Latest / Zero Shot Podcast DEMO / Revolutionizing Pancreatic Cancer Treatment with Liquid Biopsies V8
Transcript
- 0:00Arshad: In this conversation, advanced liquid biopsies can significantly enhance the understanding and treatment of pancreatic cancer by capturing tumor heterogeneity and clonal evolution.
- 0:17Thanks, everybody, for joining OneCell's webinar.
- 0:21The topic of today's conversation is advanced liquid
- 0:29biopsies.
- 0:30And in particular, we'll be discussing not just looking at circulating tumor DNA, but also the emerging
- 0:38field of single -cell -based liquid biopsies, which formerly a lot of people referred to as circulating tumor cells, also still
- 0:46referred to as circulating tumor cells.
- 0:47But we'll also describe what is new about these sort of cell -based liquid biopsies, where we can do molecular
- 0:55profiling, both in the cell level as well as at the DNA level.
- 1:01Ken Bloom: So the topic is multisource genomics to monitor clonal evolution for pancreatic cancer.
- 1:08Dr.
- 1:08Rizal Kurzok from Medical College of Wisconsin will provide an update for the talk.
- 1:14Arshad: This meeting is being recorded.
- 1:16We will have two formats for Q &A.
- 1:20As the meeting progresses, please feel free to put your questions in the chat, in the chat box,
- 1:28and then we'll accommodate as many of the questions.
- 1:32And towards the end, we'll have some time for some live questions as well.
- 1:36So 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.
- 1:44Before we continue, let’s clarify who Ken Bloom is and his relevance to this discussion.
- 1:51Ken Bloom: turn it over to Ken Bloom.
- 1:54Ken is OneCell's advisor.
- 1:57He's a strategic advisor to OneCell, also leads our CAPCLEAR certified laboratory in the San Francisco Bay Area.
- 2:06Arshad: be providing an overview of OneCell as well as our OncoInsights technology.
- 2:13Ken Bloom: after that, before I turn it over to Rizal, I will ask all of the participants to go into the chat box.
- 2:21And there's a link there, which you can click.
- 2:25And it'll take you literally not more than 10 seconds to answer questions around what topics are relevant to you guys.
- 2:31That'll be important for us to understand.
- 2:33And we'll share some of that either towards the end or as a follow -up.
- 2:41Arshad: labs hold the highest level of clinical accreditation, CLIA and CAP in the U .S., NAVAL and CAP in India.
- 2:47And these aren't just logos on the slide.
- 2:50They mean that the data coming out of our labs meets the standards required for clinical decision -making.
- 2:59Critically, this allows for the capture of the full diversity of tumor cells, not just the most common ones.
- 3:05Once the cells are captured, they are released intact using a cleavable linker system.
- 3:10No bead contamination, no cell damage.
- 3:14So the cells are ready for multi -omic analysis.
- 3:16So this is where things get really exciting because of what you can measure from these capture CTCs.
- 3:23The OncoInsights panel covers three biological layers simultaneously from the same blood draw.
- 3:29First, DNA.
- 3:311080 gene panel covering point mutations, insertions, deletions, gene fusions, copy number variations, and
- 3:39chromosomal rearrangements.
- 3:40It also gives you tumor mutational burden, microsatellite instability status, and homologous
- 3:47recombination deficiency status.
- 3:49All of the genomic biomarkers that predict response to immunotherapy, PARP inhibitors, and targeted agents.
- 4:01Ken Bloom: mission is straightforward but ambitious.
- 4:03We're going to be able to do this, democratize precision oncology, make it actionable, accessible, affordable for every cancer patient
- 4:10everywhere.
- 4:11We are working toward impacting the lives of one million cancer patients through breakthroughs in science and AI.
- 4:18For those of you in pharma, you can think of OneCell as a potential partner for clinical trial design, patient selection, biomarker
- 4:26discovery, and drug development.
- 4:28Everything that you're about to hear is built on that infrastructure.
- 4:31So now let's talk about the problem, where we've been and where we're going.
