Latest / Zero Shot Podcast DEMO / Advancements in Liquid Biopsies for Pancreatic Cancer V4
Transcript
- 0:00Interviewer: Thanks, everybody, for joining OneCell's webinar.
- 0:04The topic of today's conversation is advanced liquid
- 0:12biopsies.
- 0:13And in particular, we'll be discussing not just looking at circulating tumor DNA, but also the emerging
- 0:21field of single -cell -based liquid biopsies, which formerly a lot of people referred to as circulating tumor cells, also still
- 0:29referred to as circulating tumor cells.
- 0:30But we'll also describe what is new about these sort of cell -based liquid biopsies, where we can do molecular
- 0:38profiling, both in the cell level as well as at the DNA level.
- 0:47speakers: In this conversation, the webinar discusses advancements in liquid biopsies for monitoring pancreatic cancer, emphasizing the importance of both circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs).
- 1:08Interviewee: We've long sought biomarkers that would allow us to effectively monitor tumor progression and response to therapy.
- 1:13In my early career, this was accomplished with blood -based biomarkers like CEA, CA -125, and with
- 1:21imaging like CT and PET scans.
- 1:24While valuable, blood -based biomarkers are limited by their poor sensitivity and specificity, and
- 1:31imaging lacks sensitivity, exposes a vulnerable patient to high doses of radiation, and doesn't identify a lesion until it's of significant
- 1:39size.
- 1:41CT
- 1:45Interviewer: I'll turn it over to Rizal, and we'll go for Q &A.
- 1:51So that's the agenda for today.
- 1:55Without any further delays, I will turn it over to Ken.
- 1:59Over to Ken.
- 2:03Perfect.
- 2:03Thank you, Arshad.
- 2:04Welcome, everybody.
- 2:05My
- 2:05speakers: OneCell aims to democratize precision oncology for cancer patients. The positivity rate for detecting CTCs in metastatic patients approaches 100%, showcasing the effectiveness of the technology.
- 2:21Interviewee: name is Ken Bloom.
- 2:22I'm a surgical and molecular pathologist and the medical director of OneCell's Foster City Laboratory.
- 2:28So let's start with a quick introduction to OneCell .ai.
- 2:31We're a precision oncology company headquartered in Foster City, California, with major laboratory operations in Pune and
- 2:39Mumbai, India.
- 2:41Our
- 2:42Interviewer: labs hold the highest level of clinical accreditation, CLIA and CAP in the U .S., NAVAL and CAP in India.
- 2:49And these aren't just logos on the slide.
- 2:51They mean that the data coming out of our labs meets the standards required for clinical decision -making.
- 2:57Our
- 2:58Interviewee: mission is straightforward but ambitious.
- 3:00We're going to be able to do this.
- 3:00We're going to be able to do this.
- 3:00Democratize precision oncology.
- 3:03Make it actionable, accessible, affordable for every cancer patient everywhere.
- 3:09We are working toward impacting the lives of 1 million cancer patients through breakthroughs in science and AI.
- 3:15For those of you in pharma, you can think of OneCell as a potential partner for clinical trial design, patient selection, biomarker
- 3:23discovery, and drug development.
- 3:25Everything that you're about to hear is built on that infrastructure.
- 3:29So now let's talk about the problem, where we've been and where we're going.
- 3:33I
- 3:34Interviewer: was trained 40 years ago with the idea that tissue biopsy is the gold standard.
- 3:38And over those years, we've been able to extract multiomic data from tissue, protein data from immunohistochemistry, and increasingly
- 3:46comprehensive molecular data from next -generation sequencing.
- 3:50Tissue
- 3:54Interviewee: So the topic is multisource genomics to monitor clonal evolution for pancreatic cancer.
- 4:01Dr.
- 4:01Rizal Kurzok from Medical College of Wisconsin will provide an update for the talk.
- 4:07This
- 4:07Interviewer: meeting is being recorded.
- 4:09We will have two formats for Q &A.
- 4:13As the meeting progresses, please feel free to put your questions in the chat, in the chat box,
- 4:21and then we'll accommodate as many of the questions.
