Medicine's Future, From a Leader in Genome Editing and Stem Cells

; Chad A. Cowan, PhD


May 10, 2016

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Falling in Love With Hands-on Science

Eric J. Topol, MD: Hello. I'm Eric Topol, editor-in-chief of Medscape. Welcome to One-on-One. We're thrilled to have Chad Cowan, an associate professor at Harvard University who is at the Harvard Stem Cell Institute. Chad and I have both been principal investigators on the induced pluripotent stem cell (IPSC) grant. I have looked to Chad as a leader in this field and he has been prolific in recent years. Let's start with your background. You were in college at Kansas?

Chad A. Cowan, PhD: I'm originally from Wichita, Kansas. I was recruited to the University of Kansas where I thought I was going to be an athlete. I realized that professional swimming didn't really exist and found my way into chemistry and biology.

Dr Topol: How did you land where you are now? What were the successive steps?

Dr Cowan: A lot of the younger people that I now mentor and talk to are more directed in what they do—I was less directed. I thought I was going to be a chemist because it was a harder science and I could see the end products. Then once I saw what was available for chemists after a bachelor's degree, I wasn't as interested in that—synthetic organic chemistry was the big thing then. I was asked by a friend to go into his neuroscience lab, and I just fell in love with doing science with my hands.

Then I made a decision on a whim to go to graduate school. I applied to two graduate schools that I picked because they had no application fee. I ended up going to the University of Texas Southwestern, which I didn't know much about, but at the time they had four Nobel Prize winners—a phenomenal institute.

It furthered my love of experimental research, and when you love something, you put all your heart and soul into it. And, before you know it, you have accomplished something. At that point I thought, now that I've done something, maybe I should do something to give back. That's when I started focusing all of my efforts in service of humanity. I fell in love with the idea of human pluripotent stem cells and started surveying the United States and even Europe for who was playing in that area. I had heard whispers that a very accomplished developmental biologist, Douglas Melton, was actually starting to launch into the area. I went to interview with him. Most young kids now haven't seen the movie Love Story, but we had a "first date" that day that was very similar to Love Story. We went to the law school library and I've been at Harvard ever since.

Dr Topol: What year was that?

Dr Cowan: That was 2001.

Dr Topol: That was 15 years ago. In some ways you have followed Doug Melton's footsteps in terms of areas of interest—diabetes and metabolic diseases.

Dr Cowan: Correct. Doug and I decided to divide and conquer. There was no way that I was going to do a better job than Doug of understanding type 1 diabetes, but because of his own personal situation, having two children with type 1 diabetes, he has almost no interest in the larger spectrum of diabetes, including type 2 diabetes. So, I thought, why not focus my attention there? That's what led me by the nose to genetics—because if you're going to focus on something, the best lens to use initially is human genetics, and from human genetics to IPSC and the genome editing tools that we use today in the lab.

Dr Topol: We're right around the 10th anniversary of IPSCs; in fact, it was just weeks ago that this celebration occurred. During this 10-year stretch after Yamanaka and others, where did you come in?

Dr Cowan: We were there at the beginning. I remember being at the keystone meeting in Canada when Shinya Yamanaka first announced that he thought he had made these IPSCs. He revealed two of the factors and two "mystery factors." At International Society for Stem Cell Research—the big stem cell meeting—Yamanaka revealed one more factor. We were all on the edge of our seats.

I had already invited him to Harvard based on other work, so we actually were one of the first places to host him after he had published and announced everything. People got to ask all of their exciting questions. The demonstration of what could happen was great, and they used mice because it's a more tractable system, but what we cared about were humans. We were right there in the race for the first human IPSCs. From that point, we started expanding their use for disease modeling and understanding aspects of genetics and how it influences disease.

Dr Topol: You worked with skin biopsies first?

Dr Cowan: Yes, initially with skin biopsies or keratinocytes, and it wasn't until later that we perfected some technologies for using blood, which is much more clinically accessible.

The Art of Making Pluripotent Stem Cells

Dr Topol: This area has evolved so much, and you have been a principal part of the whole IPSC movement, and no less the editing of these cells. It's painstaking to do this. A lot of people think it's some kind of magical thing and that you create this disease in a dish. It's not just connecting a couple of dots.

Dr Cowan: It's certainly not. To give people an example of how hard it was and how it was more art than science, initially, after Shinya Yamanaka's groundbreaking publication,[1] it was more than a year before anyone reproduced it. That's how hard it was to practice the art, and then even among those of us who started to truly practice that art, it still wasn't routine. It wasn't something we could count on. When we tried to convert a skin cell into a stem cell, it didn't happen every time. It took several more years before it was something that was somewhat reliable, and now it is something you can almost routinely do. It's been a number of advances, all mostly technical.

