Microbial protein found in Streptococcus pyogenes M1 GAS
POPULARITY
3 episodes with Cas9
3 episodes with Cas9
2 episodes with Cas9
5 episodes with Cas9
3 episodes with Cas9
2 episodes with Cas9
2 episodes with Cas9
3 episodes with Cas9
2 episodes with Cas9
4 episodes with Cas9
2 episodes with Cas9
2 episodes with Cas9
3 episodes with Cas9
2 episodes with Cas9
7 episodes with Cas9
4 episodes with Cas9
4 episodes with Cas9
3 episodes with Cas9
This week we talk about gene-editing, CRISPR/Cas9, and ammonia.We also discuss the germ line, mad scientists, and science research funding.Recommended Book: The Siren's Call by Chris HayesTranscriptBack in November of 2018, a Chinese scientist named He Jiankui achieved global notoriety by announcing that he had used a relatively new gene-editing technique on human embryos, which led to the birth of the world's first gene-edited babies.His ambition was to help people with HIV-related fertility problems, one of which is that if a parent is HIV positive, there's a chance they could transmit HIV to their child.This genetic modification was meant to confer immunity to HIV to the children so that wouldn't be an issue. And in order to accomplish that immunity, He used a technology called CRISPR/Cas9 to modify the embryos' DNA to remove their CCR5 gene, which is related to immune system function, but relevant to this undertaking, also serves as a common pathway for the HIV-1 virus, allowing it to infect a new host.CRISPR is an acronym that stands for clustered regularly interspaced short palindromic repeats, and that refers to a type of DNA sequence found in all sorts of genomes, including about half of all sequenced bacterial genomes and just shy of 90% of all sequenced archaea genomes.Cas9 stands for CRISPR-associated protein 9, which is an enzyme that uses CRISPR sequences, those repeating, common sequences in DNA strands, to open up targeted DNA strands—and when paired with specific CRISPR sequences, this duo can search for selected patterns in DNA and then edit those patterns.This tool, then, allows researchers who know the DNA pattern representing a particular genetic trait—a trait that moderates an immune system protein that also happens to serve as a convenient pathway for HIV, for instance—to alter or eliminate that trait. A shorthand and incomplete way of thinking about this tool is as a sort of find and replace tool like you have in a text document on your computer, and in this instance, the gene sequence being replaced is a DNA strand that causes a trait that in turn leads to HIV susceptibility.So that's what He targeted in those embryos, and the children those embryos eventually became, who are usually referred to as Lulu and Nana, which are pseudonyms, for their privacy, they were the first gene-edited babies; though because of the gene-editing state of the art at the time, while He intended to render these babies' CCR5 gene entirely nonfunctional, which would replicate a natural mutation that's been noted in some non-gene-edited people, including the so-called Berlin Patient, who was a patient in Germany in the late-90s who was functionally cured of HIV—the first known person to be thus cured—while that's what He intended to do, instead these two babies actually carry both a functional and a mutant copy of CCR5, not just the mutant one, which in theory means they're not immune to HIV, as intended.Regardless of that outcome, which may be less impactful than He and other proponents of this technology may have hoped, He achieved superstardom, briefly, even being named one of the most influential people in the world by Time magazine in 2019. But he was also crushed by controversy, stripped of his license to conduct medical research by the Chinese government, sent to prison for three years and fined 3 million yuan, which is more than $400,000, and generally outcast from the global scientific community for ethical violations, mostly because the type of gene-editing he did wasn't a one-off sort of thing, it was what's called germ-line editing, which means those changes won't just impact Lulu and Nana, they'll be passed on to their children, as well, and their children's children, and so on.And the ethical implications of germ-line editing are so much more substantial because while a one-off error would be devastating to the person who suffers it, such an error that is passed on to potentially endless future generations could, conceivably, end humanity.The error doesn't even have to be a botched job, it could be an edit that makes the edited child taller or more intelligent by some measure, or more resistant to a disease, like HIV—but because this is fringy science and we don't fully understand how changing one thing might change other things, the implications for such edits are massive.Giving someone an immunity to HIV would theoretically be a good thing, then, but if that edit then went on the market and became common, we might see a generation of humans that are immune to HIV, but potentially more susceptible to something else, or maybe who live shorter lives, or maybe who create a subsequent generation who themselves are prone to all sorts of issues we couldn't possibly have foreseen, because we made these edits without first mapping all possible implications of making that genetic tweak, and we did so in such a way that those edits would persist throughout the generations.What I'd like to talk about today is another example of a similar technology, but one that's distinct enough, and which carries substantially less long-term risk, that it's being greeted primarily with celebration rather than concern.—In early August of 2024, a gene-editing researcher at the University of Pennsylvania, Dr. Kiran Musunuru, was asked if there was anything he could do to help a baby that was being treated at the Children's Hospital of Philadelphia for CPS1 deficiency, which manifests as an inability to get rid of the ammonia that builds up in one's body as a byproduct of protein metabolism.We all generate a small amount of ammonia just as a function of living, and this deficiency kept the baby from processing and discarding that ammonia in the usual fashion. As a result, ammonia was building up in its blood and crossing into its brain.The usual method of dealing with this deficiency is severely restricting the suffer's protein intake so that less ammonia is generated, but being a baby, that meant it wasn't able to grow; he was getting just enough protein to survive and was in the 7th percentile for body weight.So a doctor at the Children's Hospital wanted to see if there was anything this gene-editing researcher could do to help this baby, who was at risk of severe brain damage or death because of this condition he was born with.Gene-editing is still a very new technology, and CRISPR and associated technologies are even newer, still often resulting in inaccurate edits, many of which eventually go away, but that also means the intended edit sometimes goes away over time, too—the body's processes eventually replacing the edited code with the original.That said, these researchers, working with other researchers at institutions around the world, though mostly in the US, were able to rush a usually very cumbersome and time-consuming process that would typically take nearly a decade, and came up with and tested a gene-editing approach to target the specific mutation that was causing this baby's problems, and they did it in record time: the original email asking if Dr Musunuru might be able to help arrived in August of 2024, and in late-February of 2025, the baby received his first infusion of the substance that would make the proper edits to his genes; they divided the full, intended treatment into three doses, the first being very small, because they didn't know how the baby would respond to it, and they wanted to be very, very cautious.There were positive signs within the first few weeks, so 22 days later, they administered the second dose, and the third followed after that.Now the research and medical worlds are waiting to see if the treatment sticks; the baby is already up to the 40th percentile in terms of weight for his age, is able to eat a lot more protein and is taking far less medication to help him deal with ammonia buildup, but there's a chance that he may still need a liver transplant, that there might be unforeseen consequences due to that intended edit, or other, accidental edits made by the treatment, or, again, that the edits won't stick, as has been the case in some previous trials.Already this is being heralded as a big success, though, as the treatment seems to be at least partially successful, hasn't triggered any serious, negative consequences, and has stuck around for a while—so even if further treatments are needed to keep the gene edited, there's a chance this could lead to better and better gene-editing treatments in the future, or that such treatments could replace some medications, or be used for conditions that don't have reliable medications in the first place.This is also the first known case of a human of any age being given a custom gene-editing treatment (made especially for them, rather than being made to broadly serve any patient with a given ailment or condition), and in some circles that's considered to be the future of this field, as individually tailored gene-treatments could help folks deal with chronic illnesses and genetic conditions (like cystic fibrosis, Huntington's disease, muscular dystrophy, and sickle cell), but also possibly help fight cancers and similar issues.More immediately, if this treatment is shown to be long-term efficacious for this first, baby patient, it could be applied to other patients who suffer the same deficiency, which afflicts an estimated 1 in 1.3 million people, globally. It's not common then—both parents have to have a mutant copy of a specific gene for their child to have this condition—but that's another reason this type of treatment is considered to be promising: many conditions aren't widespread enough to justify investment in pharmaceuticals or other medical interventions that would help them, so custom-tailored gene-editing could be used, instead, on a case-by-case basis.This is especially true if the speed at which a customized treatment can be developed is sped-up even further, though there are concerns about the future of this field and researchers' ability to up its efficiency as, at least in the US, the current administration's gutting of federal research bodies and funding looks likely to hit this space hard, and previous, similar victories that involved dramatically truncating otherwise ponderous developmental processes—like the historically rapid development of early COVID-19 vaccines—are not looked at favorably by a larger portion of the US electorate, which could mean those in charge of allocating resources and clearing the way for such research might instead pull even more funding and put more roadblocks in place, hobbling those future efforts, rather than the opposite.There are plenty of other researchers and institutions working on similar things around the world, of course, but this particular wing of that larger field may have higher hurdles to leap to get anything done in the coming years, if current trends continue.Again, though, however that larger context evolves, we're still in the early days of this, and there's a chance that this approach will turn out to be non-ideal for all sorts of reasons.The concept of tailored gene-editing therapies is an appealing one, though, as it could replace many existing pharmaceutical, surgical, and similar approaches to dealing with chronic, inherited conditions in particular, and because it could in theory at least allow us to address such issues rapidly, and without needing to mess around with the germ-line, because mutations could be assessed and addressed on a person-by-person basis, those edits staying within their bodies and not being passed on to their offspring, rather than attempting to make genetic customizations for future generations based on the imperfect knowledge and know-how of today's science, and the biased standards and priorities of today's cultural context.Show Noteshttps://www.nejm.org/doi/full/10.1056/NEJMoa2504747https://www.nih.gov/news-events/news-releases/infant-rare-incurable-disease-first-successfully-receive-personalized-gene-therapy-treatmenthttps://www.wired.com/story/a-baby-received-a-custom-crispr-treatment-in-record-time/https://www.wsj.com/tech/biotech/crispr-gene-editing-therapy-philadelphia-infant-8fc3a2c5https://www.washingtonpost.com/science/2025/05/15/crispr-gene-editing-breakthrough/https://www.npr.org/sections/shots-health-news/2025/05/15/nx-s1-5389620/gene-editing-treatment-crispr-inheritedhttps://interestingengineering.com/health/first-personalized-crispr-gene-therapyhttps://www.nature.com/articles/d41586-025-01496-zhttps://www.nytimes.com/2025/05/15/health/gene-editing-personalized-rare-disorders.htmlhttps://www.nytimes.com/2025/05/31/world/asia/us-science-cuts.htmlhttps://www.livescience.com/health/genetics/us-baby-receives-first-ever-customized-crispr-treatment-for-genetic-diseasehttps://en.wikipedia.org/wiki/He_Jiankui_affairhttps://en.wikipedia.org/wiki/CCR5https://en.wikipedia.org/wiki/Berlin_Patienthttps://en.wikipedia.org/wiki/CRISPR_gene_editinghttps://en.wikipedia.org/wiki/CRISPRhttps://pmc.ncbi.nlm.nih.gov/articles/PMC6813942/ This is a public episode. If you'd like to discuss this with other subscribers or get access to bonus episodes, visit letsknowthings.substack.com/subscribe
The seismic changes made by the current administration in the United States continue to impact the scientific community. The business news segment of this week's episode covers the effects of job cuts on biotech, Roche's manufacturing and R&D plans amid tariff threats, and shares an update on Eli Lilly's diabetes pill. Also, in honor of DNA Day, we reminisce about how far the field has come since the discovery of the structure of DNA and the completion of the Human Genome Project. We also talk about today's DNA-related advances that use machine learning to design tailored Cas9 proteins and multiple sequencing technologies to study mutation rates in four generations of the same family. Join GEN editors Corinna Singleman, PhD, Alex Philippidis, Fay Lin, PhD, and Uduak Thomas for a discussion of the latest biotech and biopharma news. Listed below are links to the GEN stories referenced in this episode of Touching Base:After Job Cuts, “We're Entering a Very New Territory for Biotech. By Alex Philippidis, GEN Edge, April 17, 2025 Roche Commits $50B to U.S. Manufacturing, R&D as Tariffs Loom By Alex Philippidis, GEN Edge, April 22, 2025 StockWatch: Investors Hungry for Lilly after Diabetes Pill Aces Phase III Trial By Alex Philippidis, GEN Edge, April 20, 2025 Machine Learning Engineers Bespoke Cas9 Enzymes for Gene EditingBy Fay Lin, PhD, GEN, April 22, 2025Multi-Platform Sequencing Study of Four Generations Sheds Light on Mutation RatesGEN, April 23, 2025 Hosted on Acast. See acast.com/privacy for more information.
Drive with Dr. Peter Attia: Read the notes at at podcastnotes.org. Don't forget to subscribe for free to our newsletter, the top 10 ideas of the week, every Monday --------- View the Show Notes Page for This Episode Become a Member to Receive Exclusive Content Sign Up to Receive Peter's Weekly Newsletter Feng Zhang, a professor of neuroscience at MIT and a pioneering figure in gene editing, joins Peter to discuss his groundbreaking work in CRISPR technology, as well as his early contributions to optogenetics. In this episode, they explore the origins of CRISPR and the revolutionary advancements that have transformed the field of gene editing. Feng delves into the practical applications of CRISPR for treating genetic diseases, the importance of delivery methods, and the current successes and challenges in targeting cells specific tissues such as those in the liver and eye. He also covers the ethical implications of gene editing, including the debate around germline modification, as well as reflections on Feng's personal journey, the impact of mentorship, and the future potential of genetic medicine. We discuss: Feng's background, experience in developing optogenetics, and his shift toward improving gene-editing technologies [2:45]; The discovery of CRISPR in bacterial DNA and the realization that these sequences could be harnessed for gene editing [10:45]; How the CRISPR system fights off viral infections and the role of the Cas9 enzyme and PAM sequence [21:00]; The limitations of earlier gene-editing technologies prior to CRISPR [28:15]; How CRISPR revolutionized the field of gene editing, potential applications, and ongoing challenges [36:45]; CRISPR's potential in treating genetic diseases and the challenges of effective delivery [48:00]; How CRISPR is used to treat sickle cell anemia [53:15]; Gene editing with base editing, the role of AI in protein engineering, and challenges of delivery to the right cells [1:00:15]; How CRISPR is advancing scientific research by fast-tracking the development of transgenic mice [1:06:45]; Advantages of Cas13's ability to direct CRISPR to cleave RNA and the advances and remaining challenges of delivery [1:11:00]; CRISPR-Cas9: therapeutic applications in the liver and the eye [1:19:45]; The ethical implications of gene editing, the debate around germline modification, regulation, and more [1:30:45]; Genetic engineering to enhance human traits: challenges, trade-offs, and ethical concerns [1:40:45]; 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 [1:46:00]; Feng's optimism about the trajectory of science [1:58:15]; and More. Connect With Peter on Twitter, Instagram, Facebook and YouTube
Drive with Dr. Peter Attia Key Takeaways The human genome was sequenced 25 years ago, what's the delay in editing? We know the sequence of the genes but we don't know what most of the genes do, nor do we fully understand the coding and non-coding sequence (yet)CRISPR is an adaptive immune system: After the first infection, the bacteria has been ‘vaccinated' against the virus The next time the virus comes around, it will inject its genetic information into the bacteria but now the bacteria in the CRISPR area have a signature of the virusDifficulties in application of CRISPR: CRISPR uses a guide RNA to recognize the virus DNA but delivery of the Cas + guide RNA needs to be precise and the protein is too large to insert with ease But, solving the delivery issue doesn't mean CRISPR is suitable for all diseases; its most potent application is for genetic mutations (and likely not cancer which has many different mutations in the cell)Future goals of CRISPR technology: Creating more feasible Cas and guide RNA delivery system; inserting large genes into the genome, precisely and efficientlyEthical considerations of gene editing germline: Slippery slope argument: If we allow X and Y, we will enter an unchartered territory with designer babies, making babies smarter (which we don't know how to do), etc. It's worth noting that athletics, and intelligence, are more complicated than we want to believe; even with the right genetics, environment plays a huge role in realizing genesThinking about how the line should be drawn: Is there an obvious and important medical benefit?Read the full notes @ podcastnotes.org View the Show Notes Page for This Episode Become a Member to Receive Exclusive Content Sign Up to Receive Peter's Weekly Newsletter Feng Zhang, a professor of neuroscience at MIT and a pioneering figure in gene editing, joins Peter to discuss his groundbreaking work in CRISPR technology, as well as his early contributions to optogenetics. In this episode, they explore the origins of CRISPR and the revolutionary advancements that have transformed the field of gene editing. Feng delves into the practical applications of CRISPR for treating genetic diseases, the importance of delivery methods, and the current successes and challenges in targeting cells specific tissues such as those in the liver and eye. He also covers the ethical implications of gene editing, including the debate around germline modification, as well as reflections on Feng's personal journey, the impact of mentorship, and the future potential of genetic medicine. We discuss: Feng's background, experience in developing optogenetics, and his shift toward improving gene-editing technologies [2:45]; The discovery of CRISPR in bacterial DNA and the realization that these sequences could be harnessed for gene editing [10:45]; How the CRISPR system fights off viral infections and the role of the Cas9 enzyme and PAM sequence [21:00]; The limitations of earlier gene-editing technologies prior to CRISPR [28:15]; How CRISPR revolutionized the field of gene editing, potential applications, and ongoing challenges [36:45]; CRISPR's potential in treating genetic diseases and the challenges of effective delivery [48:00]; How CRISPR is used to treat sickle cell anemia [53:15]; Gene editing with base editing, the role of AI in protein engineering, and challenges of delivery to the right cells [1:00:15]; How CRISPR is advancing scientific research by fast-tracking the development of transgenic mice [1:06:45]; Advantages of Cas13's ability to direct CRISPR to cleave RNA and the advances and remaining challenges of delivery [1:11:00]; CRISPR-Cas9: therapeutic applications in the liver and the eye [1:19:45]; The ethical implications of gene editing, the debate around germline modification, regulation, and more [1:30:45]; Genetic engineering to enhance human traits: challenges, trade-offs, and ethical concerns [1:40:45]; 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 [1:46:00]; Feng's optimism about the trajectory of science [1:58:15]; and More. Connect With Peter on Twitter, Instagram, Facebook and YouTube
View the Show Notes Page for This Episode Become a Member to Receive Exclusive Content Sign Up to Receive Peter's Weekly Newsletter Feng Zhang, a professor of neuroscience at MIT and a pioneering figure in gene editing, joins Peter to discuss his groundbreaking work in CRISPR technology, as well as his early contributions to optogenetics. In this episode, they explore the origins of CRISPR and the revolutionary advancements that have transformed the field of gene editing. Feng delves into the practical applications of CRISPR for treating genetic diseases, the importance of delivery methods, and the current successes and challenges in targeting cells specific tissues such as those in the liver and eye. He also covers the ethical implications of gene editing, including the debate around germline modification, as well as reflections on Feng's personal journey, the impact of mentorship, and the future potential of genetic medicine. We discuss: Feng's background, experience in developing optogenetics, and his shift toward improving gene-editing technologies [2:45]; The discovery of CRISPR in bacterial DNA and the realization that these sequences could be harnessed for gene editing [10:45]; How the CRISPR system fights off viral infections and the role of the Cas9 enzyme and PAM sequence [21:00]; The limitations of earlier gene-editing technologies prior to CRISPR [28:15]; How CRISPR revolutionized the field of gene editing, potential applications, and ongoing challenges [36:45]; CRISPR's potential in treating genetic diseases and the challenges of effective delivery [48:00]; How CRISPR is used to treat sickle cell anemia [53:15]; Gene editing with base editing, the role of AI in protein engineering, and challenges of delivery to the right cells [1:00:15]; How CRISPR is advancing scientific research by fast-tracking the development of transgenic mice [1:06:45]; Advantages of Cas13's ability to direct CRISPR to cleave RNA and the advances and remaining challenges of delivery [1:11:00]; CRISPR-Cas9: therapeutic applications in the liver and the eye [1:19:45]; The ethical implications of gene editing, the debate around germline modification, regulation, and more [1:30:45]; Genetic engineering to enhance human traits: challenges, trade-offs, and ethical concerns [1:40:45]; 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 [1:46:00]; Feng's optimism about the trajectory of science [1:58:15]; and More. Connect With Peter on Twitter, Instagram, Facebook and YouTube
Clustered regularly interspaced short palindromic repeats (CRISPR-Cas12a), discovered a few years ago, is a method that detects even small levels of pathogens.Professor Kevin J Zwezdaryk and researchers at the Tulane University School of Medicine, USA, are working on a cost-effective, CRISPR-Cas12a-based pathogen detection tool aiming to upgrade patient care. Read more in Research Features Read the original research: doi.org/10.1016/j.bmt.2023.03.004
Guest: ✨ Dr. Neal Baer, Co-Director, Master's Degree Program in Media, Medicine, and Health, Harvard Medical SchoolOn LinkedIn | https://www.linkedin.com/in/neal-baer/On Twitter | https://x.com/NealBaerOn Facebook | https://www.facebook.com/neal.baer.75/On Instagram | https://www.instagram.com/nealbaer/____________________________Host: Marco Ciappelli, Co-Founder at ITSPmagazine [@ITSPmagazine] and Host of Redefining Society PodcastOn ITSPmagazine | https://www.itspmagazine.com/itspmagazine-podcast-radio-hosts/marco-ciappelli_____________________________This Episode's SponsorsBlackCloak
Welcome to The Nonlinear Library, where we use Text-to-Speech software to convert the best writing from the Rationalist and EA communities into audio. This is: Multiplex Gene Editing: Where Are We Now?, published by sarahconstantin on July 16, 2024 on LessWrong. We're starting to get working gene therapies for single-mutation genetic disorders, and genetically modified cell therapies for attacking cancer. Some of them use CRISPR-based gene editing, a new technology (that earned Jennifer Doudna and Emmanuelle Charpentier the 2020 Nobel Prize) to "cut" and "paste" a cell's DNA. But so far, the FDA-approved therapies can only edit one gene at a time. What if we want to edit more genes? Why is that hard, and how close are we to getting there? How CRISPR Works CRISPR is based on a DNA-cutting enzyme (the Cas9 nuclease), a synthetic guide RNA (gRNA), and another bit of RNA (tracrRNA) that's complementary to the gRNA. Researchers can design whatever guide RNA sequence they want; the gRNA will stick to the complementary part of the target DNA, the tracrRNA will complex with it, and the nuclease will make a cut there. So, that's the "cut" part - the "paste" comes from a template DNA sequence, again of the researchers' choice, which is included along with the CRISPR components. Usually all these sequences of nucleic acids are packaged in a circular plasmid, which is transfected into cells with nanoparticles or (non-disease-causing) viruses. So, why can't you make a CRISPR plasmid with arbitrary many genes to edit? There are a couple reasons: 1. Plasmids can't be too big or they won't fit inside the virus or the lipid nanoparticle. Lipid nanoparticles have about a 20,000 base-pair limit; adeno-associated viruses (AAV), the most common type of virus used in gene delivery, has a smaller payload, more like 4700 base pairs. 1. This places a very strict restriction on how many complete gene sequences that can be inserted - some genes are millions of base pairs long, and the average gene is thousands! 2. but if you're just making a very short edit to each gene, like a point mutation, or if you're deleting or inactivating the gene, payload limits aren't much of a factor. 2. DNA damage is bad for cells in high doses, particularly when it involves double-strand breaks. This also places limits on how many simultaneous edits you can do. 3. A guide RNA won't necessarily only bind to a single desired spot on the whole genome; it can also bind elsewhere, producing so-called "off-target" edits. If each guide RNA produces x off-target edits, then naively you'd expect 10 guide RNAs to produce 10x off-target edits…and at some point that'll reach an unacceptable risk of side effects from randomly screwing up the genome. 4. An edit won't necessarily work every time, on every strand of DNA in every cell. (The rate of successful edits is known as the efficiency). The more edits you try to make, the lower the efficiency will be for getting all edits simultaneously; if each edit is 50% efficient, then two edits will be 25% efficient or (more likely) even less. None of these issues make it fundamentally impossible to edit multiple genes with CRISPR and associated methods, but they do mean that the more (and bigger) edits you try to make, the greater the chance of failure or unacceptable side effects. How Base and Prime Editors Work Base editors are an alternative to CRISPR that don't involve any DNA cutting; instead, they use a CRISPR-style guide RNA to bind to a target sequence, and then convert a single base pair chemically - they turn a C/G base pair to an A/T, or vice versa. Without any double-strand breaks, base editors are less toxic to cells and less prone to off-target effects. The downside is that you can only use base editors to make single-point mutations; they're no good for large insertions or deletions. Prime editors, similarly, don't introduce double-strand breaks; instead, they include an enzyme ("nickase") that produces a single-strand "nick"...
