Bringing back the Mammoth: featuring Colossal Biosciences’ CEO Ben Lamm and Scientist Christopher Mason

May 16, 2023
Blog Article

From DeciBio Consulting, I am your host, Julia Kirkland, and this is the DeciBiome. 

Julia Kirkland: I am thrilled to introduce you all to today's discussion and guests. We are joined by Colossal Biosciences’ co-founder and CEO, Ben Lamm, as well as Colossal Biosciences' Scientific Advisor and Professor of Computational Genomics, Christopher Mason, to discuss the science behind Colossal's mission to de-extinct the woolly mammoth and furthermore, the implications their advancements in genetic engineering and embryology may have on human health applications. 

To give you a little bit of background, Colossal has sequenced DNA from multiple woolly mammoths and intends to genetically insert the cold-resistant genes of woolly mammoths into the Asian elephant genome. Once brought to term, the goal for these Asian elephant woolly mammoth hybrids is to repopulate the grasslands of the tundra and compact permafrost to help slow the release of carbon and methane into the atmosphere. Colossal's attempts to combat the climate crisis through de-extinction efforts have gained significant media attention, and the company has received $224 million in funding since their founding in 2021. Their most recent $150 million Series B funding round has allowed them to launch their Avian Genomics Group with the goal of using synthetic biology to resurrect the dodo bird. I am also joined by my co-hosts, Graham Friedman and Lauren Brodsky, who are consultants here at DeciBio. You can take it away, Lauren. 

Lauren Brodsky: Thank you for the intro, Julia, and thank you, Ben and Chris, for joining us today. We're really looking forward to hearing more about Colossal Biosciences. So, it would be great to start the discussion with the purpose behind bringing back the woolly mammoth. We understand that woolly mammoths could potentially help sequester carbon from the atmosphere by restoring grasslands. Could you describe this ecological process for us? 

Ben Lamm: Yeah, and we don't, and we still don't know exactly, right, because we didn't have a plethora of scientists doing great measurements back in the Pleistocene era, so we don't, we don't exactly have like the exact measurements, right, but what's been pretty interesting and what we have seen is that, the Sergey and Nikita Zimov's work in Pleistocene Park, as well as some additional work in other parts of the tundra, have shown that the reintroduction of coal-tolerant fauna and megafauna, has a huge opportunity, one, to create a better oxygen-nitrogen cycle in that area by just increasing biodiversity. It also has shown the potential to uproot and change the ecosystem landscape to be more of a steppe-like, or the mammoth steppe-like ecosystem with more an Arctic grassland approach versus the taiga forest that exists today. The results show that they can actually lower, in kind of concentrated locations with the right level of population densities of musk ox, camels, horses, and other species, ground temperatures by up to eight degrees in certain locations, right, in the winter months, and that obviously permeates through the summer months. That, coupled with the potential to create this Arctic grassland, they think there's, we've kind of modeled it as two to three times more efficient at the albedo effect. And so when you start to look at that, it starts to paint a really interesting potential of the application of Arctic rewilding and bringing not just the existing megafauna, but engineered, charismatic, giant megafauna back to the landscape. 

Lauren Brodsky: Great. That sounds like it could really have some amazing environmental benefits. So shifting more to the scientific feasibility of de-extincting mammoth genes, we were wondering, do you have a fully sequenced and annotated mammoth genome? And if not, what sort of material are you working with today? 

Ben Lamm: Yeah, so one of our collaborators, we work with a lot of great scientists like, Chris Mason and George Church and Lueva Dahlin from the University of Stockholm, who's amazing. He published a paper today in Cell where he's actually doing an analysis of 23 different mammoth genomes. So we have 54 today. It's a combination of some published samples, some samples that we've recovered, as well as 40 from Lueva's lab. And we work very, very closely with them as well to do the computational analysis. There's not a complete reference genome built today. It's something that we, with some of our collaborators, are actively working on. We have enough of the genome and the various assemblies put together that we've been able to derive some of the 65 targeted areas that we're making edits that we think represents the highest likelihood of cold tolerance. Everything from how nerve endings work and hemoglobin is produced at sub-freezing temperatures, as well as the subcutaneous fat layer in the iconic woolly coat and some other ones like small ears and tails for heat loss, right? So we have what we need to be successful in kind of our directed evolution work, but from a sheer scientific perspective, we would love to see that reference genome and we're working on that with some of our collaborators now. 