- 4:25And towards the end, we'll have some time for some live questions as well.
- 4:29So 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.
- 4:37I'll
- 4:37Interviewee: turn it over to Ken Bloom.
- 4:40Ken is OneCell's advisor.
- 4:43He's a strategic advisor to OneCell, also leads our CAPCLEAR certified laboratory in the San Francisco Bay Area.
- 4:52He will be providing an overview of OneCell as well as our OncoInsights technology.
- 5:00Right after that, before I turn it over to Rizal, I will ask all of the participants to go into the chat box.
- 5:09And there's a link there, which you can click.
- 5:12And it'll take you literally not more than 10 seconds to answer questions around what topics are relevant to you guys.
- 5:19That'll be important for us to understand.
- 5:21And we'll share some of that either towards the end or as a follow -up.
- 5:25And
- 5:30speakers: We've long sought biomarkers to effectively monitor tumor progression and response to therapy, but traditional methods have limitations. The topic of today's conversation is advanced liquid biopsies, focusing on both circulating tumor DNA and the emerging field of circulating tumor cells. This highlights the need for advancements in monitoring techniques?
- 5:53Interviewee: biopsy has allowed us to predict prognosis and in the era of precision medicine to predict therapy response and potential resistance mechanisms.
- 6:03Interviewer: However, as biopsies become smaller and smaller, our analysis becomes less reliable because of tumor heterogeneity.
- 6:10A 5 micron section from a 1 centimeter tumor represents only a fraction of a percent of that tumor.
- 6:17So 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
- 6:25sentence of the book.
- 6:26You get a snapshot, a static picture.
- 6:29And while that provides actionable data, it creates a gap in our ability to monitor cancer's evolution.
- 6:35And this has direct consequences for patient management.
- 6:43DNA, or circulating tumor DNA, has emerged as the latest tool in our monitoring arsenal.
- 6:48It's real -time, and it reflects what's happening now since the half -life of DNA is on the order of a few hours.
- 6:55But CT DNA only gives you the genetic sequence of the fraction of tumor cells that have recently died.
- 7:02It can miss low -frequency mutations entirely, and of course, it will likely miss emerging clones that are actively proliferating but have not
- 7:10yet died.
- 7:11But
- 7:11Interviewee: more importantly, as antibody drug conjugate therapies have emerged, CT DNA doesn't give us any useful information about
- 7:19protein expression or localization.
- 7:22This means we're all making patient selection and endpoint decisions based on incomplete, often outdated information.
- 7:29But that's a solvable problem, and it's exactly what OneCells platform addresses.
- 7:34Our solution is called OncoInsights, our proprietary platform to capture and comprehensively analyze circulating
- 7:42tumor cells.
- 7:49Interviewer: earliest systems utilized single -marker immunocapture and fixed the cells, making them largely unsuitable for comprehensive downstream analysis.
- 7:58Other systems used negative selection by depleting hematopoietic cells or size -based methods, but these suffered from
- 8:06high background noise and low purity.
- 8:09OncoInsights
- 8:10Interviewee: solves these limitations with a combination of multi -marker affinity capture and a cleavable linker allowing capture of live
- 8:17CTCs with no cell damage.
- 8:19Instead of a single hook, we use customized capture beads coated with multiple antibodies targeted to a specific cancer
- 8:27type.
- 8:28For
- 8:28Interviewer: most cancers, a combination of Epcam and Transferrin works effectively, but the beads can be customized to optimize capture.
- 8:35For example, many renal cell cancers don't express Epcam at high levels, expressions quite low.
- 8:42So adding CD70 to the beads dramatically increases the CT positivity rate.
- 8:48Critically, this allows for the capture of the full diversity of tumor cells, not just the most common ones.
- 8:54Once the cells are captured, they are released intact using a cleavable linker system.
- 9:00No bead contamination, no cell damage.
- 9:02So the cells are ready for multi -omic analysis.
- 9:06So this is where things get really exciting because of what you can measure from these capture CTCs.
