I think we're ready to go, folks. Thanks very much. I'm Josh Schimmer from the Cantor Fitzgerald Biotech Research Team. Very pleased to introduce from Boundless Bio, we have Zachary Hornby, Chief Executive Officer. Zach, welcome. Thanks for joining. Maybe give us a quick snapshot of Boundless, your area of focus, and some of the milestones we should be looking for from the company.
Great. Thanks, Josh, for hosting. Thank you, Cantor. Good to be here. Boundless Bio is a public clinical-stage precision oncology company that is trying to deliver new therapeutics for a high unmet need population of cancer patients, which is those with oncogene amplified cancers, and this is approximately 25% of all cancers. It is a very large population, and importantly, patients with oncogene amplifications generally do not benefit from targeted therapies, immunotherapies, or other standards of care, and consequently, they have worse survival, so very high unmet medical need. Our company, Boundless, was founded based on some scientific observations of the root cause of oncogene amplifications in cancer. Specifically, there's something called extrachromosomal DNA or ecDNA. These are cancer-specific circular units of DNA. They look like plasmids that reside within the nuclei of cancer cells but are separate from chromosomes, and they independently replicate and transcribe.
They give rise to a lot of oncogenic protein, and they give rise to a lot of tumor heterogeneity that allows tumors to become resistant and to migrate or evolve away from targeted therapies and other pressures. In terms of where we are as a company, we have built a platform to identify vulnerabilities or synthetic lethalities in these cancer cells that rely on ecDNA, and then to drug the targets that are these synthetic lethalities. We currently have three active drug discovery development programs, all oral small molecules. Two of those programs, BBI-355 and BBI-825, both of which were internally discovered, wholly owned, are in the clinic. They're both in first-in-human phase I and II studies in different oncogene amplified cancer settings, and we expect both to have meaningful readouts next year, two thousand and twenty-five.
All right, excellent. Is ecDNA ever normal? Do you find it in normal cells? Is there, like, some kind of threshold effect beyond which it can be oncogenic?
Right. ecDNA is not normal in normal or healthy human cells. It is a cancer-specific phenomenon, and it generally for the conditions for it to arise, relies upon a p53 loss of function or knockdown. ecDNA can be found in some other species, like yeast. In fact, it is a mechanism of resistance and survival in yeast.
How do you find it and measure it?
Yeah, great question. So historically, the gold standard for finding or seeing ecDNA was literally visualization through things like FISH and DAPI staining, but that's very inefficient. Now, with the advent of genomic technologies, it can be detected in sequencing data. Up until recently, it was detected only in whole genome sequencing through a kind of academic tool called AmpliconArchitect . But one of Boundless's strategic endeavors was to try to come up with a diagnostic to detect ecDNA using standard of care, meaning sequencing panels, think like Foundation Medicine or Caris. And so indeed, what we have created within Boundless is a diagnostic detection device, we call it ECHO, that relies on standard sequencing data to be able to detect these circular units and report them out.
In fact, we just published the validation data of this ECHO assay this past weekend at the ESMO conference in Barcelona.
How do you think about leveraging your understanding of ecDNA to come up with targeted therapeutics when it can still be challenging having a targeted therapeutic around those constructs?
Yeah, and this really gets to the essence of what are ecDNA, how do they work, why does certain standards of care not work for them, and therefore, what you must do differently? So the ecDNA, these circular units, by the way, they're about one to five megabase pairs in length. This means they can encode full-length genes, even multiple genes, regulatory regions, et cetera. So they're completely active genetic units. They can encode common oncodrivers like EGFR, FGFR, MDM2, MYC, KRAS. These are all commonly encoded on ecDNA. And so, for instance, if EGFR is encoded on ecDNA, you might just think, well, this is another mechanism for EGFR activation. Surely, you should just drug it with an EGFR inhibitor.
But herein lies the problem: If a cancer cell is amplifying EGFR, and you drug it with an EGFR inhibitor, what that cancer cell will do is it will leverage the ecDNA in one of two ways. It will either make even more copies of the EGFR, so many copies that it outcompetes the kinetics of the drug at its maximum tolerated dose, so the ecDNA can simply overwhelm a drug, or perhaps even more sinister, the ecDNA can switch to a new gene, so instead of encoding EGFR, which is under therapeutic pressure, they can switch to now encoding MET, and so now the drug, the EGFR inhibitor, is pharmacologically irrelevant because it's now MET that it's being leveraged to grow the cancer.
