Genetic Epilepsy Team Australia’s 2024 Genetic Epilepsy Conference

So thanks for, to the GETA team for inviting me and David and Kris for sending a whole bunch of emails reminding me what I need to do. I’m really delighted. I’m sorry I can’t be there. I was planning on being in Australia. Right now I’m in Boston, working on this project and others and hopefully you’ll be visiting Melbourne in July. And as Sarah mentioned, I’m really excited to be talking about some of the first in patient results. And for those of you that have been coming to the GETA meetings for a while, I’ve been talking about antisense oligos or ASOs for some time and especially working on the SCN2A ASO and it’s always said at those meetings, I’d love to come back one day and present on the results.

These are the first in patient results. So I’m very excited to be sharing it. Most of this data is only a few months old. So there’ll be more and more data coming, of course. As we, we move into more and more involved trials. So what I’m going to talk about is the gene SCN2A. I’m sorry if a lot of this has been done.

I don’t know what’s been covered in the meeting, unfortunately, but it’s a, quite a spectrum disorder. There’s, depending on the nature of the genetic change, depending on individual patient differences, the disorder can express clinically in different ways. very much. And this is a recent paper done in collaboration with Ingrid Schaeffer and others really trying to understand the presentation of the disease, but also understanding the functional consequences of the genetic changes that are seen in patients within these various groups. For today, and for the ASO and we’ve all heard about precision medicine, and what precision medicine means is that the medicine is tied to a clinical or a genetic condition. And in this case, the medicine is really tied to those patients that are in the pink and the red box here. The EI intermediate and the EI severe cases. These are what we call gain of function changes in the SCN2A gene, so it’s working harder than it should. These kids present with seizures very early in life, typically have a very severe presentation. And what we’re interested in, of course, is trying to do something about that. This is a paper that really set the tone for moving into the clinical realm. and it’s a sort of a path that you need to follow, you need to try and understand there’s a lot of beautiful genetics done by people like Ingrid and Sam and others that reveal the genes that are underlying these different disorders and then there’s now there’s a process of what we’re now we’re getting very secure in our genetic knowledge. For many of these disorders, how can we use that knowledge and that understanding to move to therapies? And that’s always the way, and this was a proof of concept study saying, can we do it in a mouse, basically. These mice have the same genetic change that patients, and that can be a bit challenging for some people, but if we want to help the children, we have to go through this step.

These mice contain the same mutation that some of the children with SCN2A contain. And you can see these mice one day of age and that middle mouse that is quite stiff is having a seizure. And so very early in life, these mice mimic aspects of the patient presentation. Unfortunately, these mice die very young. In the black curve, this is a graph showing how many are surviving over different ages, and you can see within 30 days all of the mice are dead, and they all have very strong seizures and they in many of those seizure situations they stop breathing and they die and, so it’s a very severe phenotype in these animals.

Now, the red line is using phenytoin that’s injected into these mice on a daily basis. And phenytoin is one of the first line treatments for patients. It’s one of the more effective treatments that works in people, but when you inject it at the highest levels, we can in the mouse, it only, you can see he only extends their life by a very small amount.

And with, essentially the mice don’t live much longer, but they start dying a bit later. So basically. Is this is the best we’ve got? Can we do better? And that was the question we asked when we started investigating this gene and these mutations and these developmental and epileptic encephalopathies associated with the SCN2A gene.

So we turned to antisense oligos, and this just gives a bit of chemistry that doesn’t really matter. It’s just, I just want to say what are antisense oligos. Sarah mentioned them. Eventually, if you come to enough GETA meetings, you’ll get used to hearing it and saying it. ASOs are basically a modified version of the natural DNA.

It’s in all of us the same DNA that gets mutated to cause the diseases that brings us here today. But that same DNA can be chemically modified into short stretches. These are a ASOs are short stretches only. We know that there are, hundreds and hundreds of millions of different bases in, of DNA in the human, but these are only 18 to 20 nucleotides in length. So quite short strands that we modify to make them more stable, we modify them to make them less toxic, we modify them so they don’t trigger an immune response, we modify them so they bind the RNA very tightly. So that’s why we do the chemical modifications, essentially turning DNA into a drug. And the drug that we want to create is a drug that can destroy RNA to reduce the levels of a gene. And I mentioned before that the SCN2A is a gain of function. That means that gene works too hard, so the therapeutic choice is to try and reduce the level of activity of that gene by simply reducing the amount, and we can do that with an antisense oligo.