- 4:36Arshad: was trained 40 years ago with the idea that tissue biopsy is the gold standard.
- 4:41And over those years, we've been able to extract multiomic data from tissue, protein data from immunohistochemistry, and increasingly
- 4:48comprehensive molecular data from next -generation sequencing.
- 4:53Tissue biopsy has allowed us to predict prognosis and in the era of precision medicine to predict therapy response and potential resistance
- 5:00mechanisms.
- 5:02However, as biopsies become smaller and smaller, our analysis becomes less reliable because of tumor heterogeneity.
- 5:09A five micron section from a one centimeter tumor represents only a fraction of a percent of that tumor.
- 5:16So 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 sentence
- 5:24of the book.
- 5:25You get a snapshot, a static picture.
- 5:28And while that provides actionable data, it creates a gap in our ability to monitor cancer's evolution.
- 5:35And this has direct consequences for patient management.
- 5:39Ken Bloom: We've long sought biomarkers that would allow us to effectively monitor tumor progression and response to therapy.
- 5:45In my early career, this was accomplished with blood -based biomarkers like CEA, CA -125, and with
- 5:53imaging like CT and PET scans.
- 5:55While valuable, blood -based biomarkers are limited by their poor sensitivity and specificity, and
- 6:03imaging lacks sensitivity, exposes a vulnerable patient to high doses of radiation, and doesn't identify a lesion until it's of significant
- 6:10size.
- 6:12Arshad: DNA or circulating tumor DNA has emerged as the latest tool in our monitoring arsenal.
- 6:18It's real time, and it reflects what's happening now since the half -life of DNA is on the order of a few hours.
- 6:25But CT DNA only gives you the genetic sequence of the fraction of tumor cells that have recently died.
- 6:31It can miss low -frequency mutations entirely, and of course, it will likely miss emerging clones that are actively proliferating but have not
- 6:39yet died.
- 6:41Ken Bloom: more importantly, as antibody drug conjugate therapies have emerged, CT DNA doesn't give us any useful information about
- 6:48protein expression or localization.
- 6:50This means we're all making patient selection and endpoint decisions based on incomplete, often outdated information.
- 7:05Arshad: Here's a quick refresher.
- 7:06When a tumor grows, it sheds cells into the bloodstream.
- 7:10These are circulating tumor cells, actual cancer cells floating in a patient's blood drop.
- 7:15The problem historically has been catching them.
- 7:18They are incredibly rare, maybe dozens or less, among billions of normal cells.
- 7:23The trick, though, is not just to capture them, but to capture them in a way that's suitable for downstream analysis.
- 7:30The earliest systems utilized single -marker immunocapture and fixed the cells, making them largely unsuitable for comprehensive downstream
- 7:38analysis.
- 7:39Other systems use negative selection by depleting hematopoietic cells or size -based methods, but these
- 7:47suffered from high background noise and low purity.
- 7:51OncoInsights solves these limitations with a combination of multi -marker affinity capture and a cleavable linker allowing capture of
- 7:58live CTCs with no cell damage.
- 8:01Instead of a single hook, we use customized capture beads coated with multiple antibodies targeted to a specific
- 8:08cancer type.
- 8:10For most cancers, a combination of Epcam and transferrin works effectively, but the beads can be customized to optimize capture.
- 8:18For example, many renal cell cancers don't express Epcam at high levels, expressions quite low.
- 8:24So adding CD70 to the beads dramatically increases the CT positivity rate.
- 8:33Ken Bloom: is protein expression.
- 8:35This is currently measured by immunofluorescence on individual cells.
- 8:38You can directly quantify the proteins a drug is targeting, such as HER2, TROP2, clodin -18, nectin -4, etc.
- 8:47If you're developing an antibody drug conjugate, for example, this tells you whether the target is actually present at the protein level
- 8:54on cells circulating right now during treatment.
- 9:02Arshad: overall CTC positivity rate, or our ability to detect CTCs, was 83 % for stages stage
- 9:102 through stage 4 patients, but metastatic patients had approached 100%.
