Geulah Livshits, PhD, a Senior Research Analyst at Chardan covering biotech companies, with a focus on gene editing and oncology.

Genome editing’s dazzling potential and stubborn challenges were both highlighted at Chardan’s 6th Annual Genetic Medicines Conference earlier this month in New York, held in-person for the first time since the COVID-19 pandemic.

Leaders from 72 companies presented updates on their pipeline progress and expected milestones, while speakers and other stakeholders weighed in on technologies that included adeno-associated virus (AAV)-based gene therapies, RNA-based treatments including long non-coding RNAs, base and prime editing technologies, gene regulation, and non-viral genetic medicines.

Some key inflection points for the genome editing field are expected to emerge over the coming year with clinical data readouts from leading companies in the field on drug candidates furthest along in trials.

One is exagamglogene autotemcel or “exa-cel” (formerly CTX001), the autologous, ex vivo CRISPR-Cas9 gene-edited therapy co-developed by CRISPR Therapeutics and Vertex Pharmaceuticals for sickle-cell disease (SCD) and transfusion-dependent beta thalassemia (TDT). Vertex agreed last year to pay CRISPR Therapeutics $900 million upfront to lead the global development, manufacturing, and commercialization of CTX001 following very positive early clinical results.

Another is NTLA-2001, the in vivo CRISPR-Cas9-based therapy co-developed by Intellia Therapeutics and Regeneron Pharmaceuticals to treat transthyretin (ATTR) amyloidosis. Last year researchers from the companies and their clinical partners published the first-ever clinical data supporting the safety and efficacy of in vivo CRISPR genome editing in humans. “We believe we are truly opening a new era of medicine,” Intellia president and CEO John Leonard, MD, declared.

By the end of this year, Editas Medicine is expected to announce clinical data for its two lead candidates pursuing proof-of-concept—EDIT-101, an in vivo CRISPR gene editing treatment for Leber congenital amaurosis 10 (LCA10); and EDIT-301, a cell therapy medicine also being developed for SCD and TDT. Next year, Verve Therapeutics is expected to report interim clinical data for VERVE-101, the first in vivo base editing therapy to reach the clinic, dosing its first patient in July.

Also in 2023, Graphite Bio is expected to report initial proof of concept data from its Phase I/II open-label CEDAR trial designed to evaluate the safety, preliminary efficacy, and pharmacodynamics of Nula-cel (formerly GPH101) in adults and adolescents with severe SCD. The first patient in CEDAR was dosed in August. Graphite Bio’s precision gene editing approach, is designed to “find & replace” any gene in the genome using its UltraHDR™ gene editing platform.

Geulah Livshits, PhD, is a Senior Research Analyst at Chardan covering biotech companies, with a focus on gene editing and oncology. After a busy stint at the conference, where she moderated numerous presentations, Livshits sat down to discuss the progress and challenges of developing genome editing therapies with GEN Edge. (This interview has been lightly edited for length and clarity).

GEN Edge: What emerged among the key themes as you spoke with CEOs and heard presentations during the conference?

Livshits: Clearly there’s a lot of interesting science that is being done along the genetic medicine spectrum, from gene editing to gene therapy, both on the therapeutics side and on the platform side. One of the areas that kept coming up repeatedly is the importance of delivery in various types of genetic medicines applications. Whether it’s gene editing or gene therapy, getting to the right cell and delivering the right amount is clearly important parameters for the therapeutic space.

GEN Edge: What are the key challenges involved in delivery, and how are companies surmounting them?

Livshits: The genome editing space has really leveraged a lot of the delivery modalities that have been used for other therapeutics in the past—for example, AAV vectors that have been used in gene therapy for gene delivery, and lipid nanoparticles (LNPs) for RNA modalities. The challenges within those spaces are a little bit different. The other dimension there is the tissue that companies are trying to target for a particular therapeutic application.

