CRISPR’s Second Decade: Jennifer Doudna Looks Forward and Back

The 2020 Nobel Laureate shares her thoughts on the first decade of CRISPR genome editing, where the technology is heading next, and what it needs to get there

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JenniferDoudna
Jennifer Doudna
Nobel Laureate and Professor of Biochemistry & Molecular Biology
University of California, Berkeley

Last month, Genetic Engineering & Biotechnology News hosted “The State of Biotech” virtual summit, packed full of amazing conversations with scientists, physicians, executives, and analysts driving new research and applications in biotechnology. Among them was University of California, Berkeley, biochemist Jennifer Doudna, who shared the 2020 Nobel Prize for chemistry with Emmanuelle Charpentier. Doudna is also an investigator with the Howard Hughes Medical Institute, the cofounder of the Innovative Genomics Institute (IGI), and cofounder of a number of biotech companies applying CRISPR to therapeutics, including Caribou Biosciences, Editas Medicine, Intellia Therapeutics, Mammoth Biosciences, and Scribe Therapeutics.

In a candid conversation with GEN senior science writer Julianna LeMieux during “The State of Biotech” forum, Doudna discussed a wide range of topics—what excites her most about CRISPR, where she sees genome editing making an impact on society, what it is like to win the Nobel, and much more.

(This interview has been edited for length and clarity.)

 

LeMieux: Jennifer, I do not suppose being introduced as a Nobel Laureate will ever get old, will it?!

Doudna: It still feels new. I still pinch myself…

 

LeMieux: It has been 10 years since your landmark article on CRISPR as a genome editing tool with Charpentier and colleagues in Science.1 What has been the best, and worst, part of the past decade?

Doudna: The best has been doing the science. It has been an extraordinary opportunity to work with so many amazing people, both in my own laboratory, with our collaborators, and, of course, with Emmanuelle. Before I even met Emmanuelle, Jill Banfield, my colleague at UC Berkeley, was one of the first researchers to find CRISPR sequences back before they were a thing. There have been so many other people since then. The science is still what gets me out of the bed every morning and is still very new and exciting.

The worst? Certainly, the pandemic is high up there on my list. If there is a silver lining, it pulled together scientists from different disciplines. We certainly saw this at the IGI. People came together to build a clinical testing laboratory where we were able to build a team to develop CRISPR as a diagnostic tool. There were many other things that happened scientifically everywhere, of course, that were motivated by the desire to pitch in during the pandemic.

 

LeMieux: How did life change for you after you won the Nobel Prize in 2020, beyond the coveted parking space that Berkeley gifts to Nobel laureates.

Doudna: They do not even charge me for it! Isn’t that amazing?!

It was extraordinary to see how many young scientists reached out to me after the Nobel announcement to say, “I feel inspired, I’m excited, I want to learn more.” I have heard from many, many young scientists—most of whom I do not know personally—who have reached out. That was extraordinary and it is still going on.

Because we were in a pandemic, it was an unusual time to get news like that from the Nobel. We were not able to travel to Stockholm for the events, so I was awarded the Nobel Prize in my backyard in Berkeley!

 

LeMieux: What is a typical day in your life like?

Doudna: I have done very little traveling this year. As a result, I am mostly in my laboratory every day. I spend about half of my time these days with either laboratory members or collaborators, talking about science, planning experiments, reviewing data, and writing articles. So that has been fun and exciting.

What am I doing during the other half? Primarily, I am working on building our institute. We started the IGI about 6 years ago as a partnership between UC Berkeley—where I have my primary appointment—and the University of California, San Francisco, and the Gladstone Institutes—where I have a secondary appointment. We have two primary goals: using CRISPR for health care applications and to address the challenges of climate change.

For example, we have an approved clinical trial that is running. This is probably a first for the nonprofit sector. We are certainly the only nonprofit to conduct a clinical trial that is running [a trial] for sickle cell disease with CRISPR right now. We are forging the way there. We want to make sure we can ultimately have an impact on many people and control costs in the future.

In the climate area, we have booted up a big team that includes scientists from UC Davis, one of the world’s best agricultural universities, and other national laboratories in our area. We have amazing scientists who are using CRISPR to make changes to the soil microbiome, and to plants, that will help these organisms adapt as the climate is changing.

 

LeMieux: You have just come back from the Cold Spring Harbor Laboratory (CSHL) Genome Engineering conference, which you co-organized. How was the meeting and what stood out for you this year?

