George Church, PhD: Rewriting Genomes to Eradicate Disease and Aging

George Church, PhD: Rewriting Genomes to Eradicate Disease and Aging

Show Video

[Dr. Church]: In order to understand how  something works. And also in order to develop new   technologies, you need to be able to, to write and  edit. It's like reverse engineering, electronic   circuit or some software. So I have no idea  what this code does. Let's, let's change it in   case of the biology. You'll, you'll, you'll take  a piece out and now it no longer handles glucose.

You say, okay, that's part of  the glucose monitoring system.   And, and you can just get through that and  you can get to more and more nuance changes   for discovery's sake, but it's often entangled  with not just discovering, but making   useful, uh, synthetic biology, um, that  there you'll have a challenge that you'll   have out there, and that will drive the  reading and writing technology forward. It will drive our creativity in  terms of how these things can   positively influence, uh, society and ecosystems. [Dr. Patrick]: Hey, everyone. Today I'm  extraordinarily excited to bring to you, Dr.  

George Church. It's really a special opportunity  to talk to Dr. Church because he's one of those   rare living historical figures, whose work  is so vastly influential that it can change   our perspective on the potential of an  entire field. In my opinion, this gives   his generally optimistic take on technology  and the future a very special weighting.   Through his work in the Human Genome Project,  in particular, he has directly contributed to   exponential shifts in understanding feasibility  and capability in the field of biology. The Human Genome Project began as a $3  billion moonshot shortly after Dr. Church  

first pioneered a method of  direct DNA sequencing in 1984.   The goal, to sequence a single  reference genome for humans.   Completing the initial aim of that project,  Dr. Church and his collaborators and colleagues   ultimately set us on a path to where we find  ourselves today. Sequencing is now over 10 million   fold cheaper, and most people can get their  genome sequence inexpensively if they so desire. But where do we go from there is the question.  Arguably one of the most important geneticists  

of our time, Dr. Church helped initiate the  Human Genome Project in 1984 and the Personal   Genome Project in 2005. His lab was one of  the first that showed CRISPR-Cas9 worked for   precise gene editing in normal human cells. And  he has been behind countless other scientific  

innovations and disruptions, specifically  in the world of precision genome sequencing. Dr. Church has described the key theme of his lab  as technology development, radical transformative   technologies. So, let's talk about those.  George, it's hard to know where to start,   large genome-writing history, universal donor  cells, multiplex editing, and the ability to   perform thousands of edits in a single cell,  organoids. But maybe we can just start with the  

Human Genome Project. What is the back story, and  how did we get to present day, an era of writing? [Dr. Church]: Oh, thank you, Rhonda.  Let's see. Let's start with...I   think we didn't realize that we were on an  exponential when we started sequencing. I got   introduced to it through RNA sequencing. There  wasn't DNA sequencing. And then Wally Gilbert   was my mentor as a graduate student, and he and   his team invented it in 1977. Independently.  Fred Sanger published a paper that same year.

It took a little longer for the  Sanger method to get implemented. But   what happened was, very quickly, we got to  a point where we were talking about doing   a whole genome, mainly at the Department of  Energy's bequest, in 1984. They asked a harder   problem, which was, how do you estimate mutation  rates to the consequence of energy? And we know, a handful or maybe 10 scientists  in what would later be called genomics said,   "Well, we can't do that, but what we might be able  to do is get one genome, a reference genome." That   consolation prize was big enough that Charles  DeLisi at the Department of Energy just started   writing checks. I mean, he didn't wait  for an act of Congress or anything, just  

had money for this kind of R&D because of health  effects. And then it took about three years. I was transitioning from postdoc to  professor, and my lab got one of the first   two Genome Project grants. And then the took about three years before the   NIH got involved, but they got involved in a big  way because they felt they were a more appropriate   vehicle for anything health related than  the Department of Energy. And they did it,   kind of, in a teamwork with maybe 30% DOE  and 70% NIH in the United States component,   plus lots of international collaboration,  really starting in 1990 with a 15-year goal. There was a lot of talk of cutting corners at  the beginning. I didn't necessarily call it that,   but there was a lot of people trying to  do 1X coverage, meaning doing every base   pair...reading it exactly once. And I didn't like  most of these corner-cutting things, but I was  

the most junior member of the project from  the beginning. I didn't have a lot of sway. I also felt that we should put technology  development upfront because that could reduce the   price, and then we could do a lot more than one  genome for a lot less than $3 billion. As soon as   some of the senior members of the visionary  team, like Jim Watson, who came in later,   started representing...drumming up support in  Congress, it became evident that we would have $3   billion. And then the motivation for bringing the  price down disappeared for a few years...a decade. Then instead of...some of the corner cutting  was to not worry too much about the repetitive   sequences, which in the case of the  fruit fly was about half the genome.  

Yeah. You know, it doesn't matter. And at  one point, they were going to just do the   coding regions, which is 1%. It turns out,  we still haven't identified the 1% coding   regions that would not have been a shortcut.  So a lot of these shortcuts were really   ill-conceived. But fortunately, we did get a  decent 92% of the genome and declared victory.  

I want to make sure we've got that before we go on  to writing genomes. That's a whole another topic. [Dr. Patrick]: Do we need  more reference genomes? And   what are your expectations of finding new  tools elsewhere in the evolutionary tree? [Dr. Church]: Well, so,  yes, we certainly need more   genomes. It's not just the reference. It's  the population variation that's important.   The variation is at least as important as  the reference, and it helps us make sure   we've got a good reference. So you can  call that the reference. It is growing   recognition that we can represent  the reference as a diversity.

We are finding tools in the genomes. One  of the nuances that developed, the first   kind of recommendations for maybe 1984, 1985,  1986 was the Human Genome as if there were one   and as if there weren't any other genomes. And I  kept advocating for genome comparisons because,   when you compare two genomes, that's almost as  good as an experiment, but it gives you a richer   formulation for exploration. And we have...part  of that genome comparison has resulted in   new tool discovery, and so it's kind of a  positive feedback loop. You sequence some genomes,   you find some tools, use those to read and  write genomes, find some more tools, and so on.

