Peter Attia MD323 - CRISPR and the future of gene editing: scientific advances, genetic therapies, & more
EVERY SPOKEN WORD
125 min read · 24,541 words- 0:00 – 1:32
Intro
- FZFeng Zhang
The Human Genome Project was completed in early 2000s, and with the human genome having been sequenced, and then also with DNA sequencing technology becoming cheaper and faster, um, scientists were able to start to sequence many, many more genomes. And so they can start to make comparisons between healthy individuals and also people who are affected by specific diseases to see what's different between their genomes. And by doing that comparison, they can identify the differences that may be causal for disease. And so, you know, to date, um, based on genetic analysis, researchers have probably identified more than five thousand, uh, genetic mutations that have a direct causative role in disease. And so these are called genetic diseases. They are usually, um, you know, affecting a small population of individuals. They're not, they're not as common as things like cancer or diabetes or, or these, um, what people call com-complex or, or complicated diseases. But, but nevertheless, um, these are the ones where we know the exact genetic, uh, cause. And so the tantalizing idea is then if you know the mutation in the genome, why not just go and fix it? And so that's where gene editing comes in.
- PAPeter Attia
[upbeat music] Hey, everyone. Welcome to "The Drive" podcast. I'm your host, Peter Attia.
- 1:32 – 10:05
Feng’s background, experience in developing optogenetics, and his shift toward improving gene-editing technologies
- PAPeter Attia
Hey, Feng. Thank you so much for detouring your, your trip and coming through Austin. I've been really looking forward to sitting down with you for, uh, uh, frankly, about a year. Um, so this is a topic that I don't think there's anybody who's heard this podcast who hasn't heard the term CRISPR. Um, but I think very few people can actually explain it, uh, and explain what a powerful tool it is. But I do think that before we get there, it would be really helpful to kind of understand a little bit more about your journey-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... on one hand, and then the journey of gene editing kind of as a, as a parallel. Uh, but let, let's start with, with, with yours. Um, you and I overlapped a little bit because, I mean-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... not temporally, but you were at Stanford, and you, uh, were you a postdoc in Karl Deisseroth's lab?
- FZFeng Zhang
Well, first of all, thank you for having me be on this posca- podcast. I've listened to your podcast, uh, on and off, uh, especially when I'm, um, you know, running around or, or exercising, and it's always I learn a lot from listening to the podcast.
- PAPeter Attia
Oh, awesome.
- FZFeng Zhang
Uh, thank you for having me here. Um, so back to Stanford, um, I was there as a graduate student. Uh, I was in the lab-
- PAPeter Attia
Okay
- FZFeng Zhang
... of a researcher, uh, named Karl Deisseroth, and, uh, I was there for five years.
- PAPeter Attia
That's right. You did your PhD there with Karl. Okay. Now, as you know, Karl ha- was, and I were classmates. Karl's been on this podcast. Um, and so maybe folks who either didn't listen to that podcast or who did but have forgotten, uh, give us a, a kind of a quick, uh, summary of the type of work that you and Karl did.
- FZFeng Zhang
When I was working with Karl Deisseroth, uh, we developed a technology called optogenetics, and it's a way of studying, uh, brain cells in, in the brain, um, how they are connected together and how they mediate, uh, memory, mediate different types of physiological function. The way it works is that we took a gene, uh, from a green algae, and this is a gene that senses light and converts it into, uh, electrical current, uh, in a cell. So we can put this gene from the green algae right into the brain cells in a mouse, and we can shine blue light or a yellow light, uh, and control the brain activity, uh, in these mice. So for example, if you wanted to study, uh, sleep, you can put this gene into different groups of cells in the brain and stimulate them, and you can find out which ones of these are controlling wakefulness or which one are causing the mouse to become more sleepy. Uh, so if you do this systematically one by one from one type of cell to another type of cell, you can gradually start to put together a picture of how the brain is wired together and then also what are the different components that govern all sorts of behaviors, uh, from, you know, sleep and, and wakefulness to thirst and hunger to memory and even to motivation and happiness. Um, so it was really fun to be at Stanford and working with Karl.
- PAPeter Attia
Yeah, and, and to me, the thing that always stood out about the technique was just the resolution, right?
- FZFeng Zhang
Mm-hmm.
- PAPeter Attia
It was, you know, I don't know what a great analogy would be, but it was sort of, y-you know-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... resolution at the level [clears throat] of the word rather than the page-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... if you were thinking about a book, for example.
- FZFeng Zhang
Right. Uh, what is incredible about these, um, algal proteins is that they are very, very fast. So you can control, uh, the way the s- the brain cells are able to signal to each other at the action potential level.
- PAPeter Attia
Hmm.
- FZFeng Zhang
So action potentials are these individual signals that they're basically like the, the phonemes, uh, of, of the speech that one neuron speaks with another neuron, and, uh, and you can control it at, at every single phoneme level, and, and that is, um, pretty cool.
- PAPeter Attia
And since we're gonna be talking a lot about gene editing, what was the technique that you guys used to insert those algal genes into the brains?
- FZFeng Zhang
The way that you would put a gene, uh, into the brain, uh, is usually by using a virus. Um, so this is, uh, a virus that, that exists in nature, but we have engineered it by removing everything that is pathogenic about the virus and then replacing those pathogenic genes with the gene that we're trying to put into the brain. So in this case, it's the gene from the green algae. And by injecting the virus into a brain area that you want to study, uh, the virus will infect all the cells in that region and then make those cells begin to produce this algal protein. So once, once the neuron starts to carry this algal protein, it becomes light sensitive. So you can Turn blue light on it and then be able to stimulate it
- PAPeter Attia
Yeah. Amazing. Um, what year did you finish your PhD?
- FZFeng Zhang
In 2009.
- PAPeter Attia
Okay. And then you went to MIT, or you went to Broad?
- FZFeng Zhang
Um, then, then I went to Harvard.
- PAPeter Attia
Okay.
