
The Genetics Podcast · 2026-07-09 · 38 min
Key moments - from our scoring
Substance score
78 / 100
Five dimensions, 20 points each
Walsh presents a paradigm shift in understanding neurodegenerative disease: rather than viewing somatic mutations as a minor modifier of germline disease, he demonstrates that somatic mosaicism is the primary driver of age-related neurodegeneration. His lab at Boston Children's Hospital has used single-cell whole genome sequencing - developed in collaboration with bioinformaticians Peter Park, Alice Lee, and August Huang - to reveal that neurons accumulate mutations with clockwork precision throughout life. In Alzheimer's disease, microglia carrying cancer-driver mutations in pathways like mTOR become inflammatory "angry murderers" that damage neighboring neurons. Across four distinct neurodegenerative conditions (Alzheimer's, frontotemporal dementia, ALS with C9orf expansion, and chronic traumatic encephalopathy), Walsh's team identified a shared mutational signature: oxidative damage (C-to-A changes reflecting oxoguanine) combined with topoisomerase-1-mediated two-base-pair deletions. This pattern emerges from inflammation-driven nucleotide excision repair that depletes deoxyribonucleotides, forcing incorporation of ribonucleotides into DNA and triggering genome fragmentation. The therapeutic implications are profound - targeting cancer genes in microglia or supplementing deoxyribonucleotides could become disease-modifying strategies.
Neurons accumulate ~17-20 single nucleotide variants per year, making them faster than hematopoietic stem cells but slower than metabolically active cardiomyocytes and epithelial cells like gut and lung cells, which accumulate 40-50 mutations per year.
All four conditions show oxidative damage (C-to-A changes reflecting oxoguanine) combined with topoisomerase-1-mediated two-base-pair deletions with AT-rich consensus sequences, indicating DNA fragmentation from ribonucleotide incorporation into DNA during repair.
Cancer-driver mutations in mTOR pathway and other genes make microglia hyperactive and inflammatory; because microglia cannot form tumors, these mutations convert them into cytokine-secreting cells that kill nearby neurons instead of forming cancers.
Yes - by analyzing the accumulation of somatic mutations in a single neuron and comparing it to a germline baseline, you can determine the age of the person the neuron came from, as mutation accumulation is remarkably linear across the lifespan.
Reducing microglial inflammation through cancer-drug repurposing targeting enriched genes, supplementing deoxyribonucleotides to restore DNA repair capacity, and potentially reducing or attenuating the inflammatory response of mutant microglia.
Our reviewer’s read on each dimension, with quotes from the episode.
Walsh delivers substantial novel insights about somatic mosaicism in neurons and its links to neurodegeneration, including specific mechanistic pathways (oxidative damage, ribonucleotide misincorporation, topoisomerase dysfunction). However, the episode contains notable stretches of biographical narrative and career advice that dilute the scientific density, particularly in the opening 8+ minutes and closing segment.
neurons accumulate mutations with age...about 17 or 18 SNVs per year...it's incredibly linear...15 or 20 SNVs your first year of life...15 or 20 SNVs your 100th year of life
we see an essentially indistinguishable pattern of genome damage...C to A changes which often reflect oxoguanine...two base pair deletions in a particular pattern with a particular consensus sequence
Walsh presents genuinely fresh thinking on age-related neurodegeneration by inverting the typical germline-centric model and reframing somatic mosaicism as the primary driver (analogous to cancer biology). His framework linking SBS5 signatures, oxidative damage, ribonucleotide imbalance, and TOP1 mutagenesis is specific and counterintuitive. The genome-as-clock concept and brain-as-quality-control mechanism via neuronal pruning are novel angles on development and aging.
the situation is Completely inverted...the disease is the somatic mosaicism...probably the germline risk genes for Alzheimer's are actually modifiers of the somatic process...analogous to cancer
neurons when they're originally born have an extremely high rate of...large scale chromosome level copy number variants on average in about 25 or 30% of them...this thing that we've known for a long time as programmed cell death is actually a genome quality control process
Christopher Walsh is an exceptionally qualified practitioner: Bullard Professor at Harvard Medical School, Chief of Genetics & Genomics at Boston Children's Hospital, Howard Hughes Medical Institute investigator with 30+ years of direct lab work in human genetics and neurobiology. He has authored multiple Cell papers presented during this episode and led the development of single-cell genome sequencing technology. His seniority and direct execution of the work discussed are exemplary.
