Epigenetic editing expands the reach of gene therapy

Gene editing therapies are designed to be a one-and-done fix that cure a genetic disease and last a lifetime. Yet, they have some safety risks — chief among them the potential for off-target effects that permanently alter unrelated genes. Plus, there are ethical questions related to genetic editing of germline cells, as those mutations could be passed down to future generations (1).

“Because those risks exist, why not develop alternative approaches that would stand alongside or improve on what classical gene editing can do?” said Daniel Hart, the Head of Platform at Epicrispr Biotechnologies.

Rather than cutting and permanently altering the genetic code, Epicrispr Biotechnologies is one of several companies pioneering a new kind of gene therapy — epigenetic editing. This technology is inspired by a cell’s natural epigenetic mechanisms, which work by modifying chemical tags on DNA to regulate gene expression over time.

“The safety aspect is key. If one were offered the option of a cure that would leave everything as it were, except to change the gene expression in a way that would benefit you. Or, run the risk that I introduce mutations that might affect other genes and other pathways, I think the decision would be an easy one,” said Hart.

In March, Epicrispr Biotechnologies announced plans to start a clinical trial in New Zealand later this year to test their lead compound, EPI-321, in people with the genetic neuromuscular disease facioscapulohumeral muscular dystrophy (FSHD). Using their Gene Expression Modulation System (GEMS), they are also advancing programs to treat other neuromuscular diseases and blood cancers.

“I would like to see [epigenetic editing] stand alongside the other approaches, which I think have gotten their due credit and attention,” said Hart. “I think it will get there.”

What are the main advantages of epigenetic editing?

First and foremost, we can turn genes on and off without messing around with the underlying DNA, so the DNA remains intact — no mutations, no double- or single-stranded breaks. This is important from a safety perspective since we don't want to add any burden to the cells or organs. The second thing is that epigenetic editing allows us to do a lot of things that classical gene editing does not, namely, turn genes on. With classical gene editing, we can change the sequence of DNA to turn things off or correct sequences that are deleterious. But it's often hard to imagine how we would use that to increase the expression of a gene if we wanted to. With epigenetic editing, we have that potential, and that's what we developed at Epicrispr Biotechnologies.

A visual schematic of Epicrispr Biotechnologies’ platform. — Epicrispr Biotechnologies’ Gene Expression Modulation System (GEMS) works by combining a guide protein with a non-cutting Cas protein to bind to DNA and modulator proteins that regulate the expression of genes.
Credit: Epicrispr Biotechnologies

How does GEMS work?

GEMS leverages the CRISPR-associated (Cas) proteins, which are essentially DNA cutters. Instead of using the Cas proteins to cut the DNA, we've disabled that cutting aspect, so the Cas protein now is just very good at finding whatever we want it to bind in the genome. It brings small modulators to turn genes on or off as we desire. We also add a guide RNA that determines where the Cas protein binds. It’s basically the GPS of the system. We discovered and engineered the modulator domains at Epicrispr Biotechnologies together with the Cas proteins. Specifically, we have the exclusive license to use the CasMINI protein.

What is CasMINI?

CasMINI is a protein that our Founder, Stanley Qi, identified a few years ago (2). He found a naturally occurring, nonbacterial Cas protein, and introduced mutations that made it work in human cells. He demonstrated that we could use this for gene editing, base editing, and, importantly, epigenetic editing by gene activation.

A lot of the initial efforts in the CRISPR therapeutics space focused on ex vivo applications, which means taking cells out of a patient, engineering the cells, and putting them back in. It is curative, but the burden is on the patient. The costs and risks of taking these cells, engineering them and so forth, can be prohibitive. If we go the in vivo route, we can mitigate a lot of those risks, but that requires having protein sequences small enough to fit into a gene therapy vector.

Because CasMINI is extremely small — it's less than a third of the size of Cas9 — it can fit into any gene therapy vector including an adeno-associated virus (AAV), which has a relatively small genome. That means we can use it for in vivo gene therapy. We can include sequences for a promoter, our compacted guide RNAs, our small modulators, and our very small Cas proteins, whose sequences are about 1,500 nucleotides. Everything fits very comfortably into this AAV, so we can now go in and address muscle and eye conditions and so forth.

How does your lead compound, EPI-321, work to treat FSHD?

FSHD is one of the most prevalent muscular dystrophies in people. It's characterized by progressive muscle weakness in the skeletal muscle system. It's quite debilitating; it sometimes leaves people wheelchair-bound, is disruptive for normal functioning, and has a huge impact on quality of life. The cause of this disease is a misexpression of a gene called double homeobox 4 (DUX4). This misexpression occurs through epigenetic means, so we are uniquely able to address it by restoring the epigenetic landscape around this gene to switch the gene off. In this case, EPI-321 epigenetically silences the DUX4 locus in muscle cells by leveraging the GEMS platform. We hope that it will be curative for this disease. We are planning to move this into the clinic in the second half of 2025.

What have the results showed so far with EPI-321?

It’s all preclinical data so far. We generated our in vitro data to identify the best component parts of the GEMS platform that would constitute EPI-321: the right Cas protein, the right modulators, and the right guides. We assessed its performance in FSHD patient-derived cells to read out how well we suppressed DUX4 and downstream genes (3). We then performed similar studies ex vivo in muscle organoids, and we measured physiological outcomes, which were very encouraging. After that, we completed safety studies in mice as well as in nonhuman primates. We are very excited by the results, and that encouraged us to move to the clinic.

What other indications is your team working on?

Dan Hart leads a team of scientists working to make epigenetic editing a reality to cure many human genetic diseases.

Credit: Epicrispr Biotechnologies

Familial hypercholesterolemia (FH) is an interesting one because there we're taking a different approach than other people. Whilst epigenetic editing and epigenetic regulation of genes has been well studied for a long time, a lot of the focus has been on suppression of genes. The mechanism underlying long-term suppression through epigenetics is better characterized than it is for epigenetic activation of genes. My team set up a platform to identify activators, and we found some unique ones, which, when delivered transiently to cells, induced long-lasting gene activation. We wanted to exploit this, so in a proof-of-concept study, we tested these activators in human hepatocytes placed within a mouse. We asked whether we could activate the low-density lipoprotein (LDL) receptor gene, which is the protein that needs to have increased expression in FH in hepatocytes. We successfully demonstrated that in the first-of-its-kind study (4). That's exciting because it shows what we can do for functional haploinsufficiencies, a class of genetic diseases in humans that are characterized by having about half the amount of a required protein expressed. It’s very exciting data and something that I think demonstrates the unique capabilities of our platform.

How are you planning to improve your platform?

We never stop trying to improve the platform. I think we can always look to gain more space in the AAV vector. For now, AAVs are the most clinically derisked systems for in vivo gene therapy. We're going to need even smaller cargo, so we continue to work on making our Cas proteins smaller. We’re also working on expanding the types of sequences that they can recognize so that we can increase the footprint we can target in the human genome. We also continue to improve and enhance our modulator proteins so that now we are able to do almost everything on the epigenetic side: methylate, demethylate, and so on.

What do you find most exciting about working on epigenetic editing treatments?

The most exciting thing is that for me, this has been a long time coming. From a scientific curiosity and interest point of view, we are poised to see the potential of this realized, hopefully, very soon. But there's still a breadth of knowledge that's there waiting for us to tap in terms of how epigenetic regulation controls gene expression. We're really at the initial phases of getting into that. Some of the things we're using today will look very naive and very simplistic in a few years, but this is just the start. I'm really excited about where this whole platform and technology can go.

This interview has been condensed and edited for clarity.

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