Making Sense with Sam Harris - #106 — Humanity 2.0

Episode Date: November 29, 2017

Sam Harris speaks with Jennifer Doudna about the gene-editing technology CRISPR/cas9. They talk about the biology of gene editing, how specific tissues in the body can be targeted, the ethical implications of changing the human genome, the importance of curiosity-driven science, and other topics. If the Making Sense podcast logo in your player is BLACK, you can SUBSCRIBE to gain access to all full-length episodes at samharris.org/subscribe.

Thank you. of the Making Sense podcast, you'll need to subscribe at SamHarris.org. There you'll find our private RSS feed to add to your favorite podcatcher, along with other subscriber-only content. We don't run ads on the podcast, and therefore it's made possible entirely through the support of our subscribers. So if you enjoy what we're doing here, please consider becoming one. Today I'm speaking with Jennifer Doudna. Jennifer is a biochemist. She's a professor in the chemistry and the molecular and cell biology departments at the University of California at Berkeley. She's also an investigator with the Howard Hughes Medical Institute

and a researcher in the molecular biophysics and integrated bioimaging division at the Lawrence Berkeley National Laboratory. She is one of the world's experts on RNA protein biochemistry and, in particular, CRISPR biology. And she's the author, along with Samuel Sternberg, of the book A Crack in Creation, Gene Editing and the Unthinkable Power to Control Evolution. And Jennifer is credited as one of the inventors of the CRISPR-Cas9 gene editing technology, which is the topic of today's conversation. We get into all the details and the ethics. And time was short. Jennifer is a rock star scientist, and I could only schedule about an hour with her, but I will take it. It was great to have her walk me through the details of CRISPR. And I trust you will leave this podcast as I did, knowing much more about

where this technology is at present and where it's all likely to head. So without further delay, I bring you Jennifer Doudna. I am here with Jennifer Doudna. Jennifer, thanks for coming on the podcast. Great to be here, Sam. So you are a co-inventor of CRISPR-Cas9, which is a gene editing technology that we'll talk about. Before we get into this, perhaps you can just give a kind of potted summary of your background scientifically. Well, I'm a biochemist, so I'm somebody who studies molecules and how they work. And I've always been interested in evolution and the way that cells have evolved to use their genetic information in precise ways. And that's actually how we got into the whole area of gene editing.

And you're at UC Berkeley, right? I'm at UC Berkeley, correct. Now, I know there's some controversy about who should get credit for inventing CRISPR-Cas9, and we don't really have to go into that. I think there clearly is no controversy that you are one of the world's experts on this. Is there anything you want to say about the controversy, or is it kind of a distraction as far as this conversation is concerned? Well, I guess all I would say is that my work with Emmanuel Charpentier was going on to, really, I would call it a curiosity-driven project that was aimed at

discovering how bacteria fight viral infections. So neither of us were aiming to create a technology, but the work that we did uncovered the activity of a protein that can be programmed to find and cut DNA sequences. And with that understanding, it was pretty obvious that this was going to be a great technology. And that was work that was published in 2012, so I don't think anybody argues about that. Right. Okay, well, let's talk about CRISPR and that protein. But before we do, it might be good to give a very quick remedial summary of some basic molecular biology. I think we have a fairly educated audience here, but everyone, I think, can do with a primer on DNA to RNA to protein and, you know, because we're going to be talking about just

the mechanics of gene editing here. So can you give us a few minutes of basic biology here? Sure, absolutely. So can you give us a few minutes of basic biology here? Sure, absolutely. So I guess we could start by pointing out that people probably are familiar with the idea that DNA encodes genetic information. So it's really the chemical that stores information in cells and allows cells to grow and develop and become tissues or whole organisms. And the way that cells use that

information is mostly in the form of proteins. So the information in the DNA is converted into proteins by a process that creates the protein molecules by reading the code in the DNA. And the intermediary in that process is kind of what I like to call a throwaway copy of the genetic information, which is molecules of RNA. And what has emerged over the last probably two decades is that RNA molecules are not just throwaway copies of the genome, but they are actually molecules that have a lot of interesting functions in their own right. And that's actually what I've always been interested in in my own laboratory, is the role of RNA molecules that are involved in controlling