Dr. Christopher Walsh, who's a Bullard professor of Pediatrics and Neurology at Harvard Medical School, Chief of Genetics and Genomics at Boston Children's Hospital, and Howard Hughes Medical Institute investigator
We just had a paper in Cell this week on...Alzheimer's disease where the microglia carry cancer driver mutations
Walsh grounds claims in concrete data: specific mutation rates (17-18 SNVs/year in neurons vs. sperm <5/year, cardiomyocytes fastest), named signature patterns (SBS1, SBS5, oxidative C-to-A transitions, AT-motif two-base deletions), cited collaborators (Peter Park, Alice Lee, August Huang), multiple Cell/bioRxiv papers with specific findings (microglia mutations in Alzheimer's, copy number variant elimination by birth, TOP1 covalent binding), and disease-specific neuronal patterns (Alzheimer's, FTD, ALS with C9orf, CTE). Few claims lack supporting detail, though some mechanistic steps remain partially speculative.
neurons accumulate mutations with age...about 17 or 18 SNVs per year...it's been shown now with five different technologies
the neurons when they're originally born have an extremely high rate of, ah, large scale chromosome level copy number variants on average in about 25 or 30% of them...by the time of birth, the proportion of neurons with large pseudocopping number variants is down to about 5%
Short asks intelligent opening questions (somatic mosaicism, clinical implications, healthy brain baseline) and follows up on specific points (APOE, therapeutic targets, centenarian data, selection pressures). However, he rarely pushes back or challenges Walsh's claims, instead affirming them ("Wow," "Interesting," "That's amazing"). The conversation reads more as guided discovery than critical interrogation. Short misses opportunities to probe mechanism gaps, validate speculative claims, or explore contradictions.
What insights does it give you about therapeutic potential?
So it sounds like you're seeing like, uh, is it a characteristic mutational signature across these four conditions? What. Do you have any hypotheses about what's behind it?
Computed from the transcript - who did the talking, and the words that came up most.
This week on The Genetics Podcast, Patrick is joined by Dr. Christopher Walsh, Professor of Pediatrics and Neurology at Harvard Medical School, Chief of Genetics and Genomics at Boston Children's Hospital, and HHMI Investigator. They discuss his path from neurobiology to human genetics, how somatic mosaicism in the brain drives disease from epilepsy to Alzheimer's, and what this reveals about new therapeutic targets for neurodegeneration.
Transcribed and scored by The B2B Podcast Index.
Speaker A: Hello and welcome to the Genetics Podcast. I'm your host, Patrick Short. My background is in population genomics and studying the genetic causes of rare disease. I did my PhD at the Sanger Institute and the University of Cambridge and have been in biotech since 2018, when I started Cyanogenetics. Cyanogenetics helps academic and industry researchers to run large scale genetic testing programs that speed up their clinical trials, generate data sets for the next big breakthrough, and give participants the best possible experience taking part in research. Each episode of the Genetics Podcast, we bring you insights from the leading minds in genetics and precision medicine, including household names and Nobel Prize winners, as well as early career scientists and biotechs working on the next big breakthrough. Whether you are a scientist, entrepreneur, executive, patient advocate, or simply someone curious about how genetics shapes our world, you're in the right place. Thank you for listening and let's get started.
Speaker B: Welcome, everyone, to the Genetics Podcast. I'm really excited to be here today with Dr. Christopher Walsh, who's a. Bullard professor of Pediatrics and Neurology at Harvard Medical School, Chief of Genetics and Genomics at Boston Children's Hospital, and Howard Hughes Medical Institute investigator Chris. Thank you so much for taking the time to join me.
Speaker C: It's great to be here, Patrick.
Speaker B: I'd love to just start with actually how you got interested in genetics. Can you take me back to that story?
