Latest / Zero Shot Podcast DEMO / Advancements in Liquid Biopsies for Pancreatic Cancer V2
Transcript
- 0:00Ken Bloom: In this webinar, we explore advanced liquid biopsies and their critical role in monitoring clonal evolution in pancreatic cancer. This discussion highlights the limitations of traditional biopsies and introduces innovative technologies that promise to enhance patient care.
- 0:20Thanks, everybody, for joining OneCell's webinar.
- 0:25The topic of today's conversation is advanced liquid
- 0:33biopsies.
- 0:34And in particular, we'll be discussing not just looking at circulating tumor DNA, but also the emerging
- 0:42field of single -cell -based liquid biopsies, which formerly a lot of people referred to as circulating tumor cells, also still
- 0:50referred to as circulating tumor cells.
- 0:51But we'll also describe what is new about these sort of cell -based liquid biopsies, where we can do molecular
- 0:59profiling, both in the cell level as well as at the DNA level.
- 1:05Dr. Rizal Kurzok: So the topic is multisource genomics to monitor clonal evolution for pancreatic cancer.
- 1:11Dr.
- 1:12Rizal Kurzok from Medical College of Wisconsin will provide an update for the talk.
- 1:16Ken Bloom: This meeting is being recorded.
- 1:18We will have two formats for Q &A.
- 1:23As the meeting progresses, please feel free to put your questions in the chat, in the chat box,
- 1:31and then we'll accommodate as many of the questions.
- 1:35And towards the end, we'll have some time for some live questions as well.
- 1:39So the way the agenda is going to work is I'll spend a couple of minutes on just sort of setting the stage, which I'm doing right now.
- 1:46Traditional tissue biopsies are limited by tumor heterogeneity. The OncoInsights platform captures and analyzes circulating tumor cells (CTCs) effectively.
- 2:00Dr. Rizal Kurzok: I'll turn it over to Ken Bloom.
- 2:03Ken is OneCell's advisor.
- 2:06He's a strategic advisor to OneCell, also leads our CAPCLEAR certified laboratory in the San Francisco Bay Area.
- 2:15Ken Bloom: He will be providing an overview of OneCell as well as our OncoInsights technology.
- 2:21Dr. Rizal Kurzok: Right after that, before I turn it over to Rizal, I will ask all of the participants to go into the chat box.
- 2:30And there's a link there, which you can click.
- 2:33And it'll take you literally not more than 10 seconds to answer questions around what topics are relevant to you guys.
- 2:40That'll be important for us to understand.
- 2:42And we'll share some of that either towards the end or as a follow -up.
- 2:49Ken Bloom: Our labs hold the highest level of clinical accreditation, CLIA and CAP in the U .S., NAVAL and CAP in India.
- 2:56And these aren't just logos on the slide.
- 2:59They mean that the data coming out of our labs meets the standards required for clinical decision -making.
- 3:08CTCs provide a more comprehensive view of tumor evolution than CT DNA alone.
- 3:14Dr. Rizal Kurzok: But more importantly, as antibody drug conjugate therapies have emerged, CT -DNA doesn't give us any useful information
- 3:22about protein expression or localization.
- 3:25Ken Bloom: The topic of today's conversation is advanced liquid biopsies. The topic is multisource genomics to monitor clonal evolution for pancreatic cancer.
- 3:37Dr. Rizal Kurzok: This means we're all making patient selection and endpoint decisions based on incomplete, often outdated information.
- 3:44But that's a solvable problem, and it's exactly what OneCells platform addresses.
- 3:49Our solution is called OncoInsights, our proprietary platform to capture and comprehensively analyze circulating
- 3:57tumor cells.
- 3:58Here's a quick refresher.
- 4:00When a tumor grows, it sheds cells into the bloodstream.
- 4:03These are circulating tumor cells, actual cancer cells floating in a patient's blood draw.
- 4:09The problem historically has been catching them.
- 4:12They are incredibly rare, maybe dozens or less, among billions of normal cells.
- 4:16The trick, though, is not just to capture them, but to capture them in a way that's suitable for downstream analysis.
- 4:28Ken Bloom: The OncoInsights panel covers three biological layers simultaneously from the same blood draw.
- 4:35Dr. Rizal Kurzok: OncoInsights solves these limitations with a combination of multi -marker affinity capture and a cleavable linker allowing capture of
- 4:43live CTCs with no cell damage.
- 4:46Instead of a single hook, we use customized capture beads coated with multiple antibodies targeted to a specific cancer
- 4:53type.
- 4:56Ken Bloom: For most cancers, a combination of Epcam and Transferrin works effectively, but the beads can be customized to optimize capture.
- 5:03For example, many renal cell cancers don't express Epcam at high levels, expressions quite low.
- 5:10So adding CD70 to the beads dramatically increases the CT positivity rate.
- 5:15Critically, this allows for the capture of the full diversity of tumor cells, not just the most common ones.
- 5:21Once the cells are captured, they are released intact using a cleavable linker system.
- 5:27No bead contamination, no cell damage.
- 5:30So the cells are ready for multi -omic analysis.
- 5:33So this is where things get really exciting because of what you can measure from these capture CTCs.
- 5:39The OncoInsights panel covers three biological layers simultaneously from the same blood draw.
- 5:46First, DNA.
- 5:471080 gene panel covering point mutations, insertions, deletions, gene fusions, copy number variations, and
- 5:55chromosomal rearrangements.
- 5:56It also gives you tumor mutational burden, microsatellite instability status, and homologous
- 6:04recombination deficiency status.
- 6:06All of the genomic biomarkers that predict response to immunotherapy, PARP inhibitors, and targeted agents.
- 6:17Dr. Rizal Kurzok: Our mission is straightforward but ambitious.
- 6:20We're going to be able to do this.
- 6:20We're going to be able to do this.
- 6:20Democratize precision oncology.
- 6:22Make it actionable, accessible, affordable for every cancer patient everywhere.
- 6:28We are working toward impacting the lives of one million cancer patients through breakthroughs in science and AI.
