Podcasts about rnaseq

Play Episode Listen Later May 2, 2024 6:49

With an ever-increasing global population grappling with age-related ocular ailments like cataracts, dry eyes, glaucoma, and macular degeneration, the need for new research in this domain is more pressing than ever. In a new study, researchers Kohsaku Numa, Sandip Kumar Patel, Zhixin A. Zhang, Jordan B. Burton, Akifumi Matsumoto, Jun-Wei B. Hughes, Chie Sotozono, Birgit Schilling, Pierre-Yves Desprez, Judith Campisi (1948-2024), and Koji Kitazawa from the Buck Institute for Research on Aging, Kyoto Prefectural University of Medicine, University of Cambridge, and California Pacific Medical Center shed light on a pivotal aspect of corneal health – the impact of ultraviolet-A (UV-A) radiation on corneal endothelial cells. Their research paper was published on the cover of Aging's Volume 16, Issue 8, entitled, “Senescent characteristics of human corneal endothelial cells upon ultraviolet-A exposure.” “The objective of this study was to investigate the senescent phenotypes of human corneal endothelial cells (hCEnCs) upon treatment with ultraviolet (UV)-A.” Full blog - https://aging-us.org/2024/05/uv-a-exposure-cellular-senescence-and-vision-impairment/ Paper DOI - https://doi.org/10.18632/aging.205761 Corresponding author - Koji Kitazawa - kkitazaw@koto.kpu-m.ac.jp Sign up for free Altmetric alerts about this article - https://aging.altmetric.com/details/email_updates?id=10.18632%2Faging.205761 Subscribe for free publication alerts from Aging - https://www.aging-us.com/subscribe-to-toc-alerts Keywords - aging, cellular senescence, senescence-associated secretory phenotype, RNA-Seq, proteomics, gene ontology analysis About Aging-US Aging publishes research papers in all fields of aging research including but not limited, aging from yeast to mammals, cellular senescence, age-related diseases such as cancer and Alzheimer's diseases and their prevention and treatment, anti-aging strategies and drug development and especially the role of signal transduction pathways such as mTOR in aging and potential approaches to modulate these signaling pathways to extend lifespan. The journal aims to promote treatment of age-related diseases by slowing down aging, validation of anti-aging drugs by treating age-related diseases, prevention of cancer by inhibiting aging. Cancer and COVID-19 are age-related diseases. Aging is indexed by PubMed/Medline (abbreviated as “Aging (Albany NY)”), PubMed Central, Web of Science: Science Citation Index Expanded (abbreviated as “Aging‐US” and listed in the Cell Biology and Geriatrics & Gerontology categories), Scopus (abbreviated as “Aging” and listed in the Cell Biology and Aging categories), Biological Abstracts, BIOSIS Previews, EMBASE, META (Chan Zuckerberg Initiative) (2018-2022), and Dimensions (Digital Science). Please visit our website at https://www.Aging-US.com and connect with us: Facebook - https://www.facebook.com/AgingUS/ X - https://twitter.com/AgingJrnl Instagram - https://www.instagram.com/agingjrnl/ YouTube - https://www.youtube.com/@AgingJournal LinkedIn - https://www.linkedin.com/company/aging/ Pinterest - https://www.pinterest.com/AgingUS/ Spotify - https://open.spotify.com/show/1X4HQQgegjReaf6Mozn6Mc Media Contact 18009220957 MEDIA@IMPACTJOURNALS.COM

Cover Paper: Senescent Characteristics of Human Corneal Endothelial Cells Upon UV-A Exposure