Speaker C: Yeah, there are kind of two phases to that. Uh, first in graduate school, I did my PhD with, in neurobiology, but with Ray Guillory, who had described way back in the 70s, the first genetic mutations that disrupt the wiring of the human brain. And these are mutations associated with albinism that actually cause the fibers from the retina to be misrouted at the optic chiasin. So eyes project to the wrong side of the brain. And so although I was, uh, really interested in how this miracle of the developing brain comes about, I thought it would be really cool to try to apply genetics to that. And so I took a couple of extra genetics courses as part of my neurobiology training. But then a, uh, really second pivotal event happened 10 or 15 years later. How I really became a geneticist was I finished my PhD, I went through training as an adult neurologist, and I did a postdoc with Connie Sepko, which was very basic and had. It was in a genetics department at Harvard, but it was actually just tracking the anatomy of how the neurons in the cerebral cortex develop. My postdoc project was actually taking DNA barcodes and adding them to retroviruses so that you could, uh, identify a clone wherever the daughter cells would migrate in the brain. So I set up my own lab, thinking I was again going to be doing these relatively descriptive studies in the development of the cerebral cortex. And then five months after I started my own lab, everything changed. I went to a meeting in Venice with my wife to present this cell lineage barcode stuff that I'd been doing. And one of my teachers from the University of Chicago, Peter Hutten Lauper, presented a family with an inherited malformation of the cortex where some of the neurons completely failed to migrate. He already showed that this was an X linked trait, likely dominant in females and lethal prenatally to males because he had a large family. And this for me was just like literally a moment I was listening. I could feel my palms sweating and my heart racing. Because this is where everything came together. The opportunity to use genetics to understand the development of the brain. And it was something that really hadn't seemed possible before that because most of the genetic disorders that disrupt the development of the brain are so disabling that they result in very small family sizes, are caused by de novo, we now know, caused by de novo mutations. But here was something. Because of its X linked nature, we could get our hands on a family that was large enough to do the primitive mapping that was available back then in the early 90s. And so on that day, I became a human geneticist. And I went racing down to the podium after Peter's talk because I thought everyone in the auditorium would want to be the one to map that disorder. And I said, peter, can we? And Peter had actually taught me pediatric neurology and written one of my letters for residency. And so I asked him, can we, can we work together to map that gene? And he gave me this confused expression like he thought had never crossed his mind before. And so on that day, our collaboration was born. And he was there with his wife Janellen, and I was there with my wife Mingwe. And the four of us spent the next day together talking about our collaboration. And so that also just called me to become completely hooked on human genetics and this interaction between the development of
Speaker B: the brain and human genetics that is a super story. One of the things that may be underrated in the progress of science is actually the power of some of these really strong collaborations. Are there any others throughout your career that, that you can share, that you've had, have had a really big impact on you?
Speaker C: Well, I've had tremendous effects of mentors, not just Ray and Peter, but also I Probably wouldn't have become. I came to do my residency at Mass General because this time, at that time, back in the mid-80s, it was the real, really was a hotbed of applying human genetics to neurological disease. That was when Joe Martin had recruited Jim to start mapping the Huntington's gene and then Gazella went on to map other neurological disease genes. And so I chose that residency because, again, I was interested in genetics. It was only, as I said, a couple of years later, I could see how I could apply that to studying development. In terms of collaborations, yeah, that collaboration with Peter was really, really pivotal. I mean, more recently, our studies on, um, the genomes of single cells, it would have been completely impossible without collaborations with bioinformaticians. Initially Peter park and Alice Lee, and more recently also August Huang. And I continue to collaborate with them all now for almost 20 years. And you know, again, I have, I'm a neuroscientist and I am the weakest bioinformatician in my lab. But. And so they develop these incredible new, you know, programs that allow us to call variants from a single cell's genome and, and suppress, uh, artifact. And then, you know, we add this biological program where we can put that to use and develop interesting ways of applying it. So those have been really enduring collaborations for a long period of time. And like I said, I'd be nowhere without them. I'm incredibly fortunate and privileged to be able to have people like that who share common interests.
Speaker B: We, you, you mentioned the single cell work, and I want to go down that rabbit hole because we, perhaps naively or, or probably thanks to your work, certainly naively think about our organ systems as a monolith at a cellular level. But there's a lot going on in terms of somatic mosaicism in the brain. Can you talk a little bit about what, what has changed about how you think about the brain?
Speaker A: What have we learned?
Speaker B: And then also what are the biggest things? Open questions?
