Genetics, and what is CRISPR anyway?

More episodes in the Science Sound Off Podcast

David Reiner, PhD, associate professor at the Texas A&M Institute of Biosciences and Technology, explains his genetics research, how CRISPR works and why a tiny worm can teach us about ourselves.

Episode Transcript

Christina Sumners: Welcome to Science Sound Off. I’m Christina Sumners.

Tim Schnettler: And I’m her co-host, Tim Schnettler.

Christina Sumners: And with us today we have Dr. David Reiner. Welcome to the podcast.

David Reiner: Right, thanks. Good to be here.

Christina Sumners: So, you’re from the Texas A&M Institute of Biosciences and Technology?

David Reiner: Yes, in Houston. A lot of people don’t know that we have a pretty sizable footprint in Houston. And we have a research institute there with scientists who are located full-time in Houston.

Tim Schnettler: So tell us a little bit more, before we get started on your research, tell us a little bit more about what IBT does and what kind of things go on at IBT.

David Reiner: So, we’re actually on the small side. You’d think that, we have research tower, but we’re about the size of a department here, in Bryan-College Station. And unlike a department we’re not that thematically organized, so we’re actually quite diverse. We have cardiac biologists, we have very basic scientists like me, we have clinical people, direct discovery people, cancer biologists. And the reason we do that is we’re located in the world’s largest medical center. And so, when you’re a self-contained college town, your nearby expertise is what’s there. For us, within a five-minute shuttle, or 15-minute walk are several world-class institutions. We have Rice, Valor College of Medicine, UT Health, and MD Anderson, the world’s largest cancer center. And I think 22 hospitals in the medical center. It’s the world’s largest medical center. It’s actually pretty astonishing how many people are there. And so that’s a large part of why we’re there. We’re a portal for, or a confluence of information between College Station and Houston.

Christina Sumners: So, you work closely with some of the hospitals and other institutions in the area?

David Reiner: Well, there are people in our building who are more translational, which is the word we use. From experiments in the lab to patients. And so they interact with clinicians more frequently. I’m what’s called a basic scientist. Just looking at fundamental principles of life. And so I interact with similar counterparts at other institutions. But yeah, some of my colleagues that are on my floor, my neighbor, actually interact at the clinic lane pretty regularly.

Christina Sumners: So let’s talk about some of those fundamentals of life.

David Reiner: Yeah, let’s do that. Let’s see.

Christina Sumners: You’re a geneticist.

David Reiner: I am a geneticist by training.

Christina Sumners: Okay.

David Reiner: I think, now I call myself a developmental geneticist. I’ve worn different hats in the past, including neuroscience. And what developmental genetics means is that we use mutations in animals to study how they develop, how they’re put together. And these are some of the fundamental rules of life. The operating system if you will. And so, we actually do this in a very specific organism. And it’s not a cute fuzzy organism. It’s actually a very, very tiny worm. And I always tell people if you want to know how big this is hold your fingers a millimeter apart and now you know how big a worm is. This is Caenorhabditis elegans and it’s one of the major invertebrate model organisms. Along with an organism people may be more familiar with, the fruit fly that you find on your bananas, that’s another, Drosphilia melanogaster. Is a very common research organism. So my lab works almost entirely on this although we do collaborate with humans to take our findings into. You know, people that work with cells in a dish, will find something in a worm, we’ll actually take it to human cells in a dish that a cancer researcher, say, is working on. We’ve had a couple papers where our discoveries are translated like that.

Christina Sumners: Why worms?

David Reiner: Yeah, that’s a great question. So, to do that I’m actually gonna digress into fruit flies. And they were actually readily available, like I said, on your bananas as they got older. And so in the early 1900s, fruit flies were harnessed to discover some of the most fundamental aspects of genetics. What is a chromosome? What is a gene? And worms actually, as a research organism, C. elegans was started in the 60s because they knew where some of the short comings of the Drosophila system was. And this, we’re sort of rival siblings, and C. elegans is a younger sibling, so I was taking pot shots at the older one. And so in the 60s a visionary scientist in Britain, Sydney Brenner, actually secured funding to say we can study in the simplest possible organism that you can have and still have all the issues with being multicellular. Let’s figure out key pieces of developmental biology, of neuroscience, strip it down as simple as it can be, and we’ll learn a lot. And he won a Nobel Prize. So he turned out to be a visionary scientist and he founded a field that actually now, I think, encompasses three or 4,000 people world-wide. And not quite as big as the Drosophila community and really but they are now of equal stature. And we learn a lot about biology. So to illustrate some points that C. elegans brings to the table is, it’s really fast. We get two generations per week.