I don't know where that ends, but I do think  that synthetic biology is probably ultimately   unlimited, while the diversity on earth,  even though it's vast, is more limited.   Almost by definition, we can explore  more than currently exists, at least   initially in narrow corridors, where we're looking  at, you know, specific tool-building ecosystem,   restoration, and medical consequences. I think  there's a rich field of...let's say you had   one book, and that's the only book you had.  You could read it and reread it and reread it,   and you keep learning more and more. But as  soon as you start writing books, now you've   got millions of them. That's how I think of  the synthetic biology or writing of genomes. [Dr. Patrick]: I've read a quote...kind  of reminds me of the quote that I read  

from you that stated, "I have speculated that  essentially everything that we can currently   manufacture today without biology, we will  be able to manufacture with biology and with   potential advantages. Biology is intrinsically  atomically precise, and it's scalable to cover   the whole planet essentially for free."  That's pretty revolutionary, I mean... [Dr. Church]: Yeah.   That's accurate reflection of how I felt then  and how I feel today. Why is it reasonable?  

They are atomically precise. Biology does not  yet gracefully use the entire periodic table or   all the chemical bonds that you might want to make  out of that periodic pairs of elements. It comes   pretty quick...pretty close. It uses a lot of  inorganic bonds that might surprise some people. There are biological systems if you look  widely enough. And now we're not talking  

about necessarily, you know, your enzymatic tools,  which might have been implied in the previous,   but, you know, all the things that...all  the chemistry and physics that biology   uses. They can make things that  are fiber optics like and sponges.   You can make semiconductors, ferromagnetic  materials that help like compass. There are  

all kinds of dichroics and gratings that  generate colors, you know, and the list goes on. Materials that are used, either naturally or  where the enzymatic apparatus that is used   actually can...if you give it a new set of  elements, it will incorporate those. You   could say misincorporate them. But the point  is they're atomically precise in that you can  

reproducibly make a molecule with thousands of  atoms, and the next molecule over has exactly 1000   atoms and exactly the same configuration, you  know, off by less than an atomic bond in length. This is not something that happens  in Silicon Valley or other, you know,   worldwide manufacturing of silicon-based  circuits or any other inorganic circuits.   It is so far unique to biology. Another thing  that's unique to biology is ability to replicate,   so you can make a copy of yourself. So to make a know, the idea that a cell phone can  

make a copy of a cell phone is ludicrous so far,  but there might be a use of hybrid system where we   use biological inspiration...electronics  inspiration to make hybrid devices that can   replicate use of the full periodic table  and do, you know, a few things that   electronics is a little bit better at, better at  telecommunications at certain wavelengths, very   hazardous wavelengths like X-ray and gamma, as  well as the other end of the spectrum, the radio. [Dr. Patrick]: Let's talk about how writing  the human genome may help us better understand   it. So Francis Collins described the working  draft of the human genome as the first glimpse  

of our own instruction book. But today, many  scientists believe that to truly understand   the instruction book, we also have to  write it. Can you explain why that is? [Dr. Church]: Right. Well, I'm not sure  I would say, have to, but it is certainly   very advantageous. I should mention that we  don't even have the full instruction book  

of any human being yet. We declared victory  in 2001 on a kind of a rough draft of 92%.   Actually, it was considered the final draft of a  rough draft in 2001. It was final draft in 2004,   but it was still haploid, meaning it was just  one genome, while all...essentially, all of us   are diploid, inheritance from mother and father,  except for our gametes. So, the sequence we have,   the one human genome that we have is not of  a gamete. It's of a strange haploid cell.

But that's not the big barrier to understanding.  The big barriers, as you say, order to   understand how something works and also in order  to develop new technologies, you need to be able   to write and edit and alter. And you understand it  because you'll say, "Gee, I have no idea..." It's   like reverse engineering electronic circuit or  some software. "So I have no idea what this code   does. Let's change it." And then you say, "Oh,  that changes the calendar. Okay. So then that code   does calendar." Or in case the biology, you'll  take a piece out, and now it no longer handles,   you know, glucose. So you say, "Okay, that's  part of the glucose monitoring system." And you  

can just get through that, and you can get to more  and more nuanced changes for discovery's sake, but   it's often entangled with not just discovering,  but making useful synthetic biology. You'll have a   challenge that you'll have  out there, and that will drive   the reading and writing  technology forward. It will drive   our creativity in terms of how these things can  positively influence society and ecosystems. [Dr. Patrick]: What's the goal of writing a  large or a whole genome or an entire chromosome?

[Dr. Church]: So there are a few ideas that  have come up, where something at a genomic   scale is more desirable than a single gene.  So a huge fraction of recombinant at the end,   so the GMOs and synthetic biology, historically  has been changing one or two genes. It doesn't   make sense to synthesize whole genomes if you  just want to change one or two genes. But more   and more, we're seeing advantages of changing so  many genes. You might as well rewrite the thing. As an example of that, we have a project  to change the genetic code to make   any cell resistant to all viruses. And we just  published a paper where we think we did that. And  

the way that it works is that the virus...all  viruses, as far as we know, depend on the host   genetic code, the translation ribosomal machinery.  You can change the code without hurting the host.   The host could be a cell. It could be an  organism. So far we've only done it in one  

industrial organism, E. coli. But anyway, if  you change that enough, the virus can't mutate.   There'd be too many changes that are required to  get the virus to be back to its healthy state. And we think that this is  completely general in that,   essentially, every plant, microbe, and  animal on earth, shares a very similar   genetic code to one another, and in any case,  have a genetic code that they share with the   viruses. And if you take it offline, change it  enough, like sometimes as few as two codons,   let's say two codons, a code for serine,  leucine, and arginine are our favorites ones   because they have so many codons for each. They're  triplets of ACG NT, so like AAA codes for lysine,  

the amino acid lysine. There's 64 of those, and if  you change one, you get a new genetic code. If you   can change two, and now you get something that's  multivirus resistant. So that's an example   where you have to make so many changes, tens of  thousands of changes genome-wide. And they're   interspersed throughout the genome. You might as  well just synthesize it, and that's what was done.

