Cancer Research at University of Oregon by Ben Stone

Background

About a month ago after dinner, I was eating an apple and talking to my roommate about a class he’d taken on the History of Hip-Hop. He offhandedly mentioned this brilliant, mysterious kid named Opher Kornfeld who had been in the class with him, who incidentally had won some massive scholarship for his research into cancer. I looked up.

“Seriously?” I said. “Cancer?”

“Yeah, I know,” he said. “I’m not sure, but I think he discovered some sort of new protein or something.” (This turned out to be false)

Woah. For a long time, I had been fishing around the Lokey Science Complex at the University of Oregon for interesting, multi-faceted stories that I could dive into. None of my leads were very good, or very surprising, anyway. I knew I certainly wouldn’t want to read the articles I would potentially write about those leads. But cancer research was different.

The problem of cancer is one of the most glaring issues in medicine. According to an American Cancer Society report, 577,190 Americans were expected to die of cancer. Cancer’s extreme prevalence means that there are rarely too many degrees of separation between a given person and cancer. And the compelling, horrible thing about cancer is that we still know so little about how it develops and how to effectively treat it. Cancer is still a top-tier issue: on January 3 of this year, according to the Lung Cancer Alliance, President Obama signed into law legislation that will require the National Cancer Institute to figure out how to address cancers with “survival rates of less than 50%”, namely pancreatic and lung cancers.

I soon realized that I could probably find no worthier area of investigation inside the Lokey Science Complex than cancer research. Besides Opher Kornfeld, I established contact with the rest of the UO Science faculty who lead studies on cancer: John Postlethwait, Karen Guillemin, and Bill Cresko. I succeeded in conducting three fascinating interviews with Cresko, Guillemin, and Kornfeld, but then ran into some problems I have not encountered before. First, I finished establishing contact with all of them about three weeks before the end of the term—a crushingly busy period for anyone on campus. This is especially true, it seems, of those studying cancer. I had originally planned to organize an audio slideshow with the recordings of my interviews and pictures from one of the labs of the professors. Unfortunately, by the time they were all able to meet with me, none of them had time to organize lab work to perform that I could photograph, and also could not send me pictures of their research. However, in lieu of a full e-mail Q&A with Professor Postlethwait (due to the fact that he is busy researching in Antarctica), he gave me a brief summary of what he’s doing down there, and sent me some photos to explain his research.

But what this project is lacking in multimedia, it makes up for in its content. Though it is probably not surprising to hear me say this, there is some incredibly valuable and interesting research happening within the walls of the science labs here at UO. I have been stunned by not only the complexity of the cancers that these scientists are studying and the ways that they are using to try to understand them, but most of all by the passion and patience and brilliance with which these four people operate.

Understanding Cancer Through Yeast

UO biochemistry major Opher Kornfeld makes a breakthrough of sorts

Opher Kornfeld standing by his research poster (Credit: Opher Kornfeld)

Opher Kornfeld standing by his research poster (Credit: Opher Kornfeld)

Opher Kornfeld can’t find the dots. In theory, they should be there, but they aren’t. He scans the gel under the microscope over and over, under high-intensity and low-intensity lenses. They’re nowhere to be found. Kornfeld and his advisor Diane Hawley try to grasp what they had done wrong, and start to consider reworking the experiment. Frustrated, he checks the microscope again. In one blissful second he realizes that his project will be able to continue. The dots appear.

“Whoah,” Kornfeld said at that moment. This is not something one hears very often from Opher Kornfeld. But, as Kornfeld reiterates, one shouldn’t overstate the importance of single moments in the lab like this.

“I never had that one big ‘aha’ moment that I found something brand new that I never expected before and I ran out of the lab crying or something like that,” Kornfeld says. “I definitely got excited about many things, but it was not about the scientific discovery.”

Kornfeld is a University of Oregon biochemistry major his early 20s, and already has the presence of an old man. He is wearing a large colorful sweater and sharp-edged black rectangular glasses, sitting with unusually good posture and his hand folded on the table. He is good-humored, but also matter-of-fact—grounded and realistic from his time in the lab.

“[Opher] is very selective and precise in the words that he chooses, and he’s very rational—he doesn’t really hold a lot of biased opinions,” classmate Cole Lendrum says. “It’s very hard sometimes to know how he feels about something.”