- FZFeng Zhang
I was there for about a year.
- 10:05 – 21:48
The discovery of CRISPR in bacterial DNA and the realization that these sequences could be harnessed for gene editing
- PAPeter Attia
So let's keep that story on the side for a moment-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... and let's tell in parallel another story, a story that started long before-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... um, you were even in college, right?
- FZFeng Zhang
Mm-hmm.
- PAPeter Attia
When you were, when you were a young kid.
- FZFeng Zhang
Absolutely. Right.
- PAPeter Attia
Um, and it stems from an observation-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... um, that grew out of a discovery in sequences that existed in bacterial DNA.
- FZFeng Zhang
Mm-hmm.
- PAPeter Attia
A certain type of repeating structure that had all these-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... interesting characteristics.
- FZFeng Zhang
Mm-hmm.
- PAPeter Attia
Um, so let's go back to the '80s and tell a little bit of that story and it's o- obviously I wouldn't be going through this if it wasn't gonna q-
- FZFeng Zhang
Sure. [laughs]
- PAPeter Attia
... quickly converge with your life, uh-
- FZFeng Zhang
Sure
- PAPeter Attia
... and change the direction of your life. But let's go back to the '80s.
- FZFeng Zhang
Sure. Um, I was born in the '80s.
- PAPeter Attia
Yep.
- FZFeng Zhang
Um, but, um, what was really, uh, interesting that you're pointing out is that back in the '80s, uh, there was a group of Japanese researchers who were just looking at DNA sequences of bacteria, and they were looking at, um, E. coli. And what they found is that within some of the genomes, the DNA sequences of these bacteria, there are these regions that are very repetitive, so just repeat over and over and over again. Normally, um, genome sequences are not repetitive, um, because they encode genes and different genes. Uh, but here you, they found that there are these repeat sequences that are, um, that are all grouped together, so they're clustered, and they are not tandem repeats, so it's not repeat one next to each other, but they're interspaced by a short fixed length gap. And so it's basically A, B, A, C, A, D, A, E, A, G. Um, and so it just continues to, uh, repeat itself, but in this regularly spaced pattern. And when they first found it, they had no idea what it was, what the sequence was all about.
- PAPeter Attia
And there's something else about those repeating segments that was quite interesting as well, right?
- FZFeng Zhang
Mm-hmm.
- PAPeter Attia
Which is in each direction, whichever way you read them, they were the same.
- FZFeng Zhang
Right. So they're called palindromes. Um, D- no, DNA is double-stranded, so there's a top strand and there's a double strand, uh, uh, there's a bottom strand. And so this is why, uh, they're, they, they look like a double helix, so they twist and, and turn. And, uh, what is interesting is that when they-- when you read these repeat sequences from the top and you read in the reverse way on the bottom, uh, they're almost the same. Uh, so, so they're a palindrome.
- PAPeter Attia
So you had these palindromic clustered repeats-
- FZFeng Zhang
Mm-hmm
- 21:48 – 29:48
How the CRISPR system fights off viral infections and the role of the Cas9 enzyme and PAM sequence
- PAPeter Attia
Um, let's walk through two scenarios.
- FZFeng Zhang
Mm-hmm.
- PAPeter Attia
First infection, reinfection, and explain the difference between how the bacteria defends itself with special-
- FZFeng Zhang
Sure
- PAPeter Attia
... attention to the use of the CRISPR system and the Cas9 enzyme.
- FZFeng Zhang
Sure. So, so first of all-
- PAPeter Attia
First infection now, out of the gate. You're-
- FZFeng Zhang
Right
- PAPeter Attia
... you're an E. coli. I'm a bacteriophage.
- FZFeng Zhang
Right.
- PAPeter Attia
You've never seen me before. I come along. I've in- I've just injected my viral DNA into you.
- FZFeng Zhang
Right. So, so CRISPR is an adaptive immune system, so it means this system can evolve with the bacteria to be able to a- accommodate many, many virus infections.
- PAPeter Attia
Yep.
- FZFeng Zhang
So, so when the virus, uh, which is called a bacteriophage, first infects the bacteria, it will inject its genetic information into the bacteria. The virus is usually very powerful, uh, and very potent. It will probably wipe out most of the bacterial population. But for a very small number of cells, maybe one out of a million, um, the CRISPR system will successfully recognize a piece of the DNA of that virus and begin to insert it into this repeat area, uh, in, in the CRISPR, um, system.
- PAPeter Attia
And how long a piece is that typically? How many nucleotides in that piece?
- FZFeng Zhang
It's usually 30 letters long.
- PAPeter Attia
Okay.
- FZFeng Zhang
And that is enough, uh, for the bacteria to uniquely recognize the virus. So, so anyway, so during the first infection, um, you know, most bacteria die. Very, very small number of them begin to acquire a snippet of the genetic information of this virus, and it inserts it into the CRISPR system. So those bacteria that survived have now acquired immunity against these viruses.
- PAPeter Attia
And in the process of surviving, what do they have to rapidly do to fend off that first viral infection?
- FZFeng Zhang
Well, so the bacteria has many different defense systems in addition to CRISPR. So in fact, uh, CRISPR is not the first line of defense. There are other things that are also very powerful, uh, technologies now that are called restriction endonucleases. These are proteins or enzymes that bacteria use. Uh, they don't adapt, so they don't evolve-
- PAPeter Attia
Yep
- FZFeng Zhang
... but they recognize fixed letter sequences, and sometimes these will get But these will always get activated first and, and try to fend off the virus. But if it doesn't, then there are a host of other, uh, defense systems, and, uh, one of these will eventually work. But unfortunately for the bacterial population, um, these things don't come in quick enough, and that's why most of the cells die. But the few where these things were able to keep up with the virus, that's what allows the CRISPR systems to begin to acquire, uh, the genetic information.
- PAPeter Attia
So now let's talk about that subsequent infection.
- FZFeng Zhang
Mm-hmm.
