CRISPR Pioneer Feng Zhang at the Berkeley Forum

Conversations April 8, 2019

Professor Feng Zhang appeared at the Berkeley Forum on March 1, 2017. Professor Zhang’s talk focused on how the powerful CRISPR-cas9 technology was developed, the ways in which genome editing will transform the world, and the human impact of capitalizing on nature’s diversity. The event was moderated by Michael Chien.

Michael Chien: Professor Zhang, thank you so much for taking the time to speak with us here today. I want to begin with a topic that has gained national media attention but has been especially discussed here on UC Berkeley’s campus over the last month, and that’s the relationship between your work and that of Professor Jennifer Doudna’s. Last month, the US Patent and Trademark Office upheld the validity of the Broad Institute’s patent on your research and found no interference, in fact, with UC Berkeley’s, which is still pending. What do you see as the main differences between your work on CRISPR technology and that of Professor Doudna’s?

Feng Zhang: Thank you for your question. This is a good question. So, my understanding is that, we have our patent, and Berkeley will be issued its patent, and so, we’ll all have patents. There will be patents , which is fantastic for the world. And the thing is, there’s really been a tremendous amount of contribution from many different groups. It’s great to see that the different contributions getting rewarded and through these different mechanisms, and I think it’s really great that all these work will be recognized.

Michael Chien: Well, the patent awarded to the Broad Institute last month covers the use of CRISPR-cas9 technology in eukaryotic environments, but other patents have been submitted for use in technology in other environments, like UC Berkeley’s. That being said, there are still other institutions, as you mentioned, doing their own original research on CRISPR. So, how do you think the differences in domain of all these patents, that will eventually be filed, affect every institution’s licensing potential?

Feng Zhang: There are different contributions to the field. And so these patents will reward or honor these different contributions. And I think they will do it appropriately so. In terms of licensing, one thing that we have been doing so far, is to make sure that the technology is accessible. In fact, that’s something we have been trying to do for many years now, and we’re going to be able to continue to do that, especially with this patent decision. The technology is a fundamental, foundational technology. So, we want to make sure that as many people have access to that as possible. So, MIT and the Broad Institute have been adopting a non-exclusive licensing approach. So, any party, academics, can use it freely. Commercial entities can have a nonexclusive license. That doesn’t preclude anybody else from doing it. I think that’s the way that we should approach these kinds of technologies. Make it accessible. Do not stifle progress, and really enabling as many people as possible.

Michael Chien: You spoke very thoroughly about how the methodology of your research, and I want to focus a little bit more on the ideation process and the potential applications. As you mentioned, the CRISPR-cas9 system was originally discovered in bacteria, in archaea, which use it to develop immunity through storing the genetic signature of viruses that previously attacked it. How did you initially make that connection that this system might be modified for the purpose of gene editing in other organisms?

