Jennifer Doudna - Rewriting the Code of Life: CRISPR Biology and the Future of Genome Editing

you you you you welcome to UCSB Arts & Lectures please take this moment to locate the emergency exit nearest your seat we ask that you turn off your cell phones please refrain from all cell phone use we also remind you that photography and sound recording of any sort are not permitted and that food and beverages are not allowed in the theatre thank you for coming and enjoy the event good evening welcome to Campbell Hall I'm Heather Silva the programming manager here at UCSB Arts & Lectures thank you so much for being here tonight we're delighted that you could join us for this evening's lecture by our esteemed UC Berkeley colleague dr. Jennifer Doudna before we begin I do want to thank tonight's event sponsors Monica and Timothy Babbage thank you so much and thanks as always to our corporate season sponsor saige publishing our community partners the Natalie Orfila foundation and Lou boogly Olli and to yardie for their support of our lecture program thank you very much I also want to acknowledge many UCSB students who are here with us tonight whoo it's always a great joy to have your energy in the room and also to those students who are watching the live feed nearby in Buckhannon hall so tonight's event is part of the thematic learning initiative series entitled health matters in the lead up to dr. down des event Arts & Lectures organized a number of advanced learning opportunities for the community and UCSB students including a learning opportunity about the basics of the CRISPR technology with UCSB professor of biochemistry dr. Stewart Feinstein at the Santa Barbara Public Library and earlier this afternoon dr. Doudna attended a session with students and faculty from the department of molecular cellular and developmental biology we're most grateful to Lynda Weinman and Bruce Haven for the visionary support of the a and L thematic learning initiative after dr. doubters presentation there will be a question-and-answer session moderated by dr. Feinstein which include questions collected in advance via email from ticket buyers here in the theater following that dr. Doudna will sign copies of her book here on stage called a crack in creation books are also available in the lobby at the Trotters book sale table as an internationally renowned professor of chemistry and molecular and cell biology at UC Berkeley dr. Jennifer Doudna and her colleagues rocked the research world in 2012 by first describing a simple way of editing the DNA of any organism using an R a guided protein found in bacteria this breakthrough technology called CRISPR Castine has redefined the possibilities for human and non-human applications of gene editing including opening up and accelerating the development of new genetic surgeries to cure disease novel ways to care for the environment and nutritious foods for a growing global population challenged by climate change dr. Donna is also the executive director of the innovative genomics Institute an investigator with the Howard Hughes Medical Institute and a member of the National Academy of Sciences the National Academy of Medicine the National Academy of inventors and the American Academy of Arts and Sciences she's also a foreign member of the Royal Society and was received many other honors including the breakthrough prize in life sciences the heineken prize the BBVA foundation frontiers of knowledge award the Japan prize and the Cavalier Prize she is a co-author with Sam Sternberg of a Kraken creation a personal account of her research and the societal and ethical implications of gene editing it is my pleasure to welcome to the stage dr. Jennifer Doudna [Applause] good evening good evening Santa Barbara and UCSB it's a huge honor for me to be here and I'm very grateful for the opportunity to come and and visit with you and speak with you about the science that I've been up to how are you all tonight whoo so you know I'm really grateful for that that generous introduction but I always like to start I know we have a lot of students here tonight I like to start by pointing out that I grew up in a small town in Hawaii nobody in my family was a scientist and I'm here really today and tonight doing what I do because of just you know pursuit of a passion that I had starting when I was growing up on that Island environment and interested in science and thinking about how I could eventually make a career out of the process of discovery and the story that I'm going to tell you tonight is very much an outgrowth of that passion and the interest that we had in understanding something seemingly esoteric namely a bacterial immune system and how that curiosity driven science went in a direction that none of us at the beginning could have predicted and I like to start off talking about the concept of gene editing by showing you this picture of the DNA double helix and I think the idea of genome editing really started when scientists back in the 1950s discovered this beautiful structure because this chemical helix is the code of life it's the way that all cells and organisms have the chemical information to develop and grow into a tissue or an entire organism and it's it's if we can think about it really as the the instructions for that organism and when this double helical structure was discovered scientists at that point already started imagining what you could do if you could not only read the code of life but what if you could synthesize it what if you could recode that information alter it so that you could under and the function of genes and even do things like cure the genetic basis of disease and and so really since you know since since that time over the last several decades there have been a series of scientists and and research teams that have been investigating this structure and how you could modify it and one of those wasn't me actually right so we started off working in a very different area of biology and chemistry that eventually led us to the concept of genome editing based on our work on this obscure bacterial immune system but before we get to that I wanted to first tell you a little bit about how I got interested in this area of science and especially for the students here I like to like to you know just tell you a little bit about my own process of Education and development and so for me it was back in probably I was in you know the sixth or seventh grade and my dad who was a professor at the University of Hawaii and in literature gave me a copy of Jim Watson's book called the double helix and I read this book and it was absolutely mind-blowing to me that scientists could come up with a way to understand and discover the structure of a molecule like DNA and that for me was the beginning of thinking about you know wondering gee I wonder if I could work in that field someday could I actually do work that would uncover fundamental aspects of biology that nobody's ever figured out before and I got really interested in that possibility and and then you know as time went on so I you know I was interested in chemistry and I went off to Southern California a little further south and near Pomona College to get my undergraduate degree and I was studying chemistry and I took one biology class in college and in that class we were taught about what was called the central dogma of molecular biology namely that DNA which is the code of life encodes all of the information necessary to make a cell or an organism and the and the chemical basis for this is that that information in DNA is conferred to the cell by transcription which is a process that makes a transient copy of the DNA in the form of RNA molecules that are translated by the cells machinery into proteins and we were taught that it's really the proteins that are doing all of the functional work in the cell and the DNA is really important because it's it holds the the fundamental information necessary to make all these proteins and then this molecule in the middle called RNA is you know to us in college it sounded really boring it was this throwaway copy of the genome and you know and we were told it was just kind of intermediary molecule and I didn't think much more about it but eventually when I got to graduate school I learned that sometimes RNA molecules function without encoding proteins and that in fact there was a very exciting line of research going on at that time in the mid to late 1980s that showed that a lot of these molecules of RNA can actually do really interesting things in cells and in