Founder Stories: Benjamin Oakes and Kristen Fortney, CRISPR and Aging

Hello. Today's topics are two different but fast-growing areas in our life sciences industry: CRISPR gene editing and molecular aging.

Cool. Should we just get straight to it?

Let's do it. Welcome to Discovery Matters. Please meet Dr. Benjamin Oakes, co-founder, president, and CEO of Scribe Therapeutics. His heart and soul is in CRISPR technology. In fact, he thought he was going to be a doctor growing up. Then, during his junior year of college, he shadowed ER doctors and realized that medicine needed a tech injection.

The majority of it, I'd say 70-75% of it, was that very clear diagnose and treat the symptoms in the best way you can. And that made me really switch gears. And I said, I don't think I want to be in medicine, at least with the technologies we have today. And it became really apparent that we needed better technologies. So that's where I went and I really sought out a career more in research biology. At that point in time, I was fortunate enough to get a job working on engineering first-generation genome editing molecules known as zinc finger nucleases. Back then, they were kind of the only game in town. It was the dark ages, it was BC, before CRISPR.

So never let it be said that biologists lack imagination. I mean, the names in this space are just insane, aren't they? Gene editing technologies like talons and CRISPR and paste. So for the benefit of our listeners, what's a zinc finger?

Well, bizarre. It actually sounds like a terrible affliction. Right. But as I understand it, zinc finger nucleases were the first generation of genome editing technology. And they're basically the combination of two different molecular machines harnessed from a bacterium's nucleus that has no specificity. It's like a white label bacterium. How do you like that? But actually, Ben should explain it because he does it so much better than I do.

So it has no ability to target any location in the human genome. And actually, human transcription factors, which are essentially the molecules that can turn on or off genes, you know, it's the things that make a liver cell a liver cell and a neuron a neuron. Obviously those have to go to a very specific point in the genome to make that happen. So we can harness those transcription factors and we can harness the nuclease from bacteria and we can put them together, that becomes a zinc finger nuclease. Now, however, in order to target a specific site in the human genome, in order to find a site we actually want to target and either mutate or interrogate in some way, you have to engineer these ZFNs.

So you need to make a billion different molecules and then select from that pool of a billion to find just a handful that are going to work. And that handful will work as 3 nucleotides, so 3 base pairs in the human genome. To get specificity, you need 18 different base pairs. So you have to do that again. You do a billion, a billion, another billion. Now you have half of what you need.

Okay, so that's a ton of billions, a metric ton of billions. So this is when you need computational power, right? 'Cause it's just really hard to do the maths.

This was before CRISPR, right? This is what that paradigm shift really looks like. Me in this lab with a few others basically pouring 80 hours a week of our lives into this work just to find a single pair. And then basically Jennifer Doudna comes along with Martin Jennek and Emmanuelle Charpentier, and they show the world how to harness essentially a bacterial immune system that uses an RNA to program to nearly any location in the human genome in about 15 minutes. So it takes all of that work that I've been doing and in many ways actually kind of makes it somewhat obsolete. Now, that's the paradigm shift that is CRISPR.

So it's been 10 years since the shift, and a lot happens in biotech in 10 years.

Indeed. And it all started with CRISPR-Cas9, which most of us probably think of as CRISPR in its entirety.

That is the first molecule that Jennifer discovered. And that is the molecule that I think worked well enough for most folks around the world to pick it up and apply it very quickly. At Scribe in particular, though, we've moved beyond that original platform and have started to build our own platforms on a number of new molecules, including this one called CasX. And what we are doing at Scribe is taking molecules like CasX, bacterial immune systems, And recognizing really intentionally that these are bacterial immune systems, and therefore they have not evolved all of the characteristics that you would want to build into a genome-editing scalpel or a genome-modification technology. And that's where kind of all of this creative ferment that I was talking about that we now have the time and the ability to use, we can start to apply, and we can make molecules that are much more specific, much more active, can create different outcomes at the DNA, and then also really importantly, much more deliverable, and we can engineer delivery systems as well. And that's what we're doing at Scribe that we really believe is quite distinct from what other folks are doing with the original Cas9-based technology.

So he mentions Jennifer Doudna, who along with Emmanuelle Charpentier has undeniably changed the world of gene editing. So it would be hard for Ben not to be influenced by that and carry that influence in his work.