Graham Friedman: Cool. And just drilling down even further on the science there, how do you establish the functions of these genes when you don't have them in a living organism? Is it through comparison to, you know, Asian elephants or just, just curious about the details behind that a little bit? 

Christopher Mason: Yeah, a lot of it is, I mean, there's, there's at least two ways you can get information, even if it's fragments of DNA, there's still a lot of information there. And a lot of this is through comparative vertebrate genomics where we can compare, say, for example, the last of the woolly mammoths that were there in near in Siberia, and look at the Asian elephant or other related species, and build these, these synthetic maps where groups of genes come together and compare them and often are conserved over tens of millions of years, in some cases, or hundreds of millions of years where you have these really core sets of genes that we know from other species. And so even if we get bits of them, we can impute and infer a pretty fair amount. But also, we get methylation information, so there's differential rates of degradation of CPG islands where we see methylation. So we can actually, take that as a way to determine the rate of degradation and paint a picture of the regulatory region. So we do a lot of epigenetics in my lab and some of the same principles apply there where you're basically looking at where do we see gene regulatory boundaries?, where can we see where the beginning and ends of genes are?, and even potentially nucleosome positioning, sort of, but it's very early and it's a bit degraded. But, there's a lot of information to get even from fragments of DNA and the methylation states that are still left over. Deamination, of course, occurs during degradation. And you can measure that though, where you've lost that basically that methyl group from the cytosine. But the information is all there once you start to sequence it and do multiple treatments. 

Graham Friedman: Okay, and that's another thing that we were curious to ask about is just sort of what is the state of the epigenetic information? It sounds like there's quite a lot still there, but is that a limiting factor to a large extent? Or do you feel like you have all the information that you need in that regard? 

Christopher Mason: It depends on how degraded the sample is. There's been a good number of published papers showing the correlation between the amount of degradation and the degree of preservation. Some have showed that even methylated cytosines will degrade a little bit faster in certain settings. And so it's a constant dance of degradation, but we know a little bit about how different regions degrade at different rates. And so it actually helps us- there's been enough studies on ancient DNA, we can begin to tease that out. But it's not going to be quite like some of the epigenetic clockwork where people are trying to, discern the age of the animal when it died. We probably can't quite do that. But we can get, a lot of information in terms of gene regulatory information. And again, we can look through orthologous regions through other species, we can get a fair amount of other information and impute that based on what we know by comparison. 

Ben Lamm: I think people are, I think some of those people, when they have a picture of colossal their mind, they think it's like actually taking frozen DNA and frozen things like putting it in like pipetting, like jamming it in. I think people don't recognize the amount of computational biology and work that goes on in software. Sometimes when people go into the lab, they see a lot of people working on computers. And I think it sometimes throws them for a loop because they don't expect the amount of computational analysis that goes into a lot of the decisions and even in designing RNAs and everything that we're working on.

Christopher Mason: Yeah. And also just the sequence analysis, the assembly tools, all the computational biology work that's come over decades of comparative vertebrate evolutionary studies is now being deployed at Colossal. Yeah, you might think that people are just at Colossal like mixing in cocktails with mammoth DNA and taking shots, that it feels that way, but that is not what happens. There's a lot of it's a great group and a fun lab that's there. 

Form Bio is also a company that just spit out of Colossal that is focused on this question and commercialization of some of the tools that are being built for mapping genomes, looking at multiplex CRISPR screens, assembly and also genome editing, all of which are going to be tools in their own right, they get more and more developed. So I think it's all those teams are there in Dallas and elsewhere. 

Ben Lamm: Yeah. To be successful in this, you kind of have to build the entire infrastructure. You don't get to build it in pieces, right and farm it out to other people. You actually have to kind of build the entire kind of functional system. And then when you start to look at things from that kind of system perspective, you start to notice opportunities for invention, but even more so innovation, like we do with Form Bio. And we try to target things around software, hardware and wetware that we can also commercialize, not just benefit for de-extinction efforts or, or even conservation, but human health care. And so that's something that's pretty core to how we view the world and how we design these systems. 