fact a number of scientists were starting to think that it was really RNA that gave rise to the life that we see on earth that these molecules of RNA could encode genetic information in their own right as they do in a number of viruses today and they could also carry out chemical functions and so I pursued my graduate work studying that aspect of biology and in an interesting way that led me to the technology known as CRISPR and the reason is that a number of years later when I was now running my own academic research laboratory I got exposed to a scientist who was studying how bacteria were thinking about how bacteria fight viral infection and our work studying this process and looking at how bacteria can acquire immunity to to viruses led to a technology now known as CRISPR cast that is is a technology that enables precise changes to be introduced into the DNA of cells but that's not how we got started working on it was really a question of the fundamental biology of these systems and so you can imagine me sitting in my office at Berkeley UC Berkeley it was around 2005 or so and one day I got a call from a colleague Gillian Banfield who is working in a very different area of science for me she studies the bacteria that grow in the environment most of these bugs have never been cultivated in the lab and most scientists don't even know what they are and what her research team does is go out and identify what these bugs are by sequencing their DNA and in the process they also sequence the DNA of the viruses that are interacting with these bugs to try to understand what their ecosystem is how do these bugs grow and how do they fight off viruses that they encounter and what can we learn fundamentally about life on our planet by understanding these kinds of organisms and in the process of that research her lab was one of the very first to notice that a lot of bacteria had in their DNA a very unusual sequence and it was and so what this cartoon shows you here is a picture cartoon of the bacterial chromosome this is the DNA of a bacterium and what Dan Fields lab identified was that in many of these bacteria there's a place in the genome that has a series of short DNA repeats shown by the plaque diamonds that flanked pieces of DNA that have a unique sequence shown by the colored boxes and these were really distinctive because most parts of the bacterial DNA didn't have these repetitive elements so you know she and a few others were noticing this pattern of repeats and they had come to be called crispers which stands for clusters of regularly interspaced short dramatic repeats I won't say that again and but now this this acronym CRISPR you see it in the media sometimes and you know you might think that it stands for a new kind of cracker or the place where you store your vegetables but now you know that it's actually this pattern of DNA sequences and furthermore these sequences have what are known as casts or CRISPR associated genes that are hanging out nearby in the genome and these genes encode proteins and when they were first discovered nobody knew what they did but they were distinctive because they always occurred and they sat in the genome next to these CRISPR arrays and the question was what are these doing and the reason that Banfield Jill Banfield called me up was because of two things one is that right around that time three different publications had appeared in the scientific literature reporting that in these CRISPR arrays the unique sequences came from viruses and so this was a very interesting observation and again nobody knew why but it was and I gave some scientists the idea that this might be some way of storing information about viral infection that happens in bacteria why nobody knew at the time but it was seemed interesting and furthermore Jill being a very astute scientist even though she doesn't do experimental work in the lab she wondered if these stored viral sequences were being used in cells in the form of RNA molecules and knowing that I work on RNA she thought that it might be something that our lab could investigate and so over the next couple of years there were really just a handful of labs worldwide that had started to pay attention to these these CRISPR sequences and what emerged in the scientific literature was genetic evidence that the way these these systems operate is is the following so in cells that have a CRISPR array here and the associated genes there these cells are able to detect viral DNA that gets injected into the cell during a viral and affection and once that injection occurs the cell can acquire a little piece of the viral DNA and store it in the CRISPR array so this is a an adaptive system so new sequences are being stored all the time and then the cell uses the those sequences by making an RNA copy so this is a molecule that is chemically related to DNA but it's able to exist in the cell as a single strand rather than a double helix like in DNA and these molecules of RNA produced initially as a long string of sequence are cut up into shorter units that each include a sequence acquired from a virus and importantly those RNA is then combined with proteins encoded by the caste genes to form a protein RNA complex that can surveil the cell looking for a sequence that matches the sequence in the RNA when that match occurs then the proteins are recruited to that particular molecule of DNA and the DNA is destroyed and so for bacteria it's a terrific way to acquire immunity to viruses and store it at the level of DNA and then sort of deploy it in this way that I just illustrated and so for me as a you know biochemist and somebody that's always sort of asked the Y questions in my lab or you know you know how and why does does a system operate at the molecular level we were interested at this stage in getting involved to understand how these molecules actually function and so one of the things that's really interesting about these these CRISPR systems is that they're quite diverse and this is a cartoon that just shows that there's there that if we look at the different types and numbers of genes and that's what these little boxes illustrate that are part of the these CRISPR castes immune systems you can see that there's lots of variability some of these systems had a lot of different genes that were in part of it and but and then a number of others down here had really just one or two genes some of them very large jeans that were required for this adaptive immune system to function and although we started off initially studying the the types of CRISPR systems shown at the top that had lots of genes involved I went to a conference in in 2011 and I met a scientist emmanuel sharpen CA who was studying a CRISPR system down here that had a single large gene called Cass 9 required for CRISPR based immunity and when she and I met at that conference we realized that we have complementary expertise I'm a biochemist she's a microbiologist and we decided to get together to answer this question namely what is the function of the protein that's encoded by this gene called Cass 9 and it seemed like a really interesting protein nobody knew the function of it at the time but it was known genetically to be essential for bugs that have this type of CRISPR pathway to fight off viruses and so the question was how does it work and that's what we set out to understand and that led to a fantastic global sort of international partnership she her lab was in Sweden at the time my group was in Berkeley and you know thank goodness for Skype and and and programs like that because we were able to part collaborate with our colleagues in Europe by by communicating mostly over the over the Internet and sharing data and ideas even though our students had never met each other initially right and and what what we had two fantastic scientists Martin Yannick in my lab christiansí and Emmanuel's lab who were able to work together to figure out what the what this caste 9 protein does and it turned out to be an amazing little molecular machine because it operates by recognizing a DNA molecule and I'm showing you the DNA here and just in a very schematic way to show you that this is a protein the cart the blue cartoon is the caste 9 protein that interacts with DNA by cognizing a 20 letter sequence in the DNA that matches the sequence in this molecule of RNA here that comes from the CRISPR array and remember that this is a part of the crispr RNA molecule is derived from a virus so the 20 letters on this end of the molecule recognize a DNA molecule that has a matching