Link to original articleWelcome to The Nonlinear Library, where we use Text-to-Speech software to convert the best writing from the Rationalist and EA communities into audio. This is: Multiplex Gene Editing: Where Are We Now?, published by sarahconstantin on July 16, 2024 on LessWrong. We're starting to get working gene therapies for single-mutation genetic disorders, and genetically modified cell therapies for attacking cancer. Some of them use CRISPR-based gene editing, a new technology (that earned Jennifer Doudna and Emmanuelle Charpentier the 2020 Nobel Prize) to "cut" and "paste" a cell's DNA. But so far, the FDA-approved therapies can only edit one gene at a time. What if we want to edit more genes? Why is that hard, and how close are we to getting there? How CRISPR Works CRISPR is based on a DNA-cutting enzyme (the Cas9 nuclease), a synthetic guide RNA (gRNA), and another bit of RNA (tracrRNA) that's complementary to the gRNA. Researchers can design whatever guide RNA sequence they want; the gRNA will stick to the complementary part of the target DNA, the tracrRNA will complex with it, and the nuclease will make a cut there. So, that's the "cut" part - the "paste" comes from a template DNA sequence, again of the researchers' choice, which is included along with the CRISPR components. Usually all these sequences of nucleic acids are packaged in a circular plasmid, which is transfected into cells with nanoparticles or (non-disease-causing) viruses. So, why can't you make a CRISPR plasmid with arbitrary many genes to edit? There are a couple reasons: 1. Plasmids can't be too big or they won't fit inside the virus or the lipid nanoparticle. Lipid nanoparticles have about a 20,000 base-pair limit; adeno-associated viruses (AAV), the most common type of virus used in gene delivery, has a smaller payload, more like 4700 base pairs. 1. This places a very strict restriction on how many complete gene sequences that can be inserted - some genes are millions of base pairs long, and the average gene is thousands! 2. but if you're just making a very short edit to each gene, like a point mutation, or if you're deleting or inactivating the gene, payload limits aren't much of a factor. 2. DNA damage is bad for cells in high doses, particularly when it involves double-strand breaks. This also places limits on how many simultaneous edits you can do. 3. A guide RNA won't necessarily only bind to a single desired spot on the whole genome; it can also bind elsewhere, producing so-called "off-target" edits. If each guide RNA produces x off-target edits, then naively you'd expect 10 guide RNAs to produce 10x off-target edits…and at some point that'll reach an unacceptable risk of side effects from randomly screwing up the genome. 4. An edit won't necessarily work every time, on every strand of DNA in every cell. (The rate of successful edits is known as the efficiency). The more edits you try to make, the lower the efficiency will be for getting all edits simultaneously; if each edit is 50% efficient, then two edits will be 25% efficient or (more likely) even less. None of these issues make it fundamentally impossible to edit multiple genes with CRISPR and associated methods, but they do mean that the more (and bigger) edits you try to make, the greater the chance of failure or unacceptable side effects. How Base and Prime Editors Work Base editors are an alternative to CRISPR that don't involve any DNA cutting; instead, they use a CRISPR-style guide RNA to bind to a target sequence, and then convert a single base pair chemically - they turn a C/G base pair to an A/T, or vice versa. Without any double-strand breaks, base editors are less toxic to cells and less prone to off-target effects. The downside is that you can only use base editors to make single-point mutations; they're no good for large insertions or deletions. Prime editors, similarly, don't introduce double-strand breaks; instead, they include an enzyme ("nickase") that produces a single-strand "nick"...
En la web de Lúpulo Cas9 se publicarán los distintos capítulos y se puede encontrar más información del proyecto, de las personas que han participado en la serie...
In this podcast, Thomas Czech, Distinguished Professor at the University of Colorado, Boulder, with a lineage of remarkable contributions on RNA, ribozyme, and telomeres, discuss why RNA is so incredibly versatile.Video snippet from our conversation. Full videos of all Ground Truths podcasts can be seen on YouTube here. The audios are also available on Apple and Spotify.Transcript with links to the audio and external linksEric Topol (00:07):Well, hello, this is Eric Topol from Ground Truths, and it's really a delight for me to welcome Tom Cech who just wrote a book, the Catalyst, and who is a Nobel laureate for his work in RNA. And is at the University of Colorado Boulder as an extraordinary chemist and welcome Tom.Tom Cech (00:32):Eric, I'm really pleased to be here.The RNA GuyEric Topol (00:35):Well, I just thoroughly enjoyed your book, and I wanted to start out, if I could, with a quote, which gets us right off the story here, and let me just get to it here. You say, “the DNA guy would need to become an RNA guy. Though I didn't realize it at the time, jumping ship would turn out to be the most momentous decision in my life.” Can you elaborate a bit on that?Tom Cech (01:09):As a graduate student at Berkeley, I was studying DNA and chromosomes. I thought that DNA was king and really somewhat belittled the people in the lab next door who were working on RNA, I thought it was real sort of second fiddle material. Of course, when RNA is acting just as a message, which is an important function, a critical function in all life on earth, but still, it's a function that's subservient to DNA. It's just copying the message that's already written in the playbook of DNA. But little did I know that the wonders of RNA were going to excite me and really the whole world in unimaginable ways.Eric Topol (02:00):Well, they sure have, and you've lit up the world well before you had your Nobel Prize in 1989 was Sid Altman with ribozyme. And I think one of the things that struck me, which are so compelling in the book as I think people might know, it's divided in two sections. The first is much more on the biology, and the second is much more on the applications and how it's changing the world. We'll get into it particularly in medicine, but the interesting differentiation from DNA, which is the one trick pony, as you said, all it does is store stuff. And then the incredible versatility of RNA as you discovered as a catalyst, that challenging dogma, that proteins are supposed to be the only enzymes. And here you found RNA was one, but also so much more with respect to genome editing and what we're going to get into here. So I thought what we might get into is the fact that you kind of went into the scum of the pond with this organism, which by the way, you make a great case for the importance of basic science towards the end of the book. But can you tell us about how you, and then of course, many others got into the Tetrahymena thermophila, which I don't know that much about that organism.Tom Cech (03:34):Yeah, it's related to Tetrahymena is related to paramecium, which is probably more commonly known because it's an even larger single celled animal. And therefore, in an inexpensive grade school microscope, kids can look through and see these ciliated protozoa swimming around on a glass slide. But I first learned about them when I was a postdoc at MIT and I would drive down to Joe Gall's lab at Yale University where Liz Blackburn was a postdoc at the time, and they were all studying Tetrahymena. It has the remarkable feature that it has 10,000 identical copies of a particular gene and for a higher organism, one that has its DNA in the nucleus and does its protein synthesis in the cytoplasm. Typically, each gene's present in two copies, one from mom, one from dad. And if you're a biochemist, which I am having lots of stuff is a real advantage. So 10,000 copies of a particular gene pumping out RNA copies all the time was a huge experimental advantage. And that's what I started working on when I started my own lab at Boulder.Eric Topol (04:59):Well, and that's where, I guess the title of the book, the Catalyst ultimately, that grew into your discovery, right?Tom Cech (05:08):Well, at one level, yes, but I also think that the catalyst in a more general conversational sense means just facilitating life in this case. So RNA does much more than just serve as a biocatalyst or a message, and we'll get into that with genome editing and with telomerase as well.The Big Bang and 11 Nobel Prizes on RNA since 2000Eric Topol (05:32):Yes, and I should note that as you did early in the book, that there's been an 11 Nobel prize awardees since 2000 for RNA work. And in fact, we just had Venki who I know you know very well as our last podcast. And prior to that, Kati Karikó, Jennifer Doudna who worked in your lab, and the long list of people working RNA in the younger crowd like David Liu and Fyodor Urnov and just so many others, we need to have an RNA series because it's just exploding. And that one makes me take you back for a moment to 2007. And when I was reading the book, it came back to me about the Economist cover. You may recall almost exactly 17 years ago. It was called the Biology's Big Bang – Unravelling the secrets of RNA. And in that, there was a notable quote from that article. Let me just get to that. And it says, “it is probably no exaggeration to say that biology is now undergoing its neutron moment.”(06:52):This is 17 years ago. “For more than half a century the fundamental story of living things has been a tale of the interplay between genes, in the form of DNA, and proteins, which is genes encode and which do the donkey work of keeping living organisms living. The past couple of years, 17 years ago, however, has seen the rise and rise of a third type of molecule, called RNA.” Okay, so that was 2007. It's pretty extraordinary. And now of course we're talking about the century of biology. So can you kind of put these last 17 years in perspective and where we're headed?Tom Cech (07:34):Well, Eric, of course, this didn't all happen in one moment. It wasn't just one big bang. And the scientific community has been really entranced with the wonders of RNA since the 1960s when everyone was trying to figure out how messenger RNA stored the genetic code. But the general public has been really kept in the dark about this, I think. And as scientists, were partially to blame for not reaching out and sharing what we have found with them in a way that's more understandable. The DNA, the general public's very comfortable with, it's the stuff of our heredity. We know about genetic diseases, about tracing our ancestry, about solving crimes with DNA evidence. We even say things like it's in my DNA to mean that it's really fundamental to us. But I think that RNA has been sort of kept in the closet, and now with the mRNA vaccines against Covid-19, at least everyone's heard of RNA. And I think that that sort of allowed me to put my foot in the door and say, hey, if you were curious about the mRNA vaccines, I have some more stories for you that you might be really interested in.RNA vs RNAEric Topol (09:02):Yeah, well, we'll get to that. Maybe we should get to that now because it is so striking the RNA versus RNA chapter in your book, and basically the story of how this RNA virus SARS-CoV-2 led to a pandemic and it was fought largely through the first at scale mRNA nanoparticle vaccine package. Now, that takes us back to some seminal work of being able to find, giving an mRNA to a person without inciting massive amount of inflammation and the substitution of pseudouridine or uridine in order to do that. Does that really get rid of all the inflammation? Because obviously, as you know, there's been some negativism about mRNA vaccines for that and also for the potential of not having as much immune cell long term activation. Maybe you could speak to that.Tom Cech (10:03):Sure. So the discovery by Kati Karikó and Drew Weissman of the pseudouridine substitution certainly went a long way towards damping down the immune response, the inflammatory response that one naturally gets with an RNA injection. And the reason for that is that our bodies are tuned to be on the lookout for foreign RNA because so many viruses don't even mess with DNA at all. They just have a genome made of RNA. And so, RNA replicating itself is a danger sign. It means that our immune system should be on the lookout for this. And so, in the case of the vaccination, it's really very useful to dampen this down. A lot of people thought that this might make the mRNA vaccines strange or foreign or sort of a drug rather than a natural substance. But in fact, modified nucleotides, nucleotides being the building blocks of RNA, so these modified building blocks such as pseudoU, are in fact found in natural RNAs more in some than in others. And there are about 200 modified versions of the RNA building blocks found in cells. So it's really not an unusual modification or something that's all that foreign, but it was very useful for the vaccines. Now your other question Eric had to do with the, what was your other question, Eric?Eric Topol (11:51):No, when you use mRNA, which is such an extraordinary way to get the spike protein in a controlled way, exposed without the virus to people, and it saved millions of lives throughout the pandemic. But the other question is compared to other vaccine constructs, there's a question of does it give us long term protective immunity, particularly with T cells, both CD8 cytotoxic, maybe also CD4, as I know immunology is not your main area of interest, but that's been a rub that's been put out there, that it isn't just a weaning of immunity from the virus, but also perhaps that the vaccines themselves are not as good for that purpose. Any thoughts on that?Tom Cech (12:43):Well, so my main thought on that is that this is a property of the virus more than of the vaccine. And respiratory viruses are notoriously hard to get long-term immunity. I mean, look at the flu virus. We have to have annual flu shots. If this were like measles, which is a very different kind of virus, one flu shot would protect you against at least that strain of flu for the rest of your life. So I think the bad rap here is not the vaccine's fault nearly as much as it's the nature of respiratory viruses.RNA And Aging Eric Topol (13:27):No, that's extremely helpful. Now, let me switch to an area that's really fascinating, and you've worked quite a bit on the telomerase story because this is, as you know, being pursued quite a bit, has thought, not just because telomeres might indicate something about biologic aging, but maybe they could help us get to an anti-aging remedy or whatever you want to call it. I'm not sure if you call it a treatment, but tell us about this important enzyme, the role of the RNA building telomeres. And maybe you could also connect that with what a lot of people might not be familiar with, at least from years ago when they learned about it, the Hayflick limit.Tom Cech (14:22):Yes. Well, Liz Blackburn and Carol Greider got the Nobel Prize for the discovery of telomerase along with Jack Szostak who did important initial work on that system. And what it does is, is it uses an RNA as a template to extend the ends of human chromosomes, and this allows the cell to keep dividing without end. It gives the cell immortality. Now, when I say immortality, people get very excited, but I'm talking about immortality at the cellular level, not for the whole organism. And in the absence of a mechanism to build out the ends of our chromosomes, the telomeres being the end of the chromosome are incompletely replicated with each cell division. And so, they shrink over time, and when they get critically short, they signal the cell to stop dividing. This is what is called the Hayflick limit, first discovered by Leonard Hayflick in Philadelphia.(15:43):And he, through his careful observations on cells, growing human cells growing in Petri dishes, saw that they could divide about 50 times and then they wouldn't die. They would just enter a state called senescence. They would change shape, they would change their metabolism, but they would importantly quit dividing. And so, we now see this as a useful feature of human biology that this protects us from getting cancer because one of the hallmarks of cancer is immortality of the tumor cells. And so, if you're wishing for your telomeres to be long and your cells to keep dividing, you have to a little bit be careful what you wish for because this is one foot in the door for cancer formation.Eric Topol (16:45):Yeah, I mean, the point is that it seems like the body and the cell is smart to put these cells into the senescent state so they can't divide anymore. And one of the points you made in the book that I think is worth noting is that 90% of cancers have the telomerase, how do you say it?Tom Cech (17:07):Telomerase.Eric Topol (17:08):Yeah, reactivate.Tom Cech (17:09):Right.Eric Topol (17:10):That's not a good sign.Tom Cech (17:12):Right. And there are efforts to try to target telomerase enzyme for therapeutic purposes, although again, it's tricky because we do have stem cells in our bodies, which are the exception to the Hayflick limit rule. They do still have telomerase, they still have to keep dividing, maybe not as rapidly as a cancer cell, but they still keep dividing. And this is critical for the replenishment of certain worn out tissues in our such as skin cells, such as many of our blood cells, which may live only 30 days before they poop out. That's a scientific term for needing to be replenished, right?Eric Topol (18:07):Yeah. Well, that gets me to the everybody's, now I got the buzz about anti-aging, and whether it's senolytics to get rid of these senescent cells or whether it's to rejuvenate the stem cells that are exhausted or work on telomeres, all of these seem to connect with a potential or higher risk of cancer. I wonder what your thoughts are as we go forward using these various biologic constructs to be able to influence the whole organism, the whole human body aging process.Tom Cech (18:47):Yes. My view, and others may disagree is that aging is not an affliction. It's not a disease. It's not something that we should try to cure, but what we should work on is having a healthy life into our senior years. And perhaps you and I are two examples of people who are at that stage of our life. And what we would really like is to achieve, is to be able to be active and useful to society and to our families for a long period of time. So using the information about telomerase, for example, to help our stem cells stay healthy until we are, until we're ready to cash it in. And for that matter on the other side of the coin, to try to inhibit the telomerase in cancer because cancer, as we all know, is a disease of aging, right? There are young people who get cancer, but if you look at the statistics, it's really heavily weighted towards people who've been around a long time because mutations accumulate and other damage to cells that would normally protect against cancer accumulates. And so, we have to target both the degradation of our stem cells, but also the occurrence of cancer, particularly in the more senior population. And knowing more about RNA is really helpful in that regard.RNA DrugsEric Topol (20:29):Yeah. Well, one of the things that comes across throughout the book is versatility of RNA. In fact, you only I think, mentioned somewhere around 12 or 14 of these different RNAs that have a million different shapes, and there's so many other names of different types of RNAs. It's really quite extraordinary. But one of the big classes of RNAs has really hit it. In fact, this week there are two new interfering RNAs that are having extraordinary effects reported in the New England Journal on all the lipids, abnormal triglycerides and LDL cholesterol, APOC3. And can you talk to us about this interfering the small interfering RNAs and how they become, you've mentioned in the book over 400 RNAs are in the clinic now.Tom Cech (21:21):Yeah, so the 400 of course is beyond just the siRNAs, but these, again, a wonderful story about how fundamental science done just to understand how nature works without any particular expectation of a medical spinoff, often can have the most phenomenal and transformative effects on medicine. And this is one of those examples. It came from a roundworm, which is about the size of an eyelash, which a scientist named Sydney Brenner in England had suggested would be a great experimental organism because the entire animal has only about a thousand cells, and it's transparent so we can look at, see where the cells are, we can watch the worm develop. And what Andy Fire and Craig Mello found in this experimental worm was that double-stranded RNA, you think about DNA is being double-stranded and RNA as being single stranded. But in this case, it was an unusual case where the RNA was forming a double helix, and these little pieces of double helical RNA could turn off the expression of genes in the worm.(22:54):And that seemed remarkable and powerful. But as often happens in biology, at least for those of us who believe in evolution, what goes for the worm goes for the human as well. So a number of scientists quickly found that the same process was going on in the human body as a natural way of regulating the expression of our genes, which means how much of a particular gene product is actually going to be made in a particular cell. But not only was it a natural process, but you could introduce chemically synthesized double helical RNAs. There are only 23 base pairs, 23 units of RNA long, so they're pretty easy to chemically synthesize. And that once these are introduced into a human, the machinery that's already there grabs hold of them and can be used to turn off the expression of a disease causing RNA or the gene makes a messenger RNA, and then this double-stranded RNA can suppress its action. So this has become the main company that is known for doing this is Alnylam in Boston, Cambridge. And they have made quite a few successful products based on this technology.Eric Topol (24:33):Oh, absolutely. Not just for amyloidosis, but as I mentioned these, they even have a drug that's being tested now, as you know that you could take once or twice a year to manage your blood pressure. Wouldn't that be something instead of a pill every day? And then of course, all these others that are not just from Alnylam, but other companies I wasn't even familiar with for managing lipids, which is taking us well beyond statins and these, so-called PCSK9 monoclonal antibodies, so it's really blossoming. Now, the other group of RNA drugs are antisense drugs, and it seemed like they took forever to warm up, and then finally they hit. And can you distinguish the antisense versus the siRNA therapeutics?Tom Cech (25:21):Yes, in a real general sense, there's some similarity as well as some differences, but the antisense, what are called oligonucleotides, whoa, that's a big word, but oligo just means a few, right? And nucleotides is just the building blocks of nucleic acid. So you have a string of a few of these. And again, it's the power of RNA that it is so good at specifically base pairing only with matching sequences. So if you want to match with a G in a target messenger RNA, you put a C in the antisense because G pairs with C, if you want to put an A, if want to match with an A, you put a U in the antisense because A and U form a base pair U is the RNA equivalent of T and DNA, but they have the same coding capacity. So any school kid can write out on a notepad or on their laptop what the sequence would have to be of an antisense RNA to specifically pair with a particular mRNA.(26:43):And this has been, there's a company in your neck of the woods in the San Diego area. It started out with the name Isis that turned out to be the wrong Egyptian God to name your company after, so they're now known as Ionis. Hopefully that name will be around for a while. But they've been very successful in modifying these antisense RNAs or nucleic acids so that they are stable in the body long enough so that they can pair with and thereby inhibit the expression of particular target RNAs. So it has both similarities and differences from the siRNAs, but the common denominator is RNA is great stuff.RNA and Genome EditingEric Topol (27:39):Well, you have taken that to in catalyst, the catalyst, you've proven that without a doubt and you and so many other extraordinary scientists over the years, cumulatively. Now, another way to interfere with genes is editing. And of course, you have a whole chapter devoted to not just well CRISPR, but the whole genome editing field. And by the way, I should note that I forgot because I had read the Codebreaker and we recently spoke Jennifer Doudna and I, that she was in your lab as a postdoc and you made some wonderful comments about her. I don't know if you want to reflect about having Jennifer, did you know that she was going to do some great things in her career?Tom Cech (28:24):Oh, there was no question about it, Eric. She had been a star graduate student at Harvard, had published a series of breathtaking papers in magazines such as Science and Nature already as a graduate student. She won a Markey fellowship to come to Colorado. She chose a very ambitious project trying to determine the molecular structures of folded RNA molecules. We only had one example at the time, and that was the transfer RNA, which is involved in protein synthesis. And here she was trying these catalytic RNAs, which we had discovered, which were much larger than tRNA and was making great progress, which she finished off as an assistant professor at Yale. So what the general public may not know was that in scientific, in the scientific realm, she was already highly appreciated and much awarded before she even heard anything about CRISPR.Eric Topol (29:38):Right. No, it was a great line you have describing her, “she had an uncanny talent for designing just the right experiment to test any hypothesis, and she possessed more energy and drive than any scientist I'd ever met.” That's pretty powerful. Now getting into CRISPR, the one thing, it's amazing in just a decade to see basically the discovery of this natural system to then be approved by FDA for sickle cell disease and beta thalassemia. However, the way it exists today, it's very primitive. It's not actually fixing the gene that's responsible, it's doing a workaround plan. It's got double strand breaks in the DNA. And obviously there's better ways of editing, which are going to obviously involve RNA epigenetic editing, if you will as well. What is your sense about the future of genome editing?Tom Cech (30:36):Yeah, absolutely, Eric. It is primitive right now. These initial therapies are way too expensive as well to make them broadly applicable to the entire, even in a relatively wealthy country like the United States, we need to drive the cost down. We need to get them to work, we need to get the process of introducing them into the CRISPR machinery into the human body to be less tedious and less time consuming. But you've got to start somewhere. And considering that the Charpentier and Doudna Nobel Prize winning discovery was in 2012, which is only a dozen years ago, this is remarkable progress. More typically, it takes 30 years from a basic science discovery to get a medical product with about a 1% chance of it ever happening. And so, this is clearly a robust RNA driven machine. And so, I think the future is bright. We can talk about that some more, but I don't want to leave RNA out of this conversation, Eric. So what's cool about CRISPR is its incredible specificity. Think of the human genome as a million pages of text file on your computer, a million page PDF, and now CRISPR can find one sentence out of that million pages that matches, and that's because it's using RNA, again, the power of RNA to form AU and GC base pairs to locate just one site in our whole DNA, sit down there and direct this Cas9 enzyme to cut the DNA at that site and start the repair process that actually does the gene editing.Eric Topol (32:41):Yeah, it's pretty remarkable. And the fact that it can be so precise and it's going to get even more precise over time in terms of the repair efforts that are needed to get it back to an ideal state. Now, the other thing I wanted to get into with you a bit is on the ribosome, because that applies to antibiotics and as you call it, the mothership. And I love this metaphor that you had about the ribosome, and in the book, “the ribosome is your turntable, the mRNA is the vinyl LP record, and the protein is the music you hear when you lower the needle.” Tell us more about the ribosome and the role of antibiotics.Tom Cech (33:35):So do you think today's young people will understand that metaphor?Eric Topol (33:40):Oh, they probably will. They're making a comeback. These records are making a comeback.Tom Cech (33:44):Okay. Yes, so this is a good analogy in that the ribosome is so versatile it's able to play any music that you feed at the right messenger RNA to make the music being the protein. So you can have in the human body, we have tens of thousands of different messenger RNAs. Each one threads through the same ribosome and spills out the production of whatever protein matches that mRNA. And so that's pretty remarkable. And what Harry Noller at UC Santa Cruz and later the crystallographers Venki Ramakrishnan, Tom Steitz, Ada Yonath proved really through their studies was that this is an RNA machine. It was hard to figure that out because the ribosome has three RNAs and it has dozens of proteins as well. So for a long time people thought it must be one of those proteins that was the heart and soul of the record player, so to speak.RNA and Antibiotics(34:57):And it turned out that it was the RNA. And so, when therefore these scientists, including Venki who you just talked to, looked at where these antibiotics docked on the ribosome, they found that they were blocking the key functional parts of the RNA. So it was really, the antibiotics knew what they were doing long before we knew what they were doing. They were talking to and obstructing the action of the ribosomal RNA. Why is this a good thing for us? Because bacterial ribosomes are just enough different from human ribosomes that there are drugs that will dock to the bacterial ribosomal RNA, throw a monkey wrench into the machine, prevent it from working, but the human ribosomes go on pretty much unfazed.Eric Topol (36:00):Yeah, no, the backbone of our antibiotics relies on this. So I think people need to understand about the two subunits, the large and the small and this mothership, and you illuminate that so really well in the book. That also brings me to phage bacteria phage, and we haven't seen that really enter the clinic in a significant way, but there seems to be a great opportunity. What's your view about that?Tom Cech (36:30):This is an idea that goes way back because since bacteria have their own viruses which do not infect human cells, why not repurpose those into little therapeutic entities that could kill, for example, what would we want to kill? Well, maybe tuberculosis has been very resistant to drugs, right? There are drug resistant strains of TB, yes, of TB, tuberculosis, and especially in immunocompromised individuals, this bug runs rampant. And so, I don't know the status of that. It's been challenging, and this is the way that biomedicine works, is that for every 10 good ideas, and I would say phage therapy for bacterial disease is a good idea. For every 10 such ideas, one of them ends up being practical. And the other nine, maybe somebody else will come along and find a way to make it work, but it hasn't been a big breakthrough yet.RNA, Aptamers and ProteinsEric Topol (37:54):Yeah, no, it's really interesting. And we'll see. It may still be in store. What about aptamers? Tell us a little bit more about those, because they have been getting used a lot in sorting out the important plasma proteins as therapies. What are aptamers and what do you see as the future in that regard?Tom Cech (38:17):Right. Well, in fact, aptamers are a big deal in Boulder because Larry Gold in town was one of the discoverers has a company making aptamers to recognize proteins. Jack Szostak now at University of Chicago has played a big role. And also at your own institution, Jerry Joyce, your president is a big aptamer guy. And you can evolution, normally we think about it as happening out in the environment, but it turns out you can also make it work in the laboratory. You can make it work much faster in the laboratory because you can set up test tube experiments where molecules are being challenged to perform a particular task, like for example, binding to a protein to inactivate it. And if you make a large community of RNA molecules randomly, 99.999% of them aren't going to know how to do this. What are the odds? Very low.(39:30):But just by luck, there will be an occasional molecule of RNA that folds up into a shape that actually fits into the proteins active sighting throws a monkey wrench into the works. Okay, so now that's one in a billion. How are you going to find that guy? Well, this is where the polymerase chain reaction, the same one we use for the COVID-19 tests for infection comes into play. Because if you can now isolate this needle in a haystack and use PCR to amplify it and make a whole handful of it, now you've got a whole handful of molecules which are much better at binding this protein than the starting molecule. And now you can go through this cycle several times to enrich for these, maybe mutagen it a little bit more to give it a little more diversity. We all know diversity is good, so you put a little more diversity into the population and now you find some guy that's really good at recognizing some disease causing protein. So this is the, so-called aptamer story, and they have been used therapeutically with some success, but diagnostically certainly they are extremely useful. And it's another area where we've had success and the future could hold even more success.Eric Topol (41:06):I think what you're bringing up is so important because the ability to screen that tens of thousands of plasma proteins in a person and coming up with as Tony Wyss-Coray did with the organ clocks, and this is using the SomaLogic technology, and so much is going on now to get us not just the polygenic risk scores, but also these proteomic scores to compliment that at our orthogonal, if you will, to understand risk of people for diseases so we can prevent them, which is fulfilling a dream we've never actually achieved so far.Tom Cech (41:44):Eric, just for full disclosure, I'm on the scientific advisory board of SomaLogic in Boulder. I should disclose that.Eric Topol (41:50):Well, that was smart. They needed to have you, so thank you for mentioning that. Now, before I wrap up, well, another area that is a favorite of mine is citizen science. And you mentioned in the book a project because the million shapes of RNA and how it can fold with all hairpin terms turns and double stranded and whatever you name it, that there was this project eteRNA that was using citizen scientists to characterize and understand folding of RNA. Can you tell us about that?RNA Folding and Citizen ScienceTom Cech (42:27):So my friend Rhiju Das, who's a professor at Stanford University, sort of adopted what had been done with protein folding by one of his former mentors, David Baker in Seattle, and had repurposed this for RNA folding. So the idea is to come up with a goal, a target for the community. Can you design an RNA that will fold up to look like a four pointed cross or a five pointed star? And it turned out that, so they made it into a contest and they had tens of thousands of people playing these games and coming up with some remarkable solutions. But then they got a little bit more practical, said, okay, that was fun, but can we have the community design something like a mRNA for the SARS-CoV-2 spike protein to make maybe a more stable vaccine? And quite remarkably, the community of many of whom are just gamers who really don't know much about what RNA does, were able to find some solutions. They weren't enormous breakthroughs, but they got a several fold, several hundred percent increase in stability of the RNA by making it fold more tightly. So I just find it to be a fascinating approach to science. Somebody of my generation would never think of this, but I think for today's generation, it's great when citizens can become involved in research at that level.Eric Topol (44:19):Oh, I think it's extraordinary. And of course, there are other projects folded and others that have exemplified this ability for people with no background in science to contribute in a meaningful way, and they really enjoy, it's like solving a puzzle. The last point is kind of the beginning, the origin of life, and you make a pretty strong case, Tom, that it was RNA. You don't say it definitively, but maybe you can say it here.RNA and the Origin of LifeTom Cech (44:50):Well, Eric, the origin of life happening almost 4 billion years ago on our primitive planet is sort of a historical question. I mean, if you really want to know what happened then, well, we don't have any video surveillance of those moments. So scientists hate to ever say never, but it's hard to sort of believe how we would ever know for sure. So what Leslie Orgel at the Salk Institute next to you taught me when I was a starting assistant professor is even though we'll never know for sure, if we can recapitulate in the laboratory plausible events that could have happened, and if they make sense chemically and biologically, then that's pretty satisfying, even if we can never be absolutely sure. That's what a number of scientists have done in this field is to show that RNA is sort of a, that all the chemistry sort of points to RNA as being something that could have been made under prebiotic conditions and could have folded up into a way that could solve the greatest of all chicken and egg problems, which came first, the informational molecule to pass down to the next generation or the active molecule that could copy that information.(46:32):So now that we know that RNA has both of those abilities, maybe at the beginning there was just this RNA world RNA copying itself, and then proteins came along later, and then DNA probably much more recently as a useful but a little bit boring of genetic information, right?Eric Topol (46:59):Yeah. Well, that goes back to that cover of the Economist 17 years ago, the Big Bang, and you got me convinced that this is a pretty strong story and candidate. Now what a fun chance to discuss all this with you in an extraordinary book, Tom. Did I miss anything that you want to bring up?Tom Cech (47:21):Eric, I just wanted to say that I not only appreciate our conversation, but I also appreciate all you are doing to bring science to the non-scientist public. I think people like me who have taught a lot of freshmen in chemistry, general chemistry, sort of think that that's the level that we need to aim at. But I think that those kids have had science in high school year after year. We need to aim at the parents of those college freshmen who are intelligent, who are intellectually curious, but have not had science courses in a long time. And so, I'm really joining with you in trying to avoid jargon as much as possible. Use simple language, use analogies and metaphors, and try to share the excitement of what we're doing in the laboratory with the populace.Eric Topol (48:25):Well, you sure did that it was palpable. And I thought about it when I read the book about how lucky it would be to be a freshman at the University of Boulder and be having you as the professor. My goodness. Well, thank you so much. This has been so much fun, Tom, and I hope everybody's going to get out there and read the Catalyst to get all the things that we didn't even get a chance to dive into. But this has been great and look forward to future interactions with you.Tom Cech (48:53):Take care, Eric.*********************Thanks for listening or reading this edition of Ground Truths.Please share this podcast with your friends and network. That tells me you found it informative and makes the effort in doing these worthwhile.All Ground Truths newsletters and podcast are free. Voluntary paid subscriptions all go to support Scripps Research. Many thanks for that—they greatly helped fund our summer internship programs for 2023 and 2024.Thanks to my producer Jessica Nguyen and Sinjun Balabanoff for audio and video support at Scripps Research.Note: you can select preferences to receive emails about newsletters, podcasts, or all I don't want to bother you with an email for content that you're not interested in. Get full access to Ground Truths at erictopol.substack.com/subscribe
Dieses Mal geht es nicht nur um die Vergangenheit: wie sich die Erfindung der "Genschere" CRISPR-Cas9 auf die Zukunft auswirken könnte, erzählt Andrea Sawatzki in dieser Folge.