Graham Friedman: Cool. And just thinking about sort of the ways that you're describing specific edits to the elephant genome, and how you're kind of adding elements of the mammoth genome. And also, as has been described in previous podcasts and articles and things, it seems like you're not really trying to de-extinct the mammoth in a strict sense, but you're really de-extincting traits and genes. So kind of in that vein, we're interested if you're thinking of adding any other traits, if it's all just centered around cold resistance, or if there are other things that you might try to bring back from a mammoth and put into some sort of hybrid species. 

Ben Lamm: You know, I think it maybe a function of, watching too many movies, maybe it's a function of having people like Chris and George are on the table, or the fact that some of the non biologists are on the table in software, we really kind of think of these as like engineering problems, and systems problems, right? And so sometimes we have philosophical debates on, oh, is it a mammoth or is a cold adaptive elephant that likes the cold that would de-extinct the genes and alleles from a mammoth that's been adapted and upregulated and downregulated. So a lot of times we will just default to, okay, cool, it's a boy mammoth 2.0, right? If we had the opportunity to engineer one, this is how we would do it, right? We take an architecture of like the Asian elephants that works because they are here, and, seemingly propagating, and then create the right, de-extinct to your point, the core gene to create those phenotypes that we're looking for, right? Because our goal is for ecosystem restoration, and for them to be able to thrive and be cold tolerant. But we also want that, some of those iconic traits that give us this phenotype that, when we see it, we're all really excited. And so, we do have some of those philosophical conversations with, there are certain subsets of the population that really want to have that conversation over and over and over and over again. We just like to do the work. So we are focusing right now on, to your question, just, de-extincting core genes and traits that we think will create the phenotypes and cold tolerance levels that we look like, that we're looking for in mammoths, as well as looking at where we can be smart and upregulated and downregulated and engineer in other traits. We're not, we're not trying to build chimeric animals. We're not like pulling in other traits or genes or subsystems. But we are to Chris's point, we're doing a lot of comparative analysis work, even with just how some of these mammals, including, polar bears and caribou and others, are cold adaptive and how they produce hemoglobin at sub-freezing temperatures. So we're trying to be thoughtful in that analysis approach. 

Christopher Mason: Yeah, and I think a lot of it's that you can see with comparative genomics, the regions that are very divergent between the fragments of mammoth genomes and the other elephants and see what really is different is what helps guide the light. 

Graham Friedman: Yeah, that only makes sense. And then another thing is just that we've thought about a bit is the gestation period. So woolly mammoths, I think, are believed to have a gestation period of around 22 months. And we imagine that that would probably pose some challenges sort of for the experimental process. And we're curious how you go about trying to work with an animal that has such a slow life cycle and what sorts of challenges and workarounds has that involved for Colossal?

Ben Lamm: We try to be, I would say, thoughtfully for the right response, right? All of the technology that we are developing for conservation that fall in that assisted reproductive technology world, we want to make it part of our mission. And what we talked about publicly is making that available for free. We've got an incredible, two conservation groups. And so we have an incredible animal husbandry group with Dr. Winnie Kiso and Matt James and their teams below them. That really focus a lot on animal husbandry and whatnot. We work very closely with Thomas Hildebrand, who's arguably one of the world experts with OPU and other technologies around assisted reproductive technology in the northern. He works, most famously, on the northern white rhino and a few other genetic, big genetic rescue projects. And so for us, we are estimating a 22 month gestation process, right? Because it's also the same as the Asian elephant. We're doing a lot of studies on reproductive physiology and some of the different reproductive cuing in elephants right now, and some of their related species related to being similar gestational species like hyraxes and others. And so we've been very thoughtful, I think, on the approach around that. 

And then, because these animals will be birthed through surrogates, we're starting to work on some of these other technologies that can help us both from a oocyte aspiration all the way through, which has never been done yet with elephants to our knowledge in the world, as well as gametogenesis. And that's some of the stuff we're doing in our lab with some of the IVFC and some of the other work that we're doing, as well as IVF and wild type in elephants. And some of those tools and technologies, when you look at it, it's not just the 22 month gestation that's important. It's the fact that these animals also reach sexual maturity at a very long time-so it takes about 13 years to reach sexual maturity. So outside of the challenges that represents with creating breedable populations, our mammoth 2.0, for lack of better words, it also creates an opportunity for us to iterate and build technology that can then apply directly towards elephant conservation and captive breeding elephant programs to increase elephant numbers. And so those are things that, we're working on. And because I think I mentioned earlier, we look at it as a system. We're starting to work on all of those things now. And so we have a whole team that's not just doing the IVFC work. We have a separate team that's doing animal husbandry and wild type. Our goal is to get to wild type IVF in elephants as fast as possible. We may have some news coming out hopefully this year around oocyte retrieval and aspiration in elephants, which is pretty cool because of the conservation implications of that. And then, looking to get to the point that we successfully birthed a wild type elephant because then from there it's just plugging in the edited one, right? And so, from at least an oversimplification perspective. So with all the projects that we're working on, the done art is a 13 and a half day gestation. So continuing to work out the kinks on the kind of faster iteration animals, so that we can be very, very thoughtful and have done it on newer species before we make our final attempts on the mammoth is pretty critical in our animal husbandry plan. 

