Improving Cancer Immunotherapy with Dr. Alma Cepika

On this episode of Scrubcast, Dr. Alma Cepika, assistant professor in the Division of General Surgery and chief of its new Surgical Sciences Section, explains how regulatory T cells help prevent the immune system from causing unnecessary damage. She introduces the differences between FOXP3 regulatory T cells and type 1 regulatory T cells, or TR1 cells, and makes concepts such as multi-omics, transcription, epigenetics, and in vivo research accessible through everyday analogies.

The conversation explores her team’s research identifying TR1-like cells in human cancers and investigating whether these cells may suppress antitumor immunity or contribute to resistance to checkpoint inhibitor therapy. Dr. Cepika also discusses the complex role of TR1 cells in transplantation and persistent infection.

Finally, she shares how advice from a movie helps her keep her calm, reveals her preference for punk rock in the lab, and describes opportunities for researchers and trainees to join her growing laboratory.

Read the article in Science Advances 

*Music by NastelBom*

Rachel Baker: [00:00:00] Welcome to Scrubcast, where we take a closer look at the research happening at Stanford University's Department of Surgery. I'm your host, Rachel Baker. Today we're speaking with Dr. Alma Cepika. Thank you for joining us.

Alma Cepika: Thanks for the invitation, Rachel.

Rachel Baker: Of course. Dr. Cepika is an assistant professor in our Division of General Surgery, and chief of our new surgical sciences section.

Dr. Cepika has a PhD in immunology and previously worked in the Department of Pediatrics. What brought you over to the adult side?

Alma Cepika: So my postdoctoral training before I joined Stanford was focused on identifying mechanisms of immunopathology using directly patient samples. But as an MD, not just a, a PhD, I still wanted to learn how to translate these discoveries into clinical practice, and that's why I initially joined the Department [00:01:00] of Pediatrics at Stanford.

I joined the lab of cell and gene therapy pioneer Maria Grazia Roncarolo, who developed a cell therapy to improve hematopoietic stem cell transplantation in-house as it was translating into the clinic. And once Maria Grazia retired, I started looking for independent faculty positions, and the position in Division of General Surgery seemed to be like a perfect fit.

It has a large clinical operation, which meant plenty of opportunity to collaborate with different faculty, to continue my studies of, of human immune system and its role in disease. And the division has a very supportive division chief, Dr. Electron Kebebew, who is keen on expanding basic and translational research infrastructure.

Rachel Baker: Fantastic. Well, I'm so glad he was able to woo you to our department. I try to make our episodes inclusive for all listeners, uh, particularly when we tackle a new [00:02:00] field in basic science. Would you mind if we start off with a little vocabulary lesson?

Alma Cepika: Yeah, sure.

Rachel Baker: All right, so the first word I have is Treg, T reg.

I don't even know if I'm pronouncing that right.

Alma Cepika: So it's T-reg ... it's short from regulatory T cells, and these Tregs are distinct cells from TR1 cells or type 1 regulatory T cells.

Rachel Baker: Got it. Okay. What is the difference between a Treg and a TR1 cell?

Alma Cepika: So both cell types really act as brake on the immune system.

So they- Mm-hmm ... their original purpose is to prevent our immune system from attacking things it shouldn't attack. Both cell types express key marker protein CD4, which classifies them as helper T cells, as opposed to CD8 T cells that [00:03:00] kill target cells, such as cells that are infected or tumor cells.

Rachel Baker: Mm-hmm.

Alma Cepika: And the main difference between the CD4 Tregs and TR1 cells is where they come from. Tregs are kind of born into the job. They are made in the thymus. Mm-hmm. Uh, they carry a protein, uh, which is a transcription factor called FoxP3, and they are a distinct lineage of T cells. That is, once they are exit the thymus in the peripheral blood and start circulating around the body, and their main role is to prevent autoimmune disease.

And 2025 Nobel Prize in Physiology and Medicine was actually awarded for the discovery of these cells.

Rachel Baker: Cool.

