Jennifer Doudna, “CRISPR Biology and Biotechnology: The Future of Genome Editing”

good evening ladies and gentlemen thank you for being so patient and welcome to all is a very full house as you can see we're delighted to see so many people here this evening my name is Robert Anderson I'm president of the science history Institute in case this is your first visit and you're unfamiliar with the science history Institute I'll just say a few words about what it is in short we we uncreate and we share knowledge we have very large collections here and people come and use them and write histories and indeed we have a big educational program as well we hold and build our collections to engage the public and scholarly audience about the role of Science and Technology in society and we desire to increase public understanding of how science and technology shaped the world from the mundane such as one might say the proliferation of consumer goods which we're all interested in of course to the life-altering life altering mechanisms it's important we believe that we understand science today's science it's an inseparable part of our culture at the same time science is increasingly becoming difficult to understand and to explain we give our audiences a chance to shut to deepen their perceptions and perspectives and engage in dialogue and with us and with each other about how science and technology have changed and will continue to do so and it's my pleasure tonight to welcome you all those of you who are here in person and indeed those who are joining us via our webcast for this really rather exciting occasion the 2018 earlier public affairs lecture which is tonight going to be delivered by Jennifer Doudna the aulia public affairs lecture was established in 1990 to emphasize to the general public the positive role that chemical and molecular sciences play in our lives oleate lecturers are distinguished in their fields nationally recognized and have a particular ability to communicate to a non-scientific nevertheless highly curious audience college presidents CEOs researchers of international reputation and leaders in science and government have come into this building to share their knowledge with with those who are present in Philadelphia and indeed the whole world we consider ourselves now to be an international organization fact we have we have a an office in Paris the program is due to the vision of Glenn and Barbara Elliot whom the lecture as well as this lecture or amateur I'm sitting tonight is named and today four organizations continue to carry on this vision as co-sponsors of the earlier lecture the four organizations are the department of chemistry at the university of pennsylvania department of chemistry and biochemistry at the University of the sciences the Philadelphia section and Delaware section of the American Chemical Society and indeed ourselves the science history Institute together we are pleased to bring to you the 20th orient public affairs lecture title of which is CRISPR biology and biotechnology the future of genome editing and it's going to be delivered by Jennifer Doudna so to tell you a little more about Jennifer and to invite I want to invite her Christopher Mora new president CEO of Life Sciences Pennsylvania Christopher would I come and explain please [Applause] Thank You Robert it's a it's an honor and a privilege to be here the the organization that I I lead life sciences Pennsylvania is the statewide trade association for the entire life sciences community of the Commonwealth of Pennsylvania so academic research institutions pharmaceutical companies medical devices diagnostics digital health companies the entire scientific and business ecosystem that is so strong here in Pennsylvania we represent about 2800 Life Sciences establishments and about a hundred and twenty thousand Pennsylvanians directly doing life sciences work and it's a privilege not only because of the the men and women that that we get to work with and represent but also because we sit in a unique vantage point as a trade association we get to see these emerging technologies we get to see breakthrough therapies and treatments breakthrough medical devices and technologies that are that are truly remaking the world and transforming human healthcare and it is a rare technology that really remakes the world but CRISPR casts nine gene therapy and gene editing technology is one of them it's only been around a few years but it's already a it's causing a revolution in how we think about treating and curing disease researchers have reversed mutations that cause blindness stop cancer cells from multiplying and made cells impervious to the virus that causes AIDS strains of wheat are now invulnerable to killer fungi like powdery mildew and such success suggests an engineered opportunity for staple crops that could feed ballooning populations around the world bio engineers have also used CRISPR to alter the DNA of yeast so that it consumes plant matter and excretes ethanol potentially offering another alternative fuel it's quick its precise its inexpensive and it's so simple that high school students are using it now we have high school students in the audience that was an applause line for the high school students okay so we truly are on the cutting edge of a revolution and it's a revolution brought to us by dr. Doudna by dr. Jennifer Doudna who's our our speaker here this evening so dr. Doudna is a professor in the department of chemistry and chemical engineering and the department of molecular and cell biology at the University of California Berkeley and has been an investigator with the Howard Hughes Medical Institute since 1997 since 2018 she has held the position of senior investigator at the Gladstone institutes as well as that that a professor at the University of California in San Francisco dr. Doudna first made her named uncovering the basic structure and function of the first ribozyme a type of catalytic RNA that helps catalyze chemical reactions this work helped lay the foundation for her later later work helping to pioneer CRISPR cast 9 in 2012 dr. Donna and Emmanuelle Charpentier were the first to propose that CRISPR cast 9 could be used for programmable editing of genomes which is now considered one of the most significant discoveries in the history of biology in addition to her scientific contributions dr. Doudna also takes the ethical implications of her work very seriously and has organized several conferences to discuss the ways to ensure that CRISPR casts 9 is used for good we're lucky to have that sort of mindfulness and accountability at the head of this charge and we're very fortunate to have dr. dabeh here with us tonight so please welcome dr. Jennifer down [Applause] good evening everyone it's a real pleasure to be here thank you for that very kind introduction and I'd like to start by thanking Robert and the members of the committee that selected me to come and visit with you it's been a great day here for me learning about the Institute and a little more broadly about what's happening in science and technology here in Philadelphia it's very very impressive and clearly I need to come back and spend more time and I also wanted to just start out by pointing out that you know I'm a scientist who has always done fundamental research I've always asked very fundamental questions about biology in my lab and the story that I want to tell you tonight is one that will illustrate the some of the sort of serendipity of science and in my experience the opportunities that come up as a result of curiosity driven research which i think is a little bit