Play Episode Listen Later Apr 30, 2024 4:17

BUFFALO, NY- April 30, 2024 – A new #researchpaper was #published on the #cover of Aging (listed by MEDLINE/PubMed as "Aging (Albany NY)" and "Aging-US" by Web of Science) Volume 16, Issue 8, entitled, “Senescent characteristics of human corneal endothelial cells upon ultraviolet-A exposure.” In this new study, researchers Kohsaku Numa, Sandip Kumar Patel, Zhixin A. Zhang, Jordan B. Burton, Akifumi Matsumoto, Jun-Wei B. Hughes, Chie Sotozono, Birgit Schilling, Pierre-Yves Desprez, Judith Campisi (1948-2024), and Koji Kitazawa from Buck Institute for Research on Aging, Kyoto Prefectural University of Medicine, University of Cambridge, and California Pacific Medical Center investigated the senescent phenotypes of human corneal endothelial cells (hCEnCs) upon treatment with ultraviolet (UV)-A. “We assessed cell morphology, senescence-associated β-galactosidase (SA-β-gal) activity, cell proliferation and expression of senescence markers (p16 and p21) in hCEnCs exposed to UV-A radiation, and senescent hCEnCs induced by ionizing radiation (IR) were used as positive controls.” The researchers performed RNA sequencing and proteomics analyses to compare gene and protein expression profiles between UV-A- and IR-induced senescent hCEnCs — they also compared the results to non-senescent hCEnCs. Cells exposed to 5 J/cm2 of UV-A or to IR exhibited typical senescent phenotypes, including enlargement, increased SA-β-gal activity, decreased cell proliferation and elevated expression of p16 and p21. RNA-Seq analysis revealed that 83.9% of the genes significantly upregulated and 82.6% of the genes significantly downregulated in UV-A-induced senescent hCEnCs overlapped with the genes regulated in IR-induced senescent hCEnCs. Proteomics also revealed that 93.8% of the proteins significantly upregulated in UV-A-induced senescent hCEnCs overlapped with those induced by IR. In proteomics analyses, senescent hCEnCs induced by UV-A exhibited elevated expression levels of several factors part of the senescence-associated secretory phenotype. “In this study, where senescence was induced by UV-A, a more physiological stress for hCEnCs compared to IR, we determined that UV-A modulated the expression of many genes and proteins typically altered upon IR treatment, a more conventional method of senescence induction, even though UV-A also modulated specific pathways unrelated to IR.” DOI - https://doi.org/10.18632/aging.205761 Corresponding author - Koji Kitazawa - kkitazaw@koto.kpu-m.ac.jp Sign up for free Altmetric alerts about this article - https://aging.altmetric.com/details/email_updates?id=10.18632%2Faging.205761 Subscribe for free publication alerts from Aging - https://www.aging-us.com/subscribe-to-toc-alerts About Aging-US Aging publishes research papers in all fields of aging research including but not limited, aging from yeast to mammals, cellular senescence, age-related diseases such as cancer and Alzheimer's diseases and their prevention and treatment, anti-aging strategies and drug development and especially the role of signal transduction pathways such as mTOR in aging and potential approaches to modulate these signaling pathways to extend lifespan. The journal aims to promote treatment of age-related diseases by slowing down aging, validation of anti-aging drugs by treating age-related diseases, prevention of cancer by inhibiting aging. Cancer and COVID-19 are age-related diseases. Please visit our website at https://www.Aging-US.com and connect with us: Facebook - https://www.facebook.com/AgingUS/ X - https://twitter.com/AgingJrnl Instagram - https://www.instagram.com/agingjrnl/ YouTube - https://www.youtube.com/@AgingJournal LinkedIn - https://www.linkedin.com/company/aging/ Pinterest - https://www.pinterest.com/AgingUS/ Spotify - https://open.spotify.com/show/1X4HQQgegjReaf6Mozn6Mc MEDIA@IMPACTJOURNALS.COM

Transcriptomic Modulation of Alzheimer's Disease by Activated Protein C Using Single-Cell RNA-Seq

Play Episode Listen Later Mar 13, 2024 3:16

BUFFALO, NY- March 13, 2024 – A new #research paper was #published in Aging (listed by MEDLINE/PubMed as "Aging (Albany NY)" and "Aging-US" by Web of Science) Volume 16, Issue 4, entitled, “Single-Cell RNA-seq reveals transcriptomic modulation of Alzheimer's disease by activated protein C.” Single-Cell RNA sequencing reveals changes in cell population in Alzheimer's disease (AD) model 5xFAD (5x Familial AD mutation) versus wild type (WT) mice. In this new study, researchers Mohammad Kasim Fatmi, Hao Wang, Lily Slotabec, Changhong Wen, Blaise Seale, Bi Zhao, and Ji Li from the University of South Florida, University of Mississippi Medical Center and the G.V. (Sonny) Montgomery VA Medical Center used single-cell RNA sequencing and bioinformatic analysis to analyze the effects of APC [Activated Protein C] treatment on AD transgenic mice. “In our investigation, we utilized transgenic mice that contain expression for five major amyloid pathologies that allow for rapid progression of AD and Aβ deposition known as 5xFAD mice.” The returned sequencing data was processed through the 10x Genomics CellRanger platform to perform alignment and form corresponding matrix to perform bioinformatic analysis. Alterations in glial cells occurred in 5xFAD versus WT, especially increases in microglia proliferation were profound in 5xFAD. Differential expression testing of glial cells in 5xFAD versus WT revealed gene regulation. Globally, the critical genes implicated in AD progression are upregulated such as Apoe, Ctsb, Trem2, and Tyrobp. Using this differential expression data, GO term enrichment was completed to observe possible biological processes impacted by AD progression. Utilizing anti-inflammatory and cyto-protective recombinant Activated Protein C (APC), the researchers uncovered inflammatory processes to be downregulated by APC treatment in addition to recuperation of nervous system processes. Moreover, animal studies demonstrated that administration of recombinant APC significantly attenuated Aβ burden and improved cognitive function of 5xFAD mice. “The downregulation of highly expressed AD biomarkers in 5xFAD could provide insight into the mechanisms by which APC administration benefits AD.” DOI - https://doi.org/10.18632/aging.205624 Corresponding authors - Bi Zhao - bizhao@usf.edu, and Ji Li - jli3@umc.edu Sign up for free Altmetric alerts about this article - https://aging.altmetric.com/details/email_updates?id=10.18632%2Faging.205624 Subscribe for free publication alerts from Aging - https://www.aging-us.com/subscribe-to-toc-alerts Keywords - aging, APC, Alzheimer's disease, inflammation About Aging-US Launched in 2009, Aging-US publishes papers of general interest and biological significance in all fields of aging research and age-related diseases, including cancer—and now, with a special focus on COVID-19 vulnerability as an age-dependent syndrome. Topics in Aging-US go beyond traditional gerontology, including, but not limited to, cellular and molecular biology, human age-related diseases, pathology in model organisms, signal transduction pathways (e.g., p53, sirtuins, and PI-3K/AKT/mTOR, among others), and approaches to modulating these signaling pathways. Please visit our website at https://www.Aging-US.com and connect with us: Facebook - https://www.facebook.com/AgingUS/ X - https://twitter.com/AgingJrnl Instagram - https://www.instagram.com/agingjrnl/ YouTube - https://www.youtube.com/@AgingJournal LinkedIn - https://www.linkedin.com/company/aging/ Pinterest - https://www.pinterest.com/AgingUS/ Spotify - https://open.spotify.com/show/1X4HQQgegjReaf6Mozn6Mc Media Contact 18009220957 MEDIA@IMPACTJOURNALS.COM