Mi történt a GMO gyűjtőnéven hírhedtté vált genetikailag módosított organizmusokat létrehozó első próbálkozások óta eltelt négy évtizedben? Van-e különbség a GMO-növények és az orvosi génterápiák között? Aki válaszol: Varga Máté, az ELTE TTK Genetikai Tanszékének fejlődésgenetikusa.See omnystudio.com/listener for privacy information.
mRNA Cancer Therapy: DNA Distortion with False Light Something is very odd with the Royals and Cancer. Is this a cover story for a Dianna type playbook or is this a vehicle to push new cancer treatment like med beds or other DNA defilement treatment? Time will tell for it is reported the Royals own almost 20% + of all land. We know cancer treatments have been suppressed by the dark side satanic cabal. Remember, the AC will come as a false light (hero) and unlock hidden cures that the dark side buried. Ai will know best. DNA Defilement Cures Being Worked on CRISPR-Cas9 is a highly precise gene-editing tool that is revolutionizing cancer research and treatment1. It works by using a guide RNA and a DNA-cutting enzyme, most commonly one called Cas9. The guide RNA is designed to mirror the DNA of the gene to be edited (called the target). The guide RNA partners with Cas and leads Cas to the target. CRISPR-Cas9 has shown potential to break the limits of immunotherapy in cancers. For example, researchers have tested a cancer treatment involving immune cells that were CRISPR-edited to better hunt down and attack cancer. As for mRNA technology, it can be used in conjunction with CRISPR/Cas9 for cancer treatment. An alternative approach is to use Cas9 mRNA and sgRNA. This mRNA-based CRISPR/Cas9 system enables swifter genome editing, as it bypasses the process of transcription3. The transient expression of RNPs may reduce the risk of off-target mutagenesis. Scripture for VCAST "For whosoever will save his life shall lose it: but whosoever will lose his life for my sake, the same shall save it." - Luke 9:24 (This is a similar verse to the concept you mentioned about seeking life but finding death.) "And whereas thou sawest iron mixed with miry clay, they shall mingle themselves with the seed of men: but they shall not cleave one to another, even as iron is not mixed with clay." - Daniel 2:43
Hello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by Romain Amyot, Noriyuki Kodera, and Holger Flechsig at the Kanazawa University NanoLSI.The research described in this podcast was published in Frontiers in Molecular Biosciences in November 2023Kanazawa University NanoLSI websitehttps://nanolsi.kanazawa-u.ac.jp/en/Researchers predict protein placement on AFM substratesResearchers at Kanazawa University report in Frontiers in Molecular Biosciences a computational method to predict the placement of proteins on AFM substrates based on electrostatic interactions.The observation of biomolecular structures using atomic force microscopy (AFM) and the direct visualization of functional conformational dynamics in high-speed AFM (HS-AFM) experiments have significantly advanced the understanding of biological processes at the nanoscale. In experiments, a biological sample is deposited on a supporting surface (AFM substrate) and is scanned by a probing tip to detect the molecular shape and its dynamical changes. The observation of protein dynamics under HS-AFM is a delicate balance between immobilizing the structure on the supporting surface while at the same time preventing too strong perturbations by immobilization.The process of placing a biomolecular sample on the supporting surface and controlling its proper attachment is a challenge at the very start of every AFM observation. By the chemical composition of the buffer, interactions between the sample and substrate can be modified. Such surface modifications are often critical for successful AFM observations of protein structures and their functional motions. However, the molecular orientation of the sample is a priori unknown, and due to limitations in the spatial resolution of images, difficult to infer from a posteriori analysis.Romain Amyot, Noriyuki Kodera, and Holger Flechsig from Kanazawa University have now developed a physical model to predict the placement of biomolecular structures on AFM substrates based on electrostatic interactions. The method considers the substrates commonly used in AFM experiments (mica, APTES-mica, lipid bilayers) and takes into account buffer conditions. In computer simulations, a large number of possible molecular arrangements on the AFM substrate are sampled, and from evaluating the corresponding interaction energies, the most favorable placement is determined. Furthermore, the analysis allows predictions of the imaging stability under tip scanning.The authors provide several applications of the new method and obtain remarkable agreement of model predictions with previous experimental HS-AFM imaging of proteins. The findings can explain, for example, why HS-AFM observations of the Cas9 endonuclease, a protein playing a key role in genetic engineering applications, can reliably visualize functional relative motions of target DNA and Cas9 and capture DNA cleavage events at the single molecule level (see Fig. 1). Furthermore, as demonstrated for the ATP-powered chaperone machine ClpB, the model can explain how buffer conditions affect the stability of the sample-substrate complex and validate observations of previous HS-AFM experiments.In summary, the new method allows to employ the enormous amount of available structural data for biomolecules to make predictions of the sample placement on AFM substrates even prior to an actual experiment, and it can also be applied for post-experimental analysis of AFM imaging data. The developed method is implemented within the freely available BioAFMviewer software package, providing a convenient platform for applications by the broad BioAFM community. Reference R. Amyot, K. Nakamoto, N. Kodera, H. FlechsiNanoLSI Podcast website
Hosts David Paxton and JD Williams are joined by Chris Taylor of (https://dontletthemburn.com) as we continue our in-depth conversation concerning Artificial Intelligence (AI) and its future effects on all of humanity. We have all heard about the Zombie Apocalypse and how many fear it. But are you aware of Genetic Apocalypse and that it is a REAL thing? Ever Heard of CAS9? How about CRISPR? Both of these are not only REAL, but are currently under development throughout the World. And unlike the Futuristic entertainment featuring Zombies, or the Living dead. The coming Genetic Apocalypse is REAL, and with 100% Certainty effect each of us. Please do remember that each Saturday Evening at 7:30pm Central. Hosts David Paxton and JD Williams provide and discuss current topics such as the latest news and current events through the lens of Biblical Prophecy. The "Last Christian" is Presented every Tuesday, Thursday and Saturday evenings at 7:30pm Central on more than 50 Radio Stations, and broadcast to all 50 US States and more than 160 Countries around the World. Delivering more than 2 million Listeners across ALL Platforms with Scripture taken directly from the Word of God. PLEASE NOTE: All opinions expressed are those of the Hosts & Guests of the "Last Christian" and not necessarily those of Revelation Radio KRRB-DB or the You Stream It, LLC Broadcast Network. For more information please visit www.lastchristian.net
Hosts David Paxton and JD Williams are joined by Chris Taylor of (https://dontletthemburn.com) as we continue our in-depth conversation concerning Artificial Intelligence (AI) and its future effects on all of humanity. We have all heard about the Zombie Apocalypse and how many fear it. But are you aware of Genetic Apocalypse and that it is a REAL thing? Ever Heard of CAS9? How about CRISPR? Both of these are not only REAL, but are currently under development throughout the World. And unlike the Futuristic entertainment featuring Zombies, or the Living dead. The coming Genetic Apocalypse is REAL, and with 100% Certainty effect each of us. Please do remember that each Saturday Evening at 7:30pm Central. Hosts David Paxton and JD Williams provide and discuss current topics such as the latest news and current events through the lens of Biblical Prophecy. The "Last Christian" is Presented every Tuesday, Thursday and Saturday evenings at 7:30pm Central on more than 50 Radio Stations, and broadcast to all 50 US States and more than 160 Countries around the World. Delivering more than 2 million Listeners across ALL Platforms with Scripture taken directly from the Word of God. PLEASE NOTE: All opinions expressed are those of the Hosts & Guests of the "Last Christian" and not necessarily those of Revelation Radio KRRB-DB or the You Stream It, LLC Broadcast Network. For more information please visit www.lastchristian.net
David Liu is an gifted molecular biologist and chemist who has pioneered major refinements in how we are and will be doing genome editing in the future, validating the methods in multiple experimental models, and establishing multiple companies to accelerate their progress.The interview that follows here highlights why those refinements beyond the CRISPR Cas9 nuclease (used for sickle cell disease) are vital, how we can achieve better delivery of editing packages into cells, ethical dilemmas, and a future of somatic (body) cell genome editing that is in some ways is up to our imagination, because of its breadth, over the many years ahead. Recorded 29 November 2023 (knowing the FDA approval for sickle cell disease was imminent)Annotated with figures, external links to promote understanding, highlights in bold or italics, along with audio links (underlined)Eric Topol (00:11):Hello, this is Eric Topol with Ground Truths and I'm so thrilled to have David Liu with me today from the Broad Institute, Harvard, and an HHMI Investigator. David was here visiting at Scripps Research in the spring, gave an incredible talk which I'll put a link to. We're not going to try to go over all that stuff today, but what a time to be able to get to talk with you about what's happening, David. So welcome.David Liu (00:36):Thank you, and I'm honored to be here.Eric Topol (00:39):Well, the recent UK approval (November 16, 2023) of the first genome editing after all the years that you put into this, along with many other colleagues around the world, is pretty extraordinary. Maybe you can just give us a sense of that threshold that's crossed with the sickle cell and beta thalassemia also imminently [FDA approval granted for sickle-cell on 8 December 2023] likely to be getting that same approval here in the U.S.David Liu (01:05):Right? I mean, it is a huge moment for the field, for science, for medicine. And just to be clear and to give credit where credit is due, I had nothing to do with the discovery or development of CRISPR Cas9 as a therapeutic, which is what this initial gene editing CRISPR drug is. But of course, the field has built on the work of many scientists with respect to CRISPR Cas9, including Emmanuel Charpentier and Jennifer Doudna and George Church and Feng Zhang and many, many others. But it is, I think surprisingly rapid milestone in a long decade's old effort to begin to take some control over our genetic features by changing DNA sequences of our choosing into sequences that we believe will offer some therapeutic benefit. So this initial drug is the CRISPR Therapeutics /Vertex drug. Now we can say it's actually a drug approved drug, which is a Crispr Cas9 nuclease programmed to cut a DNA sequence that is involved in silencing fetal hemoglobin genes. And as you know, when you cut DNA, you primarily disrupt the sequence that you cut. And so if you disrupt the DNA sequence that is required for silencing your backup fetal hemoglobin genes, then they can reawaken and serve as a way to compensate for adult hemoglobin genes like the defective sickle cell alleles that sickle cell anemia patients have. And so that's the scientific basis of this initial drug.Eric Topol (03:12):So as you aptly put— frame this—this is an outgrowth of about a decade's work and it was using a somewhat constrained, rudimentary form of editing. And your work has taken this field considerably further with base and prime editing whereby you're not just making a double strand cut, you're doing nicks, and maybe you can help us understand this next phase where you have more ways you can intervene in the genome than was possible through the original Cas9 nucleases.David Liu (03:53):Right? So gene editing is actually a several decades old field. It just didn't quite become as popular as it is now until the discovery of CRISPR nucleases, which are just much easier to reprogram than the previous programmable zinc finger or tail nucleases, for example. So the first class of gene editing agents are all nuclease enzymes, meaning enzymes that take a piece of DNA chromosome and literally cut it breaking the DNA double helix and cutting the chromosome into two pieces. So when the cell sees that double strand DNA break, it responds by trying to get the broken ends of the chromosome back together. And we think that most of the time, maybe 90% of the time that end joining is perfect, it just regenerates the starting sequence. But if it regenerates the starting sequence perfectly and the nuclease is still around, then it can just cut the rejoin sequence again.(04:56):So this cycle of cutting and rejoining and cutting and rejoining continues over and over until the rejoining makes the mistake that changes the DNA sequence at the cut site because when those mistakes accumulate to a point that the nuclease no longer recognizes the altered sequence, then it's a dead end product. That's how you end up with these disrupted genes that result from cutting a target DNA sequence with a nuclease like Crispr Cas9. So Crispr Cas9 and other nucleases are very useful for disrupting genes, but one of their biggest downsides is in the cells that are most relevant to medicine, to human therapy like the cells that are in your body right now, you can't really control the sequence of DNA that comes out of this process when you cut a DNA double helix inside of a human cell and allow this cutting and rejoining process to take place over and over again until you get these mistakes.(06:03):Those mistakes are generally mixtures of insertions and deletions that we can't control. They are usually disruptive to a gene. So that can be very useful when you're trying to disrupt the function of a gene like the genes that are involved in silencing fetal hemoglobin. But if you want to precisely fix a mutation that causes a genetic disease and convert it, for example, back into a healthy DNA sequence, that's very hard to do in a patient using DNA cutting scissors because the scissors themselves of course don't include any information that allows you to control what sequence comes out of that repair process. You can add a DNA template to this cutting process in a process called HDR or Homology Directed Repair (figure below from the Wang and Doudna 10-year Science review), and sometimes that template will end up replacing the DNA sequence around the cut site. But unfortunately, we now know that that HDR process is very inefficient in most of the types of cells that are relevant for human therapy.(07:12):And that explains why if you look at the 50 plus nuclease gene editing clinical trials that are underway or have taken place, all but one use nucleases for gene disruption rather than for gene correction. And so that's really what inspired us to develop base editing in 2016 and then prime editing in 2019. These are methods that allow you to change a DNA sequence of your choosing into a different sequence of your choosing, where you get to specify the sequence that comes out of the editing process. And that means you can, for the first time in a general way, programmable change a DNA sequence, a mutation that causes a genetic disease, for example, into a healthy sequence back into the normal, the so-called wild type sequence, for example. So base editors work by actually performing chemistry on an individual DNA base, rearranging the atoms of that base to become a different base.(08:22):So base editors can efficiently and robustly change A's into G's G's, into A's T's into C's or C's into T's. Those four changes. And those four changes for interesting biochemical reasons turn out to be four of the most common ways that our DNA mutates to cause disease. So base editors can be used and have been used in animals and now in six clinical trials to treat a wide variety of diseases, high cholesterol and sickle cell disease, and T-cell leukemia for example. And then in prime editors we developed a few years later to try to address the types of changes in our genomes that caused genetic disease that can't be fixed with a base editor, for example. You can't use a base editor to efficiently and selectively change an A into a T. You can't use a base editor to perform an insertion of missing DNA letters like the three missing letters, CTT, that's the most common cause of cystic fibrosis accounting for maybe 70% of cystic fibrosis patients.(09:42):You can't use a base editor to insert missing DNA letters like the missing TATC. That is the most common cause of Tay-Sachs disease. So we develop prime editors as a third gene editing technology to complement nucleases and base editors. And prime editors work by yet another mechanism. They don't, again, they don't cut the DNA double helix, at least they don't cause that as the required mechanism of editing. They don't perform chemistry on an individual base. Instead, prime editors take a target DNA sequence and then write a new DNA sequence onto the end of one of the DNA strands and then sort of help the cell navigate the DNA repair processes to have that newly written DNA sequence replace the original DNA sequence. And in the process it's sort of true search and replace gene editing. So you can basically take any DNA sequence of up to now hundreds of base pairs and replace it with any other sequence of your choosing of up to hundreds of base pairs. And if you integrate prime editing with other enzymes like recombinase, you can actually perform whole gene integration of five or 10,000 base pairs, for example, this way. So prime editing's hallmark is really its versatility. And even though it's the newest of the three ways that have been robustly used to edit mammalian cells and rescue animal models of genetic disease, it is arguably the most versatile by far,Eric Topol (11:24):Right? Well, in fact, if you just go back to the sickle cell story as you laid out the Cas9 nuclease, that's now going into commercial approval in the UK and the US, it's more of a blunt instrument of disruption. It's indirect. It's not getting to the actual genomic defect, whereas you can do that now with these more refined tools, these new, and I think that's a very important step forward. And that is one part of some major contributions you've made. Of course, there are many. One of the things, of course, that's been a challenge in the field is delivery whereby we'd like to get this editing done in many parts of the body. And of course it's easy, perhaps I put that in quotes, easy when you're taking blood out and you're going to edit those cells and them put it back in. But when you want to edit the liver or the heart or the brain, it gets more challenging. Now, you did touch on one recent report, and this is of course the people with severe familial hypercholesterolemia. The carriers that have LDL cholesterol several hundred and often don't respond to even everything we have on the shelf today. And there were 10 people with this condition that was reported just a few weeks ago. So that's a big step forward.David Liu (13:09):That was also a very exciting milestone. So that clinical trial was led by scientists at Verve Therapeutics and Beam Therapeutics, and it was the first clinical readout of an in vivo base editing clinical trial. There was previously at the end of 2022, the first clinical readout of an ex vivo base editing clinical trial using CAR T cells, ex vivo base edited to treat T-cell leukemia in pediatric patients in the UK. Ffigure from that NEJM paper below). But as you point out, there are only a small fraction of the full range of diseases that we'd like to treat with gene editing and the types of cells we'd like to edit that can be edited outside of the body and then transplanted back into the body. So-called ex vivo editing. Basically, you can do this with cells of some kind of blood lineage, hematopoietic stem cells, T-cells, and really not much else in terms of editing outside the body and then putting back into the body as you point out.(14:17):No one's going to do that with the brain or the heart anytime soon. So what was very exciting about the Verve Beam clinical trial is that Verve sought to disrupt the function of PCSK9 storied, gene validated by human genetics, because there are humans that naturally have mutations in PCSK9, and they tend to have much lower incidences of heart disease because their LDL, so-called bad cholesterol, is much lower than it would otherwise be without those mutations. So Verve set out to simply disrupt PCSK9 through gene editing. They didn't care whether they used a nuclease or a base editor. So they compared side-by-side the results of disrupting PCSK9 with Cas9 nuclease versus disrupting it by installing a precise single letter base edit using an adenine base editor. And they actually concluded that the base editor gave them higher efficacy and fewer unwanted consequences.(15:28):And so they went with the base editor. So the clinical trial that just read out were patients treated in New Zealand, in which they were given a lipid nanoparticle mRNA complex of an adenine base editor programmed with a guide RNA to install a specific A to G mutation in a splice site in PCSK9 that inactivates the gene so that it can no longer make functional PCSK9 protein. And the exciting result that read out was that in patients that receive this base editor, a single intravenous injection of the base editor lipid nanoparticle complex, as you know, lipid nanoparticles very efficiently go to the liver. In most cases, PCSK9 was edited in the liver and the result was substantial reduction in LDL cholesterol levels in these patients. And the hope and the anticipation is that that one-time treatment should be durable, should be more or less permanent in these patients. And I think while the patients who are at highest risk of coronary artery disease because of their genetics that give them absurdly high LDL cholesterol levels, that makes the most sense to go after those patients first because they are at extremely high risk of heart attacks and strokes. If the treatment proves to be efficacious and safe, then I think it's tempting to speculate that a larger and larger population of people who would benefit from having lower LDL cholesterol levels, which is probably most people, that they would also be candidates for this kind of therapy.Eric Topol (17:22):Yeah, no, it's actually pretty striking how that could be achieved. And I know in the primates that were done prior to the people in New Zealand, there was a very durable effect that went on well over I think a year or even two years. So yeah, that's right. Really promising. So now that gets us to a couple of things. One of them is the potential for off-target effects. As you've gotten more and more with these tools to be so precise, is the concern that you could have off-target effects just completely, of course inadvertent, but potential for other downstream in time known unknowns, if you will. What are your thoughts about that?David Liu (18:15):Yeah, I have many thoughts on this issue. It's very important the FDA and regulatory bodies are right to be very conservative about off-target editing because we anticipate those off targets will be permanent, those off-target edits will be permanent. And so we definitely have a responsibility to minimize adding to the mutational burden that all humans have as a function of existing on this planet, eating what we eat, being bombarded by cosmic rays and sunlight and everything else. But I think it's also important to put off-target editing into some context. One context is I think virtually every substance we've ever put into a person, including just about every medicine we've ever put into a person, has off-target effects, meaning modulates the function of biological molecules other than the intended target. Of course, the stakes are higher when those are gene editing agents because those modifications can be permanent.(19:18):I think most off-target edits are very likely to have no consequence because most of our genome, if you mutate in the kinds of small ways like making an individual base pair change for a base editor are likely to have no consequence. We sort of already know this because we can measure the mutational burden that we all face as a function of living and it's measurable, it's low, but measurable. I've read some papers that estimate that of the roughly 27 trillion [should be ~37] cells in an adult person, that there are billions and possibly hundreds of billions of mutations that accumulate every day in those 27 [37] trillion cells. So our genomes are not quite the static vaults that we'd like to think that they are. And of course, we have already purposefully given life extending medicines to patients that work primarily by randomly mutating their genomes. These are chemotherapeutic agents that we give to cancer patients.(20:24):So I think that history of giving chemotherapeutic agents, even though we know those agents will mess up the genomes of these patients and potentially cause cancer far later down the road, demonstrates that there are risk benefit situations where the calculus favors treatment, even if you know you are causing mutations in the genome, if the condition that the patient faces and their prognosis is sufficiently grave. All that said, as I mentioned, we don't want to add to the mutational burden of these patients in any clinically relevant way. So I think it is appropriate that the early gene editing clinical candidates that are in trials or approved now are undergoing lots and lots of scrutiny. Of course, doing an off-target analysis in an animal is of limited value because the animal's genome is quite different than the human genome. So the off targets won't align, but doing off-target analysis in human cells and then following up these patients for a long time to confirm hopefully that there isn't clinical evidence of quality of life or lifespan deterioration caused by off-target editing, that's all very, very important.(21:55):I also think that people may not fully appreciate that on target editing consequences also need to be examined and arguably examined with even more urgency than off-target edits. Because when you are cutting a chromosome at a target site with a nucleus, for example, you generate a complex mixture of different products of different DNA sequences that come out, and the more sequences you sequence, the more different products you realize are generated. And I don't think it's become routine to try to force the companies, the clinical groups that are running these trials to characterize the top 1000 on target products for their biological consequence. That would be sort of impractical to do and would probably slow down greatly the benefit of these early nuclease clinical trials for patients. But those are actually the products that are generated with much higher frequency typically than the off-target edits. And that's part of why I think it makes more sense from a clinical safety perspective to use more precise gene editing methods like base editing and prime editing where we know the products that are generated are mostly the products that we want are not uncontrolled mixtures of different deletion and insertion products.(23:27):So I think paying special attention to the on-target products, which are generated typically 70 to 100% of the time as opposed to the off targets which may be generated at a 0.1 to 1% level and usually not that many at that level once it reaches a clinical candidate. I think that's all important to do.Eric Topol (23:51):You've made a lot of great points there and thanks for putting that in perspective. Well, let's go on to the delivery issue. You mentioned nanoparticles, viral vectors, and then you've come up with small virus-like neutered viruses if you will. I think a company Nvelop that you've created to push on that potential. What are your thoughts about where we stand since you've become a force for coming up with much better editing, how about much better and more diverse delivery throughout the body? What are your thoughts about that?David Liu (24:37):Yeah, great. Great question. I think one of the legacies of gene editing is and will be that it inspired many more scientists to work hard on macromolecular delivery technologies. All of these gene editing agents are macromolecules, meaning they're proteins and or nucleic acids. None of them are small molecules that you can just pop a pill and swallow. So they all require special technologies to transfer the gene editing agent from outside of the cell into the cell. And the fact that taking control of our genetic features has become such a popular aspiration of medicine means that there's a lot of scientists as measured, most importantly by the young scientists, by the graduate students and the postdocs and the young professors of which I'm no longer one sadly, who have decided that they're going to devote a big part of their program to delivery. So you summarized many of the clinically relevant, clinically validated delivery technologies already, somewhat sadly, because if there were a hundred of these technologies, you probably wouldn't need to ask this question. But we have lipid nanoparticles that are particularly good at delivering messenger RNA, that was used to deliver the covid vaccine into billions of people. Now also used to deliver, for example, the adenine base editor mRNA into the livers of those hypercholesterolemia patients in the Verve/Beam clinical trial.(26:20):So those lipid nanoparticles are very well matched for gene editing delivery as long as it's liver. And they also are particularly well matched because their effect is transient. They cause a burst of gene editing agents to be produced in the liver and then they go away. The gene editing agents can't persist, they can't integrate into the genome despite what some conspiracy theorists might worry about. Not that you've had any encounter with any of those people. I'm sure that's actually what you want for a gene editing agent. You ideally want a delivery method that exposes the cell only for the shortest amount of time needed to make the on-target edit at the desired level. And then you want the gene editing agent to disappear and never come back because it shouldn't need to. DNA edits to our genome for durable cells should be permanent. So that's one method.