Dana Carroll must be considered one of the deans of genome editing. He was instrumental in the development of zinc finger nucleases (ZFNs), the genome editing tool that predates CRISPR-Cas by a full decade. Over that time, he has seen the tools he helped create make inroads into the clinic and marvel as the arrival of CRISPR has taken genome editing into myriad unchartered territories.
Carroll closed his lab at the University of Utah in 2018 but remains on the faculty and is still a vital presence on the genome editing circuit. This year, he signed onto a new part-time role at the Innovative Genomics Institute in San Francisco, where he will be leading community engagement efforts. He also serves on a commission created by the National Academies of Science, Engineering, and Medicine and the Royal Society to study the clinical use of germline editing.
Carroll joined The CRISPR Journal’s executive editor Kevin Davies for an interview in which he reflects on two decades of research advances in genome editing and ruminates on some of the broader issues impacting the scientific community.
Davies: In terms of charting a course for the successful therapeutic deployment of gene editing, whether it is CRISPR or any of the other tools in the toolbox, what do you consider the biggest hurdles?
Carroll: I think the biggest one is getting to the point where homologous repair is really the majority outcome to these editing processes. As I’ve said over and over again, all we’re doing with standard CRISPR, TALEN, and ZFN platforms is making a break in DNA. Then we’re totally reliant on what the target cells are able to do to repair those breaks. And we’re still floundering in this region where we are having trouble dramatically enhancing the homologous outcomes. People have been nibbling at the edges of this for a long time: How can we reduce nonhomologous outcomes and enhance homologous outcomes?
There are ways to do that, but none of them has been the silver bullet that has gotten to the point where we can confidently, in different cell types, get the homologous repair up to a level where we can talk more about the correction types of therapeutic applications and less about the knockout types.
The second biggest one is delivery. There is both getting things into lots of cells and then the targeted delivery to specific cells of interest.
I think some of the most effective approaches are going to be the ones where we can make modifications ex vivo and then put things back, or in in vivo situations where we can have access. For example, in the liver, almost everything goes into cells in the liver, no matter how you are trying to do delivery. Hepatocytes are a good target. And then some of the things where you can do physically targeted delivery in the eye, in skeletal muscle, and things like that.
Davies: I want to talk about some of the ethical questions surrounding this field. You’re an advisor with the Innovative Genomics Institute (IGI) that Jennifer Doudna launched and co-directs in Berkeley?
Carroll: I went to the IGI on sabbatical four years ago and spent 10 months working in Jacob Corn’s lab. Mark DeWitt, who was a postdoc in Jacob’s lab at the time, and I were the ones who initiated their project on sickle-cell disease. There’s a paper published on that.
While I was there, I started a CRISPR course, which we taught for three summers, 2015–2017. I’m going back to the IGI part-time to help them with their policy and social issue and outreach projects, a fledgling part of the IGI. I’m very interested now in being more involved in the societal aspects of genome editing. I’ve already begun to talk with public groups, less as an educator and more of a receiver of information from nonscientists.
I think the wrong forum is having Jennifer Doudna stand up and speak to a large audience from whom she will only get little bits of feedback. A better way to do it is in situations where feedback is the goal. In those situations, even though you would be working with potentially a smaller group, there should be a ripple effect, where the people who have thought about it more and begun to speak about it more will go out and do this with their friends and their friends’ friends and other groups that they are associated with.
Davies: Jennifer has played a very important role in bringing scientists and other groups together to begin talking about the ethical issues around gene editing. You were one of the attendees at perhaps the first CRISPR-focused or -inspired meeting in Napa, CA, in early 2015. What are your recollections of that discussion, which led to an important essay in Science, just as the first gene editing human embryo experiment was about to be published?
Carroll: That retreat was quite important in getting people with different perspectives, including some of us who’d been involved in the genome editing fields for a while, really focused on the things that could be done beyond what we were doing currently, and how people were going to react to it, and how we should begin to set standards within the field for how this should be approached.
There were some of us looking back at the gene therapy attempts from 15 or 20 or more years ago that had run afoul of unintended effects. There were people there who were familiar with the whole stem-cell situation, talking about trying to put constraints around going off and using stem cells therapeutically in situations where it really was not appropriate.
It was shortly after that when the first summit meeting on human gene editing took place in Washington, DC. I was there. I learned a lot from nonscientists who spoke from the podium about how other people were thinking about it. One of the questions that I saw emerge from that was: How are we going to distribute these high-tech therapies once they are finally to the point where we feel comfortable with them? How are we going to distribute them to the people who are going to need them most around the world?
Is this going to be another example of a therapy for the wealthy, while others in the world will just languish?
The diagnostic tools, including microarrays and DNA sequencing and PCR-based diagnostics, have been miniaturized and made so inexpensive, you can take them out into the wild and use a blood or saliva sample to see what viral infection somebody has got. The diagnostic tools have been miniaturized to the point where you can take them all around the world. Is there a way to conceive of making the therapeutic applications distributable?
Davies: You also attended the Summit in Hong Kong at the end of 2018. What did you take away from the appearance of He Jiankui and that story about the CRISPR babies?
Carroll: I thought it was good that all of the scientists reacted to that by saying, “This should never have been done.” Perhaps at some point we will be at the point where we are comfortable with the technology. It was really irresponsible, beyond irresponsible, for He Jiankui to have done this.
The two things that might result from this that would be distressing would be, first of all, that some other people would think the door is now open—we are doing this, too. The technology is absolutely not ready for that—as he unfortunately demonstrated.
The other thing would be that regulations would come down from authorities in various countries that would inhibit the research that is necessary to get to the point where embryo editing really would be safe and effective.
Davies: Are you persuaded that there are some scenarios where germline editing might be the only way and a prudent option to proceed? It seems like the list is very, very small.
Carroll: That is true. But there are a few, and people trot them out. I don’t think that is really the way to look at it because there are issues around the alternatives that are not appreciated as well as they should be. People always talk about using the preimplantation diagnosis ahead of implantation. There are problems with that. One is generating enough embryos in situations—particularly if you are looking at a dominant condition where half the embryos may be getting the mutant allele—generating enough embryos to be confident of finding one that is unaffected.
The procedures themselves have their potential impacts on the health of the embryos. So, although it’s true that we would at least initially think of doing the embryo editing in the context of in vitro fertilization, you can almost imagine a situation where you would not need to do the preimplantation assessment of the efficacy of the editing.
We would also need to find ways around mosaic formation because the editor will continue to act after the one-cell stage.
The other thing is something I began to be aware of at the first editing summit. Patient groups will tell you, “If you have got anything that can help us, give it to us.” I don’t think of the germline therapies as being mandated but as being made available as alternatives to things that are available for whatever the condition.
Davies: We can never close the door on the fact that there may be an even better gene editing technology still to be discovered. What do you think?
Carroll: I’ll say two things about that. I’ve been asked this question more than once. First, I have no crystal ball. The one I try to look into is really cloudy! But I think it is likely that if there is a next editing technology, it, like the previous ones, will come from nature.
*This is an edited version of an article that was published online June 21, 2019, in The CRISPR Journal, Vol. 2, No. 3, Mary Ann Liebert, Inc., publishers. To read the entire interview, go to: doi.org/10.1089/crispr.2019.29058.dca