the flow of genetic information and helping cells decide when and how to use the information that's stored in the genome, in the DNA. And the story of CRISPR, the story of this gene editing technology, is kind of interesting because it really involves all three of those types of fundamental molecules, DNA, RNA, and protein, because it's a protein that is really responsible for cutting DNA at precise positions. The places in the DNA that get cut are defined by molecules of RNA that the protein, which is called Cas9, holds onto. And the places in the DNA that get cut are the sites in the genome where editing occurs, where permanent changes are made to the genetic code. And so you discovered this in bacteria, right? CRISPR has been described as part of the bacterial

immune system. That's correct. Take me there. So what happens? Viruses periodically infect bacteria. And what does the CRISPR sequence do in that context? Right. So viruses infect bacteria actually all the time in nature. And so bacteria have a very effective way of defending against viruses by storing pieces of viral DNA in their own chromosome. And then they use that stored viral DNA sequence. There actually are multiple sequences coming, one representing each virus that has infected the cell over time. So you can think of it sort of like a genetic vaccination card. And then those stored viral DNA sequences are copied into RNA. And then those RNA molecules assemble with the Cas9 protein to direct it to sequences that match the RNA sequence. In other

words, sequences that belong to viruses. And when that match occurs, then the Cas9 protein works like a molecular scalpel and cuts the viral DNA and basically allows the cell to destroy it. So again, this is semi-dense material and you don't have the benefit of visual aids here. So I just want to make another pass on this

just to make sure everyone has a picture of what's happening here. So you have this little machine, really. It's a combination of protein molecule and RNA, which is really informing its behavior, right? So you have an RNA sequence that matches a sequence in the DNA, which determines what part of the DNA it will bind to and edit or cut. And this is something you've discovered in bacteria, but which can be used as a kind of molecular scalpel in eukaryotes, like mammals such as ourselves. And this then becomes a way of targeting, with a precision that we didn't have before, spots in the human genome that can be edited. You nailed it. That's perfect.

Okay. So I guess I'm interested a little more in the mechanics of this. So what are the chances that the CRISPR-Cas9 technology will cut in the wrong place in the genome? I mean, does there have to be a complete complementarity between the RNA and the DNA, or is there some potential for error here? Sure, there's always potential for error. I think the amazing thing about the CRISPR-Cas9 technology is that it's really pretty accurate,

and it's not perfect, but it's close to. So I think what's emerged over the last few years that people have been using this, and it's probably worth mentioning that this technology took off incredibly quickly. It was adopted very, very rapidly after our 2012 publication. And there are now probably thousands of people around the world using this as a tool in all sorts of systems. And the good thing about that, or one of them, is that it's meant that there's been very rapid development of the technology as well as understanding of how it works. development of the technology as well as understanding of how it works. And one of the things that's emerged is that this tool is, you know, it's accurate enough to make precise changes in even very large genomes, like the human genome or plant genomes. And when people have sort of, as I think as people have become more sophisticated about using it, ensuring that the Cas9 protein is used in limiting amounts in cells,

not present in huge quantities and not hanging around for too long, that it's actually remarkably accurate at generating those kinds of edits. It's possible to find off-targets, but you have to look pretty hard. And can you edit a single base pair, or do you have to deal with longer sequences than that? You can edit a single base pair, yeah. Wow. So you've described this as a scalpel. Now, what happens after the DNA is cut? Is it always a matter of inserting more DNA, a variant sequence, or can you simply cut and remove parts of the DNA? Yes, you can cut and remove or you can cut and replace. The removal part turns out to be easier technically to do than the replacing part, but both are possible.

So again, this is so counterintuitive in ways when you actually picture what's happening here, because anyone who's taken biology in recent memory will know that the genetic material inside our cells is in the nucleus, and it's bound very tight. It's just crammed in there. The chromosomes aren't laid out in the pretty way that they are when we picture them in textbooks. And now you've sent CRISPR, this little machine, into the cell. We'll talk about how you can target tissues later on, but this goes into the cell and moves all over the genome and is searching for the sequence to which it is the mate and so that it can find the place to cut. How does it search the whole genome?