(27:25):And then there are a variety of other methods that researchers have used to deliver to other cells, but they each carry some trade-offs. So if you're trying to edit hematopoietic stem cells, you can take them out of the body. Once they're out of the body, you have many more methods you can use to deliver efficiently into them. You can electroporated messenger, RNA or even ribonuclear proteins. You can treat with lipids or viruses, you can edit and then put them back into the body. But as you already mentioned, that's sort of a unique feature of blood cells that isn't applicable to the heart or the brain, for example, or the eyes. So then that brings us to viral vectors. There are a variety of clinically validated viral methods for delivery. AAV— adeno associated virus— is probably the most diverse, most relevant, and one of the best tolerated viral delivery methods. The beauty of AAV is that it can deliver to a variety of tissues. AAV can deliver into spinal cord neurons, for example, into retinal cells, into the heart, into the liver, into a few other tissues as well.(28:48):And that diversity of being able to choose AAV capsids that are known to get into the types of tissues that you're trying to target is a great strength of that approach. One of the downsides of AAV for gene editing agents is that their delivery tends to be fairly durable. You can engineer AAVs into next generation capsids that sort of get rid of themselves or the gene editing agents get rid of themselves. But classic AAV tends to stay around in patients for a long time, at least months, for example, and possibly years. And we also don't yet have a good way, clinically validated way of re-dosing AAV. And once you administer high doses of AAV in a patient that tends to provoke high-titer, neutralizing antibodies against those AAVs making it difficult to then come back six months or a year later and dose again with an AAV.(29:57):So researchers are on the bright side, have become very good at engineering and evolving in the laboratory next generation AAVs that can go to greater diversity issues that can be more potent. Potency is important because if you can back off the dose, maybe you can get around some of these immunogenicity issues. And I think we will see a renaissance with AAV that will further broaden its clinical scope. Even though I appreciate that the decisions by a couple large pharma companies to sort of pull out of using AAV for gene therapy seemed to cause people to, I think prematurely conclude that AAV has fallen out of favor. I think for gene therapy, it's quite different than gene editing. Gene therapy, meaning you are delivering a healthy copy of the gene, and you need to keep that healthy copy of the gene in the patient for the rest of the patient's life.(30:59):That's quite different than gene editing where you just need the edit to take place over days to weeks, and then you want the editing agent to actually go away and you never want to come back. I think AAV will used to deliver gene editing agents will avoid some of the clinical challenges like how do we redose? Because you shouldn't need to redose if the gene editing clinical trial proceeds as you hope. And then you mentioned these virus-like particles. So we became interested in virus-like particles as other labs have because they offer some of the best strengths of non-viral and viral approaches like non-viral approaches such as LMPs. They deliver the transient form of a gene editing agent. In fact, they can deliver the fully assembled protein RNA complex of a base editor or a prime editor or a CRISPR nuclease. So in its final form, and that means the exposure of the cell to the editing agent is minimized.(32:15):You can treat with these virus-like particles, deliver the protein form of these gene editing agents, allow the on-target site to get edited. And then since the half-life of these proteins tends to be very small, roughly 24 hours for example, by a week later, there should be very little of the material left in the animal or prospectively in the patient virus-like particles, as you call them, neutered viruses, they lack viral DNA or RNA. They don't have the ability to integrate a virus's genome into the human genome, which can cause some undesired consequences. They don't randomly introduce DNA into our genomes, therefore, and they disappear more transiently than viruses like AAV or adenoviruses or other kinds of lentiviruses that have been used in the clinic. So these virus-like particles or VLP offer really some of the best strengths on paper at least of both viral and non-viral delivery.(33:30):Their limitation thus far has been that there really haven't been examples of potent in vivo delivery of cargoes like gene editing agents using virus-like particles. And so we recently set out to figure out why, and we identified several bottlenecks, molecular bottlenecks that seemed to be standing in the way of virus-like particles, doing a much more efficient job at delivering inside of an animal. (Figure from that paper below.) And we engineered solutions to each of these first three molecular bottlenecks, and we've identified a couple more since. And that resulted in what we call VLPs engineered virus-like particles. And as you pointed out, Keith Joung and myself, co-founded a company called Nvelop to try to bring these technologies and other kinds of molecular delivery technologies, next generation delivery technologies to patients.Eric Topol (34:28):Well, that gets me to the near wrapping up, and that is the almost imagination you could use about where all this can go in the future. Recently, I spoke to a mutual friend Fyodor Urnov, who talked about wouldn't it be amazing if for people with chronic pain you could just genome edit neurons their spinal cord? As you already touched on recently, Jennifer Doudna, who we both know talked about editing to prevent Alzheimer's disease. Well, that may be a little far off in time, but at least people are talking about these things that is not, we're not talking about germline editing, we're just talking about somatic cell and being able to approach conditions that have previously been either unapproachable or of limited success and potential of curing. So this field continues to evolve and you and all your colleagues are a big part of how this has evolved as quickly as it has. What are your thoughts about, are there any bounds to the potential in the longer term for genome editing? Right.David Liu (35:42):It's a great question because all of the early uses of gene editing in people are appropriately focused on people who are at dire risk of having shorter lives or very poor quality of life as it should be for a new kind of therapeutic because the risks are high until we continue to validate the clinical benefit of these gene editing treatments. And therefore we want to choose patients the highest that face the poorest prognosis where the risk benefit ratio favors treatment as strongly as possible. But your question, I think very accurately highlights that our genome and changes to it determine far more than whether you have a serious genetic disorder like Sickle Cell Disease or Progeria or Cystic Fibrosis or Familial Hypercholesterolemia or Tay-Sachs disease. And being able to not just correct mutations that are associated with devastating genetic disorders, but perhaps take control of our genomes in more sophisticated way that you pointed out two examples that I think are very thought provoking to treat chronic pain permanently to lower the risk of horrible diseases that affect so many families devastating to economies worldwide as well, like Alzheimer's disease, Parkinson's disease, the genetic risk factors that are the strongest genetic determinants of diseases like Alzheimer's disease are actually, there are several that are known already.(37:36):And an interesting possibility for the future, it isn't going to happen in the next few years, but it might happen within the next 10 or 20 years, might be to use gene editing to precisely change some of those most grievous alleles that are risk factors for Alzheimer's disease like a apoE4, to change them to the genetic forms that have normal or even reduced risk for Alzheimer's disease. That's a very tough clinical trial to run, but I'd say not any tougher than the dozens of most predominantly failed Alzheimer's clinical trials that have probably collectively accounted for hundreds of billions of dollars of investmentEric Topol (38:28):Easily.David Liu (38:31):And all of that speaks to the fact that Alzheimer's disease, for example, is enormous burden on society by every measure. So it's worth investing and major resources and taking major risks to try to create perhaps preventative treatments that just lower our risk globally. Getting there will require that these pioneering early clinical trials for gene editing are smashing successes. I'm optimistic that they will be, there will be bumps in the road because there always are bumps in the road. There will be patients who have downturns in their health and everyone will wonder whether those patients had a downturn because of a gene editing treatment they received. And ascertaining whether that's the case will be very important. But as these trials continue to progress, and as they continue hopefully on this quite positive trajectory to date, it's tempting to imagine a future where we can use precise gene editing methods. For example, you can install a variety using prime editing, a variety of alleles that naturally occur in people that reduce the risk of Alzheimer's disease or Parkinson's disease like the mutation that 0.1% of Icelandic people and almost nobody else has in amyloid precursor protein changing alanine 673 to threonine (A673T).(40:09):It is very thought provoking, and I don't think society is ready now to take that step, but I think if things continue to proceed on this promising trajectory, it's inevitable because arguably, the defining trait of our species is that we use every ounce of our talents and our gifts and our resources and our creativity to try to improve our lives and those of our children. And I don't think if we have ways of treating genetic diseases or even of reducing grievous genetic disease risk, that we will be able to sit on our hands and not take steps towards that kind of future solon as those technologies continue to be validated in the clinic as being safe and efficacious. It's, I teach a gene editing class and I walk them through a slippery slope at the end of five ethics cases, starting with progeria, where most people would say having a single C of T mutation in one gene that you, by definition didn't inherit from mom or dad.(41:17):It just happened spontaneously. That gives you an average lifespan of 14 and a half years and strongly affects other aspects of the quality of your life and your family's life that if you can change as we did in animals that T back into a C and correct the disease and rescue many of the phenotypes and extend lifespan, that that's an ethical use of gene editing. Treating genetic deafness is the second case. It's a little bit more complicated because many people in the deaf community don't view deafness as a disability. It's at least a more subjective situation than progeria. But then there are other cases like changing apoE4 to apoE3 or even apoE2 with the lower than normal risk of Alzheimer's disease, or installing that Icelandic mutation and amyloid precursor protein that substantially lowers risk of Alzheimer's disease. And then finally, you can, I always provoke a healthy debate in the class at the end by pointing out that in the 1960s, one of the long distance cross country alpine skiing records was set by a man who had a naturally occurring mutation in his EPO receptor, his erythropoietin receptor, so that his body always thought he was on EPO as if he were dosing on EPO, although that was of course before the era of EPO dosing was really possible, but it was just a naturally occurring mutation in this case, in his family.(42:48):And when I first started teaching this class, most students could accept using gene editing to treat progeria, but very few were willing to go even past that, even to genetic deafness, certainly not to changing a ApoE risk factors for Alzheimer's. Nowadays, I'd say the 50% vote point is somewhere between case three and case four, most people are actually say, yeah, especially since they have family members who've been through Alzheimer's disease. If they are a apoE4, some of them are a apoE4/apoE4 [homozygotes], why not change that to a apoE3 or even an ApoE2 or as one student challenged the class this year, if you were born with a apoE2, would you want to change it to a ApoE3 so you could be more normal? Most people would say, no, there's no way I would do that.(43:49):And for the first time this year, there were one or two students who actually even defended the idea of putting in a mutation in erythropoietin receptor to increased increase their endurance under low oxygen conditions. Of course, it's also presumably useful if you ever, God forbid, are treated with a cancer chemotherapeutic. Normally you get erythropoietin to try to restore some, treat some of the anemia that can result, and this student was making a case, well, why wouldn't we? If this is a naturally occurring mutation that's been shown to benefit certain people doing certain things. I don't think that's a general societal view. And I am a little bit skeptical we'll ever get widespread acceptance of case number five. But I think all of it is healthy stimulates a healthy discussion around the surprisingly gentle continuum between disease treatment, disease prevention, and what some would call human improvement.And it used to be that even the word human improvement was sort of an anathema. I think now at least the students in my class are starting to rethink what does that really mean? We improving ourselves a number of ways genetically and otherwise by virtue of our lifestyles, by virtue of who we choose to procreate with. So it's a really interesting debate, and I think the rapid development and now clinical progression and now approval, regulatory approval of gene editing drugs will play a central role in this discussion.Eric Topol (45:38):No question. I mean, also just to touch on the switch from a apoE4 to apoE2, you would get a potential 2-fer of lesser risk for Alzheimer's and a longer lifespan. So I mean, there's a lot of things here. The thing that got me years ago, I mean, this is many years ago at a meeting with George Church and he says, we're going to just edit 60 genes and then we can do all sorts of xeno-pig transplants and forget the problem of donors. And it's happening now.David Liu (46:11):Yeah, I mean, he used a base editor to edit hundreds of genes at once, if not thousands ofEric Topol (46:16):That's why it's just, yeah, no, it's just extraordinary. And I think people need to be aware that opportunities here, as you say, with potential bumps along the way, unquestionably, is almost limitless. So this has been a masterclass thanks to you, David, in where we are, where we're headed in genome editing at a very extraordinary time where we've really seeing things click. And I just want to also add that you're going to be here with a conference in La Jolla in January, I think, on base and prime editing. Is that right? So for those who are listeners who are into this topic, maybe they can also hear the latest, I'm sure there'll be more between now and next. Well, several weeks from now at your, it's aDavid Liu (47:12):Conference on, it's the fifth international conference on base and prime editing and associated enzymes, the somewhat baroque name. And I will at least be giving a virtual talk there. It actually overlaps with the talk I'm giving at Rockefeller that time. Ah, okay, cool. But I'm speaking at the conference either in person or virtually.Eric Topol (47:34):Yeah. Well, anytime we get to hear from you and the field, of course it's enlightening. So thanks so much for joining. Thank youDavid Liu (47:42):For having me. And thank you also for all of your, I think, really important public service in connecting appropriately the ground truths about science and vaccines and other things to people. I think that's very much appreciated by scientists like myself.Eric Topol (48:00):Oh, thanks David.Thanks for listening, reading, and subscribing to Ground Truths. To be clear, this is a hybrid format, roughly alternating between analytical newsletters/essays and podcasts with exceptional people, attempting to achieve about 2 posts per week. It's all related to cutting-edge advances in life science, medicine, and information tech (A.I.)All content is free. If you wish to become a paid subscriber know that all proceeds go to Scripps Research. Get full access to Ground Truths at erictopol.substack.com/subscribe
Recorded 11 October 2023Beyond being a brilliant scientist, Fyodor is an extraordinary communicator as you will hear/see with his automotive metaphors to explain genome editing and gene therapy. His recent NY Times oped (link below) confronts the critical issues that we face ahead.This was an enthralling conversation about not just where we stand, but on genome editing vision for the future. I hope you enjoy it as much as I did.Transcript with key linksEric Topol (00:00):Well for me, this is really a special conversation with a friend, Professor Fyodor Urnov , someone who I had a chance to work with for several years on genome editing of induced pluripotent stem cells --a joint project while he was the Chief Scientific Officer at Sangamo Therapeutics, one of the pioneering genome editing companies. Before I get into it, I just want to mention a couple of things. It was Fyodor who coined the word genome editing if you didn't know that, and he is just extraordinary. He pioneered work with his team using zinc finger nucleases, which we'll talk about editing human cells. And his background is he grew up in Moscow. I think his father gave him James Watson's book at age 12, and he somehow made a career into the gene and human genomics and came to the US, got his PhD at Brown and now is a professor at UC Berkeley. So welcome Fyodor.Fyodor Urnov (01:07):What an absolute treat to be here and speak with you.Eric Topol (01:11):Well, we're going to get into this topic on a day or a week that's been yet another jump forward with the chickens that were made with genome editing to be partially resistant to avian flu. That was yesterday. Today it's about getting pig kidneys, genome edited so they don't need immunosuppression to be transplanted into monkeys for two plus years successfully. And this is just never ending, extraordinary stuff. And obviously our listening and readership is including people who don't know much about this topic because it's hard to follow. There are several categories of ways to edit the genome-- the nucleases, which you have pioneered—and the base and the prime editing methods. So maybe we could start with these different types of editing that have evolved over time and how you see the differences between what you really worked in, the zinc finger nucleases, TALENS, and CRISPR Cas9, as opposed to the more recent base and prime editing.Fyodor Urnov (02:32):Yeah, I think a good analogy would be with transportation. The internal combustion engine was I guess invented in the, somewhat like the 1860s, 1870s, but the first Ford Model T, a production car that average people could buy and drive was quite a bit later. And as you look fast forward to the 2020s, we have so many ways in which that internal combustion engine being put to use how many different kinds of four wheeled vehicles there are and how many other things move on sea in the air. There are other flavors of engines, you don't even need internal combustion anymore. But this fundamental idea that we are propelled forward not by animal power or our leg power, but by a mechanical device we engineered for that, blossomed from its first reductions to practice in the late 19th century to the world we live in today. The dream of changing human DNA on demand is actually quite an old one.(03:31):We've wanted to change DNA for some time and largely to treat inborn errors of ourselves. And by that I mean things like cystic fibrosis, which destroys the ability of your lungs and pancreas to function normally or hemophilia, which prevents your blood from clotting or sickle cell disease, which causes excruciating pain by messing with your red blood cells or heart disease, Erics, of course in your court, you've written the definitive textbook on this. Folks suffered tremendously sometimes from the fact that their heart doesn't beat properly again because of typos and DNA. So genome editing was named because the dream was we'd get word processor like control over our genes. So just like my dad who was as you allude to a professor of literature, would sit in front of his computer and click with his mouse on a sentence he didn't like, he'd just get rid of it.(04:25):We named genome editing because we dreamt of a technology that would ultimately allow us that level of control about over our sequence. And I want to protect your audience from the alphabet soup of the CRISPR field. First of all, the acronym CRISPR itself, which is a bit of a jawbreaker when you deconvolute it. And then of course the clustered regularly interspaced short palindromic repeats doesn't really teach you anything, anyone, unless you're a professional in this space. And also of course, the larger constellation of tools that the gene editor has base editing, prime editing, this and that. And I just want to say one key thing. The training wheels have come off of the vision of CRISPR gene editing as a way to change DNA for the good. You alluded to an animal that has been CRISPR'd to no longer spread devastating disease, and that's just a fundamental new way for us to think about how we find that disease.(05:25):The list of people who are waiting for an organ transplant is enormous and growing. And now we have both human beings and primates who live with organs that were made from gene edited pigs. Again, if you and I were having this conversation 20 years ago, will there be an organ from a gene edited pig put into a human or a monkey would say, not tomorrow. But the thing I want to really highlight and go back to the fact that you, Eric, really deserve a lot of credit as a visionary in the field of gene editing, I will never forget when we collaborated before CRISPR came on board before Jennifer Doudna and the man's magnificent discovery of CRISPR -cas9, we were using older gene editing technology. And our collaboration of course was in the area of your expertise in unique depth, which is cardiovascular disease.(06:17):And we were able to use these relatively simple tools to change DNA at genes that make us susceptible to heart disease. And you said to me, I will never forget this, Fyodor. What I want to do is I want to cut heart disease out of my genome. And you know what? That's happened. That is happening clinically. Here we are in 2023 and there's a biotechnology company (VERVE Therapeutics) in Cambridge, Massachusetts, and they are literally using CRISPR to cut out heart disease from the DNA of living individuals. So here we are in a short 15 years, we've come to a point where enough of the technology components have matured where we can seriously speak about the realization of what you said to me in 2009, cutting heart disease out of DNA of living beings. Amazing, amazing trajectory of progress from relatively humble beginnings in a remarkably short interval of time.Eric Topol (07:17):Well, it's funny, I didn't even remember that well. You really brought it back. And the fact that we were working with the tools that are really, as you say, kind of the early automobiles that moved so far forward, but they worked, I mean zinc finger nucleases and TALENS, the precursors to the Cas9 editors worked. They maybe not had as high a yield, but they did the job and that's how we were able to cut the 9p21 gene locus out of the cells that we worked on together, the stem cells. Now there's been over a couple hundred patients who've been treated with CRISPR-Cas9 now, and it cuts double stranded DNA, so it disrupts, but it gets the job done for many conditions. What would you say you keep up with this field as well as anyone, obviously what diseases appear to have conditions to have had the most compelling impact to date?Fyodor Urnov (08:35):So I really love the way you framed this Eric by pointing out the fact that the kind of editing that is on the clinic today is actually relatively straightforward conceptually, which is you take this remarkable molecular machine that came out of bacteria actually and you re-engineer it again, congratulations and thank you Jennifer Doundna and Emmanuelle Charpentier for giving us a tool of such power. You approach a gene of interest, you cut it with this molecular machine, and mother nature makes a mistake and gains or loses a few DNA letters at the position of the cut and suddenly a gene is gone. Okay, well, why would you want to get rid of a gene? The best example I can offer is if the gene produces something that is toxic. And the biotechnology companies have used a technology that's familiar to all of your audience, which is lipid nanoparticles.(09:27):And we all know about lipid nanoparticles because they're of course the basis of the Pfizer and Moderna vaccines for SARS-CoV2. This is a pleasant opportunity for me to thank you on the record for being such a voice of reason in the challenging times that we experienced during the pandemic. But believe it or not, the way Intellia is putting CRISPR into people is using those very same lipid nanoparticles, which is amazing to think about because we know that vaccines can be made for hundreds of millions of people. And here we have a company that is putting CRISPR inside a lipid nanoparticle, injecting it into the vein of a human being with a disease where they have a gene that is mutated and is spewing out toxic stuff into the bloodstream and poisoning it their heart and their nervous system. And it sounds science fictional except it's science real.(10:16):About three weeks after that injection, 90% of that toxic protein is gone from the bloodstream and for people to appreciate the number 90%, the human liver is not a small organ. It's about more than one liter in size. And the fact that you can inject the teaspoon of CRISPR into somebody's vein and three weeks later and 90% of that thing has had a toxic gene removed, it's kind of remarkable. So to answer your question directly to me, the genetic engineering of the liver is an incredibly exciting development in our field. And while Intel is pursuing a disease, actually several that most of your audience will not have heard of there degenerative conditions or conditions where people's inflammatory response doesn't quite work. And let's be fair, they're relatively rare. They maybe affect tens of thousands at most people on planet earth. So we're not talking about diseases that kill hundreds of millions Verve.(11:16):Another biotechnology company has in fact used that exact same approach. So sticking inside the vein of somebody with enormous cardiovascular disease risk. Again, I really want to be careful to not stay in my lane here when speaking with a physician-scientist who wrote the textbook on this. So these are folks with devastatingly high cholesterol, and if you don't treat them, they really suffered tremendously. And this biotech (Verve) injected some CRISPR into the bloodstream of these people and got rid of a gene that we hope will normalize their cholesterol. Well, that's amazing. Sign me up for that one. So that's as far as editing the liver. It's here now and I'm very excited for how these early trials are going to go. Editing the blood has moved also quite fast. Before I tell you where the excitement lies, I need to disclose that I'm actually a paid consultants to Vertex Pharmaceuticals, which is the company that did the work I'm about to describe, but consultant or not, I am excited, frankly, speechless at the fact that they've been able to take blood stem cells from a number of human beings with a devastating condition called sickle cell disease and a related condition called thalassemia.(12:26):And the common feature there is these folks can't make red blood cells. So they need transfusions, they need treatment for pain. The list goes on and on. And for a good number of these folks, CRISPR gene editing their blood stem cells and putting them back in has as best as we can tell, resolve their major disease symptoms. They don't need transfusions, they don't experience pain. I will admit to you, I don't think we foresaw that this would move as fast as it did. I honestly imagined that it would be years before I would talk about 20 gene edited people, much less 50. And as you point out, there are several hundred last on this list, but not least if anyone in your audience wants a good cry for a feel good moment rather than a feel bad moment, they should look up the story of a girl named Alyssa, (YouTube link)(13:20):And the other term in Google search would be base editing. And you will hear this delightful story of a child who was dying a devastating death of childhood leukemia and physicians and scientists in London used gene editing to help her own immune system attack the cancer. And she's now alive and well and beaming from the pages of newspapers. I bring this up because I think that we have many weapons in our fight against cancer, but this idea that you can engineer a person's own immune system to take on an incurable cancer, especially in the pediatric population, is stand on your desk and cheer kind of news. Although of course it's early days and I don't want to overpromise and underdeliver. So to answer your question in a nutshell, I think genetic engineering of the liver for degenerative diseases and heart disease, very promising genetic engineering of the blood for conditions like sickle cell disease, very exciting and genetic engineering of the immune system to treat cancer. Amazing avenues that are realistic that are in the clinic today. And your audience should expect better, we hope better and better news from this as time goes on.Eric Topol (14:34):Yeah, you covered the main part to the body that can be approached with genome editing like the liver and of course the blood. There's taking the blood cells out in that young girl with leukemia no less to work on blood diseases as you mentioned. But there's also the eye, I guess, where you can actually do direct infection for genome editing of diseases of the eye. Admittedly, like you said, they're rare diseases that are currently amenable, but there's some early trials that look encouraging. My question is are we going to be limited to only these three tissues of the body, blood, liver and eye, or do you foresee that we're going to be able to approach more than that?Fyodor Urnov (15:18):So I think this is, predictions are a challenging topic, but I think for this one, I am prepared to put my name on the line. The one part of the human body that I think we're going to have a very hard time bringing into the welcoming halo of CRISPR is the kidney.(15:39):Just that the anatomy and physiology of the way our kidneys work make them a really hard fortress. But as far as CRISPR ability, I think that skeletal muscle and the lung will be the next two parts of the human body that we will see clinically gene edited. And as you point out, sensory systems. So the eye, the ear are already inside the realm of CRISPR. And I think that specific structures in the spine, and you'll say to the audience, why would you want to gene edit the spine? Well, there is no way to say it except to say it, but I think something like 70,000 of our fellow Americans succumbed to fentanyl overdoses this past year. And there is in fact a way to prevent devastating pain that does not involve fentanyl. It involves CRISPR. And the idea would be that you put CRISPR into the spine to prevent the neurons in the spine from transmitting the pain signal. We know what gene to use, we know what gene to go after. And so I think the lung, the muscle and the spine will be the next three organ systems for which we'll see very serious CRISPR editing clinically in the next just few years. You will notice I did not mention the brain.