under attack right now in terms of the funding agencies that question the value of that kind of science and I'm really here to tell you that you know the kinds of opportunities that come up with with you know an open-ended approach to exploring the natural world are really on or unanticipated we can't predict where new technologies and discoveries are going to come from and so I just I really have the pleasure of sharing with you some incredibly exciting science where we're kind of at a moment in biology that is unprecedented in the sense that there are technologies now coming together and one of them I'm going to talk about tonight that provide opportunities for both manipulating DNA but in ways that will be useful clinically but also understanding more about the natural world and really who we are as humans that I find to be incredibly exciting I just feel sort of fortunate to be alive at this moment and and to be part of the the science that is going into all of this and to start to start talking about genome editing I really just wanted to start by by showing the structure of the so you know if we think about the code the code of life this is the chemical that provides all of the instructions for cells and organisms to develop the way that they do the structure of DNA was discovered back in the 1950s and at that time scientists already started imagining what would be possible if you could manipulate that code if you could sequence it read the code synthesize it write the code and maybe even someday rewrite the code alter the code and it's that latter opportunity altering the code which is really what genome editing is all about it's about being able to precisely change the DNA in cells that gives scientists the opportunity to not only do things like change DNA that might otherwise lead to disease but also to understand the genetics that underlie organisms and their properties in ways that were until very recently simply not possible so very briefly about me so I you know I started off my my life in Hawaii I grew up in Hawaii and my father nobody in my family was a scientist I'm saying this partly for the students that are here so I you know I didn't I didn't I didn't know any scientists growing up and I I I certainly didn't know any women scientists and but my dad was really interested in science even though he was not a scientist and he gave me this book when I was probably about 12 or 13 years old that is a book about the discovery of the structure of DNA written by Jim Watson and when I read this book I was completely blown away by the fact that scientists could ask a question like this about the structure of DNA and come up with experiments to answer it and I started to imagine I think at that time what it might be like if I could actually spend my life doing that kind of work too and so I went on in in science I got a degree in chemistry as a college student and I took one biology class and call and in that biology class we learned about what's called the central dogma of molecular biology which is that DNA in is the information encoding molecule in cells it's the store of the instructions for the cell and it those instructions are typically deployed as protein molecules that are coded for by the by the DNA so the proteins are on the right hand side and then at least in my college biology class that you know we were told though there's this very boring molecule in the middle called RNA which is kind of a chemical cousin of DNA and it's really just an intermediary between the DNA and proteins and so I didn't think too much more about it until I got to graduate school and I learned that in fact there were at that time this was in the mid 1980s there were interesting examples of RNA molecules that had chemical functions on their own they didn't encode proteins but they actually did interesting chemistry in cells without requiring anything else and that got me interested in the whole question of you know what RNA molecules are doing in biological systems my graduate adviser was interested in the role of RNA in the origin of life and I started investigating the way that RNA is involved in really controlling the output of the genome the way that genes are actually expressed and turned in and in the way that proteins are produced in cells and that turns out to be a very rich area of biology that said we've been able to work in a number of different on various aspects of that question over the last three decades and the story that I'm going to tell you tonight is really one that came about again through that sort of curiosity about the role of RNA in controlling the way that bacteria interact with viruses and and the opportunity to understand this by thinking about and studying this process and as all you this is really a pathway that fundamentally involves molecules of RNA and so I got I got inserted into this area that's now known by the acronym CRISPR back in around 2005 when a colleague of mine at Berkeley Jill Banfield who's shown here was researching bacterial DNA so her her line of work involves studying organisms that live in interesting Nisha's in the environment and sequencing their DNA to learn about their lifestyles and that line of work had led to a really interesting observation that she told me about in a phone call where she said that a lot of bacteria have in their DNA so this is showing you a circular chromosome of DNA and in a bacterium they have a repetitive place in the DNA sequence that is a storage site for little bits of DNA that come from viruses and this these sequences that had come to be known as crispers include repeated elements shown by the black diamonds that flanked inserted segments of DNA that are unique each one is different and each comes from a different virus so it's effectively a genetic vaccination card in bacteria a place where they these bugs store a genetic record of viruses that have infected them over time now why would bacteria do that and so in thinking about this Jill and a few others who are noticing these sequences at that time proposed that these might in fact represent an adaptive immune system a way that bacteria could acquire sequences of DNA store them and then somehow use them later to protect cells from future infection and a clue to this was the presence of CRISPR associated or cast genes that were neighbor sitting nearby and the genome that encoded proteins of unknown function but that always were present together with these CRISPR arrays so it was a hint that they might be participating some together to protect cells and what emerged over the next few years in research that was going on in just a handful of labs around the world at the time was the sort of the the fundamentals of how this adaptive immune system actually operates and so I'm showing you here a picture of a looking at a corner of a bacterial cell that's being infected by a virus and if the cell has a CRISPR system in sitting in the genome it can detect this DNA that gets injected when the virus infects and store a little piece of it in this CRISPR sequence in the CRISPR locus and then the cell is able to make copy of that sequence in the form of an RNA molecule that starts off as a long segment of RNA that subsequently chopped into individual units that contain in each case a sequence that comes from a virus these little squiggly lines here those RNAs then combine with proteins encoded by the cast genes to form surveillance complexes and these are literally proteins that are programmed with these RNA molecules to find sequences of nucleic acid typically DNA but some of these recognized RNA that have a matching letter