Using A Natural DNA Repair Process to Improve Genetic Medicines

Precision, safety, and durability are challenges for gene replacement and gene editing therapies. LogicBio Therapeutics says its GeneRide platform technology addresses these challenges by harnessing a natural DNA repair process. We spoke to Daniel Gruskin, chief medical officer of LogicBio, about the company’s platform technology, the advantages it provides, and the company’s lead experimental therapy for the rare metabolic condition methylmalonic acidemia.

Daniel Levine: Daniel. Thanks for joining us.

Daniel Gruskin: Thank you so much for having me. I really appreciate the opportunity to talk to you.

Daniel Levine: We’re going to talk about LogicBio, its GeneRide platform technology, and its effort to develop gene therapies and gene editing therapies for rare life-threatening conditions like methylmalonic acidemia. Perhaps we can start with gene editing though. For listeners not familiar with it, how does it differ from what people may think of as gene replacement therapies?

Daniel Gruskin: That’s a great question. I think it comes down to durability and the potential for durability, meaning how long will the effect last. In gene editing, you’re actually making a change to the patient’s DNA, the genetic material that is already in their cells. So, when the cells divide and multiply, whatever change you have made to that DNA gets passed along to both daughter cells. On the other hand, in canonical gene therapy/gene replacement treatments, the gene that’s being delivered remains outside of the patient’s endogenous DNA and, sort of floats around in the cell. It gets transcribed and translated as the other DNA does, but if, and when the cell divides, it does not get passed along. That’s what you’ve seen in other canonical gene therapies, the concern is that the effect that you see early on in the treatment diminishes over time as the transgene gets lost.

Daniel Levine: A big open question still for a lot of gene therapies is, how well understood or how well known is the durability of the effect of gene editing in that context.

Daniel Gruskin: That’s right. It will take long-term studies to demonstrate a true durability. We’ve seen that in our technology, which is called GeneRide, in animal studies. We are initiating our first in-human trial. In fact, the first patient was dosed with our first GeneRide product earlier in the spring. After the study, each patient will be enrolled in a long-term follow-up study to determine durability and long-term safety. Because of the mechanism of action, where, as I mentioned earlier, it’s actually modifying the genome of the patient, we do expect to see a durable life-long effect and intend this to be a single administration therapy. You can give it once and it remains there for the life of the patient potentially.

Daniel Levine: LogicBio Is actually developing a pipeline of both gene editing therapies and gene replacement therapies. What determines whether a disease would be appropriate for a gene replacement therapy rather than a gene editing therapy?

Daniel Gruskin: That’s a great question. One of the reasons that LogicBio was founded was to develop genetic therapies that could be used in children, in diseases where it’s critical to intervene early in the life of the patient to get the most benefit from the therapy. Many genetic diseases, as you probably know, are associated with irreversible tissue damage. If you don’t intervene before much of that irreversible damage takes place, then you’re not able to really make a meaningful difference in the lives of these patients. So, with the technology that LogicBio has developed, a gene-editing technology that we think has the potential to be both durable and safer than some of the existing technology, it makes it particularly well-suited for those diseases like methylmalonic acidemia, where it’s absolutely critical to intervene as early as possible.

Daniel Levine: I want to ask you about your gene editing technology platform known as GeneRide. Before we talk about that, perhaps you can explain what homologous recombination is and what its natural function in cells is.

Daniel Gruskin: Sure. It’s a natural DNA repair mechanism that all of our cells have. Over time the DNA in each of our cells has the potential to be damaged by things like ultraviolet light or a variety of other mechanisms where the DNA is damaged and there’s an incorrect coding sequence, a base is wrong, or our DNA gets damaged and is not intact due to a cut in the DNA. Evolution has provided us with this mechanism of homologous recombination, where, because the DNA can match up with a similar sequence, the cell has the ability fix whatever the defect is. This is something that’s really important for the health of a cell because mistakes in DNA happen quite frequently and are the basis for evolution. If mistakes are detrimental, there needs to be a way for the cell to repair them and homologous recombination is one of those mechanisms.

Daniel Levine: What is the GeneRide technology and how does it exploit this natural process?