- 9:14Let me put that in context.
- 9:17Our first generation of CTC capture technology yielded a mean of about 5 CTCs per sample, while our current
- 9:25platform yields a mean of about 21 CTCs per sample.
- 9:29That's a four -fold improvement, and more cells means more material for downstream analysis, more genomics, more protein
- 9:36profiling, more confidence.
- 9:43Thanks, Ken.
- 9:44Appreciate that.
- 9:45If I can ask all the participants, if you can go to the top of the chat room, there's a link there
- 9:52from, it's called forms .gle.
- 9:56If you guys just click that link, I promise this won't take more than 10 seconds.
- 10:00It's going to ask some basic questions on what are the types of areas that are important to you, and that's it.
- 10:06Just 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.
- 10:13So, over to Razelle.
- 10:17So, a pleasure to work on this project and with this
- 10:25really interesting technology.
- 10:31Ken Bloom: 83 % to 100 % positivity rate across solid tumors means that the vast majority of your enrolled patients can be monitored longitudinally
- 10:39with this platform, and that's a game -changer for adaptive trial design.
- 10:43One more important point before we move on, and this is particularly relevant for CNS cancers and thoracic malignancies.
- 10:50The technology isn't just limited to blood.
- 10:53At one cell, we've demonstrated CTC capture, or tumor cell capture, from cerebral spinal fluid
- 11:00and pleural fluid.
- 11:02In CNS tumors like glioblastoma and medulloblastoma, where a blood draw tells you almost nothing about what's happening in the brain,
- 11:09CSF -based CTC analysis opens a completely new window.
- 11:14This is significant for clinical trials and CNS malignancies, where biomarker development has lagged far behind other tumors.
- 11:21Now, generating all this data is only valuable if you can act on it, and that's what the iCORM platform is designed to do.
- 11:30iCORM is one cell's integrated precision oncology consult.
- 11:34Think of it as the intelligence layer that sits on top of the laboratory data.
- 11:39It has two primary interfaces.
- 11:41iDiscover for translational research and clinical trial support, and iCare for the treating oncologist.
- 11:48For those of you in pharma, iDiscover is the critical piece.
- 11:53Arshad: imaging, pathology images, and real -world evidence data sets.
- 11:58It uses AI and machine learning to identify patient populations most likely to respond to a given therapy, flag resistance
- 12:06markers as they emerge, and help you understand mechanisms of action in a way that bulk tumor sequencing simply can't provide.
- 12:14It also adds the missing temporal layer to AI.
- 12:18It allows AI to begin to understand how tumor cells are adapting and what to do about it.
- 12:25Imagine being able to enrich your clinical trials for responders before the trial even starts, based on real -time
- 12:32CTC protein expression in genomics, rather than on archival tissue.
- 12:37That's the promise of iCORM.
- 12:39You get smarter enrollment, more informative biomarker endpoints, and ultimately, a cheaper path to approval.
- 12:47Ken Bloom: that as background, I'll now turn the slides over to Dr.
- 12:50Curtis Rock, who's going to present her exciting data on the clonal evolution in pancreatic cancer.
- 12:56But first, there will be a few polling questions.
- 12:59So, Arshad, I guess that goes to you next.
- 13:02Yes, thanks.
- 13:09Arshad: we really wanted to concentrate on pancreatic ductal adenocarcinoma for several reasons.
- 13:15One is because our institution really has a world -class program in this cancer.
- 13:23And the second is because it is such a difficult cancer.
- 13:27The five -year survival rate is about 13%, despite advances in surgery and systemic therapies.
- 13:35And it's actually worse than that.
- 13:37There's a recent paper in JAMA that shows that the one -year survival is about 24%.
- 13:43So, we have a long way to go to learn how to deal with this cancer.
- 13:48And it is projected to become the second leading cause of cancer -related deaths in the United States.
- 13:56And so, we really need to improve our understanding of this cancer.
