#077 Rewriting genomes to eradicate disease and aging | Dr. George Church

Gene Therapy Discussion

Today's episode is an incredible treat for those of you among us that are true, bona fide believers in the ability of technical innovations to potentially change the world and even foundations of biology and...

"Today's episode is an incredible treat for those of you among us that are true, bona fide believers in the ability of technical innovations to potentially change the world and even foundations of biology and life itself. My guest today is Dr. George Church. Dr. Church is a professor at Harvard Medical School and MIT and arguably one of the most important and accomplished geneticists of our time, with crucial contributions ranging from massive advances in genome sequencing to gene editing technology to synthetic biology, and generally the increasing sophisticated application of engineering principles to biology. 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. Dr. Church has described the key theme of his lab as the development of radical transformative technologies. Time and time again, Dr. Church has found himself in what he terms the exponential, participating in and observing advances so rapid that they defy the potential of our own collective imaginings. As new technologies present themselves, like gene drive, which allows gene engineering that can bend the laws of Mendelian inheritance, in other words, how genes are inherited, or multiplex editing, which could culminate in impressive feats like writing entire genomes from scratch, recoding organisms or cells to make them immune to all viruses, or producing universal donor cells for therapeutics, which could possess superhuman qualities like resistance to DNA damage, radiation, or cryopreservation. All of these things challenge our ability to intuitively grasp the difference between the world of today versus the world in possibly just a few short years. For that reason in particular, I value conversations like these tremendously. As we discuss controversial topics like embryo and germline editing, or the ability to promote changes that could alter the genome of an entire species, a technique called gene drive technologies. The greatest danger we have as a public is not having knowledge that can help us be better prepared to have productive conversations as these advances develop. In this incredible episode, we discuss the ability to change cells or even entire organisms at the level of the DNA so profoundly that viruses cannot infect and utilize their ribosomal translation machinery, a process called genetic recoding. We talk about how projects like the Vertebrate Genomes Project, a massive project to sequence all known vertebrates, may participate in saving keystone species, protecting or reintegrating genetic diversity once it's been lost, and participate in preventing or reversing the process of extinction. We discussed the genome project WRITE and the increasingly credible goal of being able to write large or entire genomes from scratch, starting with the novel synthesis of an entire human Y chromosome. We discussed the advance from CRISPR Cas9 gene editing to what is known as base editing and why base editing may be the key to unlock the full potential of gene editing, taking us from a technology that can only do a handful of edits to tens or hundreds of thousands, or maybe even one day millions of edits. We talk about how gene editing could be used to eliminate zoonotic viruses that spill over from livestock, how a type of genetic engineering called gene drive may take insects and make them unable to carry human diseases like malaria or Lyme disease. We talk about how Dr. Church's work on making animal organs suitable for human transplant by engineering them to be universal donors, but also the possibility to engineer potential qualities like I mentioned earlier, such as DNA damage resistance and other enhancements above and beyond those of ordinary human tissues. We discuss how Dr. Church is working on a combination gene therapy to reverse age-related biomarkers, focusing on soluble factors that can rejuvenate the whole body, similar to how factors in young blood revitalized old organs in animal studies. We talk about why he thinks initially developing a veterinary product for aging dogs and his xenotransplantation project may be the ideal pipeline towards creating therapeutics that can unlock human potential. His perspectives on controversy surrounding whether there can be responsible use of germline editing and complexities surrounding practical differences and how that's compared to embryo selection, and so much more. 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It's incredibly hard to go wrong with the premium Found My Fitness membership. Check that out at foundmyfitness.com forward slash premium. That's P-R-E-M-I-U-M, premium. Or learn about the premium podcast at foundmyfitness.com forward slash aliquot. That's A-L-I-Q-U-O-T, aliquot. Okay, I know everyone is chomping at the bit. I present to you the incredible Dr. George Church. Thank you, Rhonda. Let's see. Let's start with the gene. 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 invented his team 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 felt, you 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. And then that, but that was, 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. So my lab, I was transitioning from postdoc to professor, and my lab got one of the first two Genome Project grants. And then the NIH...it 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. 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. But as soon as some of the senior members of the visionary team like Jim Watson, who came in later, started 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. but it did so with then instead of some of the corner cutting was to not worry too much about repetitive sequences, which in the case of the fruit fly was about half the genome. It doesn't matter. And at one point, they were going to just do the coding regions, which was 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 as a whole, another topic. Do we need more reference genomes? And what are your expectations of finding new tools elsewhere in the evolutionary tree? Well, so yes, we certainly need more genomes. It's not just the reference, it's the population variation that's important. We want to...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's growing recognition that we can represent the reference as a diversity. We are finding tools in the genomes. So one of the nuances that developed, the first kind of recommendations for maybe the 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 limited, more limited. Almost by definition, we can explore more than currently exists, at least initially in narrow corridors where we're looking at 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 got millions of them. So that's how I think of the synthetic biology or writing of genomes. I've read a quote, kind of reminds me of a 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. Yeah. Maybe. Yeah. I mean, that's an accurate reflection of how I felt then and how I feel today. Why is it reasonable? So 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, but it comes pretty quick. It uses a lot pretty close. It uses a lot of inorganic bonds that might surprise some people. So you can make, 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 all, you know, all the things that, all the chemistry and physics that biology uses, they can make fiber optics, things that are fiber optics like in sponges. You can make semiconductors, ferromagnetic materials that help it like compass. There are all kinds of dichroics and gratings that generate colors, you know, and the list goes on. The 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, atomically precise, and that it can reproducibly make a molecule with thousands of atoms in it, and the next molecule over has exactly the size of thousands of atoms and exactly the same configuration, at least off by less than an atomic bond in length. So it's really, this is not something that happens in Silicon Valley or other 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 the ability to replicate. So you can make a copy of yourself. So to make a copy, the idea that a cell phone could make a copy of a cell phone is ludicrous so far. But there might be a use of a hybrid system where we use biological inspiration, electronics inspiration, make hybrid devices that can replicate, use the full periodic table and do a few things that electronics is a little bit better at. It's 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."

