The Rapid Rise of CRISPR
A Conversation with Jennifer Doudna, Emmanuelle Charpentier and Virginijus Šikšnys

by Steve Koppes

For nearly two decades, scientists who studied a bacterial immune system called CRISPR did so without attracting much attention to their field. That all changed in 2012, when Emmanuelle Charpentier and Jennifer Doudna, working together, and Virginijus Šikšnys, working independently, announced their CRISPR-based invention of a powerful new gene-editing technology. Called CRISPR-Cas9, the technology offers a means of curing disease, bringing innovation to agricultural production, and controlling evolution itself.

In the years leading up to the invention of the technology, scientists knew CRISPR as an intriguing genetic sequence that plays a major role in the immune systems of certain bacteria. After viruses invade bacterial cells, they become incorporated into the bacterial genome. An enzyme associated with CRISPR, called Cas9, can be programmed to cut out the viral DNA, preventing the predatory virus from replicating. After years of studying the bacteria’s DNA sequence, scientists discovered that they could wield the enzyme to cut the DNA of other organisms like a pair of gene-snipping nano-scissors.

To learn more about this breakthrough discovery and what could come next, we had a conversation with Emmanuelle Charpentier, Jennifer Doudna, and Virginijus Šikšnys.

The following is an edited transcript of a roundtable discussion. The participant has been provided the opportunity to amend or edit their remarks.

To get started, back in 2012, you published your respective landmark papers about CRISPR-Cas9 – papers that provided the pathway for science to manipulate the genetic makeup of, really, all life. At the time, the potential of this technology was just being imagined. Now, six years later, what do you see as its most promising applications?

Emmanuelle Charpentier: The range of CRISPR technology applications has quickly been adapted by the scientific community in a very broad manner. This shows how versatile and powerful the technology is, and it’s still developing extremely fast with new applications being published almost weekly. I think the most interesting applications are in the medical field, and hopefully we’ll see the technology being successfully applied to correcting more genetic disorders.

Virginijus Šikšnys: These days, CRISPR applications span very different fields, from basic biology, to biotechnology and medicine. I agree with Emmanuelle that probably the most promising applications will be in biomedicine and human disease. We are looking forward to the application of CRISPR gene editing for curing inherited genetic disease in humans, and such experiments are going on in different labs across the world.

Jennifer Doudna: I’ll make two additional points. One is that in terms of clinical applications, I’m most excited about using CRISPR to correct disease-causing mutations in blood diseases, such as sickle cell anemia. Many groups and companies are trying to do this now, and there’s a very real possibility that there will be a genetic cure for this disease in the foreseeable future. That would be an incredible advance. It foretells what may come for other diseases in which there’s a single-gene cause and you can envision correcting it using genome editing. The big challenge there is how to deliver gene-editing molecules into a tissue. Blood diseases have been one of the early targets because of the potential to do the delivery ex vivo, in cells that are removed from a patient and then put back into them after the mutation has been corrected.

My other comment is that if you think globally about the impact of genome editing on human society, the bigger impact is likely to be in agriculture. We all have to eat, right? The potential to make genetic changes to plants that will protect them from drought or introduce other beneficial traits has gotten much easier now that we have CRISPR technology.

Šikšnys: Yes, these agro-biotech applications will come a bit quicker than applications in the biomedical field.

And the technology seems to be advancing with remarkable speed, despite the challenges.

Doudna: What’s amazing about CRISPR technology is its incredibly fast path of development. We published our work in 2012. Here it is 2018. There are already clinical trials going on with it. That is an unprecedented pace of technological adoption. And the reason why is that the timing was right for a programmable technology that would easily allow changes to be made to genomes. The technology is not perfect, that’s for sure, and there are always tweaking and further developments that can happen. But it was the fundamental research that we and others in the CRISPR field were doing that laid the foundation for this rapidly adopted, highly effective technology.

Šikšnys: Exactly. And I would add that before CRISPR there were other tools that allowed us to do genome modifications, but these tools were difficult to manipulate. CRISPR tools are readily available to the wider scientific community and they’re much easier to use than the other ones that came before.

Charpentier: The technology is very efficient and very versatile. It can become even more versatile because scientists are very innovative. There is still a wish to increase the specificity of the system and to find ways to more easily deliver the technology into various types of cells.