- 6:35For those of you in pharma, you can think of OneCell as a potential partner for clinical trial design, patient selection, biomarker
- 6:43discovery, and drug development.
- 6:45Everything that you're about to hear is built on that infrastructure.
- 6:48So now let's talk about the problem, where we've been and where we're going.
- 6:52Ken Bloom: I was trained 40 years ago with the idea that tissue biopsy is the gold standard.
- 6:58And over those years, we've been able to extract multiomic data from
- 7:05However, as biopsies become smaller and smaller, our analysis becomes less reliable because of tumor heterogeneity.
- 7:13A five -micron section from a one -centimeter tumor represents only a fraction of a percent of that tumor.
- 7:19So to put it in a little bit easier terms, that's like trying to understand the entire plot of war and peace by reading one
- 7:27sentence of the book.
- 7:28You get a snapshot, a static picture.
- 7:31And while that provides actionable data, it creates a gap in our ability to monitor cancer's evolution.
- 7:38And this has direct consequences for patient management.
- 7:45Our solution is called OncoInsights, our proprietary platform to capture and comprehensively analyze circulating tumor cells.
- 7:54Dr. Rizal Kurzok: Second is protein expression.
- 7:56This is currently measured by immunofluorescence on individual cells.
- 8:00You can directly quantify the proteins a drug is targeting, such as HER2, TROP2, clodin -18, nectin -4, etc.
- 8:09Ken Bloom: If you're developing an antibody drug conjugate, for example, this tells you whether the target is actually present at the protein level
- 8:16on cells circulating right now during treatment.
- 8:20Dr. Rizal Kurzok: Third is RNA, or whole transcriptome profiling.
- 8:23That's about 16 ,000 markers.
- 8:26This is your window into gene expression, what pathways are active, what resistance mechanisms might be turning on, and what's changing
- 8:33over time.
- 8:34Ken Bloom: For drug programs, this isn't just biomarker discovery.
- 8:38This is real -time pharmacodynamic monitoring.
- 8:41You can track whether your drug is hitting its target, whether resistance is emerging, and which patients are likely to respond.
- 8:48Any new technology lives or dies on its data, so let's look at the numbers.
- 8:53Across more than 2 ,000 patient samples spanning lung, breast, pancreatic, colorectal,
- 9:03Dr. Rizal Kurzok: radiologic imaging, pathology images, and real -world evidence data sets.
- 9:08It uses AI and machine learning to identify patient populations most likely to respond to a given therapy, flag resistance
- 9:16markers as they emerge, and help you understand mechanisms of action in a way that bulk tumor sequencing simply can't provide.
- 9:25It also adds the missing temporal layer to AI.
- 9:29It allows AI to begin to understand how tumor cells are adapting and what to do about it.
- 9:35Imagine being able to enrich your clinical trials for responders before the trial even starts, based on real -time
- 9:43CTC protein expression in genomics, rather than on archival tissue.
- 9:48That's the promise of iCORM.
- 9:50You get smarter enrollment, more informative biomarker endpoints, and ultimately, a cheaper path to approval.
- 9:57Ken Bloom: With that as background, I'll now turn the slides over to Dr.
- 10:01Curtis Rock, who's going to present her exciting data on the clonal evolution in pancreatic cancer.
- 10:06But first, there will be a few polling questions.
- 10:09So, Arshad, I guess that goes to you next.
- 10:11Dr. Rizal Kurzok: Yes, thanks.
- 10:12Thanks, Ken.
- 10:13Appreciate that.
- 10:15If I can ask all the participants, if you can go to the top of the chat room, there's a link there
- 10:22from, it's called forms .gle.
- 10:26If you guys just click that link, I promise this won't take more than 10 seconds.
- 10:29It's going to ask some basic questions on what are the types of areas that are important to you, and that's it.
- 10:35Just click on that, type in your name so that we know who responded to what, and then we can move on to the next part of the agenda.
- 10:43So, over to Razelle.
- 10:45Ken Bloom: So, a pleasure to work on this project and with this
- 10:53really interesting technology.
- 10:59Dr. Rizal Kurzok: liver, head and neck, prostate, and gallbladder cancers, the overall CTC positivity rate, or our ability to
- 11:07detect CTCs, was 83 % for stages stage 2 through stage 4 patients, but metastatic patients had
- 11:14approached 100%.
- 11:16Let me put that in context.
- 11:18Our first generation of CTC capture technology yielded a mean of about 5 CTCs per sample, while our current
- 11:26platform yields a mean of about 21 CTCs per sample.
- 11:30That's a four -fold improvement, and more cells means more material for downstream analysis, more genomics, more protein
- 11:37profiling, more confidence.
- 11:44Ken Bloom: Pancreatic ductal adenocarcinoma progression involves stepwise accumulation of key driver mutations,
- 11:51which are mainly known to be KRAS, the cyclin system,
- 11:59CDKN2AB loss, and P53.
- 12:03And tumor evolution also includes rapid genomic restructuring characterized by
- 12:11copy number variations and large chromosomal rearrangements following
- 12:17polyploidization.
- 12:20So, this is a difficult cancer.
- 12:24And the reason, one of the reasons it's difficult is because of the great heterogeneity between patients
- 12:32and even within patients with time.
- 12:35And that's really difficult to capture if what you're doing is a baseline tissue biopsy.
- 12:43Um, so, um,
- 12:49An 83 % to 100 % positivity rate across solid tumors means that the vast majority of your enrolled patients can be monitored
- 12:56longitudinally with this platform, and that's a game -changer for adaptive trial design.
- 13:02One more important point before we move on, and this is particularly relevant for CNS cancers and thoracic malignancies.
- 13:09The technology isn't just limited to blood.
- 13:11At one cell, we've demonstrated CTC capture, or tumor cell capture, from cerebral spinal fluid
- 13:19and pleural fluid.
- 13:20In CNS tumors like glioblastoma and medulloblastoma, where a blood draw tells you almost nothing about what's happening in the brain,
- 13:28CSF -based CTC analysis opens a completely new window.