Our insight as a company is that targeted therapies alone are not the right therapeutic approach when the cells have this rapid ability to evolve their oncogenic driver. Instead, we need to somehow disallow the cancer cell from invoking ecDNA at all... We need to somehow throw a wrench in the machinery for the ecDNA to either form or function properly, and that is what each of our internally discovered targets does.
So 355 is such an interesting glimpse into how one may approach targeting tumors driven by ecDNA. So maybe give us the overview of that mechanism and how that mechanism aligns with-
Yeah
with the kind of underlying biology.
355 is our first clinical program. It's an oral, highly potent, highly selective CHEK1 inhibitor. CHEK1 as a target has been known for decades and has been pursued by virtually every large pharma, but unsuccessfully up until now. Interestingly, CHEK1 inhibitors that have been taken into the clinic have demonstrated prolonged single agent activity, regressions, even complete responses. Historically, the pharma companies that developed CHEK1 inhibitors did not have a biomarker. They did not have a way to predict which patients would respond, and therefore, they were never taken through to commercialization. One of our insights based on our biology platform is that when cancer cells rely on ecDNA, and they're pumping out a lot of oncogene-amplified genes and ultimately proteins, that reliance on ecDNA causes a lot of replication stress. Replication stress is a relatively well-known phenomenon in cancer.
It is objectively measurable. When cancer cells undergo replication stress, if there's too much, it can ultimately turn into mitotic catastrophe, and the cells will die. However, the cancer cells, you know, in their quest to constantly survive, they self-regulate. They mitigate their own replication stress by invoking the DNA damage response pathway, and CHEK1 is the master regulator of the DNA damage response pathway. So in other words, if a cancer cell has replication stress, it upregulates CHEK1 to self-regulate. It kind of pauses, resolves itself, and then moves on. And so what we have observed is that these cancer cells with ecDNA have high replication stress, exquisite sensitivity or reliance upon CHEK1, and therefore exquisitely susceptible to inhibiting CHEK1 and disallowing its function.
What exactly is replication stress, and how do you measure it?
Yeah. Replication stress can arise due to various things, but in the case of ecDNA, this gets a little bit scientific, so I'll try to keep it relatively high level. But, generally, cells, their DNA is either supposed to be transcribing into RNA or replicating during mitosis, but really, both are not supposed to happen at the same time. It's kind of one or the other. Both these circular units of ecDNA that are highly accessible to the transcriptional machinery, they're basically being constitutively transcribed, so that when they go into mitosis, you do get both transcription and replication occurring at the same time, and the machinery actually collides. It's called a transcription replication collision, or TRC, and that's what causes the replication stress.
It can be measured because you get these long strands of single-stranded DNA, which I think folks know, that's kind of a susceptibility for a cell. So the cancer cells decorate that long strand of DNA with something called phospho-RPA that protects the strand of single strand of DNA. So we can measure the replication stress by measuring phospho-RPA, and that is an objective, quantifiable measure.
When we hear DNA damage response targeting, I think we often think of PARP or PARG. What makes CHEK1 a more suitable target in this setting?
It really comes down to CHEK1 is the appropriate target for this population, those with ecDNA. And in fact, Josh makes a good point, which is once we started as a company, noticing that some DDR targets might be active in this setting, we actually tested other things like PARP and PARG, kinda all the usual suspects you might think of, CHEK2, ATR, WEE1, et cetera. Empirically, we found that certain of these targets were much more relevant, much more sensitive. So it, it's not just a total class effect that any DDR agent will work in this setting, but for some reason, CHEK1 is the one that was most sensitive for ecDNA cells.
So maybe we can review the experience with prexisertib, what we've learned from that, and what you can learn from that-
Yeah
-to inform your own program.
Yeah, just to get everyone up to speed, prexisertib is a potent CHEK1 inhibitor, originally discovered by Eli Lilly. This is one of the agents that was taken into the clinic, did demonstrate some pretty profound clinical response, but in a 1,000-patient phase 2 study, I wanna say the response rate was about 11% and a fair amount of neutropenia. Lilly decided to no longer advance it. A new company in the last couple of years, another public company called Acrivon, had a somewhat similar philosophy as us, and it's not to do with ecDNA, but like us, they thought that CHEK1 could be a druggable target if you had a biomarker to predict who would respond.
So this other company, Acrivon, in-licensed prexisertib, they've renamed it ACR368, and they just had data this past weekend at the ESMO conference, where using their biomarker and in endometrial cancer, which by the way, is a high replication stress tumor, they were able to show in a small data set, a greater than 50% response rate in patients with endometrial cancer that are biomarker positive. So I think it's promising. I think it helps validate that both companies have a similar approach, meaning we believe CHEK1 is a viable target. We believe it needs a biomarker to be developed successfully. Two key differences between them and us, their drug is an IV agent administered once every other week. Ours is an oral agent administered once every other day, and then their biomarker, they haven't publicly disclosed the exact nature.