Daphne Koller: The Convergence of A.I. and Digital Biology

Ground Truths

Play Episode Listen Later Mar 10, 2024 35:16

Transcript Eric Topol (00:06):Well, hello, this is Eric Topol with Ground Truths and I am absolutely thrilled to welcome Daphne Koller, the founder and CEO of insitro, and a person who I've been wanting to meet for some time. Finally, we converged so welcome, Daphne.Daphne Koller (00:21):Thank you Eric. And it's a pleasure to finally meet you as well.Eric Topol (00:24):Yeah, I mean you have been rocking everybody over the years with elected to the National Academy of Engineering and Science and right at the interface of life science and computer science and in my view, there's hardly anyone I can imagine who's doing so much at that interface. I wanted to first start with your meeting in Davos last month because I kind of figured we start broad AI rather than starting to get into what you're doing these days. And you had a really interesting panel [←transcript] with Yann LeCun, Andrew Ng and Kai-Fu Lee and others, and I wanted to get your impression about that and also kind of the general sense. I mean AI is just moving it at speed, that is just crazy stuff. What were your thoughts about that panel just last month, where are we?Video link for the WEF PanelDaphne Koller (01:25):I think we've been living on an exponential curve for multiple decades and the thing about exponential curves is they are very misleading things. In the early stages people basically take the line between whatever we were last year, and this year and they interpolate linearly, and they say, God, things are moving so slowly. Then as the exponential curve starts to pick up, it becomes more and more evident that things are moving faster, but it's still people interpolate linearly and it's only when things really hit that inflection point that people realize that even with the linear interpolation where we'll be next year is just mind blowing. And if you realize that you're on that exponential curve where we will be next year is just totally unanticipatable. I think what we started to discuss in that panel was, are we in fact on an exponential curve? What are the rate limiting factors that may or may not enable that curve to continue specifically availability of data and what it would take to make that curve available in areas outside of the speech, whatever natural language, large language models that exist today and go far beyond that, which is what you would need to have these be applicable to areas such as biology and medicine.Daphne Koller (02:47):And so that was kind of the message to my mind from the panel.Eric Topol (02:53):And there was some differences in opinion, of course Yann can be a little strong and I think it was good to see that you're challenging on some things and how there is this “world view” of AI and how, I guess where we go from here. As you mentioned in the area of life science, there already had been before large language models hit stride, so much progress particularly in imaging cells, subcellular, I mean rare cells, I mean just stuff that was just without any labeling, without fluorescein, just amazing stuff. And then now it's gone into another level. So as we get into that, just before I do that, I want to ask you about this convergence story. Jensen Huang, I'm sure you heard his quote about biology as the opportunity to be engineering, not science. I'm sure if I understand, not science, but what about this convergence? Because it is quite extraordinary to see two fields coming together moving at such high velocity."Biology has the opportunity to be engineering not science. When something becomes engineering not science it becomes...exponentially improving, it can compound on the benefits of previous years." -Jensen Huang, NVIDIA.Daphne Koller (04:08):So, a quote that I will replace Jensen's or will propose a replacement for Jensen's quote, which is one that many people have articulated, is that math is to physics as machine learning is to biology. It is a mathematical foundation that allows you to take something that up until that point had been kind of mysterious and fuzzy and almost magical and create a formal foundation for it. Now physics, especially Newtonian physics, is simple enough that math is the right foundation to capture what goes on in a lot of physics. Biology as an evolved natural system is so complex that you can't articulate a mathematical model for that de novo. You need to actually let the data speak and then let machine learning find the patterns in those data and really help us create a predictability, if you will, for biological systems that you can start to ask what if questions, what would happen if we perturb the system in this way?The ConvergenceDaphne Koller (05:17):How would it react? We're nowhere close to being able to answer those questions reliably today, but as you feed a machine learning system more and more data, hopefully it'll become capable of making those predictions. And in order to do that, and this is where it comes to this convergence of these two disciplines, the fodder, the foundation for all of machine learning is having enough data to feed the beast. The miracle of the convergence that we're seeing is that over the last 10, 15 years, maybe 20 years in biology, we've been on a similar, albeit somewhat slower exponential curve of data generation in biology where we are turning it into a quantitative discipline from something that is entirely observational qualitative, which is where it started, to something that becomes much more quantitative and broad based in how we measure biology. And so those measurements, the tools that life scientists and bioengineers have developed that allow us to measure biological systems is what produces that fodder, that energy that you can then feed into the machine learning models so that they can start making predictions.Eric Topol (06:32):Yeah, well I think the number of layers of data no less what's in these layers is quite extraordinary. So some years ago when all the single cell sequencing was started, I said, well, that's kind of academic interest and now the field of spatial omics has exploded. And I wonder how you see the feeding the beast here. It's at every level. It's not just the cell level subcellular and single cell nuclei sequencing single cell epigenomics, and then you go all the way to these other layers of data. I know you plug into the human patient side as well as it could be images, it could be past slides, it could be the outcomes and treatments and on and on and on. I mean, so when you think about multimodal AI, has anybody really done that yet?Daphne Koller (07:30):I think that there are certainly beginnings of multimodal AI and we have started to see some of the benefits of the convergence of say, imaging and omics. And I will give an example from some of the work that we've recently distributed on a preprint server work that we did at insitro, which took imaging data from standard histopathology slides, H&E slides and aligned them with simple bulk RNA-Seq taken from those same tumor samples. And what we find is that by training models that translate from one to the other, specifically from the imaging to the omics, you're able to, for a fairly large fraction of genes, make very accurate predictions of gene expression levels by looking at the histopath images alone. And in fact, because many of the predictions are made at the tile level, not at the entire slide level, even though the omics was captured in bulk, you're able to spatially resolve the signal and get kind of like a pseudo spatial biology just by making predictions from the H&E image into these omic modalities.Multimodal A.I. and Life