Another example is of the extinction. There are  a number of changes you might have to make in   order to bring back some physiology like cold  resistance and all the traits that go along   with cold resistance, may be scattered around  enough that you' can think of it either   as highly multiplex editing or as a complete  rewrite. And even when you do a complete rewrite,  

you're not changing every single base pair, all 3  billion times 2 bases. You're leaving them mostly   intact. You've chemically synthesized it, but it's  still useful to think of it as a lot of edits. The maximum number of edits we've done by editing,  meaning having an enzyme that's targeted at a   particular place, is 24,000. The maximum we've  done by synthesis is almost the same amount,   although we have synthetic projects which  are now getting close to done at 60,000.   But then we're going to take the editing up to  a million pretty soon. They go back and forth.   There's a technical leapfrogging that goes  on between editing and writing of genomes.

[Dr. Patrick]: This, sort of, moonshot goal of  changing genomes or writing large genomes in a   way writing, editing them, where, you know,  as you mentioned, you make let's   take a human cell in a Petri dish,  make it resistant to viruses or,   you know, make it capable of synthesizing  essential micronutrients that we usually   have to get from our diet. Like, even if it  just sits in a Petri dish forever, and that's   the only place it goes, to me, there's something  very just fundamentally, you know, awe-inspiring   about that. Is it, kind of, like, along the lines  of your thinking with doing some of those things? [Dr. Church]: Yeah. I think the community,  the synthetic biology community has responded   in the same kind of awe-inspiring the initiation  of this kind of project. I hesitate to call it a  

moonshot because I actually think the moonshot  was not as inspiring to me as the satellites,   the GPS satellites, the weather  satellites, and, you know, surveillance  of land. And the same thing  goes for other big projects. The Genome Project wasn't as impressive  to me as reducing the cost project, $1000   Genome Project, sort of, the technology  development. And the Manhattan Project   was certainly not as attractive to me as say  the projects for nuclear fusion, which could   have...all of these things could have started much  earlier on. They sound may be a little bit harder,   but what they have in common is they're  very much more consciously aimed at positive   societal consequences. And I  think it's a little easier to get   everybody excited about these, sort of, things.

And I think being able to make  industrial microorganisms,   plants, and animals are important for  ecosystems and agriculture and human   stem cells. They won't stay in that Petri  plate. They will make their way into   cell therapies in humans. And if we're going to  fix something that's broken that you can fix with   blood cells, you might as well have those  blood cells be resistant to all viruses   as well if that is shown to be safe and  effective by the FDA and similar organizations. [Dr. Patrick]: You, kind of,  alluded to this earlier, but   how do you think the Vertebrate Genomes Project  will affect the field of genetics and biology? [Dr. Church]: So the Vertebrates Genome  Project, I think, is just indicative of  

our wish to sequence the whole biosphere.   Vertebrates in particular are helpful because  they often constitute keystone species   in the wild. And I hope...I think there's a reason  to believe that we will be restoring more and more   of the non-urban environment to wilderness.  Certainly, you can see about 1000 successful  

rewilding projects, a local rewilding.  So, the most famous one is probably   restoring the wolves to Yellowstone after 70  years. They had a typical keystone effect.   That ripple effect was anticipated and  worked out, which was they changed the   abundance of large herbivores, which then  changed the abundance of the willows and other   trees, which changed the beavers' behavior  which changed the lakes, which resulted in   aquaculture. So just introducing one vertebrate   had all this ripple effect. That's one  reason to do it, but there are many others. And if we are causing the extinction of many  species, we are also causing the hybridization,   which is the creation of new  species. It's not clear that we're   making extinction faster or more significant  than hybrid than new species. I think our  

gut feeling is that we are, but it's not proven  yet. But in any case, we need to do that survey   to see in detail what we're doing,  and in some cases, we need to   freeze away as many organisms as possible. But  we shouldn't be confused that freezing it away or   putting it in a database doesn't mean that it's  going to be easy or even possible to restore.   We need to do everything. We need to document,  freeze, and protect what is already there by   shrinking our agricultural use possibly by, you  know, 10 or 100 fold. I think that's totally  

feasible to do with synthetic biology  and other new tools that we have. [Dr. Patrick]: Can you talk about the advantages  of perhaps computer-aided design of genomes, the,   sort of, aspirational software, heart and soul  of the Genome Project, right? So in particular,   I'm curious about advances in AI like those  coming out of DeepMind such as the AlphaFold,   and if they have special relevance  for this, sort of, complex work.

[Dr. Church]: Right. So the genome  consists of, 1% of it codes for proteins,   and an AlphaFold is focused mostly on  the proteins. There's some software for   folding RNA and folding even the genome  itself. That can either be predictive or   it can be measured. So there's a lot of software  that's used for looking through microscopes and  

determining the structure and try and correlate  that structure, again, by synthetic biology.   You say, "Let's change the shape, not just the  sequence, and see how that...see what function   that affects." And that trial and error can go  very quickly or even exponentially. Once you   get going, you see the patterns and you start  testing more and more sophisticated hypotheses.