- PAPeter Attia
So we've obviously, through a very Darwinian mechanism, selected a subset of the E. coli in this case that indeed-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... are able to not just survive with their first and second line defense-
- FZFeng Zhang
Right
- PAPeter Attia
... against the bacteriophage, but now they've also developed the memory, so to speak, the way we would use the term.
- FZFeng Zhang
Right, right.
- 29:48 – 39:08
The limitations of earlier gene-editing technologies prior to CRISPR
- PAPeter Attia
So Feng, does this bring us more or less up to speed with the state of the art when you turned your attention to how-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... can I create a finer resolution-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... for gene editing for my optogenetics problem? Is this about where the state of the art was?
- FZFeng Zhang
Yeah. So, um, I started to, uh, work at MIT and the Broad Institute, uh, in 2011. And so when I first started, um, I went to a, a scientific, uh, presentation and they were talking about CRISPR. Uh, and they mentioned that, uh, CRISPRs are nucleases. Uh, because I was thinking about nucleases and gene editing at the time, when I heard that word, it just kind of, um, got me a- uh, interested. And so I went on to, uh, Wikipedia and looked at what CRISPR is, and, and Francis Mojica and Sylvain Moineau and Rodolphe Barrangou, they had just published the very early, uh, studies on the Cas9 system. Back then it was still called Cas5. Uh, it was only later on renamed to be Cas9. But, but there was all these papers that if you read them, there aren't too many of them, you can piece together the information and you can get a sense that this is a RNA-guided DNA targeting cleaving enzyme. And, uh, and at the time there were other, uh, gene editing systems that were being worked on by researchers in the field, something called zinc finger nuclease or, or TALEN. Uh, and, and these are systems that use proteins to recognize DNA, but not using RNA to recognize DNA.
- PAPeter Attia
So maybe let's talk a little bit about both of those because they were the state-of-the-art-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... up until fifteen years ago.
- FZFeng Zhang
Mm-hmm.
- PAPeter Attia
And, um, I wanna understand both how they work and why they may not have been sufficient for your application. In other words, why, why were you looking for something beyond two techniques that already existed?
- FZFeng Zhang
Sure. So when I first became interested in gene editing, um, i- in the, you know, uh, sort of late 2000s, um, there were people already developing gene editing technologies. In fact, um, there were multiple iterations of technologies that, that came around. Uh, there's something called meganuclease, which was very, very early. And then, uh, what got me excited was a New York Times article, I think it was two thousand and eight or two thousand and nine. Uh, it talked about, um, a system called zinc finger nuclease. Uh, there's a company, uh, in, in, uh, uh, California, um, that's called, uh, Sangamo Biosciences, and they were already developing zinc finger nucleases for gene therapy to be able to go and edit DNA and treat disease. But zinc finger was a really, uh, challenging system for scientists to adapt and use because it required very sophisticated protein engineering. Um, the way it works is that, um, zinc fingers are, are protein domains that are just one glob of protein. Each finger, each zinc finger can recognize three letters of DNA, and they occur in nature, uh, so you can find them in naturally occurring DNA, uh, binding proteins called transcription factors. And they allow transcription factors to go and recognize different genes in the genome to modulate their activity, either turn them on or turn them off or change how much they are expressed in the cell.
- PAPeter Attia
But how do you get specificity when you are only recognizing three nucleotides? The probability of three-- those three-
- FZFeng Zhang
Right
- PAPeter Attia
... nucleotides showing up seems pretty likely across the genome, right?
- FZFeng Zhang
Right. Exactly. So, so nature has solved this problem by forming zinc finger arrays. So they tether multiple fingers together-
- PAPeter Attia
Ah
- FZFeng Zhang
... to form-
- PAPeter Attia
And all of them have to hit their target of three nucleotides.
- FZFeng Zhang
Correct. That's right. So if you have an array of three fingers, it recognizes nine letters. If you have array of six fingers, then that's eighteen letters.
- PAPeter Attia
Yeah.
- FZFeng Zhang
So in a complicated genome like our genome with three billion letters, eighteen would give us uniqueness. So eighteen can allow you to find or, or define just a single position.
- PAPeter Attia
And that's because four to the power of eighteen-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... is a big enough number?
- FZFeng Zhang
It's bigger than three billion.
- PAPeter Attia
Yeah. Okay. So, um, let's now talk about the TALENs. Why-- Well, first of all, what is that technique, and why was that not necessarily going to serve your purpose?
- FZFeng Zhang
Right. So, so the challenge with zinc finger is that you have to engineer the fingers to recognize different combinations of three letters, and you have to make sure that when you tether them together to make a zinc finger array, they can recognize what you intend to recognize in that multiple three fashion. That turned out to be really cum-cumbersome, and usually it doesn't work very well. So then, um, this other system that you mentioned called transcription activator-like effector, TALE, uh, nuclease were developed. Uh, so these systems came also from bacteria. Um, they came from, uh, a s-specific pathogenic bacteria called Xanthomonas oryzae. So it lives on rice plants and is a major rice pathogen. The way these proteins work is that they're injected by the bacteria that's trying to colonize the plant into the plant cell. And once it gets inside, it homes into the genome of the plant cell, finds a gene, and then starts to turn it on. When it turns it on, it allows the bacteria to-- uh, it allows the plant to become more susceptible to the bacterial colonization.
- PAPeter Attia
Hmm.
- FZFeng Zhang
And so allows the bacteria to be able to more successfully, uh, survive on, on this host, uh, plant. So it's a, it's a, it's a major pathogenic system. But what is really cool about TALENs or TALES is that they recognize DNA in a, in a sort of a very programmable fashion. These proteins, they have repeat domains, just like zinc fingers, that form an array, but individual domains recognize single DNA letters. And so you can find these TALE proteins-
- 39:08 – 51:59
How CRISPR revolutionized the field of gene editing, potential applications, and ongoing challenges
- PAPeter Attia
So it's very interesting. I mean, I think it's worth just sort of taking a step back, right? I mean, if-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... if most people can sort of remember what they were thinking 10 years ago-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... you know, 12, 15 years ago, and-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... you know, look, the, the human genome was sequenced, uh, nearly 25 years ago.