Speaker C: Sure. Well, that's. Gosh, that's a lot of questions. I'll take them through. I'll try to take them one at a time. The, you know, the concept of mosaicism in our lab really developed because of two projects that seemed initially separate, but then ended up being thematically very linked. So the first had to do with genetics of human disease. And we had been studying now malformations of the brain, particularly other developmental genetic disorders, but especially malformations. And uh, we came upon ones actually right from the start where the disorder was very asymmetrical. It only involved one hemisphere of the frame. And so it just didn't look like it was likely to be a germline mutation. But we didn't know how to study them. But some of these cause such severe epilepsy that they undergo, as the patient undergoes surgery to remove a patch of the brain to cure the epilepsy, that which allows us to study the abnormal area. That led us to discover that these mutations, that these disorders are actually somatic disorders, where there's just a clone of, uh, abnormal cells, generally with activating mutations in the MTOR pathway, the exact same mutations in the exact same genes that are typically associated with cancer, but because they occur in neurons known as Cat 4 cancer. And so it's just an abnormal clone, instead it just turns those neurons into really bad neighbors because they're hyperactive and overstimulating, and that's what leads to the epilepsy. And then at the same time, two graduate students, particularly Gilada Vroni, wanted to study the genome of a single neuron. And we were specifically interested in that time at looking at retrotransposons, which had been claimed to frequently mobilize, particularly in the genomes of neurons, perhaps even as part of the developing neuronal identity of the diversity of neurons. And so we wanted to test that theory. We were skeptical of it because we thought that somatic mutations are probably bad for you. And so that led Lad and another graduate student, Xu Yukai, to develop the single cell whole genome sequencing. And so then having that capability also then gave us a lot of insight into the epileptic disorders. To answer your question about what's changed, I think when we originally, once we started studying mosaicism of the brain, we thought of it as a special case of many germline disorders. We studied some of these neuronal migration disorders and found that they caused a severe malformation in the germline state. We could occasionally find patients where they would have a mosaic mutation and would have a milder cause of it. And so we thought that, oh, that's a nice sort of a curiosity, you know, it makes up, uh, if you're talking about a disorder associated with a de novo mutation that has a severe, maybe lethal phenotype, about 5 or 10% of those patients will end up having a mosaic mutation instead with a milder phenotype. So we thought of the mosaic mutations as like a little bit of add on to germline neurology. But then more recently we've been studying mosaicism in age related disorders. And there it looks more like the situation is Completely inverted. That the disease is the somatic mosaicism. We just had a paper in Cell this week on, um, Alzheimer's disease where the microglia carry cancer driver mutations.
Speaker B: Wow.
Speaker C: And we know that cancer driver mutations are not good for you. And those cancer driver mutations convert, confer an inflammatory state in the microglia, which we think in that case, these cancer driver mutations are in dividing cells. And they are. But microglia are also cells that can't form cancers. And so instead of forming cancers, those cells just turn into angry murderers and start killing the neurons nearby. And here we think, as I said, the situation is inverted, that probably the germline risk genes for Alzheimer's are actually modifiers of the somatic process. Um, like the same way we think of cancer mutations, where the germline cancer mutations modify a somatic process of cancer development. Because the germline cancer mutations like Li Fraumeni or this sort of, you know, the instability, microsatellated instability disorders, they basically create, either create more somatic mutations or alter the clonal selection somatic mutations. And so we suspect, although we have not proven, that the germline risk genes for Alzheimer's, like amyloid or other ones, actually modify this process of somatic mutation analogous to cancer.
Speaker B: Do you think that's my own.
Speaker C: That's my own sort of prior now, yes. And that is a completely inversion of my, of how I first came to it. I just lost your. I didn't hear that question.
Speaker B: Do you think that's the case with APOE as well?
Speaker C: I really don't know. I. My best guess is that APOE is actually, you know, acts in microglia to make them more inflammatory and so it acts on top of the somatic mosaicism. In fact, again, my colleague Al, my colleagues Alice Lee and August1 have a paper on bioarchive where they looked at CHIP mutations in the blood of Alzheimer patients and they find that CHIP mutations are a very strong risk factor for Alzheimer's. When you discover them at depth, if you do targeted panel sequencing where you can discover them with very low variant allele frequency. And most of that risk is from very small clones, not the ones that create risk for cancer because it's a cancer like process, but in a totally different way with many, many small clones instead of a particularly dangerous large point. And interestingly, that risk that they find in Alzheimer's is completely driven by the neutral ApoE phenotypes, ApoE3 homozygotes particularly, and the ApoE4 carriers actually do not have a risk from somatic mosaicism. So in fact, it looks like these might be complementary risk factors that they basically, one way or another, a, uh, microglia has to become inflammatory and dangerous. That can either happen by germline risk, you know, maybe trem2 as well, or it can happen by somatic risk.
Speaker B: What insights does it give you about therapeutic potential?