Doudna: It was a lot of fun! It was great to be back in person after 2 years of virtual meetings, which were good in their own right, but nothing replaces the opportunity to run into colleagues. I met many students at the meeting. Many attendees had never been to CSHL before. It is a reminder that, for many, especially younger scientists, it is still kind of a Mecca. It was also a reminder of how incredibly fast the field is moving, how many different types of people are now contributing, the impact of CRISPR, and how CRISPR will likely continue to grow in the future.

 

LeMieux: What about some of the most exciting projects going on in the Doudna laboratory right now?

Doudna: We continue to have a great active collaboration with the laboratory of Jillian Banfield. For a long time, we have been interested in understanding the context of CRISPR in its natural setting, in microbes. What is CRISPR doing in microbes and how many different flavors of CRISPR systems are out there? We have most recently been focused on CRISPR pathways that are encoded by viruses, which is very interesting given that CRISPR is thought to be primarily an antiviral system. Yet, it looks like viruses have captured it and they are carrying it around and using it against their competitors!

The other big push is more on the applied side. We are trying to figure out how it will be possible to deliver CRISPR molecules into specific cell types. Whether we are talking about a patient who needs it for a medical application or using it in plants to address climate challenges. In either case, having the ability to deliver CRISPR molecules into targeted tissue types is critical. That is an effort that involves building on existing technologies for delivery, but also looking for innovative ways to do this.

This project also involves looking at how viruses do this. How do microbes get molecules into other microbial cells and tissue types? This is a fun project because it involves new biology but always with an eye toward something that can be used in a more applied setting.

 

LeMieux: You recently posted a preprint, with Jennifer Hamilton as the first author, that described a delivery mechanism.2 By displaying antibody fragments on the Cas9 envelope particles, you can target the system to specific cells. How much of your laboratory is focusing on delivery versus other areas of genome editing?

Doudna: Students are often the bellwether of the next big thing. Many students have a sense of where the next big opportunities and discoveries are going to be and many that come to my laboratory these days want to work on delivery.

It has been interesting to see that trend developing, and I think it reflects the appreciation across the field that delivery is one of the new frontiers. It is not new, though, is it? Delivery has been a challenge for a long time, but I think there is renewed interest, especially when we think about how to deliver genome editing systems and molecules into different tissue types.

 

LeMieux: There are so many new tools in the toolbox, including many new Cas enzymes. Do you think we will reach a point when people are no longer using Cas9?

Doudna: I think about it like a physical toolbox, in the sense that you have household tasks that you need to get done. Whether you need a hammer or a wrench or a screwdriver, they are all in the toolbox. That is how I think about genome editing. There are different ways of manipulating the genome in a precise manner. If you need to correct a gene or change the protein levels that are being produced or you want to image a gene, these are all different applications that require different tools in the toolbox. Over time, I think that we are going to see the genetic toolbox continue to expand.

A theme for the past several years at the CSHL meetings has been a continued expansion of the CRISPR toolbox—new ways of using CRISPR, new proteins, old proteins being used in different ways, etc. It continues to make it possible to make any kind of change to any genome with the kind of precision and accuracy that will enable both fundamental discoveries and important advances in health care and agriculture.

 

LeMieux: Considering the growing number of interesting tools—transposons, base and prime editors, etc.—and nature’s complexity, this toolbox expansion could essentially keep going for a while. Do you see a time when we have enough tools in the toolbox to do everything that we would want to edit a genome?

Doudna: I do think that that time is coming. It is hard to say exactly when. There may not even be a precise date when it happens. At some level it is a moving target but it continues to get easier to make changes and do things to genomes in a targeted manner that were just not possible, even in the recent past. Imagine making targeted integrations of tens of kilobases of DNA into a genome. That is the kind of work being done right now with different methodologies, including the CRISPR transposase that you mentioned. I think it is extraordinary that we continue to expand the kinds of manipulations that can be made using these tools.

 

LeMieux: There is a lot of excitement about the therapeutic applications of CRISPR. You have cofounded several biotech companies pursuing novel strategies, applications, and clinical genome editing. What excites you most in this field and what would you say are the safety and regulatory issues that still need to be resolved?

Doudna: Two things excite me most in the near term. The ability to make targeted changes that can correct the effects of monogenic diseases. I am thinking of disorders, such as sickle cell disease, cystic fibrosis, muscular dystrophy, and maybe even neurological disorders such as Huntington’s disease.

