Targeting Regulatory RNA to Upregulate Gene Expression to Treat Rare Diseases

Dravet Syndrome is a severe genetic epilepsy characterized by lifelong seizures and neurodevelopmental impairment that starts in infancy. Camp4 is developing an RNA therapy that it believes can reduce the frequency and severity of seizures, or eliminate them, by upregulating a gene that underlies the condition. We spoke to Ann Barbier, chief medical officer of Camp4 Therapeutics, about Dravet syndrome, the company’s platform technology to develop therapies that can upregulate gene expression, the potential to apply its approach to a broad range of conditions.

Daniel Levine: Ann, thanks for joining us.

Ann Barbier: My pleasure.

Daniel Levine: We’re going to talk about Dravet syndrome, Camp4, and its platform to address genetic diseases with programmable therapeutics that upregulate gene expression by targeting regulatory RNA. Perhaps we can begin with regulatory RNAs. What are they and what role do they play in controlling healthy gene expression?

Ann Barbier: Regulatory RNAs, or regulatory RNA, is a broad name for a group of RNAs that do not code for proteins. They can come from different parts of the genome. And it’s only in the last decade or so that people have begun to appreciate what they do. And basically what they do is they regulate gene expression at the level of transcription. And they can do that both in a positive way, enhancing transcription, or in a negative way, decreasing transcription. Now [as to] how they work; in order to understand that let’s think of how transcription typically works. You have your gene of interest and in Dravet that’s SCN1A. You also have other stretches of DNA that are located at a little bit of a distance, and those are called enhancers or promoters, and then you have the transcription proteins themselves. So people think of this as having three components: the coding section of the DNA, enhancers and promoters, and then transcriptional factors. And what we have begun to understand is that there might be, or there often is, a fourth partner, and that is where those regulatory RNAs come in. They participate in this complex and can regulate it in a positive or in a negative way. That also means, to bring us to what we want to do, is that by interfering with the regulatory RNAs in that regulation of transcription, you may, as the case may be, upregulate or downregulate the transcription of your gene of interest.

Daniel Levine: Camp4 is focused on developing RNA actuators, which it says have been largely unexploited as therapeutic targets. What are RNA actuators and why have they not been seen as therapeutic targets until now?

Ann Barbier: Just to clarify, the target are those regulatory RNAs that we just talked about. The RNA actuators is the name of the drugs that are intended to interfere with those regulatory RNAs. And in the case of what we want to do, these are antisense oligonucleotides. Now, why have they been underappreciated as therapeutic targets? Well, I think that is mainly because for a long time, the prevailing wisdom was that RNA fell into a couple of buckets and that was the coding messenger RNA, the transfer RNAs, and the ribosomal RNAs, and all these other RNA transcripts that people identified were considered to be junk or transcriptional noise without much function. It’s only in the last decade or so that people have begun to understand that these are biologically active molecules specifically at the level of regulating the transcription of genes.

Daniel Levine: Camp4 has created its RAP platform to identify regulatory RNA that targets specific genes and generating oligonucleotide drug candidates to use them to control the expression levels of genes. How does the platform work?

Ann Barbier: Well, the first step is to map, in specific human cell types, what you can find in terms of regulatory RNA and the genes they control, and that is done by applying some very sophisticated sequencing techniques. And then the second step is to apply machine learning to this, to really figure out, out of this massive data, which enhancer or which promoter controls which gene. And once you have those pieces of information, you can start to figure out where the regulatory RNAs might be produced. And then the third step is to design antisense oligonucleotides that block the interaction of the regulatory RNA with its targets.

Daniel Levine: It would seem that identifying those targets is the real challenge here. How difficult is it to know which RNA to target and how gene specific are those targets?