I think it's three different biomarkers, but it's measured through a digital IHC platform, whereas as I mentioned, for us, our biomarker is simply measured using NGS data.
Is there any reason to think that you're both honing in on the same patients, susceptible patients, despite using different biomarkers entirely?
I suspect that we are honing in to the same ballpark. I think of it maybe as like a Venn diagram, probably not concentric circles. We're probably not completely overlapping with them, but I suspect we're getting into an adjacency or some overlapping patients, where some of their patient-biomarker positive patients would be biomarker positive for us and vice versa, but not all. And then ultimately, you know, clinically, both companies will have to demonstrate how well their biomarker selects for activity.
So I guess some of the early activity is being seen in the gynecologic malignancies. I guess, and you indicated that endometrial cancer is a setting where there's high replication stress. Can we infer from that, that there are also high rates and copy numbers of ecDNA in gynecologic malignancies? And is there any reason why it would be different here than anywhere else?
Yeah. And so, yes, certain of the gynecological malignancies are known for having high replication stress. Ovarian cancer, in particular, is one of the other settings where they've demonstrated some initial signs of activity with very small numbers. Ovarian cancers are one of the most highly amplified tumors, often CCNE1, MYC or KRAS. So you might imagine both companies being in that space due to intrinsic replication stress. However, I also want to emphasize one additional way that we're pursuing our biology, which is something different than what this other company is doing, is that we, Boundless, are looking for cancers with actionable oncodrivers, where the targeted therapies have been tried in the past but failed as a single agent. So let me give you two examples.
EGFR amplifications are very common throughout cancer, and FGFR amplifications are common throughout cancer, and both of these can be found in things like gastric cancer, esophageal cancer, breast cancer, head and neck, et cetera. Historically, other companies have run studies of potent EGFR inhibitors or potent FGFR inhibitors in these amplified patients, and those studies have collectively delivered about a 15% response rate with a couple of months of durability, insufficient to warrant approval, and that's one of the reasons why there are no drugs available for these patients. There is no standard of care.
If we rewind back to what I was talking about earlier, about how ecDNA functions, our thesis and our biological observation is that the reason these single-agent targeted therapies failed in this setting is that when you put the targeted therapy pressure on the amplifications, the cells rely on ecDNA to either make more amplified gene or a different amplified gene, and they evolve away from the pressure. What we are doing in the clinic with both of our ongoing studies is we're actually giving combination of our proprietary agents, BBI-355, and we'll talk about our second program, with the targeted therapy. Let me give you an example.
If a patient has an FGFR-amplified solid tumor, they're gonna get a potent pan FGFR inhibitor, futibatinib, plus our BBI-355 program, with the premise being that you put pressure on the tumor's initial preferred oncogenic driver, but you know that it's gonna become resistant with ecDNA, so you also put pressure on the ecDNA with our checkpoint inhibitor, and the thought being that you disallow the cancer any escape route, and that combination might have synergistic activity. That is what we've observed preclinically, and that's now what we're aiming to demonstrate clinically.
Yeah. You had a poster at ESMO around the assay that you're using. Maybe you can share a little bit about what you presented.
Yeah. So the assay I mentioned earlier, that is called ECHO, that uses standard sequencing data as an input. So if you imagine, if a patient's tumor is sequenced by, like, Foundation Medicine or Tempus, they usually read out 300 to 400 genes that get sequenced, and the output is in what's called, like, a BAM file. So that, that's just how the data come out. So our assay, which we co-developed with a diagnostic company called SOPHiA GENETICS, it ingests that BAM file as its input, and it recalculates the data in a unique way that our scientists created, a unique algorithm. And so it can then use those data to determine was there a circular unit of DNA present? 'Cause normally, chromosomal DNA is linear, but this ecDNA is circular.
So if, in fact, we determine that a circle is present, then we know it's ecDNA positive, and we can also report out which specific gene or genes were amplified on the ecDNA and how many copies. So that's our ECHO output. Is it ecDNA positive or negative? Which gene is amplified? How many copies? What was presented at ESMO was all of the work that went into validating the performance of that assay using blinded, human tumor specimens, and then orthogonally analyzing those specimens with things like FISH, which I mentioned is the historical gold standard, as well as the whole genome sequencing tool. That really is not clinically viable, but is useful for research purposes.