Now, a particular form of oligo that’s called a gapmer you can see it in the top right here. I don’t know if you can see my cursor. You can see here it’s called a gapmer because of the chemical modifications. It doesn’t really matter what does matter when this type of ASO binds. So in our bodies, we have DNA, which are the master plans, messenger RNA, which are the working drawings and messenger RNA makes protein. But it really gives us life that makes up their muscle or everything in our bodies. Now, if you can reduce the amount of RNA, you can reduce the amount of protein you make. And in this case, we can reduce the amount of the aberrant SCN2A protein. So we can make this little tiny little square here that’s that’s binding to the messenger RNA. Attracts this little pac man shaped object that chews up the RNA. So this combination of a little oligonucleotide bound to this really big messenger RNA molecule causes that messenger RNA molecule to be destroyed.

The more antisense oligonucleotide we give to a patient, the more RNA that gets destroyed. So like many drugs, we can use dose. to try and have an effect to modulate the level of effect that we need. So we did this in the mouse model that I showed you. Antisense oligos were screened and we look at how potent they are in these curves at the bottom.

We look at how selective they are just for the gene of interest on the top. We don’t want it attacking related genes, these SCN8A, 9A, 10A, et cetera. So it’s very specific for what we want and we can then understand how much ASO causes what effect. And then we can really fully understand when we give it to a young animal, a medium age and an older animal, how much ASO will cause how much reduction in the RNA and protein.

Now when we do that, so if we inject mice with that, what we can see here is that I showed you before the black line, which is the mice that are uninjected, and they just die after 20 to 30 days. If, and this is injected at the day of birth if we now inject just with an ASO that doesn’t target the SCN2A it has essentially no effect on the longevity of these mice, but you can see at a 50 percent dose, you can see here that the mice start to live longer, considerably longer, up to 80 days, single dose. Now they live until about 80 days. If we give a higher dose, you can see that they go well beyond 80 days before there’s any death of these mice.

Now, that was the first finding that really showed us, you know what, maybe we’re onto something here. Certainly a lot better than that Phenytoin that I showed you. And we also started doing other experiments that said I showed you what happens when you inject once at a very early age. But if you give a booster shot at a slightly older age, you can see we can rescue all of the mice. So 100 percent of the mice survive now if we give this second booster shot at a later age. And so now we’ve got to hope so, these mice that were dying here, we just required a little bit more ASO at a later age and we could do that. And also, and importantly, If we give the ASL at the latest time possible to these mice, because they all die at day 30, if we give them at day 15. You still get a lot of rescue. So even at that last stitched age where the animals just cross over to that point where they’re dying. So here’s about day 20, here’s day 30, and they’re all dead. So we can have an effect even very late. That was important in asking what happens if you give to a kid who’s two years old or three years old? Is there still any hope? And we think this sort of these sort of experiments start to give us that hope. And then we could, I won’t go into the details here, but we can look at the effects of the mutation on the gene function with these experiments in a real nerve. So this is what happens. You can see these curves are black is the normal nerve. The red is the nerve with the gene mutation in it, and the curve shifts, and it’s just important to understand these sorts of shifts in the curve changes in the properties and excitability of these nerves that can drive the disease.

What you can see on the right, though, when we give the ASO, which is blue, that blue curve goes back onto the black curve, which means we’ve now impacted the neuron in a way that’s actually reversing the effect of the mutation. And that’s a really important thing because at one level, we say we can help the mice, we affect their longevity, but we’re fixing it at a level where the neurons are fixed and look very much like a normal, healthy neuron. That’s really important if you really want to deliver precision medicine. And that’s the whole idea of precision medicine. If you fix the root underlying cause, whether it’s genetic or something else all the consequences of that then play out.

And indeed, we can see when we do that, all the seizures go away. This gray bar is an animal that didn’t receive the SCN2A ASO, but received another one. Still having lots of seizures, and you can see here, we injected with the ASO, those animals were no longer having seizures. Older animals also, of course, we don’t have any animals alive at day 30 to measure them, but those that survived because they were treated had no seizures also.