sequence so in a Vienna bacterium this would be a DNA molecule that comes from a virus and when that match occurs the DNA helix unwinds and the protein is able to use two separate chemical centers to cut the DNA much like you might cut a ribbon or a rope just cuts apart the DNA and breaks it up at precisely the position that exists within this matching sequence that matches the RNA molecule now Martin and Kristoff in doing their experiments also recognize something else that turned out to be essential for this enzyme this caste 9 protein to function like this and that was that in addition to the crisper RNA which provides the zip code if you will for DNA recognition this system requires a second molecule of RNA called tracer which is the molecule shown right here that provides a handle for the caste 9 protein to bind to bind to and so these two separate RNA molecules are essential for a caste 9 to work and once we understood that Martin Yannick who was a very sort of mechanically minded person in the lab who was always thinking about you know how do these molecules actually work and cani cani cani rejigger them compared to what nature has done you realized that we could actually link together these two separate RNAs into a single guide RNA that would include the targeting information on one end and the handle for binding to caste 9 on the other and once we did that made that change and did experiments showing that these single guide RNAs were effective at targeting cast 9 - DNA sequences we also realized that it was now trivial to change the sequence of letters on the end of the RNA at this position to allow cast 9 to interact with any desired DNA molecule and make a precise double-stranded break so imagine having a basically a pair of scissors it's like having a scalpel or something for the genome where you can go in you can program this thing to find a particular place in all of the DNA in a Cell find one place and make a precise cut so that was kind of kind of cool and you know it was kind of really interesting that bacteria had evolved this fascinating little machine to cut viral DNA but there was actually a bigger implication of this that occurred to us as we were doing these experiments and here's the implication so in parallel with this little very niche area of CRISPR biology that was going on at the time there was a large body of work that had been focused on studying how our cells human cells and plant cells basically any kind of animal or plant system handles damaged DNA and what that line of research had revealed was that in our cells unlike in bacteria where when DNA is broken it's rapidly degraded in our cells when DNA gets broken it's actually repaired and it's repaired quite efficiently and so this is a cartoon that shows that when a double-stranded break happens in the DNA of an animal or plant cell the cell can quickly identify the broken ends of the DNA and repair them in pathways that involve either introducing a small change to the DNA during the repair process or by integrating a whole new piece of DNA at the site of the repair at the site of the break and so in this way genomes could actually be edited by introducing a double-stranded break at a position where one might want to introduce a change to this code and so the challenge for scientists and people that have been working on this for quite a while was how do you introduce a double-stranded break at a place where you might want to change the DNA sequence and there were various technologies that had come along for doing this that were powerful but they were difficult to deploy and so most labs even my own had looked at these technologies and said wow that's really cool but we don't have the money or the expertise to actually use those technologies because you know we're not we're not genome engineers and the wonderful thing about this CRISPR system in bacteria is that lo and behold Nature had already come up with a great way to break DNA in a precise fashion in a controllable programmable way we just had to find it right and that's the great serendipity of this whole field is that the discovery of this system was a curiosity driven project that led to a powerful technology so I'm going to show you a video this is a this is a kind of an artist's rendition of how we imagine these CRISPR molecules work when they get in to an animal or a plant cell so here we're zooming into a cell that has the DNA encapsulated in the nucleus and the DNA is highly compacted so this bacterial protein caste 9 with its guiding RNA has to search through all of the DNA in the nucleus to find a single place that has a 20 letter match to the RNA molecule that is the programming guide for caste 9 and when that match occurs it opens up the DNA makes the cut and then here's where the magic happens is where the editing actually happens the cell has a way of detecting that break and sending in repair enzymes to fix it in this example by integrating a new piece of genetic information during the repair process and so this has become a tool that is incredibly powerful for allowing scientists to inch a double-stranded break or more than one to make changes to genomes in essentially any kind of cell or organism that allows control over the editing process and I wanted to share with you just you know again I'm a you know sorry I've always sort of asked the how questions in my own lab and I wanted to share with you a little bit of research that we've been doing to understand how this actually works it's kind of an amazing thing when you see a video like that it might almost look like science fiction can that really happen and yet it does and so we'd love to understand that process and so we've been busily working away in our lab at Berkeley to try to figure out this mechanism of recognition how does that 20 letter sequence in the RNA actually trigger opening up of the DNA duplex and the ability of cast 9 to make this precise cut and and so this is a this is actually a 3d printed model of the cast 9 protein so it's been possible now to crystallize this complex and have a look at the molecular structure and we can make a 3d printed model that's based on that that molecular structure and this model is actually about yea big and you know it sits on my desk at home at Berkeley and when I'm there you know virtually you use it almost every day because I'm you know I'm sitting with my students and we're looking at this thing and trying to figure out how it works and thinking about the way that it is able to unwind DNA and I want to point out just a couple of things here so the protein is the white molecule it's got the orange guide RNA sitting in the center and when it grabs on to DNA it literally opens up the DNA helix annal and inserts this piece of RNA so it forms an RNA DNA helix inside the protein that's the mechanism of recognition and then because it's got the two strands of DNA separated that allows the cleavers to come in and make a precise cut and so we've been you know really wondering how this works and one of the things that's interesting about cast 9 is the it's able to open up the DNA but it does that without any external energy source right so just like a must has to tease apart these strands but it doesn't have to it doesn't have any way of providing it doesn't you know if you're a biochemist you know about ATP and gtp and using the energy of breaking the bonds and those molecules to do something else to do work well this calf slime protein doesn't do that it has to get the energy for this DNA melting from somewhere else and one of the clues to how it works is actually comes from comparing its structural States as it assembles with RNA and DNA and from doing that we know that this is a protein that undergoes a very profound structural rearrangement so this is showing you the protein changing shape as it grabs on to its RNA molecule there in orange that provides the targeting information and forms the the complex that is able to surveil the cell to look for a matching piece of DNA when it binds DNA there's an additional structural rearrangement that accommodates that rna-dna hybrid in the center and then finally this is the chemical cleaver it swings into position and then actually makes the cut and there's not showing it to you here but there's a sensor in the molecule that detects base pairing between the RNA and the DNA and that's part of its mechanism of accuracy so it makes sure that it's really associated with the right segment of DNA before the cleaver swings into position and makes the cut so it's a beautiful