On the trail of a cellular cold case

Transcript

Nick Wurm: You’re now At the Lab with Cold Spring Harbor Laboratory, where we talk about inspiring curiosity, discoveries, innovations, and the many ways that science makes life better. My name is Nick Wurm, and I’m joined today by Cancer Center Member and Assistant Professor Kate Alexander. We’ll be discussing mysterious cellular structures lurking inside the nucleus of every one of our cells. Their name? Nuclear speckles. Kate, thank you for joining me today. Let’s get started.

NW: So, I only learned about nuclear speckles a little while ago when you joined the Lab, but you’ve been studying these things for a while, right? How’d you get involved in this area of research? Like what about nuclear speckles first piqued your interest?

Kate Alexander: Growing up in science as a scientist, learning how gene expression works, you’re kind of taught a certain picture of it where the DNA is a line and the genes are kind of arrows coming off of it, and it gives you the sense of everything happening in two dimensions, but really that’s not what it looks like inside of the cell nucleus. It’s 3D. And what I didn’t realize at first was that it’s not just DNA inside the cell nucleus. It’s full of these different structures and compartments. And I realized that none of the textbooks told me about those, and especially—how does the DNA interact with them? And so, once I started thinking about nuclear speckles, I couldn’t stop. So yeah, I guess what drew me to them is that they don’t fit with what I was taught in the textbooks about how genes are regulated. And then I wanted to understand what’s actually going on.

NW: What went through your head when you realized, like, ‘wait, no one’s talking about this?’ Because it’s not like nuclear speckles are a new discovery, right?

KA: Yeah. We’ve known that nuclear speckles exist for over a hundred years, but there were some limitations in the field. It was very hard to manipulate them and say this is what they’re doing. Because if you kind of get rid of one protein in the speckle, someone might say, oh, it’s doing other functions too. So even though we’ve known about them for a long time, we’ve lacked really the technologies and the tools to know what they’re actually up to. And I think that’s led people to think like, ‘Oh, they’re not important. They’re just sitting there,’ which is not true.

NW: So, there must be so many questions to answer.

KA: Yeah, exactly. We’re at a very exciting time in the speckle field because now we have the technologies which allow us to get into how things are working, and once we know how things are working, we can manipulate them and see what their purpose is. And that’s really the fundamentals of what my lab does.

NW: With all these questions, is there any one that sort of keeps you up at night? Like, is there one question about nuclear speckles that you really want to answer?

KA: Okay. I have some background to explain before I answer that question, which is in contrast to how we think about other kind of layers of gene regulation, where it’s like, okay, a factor binds the DNA, activates one gene at a time. Nuclear speckles are different because it’s neighborhoods of genes that interface with nuclear speckles. So instead of one gene interfacing at once, it’s hundreds of genes at the same time. And so, I think about speckles as a potential way to coordinate those groups of hundreds of genes at the same time. So that’s what I really think about is like, what stimuli, what factors are changing the speckles to change those hundreds of genes, all together?

NW: Like what’s the trigger—

KA: Yeah. What is the signal that tells speckles to change those groups of genes?

NW: And are we talking about particular groups of genes, or more just like in general?

KA: Particular groups; particular but large groups of genes. So, understanding that in the field of 3D genome research, there are two main gene activating compartments: one’s at the speckle and one’s not at the speckle. And so, if you change the speckles, you’re changing potentially—this is all the idea—the relative expression of the speckle versus the non-speckle genes.

NW: So, one thing that comes to mind for me when you say changing gene expression is like a transcription factor, something that’s like switching genes on and off. Are speckles basically doing the same thing, just on a larger scale?

KA: What makes it fun is that speckles are—well, I think of them as one layer of gene regulation. And then you also have the other layers that are existing in tandem. I kind of think of it as you have on-off switches. So, is this gene going to be on or off? And then you have amplifiers. So, if this gene is on, is it going to be low and on or is it going to be high and on? And so far, it seems like the speckles are more amplifiers, rather than on-off switches for gene expression, meaning that depending on the off switch, speckles will have different impacts because you need to be on to be amplified.

NW: I’m picturing sort of like a light switch with a dimmer.

KA: Exactly. It’s like a dimmer, but also you need to get the first “ON” before you can go dim up and down.

NW: So, what are some of the effects of amplifying gene expression like that?

KA: Pretty much anything you could think about. That’s kind of the beautiful part of it. So, if you can have the amplifier, but if the amplifier does different things depending on what on-off switches are there. So, when cell type A, you have certain things going on and you amplify those certain things, cell type B, you amplify other certain things. I consider that this is a major mode of gene regulation, probably applied across all of human biology and response to stress. And so, part of our goal is to understand where it’s being applied, and we really don’t know yet. So far, we see that cancers can have kind of a more hyperactive state of nuclear speckles or not. They’re kind of different states that they can exist, but what’s driving that? And then what are the consequences? Those are huge open questions.

NW: And you’ve been looking into a lot of this in the context of kidney cancer, right?

KA: That’s right.

NW: So, in kidney cancer, you’re seeing different patterns of nuclear speckles tumor to tumor?

KA: Yes. Yeah, so different individuals will have different looking speckles in their tumors. Why? I don’t know.

NW: So, you actually just received a New Innovators award from the NIH to investigate, right?

KA: Yes. So, one big question is exactly that. What does that? We had some hypotheses about what signals may be acting on the cells to either make the speckles more like the one state or the other state.

NW: And these are those hyperactive or not hyperactive states, right?