- 9:12The OncoInsights panel covers three biological layers simultaneously from the same blood draw.
- 9:18First, DNA.
- 9:201080 gene panel covering point mutations, insertions, deletions, gene fusions, copy number variations, and
- 9:28chromosomal rearrangements.
- 9:29It also gives you tumor mutational burden, microsatellite instability status, and homologous
- 9:36recombination deficiency status.
- 9:38All of the genomic biomarkers that predict response to immunotherapy, PARP inhibitors, and targeted agents.
- 9:48Second
- 9:48speakers: is protein expression.
- 9:50This is currently measured by immunofluorescence on individual cells.
- 9:54You can directly quantify the proteins a drug is targeting, such as HER2, TROP2, clodin -18, nectin -4, etc.
- 10:02If
- 10:02Interviewer: developing an antibody drug conjugate, for example, this tells you whether the target is actually present at the protein level on cells
- 10:10circulating right now during treatment.
- 10:13Third
- 10:14Interviewee: is RNA, or whole transcriptome profiling.
- 10:17That's about 16 ,000 markers.
- 10:19This is your window into gene expression, what pathways are active, what resistance mechanisms might be turning on, and what's changing
- 10:27over time.
- 10:28For
- 10:29Interviewer: drug programs, this isn't just biomarker discovery.
- 10:31This is real -time pharmacodynamic monitoring.
- 10:35You can track whether your drug is hitting its target, whether resistance is emerging, and which patients are likely to respond.
- 10:42Any new technology lives or dies on its data, so let's look at the numbers.
- 10:46Across more than 2 ,000 patient samples spanning lung, breast, pancreatic, colorectal, liver,
- 10:54head and neck, prostate, and gallbladder cancers, the
- 10:59speakers: This technology allows for real-time pharmacodynamic monitoring, tracking whether drugs hit their targets and identifying resistance.
- 11:09Interviewee: overall CTC positivity rate, or our ability to detect CTCs, was 83 % for stages stage
- 11:172 through stage 4 patients, but metastatic patients had approached 100%.
- 11:22Let me put that in context.
- 11:24Our first generation of CTC capture technology yielded a mean of about 5 CTCs per sample, while our current
- 11:32platform yields a mean of about 21 CTCs per sample.
- 11:36That's a four -fold improvement, and more cells means more material for downstream analysis, more genomics, more protein
- 11:44profiling, more confidence.
- 11:47An
- 11:49Interviewer: 83 % to 100 % positivity rate across solid tumors means that the vast majority of your enrolled patients can be monitored longitudinally
- 11:57with this platform, and that's a game -changer for adaptive trial design.
- 12:01One more important point before we move on, and this is particularly relevant for CNS cancers and thoracic malignancies.
- 12:08The technology isn't just limited to blood.
- 12:11At one cell, we've demonstrated CTC capture, or tumor cell capture, from cerebral spinal fluid
- 12:19and pleural fluid.
- 12:20In CNS tumors like glioblastoma and medulloblastoma, where a blood draw tells you almost nothing about what's happening in the brain,
- 12:28CSF -based CTC analysis opens a completely new window.
- 12:32This is significant for clinical trials and CNS malignancies, where biomarker development has lagged far behind other tumors.
- 12:39Now, generating all this data is only valuable if you can act on it, and that's what the iCORM platform is designed to do.
- 12:48iCORM is one cell's integrated precision oncology consult.
- 12:52Think of it as the intelligence layer that sits on top of the laboratory data.
- 12:57It has two primary interfaces.
- 13:00iDiscover for translational research and clinical trial support, and iCare for the treating oncologist.
- 13:06For those of you in pharma, iDiscover is the critical piece.
- 13:11It integrates multiomic data from CTCs and CT DNA, radiologic
- 13:16Interviewee: imaging, pathology images, and real -world evidence data sets.
- 13:21It uses AI and machine learning to identify patient populations most likely to respond to a given therapy, flag resistance
- 13:29markers as they emerge, and help you understand mechanisms of action in a way that bulk tumor sequencing simply can't provide.