example of how this has evolved over many eons and bacteria to be a highly effective way of recognizing just those pieces of DNA that the bacterium wants to cut up namely viruses and and then I just wanted to show you also this picture so this is a this is a and this is also an animation that shows you the the molecular structure of casts 9 bound to a double piece of DNA so the DNA is in blue and magenta in this in this molecule in the structure and you can see the rna-dna hybrid here and the DNA opening up inside the protein it's a system that has the ability to recognize essentially any DNA sequence so the sequence of the RNA can be easily changed on this end to allow interaction with different segments of DNA and then here's this cleaver swinging into position so that it can actually make the cut once this protein has assembled with the right piece of DNA and so I wanted to just talk now a little bit about two particular aspects of this field and where they're going because I think they illustrate both where we're sort of what's happening on the technology development side of things and then how we're actually going to be able to use CRISPR cast genome editing in ways that I think are going to end up affecting all of our our lives going forward and I'll start with the technology developments and that that's really sort of this top question which is are there new kinds of CRISPR systems and you know the short answer is yes and and what's really interesting as I mentioned before is that these CRISPR systems in bacteria are found very widely across the microbial Kingdom and they're really diverse and so as people like Jill Banfield have continued to investigate all of the bugs that are in our environments and look at the kinds of CRISPR enzymes and pathways that they have she's been able to uncover a number of new examples of proteins that are part of these pathways and these are just three of the recent ones that we've identified - proteins called cast X and cast Y and then some new examples of the cast 9 enzyme and what's interesting about these proteins and cast X in particular is that it's a it's encoded by a gene that's quite a bit smaller than the gene that encodes cast 9 and that means that the resulting protein is quite a bit small and this is just showing a picture of the actual genomic locust that includes this cast X protein so here's the CRISPR array over here that tracer molecule is part of it as well we have three genes that are important for the front end of this pathway namely for recognizing viral DNA and Inter inserting those little sequences into the CRISPR array so that's the adaptive part of the immune system and then there was this other protein and we didn't know what it was but we sort of hypothesize that this might be the the caste 9 equivalent maybe the enzyme that is on the other end of the pathway responsible for actually targeting a viral or any kind of DNA molecule and so in in some very recent work and this isn't even published yet so I'm showing you some some very very new hot off the lab bench kind of results this is a picture of what this casts X protein looks like with its guide RNA and one of the things that was very interesting to us is that this protein sits right here it's sitting kind of at the top of this RNA lollipop and the RNA is a much larger component of this combined protein RNA complex than what we saw forecasts 9 don't know why that is but we do know that it's essential that the RNA be that big it's required to for this protein to be functional and furthermore it turns out that this protein works just like caffeine does it's very effective as an RNA guided DNA target and I just wanted to show you one piece of evidence for this so this is an experiment that we can do in bacterial cells so we have bacteria that are growing on a plate and these bacteria are expressing two different kinds of fluorescent proteins there for expressing a green fluorescent protein and a red fluorescent protein and when those proteins are made together the cells look kind of yellow like this and then what we do is we use the cast X protein with a guide RNA that is interacting with the gene encoding the green fluorescent protein with the idea of turning that gene off and what you can see is that when we do that now all the cells look red and that's because the cells are still alive and they're making the red fluorescent protein but they're no longer able to make the green fluorescent protein because we've used Kasich's to turn it off and it's really efficient because basically every single cell that you see growing here is now no longer able to make the green fluorescent protein so that's one of the types of experiments that can be done to test the actual ability of these kinds of enzymes to interact with DNA and have a specific kind of effect so how do we take proteins like this like whether it's castes 9 or caste X or any of these other enzymes that are you know coming out of the fundamental discoveries of these pathways and how do we turn them into effective applications whether it's in biomedicine or agriculture we need to be able to harness their capabilities for genome editing and I wanted to speak a little bit about how that's done and what the current challenges are and then tell you about some really exciting examples of what's happening right now with this kind of technology so when I think about especially the the challenges to using genome editing therapeutically I think you know there's sort of really three big ones in my mind and there's a lot of smaller ones too but these are these are kind of the big ones so the big ones are delivery so how we introduce genome editing molecules into tissues or systems where the editing is necessary how do we control the way that DNA repair happens because you now know that what CRISPR is is it's the scissors but it's not the actual repair enzyme right that's the job of the cell and so what scientists are trying to do right now is not only understand how that repair happens but also control it so we can ensure that we get the desired editing outcome when we use a system like CRISPR cast line and then thirdly and very importantly is is the the whole aspect of ethical and societal considerations especially for certain applications of CRISPR casts 9 and we'll get they're in a in a few minutes so right now there's this is a slide that just illustrates some of the many many different kinds of cells and organisms that have been edited using CRISPR Castine and if you look at this for a couple of minutes you'll see that you know it's got insects we've got plants we've got fungi we've got all kinds of human cells we've got various kinds of animals so what's been amazing over the last six years since emmanuel sharpen TA and i first published our research is that scientists around the world very quickly started adopting this system for their favorite experiment and their favorite organism and so far we found that this is an active system in in effectively every kind of cell and organism where it's been tested so it's very makes it very powerful and it's kind of a democratizing tool it makes it easy for scientists everywhere to apply this in for their research certainly and and also for we think in the future for various kinds of applications so what are those applications and I really I put them into five buckets here research of course but also healthcare therapeutics agriculture and diagnostics and these are all areas that right now are being profoundly impacted by CRISPR cast genome editing because of the ability of scientists now to control the DNA in cells and thereby really control the code of life and control the way that cells are accessing the information that they need to grow and develop so let's take a look at a few of the things that are that are happening that are that are really interesting and I think you know on the research side of things you know one of the things that happened pretty quickly in this field is that scientists realized that instead of having to restrict their studies of genetics in in organisms to just those few that had been carefully you know cultivated in labs over many years like fruit flies and certain kinds of little worms and and certain kinds of yeast now the ability to study genetics opened up to any kind of organism and this was actually a slide that I got from a graduate student working at a laboratory at New York University and Claude to splines lab where he said that suddenly his work on butterflies had totally changed because instead of having to collect