Christopher Mason: And it's helpful also for other species, like some of the work is also to monitor for cloning, like for the black-footed ferret is another project that's not related to mammoth per se, but the method of cloning and tracking embryos and seeing, because every time you create an embryo, you epigenetically reprogram and start from scratch. And then cloning that process is not always perfect, but we're now learning when things go wrong or right and exactly how and where and when you could intervene to kind of tweak it and make sure you have a fully reprogrammed and fully viable embryo along the way. So we're taking lessons from as many other creatures as we can, but all of these tools will help conservation broadly. 

Graham Friedman: Got it. And to what extent does the work in other animals contribute to understanding questions around the maternal environment and, you know, the environment that exists as the embryo develops? And I know that there's been some talk of artificial wombs, and we're just curious how you see that factoring in. And is that something that could spin out of Colossal in the future, potentially, or otherwise something that will be kind of directly leveraged for human reproductive health and medical advancements? 

Ben Lamm: Yeah, so Colossal, I think we've taken a pretty strong stance that we're focused on species preservation and de-extinction, right? And so any of the tools and technologies that we think have an application to help humanity on its journey in human health care, we'll spin those out, like teams that go work with that. Some of those are regulated industries. We really want to help support those like we did with FormBio. We have a 17-person team that just focuses on exudatory development, right? So it's very, very early. It's funny, de-extinction and some of the, like, 99% of the work that we do every day just doesn't sound crazy to me, but the work that keeps me up at night is the exudatory development. Because the applications to the exudatory development, regardless of where you think it falls in human health care long-term-I can make a case for why I think it's really important for us as a society to develop tools better than what we have in IVF and look at, long-term population collapse, or in Chris's world, long-term interspecies seeding. 

But what's key is, we are hopeful that in the next, five to six years, we can have a system in place that we feel really good about, not for, necessarily humans or anything else, but be able to demonstrate taking several different mammal types and placental types from a embryo full to term. And so I think we have a pretty thoughtful approach on it, in terms of how we are trying to architect the system. And, we've made significant progress both in marsupials and in mice. Obviously with marsupials, you get the benefits that are not really placental mammals, and you get a 13 and a half day gestation versus 24, right? So you can even accelerate faster, and there's no real implantation layer. It kind of just sticks up through the whole thing. So we're trying to be very thoughtful in the approach. Our goal, though, and the reason why we're pursuing it, is because we think it's transformative outside of potential implications as a full system for human health care. We think that just pieces of the system can be helpful now in human health care. So like we have a really novel microfluidic delivery system, and a very novel camera system, and a very novel hydrogel matrix, that we've seen better success in mouse and pig and bovine embryos than we have using traditional methods. And so we think some of the just the pieces of the system could be really helpful for and have implications for embryo manipulation and transference in human health care. But we also think that long term, as it relates to species preservation or de-extinction, is that being able to truly hit your first question of making material impact in the wild with mammoths, I think we can do it with Thylacines and dodos and other animals, but to really create kind of the impact scale we need in the Arctic Circle and the Ancircle polar north, we will need exudero systems because you just can't rely on a 22 month gestation and 13 year sexual maturity cycle to get the stable populations that make the impact level at the scale that George wants. And so it is critical for our, I think, our long term goals, not critical for our de-extinction success, but we're spending a lot of time on it. 

Christopher Mason: And with other related organisms, there's some work on looking at marsupials and comparing it to other things that are sort of like exudero technologies, but just in kangaroos and related marsupials, but there they have pouch jam, which we're also investigating, which is a term I didn't know until I started hanging out with Ben is pouch jam. 

Ben Lamm: Potion to pouch jam. 