Slowly and thoughtfully, Kornfeld shrugs off any sort of dramatic narrative that could be assigned to his research. Which is vexing, especially considering that last year Kornfeld was awarded the nationally prestigious Goldwater Scholarship for the way he explained this project’s potential implications for our knowledge of cancer.

Cancer has such a powerful physical and emotional effect on those afflicted with it and the people around them that it may be surprising to know how it is sometimes viewed at a scientific level. Kornfeld wasn’t drawn to cancer out of emotion—he was drawn to it because it was a compelling problem to solve. Actually, he wasn’t originally drawn to cancer at all. His interest is much more basic than that.

When Kornfeld was a freshman looking to cut his teeth in the lab, he looked at the descriptions of the UO science labs open to the undergraduates. One of the only descriptions he understood at the time was of a lab run by Professor Diane Hawley dealing with RNA polymerase. Kornfeld e-mailed her and got into the lab, subsequently spending much of his free time there for the last three years.

To understand what Kornfeld does in Hawley’s lab, what RNA polymerase is, and how it all relates to cancer, requires a bit of background in the cellular process of transcription. Inside every cell in our bodies, Kornfeld explains, our genome codes for many genes that result in many proteins. The entire code, which is basically a “library of blueprints”, stays inside the nucleus. Proteins, however, are made outside of the nucleus in the cytoplasm. So, a molecule called messenger RNA has to be made so that it can travel from the nucleus to the cytoplasm in order to code genes and start the process of transcription. The enzyme that creates messenger RNA is called RNA polymerase.

To be even more specific, Kornfeld’s assignment within his lab deals with how RNA polymerase is related to the sinister-sounding final stage of transcription: termination.

“My project seeks to understand whether RNA polymerase, this big enzyme, affects, or mutations in this big enzyme, affect which ‘stop sign’ the cell chooses to use [to end transcription] and also whether mutations in RNA polymers affect the recognition of these stop signs.”

To this end, Kornfeld scopes the gelled dots of budding yeast cells, the same kind of yeast we use to make bake bread and brew beer. The main thing he does with the cells is crush them, extract the mRNA from inside the cells, and then examine the fragments of DNA from the mRNA molecules under a microscope to compare their lengths. And, over time, Kornfeld has indeed collected “some data to prove” that RNA polymerase does affect which “stop sign” a cell chooses. Last year he wrote about his findings in an essay, which he successfully submitted for the Goldwater Scholarship.

In his essay, Kornfeld wrote that far in the future his data could indeed contribute to knowledge of the cancer formation process. He explains that the way tumors form has to do with the way certain genes are expressed. When genes are over-expressed, an excess of the protein is made and cells begin proliferating very quickly, forming a tumor.

“If you understand the process of cell proliferation to a very fundamental level, you’re able to manipulate it a lot more,” Kornfeld says. “So if you want the process to stop, which you do if you want to cure cancers, the more you know about the process, the more you’re able to find ways to inhibit it.”

Evidently, there are no easily-defined endings or answers in Kornfeld’s line of work. And just as his research had no clear discovery and no conclusive results, Kornfeld will completely drop this project when he leaves UO this spring and prepares to enter the Stanford graduate school in the fall. His time has come to move on, regardless of where this project could lead. To be a rolling stone, according to Kornfeld, is wise in the science community. Besides, he was never in it to cure cancer.

“I am so excited to the point that I decided to pursue a career in it because I just really enjoy the day-to-day—I really enjoyed it when things got complicated,” Kornfeld says.

Though it may not make a tidy story, hungry scientists like Kornfeld are probably exactly what we need to solve our greatest medical problems—people who most of all love the hunt of science, and searching for the dots that don’t appear to be there.

Q&A With Karen Guillemin 

Karen Guillemin is an Associate Professor of Biology at University of Oregon, and operates her own research laboratory, the Guillemin Lab, on the second floor of Klamath Hall. I talked with her about one project her lab is conducting on the way a certain stomach pathogen relates to the formation of stomach cancer. We covered many topics, including the unique relation between bacteria in a host and cancer, her experimentation with zebrafish, and some potentially very valuable discoveries that her lab has made. Our conversation became a bit tense at the end, and we finished on an interesting note, as she addressed the importance of journalism in portraying the value of animal experimentation in finding therapies for humans.