- FZFeng Zhang
Mm-hmm.
- PAPeter Attia
And the promise of gene therapy-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... um, was sort of hailed as right around the corner.
- FZFeng Zhang
Mm-hmm.
- PAPeter Attia
And yet here we are, a decade, more than a decade after the sequencing of the human genome-
- FZFeng Zhang
Right
- PAPeter Attia
... and it doesn't appear that gene therapy through gene editing was-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... any closer than it really was from a practical standpoint-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... a decade earlier.
- FZFeng Zhang
Mm-hmm.
- PAPeter Attia
I think that's a bit of a disconnect for people. I think most people who necessarily aren't in a lab would be-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... surprised to understand that simply knowing what the sequence of genes are, I mean-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... A, we've talked about this a lot in the podcast.
- FZFeng Zhang
Mm-hmm.
- PAPeter Attia
We still have no idea what most of these genes do anyway.
- FZFeng Zhang
Mm-hmm. Right.
- PAPeter Attia
Uh, we have no idea why there are coding segments, and the majority of the DNA is non-coding segments.
- FZFeng Zhang
Mm-hmm.
- 51:59 – 57:55
CRISPR’s potential in treating genetic diseases and the challenges of effective delivery
- PAPeter Attia
what diseases are currently amenable to that type of gene therapy? And we'll put aside the regulatory stuff, which we can talk about.
- FZFeng Zhang
Mm-hmm.
- PAPeter Attia
But if we were dealing, if we pretended that humans were laboratory animals-
- FZFeng Zhang
Right
- PAPeter Attia
... um, where we could do an experiment and actually do this, what, what are some of the diseases that we could directly-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... affect in that manner?
- FZFeng Zhang
So, um, so there are a lot of genetic diseases, uh, where there is a mutation that is pathogenic.
- PAPeter Attia
Overexpression. Well, in this case, overexpression if you want to deactivate it, but-
- FZFeng Zhang
Right
- PAPeter Attia
... some would be underexpressed, of course.
- FZFeng Zhang
Yeah. So, so these are genes that are usually important for the body, um, but there's a mutation in it, um, and, uh, and that makes the, the resulting protein, uh, the mutant protein, um, deleterious for, for, for the patient. And so, so if you can inactivate these genes, uh, then, then you can, you can treat disease. So for example, there are diseases of the liver where there are certain proteins that cause, uh, amyloidosis, um, and, and that can lead to, uh, serious problems. And so by using CRISPR, you can go in and cleave these genes, inactivate them so that they no longer produce these toxic gene product. Uh, Huntington is another example, uh, where there are mutations that are occurring in the gene that makes the, the gene deleterious and, um, and so if you can go and try to inactivate these deleterious mutations, it may be possible to, to treat the disease.
- PAPeter Attia
Is it generally the case that autosomal dominant diseases are an overexpression problem or an expression of something harmful problem, whereas-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... recessive diseases-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... are, uh, the opposite, where you tend to not be producing enough or something of that nature? Is that a, is that a-
- FZFeng Zhang
Yeah, I think that-
- PAPeter Attia
... overly simplistic, but-
- FZFeng Zhang
I think that, yeah, I think that's a good, um, good explanation.
- PAPeter Attia
So many people are probably familiar with Huntington's because it is one of the most devastating neurodegenerative diseases imaginable, perhaps second only to-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... Lou Gehrig's disease or ALS.
- FZFeng Zhang
Mm-hmm.
- PAPeter Attia
Um, but unlike ALS, where we don't really know the etiology, we clearly-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... know the etiology of Huntington's disease, which is-
- FZFeng Zhang
Right
- PAPeter Attia
... a gene, right?
- FZFeng Zhang
Right, right.
- 57:55 – 1:05:51
How CRISPR is used to treat sickle cell anemia
- PAPeter Attia
so-
- FZFeng Zhang
Sure
- PAPeter Attia
... um, tell people what sickle cell anemia is and why it's amenable to this type of therapy.
- FZFeng Zhang
Right. So sickle cell ane- anemia is caused by a mutation that causes the red blood cell to sickle, so they form a sickle form. And so they are, they're not able to, uh, sort of, um, you know, properly function, and sometimes they can aggregate, and then this can c- cause occlusion in the blood vessel and can cause serious problems. And, um, and so these red blood cells are made by, uh, progenitor or stem cells, uh, in the body, um, that produce these red blood cells. And so one idea for treating-
- PAPeter Attia
And it's a simple mutation.
- FZFeng Zhang
It's a simple, it's a single-
- PAPeter Attia
It's a, it's a single point mutation-
- FZFeng Zhang
Correct
- PAPeter Attia
... that changes one amino acid.
- FZFeng Zhang
That's right.
- PAPeter Attia
And that one amino acid based on one base pair change-
- FZFeng Zhang
Yep
- PAPeter Attia
... I can't remember what it is. It's an-
- FZFeng Zhang
Right
- PAPeter Attia
... alanine to a glycine or something. It's-
- FZFeng Zhang
Right
- PAPeter Attia
... it's quite trivial-
- FZFeng Zhang
Yeah
- PAPeter Attia
... um, is what leads to all of this bad, this downstream bad-
- FZFeng Zhang
Exactly
- PAPeter Attia
... badness you talk about. Um, but now if you-- So current treatment for these patients is blood transfusions, right? I mean, it's a-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... it's a, it's an awful disease.
- FZFeng Zhang
Yep.
- PAPeter Attia
And these patients experience-
- FZFeng Zhang
Very painful
- PAPeter Attia
... unbearable pain.
- FZFeng Zhang
Right.
- PAPeter Attia
Um, as an aside, some might ask, why does this disease exist? Why didn't Darwin get rid of this?