Šikšnys: The development of CRISPR technology and tools based on CRISPR is going through the stages that all technologies based on tools usually experience. Even in early prehistory, stone tools were not perfect, but over the millennia they developed into sharper, more precise tools. The same is happening in the CRISPR field. This is a typical development in science.

When you started working on the CRISPR gene-editing technology, you were all doing fundamental research in bacterial immune systems. The late paleontologist Stephen Jay Gould once said that life on our planet has always been in the Age of Bacteria. How much of the richness of the bacterial world have we sampled, not necessarily just through the gene editing technology, but also through more fundamental studies of the CRISPR genetic sequence itself?

Doudna: Just a tiny fraction of the microbial world has been sampled. Most microbial organisms haven’t been investigated by science because they can’t be grown in a laboratory. Imagining what’s out there in the microbial universe is one of the things I find so fascinating right now about the science we’re doing.

In fact, most of the technologies that have been so instrumental in bringing molecular biology into the modern era and serve as the foundation for so many biotechnology companies today come from studying microbes. It’s exciting to think about what’s in the future as more and more people investigate aspects of the microbial world that haven’t been studied yet.

Charpentier: We need to continue to support fundamental research in microbiology. It is by studying the diversity of the microbial world that we will continue to find interesting mechanisms that can be exploited to improve the genetic toolboxes that already exist.

Šikšnys: Actually, CRISPR was discovered as an anti-viral defense system in bacteria. But there are many others, including one called restriction-modification system, which was behind the revolution in biology in the 1980s that Jennifer mentioned. I’m sure that further studies of bacteria will lead to new discoveries.

Let’s talk about your pathways as researchers. Dr. Doudna, you’ve mentioned that your love of science really took root in large part because of a high school chemistry class. What was it about that class that made science so compelling for you?

Doudna: I had a chemistry teacher, Miss Wong, when I was in tenth grade at Hilo High School in Hilo, Hawaii. She taught us that science is about discovery. It’s not about memorizing facts in the textbook. It’s about asking questions about the natural world and coming up with ways to figure out answers, and I absolutely love that. I love the idea that you’re posing and trying to answer a series of questions and learning things that potentially nobody ever has understood about the natural world. I still feel very excited about the way science works. It’s an incredibly fun process of discovery. It’s not without frustration, for sure, but that’s part of the process, and it’s something that I learned when I was in that chemistry class.

Dr. Charpentier, when you were growing up, you had many interests, ranging from the piano to ballet to medicine. How did science float to the top?

Charpentier: It was a gut feeling, mainly, but at least one or two teachers during high school certainly influenced me. Between them and my gut feeling, it was my curiosity and my pure scientific interest in what the world is made of, biologically speaking. I was also interested in going to university because I understood very early on that there one could continue to acquire knowledge. I was also interested in the teaching and teamwork aspect of research.

And Dr. Šikšnys, what factors influenced your career decisions and interest in science?

Šikšnys: My path to science was similar to Jennifer’s because I had a really great chemistry teacher in high school. She boosted my interest in chemistry. She trusted me with the key to the chemistry laboratory where I was allowed to do some simple experiments. And Lithuania had a system of chemistry competitions, called Olympiads. Encouraged by the teacher, I started to actively participate in these competitions, and there was no question what I would do when I graduated from high school.

After graduating from Vilnius University with a degree in chemistry, I had limited choices in terms of where to continue my studies. At that time, we were behind the “Iron Curtain” and the borders of the former Soviet Union limited where you could go. Therefore, I went for PhD studies to Moscow University, which was the best place to go at that time. When Lithuania restored its independence in 1990, the borders opened bringing a lot of exchange opportunities for students and researchers. I used this opportunity to initiate research collaborations with many scientists around the world and to become familiar with new techniques, like X-ray crystallography, which was not available for us at that time. This exchange made a huge impact on my own career and on research in Lithuania.

Dr. Charpentier, you have talked about how resourceful you needed to be in overcoming funding challenges for your research. For example, you’ve had to establish your lab multiple times as you’ve moved from university to university to advance your work. Funding aside, what are some of the other challenges that each of you has faced?

Charpentier: I’ve had to adapt quickly to new places, new colleagues and new funding situations. Another challenge was to rapidly establish my labs, which is linked to the challenge of hiring the right people and bringing the two together in the right way. And it’s always a challenge to find the right scientific niche and develop research projects within the frame of topics that are of interest to the scientific community and that could have potential impact beyond fundamental research.