And then when we looked at a whole bunch of different behaviors, what was really important here, Is that when we gave the mid level dose of ASO, this ED50 dose, we could not distinguish a treated animal from a normal wild type litter made animal. And that’s that’s a really important thing. So the animals were that were impacted, not just on their survival, not just on the neuronal properties, but on motor, psychosocial and cognitive domains. So we saw a correction across and this is what everybody wants of course. We want the kids to not just have seizures. We want them to, have better ambulation to have proper higher levels of cognition and other things. We can’t promise this will happen in a human. It’s going to be a lot more work for us to be able to get here. And of course, we all want a reduction in the seizures because that can have a lot of downstream consequences of not seizing all the time. But there’s hope when you see data like this, that you can have a bigger consequence than just seizures.

The second question we asked, what patients can actually receive? And ways of doing that is trying to understand what does the patient look like clinically? What does the gene look like when we study just the gene in isolation? And we developed a method I call this dynamic action potential clamp method. I won’t go into any of the details here, but it lets us really get a very strong handle on how the gene is broken at a functional level. And we get readouts like this again, I won’t belabor these, but what’s important to understand is that we can say we understand the clinical presentation, we measure your gene function, because we want to be very cautious, of course, when we give a precision medicine like this, for some patients with different types of mutations, you wouldn’t want to give this particular therapy, but for others, it would be key.

And now we’ve we, and because when we think about how we’re going to move forward with this program. How are we going to design our trials? Who’s going to come into them? Who’s going to benefit? We need to develop these essays. So it’s a really important step in patient selection. And this is 1 example of a mutation in a patient that even though it looked like it, the current here, if you compare it to here, it looks like it’s a lot more, which is typical gain of function. But when you look at it in this other assay we developed, you can see that it actually results in less neural activity than a normal channel. And so a patient with this mutation, despite this, in one functional test says, maybe you should get it. But in this other functional test says, no, it wouldn’t be a good idea. And so it’s really important to have these different levels of analysis to pick patients. We don’t want to make anything worse than it already is.

And again, I mentioned this before. We can now say that we can really hone in on these two classes of people here. Most of our trials so far have been in this dark red box, and I’ll show you the data from that next. It’s complex, but we think it’s solvable, and I won’t go into the details of this.

So I think we’ve got, we’ve shown that the ASO is effective we think it’s going to be a very specific therapy for early seizure onset gain of function patients, ASO is ready and the first patient trials were started last year.

Now this was the report, this is the first child, first human that ever received this ASO. It was in Munich. And it was a team of neurologists and epileptologists from Munich, Ingo Borggraefe and Mathias Wagner. And this is a poster that we presented at the American Epilepsy Society meeting last year describing our experience with this ASO.

There was a preterm infant. She was born around 10, 12 weeks preterm. She was born in status epilepticus, and she was in status epilepticus for 13 weeks. So seizing, and so that’s not a great start to life. And it may have its own consequences on how effective even an ASO can be,if that child’s brain has been undergoing that level of activity for some time.

They did an exome when they realized there might have been a problem prenatally. They did some prenatal exome sequencing. They found the mutation in SCN2A, and they reached out to us via a colleague of mine to access the ASO that we were developing, Prax222. Fortunately, we had done all the work to make it to be able to deliver it to people and we hadn’t done a trial yet, but we had clinical grade molecule we had everything ready. We done all our toxicology, et cetera. So we were in a position to help these physicians and to help this child. So the patient was 13 weeks old. And as I said, a very poor prognosis due to the continuous status epilepticus.

We analyzedthe mutation, showed it was actually gain of function. So we were very motivated and we knew that we’ve got the right drug for this patient was really important that we understood that prior to delivering the ASO. So that was clear.