Feng Zhang: So, I had been working on genome editing for a while before I started work on the CRISPR-cas9 system. So, there were earlier generations, like I showed on slides, there’s sometimes meganucleases. So, when I was a graduate student at Stanford, at one time I worked on optogenetics. So optogenetics has three needs that I needed to solve. The first is, how do you get neurons to become light sensitive? And that was done by developing these microbial opsin proteins so that we can express the neurons to confer light sensitivity. The second challenge was, how do you deliver light into the brain when the skull is opaque? So, if you just shine light the frontal skull, it doesn’t work. So, then I developed a way to use optical fibers to implant into a specific brain region, and then be able to see into the cells. The third one is, how do you get the opsins to express in a specific group of cells, not any kind of neuron, only a subset of neurons. So, as a graduate student I had developed a ton of different methods to do that using either viral vectors or using a crude recombinant system with CRE Driver mice to get cell-specific expression. But I really wanted to get access to specific cell types in any kind of organism. Maybe eventually even human for clinical translation. So, when I thought about how to do that, one of the things that I thought about is to develop nucleuses to be able to cleave a specific promoter in the genome, that’s specific to a subtype cell, so that you can insert the opsin genes into that specific genomous region, so that is expressed only in the cell that we’re interested in, in the nuclei. When I started to work on CRISPR, after I left Stanford, I realized that these nucleuses are pretty challenging to use. And so that’s really problematic. And also, a lot of the reagents were not readily available at the time. So, it’s around that time that I started to read about other kinds of systems, and I stumbled upon a system called TALE. Transcription activator-like effector. It was in 2010, it was just starting to become understood how TALE proteins are able to recognize DNA sequences. So, I worked on developing that, and so that turned out to be an efficient system to reprogram and recognize specific DNA sequences. So, I started my lab in the beginning of 2011, and I thought maybe I can start using TALE systems to study neurobiology. I can teach students to build them, and to be able to engineer specific cell types in the brain. But that turned out to be quite cumbersome. As I was teaching students to build TALEs, I realized that each TALE construction project is really a serious project on its own. And so, if we had to build these complicated systems, it is quite challenging. So, I started to think about, are there other systems that you can also use for reprogrammable genome editing? It was in the beginning of 2011 when I just started lab, that I went to a talk at the Broad Institute. Mike Gilmore was a professor there, and he had a talk on his work on Enterococcus bacteria. But he had casually mentioned that in Enterococcus he also find these CRISPR systems. And so, when I heard about CRISPR systems, I didn’t know what it was. And so, I went to try to look it up. When I started to look it up on Wikipedia, and also started to read some of the papers, I realized that this is an endonuclease. This is, furthermore, an RNA guided endonuclease. So, it’s also around that time that Sylvain Moineau from the Laval University in Canada, had published a paper in Nature showing that the cas9 system is an RNA guided single nucleus that can make a double strand breaks inside the bacterial cells. When I saw that, I got really excited. I thought…there’s this new system CRISPR-cas9 that maybe you can harness to be able to reprogram by just giving it a short RNA guide. And so that’s how the idea started. If I wasn’t thinking about genome editing of nucleuses before, when I heard that talk in the beginning of 2011, I probably wouldn’t have realized the potential.

Michael Chien: Well the progression of your research, from not only your graduate schooling but all the way up until now, has shown immense potential for really curing diseases. That being said, there are a lot of ethical implications of this kind of technology. In 2015, researchers at Sun Yat-Sen University in China used CRISPR-cas9 technology to edit the genomes of human embryos, which result in genetic changes that are potentially heritable. As a result of your now successful patent, the Broad Institute has the ability to restrict ethically controversial applications of this technology. How does the Institute really come to decide what types of regulations should be enforced when licensing that technology?

Feng Zhang: You must have read the licensing statement from the Broad Institute. So, one of the things that the Broad does not provide license for is germline self-editing, exactly because the controversial issue that’s surrounding the technology. The other thing that it doesn’t provide license for is the production of survival. So, things that have known health consequences for humans. So, the ethical issues surrounding germline editing is a very important issue. And that’s something that has been highlighted and also thoroughly discussed. And I think it’s something that we really need to pay serious attention to, to make sure that we are really thinking and understanding these problems and doing our best to try to think about ways to be able to move forward.

Michael Chien: Speaking of that licensing agreement though, part of the complicated nature of licensing is the disparity in size and intent of all the private companies involved. And so, the Broad Institute has already licensed the technology to Monsanto, one of the world’s largest agricultural conglomerates. And UC Berkeley has partnered with Dupont Pioneer, a subsidiary of the chemical giant Dupont. Do academic research institutions forfeit autonomy over the direction of their technology’s use when they allow large corporations to use that technology for financial gain?

Feng Zhang: I think that the most important thing is to make sure that foundational technology, like CRISPR-cas9, are broadly distributed. We enable as many people as possible so let 1,000 flowers bloom. So many people have created ideas, but each one of them not be limited by what they can do, but really enable them with all these tools. Broad has licensed to many different companies – we have distributed this to 2,100 laboratories around the world, really trying to enable as many people as possible so then they have access to this tool to be able to do what they want to do.