- 13:37It also adds the missing temporal layer to AI.
- 13:41It allows AI to begin to understand how tumor cells are adapting and what to do about it.
- 13:47Imagine being able to enrich your clinical trials for responders before the trial even starts, based on real -time
- 13:55CTC protein expression in genomics, rather than on archival tissue.
- 14:00That's the promise of iCORM.
- 14:02You get smarter enrollment, more informative biomarker endpoints, and ultimately, a cheaper path to approval.
- 14:10With that as background, I'll now turn the slides over to Dr.
- 14:14Curtis Rock, who's going to present her exciting data on the clonal evolution in pancreatic cancer.
- 14:19But first, there will be a few polling questions.
- 14:22So, Arshad, I guess that goes to you next.
- 14:25Yes, thanks.
- 14:26Thanks, Ken.
- 14:27Appreciate that.
- 14:28If I can ask all the participants, if you can go to the top of the chat room, there's a link there
- 14:36from, it's called forms .gle.
- 14:40If you guys just click that link, I promise this won't take more than 10 seconds.
- 14:43It's going to ask some basic questions on what are the types of areas that are important to you, and that's it.
- 14:49Just 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.
- 14:56So, over to Razelle.
- 15:01So, a pleasure to work on this project and with this
- 15:08really interesting technology.
- 15:11And we really wanted to concentrate on pancreatic ductal adenocarcinoma for several reasons.
- 15:17One is because our institution really has a world -class program in this cancer.
- 15:25And the second is because it is such a difficult cancer.
- 15:29The five -year survival rate is about 13%, despite advances in surgery and systemic therapies.
- 15:37And it's actually worse than that.
- 15:39There's a recent paper in JAMA that shows that the one -year survival is about 24%.
- 15:45So, we have a long way to go to learn how to deal with this cancer.
- 15:51And it is projected to become the second leading cause of cancer -related deaths in the United States.
- 15:58And so, we really need to improve our understanding of this cancer.
- 16:04speakers: ductal adenocarcinoma progression involves stepwise accumulation of key driver mutations,
- 16:11which are mainly known to be KRAS, the cyclin system,
- 16:18CDKN2AB loss, and P53.
- 16:23And tumor evolution also includes rapid genomic restructuring characterized by
- 16:30copy number variations and large chromosomal rearrangements following
- 16:36polyploidization.
- 16:40So, this is a difficult cancer.
- 16:43And the reason, one of the reasons it's difficult is because of the great heterogeneity between patients
- 16:51and even within patients with time.
- 16:54And that's really difficult to capture if what you're doing is a baseline tissue biopsy.
- 17:02Um, so, um, there are a lot of limitations to bulk sequencing.
- 17:10Um, and, uh, some of them are illustrated here.
- 17:15Uh, so, we use bulk sequencing to understand, um, cancer.
- 17:22But the problem is that it doesn't really show us what happens with time, what happens with
- 17:29successive, um, mutational events.
- 17:33And, um, it cannot, um, extinguish, it cannot distinguish what is
- 17:41happening in different clones of cells.
- 17:44So, if we see, do single cell sequencing, we can see, are there co -occurring versus
- 17:52mutually exclusive alterations in different cells?
- 17:56Might this explain, um, mixed responses to drugs, uh, like PARP inhibitors, KRAS inhibitors,
- 18:04and immunotherapy.
- 18:06And so, single cell DNA sequencing is really required to resolve the clonal
- 18:14architecture of pancreatic ductal adenocarcinoma from early invasion through systemic,
- 18:21uh, dissemination and to identify molecular vulnerabilities targetable with precision
- 18:29therapies as the, as the disease evolves.
- 18:32Uh, so, this is a study that we initiated, um, and, uh, the purpose of
- 18:40the study was to isolate single circulating tumor cells from pancreatic cancer patients prior to treatment
- 18:48and perform genomic profile to characterize cellular level genomic heterogeneity, and also to
- 18:56follow these patients during treatment.
- 18:58And, uh, uh, this, uh, study is led by Dr.