At this point, I think we’ve seen great delivery to the liver using lipid nanoparticles that encapsulate mRNAs that can code either the gene that expresses the liver protein, or the genome editor, as we’ve seen from Intellia’s data, where they reported clinical results in humans. And Verve Therapeutics is also in the clinic. Now we haven’t seen clinical data there yet, but from Intellia’s data, we’ve seen good translatability between preclinical models such as mice and non-human primates over into the clinic.

For liver, at least in the genome editing space, LNPs are seen as the most advanced approach. But LNPs are less mature as a delivery form to other tissues. Now, that’s an area where we’ve seen some activity in recent years, in terms of adapting LNPs to target different tissues and cell types. This is either done by changing the chemical properties of LNPs to select for versions that can better deliver genetic material or cargo components into other tissues, such as lung or immune cells or hematopoietic stem cells. There are additional approaches that you could use to try to target them. That’s the non-viral component.

Then on the viral side, AAV delivery in itself, within the gene therapy space, is an evolving area. The next-gen versions of AAV vectors can potentially either avoid the liver or reduce exposure to the liver, which is one of the sources of some toxicities that we’ve seen in the space, and/or show better tropism to different target tissues, such as the central nervous system or muscle, that could potentially enable lower dosing. And that, again, could help improve a benefit-risk profile in terms of safety.

So on the gene editing side, companies could piggyback off of those advances incorporating different AAV vectors. The challenge there is making sure that the genome editing enzyme can actually fit as a cargo in a viral vector, because viral vectors have pretty defined constraints in terms of the size of the cargo that you can package. The traditional Cas9 nuclease that has been used in the clinic is typically challenging to package. Editas does have a different version of Cas9 that they use in their clinical program that does work in an AAV vector, but having a smaller nuclease affords more flexibility in incorporating additional regulatory elements or next-gen precision editing domains, using viral vectors, such as AAV and other next-gen viral vectors that might be in development.

GEN Edge: Until now, the types of tissues and organs seem to decide when companies go to a viral or a non-viral delivery approach. How much will that change?

Livshits: We’re seeing the confluence of the cargo technology advancements as well as the delivery technology advances guiding where the pipelines go. Typically, companies take a balanced risk management approach where, if they’re advancing a new, let’s say, editing technology, they may want to mitigate other sources of risk by going after a target that’s well understood, and using a delivery mechanism that is also well characterized, such that the risk is isolated as much as possible to this specific technology that they’re advancing, whether that be in a novel nuclease system, or a base editor, or something of that sort.

As the delivery technologies mature, we’ll see, pipelines may follow. In the case of AAV, we see delivery to the liver as well as muscle and the central nervous system. And again, those are continuing to iterate with new and potentially improved versions of those technologies. And in the lipid nanoparticle setting, there’s early-stage programs that will be looking at delivery to the lung and the immune system. We’ve seen a fair amount of interest in in situ cell therapies.

In our 2022 preview commentary, we asked if the future of cell therapy could be in vivo. Obviously that’s an unknown, potentially long-term time horizon, because there’s a lot of science to be done. But that’s an area where we’ve seen a lot of interest, for example, with developing in situ CAR-T, such as Orna Therapeutics is doing, or in situ CAR macrophages, such as Carisma Therapeutics is doing with Moderna, or with myeloid cells as Myeloid Therapeutics is doing. We heard from each of those companies a bit at our conference, discussing those different strategies. Again, it’s early days for those types of technologies.

GEN Edge: Where do base and prime editing have a place in the toolbox that therapy developers are creating? Will these be widely used or selectively?

Livshits: I think a lot of it comes down to matching the right tool to an indication or patient swath, where it provides an advantage over other available systems or technologies. So for something like base editing, where it can correct the specific mutation, it may represent an advance, and an attractive strategy in settings where, let’s say, there’s one common mutation, or one or two common mutations that a large swath of patients with an indication have, such that they could all be treated with the same therapy.

