Stoking Functional Copies of Genes to Compensate for Mutated Ones

May 20, 2022

Stoke Therapeutics platform technology allows it to target genetic diseases where people have one functional copy of a gene and one mutated copy. As a result, they can only produce half as much protein as they need to maintain health. Stoke seeks to restore missing proteins by increasing the protein output from healthy genes to compensate for the non-functioning copy of the gene. The company’s lead experimental therapy is an antisense oligonucleotide to treat the rare and progressive genetic epilepsy Dravet syndrome. We spoke to Ed Kaye, CEO of Stoke, about the company’s platform technology, how it works, and its lead program in Dravet syndrome.

Daniel Levine: Ed, thanks for joining us.

Ed Kaye: You’re welcome. And thank you for the invitation.

Daniel Levine: We’re going talk about Stoke Therapeutics, its platform technology, and its efforts to develop antisense oligonucleotides to treat rare genetic diseases. Perhaps we can start with antisense nucleotides. Listeners may be familiar with this emerging area of therapeutics, often referred to as ASOs. What are these and how do they work?

Ed Kaye: The way to think of these antisense oligonucleotides is they work by pairing up with certain genes on the human genome. And what we’re trying to do, it’s a genetic medicine, but it’s not that we’re trying to replace an entire gene, like what you would do for gene therapy. What we’re doing is we’re changing splicing and we’re altering some of that RNA output, and in our particular case, what we’re trying to do is to compensate for a very low level of protein that was inherited as a genetic defect. And we’re utilizing the normal RNA to increase the amount of full length, messenger RNA and protein to compensate for what’s going on in the body. It’s a way of taking care of a genetic mutation without actually having to alter the mutation or put in a new gene. But just by changing splicing, we’re able to correct for the deficiency.

Daniel Levine: Stoke has a proprietary platform technology called Tango, what is Tango and how does it work?

Ed Kaye: Tango stands for Targeted Augmentation of Nuclear Gene Output, and it’s a fancy name for a process where—and this was an idea that was discovered by one of our scientific founders Adrian Krainer who was at Cold Springs Harbor in Long Island. What he found is there were naturally occurring, retained elements on the pre-messenger RNA. And if you remember your biology, you go from pre-messenger RNA to messenger RNA, and you do that by splicing out introns and other things, and getting kind of the business section of the gene, which is really encoding for the protein. What he found is that business section wasn’t rewritten correctly and there were certain things that were stuck on, certain elements, but if you spliced them out, you could actually increase the amount of protein that you were making. And the analogy that we’ve come up with is if you have your bathroom sink and you have a cold and a hot water handle. If you turn both of them on—on half—you’ll get a certain amount of water that’s going to enter into the bowl. And if you turn off the hot water, you’re going to have half the amount of water in the bowl. But there’s two ways to compensate for it. Either you can turn back on that hot water, or the other way you can do it is basically to open completely that other spigot. And that’s what we’re doing. We’re opening that faucet to compensate for the one faucet that’s not working as well as it should. And we do that by taking a normal copy of the gene and upregulating and compensated for the bad copy of the gene. Does that make sense?

Daniel Levine: Yeah. Given that approach, what’s the potential range of conditions you can treat with this? Is it always a case where there’s one functional copy of the gene?

Ed Kaye: We do need at least one functional copy of the gene that is correct for the most part, and we have a few different approaches. We’re focusing on dominant diseases. That means diseases that are passed on from one generation to another and 50 percent of the offspring, and where you’re missing 50 percent of the protein. That’s the easiest approach that we can use for this particular Tango mechanism, but we can also upregulate other genes and pathways. That could be very important. When we look at all the genes and all the various different types of Tango signatures, we see that about 50 percent of genes actually could have a Tango signature that might be able to be upregulated, and just looking at genetic diseases, we have about 1600 diseases that we’ve identified that could be upregulated. It’s a lot of diseases that we could go after, but right now, we’re focusing on the central nervous system and the eye, primarily because those are very well credentialed delivery mechanisms, if you give the ASO through a spinal tap in the back and the spinal cord, you can introduce it into the brain. And if you give it in the eye through an intravitreal injection, a lot of what’s done for macular degeneration, drugs like Lucentis, you get very good biodistribution in the retina. We’re using that mechanism of biodistribution to go after some of these targets that are a little bit easier to approach, and we don’t need any really sophisticated delivery systems to get into the organ.