- 13:32This is significant for clinical trials and CNS malignancies, where biomarker development has lagged far behind other tumors.
- 13:40Now, generating all this data is only valuable if you can act on it, and that's what the iCORM platform is designed to do.
- 13:52there are a lot of limitations to bulk sequencing.
- 13:57Um, and, uh, some of them are illustrated here.
- 14:02Uh, so, we use bulk sequencing to understand, um, cancer.
- 14:08But the problem is that it doesn't really show us what happens with time, what happens with
- 14:16successive, um, mutational events.
- 14:20And, um, it cannot, um, extinguish, it cannot distinguish what is
- 14:27happening in different clones of cells.
- 14:30So, if we see, do single cell sequencing, we can see, are there co -occurring versus
- 14:38mutually exclusive alterations in different cells?
- 14:43Might this explain, um, mixed responses to drugs, uh, like PARP inhibitors, KRAS inhibitors,
- 14:50and immunotherapy.
- 14:53And so, single cell DNA sequencing is really required to resolve the clonal
- 15:00architecture of pancreatic ductal adenocarcinoma from early invasion through systemic,
- 15:08uh, dissemination and to identify molecular vulnerabilities targetable with precision
- 15:15therapies as the, as the disease evolves.
- 15:19Uh, so, this is a study that we initiated, um, and, uh, the purpose of
- 15:27the study was to isolate single circulating tumor cells from pancreatic cancer patients prior to treatment
- 15:34and perform genomic profile to characterize cellular level genomic heterogeneity, and also to
- 15:42follow these patients during treatment.
- 15:45And, uh, uh, this, uh, study is led by Dr.
- 15:49Mondana Kamgar and myself
- 15:54iCORM is one cell's integrated precision oncology consult.
- 15:59Think of it as the intelligence layer that sits on top of the laboratory data.
- 16:03It has two primary interfaces.
- 16:06iDiscover for translational research and clinical trial support, and iCare for the treating oncologist.
- 16:12For those of you in pharma, iDiscover is the critical piece.
- 16:17It integrates multiomic data from CTCs and CT DNA,
- 16:25at MCW and Dr.
- 16:27Kremolini at, uh, University of Pisa.
- 16:31And, uh, we've collected quite a few samples and I think, um, I'm happy to share with you some of the
- 16:38insights, uh, from these samples.
- 16:41Next, uh, slide, please.
- 16:44So, all together, uh, we now have 26 patients, 63 total samples,
- 16:52um, and, uh, five time points tracked.
- 16:56And remembering that we're looking, um, both at CTCs and CT DNA.
- 17:03And we're also continuing to expand, uh, this, uh, project.
- 17:08Uh, but I'm going to show you, I think we have some fascinating insights, um, at this, uh, time.
- 17:15And, um, I want to share those with you.
- 17:18So, uh, first, um, uh, this slide, I think really illustrates, uh, some of the
- 17:25insights, uh, from the study.
- 17:27Um, so if we look at, uh, patients that have CT DNA only
- 17:34versus, uh, CTC DNA only, we're getting a lot more alterations
- 17:42from the CTCs, which you can see on the right, than we are getting from the CT DNA.
- 17:49And this in the middle are some of the shared alterations, um, that you see.
- 17:55So there's a lot of common things, but themes.
- 17:59But in addition, I think that both the CT DNA and the CTCs bring their
- 18:06own information.
- 18:08And I think you can see how rich the information is that is coming, um, from the CTCs.
- 18:15Um, so this, uh, slide shows, uh, the longitudinal, uh, CTC,
- 18:23uh,
- 18:25DNA and, uh, CT DNA longitudinal mutational landscape.
- 18:31And I'm going to go into, um, more detail in a moment, but if you go to the
- 18:39right side, this is patient by patient.
- 18:42And if you go to the right side of the slide, you can see, um, on the, um, Y axis on the
- 18:50right side, uh, the red is CT DNA and the green is CTCs.
- 18:56And we're going to go to higher level magnification, but at, uh, but you can see already from these slides
- 19:04that the CTCs and the CT DNA do not always tell you the same thing.
- 19:11Um, they give complimentary information sets.
- 19:17Um, so this, uh, focuses in, um, on, uh, what we see
- 19:24in, um, for instance, CT DNA, which is in the red and CTCs, which is in the green.
- 19:32And, um, what you can see is that in some, in some situations we're seeing the same thing,
- 19:39but in other situations we actually see, um, uh, more of certain mutations
- 19:47in the CT DNA than in the CTCs.
- 19:51Um, and, um, so one of the interesting things that we found
- 19:59with this is that, um, as we began to look at the CTCs
- 20:07versus the CT DNA, um, the, uh, we began to see something that we found
- 20:14initially confusing, but now we think it is absolutely fascinating and really goes again,
- 20:23uh, along with
- 20:24evidence published very recently in, uh, nature genetics by the Sloan Kettering group.
- 20:31Um, so in the CTCs, we're finding, for instance, we find alterations not found
- 20:39in the CT DNA.
- 20:40In the CT DNA, we find alterations not found in the CTCs.
- 20:45And, um, if we put, and some, of course, uh, of the alterations are found both in the CTCs
- 20:53and the CT DNA.
- 20:54Um, but this is, I'm going to give you an example of something that we thought was really fascinating and actually
- 21:02very relevant to therapy.
- 21:05Um, so a subset of, uh, patients with KRAS, as the tumor evolves,
- 21:13there are CTCs that appear to lose, uh, their KRAS.
- 21:18And, um, this was at first a bit confusing to us, but it turns out this
- 21:26is very consistent with what other, um, investigators are finding when they're looking at single cell
- 21:33populations.
- 21:35Um, and, uh, for instance, the Sloan Kettering group in nature genetics about a year ago
- 21:42published that about 40 % of the individual clones in pancreatic cancer were
- 21:50losing their KRAS.
- 21:52And, um, this is precisely what we're seeing as we follow individual
- 21:59CTCs and, um, uh, see that there are different clones of CTCs and not
- 22:07all of them retain, for example, um, their CTCs.