- 14:02Ken Bloom: ductal adenocarcinoma progression involves stepwise accumulation of key driver mutations,
- 14:08which are mainly known to be KRAS, the cyclin system,
- 14:16CDKN2AB loss, and P53.
- 14:20And tumor evolution also includes rapid genomic restructuring characterized by
- 14:28copy number variations and large chromosomal rearrangements following
- 14:34polyploidization.
- 14:38So, this is a difficult cancer.
- 14:41Arshad: reason, one of the reasons it's difficult is because of the great heterogeneity between patients
- 14:49and even within patients with time.
- 14:52And that's really difficult to capture if what you're doing is a baseline tissue biopsy.
- 15:00Um,
- 15:00Ken Bloom: are a lot of limitations to bulk sequencing.
- 15:05Um, and, uh, some of them are illustrated here.
- 15:10Uh, so, we use bulk sequencing to understand, um, cancer.
- 15:16But the problem is that it doesn't really show us what happens with time, what happens with
- 15:24successive, um, mutational events.
- 15:28And, um, it cannot, um, extinguish, it cannot distinguish what is
- 15:35happening in different clones of cells.
- 15:38So, if we see, do single cell sequencing, we can see, are there co -occurring versus
- 15:46mutually exclusive alterations in different cells?
- 15:51Might this explain, um, mixed responses to drugs, uh, like PARP inhibitors, KRAS inhibitors,
- 15:58and immunotherapy.
- 16:01And so, single cell DNA sequencing is really required to resolve the clonal
- 16:08architecture of pancreatic ductal adenocarcinoma from early invasion through systemic,
- 16:16uh, dissemination and to identify molecular vulnerabilities targetable with precision
- 16:23therapies as the, as the disease evolves.
- 16:27Uh, so, this is a study that we initiated, um, and, uh, the purpose of
- 16:35the study was to isolate single circulating tumor cells from pancreatic cancer patients prior to treatment
- 16:42and perform genomic profile to characterize cellular level genomic heterogeneity, and also to
- 16:50follow these patients during treatment.
- 16:53And, uh, uh, this, uh, study is led by Dr.
- 16:57Mondana Kamgar and myself at MCW and Dr.
- 17:01Kremolini at, uh, University of Pisa.
- 17:05And, uh, we've collected quite a few samples and I think, um, I'm happy to share with you some of the
- 17:12insights, uh, from these samples.
- 17:15Next, uh, slide, please.
- 17:18So, all together, uh, we now have 26 patients, 63 total samples,
- 17:26um, and, uh, five time points tracked.
- 17:30And, uh, we're also continuing
- 17:38to expand, uh, this, uh, project, uh, but I'm going to show you, I think we have some fascinating insights,
- 17:46um, at this, uh, time.
- 17:48And, um, um, I want to share those with you.
- 17:52So, uh, first, um, uh, this slide, I think really illustrates, uh, some of the insights,
- 18:00uh, from the study.
- 18:01Um, so if we look at, uh, patients that have CT DNA only
- 18:08versus, uh, CTC DNA only, we're getting a lot more alterations
- 18:16from the CTCs, which you can see on the right, than we are getting from the CT DNA.
- 18:23And this in the middle are some of the shared alterations, um, that you see.
- 18:29So there's a lot of common things, but themes.
- 18:33But in addition, I think that both the CT DNA and the CTCs bring their
- 18:41own information.
- 18:42And I think you can see how rich the information is that is coming, um, from the CTCs.
- 18:49Um, so this, uh, slide shows, uh, the longitudinal, uh, CTC,
- 18:57uh, DNA and, uh, CT DNA longitudinal
- 19:04mutational landscape.
- 19:06And I'm going to go into, um, more detail in a moment, but if you go to the right
- 19:14side, this is patient by patient.
- 19:17And if you go to the right side of the slide, you can see, um, on the, um, Y axis on the
- 19:25right side, uh, the red is CT DNA and the green is CTCs.