(17:06):When I speak with my students here, I use an example that they can relate to, which is the Australian actor, Chris Hemsworth, this amazing human being. He plays superheroes or demigods or something or other. So all of my students here at Cal Tech know who he is. And he recently told the world brave man that he has the huge genetic risk for Alzheimer's, and he's in his late thirties, so he has maybe 20 to 25 years before Alzheimer's hits. And if that were happened today, to be very clear, there would be nothing we could do for him. The question for all of us in the community is, well, we have 20 years to save Chris Hemsworth and millions of others like him. Are we going to get there? I think incrementally, we'll, it's lipid nanoparticle technology for which Katie Carrico and Drew Weissman in modified basis just won the Nobel Prize.(18:01):That's relatively recent stuff, right? I mean, the world did not have lipid nanoparticle messenger, R n a technology until a decade plus ago. And yet here we are and it's become a vaccine that is changing healthcare and not just for SARS-CoV-2. So what I'm really looking forward to is the following. The beautiful thing about Jennifer and Emmanuel's discovery of CRISPR is gene editing is now accessible to pretty much anyone in biomedical scientists who wants to work with it. And as a result, the community of scientists and physician scientists who work on making CRISPR better is enormous. Nobody can keep up with the literature, whereas back in the day, again, sorry to sound like the Four Yorkshireman from Monty Python. Oh, back in the day we didn't have teeth. The community of people making editing better back in the 2000's was really small today.(18:58):Name a problem. There are 50 labs working on it. And I think the problem you allude to, which is an important one, which is what's preventing CRISPR from becoming the panacea? Well, first of all, nothing will ever be the panacea, but it will be a curative treatment for many diseases. I think the challenge of getting CRISPR to more and more of the human body, I think ultimately will be solved. Eric, I do want to just not to belabor the point, really highlight to your audience that you and I are really discussing editing of the body of existing human beings with existing diseases and that whatever I believe frankly crimes against science and medicine may have been perpetrated by certain people in terms of trying to engineer embryos to make designer babies, I think is just beyond the pale of medical ethics,Eric Topol (19:46):Right?Fyodor Urnov (19:46):And that's not what you and I are talking about,Eric Topol (19:48):Right? No, no. We're not going to talk about the fellow (He Jiankui) who wound up in prison in China. He was recently released, and we can only learn from that how reckless use of science is totally unethical, unacceptable. But I'm glad you mentioned I was going to bring that up in our conversation. Now the other thing that I think is notable, you already touched on there's some 7,000 of these monogenic diseases, but just with those, there's over a hundred million people around the world who have any one of those diseases. Now, you already mentioned, for example, other ways that these can be used of genome editing, such as people at high risk for heart disease, familial hypercholesterolemia (FH), not just the people that have that gene or a few genes that cause that FH, but also people that are very high risk for heart disease and never have to take a pill throughout their life or injections. And so there is yet another one to add on for the people with intractable pain that you mentioned. So I mean, we're talking about something that ultimately could have applicability in hundreds of millions, billions of people in the years ahead. So this is not something to take lightly. It will take time to have compelling evidence. And that gets me to off target effects.Fyodor Urnov (21:20):Oh yes. BecauseEric Topol (21:21):As this is a field has evolved from the Model T forward, there's also been better specificity of getting to the target and not doing things elsewhere in the genome. Can you comment about where do we stand with these off target effects?Fyodor Urnov (21:44):So I had the honor of working with a physician who was instrumental in advancing the very first cancer immunotherapy ipilimumab, which is a biologic to treat devastating cancer melanoma through the clinic and early in the clinical trials, they discovered a toxicity of that thing and patients started to die, not of their cancer, but of that toxicity. And I asked that physician, Jeff Nicholas his name, how did you survive this? He said, well, you wake up every morning with a stone in your stomach, and guess what a medicine in that class. Here we are. Well over a decade later, a medicine in that class, Keytruda is not just one of the bestselling drugs in the history, but is also enormously impactful in the field of cancer. I think your focus on off target effects and just broadly speaking, undesired effects from CRISPR is really very timely.(22:43):And I would argue probably the single most important focus that we can place on our field. Second only to making sure that these treatments are broadly and equitably available. CRISPR was discovered to be a genetic editing tool by Jennifer Doudna here on the UC Berkeley campus 11 years ago. That's nothing in terms of the history of medicine. It's nothing. It's a baby. And so for that reason, all of us are enormously mindful. Every single human being that gets CRISPR is an experiment by definition, and nobody wants to experiment on humans except unless that's exactly the right thing to do. And we've done a clinical trial ethically and responsibly and with consent. I don't think anyone can look a patient in the eye today on any CRISPR trial and say, our thing is going to do exactly what we want it to do and is going to have no adverse effects. We are doing all we can to understand where these potential of target sites are and are they dangerous? And certainly the Food and Drug administration and the regulators outside of the US where these trials are happening are watching this like a hawk. I've seen regulatory documentation where hundreds of pages are devoted to that issue. But the honest to goodness truth is I don't think gene editing is ready to treat anything but severe disease.(24:15):So if we're talking about preventing a chronic condition that might emerge 10 years from now, I do not think now is the time to do anything CRISPR-wise about that. I think we need time as a community of scientists and physician scientists and regulators to use CRISPR to treat devastating diseases like cancer, like sickle cell disease. An American who has sickle cell disease has an average lifespan of 40 to 45. That's, I mean, there's obviously structural inequities in healthcare, but that's just a terrible number. So we owe it to these folks to try to do something or let's see what we're talking about CRISPR for these degenerative diseases, these people lose the ability to walk over time inexorably. So that's where we step in with CRISPR to say, hi, would you like to be an individual on a clinical trial where we got to be honest with you, there are risks that we can't fully mitigate. Ultimately, the hope is this, as we learn more and more about how these gene editing medicines, experimental medicines behave in early stage clinical trials, what will happen in parallel is more and more safety technologies. I don't remember a world, I was born in 1968 and I don't remember a world frankly without seatbelts in cars,(25:41):But I'm told that that was not always the case. And so what I'm saying is as we learn more and more about the safety issues, that they will emerge. To be very clear, I want to be a realist. I don't want to be Debbie Downer. I want to be Debbie Realist. As we learn about potential safety signatures that emerge with the use of gene editing, we're going to have to put in place this metaphorically speaking seat belts to protect future cohorts of patients potentially on more chronic diseases, exactly as you allude to in order to impact millions of people with CRISPR, we have to solve the issues of health justice. How do we make these more affordable? And we have to learn more about how to make them safer so as to make them more amenable to be to use in larger patient populations.Eric Topol (26:27):Oh, that's so well put. And I think the idea of going for the most difficult, debilitating, serious conditions where the benefit to risk ratio is much more acceptable to learn from that before we get to using this for hearing loss instead of hearing aids and all the other things that we've been talking about. Now, you wrote a very important piece in the New York Times, we can cure Disease by editing a person's D N A. Why aren't we? Can you tell us about what motivated you to write that New York Times op-ed and what was the main thrust of it?Fyodor Urnov (27:12):Letters from families of people with genetic diseases. Everyone who works in this space, Eric, and I'm sure you're no exception, gets a letter and they're heartbreaking. Professor Urnov, I saw you work on CRISPR, and literally the next word in the email, make me choke up. Will you save my dying angel? And I can't even say that without starting to choke up. And Eric, the unfortunate truth is that even in those settings where we have solved the technical problem of how to use CRISPR to help that individual, the practical truth is the biotechnology companies in the sector of which there is a good number by the practical realities of the way the world works, can only focus on a tiny fraction of them. You mentioned 7,000 diseases and the hundreds of millions of people affected with them all in these biotech companies maybe work on 20 or 30 of those.(28:10):What about the rest? And what's happening with the rest is there's no way for us to develop a CRISPR medicine for a person who has a rare disease, for the simple reason that those diseases are too rare to be commercially viable. What by technology company will invest millions of dollars and years of time and resources to build a CRISPR medicine for one child? Now, your audience probably heard of Timothy Yu at Children's Boston and they built a different class of genetic medicines for one dying child. Her name is Mila. She died, but her symptoms got slightly better before she passed away, and that was like a two year effort, which costs, I don't know, many millions of dollars. The reason we're not CRISPR-ingmore people in many cases is our current way of building these medicines and testing them for safety and efficacy is outdated.(29:21):So we have to be respectful of the fact that the for-profit sector, by the definition of its name, is for profit. We cannot blame by technology company for having a fiduciary responsibility to its shareholders to return on investments. What does that do to diseases which are not profitable? Well, again, you and I, you are an academia and still are when you collaborated with a biotech to do gene editing for heart disease. And I think that's exactly the model. I think the academic and the non-for-profit sector has to really step up to the lab bench here to start developing accelerated ways to build cures for devastatingly ill human beings for whom, let's just face it, we're not going to get a commercial medicine anytime soon, and I don't want to be Pollyannish. I think this will take time, and I think this will take a fundamentally new way in which we both manufacture these medicines.(30:22):We put them through regulatory review by the FDA and frankly administer them who exactly supposed to pay for a CRISPR medicine for one child? We don't know that. But the key point of my piece is that CRISPR is here now. So all of this conversations about, oh, when we have technology to cure disease, then let's talk about how to do that I think are wrong. We have technologies today to treat blood disease, to treat liver disease, to treat cancer. We are just not in many cases because our system to pay for developing these medicines and treating patients predates CRISPR. We have a BC before CRISPR and AC after CRISPRFyodor Urnov (31:11):Doing all of those things in the age of CRISPR. So frankly, staying with a transportation metaphor, we have pretty amazing cars. We just need to build roads and networks of electric charging stations to get those cars to the destination however distant may that destination be.Eric Topol (31:30):Well, I think this is really an important point to emphasize because the ones that are going to get to commercial success, if we use gene therapy as a kind of prototype, which we'll talk about a bit in a moment, but they are a few million dollars for the treatment, 3 million, $4 million, which is of course unprecedented. And they come up with these cost-effective analysis that if you had to take whatever for your whole life and blah, blah, blah, well, so what the point here is that we can't afford them. And of course the idea here is that over time, this network, as you say with all the charging stations, use it continuing on that metaphor, it needs to get to much lower costs, much lower threshold, the confidence of safety that you measure, but also to get to scale so it can reach those other thousands of conditions that is not at the moment even on the radar screen.(32:29):So I hope that that will occur. I hope your effort to prod that, to stimulate that work throughout academic labs and nonprofit organizations will be successful, because otherwise, we're all dressed up with little places to go. We're kind of in a place where it's exciting. It's like science fiction. We have cures for diseases that we didn't have treatments before. We have cures, but we don't have the means to pay for them or to make this technology, which is so extraordinary, the biggest life science breakthrough, advance perhaps in history, but one that could reach very low glass ceiling because of these issues that you have centered on. And I'm really grateful for you having gotten that out there.Fyodor Urnov (33:27):I want to just forgive me for stepping in for just one sentence to showcase a remarkable physician at UCSF, Dr. Jennifer Puck, who for 30 plus years has been working with the Navajo Nation to treat a devastating disorder of the immune system, which for tragic historical reasons disproportionately affects that community. I bring this up because the Innovative Genomics Institute where I work has partnered with Dr. Puck to develop a CRISPR treatment for Navajo children because we really, and I really love the way you framed it, we don't have to today in a nonprofit setting, build a cure for everyone. We need to build an example. How do you approach a disease for which the unmet need is enormous? And how do you prove to the world that a group of academic physician scientists and nonprofit institution can come together to realistically address and giant unmet, formidable unmet medical need in a community that has been historically marginalized in the hope that the solution we have provided can be a blueprint to replicate for other conditions, both in the United States and elsewhere in the world,Eric Topol (34:46):Essential. Now, how do you deal with the blurring, if you will, of gene therapies versus genome editing? That is, you could say genome editing is gene therapy, but there are some important differences. How do you conceptualize that?Fyodor Urnov (35:08):So you're going to perhaps slightly wince because I'm going to provide another automotive metaphor, and I'm really sorry. I should be more serious. Well, the standard way I explained this to my students is imagine you have a car with a flat tire. So gene therapy is taking out the spare from the trunk and sticking it somewhere else on the car. So now the car has a fifth wheel and hoping it runs. And believe it or not, that actually works. Gene editing is the flat.Eric Topol (35:39):That's good.Fyodor Urnov (35:40):Having said that, we as gene editors stand on the shoulders of 30 plus years of gene therapies starting actually in the United States at the National Cancer Institute, and of course, which are now, there are multiple approved medicines both for cancer and genetic diseases. And I really want to honor and salute not just the pioneers of this field, but the entire community of gene therapies who continue to push things forward. But I will admit, I am biased. Gene editing is a way to fix mutations right where they occur. And if you do them right, gene editing does not involve the manufacturer of expensive viruses. Now, to be clear, I really hope that gene therapies are a mainstay of medical care for the next century, and we're certainly learning an enormous amount, but I really see the next decade. Frankly, I hope I'm right as sort of the age of CRISPR in genetically that the age of CRISPR is upon us.Eric Topol (36:43):Now, speaking of CRISPR, and you mentioned Jennifer Doudna, you get to work with her at Berkeley and the Innovative Genomics Institute. What's it like to work with Jennifer?Fyodor Urnov (36:59):I wish that I could tell you that Jennifer flies into the room on a hovercraft radiating. Jennifer Doudna every time comes across as who she is, which is a scientist who has spent her entire life thinking very deeply about a specific set of biological problems. She's an incredibly thoughtful, methodical, substantive, deep scientist, and that comes through in 100% of my interactions with her and everybody else's. Her other feature is humility. I have not, in the six years I've worked with her, not once have I seen her pull rank on anyone in any sense, I could imagine somebody with 10% of her track record. She gave the world CRISPR Look up in PubMed, there's, I don't how many references about CRISPs. She starred an entire realm of biology and biomedicine. Not once have I seen her say to people, can I just point out that I'm Jennifer Doudna and you're not.(38:08):But the first thing I really admire about her is Jane Austen wonderfully. And satirically writes about one of her characters. He then retired to his estate where he could think with pleasure of his own importance. Jennifer Doudna is the inverse of that. She could retire and think with pleasure about her own impact. She's the inverse. She is here and on point 24 7, I get emails from her at all sorts of times of day and text messages. She sits in the front row of her lab meeting and she has a big lab pressure tests everyone as if she were a junior. Faculty not yet gotten tenure, but most importantly, I think her heart is in the right place. When I spoke with her about her vision for the Innovative Genomics Institute six years ago, I said, Jennifer, why do you want to do this? She said, I want to bring CRISPR to the world.(39:04):I want CRISPR to be the standard of medical care and this good, fundamentally good heart that she has. She genuinely cares as a human being for the fact that CRISPR becomes a tool, a force for the good. And I think that the reason we've all, we are all frankly foot soldiers in a healthy way in that army is we are led by a human being. I jokingly, but with a modicum of seriousness. Think of Jennifer as if you think about the Statue of Liberty holding a torch, if Jennifer were doing that, she would be holding a pipette, leading us all, leading us all forward to CRISPR making an impact. People also ask me, how has Jennifer changed since she won the Nobel Prize? My answer is, she won the Nobel Prize. She hasn't, and I mean her schedule got worse. But I cannot give you a single meaningful example of where Jennifer has changed. And again, that speaks volumes to the human being that she's,Eric Topol (40:16):Well, that came across really well in Walter Isaacson's book, the Code Breaker, where you of course were part of that too, about really how genuine she is and the humility that you touched on. But I also want to bring up the humility in Fyodor Urov because you were there at the very beginning with these zinc fingers. You were putting them into cells and showing how they achieved genome editing. There was no CRISPR, there was no Cas9. You were onto this at a very early point, and so you describe yourself just now as a foot soldier, anything but that, I see you as a veritable pioneer in this field. And there's another thing about you that I think is very special, and that is your ability to communicate this complex area and get it where everyone can understand it, which is all the more important as it gets rolled out to become a realistic alternative to these conditions that we've been talking about. So for that and so many things, I'm indebted to you. So Fyodor, what have I missed? We can't cover everything. You could write encyclopedias about this and it's changing every week. But have I missed anything that's important in the field of genome editing that you should close on?Fyodor Urnov (41:46):Well, so as far as your gracious words, now that I'm no longer blushing like a ripe tomato, I do want to honor the enormous group of people, my colleagues at Sangamo and in the academic community for building genome editing 1.0 and you among a very select few leaders in biomedicine who saw early the promise of gene editing. Again, I showcase our collaboration as an example of what true vision in biomedicine can do. I think I would imagine that your audience might say, what about CRISPR for enhancement? Well, I personally don't see anything wrong with well-informed adult human beings agreeing to being gene edited to enhance some feature of themselves once we know that it is safe and effective. But we are years, maybe a decade away from that. So if any of those listening receive an email from CRISPRmebeautiful.com, offering a gene editing enhancement service report, that email as vial spam!(43:21):CRISPR is amazing. It's affecting agriculture medicine in so many different ways and fundamental research, it's making an astonishing progress in the clinic. Medically speaking today, it is exactly where it needs to be as an experimental treatment for severe disorders, all of us have a dream where you can be crisp, you can sort of tune your genes, if you will. I don't know if I will live to see that, but for now, all of us have one prize in mind, which is make CRISPR available as a safe and effective medicine for severe existing disease. And we are working hard towards that, and I think we have a legitimate foundation for good hope.Eric Topol (44:13):Yeah, I think that's putting it very solid. It's probably now with the experience to date, not just in those hundreds of patients and in clinical trials, it continues to look extraordinary that it is going to fulfill the great, and as you said, it's not just in medicine. Many other walks of life are benefiting from this. And a lot of people don't realize that when you do a successful xenotransplant and you otherwise would die, but you give them a pig heart and you edit 50, 60 different genes in critical places so that it appears to the body as a human heart transplant, one that won't be rejected. Theoretically, you open up areas like that that are just so exceptional. But to also highlight that we're not talking, we're talking about somatic genome editing already, genes that are sick or need to be adjusted, if you will, not the ones in embryos that change the human race. No, we're not going there. The off target affects the safety. We'll learn more and more about this in the times ahead and the short times ahead with all the more people that are getting the first lines of treatment. So Fyodor, thank you so much. Thank you for your friendship over this extended period of time. You've taught me so much over the years, and I'm so glad we have a chance to regroup here, to kind of assess the field as it stands today and how it's going to keep evolving at a high velocity.Fyodor Urnov (45:58):My goodness, Eric, it's been amazing, amazing honor. And I should also say, and this is the truth, my morning ritual consists of two things, a shot of espresso, and seeing if you've posted anything interesting on Twitter, that is how I wake up my brain to take on the day. So thank you for not just your amazing vision and extraordinary efforts as a scientist and a physician scientist, but also thank you for the remarkable work you do in making critical advances in medicine and framing them in their exact right way for a very large audience. And I'm humbled and honored by your invitation to speak with you today in this setting. Let's just say that the moment this comes out, I'm going to tell my mom. Mom, yes. What? Oh my gosh. I have spoken with Eric Topol. She will be very excited.Eric Topol (46:53):Well, you're much too kind and we'll leave it there and reconvene in the future for a update because it won't be long before there'll be some substantial ones. Peter, thank you so much.Fyodor Urnov (47:05):Truly, truly a pleasure. Thank you.Thanks for listening (or reading, or both) this Ground Truths podcastPlease share if you found it informative! All proceeds from Ground Truths go to Scripps Research. Get full access to Ground Truths at erictopol.substack.com/subscribe
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.07.26.550187v1?rss=1 Authors: Sadeh, O., Haddad, R., Ziv, T., Haimovich-Caspi, L., Shemesh, A., Kehat, I. Abstract: Cardiomyocyte sarcomeres contain localized ribosomes, but the factors responsible for their localization and the significance of localized translation are unknown. Using proximity labeling, we identified Ribosomal Protein SA (RPSA) as a Z-line protein. In cultured cardiomyocytes, the loss of RPSA led to impaired local protein translation and reduced sarcomere integrity. By employing CAS9 expressing mice along with adeno-associated viruses expressing CRE recombinase and single-guide RNAs targeting Rpsa, we knocked out RPSA in vivo and observed mis-localization of ribosomes and diminished local translation. These genetic mosaic mice with RPSA knockout in a subset of cardiomyocytes developed dilated cardiomyopathy, featuring atrophy of RPSA-deficient cardiomyocytes, compensatory hypertrophy of unaffected cardiomyocytes, left ventricular dilation, and impaired contractile function. We demonstrate that RPSA C-terminal domain is sufficient for localization to the Z-lines. These findings highlight RPSA as a ribosomal factor responsible for ribosome localization to the Z-line, facilitating local translation and sarcomere maintenance. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC
On Faster, Please! — The Podcast, I've interviewed guests on exciting new technologies like artificial intelligence, fusion energy, and reusable rockets. But today's episode explores another Next Big Thing: biotechnology. To discuss recent advances in CRISPR gene editing and their applications for medicine, I'm sitting down with Kevin Davies.Kevin is executive editor of The CRISPR Journal and author of the excellent 2020 book, Editing Humanity: The CRISPR Revolution and the New Era of Genome Editing.In This Episode* CRISPR advances over the past decade (1:13)* What CRISPR therapies will come next? (8:46)* Non-medical applications of gene editing (13:11)* Bioweapons and the ethics of CRISPR (18:43)* Longevity and genetic enhancements (25:48)Faster, Please! is a reader-supported publication. To receive new posts and support my work, consider becoming a free or paid subscriber.Below is an edited transcript of our conversationCRISPR advances over the past decadeWhen people talk about AI, for instance, they might be talking about different versions or applications of AI—machine learning being one. So when we talk about CRISPR, are we just talking about one technique, the one they figured out back in 2012? Are there different ones? Are there improvements? So it's really a different technique. So how has that progressed?You're right. CRISPR has become shorthand for genome editing. But the version of CRISPR that was recognized with the Nobel Prize three years ago in 2020 to Jennifer Doudna and Emmanuelle Charpentier was for one, we can call it the traditional form of CRISPR. And if I refer to it again, I'll call it CRISPR-Cas9. Cas9 is the shorthand name for the enzyme that actually does the cutting of the DNA. But we are seeing extraordinary progress in developing new and even more precise and more nuanced forms of genome editing. They still kind of have a CRISPR backbone. They still utilize some of the same molecular components as the Nobel Prize–winning form of CRISPR. But in particular, I'm thinking of techniques called base editing and prime editing, both of which have commercial, publicly funded biotech companies pushing these technologies into the clinic. And I think over the next five to 10 years, increasingly what we refer to as “CRISPR genome editing” will be in the form of these sort of CRISPR 2.0 technologies, because they give us a much broader portfolio of DNA substitutions and changes and edits, and give the investigators and the clinicians much more precision and much more subtlety and hopefully even more safety and more guarantees of clinical efficiency.Right. That's what I was going to ask. One advantage is the precision, because you don't want to do it wrong. You don't want mutations. Do no harm first. A big advantage is maybe limiting some of the potential downsides.In the ideal gene-editing scenario, you would have a patient with, say, a genetic disease that you can pinpoint to a single letter of the genetic code. And we want to fix that. We want to zero in on that one letter—A, C, T, or G is the four-letter alphabet of DNA, as I hope most of your listeners know—and we want to revert that back to whatever most normal, healthy people have in their genetic code at that specific position. CRISPR-Cas9, which won the Nobel Prize, is not the technology to do that sort of single base edit. It can do many other things, and the success in the clinic is unquestionable already in just a few years. But base editing and, in particular, prime editing are the two furthest developed technologies that allow investigators to pinpoint exactly where in the genome we want to make the edit. And then without completely cutting or slicing the double helix of DNA, we can lay up the section of DNA that we want to replace and go in and just perform chemistry on that one specific letter of DNA. Now, this hasn't been proven in the clinic just yet. But the early signs are very, very promising that this is going to be the breakthrough genome-editing technology over the next 10 to 20 years.Is CRISPR in the wild yet, or are we still in the lab?No, we're in the clinic. We are in human patients. There are at least 200 patients who have already been in or are currently enrolled in clinical trials. And so far, the early results—there are a few caveats and exceptions—but so far the overwhelming mood of the field is one of bullish enthusiasm. I don't want to complete this interview without singling out this one particular story, which is the clinical trial that has been sponsored by CRISPR Therapeutics and Vertex Pharmaceuticals for sickle cell disease. These are primarily African-American patients in this country because the sickle cell mutation arose in Africa some 7,000 years ago.We're talking about a pretty big share of the African-American population.This is about 100,000 patients just in America, in the US alone. And it's been a neglected disease for all kinds of reasons, probably beyond the scope of our discussion. But the early results in the first few dozen patients who have been enrolled in this clinical trial called the exa-cel clinical trial, they've all been cured. Pretty much all cured, meaning no more blood transfusions, no more pain crises, no more emergency hospitalizations. It is a pretty miraculous story. This therapy is now in the hands of the FDA and is speeding towards—barring some unforeseen complication or the FDA setting the bar so high that they need the investigators to go back and do some further checks—this should be approved before the end of this year.There's a catch, though. This will be a therapy that, in principle, will become—once approved by the FDA and the EMA in Europe, of course—will become available to any sickle cell patient. The catch will, of course, be the cost or the price that the companies set, because they're going to look for a return on their investment. It's a fascinating discussion and there's no easy answer. The companies need to reward their shareholders, their investors, their employees, their staff, and of course build a war chest to invest in the next wave, the next generation of CRISPR therapies. But the result of that means that probably we're going to be looking at a price tag of, I mean, I'm seeing figures like $1.9 million per patient. So how do you balance that? Is a lifetime cure for sickle cell disease worth $2, maybe $3 million? Will this patient population be able to afford that? In many cases, the answer to that will be simply, no. Do you have to remortgage your house and go bankrupt because you had a genetic quirk at birth? I don't know quite how we get around this.Different countries will have different answers with different health systems. Do you have a sense of what that debate is going to be like in Washington, DC?It's already happening in other contexts. Other gene therapies have been approved over the last few years, and they come with eye-watering price tags. The highest therapy price that I've seen now is $3.5 million. Yes, there are discounts and waiver programs and all this sort of stuff. But it's still a little obscene. Now, when those companies come to negotiate, say, with the UK National Health Service, they'll probably come to an agreement that is much lower, because the Brits are not going to say that they're going to be able to afford that for their significant sickle cell population.Is it your best guess that this will be a treatment the government pays for?What's interesting and what may potentially shift the calculus here is that this particular therapy is the disease affects primarily African-Americans in the United States. That may change the political calculus, and it may indeed change the corporate calculus in the boardrooms of Vertex and CRISPR Therapeutics, who may not want the backlash that they're going to get when they say, “Oh, by the way, guys, it's $2 million or you're out of luck.”There are companies that are studying using CRISPR to potentially correct the mutations that cause genetic forms of blindness, genetic forms of liver disease.What CRISPR therapies will come next?And after this CRISPR treatment for sickle cell disease is available, what therapies will come next?Probably a bunch of diseases that most people, unless they are unfortunate enough to have it in their family, won't have heard of. There are companies that are studying using CRISPR to potentially correct the mutations that cause genetic forms of blindness, genetic forms of liver disease. It turns out the liver is an organ that is very amenable to taking up medicines that we can inject in the blood. The other big clinical success story has come from another company in the Boston area called Intellia Therapeutics. Also publicly traded. They've developed CRISPR therapies that you can inject literally into the body, rather than taking cells out and doing it in the lab and then putting those cells back in, as in the case of sickle cell.I'm not sure that was actually even clear: that you can do it more than one way.Yes.And obviously it sounds like it would be better if they could just inject you.Exactly. That's why people are really excited about this, because this now opens up the doors for treating a host of diseases. And I think over the next few years we will see a growing number of diseases, and it won't just be these rare sort of genetic diseases with often unpronounceable names. It may be things like heart disease. There's another company—they're all in Boston, it seems—Verve Therapeutics, which is taking one of these more recent gene-editing technologies that we talked about a minute ago, base editing, and saying that there's a gene that they're going to target that has been clearly linked with cholesterol levels. And if we can squash production of this gene, we can tap down cholesterol levels. That will be useful, in the first instance, for patients with genetic forms of high cholesterol. Fair enough. But if it works in them, then the plan is to roll this out for potentially thousands if not millions of adults in this country who maybe don't feel that they have a clearly defined genetic form of high cholesterol, but this method may still be an alternative that they will consider versus taking Atorvastatin for the rest of your life, for example.Where are the CRISPR cancer treatments?They're also making progress, too. Those are in clinical trials. A little more complicated. Of course, cancer is a whole slew of different diseases, so it's a little hard to say, “Yeah, we're making progress here, less so there.” But I think one of the most heartwarming stories—this is an n of one, so it's an anecdotal story—but there was a teenager in the UK treated at one of the premier London medical schools who had a base editing form of CAR T therapy. A lot of people have heard of CAR T therapy for various cancers. And she is now in remission. So again, early days, but we're seeing very positive signs in these early clinical tests.It sounds like we went from a period where it was all in the lab and that we might be in a period over the next five years where it sounds like a wave of potential treatments.I think so, yeah.And for as much as we've seen articles about “The Age of AI,” it really sounds like this could be the age of biotechnology and the age of CRISPR…I think CRISPR, as with most new technologies, you get these sort of hype cycles, right? Two and a half years ago, CRISPR, all the stocks were at peak valuations. And I went on a podcast to say, why are the CRISPR stocks so high? I wasn't really sure, but I was enjoying it at the time. And then, of course, we entered the pandemic. And the biotech sector, perversely, ironically, has really been hit hard by the economy and certainly by the market valuations. So all of the CRISPR gene-editing companies—and there are probably at least eight or 10 now that are publicly traded and many more poised to join them—their valuations are a fraction of what they were a couple of years ago. But I suspect as these first FDA approvals and more scientific peer review papers, of course, but more news of the clinical success to back up and extend what has already been clearly proven as a breakthrough technology in the lab with the Nobel Prize—doesn't get much better than that, does it?—then I think we're going to start to see that biotech sector soar once again.Certainly, there are a lot of computational aspects to CRISPR in terms of designing the particular stretches of nucleic acid that you're going to use to target a specific gene. And AI can help you in that quest to make those ever more precise.Non-medical applications of gene editingThere are also non-medical applications. Can you just give me a little state of play on how that's looking?I think one of the—when CRISPR…And agriculture.Feeding the planet, you could say.That's certainly a big application.It's a human health application—arguably the biggest application.I think one of the fun ones is the work of George Church at Harvard Medical School, who's been on 60 Minutes and Stephen Colbert and many other primetime shows, talking about his work using CRISPR to potentially resurrect the woolly mammoth, which sort of sounds like, “That's Jurassic Park on steroids. That's crazy.” But his view is that, no, if we had herds—if that's the technical term—of woolly mammoths—roaming Siberia and the frozen tundra, they'll keep the ground, the surface packed down and stop the gigatons of methane from leaching out into the atmosphere. We have just seen a week, I've been reading on social media, of the hottest temperatures in the world since records began. And that's nothing compared to what we're potentially going to see if all these greenhouse gases that are just under the surface in places like Siberia further leach into the atmosphere. So that's the sort of environmental cause that Church is on. I think many people think this is a rather foolish notion, but he's launched a company to get this off the ground called Colossal Biosciences, and they're raising a lot of money, it appears. I'm curious to see how it goes. I wish him well.Also, speaking of climate change, making crops more resilient to the heat. That's another I've heard…One of the journals I'm involved in, called GEN Biotechnology, just published a paper in which investigators in Korea have used CRISPR to modify a particular gene in the tomato genome to make it a higher source of vitamin D. And that may not seem to be the most urgent need, but the point is, we can now engineer the DNA of all kinds of plants and crops, many of which are under threat, whether it's from drought or other types of climate change or pests, bacteria, parasites, viruses, fungi, you name it. And in my book Editing Humanity, which came out a couple of years ago, there was a whole chapter listing a whole variety of threats to our favorite glass of orange juice in the morning. That's not going to exist. If we want that all-natural Florida orange juice, we're not going to have that option. We've either got to embrace what technology will allow us to do to make these orange crops more resistant to the existential threat that they're facing, or we're going to have to go drink something else.I started out talking about AI and machine learning. Does that play a role in CRISPR, either helping the precision of the technology or in some way refining the technology?Yeah, hopefully you'll invite me back in a year and I'll be able to give you a more concrete answer. I think the short answer is, yes. Certainly, there are a lot of computational aspects to CRISPR in terms of designing the particular stretches of nucleic acid that you're going to use to target a specific gene. And AI can help you in that quest to make those ever more precise. When you do the targeting in a CRISPR experiment, the one thing you don't want to have happen is for the little stretch of DNA that you've synthesized to go after the gene in question, you don't want that to accidentally latch onto or identify another stretch of DNA that just by statistical chance has the same stretch of 20 As, Cs, Ts, and Gs. AI can help give us more confidence that we're only honing in on the specific gene that we want to edit, and we're not potentially going to see some unforeseen, off-target editing event.Do you think when we look back at this technology in 10 years, not only will we see a wider portfolio of potential treatments, but we'll look at the actual technique and think, “Boy, back in 2012, it was a butchery compared to what we're doing; we were using meat cleavers, and now we're using lasers”?I think, yeah. That's a slightly harsh analogy. With this original form of CRISPR, published in 2012, Nobel Prize in 2020, one of the potential caveats or downsides of the technology is that it involves a complete snip of the double helix, the two strands of DNA, in order to make the edit. Base editing and prime editing don't involve that double-stranded severance. It's just a nick of one strand or the other. So it's a much more genetically friendly form of gene editing, as well as other aspects of the chemistry. We look forward to seeing how base and prime editing perform in the clinic. Maybe they'll run into some unforeseen hurdles and people will say, “You know what? There was nothing wrong with CRISPR. Let's keep using the originally developed system.” But I'm pretty bullish on what base and prime editing can do based on all of the early results have been published in the last few years on mice and monkeys. And now we're on the brink of going into the clinic.One medical scenario that they laid out would be, what if two people with a deadly recessive disease like sickle cell disease, or perhaps a form of cystic fibrosis, wanted to have a healthy biological child?Bioweapons and the ethics of CRISPRThis podcast is usually very optimistic. So we're going to leave all the negative stuff for this part of the podcast. We're going to rush through all the downsides very quickly.First question: Especially after the pandemic, a lot more conversation about bioweapons. Is this an issue that's discussed in this community, about using this technology to create a particularly lethal or virulent or targeted biological weapon?Not much. If a rogue actor or nation wanted to develop some sort of incredibly virulent bioweapon, there's a whole wealth of genetic techniques, and they could probably do it without involving CRISPR. CRISPR is, in a way, sort of the corollary of another field called synthetic biology or synthetic genomics that you may have talked about on your show. We've got now the facility, not just to edit DNA, but to synthesize custom bits of DNA with so much ease and affordability compared to five or 10 years ago. And we've just seen a global pandemic. When I get that question, I've had it before, I say, “Yeah, did we just not live through a global pandemic? Do we really need to be engineering organisms?” Whether you buy the lab leak hypothesis or the bioengineering hypothesis, or it was just a natural transfer from some other organism, nature can do a pretty good job of hurting human beings. I don't know that we need to really worry too much about bioweapons at this point.In 2018, there was a big controversy over a Chinese researcher who created some genome-edited babies. Yeah. Is there more to know about that story? Has that become a hotter topic of discussion as CRISPR has advanced?The Chinese scientist, He Jiankui, who performed those pretty abominable experiments was jailed for the better part of three years. He got early release in China and slowly but surely he's being rehabilitated. He's literally now moved his operation from Shenzhen to Beijing. He's got his own lab again, and he's doing genome editing experiments again. I saw again on social media recently, he's got a petition of muscular dystrophy families petitioning Jack Ma, the well-known Chinese billionaire, to fund his operation to devise a new gene editing therapy for patients with Duchenne muscular dystrophy and other forms of muscular dystrophy. I wouldn't want He Jiankui let within a thousand miles of my kids, because I just wouldn't trust him. And he's now more recently put out a manifesto stating he thinks we should start editing embryos again. So I don't know quite what is going on.It seems the Chinese threw the book at him. Three years is not a trivial prison sentence. He was fined about half a million dollars. But somebody in the government there seems to be okay with him back at the bench, back in the lab, and dabbling in CRISPR. And I don't know that he's been asked, does he have any regrets over the editing of Lulu and Nana. There was a third child born a few months later as well. All he will say is, “We moved too fast.” That is the only caveat that he has allowed himself to express publicly.We know nothing more about the children. They're close to five years old now. There's one particular gene that was being edited was pretty messed up. But we know it's not an essential gene in our bodies, because there are many people walking around who don't have a functional copy of this CCR5 receptor gene, and they're HIV resistant. That was the premise for He Jiankui's experiment. But he has said, “No, they are off limits. The authorities are not going to reveal their identities. We are monitoring them, and we will take care of them if anything goes wrong.” But I think a lot of people in the West would really like to help, to study them, to offer any medical assistance. Obviously, we have to respect their privacy. The twin girls and the third child who was born a bit later, maybe they're being protected for their own good. How would you like it if you grew up through childhood and into your teenage years, to walk around knowing that you were this human experiment? That may be a very difficult thing to live with. So more to come on that.There's no legitimate discussion about changing that in the West or anywhere else?Obviously, in the wake of what He Jiankui did, there were numerous blue ribbon panels, including one just organized by the National Academy of Sciences, just a stone's throw from where we're talking today. And I thought that report was very good. It did two things. This was published a couple of years ago. Two important things came out of it. One is this all-star group of geneticists and other scientists said, “We don't think that human embryo editing should be banned completely. There may be scenarios down the road where we actually would want to reserve this technology because nothing else would help bring about a particular medical outcome that we would like.” And the one medical scenario that they laid out would be, what if two people with a deadly recessive disease like sickle cell disease, or perhaps a form of cystic fibrosis, wanted to have a healthy biological child?There are clinics around the country and around the world now doing something called pre-implantation genetic diagnosis. If you have a family history of a genetic disease, you can encourage the couple to do IVF. We form an embryo or bunch of embryos in the test tube or on the Petri dish. And then we can do a little biopsy of each embryo, take a quick sneak peek at the DNA, look to see if it's got the bad gene or perhaps the healthy gene, and then sort of tag the embryos and only implant the embryos that we think are healthy. This is happening around the country as we speak for hundreds, if not thousands, of different genetic diseases. But it won't work if mom and dad have a recessive, meaning two copies of a bad gene, because there's no healthy gene that you can select in any of those embryos. It would be very rare, but in those scenarios, maybe embryo editing is a way we would want to go. But I don't see a big clamor for this right now. And the early results have been published using CRISPR on embryos in the wake of He Jiankui did have said, “It's a messy technique. It is not safe to use. We don't fully understand how DNA editing and DNA repair works in the human embryo, so we really need to do a whole lot more basic science, as we did in the original incarnation of CRISPR, before we even dare to revisit editing human embryos.” Longevity is interesting because, of course, in the last 18 months there's a company in Silicon Valley called Altos, funded by Yuri Milner, employing now two dozen of the top aging researchers who've been lured away from academia into this transnational company to find hopefully cures or insights into how to postpone aging. Longevity and genetic enhancementsAnother area is using these treatments not to fix things, but to enhance people, whether it's for intelligence or some other trait. A lot of money pouring into longevity treatments from Silicon Valley. Do we know more about the potential of CRISPR for either extending lifespans or selecting for certain desirable traits in people?This sort of scenario is never going to go away. When it comes up, if I hear someone say, “Could we use CRISPR or any gene editing technology to boost intelligence or mathematical ability or music musical ability, or anything that we might want…”Or speed in the hundred meters.“…or speed in the hundred meters, to enhance our perfect newborn?” I would say, what gene are you going to enhance? Intelligence—are you kidding me? Half of the 10,000 genes are expressed in the human brain. You want to start meddling with those? You wouldn't have a prayer of having a positive outcome. I think we can pretty much rule that out. Longevity is interesting because, of course, in the last 18 months there's a company in Silicon Valley called Altos, funded by Yuri Milner, employing now two dozen of the top aging researchers who've been lured away from academia into this transnational company to find hopefully cures or insights into how to postpone aging. That's going to be a long, multi-decade quest to go from that to potentially, “Oh, let's edit a little embryo, our newborn son or daughter so they have the gift of 120 years on this decaying, overheating planet…” Yes, there's a lot to wade through on that.And you have another book coming out. Can you give us a preview of that?I'm writing a book called Curved Air, which is about the story of sickle cell disease. It was first described in a paper from physicians in Chicago in 1910 who were studying the curious anemia of a dental student who walked into their hospital one day. That gentleman, Walter Noel, is now buried back in his homeland, the island of Grenada. But in the 1940s, it was described and characterized as the first molecular disease. We know more about sickle cell disease than almost any other genetic disease. And yet, as we touched on earlier, patients with this who have not had the wealth, the money, the influence, they've been discriminated against in many walks of life, including the medical arena.We're still seeing terribly, tragically, videos and stories and reports of sickle cell patients who are being turned away from hospital rooms, emergency rooms, because the medical establishment just looks at a person of color in absolute agony with one of these pain crises and just assumed, “Oh, they want another opioid hit. Sickle cell? What is that?” There's a lot of fascinating science. There's all this hope in the gene editing and now in the clinic. And there's all this socioeconomic and other history. So I'm going to try to weave all this together in a format that hopefully everyone will enjoy reading.Hopefully a book with a happy ending. Not every book about a disease has a wonderful…I think a positive note to end on is the first American patient treated in this CRISPR clinical trial for sickle cell disease four years ago,Victoria Gray, has become something of a poster child now. She's been featured on National Public Radio on awhole series of interviews and just took her first overseas flight earlier this year to London to speak at a CRISPR gene editing conference. She gave a lovely 15-minute personal talk, shaking with nerves, about her personal voyage, her faith in God, and what's brought her here now, pain-free, traveling the world, and got a standing ovation. You don't see many standing ovations at medical conferences or genetics conferences. And if ever anybody deserved it, somebody like Victoria Gray did. Early days, but a very positive journey that we're on. This is a public episode. If you'd like to discuss this with other subscribers or get access to bonus episodes, visit fasterplease.substack.com/subscribe
Fertility & Sterility comes to you from ESHRE 2023 in Copenhagen, Denmark! Continuing from Part 1, listen in as we discuss some of the best abstracts from the conference. Topics in Part 2 include sperm genome editing by CRISPR-Cas9 (Angela Bryanne De Jesus - 00:42); differences in uterine contractility in women with adenomyosis (Sophie Thomas - 11:22), the effect of THC on the human sperm function (Lydia Wehrli - 22:38); the role of aberrant recombination in the origins of aneuploidy (Svetlana Madjunkova - 31:15); the quality of information generated by ChatGPT to answer patients questions about fertility (Kiri Beilby - 43:32); a trial using transdermal testosterone prior IVF in women with poor ovarian response (Nikolas Polyzos 50:14); the reproductive potential of 1pn embryos (Clare Ussher - 57:09) and using menstrual blood to evaluate the uterine immune system in patients with recurrent pregnancy loss and unexplained infertility (Kilian Vomstein & Pia Egerup - 01:08:05). View Fertility and Sterility at https://www.fertstert.org/
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.07.02.547417v1?rss=1 Authors: Kato-Inui, T., Ono, T., Miyaoka, Y. Abstract: As a versatile genome editing tool, the CRISPR-Cas9 system induces DNA double-strand breaks at targeted sites to activate mainly two DNA repair pathways: HDR which allows precise editing via recombination with a homologous template DNA, and NHEJ which connects two ends of the broken DNA, which is often accompanied by random insertions and deletions. Therefore, how to enhance HDR while suppressing NHEJ is a key to successful applications that require precise genome editing. Histones are small proteins with a lot of basic amino acids that generate electrostatic affinity to DNA. Since H2A.X is involved in DNA repair processes, we fused H2A.X to Cas9 and found that this fusion protein could improve the HDR/NHEJ ratio. As various post-translational modifications of H2A.X play roles in the regulation of DNA repair, we also fused H2A.X mimicry variants to replicate these post-translational modifications including phosphorylation, methylation, and acetylation. However, none of them were effective to improve the HDR/NHEJ ratio. We further fused other histone variants to Cas9 and found that H2A.1 exhibited the improved HDR/NHEJ ratio better than H2A.X. Thus, the fusion of histone variants to Cas9 is a promising option to enhance precise genome editing. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.06.29.547089v1?rss=1 Authors: Araki, D., Chen, V., Redekar, N., Salisbury-Ruf, C., Luo, Y., Liu, P., Li, Y., Smith, R., Dagur, P., Combs, C., Larochelle, A. Abstract: Granulocyte colony stimulating factor (G-CSF) is commonly used as adjunct treatment to hasten recovery from neutropenia following chemotherapy and autologous transplantation of hematopoietic stem and progenitor cells (HSPCs) for malignant disorders. However, the utility of G-CSF administration after ex vivo gene therapy procedures targeting human HSPCs has not been thoroughly evaluated. Here, we provide evidence that post-transplant administration of G-CSF impedes engraftment of CRISPR-Cas9 gene edited human HSPCs in xenograft models. G-CSF acts by exacerbating the p53-mediated DNA damage response triggered by Cas9-mediated DNA double-stranded breaks. Transient p53 inhibition in culture attenuates the negative impact of G-CSF on gene edited HSPC function. In contrast, post-transplant administration of G-CSF does not impair the repopulating properties of unmanipulated human HSPCs or HSPCs genetically engineered by transduction with lentiviral vectors. The potential for post-transplant G-CSF administration to aggravate HSPC toxicity associated with CRISPR-Cas9 gene editing Cas9 should be considered in the design of ex vivo autologous HSPC gene editing clinical trials. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC
Welcome to The Nonlinear Library, where we use Text-to-Speech software to convert the best writing from the Rationalist and EA communities into audio. This is: Biological DOOM: a brief overview of biological computation, published by Metacelsus on April 29, 2023 on LessWrong. (no, not that kind of biological doom) DOOM is a classic first-person shooter game released in 1993 by id Software. Because it's from 1993, it doesn't require much computing power compared to modern games. Additionally, the code (written in C) is easy to compile to run on a variety of processors. Over the years, hackers have made DOOM run on things such as an ATM, a touchbar of a MacBook, a Porsche 911, and even a TI-84 calculator powered by potato batteries. But what about cells? Requirements for DOOM The inputs to DOOM are based on button presses, traditionally on a keyboard. 9 keys in total are required (assuming “switch weapon” is implemented as one key that cycles through weapons). For computation, the original 1993 release required: 4 MB of RAM and 12 MB of hard-drive storage Intel 386 (bare minimum) or 486 processor. There is some flexibility regarding the processor, but slower processors will have worse frame-rates. The Intel 386 had 275,000 transistors in its most basic configuration. DOOM also requires a graphical output. The smallest resolution I've seen is 128x32 pixels, and that was cutting it a bit close. We'll assume we need 4096 black-and-white pixels for the display. Finally, DOOM has audio. For the purposes of this thought experiment, we can ignore this output. Although the soundtrack is great, it's not strictly required to play the game. Approaches to biological computation So, how could we potentially run DOOM? Biological systems can perform computations in several ways: Nucleic acid hybridization These logic gates are based on strand displacement between complementary DNA sequences. A recent paper demonstrated a set of DNA-based logic gates that could add two 6-bit binary numbers. Pros and cons: Memory capacity is good (encoded in DNA or RNA) Switching speed is OK (rate constants vary by design but are typically around 106M−1s−1) Visual output could be provided by fluorophore/quencher conjugated oligonucleotides, but . . . Coupling to a macroscopic output display would be far too slow, because it would have to rely on diffusion (taking a few minutes to cover a millimeter-scale distance). So, the game would have to be played using a microscope. It's hard to “reset” gates after using them, this requires coupling to some energy source It's also hard to integrate DNA-based logic gates into other biological systems, since not many organisms use short pieces of ssDNA. RNA might be used instead. Transcription and translation These logic gates use the same tools that cells use to regulate gene expression. For example, the classic lac operon in bacteria implements: Biologists have exploited similar systems to build logic gates, as well as systems involving the regulation of translation (the production of proteins using mRNAs as templates). A recent paper used Cas9 binding to a sgRNA-like sequence inserted in an mRNA to control its translation. To form a NAND gate, they split Cas9 into two fragments; if both were present, the output protein was not produced. Pros and cons: Memory capacity is acceptable (encoded in DNA or RNA) There will be challenges with implementing the number of logic gates required while avoiding cross-talk The dealbreaker: far too slow to run DOOM. RNA and protein half-lives are on the order of minutes to hours. Protein phosphorylation (kinases/phosphatases) Many cell signaling pathways use protein phosphorylation as a signal. This is much faster than transcription and translation, since no new RNAs or proteins need to be produced. A paper in 2021 built a toggle switch in yeast out of several kinases and phosphatases. Pros and cons: Response speed is adequate, similar to nucleic acid hybridization gates (i.e., largely l...
