RARE Daily

Differentiating Gene Therapies Through Regulatory Elements

May 30, 2024

Encoded Therapeutics is developing gene therapies that can target any cell type that has a unique genetic profile. The company’s lead experimental therapy is in development for the epileptic encephalopathy Dravet syndrome, although the company expects to pursue metabolic, liver, and cardiovascular conditions in the future. We spoke to Salvador Rico, chief medical officer of Encoded Therapeutics, about its lead program in Dravet syndrome, its efforts to develop gene therapies with optimized regulatory elements to target specific organs, and why he believes its approach is a point of differentiation for the company.

Daniel Levine: Sal, thanks for joining us.

Salvador Rico: Thank you for having me Danny.

Daniel Levine: We’re going to talk about the rare seizure disorder SCN1A+ Dravet syndrome, Encoded Therapeutics, and its efforts to develop gene therapies with optimized regulatory elements to target specific organs. I’d like to start with some gene therapy basics for listeners. Can you break down the elements of a gene therapy, what the regulatory elements include and the role that they play?

Salvador Rico: Absolutely. And to be more specific, what I’m going to be describing now are the components of adeno-associated virus gene therapy, or AAV gene therapy. This type of therapy comprises three main elements. On the one hand, we have the capsid, which is a non-infectious, non- replicating capsid that is going to be used as a delivery vehicle for the drug. The second component is the transgene, and this is the genetic sequence that is introduced into an organism, and it’s used to alter the biological properties of a cell to correct a genetic defect or to produce a therapeutic protein. And then the third part are the regulatory elements. These are sequences of DNA that control where and how a gene is expressed. And these elements include promoters which initiate the transcriptions of a gene, enhancers which increase the transcription rate of a gene or the targeting sequences that prevent expression of a gene in a given group of cells. And so, in summary, regulatory elements ensure that the transgene is expressed in the correct cells at the right time and at appropriate levels, which is crucial to get the desire effect without the unintended consequences.

Daniel Levine: Most gene therapies to date have used standardized regulatory elements. What limitations has that caused?

Salvador Rico: Yeah, you’re absolutely right. Many of the gene therapies developed to date or are in development utilize nonspecific regulatory elements that express the respective transgenes in many types of cells. We believe that by achieving expression in disease relevant cells, you have the best potential to show efficacy. And by preventing the expression in non-disease relevant cells, you avoid most of the undesirable effects.

Daniel Levine: Encoded has put an emphasis on the regulatory elements as a point of differentiation. What’s the case for this as a point of differentiation?

Salvador Rico: I like to think of this as an evolution in the design of gene therapy in that we’re moving away from using the first generation standard regulatory elements, such as ubiquitous promoters that led to widespread expression in many cell types, into the use of more selective and precise regulatory elements that help us achieve robust and precise expression in the target cells of interest. So this may enable the use of lower doses and hopefully safer and more efficacious products.

Daniel Levine: Encoded has developed platform technology for designing gene therapy constructs. How does this work and what benefits are you able to achieve with this? What improvements in performance of a therapy can this provide?

Salvador Rico: We bring together two platform capabilities to create our gene therapies. The first one are our regulatory elements, and then the second one are novel transgenes with unique functionality. So, our regulatory elements are identified via proprietary genomics-driven screening methods where we identify thousands of sequences in our genome that drive precise and robust expression in target cells. We then apply machine learning algorithms to these uncovered sequences to identify motives driving the design pattern of gene activity. And then we test that in mouse models where we try to ascertain whether the expression pattern is the one that was predicted by algorithm. We feed our algorithms and we do it all over again so that in the end, and by understanding the principles underlying transcriptional regulation, we can engineer synthetic regulatory elements that are more selective, more potent, and smaller than those found occurring in nature. So, the other platform capability that we bring to the table, as I mentioned, are the transgenes with unique functionality. And this is how we are also differentiated from other companies. As you know, the most common form of transgene is CDNA that is used to replace a missing or a malfunctioning gene. And one good example of how we have approached this challenge differently is with our Dravet program that we have at Encoded where we have designed an engineered transcription factor that operates the expression of the SCN1A gene. And we needed to do this because the SCN1A gene is just too large to fit into one capsid. And this is just one example besides the syngenic transcription factor., We’re also developing novel transgenes that modulate RNA or marker RNAs for other indications. So again, these are the two capabilities that we’re bringing to the table.