set of letters in the in the DNA or RNA when that match occurs these cast proteins are recruited to that molecule and they lead to its degradation so it's a fantastic way that bugs can acquire immunity to phage kind of in real time store these sequences and then use them to protect the cell from future infection and one of the things that turned out to be really interesting this is again work that was done initially in largely Injil Banfield's lab and another guy named Eugene Koonin and his partner Kira Makarova at the National Institutes of Health was that these are pathways that are very diverse in nature and this is showing a cartoon oonh of some of the different kinds of genes that are part of these pathways so I'm just showing you cast genes and they're color coded according to their function so some of these were known to be involved in this actual interference step of protecting cells and destroying foreign DNA some of them were involved in production of the molecules necessary for this immune system to work and then the ones over here were part of the adaptation part of the pathway integrating new sequence of sequences of DNA and we were initially studying one of the systems shown up here called type 1 that has multiple proteins that come together and protect cells from infection but I was intrigued by the finding that there are CRISPR systems corresponding the class two pathways down here on the bottom that instead of having many proteins required for the system to operate they have in each case one large gene that encodes one large protein that's necessary for protecting cells from infection and so when I met my collaborator emmanuel sharp NTA at a conference in 2011 we decided to collaborate to answer this question what's the function of one of these big genes that encodes a large protein called cass 9 which seemed like a really interesting protein because it was the only protein necessary in these bugs to protect the cells from infection using the CRISPR pathway but at the time nobody knew how it worked and so that's what we we investigated and it led to a really interesting finding that was the work of two fabulous scientists in our labs Martin Janek who was working in my lab at Berkeley and christiansí who was working in a manuals lab in Europe and these two guys even though they had never met they were working you know thousands of miles apart they were doing experiments together and sharing ideas and data over the Internet and over Skype and they figured out that cast is a fascinating protein that has the ability to recognize double-stranded DNA molecules and cut them precisely at a place that matches the letter sequence of the RNA molecule here coming from the CRISPR array and so this molecule has a 20 nucleotide or 20 letter sequence on its end that is the recognition it's really the zip code for this molecule and when that interaction with DNA occurs the protein unwinds the DNA and uses two separate active sites to make a chemical cut to the double helix so it literally cuts apart the double helix of DNA and leads in bacteria to destruction of that DNA molecule now importantly so Martin and Kristoff were doing biochemistry which means they were working with purified molecules in the lab so we could really figure out what was necessary and sufficient for this DNA cutting reaction to work and that revealed that in bacteria there's a second type of RNA called tracer this red molecule that is essential for cast 9/2 function it has to be there because it provides a structural handle that allows cast 9 to hold on to these RNA molecules and so that allowed us to you know manipulate this this protein and program it to recognize different DNA molecules by making changes to this letter sequence here it also led martin jeanette to recognize that he could simplify the system compared to what nature has done by linking together these two rnas to have a single what we called a single guide RNA that would have the address for DNA recognition on this end and the handle for cast 9 binding on the other end and this was for us kind of the moment when this project which started as a curiosity driven research effort when we realized this was science that was going in a very different direction for what we anticipated because here we had a two-component system with the single guide RNA being used to program cast 9 for DNA binding and cutting that could be introduced into cells and used to cut apart essentially any DNA sequence and you might be wondering why does that how does that relate to gene editing and to answer that question I have to introduce you to a summary of a lot of the research that had gone on in many labs over the previous two decades or so with scientists discovering and trying to understand how cells deal with DNA damage and that line of research had revealed that unlike in bacteria where the cells are growing very very fast and when a double-stranded DNA break happens the DNA is quickly destroyed in cells like human cells ourselves plant cells other kinds of what are called eukaryotic cells these are cells that are growing a lot more slowly and they have to deal with DNA damage as a sort of in the course of DNA replication and cell division and so these are cells that have machinery to detect double-stranded breaks like this one and repair them in pathways that include either linking together the broken ends of DNA and sometimes in the process making a little deletion or insertion to the DNA sequence or by using a DNA template that has some sequence matching the flanking the site of the break that can lead to incorporation of new genetic information during the repair process and so scientists have studied this and had recognized that if you could introduce a double-stranded DNA break into a cell's genome you could trigger this kind of repair and in the process trigger a change to the DNA sequence in other words genome editing and the challenge was how to introduce a double-stranded break not so easy and so earlier technologies for doing this had been developed relying on Prout that could be engineered to bind and cut DNA and they worked very well but they were very cumbersome you had to have extensive experience with proteins and how to engineer them it often took significant time to make each protein that was necessary for a single engineering change to a particular genome and so it was just not possible for most labs to rapidly adopt that kind of technology even though we could all see that it would be really cool if you could do that and the fantastic thing about the CRISPR cast nine protein with its programming that happens through this single guide RNA is that here we finally had a way to easily alter the DNA recognition properties of casts 9 to allow it to use its chemical cleaver at any place where you might want to introduce a break and thereby trigger a genome editing event and I wanted to show you a this is a little video created by a wonderful artist Janet iwasa that shows how we imagine this system operating in eukaryotic cells these are cells that have DNA inside the nucleus and the DNA is highly compacted in the form of chromatin and what this protein casts nine has to do is search through all of that DNA in the human genome 3 billion base pairs of DNA to find a single stretch that has a 20 base pair match to the 20 letters of the guide RNA when that match occurs the DNA unwinds inside the protein the protein is able to cut the double helix and then in a process that we don't fully understand sort of magic happens this is where the editing actually happens the cell detects that broken DNA sends in repair