If there is an indication where patients have a variety of different mutations, a gene delivery strategy might be better—whether that’s a gene therapy strategy, or something that inserts the replacement into the genome. That way patients with lots of different mutations might be amenable to treatment with a single therapy. In the longer term, eventually maybe, there could be the pathways for really personalized gene correction strategies. That’s a longer-term vision for the space. There’s a lot to be done between here and there.

For prime editing, it’s a similar question, where that could be amenable to treating indications where there’s, let’s say, a mutation or a hot spot of several mutations that could all be treated with the same kind of smaller insertion fragment or rewriting fragment. So those are the dimensions on the indication side. Again, for each of those modalities, there’s also constraints in terms of delivery, and the size of the enzyme, and the technology that’s doing the activity. I think there’s space for multiple different technologies based on what is needed for a particular indication.

The other dimension here is efficiency. In some cases, it may be important to have high efficiency, and the exact consistency of the editing outcome may not be as critical. For example, in the setting of gene knockdown, you don’t necessarily need to do the precise correction as you would if you were trying to maintain expression of the protein and didn’t want to accidentally create a deficient allele.

GEN Edge: How much have base and prime editing driven efforts to shrink the nucleases used by genome editing therapy developers?

Livshits: Part of the push for the smaller nucleases is to be able to hook on these additional functionalities. Again, whether it’s a base editor or prime editor, or an epigenome editor, having a smaller nuclease could in principle, leave space for an additional functional element to be attached there. Some of the companies that presented at the conference also mentioned advantages for lipid nanoparticle delivery, in terms of packaging efficiency and parameters there. I think that’s less widely understood or characterized as compared to the AAV vector packaging constraints, which are very well known from the gene therapy space.

Attaching a base editing domain or a prime editing domain—adding these different functional elements increases the size of the cargo. This is where potentially having a smaller enzyme can help increase the flexibility, in terms of fitting into a viral vector along with whatever kind of regulatory elements might be needed, such as a tissue-specific promoter or something of that sort.

GEN Edge: Is there still a place for Cas9 in genome editing? Or will that be supplanted by newer and smaller nucleases?

Livshits: I don’t think supplanted is the right word. Companies will look at what is needed for a particular indication, and should be matching the appropriate tool for the job, rather than holding a hammer and assuming everything is a nail, basically.

Each of the nucleases is likely to be different with regard to the biochemical details. People want to generalize a lot regarding the space, but the details really do matter, when you come down to the biochemical edits that you’re trying to achieve at the therapeutic level. Different nucleases will likely have different PAM preferences, different abilities, and different biochemical properties with respect to DNA binding, specificity or off-target. So I think there’s room for multiple different flavors of nucleases, and it’s more about matching the right one in the toolbox for the job.

Clearly Cas9 has worked in the clinic so far in terms of at least showing target knockdown from Intellia’s programs. There’s potential for other nucleases to also have effects there, but there’s the important parameter is to match the appropriate tool for the therapy itself.

GEN Edge: Intellia and Regeneron recently announced positive data for their single-dose CRISPR therapy NTLA-2001 for transthyretin amyloidosis. CRISPR Therapeutics and Vertex have reported positive results for nearly two years. And Editas has retooled with a new CEO and announced the first patient successful patient engraftment in a sickle cell disease trial. How soon are we from seeing treatments win approval and reach patients?

Livshits: CRISPR Therapeutics and Vertex have guided to regulatory filings in towards the end of this year in Europe, and they plan to start a rolling submission, I believe, by the end of this year to be completed in the beginning of 2023. So, we’re not too far away from having these therapies potentially reach the regulatory approval stage and making the way to patients, potentially, in the 2023 timeframe, at least on the ex vivo side.

On the in vivo side, Intellia is engaged a little bit with the FDA. They plan to provide an update on a pivotal path for their lead program in transthyretin amyloidosis later this year. So at that point, we’ll have a better sense of the exact timelines to approval or a filing on that one. Whereas on the ex vivo side, we might be pretty close, actually.