Daniel Levine: The company has started with a focus on pediatric neurological conditions. Why start there?

Salvador Rico: There have been both external and internal factors that have led us to this decision. On the external front, we recognize that there’s a huge unmet medical need for degenerative disease modifying therapies in the CNS field and includes many monogenic disorders that are highly amenable to therapies. In parallel, we’ve observed how over the past few years there’s been a tremendous progress in the CNS field and a deeper understanding of the genetic drivers of disorders as well as understanding of potential biomarkers and clinical trial endpoints that may be acceptable to regulators in many CNS disorders. And we have also been observing how there are many gene therapies delivering positive clinical data, especially with AAV9 capsids, which is the one that we are proposing for our drug program. On the internal front, we believe that our platform is uniquely suited for the development of CNS gene therapies. A good example again, is our Dravet program where we have generated and cell selected transgene thanks to GABA-selective regulatory elements and leveraging those regulatory elements. We are also thinking of other indications such as our preclinical program that we unveiled today for Lennox-Gastaut syndrome. Additionally, we have engineered regulatory elements that drive potent neuro specific expression in the brain while the targeting expression in the dorsal root ganglia, enabling the use of efficacious doses in other indications, while minimizing the side effect that has been observed in some preclinical programs. And now we also have a very promising pipeline of microRNAs to treat other indications such as Angelman syndrome. I would also say that although pediatric indications are a starting point, our early pipeline also includes candidates for non-monogenic disorders that impact adults, including neurodegeneration and pain. And in fact, today we unveiled additional preclinical programs in Alzheimer’s disease as well as neuropathic pain, each of which demonstrate robust gene silencing with these microRNAs, or knockdown in the respective targets. So again, the platform innovation and infrastructure that we built for Dravet is serving as the foundation for the expansion into more common disorders.

Daniel Levine: Let’s talk about Dravet syndrome. For listeners not familiar with the condition, what is it?

Salvador Rico: SCN1A+ Dravet syndrome is a devastating developmental and epileptic encephalopathy that is characterized by a highly refractory seizure burden that includes prolonged and frequent seizures and episodes of status epilepticus. It also carries an unacceptable mortality risk of up to 20 percent before adulthood, mostly due to sudden unexpected death in epilepsy. It carries a very high risk of developmental stagnation affecting communication, cognition, and it also leads to more problems, behavioral issues, very poor sleep quality, and as you may imagine, a huge impact on the lives of those people living with the disorder and their families. In most cases, Dravet syndrome is the result of a single allele mutation or variant of the SCN1A gene. The SCN1A gene encodes for the alpha subunit of the nav 1.1 sodium channel, which controls the release of GABA, an inhibitory neurotransmitter in our brains. So, we have the density of the nav1.1 channels in the brain. There’s not enough inhibition. There’s runaway excitation that leads to all the phenotypes of the disease.

Daniel Levine: What treatment options exist today, if any?

Salvador Rico: There are unfortunately no disease modifying treatments for Dravet syndrome. There are three antisense medications and several anti-seizure medications that are used off label for the treatment of seizures associated with Dravet syndrome. So it’s only symptomatic treatment for the seizures. And in combination they do reduce the seizure burden, but even in combination, they fail to render patients seizure-free and they do nothing to address their mortality risk as well as the developmental stagnation.

Daniel Levine: And what’s the prognosis for someone diagnosed with the condition today?

