cilium senses the signal, it can then transduce the signal to the nucleus, for example, or maybe non-nuclear signals, and that tells the cell how to behave appropriately. So I guess in a nutshell, your primary cilia there like these are GPS signaling receivers that are essential for cell behavior. And of course, that’s essential for, developmental processes, which is probably why you see developmental defects in ciliopathies.

Ben Jussila (Host): [00:06:16] Yeah. Well, and it’s – they’re so, they’re so – one: they’re so ubiquitous, and two: they have, it seems like they’ve got -they’re fitted out with all the things. They’ve got mechanosensory, they’ve got ligands, they’ve got all of the different receptors and everything. And they’re involved in, like, the patterning from from square one, right?

 Dr. Oliver Blacque (Guest) : [00:06:37] Yeah. And in fact, you some of the most important developmental cell-cell communication signaling molecules like Sonic Hedgehog. So any developmental biologist who is listening will know about that. Or some of the wingless molecules or some growth factors. You know, the receptors to those signaling agents are frequently highly clustered in the ciliary parts of the cell surface. So for some reason, cells have evolved the cilium as a place on the surface of cells to house these sensory molecules presume – or signaling molecules, presumably because you can regulate the signaling pathways better by having them in a defined place. And we don’t exactly know how that might have happened. There are plenty of theories, but that’s certainly the context to this little organelles signaling function, I think.

Ben Jussila (Host): [00:07:27] Yeah, it’s I mean, I can see why they maybe initially thought that it was sort of the appendix of the cell, but it seems like it is actually completely opposite. That it is a very crucial and an essential component and that it actually houses a lot of things. I mean, I know that the appendix has also gotten a lot of crap over the years, but that it serves important functions. But so OK, so so that, that kind of lays the groundwork for how it’s how cilia are related to human diseases. So what diseases are you currently focused on? I know that there are a lot, and there are a lot of different aspects even within, you know, syndrome ciliopathies. So are there certain ones that you’re focusing on right now?

 Dr. Oliver Blacque (Guest) : [00:08:16] Yeah, there are, actually. So we’re particularly interested in one of the diseases called Joubert syndrome (JBTS) and a related disease, well they’re all related, I guess, with ciliopathies, but particularly related to Joubert is Meckel-Gruber syndrome. And Joubert syndrome patients are actually diagnosed by a characteristic malformation their brains, which you see in an MRI. It’s called a molar tooth sign. And that’s because those patients have defects in midbrain and hindbrain structures, the cerebellar vermis, for example is disrupted. And patients therefore have, you know, motor and speech problems, you know, various types of muscle twitching and intellectual issues. And they also suffer from other symptoms in other organs, as you might imagine, for ciliopathies like eye problems, blind assisted kidneys. So we’re interested in Joubert, not just for that reason, but also because all of the Joubert, or many of the Joubert proteins – that the genes mutated in Joubert, the encoded proteins, they’re all clustered right at the bottom of the cilium. That’s really quite fascinating. So the bottom of the cilium, there’s a little subcompartment, which we call the transition zone. It’s only about point one to one micron in length. It’s the first little piece of the cilium. And we think this little part of the cilium acts as a kind of gate. It’s a regulated gate, because we can’t have molecules just wandering in and out of the cilium. It’s such an important organelle for signaling, we have to control the composition of the cilium. So this then gate, at the base seems to regulate what’s allowed and what’s not. So we think it does that by establishing some kind of molecular diffusion barrier. So there’s diffusion barriers at the membrane, at the cytosol of this base region at the gates and somehow the Joubert syndrome proteins are part of this. They’re clustered there. We think some of them could be part of the structure of the gate, which we don’t fully understand that structure, yet. And I can talk about that in a little bit, but I find the ciliary gate fascinating because in all of the biology we wonder how do signals – how do pieces of the plasma membrane get compartmentalized? How do you make a little patch different from another? The ciliary membrane is a unique patch of the plasma membrane, and having these barriers at the base is a way in which you can regulate the uniqueness of the ciliary membrane. And in fact, we know very little about barriers regulating any patch of any plasma membrane surface. The cilium is a really good test case to actually try and understand this important basic problem. And because Joubert intersects with that part of the cilium and is somehow part of the barrier regulation, I find that a very interesting test case to actually bring to my lab.

Ben Jussila (Host): [00:10:59] Yeah. No, that’s – it’s for being such a small, a small actual space within the cell there is a lot that happens there and it’s got just a myriad of functions that are disrupted when you when you mess with that zone or that compartment. Yeah. Sorry, I’m sitting here lost in thought a little bit about – my whole day is looking at transition zone proteins. And it’s just that it is a long list of genes that are that are involved there, localized there.