But what we were able to show is that our new assay has about 90% accuracy, including 80% sensitivity and more than 90% specificity in correctly determining whether a tumor sample has ecDNA or not.
... So you have a number of preclinical models showing the benefit of 355 in the settings of high ecDNA. Do you have the corollary showing that it's not efficacious where there is no extrachromosomal DNA, or are there exceptions where it can still work even though-
Yeah.
ecDNA is not present?
Right. So 355, we've demonstrated preclinically works best, in settings where there's ecDNA. However, as I mentioned before, there are other causes of replication stress. ecDNA is not the only one, so we have demonstrated that 355 can be active in other replication stress settings, including just normal oncogene amplifications. Even with their chromosomal in nature, they do still afford some replication stress, and so, 355 has demonstrated activity in that setting. But outside of that, it does not just necessarily demonstrate activity in all tumors or all tumor models. So we really do think its highest activity is in these amplified settings.
Maybe can you review the design of the phase 1/2 program? And you recently gave a timeline update, so what was going on there?
Yeah. So the phase 1/2 first-in-human study for 355 is called the POTENTIATE Study. It is a three-part phase 1/2 study. The Part 1 is a single-agent dose escalation to determine the safety, tolerability, maximum tolerated dose of the single agent. Part 2 is dose escalation of 355 with the various combination therapies, and there's actually three modules to Part 2, so we're going into EGFR-amplified patients. These are wild-type EGFR amplifications. They're not T790M or other EGFR mutants. Therefore, we're combining with a potent wild-type EGFR inhibitor, which is erlotinib. Module two is patients with FGFR amplifications. We're using a pan-FGFR inhibitor, futibatinib, which is supplied to us by Taiho, and then Module three is patients with CDK4 or CDK6 amplifications. There, we are combining with the drug abemaciclib, which has been supplied to us by Eli Lilly.
And so Part 2 is determining the optimal combination of 355 with these various agents. Part 2 is currently ongoing for both the EGFR and FGFR arm, and then once we have the optimal combination doses, we will move into Part 3, which is a dose expansion using Simon two-stage design to really try to seek efficacy signal and see whether there's something here worthy of pursuit. And with respect to timelines, what we've shared is that we expect to have meaningful efficacy data to determine whether there's a signal there by the second half of next year.
Will you be enriching for patients with high ecDNA? And for the monotherapy portion, how many patients, and what specifically are you looking to show there?
Yeah, that's an important question, so for the combination arms, Part 2 and Part 3 can actually enroll patients with any amplification, including locally tested, of the relevant genes like EGFR, FGFR, CDK4/6, so a patient can be determined, let's say, by a Guardant assay of having a high amplification. They can enroll into the study, but we then test them with ECHO to determine are they ecDNA positive or ecDNA negative, and depending on the answer, we're gonna separate them into two different efficacy analyses, so that'll be part of testing this hypothesis of whether the biomarker truly does matter to response rate or not.
Mm-hmm.
That's something we will assess objectively based on that binning. For Part 1, which is single agent, where we're going to expand into these gynecological malignancies we talked about, like ovarian, endometrial, we are not requiring any ecDNA status for that. It really is just the presence of an amplification, and as mentioned before, the common amplifications in these settings would be CCNE1, MYC, or KRAS. Two out of those three are not even directly druggable, hence there is no combination approach there.
Why not select by ecDNA for the monotherapy group?
Partly because of just the historical clinical data, and even as I mentioned what Acrivon was doing, that there appears to be activity of CHEK1 inhibitors, probably just more linked to replication stress writ large, as opposed to an ecDNA specificity.
Maybe we can turn to, 825 , and, describe what an RNR inhibitor is.
Yeah
... and what that has to do with ecDNA.
So BBI-825 is another internally discovered, wholly owned compound. This is a highly selective oral ribonucleotide reductase inhibitor, RNR. A little of the biology, which is kinda interesting, is that all cells require dNTPs or nucleotides to form DNA and then RNA. There are two mechanisms by which cells can create dNTPs. One mechanism is called the salvage pathway, and it's kinda what it sounds like. They're basically recycling dNTPs within the cell for new DNA synthesis. This is the more energy-efficient pathway for creating dNTPs, and it's kind of the preferred or default pathway. The second pathway is called de novo synthesis, where dNTPs are made or are, like, metabolically synthesized anew. This is less energetically efficient, so it's not the preferred pathway.