Daniel Gruskin: Sure. First of all, the GeneRide technology is built from an AAV-based capsid that has, at least in this current iteration, a high level of tropism for the liver. After it’s infused intravenously, it’s delivered almost exclusively to the hepatocytes. The exciting innovation with GeneRide is what’s inside the capsid, it’s the cassette, which we feel is elegant in its simplicity. It’s comprised only of the gene of interest, the transgene. In LB001, which is the drug for methylmalonic acidemia, the gene is called a methylmalonyl-CoA mutase. This gene is flanked by very long homology guide arms. So, it has DNA that’s a thousand base pairs long on each side. In addition to the long homology guide arms, there’s a short sequence that codes for a peptide called 2A, and this is critical and I’ll get to why it’s there in a minute. That’s all that’s inside there, the gene, these long homology arms, and the 2A sequence. We don’t need to package this with promoters and we don’t need to package this with nucleases because we’re utilizing this natural process of homologous recombination. So, what happens is these very long homology guide arms direct the gene in a very precise site-specific way. We’ve chosen the guide arms to match up with the albumin locus. You probably know that albumin is a protein produced by the liver and it’s the most active gene in the liver. We chose it for that very reason. The transgene is inserted, again in a very site-specific to the nucleotide level way, just adjacent to the end of the albumin locus, where it is integrated in a non-disruptive way next to albumin and therefore can take advantage of the highly active albumin promoter. This is why we don’t need to package this with an exogenous promoter. Also, because it uses this homologous recombination, we don’t need to cut the DNA like other gene editing techniques. It’s this lack of a promoter and lack of nucleases that we think will allow for a better safety profile and less likelihood of off-target effects. Once the gene is inserted next to albumin it is transcribed as a fused mRNA. So, there’s the albumin gene, this 2A sequence, and then mutase, which are produced as a single transcript. This is where the two-way sequence comes into play because as the single transcript is translated, the two-way sequence induces a ribosomal skipping event, which means that two separate proteins are produced, one of which is the goal. We’re trying to produce the mutase enzyme which is deficient in these patients. This mutase enzyme, once it’s cleaved by this ribosomal skipping event, is directed to the mitochondria, which is where it performs its function. The other protein that’s produced is albumin, but it has this short 2A tag, it’s about 20 amino acids or so. This albumin 2A molecule, which is a feature of the technology and not a bug because it doesn’t interfere with the function of albumin, but what it does do is provide us with a circulating biomarker. Then, we can perform a simple blood test that circumvents the need for a liver biopsy. The production of albumin 2A correlates with genomic integration and protein expression. So it can give us an early readout on how well the drug is working without having to get a big long needle to get a piece of liver.

Daniel Levine: Your lead therapeutic candidate, LB001, is a gene editing therapy in development for methylmalonic acidemia or MMA. What is MMA?

Daniel Gruskin: So, MMA is a potentially life-threatening and certainly life-altering inherited disease. It’s caused by the inability to properly metabolize certain amino acids and fats. The block in this pathway leads to the buildup of toxic metabolites. One of these toxic metabolites is methylmalonic acid, and that’s why it’s called methylmalonic acidemia, but there are other toxic metabolites formed. It’s the block in this metabolic pathway that drives systemic organ dysfunction particularly in tissues with high energy needs like brain, liver, or kidney. There are a few enzymes involved in this pathway, but the most common form of MMA is caused by deficiency of a mitochondrial enzyme called methylmalonyl-CoA mutase. The disease is genetic, it’s autosomal recessive. Because it’s genetic, it’s inherited and the underlying defect is clearly present at birth. The clinical manifestations often arise in the first few days of life with an event that’s called a metabolic decompensation or a metabolic crisis where the child becomes severely acidotic and ammonia levels get very high. If the crisis isn’t managed aggressively and quickly, this metabolic dysfunction can lead to significant neurologic damage, respiratory distress, and even coma or death. If the baby does survive the initial event, the clinical course of MMA is characterized by recurrent metabolic crises like these that can be triggered by conditions that induce catabolism. Not just dietary intake of protein, but even minor viral infections, physical or emotional stress, or a change in the nutritional status—so if a baby is not eating because he or she doesn’t feel well—can induce catabolism. Increased flux through this pathway can cause one of these devastating metabolic crises. Because the chronic metabolic imbalance and the intermittent crises can lead to significant and irreversible long-term complications, like impaired growth, feeding problems, or neurodevelopmental disability, any effective treatment needs to be initiated as soon as possible. MMA is on the newborn screening panel of every state in the country because early intervention is so critical. Unfortunately there aren’t any current treatments available that address the underlying cause of the disease. Current standard of care is essentially limited to changes in the diet. These patients have a strict limitation on the amount of dietary protein that they can take in. They need to be on special formulas and keep a very close eye on what they’re taking in through their diet particularly in regard to protein. In fact, many patients require G-tubes, both because of the feeding difficulty, but also to help manage the strict diet. Even with the most obedient adherence to the prescribed diet, outcomes in these patients are, almost uniformly, poor. Because of this, in many centers of excellence, liver transplantation is being offered to these children more frequently and at a younger age. The idea here is, most of the activity of the mutase enzyme takes place in the liver, not all, but much of it, and replacing the liver is done in an attempt to replace this enzymatic activity. Of course, a liver transplantation is an invasive surgery and comes with its own set of risks and complications. Not to mention there’s a finite availability of livers to transplant. While MMA is certainly a rare disease, it affects about one in 50,000 newborns, still the unmet need is enormous. There’s a huge desire among families, caregivers and physicians for a better therapy. We’re hopeful that our technology, GeneRide and LB001, an in vivo gene editing technology, is durable and safe. This can serve as a molecular liver transplant through gene therapy where you get the benefits of providing a new liver, but without the need for a surgery. Hopefully, this can generate enough mutase activity to provide better metabolic stability to these children, avoid metabolic decompensations, and get them and their families a better quality of life.