 Dr. Oliver Blacque (Guest) : [00:11:32] Yeah, there’s a whole bunch there and there’s been some great studies trying to understand the interactome of the transition zone. We know different protein complexes are in there. And the other cool part about that that part of the cilium is it’s right stuck at the beginning of a railroad track using microtubules. So there’s another track, there’s a system in C.elegans – or cilia, I should say, whereby proteins are moved in with motors out of the cilium and into the organelle, and the first part of the track has to actually go through this transition zone barrier. We think there’s some really interesting connections and crosstalk between the gate, which is like the exit to the train station, if you will, and these motor-driven assemblies, which are all bringing things into and out of cilia.

Ben Jussila (Host): [00:12:18] Oh, yeah, so that kind of helps me transition to one of the next questions here, so how are C. elegans suited to to this kind of research? So I mean, you can imagine that if I’m thinking about a syndromic, a human disorder, I’ve got eyes, I’ve got a spinal cord and I’ve got a bunch of things a worm doesn’t. But what, so what – maybe you can shed a little light on that.

 Dr. Oliver Blacque (Guest) : [00:12:43] Well, I’m very good in this question from trying to rebut reviewers’ comments from grant applications over the years: ‘Why would you want to use the worms to understand cilia biology?’ Well, there’s a whole bunch of reasons. So the first thing, you know, the genes that build and maintain cilia, they tend to be conserved in C. elegans. Second thing is many of the ciliopathy genes are conserved in C. elegans. And so for example, these 35 Joubert syndrome genes that cause Joubert syndrome in humans, 23 of them, I think, are conserved in C. elegans. And so therefore we can actually understand and study the – how these disease genes function in the context of a simpler organism like C. elegans. It’s simpler, but it’s still conserves the pathways and components. So that’s very, very important. And for, for example, in the case of Joubert syndrome, in the transition zone, the human – uh, Joubert syndrome proteins are also stuck in the transition zone just like the worm one. So we’ve got very good conservation of biology. Even the complexes that are formed between the different Joubert syndrome proteins at the transition zone seem to be very similar. So some great conservation, and we can use that to our advantage in C. elegans. Of course, worms like any model organism like drosophila or yeasts – some great genetic tools. We can manipulate genes very easily. We can knock out genes at will and recently using CRISPR Cas9, and hopefully I have time to say something about this later, you know, we can do gene editing and make very specific changes in the gene. That’s very, very useful for understanding very specific mutations in human disease. Of course, in the C. elegans, we’ve got a transparent organism. So imaging is great. We can even do super resolution microscopy using SEM (scanning electron microscopy), we’ve even done, SEM microscopy in living worms on the slide. We published that data and in fact, using that, we were able to define maybe one of the first architectures for the, for the transition zone diffusion barrier. So that was very exciting. And of course, in C. elegans, we’ve got speed of experimentation and cost, very important – [they are] not expensive.

Ben Jussila (Host): [00:14:43] Yeah. Yeah, I mean, I mean, for any other organism, I guess “higher order”, I don’t like to always say that that way, but I feel like that’s the gentlest way to say it. Any vertebrate models, even zebrafish that are supposedly more high throughput, they can’t hold a candle to C. elegans in terms of throughput and speed and ease of manipulation.

 Dr. Oliver Blacque (Guest) : [00:15:09] That’s right, that’s right. And the C.elegans community are super collaborative. Of course, the zebrafish community are as well, I don’t want to hold anything against any individual community. But you know, for example, when CRISPR-Cas9 was first discovered, as you know, only in the early 2010, 2011, the C. elegans community jumped on this, and within a couple of years they had developed really robust techniques because the community needed it. Everything was shared from the very beginning. And, and this type of environment really helped to push technical developments in the worm field. And I think that, that’s one of the reasons C.elegans, you know, can be and is very successful as a model for many different things.

Ben Jussila (Host): [00:15:51] Yeah. So I’m just keeping an eye on the time here. So one of the next questions here is that many people use C. elegans to study disease, but you’ve chosen specifically to focus on rare diseases, and I maybe would like to roll that into another question of is there one particular project that you’re working on right now in the rare disease space that you’d like to tell us a little bit more about, and why you’re focusing on on a rare disease as opposed to it, maybe a more abundant or more pop- or you know, more –