- 22:12So we're, uh, their KRAS.
- 22:14So for instance, we're seeing KRAS negative, uh, CTCs.
- 22:19Um, sometimes in the KRAS negative CTCs,
- 22:23Dr. Rizal Kurzok: the MEC pathway is still, um, a driver.
- 22:28For instance, they may have SMOD4 or they may have other alterations in that pathway, but not always.
- 22:35Some of these, uh, CTCs are probably losing different pathways or exploiting different
- 22:42pathways in order to, um, propagate, uh, the pancreatic cancer.
- 22:49Uh, so this goes back to our prior slide and I want to now focus on
- 22:56the Y -axis to the right and, um, um, the green
- 23:04part of that access.
- 23:05And that's the CTCs.
- 23:08And you can see that there's, um, multiple alterations that can be found in CTCs that cannot
- 23:16be found in the CT DNA.
- 23:19Um, so before we focused on some of the alterations, some of the CTCs that were losing
- 23:26alterations, now we're going to focus on, um, some of the alterations found in CTCs that
- 23:34cannot be found, um, in the CT DNA.
- 23:38And, uh, so you can see there's a whole, um, group of alterations
- 23:45that were being, that were finding in the CTCs.
- 23:49And, um, these alterations are not found in the bulk, uh, CT DNA.
- 23:55And since the CTCs may reflect the evolution of cancer, pancreatic cancer, and other
- 24:03cancers, and also may be seeding some of the metastatic sites, these additional alterations
- 24:11may be critical to thinking about therapy.
- 24:14And then, um, the final, um, part of this, uh, slide, if you look on the, on
- 24:22the Y axis
- 24:25Ken Bloom: CTCs provide insights into tumor heterogeneity, revealing alterations not captured by CT DNA. This dual approach enhances our understanding of individual patient profiles and treatment responses.
- 24:42Dr. Rizal Kurzok: to the right, uh, the bottom of the right axis, you can see the red dots.
- 24:48And this is the CT DNA only.
- 24:50So there are alterations also found in CT DNA that are not found in CTCs, um,
- 24:58less so than vice versa, but there are certain alterations in some of our patients.
- 25:04Uh, this shows, um, some of the alterations found in individual patients in the CT DNA and not
- 25:11found, um, um, in the CTCs.
- 25:14So when we put all of this together, the bottom line is we need both sources of information.
- 25:22We need the CT DNA and we need the CTCs.
- 25:26And this again puts together, um, some of the alterations found in the CT DNA only, some of the
- 25:34alterations found in the CTCs.
- 25:38And, uh, there's a lot of alterations that are found in the CTCs that are not found in the CT DNA and then some of
- 25:46the shared alterations.
- 25:48So these are complementary techniques and this type of liquid biopsy is really unique in that it can
- 25:55give, um, investigators the full picture of what is going on in an individual patient.
- 26:03And, um, likely the difficulty with pancreatic cancer, metastatic pancreatic cancer, and
- 26:11probably many other, uh, cancers is that we've been getting a very partial picture.
- 26:18Um, if we do tissue biopsy, we get a picture at one point in time of one small piece of tissue.
- 26:26If we do a liquid biopsy, a blood biopsy, but we do CT DNA, we can get a serial picture
- 26:34of what is happening in the cancer, but it's a bulk serial picture.
- 26:39And we're not seeing what is happening in individual
- 26:44Ken Bloom: Understanding the molecular evolution of pancreatic cancer through CTC analysis is crucial for tailoring therapies. This approach allows for real-time monitoring of clonal dynamics and resistance mechanisms.
- 26:59Dr. Rizal Kurzok: cells, which may reflect a tremendously important, um, biology of the
- 27:07cancer and also may reflect, um, seeding of new metastatic sites and how those
- 27:14clones may be different, um, may be the key, uh, to understanding, um, our next, uh,
- 27:22step in steps in therapy.
- 27:25So, um, this, um, emphasizes the point that we
- 27:32kind of always known, but here we have clear cut evidence for it, um, pancreatic
- 27:40cancer and probably every other cancer has a lot of tumor heterogeneity.
- 27:45And in addition with time that tumor heterogeneity, um, becomes
- 27:53worse.
- 27:54It undergoes molecular evolution and, uh, there are, uh, new alterations that are appearing.
- 28:02There may be old alterations that are muted or disappear.
- 28:10And, um, to reiterate tissue biopsy or just bulk CT DNA
- 28:18cannot outline all that is happening at a single cell level.
- 28:24And so CTCs demonstrate molecular diversity of the tumor at the baseline, uh, which is
- 28:32hidden with bulk CT DNA and tissue analysis.
- 28:37CTCs allow you to follow that on a regular basis and see what is
- 28:44happening at a single cell level as the cancer progresses.
- 28:49So, uh, they're important at baseline and they're important through the life cycle of that, uh, cancer.
- 28:57Um, so single
- 29:01Ken Bloom: cell CTC genomics provides biologic insights beyond conventional, um, liquid
- 29:08biopsies and it, uh, reveals tumor subpopulations and genomic alterations not captured by
- 29:16CT DNA, broadening the detectable molecular landscape and metastatic pancreatic cancer beyond what
- 29:24circulating DNA alone can resolve.
- 29:26And again, we're talking about pancreatic cancer, but it's very likely, and that's what our project was on, but
- 29:34it's very likely that this really applies to all tumors that tend to metastasize.
- 29:40Um, so I want to loop back to this really interesting finding,
- 29:47um, that our, uh, project has confirmed prior results, um, from,
- 29:56uh, uh, that were published in nature genetics about a year ago.
- 29:59Um, so, um, to our surprise and probably to the Sloan Kettering group surprise, uh, when they
- 30:07published this, um, we identified CTCs that have KRAS, that are KRAS independent.
- 30:15They appear, this is one example, but they appear to have lost their KRAS, um, and they're circulating
- 30:23in the bloodstream.
- 30:24Um, so this would be invisible to CT DNA based assays, um, that, uh,
- 30:33track, uh, tumor DNA in bulk.