Salvador Rico: Well, first I would like to just go back a little bit to the trajectory of Dravet syndrome. So, the first seizure that patients experience is typically around four to six month of age. And these are prolonged seizures typically associated with fever. They increase in type of severity and frequency over the ensuing months and they persist into adulthood. Then around two years of age, there are signs of developmental delay or stagnation, mainly affecting communication. That is what is more significant for the families at the beginning. And then around four to five years of age, patients experience some motor problems and they start experiencing behavioral issues that are reminiscent of autistic spectrum disorder traits, OCD traits, ADHD, oppositional defined disorder, et cetera. The developmental stagnation is more, gets more pronounced over time. So, by the time a kid is seven years of age, they’re performing like a two to 3-year-old neurotypical patient. The seizures typically follow a time course where they shift from prolonged, provoked, and focal seizures occurring while awake during childhood to shorter generalized seizures occurring in sleep during adolescence and adulthood. Over time, the mortality beast doesn’t really change, as I mentioned, up to 20 percent before adulthood. There is refractory epilepsy into adulthood in spite of multiple anti-seizure medications. And some of these patients receive up to six anti-seizure medications. The risk of developmental stagnation is almost a certainty, unfortunately. In a recently completed natural history study, we learned that a hundred percent of the participants in our study experienced developmental stagnation. And as you imagine, in combination, all of these symptoms affect the ability of patients to live independently and most of the adults live with their parents or in a specialized facilities, and it carries a tremendous clinical, humanistic, and economic burden on those living with a disorder and their families.

Daniel Levine: Let’s talk about your experimental therapy ETX101. What is it and how does it work?

Salvador Rico: ETX101 has the potential of being a one-time disease modifying therapy for Dravet syndrome as it addresses the underlying pathophysiology of the disorder. And this is an AAV9-based gene regulation therapy that carries an engineered transfection factor that operates expression of the SCN1A gene preferentially in GABAergic inhibitory neurons where the problem resides in this disease. To better explain the mechanism of action of ETX101, I like to think of an analogy where we compare the two alleles of the SCN1A gene assembly lines in a manufacturing facility. And in most patients living with Dravet syndrome, one of those assembly lines that is manufacturing that 1.1 channels is not working. So, you only have one of the assembly lines working. What ETX101 is doing is it is boosting the output of the healthy allele or the working assembly line to compensate for the loss of the other assembly line. And this is done preferentially again in GABAergic inhibitory neurons.

Daniel Levine: And how is it delivered?

Salvador Rico: This investigational drug will be delivered directly into one of the brain ventricles. This route administration is called intracerebral ventricular or ICD. And this is a route of administration that is typically used for the delivery of antibiotics, chemotherapy agents, or enzyme replacement therapy. And the main difference in all of those cases is that the administration is repeated or chronic, whereas in our case, this is a single administration. We put a lot of thought on the selection of our route of administration, and we did this in a data-driven way. We conducted some experimental work in non-human primates some years ago where we learned that via ICD, you are able to get the broadest biodistribution in the brain with the lowest possible dose, which is important from a safety perspective.

Daniel Levine: What’s known about it from preclinical studies,

Salvador Rico: We have tested ETX101 in two mouse models of Dravet syndrome, and also in wild type non-human primates. The mouse models of Dravet syndrome are haplo-sufficient, and they recapitulate many of the phenotypes of disease. And one of the key ones is the early mortality. So, the mouse model of Dravet syndrome shows that 50 percent of mice die within 60 days of birth, and upon receiving a single dose of ETX101 on Day 1 postnatally, we show a very robust survival at Day 60, 90, and up to 470 days in what is now the longest study of its kind that we have knowledge of. Besides that, a single administration to these mice reduces the seizure frequency in a substantial way and shows an increase in the threshold to the hyperthermic induced seizure assay. This is an interesting assay that we believe is quite apropos, relevant, and translatable. In short, you place mice under a headlamp and you increase their body temperature all the way to 43 degrees Celsius, which is about 110 Fahrenheit, and you assess the proportion of mice who seize at different temperature thresholds. And we’ve shown that ETX101 has a dose response in increasing the threshold of this hyperthermic seizure assay. These assays are also quite stringent and many anti-seizure medications typically fail to show an effect in this assay or require super therapeutic doses to show an effect in non-human primates. We have shown that a single administration of ETX101 is safe, is well-tolerated and leads to broad biodistribution in key areas of the brain that are associated with cognitive function and behavior.