Alma Cepika: So on the other hand, TR1 cells have a very similar functional role, and they act, uh, in a similar way. So they use the tools as FOXP3 T-regs to prevent this excessive [00:04:00] inflammation, but they do not have FOXP3.

They are not born in the thymus, but they are actually made from CD4 T cells that have already left the thymus, that are so-called conventional CD4 T cells.

Rachel Baker: Okay.

Alma Cepika: And these T cells become TR1 cells when they see the same antigen over and over again, or a lots of the same antigen at the same time in the presence of certain anti-inflammatory proteins that facilitate this conversion.

And in that way, TR1 cells are evolutionary adaptation of our immune system that was probably arose to prevent chronic or severe acute inflammation that can cause more harm than good. Now, this is something that can be exploited by cancer

Rachel Baker: [00:05:00] What is multi-omics?

Alma Cepika: Oh, multi-omics. So, it means that we are capturing each type of genomic data at once at the same time.

Mm-hmm. Uh, and then we are kind of stacking these layers on top of each other and using bioinformatics to, to connect all of it. A good analogy would be, like, all the different ways that can use Google Maps. So you have just a street layer, but then you have a traffic layer, you can have

Rachel Baker:  The satellite layer

Alma Cepika: the satellite view. Exactly. And by using all of these layers together, you can actually see how the city works and not just the names of the streets.

Rachel Baker: Cool. The next word I have is transcription, which for me is when I make a Word document from an audio file, but I'm imagining that's not how you use this word.

Alma Cepika: No, actually, it's really the same idea. So, the... Using your analogy, a [00:06:00] reporter writing a news story after they- Mm-hmm ... interviewed someone would transcribe the audio interview into a Word document. And for a cell, it's a DNA, so the genetic material that is cr- transcribed into RNA. And DNA is the archive, so it, it codes the genes that are exactly the same in every cell that, that we have in our body.

But the RNA is the working copy of the DNA, those genes. That cell makes what it needs to use some of the genes and build something into a protein. So, when we say transcribed, it means that the cell went to the archive, to the DNA, and made a working copy of the DNA that is going to be translated into a protein, and this working copy we can measure, uh, by measuring RNA.

Rachel Baker: I love that. Okay, next word, epigenetic. It's like genetic, but with an epi- pen

Alma Cepika: Yeah, yeah. Exactly. Epi means on top, and this means basically there is a layer of information [00:07:00] that is distinct from DNA and RNA. It sits on top of the DNA. It's not heritable, but it's... this is a very important layer because it really decides which part of the DNA gets read and transcribed into a protein.

Rachel Baker: All right. Last word. Well, it's, it's two words. It's in vivo. So for all of us that didn't take Latin, this means that you're doing experiments in a living model?

Alma Cepika: Yes, it's correct, in a living model, in a... it means a living org- organism, so not just in a model like in the mouse model, but also it includes people.

So clinical trials are in vivo experiments. When we look at data in, let's say, a protein expression in vivo, it means that we analyzed, for example, patient tissue without modifying it in a dish. Got it. If we, for example, take the patient tissue out and modify it in a dish, we call these experiments ex vivo, so we did [00:08:00] something with it when we analyze it.

And if we modify it a lot, like for example, we edit the genes or we convert the primary tumor cell into a cell line, then these become in vitro experiments, like in a glass dish.

Rachel Baker: Fabulous. All right. I feel like I'm on much more solid footing now. Let's talk about this recent paper that you published in the journal Science.

It came out on July 10th. Here's the title, Epigenetic Landscape, Key Transcriptional Regulators, and In Vivo Identification of Human TR1 Cells.

Okay, so reading the paper, I think the first sentence that really stood out to me was this one, "Data from solid tumors indicate that TR1 cells suppress anti-tumor immunity."

Are you saying what I think you're saying here? Did, did cancer figure out how to use our immune systems against us?

Alma Cepika: Uh, yes. [00:09:00] Yes, in short, yes, although I would say the tumor didn't invent anything. It exploited something that we already have. You know, if you think about the tumor microenvironment, we have persistent antigens-such as tumor antigens, and we have lots of anti-inflammatory proteins because tumors tend to hide themselves from the immune system and create this tolerogenic environment.

