This Science Snapshot episode highlights oncology research-related conversations from past Absolute Gene-ius interviews, featuring expert insights on CAR-T research, CRISPR-generated animal models, cell-free DNA, circulating tumor DNA, and multiplex digital PCR assay design. Together, the clips show how molecular biology tools are helping researchers ask better questions and study cancer with greater analytical sensitivity, precision, and biological relevance.
Cancer research is moving fast, and molecular tools are helping scientists see more, measure more, and ask better questions.
In this Science Snapshot episode of Absolute Gene-ius, Jordan Ruggieri and Lisa Crawford revisit memorable oncology-related clips from past conversations. Dr. Raquel Munoz explains how CAR-T cells are engineered to recognize and kill cancer cells, and how PCR-based methods can help confirm successful modification and track CAR-T expansion. Dr. Dustin Rubinstein shares how CRISPR and genome editing are being used to create pig models, including “onco-pig,” that may better reflect aspects of human cancer biology than traditional models. The episode also connects cell-free DNA research from Dr. Lee Ann Baxter-Lowe to oncology applications, before turning to Dr. Kathie Sollweck’s discussion of circulating tumor DNA and the sensitivity needed to detect low mutational burden in liquid biopsy research. Finally, Valeria Rangel offers practical perspective on multiplex PCR assay design.
And because it is Absolute Gene-ius, the science comes with some laughs, a few pig jokes, and a reminder that even complex oncology methods can be surprisingly fun to talk about.
Lisa Crawford 00:00
Me too.
Jordan Ruggieri 00:00
I've enjoyed it. I've enjoyed it.
Lisa Crawford 00:02
I enjoyed it. I've enjoyed. Okay.
Jordan Ruggieri 00:10
I've really, really enjoyed it.
Lisa Crawford 00:13
Okay, I didn't enjoy that much.
Jordan Ruggieri 00:15
Welcome to a Science Snapshot episode of Absolute Gene-ius. I'm Jordan Ruggieri.
Lisa Crawford 00:32
And I'm Lisa Crawford.
Jordan Ruggieri 00:33
In this episode, we bring you highlights from past interviews focused on oncology-related research. We'll hear from experts about their innovative oncology research and the cutting-edge technologies being used in their labs.
Lisa Crawford 00:45
Absolutely. We've handpicked some really great clips from past genius conversations to give a sense of how science is transforming oncology. Let's kick things off with Dr. Raquel Munoz, who talked about CAR-T therapy research in season two. Many of us have probably heard of CAR-T therapy, but Raquel did a great job of explaining CAR-T and how this immunotherapy research is changing the way we fight cancer.
Raquel Munoz, PhD 01:08
It's a type of immunotherapy. We can use the immune system to protect from an illness. So we can modify the immune system, and for the treatment of this illness, and for example, with the CAR-T cell therapy, we obtain T cells that are immune cells. These are the fighters of the immune system. We can modify them in the lab and put a receptor, a specific receptor that can find and kill cancer cells. So we create the CAR-T cell that is the crowning of chimeric antigen receptor T cells, because we have added this chimeric receptor in the cell surface. So when we create these CAR-T cells, we can reintroduce them into the into a subject, and the CAR-T cells will find and kill the cancer cells in a specific way.
Jordan Ruggieri 02:18
That is, that is incredible. So when you are working with CAR-T, can you describe a little bit of how you know a modification was made properly?
Raquel Munoz, PhD 02:33
Yeah, we have markers gene. So we try to, we try to amplify these marker genes, so we know that the CAR-T cells that we have made have a specific gene. So if we amplify this gene, we know that we have done the CAR-T cell well, and if we don't see any amplification, we have failed with the with the construction of the CAR-T cell.
Jordan Ruggieri 03:07
Do the CAR-T cells stay a long time in a subject or do they do they degrade over time?
Raquel Munoz, PhD 03:16
We are researching about this because it's important to know how many days or even months the CAR-T cells still and do the work. Because we want that they work only in a period of time, because if they still, and they still killing, maybe we can have side effects we don't want to have it. Our main that we want to achieve is to measure how many times these cells is still in, in the blood, so we try to measure and describe what is the curve of the expansion of these CAR-T cells.
Jordan Ruggieri 04:14
I remember that conversation well, Lisa. CAR-T is truly a game changer, researching how to harness the immune system's own fighters to target and destroy cancer cells. It's pretty cool stuff. I remember her talking about how dPCR's precision and reproducibility are helping provide confidence in her CAR-T expansion studies. This was episode two of season two. If anyone wants to listen to the full conversation.
Lisa Crawford 04:38
Let's shift gears to genome editing and an example of how CRISPR technology is being used in conjunction with PCR and oncology research. Dr. Dustin Rubinstein from the University of Wisconsin-Madison shares how CRISPR is transforming disease research by creating powerful new models using an unexpected animal. Here's Dustin.