ScienceDaphne Koller (08:44):So there are I think beginnings of multimodality, but in order to get to multimodality, you really need to train on at least some data where the two modalities are simultaneously. And so at this point, I think the rate limiting factor is more a matter of data acquisition for training the models. It is for building the models themselves. And so that's where I think things like spatial biology, which I think like you are very excited about, are one of the places where we can really start to capture these paired modalities and get to some of those multimodal capabilities.Eric Topol (09:23):Yeah, I wanted to ask you because I mean spatial temporal is so perfect. It is two modes, and you have as the preprint you refer to and you see things like electronic health records in genomics, electronic health records in medical images. The most we've done is getting two modes of data together. And the question is as this data starts to really accrue, do we need new models to work with it or do you actually foresee that that is not a limiting step?Daphne Koller (09:57):So I think currently data availability is the most significant rate limiting step. The nice thing about modern day machine learning is that it really is structured as a set of building blocks that you can start to put together in different ways for different situations. And so, do we have the exact right models available to us today for these multimodal systems? Probably not, but do we have the right building blocks that if we creatively put them together from what has already been deployed in other settings? Probably, yes. So of course there's still a model exploration to be done and a lot of creativity in how these building blocks should be put together, but I think we have the tools available to solve these problems. What we really need is first I think a really significant data acquisition effort. And the other thing that we need, which is also something that has been a priority for us at insitro, is the right mix of people to be put together so that you can, because what happens is if you take a bunch of even extremely talented and sophisticated machine learning scientists and say, solve a biological problem, here's a dataset, they don't know what questions to ask and oftentimes end up asking questions that might be kind of interesting from machine learning perspective, but don't really answer fundamental biology questions.Daphne Koller (11:16):And conversely, you can take biologists and say, hey, what would you have machine learning do? And they will tell you, well, in our work we do A to B to C to D, and B to C is kind of painful, like counting nuclei is really painful, so can we have the machine do that for us? And it's kind of like that. Yeah, but that's boring. So what you get if you put them in a room together and actually get to the point where they communicate with each other effectively, is that not only do you get better solutions, you get better problems. I think that's really the crux of making progress here besides data is the culture and the people.A.I. and Drug DiscoveryEric Topol (11:54):Well, I'm sure you've assembled that at insitro knowing you, and I mean people tend to forget it's about the people, it's not about the models or even the data when you have all that. Now you've been onto drug discovery paths, there's at least 20 drugs that are AI driven that are in the clinic in phase one or two at some point. Obviously these are not only ones that you've been working on, but do you see this whole field now going into high gear because of this? Or is that the fact that there's all these AI companies partnering with big pharma? Is it a lot of nice agreements that are drawn up with multimillion dollar milestones or is this real?Daphne Koller (12:47):So there's a number of different layers to your question. First of all, let me start by saying that I find the notion of AI driven drugs to be a bit of a weird concept because over time most drugs will have some element of AI in them. I mean, even some of the earlier work used data science in many cases. So where do you draw the boundary? I mean, we're not going to be in a world anytime soon where AI starts out with, oh, I need to work on ALS and at the end there is a clinical trial design ready to be submitted to the FDA without anything, any human intervention in the middle. So, it's always going to be an interplay between a machine and a human with over time more and more capabilities I think being taken on by the machine, but I think inevitably a partnership for a long time to come.Daphne Koller (13:41):But coming to the second part of your question, is this real? Every big pharma has gotten to the point today that they realize they need some of that AI thing that's going around. The level of sophistication of how they incorporate that and their willingness to make some of the hard decisions of, well, if we're going to be doing this with AI, it means we shouldn't be doing it the old way anymore and we need to make a big dramatic internal shift that I think depends very much on the specific company. And some companies have more willingness to take those very big steps than others, so will some companies be able to make the adjustment? Probably. Will all of them? Probably not. I would say however, that in this new world there is also room for companies to emerge that are, if you will, AI native.Daphne Koller (14:39):And we've seen that in every technological revolution that the native companies that were born in the new age move faster, incorporate the technology much more deeply into every aspect of their work, and they end up being dominant players if not the dominant player in that new world. And you could look at the internet revolution and think back to Google did not emerge from the yellow pages. Netflix did not emerge from blockbuster, Amazon did not emerge from Walmart so some of those incumbents did make the adjustment and are still around, some did not and are no longer around. And I think the same thing will happen with drug discovery and development where there will be a new crop of leading companies to I think maybe together with some of the incumbents that we're able to make the adjustment.Eric Topol (15:36):Yeah, I think your point there is essential, and another part of this story is that a lot of people don't realize there's so many nodes of ways that AI can facilitate this whole process. I mean from the elemental data mining that identified Baricitinib for Covid and now being used even for many other indications, repurposing that to how to simulate for clinical trials and everything in between. Now, what seems like because of your incredible knack and this convergence, I mean your middle name is like convergence really, you are working at the level of really in my view, this unique aspect of bringing cells and all the other layers of data together to amp things up. Is that a fair assessment of where insitro in your efforts are directed?Three BucketsDaphne Koller (16:38):So first of all, maybe it's useful to kind of create the high level map and the simplest version I've heard is where you divide the process into three major buckets. One is what you think of as biology discovery, which is the discovery of new therapeutic hypotheses. Basically, if you modulate this target in this group of humans, you will end up affecting this clinical outcome. That's the first third. The middle third is, okay, well now we need to turn that hypothesis into an actual molecule that does that. So basically generating molecules. And then finally there's the enablement and acceleration of the clinical development process, which is the final third. Most companies in the AI space