Sydney Brenner put it best by saying that often it's techniques that open up opportunities in research. Once again, technical advances have made it routine but not simple. Even if we can reprogram blood, if we get blood from an individual who we want to make a stem cell from, it still takes 6 months and about $15,000. And a lot of additional work must be done if you want to use those stem cells to understand something about disease. I usually tell the brave students who join my lab that it may be 2 or 3 years before they have an answer to a question that seemed very simple upfront.

Dr Topol: When we talk about IPSCs, are we talking about being able to differentiate to any cell?

Dr Cowan: In theory, that is the exact definition of pluripotency—that they can make every cell in the adult human body. That's easy to say, but it's very difficult to do in practice. When we first started doing this, there were two examples of cells that people could reliably make. The spectrum of those cells has grown enormously so that now, reliably, people can make many of the cells that you might be interested in. In my lab, we have focused on those that are involved in metabolic disorders. We can make insulin-producing beta cells, liver cells, fat cells, endothelial cells, and vascular smooth muscle cells.

Making Fat in a Dish

Dr Topol: You are noted for many things, but one is that you are the first scientist to create fat in a dish. Was it white fat?

Dr Cowan: White and brown fat.

Dr Topol: For those who aren't initiated, what is the difference?

Dr Cowan: White fat is the fat that everybody thinks of when they think of fat. It's the stuff that stores excess energy, and eventually its expansion is what leads to diseases like diabetes and coronary artery disease. It's the unseemly fat that we are all going to the gym to try to get rid of. More recently it has been appreciated that adults also have brown fat. The job of brown fat is not to store energy but rather to use it to keep us warm in a process known as nonshivering thermogenesis. Just before you get so cold that you start to shiver, this fat gets turned on and it burns the energy stored by other fat cells to make heat. It's a fascinating process, and it has made people very interested in it because it looks like people who have more brown fat are protected from the same metabolic diseases caused by white fat.

Dr Topol: Before we talk about editing IPSCs, can you tell us about the Harvard Stem Cell Institute?

Dr Cowan: Most people think of institutes as singular places, like the Broad Institute or the Stowers Institute. The Harvard Stem Cell Institute realized that Harvard is a large and vast research network with hospitals, medical school, and the college campus. If an institute was going to capture the intellectual firepower that they had in stem cells, it was going to have to operate as a spoke-and-hub operation. There is a central location where the Stem Cell Institute has its administrative offices, and that's on the college campus. But then it reaches into every single research area and research lab that wants to be involved in the Harvard diaspora. It has over 200 faculty members and more than 400 principal members, and its mission is to do just what you would imagine: to use stem cells to cure devastating diseases in people.

I got to see it launch. I saw the Harvard Stem Cell Institute go from a secretary at the end of the hall in our lab to a real institute. I had thought, there is just no way to break down these barriers at Harvard, with its siloed research places, to get people to come together. It worked far better than I would have imagined.

From Difficult First Gene Edits to 'Mutations Gone Wild'

Dr Topol: Now you can order up almost any IPSCs—differentiated cells—and you are thinking about editing them. You have gone from zinc finger nuclease to TALENs (transcription activator–like effector nucleases) and CRISPR (clustered regularly interspaced short palindromic repeats). Where are you in the use of editing tools to help the quest of understanding, and eventually even treating and preventing, disease?

Dr Cowan: I became convinced that to try to understand a disease as complex as type 2 diabetes, I was going to have to stare hard at what geneticists like you were teaching us about these diseases. I also knew that to understand how they actually influence the molecular mechanisms that result in disease, we were going to have to change the genome to insert the changes that we think are influencing diabetes, or correct them. In the early ages of genome editing, I picked up some of the first tools—zinc fingers among them—and while we could get them to work occasionally, it was really hard.

I often tell people that for the very first "gene edit" we made in a stem cell, it took us over a year to build the tool and make the edit. Before that, I had used the technology pioneered by Oliver Smithies and colleagues, which was homologous recombination. With that, it took more than 2 years to make my first knock-in or knock-out cell line. Then we stumbled upon TALENs—much thanks goes to George Church for introducing us to TALENs—and they turned out to be very rational to design, and they worked more effectively and most of the time in our hands. We got so excited that, in our first publication, we actually made 20 different mutations even though you can't study 20 mutations rigorously in terms of their functional relevance to disease. We studied about two or three. But we were so excited that we could finally do it, that we did it to everything that we wanted to study.

Dr Topol: Mutations gone wild.

Dr Cowan: It's still hard to understand disease biology from the mutation. In fact, we had known about the CRISPR-Cas revolution first from Feng Zhang, who was a collaborator with us on gene editing even with the TALENs and differentiating stem cells. We were helping his lab get used to culturing and differentiating the cells, and he told me in a hallway conversation, "There's this new system." I asked, "Does it work?" He said, "Not yet—not in my hands." Then the revolution took off with the work by Jennifer Doudna and Emmanuelle Charpentier and its movement into mammalian cells by George Church and Feng Zhang. Just prior to publishing, Zhang said, "I think it's really working now, Chad," I thought, maybe we'll give it a try. At the time, I wasn't extremely eager to do it—I don't know why. I thought, we have a tool that finally works.