enzymes that can fix it by in this example actually integrating a new piece of genetic information at the site of the break and what's amazing about this enzyme even though it comes from bacteria is that it turns out to be highly effective at doing this kind of chemistry in any kind of cell or organism where contested and so in the six years since Emmanuelle Charpentier and I published our research in the summer of 2012 this crisper cast nine technology has been widely adopted by labs around the world for all sorts of genome editing applications and fundamental research and so in our own lab you know we've been continuing to try to understand how it works it's sort of an amazing thing like you see a video like that and it almost looks like science fiction right how can something really work like that and how can it work accurately and how did how can it work quickly and how can it deal with really highly compacted DNA and all of those kinds of questions so we as as biochemists and structural biologists in my lab this is these are the kinds of questions that we like to dive into and so we've been investigating this question of how cast nine works and I'm just going to share a couple of the insights that we've had with you one is that this is a protein that works by using its guide RNA to interact with DNA by forming base pairs that mimic what happens in a normal DNA double helix and this is a this is actually a 3d printed model of cast 9 that's based on a real molecular structure of the molecule the protein that shows how it works and so we've got the protein in white it's got a guide RNA here in orange and when it finds a matching sequence to the 20 letters in the guide RNA in a DNA substrate this blue molecule the DNA opens up inside the protein and RNA DNA helix forms that's the orange and blue helix and this displaced strand of DNA is then positioned for DNA cutting as well as the Strand that's associated with the RNAs and there are two separate chemical centers we call them active sites in the protein that are each responsible for cutting one of the DNA strands so it makes a blunt double-stranded break in the DNA and I won't show you the data for this but one of the things that's very interesting about this protein is that it's clearly evolved in bacteria to have a sensor that is detecting the base pairs that form in this RNA DNA helix so that it only is position to cut DNA when it's associated with a correct sequence of DNA it's really the the interaction is able to trigger active cutting of DNA only when it's associated with a correct site and so one of the curiosities about this protein is you notice here that they're fundamental to the way it works is that it has to melt apart the DNA strands at the place where recognition and cutting is happening and we know that that's essential for its function as a DNA cleaver and yet it doesn't have an external energy source so it's truly somehow prying apart the DNA strands but it doesn't have a way of in in bio for those of you that know biochemistry you know that a lot of enzymes that have to do work in the cell get energy to do that work by hydrolyzing ATP or gtp but this molecule doesn't do that so we've been wondering how does it actually unwind and melt DNA since that's so fundamental to the way it operates and we don't fully know the answer yet but one clue has come from comparing different structural states of the enzyme this caste 9 protein as it binds to RNA and then DNA molecules and I wanted to show you a little animation that compares these structural states showing the the way this protein changes its shape as it binds to a guide RNA the orange molecule you saw a big rearrangement than that part of the enzyme it opens up a channel in the center of the protein where DNA recognition can happen and then when DNA binding occurs there's an additional rearrangement of the structure to accommodate that that RNA DNA helix and we think that that structural change also has to do with opening up of the DNA duplex and then finally this part of the enzyme in yellow is one of the chemical cleavers that swings into position to cut the DNA and we know that that final structural change only happens when this when this protein is associated with a true DNA substrate and not a sequence that has a mismatch for example to the guide RNA so I let's see this is a this is this slide deck looks a little bit different from the one that I wanted to show you but it's okay I will we'll go in it so this is a this is actually a more recent three-dimensional structure of the enzyme bound to a true double stranded DNA molecule in blue and in magenta showing how the DNA unwinds and the protein and based on this structural work as well as some chemistry that we were able to do we figured out that this is a protein that does under in fact undergo these rearrangements in shape as it assembles with DNA and we think that that's really part of its mechanism of prying apart those DNA strands so I was not going to get into too much scientific detail here but I think when they put up my slide deck they picked the wrong file so that's okay that's okay that's okay but you're gonna hear a little more science than I was actually going to tell you sort of a little bit more detail but that's okay because I'll try to I'll try to explain it and tell you why we're doing what we're doing so one of the things that we've been studying and working on in the lab is to ask whether there are you know how many different kinds of CRISPR systems are out there we know these are diverse so we know there's lots of different flavors of these and can we understand how they work and as I'll show you very briefly with their the answer is there are new ones and and they have interesting properties so I'll show you a little bit of that and then I also wanted to tell you in the last part of the talk really where this technology now is going it's an exciting moment and what's happening how are people using this technology and what do we need to think about and how is it going to affect all of us in the future so in terms of thinking and discovering new crisper caste systems I've been working with Jill Banfield's lab so she was the person who first told me about CRISPR systems back in 2005 so she continues to investigate organisms that grow in the environment and that research has led to appreciating the incredibly interesting diversity of these pathways it turns out that because bacteria and their viruses are evolving very quickly there's been lots of you know variations on this theme of RNA guided protection of the genome and one of the things we found recently is that there are two proteins called Cass X and Cass Y that are also RNA guided enzymes that operate by cutting DNA as I showed you forecast 9 but they're interesting to us because they don't look anything like caste 9 they're completely different and they're also a lot smaller in terms of their their actual the actual size of these proteins and that could have interesting implications for the way that ultimately we might be able to introduce these into cells for genome editing applications so I'll tell you just a very little bit about Cass X and this is actually really new research it's not even published yet and but it came out of this study that we did in collaboration with Jill Banfield wonderful guy David Burstein who is a computational biologist who basically said can I find CRISPR arrays and those are relatively easy to find in these kinds of datasets that are next door to a gene that is of unknown function so it's proximal to the CRISPR array it might be involved in this adaptive