animals in the wild and just look and observe the wing patterns and try to discern things about their genetics by observation they were actually able to use CRISPR cast nine to make changes to the DNA of these butterflies and figure out what the genetics were for wing pattern formation and and and color patterns and this this you know capability is now possible in many kinds of organisms where people can suddenly do genetics in a way that wasn't possible just a few years ago so so one of the things that that does then is to make possible again the kinds of experiments that until recently would have been absolutely in the realm of science fiction here's here's an example of that so a guy named sponte Paabo has been become quite well known for his work sequencing the genome of Neanderthals a huge accomplishment and is starting to tell us a lot about the molecular evolution of Homo sapiens and sort of who we are at the level of our genes and so one of the questions that's emerging from that line of experiment is the fact that there seem to be differences in genes that are that correspond to brain development in Neanderthals versus modern humans and yet until recently it wasn't possible to ask questions experimentally about that and so what's Fonte Pavel's lab is now doing is they're using pieces of tissue called organoids that can be grown from human cells that develop into these sort of brain like or at least have some properties of the brain and they can engineer those cells to have genes that come from the Neanderthal genome that are thought to affect brain development and they can use that as a way to study the effect of these Neanderthal genes on neuronal development in an otherwise context of a human genome so fascinating don't know the outcome of that yet but that's the kind of thing that's now possible using CRISPR cast gene editing and then I went on the on the topic of healthcare I wanted to point out that in addition to ways that we may have in the future to correct genetic diseases in humans I think other ways that may impact human health come from the ability to manipulate the genomes of animals and this is an example using CRISPR cast to modify the pig genome to do two things one is to remove endogenous viruses that are part of these Pig genomes and the other is to create animals that have more human-like organs that could be better suited to organ donation something that both companies and academic labs are actively pursuing in our own lab so one of the things that I would have never imagined doing and my previous life was being able to you know think about an actual strategy for dealing with neurodegenerative disease and so we've been working on an idea where we take CRISPR Cass 9 so that's this little cartoon here and modify the surface of the protein to give it the ability to penetrate neuronal cells and then what we do is to take these programmed calf's 9 enzymes and inject them across the blood-brain barrier and this is we're doing this in a right now in a mouse model of a neurodegenerative disease so that we can observe DNA editing in just particular areas of the brain and this is an example where we use a mouse that's been engineered so that when the cells are edited they turn red makes it very easy to see the extent of editing that occurs and you can see here that when we do injections on both sides of the brain we get a reasonable volume of tissue that gets edited on both sides using CRISPR cast line and and our current work focuses on using this kind of a delivery strategy in an animal model of Huntington's disease which is a well known genetic neurodegenerative disease with the idea that eventually if we can get therapeutically meaningful levels of editing in this animal model we'd like to move towards clinical trials and humans partnering with clinicians that work with these patients and and I I don't want to neglect to point out that I think in addition to all of these applications that are important in in thinking about human healthcare I think that the impact and agriculture will be equally large or potentially much larger because of the ability now to modify plant genomes in a precise fashion and just one quick example of this is work going on by Zack Lippmann who is a scientist at Cold Spring Harbor Laboratory who has been doing beautiful work modifying Tomatoes using CRISPR Castine to have different numbers of flowers and hence different numbers of fruits and he had this incredible presentation that I saw in New York a few weeks ago where he's now been able to do this where he had a slide showing a home you know something like 15 different variants of tomatoes that had exactly the same genes except for one that was responsible for the the number of flowers on the plant so that the plants went from producing no tomatoes to you know dozens of tomatoes and it was really really powerful demonstration of how gene editing can be used now to control crop yields and and we think in the near future many other traits in plants that will be very valuable in different environments around the world and the less I leave off I didn't want to leave off this last point which is the development very recently of CRISPR cast enzymes that are likely to be useful for diagnostics and this came about again from fundamental research going on in my lab and a few others that were studying activities of these CRISPR cows proteins that showed that some of them can be harnessed as a detection system for DNA that instead of cutting up making a double-stranded breaks to DNA is actually able to recognize as a target sequence and by engineering the system you can use a fluorescently labelled substrate molecule in this case a single-stranded DNA that is cleaved very rapidly when this protein finds its target and that releases a fluorescent signal that says I found my target and it makes it very easy to detect DNA or even RNA molecules in samples and we think this is going to be useful for all sorts of applications not only for detecting viruses and bacteria but potentially even for screening for DNA molecules associated with cancer so I just want to close by by circling back to this question of ethics and you know you can maybe appreciate that you know I'm a I'm a biochemist and you know I sort of I've always been interested in the fundamental questions in biology I never really imagined that my work would have much of a you know I mean I hoped it would have some kind of a little impact in the world but you know I never imagined that it would be something that people would someday be you know really talking about in the media and people would be speculating about you know governmental use of something like this and so when this technology began to really take off in in 2013 and 2014 I realized that you know we needed to really think hard about how it's going to be deployed in the future and in particular there's this question of using it in what's called the germline so we can imagine gene editing and sort of two kinds of cells if we do gene editing and cells that are fully developed and differentiated then they affect that one organism or person but they don't affect their progeny they don't affect their children but what if we did gene editing in what are called germ cells so that would be eggs or sperm or embryos well then those DNA changes become part of the entire organism and they can be passed on to future generations and so we now have a technology that allows us in principle to control our own evolution or the evolution of anything else right it's a very powerful thing and so I started thinking about this and you know I started realizing that you know people were already sort of doing germline editing and various kinds of animals and implants why not humans it seemed like there was no technical reason why one couldn't do this and this is actually showing you a pipette tip that's holding on to a fertilized Mouse egg with a needle that's injecting CRISPR cast nine right here and when you do this in a mouse embryo you can you know pretty easily make changes in the germline that become part of that entire animal and in fact we now know that you know from research that published just in the last year we know that this is now possible to do in viable human embryos as well and it looks like it works and and so people are you know asking and have been asking for a few years now should we do this and you know how do we how do we regulate it how do we think about the ethics and the safety and efficacy of this under what circumstances would we want to do this and of course