Now this is her EEG. It’s a particular type of EEG that Ingrid, I’m sure, can explain a lot better than me. But in, the neonatal intensive care units they often do this amplitude integrated EEGs. You don’t need as many electrodes, but basically what you can see is that her EEG, she’s just continuous firing. And there’s very high levels of phenytoin. And you can see here where a dose of phenytoin was happening, you still get, still seeing status epilepticus across the board. Now the top was that amplitude EEG that I mentioned before, ongoing seizure activity. And what you can see underneath is about a week after the administration of the first ASO dose. ASOs take time to act because they have to degrade the RNA, then reduce the levels of protein, and it takes about a week for their effect to start to stabilize. And immediately we could see an effect, and remarkably, for the first time, the patient was no longer in status. And that was quite an amazing observation given how sick this little girl was. And this just goes to show some of the the seizures per hour count here in this blue line you can see over the course. And at the top you can see that when the first ASO and then we started increasing the amounts of doses and we can see a decline in the amounts of seizures over time. And then the, phenytoin was still on board in this girl. And she was undergoing all sorts of aspirational pneumonia, all these other things happening clinically. There were, of course, triggers and making the condition a lot worse, but I’m happy to say she’s and this data was current as of the end of September last year (2023), you can see the seizures have reduced enormously and not only the count, but if you actually look at the severity of these seizures, they’re almost impossible to pick up. And it can be a shudder or a little jerk versus a prolonged tonic clonic seizure that we were seeing earlier.

So that’s not reflected here, and this is only reflecting the actual count, but all the seizures down here are much less severe than the seizures up here as well. So there seems to have been a prolonged effect. This little girl is still alive. The physicians, estimated that up to about, five months of age, she’d have somewhat like 20 to 30, 000 seizures. So that’s a terrible burden for any brain. And we think there will be some permanent effects of that. But we also think there’s a huge amount of benefit that this girl has received from this treatment. This just summarizes some of the findings that we found there that I’ve already spoken about.

Now what I will also end on is, and I’ve probably gone over time and I apologize. It is just the, there’s a couple of slides really. On the first trial results run by Praxis. I was one of the co founders of Praxis and this has been one of the projects I first started working on this project in 2015 in the animal models or maybe even earlier and just delighted to see that it’s actually matured and it’s now in patients. This is a formal trial. We got four patients. And what we did in this first trial, really a very low dose, one milligram. I don’t know if any of you have been looking at the Stoke trial, they’re injecting amounts like 45 and 70 milligrams a day of ASO there. This is a very low dose just to see basically, is there going to be any bad reactions, what the safety signal is, and is there any inkling of an effect?

And I’ll show you that every four weeks. We’ve got a baseline period and then every four weeks we gave each of the patients an intrathecal dose of one milligram of the human ASO and there’s two slides that really, that basically show all the data. This, and this is really somewhat surprising that even at 1 mg, we’re seeing a remarkable reduction in median seizures across the first 3 doses, up to a 58 percent reduction in the numbers of seizures, above and beyond the standard of care. So these kids are already on their phenytoin. This is an effect and couldn’t tolerate it anymore. Couldn’t get any other efficacy. And it was just remarkable to see this additional benefit at the three different dose periods for the different patients. Not only that at baseline, there were only 21 percent seizure free days for these kids. So that means only one day out of five were they seizure free. And we saw about a 70 percent increase in that. So they were getting at least two or three days a week where they were the median was 35%, free of seizures, which is a remarkable, improvement for quality of life for the, obviously for the kids and also for the carers. When you’re not dealing with seizures every day in day out, so we were really excited to see this and I’m really excited to see as we move to broader trials. How this effect plays out in this patient population and are really doing whatever we can to try and get this drug out as quickly as we possibly can.

And there’ll be work to be done after we get it out as well. There’ll be other studies done to really understand how we really optimize the use of this. But we’re very keen to try and get it into the hands of patients as soon as possible. Importantly, and this was a safety trial, obviously the first one there were no what we call TEAs treatment emergent AEs, nothing related to the treatment. No serious adverse events considered related to the study. So we’re really pleased with the safety profile and the data monitoring committee really gave us an independent committee of key opinion leaders and not in the company, of course, gave the opinion that they should continue dosing without modifications.

So we’re in the point now where there’s a lot of planning and discussions internally and externally to really decide next steps for this program. So I’ll leave it there. I think it’s just great to see these first data. I’d love to come back in a year or two and show you the next steps. And of course, we do have other programs in development on things that have started in The Florey and will be moving to Praxis, we hope in the near future for development from out of the lab into patients and we can start to talk about those in the coming years. So thanks very much everybody.