Ben Stone: So you study the way stomach pathogens lead to cancer specifically?

Karen Guillemin: That’s one area of research in my lab. There’s a specific stomach pathogen called helicabacter pylori that is implicated in stomach cancer, and we’re interested in understanding in what way does this pathogen manipulate host cell programs that could lead to cancer. So that’s one area of research in my lab.

And is that the only one that links directly to cancer in your lab?

No, there are other ways in which our work relates to cancer, but that’s the most direct one. And that’s research that has in the past been funded by the American Cancer Society.

And you work with zebrafish…

That’s right.

Is that the only organism that you…

No, we also use a fruit fly model, as well as a zebrafish model, and we also look in human cultured cells. And then in other research in the lab we use mice as the model for studying properties that are related to cancer risk. More broadly, we study how bacteria interact with animals. Many of those interactions are beneficial for animals. Some of those interactions can stimulate processes that under certain circumstances could be carcinogenic, could lead to the development of cancer. One of the processes that we study is inflammation, so that’s the body’s reaction to an infection or a wound that is designed to try to treat that problem. There’s a growing body of evidence that inflammatory processes can also encourage the development of cancers, and can exacerbate cancer progression.

So, anywhere, not just in the stomach.

That’s right, yeah. So there’s also interest in the role of inflammation in all sorts of cancers.

In your lab?

No, our work focuses on inflammation, and we think a lot about inflammation in the gastrointestinal tract. But there are other precedents of research in the cancer field that looks at inflammation in other types of cancer.

Were you drawn to study this pathogen for a particular reason?

Yes, I was drawn to it for a particular reason, yes. I was broadly interested in how bacterial and animal interactions occur and how those influence animal biology. And this particular bacterial pathogen is a really interesting example of a bacterium that influences the biology of its host. It has long-term associations with the animal host, and in this time period, it can change the biology of the host and even cause cells in the stomach to become cancerous, so I was interested in that process: how does a bacterium interact with an animal and change its developmental program? This is an example where cells in the stomach, some of the cells that are in there interacting with the bacteria are now transforming into cancer cells, and so that was a question that fascinated me.

Okay. Now what are you exactly doing right now in that project—is this project current?

Yes, we’re doing a number a number of things, but we’re interested in understanding how this bacterial pathogen distributes itself through the stomach. That’s an important question because in humans the distribution of the bacterium in the stomach is correlated with disease outcome. So people who have this bacteria more broadly distributed through the stomach are at higher risk for developing stomach cancer. We are studying some of the chemical cues that the bacteria receive and that they direct their motion towards in the stomach, so understanding how is the bacterium navigating through the environment of this organ and distributing itself. That’s one type of the question we’re asking.

We’re also asking about the particular activities of a protein this bacterium produces that ultimately ends up inside the host’s cells. Inside the host cell it alters some of the biology of that cell, and this particular protein seems to be key to the tumor formation process, so we’re understanding the biological activities of this protein.

And to do this you take cells out of the…

No, what we do is we cause that bacterial protein to be produced inside the host cells of an intact organism, and we study how does that tissue change when the protein is present.

One characteristic of cancer is that you get uncontrolled proliferation, uncontrolled division of cells. So, do we get higher rates of proliferation in these animal cells that now have this bacterial protein present? And we do, so then we’re asking why is it that those cells are now proliferating more.

How do look inside of the animal and see…you’re looking through the skin and into the cells?

We can do various things. We can look through the animal into the skin, taking advantage of the fact that zebrafish, unlike icefish, are transparent. But we can also allow that protein to exist within the tissue. Then we would euthanize the animal and then we can look in tissue that’s been preserved and look at the pattern of proliferating cells in that preserved tissue.

I’ve done interviews with professors and students and they always seem to be displeased at the way I phrase this, but are you making progress in any way? Have you discovered something new that has pushed you in a new direction? Where are you at with this specific project?

I think that one reason that people would take offense to that is because, of course we’re making progress. There are different landmarks that you can use to mark progress. One landmark for us is that we just recently published a paper describing the system. And one of the major findings in that paper is that we found in our zebrafish model where we are producing this bacterial protein inside the zebrafish, that if we did that in conjunction with causing a mutation in the zebrafish that’s a really common mutation in most tumors and stomach cancer…

And, sorry, what do you mean by causing?