 Dr. Oliver Blacque (Guest) : [00:16:29] Well. Yeah, well, pure serendipity. I fell into the rare disease field purely by chance because as a postdoc, we were interested in Bardet-Biedl syndrome, back in 2003, knew nothing about it, and then basically figured out it has something to do with cilia. And as any scientist will know, once you have some success and make some discoveries, suddenly that becomes your interest. So then I became cilia biologist. I was using C. elegans, and so therefore I became a C. elegans geneticist – well that probably took ten more years. And so because cilia, so many of the diseases are rare, I guess I became a rare disease biologist. I would also say that I think every every person deserves their illness to be addressed in the lab, and I do take some level of satisfaction in knowing that some ignored diseases are actually being addressed, for example, by my lab. So I think that sort of point of view, it’s it’s quite satisfying. In terms of the second part of your question. Yeah. So I mean, if I could turn back to Joubert syndrome as an example of something we’re doing in my lab, I mean, we’re very interested in trying to interpret human genetic variation in C.elegans. So one of the big problems that has arisen from genome sequencing is that we now know of many, many different mutations in genes and patients. But many of those mutations, we actually have no idea if they’re actually disrupting gene function or not. And so the clinical geneticists, when they come to classify for a particular missense mutation, for example, is causative they often have to say, ‘Well, we just don’t know.’ And they classify those types of mutations as variants of uncertain significance: VUS [pronounces V-O-O] or VUS [pronounces V-O-S], if you are less posh, I guess, as somebody said to my lab. And so we need ways to understand if these variants are actually causing disease. So we need ways to reclassify VUS to either pathogenic or benign. Very important for patients because the clinical geneticists, you know, if they have a VUS classification, you can’t push that patients into disease management as quickly. And it also prevents that patients from accessing things like genetic trials. So we have to reclassify them. So we’ve been doing this in C. elegans. We’ve been basically knocking in using gene editing the very same mutations that you find in patients into the worm version of the gene. And then we look at the worm phenotypes and ask, well, you know ‘do we see defects in cilia or not?’ If we do see defects in cilia, we would say that this is pathogenic likely if we don’t see defects in cilia, then we would say it’s benign. And we’ve done this actually on two different Joubert genes and so far has been great. The pathogenic mutations the missense mutations turn out to be pathogenic in a worm, the benign ones turn out to be benign. And of the VUS we’ve looked at, the two genes, some of them turn out to look like pathogenic, some turn out to look like benign. And we would hope that this type of data is evidence to reclassify VUS. And in a way to provide a route to diagnosis for patients carrying these mutations. And we think this is very, very important. We’re also trying to validate some of our data in human cells so we could have two models perhaps, providing a combined piece of evidence to help with the reclassification of these very important mutations.

Ben Jussila (Host): [00:19:42] Yeah, that’s I mean, that’s very and very near and dear to our hearts. We’ve, you know, being doing a lot of humanization – similar humanization work to to figure out, OK, a lot of these patients for these severe debilitating disorders, they don’t have years to wait. They they don’t have – and, or they don’t have a gigantic body of funding and research focused on them. So, C. elegans, for the reasons that you mentioned before: the speed, the amenability to touch genetic manipulation, those are all things that are really well-suited to modeling these and addressing these questions in a rapid and effective manner.

 Dr. Oliver Blacque (Guest) : [00:20:26] Exactly, exactly. I mean, you could if you had several people in a team, you could easily make, you know, 100, 200 mutations quite quickly. In fact, with really efficient CRISPR editing, it only [00:20:37] takes two to three. You got the idea of having a work train, [00:20:42] you know, and and this is a very clean experiment and thus with good assays, good quantification assays comparing everything to a null allele you can really classify the effects in C. elegans very robustly, for sure.

Ben Jussila (Host): [00:20:58] Yeah. Well, I don’t know if you heard our timer went off here.

 Dr. Oliver Blacque (Guest) : [00:21:03] Yes.

Ben Jussila (Host): [00:21:03] But we were on a good train of thought, so I wanted to let us see that to the station. Yeah, no. Thank you so much for talking, talking with us about this. I think the work that you’re doing is extremely impressive and important. I mean, your publication record is phenomenal. And I spent a little time this morning crawling through it and it’s like, ‘Oh, I know that one. Oh, I know that one. Oh, I need to read that one and that one and that one.’ But there’s there’s a lot of really cool work to be done. I’m glad to see researchers like you out there, you know, focusing on this and really representing and advocating for the value of this, of this tool in this system to address these questions.

 Dr. Oliver Blacque (Guest) : [00:21:45] Well, thank you, Ben, I mean, it’s it’s great to get some validation and and I’m very excited also by what InVivo Biosystems is doing on the reclassifications because we’ve noted how you’re also using C.elegans to classify them, and that is great validation for the work we do. And yeah, and I appreciate the comments and I look forward to talking again sometime, hopefully.

Ben Jussila (Host): [00:22:08] Yeah. Yeah, likewise. Well, everybody, thank you for joining us today on this episode of 17 Minutes of Science. We will post all of the – we’ll post the video, some links to Oliver’s work so you can learn more about what they’re doing. And until then, stay safe, stay well, and we’ll see you next time.

Accelerate your research with our top-notch gene editing services – Get in touch today!