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

Salvador Rico: Well, the first step that we gave in our thinking on the development plan for ETX101 for Dravet syndrome was to lay a strong foundation for clinical trials. And we did that by launching three initiatives back in 2020, slightly before the pandemic. One of them was called Dravet Engage, then Ambition, and then Elucidate. Dravet Engage is a patient-focused initiative where we have generated qualitative and quantitative data on the perspectives and needs of caregivers and parents of patients living with Dravet syndrome. And through Engage, we learned that the seizure burden is the most important concern that families have, followed by their inability to communicate with their children. And Ambition is a recently completed longitudinal prospective natural history study where we recruited almost 60 children in collaboration with 16 expert sites in four countries in the world. All of these kids were under five years of age and receiving standard treatment with anti-seizure medications for Dravet. And it was our intent to follow them up every three months for up to a couple of years to understand the trajectory or the progression of the disease. Importantly, half of these patients, so almost 30 patients. were patients under two years of age where there was really a dearth of data, especially contemporary data on the trajectory of the different symptoms associated with the disease. Not only did we learn a lot from this recently completed study from the disease perspective, but we also tested several of the instruments, especially some of the neuropsychological assessments that we’re going to be using in our upcoming clinical trials. And last but not least, as part of the foundation, we also launched a project called Elucidate, which is a multi-pronged biomarker discovery project where we sought to understand whether there are potential biomarkers of target engagement via analysis of blood samples, functional neuroimaging, or quantitative electrophysiology. So, with that solid foundation in mind, we have designed now our clinical development program for ETX101 that we have adopted—Polaris as our North Star, and Polaris current comprises three open label dose ranging studies that are going to assess the safety and the preliminary efficacy of ETX101 in patients under seven years of age. The three studies that I just mentioned are called Wayfinder that is being initiated in Australia, Expedition in the UK, and Endeavor Part 1 in the U.S. Importantly, this Endeavor study has a second part that is much more pathologically proposed that has already been vetted and approved by the U.S. FDA. It follows a randomized double-blind sham delayed treatment control type of design. And this is a potentially confirmatory study in nature. So, the plan is that once we generate data in an open label setting in Wayfinder, Expedition, and Endeavor Part 1, we hope to seamlessly transition into what could be a potential confirmatory study in Endeavor part 2 to confirm again the potential benefit of ETX101 and its safety.

Daniel Levine: And why the age limit on the enrollment?

Salvador Rico: This is our starting point. We really want to initiate in the age range where, based on literature and other gene therapy programs, we believe that we’ll see the greatest magnitude of the effect in the shortest amount of time. That’ll be fundamentally important in our discussions to argue for the optimal dose levels with regulators for our confirmatory study. But, as I said, that’s just the starting point, and then once we have the data on the optimal dose, we haven’t, we will be discussing with regulators the next steps as it relates to the assessment of safety and efficacy of ETX101 in older patients. But you’re absolutely right. What we have as an objective at Encoded is to develop a drug that can help hopefully all patients and families living with the disorder.

Daniel Levine: How is Encoded funded to date?

Salvador Rico: We have raised over $300 million from premier biotech investors, and our current funding will take us into 2026.

Daniel Levine: And what’s the plan for raising additional capital?

Salvador Rico: We’re tremendously fortunate to have a highly committed investor base, and we continue to field increase from new groups that are interested in investing in Encoded. Our focus this year is really to execute against our ETX101 Polaris Clinical Development Program, as well as to advance our promising pipeline of CNS gene therapies. And then in 2025, we’ll be providing further guidance on our fundraising strategy.

Daniel Levine: Salvador Rico, chief medical officer of Encoded. Sal, thanks so much for your time today.

Salvador Rico: Thank you for the opportunity, Danny. Really appreciate it.

This transcript has been edited for clarity and readability.


The RARECast podcast is made possible through support from the Global Genes’ Corporate Alliance. The members of the Corporate Alliance support Global Genes’ mission and programs, work to meet the vital needs of people with rare diseases, and address inequities they face. To learn more about the Corporate Alliance or how your organization can become a member, click here.



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