GEN Edge: What are the greatest successes for genome editing over the past decade, and the key challenges that need to be surmounted going forward?

Livshits: The success of this so far has been the translatability that we’ve seen in the in vivo genome editing technology. As an academic scientist, I like to see when mouse data translates to non-human primate data and ultimately to the clinical setting. I’m very encouraged by good translatability in any setting when I see it, because then that helps de-risk future programs. That’s the advantage of a pipeline that does incorporate a particular genome editor, and where the thing that changes is, let’s say, the guide RNA and the target.

In addition to translatability on the in vivo side, another success is the efficiency that we’ve seen on the ex vivo side from CRISPR Therapeutics and Vertex’s program, and just in general the editing efficiencies. The challenge on the ex vivo side is not so much a challenge related to editing, but how it’s necessarily applied. In many cases, companies are using genome editing to enable immune evasion in an off-the-shelf cell therapy context. And the field has, I think, not quite finalized the optimal actual targets to the editing.

It’s not necessarily that the editing doesn’t work. The editing seems to work well, but which targets need to be edited is an in-progress question. That’s something that there’s different strategies that that are in play, that we might learn more about over the next couple of years.

The other open question in this space is, when you do edit multiple genes at a time in a cell therapy, whether that multiplex editing could create translocations? We know it does at some low level. But whether that is positioned to create problems in terms of the therapy is an open question. So that whether base editing is the more attractive strategy in that setting is an open question at the functional level.

GEN Edge: One challenge the field still faces is ensuring broad, patient access to the treatments that will emerge in coming years. Some gene therapies carry list prices as high as $23 million. How much more affordable can genome editing therapies be? And how will that affordability come about?

Livshits: Yes, it’s a good question. At least initially, a genome editing therapy might be fairly similar to a comparable gene therapy or other genetic medicine approaches that are using similar modalities. For example, in a cell therapy setting, the cell processing and manipulation components do contribute to the cost. It’s not necessarily that different, although being able to avoid having to use a viral vector does reduce some of the costs associated with the genome editing program.

At a broad level, it might be fairly similar on the cell therapy side. And then in the in vivo editing setting, there are comparable reference points using LNPs or other in vivo genetic medicine deliveries. Typically, when we think about modeling out a gene therapy approach, we often think about estimating its effect over four or five years, such that you can expect that a one-time dose might save five years of repeat treatment.

In terms of access to in vivo lipid nanoparticles, we’ve seen broad distribution with the COVID vaccines, so that’s less of a hurdle in terms of access at this point in that we’ve seen scalable manufacturing and distribution in that setting. In the cell therapy setting, it does remain a challenge.

From our perspective, the CRISPR/Vertex program benefits from Vertex’s broad expertise and global footprint. On the logistics front, we think that they could fare pretty well. We see other companies on the ex vivo cell therapy side, such as Bluebird Bio, run into challenges in Europe. We’ll see how they do in the U.S. now that they’ve gotten their approvals. But I think that’s the reference point that we would think of for the sickle cell programs.

GEN Edge: What stories, trends, or developments will you be watching to see unfold as we move into 2023?

Livshits: In the fourth quarter [2022], we’ll have a couple of areas of regulatory path visibility and guidance from some of the programs. Intellia will have a little bit more visibility on their path in transthyretin amyloidosis. We’ll also have some visibility on Rocket [Pharmaceuticals]’ gene therapy program in Danon disease, which is also an area that we’re closely watching. They recently reported data, and we’ll be interested to see what kind of a pivotal study design they’ll come up with.

I think it’s an exciting time in the genetic medicine space overall. The science continues to move forward, both on the platform side, and as pipelines continue to mature. We just had two BLA filings [September 2022] in the gene therapy space as well, so that area continues to move forward on the clinical side for sure.

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