immunity but we don't know what it does and the answer was yes and one of these was this protein that we ended up calling Cass X so it was sitting in a bacterial genome here's the CRISPR array over here and that molecule called tracer we found a place in the genome that encodes that these are three genes that are involved in the adaptive step of the pathway integrating new DNA sequences into the array and then there was this Kasich's that had an unknown function so it was a hypothesis that this might be a maybe RNA guided protein and that turned out to be true so in recent experiments we've been able to look at molecular structures of Kasich's and it turns out to be a very interesting making a very interesting partnership with RNA and this molecule what you can maybe see here as the protein is sitting here at the top and all of this other stuff all of these HeLa C's here and here this is all of the RNA that's part of the system so it has a much bigger component of RNA than we saw forecast 9 and it seems to be essential for it for its function and furthermore it's active for gene silencing and regulation so this is one kind of experiment that we did doing using the caste X protein to turn off expression of a gene encoding a green fluorescent protein in bacteria so this shows cells that are making the green fluorescent protein and these cells are actually making both green and red fluorescent proteins so when you they're made together in these cells they look yellow and when we use caste X programmed with a guide RNA that recognizes that green fluorescent protein gene we turn off just that gene so the cells keep growing and they keep making the red fluorescent protein but now they don't make the green one anymore and you can see that that's been turned off and this shows you gives you a sense of the efficiency of this right all of the cells are basically have received that that editor they they've made that change so in terms of thinking about how do we how we think about then taking caste X or of course caste 9 and these other other related RNA guided proteins and using them it for various applications including for therapeutics and I think there really are three big challenges to this that are still very much under active development one is delivery how we introduce these molecules into cells or tissues or how eventually we could actually put them into a a person we wanted to use this therapeutically how we control the outcome of editing so you saw that what these RNA guided proteins do is they're the cleaver right they make the cut but the cell has to take over and make the actual edit and so scientists are very actively working on how to control that repair process and then finally as I'll mention at the end there are some I think very interesting and important ethical and societal implications for certain applicant uses of gene editing that we need to really grapple with right now so this is a slide that just illustrates some of the many many organisms and cell types that have been edited now using CRISPR caste 9 and that's still the primary molecule that's being used for these experiments and if you look at this briefly you'll see that you know we have mushrooms we have flies we have you know all kinds of self various kinds of plants pets all kinds of organisms so it's truly a democratizing technology it works across all of biology and it enables incredible opportunities for both research and applications and and so what are some of those applications and I wanted to just highlight for you a few examples of things that I think are really interesting that are happening right now with genome editing and that are going to lead to interesting things in the near future and these are some of the categories right so there's fundamental research but there's also uses in healthcare therapeutics agriculture and diagnostics and and just to highlight this I thought I would show you to two things that are happening on the research front that are sort of illustrating changes that are really you know profoundly affecting the way that scientists decide what to study and then how to study them so this was a slide I got from Claude to spline flat New York University Michael Perry a student in his lab who was doing work on butterflies and they were studying the gym there were hoping wanting to study the genetics of butterfly wing pattern development but until until cast nine came along it was impossible to do genetics in these organisms they could only collect animals in the wild and try to look and correlate changes in wing patterns with you know various you know things diet environment etc but with cows 9 they're actually able to control the genes that lead to these wing pattern developments and they've been able to dissect these patterns now beautifully and this illustrates what's happening in lots of other fields to where now organisms that previously were not genetically tractable can be altered and studied at the level of their genes so another example of this kind of research is what's happening with understanding and trying to make sense of of what the Neanderthal DNA genome can tell us about who we are as homo sapien so you may know that over the last few years scientists like Svante Paabo and others have been able to collect samples from Neanderthal remains and sequenced the genome of these Neanderthals and and then the question is so we've got the sequence what does it mean and how do we understand or try to answer questions that are still mysterious like why didn't the and earth also go extinct and why how and why were they different from modern humans and so an experiment that's going on right now is that scientists are using little sort of what we call organoids these are tissues that grow in the laboratory that have some properties they're not really little brains but they have some properties of neurons that mimic what happens in the in you know mammalian brains to investigate how genes in the Neanderthal genome might change the way that these mini brain these little brain organoids can develop and function and in doing those kinds of experiments they use gene editing to cut out and then introduce those Neanderthal genes into the the human modern human genome in the context of these orgonites so that's research that again would not have been possible that weren't possible to edit DNA precisely and accurately and then a couple of other examples so in healthcare there's been interest in using the gene editing technology to make changes to animal genomes that will have an impact in health care and one of the ones that's gotten some attention lately is using it in pigs because there's a an opportunity to use these animals for organ donation but they need to be we need to make some changes to the DNA to make that possible one is to remove virus sequences that are part of the naturally of the pig genome and it could infect humans if they were if they were organs were put into humans directly and the other is to make changes to DNA and pigs that will make their organs more human-like so they don't get rejected by our immune system and that's happening now and so these are efforts that are underway both in companies as well as in various academic labs and then in terms of a direct clinical use of CRISPR technology I wanted to share with you one experiment from our own labs this is something that wonderful postdoc Brett Stoll has been working on now for several years where he's been modifying the Cassadine protein chemically so that it has the ability to get into cells in the brain and so we do what we do in these experiments is we have the Cassadine