have really focused in on that middle third because it is well-defined, you know when you've succeeded if someone gives you a target and what's called a target product profile (TPP) at the end of whatever, two, three years, whether you've been able to create a molecule that achieves the appropriate properties of selectivity and solubility and all those other things. The first third is where a lot of the mistakes currently happen in drug discovery and development. Most drugs that go into the clinic don't fail because we didn't have the right molecule. I mean that happens, but it's not the most common failure mode. The most common failure mode is that the target was just a wrong target for this disease in this patient population.Daphne Koller (18:09):So the real focus of us, the core of who we are as a company is on that early third of let's make sure we're going after the right clinical hypotheses. Now with that, obviously we need to make molecules and some of those molecules we make in-house, and obviously we use machine learning to do that as well. And then the last third is we discover that if you have the right therapeutic hypothesis, which includes which is the right patient population, that can also accelerate and enable your clinical trials, so we end up doing some of that as well. But the core of what we believe is the failure mode of drug discovery and what it's going to take to move it to the next level is the articulation of therapeutic hypotheses that actually translate into clinical outcome. And so in order to do that, we've put together, to your point about convergence, two very distinct types of data.Daphne Koller (19:04):One is data that we print in our own internal data factory where we have this incredible set of capabilities that uses stem cells and CRISPR and microscopy and single cell measurements and spatial biology and all that to generate massive amounts of in-house data. And then because ultimately you care not about curing cells, you care about curing people, you also need to bring in the clinical data. And again, here also we look at multiple high content data modalities, imaging and omics, and of course human genetics, which is one of the few sources of ground truth for causality that is available in medicine and really bring all those different data modalities across these two different scales together to come up with what we believe are truly high quality therapeutic hypotheses that we then advance into the clinic.AlphaFold2, the ExemplarEric Topol (19:56):Yeah, no, I think that's an extraordinary approach. It's a bold, ambitious one, but at least it is getting to the root of what is needed. One of the things you mentioned of course, is the coming up with molecules, and I wanted to get your comments about the AlphaFold2 world and the ability to not just design proteins now of course that are not extant proteins, but it isn't just proteins, it could be antibodies, it could be peptides and small molecules. How much does that contribute to your perspective?Daphne Koller (20:37):So first of all, let me say that I consider the AlphaFold story across its incarnations to be one of the best examples of the hypothesis that we set out trying to achieve or trying to prove, which is if you feed a machine learning model enough data, it will learn to do amazing things. And the space of protein folding is one of those areas where there has been enough data in biology that is the sequence to structure mapping is something that over the years, because it's so consistent across different cells, across different species even, we have a lot of data of sequence to structure, which is what enabled AlphaFold to be successful. Now since then, of course, they've taken it to a whole new level. I think what we are currently able to do with protein-based therapeutics is entirely sort of a consequence of that line of development. Whether that same line of development is also going to unlock other therapeutic modalities such as small molecules where the amount of data is unfortunately much less abundant and often locked away in the bowels of big pharma companies that are not eager to share.Daphne Koller (21:57):I think that question remains. I have not yet seen that same level of performance in de novo design of small molecule therapeutics because of the data availability limitations. Now people have a lot of creative ideas about that. We use DNA encoded libraries as a way of generating data at scale for small molecules. Others have used other approaches including active learning and pre-training and all sorts of approaches like that. We're still waiting, I think for a truly convincing demonstration that you can get to that same level of de novo design in small molecules as you can in protein therapeutics. Now as to how that affects us, I'm so excited about this development because our focus, as I mentioned, is the discovery of novel therapeutic hypotheses. You then need to turn those therapeutic hypotheses into actual molecules that do the work. We know we're not going to be the expert in every single therapeutic modality from small molecules to macro cycles, to the proteins to mRNA, siRNA, there's so many of those that you need to have therapeutic modality experts in each of those modalities that can then as you discover a target that you want to modulate, you can basically go and ask what is the right partner to help turn this into an actual therapeutic intervention?Daphne Koller (23:28):And we've already had some conversations with some modality partners as we like to call them that help us take some of our hypotheses and turn it into molecules. They often are very hungry for new targets because they oftentimes kind of like, okay, here's the three or four or whatever, five low hanging fruits that our technology uniquely unlocks. But then once you get past those well validated targets like, okay, what's next? Am I just going to go read a bunch of papers and hope for the best? And so oftentimes they're looking for new hypotheses and we're looking for partners to make molecules. It's a great partnership.Can We Slow the Aging Process?Eric Topol (24:07):Oh yeah, no question about that. Now, we've seen in recent times some leaps in drugs that were worked on for decades, like the GLP-1s for obesity, which are having effects potentially well beyond obesity didn't require any AI, but just slogging away at it for decades. And you previously were at Calico, which is trying to deal with aging. Do you think that we're going to see drug interventions that are going to slow the aging process because of this unique time of this exponential point we are in where we're a computer and science and digital biology come together?Daphne Koller (24:52):So I think the GLP-1s are an incredible achievement. And I would point out, I know you said and incorrectly that it didn't use any AI, but they did actually use an understanding of human genetics. And I think human genetics and the genotype phenotype statistical associations that they revealed is in some ways the biological precursor to AI it is a way of leveraging very large amounts of data, admittedly using simpler statistical tools, but still to discover in a data-driven way, novel therapeutic hypothesis. So I consider the work that we do to be a progeny of the kind of work that statistical geneticists have done. And of course a lot of heavy lifting needed to be done after that in order to make a drug that actually worked and kudos to the leaders in that space. In terms of the modulation of aging, I mean aging is a process of decline over time, and the rate of that decline is definitely something that is modifiable.Daphne Koller (26:07):And we all know that external factors such as