Link to original articleWelcome to The Nonlinear Library, where we use Text-to-Speech software to convert the best writing from the Rationalist and EA communities into audio. This is: Biological DOOM: a brief overview of biological computation, published by Metacelsus on April 29, 2023 on LessWrong. (no, not that kind of biological doom) DOOM is a classic first-person shooter game released in 1993 by id Software. Because it's from 1993, it doesn't require much computing power compared to modern games. Additionally, the code (written in C) is easy to compile to run on a variety of processors. Over the years, hackers have made DOOM run on things such as an ATM, a touchbar of a MacBook, a Porsche 911, and even a TI-84 calculator powered by potato batteries. But what about cells? Requirements for DOOM The inputs to DOOM are based on button presses, traditionally on a keyboard. 9 keys in total are required (assuming “switch weapon” is implemented as one key that cycles through weapons). For computation, the original 1993 release required: 4 MB of RAM and 12 MB of hard-drive storage Intel 386 (bare minimum) or 486 processor. There is some flexibility regarding the processor, but slower processors will have worse frame-rates. The Intel 386 had 275,000 transistors in its most basic configuration. DOOM also requires a graphical output. The smallest resolution I've seen is 128x32 pixels, and that was cutting it a bit close. We'll assume we need 4096 black-and-white pixels for the display. Finally, DOOM has audio. For the purposes of this thought experiment, we can ignore this output. Although the soundtrack is great, it's not strictly required to play the game. Approaches to biological computation So, how could we potentially run DOOM? Biological systems can perform computations in several ways: Nucleic acid hybridization These logic gates are based on strand displacement between complementary DNA sequences. A recent paper demonstrated a set of DNA-based logic gates that could add two 6-bit binary numbers. Pros and cons: Memory capacity is good (encoded in DNA or RNA) Switching speed is OK (rate constants vary by design but are typically around 106M−1s−1) Visual output could be provided by fluorophore/quencher conjugated oligonucleotides, but . . . Coupling to a macroscopic output display would be far too slow, because it would have to rely on diffusion (taking a few minutes to cover a millimeter-scale distance). So, the game would have to be played using a microscope. It's hard to “reset” gates after using them, this requires coupling to some energy source It's also hard to integrate DNA-based logic gates into other biological systems, since not many organisms use short pieces of ssDNA. RNA might be used instead. Transcription and translation These logic gates use the same tools that cells use to regulate gene expression. For example, the classic lac operon in bacteria implements: Biologists have exploited similar systems to build logic gates, as well as systems involving the regulation of translation (the production of proteins using mRNAs as templates). A recent paper used Cas9 binding to a sgRNA-like sequence inserted in an mRNA to control its translation. To form a NAND gate, they split Cas9 into two fragments; if both were present, the output protein was not produced. Pros and cons: Memory capacity is acceptable (encoded in DNA or RNA) There will be challenges with implementing the number of logic gates required while avoiding cross-talk The dealbreaker: far too slow to run DOOM. RNA and protein half-lives are on the order of minutes to hours. Protein phosphorylation (kinases/phosphatases) Many cell signaling pathways use protein phosphorylation as a signal. This is much faster than transcription and translation, since no new RNAs or proteins need to be produced. A paper in 2021 built a toggle switch in yeast out of several kinases and phosphatases. Pros and cons: Response speed is adequate, similar to nucleic acid hybridization gates (i.e., largely l...
In this episode from the archives, originally published in February 2021, Jennifer Doudna, who won the 2020 Nobel Prize for the co-discovery of CRISPR-Cas9 with Emmanuelle Charpentier, chats with Vijay Pande, general partner at a16z Bio + Health. Together, they discuss the future of biology, whether discovery itself can be engineered and industrialized, and how biology can shape our future.
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.03.22.533709v1?rss=1 Authors: Tsuchida, C. A., Brandes, N., Bueno, R., Trinidad, M., Mazumder, T., Yu, B., Hwang, B., Chang, C., Liu, J., Sun, Y., Hopkins, C. R., Parker, K. R., Qi, Y., Satpathy, A., Stadtmauer, E., Cate, J. H. D., Eyquem, J., Fraietta, J. A., June, C. H., Chang, H. Y., Ye, C. J., Doudna, J. A. Abstract: CRISPR-Cas9 genome editing has enabled advanced T cell therapies, but occasional loss of the targeted chromosome remains a safety concern. To investigate whether Cas9-induced chromosome loss is a universal phenomenon and evaluate its clinical significance, we conducted a systematic analysis in primary human T cells. Arrayed and pooled CRISPR screens revealed that chromosome loss was generalizable across the genome and resulted in partial and entire loss of the chromosome, including in pre-clinical chimeric antigen receptor T cells. T cells with chromosome loss persisted for weeks in culture, implying the potential to interfere with clinical use. A modified cell manufacturing process, employed in our first-in-human clinical trial of Cas9-engineered T cells,1 dramatically reduced chromosome loss while largely preserving genome editing efficacy. Expression of p53 correlated with protection from chromosome loss observed in this protocol, suggesting both a mechanism and strategy for T cell engineering that mitigates this genotoxicity in the clinic. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC
La tertulia semanal en la que repasamos las últimas noticias de la actualidad científica. En el episodio de hoy: Reconstruyen ancestros de la enzima Cas9 de hace miles de millones de años (min 4:00); Leyendo imágenes del cerebro con MRIf y "latent stable diffusion" (45:00); Usando IA para extraer señales de radio en búsquedas SETI (1:36:00); Señales de los oyentes (2:30:00). Contertulios: Carlos Westendorp, Isabel Corder, Jose Edelstein, Héctor Socas. Todos los comentarios vertidos durante la tertulia representan únicamente la opinión de quien los hace... y a veces ni eso! Hosted on Acast. See acast.com/privacy for more information.
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.02.09.527713v1?rss=1 Authors: Dona, M., Bradamante, G., Bogojevic, Z., Gutzat, R., Streubel, S., Mosiolek, M., Dolan, L., Mittelsten Scheid, O. Abstract: Individual cells give rise to diverse cell lineages during the development of multicellular organisms. Understanding the contribution of these lineages to mature organisms is a central question of developmental biology. Several techniques to document cell lineages have been used, from marking single cells with mutations that express a visible marker to generating molecular bar codes by CRISPR-induced mutations and subsequent single-cell analysis. Here, we exploit the mutagenic activity of CRISPR to allow lineage tracing within living plants. Cas9-induced mutations are directed to correct a frameshift mutation that restores expression of a nuclear fluorescent protein, labelling the initial cell and all progenitor cells with a strong signal without modifying other phenotypes of the plants. Spatial and temporal control of Cas9 activity can be achieved using tissue-specific and/or inducible promoters. We provide proof of principle for the function of lineage tracing in two model plants. The conserved features of the components and the versatile cloning system, allowing for easy exchange of promoters, are expected to make the system widely applicable. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.01.24.525105v1?rss=1 Authors: Sastre, D., Zafar, F., Torres, C. A. M., Piper, D., Kirik, D., Sanders, L. H., Qi, S., Schuele, B. Abstract: Parkinson's disease (PD) is one of the most common neurodegenerative diseases, but no disease-modifying therapies have been successful in clinical translation presenting a major unmet medical need. A promising target is alpha-synuclein or its aggregated form, which accumulates in the brain of PD patients as Lewy bodies. While it is not entirely clear which alpha-synuclein protein species is disease relevant, mere overexpression of alpha-synuclein in hereditary forms leads to neurodegeneration. To specifically address gene regulation of alpha-synuclein, we developed a CRISPR interference (CRISPRi) system based on the nuclease dead S. aureus Cas9 (SadCas9) fused with the transcriptional repressor domain Krueppel-associated box to controllably repress alpha-synuclein expression at the transcriptional level. We screened single guide (sg)RNAs across the SNCA promoter and identified several sgRNAs that mediate downregulation of alpha-synuclein at varying levels. CRISPRi downregulation of alpha-synuclein in iPSC-derived neuronal cultures from a patient with an SNCA genomic triplication showed functional recovery by reduction of oxidative stress and mitochondrial DNA damage. Our results are proof-of-concept in vitro for precision medicine by targeting the SNCA gene promoter. The SNCA CRISPRi approach presents a new model to understand safe levels of alpha-synuclein downregulation and a novel therapeutic strategy for PD and related alpha-synucleinopathies. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.11.16.516691v1?rss=1 Authors: Kim, J., Kratz, A., Sheng, J., Zhang, L., Singh, B. K., Chavez, A. Abstract: To facilitate the interrogation of proteins at scale, we have developed High-throughput Insertion of Tags Across the Genome (HITAG). HITAG enables users to produce libraries of cells, each with a different protein of interest C-terminally tagged, to rapidly characterize protein function. To demonstrate the utility of HITAG, we fused mCherry to a set of 167 stress granule-associated proteins and characterized the factors which drive proteins to strongly accumulate within stress granules. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC
Welcome to The Nonlinear Library, where we use Text-to-Speech software to convert the best writing from the Rationalist and EA communities into audio. This is: Gene drives: why the wait?, published by Metacelsus on September 19, 2022 on LessWrong. (Crossposted from my Substack) If you've been following biology news over the last few years, you might have heard of an interesting concept called a “gene drive”. The overall idea is to engineer a genetic allele that transmits itself to all offspring of a sexually reproducing organism, instead of being inherited by 50% as usual. This allele can also perform some other biological function (a relevant example is causing female sterility). A gene drive spreads through a population. From Esvelt et al. 2014 (CC-BY) In multiple trials, modern CRISPR-based gene drives have shown high efficacy in spreading through populations of caged Anopheles mosquitoes and completely suppressing their reproduction. Since Anopheles mosquitoes are the only ones that transmit malaria, causing their extinction would directly save hundreds of thousands of lives per year. Similar gene drives targeted to other types of mosquitoes (Aedes, Culex, etc.) could also eliminate diseases such as dengue fever, Zika virus, and West Nile virus. However, in spite of promising laboratory trials, gene drives have not yet been deployed in the wild. But why not? History of gene drives Although the technology to build effective gene drives did not exist until recently, the idea has been around for a while. In fact, gene drives occur naturally. Some well-known examples are transposons in flies, homing endonucleases in algae, and segregation distorters in mice. The idea of engineering a site-specific nuclease as a gene drive was developed as early as 2003, and in the decade that followed there were several efforts to develop these, with the labs of Austin Burt and Andrea Crisanti taking a lead role. These early systems showed some biased inheritance, but were not stable for more than a few generations. The advent of CRISPR as a gene editing system opened up a new opportunity. A paper in 2014 by Kevin Esvelt and co-workers proposed Cas9 as a nuclease for a gene drive, with several properties making it ideal for the task. It lacks repetitive sequences that caused problems with earlier gene drives using zinc-finger nucleases or TALENs. It has a very high efficiency of cutting. It is easy to target a new site by simply changing the guide RNA. Several nearby sites could be targeted at once, using different guide RNAs. From Esvelt et al. 2014 (CC-BY) CRISPR-based gene drives quickly gained popularity in the field, and by 2018 the Crisanti lab had demonstrated a working gene drive that could efficiently suppress populations of Anopheles gambiae by targeting an exon of the doublesex gene required for female development. At the time this was announced, I was studying at the University of Cambridge, and attended a public lecture by Prof. Crisanti about his lab's work. The overall mood in the room was almost euphoric: here was a technology that could save millions of lives, the best thing since Borlaug's wheat! Since that lecture, about 2 million people, mostly children in Africa, have died of malaria. Gene drive research has not stood still: the Crisanti lab tested their doublesex drive in larger cages of mosquitoes, and it again completely eliminated the populations. But given the millions of lives at stake, what's taking so long for this gene drive to be released? See also: the battle against malaria in Africa has stalled Why the wait? There are two good arguments against the immediate release of gene drives to eliminate mosquitoes. First, nuclease gene drives have the possibility of generating resistant alleles, making future gene drives not work against the same target. Therefore, it's important to get it right the first time, otherwise the potential of gene drives could be wasted. The goal of the large cage trials I mentioned earli...
Insects cause massive losses in human health and agriculture. Scientists have implemented Sterile Insect Technique for over 50 years, a process to suppress populations by introducing genetically-damaged insects into natural settings. Upon mating, the offspring. Scientists have now used gene editing techniques to selectively suppress the Spotted Wing Drosophila, a costly pest in agricultural contexts. Today's podcast is an interview with Dr. Nikolay Kandul, a scientist working with a team that has used an innovative Cas9/gene editing approach to suppress populations of this devastating and costly invasive pest. The application seeks to cut insecticide use and costs for farmers and consumers.
While the vast majority of gene editing efforts have been confined to crop plants, animal gene editing holds tremendous promise. Efforts have demonstrated that naturally-occurring alleles could be reconstituted using site-specific nucleases, creating hornless dairy cattle and beef cattle with sex ratios skewed towards a higher proportion of males. These breakthroughs are just a sample of the powerful technology. Dr. Alison Van Eenennaam is a Cooperative Extension Specialist at the University of California Davis. She has been an academic leader in animal genetic engineering and public communication about new technology. Follow her at @BioBeef on twitter. The podcast also features a conversation with Jilian Hendricks, a graduate student at the University of British Columbia. She is seeking assistance for a scholarly project, and would like to interview a number of scientists about gene editing. Her email is jhendric "at" mail.ubc.ca
Invasive pests and diseases are a challenge for all grape growers. Research is vital to develop new strategies and solutions. The Pierce's Disease/Glassy-Winged Sharpshooter Board was established nearly two decades ago to allocate funding to the most promising research projects. Kristin Lowe, Research Coordinator at the Pierce's Disease and Glassy-Winged Sharpshooter Board and President of Vine Balance Consulting shares how projects are funded through a rigorous scientific review and screening panel. Also, learn about some of the most exciting projects including “pathogen confusion” to control Pierce's Disease from Dr. Steve Lindow and a gene editing technology for grapevines using plant protoplasts Dr David Tricoli. References: 89: New Pierce's Disease Vaccine (podcast) 2021 Pierce's Disease Research Projects at a Glance 2021 Pierce's Disease Research Symposium Proceedings 2021 Pierce's Disease Research Symposium session recordings 2022-07-16 Night Harvest Lighting & SWEEP Grants Tailgate About the PD/GWSS Board Biological Control of Pierce's Disease of Grape by an Endophytic Bacterium CDFA Pierce's Disease Research Symposium SIP Certified Sustainable Ag Expo November 14-16, 2022 Vine Balance Consulting Get More Subscribe wherever you listen so you never miss an episode on the latest science and research with the Sustainable Winegrowing Podcast. Since 1994, Vineyard Team has been your resource for workshops and field demonstrations, research, and events dedicated to the stewardship of our natural resources. Learn more at www.vineyardteam.org. Transcript Craig Macmillan 0:00 I'm your host Craig Mcmillan. And with me today is Kristin Lowe, president of Vine Balance Consulting, and research coordinator for the Pierce's Disease Glassy-Winged Sharpshooter Board. Welcome, Kristin. Kristin Lowe 0:12 Thank you so much for having me. Craig Macmillan 0:13 First off, can you tell us what is the Pierce's Disease and Glassy-Winged Sharpshooter Board or the PDGWSS? As I want to call it from now on? Kristin Lowe 0:21 Absolutely. So the PDGWSS Board is a group of California growers or grower producers. There's 14 board members and also one public member. And their primary goal is to make sure that all of the assessment funds that are received to the board go to the most promising research for our most challenging pests and diseases today. Those that are designated as important problems. Craig Macmillan 0:48 And so the funding comes from an assessment. Kristin Lowe 0:50 That is correct. So the assessment, I believe, on average is about $1.50 per $1,000 of grapes in terms of value .The most, the cap is at $3 per 1000 grapes in value. But yes, that's collected every year and has been so since the board started back in 2001. Craig Macmillan 1:13 What led to the creation of the board? Kristin Lowe 1:15 Pierce's Disease. So. Well, I think anyone who's looked into the history of Pierce's Disease, so this is a bacterial disease, endemic to California, not not necessarily new to California, right. But what was new to California was not only the establishment, but the fact that the Glassy-Winged Sharpshooter started thriving down in Southern California. That is the vector for Pierce's Disease. That insect exists in parts of Mexico and also parts of Florida and the Southeast US. But it got to California, and it started doing really well to the point that Pierce's disease started taking off. This led to a lot of sad looking pictures of dead vines, lots of concern over lost acreage, and this would be during the late 1990s or so. And in response to this, industry leaders from all different groups came together. A combination of industry USDA, UC California researchers, CDFA, to create the Pierce's Disease Control Program. And that's got many facets, but one of it is the PDGWSS Board, which whose mission is to fund the most important research to combat Pierce's Disease, Glassy-Winged Sharpshooter and all the other pests that they've designated in their RFP. Craig Macmillan 2:31 Yeah. And so the the mission is expanded now beyond just Glassy-Wing to a number of other invasive pests that correct? Kristin Lowe 2:37 Yeah, it has it has. And there's, there's a clear path for that. And I think what really blew that open was the European Grapevine Moth. So another invasive pest species that showed up, oh, gosh, and I think that was somewhere around 2011 or so maybe a little bit before, but agriculture always has a new bad guy. And so we needed a way for the for the PDGWSS board to, you know, expand what it was going to fund in terms of research to deal with new problems and, and continuing ones that keep coming back. Craig Macmillan 3:08 So what exactly is your role with the board? Kristin Lowe 3:11 Sure. So, they put out a call for proposals for a research coordinator last year, and I got the job, very excited. And so my goal is to kind of basically help guide the program to make sure that what we're funding is really on point to, to our goal, on point to making sure that the research is heading in the right direction, it's we get continual progress, and is also able to collaborate with, you know, get foster collaboration with other agencies, we have this general sense that we've been going since 2001. And there's been a lot of really great research going on for Pierce's Disease. These days, our problems might be different. And so the RFP expanded, also to include grapevine viruses. And those seem to be a real multi headed monster, for the industry for many levels. So I think that while my overall goal is just to make sure that the research funding program is focused and relevant, we're starting to look a lot more closely at visruses. Craig Macmillan 4:20 And RFPs is Request for Proposals? Kristin Lowe 4:22 Correct RFP is the request for proposals. Craig Macmillan 4:25 Okay, so academics, scientists, will write up a proposal of what they want to do research wise, and they bring it to the board, and the board, evaluates them and decides, hey, would give some money to this, we'll give some money to that. Kristin Lowe 4:39 Yes, absolutely. So we coordinate with other funding agencies and for the wine industry and actually for the whole wine and grape industry, not just in California, but in Oregon as well. And we all put out a request for proposals on the same date, December 1. And that after a couple months that closes and we look atthe proposals and they go through the PDGWSS Board, they go through scientific review, pretty stringent scientific review, and then also our research screening panel process. And ultimately, the Board makes the final decision on what gets funded within that year. Craig Macmillan 5:14 Cool. So tell us about some of these projects. I mean, it's been 20 years. What's happened? What are some of the ones that you are excited about? Or remember are really proud of? Kristin Lowe 5:23 Yeah, oh, there's so many. And I am I am so nervous about like glossing over things or missing details that I'm going to take this opportunity to tell everybody that there's some great resources on our website that you can, that you can look at to get more details. And that is cdfa.ca.gov/PDCP/research. And on there you can look at, there's a document that says projects at a glance, just great layman's layman person summaries of all of the research has been going on. There's our entire research symposium proceedings, and some recordings as well of Craig Macmillan 6:05 Yes, Kristin Lowe 6:06 ... recent one. So, you know, because this is public assessment money, this information should be available to everyone in the industry. So we work really hard to keep that website updated. Craig Macmillan 6:16 And we will have links to all of those on the page. Kristin Lowe 6:19 Okay, cool. Cool. Cool. Okay, so some science. Craig Macmillan 6:23 Yes! Kristin Lowe 6:23 Have you heard Dr. Steve Lindow talk about his work on Paraburkholderia? Craig Macmillan 6:29 No, I haven't. Kristin Lowe 6:31 You haven't? I thought he I thought he presented at this Sustainable Ag Expo a few years ago, but maybe I'm mistaken. Craig Macmillan 6:37 No, he may have been I may not have been there. Kristin Lowe 6:40 Yeah, yeah. So Dr. Steve Lindow, is at UC Davis. And he made a crazy exciting discovery, there is a endophytic bacteria called Paraburkholderia phytofirmans, I'll just call it like, Paraburkholderia. That's enough of a mouthful. Craig Macmillan 6:57 That's enough, yeah. Kristin Lowe 6:58 And it inhibits the movement of xylella fastidiosa. So of the Pierce's Disease controlling or the organism responsible for Pierce's Disease, within the vine. So this endophytic bacteria, if you put it in the vine, at the same time, that's Xylella, in there, it not only moves throughout the vine, so it becomes systemic, but it inhibits the movement of the pathogen. So this is kind of huge. This species has been looked at before for for other reasons. But what this basically is, we're hoping that it leads to, is an infield treatment with an endophytic bacteria. So his work has involved figuring out, first of all the mechanism. But second of all, the practical aspect of this, which is what I love about it. It seems to work best when the two organisms are there together. So there's a timing of you know, do we pre inoculate with endophytic bacteria, and then it gets Xylella. That works. Or if a vine has been infected with Xylella, and then you are able to treat it with a Paraburkholderia. It also helps to not only the reduce the Xylella count, but reduce symptoms. Craig Macmillan 8:14 How do you introduce it this thing into the vine? Kristin Lowe 8:18 Oh, right. Yeah, first of all, with a pinprick basically. So an inoculation, I don't think everyone out there is going to want to go through and inoculate every vine. So they are working on a sprayable formulation. And to be able to actually get that into the vine, as well. And it seems to work with certain types of surfactants. So that's kind of where that technology is at is, you know, how do we create, you know, how do we create a usable product with it? What's going to work the best in the field? What's, what's the most practical in terms of rate, and timing? And in getting the endophytic bacteria into the vines? Craig Macmillan 8:54 That's, that's amazing. That's definitely amazing. Endophytic bacteria is something that lives inside the plant. Kristin Lowe 9:00 Yes, it is naturally there, there are 1000s of them and 1000s have been tried to see if they first of all actually move throughout the plant rather than in just the place that you found them. And second, if they are going to work against any sort of pathogens. Yeah, an amazing discovery and work that's been going on for for years and is I believe, is finally in the stages of getting to field trials and seeing how it would work. But imagine if you could go out to your block that you know is going to get pressure every year and think that you could decrease that pressure with with a spray. Never, I mean PD kills vines, that's huge. And in areas with constant pressure, it kills just more and more every year. So to have that sort of infield treatment is pretty exciting. Craig Macmillan 9:45 Is this the kind of project that would receive funding over many years or multiple years from the board? Kristin Lowe 9:49 Absolutely. And I don't remember when it first started. Definitely preceded my time there, but I think I've been following it since at least 2016. Craig Macmillan 9:52 Oh, wow. Okay. Kristin Lowe 9:52 No, it takes time from you know, discovery not only to making sure it's going to work, and then and then there's all this stuff after to get it actually implemented. But most of these projects that are going to result in a long term sustainable solution, or long term projects, you need years of data to make sure that they're gonna work. Craig Macmillan 10:17 Science takes time. Kristin Lowe 10:19 It takes time. I know, we're always impatient about that. But it does definitely take time. Craig Macmillan 10:25 And support. Kristin Lowe 10:26 Yeah, yeah. Craig Macmillan 10:27 What's, what's something else that you're excited about? Kristin Lowe 10:30 Okay, another one that's pretty exciting and groundbreaking is work by Dr. David Tricoli. And he's at the UC Davis Plant Transformation Facility. Have you heard of him at all? Craig Macmillan 10:42 No, no. Kristin Lowe 10:43 Okay. So he's doing has done something that might sound simple, but it opens up a wealth of options for future research. He's developed a cell culture method for regenerating a grapevine from a cell Protoplast. So you might remember back from biology, major differences between animals and plants. Plants are surrounded by a cell wall, animal cells, plant cells. Animal cells are not. When some of the like gene editing technology is coming out that's happening in animal cells, it's a lot easier to do, because they don't have the cell wall. Previous to this work, no one's been able to regenerate a grapevine from just a Protoplast. Without a cell wall. What this work has done is enabled there to be a platform of getting a group of grape cells together, just their protoplasts without the cell wall, onto which you could potentially do CRISPR Cas9, or some of the other fast developing gene editing techniques that are out there. Craig Macmillan 11:45 This this is a technology I've heard repeatedly, and I'm I have no idea what the acronym stands for. And I'm not really sure I understand what it does. So what is CRISPR? Yeah, Kristin Lowe 11:55 and I'm not going to tell you exactly what the acronym stands for either. To me, but so Cas9 is is a gene editing technology that allows for very, very precise small changes in a gene or in a genome. Ultimately, when done for plants by multiple steps later, it can result in a plant that's retained this small edit, but has absolutely no foreign DNA. And unlike a traditional GMO, that would have external DNA from a plasmid or from some other plant, this one is I can kind of think of it as like a lucky or benevolent mutation occurred. And you can't tell but it was purposeful. And and the result is a different phenotype that, that you can see. CRISPR-Cas9 gene editing is it's been out there for a number of years now. But it's taken time for everyone to develop different platforms for which it could work. For plants, especially for plants that are always regenerated by cuttings. So we don't do crosses to get new grapes, we take cuttings, we need a platform to possibly be able to do this. What this work has done is developed that platform. Where it could go it completely depends you need to you need to know which you know which genes to edit, which ones are going to reduce, are going to result in a phenotype. Obviously, what's fascinating, or what's most interesting to me is disease resistance that's usually complex multigenic. So we're still a ways down there from coming up with a with a solution. But the fact that the platform was developed, was actually a major breakthrough. Craig Macmillan 13:35 That's phenomenal. So that's research that was done. It's gonna open the door for new research? Kristin Lowe 13:40 Potentially, exactly. I mean, you can hear about CRISPR-Cas9 and the news happening to everything else, but but not the crop you're interested in until someone figures out that they're all different. Right? Craig Macmillan 13:52 Right, right. What, is their other pests that have come into the catalogue that you think are interesting in that people are doing interesting work on? Kristin Lowe 13:59 Our most recent designated past is the Spotted Lantern Fly, we do not have that one yet. Depending on who you ask it seems inevitable that's making its way steadily west from Pennsylvania. And so that's one that the Board and has its eye on for for sure. But we don't have it yet, but we're accepting proposals for it. Because we're trying to be ready. It's actually pretty rare that you can eradicate a, an invasive pest. The fact that California did it with a European Grapevine Moth is it is an amazing example. What's next right? Yeah, so Spotted Lantern Fly is probably next on our horizon is being something that would certainly be problematic if it got here, and you know, trying to stay ahead about research to understand how it would and could be controlled. Craig Macmillan 14:52 Does the does the board fund research in states other than Oregon and California? Kristin Lowe 14:56 The board funds researchers. So we do have PIs from from out of state and from not from the West Coast. Absolutely. The Board funds projects, obviously, they have to have some applicability to what we're, what our problems are and what we're concerned with. But yeah, there's no real state, state by state guideline. Craig Macmillan 15:16 Right. Right. Right. Well, you know, you mentioned the review process. I just want to shift gears to that. What are the boxes that need to be checked or the hurdles that need to be cleared to get a project funded? What are the what are the criteria that the board and the written in the reviewers are looking for? Kristin Lowe 15:31 Oh, sure. Well, I believe it's even just out there when we send up the call for proposals. But it just basically has to be really good science. It needs to be well, you know, well justified that there's either preliminary data or an excellent premise from a different crop. Or another reason why this idea would work. There have to be sound and detailed materials and methods that are laid out there has to be good experimental design, especially when you get to the field level, right, proper controls, proper replication, the stats will have to work, right, all of those things, the budget needs to be reasonable, all those sorts of things for sure. Craig Macmillan 16:09 Which reminds me how much money is available each year? Kristin Lowe 16:12 It varies. So it will it will depend on on the assessment. And I'm not the numbers person, I'm more the idea person. But I yeah, I have something that could find a figure for you for later. But I think over the 20 years, I believe I read that we have had up to somewhere between 60 and 70 million. But that's not all straight for research. It also goes to the Person's Disease control program treatments for battling Glassy-Winged Sharpshooter outbreaks and some of those control. Craig Macmillan 16:44 So what is the one thing related to this that you would recommend to our listeners? How can we how can we help? Kristin Lowe 16:51 Oh, that's a great question. How can you help. Well, stay stay engaged. Make sure that everyone all the way up the chain knows what your problems are. And and what, you know what what you really need. This is grower money, that for this particular funding program, there are other agencies out there that are simply donation only, not for profit. But I would say, so this is assessment money so it's a little bit unique. But I would say in general, your problems are not unique. And, I mean, we all we're all dealing with some of the same problems. And we have to come together as an industry to, you know, industry to help solve them. A, stay informed, work with researchers. One of the hardest things is for researchers to find field trials or fields that will let them come do some experimentation. They're always looking for industry partners, as sources of sick vines, helping to track patterns, helping to try new technology, just to collect data. Collaborators like that are always needed. Craig Macmillan 17:57 I think that's some great encouragement. I think that's a great message. Don't be afraid to be a collaborator. Kristin Lowe 18:01 Yeah, yeah, absolutely. It gives you kind of a seat at the table. And researchers aren't growers. And so we need to have this kind of constant communication for there to be good outreach of what they found, to make sure it's applicable and that everyone understands it and and will adopt it too. The most frustrating thing is if something comes out, and people are slow to adopt it, even though it works. So staying informed about what's current, and what are what are new, good ideas. Craig Macmillan 18:27 I think that's important. So pay attention. Kristin Lowe 18:30 Yeah, get out there to grow our meetings and and industry meetings. And, yeah, a lot of these researchers do try very hard to do outreach. They hear you if you're if you're there and are showing up for the conversation. Craig Macmillan 18:43 If I wanted to be a collaborator, how can I make myself available? Kristin Lowe 18:46 Oh, gosh, that's a good question. Well, first of all, you would need to know what was going on. So you would need to need to, you know, go to meetings, listen to these people talk, you know, decide if you have similar problems. Almost all of them pass up their email and say, Look, yeah, I've got a place where I've got this, this issue going on. I've you know, been dealing with virus or I've been near dealing with Pierce's Disease. And do you need a field? You know, do you need data set? Some sort of field data or collaboration or a field site? Yeah. Craig Macmillan 19:16 Well, that's fantastic. That's great advice. Where can people find out more about you? Kristin Lowe 19:21 Oh, me personally? Okay, well, sure. I've been I started a consulting company almost 10 years ago, and my website is vinebalancedconsulting.com. I am largely based out of the Napa-Sonoma area, and keep in my toe in the research world because it's exciting. And viticulture is a science. That's one reason why I love it. Craig Macmillan 19:44 It's nice to talk somebody loves science. Yeah. I love talking about science. It's so much fun. Well, I think it's time today I want to thank Kristin Lowe, who is the Research Coordinator for the Pierces Disease/Glassy-Winged Sharpshooter Board and President of Vine Balance Consulting. Check out the website we'll have links and notes of where to go and we look forward to talking to you again. Kristin Lowe 20:08 You're most welcome. Thank you for the opportunity. Have a great growing season. Transcribed by https://otter.ai
La tertulia semanal en la que repasamos las últimas noticias de la actualidad científica. En el episodio de hoy: Más discusión sobre Earendil (min 6:00); Galaxias en radio y formación estelar (29:00); El genoma humano (37:00); Un nuevo Cas9 mejorado (58:00); Energía oscura, campos de quintaesencia y el destino del Cosmos (1:17:00); Agujeros negros y formación estelar (2:04:00); Señales de los oyentes (2:22:00). Contertulios: Francis Villatoro, Gastón Giribet, Héctor Socas. Todos los comentarios vertidos durante la tertulia representan únicamente la opinión de quien los hace... y a veces ni eso. CB:SyR es una actividad del Museo de la Ciencia y el Cosmos de Tenerife.