Dr Topol: The TALENs, which you worked so hard to get?

Dr Cowan: We worked so hard to get them; they were finally doing something, and here is this new tool. I thought to myself, maybe it's going to be like zinc fingers—sometimes it works, sometimes it doesn't.

Dr Topol: And it's a big investment of time.

Dr Cowan: It's a big investment of time and energy, but I had a very brave post-doc who said, "I really want to do it." I said, "Sure." But I made her a bet, and it's one of the few I've lost. I bet her a six-pack of Diet Coke that it was probably going to be a lot like our experience with the other genome-editing tools. It might work a little bit or better at one place but not at another place. Boy, did she prove me wrong. When she compared it to the TALENs at 10 different places in the genome, there was—hands-down—no competition. The CRISPR-Cas system was far more efficient. It was right then when I was staring at the data that I thought, well, if we were really smart, we could do something special with this technology. It was about a week later after a run that I thought, maybe I don't have to be that smart. Maybe what I need to do is all the things people have been talking about doing with gene-editing technologies that were more limited in their effectiveness. That launched us on our path towards pushing to see how far this technology could be used in IPSCs, but also in real therapeutics in people, at least in a proof-of-concept way.

Real Functional Cures

Dr Topol: Beyond the fact that for science's sake you are trying to understand mechanistically and functionally the genomic impact of IPSCs in a dish, you are also now getting into the treatment side. What's the future of genome editing and clinical intervention?

Dr Cowan: It's almost certain that for some devastating monogenic conditions—such as cystic fibrosis or sickle cell disease—from which patients suffer now with no cure and very few medicines, there is the opportunity that in our lifetimes we are going to see those reversed. We're going to see an actual cure. For me, it was Earth-shattering to start talking in those terms. As a scientist, I'm sure you also feel a little bit stunned, because we always think that maybe what we'll do is understand the mechanism so well that we can interfere with disease biology to ameliorate the disease and reduce its symptoms. But we are now talking about fixing the underlying genetic cause and thereby just abolishing the disease. We're talking about real functional cures.

Dr Topol: For example, when I was in college, my thesis in 1975 at the University of Virginia was "Prospects for Genetic Therapy in Man." That was a long time ago, before you were born, and finally there is a prospect.

Dr Cowan: It can happen. I remember the moment for me when it struck home. I was having hallway conversations or lunches with my colleagues and talking about some of the diseases we think we could use this technique to cure. The word "cure" was coming out of my mouth, and at this point I thought we should take this seriously and put our money where our mouths are. Start doing the research that would prove that it might be possible. Then, of course, I spent about a year of my life trying to rally the troops around trying to form a company. I'm a big believer that you can do only so much in an academic lab, and the only way you are going to get a medicine into people is to do it through biotechnology or pharmaceutical companies. That's what they do.

The CRISPR Patent Fight

Dr Topol: Have you done that?

Dr Cowan: We have. I was lucky enough to be cofounder of a company known as CRISPR Therapeutics. That was a thrilling ride because it was fun, and at the same time, we were talking with George Church and Jennifer Doudna and the people who formed two other CRISPR therapeutic companies. I actually think that there is plenty of space. There are so many genetic diseases that could use this tool to make a difference, that two, three, or four companies could all work together on it.

Dr Topol: Except for the patents. What are you going to do about that?

Dr Cowan: If I got to decide, I can tell you what I would do. There are two warring patent families. One was out first and the other thinks it had the original art. They are going to battle in the courts for years to try to decide this. As a rational person, I would say, "We both agree that there are important things in both patents. Why don't we make an agreement about cross-licensing so that we can all move ahead and make the medicines? But I'm not the person making the decision.

Dr Topol: Do you think the intellectual property–patent issue will hold the field back?

Dr Cowan: I don't think so. Some very smart business people taught me this: In terms of therapeutics, no patent has ever prevented a therapeutic from getting to a human. It turns out that the way a lot of the people who back companies financially think about it is like a speeding ticket. In the worst case, if you get your technology—and it's using somebody else's patent—into the clinic and you say, "I'm about to commercialize it," then you just have to write the check to pay for the access to the activity. No one holding a patent would prevent you from actually therapeutically curing someone. In fact, there is a way that you can use an injunction in the United States to require that.

Dr Topol: That's reassuring.

Dr Cowan: It is reassuring because it won't stop any of the wonderful research that is going on both in companies and in labs that rely on these patents and intellectual property.