KA: That’s right. That’s right. And we think that this is not something specific to cancer, but that it could be used in our normal cells as a response to any sort of environmental cue. And so, that’s one thing we’re looking into. Our hypothesis is that energy metabolism signals may make speckles go, transiently, one direction or the other to help the cells respond to the nutrient environment.

NW: So, let’s say you get to the bottom of all of this. What comes next? Like, where do you hope it ultimately leads?

KA: Ultimately, our goal is to understand the fundamentals of how gene regulation by speckles work. And so, one of it is to understand: how did speckles change in response to signals to alter this expression of these large groups of genes? And then the second is to understand: how is chromatin positioned at speckles? So, what decides what parts of the DNA are next speckles? By understanding those fundamental principles of gene regulation, we think that this will apply a new lens for understanding the gene dysregulation that occurs across human pathologies, as well as how normal, let’s say, development or response to signals occurs.

NW: And you’ve been focusing a lot on kidney cancer with this, but you’re also interested in macrophages—like, immune cells that cause inflammation—and another cancer called neuroblastoma, right?

KA: So, we initially looked into kidney cancer and found that depending on how the speckles look, it correlates with patient outcomes. So, in kidney cancer, this is important because it can perhaps help sort patients into people who are more likely to respond to a certain therapy. So, if you have speckles that look like this, you should receive therapy. If they look like this, you can—maybe you just get your tumor removed.

NW: So, there’s the potential to make treatments much more personalized.

KA: Exactly. And in an easier way than, let’s say, sequencing their whole genome or sequencing their RNA. It’s an imaging-based approach where we can kind of see what’s going on. So that’s kidney cancer. Neuroblastoma is another ball game because—I dunno if that’s the right analogy.

NW: I mean, when I hear neuro, I automatically think brain—and brain cancers in general are just super difficult to treat compared to other types, but, like, is neuroblastoma actually a type of brain cancer?

KA: It’s not a brain cancer per se. It’s from cells like neuronal progenitor cells, but they’re migrating during development and actually create tumors all over the body in different locations, but usually not so much the brain. That aside, it’s true, treatment is horrible. This happens in babies and infants, and if it’s high-risk neuroblastoma, the first line of therapy is chemotherapy, and that’s horrible in little babies. And high-risk neuroblastoma has only 50% survival rate even after all that chemotherapy. So, the goal for neuroblastoma is to help develop new understanding of the disease to know not who should we treat, but let’s try to get some better therapies that are actually going to work. Let’s understand the fundamentals of why are speckles driving poor risk, poor outcomes in neuroblastoma, what are speckles working with? And we think they’re working with a specific transcription factor called MCN in neuroblastoma. And based on a bunch of information, we think that MCN might be one of the transcription factors that’s binding specific sites in DNA and maybe repositioning that DNA relative to nuclear speckles. So that’s the part we’re trying to understand for neuroblastoma.

NW: So where do the macrophages come in?

KA: Macrophages are very interesting. They’re [an] immune cell type, and they do a lot of stuff. And so, the idea is, could we identify potential treatments that might specifically inhibit the ability of factors like MCN to drive association between genes and speckles? We want to do that because there are therapies that just say, ‘okay, let’s take this factor, get rid of it’ to all of its functions.

KA: And those therapies do so show some promise. But what if instead of getting rid of all of the protein’s functions, we could just get rid of the speckle-related functions of the proteins and leave the other parts of the protein intact? This leads me into why we got into macrophages, because there’s a protein that our colleague was screening through a library of compounds, and he found one that specifically binds to the region of the protein that we think is responsible for the speckle functions, and that protein happens to be involved in signaling pathways in macrophages.

NW: But the ultimate goal, as far as that’s concerned though, is to not just completely kill that one protein, but to stop it from interacting with the speckles while making sure it can do whatever else it needs to do.

KA: Yeah. Not really so much the macrophage part though. We want to test it on this protein first, and then we can apply it across all proteins we might be interested in that might work with speckles.

NW: And that could potentially mitigate side effects, at least compared to what might happen if you shut off a protein completely.

KA: Yeah, that’s the idea, if we can just turn off some of the functions and leave the others intact—but we have to test and see.

NW: Are there other cancers that you think could benefit, like therapy-wise, from this?

KA: I think so. We still need to identify them. So, part of our approach is to take the data that’s all out there and publicly available, and then to ask the question, can we find evidence that speckles are important?

NW: Just the idea that there’s this other layer of gene regulation—this whole other avenue of research that we’ve only ever been able to take one or two steps down that now we can really start exploring is just so cool to me. Like, you’re really just getting started.

KA: Exactly.

NW: It’s like the definition of cutting-edge. So, if there was one thing you could tell someone about it, what would that be?

KA: Usually, I tell them about the neighborhood things. So, I think what’s very interesting about this is thinking about the importance of different layers of gene regulation, where if you combine one with another, you get a completely different outcome than if you have just one or just the other. That’s what speckles are. They’re an additional layer that needs to be considered across any context where you’re studying gene regulation.

KA: Because then the big picture is: in the clinic, can people—can clinicians use this? But we have a lot more work to do to find the extent to which it will be important for others.

NW: Science is a shared, collaborative story. Discovery and innovation come from the curiosity inherent in each of us. Thank you for supporting science by listening and learning right alongside us. If you’re interested in more news about Cold Spring Harbor Laboratory research, subscribe to this podcast, sign up for our newsletter, and follow us on social media. To philanthropically support research at Cold Spring Harbor Lab, visit give.cshl.edu. Because science makes life better