AudioHelicase Special: RNA in health and disease

Whitehead Institute researchers Silvi Rouskin, Ankur Jain, and David Bartel discuss how their RNA research connects to health and disease, including viral infections and neurodegeneration. This story is part of our series, Sculptors of the Cell: RNA research at Whitehead Institute: RNA Research at Whitehead Institute. Click here to see all stories in this collection. 

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Transcript:

Greta Friar: RNA molecules play important roles in cells throughout the body. Messenger RNA carries instructions from DNA in the nucleus out into the cell to be made into protein. Our cells also contain other types of RNA, and many of these regulate gene expression, controlling how much or how little protein is made from a given gene. Some organisms, like certain viruses, use RNA instead of DNA to store all of their genetic information. Through its many important roles, RNA is a key player in health and disease. Researchers at Whitehead Institute are studying RNA and its role in normal health, infectious disease, neurodegeneration, and more. 

Friar: Welcome to AudioHelicase, the podcast of Whitehead Institute, unwinding the science and the people behind some of the Institute’s most exciting discoveries. I’m Greta Friar, science communications officer at Whitehead Institute. In this special episode of AudioHelicase, I’m speaking with three Whitehead Institute researchers, Silvi Rouskin, Ankur Jain, and David Bartel, about their work on RNA and its role in health and disease.

Silvi Rouskin: I'm Silvi Rouskin. I'm the Andria and Paul Heafy Whitehead Institute Fellow.

Friar: Rouskin studies RNA viruses, viruses that store their genetic information in RNA rather than DNA. These include SARS-CoV-2, the virus responsible for the Covid-19 pandemic, and HIV-1, the virus that causes AIDS. 

Rouskin: The top 12 deadliest viruses, as classified by the World Health Organization, are all RNA viruses. And RNA is this molecule that my lab specializes in. We study specifically the shapes of RNA molecules, and we are interested in developing therapeutic approaches that basically interfere with those shapes, with the way the RNA folds in 2d and 3d space. Those shapes are so important for the function of the molecule, so the idea is that by interfering with the shape, then you can cripple the virus.

Friar: Rouskin’s lab began studying RNA shape in HIV, but when Covid-19 began to spread, she quickly turned her attention to SARS-CoV-2. Her lab was the first to publish complete characterizations of the structures of both HIV-1 and SARS-CoV-2’s genomes. Rouskin found that the viruses can fold parts of their RNA genomes into different shapes, and use those different shapes to affect which proteins they produce. Knowing this provides researchers with a new way to disarm the virus, for example by learning how to interfere with it making the proteins it needs to infect a cell or to replicate itself.

Rouskin: One of the things that wasn't known before is right in the middle of this RNA genome in Coronavirus, it actually forms multiple different shapes on different molecules of the same sequence. This is very important so that this RNA molecule can be read out differently by the cellular machinery and produce a full set of all of the viral proteins. And so if we, let's say, have some drug that locks the Coronavirus RNA in the middle of the genome in one particular shape, then the virus will not be able to produce a full set of its viral proteins.

Rouskin: This idea of targeting RNA directly is a newer idea. It was thought that targeting RNA directly wouldn't be possible, but a few years ago, there was some precedent. There are a couple of different companies that developed small molecules that bind directly to RNA.

Friar: Rouskin and collaborators are now working on developing drugs that target RNA to interfere with SARS-CoV-2 replication. Instead of using small molecules, they are working with something called antisense oligos. 

Rouskin: Antisense oligos. So those are nucleotides. They're just the building blocks of the RNA. The nice thing about them is that they're very sequence specific. You can design a sequence that's going to target only the sequence in the viral genome because it's the only match for that sequence. And then, because this antisense oligo is competing to bind to the viral genome, it's going to interfere with how this viral genome is trying to fold, and it's going to interfere with the structure and then the function. That's the idea and we're doing a lot of that for the SARS-CoV-2. And that's in collaboration with Anders Naar at Berkeley. Now the issue with this strategy is that it's a little bit harder to deliver them. For SARS, it's more fortunate because you can inhale them, so they will reach the lungs.

Friar: Rouskin is also working on ways to improve finding potentially therapeutic antisense oligos. Finding a good candidate to treat Covid-19 requires testing many, many different antisense oligos to see which would be most effective. 