lifestyle, diet, exercise, even exposure to sun or smoking, accelerates the aging process. And you could easily imagine, as we've seen in the GLP-1s that a therapeutic intervention can change that trajectory. So will we be able to using therapeutic interventions, increase health span so that we live healthy longer? I think the answer to that is undoubtedly, yes. And we've seen that consistently with therapeutic interventions, not even just the GLP-1s, but going backwards, I mean even statins and earlier things. Will we be able to increase the maximum life span so that people habitually live past 120, 150? I don't know. I don't know that anybody knows the answer to that question. I personally would be quite happy with increasing my health span so that at the age of 80, I'm still able to actively go hiking and scuba diving at 90 and 100 and that would be a pretty good place to start.Eric Topol (27:25):Well, I'm with you on that, but I just want to ask though, because the drugs we have today that are highly effective, I mean statins is a good example. They work at a particular level of the body. They don't have across the board modulation of effect. And I guess what I was asking is, do you foresee we will have some way to do that across all systems? I mean, that is getting to, now that we have so many different ways to intervene on the process, is there a way that you envision in the future that we'll be able to here, I'm not talking about in expanding lifespan, I'm talking about promoting health, whether it's the immune system or whether it's through mitochondria and mTOR, caloric, I mean all these different things you think that's conceivable or is that just, I mean companies like Calico and others have been chasing this. What do you think?Daphne Koller (28:30):Again, I think it's a thing that is hard to predict. I mean, we know that different organ systems age at different rates, and is there a single bio even in a single individual, and it's been well established that you can test brain age versus muscle health versus cardiovascular, and they can be quite different in the same individual, so is there a single hub? No, that governs all forms of aging. I don't know if that's true. I think it's oftentimes different. We know protein folding has an effect, you know DNA damage has an effect. That's why our skin ages because it's exposed to sun. Is there going to be a single switch that reverts it all back? Certainly some companies are pursuing that single bullet approach. I personally would probably say that based on the biology that I've seen, there's at least as much potential in trying to find ways to slow the decline in a way that specific to say as we discussed the immune system or correcting protein, misfolding dysfunction or things like that. And I'm not dismissing there is a single magic switch, but let's just say I think we should be exploring multiple alternatives.Eric Topol (29:58):Yeah, no, I like your reasoning. I think it's actually like everything else you said here. It makes a lot of sense. The logic is hard to argue with. Well, I think what you're doing there at insitro is remarkable and it seems to be quite distinct from other strategies, and that's not at all surprising knowing your background and your aspiration.Daphne Koller (30:27):Never like to follow the crowd. It's boring.Eric Topol (30:30):Right, and I do know you left an aging directed company effort at Calico to do what you're doing. So that must have been an opening for you that you saw was much more diverse perhaps, or maybe I'm mistaken that Calico is not really age specific in its goals.Daphne Koller (30:49):So what inspired me to go found insitro was the realization that we are making medicines today in a way that is not that different from the way in which we were making medicines 20 or 30 years ago in terms of the process by which we go from a, here's what I want to work on to here's a drug is a very much an artisanal one-off each one of them is a snowflake. There is very little commonality and sharing of insights and infrastructure across those efforts except in relatively limited tool-based ways. And I wanted to change that. I wanted to take the tools of engineering and data and machine learning and build a very different approach of going from a problem definition to a therapeutic intervention. And it didn't make sense to build that within a company that's focused on any single biology, not just aging because it is such a broad-based foundation.Daphne Koller (31:58):And I will tell you that I think we are on the path to building the thing that I set out to build. And as one example of that, I will use the work that we've recently done in metabolic disease where based on the foundations that we've built using both the clinical machine learning work and the cellular machine learning work, we were able to go from a problem articulation of this is the indication that we want to work on to a proof of concept in a translatable animal model in one year. That is pretty unusual. Admittedly, this is with an SiRNA tool compound. Nice thing about things that are liver directed is that it's not that difficult of a path to go from an SiRNA tool compound to an actual SiRNA drug. And so hopefully that's a fairly linear journey from there even, which is great.Daphne Koller (32:51):But the fact that we were able to go from problem articulation to a proof of concept in a translatable animal model in one year, that is unusual. And we're starting to see that now across our other therapeutic areas. It takes a long time to build a platform because you're basically building a foundation. It's like, okay, where's the fruit of all of that? I mean, you're building and building and building and nothing comes out for a while because you're building so much of the infrastructure. But once you've built it, you turn the crank and stuff starts to come out, you turn the crank again, and it works faster and better than the previous time. And so the essence of what we've built and what has turned into the tagline for the company is what we call pipeline through platform, which is we're building a pipeline of therapeutic interventions that comes off of a platform. And that's rare in biopharma, the only platform companies that really have emerged by and larger therapeutic modality platforms, things like Moderna and Alnylam, which have gotten really good at a particular modality and that's awesome. We're building a discovery platform and that is a fairly unusual thing.Eric Topol (34:02):Right. Well, I have no doubt you'll be discovering a lot of important things. That one sounds like it could be a big impact on NASH.Daphne Koller (34:14):Yeah, we hope so.Eric Topol (34:14):A big unmet need that's not going to be fixed by what we have today. So Daphne, it's really a joy to talk with you and palpable enthusiasm for where the field is going as one of its real leaders and we'll be cheering for you. I hope we'll reconnect in the times ahead to get another progress report because you're definitely rocking it there and you've got a lot of great ideas for how to change the life science medical world of the future.Daphne Koller (34:48):Thank you so much. It's a pleasure to meet you, and it's a long and difficult journey, but I think we're on the right path, so looking forward to seeing that all that pan out.Eric Topol (34:58):You made a compelling case in a short visit, so thank you.Daphne Koller (35:02):Thank you so much.Thanks for your subscription and listening/reading these posts.All content on Ground Truths—newsletter analyses and podcasts—is free.Voluntary paid subscriptions all go to support Scripps Research. Get full access to Ground Truths at erictopol.substack.com/subscribe