Daniel Levine: Your lead experimental therapy is targeting Dravet syndrome. For listeners not familiar with the condition, what is it and how does it manifest itself and progress?

Ed Kaye: It’s a disease that is present in every ethnicity all over the world. It occurs at about the same incidence in about one in 16,000 births, and it’s a spontaneous mutation. In other words, it means that the parents don’t carry it, but the child is born and has a mutation, and it’s called the SCN1A gene, and that it codes for the nav1.1 protein. And that’s an ion channel, a sodium channel. Um, and it’s a subunit of the sodium channels. You need an alpha and a beta subunit to come together in order to have it work. These children are born and they’re missing 50 percent of this ion channel, the sodium channel.  This tango mechanism that we’re using is actually present in development, and these children don’t really start to develop symptoms until they’re about nine or 10 months of age. And the reason why that’s the case is that the nnav1.1 protein is not essential at birth. The level of this protein at birth is fairly small, but what happens is this same mechanism that we’re manipulating goes up and it reaches its adult stage at about nine months of age. that’s when these children start to get symptomatic and they are absolutely normal at birth. And what they have is seizures that are precipitated by fevers. If you have children you’ll know that children can have fevers precipitated by a lot of infections that are associated with a high fever. Any child can and have a seizure with a high fever, but what happens in children with Dravet syndrome? They don’t just have a 10 second or a 30 second seizure. They have a seizure that could last for hours and needs medical attention, and they have to be given medication to stop the seizure. Well, that’s very unusual for a simple febrile seizure. And what happens is that they continue to have seizures, often again with fevers, but then they start having seizures without fever. And that’s when they seek medical attention. And they realize that they have some other inherited disease that’s causing the seizures. And typically, what’ll happen is a clinical diagnosis of Dravet syndrome will be made and they’ll have genetic testing that shows that there’s a mutation in the SCN1A gene. That’s how these children are identified. The problem, of course, is it’s not simply a disease that just causes seizure. It’s a syndrome that’s associated with many other aspects in addition to seizures. And what we see is that these children, and as I mentioned, they’re perfectly normal at birth, but then when the seizures start, they begin to have a slow loss of some of their cognitive abilities. They have problems with behavior and other psychological problems, problems with gait that develop typically by the teenage years, problems with speech, sleep, and unfortunately about 20 percent of these children will die related to a seizure. It’s called a sudden unexpected death, related to epilepsy or a SUDEP. And that is one of the most terrifying things for the parents because they’re afraid that when these children go to bed at night, in the morning, they may not wake up because they may not wake up from the seizure. And that’s typically thought to be related to an apnea, a central breathing problem that occurs with a seizure. And even though you can address the seizures with a lot of different medications, anti- epileptics, we don’t address the other underlying problems with Dravet syndrome, and these other symptoms, which are very worrisome, certainly to the families and to the children, are not addressed. What we’re trying to do is to come up with the first genetic therapy that addresses the underlying cause of the syndrome, and to try to take care and improve the seizures, but also to improve some of the other non-seizure comorbidities that happen in the syndrome.

Daniel Levine: I want to get into that, but before we do, what’s it like to live with this condition? How frequent are the seizures and what happens in a household when they occur?

Ed Kaye: Yeah, that’s obviously an important part of this disease. We’ve certainly spoken to families and have gotten an understanding, I think, of what happens to the families when these children become symptomatic. There was also a recent conference that was held by the FDA and it was really to talk about these other aspects of the disease. Typically, as a parent, you always want and you think your children are always going to be perfect and nothing’s ever going to be wrong with them. And you have a child up until the first nine months of age that you think is perfectly healthy and doesn’t have any medical problems. And then suddenly you realize you have this intractable seizure disorder, and then even, I think, worse, you realize that the child is not developing normally and, in fact, is losing some milestones that they previously had and they have problems with the sleep. I think the biggest concern with these families is that—and we’ve heard from mothers and fathers—they’re afraid to go to sleep at night because they’re afraid that their child could could die during their sleep. And that’s just a terrifying concept for any parent to have to deal with. And what you find is that at least one of the parents is really a full-time caregiver. These children have such a complicated medical story that one, or often both, of the parents are focused on just taking care of this child and keeping this child alive. Obviously that influences the rest of the family relationships. The other children are not receiving the same level of attention because they can’t because this child needs so much medical attention. I think the entire family dynamic has to change. Fortunately, a lot of families have extended family members that help with this. It’s a disorder that affects the entire family and even the extended family. What we’re hoping to do is if we can make these children a little bit more like back to normal children, then that would really believe the burden on the families, and certainly on these patients.