Rouskin: The ultimate goal is to be able to predict all this from pure sequence, to understand enough about the contributing forces, and then say, Okay, I have the sequence of this virus or the sequence of this gene, then I know exactly what kind of shape this RNA sequence is going to form. Or maybe it's going to be a few different shapes that it's going to form. And then from there, also knowing what kind of molecule or antisense molecule this shape can bind. So you don't need to screen a million molecules to find one that gives them the right function. 

Friar: Rouskin is also interested in exploring the role of RNA shape in and using antisense oligos to treat other diseases, including neurodegenerative diseases. Whitehead Institute Member Ankur Jain is already exploring the role of RNA dysregulation in neurodegeneration.

Jain: My name is Ankur Jain. I'm a Member of the Whitehead Institute and an assistant professor of biology at MIT.

Friar: Jain studies how strands of RNA that are overly prone to clumping together might contribute to a category of neurodegeneration called repeat expansion disorders, which includes diseases such as amyotrophic lateral sclerosis (ALS) and Huntington disease. The RNA associated with the disease genes in people with these disorders has too many repeating sequences, which causes the RNA to clump together and form aggregates or gels.

Jain: Nucleic acids, as we know, can form base pairs: A can base pair with T, G can base pair with C. And if you have a repetitive stretch of C, A G, or GGCC, there are many, many sites where a single RNA molecule can bind to another one. A good analogy is thinking about a long piece of sticky tape, and the tape can bind to itself at many different sites, and it becomes naturally prone to clumping together. So it's the same physical principle by which hair gets tangled or any long floppy piece of rope gets entangled, here applied at a molecular level. And this leads to self-assembly into very large structures, which are irreversible, which potentially contribute to the disease state.

Friar: How do RNA aggregates, made up of this long, sticky RNA, contribute to repeat expansion disorders? 

Jain: One proposed mechanism is that these repeats can encode for proteins that are also susceptible to aggregation. So, the same analogy that I used for a piece of tape applies to protein, which are translated from these repeats. So, for instance, polyglutamines, which can be made out of CAG repeats, are also susceptible to aggregation. And those clumps result in neuronal death and disease.

Friar: Another proposed mechanism is that the RNA aggregates themselves are gunking up the cells. For now, these explanations are theories. Jain is working on tests that will more definitively answer the question of whether the RNA aggregates found in repeat expansion disorders are a contributing factor in the disease.

Jain: One way to prove that these aggregates are actually contributing to disease is to disrupt them, and observe the cells returning to normal function, or if we do it in a model organism which is suffering from the disease, and we disrupt these aggregates and it benefits the organism, or prevents the disease state, that's a good proof that these aggregates are actually directly contributing to the disease. So right now, we are using a few different strategies, we are screening for small molecules, drug molecules, which could disrupt RNA aggregates, specifically. We are also running genetic screens to identify proteins whose upregulation or downregulation could change RNA aggregation.

Friar: If the small molecules that Jain finds disrupt RNA aggregates in the lab and appear to prevent disease when tested in animals, then further down the line they could be good candidates to treat repeat expansion disorders in patients.

Friar: In the meantime, Jain and other researchers at Whitehead Institute are also studying the roles that RNA aggregates play in healthy biology. Normal RNA aggregates, which can be useful for the cell, are capable of dissolving when needed, unlike the permanently clumped aggregates caused by excess repeats in diseases like ALS.

Friar: Whitehead Institute Member David Bartel doesn’t primarily study RNA in the context of disease. Instead, his work has provided an in-depth understanding of regulatory RNAs, types of RNA that control gene expression, and that understanding has proved necessary as a foundation for connecting regulatory RNAs to health and disease.

Bartel: My name is Dave Bartel, and I'm a faculty member at MIT and a Member of Whitehead Institute, HHMI.

Friar: One type of regulatory RNA that Bartel’s lab studies is microRNA. These are tiny RNAs that can regulate the activity of genes by causing the messenger RNAs that are copies of those genes to be destroyed, so they stop being translated into proteins. Each microRNA pairs with particular messenger RNA sequences, and by binding to the messenger RNA, initiates its destruction. Bartel’s lab was one of the first to characterize microRNAs and figure out what they do in cells – which, it turns out, is a lot.