Moving at Breakneck Pace

Dr Topol: That's interesting. In a way, you have widened your horizons because you are working on brown fat, white fat, diabetes, and metabolic diseases, and now the editing world has opened up curing monogenic diseases. You are still doing both.

If we were to reconvene 5 years or more from now, are we going to see the beginning of these cures for various diseases?

Dr Cowan: I really do [think so]. What has convinced me is some of our own research. I first thought to myself, could you do this? Let's think of the easiest way. What cells do we use every day in therapeutics? It's blood cells. Could we cure some of the diseases in blood by making gene edits? That was the question we set for ourselves in the laboratory. Just using very crude laboratory protocols and techniques, we were able to make a functional cure for HIV to a level at which many doctors say, "That's almost there." That is so close to being something that you could think about using in the clinic, that there's no reason why this couldn't proceed in other areas.

Now when I see how it's done so professionally at the companies that are embarking on this, I have very little doubt that eventually they will figure it out. Maybe in 5 years it won't be their best medicine, but in 10 years some diseases will, in essence, be eradicated. A friend of mine tells me that CRISPR seems almost too good to imagine. I said, "Maybe it is." He said, "You guys are only going to cure three or four, maybe five diseases." I said, "I'll take it. I'll take three diseases."

Dr Topol: Then eventually it could be used well beyond that. Because the polygenic diseases are so complicated, it will take quite a bit longer.

Dr Cowan: It will take a little longer, but one of the other things we did was to try to show how you might use it to affect polygenic disease. One of the leading risk factors for heart attacks is low-density lipoprotein cholesterol (LDL-C). Right now, many people who are at risk for that take a statin.

One of the newest drugs actually targets a gene called PCSK9. We know from human genetics that people who have deletions in that gene—they don't have it at all—are perfectly normal except that they have the lowest levels of LDL-C and almost no risk for heart attack. We thought to ourselves, maybe we can use CRISPR-Cas to actually knock it out.

We did it in a mouse, not in a human. We completely abolished LDL-C. You can think of this as a vaccine for heart disease. You can in essence be giving people a one-time, lifetime dose and remove this gene that they don't need once they are an adult, and have abnormally low LDL.

Dr Topol: I got the scenario. You do the fetal sequence at 10 weeks, you find out that the genomic risk score for heart disease is really high. Then at birth you start this PCSK9 modification?

Dr Cowan: The key, of course, is the safety profile. Everything, whether it's a drug or a gene therapy, has what people refer to as "unwanted" or "off-target" effects. You would have to know through many years of research with this technology on more devastating diseases where you could accept that risk, that it was really safe—as safe as drinking water to use in an infant, as in the example you gave.

I'm encouraged, being involved in two fields that have moved at breakneck pace, to see how fast they have moved and come together. You just reminded me that only 10 years ago, IPSCs were discovered, and we are already embarking on tons of clinical trials using IPSC-derived cells. It blows me away that in 10 years we are getting treatments to people. CRISPR-Cas is just a few years old.

First Diseases to 'Take Out'

Dr Topol: It's zooming. You have pointed out that we have already seen the initiation of pure IPSC trials in Japan for macular degeneration. Only one person was treated, but what do you think about that? Without the need to do editing—just taking someone's cells, making the desired differentiated cells, and putting them back.

Dr Cowan: I'm extremely bullish on that. That has been my entire research career—trying to see and realize the promise of what we often term "regenerative medicine"—taking cells and replacing damaged or lost cells that have resulted in disease. The first place this is happening is in macular degeneration. There are now trials for Parkinson's disease, which is going to be amazing, and two or three trials are opening up for type 1 diabetes.

Dr Topol: You would think that in the 5 years it takes for a young child's islet cells to be destroyed, that we could diagnose that early on and intervene.

Dr Cowan: That's exactly right. In fact, the Harvard Stem Cell Institute hasn't announced it yet, but there is an effort underway to launch a clinical trial using that type of technology at Harvard.

Dr Topol: That's very exciting. If you can control the immune response from before the IPSC, you could win on that one.

Dr Cowan: People think that might be one of the first "wins" or diseases that we take out.

Dr Topol: It's an enormous thing to accomplish, especially since you and Doug have been working so assiduously on that. This has been fascinating—I could talk to you all day. You have been leading the charge. In our group of the nine centers—and these are not slouch centers, with Stanford, Hopkins, Scripps, and many other fine centers—you are the go-to guy: "What does Chad think?"

Dr Cowan: It has been enormously educational for me to see so many world-leading geneticists and what they deal with and what you guys have revealed to us. Without the two groups coming together, I don't think we would have had the success we have had.

Dr Topol: Keep up the great work. We are going to be following you with tremendous interest, and the medical community is going to get to know you even more.

Thank you so much for joining us for this fascinating discussion with Chad Cowan. He is one of the most interesting people in the whole biomedical sphere.


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