- 30:37Interestingly, in these KRAS independent clones, in some of them, alternate pathways are
- 30:45activated in the MEC signal, MAPK, SMOD.
- 30:51Um, and in some cases, um, and in some cases, just completely alternate pathways are activated.
- 30:58PI3 kinase, AKT,
- 31:00genomic instability, JAK -STAT.
- 31:03And I think we really have to have a good understanding of exactly what is happening in all these different clones if we
- 31:11are really going to impact what happens to pancreatic cancer patients.
- 31:16So, uh, CTCs demonstrate significantly greater intrapatient heterogeneity
- 31:24than CT DNA.
- 31:26And I showed this to you several slides back.
- 31:29Um, but it's, appears that patients have multiple, each patient has multiple
- 31:37different clones that may vary from each other.
- 31:41And, um, CTCs enable this high resolution delineation of
- 31:49coexisting clonal population and the genomic underpinnings of, uh, what is probably
- 31:57emerging resistance mechanisms when we treat.
- 32:01Um, so, um, uh, looking at both CT DNA and CTCs,
- 32:09it enables dynamic longitudinal tracking.
- 32:14Serial single cell CTC analysis enables real -time monitoring of clonal evolution during
- 32:22therapy, and it offers a direct window into tumor adaptation, uh, selective pressure responses,
- 32:30and treatment -driven genomic shifts over time.
- 32:35Um, so, key takeaway.
- 32:38We need all of these modalities.
- 32:41Um, CTC genomics is a complementary modality for understanding intratumoral heterogeneity,
- 32:49clonal dynamics, and resistance evolution in metastatic pancreatic ductal carcinoma.
- 32:55Um, and the fact that this platform gives
- 33:00us both CT DNA and CTCs at a single cell level, I think these are complementary,
- 33:07um, technologies in one platform and really allows us a very high high -level
- 33:14understanding of, um, um, what is happening in these patients.
- 33:20Um, uh, it gives us a window into an expanded, uh, molecular landscapes into clones that
- 33:28might be losing, uh, key drivers like KRAS, maybe replacing them with other drivers,
- 33:36maybe not, um, gives better clonal resolution, um, gives better clonal resolution and really allows longitudinal
- 33:44tracking of what is happening in an individual patient with treatment.
- 33:49Um, so this is one example of a patient, um, uh, treated, uh, and a
- 33:57longitudinal assessment.
- 33:59And, um, I, I think the things that I'd like to point out is, uh, that these
- 34:07patients, which we showed you, um, a high -level view, but you can see this in an
- 34:14individual patient, um, with time, the CTCs change.
- 34:20Um, so, uh, this patient starts off, uh, with NRAS, P53, and
- 34:28SMOD4.
- 34:29Uh, SMOD4 activates the MEC pathway.
- 34:32It can activate EGFR and HER2 and other pathways as well.
- 34:39And then with treatment, um, an HRAS emerges, uh, patient retains the P53.
- 34:47Now other alterations are emerging, which may be very important, including BRCA, uh,
- 34:54RAD51L, and, um, MUTYH.
- 34:59Um, a couple of these alterations like BRCA and RAD51 may be causing HRD
- 35:06and, uh, could be, uh, targeted with, um, PARP inhibitors or platinums.
- 35:13And then with more time, uh, the BRCA is retained and the P53 is retained.
- 35:20Um, but a P53CA alteration emerges.
- 35:24And so I think, um, this is really, um, important for understanding what's happening in the
- 35:32patient and how is resistance emerging and how should we mold our
- 35:39therapies, um, to this evolution that is occurring in an individual patient.
- 35:47And that is really what the ultimate goal is of precision or personalized medicine is to understand
- 35:55each patient in detail at each point in time of their disease.
- 36:00So we can mold the therapy that it would be best suited to that patient rather than guessing at what the
- 36:08next therapy should be.
- 36:10Um, I think this is really next generation precision oncology.
- 36:15Um, and, uh, this allows us to break the resolution barrier in precision oncology, allows us to understand
- 36:23biologic, uh, resolution, resistance detection, uh, tumor heterogeneity, um,
- 36:30all the different mutations and alterations.
- 36:33Um, and, um, um, um, we can go from population average genomics to single
- 36:41cell tumor biology, single cell genomics.
- 36:45Um, and in addition, uh, CTCs allow one to go beyond DNA.
- 36:51And this is really important.
- 36:53Um, CTCs allow one to look at, uh, DNA, but it, one can look at RNA.
- 36:59One
- 36:59can look at proteins on the same cell.
- 37:02One can even do functional tests on these cells.
- 37:05Um, so this is really an integrated cell biopsy platform, um, that,
- 37:13uh, can, uh, really help us understand diagnostics and, uh, drug
- 37:21development, tumor evolution, and what pressure points we need to apply to the tumor at any individual
- 37:29time point, um, of that tumor's, uh, progression.
- 37:34Rizal, is there any other slide you wanted to discuss in terms of alternative pathways?
- 37:38No, that's it.
- 37:38I'll just say, okay, perfect.
- 37:40Thank you, Rizal.
- 37:41Really appreciate, uh, the presentation.
- 37:43Uh, we already have some questions coming in, but just to remind you guys, as you can see on the slide, uh, we will be at
- 37:51AACR and I know most of you are likely to be at AACR.
- 37:55So would, if there are any questions or if you would like to meet us, you can easily, uh, take a picture of our, put your camera in front of this
- 38:03QR code and schedule a meeting with us.
- 38:07It could be 15 minutes, it could be 30 minutes, but it'll be great to see you guys.
- 38:12Okay.
- 38:12Okay.
- 38:12Let's move to the Q and A part.
- 38:14Um, I see some questions coming in already.
- 38:18Um, excellent.
- 38:20So we have, okay.
- 38:21So Sejong Chun, uh, asked a question on, yeah.
- 38:26So what's the, what's the difference you think, Rizal between the difference that why does CTCs, do you
- 38:34have a thesis on why they pick up unique and more mutations in ctDNA?