I was not actually just in Jennifer's lab. I was also jointly mentored by someone else by the name of Dave Savage. Specifically, when I saw the CRISPR papers were published, I told my boss at the time who I was engineering zinc finger nucleases with. I was like, Marcus, I'm gonna go to grad school. And I came out to UC Berkeley specifically to work with Jennifer Doudna and Dave Savage. And there was a really interesting combination of skill sets for me because Dave has been very focused on synthetic biology and how we build better molecules. And we developed a whole new set of techniques on how to build CRISPR systems. In fact, a lot of the inlaying of domains into CRISPR systems that people are doing now, we pioneered in 2014. But in Jennifer's lab, I was joining specifically to work on CRISPR-Cas9 at that time, which, funny enough, actually was not what her lab was focused on doing, right? Jennifer was an RNA biochemist, and there was still a whole suite of people there who were not working on CRISPR, were working on many different types of RNA biochemistry and many other different types of molecules that interact with RNA and DNA. And I was fortunate to be supported enough by Jennifer to say, yeah, sure, you want to do protein engineering? We don't do protein engineering here, but like, Dave and you can do protein engineering.

So for Jennifer to support Ben's work with CRISPR and the unknown, despite it not being the purpose of her lab, it's a real testament to the importance of creative freedom in research and in this industry as a whole, right?

Absolutely. She inspired Ben to always encourage young and hungry people to nurture creativity. In fact, Ben has instilled that into the fabric of Scribe.

So how does this exploration of the unknown affect the areas that Scribe is focused on?

I know nuance is not friendly to communication, but what we're trying to do is enable the use of CRISPR technology in a much broader subset of genetic diseases where we do understand the underlying cause, and then actually even be able to push beyond just genetic diseases to understand how we can create systems that are safe enough to treat much larger patient populations. Because we really believe genetic medicine shouldn't just be restricted to the rare and orphan diseases, but could be used in much broader patient populations. But in order to do that, we really believe we need to move beyond that bacterial immune system and actually reforge it into a therapeutic tool.

Okay, so because rare diseases are often monogenic, caused by one single mutation that can be corrected by editing, but most of the world's diseases are caused by multiple factors in combination, so how do we parse that out?

There are a number of neurological diseases that we understand the underlying cause of. We're working towards actually trying to build molecules that can get at that underlying cause of a neurodegenerative disease. We just announced this partnership with Sanofi where we're focused on providing them with the tools that actually will enable them to modulate their cell therapies and do so with much greater efficiency and specificity than we believe they would've been able to do so before. And we're really excited about what the results of that will be, and those cell therapies will be used in oncology.

Now, despite all the possibilities of CRISPR, Ben is keen to point out that, it is not the solution to everything.

People believe that CRISPR is primetime and ready for everything. And I think what's going to pose a challenge in the future is when we have to roll it back and tell people, well, that original technology maybe isn't. I'm hoping that Scribe will be able to fill in that gap when we start to realize all the limitations or start to be honest about all the limitations. That's what we're really aiming at being poised to step into.

Yeah, this is a really good point. You know, when the new modalities appear or a new avenue of treatment, there's always a hype cycle and we see a lot of enthusiasm turn into a belief that, yay, it's the answer to all of our problems, it's nirvana. And that just isn't the case.

Totally. The search for that panacea. And that makes it interesting and important that Ben has his eyes fixed on future what-ifs. So when we had the conversation with Ben, he had recently become a father. So naturally I asked, what would he want his son to experience from his scientific discoveries and work? And how is his son going to benefit from what he has been bringing into the world. And I loved this because from his answer, you could really tell how family is driving his work.

So my father had a heart attack at 40. He's still with us. He's still kicking. He's— but he's had 3 more since then. I would hope that my son will live in a world where, number 1, I don't have a heart attack. I'm not past 40 yet, but I'm going to hope that actually some of the genetic medicines, maybe not CRISPR yet, will help us treat potential patients like me or like my father and create a world where even if that does happen the first time, you can go get treated in a durable way that fundamentally alters the trajectory of your disease. So maybe you don't have that second heart attack and that third heart attack. And I think that's where CRISPR genetic medicine is going to make the largest impact. Our goal at Scribe is to treat broader and broader patient populations that will, just by nature of affecting more people, continue to grow in their impact. That's what I would hope that our research will look like or enable for future generations.

And speaking of disease trajectory in future generations, that brings us nicely into molecular aging and the field of longevity.

Okay, so aging, we're doing that well or otherwise. Who is our guide on the topic of molecular aging today?

Kristin Fortney, the CEO and co-founder of BioAge, which is a clinical-stage biotechnology company developing therapies that treat disease by targeting the biology of aging.

And like Ben, Kristin set out early for a scientific career.

I was always really motivated by the idea of developing medicines that really help humanity, right? Like the really big vision. And that got me really excited to apply some of these skills to tackle interesting problems in biology. So yeah, I did my PhD in medical biophysics, got to work with some really cool new data modalities. Like, I think technology development is a really important driver of novel science, whether measurement technologies like the proteome, where you can now measure like 7,000 proteins in a sample, or the metabolome. So as a graduate student, I got to work with some of these really cool data sets to try to build biomarkers of aging. And after that, I joined a lab for my postdoc at Stanford. And at Stanford, part of the appeal was that it was an aging lab, a lab just focused on aging.