How do you get full coverage of a genome? And how quickly does this happen? If we could take a video camera inside a cell, what would we be seeing there? Well, we've sort of done that. Not quite a video camera, but it's been possible to make fluorescently labeled versions of the Cas9 protein that can be visualized in live cells. So you can basically watch these little dots of light moving around in the nucleus. And when you do that kind of experiment, what emerges is that this is a protein that has very fast kinetics, so it's moving around the nucleus incredibly quickly,

much more quickly than what you see for other kinds of proteins that are existing in the nucleus. And what's thought to happen is that this protein is rapidly sampling different sections along the sequence of DNA. And it is quite remarkable to think about it because, you know, we're talking about billions of base pairs of DNA in the cell. But somehow this protein very quickly samples along the DNA sequence looking for a match to the guide RNA sequence. And one thing that's important to keep in mind is that it's not a single protein that would be in the nucleus, but instead many, many copies of this. There might be, you know, thousands or

tens of thousands of copies that are all searching. And when one finds its target site, then it makes a cut and the edit occurs. Now, are the sequences of DNA unique enough so that we're not getting redundant cuts? I mean, if you send a, younucleotide sequence as your kind of search code, are we expecting that to be the only place in the genome that would get modified? Or just by dint of numbers, you're going to be altering something you didn't expect to alter if you do that? Well, in one of those interesting serendipities of science, this Cas9 protein actually uses a 20-nucleotide RNA sequence. So it's 20 letters that it's looking for, 20 letters in a row. And if you do the math, that's just about what you need to uniquely define a sequence in the human genome, for example. Good. Numbers were on our side.

Right. Let's back up. So now we have a human being who has a variety of genes that are not as perfect as they might be. And we'll talk about the conditions for which we have some understanding of the underlying genetics and what could be modified here. understanding of the underlying genetics and what could be modified here. But let's say we know what genes we want to alter. How would we target CRISPR to specific sites in the body? And presumably, these insertions would sometimes need to be tissue-specific. You wouldn't want

to send this everywhere, right? Right. And I think you're putting your finger on what I think is one of the critical challenges for gene editing in the clinic going forward, which is just what you said. How do we deliver these editing molecules into the right cells at the right time? One of the ways that this can be done today is actually by delivering into cells that are temporarily taken out of the body. So, for example, people are working hard on correcting mutations that cause blood disorders because the blood cells can actually be taken out, edited, and replaced. So, I think that's one strategy that gets around the issue of trying to deliver something like this into specific tissues in a person. That's a much bigger challenge.

And why is it a challenge? What would be the mechanism? Would you use some viral vector to deliver it? If you wanted to get it into every cell in the body, what would be the methodology? Well, that would be hard. to get it into every cell in the body, what would be the methodology? Well, that would be hard, even using a virus, because viruses tend to target particular kinds of cells. So you might have to use a cocktail of viruses that are able to get into many different types of cells. But I think what is typically envisioned is that you might be able to use viruses that would deliver into specific

parts of the body, for example, into the liver or into the brain, and create edits that would alleviate disease in cases where the gene edit is necessary just in those kinds of cells. And what is the time frame over which this would occur? I mean, just so again, it will talk about how difficult this might be in practice, but let's say we know the gene we want to edit and we have the way to target the relevant tissue and someone has a disease born of this malfunctioning gene, how quickly would CRISPR change their genome and cancel the disease? Well, in principle, very quickly. I've seen some data in animal models of disease, for example, in mice,

where mice get an injection, and within a matter of, you know, a couple of days, you can start to detect edits in the DNA of the cells that have been targeted in the treatment. So I think the idea in principle, and I think this is something the field is working towards doing, is that gene editing would be a fairly fast kind of treatment. And furthermore, and this is actually very important to appreciate, is that it's a different kind of therapy because it's really a one and done treatment in principle, right? The idea is you would do this once and then you don't have to do it again. Yeah. I really want to get into the ethics of all of this because that is quite interesting. And obviously this worries a lot of people. But before we do,

so what are the most plausible first uses of this? If you'd like to continue listening to this conversation, you'll need to subscribe at SamHarris.org. Once you do, you'll get access to all full-length episodes of the Making Sense podcast, along with other subscriber-only content, including bonus episodes and AMAs and the conversations I've been having on the Waking Up app.

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