- 38:40Um, why do CTCs, well, I think your, um, one reason you may be picking up, uh, more mutations than
- 38:48ctDNA is because, um, uh, you're looking at multiple different CTCs and you have different clones.
- 38:54And, um, so, uh, that may be a reason
- 39:00Serial single cell CTC analysis enables real-time monitoring of clonal evolution during therapy. The ongoing study aims to clarify the relationship between clonal changes and therapy resistance, emphasizing the need for continuous monitoring of CTCs in pancreatic cancer treatment.
- 39:21Dr. Rizal Kurzok: to pick up, uh, more mutations than ctDNA.
- 39:24Uh, the ctDNA is bulk and there might be, uh, subclones of CTCs that are,
- 39:33um, smaller in number and harder to pick up in the ctDNA.
- 39:36Um, but I, I think the bottom line is that these are complementary techniques and that we're
- 39:44getting important information from both of them, but the information from the CTCs is unique because we can see it at a
- 39:52single cell level.
- 39:53And what it is showing us is that there's a lot of heterogeneity there and that heterogeneity cannot be picked up in the
- 40:01ctDNA.
- 40:03Sejong, feel free to add any follow up on that.
- 40:06Go ahead.
- 40:06Yes.
- 40:07Thank you so much for that, um, response.
- 40:09So another question that I had on that regards is that with the ctDNA, if you increase the read deaths sufficiently,
- 40:16would that divergence, um, lessen or would there still be a difference in your perspective?
- 40:25So I'm not the technical person.
- 40:27Um, uh, so I want the technical person to answer it, but I'm going to tell you what I think.
- 40:32Um, I think there would still be a difference, uh, because there may be, um, uh, a, a, uh,
- 40:41small numbers of CTCs that have a difference and that technically can't be picked up in the bulk
- 40:48ctDNA.
- 40:49And yet, even though it's small numbers of CTCs that have that difference, those CTCs may be critical to, um,
- 40:57what is happening in the patients with, um, seeding of new metastatic sites or, or reflecting resistant clones.
- 41:05So that's my answer, but somebody who's more technical than me might, um, have, uh, be able to add to that.
- 41:12Sure.
- 41:13I'll chime in on that one.
- 41:15Uh, there, there's definitely differences, but before I get into that, I'd just like to add one other point.
- 41:20If you
- 41:23Ken Bloom: draw CtDNA at, you know, draw, take a sample, send it to your favorite CtD, you know, garden, your
- 41:30favorite CtDNA lab.
- 41:32Draw it in the afternoon, send it to Tempest, draw it in the evening, send it someplace else.
- 41:37You won't get the same mutations back, right?
- 41:39You're going to get, you're getting basically a small window of cells that are dying at that point of time.
- 41:44Now, your question I think was more to the sensitivity.
- 41:47And if I raise the sensitivity of the assay, will I be able to detect things?
- 41:51And the problem with assays is generally when you raise the sensitivity, you lower the specificity.
- 41:56So now I start picking up, you know, it, where do you want to live and die, right?
- 42:01You want to get more false positives, more false negatives.
- 42:04But in the pharma's perspective, that might be slightly, um, not the way you think.
- 42:08So we would like to see the drivers or the targetable ones, which would probably, um, consist of the, um, the larger proportion of the
- 42:16mutations detected, which would be relatively consistent across different vendors and, um, different time points as well.
- 42:23So that, um, that, that's, that's a conundrum that we're facing all the time.
- 42:27But, um, this sort of leads to my next question where with the CTCs across multiple different time points, there were a few mutations that were
- 42:35consistent, but there were other ones that appeared and then went away.
- 42:38So I'm a little curious on how those were calculated.
- 42:41Um, do you think they're drivers of, let's say resistance because, um, in, in that patient, you have the biomarkers going down and eventually
- 42:49down the line as tumor burden starts to increase, you see more mutations happening, but at the end of the day, it did seem that TP53
- 42:56was the, let's say, surviving clone later.
- 43:03I, uh, do you want me to try to answer that?
- 43:07Yeah, Ray, that's for you.
- 43:08Yep.
- 43:09Yep.
- 43:09Um, yeah.
- 43:11So we actually found that fascinating and, um, uh, uh, we, uh, especially
- 43:18found, uh, yes.
- 43:21So P53 was the surviving
- 43:22The findings regarding KRAS loss in CTCs underscore the need for further investigation into the implications of clonal evolution. The variability in mutation detection between different labs highlights the importance of standardizing liquid biopsy protocols.
- 43:42Dr. Rizal Kurzok: clone in that patient, but we, with time, we don't know what else will come up, but what we found most fascinating,
- 43:50I think was the loss of some of those clones, like the loss of K -RAS.
- 43:55And, um, uh, to be frank, uh, that totally surprised me, but it was completely
- 44:02consistent with the Sloan -Kettering Nature Genetics paper, which, um, I think also surprised us.
- 44:09And the reason I think that's really important is from, to me, I'm, um, precision medical
- 44:17oncologist, is because if we're looking at therapies, if, um, the clones change, this may
- 44:24explain, uh, resistance.
- 44:26So if the remaining clones, uh, no longer have K -RAS, that may explain, um, I mean, I
- 44:34had all sorts of other explanations before some of this data came out for why patients might be resistant.
- 44:41And I think some of those explanations still hold that there may be co -drivers, but now we can add to that explanation
- 44:48that there may be loss of certain clones.
- 44:51We may have actually killed off certain clones.
- 44:54Um, and that means we have to adjust our therapy, um, accordingly.
- 45:03Thank you.
- 45:04All right.
- 45:04Excellent.
- 45:05Um, Dean, uh, you had a question.
- 45:08I can ask it, but it's better coming directly from you.
- 45:11I don't need to put you on the spot.
- 45:12Are you still there, Dean?
- 45:14Yeah, I'm here.
- 45:16Go for it.
- 45:17Yeah.
- 45:18So, uh, how often are the, how often do you see consistency between the clonal profiles and
- 45:26frequencies or profiles say at day one versus after targeted therapy?