But cancer cells, which are replicating and transcribing so quickly, they rely on this second pathway, the de novo pathway, because the salvage pathway alone is insufficient for their dNTP needs. We have found that RNR is the rate-limiting enzyme for the de novo pathway. So if you inhibit RNR, you disallow the use of the de novo pathway. That's not a problem for the healthy cells, 'cause they don't really need the de novo pathway. They're fine with the salvage pathway, but it is a problem for cancer cells who do need this de novo pathway, and so that is why RNR is thought to be a very interesting target, and it turns out, particularly ecDNA, again, back to the high copy numbers, high transcription, they have an even higher need for this dNTPs and for this pathway, so they are exquisitely sensitive to RNR inhibition.
And then finally, cancers that are MAP kinase activated, like KRAS or BRAF, also have a high dependency on RNR, and so that's a particular setting that we're very interested in for this program.
I guess you can target on some of the MAP kinase or focus on some of the MAP kinase pathway patients, but as we think about the ecDNA patient targeting, is there gonna be significant overlap with the CHEK1 inhibitor?
Right.
And how do you think about balancing effort and recruitment?
That was something we worried about early on. When we came up with the whole premise of the company and were discovering targets, we were wondering, are they ultimately all just gonna cannibalize each other? Are they all gonna work in the same setting, and at some point, you just kinda don't need more targets, not more drugs? But that was something we didn't know, and we had to assess empirically with different tumor models representing different tumor types, different oncogene amplifications, even different combination partners. It turns out that our different targets each seem to work differently and in different settings, and we couldn't have a priori predicted, like, which ones are gonna necessarily work where. But, empirically, they just... They have different activities.
For instance, this RNR program, as I mentioned, seems to work particularly well in the MAP kinase-activated tumors, and on top of that, and this is where it's different from 355, is most of these tumors start with a point mutation as their initial driver. So, like, right now, everyone's highly familiar with KRAS G12C 'cause it's a very active area, and we're getting better and better drugs from sotorasib, Amgen, to adagrasib, Mirati, now divarasib from Roche, and perhaps better ones are still coming. But what we're finding is that the better the inhibitors are, the more clinical resistance we're observing that is due to amplification. So when the inhibitors are kinda lousy, the way the tumor becomes resistant is they just do a point mutation that the inhibitor can't overcome.
But the more potent the inhibitors are, the tumor has to resort to something else, and as we've been talking throughout this presentation, amplifications are one of tumor's preferred resistance pathways. So these better and better KRAS inhibitors are leading to more clinical resistance with amplification, and once again, that's where our biology comes in. So our study of BBI-825 in the clinic, it's called the STARMAP study, we're specifically giving our agent in combination with KRAS or BRAF inhibitors to either prevent resistance from occurring or treating it once it's already manifest in the patient.
When, do you expect to report data, and how are you gonna be able to discern the contribution of,
Right
... of the product on top of that-
Yeah
-agent?
So we're currently in the part one single-agent dose escalation of the STARMAP study. We're hoping to get into the combos by about end of this year, and then, you know, assuming we're at the right exposures, then I think there's an opportunity for us to have initial clinical data second half of next year. That is, of course, contingent on some of the factors I just mentioned. And sorry, what was the second part of the question, Josh?
Discerning the signal from the noise.
Oh, right. That's an important question because we're giving with multiple agents. The easiest way to discern the signal from the noise is if we treat patients who have become relapse refractory and then show a secondary response, and we think that that will be the majority. Probably 90-plus% of the patients enrolled will basically have received a standard of care... By the way, the study's in colorectal cancer initially, but we intend to go pan-tumor. So the standard of care in colorectal is a combination with an EGFR inhibitor, cetuximab. So for instance, if they have a KRAS G12C mutation, they'll get adagrasib plus cetuximab.
About 50% of those patients will be predicted to develop resistance with an amplification, at which point we will layer on our agent, 825, and then hope to show a secondary response, and then that would clearly be discerning the contribution of our component.
Maybe in a minute or less, a review of the kinesin inhibitor and what that has to do with ecDNA.
Yeah, and I'm glad we spent... We're keeping one minute for it-
Mm-hmm.
Because the kinesin is our third program. It's a very exciting novel target discovered by Boundless. To our knowledge, no other company is or ever has worked on this. Kinesins are molecular machines that help things move around the cell, and what we have found is that there is a non-essential kinesin, so cells with this knocked out are viable, but it is essential for proper localization of ecDNA during mitosis or cell division. And so when we knock out or pharmacologically inhibit this kinesin, the ecDNA, they inappropriately aggregate, and that actually is cytotoxic to the cells. It kills the cancer cells.
All right. Excellent. I think we're out of time. Zach, thanks so much for giving us the overview of Boundless Bio and your work on ecDNA. Thanks, everyone.
Thanks, Josh. Thanks, everybody, for your attention.