This lab really piqued Kristen's interest in what it meant to age. Kristen's supervisor had blood samples from humans who lived to be over 110, which in itself is just amazing. Do you think you're going to live to 110, Kristen?

Connor? I'm gonna die trying, that's for sure. Yeah, why not? Wouldn't you?

Really?

I mean, die—

yeah, nicely done, nicely done. I don't think I'll make it past 90, let's say that. That's my personal prediction. Okay, okay, back to the topic at hand. So they did this entire genome sequence analysis and next-generation sequencing analysis of those people who are living exceptionally long lives.

Okay, so one of the best ways to understand aging, and human aging in particular, is to study people who are are beyond you and me already doing it successfully. And that doesn't mean kind of gracefully, it just means successfully, right?

Yes, yes. There are all these people out there now who make it to 100 and they get that letter from the King of Sweden, or a telegram from the King of England, or 110 or older with functional muscle, with functional brain. And you need to understand what's different about their biology. And that is what motivated Kristin's career as a scientist.

Aging, it's natural, quote unquote. I mean, so is any disease in that it unfolds all the time in natural populations. But what's interesting about aging is the extent to which it drives so many different chronic diseases, right? I mean, the two biggest killers in the US and in most developed countries are heart disease and cancer. These are totally different diseases in terms of their biology, in terms of how they unfold over time. But one of the big things they have in common is that they're by and large not diseases that happen to 20-year-olds. They're vastly more likely to happen to 80-year-olds. And part of the promise here is that by understanding these pathways that underlie aging, we're going to unlock new targets that might help treat and in the long run even prevent some of these diseases.

We've learned from nature that aging is incredibly malleable. Work in the early 1990s in the C. elegans worm was key to understanding the aging process. Bless the worms.

It's incredibly easy to study aging in this animal because it only lives for 2 weeks. So you can give it a drug or you can, you know, modify some genes and then do a lifespan experiment and ask what's different. And in the worm, they've tried knocking out like every single gene to see what the impact is on lifespan. One of the cool things is that like over 100 work. So it's like, you know, there's nothing special about the natural lifespan. It's very malleable. And by doing a combination of things in the worm, they've as much as like 10x the lifespan, which is crazy, right? So I don't expect those same things to translate to us. Like, we are not worms. But I do think that as another species, there are going to be lots of different levers on healthy aging.

So what is BioAge's area of focus?

At BioAge, we've deliberately focused on the immune system, the brain, and the muscle for a few different reasons. What we like about those is that, one, we can learn a lot about human aging in those organ systems from some very special biobanks that we have at BioAge that track human longitudinal aging over decades. Two, from a clinical perspective and clinical trial, there's really a lot of unmet need there in certain indications like Alzheimer's or diabetes where clinical development is very challenging and maybe better suited to a larger pharma. And third, we also are deliberately choosing first indications and first focus areas. We believe we can do translational animal work because again, like, there are so many, you know, translation is really hard, right? Like, that's one reason why at BioAge we're focused on understanding how humans age, looking for signals that matter in large populations, populations of humans.

So Kristen is building a molecular map to understand why those that make it to the age of 100 are often in better health than the average person.

Yeah, like a flow diagram of information from biobanks. So using modern technologies to look at every molecule in there that we possibly can, and making a big list of things in each person, starting to ask questions like, what is different about those middle-aged people who go on to live to 90+ in great health versus those who and what is the molecular map of differences, and which of those could be a lever to help the rest of us age better.

So our whole approach really is to partner with some really special biobanks that started collecting samples from healthy middle-aged people as long as 50 years ago. So these are like really precious samples that have been saved for decades and are connected to health records that track information on how long those people went to live. The diseases they got as they aged, but also healthspan variables like their walking speed and how that changed over time, their muscle function and how that changed over time, their cognitive function and how that changed over time.

In December, BioAge had that really great set of results from a Phase 1B clinical trial which confirmed that what they believed about muscle aging was true.

This was the highlight of the year, I think, for us, for the company. We announced some positive data in a Phase 1B trial, our very first look at a drug that we think has the broad potential to impact muscle aging. And this is exactly the kind of pathway that we're looking for. There's a molecule peptide called epilin. It circulates in your blood. Interestingly, it's released by exercise. And we saw in our data sets that middle-aged people with more apolin were living longer, had better muscle function, had also better cognitive function as they aged in a linear way, right? So the more the better.

Based on that finding, the team tried giving a drug that basically mimicked APL to two older mice to see if it could improve their muscle function, and they saw some compelling results. So spurred on by those results, they looked at some older volunteers on bed rest, and normally after around 10 days there is substantial muscle atrophy in older populations.