there's been lots of media speculation right this was a cover of The Economist a few years ago under the banner editing humanity and people thinking about what about enhancements and the short answer to that is that you know for the most part we don't know enough about the genome to be able to make genetic changes that would lead to these kinds of enhancements but it's coming you know it's I think many of us in in science you know we can see that this is a this is a direction that that is being pursued in in many parts of the world in labs that are you know around the world and so I've been very actively involved in sort of encouraging scientists in particular to be involved in this discussion and and recently there was a report this was issued last year from the National Academies on human genome editing and in particular human germline editing making recommendations at the time that suggested that scientists should refrain from using human germline editing clinically in other words to create a an actual baby or person that would have those kinds of edits but you know the field is moving ahead quickly and we're actually having a meeting in two weeks in Hong Kong to revisit this issue with a particular focus on what's happening in Asia because there's lots of developments there and I think that you know that this this is just a you know it's an it's a very active area of discussion right now about how we can to collectively understand and regulate this kind of use of genome editing so we'll open that up maybe to the questions afterwards but I just want to conclude by pointing out that what I call RNA guided genome editing is powerful technology from manipulating genomes and there's I didn't go into it all tonight but there's many sort of ways of using it to control the flow of information from DNA that are really impacting everything sort of essentially all fields of biology where that kind of DNA manipulation is useful applications of editing are going to depend on both delivery in the cells and also control and I mean control both in a chemical sense but also in a societal sense and finally we know that continuing investigations of fundamental biology and in particular biology of bacteria for example studying new CRISPR systems will continue to drive new technology development as these ideas lead to understandings that fundamental functions of these proteins that can be harnessed for various purposes I would be remiss in not showing you a picture of my lab so these are my lab members at Berkeley and this includes a you can look here a very diverse group of people these are students ranging from undergraduate students at Berkeley to all the way to people that have had several years of postdoctoral training that are all working together on these problems so it's an incredible honor to work with them and you know for me science has always been very collaborative so Immanuel sharp and ta was person who we started off working on cast 9 with so huge kudos to her and her laboratory we have a number of colleagues at Berkeley that we've worked on various aspects of this research with and we've also started to increasingly work with clinical teams and I'm just mentioning one of them here Joel poleski so he's a clinician who works on human papilloma virus and the kinds of cancers that it causes and we've been working with his team to develop CRISPR as a diagnostic for sample patient samples to be able to tell people very quickly if they have this type of infection and if they do how they can quickly take steps to mitigate and prevent cancer and finally as you probably know scientists like me have to get funding for our work and we get it by writing grants and trying to convince our peers to give us money so I want to thank all of these groups and in particular to point out that in my case the research on CRISPR would have never happened if it wasn't for these two organizations the Howard Hughes Medical Institute and the National Science Foundation so these two groups were both funding my research and gave us a money that allowed us to pursue this crazy bacterial immune system called CRISPR back before anybody knew where it was headed so I'll be forever grateful to them and I'm gonna stop there thank you for your attention and I look forward to the discussion to follow [Applause] you want my mic so we're just gonna bring out two chairs here dr. stuart feinstein from UCSB molecular cellular and developmental biology department we'll be asking the questions we've collected some of those from audiences via from the audience via email from ticket buyers and then after that I want to remind everyone that a doctor down there will be signing copies of her book up here on the stage chaucer's is in the lobby with copies of the book and it's a very interesting and beautiful book so she's very kindly agreed to do that so I think we're ready to start so dr. Fontan you want to join us up on stage [Applause] okay Thank You Jennifer for a wonderful talk we have questions here this is very different i lecture in this hall all the time but this is very different to be sitting up here with somebody so we have some questions and since this is sort of a broad audience of students and some faculty and lots of community members I will try to make the questions a little something for everybody so let's start with the students since that's why we're all here one of the questions from a student was what people or events were most influential in your career development I think I've certainly had several teachers who were incredibly important to me all the way from as I talked about with students today from my third grade teacher who I recently saw Hawaii it was a great all the way up to my you know graduate and postdoc mentors and I think the the common theme for those folks is that they were all people who kind of saw my insecurities I guess at different stages of my development and were able to work with me to build up my self-confidence and help me to achieve you know what I what I was really excited about doing so I'm forever grateful to them and I also want to give a special shout out to two other people one is my dad so my father was not a scientist but you know was somebody who was very interested in science and I think that he saw in me very early on this little spark of you know maybe scientific inclination and he encouraged it and you know that's that's really great sadly he didn't he didn't live to you know see me do all this but you know but he's there in spirit all the time with me and the other the other person I really want to give a shout out to is my my spouse so Jamie Kate professor Berkley who is someone who again is you know always been interested in the how questions in science and we do a lot of debating at our house about you know what happened in your lab today and what does it mean and and you know that's that kind of discussion has always been incredibly motivating to me and believe me there's been plenty of times when I'm tearing my hair out over some experiment or something and he's sort of always always there and he knows you know under stands this sort of crazy passion that we have so okay this is another student e-type question what advice do you have for students just beginning their careers in biology well I think my advice starts with pursuing your passion and and I think what goes hand in hand with that is figuring out what really gets you excited you know what really gets you out of bed in the morning because I think you know what I see in my students I I saw this and myself too when I was you know in my earlier stages was you know trying to figure out what kind of science do I want to do and what kind of answer do I feel satisfied with and I realized for myself that I'm more on the chemistry side of things I really like thinking about things at the level of molecules and you know the atoms how are they organized and how they work and how do they do chemistry that's always gotten me excited but I you know when I have students that come to my lab I realize that you know people are you know people have different different kinds of problems that they get excited about and different kinds of answers they want to pursue and I think once you figure that out if you get in that groove you can do anything you know and that's what I see over and over people in my lab you get them on to help them find the right project that really drives with what they're excited about doing and they just go farther than you could ever predict this one may embarrass you a little bit but