protein programmed with guide RNAs that recognize a gene responsible for a neurodegenerative disease called Huntington's disease this mutation has been known for a long time but up until now there's been no way to deal with it or even you know think about correcting it and what Brett's don't doing is injecting these modified proteins with guide RNAs into the brain he's doing this in in a mouse model of Huntington's and these molecules go in and they start editing neurons that are located around the site of the injection and just to show you how this works this is an actual slice out of a mouse brain this mouse has received injections on both sides and you can see that a large number of cells become edited after these injections occur and we can tell because we're using a mouse that's been engineered so that the cells turn red when they receive a precise edit and we're actually quite excited about the potential for this to be useful not only for treating a disease like Huntington's but also for understanding the fundamental genetics of brain disorders like this and lest I ignore I didn't want to ignore a huge area of impact for gene editing which is agriculture and I'm just gonna give you one really interesting example and that's work that's being done by zack Lippmann at Cold Spring Harbor labs where he's been able to use CRISPR Castine to make changes to the DNA of tomatoes that alter their their crop yields and so he had a I don't have it on this slide because it's so recent but he showed at a recent conference I attended a slide where he had 15 different tomato plants that had been generated using CRISPR cast nine where he could alter the amount of fruit that these plants produce simply by dialing up or down the expression of one specific protein in these plants something that in the past would have been impossible to imagine doing in any kind of controlled way and now it's possible using this kind of technology and this was on the cover of a scientific journal because scientists could see from this example that this would be possible potentially in a lot of other kinds of plants because they share similar genetics so you could target this gene controlling crop production and other kinds of plants and altered yields in those crops as well and then finally I just wanted to mention that recent research and this kind of gets back to you know why do we why do we care really about how these molecules actually work and what their biochemical functions are and um I think that you know we really care because we you know at least if you're me you know you actually want to understand the fundamental biology and where how these evolved and understand how they fit into the whole sort of you know bacterial milieu and what they're doing and in their natural settings but once we understand their functions we can also think more rationally about how to harness their functions for technology and this is a example we're researched by Janice Chen and Lukas Harrington in my lab showed that another RNA guided protein related to cast 9 but called cast 12 is an enzyme that has the ability to not only recognize and cut double-stranded DNA but once it finds its target it turns on a nonspecific DNA sack tivity that cuts up single-stranded molecules not in a sort of a non sequence specific fashion and if you include in a in a reaction a short strand of DNA that has a fluorescent molecule bound to it once it's cut this little molecule of DNA releases this fluorescent dye and it becomes visible and so using this as a strategy for DNA detection is exciting because it allows it in principle allows real time in interrogation of a sample to find out if it has a particular DNA sequence present in that material so you can imagine having a doctor's off this kind of kit where somebody could spit in a tube and use this as a way of detecting whether they have an infection for example by looking for the presence of virus DNA and then finally I just wanted to circle back to this whole question of ethics and you know there's there's a few uses of gene editing or maybe at least a few that you know that I think really require careful thought and one of the ones that is probably you know attracts the most attention in a way is this business about heritable genome editing and I wanted to point out that you know we can really divide genome editing into two different kinds if we're doing it in fully developed cells or fully differentiated organs that we call that somatic cell editing but if we're doing it in cells that can propagate into an entire organism then we call that germline editing and the thing about germline editing is that it's heritable so it affects the entire organism and all of its future progeny right future generations and so this type of use of crisper cast 9 started very early in the field so people using this in animals and plants but what about humans and people have of course been you know thinking about this and in fact actually doing this kind of genome editing so far not for clinical use but certainly in research laboratories and the idea here is that we can have a fertilized egg this is actually a mouse egg not human but this is a mouse egg fertilized egg that has a we have a needle coming in and injecting the CRISPR cast 9 molecules into this egg we're editing occurs and then those resulting genetic changes are passed on to the cells of this entire developed Mouse when it grows up and can be passed on to its progeny and you know so people have been thinking about this and starting to investigate how this might work in humans and I think it's been incredibly important to also think about you know how we how do we regulate that how do we make sure that we have responsible use of this kind of technology that's definitely not an easy question to answer and thinking about global regulation is certainly a big challenge but I think it's critical to be addressing this right now because we know that the day is coming at some point in the future when people will use this clinically and and then of course that opens the door to all of the things that you might at least imagine doing if you could make changes to the DNA of of kids and this this was actually a this was actually a picture on the cover of The Economist from a couple of years ago you saw this under the banner editing humanity and it was a actually great article it really talked about this was the first sort of mainstream article that really talked about this application of genome editing and what it might mean and then since then there have been you know lots and lots of articles about this and and the other thing that's happened is that you know scientists just in the last year in the UK the United States and in in China have been able to use CRISPR cosine and viable human embryos in the laboratory so we know that this kind of gene editing is possible in in embryos and there's still a lot of scientific debate about the outcome of those experiments and how the genome editing is actually working but but in principle that open it does open the door to using it clinically and I do also want to point out that you know this is still quite a fanciful slide because these are you know these are all properties that come from many genes we mostly don't know what those genes are that are interacting to create certain traits and so it's not going to be possible anytime in the near future to do this kind of editing even if we wanted to but I think it's still important to be thinking about where this is all going what does it mean and how do we ensure that it's a technology that's used for for good and for improving