Christopher Mason: That's right. You know, but I wanted to comment, it's not just the genetics or the embryology or epigenetics, but also the microbiome, like of these pouches and the gas exchange, the nutrients, the fluidics, all of these, like every cell of any kingdom of life is in play. And we're trying to model and map all of it. So, because any one of them might be the difference between a successful versus failed exudero system. So keeping an eye on anything that could help us better understand it. 

Julia Kirkland: Yeah so, to wrap things up here, what would be success to you? And then conversely, what would constitute failure? 

Christopher Mason: Sure. I guess success would be we have a large armamentarium of technologies that work for mammoth, but then could help any species that's endangered or has already gone extinct to preserve as a real manifestation of our guardianship duty towards all life past, present, and future. That would be success. Failure would be a complete collapse of like the earth and it's crashing into the sun and we lose all life because we, I mean, like we stopped the magnetic core spinning on the earth somehow, and then we lose the magnetic field that, no, I mean, that would be, I don't even know how we'd do. 

Ben Lamm: If Colossal is responsible for stopping the mantle from turning, then yeah, that would be, I mean, that would be, I didn't, you know, Chris.

Christopher Mason: I think the biggest risk is if people don't understand the value and give headwinds to the technology and how it  is essential for proper conservation and quite literally how we, you know, I think we serve as shepherds of life and caretakers of this planet and potentially others. And I think a failure might be if there's, if we didn't roll that out correctly and there's too many people that just don't understand it. I mean, there's examples where genetics can have a good role, but it gets controversial. Like genetically modified foods, it isn't as bad as its critics thought, but it's not been as good as we hoped it would be. But I think it was so controversial, like we'd never even had a chance to get its chance, I think. And I'd want to make sure we don't have that happen in this case. 

Ben Lamm: I think that is really important, outside of protecting and building tools that I think can help stitch together to build the extinction toolkit that anyone can use. I think it's really important for us too, I think there's an opportunity for Colossal to return and undo some of the kind of sins of the past, if you will, that mankind had a role in. And in some cases it didn't. One of the things that I'm really passionate about in terms of what I think looks like success is I was on the phone with the Tasmanian government the other day and they asked me the same question. So this is probably a different answer than what you heard before. But my answer was, I really hope that one day that the excitement level that you have with the dialysin doesn't exist. And they were like, wait, what does that mean? I was like, well, you know, I hope that we were so successful that we successfully rewilded species and we create a creatable population. They're like wallabies and you're not, you don't have, you've not pulled together this incredible consortium of government and aboriginal and leaders and landowners and other government officials that really need to spend time on this problem because we've helped fix that ecosystem. And there's so many, there's such, there's the right balance of Thylacines back in the ecosystem that when you see one, it's not like this mythical creature to you. Right. And so that's success, right? I think that making this normal is a part of success and that's not going to be through the science that's going to be through the rewilding efforts. 

Julia Kirkland: Thank you both again for taking the time to come on today, I guess to wrap things up here and kind of summarize what we've discussed. We understand that to date, Colossal has well preserved genomic material from 54 mammoths. From this, they've been able to derive 65 target gene areas related to cold tolerance and other essential traits for surviving in the tundra. They've been able to garner what the functions of these genes are through comparative vertebrae genomics and preserve methylation in conjunction with advanced computational techniques. We also learned that markers of degradation can unveil some important epigenetic information used to inform their genetic engineering, but we also know that there are certain limitations on this still. 

As for the future, it seems like Colossal is well on their way to help drive forward conservation through the de-extinction of numerous species, as well as rewilding in addition to advancing a plethora of cutting edge technologies. I think what will be interesting to watch play out is, you know, this is a huge operation and it seems like there is significant opportunity for pieces of the system to advantage and benefit all different facets of not only the biotech space, but also the human health care system and conservation efforts in general. Form Bio is just one of the examples of this as it facilitates commercialization and multiplex CRISPR editing, as well as complex genome assembly. They're actively working on various aspects of embryology, including ex-utero development and advanced IVF methods that could be applicable to other endangered species, as well as human medicine. We are very excited to see how Colossal fulfills their mission and we'll be keeping a close eye on the advancements they make in the future. 

Thank you to everyone who participated in this episode. And of course, thank you to all of our listeners for tuning in. Hope to catch you next time on the DeciBiome.

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