Christina Sumners: Oh, wow. Okay.

David Reiner: They’re also really small and easy to culture. So they’re a millimeter in size, like I said. They have 959 normal cells and then about a thousand reproductive cells. And every single cell is in the same place in every animal. And this is actually the only experimental animal that’s the case. So if you’re looking at a neuron and say, or some developing skin cell, we know it’s ancestry all the way back to the single-cell that started the animal. And that’s actually a tremendous advantage for experimentalists. We can shoot DNA into them to make transgenics pretty easily. So experiments are great. We can do mutant screens where we just randomly pick up interesting biological defects. So that’s why we do it. We learn a lot about human biology and the real thing that’s amazing, is actually that an astonishing number of genes that you find in a human that are clinically important, you can find in a worm or a fruit fly.

Christina Sumners: So what sort of genetic manipulations are you doing? Are you using traditional gene editing, CRISPR, what?

David Reiner: Yeah, so the old school method is you dump a chemical mutagen on the animals and you look for random effects in the process you’re interested in. The new school method, actually, the maybe less old method is to shoot in DNA that will be inherited and make what we call transgenic. You can do this in other, you know, more complex systems will take you months or even years. In a worm we can do it in a week or two. But now, of course, we’re doing CRISPR, and I was enthusiastic passenger on the bandwagon right from day one. CRISPR in C. elegans I was fortunate enough to collaborate with people that did the first CRISPR knock-ins in C. elegans. So we published that in 2013 and we went in whole hog. We were into CRISPR, it’s enormously powerful tool for us. And everybody hears about it in the news. It’s a big deal and it makes our research much more powerful and quick. We can do stuff we never dreamed of doing before.

Christina Sumners: Could you explain just what CRISPR is for people who may not know?

David Reiner: Yeah, so CRISPR is molecular scissors. And the genome, the entire DNA compliment in every cell you have, the chromosomes, is huge. Humans have three billion letters in their code. Worms have 100 million. So it’s three times smaller. Same number of genes. That always surprises people. People think that because we’re humans we must have,

Christina Sumners: So many more genes, yeah.

David Reiner: That many more genes. I said we have a lot more cells, but not necessarily that many more genes. And what CRISPR does, the things that makes it different than everything that came before it, it’s remarkably precise. So you can cut one spot in the genome. You just cut the chromosome. And then the other thing is, it’s efficient. So the scale is you can look thorough 100 or 200 animals or something and find this change. Whereas old technologies were very expensive and you’d have to screen through tens of thousands. So very difficult. So who cares? Why would you want to break in chromosomes? So we can actually break genes to look at their function. We can also insert things into genes. One thing we call tagging. So we put a piece of fluorescent protein and then a little barcode on these and we can actually track now, the gene. It will make a protein and we can see where the protein goes in the cell. And we’re doing this during development we’ll see proteins that we’re studying actually suck up against the surface of the cell. And we’ve never seen this kind of stuff before in biology. And the reason is, when we do it with the old transgenic method, we just flood them with tons of protein and we swamp out that delicate little signal. So of course, you also need advance microscopy to see this. So CRISPR’s changing how we do stuff. Now, I know everybody’s thinking about what was in the news recently, with editing a baby in China. Twins actually, I think it was. So that’s very controversial. I don’t endorse that. Just so we’re clear. But as an experimental, eventually CRISPR can probably be used as a therapeutic.

Christina Sumners: For severe genetic diseases?

David Reiner: Yeah, and we could talk about that. I actually go to CRISPR workshops occasionally. But, for us, it’s a fantastic experimental tool.

Christina Sumners: Just because you can be so precise with…

David Reiner: Yeah, you can change just one letter in that whole code. And you can really do designer genetics. Whereas before, I felt we were bashing with a sledge hammer, now we have a scalpel. And that’s what I always tell people. The difference between a sledge hammer and a scalpel. And it’s really fantastic. And it’s me and 10,000 of my closest friends doing this. So it’s not like, I invented CRISPR and, but it is something that everybody is just so enthusiastic about.

Tim Schnettler: Well, and one of the things that y’all have used that for deals with cancer treatment, chemotherapy, and drug resistance by cells. Can you talk a little bit about that?