- 45:32And, and do they get killed in a way that's consistent with the mechanism of the targeted therapy?
- 45:41Ken Bloom: Uh, is that for me?
- 45:44Sure.
- 45:45Yeah.
- 45:46Um, so I don't think we know that answer completely.
- 45:49Um, uh, this is why we're doing the study.
- 45:52Um, uh, so, uh, in order to determine, so I, I can't answer that.
- 45:58Um, I, I, I just don't think we have enough data to know.
- 46:02We have done other prior studies, uh, that suggest, um, that, uh,
- 46:10the clones do disappear consistent with the, uh, mechanism of the targeted therapy and the emerging
- 46:18clones, um, have different alterations or, uh, new mutations.
- 46:24Uh, but this is part of this study trying to figure out, um, is this consistent with the therapy that
- 46:32we are giving?
- 46:33So I don't think we have the data yet.
- 46:36Okay.
- 46:37Thank you.
- 46:37And the follow up question was around, um, you know, it's 10, it looked like the early graph said between 10 and 50 CTCs
- 46:45per patient per draw.
- 46:47Um, is, could you do some statistics on those?
- 46:51I, I see they only reported, you only reported presence or absence of a mutation in each sample, but if you had 10 or
- 46:5920, you could say 15 % were, had the mutation.
- 47:05Have you looked into that?
- 47:07We haven't looked into it, but it's a good idea.
- 47:10Okay.
- 47:11Um, but I still think, um, if there's substantial numbers of cells that are losing the mutation,
- 47:19that's telling you something important, but the actual percentage would be good to look at.
- 47:24We agree.
- 47:26Thanks.
- 47:29All right.
- 47:30Feel, guys feel free to either raise your hand and ask a question directly or add it to the, to the chat box.
- 47:37Um, Ray, I had a question for you.
- 47:44The exploration of mutation types in CTCs versus CT DNA is essential for understanding the full spectrum of tumor evolution. The ongoing research into the dynamics of CTCs and their mutations is vital for understanding the complexities of pancreatic cancer treatment.
- 48:05Dr. Rizal Kurzok: is there, uh, so you've shown the differences and the overlaps, right?
- 48:09In terms of number of mutation and the types and the, and the actual mutation.
- 48:13Did you observe any differences in the types of mutation between CTD and a versus CTCs?
- 48:20Miss sense versus nonsense versus so on and so forth.
- 48:24Frame shift.
- 48:26Uh, yeah.
- 48:27So I think that, uh, some of the slides show that, um, uh, there, there are different, there are definitely differences in the mutations
- 48:35that we see in the CTCs and the CT DNA.
- 48:39Um, I, I don't know that we can say that there are certain structural, uh, differences, frame shifts
- 48:46versus, uh, fusions or, uh, single nucleotide variants.
- 48:52Um, uh, maybe, um, the one cell people have more information in that regard.
- 48:59Um, but, um, I, I, I think that there's definitely differences in the
- 49:06types of mutations that we're picking up.
- 49:09There's also convergence in the types of mutations, um, that we see on CTD and a and CTCs, but there's differences.
- 49:17And one of the things that I found really interesting was in, uh, some of the CTCs, uh, maybe
- 49:25there would be loss loss of KRAS, but there would be other, um, mutations that activate the MEC pathway,
- 49:33uh, that would emerge, um, at the same time.
- 49:37Sometimes those other pathways didn't emerge, but sometimes they do emerge other mutations that keep that pathway going.
- 49:46Yeah.
- 49:47Yeah.
- 49:47Arshad, just to add on a, just a quick comment.
- 49:50That this is one of the reasons why having an AI platform supporting all this is so important.
- 49:56You know, we're, we're in brand new territory.
- 49:58All these are fantastic questions.
- 50:00We don't know the answers to the most of them because the data is just being
- 50:06Ken Bloom: generated now.
- 50:07And I think it's also highlighting how difficult it is to, to understand what these all really mean.
- 50:13We have to come up with a hypothesis and then we just look and say, does it support it or not support it?
- 50:18But there's a lot of data hidden in all of this.
- 50:23Great.
- 50:23Uh, and so this is a question to both you and Ken, um, put yourself in the shoes of a, a, someone
- 50:31leading a clinical trial, um, either for a targeted therapy or for an ADC.
- 50:37I know, Ray, you talked about ADCs as well.
- 50:39Um, how, what's the implications for them in terms of how is this approach of
- 50:47advanced liquid biopsies useful to them from a clinical development perspective?
- 50:52Um, so I think from, um, my, uh, perspective, uh, there are several, uh, ways it's useful.
- 51:00Uh, the first is, uh, the baseline liquid biopsies, both CTCs and CT DNA, um,
- 51:09may be predictive of, um, which patients will respond with, to which targeted agents.
- 51:16Um, the second is, uh, with time, um, if we look at what is
- 51:24happening with the CTC evolution, um, it can probably tell us early
- 51:31on, um, if the patient's going to respond.
- 51:35Um, so we haven't yet done, um, these studies, um, here, uh, but we know from
- 51:43other studies, uh, that we can tell, uh, response with liquid biopsy, uh, way before,
- 51:51uh, two months, um, with a scan.
- 51:54And that, um, is true with targeted therapies is true with chemotherapy.
- 51:59So there may be early indicators of response, which we have not had the opportunity yet to, um,
- 52:06show here, but I think that, um, there's a lot, there are several studies, some of which we have done that show, um, that,
- 52:14um, looking at these serial liquid biopsies, we can see early indicators of response.
- 52:19Um, third, um, it may tell us, um, early indicators of resistance, um,
- 52:27and not only which patients may be resistant, but why they may be resistant.
- 52:35Uh, so it may be because the CT DNA increases.
- 52:39It may be because the CTCs increase, but there may be resistance even with a
- 52:47decrease in CTCs, if the CTC clones no longer have the target.
- 52:52Uh, so I, I think this allows us to decipher, um, uh, the
- 53:00heterogeneity in response and resistance, um, that, um, is probably more
- 53:08complicated and more interesting and more informative, um, than we previously thought.