- 19:31And we're going to go to higher level magnification, but at, uh, but you can see already from these slides
- 19:39that the CTCs and the CT DNA do not always tell you the same thing.
- 19:46Um, they give complimentary information sets.
- 19:52Um, so this, uh, focuses in, um, on, uh, what we see
- 19:59in, um, for instance, CT DNA, which is in the red and CTCs, which is in the green.
- 20:07And, um, what you can see is that in some, in some situations we're seeing the same thing,
- 20:14but in other situations we actually see, um, uh, more of certain mutations
- 20:22in the CT DNA than in the CTCs.
- 20:26Um, and, um, so one of the interesting things that we found
- 20:34with this is that, um, as we began to look at the CTCs
- 20:42versus the CT DNA, um, the, uh, we began to see something that we found
- 20:49initially confusing, but now we think it is absolutely fascinating and really goes again,
- 20:58uh, along with evidence published very recently in, uh, nature genetics by the Sloan Kettering group.
- 21:06Um, so in the CTCs, we're finding, for instance, we find alterations not found
- 21:14in the CT DNA.
- 21:15In the CT DNA, we find alterations not found in the CTCs.
- 21:20And, um, if we put, and some, of course, uh, of the alterations are found both in the CTCs
- 21:28and the CT DNA.
- 21:29Um, but this is, I'm going to give you an example of something that we thought was really fascinating and actually
- 21:37very relevant to therapy.
- 21:40Um, so a subset of, uh, patients with KRAS, as the tumor evolves,
- 21:48there are CTCs that appear to lose, uh, their KRAS.
- 21:53And, um, this was at first a bit confusing to us, but it turns out this
- 22:01is very consistent with what other, um, investigators are finding when they're looking at single cell
- 22:08populations.
- 22:10Um, and, uh, for instance, the Sloan Kettering group in nature genetics about a year ago published
- 22:18that about 40 % of the individual clones in pancreatic cancer were losing
- 22:25their KRAS.
- 22:27And, um, this is precisely what we're seeing as we follow individual
- 22:34CTCs and, um, uh, see that there are different clones of CTCs and not
- 22:42all of them retain, for example, um, their CTCs.
- 22:47So we're, uh, their KRAS.
- 22:49So for instance, we're seeing KRAS negative, uh, CTCs.
- 22:54Um, sometimes in the KRAS negative CTCs, the MEC pathway is still,
- 23:02um, a driver.
- 23:04For instance, they may have SMOD4 or they may have other alterations in that pathway, but not always.
- 23:10Some of these, uh, CTCs are probably losing different pathways or exploiting different
- 23:18pathways in order to, um, propagate, uh, the pancreatic cancer.
- 23:25Uh, so this goes back to our prior slide and I want to now focus on
- 23:32the Y -axis to the right and, um, um, the green
- 23:39part of that access.
- 23:41And that's the CTCs.
- 23:44And you can see that there's, um, multiple alterations that can be found in CTCs that cannot
- 23:52be found in the CT DNA.
- 23:54Um, so before we focused on some of the alterations, some of the CTCs that were losing
- 24:02alterations, now we're going to focus on, um, some of the alterations found in CTCs that
- 24:10cannot be found, um, in the CT DNA.
- 24:13And, uh, so you can see there's a whole, um, group of alterations
- 24:21that were being, that were finding in the CTCs.
- 24:25And, um, these alterations are not found in the bulk, uh, CT DNA.
- 24:31And since the CTCs may reflect the evolution of cancer, pancreatic cancer, and other
- 24:38cancers, and also may be seeding some of the metastatic sites, these additional alterations
- 24:46may be critical to thinking about therapy.
- 24:50And then, um, the final, um, part of this, uh, slide, if you look on the, on
- 24:58the Y axis to the right, uh, the bottom of the right axis, you can see the red dots.
- 25:04And this is the CT DNA only.
- 25:07So there are alterations also found in CT DNA that are not found in CTCs, um,
- 25:14less so than vice versa, but there are certain alterations in some of our patients.