it's right from a student while studying to become a scientist did you believe you were destined to accomplish something great no no absolutely it's a great question because you know I think I often think back these days to you know when I was growing up in Hawaii and I was actually recently back you know visiting my my home down doing kind of an event like this and and I couldn't have I couldn't have imagined it I remember this one time when I was in high school and you know I was I was at I was at a party and we were sitting in somebody's backyard at night you know and having a couple of beers and and you know we were talking about what do you want to do and when you grow up you know and I was talking to a good friend of mine and you know I said I said what do you want to do when you grow up and he said well I want to be a I want to I want to have a brew pub you know and I thought that's kind of cool and he said what do you want to do and I said I want to be a biochemist he's like you know that sounds really weird and nerdy and but here we are you know I won't say how many years later but Oh number of years later and we're both doing that so he became a great a very famous Brewer he's won tons of international prizes and highly successful and you know I'm a biochemist and and so you know we got together recently and we're like wow do you remember that time we were like 15 and said so my point is you just you know you just have to I think you have to pursue what you're passionate at doing and and again it's a great example of you know each of us were passionate about something and we just didn't let anybody dissuade us from doing it okay let's move a little bit more over to the science and this is redundant to a question I asked you this afternoon so I apologize but it's a different group and you alluded to this in your talk a couple of times but I thought it might be a good thing for everybody to hear your thoughts about the importance of basic science in the development of genetic engineering if you go back even restriction enzymes in a way that was a study of a similar question to what you were asking how to virus out of bacteria evade a viral infection or plasmids so basic science in general and then also specifically with respect to CRISPR well you know if you think about the and you just you just brought up a great example of restriction enzymes but you know if you think about some of the key technologies that have come along in the sort of you know what we call the era of molecular biology really since the 1970s or so a lot of those those technologies have actually come from bacteria right restriction enzymes is one example but the polymerase chain reaction which is a way of amplifying DNA that's also come from enzymes that are found in bacteria and way of lighting up proteins called the green using the green fluorescent protein came from studying organisms that have the ability to you know use a fluorescent protein in response to signals in the environment so you know these are great examples where scientists were working on very fundamental questions in biology that might have seemed kind of kind of wonky at the time but they led to technologies that had a profound impact and I think that you know this really just underscores the importance of curiosity driven science and the value of funding scientists who are interested in all sorts of things that don't necessarily have any clear application to a disease but lead to discoveries that none of us could predict that in fact have very very profound impacts on human health it sort of broadly defined so several people wrote questions that in one form or other asked about the potential for using non genome non gene non germline editing for example in blood disorders so I used the expression earlier today if you had a crystal ball a few at a crystal ball what sort of duration do you think it'll be before that'll be in clinical testing I'm aware of a couple of groups that are in discussions right now with the Food and Drug Administration to begin clinical trials for sickle cell anemia which is a well-known blood disorder well-known genetic basis and so I think you know I hate those trials beginning in the next you know somewhere between 12 to 18 months and so I you know and it's hard to always predict of course how these will turn out but I think you know the opportunities for treating blood disorders in general like other diseases known as thalassemias that also have clear genetic causes that are are well-defined I think or other other good targets for initial uses of gene editing and part of the reason is that it's easier to do that editing because it can be done in blood stem cells that are taken from a patient edited and then put back into the body so it kind of removes this whole issue of delivery but I think down the line we're gonna see you know there's lots of interest in using gene editing in the eye for genetic causes of blindness and again it's a the eye is a tissue that at least in principle is maybe easier to deliver to than having to deliver something systemically and also liver disorders for the same reason it's a tissue that tends to be easier to deliver to and then farther be out from that but places you know as you saw briefly in my talk you know we really would love to see this utilized eventually for treating neurodegenerative disease so this is again a repeat from this afternoon but how do you grapple with the duality of knowing all the great potential and applications of CRISPR well at the same time you clearly appreciate that's a technology that could be abused look I mean I think CRISPR is not unique as a technology in the sense that you know like like many things it can be used to do very very things that I think we would all agree are very wonderful and powerful in a positive way but it also has the potential to be used to cause great problems and and and things with real ethical challenges so I deal with that by focusing on what I can do to both advance the science in ways that I think will be important and and positive but also to be very actively engaging in a discussion about the use of the technology not only with scientists but with audiences like this and and also with people in our governments and in our regulatory agencies who need to understand the science and the technology so that they can do their jobs of thinking about how we regulate the uses of the technology about a half an hour ago is rereading the prologue well about an hour and a half ago half an hour guys listening to you but I was struck by something you wrote here and this was in reference to the Napa meeting in 2015 so dr. Doudna organized a meeting of many different stakeholders to begin to discuss the ethical issues of this back in 2015 and you were speaking about germline gene editing and you said my own views on the subject are still evolving but I was struck by a comment made during the January 9 2015 meeting I organized to discuss human germline editing in embryos 17 people including the co-author of this book my former PhD students damned Sternberg we're sitting around a conference table in California's Napa Valley having a heated debate about if and when germline editing could be allowed suddenly someone leaned into the group and said very quietly someday we may consider it unethical not to use germline editing to alleviate human suffering the remark turned our conversation on its head and it still comes to mind whenever I meet with parents or would-be parents who are facing a devastating effects of genetic disorders so my question is how did that conversation end and has sentiment on it evolved since that time well so so that description is is is really apt because that's exactly what happened and when that person made their comment it kind of shut the whole thing didn't you know everybody just stopped and realized whoa you know that's a different way to think about this and and I think that the thinking in the field and certainly my own personal abuse of human germline debating have really evolved since then because I think initially my thinking was it almost felt it felt gimmicky it felt like you know something that you know science some scientists might try to rush to do for publicity purposes but over the last few years I've had an opportunity to meet with many many people who have very very generously their personal stories of you know grappling with genetic disease or sporadic genetic mutations that arise in their kids and and I've seen the the just very you know very in a very raw way the the