- 53:16And certainly gives us a lot more information than doing a scan every two or three months or, uh, just looking at CT
- 53:23DNA.
- 53:26Great.
- 53:27Thank you.
- 53:28Ken, was there any follow up on that?
- 53:29Yeah.
- 53:30I'll just add from a pathologist perspective, certainly with ADCs, a lot of the patient selection is based off of biopsy
- 53:38material, some of which can be actually quite old.
- 53:42Uh, sometimes you can't even find the biopsy on the patient.
- 53:45Uh, but you should know anytime you take a biopsy and it's fixed in formalin and prepared for, you know,
- 53:53immunohistochemistry, those epitopes have been severely altered by the pre -analytics of, uh, of getting the sample to begin with the
- 54:01ischemic times, et cetera, fixation, cross links, proteins,
- 54:05and all sorts of bizarre ways.
- 54:07We have to do retrieval mechanisms to try to bring those epitopes back.
- 54:11Sometimes we bring them back.
- 54:13Well, sometimes we open up, uh, to nonspecific findings.
- 54:17And so the ability to be able to capture a CTC at the time point of therapy and probe it for proteins
- 54:25without any of those effects.
- 54:27And I think maybe that wasn't really clear.
- 54:29When you capture a live CTC, you don't have to worry about ischemic time fixations, antigen retrieval, all of the things that
- 54:37are negatives for immunohistochemistry, wind up going away with CTCs.
- 54:42And most importantly, when it's intact, we can absolutely identify and quantify the amount of protein on the surface of the
- 54:50cell that their drug would be, uh, available for rather than relying on pathologist eyeballs or AI techniques to
- 54:58delineate membrane from cytoplasm.
- 55:00I think there's a lot of advantages now.
- 55:02Everything else I agree totally with Dr.
- 55:04Kershra said, I think she eloquently pointed out all the advantages.
- 55:08All right.
- 55:09We have two more questions.
- 55:10I'm going to quickly go through those.
- 55:11So Langdon Miller asked, uh, that one of the critical challenges, uh, is when you're measuring resistance as baseline is what are the
- 55:19intrinsic, uh, mechanism resistance or sensitivity mechanisms that may steer the therapy towards one patient or another.
- 55:26Are there any known genetic profile in pancreatic cancer that predicts sensitivity or resistance to agents that are commonly employed to treat the
- 55:34disease?
- 55:35For example, taxanes, gemcitabine, 5 -FU, oxapleton, illinotican, et cetera.
- 55:42Uh, so, uh, okay.
- 55:46So, uh, in pancreatic cancer in particular, and with chemotherapy in particular, I think that, um,
- 55:54uh, we don't know profiles very well, um, and what predicts, um, but I think we're learning and I'm going
- 56:02to give you, um, just a couple of examples.
- 56:05uh, profile, uh, cells that have, uh, homologous repair deficiency are likely to respond to platinums
- 56:13or, uh, to PARP inhibitors.
- 56:17Um, we have a paper, uh, out that, uh, shows that, uh,
- 56:25uh, uh, profiles that include ATM, um, or check to alterations, um, which
- 56:33are usually thought of HRD related genes, but they're actually, um, they can cause HRD, but mostly they don't,
- 56:41uh, but they sensitize to topo one, uh, inhibitors, topo one isomerase inhibitors, such
- 56:48as irinotekin.
- 56:49Um, as far as gemcitabine and taxane, I think that there's a lot less known about what
- 56:57profiles, um, might sensitize to those chemotherapies.
- 57:01But I will also say that I think the next generation of therapies, uh, for pancreatic
- 57:09cancer probably needs to be better than gemcitabine and, uh, abroxane.
- 57:15Um, I, I think there's a lot of new drugs coming out and this can inform our use of next generation drugs.
- 57:22Okay.
- 57:23Before we end, one last question.
- 57:24Apparent loss of KRAS, is that supported by orthogonal biopsy methods such as IHC or histology?
- 57:33Um, we, uh, yeah, so that's a really good question.
- 57:37Um, so we are now cross -checking this loss of KRAS with, um, um, really looking at the cells, making sure
- 57:45that, um, uh, that the IHC profiles are correct for pancreatic cancer and so forth.
- 57:52Um, but, um, the bottom line is that I feel very confident that this is a real result.
- 57:58And the reason I feel confident that this is a real result is first of all, because the technology is
- 58:05The confirmation of KRAS loss through advanced liquid biopsy techniques highlights the need for ongoing research into the implications of clonal evolution. The challenges of capturing CTCs and their implications for therapy highlight the need for advanced techniques in liquid biopsy. The ongoing investigation into the relationship between CTCs and therapy resistance is crucial for developing personalized treatment strategies. The integration of CTC analysis into clinical trials can significantly enhance patient selection and treatment personalization. The exploration of genetic profiles in pancreatic cancer is essential for predicting treatment responses.
- 58:46Dr. Rizal Kurzok: really good.
- 58:47And second of all, um, we, we are basically, uh, confirming that this technology shows
- 58:55exactly what Sloan Kettering, uh, showed when they looked at single cell, uh, technology.
- 59:00Uh, when you look at this in bulk, you don't see the loss, but when you look at single cell technology, um, in the nature,
- 59:08uh, genetics paper, it's a paper by Zhang, Z -H -A -N -G.
- 59:13If you want to look it up and it was published at the end of 2024, they found that 42 % of, uh, the clones were
- 59:20losing KRAS, which I think is a real surprise.
- 59:23But the single cell technology gives you that and bulk technology cannot.
- 59:29Great.
- 59:30Thank you.
- 59:30That was from, uh, Amar Adam.
- 59:31So thank you, Amar, for that question.
- 59:33With that, uh, really appreciate Ray, uh, for taking your time to, to speak to us and sharing your, your insights.
- 59:41Uh, Ken, thank you as well.
- 59:43And I really appreciate all of the participants.
- 59:45Uh, and we will look forward to speaking to you and seeing you, uh, at, uh, AACR.
- 59:51All right.
- 59:51Thank you.