Speaker C: Golly. Well, again, as in the case of cancer, again, when we think about cancer, we think not about necessarily curing the germline genes. We think about curing the somatic mutations. Yeah, the RAS inhibitors or whatever. And so I think with this, I like to think that this gives us all new window on thinking about therapeutics for Alzheimer's. That basically some of the therapeutics that are already being developed for cancer can potentially be repurposed for the treatment of Alzheimer's. Specifically those that target the genes that we show are enriched in Alzheimer's disease microglia in a totally complementary fashion. We have another paper that's coming out online next week at Cell. It focuses on those single neuron genomes in Alzheimer's disease. There we find that neurons in Alzheimer's have a particular pattern of DNA damage that is actually shared among four different major neurodegenerative diseases. That particular pattern of, uh, genome damage we think also presents other therapeutic possibilities. Yeah, you actually treat the excessive DNA damage. And that's a kind of a complicated thing to get into. So that's a real rabbit hole to explain that. But, uh, and I'm happy to do that if, if we want to go that. If we want to go down that rabbit hole. But that. But I do think that it gives. So we had. Think the work gives us kind of two new ways of thinking about therapeutic for degenerative diseases.
Speaker B: So it sounds like you're seeing like, uh, is it a characteristic mutational signature across these four conditions? What. Do you have any hypotheses about what's behind it?
Speaker C: Yes, we've looked at four degenerative conditions. Alzheimer's disease, frontotemporal dementia and ALS. In those cases, both associated with C9orf expansion specifically, and chronic traumatic encephalopathy after playing American football, which is another tauopathy, but a little different from Alzheimer's in its pattern of distribution. In each case, we looked at the genomes of single neurons. And amazingly, in all of these four diverse conditions, both tauopathies and TDP 43 opathies, we see an essentially indistinguishable pattern of genome damage. Two things, a pattern of single nucleotide variation which appears to reflect oxidative Damage, it often has C to A changes which often reflect oxoguanine. And then there's a second pattern of damage which is predominantly single stranded but occasionally double stranded. And this represents two base pair deletions in a particular pattern with a particular consensus sequence, A, T and thimotif. And specifically, it's a pattern that's been described before by Andrew Jackson and Martin Taylor as being associated with topoisomerase 1 mutagenesis. They describe this as a defect of ribonucleotide excision repair where ribonucleotides get falsely incorporated into the DNA and they can be repaired by rnase H or they can be repaired by an alternate pathway where the first step is top one basically binding covalently to the DNA and creating a two base pair nick. We find that in fact top one is covalently bound to the DNA. In the conditions where we've looked, we haven't looked in all four conditions that look in Alzheimer's and ftd and we see these nicks. And in these conditions, literally you can show that the DNA is fragmented, it's literally falling apart, um, in the cerebral cortex, which is the involved part of the brain. But in fact, if you take the cerebellum from the same patient, the DNA DNA there is just fine. And so it's literally tearing the genome apart. And this appears to be essentially due to a starvation of deoxyribonucleotides. G0 cells in general and neurons specifically had low levels of deoxyribonucleotides in the nucleus. This seems to be partly an antiviral mechanism.
Speaker B: Oh, interesting.
Speaker C: But they're not replicating, so they don't need a lot of DNPs. But, uh, what we think is happening is that this, these SNVs, the oxidative SNVs I mentioned, so that you basically have inflammation. Inflammation results in cytokine secretion from these angry murderers. Microglutin I was just telling you about, that creates reactive oxygen. That's been shown by other people in the neuron. That creates DNA damage in the form of oxoguanine. That activates nucleotide excision repair, which demands a lot of deoxyribonucleotides. That uses up the supply of deoxyribonucleotides in the nucleus, that changes the balance of DNTPs and RNTPs. Now ribonucleotides start getting incorporated into DNA and that activates this second pathway of alternate ribonucleotide excision repair, which results in essentially DNA fragmentation because the process can't
Speaker B: be completed and complex. How do you think about getting upstream or where is, where do you intervene in that process?
Speaker C: Well, I think the best option for therapy would be, would be reducing the inflammation at the level of the microglia. Yeah, it's possible that deoxyribin nucleotide supplementation, you know, might help. That's been shown to work for some other DNA repair conditions. And so it's worth thinking about. Yeah, but the more important thing, I think the more durable therapy would be either reducing the number of mutant microglia or perhaps attenuating their inflammatory response or blocking the cytokines that they may be secreting.
Speaker B: What do we know about the quote, unquote healthy brain or presumed healthy brain with respect to somatic mosaicism?