Michael Chien: In line with that method of thinking, you’ve also co-founded a company, Editas Medicine, a startup dedicated to using CRISPR for gene therapy. Is there a clear delineation between what applications of CRISPR are best suited for the academic environment versus, say, a corporate research environment?

Feng Zhang: I think it’s really great that many groups are actively developing the CRISPR applications. There are things that are developing in clinics by academics, things that are developed for a clinical application by commercial groups. I think it’s really great that many people are so excited about this and developing this to its maximum potential. There are a lot of challenges that we still face today with these genome editing tools. We need to understand how efficacious it is, how safe it is. Does it cause a neurogenic effect when you put it into the body? So, the more groups that work on it, I think, the better. There are enormous challenges, and fundamentally, the way that I got excited about the research partly was motivated by a friend who was sick. I think it’s really important that we keep that in mind. The quicker that we can get to these health solutions, to actually impact the lives of the patients, the better. So, I think the more groups really, the better for the world.

Michael Chien: For the sake of time, this will be my last question before we turn things over to the audience. My last question really is about what you said, which is to solve health problems across the world. CRISPR-cas9 has become very notable for its potential. In your eyes, probably being one of these individuals closest to the technology, what do you think is the best-case scenario for curing diseases of all sorts as they impact across all lives in this world?

Feng Zhang: I think CRISPR-cas9 is really just the beginning of molecular medicine. As we sequence the human genome more, we will understand genetic contribution to this much more. We’ll know the mechanisms of these problems a lot more clearly. And then all that will enable us to develop next generation medicine. CRISPR is also enabling researchers to accelerate their research. Drug companies can now screen and validate drugs with a fraction of the time that it used to take them. And all of these combined together I think is going to make a huge impact on the future of medicine.

Audience Member: Hi Professor Zhang. I have a question regarding the C2c2 enzyme you mentioned just now. Did you observe any off targeted effect for the C2c2, and if there is any off target effect, how sensitive, or how specific it is for the RNA that you wanted to target?

Feng Zhang: In some of [way, it’s] very similar to cas9 or Cpf1. The way you increase the number of these batches and then it becomes quite specific. And I think just like the way we’re able to engineer the cas9 to make it more specific by reducing non-specific interactions, we’ll push it out to be able to make C2c2 even more specific.

Audience Member: Hi Professor. You mentioned the great documentary, Jurassic Park. In a related note, I’d your thoughts on the work being done at the UC Santa Cruz and also at MIT by George Church on the resurrection of mammoths using CRISPR. What do you have to say about that?

Feng Zhang: I think that’s pretty difficult to do. To say the least. I think there are a lot of ideas like this, and it’s thought provoking. But I think in practice, is actually pretty challenging to realize that.

Audience Member: Hi Professor. My name is Mark. So, I actually currently work as a software engineer. I don’t have too much context around this, but I’m actually curious. So, I followed your collaborators, the Broad’s Ramnik Xavier. And in an age where autoimmune disease and a lot of chronic diseases, not just DNA the whole philosophy of nature versus nurture. What are your general thoughts on the microbiome and therapeutics within that area, and where you see things being malleable with regard to microbiome?

Feng Zhang: I think microbiome is really an exciting area. There is actually a lot of really interesting research being done here in California that highlights the importance of micro biomes for a variety of different health consequences: Alzheimer’s disease or Parkinson’s disease, autism even. And we don’t know enough about what the interactions of microbiome in the body is. Is it entirely going through the immune system, or is it also direct interface with the nervous system in the body? I think it’s very exciting. And I think it’s a very powerful direction to be able to develop new categories of therapeutics. And as already being shown to be very efficacious for some diseases. So, it’s a very, very exciting area and I think we should do more there.