But AlphaFold is not the only way to do it. So  there are other machine learning-based methods,   in fact, machine learning plot coupled with   multiplex libraries, which can be in the millions  or billions of synthetic molecules that act   as...there are subtle variations or sometimes  not so subtle various ones together. If you   do machines and everything plus mega libraries,  you're focusing on functionality rather than on   structure. AlphaFold predicts a 3D structure.  And to illustrate this, you have...let's  

say you take a serine protease. It's called  a serine protease because there's a very   key serine right at the active site. And that  serine has an oxygen that's part of the mechanism.   If you change that oxygen, that hydroxyl to a  hydrogen, it now becomes an alanine, and it's   completely functionless. But the three-dimensional  structure is completely preserved. It is  

atomically precise throughout the  structure, but it's a dead enzyme. So what's more interesting, I think, for most  practical applications is studying what functional   consequences are of substituting. And that applies  not just to proteins, which AlphaFold predicts,   but also the RNAs and DNAs. You want to know what  the landscape of functionality is. And that can be   done partly by phylogenetic evolutionary trees,  where you line up. We now have tens of thousands  

of examples of almost every major macromolecule  in the cell, proteins, RNAs, and DNAs. And then using that, or you can...if you feel  that's not enough that evolution hasn't provided   you with enough diversity for your machine  learning, you can generate your own data set. So,   when they were learning chess, and Go, they would  have the computer play these games against itself   to generate more data. Big data is good in  the case of machine learning. And in our case,   we use these mega libraries, these millions and  billions, even trillions, that act as a kind of a   wetware computer. It can do all this computing,  and you can read it out in terms of the sequencing  

that you were talking about earlier and barcodes.  So you can barcode all these molecules and   combinations of molecules. And so you can think of  these synthetic biology libraries as an honorary   computation device, what you use together with  the machine learning, which is typically done on   a classic von Neumann machine, meaning an ordinary  kind of computer that most of us would recognize. [Dr. Patrick]: In your opinion, how  has the idea of biology as a software,  

reading, writing, programming, and  debugging, sort of, held up over time? [Dr. Church]: Well, metaphors are imperfect. I  think the advantages outweigh the disadvantages   of using these metaphors. I'm a programmer since,  you know, the mid-60s as a pre-teen, and I've been   programming both computers and biology. And I find  that the metaphor really works for me personally. Where it breaks down a little bit is when  you say that your goals should be set by   the goals of the metaphor, in other words,  that in the early days of synthetic biology,   there were multiple camps. And one of them  was the camp where we're going to have   "AND" gates and "OR" gates, and  "if-then-elses," and all the Boolean logic   that might characterize a certain  category of computation electronics. And I felt and I still feel that there's  a lot to be...a lot of interesting biology  

that occurs with analog circuits.  And we've kind of lost track (or   some of us) have lost track of  that key component of electronics,   but it is there. But anyway, the analogs,  there's the evolution, where you, - typically,   when you make a cell phone, as far as I know, you  make a very small number of prototypes that are   very similar to one another, and you test  them out. But in biology, like I've said   a couple times now, you can make billions and  trillions, and you can do accelerated evolution,   while with most, you know, bridge building  and building trains and jets and cell phones,   you really don't have that luxury of making  trillions of them and seeing which one works best. [Dr. Patrick]: How fast is the field  of synthetic biology advancing?   Are you excited about where the field's  going? Do you have any concerns or fears? [Dr. Church]: Yeah. I would say both excitement  

and concerns. And I think that applies to  all technologies. I think that we need more   radical and just... You know, it could  be positively disruptive, but you have to   think of all the potential negatives. So, it is  happening exponentially. How fast? It's doubles   at least once a year. Sometimes we'll get a  factor of 10 per year as measured by both reading  

and writing DNA. Most of the 10, 20, 30 million  fold has occurred within the last decade or two.   So it's potentially faster than  Moore's Law for electronics.   And it has, kind of, this atomic limit that's very  comfortable programming precise atomic positions   using biology. Now, those sorts of tools  we've got. We're getting more and more. Now, on the negative side, we need to be...we have   good government agencies that we should be very  supportive of, both intellectually and financially   like the FDA, the EPA, the USDA,  and their foreign equivalents.  

These are not sufficient, though, because  they're things like equitable distribution   of technology. We want everybody on the  planet to least have a chance to,   not only theoretically have access to because the  price is right, but also have the education or the   dialogue that allows them to evaluate whether know that it exists and to evaluate,   what, they want to use it or not  and whether it's good for them. So, it's not sufficient to just, like, lob  over a free piece of software like, you know,   GPS software, and they don't know what the  satellites are doing and so forth. Now,   modern uses of GPS like Google Maps is fairly  accessible, but there's almost no technology   that's completely equally accessible.  You know, clean water, roads, you know,   cell phones are getting accessible in remote  parts of the world. The only thing that is truly  

accessible equally that I can think of offhand  is a biotechnology, and that is smallpox. It's   completely extinct, and so you don't have to  constantly be bringing out a new drug or a new   vaccine that maybe not everybody can afford,  every government can give out for free. But   smallpox extinction is something we can give  out for free generation after generation.   So, I'm looking for more and more  of those. You know, bringing down   the price of reading and writing DNA  by 10 million fold is just a start.  

We should look for that in almost  everything we do with synthetic biology. [Dr. Patrick]: Do we need the NIH  to embrace the Human Genome Write   Project like they did the read? Or  is that, sort of, already happening? [Dr. Church]: I think it would be  lovely if they did. I think we need to  

pursue multiple routes, philanthropy,  industry, government, multiple...again,   having DOE and NIH in the game was helpful, but  there's a number of others that are interested   in the Genome Project Write,  NSF, ARPA, DARPA, and IARPA.   And these have supported it in various forms, have  supported synthetic biology, Genome Project-write,   has, yeah,'s the heir of  all those wonderful funding sources. As long as it has a vision that includes something  that is net positive for society, there will be   a way and hopefully multiple  different ways for different   flavors of it. One of the early flagship  challenges is this resistance to all viruses   in multiple organisms. I think that's  something that can be clearly articulated, and  