Speaker C: So one of the biggest surprises of, um, the work that we started doing on sequencing the genomes of single neurons is that they, that the neurons accumulate mutations with age. And so we originally thought it was about 20 or 25 SNVs per year. Then with better technology, we're able to, we were able to find that it's about 17 or 18 SNVs per year. And that's been shown now with five different technologies. And it's really converging on, um, a. And it's incredibly linear. It's, you know, it's 15 or 20 SNVs your first year of life. It's 15 or 20 SNVs your 100th year of life, if you live to be 100 and you don't get Alzheimer's disease. And then in addition, there are two or three indels per year. And the indels are actually more damaging than single, uh, nucleotide variants. And so this is about 20 point mutations per year. And it, uh, seems to be predominantly driven by transcription, particularly the indels. And so sadly, it's enriched at the genes that are expressed at the highest levels in that particular neuron. And there's also enrichment at promoters and enhancers. These mutations are also some of them epigenetic marks. They're EPI mutations. Essentially. They have the potential to alter the pattern of transcription of the neuron. So this 20 point mutations per year is scary. So there's several things about that. First of all, how does that stack up against other cells? Well, it's actually just a little bit faster than the rate of accumulation of mutations of hematopoietic stem cells. So even though neurons are not dividing, they're accumulating mutations faster than many dividing cells. It turns out it really doesn't matter whether a cell is dividing or not in terms of its rate of accumulation of mutations. The cell with the slowest rate of mutations is sperm, which are obviously dividing or formed from recently dividing cells, and that's less than 5 per year. The one with the fastest recorded rate of accumulation of mutation of cardiomyocytes, which again are post mitotic but are very metabolically active. They have a lot of oxidative damage. Neurons are about in the middle somewhere. The second puzzle is how does that happen? Why does a. You know, we would have thought that being post mitotic was a bargain that neurons made with nature so that they could at least have a decent genome for their whole life because they're long lived and they're post mitotic and we need them to remember things. But turns out they accumulate mutations just like other cells. And as I say, it's in a particularly damaging pattern because of its relationship to transcription, although still probably that 20 per year. Since they're all over the whole genome and only a couple of percent of them are in exons, it's still something we can generally live with. It's just when you get into a disease state where the process is accelerated that it starts becoming likely to be functionally important. And then the third puzzle is what do these things do? They mark time, they mark age. So a neuron constantly knows how old it is. You could sequence the genome of a neuron that you found in the street and could determine how old the person was from that neuron, provided that you had a germline to sample from the same.
Speaker B: You need to be careful. The longevity people will get a hold of this and design a test, Right?
Speaker C: Exactly. So it's quite possible then. And so what we'd like to know is whether they have some sort of normal function or whether they're just bad news.
Speaker B: You have. I rarely have a script, but if I had one, I would be completely off script with this because you just have me spinning with the implications. Where, where does the, the neurons sit relative to. If you've got sperm on one end, cardiomyocytes, the other end, like not just in rate of change, but are there other factors where it's really very different from other organ systems?
Speaker C: Yeah. So every cell is a little different. And, and I would. And I just want to put in here a plug for the IH is supporting the somatic mosaicism across human tissues network where we're trying to look at this in all different cell types. And it's really an amazing collaboration between many sites and so different sites are looking at different cell types but there's already a fair amount of information based as you know, largely from work from the Sanger center, from you know, Anandal Martin Karena and Peter Campbell and others. So, so you know, the neurons are as I say are about 15 or 20 per year. The first one that really was well determined was like the gut cells which are about 40 or 50 per year. The lung is maybe about the same rate and so epithelial cells are a little faster than neurons. The hematopoietic stem cells are dividing cells but they do divide very slowly. And lymphocyte lymphocytes are actually about the same as neurons, so about 15 or 20 per year. So then every then cell has not only its own rate but it also has its own pattern of nucleotide substitution which reflects the pathogenic mechanisms driving that accumulation. In all cells there tend to be two patterns of substitution that are fairly commonly shared. They're called sbs, single base substitution patterns determined by the cosmic, the cosmic cancer signatures again from the Sanger 1 is SPS 1 which reflects cycine deamination during the cell cycle. Neurons seem to accumulate a little bit of that and I'm not exactly sure why, but it seems like it accumulates a little bit in non dividing cells as well. And then the main driver of this age related thing is SPS5 which is nobody knows what causes it. It's basically mostly C to T's and T to C changes. It's seen in every single tissue of the body. The slope of the line is slightly different from tissue to tissue. And so it's a universal aging signature uh, whose underlying pathogenesis is really not totally clear. Molly Pisorski has suggested it might reflect the inherent error rate of the DNA repair mechanism that is repairing particular transcription related damage. And again SPS5 accumulates out of is the main driver in neurons. It accounts for about 80% of the age related accumulation in neurons. And then what happens in neurons is that the disease signatures are added. On top of that they represent new pathogenic processes attacking the genome of the neon that are not that are rare in the normal brain.