- 19:03Mondana Kamgar and myself at MCW and Dr.
- 19:07Kremolini at, uh, University of Pisa.
- 19:10And, uh, we've collected quite a few samples and I think, um, I'm happy to share with you some of the
- 19:18insights, uh, from these samples.
- 19:20Next, uh, slide, please.
- 19:24So, all together, uh, we now have 26 patients, 63 total samples,
- 19:32um, and, uh, five time points tracked.
- 19:36And, uh,
- 19:48uh, uh, uh, uh, this slide, I think we have some fascinating insights, um, at this, uh, time.
- 19:54And, um, um, I want to share those with you.
- 19:57So, uh, first, um, uh, this slide, I think really illustrates, uh, some of the insights,
- 20:06uh, from the study.
- 20:07Um, so if we look at, uh, patients that have CT DNA only
- 20:14versus, uh, CTC DNA only, we're getting a lot more alterations
- 20:22from the CTCs, which you can see on the right, than we are getting from the CT DNA.
- 20:28And this in the middle are some of the shared alterations, um, that you see.
- 20:34So there's a lot of common things, but themes.
- 20:38But in addition, I think that both the CT DNA and the CTCs bring their
- 20:46own information.
- 20:47And I think you can see how rich the information is that is coming, um, from the CTCs.
- 20:55Um, so this, uh, slide shows, uh, the longitudinal, uh, CTC,
- 21:02uh, DNA and, uh, CT DNA longitudinal
- 21:10mutational landscape.
- 21:12And I'm going to go into, um, more detail in a moment, but if you go to the
- 21:19right side, this is patient by patient.
- 21:22And if you go to the right side of the slide, you can see, um, on the, um, Y axis on the
- 21:30right side, uh, the red is CT DNA and the green is CTCs.
- 21:37And we're going to go to higher level magnification, but at, uh, but you can see already from these slides
- 21:45that the CTCs and the CT DNA do not always tell you the same thing.
- 21:52Um, they give complimentary information sets.
- 21:58Um, so this, uh, focuses in, um, on, uh, what we see
- 22:05in, um, for instance, CT DNA, which is in the red and CTCs, which is in the green.
- 22:12And, um, what you can see is that in some, in some situations we're seeing the same thing,
- 22:20but in other situations we actually see, um, uh, more of certain mutations
- 22:28in the CT DNA than in the CTCs.
- 22:32Um, and, um, so one of the interesting things that we found
- 22:39with this is that, um, as we began to look at the CTCs
- 22:47versus the CT DNA, um, the, uh, we began to see something that we found
- 22:55initially confusing, but now we think it is absolutely fascinating and really goes again,
- 23:03uh, along with evidence published very recently in, uh, nature genetics by the Sloan Kettering group.
- 23:11Um, so in the CTCs, we're finding, for instance, we find alterations not found
- 23:19in the CT DNA.
- 23:21In the CT DNA, we find alterations not found in the CTCs.
- 23:26And, um, if we put, and some, of course, uh, of the alterations are found both in the CTCs
- 23:33and the CT DNA.
- 23:35Um, but this is, I'm going to give you an example of something that we thought was really fascinating and actually
- 23:42very relevant to therapy.
- 23:45Um, so a subset of, uh, patients with KRAS, as the tumor evolves,
- 23:54there are CTCs that appear to lose, uh, their KRAS.
- 23:59And, um, this was at first a bit confusing to us, but it turns out this
- 24:07is very consistent with what other, um, investigators are finding when they're looking at single cell
- 24:14populations.
- 24:15Um, and, uh, for instance, the Sloan Kettering group in nature genetics about a year ago
- 24:23published that about 40 % of the individual clones in pancreatic cancer were
- 24:30losing their KRAS.
- 24:32And, um, this is precisely what we're seeing as we follow individual
- 24:40CTCs and, um, uh, see that there are different clones of CTCs and not
- 24:48all of them retain, for example, um, their CTCs.
- 24:53So we're, uh, their KRAS.
- 24:55So for instance, we're seeing KRAS negative, uh, CTCs.