Doudna: I do a lot of work with graduate students and undergraduate students because I’m at a large public university, the University, of California, Berkeley. And so one of the challenges is working with people from all over the world who come to the university to learn and to do science together, and facing not only the intrinsic challenges of doing science, but also trying to learn enough about each person I’m working with that I can find out what they’re really good at, what they enjoy doing, then help them get onto projects that really maximizes their skills.

I have many fascinating examples over the years of students who have come to the lab from backgrounds that are highly diverse and they have been able to find their footing. One of the stories I love the most was an undergraduate, an older student who realized that she was fascinated by the chemistry of nail polish and other cosmetics. To learn more about that, she went to a community college and started taking chemistry classes. She loved it so much that she enrolled at UC Berkeley, and several years later graduated with highest honors in chemistry. She ended up working in our lab for several years as a technician. She was incredible because she had a background that was very different from most of our students, but her intrinsic love of chemistry allowed her to address the scientific challenges that came up in our lab.

Šikšnys: One of the challenges that I sometimes encounter is to convince local funding agencies that doing basic research is very important, because these days there is a clear bias toward applied science. Funding agencies ask you about innovation or new technologies, but usually these innovations and new technologies emerge from simply trying to answer very basic biological questions. This is important to point out.

Turning to the public’s understanding of gene editing generally, what are the most dangerous misconceptions that you feel need to be corrected?

Charpentier: Overall, I’m satisfied that the public understands the benefits of the technology, that it’s transformative for research and development and for our own well-being. And actually, the media treat the field very well. There has been some hype with regard to the danger of the technology, some of which was not really justified. But overall, the media have highlighted the benefits and the fundamental research origin and potential of the technology.

Šikšnys: Fears arise when people encounter new technologies that they do not understand. The same thing happened in the 1980s when genetic engineering started to be introduced to the world. There were fears that scientists would create super bugs that would exterminate people and so on. But now, if you look retrospectively, after 40 years, nothing very terrible happened. In contrast, these genetic engineering methods were used to develop really useful bacteria that produce drugs and provide tools that could improve human health and contribute to the development of society.

Dr. Doudna, after a meeting in 2015, you and a number of colleagues issued a statement discouraging the use of CRISPR technology to make changes in the human genome that could be passed to offspring, or germline editing. Since that time, do you think that scientists themselves have been properly engaged with the ethical implications of gene editing?

Doudna: That meeting and the statement published in 2015 was a real call to action in the scientific community. I’ve been quite pleased by the response. There’s been a very active effort to engage with scientists across disciplines to discuss not only applications of genome editing in the human germline, which means making heritable changes to human cells, but also applications in other areas that have potential environmental and certainly ethical implications.

There’s still a great need to have transparency about what’s happening as a result of technological developments in general. I’m part of an organizing committee that’s putting together a second international summit meeting on human germline editing that will be held in Hong Kong in November. This is an opportunity for scientists to come together again with members of the non-scientific community and discuss where we are today with this technology, how fast it’s moving forward, and specifically how we think about responsible use in human germline editing. I have no doubt that germline editing is coming. It’s just a question of when and how it gets deployed.

The U.S. BRAIN Initiative is focused on spurring the development of new technologies that make it possible to understand the brain in ways never before thought possible. Now that we have the CRISPR technology, what fundamental questions in biology do you expect we might be able to answer?

Šikšnys: CRISPR technology could be used to answer very different biological questions. For example, it could help us to better understand mechanisms of cancer and other diseases. CRISPR screens already look promising for identifying new drug targets that could facilitate creation of new treatments for cancer and other diseases. There are also many open questions in developmental biology, and CRISPR technology could help to tackle these questions, paving new ways to treat diseases or improve plants for better crops.

Charpentier: With the CRISPR-Cas9 technology, there is now work for a lot of researchers to study the diversity of organisms and thereby discover new types of mechanisms and maybe challenge certain dogmas associated with the study of certain types of cells. Researchers could possibly apply the CRISPR technology to study mechanisms that are important in the early development of life. Looking at the same types of mechanisms in a large variety of cells may reveal that some of the inner workings of cells are far more sophisticated than we’ve been otherwise thinking. I find this extremely fascinating. If funding increases, that would increase the number of biologists seeking to answer these kinds of still-unanswered questions. CRISPR gene editing is really useful in this regard.

