The Potential of Programmable Genomic Integration

John Finn, PhD

Tome Biosciences is currently working on platforms based on programmable genomic integration (PGI) technology, which is intended to overcome the limitations of some of the other methods used for therapeutic gene transfer and gene editing. At the American Society of Gene & Cell Therapy (ASGCT) 27th Annual Meeting, held May 7 to 10, 2024, the company presented some of its preclinical work on this area of research.

Shortly after the conference, CGTLive® interviewed John Finn, PhD, the chief scientific officer of Tome Biosciences, to get an overview of the key data the company had presented. Finn explained how PGI works and described how the company is utilizing it for various potential therapeutic applications.

CGTLive: Can you give some background context about Tome and what the company presented at ASGCT this year?

John Finn, PhD: Tome is the PGI company, and this is essentially what we introduced last week. When we talk about PGI, essentially, this is a concept, right? This concept is basically the ability to put any sequence of DNA of any location of any size—and that sounds like a pretty bold statement, but essentially, what we did at at the conference last week is we had 5 different presentations where we kind of showed snapshots of what we're doing that really shows that yes, we can in fact actually put large pieces of code in very specific locations.

Just to elaborate a little bit more, when we're talking about PGI, there's a number of things that we mean actually when we talk about this. I have been working in gene therapy since 1999 so actually this is my 25th year working in gene therapy. Over that time, in my view, the holy grail has really been: if a patient has a broken gene, we can put a healthy copy of that gene in the right location. Now with PGI, this is absolutely something we can do.

When we talk about PGI, there's a few things we mean. So first, the P stands for Programmable. This is not random integration. This is not safe harbor somewhere. The entire thesis behind Tome is that it matters where you put the gene. That's the first thing. Second, all the inserts go the right way. There's some other technologies where you can kind of make a double stranded break and half of them go in this way, half go that way—we're not talking about that. Every single insert is the right direction.

One of the most important things is that this is efficient, and not just in HEK 293 cells in a dish, but in primary human dividing and, more importantly, nondividing cells. This has been a major challenge at Tome that we've spent a lot of time optimizing. I do think this is important, because most of the cells in the body that we care about are actually nondividing. So if the system isn't efficient in relevant cells, that's not PGI.

One of the other things that's important is that we are agnostic to size, and so we can essentially do 1 base up to over 30,000 bases. Now, of course, we'll always be limited by delivery. If you can't get that big piece of DNA to the right cell, then of course, that's a factor, but we've already shown in our labs we can put over 30,000 bases in 1 specific location.

Then the last 2 things really are a property of the fact that our technology is not dependent on making a double-stranded break. What that means is that we can multiplex. Because we're not making breaks, we can actually put multiple pieces of code in multiple sites at the same time. Secondly, while I think the jury's still out on what is the safety risk of a break I think everyone would agree, if you can minimize that risk, I think you probably should. So when we're talking about PGI, that's what we're talking about.

At ASGCT last week, we actually had our first data presentations. Essentially, we had 5 talks that covered a number of different topics, all the way from integrase off-target method discovery, mouse biology—actually, where we uncovered some interesting challenges with the current ways of actually making small RT-based edits in mice. But, I think the most impactful work that we showed was probably our 2 major platforms at Tome. When we have a tool like PGI, we spend a lot of time talking about, "well, what do we do with it? And what don't we do with it?" Essentially, we have 2 different pillars within Tome. One, is really focused on cell therapy, where we've really focused on induced pluripotent stem cells (iPSCs). These are the stem cells that essentially make all the other cells. If there's 1 cell type really to have this technology work in, that's the cell. Essentially, what we show is that from a platform side, we can put large pieces of code in very specific locations, we can multiplex, and we can do this all with high efficiencies. The way that we're using that actually, is we unveiled our invariant natural killer (iNK) cell program for the autoimmune population. We are essentially building a best-in-class iNK cell for that population. This is probably the most highly-edited cell yet. One of the reasons why we're doing this is because with this technology, we can simultaneously do knockouts and large gene insertions. Our lead program actually has 3 knockouts, and then we're putting in over 12,000 bases worth of code. We have dual CARs, we have safety switches, we have allo-evasion edits. Essentially, we're building a cell that's custom-made for the autoimmune population. We're not repurposing oncology assets. We really designed the cell from the ground up for the autoimmune population.

The other pillar of the company is our integrative gene therapies (IGT). This is a completely separate application of the same technology. Here, we're not making really advanced cells. Here, actually, the concept is very simple. A patient has a broken gene. Now we can put a healthy copy of that gene in the right location, in the right cell. What this means is that not only will that gene now be regulated the way that normal gene was, and so it will only be expressed at the right time and the right amount, and not too high, not too low—but it also means that we are essentially agnostic to what mutation that patient has. The way that we're going after this is we're not going after indications where all the patients have the same mutation. There are other technologies that can do that—base editing, prime editing, those are great applications. Unfortunately, for most indications, there isn't just 1 mutation. There are tens, hundreds, if not thousands of separate mutations. Essentially what we're doing is we're making 1 product that will work for most, if not all, of the patients.

Essentially what we showed is how we've been able to improve the efficiency of full PGI in nondividing primary human hepatocytes. These are the cells actually that matter, because for the IGT program, we will be starting with the liver. This is something we talked a lot about. Because our platform is new, we didn't want to start stacking risks, and so we started with an organ where the delivery was essentially derisked. There are other people that have already used lipid nanoparticles and adeno-associated viruses to actually get efficient delivery into the liver. That's where we're starting. We did a lot of work optimizing every single component of our system for that cell type. Now actually, we had data where we showed for at least 7 different genes, we can actually get pretty good levels of PGI. Then for the PAH gene, which is actually the positive gene for our lead indication, phenylketonuria (PKU), we spent a lot of time optimizing. There actually we can get quite robust levels of full PGI in, again, nondividing primary human hepatocytes.

We also showed a bit of data with some of the interest in biology and challenges when we tried moving this technology into mice. But I think really the punchline is that we also unveiled data showing that we've already been able to achieve clinically relevant levels of editing in a nonhuman primate. I think this is a real milestone, certainly for Tome, and maybe for the field. Essentially, we've reached the levels of gene insertion, which is over 10%, which we think is actually curative for patients with PKU. I don't know if you know me well, but I usually have a big gray beard, but I told the team, if you can show me a monkey where, if we got that same level in a human, we'd cure them, then I'd shave my beard. And I shaved it about a month ago or so. It's very exciting.

This transcript has been edited for clarity.

Click here to view more coverage of the 2024 ASGCT Annual Meeting.

REFERENCES
1. Tome Biosciences presented data on its programmable genomic integration technologies at ASGCT. News release. Tome Biosciences, Inc. May 10, 2024. Accessed July 12, 2024. https://tome.bio/news/tome-biosciences-presented-data-on-its-programmable-genomic-integration-technologies-at-asgct/