Reimagining In Vivo Gene Editing Through Base Editing and Targeted Delivery with Gopi Shanker, Ph.D.

Erin, thank you very much for the invitation. It's a pleasure to be on this series with you, and thanks for the opportunity to tell your listeners and viewers about Beam Therapeutics. So at Beam, our vision is actually rather straightforward but ambitious. It's to provide lifelong cures for patients that are suffering from serious diseases. And everything we do at Beam, it's in the service of that vision. And it's driven by our values, which are fearless innovation guided by rigorous and honest research, and our commitment to each other at Beam, but also to our patients. Right? So in honor of that commitment, what we're doing here is building a leading fully integrated platform for precision genetic medicines. And we've assembled that platform with internal capabilities for gene editing, for delivery, and for manufacturing. And we're using this platform to advance a diversified set of programs, some of which are now in the clinic. So we're really excited about it. At the center of it all, of course, is our suite of gene editing technologies. It's anchored by base editing, which is a proprietary technology that's next-gen CRISPR 9. It's designed to enable really efficient single-base changes at precise locations in the genome in a predictable manner without making double-stranded breaks on the DNA, which we think is very important to the mechanism by which base editing works and to its efficiency and predictability.

Yeah. So when Beam started about nine years ago, it was, you know, base editing, we were developing it as a new technology. We weren't necessarily sure what is the best sort of context in which it's going to work. So in fact, right from the get-go, Beam invested in both ex vivo and in vivo approaches in parallel. So we had our BEAM-101 and BEAM-2011 programs for ex vivo, and then BEAM-301 and 302, which are the in vivo liver-targeted programs that you just mentioned. So it wasn't really a single aha moment, I would say, or a technical milestone. It's really, and I think, an acknowledgement of the advantages that come with in vivo delivery. So ex vivo approaches are incredibly effective, and our data with exa-cel for sickle cell disease really demonstrates that, you know, it can be fundamentally curative for patients. But the challenge is that the process can be quite arduous, both for the patient and from a manufacturing point of view for the companies, because you first have to extract the cells from the patient. You then have to edit the cells, manufacture the dose, then you would condition the patient, and then eventually transfuse those edited cells back to the patient for the therapeutic effect to take place. Right? Now, in in vivo editing approaches, they have the ability to deliver that same meaningful benefit to the patients with a one-time IV infusion without the need to take cells out and put cells back in. So it vastly simplifies the process. It removes many of the challenging steps that are associated with ex vivo therapy. I'd be remiss if I didn't note that base editing is equally effective both ex vivo and in vivo, it's equally impactful, but I think it's really the patient journey and then the reduced technical complexity that really give the in vivo therapies that edge.

Yeah. So as I mentioned earlier, base editing is a next-generation editing technology that avoids the double-stranded breaks, and it results in these consistent gene sequence outcomes, durable correction, and potentially less genotoxicity than traditional gene editing approaches. Right? So I think it's worth actually taking a step back and understanding the mechanism by which traditional CRISPR-Cas9 works. So the Cas9 enzyme, it's a nuclease, and it's directed to a specific location in the genome using a guide RNA, and that guide RNA then enables the Cas9 enzyme to reach that particular site in the genome and then cut the DNA by introducing a double-stranded DNA break. And then what happens is the cells have a surveillance mechanism to sense any damage to the DNA, and so a double-stranded break to the DNA is DNA damage. The cells want to prevent genomic instability, cancers, etc. And so they immediately activate this pathway called the comprehensive DNA damage response pathway, or the DDR pathway. It halts cell division checkpoints. It initiates repair mechanisms, manages chromatin changes to fix any damage. And during this process of DNA repair, the cell can, you know, it's trying to basically join the two ends of the broken DNA strand. It can add a few bases. It can remove a few, called insertions or deletions, indels for short. And that's how when that repair process is done, the reading frame of the gene, which is used to then make the protein, gets disrupted. And that's why actually CRISPR-Cas9 is so effective at disrupting gene function, right, to create knockouts. Now there's two things I think that's worth noting as a consequence of this process. One is when you look at the sum total of the editing outcomes of the DNA with the traditional CRISPR-Cas9, it's a heterogeneous mixture of insertions and deletions because the cell is just focused on joining those two broken ends of the DNA and put them back together and repair the DNA. It doesn't particularly care about the sequence, you know, what length is it inserting or deleting and what exact sequence it's putting. So when you look at it, you get a mixture of editing outcomes. The second one is, as you can probably imagine, the process is stressful to the cells because it's DNA damage that it's trying to repair, and so it activates these DNA damage pathways, and so that stress can actually impact cell health.

Now the way base editing works, as I said, is it uses the Cas9 enzyme, but we've removed the nuclease function, right? So it's no longer introducing double-stranded DNA breaks. It's really being used to direct the base editor with the guide RNA to the precise location in the genome. So we still retain that same precision that you get with traditional CRISPR-Cas9, but the Cas9 enzyme is now fused to another enzyme called a deaminase, a DNA deaminase base, that can essentially through biochemistry convert one base into another base. So an A to a G or a C to a G. So we're doing this precise chemistry on the genome. And as a result, what we see is homogeneous editing outcomes, consistent and highly predictable outcomes across the population of cells that are edited. So you don't see this mixture. And the second thing is because we're not introducing any double-stranded breaks to the DNA, the process is gentler on the cells. The stress pathways, the DNA damage pathways that I just alluded to, they're not activated. This has been demonstrated now in literature with data. And so there's higher chances for these edited cells to regain their functional status as a result of that therapeutic edit and the lack of the stress from these DNA damage pathways. So that's why we think it gives us an advantage both from an efficacy, efficiency, predictability point of view with consistent outcomes, as well as from a cell health point, reducing the stress to the cells.