David Reiner: So what we, I’m sorry, I said I’m a development geneticist. What we study and everybody kind of glazed over when I said this, is signaling networks in a cell. And they said, oh, what’s that? And my response is, think of it like a spider web. There’s a really, or an internet hub and a bunch of connections. Or cell phone towers, whatever. Something that’s decentralizing communicating information. The signals that bounce around a cell and between cells are similar. And so one of the things we’re learning is that in cancer, if you have really strong driver of cancer, this thing is driving the tumor, there are actually fantastic drugs there in the clinic that’ll target that. The tumor will regress astonishingly. And you know, I actually use a picture of humans with metastatic melanomas so it’s spread all over the body. It’s a really striking picture because the person’s covered with lumps, you treat them with a small molecule inhibitor and it’s a really specific and good one. The lumps go away in, I don’t know, three or four months, and then a couple months later they come back. And that’s really the problem because if you imagine a spider web, you can snip one strand but the web’s still there. And so what tumors do is they’re enormously flexible and so they can find a rewiring. And probably what happens is that in the billions of cells in a tumor, some of those are going to already have been mutated by chance. And they’re not doing so hot within the context of the tumor, but then you hit them with a drug that hits 99.99% of their neighbors and now they’re the only one that survives. They grow back out, now you have new tumor right where the old one was. And so thinking about them as a network and understanding how networks work. How is this spider web put together? And we can see what happens and actually understand how this affects development. And almost everything in disease is something, a natural healthy process that’s been messed up. It’s been perverted, it’s been broken. Whatever, however you want to put that. And so understanding how they normally work is a big part of understanding how they work in disease.

Christina Sumners: That makes sense.

David Reiner: Does it? Great.

Christina Sumners: The goal is to make these tumors more susceptible to the chemo therapy drugs?

David Reiner: Yes, that is a great question. And, yeah, the idea there is actually the analogy I use for people is to think back to HIV and AIDS. And most people know now that HIV infection is not a death sentence. It’s actually treatable and people have good long, high-quality lives, right? And the trick, and HIV actually just as a little digression, HIV is also what we call hypermutable. It changes. And so even one person can now develop multiple HIV populations in their body. Same deal. Treating with one drug, it regresses, they’re happy, they’re healthy, and then it will come back. The trick there was to identify a triple drug cocktail that hit three different parts of the virus. And when you’re hitting three things, it can’t actually bypass all simultaneously. And so that combination, as long as the patient takes the drug regularly, all right. As long as they don’t miss a dose or mess around, that triple drug cocktail has been fantastic. And this actually happened in the 90s. We’ve known for a long time that this is possible with cancer. You know, the old school treatments are actually to poison somebody essentially. But the tumor’s more sensitive. So you feel safe, but the tumor dies. There are problems with that, the obvious one being that you feel really sick. The designer drugs that specifically target one part of the tumor, and that’s the one I described with the metastatic melanoma. Is they are very, very, very specific and it’s not poisoning. You’re actually blocking one thing in the cell. But the multi-drug cocktail is probably going to be the ticket here. And not even just drugs. I mean, this year’s Nobel Prize was immunotherapies and treating cancer by harnessing your own immune system. So there are multiple prongs of an attack on this kind of thing. And that’s because cancer’s 200 different disease, minimum. And they can change really quickly. And so, that’s why you need multi-prong attacks. And everybody always says, why haven’t you guys cured cancer yet? It’s a great question, the problem is it’s like 200 diseases that are constantly changing. So some of them for technical reasons we can get at pretty quickly. Others you can’t. And so if we understand the networks then the smart chemists and medical oncologists and folks like that can actually figure out how to put together multi-drug cocktails. And some of those strands in the spider web we don’t even know exist yet. And that’s what my lab does. We try to understand what those strands are. And if we can identify those and figure out how they relate to the other strands, cancer biologists can take that information and maybe develop those triple-drug cocktails.

Christina Sumners: And take it from there and actually come up with a drug to treat patients.