Mapping the Core Senescence Phenotype of Human Colon Fibroblasts

Play Episode Listen Later Feb 29, 2024 3:30

BUFFALO, NY- February 29, 2024 – A new #research paper was #published on the #cover of Aging (listed by MEDLINE/PubMed as "Aging (Albany NY)" and "Aging-US" by Web of Science) Volume 16, Issue 4, entitled, “Mapping the core senescence phenotype of primary human colon fibroblasts.” Advanced age is the largest risk factor for many diseases and several types of cancer, including colorectal cancer (CRC). Senescent cells are known to accumulate with age in various tissues, where they can modulate the surrounding tissue microenvironment through their senescence associated secretory phenotype (SASP). Recently, researchers showed that there is an increased number of senescent cells in the colons of CRC patients and demonstrated that senescent fibroblasts and their SASP create microniches in the colon that are conducive to CRC onset and progression. However, the composition of the SASP is heterogenous and cell-specific, and the precise senescence profile of colon fibroblasts has not been well-defined. In this new study, to generate a SASP atlas of human colon fibroblasts, researchers Namita Ganesh Hattangady, Kelly Carter, Brett Maroni-Rana, Ting Wang, Jessica Lee Ayers, Ming Yu, and William M. Grady from Fred Hutchinson Cancer Center and the University of Washington School of Medicine induced senescence in primary human colon fibroblasts using various in vitro methods and assessed the resulting transcriptome. “[...] we utilized various relevant stressors to induce senescence in primary cultures of colon fibroblasts and perform RNA sequencing (RNASeq) to define an atlas of stressor-specific senescent profiles and a core senescent profile that is commonly regulated by all senescence inducers.” Using RNA Sequencing and further validation by quantitative RT-PCR and Luminex assays, the team define and validate a ‘core senescent profile' that might play a significant role in shaping the colon microenvironment. They also performed KEGG analysis and GO analyses to identify key pathways and biological processes that are differentially regulated in colon fibroblast senescence. These studies provide insights into potential driver proteins involved in senescence-associated diseases, like CRC, which may lead to therapies to improve overall health in the elderly and to prevent CRC. “Further studies will be needed to address the limitations of our study and to translate our understanding of the SASP and disease into clinical care.” DOI - https://doi.org/10.18632/aging.205577 Corresponding authors - William M. Grady - wgrady@fredhutch.org, and Ming Yu - myu@fredhutch.org Sign up for free Altmetric alerts about this article - https://aging.altmetric.com/details/email_updates?id=10.18632%2Faging.205577 Subscribe for free publication alerts from Aging - https://www.aging-us.com/subscribe-to-toc-alerts Keywords - aging, senescence, senescence associated secretory phenotype, SASP, colorectal cancer, cancer About Aging-US Launched in 2009, Aging-US publishes papers of general interest and biological significance in all fields of aging research and age-related diseases, including cancer—and now, with a special focus on COVID-19 vulnerability as an age-dependent syndrome. Topics in Aging-US go beyond traditional gerontology, including, but not limited to, cellular and molecular biology, human age-related diseases, pathology in model organisms, signal transduction pathways (e.g., p53, sirtuins, and PI-3K/AKT/mTOR, among others), and approaches to modulating these signaling pathways. Please visit our website at https://www.Aging-US.com and connect with us: Facebook - https://www.facebook.com/AgingUS/ X - https://twitter.com/AgingJrnl Instagram - https://www.instagram.com/agingjrnl/ YouTube - https://www.youtube.com/@AgingJournal LinkedIn - https://www.linkedin.com/company/aging/ Pinterest - https://www.pinterest.com/AgingUS/ Spotify - https://open.spotify.com/show/1X4HQQgegjReaf6Mozn6Mc Media Contact 18009220957 MEDIA@IMPACTJOURNALS.COM