Daniel Levine: As you mentioned, you recently dosed your first patient in a clinical study. What is the current study and what’s the development path forward?

Daniel Gruskin: Sure. Very exciting news, from a couple of weeks ago, we were able to dose our first patient. We think this is the first pediatric patient ever given an in vivo systematic gene editing technology. Very exciting for us in the gene therapy community. The first in-human trial for LB001 is called, SUNRISE. It’s a phase 1/2 study. The primary endpoints are safety and tolerability, but we’re looking at efficacy as well, both biochemically and clinically. Importantly, we are looking at albumin 2A which I mentioned earlier as a pharmacodynamic marker of genomic integration and protein expression that will give us our first signal that the product is working. Then, later in the study, we’ll be looking at biochemical markers like methylmalonic acid and some clinical features as well. It’s a small study. We’re looking to enroll up to eight patients. It’s a single administration of LB001 and there’ll be two dose cohorts. As I’ve mentioned a few times when I talked about early intervention, we feel very strongly that it’s important to treat children with this disease. We were able to generate a strong enough preclinical package to work with the FDA on designing a clinical program that treats those patients most in need and most likely to benefit. We are starting the trial in patients 3 to 12 years of age. After dosing two patients in that age group, as long as there’s no significant safety signals and we see a presence of albumin 2A, we’re able to, in the next patient, go down to as young as six months of age. We think this is really exciting and a major accomplishment if we’re able to provide a gene editing technology in patients so young,

Daniel Levine: What’s known about LB001 from the preclinical studies that were performed?

Daniel Gruskin: In our preclinical program the data was strong enough to show a prospect of direct benefit and provide FDA with the reassurance that we were able to start in children. LB001 in mice and non-human primates was found to be safe, with a very clean safety profile. We saw transduction of hepatocytes, site-specific genomic integration, and transgene expression. LB001 corrected hepatocytes in the mouse model of MMA. We were able to demonstrate preferential survival and expansion of those cells and this contributed to a progressive increase in mutase expression over time. In other words, the corrected hepatocytes were healthier than the remaining cells in the liver and had an advantage, and over time took over a larger proportion of cells in the liver. We saw that as an increase in albumin 2A and mutase expression. In terms of more clinically relevant endpoints, LB001, both in neonatal mice and in adult mice, resulted in improved growth, improved metabolic stability as shown by methylmalonic acid levels, and improved survival at both the doses that we’re using in the SUNRISE trial.

Daniel Levine: A lot of your early focus is on diseases that are related to the liver. How scalable is this technology? How easily can you take the basic approach being used in MMA to address other monogenic conditions?

Daniel Gruskin: That’s another thing that’s so exciting about the technology. It’s modular, essentially. We have these homology guide arms that take advantage of the albumin promoter. So, theoretically all we need to do is swap out the transgene and the mechanism of action will be the same. For example, we have a partnership with Takeda where we are working on Crigler-Najjar syndrome. This is another rare pediatric disease where children have a defect in bilirubin metabolism and end up with high levels of bilirubin potentially causing permanent neurological damage. We’ve demonstrated in an animal model that GeneRide, using the same homology guide arms for albumin but just swapping out the mutase gene for the gene that causes Crigler-Najjar, is effective in the Crigler-Najjar mouse. We also have some non-disclosed indications for the liver that we intend to utilize GeneRide for and a recently announced partnership with Daiichi Sankyo for a couple of undisclosed GeneRide indications. We are really excited about MMA and the potential for GeneRide in similar liver indications,

Daniel Levine: Daniel Gruskin, chief medical officer of LogicBio Therapeutics. Daniel, thanks so much for your time today.

Daniel Gruskin: Thank you. I really enjoyed talking with you.

This interview has been edited for clarity and readability.