- 24:59Um, sometimes in the KRAS negative CTCs, the MEC pathway is still,
- 25:07um, a driver.
- 25:09For instance, they may have SMOD4 or they may have other alterations in that pathway, but not always.
- 25:16Some of these, uh, CTCs are probably losing different pathways or exploiting different
- 25:23pathways in order to, um, propagate, uh, the pancreatic cancer.
- 25:30Uh, so this goes back to our prior slide and I want to now focus on
- 25:37the Y -axis to the right and, um, um, the green
- 25:45part of that access.
- 25:46And that's the CTCs.
- 25:49And you can see that there's, um, multiple alterations that can be found in CTCs that cannot
- 25:57be found in the CT DNA.
- 26:00Um, so before we focused on some of the alterations, some of the CTCs that were losing
- 26:07alterations, now we're going to focus on, um, some of the alterations found in CTCs that
- 26:15cannot be found, um, in the CT DNA.
- 26:19And, uh, so you can see there's a whole, um, group of alterations
- 26:26that were being, that were finding in the CTCs.
- 26:30And, um, these alterations are not found in the bulk, uh, CT DNA.
- 26:36And since the CTCs may reflect the evolution of cancer, pancreatic cancer, and other
- 26:44cancers, and also may be seeding some of the metastatic sites, these additional alterations
- 26:52may be critical to thinking about therapy.
- 26:55And then, um, the final, um, part of this, uh, slide, if you look on the, on
- 27:03the Y axis to the right, uh, the bottom of the right axis, you can see the red dots.
- 27:10And this is the CT DNA only.
- 27:12So there are alterations also found in CT DNA that are not found in CTCs, um,
- 27:20less so than vice versa, but there are certain alterations in some of our patients.
- 27:26Uh, this shows, um, some of the alterations found in individual patients in the CT DNA and not
- 27:33found, um, um, in the CTCs.
- 27:36So when we put all of this together, the bottom line is we need both sources of information.
- 27:44We need the CT DNA and we need the CTCs.
- 27:48And this again puts together, um, some of the alterations found in the CT DNA only, some of the
- 27:56alterations found in the CTCs.
- 28:00And, 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
- 28:08the shared alterations.
- 28:10So these are complementary techniques and this type of liquid biopsy is really unique in that it can
- 28:17give, um, investigators the full picture of what is going on in an individual patient.
- 28:25And, um, likely the difficulty with pancreatic cancer, metastatic pancreatic cancer, and
- 28:33probably many other, uh, cancers is that we've been getting a very partial picture.
- 28:40Um, if we do tissue biopsy, we get a picture at one point in time of one small piece of tissue.
- 28:48If we do a liquid biopsy, a blood biopsy, but we do CT DNA, we can get a serial picture
- 28:56of what is happening in the cancer, but it's a bulk serial picture.
- 29:01And we're not seeing what is happening in individual cells, which may reflect a tremendously
- 29:08important, um, biology of the cancer and also may reflect, um,
- 29:16seeding of new metastatic sites and how those clones may be different, um, may be the key, uh,
- 29:24to understanding, um, our next, uh, step in steps in therapy.
- 29:30So, um, this, um, emphasizes the point that we
- 29:38kind of always known, but here we have clear cut evidence for it, um, pancreatic
- 29:45cancer and probably every other cancer has a lot of tumor heterogeneity.
- 29:51And in addition with time that tumor heterogeneity, um, becomes
- 29:59worse.
- 29:59It undergoes molecular evolution and, uh, there are, uh, new alterations that are appearing.
- 30:07There may be old alterations that are muted or disappear.
- 30:15And, um, to reiterate tissue biopsy or just bulk CT DNA
- 30:23cannot outline all that is happening at a single cell level.
- 30:29And so CTCs demonstrate molecular diversity of the tumor at the baseline, uh, which is
- 30:37hidden with bulk CT DNA and tissue analysis.
- 30:42CTCs allow you to follow that on a regular basis and see what is
- 30:49happening at a single cell level as the cancer progresses.