it has, I think, a much higher positives and  negatives. And most of the negatives, I think,   we can mitigate by thinking of all the possible  downsides and how to protect against them. [Dr. Patrick]: Let's take a dive into some of  the gene editing tools and whatnot a little bit.   Over the last 10 years since Jennifer Doudna and  colleagues first developed CRISPR gene editing,   there's been a lot of excitement about it. Your  lab was one of the first to show that gene editing   using CRISPR-Cas9 could be done in normal human  cells. So acknowledging the undoubtedly, like,  

revolutionary impact of CRISPR, do you think  it's possible it's been overhyped from the   standpoint of the public at large not having a  more comprehensive or appropriate understanding of   where it, sort of, fits within the  existing toolsets of synthetic biology? [Dr. Church]: Yeah. I hesitate to use the  word hype because it implies somebody is   being hyperbolic. It was kind of a team effort's wonderful that we're bringing it,   any part of reading and writing genomes  in synthetic biology to people's attention   or science, for that matter.  This is one of the more exciting   things in science right now is getting  people... It's not just about CRISPR. First of all, you can't really edit if you can't  read. So I think the big revolution here is being  

able to read the genomes. You read them at the  beginning to find the tools. You read them again   to decide what your goals of editing are. And then  you read it a few times to make sure your editing   is going well. Then you read it again to see  that the edit that you made has the physiological   consequences, which increasingly we're using DNA  reading as a way of or RNA reading to see how the   physiology is going, the so-called epigenomics  for physiology. So, that reading is important. Another thing that's important is there  was some pretty good editing methods   that are still in use to predate CRISPR,  notably homologous recombination, which   Smithies and Capecchi got the Nobel prize  for decades before Jennifer and Emmanuelle.  

I'm a big fan of Jennifer and Emmanuelle, by  the way. We've started a few companies together,   Jennifer and I. But there's homologous  recombination, which is very powerful. It's   precise and over large distances, while CRISPR  tends to be imprecise and/or small in scope. Another one that dates back two decades  before CRISPR is SSAPs or lambda red as it's   sometimes called is a way of getting precise  editing. And that's what we actually used  

to...around 2009 to make libraries  of billions of edited cells   in a day, a single person. That shows some of  the power. And the other evidence of its power   was that that was...the first completely recoded  genome was done mostly a combination of SSAPs and   recombinases, which is also very precise.   CRISPR was basically a hatchet, and  I sometimes call it genome vandalism.

So, I think we need to embrace all of these  methods and a few more that are coming now,   deaminases that can be done with and without  CRISPR and more sophisticated SSAPs and   integrases, transposonases. So, it's a rich...  I think it's okay if the public just latches   onto one aspect of it, but it'd be is  nice whenever a more nuanced and visionary form   where it illustrates the importance of reading  and other more precise and larger scale editing   and writing where you write...synthesize something  from scratch, and usually pop it in by  

could be popped in by CRISPR but more commonly  is popped in using recombinases or integrases. [Dr. Patrick]: What about some of the existing  capabilities of, you know, gene editing therapy,   you know, things that have been done, you  know, in transgenic models for, you know,   a decade at least or more, you know, so deleting  versus addition, you know, of a missing gene? [Dr. Church]: Right. Yeah. So, you can  think of CRISPR as a subset of editing.   Editing is a subset of genome engineering,  and genome engineering is not a subset of,   but it's kind of a Venn diagram overlapping set  with therapies and GMOs and so forth. So, most   gene therapies that have been approved are adding  genes, and this is done typically without CRISPR. And, you know, when you have a genetic disease,  you're missing a gene, so you don't really want   to edit necessarily. You want to add it back  in. As you grow older, a lot of your gene  

products...your gene expression  is dropping down. One way to deal   with that would boost it back up, and  we've explored these sorts of things. The use of gene therapy, putting in a missing  gene, and, in fact, editing for that matter   for rare genetic diseases is by its nature  expensive. It's millions of dollars per person   over a lifetime, partly because the R&D costs and  the palliative care and all sorts of health care   for someone who has a very severe disease that  might have died young years ago, but thanks to   the Orphan Drug Act and others, they can now lead  closer to normal life but at millions of dollars. It's great that we'll keep developing these  gene therapies and better ways of delivery. Oh,  

I forgot to mention, delivery is another thing  that's sometimes missed when people just shout   CRISPR. You have to get it to the right place, the  right dose, the right time, maybe to turn off when   it's done its job. So keep it off target...keep it  off target, so minimum. So anyway, the delivery. An alternative to this expensive solution is a  much lower cost one, which is genetic counseling,   where you basically tell people before  they get married, before the preconception   or sometimes post-conception, that they're  at risk. They themselves are carriers. They   are healthy. They will be healthy. But if they  marry someone that has the same carrier status,   they put their children at risk.  So there's the two methods.

I think a lot of the Western world tends to  go towards the interventionism, you know,   reactive medicine where we'll spend millions of  dollars, you know, by not pursuing preventative   medicine. But the preventative medicine, in  this case, is, you know, low hundreds of dollars   just to know yourself to know how to keep your  children healthy by making preconception choices. [Dr. Patrick]: Yeah. I will probably circle  back to a little bit more of that in a minute,   but since we're talking  mentioned a few other types of,   you know, gene editing, the deaminases, and  you've talked about this multiplex editing.  