Yeah, that's it, the decline in muscle mass as you age. I feel it happening to me, the muscle dimensions, the quality. Yep, that's absolutely happening. So what do we do?

Okay, go to the gym. Anyway, so what they saw was that for older people taking the drug, there was a significant improvement on several different dimensions.

So we're very excited by this initial data. We think this has very broad potential for some serious indications driven by muscle aging, and the first Phase 2 trial that we're going to initiate for this 2023 is looking at something called diaphragmatic atrophy. So this is for mechanically ventilated patients in the ICU. You're on a ventilator. It's millions of people every year. And if you think about it, your diaphragm muscle, it's one of those muscles that works 24/7. And if you shut that off, it can atrophy in a matter of days, like 3 to 4 days. And this happens in a very large percentage of patients. And when it does, it's very serious. It increases the length of stay in the ICU. It increases your risk of dying. So we think that if this mechanism can prevent atrophy of this really important muscle in this really serious condition, it could have a lot of potential to help these patients.

And that's not an area people consider when they think of aging.

So how does Kristen intend to take this research further?

Any older patients that are in the ICU at rest for an extended period of time, it's just incredibly hard for them to recover from. When you're older and just in bed for 10 days, you see these significant declines. It takes a month or more to similar declines in younger people. So it's just much harder to recover from. So that's the first indication where we think it can sort of help this really huge unmet need. But in the longer run, I mean, everybody loses muscle mass as they age. This has functional consequences for a very large proportion of people. And there's, you know, broader indications like sarcopenia, like frailty, where the mechanism could have potential.

Well, it seems that Kristen and BioAge are really driving forward our knowledge of what the biomarkers are for aging. I mean, as well as wrinkles and feeling a bit creaky, we can consider aging just more than a consequence of living a long time. Perhaps it's a pathology, and it's clearly a whole load more complex complicated and nuanced than that.

Biomarkers of aging are hard, right? Because even if we do a clinical trial, you might see the disease improve, but how do you really know that you're impacting aging? So I think that as a field, we have to learn what reliable biomarkers look like that actually predict future function 10 years in the future, and it's going to help accelerate how things go. What I often say, right, is there's examples out there like statins. That today are prescribed like an aging drug, right? Like if you're 40, you have a couple of risk biomarkers, take a statin for prevention. And statins were first approved for a very narrow orphan disease, familial hypercholesterolemia, and the label was expanded over time. So there is this sort of recipe that's used before in drug discovery and development that I think we can apply again for other aging mechanisms where you start with a narrow disease and you learn over time, right, what else it's doing that's beneficial and you expand that indication.

All right, Connor, shall we move to the segment that we call What We Learned This Week? Shall I start with something that I think is related to the topic that we just talked about? And it's really a reflection. Lars and I were watching the show The English, which is about, you know, the Old West and settling America and stealing land from the indigenous population. And I started rereading a book which is diaries of women who were settling in the Old West from the East Coast of America. And what I reflected on was, you know, these diaries are about, oh, we traveled 10 miles today, we traveled 15 miles today. And they're looking at the landscape, which was so open back then, and observing the mountains and the trees and the animals that we no longer have with us. And I thought about that is recent history. And aging back then, it, you know, we didn't reach 90 or 100, or if you did, you were an absolute treasure. So I guess the reflection and what I've learned is, gosh, we travel time and distance in such a way that we take for granted, but it really is an incredible accomplishment.

So something that I learned this week that was incredibly exciting and made me feel great was that for the first time, farmers in The Philippines have grown what's known as golden rice, genetically engineered rice, on a massive scale, and they've harvested almost 70 tons of it. And this rice is a rice which is rich in vitamin A, because vitamin A deficiency is a major health problem in many areas in the developing world, especially the Philippines. It causes children to go blind and suffer cognitive impairments, and they can die from a weak immune system. So this is really good news showing that genetic engineering can really bring great advances to human health. So very exciting stuff.

Those are really optimistic things to learn. And just like we just talked about on this episode is the developments in gene editing, the developments in looking at longevity and our biology and what makes us live longer, healthier lives. So absolutely, thank you. Wow. So I've just learned what you learned and you just learned what I learned. All right. And this podcast is produced with the help of Beth Armit Brewster editing and mixing, and our theme music is by Tom Henley and Banda Productions. Other music is from Epidemic Sound. My name is Dodie Axelson.

And I am still Conor McKechnie. Make sure you rate us on Spotify or wherever it is that you listen to our podcast. Tell your friends and family. We'll be back soon, a little bit older, a little bit wiser, but probably not genetically engineered, and we'll have another episode of Discovery Matters.