As Jennifer mentioned, CRISPR gene-editing technology is having a huge impact on fundamental research. I like very much that it’s a system originating from the microbial world. Now, we have a versatile technology that allows us to study the diversity of organisms and modify genomes of organisms that were very difficult to manipulate prior to CRISPR.

Doudna: I’ll give you an example that epitomizes what’s so powerful about genome editing and the opportunities to address questions that have never been possible to answer before. When Emmanuelle and I were at a U.S. National Academy of Sciences meeting earlier this year, a group of scientists was being honored for their research using CRISPR gene editing to study the genetic basis of butterfly wing patterns. [MOU2] This is an incredible example of how genome editing is opening up investigations in organisms that in the past were genetically intractable. Before CRISPR, we could only study butterflies that were captured in the wild and try to make inferences about the genetic basis for their wing pattern on the basis of observation. Now there’s a tool to interrogate the link between genetics and wing pattern in a molecular way.

At the CRISPRcon 2017 meeting, the director of former U.S. Vice President Biden’s Cancer Initiative said that CRISPR is not a light on the nation, that it’s a mirror. What do you think we’ll see in that mirror decades from now?

Doudna: Over the next decade or more we’ll see the CRISPR gene editing becoming woven into the fabric, if you will, of everything that we do. We’ll be purchasing food products that are generated using genome editing. We’ll go to the doctor and find standard-of-care treatments that involve genome editing for certain kinds of diseases. And certainly we’ll see that genome editing is going to underscore a lot of the research that goes into developing solutions to problems that involve making changes to DNA. We’re living through an incredible development right now, seeing a dance of technology that’s going to permeate every aspect of the biological world that we inhabit.

Šikšnys: I agree that in the next 10 or 20 years the CRISPR technology will be used in more and different applications, starting from the agro-biotech sector to human medicine. And CRISPR will become a tool that is used not only in the lab but also in the clinic and biotech industries. In fact, successful CRISPR applications for curing human disease could also help increase the public perception of this new technology. And I am pretty sure that scientists exploring the microbial universe around us will discover new systems and tools to complement and further improve CRISPR technology.

Charpentier: With regard to the point about how the public understands and perceives CRISPR technology, the notion of modifying genomes of plants and organisms will be better accepted by the public. People will understand that it is beneficial and that they should not be concerned or scared about genome editing.

I really hope that 10 years from now we will see the first proof of concepts with regard to the development of the technology to treat certain genetic disorders, and that on a larger scale and in more indirect way, the technology will show use for treating certain types of cancer. And, as I’ve already mentioned, at the level of understanding biological mechanisms, we will know much more about the diversity we find in our world. There will also be many different technologies developed along with CRISPR gene-editing or that CRISPR technology benefits.

To wrap up our conversation, is the terminology of CRISPR a bit of a liability in advancing the public discussion about its benefits or its challenges? “Clustered Regularly Interspaced Short Palindromic Repeats,” or CRISPR, and “CRISPR-associated protein 9,” or Cas9, are rather awkward! If you could make the terms a little more lay friendly, what would you replace them with?

Šikšnys: “Molecular scissors” or “DNA scissors” could be an easier term for the technology that also conveys how it works.

Charpentier: We were working on CRISPR for a while before I first met my CRISPR colleagues in 2010, when I first presented our work on the components of the CRISPR-Cas9 system that was published in Nature in 2011. Only then I realized that I was not pronouncing CRISPR correctly. I and everyone in my lab was saying “crispr,” with a French accent. I arrived at this meeting and thought, “Oh, my God, I am going to make people smile.” But it was OK, and I just continued to pronounce “crispr” with a French accent. Later I tried to adopt the right accent. I had no idea how to pronounce this acronym. But, in a way, the fact that “crispr” is difficult for me to pronounce makes it appealing and catchy.

Doudna: Actually, we’re a bit fortunate to have an acronym that has a catchy sound to it. When I randomly run into people who have heard of CRISPR, whether it’s a taxi driver, or my neighbor, or people at my son’s school, they don’t know what it stands for, but they do know that it symbolizes a powerful technology. They may not know any details about how it works, but they’ve seen this word in the media, and it sticks in their mind. I would stay with the acronym and not worry so much about what it stands for literally, but just think about it as this powerful tool symbolizing this new era that we’re in.