What does it mean to be able to go, you know,  to performing 26,000 edits or you said, I mean,   a million...potentially a million  edits in human cells, you know,   versus the previous record of something  like 62? I mean, what applications does this   most impact? Is it, you know, the large genome  creation or tissue engineering or germline? [Dr. Church]: Right. Our previous record of 62 or  42, depending on how you count it, was in pigs,   and it was for tissue engineering. It was  germline. So germline is kind of off the   table for humans, in part because there  is no clearly articulated medical need,   and the time for discovering safety and  efficacy is over a lifetime which is,   you know, unaffordable and ill-advised. So anyway. But germline certainly work, gets into humans via  pigs. This has been...the idea of transplanting  

organs from animals to humans goes back at  least to the 1960s, where a chimpanzee kidney   survived for nine months in a school teacher  who went back to teach and, you know,   was normal for nine months. That was the exception  then and it would be the exception now except for   the synthetic biology that we do on the germline  of pigs, which now made it into many pre-clinical   primate transplant trials, pig-to-primate, and  a few pig to human trials that are going on. Primate survival looks like around  600 days so far, and they're still...a  

couple of them are still alive at 500, 600  days. We're going to keep improving these.   That's in the order of 40 to 60  edits per genome in the germline.   The multivirus resistance requires more  than that. Some things that are done for   diversity and ecosystem maintenance may involve  even more. They're a type of tape recorder,   something that's called a flight recorder,  so it's analogous to planes, that   record a lot of data. But typically, you don't  read it, so a lot of writing, not much reading,  

unless the plane goes down. Then you'll look at  selective regions for debugging what went wrong.   That same thing could be put into the bodies  of plants, animals, and even humans because   it's a very compact reporting device of the  physiological states of every cell in the body. We've shown this works, sort of, in the scale of   60 to 24,000. That's probably...our first  effort at making a million edits will be in   the form of these molecular flight recorders.  So those are a few examples, but the number  

will grow as soon as we get more than a handful  of people working on these visionary projects.   But we'll see a blossoming of all  sorts of creative uses of making   multiplex editing. I think non-multiplex  editing will become the exception. [Dr. Patrick]: So as you mentioned your lab, you  know, gene-edited pigs, and you enhance them by  

making them resistant to some retroviruses. Do  you think, you know, as a more visionary, kind of,   question, that you could use, you know, more  precise gene editing, the deaminases or CRISPR,   whatever, to eliminate viral spillover  events from livestock to humans? So, I mean,   there's a lot of viruses that originate from  livestock when we're raising animals in captivity. [Dr. Church]: Yes, this is important. The viruses  that we got rid of were endogenous retroviruses,  

meaning they're built into the pig genome of  every pig on the planet. And they have been   shown to infect human cells and to replicate and  go into other human cells. So this is particularly   bad scenario in immune-compromised patients. And  the FDA recognized this decades ago and really   was, I think, pleased to see progress being made  on eliminating them from the germline of the pigs. But in addition to viruses that are built  into the germline of animals and humans,   there are viruses coming in from outside.  And we just published the first example. This   is with Luhan Yang's team. She was a graduate  student and a postdoctoral fellow in my lab and  

co-founded eGenesis and Qihan for making cell  therapies and organ therapies. But anyway. As a side project, we published a paper on getting  rid of African swine fever virus by making CRISPR   to attack the viral DNA. What CRISPR originally  evolved to do is to take out bacterial viruses.   We think this is the first case of using CRISPR  in a practical sense for eliminating mammalian   viruses from the environment. It's  using CRISPR against mammalian viruses. But zoonotic diseases is bigger than that.  If we could make a huge fraction of plants,   animals, and humans resistant to those  viruses because of their genetic code,   that actually anticipates viruses we haven't even  seen yet. It should handle all natural viruses,   so like, you know, Marburg, Ebola, HIV, CRISPR.  These would not have been surprises. They would  

have been surprises to scientists but not to this  cancer resistance...sorry, virus-resistant cells. [Dr. Patrick]:   So it sounds like CRISPR seems to be uniquely  positioned for that, you know, type of use. [Dr. Church]: Well, not necessarily... so I like  CRISPR. I love CRISPR. I personally benefited from  

it, but it is...I like to balance it. There are  other nucleases that some people claim are more   specific, less off target. There are deaminases  that don't involve CRISPR. So I wouldn't   say...term unique is too strong. We have a lot of  tools in the toolbox. A lot of it has to do with   delivery and testing too. Testing is a big  deal, which is somewhat swept under the rug  

when we're's just like, "All we have  to do is design, you know, CRISPR to take care   of everything." But there's a lot of reading  and, you know, synthesis which isn't CRISPR. And   then the delivery and testing. So it's  integrated whole. It doesn't require CRISPR. [Dr. Patrick]: So another technology  would be base editing, which, you know,  

doesn't involve double-stranded breaks and DNA.  And I know there's a phase 1B trial with the   PCSK9 target. They're targeting at gene target  for the liver as a potential treatment for the   hypercholesterolemia familial form. You know, I  just read about this recently and pretty excited.   You know, I know people that are taking the  anti-PCSK9 antibodies, which are very expensive,   and you have to get them every two to four  weeks. It'll be interesting to see, you know,   if the base editing could be a  one-and-done treatment, do you think? [Dr. Church]: That is one of the  advantages of gene therapy in general,   whether it's editing or adding genes.  

Yeah, I think that a lot of our diseases are  diseases of wealth. I mean, we used to have   much more active vegan diets, you know, low in  overall carbohydrates mainly because it was low in   calories altogether. And so diabetes and  some of the cardiovascular diseases didn't   affect us. Also, we didn't live as long  in general. So it was less of an issue. But PCSK9 looks like it's shaping up to  be a terrific example of something that basically   all humans can be thought of as having the same  disease, and therefore it's a large market could   be low cost. Aging is another or a variety of  age-related diseases that might have a common core  

where we are programmed to die at a certain age.  The mice diet at two years old, bowhead whales at   200, humans somewhere in between.  And so that's probably negotiable. Now, PCSK9 is not solving aging in general. It's  a very specific thing that may be common to most   humans. It was de-risked because there were a  few humans that were walking around that were   basically double null for both copies of their  PCSK9 from mom and dad. That kind of showed   us that it was going to be safe and effective,  although there's still quite a bit of long-term   studies that have to be shown to make sure it  doesn't cause early onset neurodegeneration in   the particular way that we're implementing it,  which is not germline, which is how it...the  