Dustin Rubenstein, PhD 04:56
I think one of the fun things, probably one of the big projects that we've had throughout my time here is developing models for neurofibromatosis type one, which is a rare monogenetic disorder. So, there's a single gene that causes it. It's rare in that it's like one in 3000 people, but if you think of 3000 people, that's not that many, and one of them probably has it. In a nutshell, we built some genome-edited pig models to recapitulate the mutations that we see in patient kids, and then you know used all kinds of genomic tools, imaging tools to try and better understand the disease. That's been a really exciting project. We've got a number of other projects too. We've just developed, I guess I'm just naming pigs here, but we do more than pig stuff, but we've created a pig that we call onco-pig, that we can actually induce genes that induce cancer. So, if you want to, if you have an, if you think you're, if you're a drug company, and you think you might have a new drug for kidney cancer, you know, we could give them, like, you know, kidney cancer, and if you think it might work well for, you know, liver cancer, we can give the pig liver cancer and induce cancers that way.
Jordan Ruggieri 06:06
Can you talk a little bit about why are pig models beneficial for things like cancer research? Why not other models like zebrafish or mouse, or, you know, there is there a particular reason that pig models are useful?
Dustin Rubenstein, PhD 06:20
The problem is that mice generally get cancer and die. Whereas, you know, with humans we're talking about, you know, managing this problem that is cancer. With mice, it's they get cancer and then they, then they die. So that is not really a great model for the way cancer actually works in humans. Pigs have a much similar developmental trajectory to humans, they're much more similar in size, right. So I'm like from, like, from the suburbs, so I always think when I heard pigs, I always thought, like, Charlotte's Web, like cute little pigs, but I didn't realize that pigs are basically like horses with short legs, like they're enormous. So if you want a pig that's actually going to match a human size, you have to use what are called mini pigs. So, when I'm talking about biomedical pigs, it's often these mini pig varieties that, again, are not that many - they're not like the cute ones you carry in your purse, right. That you know they are super adorable, you know, they're 150 pounds-ish, or a little higher. The idea is that they match humans.
Jordan Ruggieri 07:22
This onco-pig episode from season three really stuck in my mind, like mud to a pig, you might say, Lisa.
Lisa Crawford 07:28
Oh my god, Jordan.
Jordan Ruggieri 07:30
Oh man, Dustin was such a fun guest that made the topics and their complexity so approachable. Onco-pig is really a great example of how animal models are providing powerful platforms to research cancer progression in a setting that closely mimics human biology, so that these findings are more likely translational in the end. In fact, I think animal models could be a great future topic for one of these science snapshot episodes. Hint, hint.
Lisa Crawford 07:57
I agree on the animal models, and getting back to Dustin, I think he also did a great job shedding light on the diversity of CRISPR technologies being used to create animal models and monitoring disease progression in them.
Dustin Rubenstein, PhD 08:08
It's really exciting. So, I mean, I think from a fundamental perspective, we've always thought of genomes - we, it would be described in terms of like hard copies, right? It would be like if the human genome was printed, it would be like volumes that would go from the floor to the ceiling, you know, because we always talked about reading the genome and what's the genome sequence, but you know, for the first time we actually had the ability to not just, you know, read it in a printed form, but to actually like open it up in Word and change it. What you need to do in any science experiment is actually make the manipulation, and that's what CRISPR really finally allowed us to do. So there are actually versions of CRISPR now, where you don't even have to cut the DNA, right. And whether it's base editing or prime editing, some of these other really exciting things, where I mean you're just using CRISPR as a homing device into like a certain spot of the genome, and then once it's there, you can stick whatever kind of funky tools you want on it. There's all kinds of really creative ideas, and some of them are working, which is great.
Lisa Crawford 09:00
It's exciting to hear real-world examples of how gene editing is opening new doors. It makes the science all that more interesting, and the eventual goals that much more believable.
Jordan Ruggieri 09:09
Now, let's shift back to our roots and digital PCR with this next clip. Dr. Leanne Baxter-Lowe from Children's Hospital Los Angeles was a guest in season two, and she talked about detecting donor-derived cell-free DNA to research organ transplant health and rejection. While her work to detect cell-free DNA is not oncology-focused oncology, it’s fairly transferable in thinking about detecting circulating tumor DNA. Here's an exchange from that conversation about the challenges of detecting cell-free DNA.
Lee Ann Baxter-Lowe, PhD 09:38
First, the levels of cell free DNA in the blood are very low. Zero to 100 nanograms per mil.
Jordan Ruggieri 09:46
Oh, wow. Okay.