So this kind of environment, can induce TR1 cells, and basically the tumor is kind of running the same protocol that we use in the lab to induce TR1 cells in the dish, and it teaches the immune system to tolerate it So, you know, what we did in this study, and it was study in Science Advances, not in Science

Rachel Baker: oh no!

Alma Cepika: No, it's okay. I would love that it's in Science, but it's the same family of journals.

Rachel Baker: ohhhhhh.

Alma Cepika: So what we did in this study is we have found cells that were very eerily similar to TR1 [00:10:00] cells in couple of different cancers. And we also found that these cells that look like TR1 cells were clonally expanded inside of the tumor, which mean the s- the one cell that found the antigen that they recognize--it just started multiplying.

Rachel Baker: Oh.

Alma Cepika: So they didn't really wander into the bloodstream by random. They are actually responding to an antigen inside the tumor. So this is what we found in human. And we found, using the method that we use to find these cells in human cancers, we also managed to identify TR1 cells in one published mouse model, which was very important because it validated the technology, this transcriptional signature that we used to identify these cells.

And this mouse model was very, very informative. So it was a very [00:11:00] beautiful nature paper published in 2024 from a WashU lab in St. Louis showing that TR1 cells in a murine sarcoma model actively cause resistance to checkpoint inhibitor therapy, to anti-PD-1, independently of FOXP3 Tregs. And this really convinced us that we need to keep digging, and this is what my lab is currently focused on, to better understand whether these TR1 cells we have identified in the tumor also function in a similar way as in the mouse.

So they are the bad guys in the tumor, and they can inhibit this anti-tumor immunity. The reason it matters right now especially is because there is a class of drugs that has been developed called antibodies that bind to a certain protein expressed on FOXP3 T regs called CCR8. And these are [00:12:00] tested in at least eight or more clinical trials as means to deplete FoxP3 Regs from the tumors.

Rachel Baker: Right.

Alma Cepika: But TR1 cells do not express CCR8. So if a meaningful part of the suppression in a given tumor is coming from TR1 cells, those drugs will just walk straight past them. So we need to know if solid, human solid tumors contain TR1 cells, and if they're the bad guys like in that mouse model.

Rachel Baker: Makes sense. But even if they are the bad guys, it's not like you can just turn them off, I'm guessing, because then wouldn't we all just end up with chronic inflammation and autoimmune diseases?

Alma Cepika: So with these TR1 cells that are inducible, they seem to disappear when there is no more antigen.

Rachel Baker: Ah, okay

Alma Cepika: And this is kind of the difference between [00:13:00] FOXP3 Tregs and TR1 cells.

They serve, I think, two different evolutionary purposes. FOXP3 T regs are really geared to recognize self-antigens. So if we don't have FOXP3 T regs, like some patients with diseases that have mutations that prevent the development or function have, these patients develop very severe multi-organ autoimmunity.

So they have their own T cells start attacking their pancreas, so they will develop diabetes. They have autoimmune thyroiditis. They have lung disease, dermatitis. So it seems to be that the primary role of FOXP3 T regs is to defend against autoimmune disease. Now, what happens if there are some antigens that these T regs do not encounter during their development in the thymus?

Rachel Baker: Mm-hmm.

Alma Cepika: So this could be where [00:14:00] TR1 cells jump in. For example, if, if you have a chronic infection, and this chronic infection is persisting, so you need to make sure that the immune system is not constantly in the on phase and bringing in these CD8 T cells that kill target cells, because you're going to have so much collateral damage you can kill the patient by trying to cure the disease.

So you can think of the TR1 cells, if FOXP3 T regs are not recognizing this particular antigen, TR1 cells could be very useful. But then when this antigen is gone, we don't see TR1 cells persisting in the peripheral blood as FOXP3 T regs do- which circulate all the time because our self-antigens, our autoantigens, they never disappear.

Rachel Baker: Got it.

Alma Cepika: The instances [00:15:00] where we see TR1 cells  that are persisting are, for example, in allogeneic transplantation where we give stem cells from one donor into a patient that has a different HLA makeup.