Ann Barbier: Well, that is where that machine learning model comes in, because it is capable of using all the data generated by the transcriptional maps to then identify which regulatory element is controlling which genes. And once you have made that map it is, by and large, an insilico exercise to figure out where these regulatory RNAs then are made. In terms of the specificity, what we have found is that these regulatory RNAs are typically very specific for either a single gene or sometimes for a couple of genes that you can find within the so-called insulated neighborhoods in the DNA, at least for the regulatory RNAs that are transcribed from enhancers and promoters, and they tend to act while they’re still being transcribed. So one end of the molecule is still tethered to the DNA so that it can diffuse far away and start interacting with other sequences, other parts of the gene. Now, in terms of the specificity of the interaction of the antisense oligonucleotide with its target, that is achieved by base pairing, the well-known mechanism of specificity between DNA and RNA, or double stranded nucleotide strands.

Daniel Levine: There have been challenges in the delivery of RNA therapies to different cells and tissues throughout the body. How much of an issue is this for the indications you’re pursuing?

Ann Barbier: Well, we have chosen our indications in order to be able to deliver there. The regions where success has been achieved are the central nervous system, the liver, and the eye. For the central nervous system and the eye, it really has to do with the route of administration. If you inject antisense oligonucleotides in the spinal canal, in the cerebral spinal fluid somewhere in your lumbar region, the antisense oligonucleotide mixes with the cerebral spinal fluid, which is constantly in motion, and that carries it from the lumbar region to the brain. It bathes the brain in this ASO-containing liquid. And so that’s how you deliver it. For the eye, it’s something very similar by direct injection into the relevant part of the eye. You can deliver it there. For the liver, there is a specific type of molecule you call GalNAc, which you can attach to your antisense oligonucleotides. And the result of that is that if you administer this GalNAc-conjugated antisense oligonucleotide, whether it’s intravenously or subcutaneously, it will find its way pretty selectively to the liver. The liver takes up these GalNAc-conjugated molecules very effectively. So that is a specific technique to deliver to the liver.

Daniel Levine: And by focusing on the regulatory RNA, how broad a set of indications do you think you might be able to pursue?

Ann Barbier: Well, probably a couple of thousand. There are so many genetically determined diseases. And if you just look at those diseases that are called haplo-insufficiency diseases, which essentially just means that you have about 50 percent of the messenger RNA and protein that you need—that is a group of several hundreds of diseases.

Daniel Levine: Given that broad potential, how do you go about determining which indications to focus on?

Ann Barbier: Well, we start, as I said, by looking for haplo-insufficiency diseases. These are diseases where one gene is mutated and the other one is functioning fine. That is one group of diseases. Then we look at the question of whether we can get our antisense oligonucleotides there. So, this means the liver, the CNS, and potentially the eye, although that is not something that we as a group want to focus on right now. So, that eliminates some other diseases. Then we look at factors such as unmet medical need, the number of patients that exist, what the manifestations of the disease are. Neurodegenerative diseases, for instance, are always much harder to treat because once a neuron is gone, it’s really hard to recover. Dravet, for instance, is not a neurodegenerative disease. Neuronal function in the brain is affected, but the neurons don’t really die off. That, for instance, is an attractive feature for a treatment like this.

Daniel Levine: Your lead indication is a preclinical program for the rare epilepsy Dravet syndrome. What is it and how does it manifest itself and progress?

Ann Barbier: Yeah, Dravet syndrome is a rare, genetically determined epilepsy. It starts in the first year of life. And typically, it manifests in a child that was born healthy, has developed healthy for several months and manifests as a febrile seizure, so seizure while temperature is elevated. It can be because of a fever. It can be in a hot bath. Now this happens in a lot of otherwise healthy children. So, the first seizure perhaps does not cause so much concern, but as time goes on, the child starts to develop more seizures and more severe seizures and longer lasting seizures and different types of seizures. So, it becomes clear pretty fast that there’s a serious form of epilepsy going on. On top of that, the family then starts to notice that the child doesn’t develop normally. That is, those developmental milestones of the early years are not met in terms of talking, communication, in terms of motor function, in terms of information processing and cognitive function. And over the years, additional features are noted [such as] behavioral abnormalities. Sometimes these children are described as having autistic like features or hyperactivity type features. Motor function can be affected. Sometimes in the late teens, these children can end up in wheelchairs. Then finally there is a particularly frightening feature which is called SUDEP, sudden death in epilepsy, whereby these children might just die, probably as a result of a seizure, and this can happen during the night. So parents have this intense fear of not being able to wake up their child in the morning. Those are the main features of this disease, a terrible, terrible disease that we hope to do something about.