So, there are available to us mutant lines of zebrafish that have mutations in specific genes that capitulate genes that are often mutated in cancers, so this is not something we made ourselves but were able to obtain from colleagues who discovered such a mutant line of zebrafish. So we could take that mutant line of zebrafish and combine that with our technology where we can express the bacterial protein in those fish. And when we do those two things, now we cause tumors to form. So, either one alone is not sufficient to see overt tumors, but now together we can capitulate tumor formation.

Was this something that you were trying to work up towards, or was this unexpected that you would be able to do this?

We were testing a hypothesis, and the hypothesis was that, in the context of this one common mutation, the presence of this bacterial protein would be sufficient to cause a tumor. An alternative finding could have been that we could not see the tumor formation, and that tumor formation could require additional hits, additional mutations, additional insults. So this was a not a totally surprising finding, but it was an important advance in our understanding of how cancers in the stomach can arise. We’re learning that you just need these two factors to come together, and that’s enough to get a tumor.

So I guess the major purpose, or a major purpose, of studying cancer in animals would be for application in figuring out ways to deal with cancer in humans…

Right, so there are two primary goals of translating this type of research into a clinical practice. One is to understand the course of cancer, and so you’d like to have a better diagnostic and prognostic ability. So, for example, if a clinician had a patient who was infected by helicabacter pylori, maybe based on this information they would like to genotype them and see, is this patient also a carrier of this oncogenic mutation. If so, they are at much higher risk of developing stomach cancer than a patient who doesn’t have that mutation. So, that information, so that these two things factor together greatly increase their risk of cancer, is useful in that sort of prognostic, diagnostic setting.

The other motivation for this type of research is that, if we can understand the progression process better, then we can develop new therapies that could prevent that cancer process from going forward. So, another application of this: the gene we mutated in our fish and that’s mutated in so many cancers, is a gene that’s important for repairing DNA. So, what this finding tells us is that, in the context of a helicabacter infection, there is a real danger if you’ve got DNA damage. So you can say, can we do something to bolster the DNA repair process to prevent cancer progression from happening.

So the genes of the zebrafish are also similar to humans in the sense that it would work in the same way?

Yes. That’s a really important thing for you to communicate, is that the gene function conservation between all animals is really enormously high, so we are very, very similar in our biology and in the genes that we contain. Very similar to a fruit fly, and to a zebrafish, and to a yeast cell…

(I smile)

And, it’s not funny, it’s really important for you to understand that there is real benefit for studying these experimental model systems because we are so similar in our biology of things like how a cell manages its genetic material. Every single cell on the planet contains DNA as its genetic material. That’s the same molecule, and evolution has basically come up once with the same way in which that molecule is replicated, and how its integrity is maintained. So, the DNA repair mechanisms that we’re mutating in our fish—that’s the exact same gene that’s mutated in humans and in so many cancers. It’s working in the same way in zebrafish, in fruit flies, and in yeast.

You thought it was amusing that I was saying that, but it really is true that the vast majority of effective drugs that are used for, not just cancer, but most diseases in humans, are based on our knowledge that didn’t come from our studies in humans, it came from our studies in more tractable systems, where you can do experimental manipulation. It’s less tangible in that you can’t say, that one experiment that one person did in yeast that one time led to this discovery, it’s that whole field that generated this body of knowledge that informs our basic understanding of the biology of cancer and how to treat it.

Yeah, I just thought it was amusing just because it’s kind of humbling, to think that these are the ways we study humans—with yeast.

Yeah, but there’s a public perception of scientific research that it’s trivial, and for example, Sarah Palin made this comment once that, ‘these crazy researchers, they’re studying fruit flies, for God’s sake!’ And she fails to recognize that actually fruit flies were the foundation for most modern genetics. It’s not absurd, it’s really important that we do that research, and I think it’s a real problem that the public is so scientifically illiterate that they would think that that seems like an absurd thing to spend money on.

I’m not attacking you at all, I just feel really passionately about the fact that it’s really important to be able to communicate to the public as you are doing in this article, the value of basic investigations which are the basis for the [future] of human health.