- 25:20Uh, this shows, um, some of the alterations found in individual patients in the CT DNA and not
- 25:28found, um, um, in the CTCs.
- 25:31Arshad: So when we put all of this together, the bottom line is we need both sources of information.
- 25:38We need the CT DNA and we need the CTCs.
- 25:43And this again puts together, um, some of the alterations found in the CT DNA only, some of the
- 25:51alterations found in the CTCs.
- 25:55And, 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
- 26:03the shared alterations.
- 26:05So these are complementary techniques and this type of liquid biopsy is really unique in that it can
- 26:12give, um, investigators the full picture of what is going on in an individual patient.
- 26:20And, um, likely the difficulty with pancreatic cancer, metastatic pancreatic cancer, and
- 26:28probably many other, uh, cancers is that we've been getting a very partial picture.
- 26:35Um, if we do tissue biopsy, we get a picture at one point in time of one small piece of tissue.
- 26:43If we do a liquid biopsy, a blood biopsy, but we do CT DNA, we can get a serial picture
- 26:51of what is happening in the cancer, but it's a bulk serial picture.
- 26:55And we're not seeing what is happening in individual cells, which may reflect a tremendously
- 27:03important, um, biology of the cancer and also may reflect, um,
- 27:10seeding of new metastatic sites and how those clones may be different, um, may be the key, uh,
- 27:19to understanding, um, our next, uh, step in steps in therapy.
- 27:24So, 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.
- 28:36CTCs 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 cell CTC genomics provides biologic insights beyond
- 29:04conventional, um, liquid biopsies and it, uh, reveals tumor subpopulations and
- 29:12genomic alterations not captured by CT DNA, broadening the detectable molecular landscape and metastatic
- 29:19pancreatic cancer beyond what circulating DNA alone can resolve.
- 29:25And again, we're talking about pancreatic cancer, but it's very likely, and that's what our project was on, but
- 29:32it's very likely that this really applies to all tumors that tend to metastasize.
- 29:38Um, so I want to loop back to this really interesting finding,
- 29:46um, that our, uh, project has confirmed prior results, um, from,
- 29:54uh, uh, that were published in nature genetics about a year ago.
- 29:58Um, so, um, to our surprise and probably to the Sloan Kettering group surprise, uh, when they
- 30:05published this, um, we identified CTCs that have KRAS, that are KRAS independent.
- 30:14They appear, this is one example, but they appear to have lost their KRAS, um, and they're circulating
- 30:21in the bloodstream.
- 30:23Um, so this would be invisible to CT DNA based assays, um, that, uh,
- 30:31track, uh, tumor DNA in bulk.
- 30:36Interestingly, in these KRAS independent clones, in some of them, alternate pathways are
- 30:44activated in the MEC signal, MAPK, SMOD.
- 30:49Um, and in some cases, um, and in some cases, just completely alternate pathways are activated.
- 30:57PI3 kinase, AKT, uh, genomic instability, JAK -STAT.
- 31:02And I think we really have to have a good understanding of exactly what is happening in all these different clones if we
- 31:10are really going to impact what happens to pancreatic cancer patients.
- 31:15So, uh, CTCs demonstrate significantly greater intrapatient heterogeneity
- 31:22than CT DNA.
- 31:25And I showed this to you several slides back.
- 31:28Um, but it's, appears that patients have multiple, each patient has multiple
- 31:36different clones that may vary from each other.
- 31:40And, um, CTCs enable this high resolution delineation of
- 31:48coexisting clonal population and the genomic underpinnings of, uh, what is probably
- 31:56emerging resistance mechanisms when we treat.
- 32:00Um, so, um, uh, looking at both CT DNA and CTCs,
- 32:08it enables dynamic longitudinal tracking.
- 32:13Ken Bloom: Serial single cell CTC analysis enables real -time monitoring of clonal evolution during
- 32:21therapy, and it offers a direct window into tumor adaptation, uh, selective pressure responses,
- 32:28and treatment -driven genomic shifts over time.