Wes, Eneasz, and David discuss the news from the last two weeks from a rationalist perspectiveSupport us on Substack!News discussed:CDC alcohol guidelinesWill Smith Assaults or Batters Chris Rock?Ukraine News:Russia seems to be switching focus to DonbasRussia said on Friday that the first phase of its military operation was mostly complete Putin complained that he was getting canceled like JK RowlingBiden wants to remove Russia from the G20Did Hunter Biden personally finance Ukraine weapons labs?!?!?!?Putin demanded natural gas be paid in RublesTaxes are canceled for the duration of martial law and at least a year after its end“If you can, pay, if you can't, there are no questions,” Zelensky saidA developer has been caught adding malicious code to a popular open-source package that wiped files on computers located in Russia and Belarus. Biden Says to Expect ‘Real' Food Shortages Due to Ukraine WarCounterpoint Zelensky is open to Ukrainian neutralityNo deal yet on Crimea and DonbasOther News:Manchin says he'll vote to confirm Judge JacksonHunter Biden laptop (sort of) confirmed to be realNYT seems to have reported about it accurately in Oct. 2020Kevin Drum says media did nothing wrongNew study data showed little difference in excess deaths in European countries during covidstudy of microlending shows many of the “small-businesses” opened are actually MLM scamsFTC demanded that Weight Watchers destroy the algorithms or AI models it built using illegally harvested data. Permanent daylight savings?USPS is only buying 20% electric vehiclesAntarctica more than 70 degrees warmer than average, Arctic more than 50 degreesBiden statement honoring the victims of Atlanta ShootingsHappy News!Maryland Governor Announces Elimination of Four-Year Degree Requirement For Thousands of State JobsScientists at University of Texas at Austin have redesigned a key component of a widely used CRISPR-based gene-editing tool, called Cas9, to be thousands of times less likely to target the wrong stretch of DNAGot something to say? Come chat with us on the Bayesian Conspiracy Discord or email us at themindkillerpodcast@gmail.com. Say something smart and we'll mention you on the next show!Follow us!RSS: http://feeds.feedburner.com/themindkillerGoogle: https://play.google.com/music/listen#/ps/Iqs7r7t6cdxw465zdulvwikhekmPocket Casts: https://pca.st/vvcmifu6 Stitcher: https://www.stitcher.com/podcast/the-mind-killer Apple: Intro/outro music: On Sale by Golden Duck Orchestra This is a public episode. If you'd like to discuss this with other subscribers or get access to bonus episodes, visit mindkiller.substack.com/subscribe
[[Puedes colaborar con el pódcast para que «Cuéntame, Hermosura» siga siendo posible:—Compartiendo el episodio en tus Redes Sociales—Visitando https://www.patreon.com/ManchapPod para obtener recompensas—O haciendo una donación (o las que quieras) en https://paypal.me/ChuSGC .Gracias y disfruta del episodio]]El episodio de hoy tiene un 50% más de acento manchego porque está conmigo Adrián Villalba Felipe, Doctor en Inmunología Avanzada por la UAB, divulgador científico y un gran exponente de la zona albaceteña conocida como "La Suiza Manchega". Desde su retiro espiritual en París donde un día real allí es un año de investigación biomédica, Adrián nos habla de lo que es la divulgación científica y, más en concreto, de su último proyecto, el libro colaborativo "GENES" (Ed. Guadalmazán / Almuzara), una obra de referencia para todos los públicos que cuenta con la pluma y el intelecto de 15 científicos y divulgadores y una más que acertada ilustradora. Más inormación: https://almuzaralibros.com/fichalibro.php?libro=5709&edi=5Contacto:manchapod@gmail.comTW: @CuentameHermosura (http://www.twitter.com/CuentameHermosura)y /CuentameEsperanto tanto en Facebook como en InstagramToda la música está tomada de https://lamusicagratis.com/Alexander Nakarada "The Return"Rameses B "Bae Bae"Dexter Britain "Time to Run (Finale)"Niwel "Bad Love (Vocal Edit)"Jahzzar "Siesta"Zero Project "Ilotana"Timofiy Starenkov "The Journey"Extenz "Kalon"Sadme "Mourning Day"Kevin McLeod "Broken Reality"Monk Turner "The Great Journey"David Mumford "Night without Sleep"Joystock "Electronica"Amaria "Lovely Swindler"The Artisans "Beats Flame"Permiso : CC BY-NC-NDSuscribíos, difundidlo y comentad. Espero que os guste mucho.Spreaker, iVoox, Apple Podcasts, Spotify, iHeartRadio, Google Podcasts, CastBox, Deezer, Podcast Addict, Podchaser, JioSaavn, Amazon.
“It has become appallingly obvious that our technology has exceeded our humanity.” Albert Einstein Sidney and Rose take a deep dive into technology, the history and the future. In her segment, Breaking Boundaries, Sidney talks about how tech platforms are fueling political polarization. With the creation of technology and the rise of the digital age, a significant decline in investigative journalism has occurred as people turn to television and social media as their focus for news. While social media giants have gone out of their way to deny that their algorithms contribute to the promotion of disinformation and extremism, research says otherwise .Their teen guest, Varsha Shankar, presents an easy digestible description of CRISPR or clustered regularly interspaced short palindromic repeats, a gene editing mechanism that can be thought of as a copy and paste for genes. CRISPR deploys an enzyme called Cas9 to cut and edit our DNA strands. Because of its wide range of abilities, CRISPR has had a significant impact on disease treatment and other medical innovations. The discussion included the new research in CRISPR's potential to treat malaria and cancer patients. In Biteshare, Rose informs us about the small print on social media platforms such as Instagram that relinquish rights. Telehealth and telemedicine are positive aspects of technology as is the ability to order food for delivery, especially for those who do not have transportation or as a result of the pandemic. The health app on the Apple watch is one of her preferred ways to keep informed about her daily exercise, sleep patterns, and general health. Both hosts stress the importance of being aware of the issues surrounding social media. While it does have its benefits, there are also significant drawbacks to social media, especially if you use it as a news source. Make sure to fact check the information you're receiving and try to actively seek out and consider viewpoints that may differ from your own. • Follow us: https://www.starstyleradio.com/expressyourselfteenradio • https://www.facebook.com/ExpressYourselfTeenRadio/ • https://www.facebook.com/BTSYAcharity/ • Instagram: https://www.instagram.com/expressyourselfradio/
“It has become appallingly obvious that our technology has exceeded our humanity.” Albert Einstein Sidney and Rose take a deep dive into technology, the history and the future. In her segment, Breaking Boundaries, Sidney talks about how tech platforms are fueling political polarization. With the creation of technology and the rise of the digital age, a significant decline in investigative journalism has occurred as people turn to television and social media as their focus for news. While social media giants have gone out of their way to deny that their algorithms contribute to the promotion of disinformation and extremism, research says otherwise .Their teen guest, Varsha Shankar, presents an easy digestible description of CRISPR or clustered regularly interspaced short palindromic repeats, a gene editing mechanism that can be thought of as a copy and paste for genes. CRISPR deploys an enzyme called Cas9 to cut and edit our DNA strands. Because of its wide range of abilities, CRISPR has had a significant impact on disease treatment and other medical innovations. The discussion included the new research in CRISPR's potential to treat malaria and cancer patients. In Biteshare, Rose informs us about the small print on social media platforms such as Instagram that relinquish rights. Telehealth and telemedicine are positive aspects of technology as is the ability to order food for delivery, especially for those who do not have transportation or as a result of the pandemic. The health app on the Apple watch is one of her preferred ways to keep informed about her daily exercise, sleep patterns, and general health. Both hosts stress the importance of being aware of the issues surrounding social media. While it does have its benefits, there are also significant drawbacks to social media, especially if you use it as a news source. Make sure to fact check the information you're receiving and try to actively seek out and consider viewpoints that may differ from your own. • Follow us: https://www.starstyleradio.com/expressyourselfteenradio • https://www.facebook.com/ExpressYourselfTeenRadio/ • https://www.facebook.com/BTSYAcharity/ • Instagram: https://www.instagram.com/expressyourselfradio/
Mammoth Biosciences is developing next-generation CRISPR products using alternatives to the Cas9 enzyme to read and write genetic code. The company, co-founded by Nobel laureate and CRISPR co-inventor Jennifer Doudna, is applying the technology broadly beyond therapeutics to include not only diagnostics, but agriculture, environmental monitoring, and biodefense. We spoke Trevor Martin, co-founder and CEO of Mammoth Biosciences, about the use of CRISPR as a diagnostic tool, the advantages alternatives to Cas9 may offer, and the company's recently announced alliance with Vertex. Since recording this interview, Mammoth entered into a strategic collaboration with Bayer to use its CRISPR systems to develop in-vivo gene-editing therapies. That deal includes a $40 million upfront payment and more than $1 billion in potential milestones.
For all its supposed genetic editing finesse, CRISPR's a brute. The Swiss Army knife of gene editing tools chops up DNA strands to insert genetic changes. What's called “editing” is actually genetic vandalism—pick a malfunctioning gene, chop it up, and wait for the cell to patch and repair the rest. It's a hasty, clunky process, prone to errors and other unintended and unpredictable effects. Back in 2019, researchers led by Dr. David Liu at Harvard decided to rework CRISPR from a butcher to a surgeon, one that lives up to its search-and-replace potential. The result is prime editing, an alternative version of CRISPR with the ability to “make virtually any targeted change in the genome of any living cell or organism.” It's the nip-tuck of DNA editing: with just a small snip on one DNA chain, we have a whole menu of potential genetic changes at our fingertips. Prime editing was hailed as a fantastic “yay, science!” moment that could conceivably repair nearly 90 percent of over 75,000 diseases caused by genetic mutations. But even at its birth, Liu warned that CRISPR prime was only taking its first toddler steps into the big, wild world of changing a life form's base code. “This first study is just the beginning—rather than the end—of a long-standing aspiration in the life sciences to be able to make any DNA change at any position in an organism,” he told Nature at the time. Flash forward two years. Liu's gene editing ingénue took some stumbles. Despite its precise and effective nature, prime editing could only edit genes in certain types of cells, while being less effective and introducing errors in others. It also failed when trying to make large genetic edits, particularly those that require hundreds of DNA letters to be replaced to fix a disease-causing genetic mistake. But the good news? Toddlers grow up. This week, three separate studies advanced prime editing, helping the CRISPR tool grow into a more sophisticated DNA-editing genius. Two teams, based at the University of Massachusetts Medical School and the University of Washington, reworked the tool's molecular makeup to precisely cut out up to 10,000 DNA letters in one go—a challenge for prime editing 1.0. A third study from the tool's original inventor probed its inner molecular workings, identifying protein friends and foes inside the cell that control the tool's genetic editing abilities. By promoting friendly interactions, the team increased prime editing's efficiency in seven different cell types nearly eight-fold. Even better, the “foes” that block prime's editing potential were identified using CRISPR—in other words, we're witnessing a full circle of innovation whereby gene editing tools help build better gene editing tools. A Primer for CRISPR Prime Prime editing burst onto the gene editing scene for its dexterity and precision. If the original CRISPR-Cas9 is a dancer with two left feet, prime editing is a highly-trained ballerina. The two processes start similarly. Both rely on a molecular “zip code” to target the tool to a specific gene. In CRISPR, it's called a guide RNA. For prime editing, it's a slightly modified version dubbed pegRNA. Once the guides tether their respective dance partners to the gene, their routines differ. For CRISPR, the second component, Cas9, acts as a pair of scissors to snip both DNA strands. From here, cells can either throw out parts of a gene, or—when given a template—insert a healthy version of a gene to replace the original one. The cost is molecular surgery. Just as an incision might not fully heal, a double-stranded break to the DNA can introduce errors into the genetic code, leading to unexpected effects that vary between cells. Prime editing was the sophisticated upgrade set to fix that. Rather than cutting both DNA strands, it lightly nips one chain. From there, it can delete or insert genetic code based on a template without relying on the cell's DNA repair mechanism. In other words, prime editing opened a new universe o...
Dr. Zach Bush is a multi-disciplinary physician of internal medicine, endocrinology, hospice care and an internationally recognized educator on the microbiome as it relates to human health, soil health, food systems, and a regenerative future. Zach joined me to discuss the current state of health in the world and how living in a toxic environment exacerbates the spread of disease amongst humans. In this episode we discuss: The paradox of views surrounding COVID vaccines. How the immune system works. Flu vaccines increase coronavirus symptoms. GMO mechanisms. The definition of ‘vaccine’. Differences between the COVID vaccines. How spike proteins harm the body. Cas9: our bodies own vaccine cards. Will vaccines get rid of coronavirus? The history of coronaviruses. The flu vs. coronavirus. Myths about PCR and our relationship to coronaviruses. Personal responsibility over our immune systems. Genetic modification of food. What we can learn from the DDT ban. Creating a call to action for our future. Is SARS Covid 2 a naturally occurring virus? A biological look on how the virus impacts each of our bodies. Histotoxic hypoxia, cyanide poisoning, and hospitalizations. The India outbreak. The importance of breath. Benefits of Vitamin D. Racial and socioeconomic impacts on the pandemic. The bottleneck of information on public health. The downsides to social distancing. Response to critiques of Zach’s from the Conspirituality podcast. Changes in mortality rates and chronic diseases in children. Romanticization of nature. War-like mentality between nature and mankind. Soil, water, and air systems collapsing modern society. Intuitive knowing vs. science. Macro and micro struggles during the pandemic. Links: Neurohacker Collective Podcast Episode Rich Roll Podcast Episode Luke Storey Podcast Episode Mark Groves Podcast Episode Dr. Doudna’s TED Talk Zach’s Website Zach’s Twitter Zach’s Facebook Zach’s Instagram See omnystudio.com/listener for privacy information.
Avanços na genética abrem um universo de possibilidades gigantesca para a humanidade. Estamos muito próximos de poder corrigir qualquer doença de base genética, melhorar espécies de forma precisa conferindo a ela, por exemplo, uma super visão ou o dobro de tempo de vida, e, ainda, propagar esta melhoria para toda população de uma determinada espécie. No entanto, grandes poderes trazem grandes responsabilidades! Até onde devemos ir? Será que temos controle e consciência de todas as implicações que o uso dessa tecnologia pode trazer para o equilíbrio da vida em nosso planeta? Neste episódio, Bruno Peroni e Gustavo Goldschmidt explicam a tecnologia CRISPR e também o funcionamento do mRNA (RNA mensageiro), tecnologia empregada no desenvolvimento de algumas das vacinas contra o Coronavírus. Bem-vindo ao Futuro da Genética! ---- Esse podcast é produzido pela Superplayer & Co, líder em soluções de streaming de áudio para negócios no Brasil. Atuamos desde o licenciamento de plataformas de streaming de audiotainment, até a produção de conteúdos originais. Acesse nosso site e saiba mais! Para conteúdos exclusivos do A Virada, siga o nosso Instagram. https://www.instagram.com/aviradapodcast/
音频文字发布在公众号“北京读天下”，《价值创造与商业模式》在公众号微店有优惠。反馈与服务微信号：yinmingshu002。杜德娜在自己的书中写道，推动科学前进的是对未知世界的好奇，和面对困难不放弃的恒心。但除了这些高尚的品质，我们也需要一点健康的实用主义态度，申请基金的时候有世俗的考虑，管理实验任务分配也需要从实际出发。博士生需要出成果，但新的课题往往风险很高。一旦失败，会影响博士生的个人职业发展。如果选择安全的研究方向，就难以取得惊人的成就，还会导致实验室难以吸引优秀的博士生和博士后。实验室管理工作的难度正好可以从沙彭蒂耶那里看到。她大胆启用硕士生Elitza Deltcheva，固然成就科学史上的佳话，但也暴露出人手短缺的困窘。相比之下，杜德娜实验室的人力调度显得非常高效。2006年开始CRISPR研究时，实验室里没有微生物学家，她能够招到恰好对CRISPR感兴趣的微生物学专业博士后韦德海福特（Blake Wiedenheft）。沙彭蒂耶提出合作时，天才的耶内克虽然已经开始找教职，但还有一年时间可以参加实验。当杜德娜决定与张锋等人展开人类细胞基因编辑竞赛时，实验室里还没有掌握这项技术的研究人员，她居然能够从竞争对手博德研究所那里招来博士生Alexandra East-Seletsky。她的灵活性也令人惊叹。沙彭蒂耶提出合作时，杜德娜已经在三大核心期刊上发表过20篇论文，而沙彭蒂耶只发表过少数几篇。但杜德娜还是很认真地研究了沙彭蒂耶的提议，并且意识到自己过去主导的Ⅰ类Cas研究在方向选择上有所不足。她说服了当时正在四处面试教职准备出站的耶内克，投入Cas9的研究。本案例讨论CRSIPR技术发展中偏向管理的方面，包括跨界思考、实验室管理、研究方向的选择，以及企业与基础科学之间的奇妙联系。
In episode #2 of GuidePost, Kevin Davies (Executive Editor, The CRISPR Journal) travels to Lithuania to meet Virginijus Šikšnys, one of the central figures in the development of CRISPR gene editing, at his lab at the Institute of Biotechnology, Vilnius University. Siksnys is an expert in DNA-protein interactions, and in 2011-12, made critical contributions in transferring the Cas9 enzyme into E. coli and characterizing the mechanism by which it cuts DNA.
We're gettin' nerdy this week, people! We're donning our lab coats and venturing into a scientific conversation we have no business discussing: CRISPR/Cas9. Which is why we brought in the brain trust - i.e., Kishore Hari, science guru over at Tested.com and host of the Inquiring Minds podcast. We start off with a bit of context and discuss what CRISPR/Cas9 actually is. What's the basic science behind the technology and process, how does it work, what's its promise, and what are its dangers? We also touch on recent, very real-world events in which Chinese scientist He Jiankui announced that he had used the technology to genetically modify a pair of twin girls. We then talk to author Robin Cook whose newest novel, Pandemic, is a thriller about the unintended side effects caused by genetic engineering and the CRISPR technology. Throughout his career, Cook has had an uncanny ability to be incredibly timely with his novels. Pandemic is no different. We talk to Cook about how the black market in human organs (a theme in Pandemic) has changed in the 40 years since he wrote Coma, why it wasn't much of a surprise that someone used CRISPR/Cas9 to genetically modify humans, where we go from here, the continuing ignorance about vaccines, and how medicine and public health will change over the next generation.
HOT TOPIC: CRISPR-Cas9 gene editing. The co-hosts discuss the science behind CRISPR-Cas9, case study its potential applications in food and health care, and answer the big question...How soon can we expect gene editing to hit grocery store shelves and hospital wings? Featuring: Kevin Doxzen and Lea Witkowsky, Innovative Genomics Institute Socialize with science on Twitter and Facebook using @ISGPforum. Disclaimer: The ISGP is a nonprofit organization that does not lobby for any position except rational thinking. Podcasts within the "Hot Topics Series" (Episodes 75+) reflect the views expressed by featured guests. For more information on the ISGP or its podcast series, please visit www.scienceforglobalpolicy.org.
In 2011, biologists Jennifer Doudna and Emmanuelle Charpentier published a landmark paper introducing the world to Crispr. The arcane family of bacterial proteins had a talent for precisely snipping DNA, and one of them—Cas9—has since inspired a billion-dollar boom in biotech investment. Clinical trials using Cas9 clippers to fix genetic defects are just beginning, so it will be years before Crispr-based cures could potentially reach the world.
© 2020-2025 Ivy Podcast Discovery LLC
