See Part 1 to read about Dr. Carroll's experience starting his own lab. In the second half of our two-part interview, we spoke with Dr. Carroll about developing the zinc-finger nuclease technology and his views on the gene-editing field.
Q: How did your scientific path lead you to zinc-finger nucleases (ZFN)? Tell us a bit about what it was like to develop that technology.
Well, ZFNs came sort of late in my career. We began working on ZFNs a little over 20 years ago, but I was already a full professor and department chair by the time we started working on them. My path to working on ZFNs led pretty logically through my work in genetic recombination and DNA repair. By the late 1980s and into the early 1990s, we understood that genetic recombination was a process that cells use to repair double strand breaks in DNA. Looking at it from the other side, double strand breaks stimulate recombination.
ZFN interacting with DNA
So we began working in my lab in the early 1990s on other methods that might make damage in DNA to stimulate recombination. We were primed, when we saw a paper by Chandrasegaran in 1996 describing the ZFNs to appreciate the potential impact of those nucleases. It was sort of a fantasy at that point, but I initiated a collaboration with Chandra to test the idea that we could make targeted breaks. And it turns out that that's true, but we had to figure out how to do it. The most important step was when we finally expressed a pair of ZFNs in Drosophila and made new mutations in the target gene - and actually saw those mutant phenotypes in living flies. That was the most important moment for me in the development of the ZFN technology.
The most important step was when we finally expressed a pair of ZFNs in Drosophila and made new mutations in the target gene - and actually saw those mutant phenotypes in living flies.
I'll say that one of the biggest challenges in developing the technology was getting money to do the research. Even after we had some early results, I applied to the NIH for support, and the first two times I received funding, I got a non-fundable score from the study sections and had to appeal; thankfully, the council took pity on me and decided to support the work. But there's another piece of advice I would give to junior faculty: you shouldn't give up on your ideas if you're really convinced that they're good. If you fail to get funding the first time around, keep at it.
You shouldn't give up on your ideas if you're really convinced that they're good.
Q: Where do your scientific interests lie today, and what is your lab working on now?
I'm still very interested in some of the fundamental aspects of how genome editing technology works. We're working with CRISPR, have worked with TALENS, still are working with ZFNs a little bit. The question we're addressing now is the extent to which chromatin structure limits the accessibility of targets for the programmable nucleases.
Q: How has mentorship shaped your career path - both being a mentee and mentoring others?
I would say that the mentoring I've received and most of what I've given has been by way of example. As I was being trained in research, I had several different PIs that I worked with, and PIs in labs nearby. Nobody ever sat me down and said you should do things this way or that way. It was mostly just watching how people dealt with things.
Particularly when I was department chair, I did a certain amount of advising people on how to proceed with their careers, but a lot of it again was by setting examples and by trying to run interference. I think one of the things I did pretty well was to run interference for the faculty members in my department by taking care of issues that involved dealing with the administration or other external factors, thereby allowing them to get a running start on their scientific careers.
Q: Do you have any tips for balancing an exciting scientific career and life outside of the lab?
Dr. Carroll hiking with two of his grandchildren
I'd say I've managed to maintain some interests outside of the lab. I love the outdoors; I've played a variety of sports; I've raised a family. Some of the things that I've done outside the lab I think have helped me to maintain perspective in the lab. The two things that I cite are playing sports and playing music, because they require you to focus completely on the thing that you're doing at the time. When I'm playing squash, I'm only thinking about placing the squash ball and how to keep it away from my opponent. If I'm playing music, I'm really just focused on trying to produce the notes called for on the page in a pleasing fashion. Everything that's gone on earlier in the day has left my brain, and when I come back to my issues at work, I'm not tied up in the same knots I was in. I think having interests – particularly intense interests – outside the lab helps your career.
I think having interests – particularly intense interests – outside the lab helps your career.
Q: What are some of the key challenges that the gene editing/genome engineering field will face in the near future?
On the technical side, I think one of the biggest challenges is enhancing the frequency of homologous repair in a very broad sense. Some cells are pretty good at homologous repair, but other cell types are just terrible at it. If there were a general way to enhance homologous repair that's applicable to many different cell types, it would be a huge boon. The other technical limitation that I see is delivery of the genome editing components. In the medical arena, delivering the genome editing components to human beings can be a very severe challenge. Other methods of delivery are going to be very useful as they're developed.
Q: What are you most excited about in the genome editing field?
I'm excited by how much people are excited about it – how much it's been adopted in academic labs and the private sector.
It's amazing to see the applications to which this relatively recent development has been put.
There are agricultural products that have hooves on the ground on farms and roots in the ground in fields. It's amazing to see the applications to which this relatively recent development has been put.