Daniel Levine: You mentioned some of the limitations of the existing therapies, but what treatment options exist today and how effective are they?

Ed Kaye: Really the only thing that has been available and there’s been two recent products that have been approved by the FDA for seizures in Dravet and there’s probably 25 different anti-epileptics that have been used in the syndrome. Despite all these therapies, about 90 percent of these children continue to have seizures that are uncontrolled. Even with some of the newer therapies, they’re still continuing to have seizures. On our study, when we looked at these patients, we realized that at least 50 percent of the patients were on the most recently approved therapy and even the best and the most recently approved therapy was inadequate to control the seizures. Certainly, it was inadequate to control the other aspects of the disease. Despite a lot of work that has been done in the last few years in Dravet syndrome, there’s still a huge need for a therapy that not only can improve the seizures at a better rate, but also really try to address some of these other non-seizure problems that are occurring in these children.

Daniel Levine: What is STK-001 and how does it work?

Ed Kaye: As you started out at the beginning of the call, it’s an antisense, oligonucleotide. What we’re doing is we’re pairing up a nucleotide, and typically it’s around 18 base pairs and it is modified to not be broken down by the normal endonucleases that are present within the body. It’s an artificial molecule that pairs up with the RNA, the pre-messenger RNA, and what it does is it alters splicing. It interferes with some of the splice proteins that are on that site and it’s very specific for that site. For instance, there’s 10 other different sodium channels that are present in the body and they’re all very, very similar. They were made by homologous recombination. And despite that they are almost identical, we only could upregulate the nav1.1, so it was very, very specific. The SCNA1 gene was the only one that we affected. We know that it’s very specific for that particular protein, because you don’t want to upregulate other things in the body, and certainly you don’t want to upregulate the wrong protein. From what we’ve seen, this is very specific. The other feature is that can only upregulate this protein if the ASO is in a cell that naturally contains the messenger RNA. In other words, if it gets in the wrong location where you shouldn’t make this protein, it doesn’t matter because if that message isn’t there, we cannot upregulate it. So, it’s a very specific therapy that only really upregulates, as far as we know, only one protein, and it can only do it in the cells where it normally should be found. It gives us an advantage. Everyone always asks us, “well, why don’t you just use gene therapy?” Well, gene therapy would require us to take the entire gene, which is too big to package right now in the normal vectors that are used. And also, it wouldn’t give us the specificity. We wouldn’t be able to titrate it, because we can use our ASOs like a drug and get what we’re trying to do is get it from a 50 percent level and bring it up to a 100 percent level. With gene therapy that’s almost impossible to do, you can overshoot or undershoot, but trying to get it at exactly the right amount in the right cells is a very challenging problem. And also, CRISPR gene editing, people have looked at this too, but unfortunately for Dravet syndrome, there’s over 1700 different mutations. You’d have to have 1700 different drugs if you try to do a gene editing approach for this disease. We believe that our Tango approach is the right method right now to try to address this underlying disease and upregulate that missing protein.

Daniel Levine: If I understood you earlier, the belief here is that this would address not just seizures, but other comorbidities related to the condition.

Ed Kaye: Yes, that is the hope because we are really trying to attack that underlying cause, which is that missing 50 percent missing protein. The hope would be that not only will we improve seizures, but we could improve some of the cognitive and the behavioral and the gait and sleeping and things like that. That is the hope because Dravet syndrome is not a neurodegenerative disease. In other words, you’re not losing nerve cells. What’s happening is they’re not able to connect and talk to each other because you’re missing this essential ion protein that’s necessary for that electrical discussion that occurs within the brain. And what we’re trying to do is to really reroute these electrical circuits by replacing that protein, and the hope would be not only can we improve the seizures, but since those cells are still alive, remodeling can occur, and there’s evidence in animals that even in adult mice, you can have some improvements, not only in the seizures, but in the behavioral problems in the mice, the mouse model for Dravet syndrome. The hope would be that even much later on in the course of the disease, we’ll be able to have some impact by rewiring some of those brain circuits.