Bartel: We know that microRNAs have many important roles in normal biology. They're important for proper development but also for normal physiology, for behavior. And they can influence diseases, play lots of roles in diseases. So the reason that we know this is because many labs have been studying these microRNAs, and they mutated the microRNAs or microRNA families in mice. We have about 300 microRNAs that are the same in mice and in humans, and 200 of those microRNAs are conserved throughout all vertebrate animals. And these fall into 90 families, and people have gone in and mutated individual members of many of these families or multiple members of the same family, and what they see is that these mice that are mutant, no longer have particular microRNA, they will have pretty severe defects, often in development, but also in physiology, behavior, etc. Many of these microRNAs are needed for the actual survival of the fetus or of the pup once it's born, and even those in cases where the mutant mice don't die, they can have very severe defects like if a microRNA’s removed they’ll have epilepsy or a bunch of different microRNAs will cause infertility, and others will cause cancer. That's our evidence that these microRNAs have such important roles in normal biology. The reason that they're so important is that they each regulate many genes. The microRNAs are regulating about two thirds at least of the human messenger RNAs. So when we saw that, we realized that it's going to be really hard to find a developmental process or disease that isn't somehow influenced by microRNAs.

Friar: Bartel’s lab developed an online tool called TargetScan as a resource for researchers studying RNA.

Bartel: We provide this website called TargetScan, which allows biologists to go on the website and they can focus on a particular microRNA and see which are the protein coding genes that we think are going to be most severely influenced by that microRNA, or they can focus on a particular protein coding gene of interest and then we can tell them which of the microRNAs that are most likely to influence that gene. And so, this is a broadly used resource that we hope and think that is helping to accelerate microRNA research globally. TargetScan is I guess helping a lot of other people who are connecting microRNAs to diseases and we hope to continue to, by better understanding how microRNAs recognize their targets, you can better improve these predictions.

Friar: Indeed, researchers have used TargetScan in work delving into the links between microRNAs and cancers, diabetes, neurological and psychiatric disorders, and more. 

Friar: Another area of Bartel’s research that has impacted biomedicine is his work on RNA interference, or RNAi. This is a tool that researchers use to silence genes and is based off of a process that was first discovered in the well-researched model organism C. elegans, a tiny roundworm that was the first multicellular animal to have its genome sequenced. 

Bartel: Researchers working in C. elegans were trying to develop better methods for knocking down gene expression, and they discovered that you could add double stranded RNA, that would cause the messenger RNA that corresponded to that double stranded RNA to get degraded. And so you get less protein. You get less protein, you can see what happens in that animal when it no longer had that protein, and that could tell you about the function of the protein. It was hard though to use this in mammalian cells because when our cells get long double stranded RNAs, they think they're infected by a virus, and they basically shut down all translation. So, to use this as a tool, we need to learn more about how this, what's called RNA interference, this use of double stranded RNA to knock down genes, how it works. And so, in my lab we were working in a collaboration of Phil Sharp and a couple postdocs in the lab, Tom Tuschl and Phil Zamore, started to investigate the biochemical mechanism of RNAi. 

Friar: The researchers uncovered important information about how RNAi works, and ultimately Tom Tuschl, after he started his own lab, figured out a way to synthesize short versions of the double stranded RNA, short enough that they did not set off the body’s anti-virus defenses, allowing RNAi to be used in human cells.

Bartel: By using what are called these short interfering RNAs, Tom had developed this tool and extended RNAi to mammalian cells, which is very useful for trying to understand and determine the functions of different mammalian genes. It also turns out to be quite useful for treating diseases. And so, together with Phil Sharp and Tom Tuschl, Phil Zamore, Paul Schimmel, and I, we started this company called Alnylam, which is at the forefront of making these chemically synthesized siRNAs, small interfering RNAs, to treat diseases in human patients. And they have three different drugs that are currently being sold and used to treat patients for different rare genetic diseases. And they're developing additional drugs, sometimes in collaboration with other companies, to treat much more common diseases like high blood pressure, high cholesterol, etc. So, this is a very exciting area of therapeutic development.

Friar: Along with RNAi-based therapies, interest in therapies that either use or target RNA has been skyrocketing of late, in no small part due to the Covid-19 pandemic. 

Bartel: The reason that we're all going to be able to go back to work soon is because of these vaccines that are made using messenger RNAs. 

Friar: With such a remarkable demonstration at hand of the potential impact of RNA research, and RNA-based drugs, on our society, Whitehead Institute researchers are eager to continue their work discovering new insights into how RNA influences health, and how it could be used to treat diseases from viral infections to neurodegeneration.

Friar: You can learn more about RNA research at Whitehead Institute on our website at wi.mit.edu. Find past episodes of AudioHelicase and stay tuned for new ones by subscribing on Soundcloud and iTunes. Thanks for listening.