the human condition and not for outcomes that would be detrimental and so I've been involved in in a number of these conversations and I wanted to point out that the National Academies around the world have been very active in this area so this is a report that was produced published last year from the National Academies that were built on a meeting that happened at the end of 2015 and provided a set of guidelines really for the use of human genome editing especially in the germline in the human germline and it basically you can download this report if you want to and it basically recommends not using it clinically until there's opportunity for societal consensus around around this kind of application but you know the reality is that you know people around the world are you know there's lots of science that's going on and not everybody subscribes to the same set of you know set of ideas about how this should be utilized and so for partly for that reason we're having another meeting it's happening in a week in Hong Kong again sponsored by these national academies and the goal there is to reassess you know where are we today this is now three years later where are we the science and also what's happening in terms of applications for things like human genome editing so stay tuned there will definitely be articles and reports about this meeting and the hope is that that also you know continues this discussion and sets guidelines for use that we hope scientists around the world will respect and and then finally I just want to conclude by summarizing a couple of things that I've told you so you know RNA guided gene editing is clearly a powerful way of manipulating genomes and I mentioned just a few things to you tonight but you should know that there's lots of I would say kind of auxiliary technologies that are built around these kinds of enzymes that allow things like imaging DNA in cells and and controlling the output of genomes without actually chemically altering the DNA sequence so you know lots of things that are now possible with this these this sort of family of molecules that's you know very exciting and we know that the applications of these enzymes and for genome editing in general is going to require both understanding the chemistry of those edits how that how the edits happened and how we can control them but also in a societal sense how we can regulate this and ensure that it's used responsibly and then finally you know the new biology and fundamental science is going to continue to drive this field forward and as I was talking about today with several people you know there's a really interesting interchange between fundamental research and technology and I think they they kind of to me they always feed back on each other you know you have new technologies that enable new fundamental discoveries and then those discoveries require you know posed questions that need new technologies to be addressed and so it's just you know it's sort of the process of science that you know the technology and new discoveries kind of go hand in hand and none of this would be possible without a fabulous group of people that I've had the pleasure to work with so this is a picture of members of my laboratory at the University of California Berkeley and I've got everybody in here so this was a summer photo from I think last just the end of last summer we had 10 undergraduate students working in the lab so this great and they're all in there and and then we've also had the good fortune to work with some wonderful scientific collaborators Emmanuel sharpen TA of course with whom we did the original work on cast night and then we're recently with various colleagues at Berkeley I mentioned Jill Banfield and these other folks have been involved in a lot of them were fundamental mechanistic work that we're doing and increasingly we work with colleagues at University of California San Francisco our our local internationally famous medical school for applications that include things like with Joel Paulette Sookie's lab using CRISPR casts for detection of cancer sort of cancer-causing viruses in patient samples in real time and he's actually doing this in clinics in Africa where there could be an incredible value in having a point-of-care diagnostic for this kind of thing and then of course in academic research we can't do anything without money and all of these I don't want to acknowledge these groups and in particular the Howard Hughes Medical Institute and the National Science Foundation were the organizations that first funded me to work on CRISPR biology back before anybody knew where this would be going and I'm forever grateful that they gave us the opportunity to do the kind of curiosity driven science that I think is so important for the future of both fundamental understanding and then for technology development so thank you very much [Applause] thank you very much indeed dr. Dodman for a really rather remarkable survey of the work you've been doing I'm also asking very many questions I think which really for society we have to think about and perhaps even answer now there is time for questions perhaps ten minutes or so and we have a microphone in the middle of the room we're not going to attempt to sort of try to get a microphone through to you you've got to come to the microphone so Mountain is coming to Mohammed or the other way around I'm never quite sure which way so can we um can we put up your hand if you wish to ask a question and perhaps former an orderly queue behind the microphone and ask the questions would and don't make your questions too long so we get as many in as week so the first question is there's one there please find your way to the microphone thank you could you describe the moment when you've recognized the potential implication for the technology what were you thinking what was the sort of the point where you recognized that this could be more than what you thought before and if in a hundred 50 years what do you think is the most pertinent or important question that you think the technology can answer oh that's that's tough well the moment was I remember well you know Martin Jenek my postdoc who did this work in our lab was in my office and he was showing me his biochemical data about cast 9 and we realized that this is a programmable enzyme and not only that it could be simplified to have this used the single guide RNA and in that way easily be programmed to recognize essentially any DNA sequence and make an efficient double-stranded break and when he showed me those data we really looked at each other and said gosh this could be a really powerful tool you know for genome editing because of all the research that was going on with other tools for gene editing that we're kind of working but not not not that well and so that that was really the you know and I interesting I was actually on sabbatical that year in Berkeley and I just saw Martin and he was reminding me of this that I it started my sabbatical and I was only about three weeks into my sabbatical when he showed me those data and I thought well that's my hope of doing my own experiments are over because because he's got so many interesting things to do with this so that was the moment and then you know the way where do I see this going in the future I think it's boy I mean I can't honestly even predict where we're gonna be in five years much less 150 but if I had to guess I think that we're gonna see genome editing and you know this this you know this won't be the last technology for it either but you know there will be I think continued developments around this and you