CRISPR today has the capability to make those corrective changes. The challenge there is delivery. That is where the field is pushing forward. But, in terms of the CRISPR technology, those tools are in hand now, which is quite amazing. There are already results from clinical trials for sickle cell disease that are just extraordinary. They show patients being relieved of their symptoms and, for all intents and purposes, effectively cured of their disease.

On the more societal side is the question of cost and access, which is motivation for IGI to work in this area so that we can address some of those challenges. The science is already there to do this, which is just amazing.

When I think ahead to the next 10 years, I do think we are going to see genome editing used in ways that affect broader swaths of individuals. There are already efforts to use CRISPR to protect against the high cholesterol that can lead to cardiovascular disease. If that were to become a more mainstream application, it has tremendous potential to affect many people in a positive way. I suspect, over the next decade, we will increasingly see that type of preventive health care application of CRISPR.

 

LeMieux: Let us talk about the high prices of these medicines. How do you think about getting that price down?

Doudna: We must first ask what drives that price? In the case of sickle cell disease, for example, one of the drivers is the delivery strategy. Today, that therapy is delivered ex vivo. This means that a patient must have their cells extracted and edited in the laboratory and then reinfused through a bone marrow transplant. That requires 6 weeks of hospitalization and follow-ups. Imagine if we have a delivery strategy that avoided all of that, where you could do a one-time injection. The editors would hone to the correct cells in the bone marrow to do the therapeutic editing without requiring all that ex vivo manipulation and the bone marrow transplant. I think this would be extraordinary.

Is that going to be possible? My answer is yes. Is it possible today? No. But that is why we must work toward that goal.

Anytime there is a new technology on the horizon, it tends to be the case that the initial experimentation is expensive. It is costly. There are small number of people, so it is a very ad hoc approach. The more that we can turn CRISPR into a pipeline that is well established, where we know how to make the molecules and scale, the more we can help reduce the cost. This is where many companies will be contributing over time. They will help figure out how to ramp up the current scale, so that it can reduce the cost for individuals.

 

LeMieux: You have previously said that one of the biggest areas that CRISPR can impact is agriculture. Why is that?

Doudna: For one thing, we all have to eat! There are more and more of us on this planet all the time, so there is a large market. Plants have an enormous impact on our environment, which is very closely connected to our health and lifestyle.

The scale of the impact of agricultural applications is huge. There are different barriers to using CRISPR in agricultural systems compared with using that technology in humans. The barriers are not necessarily easier, but they are different. You do not have to run clinical trials, but you do have to get appropriate approvals.

If we are using a technology like this in the environment, we must be very thoughtful about the safety and efficacy of the application. Primarily, I think that there is such an enormous need to address rapid climate change. Here in California, we are experiencing this in real time. I feel very aware of the importance of technologies that can reduce carbon emissions and help farmers do their cultivation in a way that is carbon neutral in the future. I was surprised to learn that about 25% of global carbon emissions come from commercial agriculture. It is a very large contribution and an area where we think CRISPR could have a big impact.

 

LeMieux: The IGI has devoted resources to studying CRISPR and agriculture. Was the decision to focus on agriculture because of your own personal interest? Or is it that the CRISPR community is moving in that direction in a more general sense?

Doudna: We made the decision to focus on agricultural applications several years ago at the institute. Why? It was a combination of recognizing the tremendous need and opportunities for genome editing, with plants and the soil microbes that support agriculture. We are at the University of California. One of our sister campuses, UC Davis, is one of the world’s best agricultural universities. We have, in our community, some of the most extraordinary plant biologists and microbial scientists. Putting those things together, it seemed like an opportunity not to be missed.

 

LeMieux: It is perhaps not as easy to spot progress in the field of genome editing and agriculture, especially when there is so much attention on success using CRISPR in the clinic. Where do you see progress being made?

Doudna: One area is the study of Pam Ronald, a professor at UC Davis and one of our IGI affiliates. Her laboratory has been working on rice for a long time. They have created a strain of rice that is naturally [flood] resistant that is now in the hands of more than 10 million farmers globally and having a very tangible impact. However, she started that work before CRISPR came along. It ended up taking 15 years for her laboratory to do that project, end to end, and have it [reach the] hands of real-world people who are using it now.

What CRISPR does is to vastly accelerate that pipeline. We can use CRISPR to understand the genes that need to be edited so that you can use it quickly to do genetic screening. This is something that David Savage is actively doing at the institute. You can also use CRISPR to make the actual manipulations in plants and create those new types of plants that will have that real-world impact. This speaks of the opportunities that lie ahead.