- FZFeng Zhang
Mm-hmm.
- 1:05:51 – 1:13:10
Gene editing with base editing, the role of AI in protein engineering, and challenges of delivery to the right cells
- FZFeng Zhang
The latter is a harder problem, but there's also very good progress on that front.
- PAPeter Attia
Okay.
- FZFeng Zhang
Uh, so for example, David Liu, uh, developed a methodology-
- PAPeter Attia
Also at Harvard.
- FZFeng Zhang
Yeah, also.
- PAPeter Attia
Yeah, yeah.
- FZFeng Zhang
Yeah. Uh, he's a colleague of mine-
- PAPeter Attia
Mm-hmm
- FZFeng Zhang
... and he developed a technology called base editing, and base editing allows you to use Cas9. You, you get rid of the DNA cleaving activity of Cas9. And so, so it simply goes in, binds to DNA. So you use it as kind of a guidance system to direct a different enzyme called a deaminase-
- PAPeter Attia
Hmm
- FZFeng Zhang
... to be able to go in and chemically modify a single base.
- PAPeter Attia
It's amazing to me, Feng, that that is easier-
- FZFeng Zhang
Uh-huh
- PAPeter Attia
... than what we just wish we could do, which is Change that C to a G.
- FZFeng Zhang
Mm-hmm.
- PAPeter Attia
Take out the C, make it a G.
- FZFeng Zhang
Mm-hmm.
- PAPeter Attia
And that will give me the amino acid I want. Like the fact-
- FZFeng Zhang
Right
- PAPeter Attia
... that we're chemically having to modify-
- FZFeng Zhang
Yeah
- PAPeter Attia
... it with a deaminase.
- FZFeng Zhang
Mm-hmm.
- PAPeter Attia
Um.
- FZFeng Zhang
Yeah.
- PAPeter Attia
What do you think is necessary-
- FZFeng Zhang
Uh-huh
- PAPeter Attia
... to take this next-- 'Cause we've already had, as you described it, a big step function-
- FZFeng Zhang
Right
- PAPeter Attia
... from where we were 10 years ago.
- 1:13:10 – 1:17:43
How CRISPR is advancing scientific research by fast-tracking the development of transgenic mice
- PAPeter Attia
Let's go back to animal models for a moment.
- FZFeng Zhang
Hmm.
- PAPeter Attia
Um, you touched briefly on the idea of a transgenic mouse, and again, people who have listened to this podcast for years-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... are no stranger to the transgenic mouse.
- FZFeng Zhang
Mm-hmm.
- PAPeter Attia
So many amazing breakthroughs in science-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... have come through these, and, and frankly just through genetic understanding of, of mice, making changes to a mouse gene. You know, we recently had Denina Dubal on the podcast.
- FZFeng Zhang
Oh.
- PAPeter Attia
We talked about Klotho, to me-
- FZFeng Zhang
Uh-huh
- PAPeter Attia
... one of the most interesting proteins out there.
- FZFeng Zhang
Right.
- PAPeter Attia
And of course, we learned the story of how Klotho came about, and it be- you know, silencing a gene found this thing, overexpress the gene, found this thing. Okay. How-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... does CRISPR enable that today? Has it changed the ability of people working on totally other problems to get there quicker using, uh, laboratory animals?
- FZFeng Zhang
Right. So the transgenic mouse technology, uh, really revolutionized biology.
- PAPeter Attia
Mm-hmm.
- FZFeng Zhang
Um, um, and, and when the transgenic mouse technology was developed, um, the way it worked is that you would start with stem cells from mice. You would modify these stem cells, and then you put the stem cells back into a embryo, and then you transplant the embryo into a, a mouse so that the embryo can develop into a full, um, e- develop into fetus and then, then be born as a new mouse. That is a very long process, and then once the mouse is born, usually that mouse does not have 100% of that, uh, genetic-
- PAPeter Attia
Mm-hmm
- FZFeng Zhang
... modification. So the mouse is called a mosaic, and then you have to take that mouse and breed the mouse again with a- another mouse in hoping that, um-
- PAPeter Attia
That the mosaic part is the one that gets expressed and you-
- FZFeng Zhang
Sh- gets transmitted
- PAPeter Attia
... yeah, you basically try to concentrate the mosaic portion of it.
- FZFeng Zhang
Exactly.
- PAPeter Attia
Yeah.
- FZFeng Zhang
So when you use this methodology, um, it can take probably a year or maybe even longer, uh, to be able to generate a specific transgenic mouse. So it used to take a long time to do this, um, but, but now with CRISPR technology, uh, what people can do is they can directly inject the gene editing Cas9 and guide RNA into a embryo, into a single-cell embryo and then modify it there.
- PAPeter Attia
Ah. So again, this is so brilliant because we can't do this in humans, of course.
- FZFeng Zhang
Mm-hmm.
- 1:17:43 – 1:27:55
Advantages of Cas13’s ability to direct CRISPR to cleave RNA and the advances and remaining challenges of delivery
- PAPeter Attia
Now, we've talked a lot about Cas9, um, but you've also specifically done quite a lot with another protein, another-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... CRISPR-associated protein called Cas13.
- FZFeng Zhang
Mm-hmm.
- PAPeter Attia
What's the difference, and, uh, w- how does this potentially impact future work?
- FZFeng Zhang
Sure. CRISPR is, uh, a bacterial immune system, and there are many, many different types of CRISPR. And so in nature, um, bacteria are invaded by DNA viruses, by RNA viruses, all sorts of different viruses. Cas9 protects bacteria against DNA viruses, but then there also needs to be a CRISPR system that protects against RNA viruses. So Cas13 is the, the RNA analog of Cas9. It uses a guide RNA to recognize the RNA virus and then cleave the RNA genome. And what is really interesting about Cas13 is that, um, unlike Cas9 It not only cleaves the recognized RNA, but once it recognizes a piece of RNA, it also turns on almost a suicidal function. It goes and cleaves any other RNA that's in the bacterial cell. And so in the infection cycle, uh, you can think of this as a altruistic, um, sort of a, a system where, um, when a, when, when the Cas13 recognizes, um, my, my s- my cell has been infected by RNA virus, I want to shut myself down, kill the cell, and save the population.