Speaker B: This is amazing. What do you see as the, as the next layer on top of what we are understanding today about somatic mosaicism? We're probably going to spend a decade plus really under uncovering what's going on on the somatic side. What do you see as the either parallel waves or next waves after that?
Speaker C: I mean I think it's going to be a while until we sort of digest the implications, uh, of somatic mosaicism. You know, we have a paper, again, it causes me to look at every disorder differently. We have a paper that's on bioarchive looking at the normal development of uh, copy number variation and in the brain, in neurons specifically. And what we find there is that it's been long known that the brain of humans and other species generates about 20 or 30% more neurons than it actually needs. And that 20 or 30% of those neurons die, typically in humans in the second half of gestation after the neurons become post mitotic. And it's been known that that programmed cell death process can be modified. It represents a Darwinian competition to form synapses. What we show recently, what we show in our work on bioarchive, is in fact the neurons when they're originally born have an extremely high rate of, ah, large scale chromosome level copy number variants on average in about 25 or 30% of them. Then by the time of birth, the proportion of neurons with large pseudocopping number variants is down to about 5%. And so in fact this thing that we've known for a long time as programmed cell death is actually a genome quality control process where neurons compete for survival and the strong survive. And those that have large scale copy number variants are weak and they're preferentially eliminated. But it's an interactive, non cell autonomous. And recently we've looked at some developmental disorders and they appear to retain these copy number variant containing neurons. And so what the hell's going on with those brains? And so again we see there that the germline is a modifier of somatic mosaicism. And uh, instead of the mosaicism being a modifier of the germline, which was my original prior, but again it causes me to think a completely different way about autism spectrum disorders in terms of this process of essentially synaptic pruning.
Speaker B: So yeah, complete that for me. What does it, does it give you a new way of thinking about autism? What would it be?
Speaker C: Well actually, so what we find in this paper is that at the large scale, the large scale copy number variants are mostly eliminated by the time of birth, but in fact at birth there are still another 20 or 30% of neurons that have small scale, right, but still pretty big.
Speaker B: So what is small scale but big,
Speaker C: like less than a chromosome but you know, multiple, maybe multiple megabases. So those neurons um, in fact continue to be eliminated throughout life. They get gradually a little less common as we age. And so our neuro, our brain is constantly trying to pruning itself. Yeah, uh, by a constant process of pruning and competition, which actually makes perfect sense that neurons are constantly competing to make synapses. And so that's great news. Our brain is always trying to be perfect. However, the downside of that is that I just told you about, although copy number variants Decline with age, SNVs and Indels accelerate with age. And so in fact our genomes are becoming damaged again as we age, but by a different mechanism. And so the brain actually already has a mechanism in place to kill those neurons when they reach a certain level of DNA damage. We don't need to invoke a new mechanism to think about why neurons die in degenerative conditions. We can think of it as a purely genomic process where their genomes just get progressively damaged and they can no longer compete.
Speaker B: Do you know or do you have a hypothesis around what might be happening in the brains of very healthy super centenarians? What do we think might be going on there? Healthy from a brain perspective?
Speaker C: So I have lots of theories and not much data. We looked at one or two centenarians. We originally thought that maybe the clock, the mutational clock in neurons runs at a slightly different slope in centenarians. We looked at one or maybe two greater than 100 year old people and who were healthy at the time of, who had no diagnosis of a neurodegenerative condition. To our surprise, their neurons fell right on the line. And so they doesn't seem that they have an inherent more perfect DNA repair pathway that they don't accumulate these H related mutations. I favor the idea that a significant driver of healthy aging has to do with how the brain manages the clonal selection, particularly in microglial cells. Obviously the clonal selection in glial progenitors, that would lead to cancer, brain cancer would be one determinant. But I suspect, you know, these, these cancer driver mutations are not unique to Alzheimer's disease. They're just more common and they have, and they form larger clones and they're under stronger clonal selection in the Alzheimer brain than they are in normals, but normal folks have them too. And so, uh, just as in terms of, again, thinking of things in terms of cancer, people avoiding cancer, you can avoid cancer a couple of different ways. You cannot have an uh, inherited defect of DNA repair, but you also can get lucky in terms of clonal selection or you can live well in terms of modifying that clonal selection by not smoking or not living in a city with a lot of air pollution. I think of it somewhat Analogous way to the class selection that particularly might affect megal cells.