Lee Ann Baxter-Lowe, PhD 09:47
Yeah, very little. In a situation such as ours, we're interested in studying pediatric patients, so we want to be able to get results from a milliliter of blood. So that means we have to have an assay that can work with very little DNA input. Beyond that, when you're looking at the amount of donor-derived cell-free DNA in the midst of all the host cell-free DNA, there isn't very much most of the time. So, if you have a healthy graft, some of the literature suggests it might be as low as point 2% so you can imagine why I think digital PCR is a godsend.
Jordan Ruggieri 10:33
Definitely. How is this looked at? Let's say prior to digital PCR? How, and even maybe some of these techniques, how would somebody determine that there, there might be a response against that transplanted organ? Is it done molecularly, or is it done maybe proteomics, immunology? How does that work?
Lee Ann Baxter-Lowe, PhD 11:01
Historically well, actually, still a standard practice would be to use some sort of markers or indicators of organ function, and they're very insensitive. So in the case of kidney transplantation, sero creatinine is used as a biomarker, and then an invasive biopsy is generally used to determine if there's some pathology in the organ. There's a lot of new things coming out. There are assays that are looking at RNA, either in biopsy material or in blood, and looking at whether or not they can be useful biomarkers. It's a rapidly advancing field, and very exciting. It's providing new insights into the diagnosis of rejection, the pathways involved in rejection, and ultimately we believe that it's going to lead to better therapeutic interventions, as well as preventing damage in the first place.
Lisa Crawford 12:06
Digital PCR sensitivity is a topic that comes up in almost every conversation. It's almost always one of the primary reasons researchers are using it.
Jordan Ruggieri 12:13
Oh, definitely, Lisa. And to your point, let's parlay to a conversation that's specific to oncology and ctDNA research. In our recent conversation with Kathy Sollweck, she shares insights on the challenges of liquid biopsy research and how digital PCR sensitivity is key to detecting low levels of tumor DNA.
Kathie Sollweck, PhD 12:33
The challenge that we have is the quantity that's in there, obviously there is not much. So and that's again where digital PCR also comes into play. We need methods that are highly sensitive to be able to analyze this type of DNA. Because imagine your breast cancer sheds a lot; majority of that DNA will still be a normal, healthy, wild type DNA, so even though you might have okay amounts of DNA in there, I don't know, 20, 40 nanograms, your mutational burden and is usually pretty low. So you still have to have find a method that is able to detect those low level of mutational burden, so that is definitely a challenge, and also we have to be aware that with anything liquid, we have to be very stringent with pre-analytics. So we have to make sure that the general amount that we find is actually cell-free DNA, and not some, you know, blasted blood cells that shed all of their genomic DNA in there.
Jordan Ruggieri 13:32
More good stuff there. Leanne's and Kathie's clips really underscore how dPCR sensitivity is critical, helping detect and quantify rare events to inform research decisions, like you said earlier, Lisa. It makes progress and hope so much more real. Let's wrap this up with one more clip. This one is Valeria Rangel from UC-Irvine, sharing best practices for designing multiplex digital PCR assays to get more information from precious samples, which is really important in oncology research.
Valeria Rangel 14:01
I will say that for our most of our assays, we try to design both the primers and the probes to have similar melting temperatures. So then that way we don't really have to mess much with the annealing temperature once we move into the digital PCR aspect of things. I usually do test the primers by themselves using regular PCR, just to make sure I'm not getting any nonspecific annealing elsewhere in the genome. But yeah, I think once that's settled with regular PCR, and I know that I'm only getting one product at a specific temperature, I'll kind of move into digital PCR and use a similar annealing temperature. What has really helped me is there are different tools online where you can kind of put in your primer concentration to kind of dictate what the annealing temperature should be. For digital PCR, those primer concentrations and probe concentrations are very different from what you would use in a regular PCR. So making sure that I'm, you know, taking note of what the concentration is, so that way I get, you know, an accurate number from these tools has been pretty important, as far as you know, optimizing the assay, using the correct annealing temps, and whatnot.
Lisa Crawford 15:12
I'll admit that one's a little over my head on the science, but what I hear is that there are lots of details that need to be considered and balanced to develop the PCR and dPCR assays people use for oncology research and other applications?
Jordan Ruggieri 15:24
You got it right, Lisa. We cover a lot of research and application areas on this series, so it's been nice to narrow and highlight how molecular methods are helping progress oncology research specifically. I've enjoyed it.
Lisa Crawford 15:37
Me too. And with that, let's wrap up today's Science Snapshot. We hope these expert insights inspire you as much as they inspire us. Stay tuned for more upcoming episodes and be sure to subscribe to Absolute Gene-ius to get the latest content as soon as it's available. Until then, stay curious. This episode was produced by Sarah Briganti, Matt Ferris, and Matthew Stock.
Jordan Ruggieri 15:56
Products mentioned in this episode are for research use only, not for use in diagnostic procedures