people that previously had PCSK9 nulls  for germline via natural mutations. [Dr. Patrick]: Since you mentioned  aging, it sounds like...and I think you   think aging is fundamentally a program.  It's a really interesting idea,   one that's's got many  implications, especially when we're   thinking about whether or not we can mitigate  aging or potentially cure it. So could you talk  

about your perspectives on that, what you think  it might mean for the future of human aging? [Dr. Church]: Well, so what we're mostly aiming  for is serious diseases of aging. They may have   relatively little in common in terms of what organ  is affected, you know, what system. There may be   9 or 10 different pathways that can be affected,  the so-called hallmarks of aging. So it's a great   diversity. There is a school of thought that  they have a small core set of systems biology,   systems medicine that if you get at that core,  you can change the clock. You can make it shorter  

as in mice or longer as in bowhead whale. And  then you can rejuvenate. There is rejuvenation   that occurs whenever you go through gametogenesis  and fertilization, sort of, normal reproduction.   You reset the age clock, and you also reset it  when you do something unnatural, which is cloning   where you take the nucleus from an old animal and  put it into rejuvenating environment of an egg.

And there's also a rejuvenation process that  occurs unnaturally when you use transcription   factors. These are DNA binding proteins  that regulate the expression of genes. Four   of them so-called Yamanaka factors or OSKM as an  abbreviation. These will very convincingly take a   very old cell and turn it into a very young cell,  maybe like, say, a skin cell from 80 year old. It   will take on many of the characteristic...most of  the significant characteristics of an embryonic  

cell in that it can produce almost all the tissues  of the body, probably all of them, except for the   extra-embryonic. And the parts aren't part of the  body that contribute to the early embryogenesis. So those are a few, and there are many  others that shown that the blood...what's   in the blood of older and younger animals  can influence one another. The older blood   makes the younger ones old, and the young blood  makes the older animals younger by a variety of   biomarkers and disease-related things. I fall into the...there's two schools, at least  two schools of thought here. There's a damage  

school where you have to go in there and kind of  micromanage a surgery to fix the damage as your   surgeon might fix a damaged broken arm.   Then there's the epigenetics school where  it says that if you convince the cell that   it's young, it will fix itself to a large  extent. There will be some exceptions.   And we've seen that over and over these, you  know, fertilization, cloning, and OSKM factors   are three. Again, the bloodborne  factors are four examples. And we need to reset all of the mechanisms, all  nine hallmarks of aging in probably all of the   tissue types of the body, at least the stem  cells for each of the body parts, to have a shot   at...we're aiming for youthfulness, lack  of age-related diseases, so you should be   youthful at an age where you normally  would be unhealthy, even if you're not   dying of any particular disease. That's what  we're aiming for. It will be approved by the FDA  

for specific indications for  specific diseases of aging. But then if it really is getting at the core  of aging, will it be immediately applicable to   almost all of the diseases of aging? And aging  just affects everything, almost every morbidity,   mortality, even like accidental death.  Infectious diseases like COVID has a very...and   its cognitive consequences have very  steep increases at around 60 years old. [Dr. Patrick]: So I recall, like, one of  your former publications. I forgot what   year. I think it was a PNAS one where  you did gene therapy and added three  

transcription factors to rodents, to mice, and  there was some reversal of aging or biomarkers.   And it was a TGF beta receptor and FGF21 and... [Dr. Church]: Alpha-klotho. Yeah.

[Dr. Patrick]: Klotho. Yeah. [Dr. Church]: Those were not transcription  factors. Those were soluble factors. [Dr. Patrick]: That's right. Okay. [Dr. Church]: But we also did a separate  experiment where we took three transcription  

factors, OS and K, of OSKM, separate  experiments, but delivered in similar ways,   adeno-associated virus. Then we did some other  experiments with follistatin and telomerase,   so it affects the ends of the chromosomes,  the telomeres. Follistatin is mostly muscle. But each of these has,   you know, reproducible impact on hallmarks  of aging, on biomarkers of aging,   and diseases of aging. And it affects multiple  diseases with about seven different categories   of diseases that we've done now in mice. A  subset of those have been tested in dogs now,   aiming for a veterinary product.

The three that you mentioned, I think, have  slight advantages, the fibroblast FGF21   and TGF beta. I should mention, that is an...the  other two are natural alpha-klotho and fibro   FGF21. But the TGF beta receptor is normally  membrane-bound. We made a soluble form of it. So   all three of them tend to be soluble, and  they effectively act like the young blood in   rejuvenating these mice and dogs, and hopefully,  soon there'll be in human clinical trials.   And that has the advantage  that we don't yet have a   good way of delivering to every cell in  the body or every stem cell in the body.   Remember I said delivery was very important  and it's so important. We need to fix it. But anyway, in the meantime, we can  deliver the genes to a subset of cells   in various parts of the body, and then those  subset will deliver the proteins, those three   proteins you mentioned, more broadly. And so you  can, in principle, affect the whole body by that  

combination of two kind of tiers of delivery.  That's the idea behind that. And the dogs is   a particularly good conduit to humans because  they're large mammals like humans. They live   often in a human environment, eat  sometimes eat human food. They have similar kind   of emotions and bonding and eye contact and  all the rest. And the owners can really sense  

their states so they can get at more subtle,  positive and negative consequences earlier.   So anyways. And it's a product now that  people care deeply about their pets. So,   I'm very excited about, you know, Rejuvenate  Bio, and Noah Davidson was a postdoc in my lab,   and he started Rejuvenate Bio. It seems to  be shaping up to be a good product line. [Dr. Patrick]: Yeah. It'll be exciting to  follow these results. You kind of answered  