David Reiner: That’s the goal. The other thing that I would talk about is actually the law of unintended consequences. So, you know, I actually had dinner Tuesday night with some folks over at Baylor College of Medicine. We’d had a speaker, I had, sort of related work so they invited me. We’re very collegial in the team so I know people that all these other institutions. And there was a Drosophila person at the table and to go back to that joke, we were quite civil for siblings. But he was reciting some facts that I’d heard before is that if you look at the total NHI budget for research, about 3% is for just fruit fly research. And about 2% is for C. elegans research. We’re cheap as well as fast. And he pointed out that if you look at Nobel Prizes as a rough measure for mind blowing breakthroughs, that if you looked at simple organisms where research was done, that would be bacteria, yeast. People are always surprised that, you know, if they like beer or bread, but that yeast is actually great experimental organism for a single-cell, how does a single-cell work. One of my professors in grad school got a Nobel Prize for working on this kind of stuff. And then worms and fruit flies. That actually accounts for about half of all Nobel Prizes. So in terms of return on investment, that’s a great return. Now if you add mice into that, now you’re close to 100%. And mice, of course, are the gateway, the closest thing to a human. If you look at all that, that actually spells out the justification for these model organisms whether they’re a vertebrate like a mouse. Or the invertebrates or even the single-celled yeast. This is why we do it. Because history has told us that the things that change the world are unexpected and come from just digging around and doing good science. And you don’t even have to say, I’m gonna cure this disease. You have to say I’m gonna do good science and figure out what these things do. And surprisingly, we’re just terrible at predicting them. And it’s almost because it’s so mind blowing we can’t possibly imagine it. If we could we would just do it. So they come out of, I don’t know, left field. The CRISPR’s the best example. It actually started for people working on really obscure bacteria and not even pathogenic bacteria. Just stuff that grows out in the world. And they found that these bacteria have an immune system. And the enzyme that governs that is called Cas9 So people, sometimes for CRISPR Cas, or CRISPR Cas9. And they said wow this thing’s really targeted to cut things with enormous specificity. This was done, that breakthrough was done at Berkeley in California. And somebody at MIT said, oh, yeah, we can put that in a cell and cut specific things. Those people are probably going to win a Nobel Prize. So that sometimes our betting pools. And I don’t want to overemphasize the importance of a Nobel Prize because there are tens of thousands of scientists who do great work and never get tuxedos and meet the king of Sweden. But this is why we do science, right? And the law of an unintended consequence is actually one of the most profound things if you know about science. Closest, the shortest distance between two points is not necessarily a straight line. Right, and often in science it looks like somebody just working out in left field. They’re doing something far more important than you are. We just don’t know it yet. And that’s why science seems so broad. And people say, why is somebody working on a worm? Well, you know, there are a few Nobel Prizes and then a lot of Lasker Prizes and a bunch of other prizes. And top papers and top journals that tell you why. And connections like we try to translate to cancer biologists. And so this is why we do this kind of stuff. The other thing is, it’s so simple that we can do research in a way that’s really elegant. And our findings can be really concrete because with a quick life cycle we can test them every which way. So there’s really not any ambiguity.

Christina Sumners: And you know the genetics of these organisms so well that …

David Reiner: Yeah, so the C. elegans was the first multi-cellular organism to have its genome sequenced. This was so important that when I was in grad school, I actually switched projects.

Christina Sumners: Really?

David Reiner: Yeah, the gene I was interested in was a wasteland. And I’d been trying to find it like a needle in a haystack for about a year. And then the sequence project mowed through chromosome three where there was another gene I was interested in and I found it in a month. And so, soon after that the whole genome was sequenced. But this technology frequently drives, you have to be aware of it and be prepared to change your approach. You have to stay nimble and flexible. True for all of science, not just me.

Christina Sumners: So what were you working on in grad school to begin with? And then what’d you switch to?

David Reiner: Behavior, actually.

Christina Sumners: Behavior, okay.

David Reiner: So C. elegans actually, so the C. elegans nervous system is largely dispensable for viability so they can actually reproduce without most of the nervous system there. Because they self-fertilize. And this was actually why Sydney Brenner selected them in the first place. Self-fertilizing, check, that’ll make studying nervous system function a lot easier. They don’t need to mate. A fly, you know, you actually have a male and a female and they have to get together. And that requires locomotion and—

Christina Sumners: And then their genes get mixed up when they—

David Reiner: Yeah, right. Yeah, so, a worm, they just sit there and they reproduce. And so it’s actually, we actually did a variety of behaviors. It was a lot of fun. We had to develop, we were actually making it up as we go along. Developing new assays. Well, how do we measure behavior? How do we look at this? What do we track? And so there are a variety of behaviors and like everything else, C. elegans is fairly simple. They move, they eat, they poop, they lay eggs. That’s about it. But the truth is, we worked, there were some really remarkable behaviors that they do. They can do associative learning, right? So if you feed them and put some neutral chemical in there. Butanone is, I know that’s just a random collection of syllables. Butanone is an organic chemical that doesn’t hurt a worm. And they don’t care about butanone, but they can smell it. Or taste it, however you want to say it. And they don’t have eyes, but they can smell and taste really well. And if they sense that, and there’s a lot of food, and then now you put them on a plate without food, and they get to choose between a neutral spot and something where butanone is, they make a beeline for the butanone. And they can remember that.

Christina Sumners: So, they’ve associated that with the food.