know it's going to become routine I think to manipulate genomes in various ways and you know where we're today it's a little bit you know it's it's quite easy to knock out a gene it's not so easy to knock in a gene I think that will become trivial in the future I think that you know ensuring that you know that you can deliver these molecules into cells efficiently over time that's going to become possible and maybe even trivial to do in the future so you know I think that this will become a part of the fabric of all of the kinds of research projects that people are doing and effectively any area of biology and so then it really does open the door to saying you know what do we do with the tool like that and how do we use it in ways that will be productive and not destructive thank you next question that here Jeff I wonder if you would comment about the possibility of eliminating the Anopheles mosquito in order to eliminate malaria and the controversy about eliminating species which is so destructive right so thanks for bringing that up because this is an application of gene editing that I did not mention but is is also very very much under active development and and you know has a real potential you know environmental and ethical impact and that is using it in the context of gene drives where you can use gene-editing to introduce a genetic change into a whole population of organisms very quickly and so there's been lots of interest in using it to control mosquito-borne disease and and you know you can imagine at least two probably many more but two ways of using it one would be as you said to actually destroy this species and create sterile mosquitoes that can't propagate but you could also use it to not to do that but just to create mosquitoes that can't pass on the pathogen and so I think that's the application that's the mode of using it that people are pursuing now that I'm that I'm mostly aware of and and the idea there is not that anyone likes mosquitoes but we're appreciative that there's a whole ecosystem that depends on these insects food supply and so you don't want to have an inadvertent outcome and believe me coming from a Hawaii I'm familiar with unintended consequences of you know even the best intentions of manipulating the environment so I think it's really important to pay attention to that there's a lady behind you and then thank you for your work and a great talk I think we're starting to understand that there's pre-existing antibodies and human populations which will probably be a barrier for translating these cassadine into clinical trials and I was wondering if you could just comment on that and then what you're excited about kind of how we can overcome our own immune system yeah so um thanks again for for bringing up that point too because that's also very important so what has emerged is that these particular enzymes especially the one that Emmanuel and I first started working with which comes from a human pathogenic bacterium is and because of that a lot of people have been exposed over time to this bacterium and so they have naturally-occurring antibodies against this particular form of cast 9 and so in the end you know will that be a barrier to clinical use it's possible that it will no-one's demonstrated that yet but what I think is to appreciate is that there's lots of natural variants of cast line that exist in bacteria that are not infectious to people so we would have probably no antibodies to those types of cast night proteins and also there's a very active effort among lots of bioengineering labs to engineer new versions of this enzyme that are not immuno genic in humans so I don't really see that as a long term barrier but I think what's important to appreciate is that this is something that has to be anticipated and we have to plan for it yes we've seen many times in the past we're like we learned to weaponize chlorine we learn to weaponize nuclear devices how can we prevent even with a treaty if we have governments like in Moscow Washington toran Korea that can or cannot live with agreements and decide to weaponize CRISPR yeah it's it's a good question I think I would say to that that CRISPR technology is you know like like any technology it has the potential to be used for ill intent right and and so how do we how do we ensure that that it's not I mean it's it's a hard question to answer I think that personally I I think there are easier ways to you know create bioweapons if people wanted to do that then using gene editing right now so not that that should give us comfort I suppose but you know but but it's just it's just I think we need to just keep it in perspective that there's nothing special about CRISPR technology that makes it more weaponize abow than other things and and the other thing is that I think it's it's really important to be openly discussing this and you know having these kinds of conversations because part of what will will happen I think is that you know as people become more aware of this technology and what it's doing they well I hope at least some of them get involved in this conversation get involved with government regulators and and create a you know a you know we hope it's sort of at least a consensus around the way that these technologies will be used in the future but you know there's no guarantees thank you very much indeed um I must say that some it's it's amazing that when I consider that um when I started studying chemistry in 1963 the structure of DNA had only been discovered ten years earlier than that it had a bit of a slow start I think in in developing ideas from but there's been an acceleration I'm not quite sure whether it's a revolution I think would one could argue that but it does seem to me that um life is fundamentally different from when I first started my chemistry anyway there's one more piece of business which we need to transact and that is the presentation of the of the Liberty Bell which is standing on the table in front of us and I'd like to ask Gary melanda Hirshman Meccan any professional chemistry at the University of Pennsylvania to come to the stage and say a few words so Joe thanks for a fantastic seminar and there's this tremendous tradition of presenting handmade porcelain bull to the yacht lecturer every year in all previous years there has been the Philadelphia Bowl presented and Jennifer will be the first recipient of the Liberty Bowl that's not to be confused with the football game on January 1st for those who were football fans this is a handmade porcelain bowl in the inside there's a description an inscription of from the Declaration of Independence there's also for those of you can't see it there's various scenes from historic Philadelphia including the University of Pennsylvania Independence Hall Liberty Bell and and many of the other historic buildings in downtown and you can't imagine how many times in the last few days I've heard the phrase don't drop the ball so without without dropping the bowl I'm going to present this to Jennifer well thank you very much indeed and there's only I think one more thing to say and that is we have a reception for everyone on the third floor of this building so you can discuss the meeting amongst yourselves indeed if you're lucky even perhaps have a word with dr. doubtful so thank you all very much for coming but especially thank you very much [Applause] oh yeah thank you very much I'd like to do is

Channel: Science History Institute

Views: 7,396

Rating: 4.9622641 out of 5

Keywords: genetics, gene editing, crispr

Id: mO0xFBQox-Q

Length: 71min 0sec (4260 seconds)

Published: Fri Nov 16 2018