Audience Member: Hello Professor. I’m a third-year molecular biology student here at the University. And as an MCB student, I am very much interested on the human clinical trials of CRISPR that has been going on. My question is, if you were to direct one of these clinical trials, what disease, what genetic disease would you like to target or possibly cure?

Feng Zhang: I would like to be able to treat as many as possible of genetic diseases. I think you also have to be a realist. You have to start with the ones that are tractable. And so right now, tractability is defined by areas that we can have efficient delivery. Mutation types that we can have high efficiencies in correction. And I think if you go through the list and evaluate based on those criteria, you will find that blood disorders are probably things that are tractable right now. And so, like sickle cell disease or beta thalassemia, and also eye diseases or ear, hearing diseases, are areas that are tractable to deliver.

Audience Member: Hello Professor. I have questions regarding the C2c2 switch to the non-specific RNA’s activity. What is the current status, or what do we know about the mechanism of that switch?

Feng Zhang: Good question. So, we don’t know a lot about that. Very recently the crystal structure for C2c2 has been recorded. And that shows some conformational flexibility in the enzyme that may provide that collateral activity. We have also trans mutagenesis of the proteins, so we know what are the [domains]. It’s happened though in the genes that are responsive partly involved in the collateral activity. And so, it’s still early days. But I think in the next year we’ll probably learn a lot more about what’s happening.

Audience Member: Hi Dr Zhang. I have two questions. So, the first one, is where do you see the direction of your research where your lab in the next 5,10 years? Will it be more application-based genetics? And then my second question would be, where do you see the future of the field genetics?

Feng Zhang: Thank you. These are tough questions. Where’s my lab going to go? I think for one thing is where we are very actively working on trying to address challenges that face the genome editing technologies, especially with translating this into therapeutic applications. Making the enzyme more specific. Making the editing mechanism more robust. And also working on delivery approaches that makes it possible to target more tissues beyond just  a system or the other. In terms of the field of genetics, I think we are in a renaissance for genetics. There are so many exciting discoveries. So many model technologies that all converging right now. And that’s really making our understanding of genetic contributions of any process disease or non-disease much more likely to be addressed. And I think in the next 10 years, we’ll learn so much. It’s hard to predict how far we’ll be. Certainly, 10 years ago predicting where genetics is today would be difficult to make an accurate prediction. So, I think in 10 years, I think diseases will be treatable, some diseases. And we will know a lot more and we will be able to develop more personalized mechanism-based therapeutics of so many health problems.

Audience Member: Hi Dr Zhang. Thanks for coming to Berkeley and thanks to Forum for organizing this event. We all understand that CRISPR technology should be promoted as much as possible in that academic field. But from the commercial perspective, so if there was a start-up company that wants to use this technology, what kind of licensing agreement would this company to do with the public company or the research institute in the field? Does the start-up only need to do one, or if problem is to do several licensing agreements with the different institutes?

Feng Zhang: I think what we’re trying to do at MIT and Broad is, we’re trying to make the technology as accessible as possible. So, we are non-exclusively licensing it to anybody who wants to come in and get a license. And so, whether you are a start-up company or you’re a Fortune 50 company or you’re an academic course facility, you get the same treatment to get access to the technology.

Audience Member: Hello Professor Zhang. I was curious. Recently, there’s been a huge push for genomic, genetic, I guess, general nucleic acid based technologies and solutions to disease. Do you see that as a be all, end all? Or do you think that as we’re exploring these, there’s going to be a combination of that and, maybe, some other approaches that are going to be required to solve these diseases?

Feng Zhang: When we’re thinking a multiple-choice question, usually it’s A, B, C, or all of the above. Usually, all of the above is a good guess to choose. So, absolutely. Genomics approaches is a very powerful approach. Or vary so much from these genetic sequencing or genetic analysis approaches of that disease. But that’s probably not going to be everything. We need other methodologies. And I think that’s where interdisciplinary approaches that combine sophisticated computation with chemistry with physical methods, and also all of the different arrays of biological interrogation of this. Conversion, then, is going to be critical for us to make a huge push.