- PAPeter Attia
So hang on. Why is that the case, um, if we-- So, so why does the cell not choose to do that with the DNA virus? Are RNA viruses necessarily more lethal to bacteria?
- FZFeng Zhang
RNA is usually more abundant, and so usually there are many, many-- Once, once the RNA gets produced, there are many copies, and so it's difficult to, to shut down every single copy of RNA. Whereas with DNA, there's usually just one copy of DNA, so if you can shut it down-
- PAPeter Attia
So when a DNA virus infects a bacteria-
- FZFeng Zhang
Right
- PAPeter Attia
... so again, w- let's just talk about a very specific bacteriophage latches on the outside of an E. coli. It's gonna shoot in-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... a piece of DNA.
- FZFeng Zhang
The DNA. Right.
- PAPeter Attia
We've already talked at length about how that works-
- FZFeng Zhang
Right
- PAPeter Attia
... and the role Cas9 plays in that.
- FZFeng Zhang
Right.
- PAPeter Attia
When a different bacteriophage comes along-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... you're saying it inserts a lot of RNA.
- FZFeng Zhang
No. Um, so one of-
- PAPeter Attia
Or just the RNA replicates much quicker.
- FZFeng Zhang
RNA replicates quicker.
- PAPeter Attia
Got it. Okay.
- FZFeng Zhang
And-
- PAPeter Attia
So it inserts a small amount of RNA.
- FZFeng Zhang
Right.
- PAPeter Attia
But remind me why a small amount of RNA will be amplified much quicker than a small amount of DNA. Is it because it's one step less? It's already made the-
- FZFeng Zhang
Correct. For sure
- 1:27:55 – 1:40:15
CRISPR-Cas9: therapeutic applications in the liver and the eye
- FZFeng Zhang
capabilities that we want to realize.
- PAPeter Attia
Okay.
- FZFeng Zhang
For example, how do you insert large genes into the genome precisely and efficiently? Um, I think that is, is, you know, just as important of a problem. Um, Cas9, even though it's large, um, we can deliver it, um, to some cells already. And, and, uh, so there's already-
- PAPeter Attia
In vivo or only in vitro?
- FZFeng Zhang
In vivo.
- PAPeter Attia
What, what cells can be delivered in vivo using Cas9 currently?
- FZFeng Zhang
So liver.
- PAPeter Attia
Okay.
- FZFeng Zhang
Yeah, liver is a place where we can use lipid nanoparticles-
- PAPeter Attia
Oh
- FZFeng Zhang
... to deliver Cas9 and guide RNA into. Uh, you know, the COVID vaccine is made using mRNA-
- PAPeter Attia
Mm-hmm
- FZFeng Zhang
... and lipid nanoparticle, and, uh, and so it's a very similar approach where you formulate, uh, these, uh, lipids with the Cas9 mRNA and guide RNA.
- PAPeter Attia
And what is it about the liver that makes it amenable to a lipid nanoparticle?
- FZFeng Zhang
Lipid, um, there's a lot of lipid recycling happening in the liver.
- PAPeter Attia
Mm.
- FZFeng Zhang
And so when you have a lipid nanoparticle, uh, they, they get bound by these recycling proteins and they get taken up.
- PAPeter Attia
Interesting. And this is, does it matter the manner in which it's given, intravenous, intramuscular? Does it, do all lipid nanoparticles end up there-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... provided they're not ingested orally and presumably digested?
- FZFeng Zhang
Mm-hmm. A lot of it goes to liver. Um-
- PAPeter Attia
Yeah.
- FZFeng Zhang
Yeah, because liver also, you know, it's one of the areas in our body that filter out all the toxins.
- PAPeter Attia
Yeah.
- FZFeng Zhang
And, uh, so, so everything gets trapped there.
- PAPeter Attia
So in other words, if you were thinking about one of the rare inborn met- diseases of metabolism, these are-
- FZFeng Zhang
Mm
- PAPeter Attia
... the really rare diseases where children are born-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... without, you know, a particular enzyme that allows them to either metabolize a-
- 1:40:15 – 1:52:45
The ethical implications of gene editing, the debate around germline modification, regulation, and more
- FZFeng Zhang
is.
- PAPeter Attia
Is there any, um, foundational roadblock to doing this, or is it simply just more-- like, you know, if we think about, again, like a M- is there a Moore's law aspect to this where it's-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... just going to get significantly-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... cheaper over time in the same way that, uh, transistors just get significantly cheaper over time?
- FZFeng Zhang
Um, I'm not an expert on, on this, uh, but, but I think there, there will definitely be, uh, efficiencies from scale. Um, enzymatic processes for making these, uh, RNAs, uh, is getting much better. Um, purity is g- uh, is improving. Uh, so all those things, I think, uh, they will compound and, and that will result in significant cost reduction.
- PAPeter Attia
How much do you, uh, follow/pay attention to-
- FZFeng Zhang
Uh-huh
- PAPeter Attia
... um, sort of the, the regulation of gene editing? Um, I know that, gosh, sometime in the last six, seven years-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... there was a very controversial case in China-
- FZFeng Zhang
Right
- PAPeter Attia
... with a scientist who had, it seems somewhat nefariously from my reading of the story-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... um, j- uh, edited the embryos of kids to render them, on the surface this sounds like a great idea, but rendered them, um, immune to HIV, and I believe one of their parents was HIV positive.
- FZFeng Zhang
Mm-hmm. Right.