Gene Therapy: How To

You know, clean water, roads, you know, cell phones are getting accessible in remote parts of the world.

"Yeah, I think...I hesitate to use the word hype because it implies somebody is being hyperbolic. I think it was kind of a team effort of just...it's wonderful that we're bringing any part of reading and writing genomes and synthetic biology to people's attention, or science for that matter. This is one of the more exciting things in science right now. It's getting people... But 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. And then you read it again to see that the edit that you made has the physiological consequences, which increasingly we 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 that predate CRISPR, notably homologous recombination, which Smithies and Capecchi got the Nobel Prize for decades before Jennifer and Emanuel. I'm a big fan of Jennifer Emanuel, 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, it's sometimes called. It's a way of getting precise editing. And that's what we actually used around 2009 to make libraries of billions of edited cells in a day, a single person. So that shows some of the power. And the other evidence of its power was that 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, though, and a few more that are coming now, deaminases that can be done with and without CRISPR, and more sophisticated SSCPs and integrases, transposinases. So it's a rich, I think it's okay if the public just latches on to one aspect of it, but it would be nice, it 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 synthesize something from scratch and usually pop it in by some...could be popped in by CRISPR, but more commonly it's popped in using recombinases or integrases. 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 versus, you know, of a missing gene. Right. So, 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., 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 healthcare for someone who has a very severe disease that It 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 minimal. 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 they...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 are two methods. I think a lot of the Western rule tends to go towards the interventionist reactive medicine where we'll spend millions of dollars by not pursuing preventative medicine. But the preventative medicine in this case is low hundreds of dollars just to know yourself, to know how to keep your children healthy by making preconception choices. We'll probably circle back to a little bit more of that in a minute, but since we're talking about, you mentioned a few other types of, you know, gene editing, the deaminase, 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? Right. So we did 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's no clearly articulated medical need. And the time for discovering safety and efficacy is over a lifetime, which is unaffordable and ill-advised. So anyway, but germline certainly gets into humans via pigs. So 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 was normal for nine months. But that was the exception then, and it would be the exception now, except for the synthetic biology that we do on the germ line of pigs, which now made it into many preclinical 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 a couple of them are still alive at 500, 600 days. We're going to keep improving these. But 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. There are a type of tape recorder, sometimes 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 and 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 recording 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, and 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. So as you mentioned in 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 deaminase or CRISPR or 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. So... Dr. Yes, this is important. So 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 a 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 and eGenesis and Kihon 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. This is 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 these virus-resistant cells."

Alzheimer Prevention Discussion

Pigs are very close to humans in their organs. That's why they're being used as transplants, but they're also imperfect.

"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. Right."

Gene Therapy Discussion

And, you know, I'm just sort of interested in the public response to that sort of medical technology and use of it versus the CRISPR editor babies in 2018. If they were proportional.

"And, you know, I'm just sort of interested in the public response to that sort of medical technology and use of it versus the CRISPR editor babies in 2018. If they were proportional."

Vaccine Science Discussion

It's a set of technologies, tools, possessions. That multiplex editing will be something that won't be germalined, but it will be just as surely inherited.

"It's a set of technologies, tools, possessions. That multiplex editing will be something that won't be germalined, but it will be just as surely inherited. Right."

Gene Therapy Discussion

The latest round of vaccines are kind of in a format of gene therapy and are very inexpensive compared to most gene therapies that are typically $2 million.

"But the number of embryos that could be made by in vitro for desolation could skyrocket without in any way interfering with the germline and so forth by epigenetically reprogramming cells to become pluripotent stem cells, and then the pluripotent stem cells can become eggs. And then those eggs, they might be randomly mutated, and if you sequence enough of them, you'll find one that is what you want. So I said, if you haven't induced the mutation with CRISPR, it just happened the way it happens in the world. This is far from efficient compared to editing, but it illustrates how we have this kind of double standard, that if you do it, if you achieve the same goal, germline engineering, this way it's okay, this way it's not okay. It's same as GMO argument, that if you mutate a tomato or soybean by random ultraviolet mutation, where you're making hundreds of mutations random with no control, that's somehow more attractive than if you do a precise edit and you make sure the rest of the genome is clean and you haven't touched anything else. It just doesn't, you know, for some people that make sense, for other people it doesn't. It's like saying that, oh, if I'm going to, you know, fix my car engine, I'm going to, you know, throw all kinds of random chemicals and shotguns and stuff into it and hope that one of those things makes the right fix to the car. But anyway, I think that's what's going on in general line is very similar to what's going on in GMOs. You can radically change the plant species by one method, but not by another. You can change an embryo's fate negatively with chemotherapy or positively by IVF, but not by germline editing. It's double-think. It's a good topic of conversation, And eventually, I think it will sort itself out. What about understanding the unknown? You know, so there's a lot of genetic variants that are thought to be mostly deleterious or, you know, quote unquote, not beneficial."

Vaccine Science Discussion

So, I think one approach to...so the extinction of species is one part of it. So, for example, you could make mosquitoes resistant to malaria.

"So, I think one approach to...so the extinction of species is one part of it. So So you can do gene drives whose intention is to make a species resistant to something that's bad for a third species."