John Postlethwait’s Zebrafish Research in Antarctica

Professor John Postlethwait, like Professor Guillemin, studies cancer through a zebrafish model. Currently he is living in Antarctica and utilizing zebrafish in his search for therapeutic molecules for a bone marrow failure disease called Fanconi Anemia. Fanconi Anemia isn’t cancer, but according to the Fanconi Anemia Research Fund, people who have it are “extremely likely” to develop cancer at a young age, particularly myeloid leukemia. In addition, about 60% of Fanconi Anemia patients are born with a major physical anomaly. Postlethwait hopes that he can find compounds to help zebrafish with Fanconi Anemia that will also help human patients. What follows is a visual representation of his research.

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The zebrafish that Postlethwait works with (Credit: John Postlethwait)

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A graphic representation of the process of putting mutant genes into the zebrafish genome (Credit: John Postlethwait)

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Magnifications of ovarian tumors in mutated zebrafish (Credit: John Postlethwait)

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Magnification of normal and mutated zebrafish eggs, Postlethwait’s goal stated at top (Credit: John Postlethwait)

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Rough visual diagram of Postlethwait’s process for examining zebrafish cells for changes (Credit: John Postlethwait)

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A more technical computational view of the zebrafish cell analysis process (Credit: John Postlethwait)

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A finished, counted set of zebrafish cells (Credit: John Postlethwait)

Q&A with Bill Cresko

Bill Cresko is an Associate Professor of Biology, and leads his own laboratory, the Cresko Lab, in Pacific Hall at the University of Oregon. I talked with him about his current involvement in a project with former UO Biology Professor Hui Zong focused on understanding a type of brain cancer called glioma. We discussed how the two unique parts of this collaboration complement each other, two amazing technological advances that have allowed them to sequence the full genome of mice from thin brain samples, and the wonderful moment when you think you have something figured out and nature throws you a curveball.

Ben Stone: I’m not sure what the status of it is right now, but you and Professor Zong were working on this project on glioma—where is it at right now, now that he is [working at the University of Virginia]. Is it still a working project?

Bill Cresko: Yep, we’re in the middle of the project right now, and so it’s a three-year project that will actually extend to four years. And we’re really thick in the middle of the data collection and data analysis on the project, so we’re at about the end of year two. We’ve got a lot of work done and a lot more to do on it.

So, one thing I picked up from the research that I was able to do, is that, so you are a geneticist, and he’s a [cell] biologist. Are those fields that usually that usually mix in a project like this?

They can. In this case, it’s a little bit different. We normally wouldn’t work together, because my specialty in genetics is evolutionary genetics, [in] which we think about how genes and genomes evolve over millions and millions of years of time so that we might ask questions about, how are humans similar and different from different regions around the world at the genetic level. Whereas Hui’s focus is on the brain, wanting to know how cells that are undifferentiated, that could become a variety of different things, then take on their new fates, and become, eventually, different cells in the brain that perform different functions. And in his case in particular he wants to know what can happen when a cell that’s supposed to form a glia, which is a certain type of cell in the brain, undergoes a transition and becomes a cancer, and then functions out of control.

Our project is unique in that, we decided to think about the changes in the cells in the brain, in way that’s similar to the changes in populations of organisms that I’d been studying for evolution over time. So, in cases of thinking of how humans evolved from a common ancestor with chimpanzees, we would think about each human as the unit changing over time. And so, parents give birth to offspring and so on and so forth, and as they do they accumulate mutations that then lead to differences. The same process occurs in your body. When a cell then divides it leaves two daughter cells, and those two daughter cells leave subsequent daughter cells, and as they do, they’ll often stay the same, but every once in a while they’ll obtain mutations—changes in the DNA sequence—that will then confer a different state on the daughter cells.

What cancer basically is, any type of cancer, is cells that no longer limited by their internal genetic machinery, or the neighboring cells around them. They basically break their bonds and say, well I know I’m not supposed to be growing out of control, but I’m going to ignore that. So somehow there’s genetic changes in the cell, and when those genetic changes happen in the cell, then they basically have evolved to a state where they become a cancer. So what we’re doing is studying cancer as an evolutionary process.