Daniel Levine: And how are patients with the condition generally treated today and what’s the prognosis for them?

Ann Barbier: Yes, the current treatment of Dravet syndrome is really focused on controlling the seizures. There are maybe two dozen older anti-epilepsy medications that are used in these patients. There are three drugs that in the U.S. at least have been approved specifically for Dravet syndrome. But they don’t control the seizures completely. Some of these drugs work very well for some patients and they don’t work at all for other patients. Then there is the supportive therapy speech therapy, helping with the motility, things like that. There is currently no therapy that really goes to the root cause of the disease, which is the fact that one of the two SCN1A genes is not sufficiently expressed and that you have only about 50 percent of the product of that gene, which is that voltage-gated channel in the brain.

Daniel Levine: What would your RNA actuator target, in the case of Dravet syndrome, and what would it do biologically?

Ann Barbier: So, the molecule that we have for Dravet syndrome is an antisense oligonucleotide that works on a very specific type of regulatory RNA called naturally occurring antisense transcripts. And that is just one of those types of regulatory RNAs that can suppress the expression of the gene, the SCN1A gene. The antisense oligonucliotide will bind to that naturally occurring antisense transcript by base pairing and block it from exerting its function and thereby increase the level of transcription of the SCN1A gene. So, it’s a matter of blocking the blocker or removing the inhibitor.

Daniel Levine: We recently featured Stoke Therapeutics on the show, which is also developing an oligonucleutide to upregulate the healthy gene in this condition. Are you essentially doing the same thing? Do you just talk about it in different ways?

Ann Barbier: At a fundamental level, we do the same thing. We want to increase the amount of functional messenger RNA that codes for the healthy form of the protein. The way we get there is slightly different. What Stoke does is to improve the improper splicing of some of the messenger RNA transcripts and what we do is to increase the overall production of messenger RNA transcripts. So, if you think of this as a two-step process, we work maybe at step one and Stoke’s molecule works at step two, but ultimately we want to get to the same destination.

Daniel Levine: And to what extent can you upregulate gene expression? How significant an increase is needed to obtain a meaningful therapeutic benefit?

Ann Barbier: Yes, in a disease like Dravet and all these haplo-insufficiency diseases, if you start out with 50 percent and you can double that, you would be back to the levels of a healthy individual, and there is a very reasonable expectation that that would have a therapeutic effect. Now what it turns out, though, is that you don’t need to, or probably don’t need to get from 50 percent to exactly 100 percent. If you can get from 50 percent of a healthy person to maybe 70 percent of a healthy person that might enough to make quite a difference. And the reason why I say this is that based on animal experiments in a Dravet mouse, we have seen that if you upregulate that messenger RNA level by maybe 25 percent, you can decrease the seizures in that animal model by 70 percent. That is certainly very encouraging.

Daniel Levine: And what’s the clinical path forward?

Ann Barbier: Well, the first thing we need to do is talk to the FDA and present to them the plan that we have to move forward, and that is happening in a couple of weeks. That happens this summer. Based on the feedback we receive there, we can either move forward with the plan we have already put in place, or we might have to adjust it a little bit. That’s why you go and talk to the FDA. But if all goes well, our plan is to submit the IND by the end of this year, and to be in the clinic sometime early in 2023.

Daniel Levine: In 2021, the company raised $45 million in a venture round. How far will existing funding take you?

Ann Barbier: Well, I can’t give you the exact numbers or the exact date, but we’re well capitalized, and certainly looking forward to taking the molecule into the clinic and taking it to some important readouts.

Daniel Levine: Ann Barbier, chief medical officer of Camp4 Therapeutics. Ann, thanks so much for your time today.

Ann Barbier: Thank you for having us.

This transcript has been edited for clarity and readability.