one of my questions, which was, you know, a lot  of the rodent research, particularly with aging,   not a lot of it translates, you know,  to humans. And, you know, one thing,   in particular, I think, that is  important to consider with human aging   is that, you know, humans are exposed to  disease and viruses. We're not in this,   like, sterile lab environment, and we have these  periods of real, like, illness and muscle disuse,   and it's just very different than a rodent.  But there's advantages to   using rodents. What do you think? Why  should we use rodents to study aging? [Dr. Church]: So, as a prelude to the experiment  that you mentioned where we use three soluble  

factors in dogs, we did 45 different gene  therapies singly, one at a time, in rodents,   mice to make find the subset of  three that we wanted to test in rodents in   combinations...various combinations. And then  once we had settled on the 3 factors out of 45,   then we moved into dogs, and  then we'll next move into humans. So, you shouldn't blindly expect the rodent  model to work. They're advantageous because   they only live two years, so it's easy to  see a longevity effect. We're not always  

looking for longevity. We're usually looking for  aging...reversal of age-related diseases because   that's what the FDA wants as well. But we do  occasionally measure longevity in the case of   the follistatin and telomerase treatments. Those  did show a pretty significant...very significant   longevity effect on the rodents. So, even primate trials can be deceptive.  There's a lot of differences in the way that  

they're treated. In fact, in certain ways, dogs  have, I think, a more similar environment, maybe,   you know, more to their liking, more natural for  them since they've been our companion for tens of   thousands of years. But even dogs are not an ideal  of larger... You know, pigs are very close to   humans and their organs. That's why they're being  used as transplants, but they're also imperfect. So an alternative to all of the animal models  is human organoids, and those are getting   increasingly accurate. Also, we can basically skip  a lot of the developmental biology and go straight   to a particular organ. We can't go via normal  human development because there's a ban on letting   human embryos develop past 14 days in a dish. But  it's considered ethical to make an isolated heart  

or even heart plus lungs, plus muscle, plus  liver, plus neurons, but not a whole brain.   As this is rapidly developing, we're exploring  collectively with diverse set of voices,   you know, how to do this in a way that's humane  to the animals or develop know,   completely animal-independent strategies for both  testing therapies, but also being the therapies. The organoids are increasingly moving their way  into clinical trial. So for example, we showed   restoration of a demyelinating disease in rodents  by putting human organoids, brain organoids that   contain...that remyelinate and are protected  against the demyelinated mechanisms. So they're  

supercells and that they are not just replacing  the cells that were damaged because they just get   damaged themselves, but they are resistant to the  damage. And I think that is repeated over and over   again in both cell therapies and organ therapies  we're developing, is that the goal is not just   to deal with the organ shortage or it's to have  something that's enhanced is immunologically   superior that is less rejected, resistance to  pathogens, resistance to cancerous senescence,   cryopreservation. All of these things  have been demonstrated in animals,   and now we want to either get them into  the humans via cell or organ transplants. [Dr. Patrick]: If I remember correctly,  you enhanced the brain organoid to...I   think you edited it from APOE4, which if you're  homozygous, you have like a 20-fold increased   risk for Alzheimer's to APOE3, so making it  more resilient against Alzheimer's, I guess.

[Dr. Church]: Correct. So  that's somewhat...depending   on how you look at the composition of various  genes, now that particular case E4 is not   the predominant allele. And so you might call  it an enhancement. PCSK9 is very rare in the   population, and so if you make everybody or a  large fraction of population PCSK9 negative,   that could be called an enhancement relative to  the average. But it's not an enhancement relative   to the minority. In the case of APOE3 or even  APOE2, which is...that is rare than the E3 plus   E4, and that would be an enhancement. But E3  over E4 is probably about closer to average.

But this whole definition of or this whole  obsession of an enhancement seems odd   because a huge fraction of our popular  technologies are enhancements, you know,   a smartphone makes us smarter in a certain way.  It can also make us dumber. But the point is it   has the capability of helping us navigate, help  getting access to the world's facts and factoids.   Cars, jets, so forth enhance  our ability to locomote. So I think increasingly, we're going to recognize  that the biotechnologies we're producing are not   just reactive medicine where we're putting  out fires. They're preventative medicine   where we' enhancement, we're protecting  ourselves. Like vaccines is a beautiful example of   enhancement that protects us. We're far healthier  than our ancestors were because of vaccines.

[Dr. Patrick]: I kind of would like to just  move into...a little bit to the germline   editing. We've kind of talked...alluded  to it a little bit here and there. But   you've said and previously that you felt like an  obligation to be balanced. But you've also, of   course, said it's important to focus on outcomes  and not to rationalize addictions to future. And   you're even involved in calling for a  temporary moratorium on germline editing? [Dr. Church]: No. [Dr. Patrick]: No.

[Dr. Church]: I was opposed to the obsession with  moratorium because we already have a moratorium on   all new drugs. We don't allow anybody to use new  drugs that haven't been through the FDA testing.   So, yeah. So it sounds subtle, but I was  concerned that we would be developing  

germline where there's no need. But there's also  no need for a moratorium because we have very   good regulatory mechanisms for preventing that,  sort of, thing from happening at a market scale. Now, a moratorium would not do anything more at  the market scale and also would not do anything   more at the individual scale. Both the FDA...and,  in fact, most laws do not work on individuals   that want to break the laws that are willing to  accept the consequences or think they're above   the consequences. And that's what happened in the  case of germline. Someone either misinterpreted  

willfully the guidelines or didn't think it  was a law. In fact, he didn't get convicted   of germline manipulation. This is He Juankul  from China. He got convicted of, you know, not   following the rules for getting the consent of the  funding agencies and the patients and so forth. He actually did a pretty good job of getting  the consent by some criteria. He spent an   hour of videotaped counseling to make sure  they understood what they were getting into.  

But anyway, as far as I know, he was not convicted  of germline therapy, but something more nuanced.   And he's out now. The three years is up and he's  out. And as far as we know, the children are   healthy, which is more than you can say for the  most revolutiona

2022-08-27 03:10

Show Video

Other news