- PAPeter Attia
This was an IVF case. But it turned out that there was an enormous amount of backlash-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... from the scientific and medical community because, I guess, one, he did it without the full consent-
- FZFeng Zhang
Right
- PAPeter Attia
... of the medical community, um, and also the belief that you actually didn't-- the risk of transmission of HIV was quite low to the child in the first place.
- FZFeng Zhang
Right.
- PAPeter Attia
Can you say more about that case in particular, and then also what the current state of, um, the, of, of the, of genetic, uh, manipulation is from a sort of ethical legal standpoint?
- FZFeng Zhang
Right. So, so this was back in twenty eighteen. Um, there, um, so, so, so there was a, there was a couple, uh, who wanted to have children. Uh, the father was HIV positive, and so they wanted to make sure that their, uh, children, uh, are not HI- are, are not infected by HIV. And, um, and so, so scientists, um, uh, made a mutation, uh, in the embryos, um, that is a gene in, uh, called, called CCR5.
- PAPeter Attia
Mm-hmm.
- FZFeng Zhang
And, uh, and, and this, a CCR5 mutation is a naturally occurring mutation in the human population. Single digit percent of individuals carry this mutation, and, uh, and these individuals are naturally immune to HIV infection because they don't have a specific-
- PAPeter Attia
This is the Magic Johnson mutation.
- FZFeng Zhang
Right. They don't have this specific protein on the surface to allow HIV to bind and, and enter the cell. Um, and so the scientists edited the embryo, a human embryo, um, to remove this PC- uh, this CCR5, uh, gene. But it turned out that that edit wasn't complete. Um, like earlier we were talking about mosaicism.
- PAPeter Attia
Mm-hmm.
- 1:52:45 – 1:58:25
Genetic engineering to enhance human traits: challenges, trade-offs, and ethical concerns
- FZFeng Zhang
Right.
- PAPeter Attia
Um-
- FZFeng Zhang
Right
- PAPeter Attia
... so then it gets to maybe a, a more complicated question-
- FZFeng Zhang
Right
- PAPeter Attia
... which is, is there a role for genetic engineering-
- FZFeng Zhang
Choice, yeah
- PAPeter Attia
... within, um, well, within in utero, for example?
- FZFeng Zhang
Yeah.
- PAPeter Attia
Um, or is that just so technically challenging that it's much easier to focus on just the IVF side of things?
- FZFeng Zhang
So certainly on the disease treatment, monogenic genetic disorder, IVF, I think that that is probably the most likely application. Um, further down the road, um, there are some obstac- obstacles to solve. One, we don't really understand biology enough, so if you wanted to make your kid, you know, 30 IQ points smarter-
- PAPeter Attia
Nobody knows how to do that today
- FZFeng Zhang
... we don't really know how to do that, and so the biology needs to catch up.
- PAPeter Attia
Yep.
- FZFeng Zhang
But I do think that as society continues to develop, if the science is there and the technology is also there, I think people will opt to, um, to do that. Uh, and of course, you consider whether or not there are other-
- PAPeter Attia
Sorry, meaning i- let's just assume, and by the way-
- FZFeng Zhang
Yeah
- PAPeter Attia
... I think this is personally, you know, Feng, my view is I think these problems are way harder than people think. I think these polygenic-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... nuanced traits like intelligence-
- FZFeng Zhang
Right
- PAPeter Attia
... athletic performance-
- FZFeng Zhang
Right
- PAPeter Attia
... resilience-
- FZFeng Zhang
Right
- PAPeter Attia
... happiness.
- FZFeng Zhang
Right.
- PAPeter Attia
All of those things I think are infinitely more complicated-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... than we believe, and probably just as environmental as they are genetic.
- 1:58:25 – 2:13:15
Feng’s early life, the influence of the American education system, and the critical role teachers played in shaping his desire to explore gene-editing technology
- FZFeng Zhang
long run.
- PAPeter Attia
So I wanna talk a little bit about kind of your s- your story going back. So you, you grew up in China. You came-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... to the middle of the country, right? Where'd you grow up?
- FZFeng Zhang
Yeah, I grew up in Iowa. So I moved to Des Moines, Iowa, when I was 11 years old.
- PAPeter Attia
What brought your parents here?
- FZFeng Zhang
Uh, my mother came to the U.S. first. Uh, she was a exchange scholar, uh, in computer science, and, um, and she, she had a chance to visit, uh, one of the schools in Iowa, and she saw that the educational system in Iowa was much more hands-on-
- PAPeter Attia
Mm-hmm
- FZFeng Zhang
... uh, as opposed to just old memorization. And, uh, and because of that, uh, she thought I would maybe benefit more from that type of instruction, so she decided to, uh, to, uh, stay in the U.S. and, and, uh, and immigrate here.
- PAPeter Attia
And when did you start to become aware of your, uh, your, your, your intellectual abilities, for lack of a better term? I mean, was it, was there a, was it just, was school always so easy for you? Were you sort of breezing through high school-
- FZFeng Zhang
[laughs]
- PAPeter Attia
... acing every test put in front of you or, or what, what was it like?
- FZFeng Zhang
No, I, I, I don't think I'm all that smart. Um, I think, um, I, I, I've always been interested in science. I've always been very curious. Um, so I think I've just always kind of followed my, my curiosity, uh, to do something that, that is enjoyable and fun. Um, I think, um, uh, what, what is really interesting is I, um, I didn't like biology at all, uh, when I-
- PAPeter Attia
You preferred physics and chemistry and mathematics.
- FZFeng Zhang
Yeah, and math. It was more logical.
- PAPeter Attia
Mm-hmm.
- FZFeng Zhang
Um, predict, um, things that I can understand and build a mental model for and then be able to predict things. Biology was very much just old memorization. Uh, so when I first moved to Iowa, um, in seventh, seventh grade, there was life science in middle school. And, uh, I remember it was really about memorizing trees and dissecting frogs and identifying anatomical parts. Uh, it wasn't so much sort of, um, based on logic.
- PAPeter Attia
Yep.