human need and so I think that you know there and and the other thing that's happened of course is that you know the technology has advanced incredibly in you know in and and continues to do so so you know just in the last few months there have been studies done with with human embryos that start to show how you could in principle use this kind of technology if you wanted to correct a disease-causing mutation in that sort of setting and I think it's still very unclear you know exactly when and how this this this will be utilized for what purposes it will be most useful I think that's still very much a question also there's the whole issue of understanding the basics of human very early human development and I I didn't you know I wasn't this isn't my field so I didn't I wasn't aware of this until I looked into it and heard from my colleagues that in fact with this kind of technology you can now study the genetics of early human development in a way that you know is really really enabling and opening up new you know really new avenues to understand human genetics and development so these are all things that I think are both very very important to continue to develop and and also to really stay on top of the ethics of it because I think it has the potential to get out of hand and I'd like to I'd like to you know hope that we can avoid that if possible there's another paragraph here that caught my eye you've seen all this before you wrote it and you alluded to this in your talk the importance of distinguishing between germline and non germline applications and yet when I talk to people I find that that's a source of considerable confusion and the knee-jerk reaction is just to assume it's all the dangerous or the controversial kind and you're out in here after speaking about germline modification there's just full alarm over there was justifiable arm over developments like these yet we can't overlook the fantastic medical opportunities that gene-editing gives us to assist people who suffer from debilitating genetic diseases imagine if someone who were and she carried the mutated copy of the huntington gene which virtually guarantees early onset dementia had access to her Christopher based drug that could eliminate the DNA mutations before any symptoms appeared never before have curative treatments seemed so close and it's essential that as we debate germline editing we take care not to turn public opinion against CRISPR or obstruct clinical uses of gene editing that are not heritable so can you just comment on that further well I think the we talked about this a little bit earlier today with the students but I think for me you know one of my one of my one of the things I feel most strongly about is exactly sort of that last sentence that you just read which is namely trying to ensure that that there's a an honest transparent and fact-based communication about CRISPR technology to people that are not scientifically trained so that they can understand both the the power of this technology and at least enough about how it works so that they can start to make decisions about things that will come to affect them in the future whether it's you know do I want to use this during my in vitro fertilization you know procedures or do I want to purchase food that has been edited using CRISPR and lots of other you know impacts in I would say you know environmental settings like using CRISPR to control the spread of mosquito-borne diseases and the potential risks that come with along with that but also the potentially very profoundly powerful and and and good benefit to human health globally so these are the kinds of things that decisions that are going to come along and I think we we need an educated public so that they can work on those decisions together I have a wonky science question for you great so imagine a bacterias being did by a virus it's never seen before how does it have a that infection and how does the DNA end up in the CRISPR cluster if it has a CRISPR array and it gets infected by a new virus then you know you have to imagine what's actually happening right in this setting so you've got you know millions of bacterial cells they're all kind of you know they all have the same essentially the same genome and if they have a CRISPR system all of those cells are given an opportunity to sample the viral DNA that's getting injected during the infection and grab a little piece of the viral sequence and stuff it into that you know store it in the CRISPR array and what we think happens is that first of all is that most cells don't do that so the integration system the adaptation step is actually not that efficient because it doesn't have to be right because all we need is we need one or a few of those millions of cells to acquire a useful piece of DNA that's protective and then they give rise to a whole new colony of bacteria so it's not a very efficient system but it's incredibly effective when it does happen because when they do grab a useful piece of DNA and store it then the system works like I showed you and we know that these these these surveillance proteins like cassadine are incredibly good at finding DNA and cutting it up that's what makes them good as tools but it also makes them very effective as an immune system I have one more question for you and again from this afternoon but it's a different audience and that has to deal with oversight of this technology and so we have various oversight mechanisms to deal with the proper and humane use of animals in research and teaching we have oversight mechanisms for the use of stem cells what's your vision of how oversight by government or other regulatory bodies will impact on this technology over say the next decade well I sort of have two thoughts about that one is that we're fortunate that back in the 1970s when restriction and were first discovered and people were recognizing that now we had a tool that allowed pieces of DNA from one organism to be copied and replicated in a different organism and so scientists were taking pieces of DNA from you know all sorts of contexts biologically and replicating them in bacteria and there was concern initially that you know they were using the kind of bacteria that grow in the human gut so the concern was hmm you know would that create bacteria that are making proteins or other molecules that are toxic or dangerous to humans and that would then somehow you know invade our bodies and you know cause problems and so there was lots of discussion about this and that will actually led to a whole infrastructure at the national level that regulates molecular biology and kind of in particular what we call you know molecular cloning and fortunately a lot of that infrastructure turns out to apply very nicely to the ways that people are deploying CRISPR caffeine especially for research purposes and and then the the what happened with in vitro fertilization and all of the technology around you know human fertility and and and sort of doing you know being able to fertilize eggs in in in the laboratory so all of the technology and regulation around that applies in the realm of you know using CRISPR cast nine in those systems so I think we're we're fortunate that we have already a nice infrastructure in place in the United States and a lot of other countries follow that as well for governing this but that being said you know there's there's you know as I mentioned this technology continues to develop very quickly and so I think there is an ongoing need to be revisiting those regulatory guidelines to ask are they sufficient do we need to have other or different regulations in place how do we encourage I don't think I don't say enforce because I think that's probably impossible but how do we certainly encourage our our international neighbors and partners to respect those same guidelines you know how do we kind of ensure that there's responsible use of these technologies going forward and that's just going to continue to be a very active area of discussion okay on that note on behalf of everybody here at Santa Barbara I'd love to thank you for coming it's been an honor to have you now for those of you who are wise enough to buy a copy of Jennifer's book she'll be gracious enough to sign them and talk to everybody thank you everybody for coming

Channel: UCSBArtsLectures

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Keywords: university of california, Santa Barbara, lectures

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Length: 84min 22sec (5062 seconds)

Published: Fri Nov 09 2018