 

LeMieux: About 12 years ago, before CRISPR took off, you briefly left academia to take a senior role at Genentech before returning to academia. Why did you move to industry and why did you come back?

Doudna: I was at an interesting point in my career. This was back in early 2009. I had been running my academic laboratory for about 14 years. I had started my laboratory at Yale in 1994 and then I moved to UC Berkeley in the early 2000s. I loved my science, but I started to ask myself whether my science was having impact? I loved the work that we were doing, but my hope was that our science was going to make the world a better place in some way.

When I had the opportunity to go to Genentech, I felt it was an interesting path to explore. However, I realized quite quickly that I really missed my academic colleagues. You take your life and colleagues for granted, until you realize that they are not there anymore! I also realized that I value the opportunity to do curiosity-driven research that is not restricted by company milestones. This is, by the way, no negative reflection on Genentech. I think they are a great organization. But they are a company. They have to make money in the end, and I get that. For me, for the kind of science that I like to do, and the kind of person that I am, it was a better fit for me to be back at Berkeley. I was lucky that my Berkeley colleagues welcomed me back.

 

LeMieux: There have been several successful CRISPR companies that have spun out of your laboratory. What do you think is the key component to cultivating that type of environment?

Doudna: It all ultimately stems from great people who like to work together. I love building teams, I really do. It has been a lot of fun in my academic laboratory. [In academia], we are always rebuilding our laboratories, right? We have students who are graduating all the time. We have postdocs who come in for a short period of time and then go off for other jobs. There is constant turnover. I am always building a team, in a way. In companies, that is what one is doing. It is creating a culture that focuses people on a goal or maybe multiple goals, but where people are aligned around a project. I love that.

It is amazing to see how fast things can happen when you have a focused team with resources. They can run after a problem in a way that is often, frankly, not so easy to do in an academic setting. I think there is a place for both. We certainly need to have great companies that are taking discoveries and innovations, that often start in an academic setting, but are able to scale them and focus on them in ways that are hard to achieve in academic laboratories.

At IGI, we are very interested in supporting entrepreneurs. We are proud of a couple of programs we started with philanthropic donations that encourage young entrepreneurs to get money and space where they can develop their idea to either start a company or license their technology into an existing company.

 

LeMieux: Let us talk about ethics. It has been quieter over the past few years on the bioethical front. After all the furor surrounding the CRISPR babies scandal, there are no more headlines and no moratorium. Genome editing in humans is likely going to happen again, whether it is here or internationally. What are your big concerns on this front at this moment?

Doudna: My major concern is ensuring that the topic stays on the minds of people who are practitioners of genome editing. It is essential that we maintain some degree of transparency and that people are aware of where the field is headed.

I was a novice to the whole field of embryo manipulation. I knew very little about the science of in vitro fertilization before I had a crash course so that I could understand how CRISPR might be used in that context. As a result, I have come to appreciate how much biology is still to be discovered about early embryo development. I frankly think a lot of that can be done in animal systems. But some of it cannot. I think there will rightly continue to be important research that gets conducted with CRISPR as a tool.

However, I think you are really talking more about the application of CRISPR in a clinical setting. For example, making changes to embryos to create a pregnancy where the changes that are made are heritable. I do think that remains very much a possibility. It has already been done, as you know. Even more reason why we need to have transparency and discussion around that application of genome editing, including what conditions would be appropriate for that use of CRISPR and all the societal and ethical implications. I do not think those are easily addressed and they really do need to be actively discussed.

 

LeMieux: Does it worry you?

Doudna: Not very much right now, largely because I think there are other things to worry about, for better or worse. The reality is that there are still technical barriers to using CRISPR in that manner. If we (the scientific community) keep on top of it, I think we have an opportunity to have the ethical and societal considerations developing alongside the technology.

 

LeMieux: On the preprint we were talking about earlier, all five coauthors are women. After your Nobel Prize, there was a lot of talk about the impact of two women being awarded the prize in chemistry. I am wondering whether some of that optimism has been realized, and if so, how?

Doudna: Great question. I have been quite struck by the number of women who have reached out to me to say that they were touched by this in some way. They were excited by the fact that two women won the Nobel Prize in chemistry, and that it meant something to them. That has been really inspiring to me personally and it makes me reflect on my own experiences. I feel very fortunate that I have had both female and male mentors in my career. But, in some ways, the women who were inspirational to me were particularly inspiring. I think it is very natural, especially when you are a young person, and thinking about your future career, to feel inspired when you see people who look a little bit like you. To be able to say that I could see myself as that person in the future—it really does mean something.