Rachel Baker: Mm-hmm.

Alma Cepika: And then we have TR1 cells seeing hostile antigens, and because they are there in the body and the antigen makeup of the host is different, these TR1 cells do not go away.

And we see them, for example—and this was a collaboration my former mentor had at Stanford—in patients that have persistent or recurrent malaria infection.

Rachel Baker: Hmm.

Alma Cepika: So it seems every time these kids get reinfected with malaria, the TR1 cells come up. And when the infection is clear, they go away, and then they come up again, and then they go away.

And in this case, it is very hard to understand: were they good guys or [00:16:00] bad guys- because they could actually prevent this very, very severe inflammation that malaria is known for, but they could also maybe facilitate reinfection.

Rachel Baker: Gotcha. So TR1 cells are the Batman of superheroes. We're not sure if you're a good guy or a bad guy. We will find out in a later episode, hopefully.

Alma Cepika: We will find out, hopefully, yes. At least in, in tumors.

Rachel Baker: Well, so that sound means it is time for our lightning round. On each episode of Scrubcast, we ask each of our guests the same three questions, uh, with a few adjustments for our researchers.

The first one is, who is a researcher you admire and why?

Alma Cepika: You know, I tend to, not to idolize people.

Rachel Baker: Hmm.

Alma Cepika: Uh, because it could be dangerous to meet the hero. So, you know, instead, I appreciate the work people do. For example, like [00:17:00] this Nature paper that I mentioned from WashU, did these very, very elegant experiments with fantastic controls. I do admire scientists I have the opportunity to meet and interact with, and know them as people. But, you know, it's very hard for me to single out one of them because then the other ones could be offended, so: Next question.

Rachel Baker: The second question is, what is the best advice you have received in 10 words or fewer?

Alma Cepika: Can I do it in 10 words, words or fewer? So it is from a movie called Bridge of Spies.

Rachel Baker: Okay.

Alma Cepika: and the Tom Hanks is playing a lawyer that is defending this spy, and the spy is facing some very dire consequences, and the things are not going his way.

Rachel Baker: Oh! I've seen this!

Alma Cepika: And Tom Hanks keeps asking [00:18:00] him, you know, "Why are you not stressed? Why do you not worry?" And, and the spy ask, "Would it help?"

Rachel Baker: Hmm.

Alma Cepika: And these three words, it's really kind of something clicked in me. And I understood that there is absolutely no point in getting upset about things that may happen in the future but will not happen yet, or things that are completely out of your control.

Rachel Baker: Oh, I like that. Okay. Final question, what is your preferred lab music?

Alma Cepika: So, I listen to many different genres of music, including classical music. My mom is a piano teacher, so in case she listens to this interview, I have to mention that I'm not just defined by one style. But if it comes to lab music, it's punk rock.

Rachel Baker: Ah, okay ...

Alma Cepika: You know, either, either the classics, is like Clash or Green Day or, or- Mm-hmm ... or newer bands, like [00:19:00] Australian girls called Amyl and the Sniffers. So. Yeah.

Rachel Baker: Oh, I'll have to look them up. Um, well, that's fantastic. It has been such a pleasure chatting with you, and I'm so happy that we got to sit down and have this conversation. Before we go, final question as always, what is next for Dr. Cepika?

Alma Cepika: Next, I am trying to expand my lab. I am, uh, recruiting another postdoc. My first postdoc, Saul, is doing an amazing job. Hopefully, a research assistant, and I'm happy to welcome PhD students for rotations, for projects, as well as any residents that might be interested in doing basic and translational research.

Rachel Baker: Ooh, fantastic. Hear that, everybody? She's got some positions. Awesome. Well, I look forward to, you know, seeing everything that your lab comes out with and reading your future papers. Thank you so [00:20:00] much for coming on the show.

Alma Cepika: Thank you. Thank you so much, Rachel. Bye.

Rachel Baker: And thank you to our listeners for tuning in to this episode of Scrubcast. Don't miss our other conversations just like this one. Subscribe to Scrubcast wherever you listen to your podcasts. Until next time, stay sharp