What we’re doing is taking, in this case, mice that have been engineered to allow us to do this work, and we’re looking at those mice at different time points along the way of going from not having a tumor to developing the tumor. We’re isolating the cells and we’re completely re-sequencing the genome, so taking, and it ends up that there are 3 billion base pairs of DNA, and every one of those cells in the body, so we’re isolating those cells and sequencing them completely to figure out what those mutations are that turn normal cells into cancer.

But specifically with glioma in mice.

Yep, and it’s pretty difficult to do this and one of the benefits of working in a collaboration like this is there’s two really key bits of technological advances that needed to come together to make this happen. The first is a breakthrough that Hui Zong’s lab made, which is the ability to do something called “recombineer”, which mean that you take pieces of DNA that come from somewhere else and he put them into the mice and they integrated into the genome of the mice so that when, from the very first stages, a cell that will end up becoming a tumor [will] glow green, so that there are green-glowing cells inside the brains of the mice. So what that allows us to do then is to take the mice, and sacrifice them at certain points, and then slice the brain in very thin sections and then use a very fancy microscope up the hall called a “laser capture microdissection microscope”, and that microscope actually has a laser in it, that on the slide will cut out and shine a tiny little laser and then will circle the cells and we can pull the cells out one by one. The ones we know that we want are green, because they’re glowing green.

The infamous laser capture microdissection microscope (Credit: Ben Stone)

The infamous laser capture microdissection microscope (Credit: Ben Stone)

The last thing are the advances my lab has made in terms of generating and analyzing huge amounts of DNA sequence data, using new sequencing approaches that weren’t available more than a few years ago. Now we can, at the UO, we have a sequencing facility that allows us to pull out these cells and then decode the entire genome within a few days, which, five years ago, would have cost millions of dollars. Now it costs thousands of dollars, so we do this continuously, we decode entire genomes.

The machine costs thousands of dollars, or the process?

The actual process, yeah, the machine itself cost a million dollars to do, so we have one of those, and a lot of universities have those now. Because we put [these two technological advances] together, then we’re actually able to make progress on this and, in our case, we’re starting to identify key changes that happen really early on during cancer evolution.

And why particularly are you studying glioma?

For me, it was because those are the cells that Hui’s lab was studying. So for our lab it could have been any type of cancer. His interests have been in brain cancer for a number of years. It’s a very deadly cancer, it’s very hard to treat, and so part of it is if we could come up with a diagnosis for some of the earliest stages of brain cancer, then this would be a huge benefit to the field, because instead of waiting to the point that, really what happens now is, people get diagnosed with cancer when they’ve got a tumor—usually when it’s too late. Because by the time you have a tumor, there are hundreds of thousands, if not millions, of mutated cells in there that are in that tumor, metastasizing and spreading throughout the body.

So, potentially, our research could lead to therapeutics, but also for early diagnoses, so that early on during the process we could take some blood out of someone and say, there’s likely a brain tumor that’s just a few cells, and then remove it before it actually becomes too dangerous.

So what comes at the end of this four-year sequence, what are you working towards?

Our goal is a “basic science” one. We, meaning the entire field, no one can say what genes or suites of genes, have to be mutated first to make a glial cell become a glioma. And we want to know that. We want to know what has to happen for healthy, normal, glial cell to transition into a glioma. It’s as simple as that.

And right now in the project, are analyzing a new set of genes?

Yeah, we’re analyzing piles and piles of sequence data, to go through and look for the changes. It’s a difficult computational task to do this; we have a big computer cluster, a bunch of computers that are linked together with huge amounts of memory and storage. Every night, from our sequencer we produce two terabytes, and each byte is a thousand gigabytes of data. So there’s a huge amount of data, and all of that takes a long time to sort through, even doing things like, just organizing it takes hours of the computer running. So that’s where we are right now is doing a lot of the brute force computer science work.

Are you excited about this project?

Very excited, it’s very cool. Yeah it’s really neat, and the results that we’re starting to see come out are telling us it’s like many things in science: we expected one of two options, and it wasn’t either of those. It was a third. And without going into the details of that, because it’s a little bit messy…Basically, this happens a lot in science. You think ahead of time that you’ve got all the options covered in your mind, but then nature shows you a nice little surprise, that, hey, there’s a third possibility here, that to my knowledge wasn’t expected by any cancer biologist in the field. So our results will be pretty high-impact.

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