- FZFeng Zhang
It was during seventh grade, um, that I attended a Saturday enrichment class. Uh, it was on molecular biology. Um, I didn't know what molecular, uh, what, what, what, what biology had to do with molecular things, so I went to it. And in that class, that's when I started to learn about the advances in modern biology. Uh, the teacher was very passionate. He taught us about DNA, RNA, protein, the central dogma. Uh, but he also, uh, had us do fun experiments like, um, extracting DNA from strawberries and putting a antibiotic resistant, resistance gene into a bacteria so that it can-
- PAPeter Attia
Wow
- FZFeng Zhang
... survive on ampicillin. And, uh, he also, at the same time, showed us this, I call it a documentary, but it's actually a Hollywood movie called Jurassic Park.
- PAPeter Attia
[laughs]
- FZFeng Zhang
Um, because think, if you, if you put yourself, uh, in my shoes at the time where you're learning all these molecular biology fundamentals ... gene splicing, all that. And then watching Jurassic Park to see all those theories being so tangibly there to make a dinosaur, um, you know, the movie really felt like a documentary. Uh, but, but it was also just so inspiring and, and exciting. And, um-
- PAPeter Attia
'Cause that's about when Jurassic Park came out, would've been the mid-'90s-
- FZFeng Zhang
Yes, that's right
- PAPeter Attia
... which is when you were in middle school.
- FZFeng Zhang
Yeah, it was '94. Nine-
- PAPeter Attia
Yeah
- FZFeng Zhang
Yeah. And, uh, so anyway, so I, so I saw that, and I, I became really interested in learning more about molecular biology. We also learned about gene therapy and the promise of using, uh, molecular biology to build rational design medicine. Uh, so, so that really captivated my imagination. The teacher was amazing. Uh, his name is Ed Pelkington, and, uh, he, um-
- PAPeter Attia
Was he only the teacher of the enrichment class, or did he also have r- a regular class that he taught in high school or middle school?
- 2:13:15 – 2:18:45
Feng’s optimism about the trajectory of science
- PAPeter Attia
So you're, you know, barely forty years old. Um, you're one of the most prominent scientists in your field. Um, do you-- are you optimistic about the state of science? Are you, um... And I, and I'll point out two things-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... that are negative that you don't need to comment on.
- FZFeng Zhang
Uh-huh.
- PAPeter Attia
Um, 'cause I don't wanna put you in hot water, but, but just sort of, uh, there's been a clear attack on meritocracy in the United States.
- FZFeng Zhang
Mm-hmm.
- PAPeter Attia
So a lot of the opportunities that, that served you well might not have served you well today.
- FZFeng Zhang
Mm-hmm.
- PAPeter Attia
They might not have been available to you today for various reasons, including your race.
- FZFeng Zhang
Mm-hmm.
- PAPeter Attia
And similarly, um, I think Despite all of the remarkable scientific advances during COVID, there was also a loss of public faith in science during COVID, where some of the lines between science and advocacy got blurred greatly, um, in addition to a whole bunch of other things. So in other words, I guess what I'm saying is there are a lot of things today that-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... don't look as promising as they did maybe 10 years ago vis-a-vis, um, the field, um, and, and just sort of the, the state of the art. Despite those things, do you remain as optimistic as ever, or do you have concerns?
- FZFeng Zhang
I am an optimist. I think that's the only way to be, because if you're not optimistic, then, then there's only downside, uh, when, when you are like that. Uh, but I am optimistic about science. I mean, I'm so excited about all of the rapid advances that are happening. Um, knowledge about biology, about the human body, physiology is accumulating at a very rapid pace. Every week there are interesting and exciting discoveries that are being reported, and our technologies for studying biological systems are also accelerating with, you know, sequencing technology development to protein, uh, mass spectrometry, to gene editing, uh, to new microscopy. Um, that is allowing us to collect new and more rich data, uh, cheaper and faster. And then there's AI. Um, with the, the advance of AI and larger computing, um, platforms, uh, we can analyze and learn and, and build models around those data, um, that are much more, for- much more powerful and much more, uh, predictive, predictive and generative, uh, than ever before. And that, combined with future advances in robotics, where we can have automation of experimentation and maybe even building a closed loop system where AI and, and with human intervention can design and iterate our experiments, uh, rapidly-
- PAPeter Attia
Mm
- FZFeng Zhang
... I think it's gonna accelerate science and medicine and human health, uh, beyond our imagination. So I think that's really exciting. Um, at the same time, I think we need to continue to motivate people's interest in science. Um, we, we need to make sure that the best talent are going into science.
- PAPeter Attia
Do you worry that we've lost the focus on STEM that-- I mean, obviously people talk about the heyday of science, right? During the 1960s-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... when kids growing up saw the space program, saw the Cold War-
- FZFeng Zhang
Mm-hmm
- PAPeter Attia
... the best and the brightest wanted to do science. They wanted to do engineering.
- FZFeng Zhang
Mm-hmm.
- PAPeter Attia
Um, do you, do you feel that's slipping away? And if so, what do you think is necessary to bring it back? How do we get the absolute best people into STEM?
- FZFeng Zhang
I think we can do more, for sure. Um, I think we need to get kids more excited about science. Um, and I think we need to, um, we, we need the education system to, to support, um, kids who are curious and, and, uh, who have special interests in the science and technical things and, and to give them opportunities like the ones that I had-
- PAPeter Attia
Yeah
- FZFeng Zhang
... to, to really explore those curiosities and interests. Um, when they're young, um, they are optimistic, and they have energy, and if we can nurture that and help them maintain that curiosity and energy, I think that's how we get the best people to continue in science.
- PAPeter Attia
Yeah. I, I couldn't agree with you more. Um, and this is not an investment that pays off in a year.
- FZFeng Zhang
Mm-mm.
- PAPeter Attia
Right? You've got to be doing this today, and then you'll get your payoff in a decade, in two decades.
- FZFeng Zhang
Right.
Episode duration: 2:18:46
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