David Reiner: Yeah, and the talk, I was over at Baylor this week, I was talking about that particular test with aging. And how long-term memory works. And so this, worms are also famous for aging research. In 1993, Cynthia Kenyon at UCSF published the first genetic mutant that lived longer. And it happened to be a reduced function mutation in the insulin receptor and it’s really related to food and metabolism. And so, this has become a huge cottage industry in many different systems where people study this kind of stuff. But it’s a big deal in worms because when they only live half a week, you can do a lot of aging tests. So that’s another big thing we do.

Tim Schnettler: That’s amazing that you can get so much from such a, from a worm. Something that people see and get squeamish.

David Reiner: Yeah, well, and I will say, you know, you’ve seen an earthworm, these things you can’t even see. So somebody in the room probably has some on their shoes dried up. I tell you, if you’ve walked across some grass, there’s a decent chance. And there’s one little story, when I was a sophomore in college, I was taking a plants class. And we went out and grabbed moss. You know, just fuzzy little moss. And put it in a plate and looked at it under a scope, and there’s this little guy waving at me. And it was a worm. And I had taken a basic animals biology course before and I said, I think that’s a nematode. And little did I know I was destined to spend my life researching, it may have actually been C. elegans or one of his close relatives. I’m sure it was. But it was, had I known, there would have been a, dun, dun, dun. In the background, lighting striking. Something like that.

Christina Sumners: If it was movie of your life.

David Reiner: This is your future and you’re gonna look at tens of thousands of these things.

Christina Sumners: I know you and your lab had a featured article in the journal Genetics, a little while ago. So, could you tell me about that research and what you found?

David Reiner: Sure. So I have to give you a little background but we’ll keep it non-technical wherever possible. So first I have to say the work RAS, R-A-S. And the reason is, RAS is the big one. It is by far the most mutated cancer driver. We call them onco genes or cancer genes. And about a third of all human tumors have a RAS mutant that turns it on. Locks it in the on state. This is bad. RAS is also a greasy ball. So you can’t target it with drugs. So we’ve really struggled in 35 years and we, again, I’m using the community. Has struggled how to figure out how to handle RAS. Should also add, particularly lethal cancers, like certain types of pancreatic cancer are 95% RAS mutants. So they’re essentially 100% RAS. And so, we’d still really like to know how it does that. So we’re studying, we actually study RAS-related molecules. Proteins in the worm. Genes. And one of them is call RAP1 and RAP stands for RAS-proximal. We also study a gene called RAL, which stands for RAS-like. And so you get a lot of RA something and the alphabet soup tends to drown people. So we’ll keep it to RAP1. And so we’re studying RAP1 and RAP1 is actually super similar to RAS. I would call them siblings or first cousins or something like that. And they actually, the part of the protein that sticks to partners is identical. So it’s long been a mystery in the cancer world, why RAP1 is not mutated in cancer. And what is its relationship to RAS. For various technical reasons, there have been a lot of red herrings. Misleading, false leads. RAP1 has been very enigmatic. The nice thing is, worms have a single RAS. And a single RAP1. And if you look at humans, they have three RAS proteins and two RAP1s. Or mouse, or any other animal with a backbone has these multiple genes. So from a geneticists point of view, that’s a nightmare. In a worm that’s simple. So what we did is we used CRISPR. We locked RAP1 in the on state like a cancerous RAS would look like. And it caused a weak but measurable RAS-like phenotype. So the post-doc in lab who did this work, Neil Rasmussen, likes to refer to a movie for this. And the movie is, I don’t know if you remember those old Austin Powers movies, the James Bond spoofs. He says RAS is Doctor Evil, right? The evil scientist who’s bald, he’s got the gray suit, Mike Myers really hams this up. It’s a great role. And he’s gonna take over the world and do evil things. I can’t even remember what the plot was. It’s a James Bond movie with humor. And so RAS is Doctor Evil. And RAP1 is Mini Me. And this is a really good way of thinking about it. As it turns out, that RAP1 is actually, we think it’s, we call it a shadow RAS. But really Mini Me is a great way of putting it. And it’s basic, what we think is it’s actually reinforcing whatever RAS does in development. And so we got a smoking gun experiment by locking RAP1 in the on position and getting some RAS-like biological effects that came out of that. And so that’s why this is a featured paper ’cause this has been a mystery for a long time.

Christina Sumners: About why one is cancerous and one isn’t?

David Reiner: Mm-hmm.

Christina Sumners:  Okay. Thank you so much for joining us today on the podcast. And telling us all about your work with genetics and cancer and explaining what CRISPR is.

David Reiner: Oh, my pleasure. Thanks for having me.

Christina Sumners: And thank you all so much for listening. And we will see you next time.