Jason F. Cole has been working to make gene therapy a reality for patients since he joined Bluebird about ten years ago. This gave him a front-row seat to the first generation of gene therapies, typically delivered with lentivirus in an ex vivo setting. Cole was part of the journey of taking state-of-the-art technology at the time into early clinical trials, dealing with setbacks, and navigating regulators that resulted in three approvals: Zynteglo, Skysona, and Lyfgenia.
Upon leaving Bluebird, Cole began searching for a company operating where the puck would be going. That’s when he came across SalioGen Therapeutics.
“I believe the future of genetic medicine is nonviral, in vivo, and integrative,” said Cole. “It is these permanent, full solutions to a lot of these other genetic diseases that we haven’t been able to address yet. I was looking around doing diligence and consulting work when I came across SalioGen, and what really attracted me to the company were the core differentiators of the technology: the ability to deliver large genes nonvirally into specific places in the genome with better safety compared to some of the existing editing approaches. What that does is it brings the opportunity to go after some therapeutic areas where we’ve seen no progress or a bunch of failures because the tools and maybe the first- and second-generation companies are not fit for purpose.”
Eight months ago, Cole came on board as the CEO and chairman of the board at SalioGen and immediately focused the company on just one area of their pipeline, inherited retinal diseases, to get to the clinic quickly and safely.
“When the company was founded, it was exploring the applications of this technology pretty broadly and that generated a lot of data,” said Cole. “When I joined, I really drove toward a data-driven decision around what applications of our technology are unique to us and are truly differentiated. There are a lot of folks working in the genetic medicine space now, and you see all the crowding around certain indications, whether it’s sickle cell or hemophilia—you name it. I want us to focus on things where, if SalioGen didn’t exist, neither would those therapies. That’s the kind of level of impact we want to have.”
Cole and SalioGen are showing some of their first work at ASGCT 2024 that shows how their nonviral in vivo gene insertion technology can be used. This technology uses a bioengineered mammalian transposase to integrate large DNA constructs permanently.
“It’s an exciting conference this week because a bunch of us ‘new kids’ are starting to share data for the first time, largely preclinical data but in higher species,” said Cole.
The results will show preclinical evidence that SGT-1001 is safe and effective in living organisms. It is being developed as a possible one-time treatment for Stargardt disease, a genetic condition that causes progressive vision loss. A different program being worked on for cystic fibrosis (CF) will successfully target the integration of the CFTR gene into the native CFTR intron 1. The data demonstrated by SalioGen is the beginning of what could be a big step for the genetic medicine field in the targeted delivery of a large genetic cargo.
Bioengineered mammalian transposases
At the heart of SalioGen’s genetic medicine technology is a lipid nanoparticle (LNP) that surrounds a plasmid DNA of large size and an mRNA that encodes Saliogase, a bioengineered mammalian transposase.
Saliogase can be designed to target specific recognition sequences. In its default form, saliogase was designed to form a dimer that grabs onto two inverted terminal repeats in donor DNA and then inserts it into a specific recognition sequence, TTAA. According to Cole, these TTAAs are all over the genome and are predominantly in intronic or intergenic regions, where there is less risk of a problematic integration.
“They very rarely go into exons and places where you could really disrupt something,” said Cole. Probabilistically, it’s very unlikely we are going to hit the same spot in two alleles, and it’s one in 300 billion that will hit two oncogenes. So, the way to think about transposase safety is less about guide and target and more about benign patterns where it lands.”
The enzyme looks for a certain number of these target sites and then inserts the whole payload through a chemical reaction instead of reverse transcription (also known as prime editing) or making a double-stranded break and relying on homology-directed repair (also known as CRISPR-Cas9).
“If you were to run those same experiments around CRISPR-based approaches, you would see indels; you would see things like chromothripsis,” said Cole. “We don’t see that, and this is the underpinning of data we’re going to talk to the [United States Food and Drug Administration (FDA)] and other regulatory agencies about to educate them, so they don’t do sadly what a lot of the agency did with these first in vivo gene therapies and slap on clinical holds. We believe that many of those clinical holds were based on either a lack of understanding or a lack of preparation by the sponsor. So, we’re trying to address that issue right up front with lots and lots of data.”
At ASGCT, SalioGen will also share genomic profiling data on the gene coding technology to add large DNA constructs (up to 100 kb) to the genome. The poster will also show the characterization of the insertion patterns of saliogase technology in multiple cell types.
“The main takeaway is that we have this tool that can put a large gene or construct with full fidelity into the genome,” said Cole. “You would expect it to leave a scar and to have some impact that you can detect. But again, back to the no double-stranded breaks, the elegance of how it integrates, we’ve done all these different techniques comparing the DNA we see with our integrations with regular DNA from a donor, and you can’t tell meaningful differences.”
Large DNA insertions
The saliogase approach works great in the context of Stargardt’s disease, where the goal is to rescue expression of ABCA4 via gene insertion that does not require any modification of the existing alleles.
“What really attracted me to the company was Stargardt’s program because we have the right genetic tool to put in a large gene of 6.8 kilobases,” said Cole. “Others have to do a dual adeno-associated virus (AAV) approach to get that in, and it’s unclear if it gets together in the nucleus or even in the cells. We’ve built a set of annotations around where they prefer to go. We’re sharing data with the FDA as we move our Stargardt’s program forward to give them confidence that not only are we not doing the genetic violence of a double-stranded break, we’re sort of efficiently putting it in; where we put it in is not like the random integration of lentiviruses that I lived through at Bluebird.”
For their CF program, SalioGen had to shake up their approach because the goal is to insert genetic material into a very specific place for gene function. To do this, SalioGen has changed how their bioengineered mammalian transposases work by using artificial intelligence (AI) to make them more selective and aim for a certain sequence with zinc fingers.
“Over time, what we plan to do with our enzymes is to have a version that integrates and doesn’t need to be hyper-targeted, and then we’ll have versions that are more targeted either for the disease we’re going after or maybe in the case of a T cell in some genomic safe harbor locus,” said Cole.
Nonviral in vivo delivery
SalioGen uses cell-type-specific LNPs to deliver their bioengineered transposases. For patients with Stargardt disease, SalioGen developed its own LNP that targets photoreceptors in the eye upon sub-retinal injection. Cole said that for successfully edited photoreceptors, they see one copy of the inserted sequence per genome.
When it comes to the CF program, Cole said that he’s a bit skeptical of the first wave of genetic medicines that are pursuing an inhalation-based delivery like Moderna because he doesn’t think that aerosolized approaches will be able to hit mucus-covered cells in the lungs. Instead, SalioGen is developing a systemically administered LNP that avoids the liver and targets the lung.
SalioGen’s Stargardt program is a bit ahead of the cystic fibrosis one, as demonstrated by the data in nonhuman primates revealed at ASGCT 2024 for evidence of safety, integration, and expression of SGT-1001. Cole said that SalioGen is planning to be in the clinic with its Stargardt program in the first half of 2025.
“Clinical advisors are really excited about this data because Stargardts has been a disease for which many have tried in vivo lentiviruses and other approaches that failed,” said Cole. “It’s exciting to make that transition to a clinical company.”