Speaker B: And is it my assumption would be that this, uh, because I know a little bit more about germline mutation where you find hypermutators, but you don't really find people who are hypo mutators, at least I'm not aware of it. Or they may be vanishingly rare. It sounds like that's the same case here. Is there a similar selection principle going on? But they're very different regimes of selection that we're thinking about.
Speaker C: Yeah, I mean that's how I think of it, that the selection regimes might be very different. And I mean, so there are, you know, again, there's been studies of a couple of studies, single cell studies of people that have genetic defects of DNA repair and they do often have, they do have higher rates of uh, somatic mutation. Although interestingly some of these conditions have higher rates of cancer and some don't. And in a study of one hypermutator, where there's not a large cancer risk, in fact they hypermutate, but in fact a lot of the mutations are bunched in non coding parts of the genome.
Speaker B: Interesting.
Speaker C: Their level of exonic hypermutation is actually not greatly increased.
Speaker B: Wow.
Speaker C: And so that probably has to do with the, the particular DNA repair aspects that, that that pathway is involved in.
Speaker B: Lucky them. As, as we wrap up here, is there one or two things that you want to leave the audience with? Either something you're working on right now or, or also just learnings from your career? A lot of people who listen to this are earlier in their career and maybe looking for advice on where to focus, how to focus. Is there anything you want to leave people with?
Speaker C: Sure. I think that, what, what I would think about is going back to that episode I told you about, about the day I became a human geneticist. You know, I've been, I was, I'm trained as an anatomist originally, you know, and I was comfortable doing molecular biology and PCR and charting these cells as they migrated to the brain. But on that day when I decided I was going to become a human geneticist, you know, I had no experience in human genetics and so I thought, well, how am I going to do this?
Speaker B: Yeah.
Speaker C: And. But I just, I basically said, but this is something I want to do and I just think I'm going to be able to figure it out. And it was not hard to figure it out. You know, there's colleagues, there's friends you can ask for advice. And so that just seemed like something that was worth doing. And so I encourage people. So that's when you have an opportunity like that to do something and you aren't sure whether you can do it or not. You can definitely do it. And the same thing happened when those students developed single cell health genome sequencing. It's like, okay, first we said, well, this sounds like it's going to be really complicated. How could we. Who knows what's going to happen to the genome of a single neuron? You put it in a tube, maybe some of the chromosomes will stick to the side and won't amplify. It was a miracle when we found that, by and large, you actually get the whole genome of a single cell. And then we're like, well, how are we going to analyze this? But, you know, there's people that you can. I mean, I'm particularly fortunate to be in this environment where it's such an intense scientific environment, intensely rich scientific environment. It's no more intense than anywhere else. But, uh, people are very friendly and they're always happy to chip in, but you can always find people to help you get over that. And so I would tell. I would encourage people not to be shy or to have, like, imposter syndrome if they want to do something that they think is going to be impactful and they're not sure if they'll be able to figure out how to do it or not. I just want to give them the confidence to know that they will be able to, because, uh, like I say, I still don't know how to do, like, much of this stuff, but there's people that have been able to lead me through it.
Speaker A: Yeah.
Speaker B: Science is a very social sport, isn't it?
Speaker C: It is. That's the best part about it, in fact, is to do something that's really hard but worthwhile. And it's usually not hard to recruit people to work with you on it.
Speaker B: Yeah. Well, amazing. Chris, thank you so much for taking the time today.
Speaker C: All right, thanks, Patrick. I really appreciate the opportunity to chat with you.
Speaker B: It's my pleasure. And thanks everybody, as always, for listening and we will see you next time.
Speaker A: Thanks, as always for tuning in to the Genetics podcast. If you enjoyed today's conversation, the best way you can support the show is by sharing it with a, um, or colleague who might find it interesting as well. We'd also really appreciate if you could subscribe, rate and review us on Apple Podcasts, Spotify, or wherever you listen to podcasts. This helps other people discover the show when they're searching for content on genetics, precision medicine, or biotech. We always want to hear from you as well.
Speaker B: If you have feedback or questions or
Speaker A: want to be featured on the show, you can email us@podcastanogenetics.com you can find me on LinkedIn. Patrick Short, you can find us as well Sonogenetics on LinkedIn or reach out on Instagram. Uh, the Genetics Podcast. And finally, a special thank you to the team behind the show who makes this possible. Joy Ismail produces and manages the show. And James Pierce from Selective Frequencies for his expert audio engineering. I'm Patrick Short, your host. Thanks again for listening and we'll see you next time on the Genetics Podcast.
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