Daniel Levine: What’s known about it from studies you’ve done to date?

Ed Kaye: We’ve done a lot of work on mice, that is in the murine model for Dravet, and what was done by investigators at Vanderbilt University a number of years ago, is it created a mouse model that contained a human mutation that’s missing 50 percent of the protein and has many of the symptoms that people would have with this mutation. And what we found when we gave the drug on the second post-natal day in these very severe animal models that without the medication, we have an 80 percent loss of life, but we have about a 97 percent survival if we give the medication, so a dramatic improvement in survival that occurs. We wanted to know, in addition to the survival, what happens to the seizures? What we were able to do is to implant electrodes within the brain in these animals, and then follow them for a time. And what we saw was a dramatic reduction in the number of seizures that occur these animals. Not only did they survive, but their seizures were also much better. Obviously having a proof of concept in a mouse is one thing, but what happens in a much larger brain? What we were able to do is to use non-human primates and to inject intrathecally the ASO in these animals and we saw, two to threefold upregulation of that missing protein, the nav 1.11. Now, again, these were in normal animals, they already had a hundred percent. We were able to get up to 200 to 300 percent of the amount of protein. We also demonstrated that the ASOs got into many areas of the brain and they really went throughout the brain and we showed very nice upper upregulation, even in some deeper structures. What we found is that most of the nav 1.1 is found in the cortex, but that there are other structures such as the cerebellum and pons and thalamus that also contained nav 1.1. And we were able to show—although not as much as what we saw on the cortex—but we were able to upregulate the nav 1.1 in some of those deeper structures of the brain, also suggesting that hopefully we can have an impact not only on the seizures, but on other aspects of the disease that are present.

Daniel Levine: What’s the regulatory path forward?

Ed Kaye: The regulatory path. We are in a phase 1/2 study, both in the U.S. and the U.K. and we will be reporting on seizure and safety aspects in the second half of this year. Once we find the dose, and we hope that with this phase 1/2 data, we’ll be able to know what the dose is. And we’re also doing an open label extension study and we’re dosing every four months, so we’ll know the duration of therapy and we should have a very good idea of what the frequency of therapy should be. Once we complete our phase 1/2 study, then what we would do is have discussions with the regulatory authorities and go into a phase 3 study. And there is a precedent for this. A couple of other therapies have recently been approved and it was really looking at seizure reduction, but what we would do in addition to seizure reduction, which would be the primary endpoint, we would also look at cognitive and behavior aspects and quality of life, as secondary endpoints, because we believe that it’s critical for the success of this therapy to show that not only does it improve seizures, but improves other aspects of the disease.

Daniel Levine: Listeners may remember you from your days as CEO of Sarepta. What did you learn from your time there about developing and commercializing ASOs that you’re applying to Stoke?

Ed Kaye: Well, I think one of the things that’s always challenging, and certainly what we did at Sarepta, it’s always difficult being the first one in a space and what you end up having to do. And one of the things I think we’d learned is it’s really important to understand the natural history. We were fortunate in Duchenne muscular dystrophy, that there already had been a natural history that we could compare to, but for what we needed in Dravet syndrome, there wasn’t really a very good natural history that we could really know how these patients decline. And also, importantly, what behavioral and neurocognitive tests we should use to follow these patients. So, we did that, we learned that that was really important. That was probably the first step. And then I think what we learned is to really make sure that you understand the safety and really some of the characteristics of the drug. And we were able to show that the pharmacokinetic models that we developed in animals predicted what we needed to do in humans. And I think what we learned is that you need to make sure that you understand the dose that that’s required. How much do you have to give and how often do you have to give it? And then once you’re ready for commercialization, you really have to be able to be very well developed, speak not only with the patients and the families, but also have the physicians who really understand the drug and how to use it and make sure that people know that this therapy could be very valuable, and really make sure that people understand how to use the therapy, but also that this is an important medicine to make your child hopefully function in a much more normal way.

Daniel Levine: Ed Kaye, CEO of Stoke Therapeutics. Ed, thanks much for your time today.

Ed Kaye: Thank you very much. Appreciate it.

This transcript has been edited for clarity and readability.


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