That is what I am finding now, with the Nobel, is that there is a sense that other women feel empowered in a way. They feel like, “that could be me.”

 

LeMieux: It was absolutely inspirational and very exciting, not only to young women scientists, but also to all scientists.

Doudna: You are right, it is all ages! I have had women in their 90s come up to me and say that this means a lot. It feels good to feel empowered. For many women, we did not feel that way in the past.

 

LeMieux: We know that the IGI mobilized very quickly 2 years ago to provide COVID-19 testing. What role do you think the IGI is going to play going forward for virus detection and pandemic prevention, if any?

Doudna: I was very proud that our team could boot up a clinical laboratory3 as quickly as we did. Many people contributed to make that possible. As a result, we have had a clinical laboratory operating in our building now since early 2020, doing primarily COVID-19 testing until recently (Figure 1). Now we are doing more sequencing-based analysis of genome-edited tissue samples in support of our ongoing clinical trial and in preparation for future medical applications of CRISPR.

Laboratory at the Innovative Genomics Institute
Figure 1. Researchers working in the COVID-19 testing laboratory at the Innovative Genomics Institute.

It has been interesting to see the evolution of this laboratory. We have recognized that it enables a lot of science that is difficult otherwise. You brought up the aspect of CRISPR-based diagnostics. We have had an amazing consortium of laboratories working across both sides of the San Francisco Bay to develop CRISPR as a diagnostic tool initially for COVID-19, but potentially applicable to many other kinds of targets. We were greatly enabled by the clinical laboratory because of getting access to patient samples that came in through the laboratory. I am hopeful that going forward, the laboratory will continue to pivot.

It seems like we will not need as much COVID-19 testing in the future. We will increasingly pivot to other kinds of diagnostic testing that will largely be in support of the programs that we have running at the institute, such as the sickle cell trial.

 

LeMieux: Is there anything that you would have changed about the past 10 years?

Doudna: No, probably not! That is not to say that everything that happened in the past 10 years was great. Believe me, a lot of it was not great in certain ways. But [the whole journey] is part of the path that I am on collectively with my colleagues. Whether it is dealing with the pandemic or celebrating the scientific successes that we have had or educating the next generation of scientists. All of these things have shaped where we are right now. Even with the pandemic, which has obviously been extraordinarily difficult for everyone.

I think there is, in some ways, an interesting silver lining where we are able to find a path toward different and better diagnostics in the future. We hope we all have better ways of being prepared for future pandemics through all of this. And of course, work that has gone on elsewhere to bring us mRNA vaccines as quickly as those that came about is truly exceptional. All these experiences are part of the journey.

 

LeMieux: If you could go back 10 years and give yourself a piece of advice, what would it have been?

Doudna: It would be something like, “just go with it.” Challenges come up all the time for all of us, right? But what I have found in my life is to view those challenges as opportunities in some way. Whether it is to make myself a better person, to learn from mistakes and move forward in new directions, and to celebrate successes when they happen. And, of course, to embrace wonderful colleagues. I try to tell myself to go with it and take the long view. There are always short-term setbacks for things, but if you keep your eye on the ball, that often is a good strategy for keeping up your morale and continuing to take the next step forward.

 

LeMieux: Great advice. Finally, where do you think we will be in 10 years’ time when we invite you back for “The State of Biotech 2032”?!

Doudna: Whoa, boy! You have saved the hardest one for last! I cannot predict what will happen next year, you know? But, if you pushed me, I think we will be at a point in 10 years where the toolbox we have been discussing has continued to expand in directions that are hard to even imagine right now. It will not just be CRISPR. The toolbox gets bigger all the time. I think the opportunities to use CRISPR to improve people’s lives will continue to advance. And I certainly hope that within 10 years, we have figured out how to create a smoother pipeline that will take innovations and allow us to transfer them and translate them as quickly as possible into real-world applications.

In the end, that is what our institute is all about. It is about fostering fundamental innovation, but importantly, connecting it to the investors, the entrepreneurs, etc., who are going to be able to take those discoveries and turn them into actual practical applications.

 

The above article was first published in the October, 2022 issue of GEN Biotechnology. GEN Biotechnology is the new peer-reviewed journal from Mary Ann Liebert, Inc. and Genetic Engineering & Biotechnology News (GEN) delivering exceptional research breakthroughs, news, and analysis directly impacting biotech.

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