High-throughput transcriptomics and AI for drug discovery

Speaking of Mol Bio

Play Episode Listen Later Feb 15, 2024 31:56

Doing something complex and meaningful in a new way requires thinking and acting a bit differently. This is the case with how Dr. Joey Azofeifa, from Arpeggio Bio, is using systems biology to discover new drug candidates. Join us in this Season 2 kickoff episode where we dive headlong into transcriptomics, systems biology, machine learning, and learn how they're being used to innovate drug discovery. We learn about 3'-end mRNA barcoding and in-cell reverse transcription methods that allow the pooling of up to 1,536 samples so that only a single library preparation is required while still allowing the deconvolution of RNAseq results. This reduces their RNAseq costs by up to 400-fold, which enables them to generate enormous transcriptomic data sets. We also learn about how they're using generative adversarial AI networks to use this transcriptomics data to design potential drug candidates. We even hear how one of their drug candidates, which targets iron homeostasis pathways, has progress to successful testing in mice. To access the transcript for download, please visit - https://www.thermofisher.com/us/en/home/brands/invitrogen/molecular-biology-technologies/speaking-of-mol-bio-podcast.html Subscribe to get future episodes as they drop and if you like what you're hearing we hope you'll share a review or recommend the series to a colleague.  Download Transcripts: Speaking of Mol Bio Podcast | Thermo Fisher Scientific - US Visit the Invitrogen School of Molecular Biology to access helpful molecular biology resources and educational content, and please share this resource with anyone you know working in molecular biology.

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Ep. 238 - Do Steroids Give a Permanent Advantage? (feat Dr. Alex Kolliari-Turner)

Iron Culture

Play Episode Listen Later Sep 4, 2023 78:03

It's the four-year anniversary of the last appearance of then MR. Alex Kolliari-Turner, now DR. Alex Kolliari-Turner, who returns to Iron Culture to share the results of his now-completed Ph.D. research on the long-term performance-enhancing effects of anabolic steroids (if any). A lot has changed in this burgeoning area of research, as it hinges on a theory of muscle physiology: myonuclear domain theory. Our understanding of the mechanisms of “muscle memory” leads to the possibility of anabolic steroid use providing permanent long-term effects…but what if myonuclear domain theory comes under scrutiny? That's exactly where the science is at the moment. As new mechanisms of muscle memory are being explored and the first human data emerges, the picture becomes more complicated. Join us in this fascinating episode as we explore the intersection of muscle physiology, performance-enhancing drug mechanisms, and anti-doping! 00:00 Introduction to an anabolic episode of Iron Culture and Dr Kolliari-Turner Iron Culture Ep. 29- The Science & History of Steroids (And Drug Testing) https://www.youtube.com/watch?app=desktop&v=XN7u4-ckZK8 Kolliari-Turner 2023 An observational human study investigating the effect of anabolic androgenic steroid use on the transcriptome of skeletal muscle and whole blood using RNA-Seq https://pubmed.ncbi.nlm.nih.gov/37138349/ Kolliari-Turner 2021 Analysis of Anti-Doping Rule Violations That Have Impacted Medal Results at the Summer Olympic Games 1968-2012 https://pubmed.ncbi.nlm.nih.gov/33835351/ Kolliari-Turner 2021 Doping practices in international weightlifting: analysis of sanctioned athletes/support personnel from 2008 to 2019 and retesting of samples from the 2008 and 2012 Olympic Games https://pubmed.ncbi.nlm.nih.gov/33415428/ 07:42 Myonuclear permanency Gundersen 2016 Muscle memory and a new cellular model for muscle atrophy and hypertrophy https://pubmed.ncbi.nlm.nih.gov/26792335/ Snijders 2020 The concept of skeletal muscle memory: Evidence from animal and human studies https://pubmed.ncbi.nlm.nih.gov/32175681/ Yu 2020 Potential effects of long-term abuse of anabolic androgen steroids on human skeletal muscle https://pubmed.ncbi.nlm.nih.gov/32343079/ 24:42 Myonuclear domain flexibility? Murach 2018 Myonuclear Domain Flexibility Challenges Rigid Assumptions on Satellite Cell Contribution to Skeletal Muscle Fiber Hypertrophy https://pubmed.ncbi.nlm.nih.gov/29896117/ Bagley 2023 The myonuclear domain in adult skeletal muscle fibres: past, present and future https://pubmed.ncbi.nlm.nih.gov/36629254/ 31:04 Myonuclear domain theory 36:31 Dr Kolliari-Turner's research Doctoral Thesis Anabolic Androgenic Steroid doping in Weightlifting and the Summer Olympic Games alongside their impact on muscle memory and the human transcriptome https://research.brighton.ac.uk/en/studentTheses/anabolic-androgenic-steroid-doping-in-weightlifting-and-the-summe Lima 2023 The MMAAS Project: An Observational Human Study Investigating the Effect of Anabolic Androgenic Steroid Use on Gene Expression and the Molecular Mechanism of Muscle Memory https://pubmed.ncbi.nlm.nih.gov/35533133/ Smit 2021 Positive and negative side effects of androgen abuse. The HAARLEM study: A one-year prospective cohort study in 100 men https://pubmed.ncbi.nlm.nih.gov/33038020/ 57:05 Other research on past-AAS use and higher myonuclei density Nielsen 2023 Higher myonuclei density in muscle fibers persists among former users of anabolic androgenic steroids https://pubmed.ncbi.nlm.nih.gov/37466198/ Eriksson Doctoral Thesis 2006 Strength training and anabolic steroids: a comparative study of the trapezius, a shoulder muscle and the vastus lateralis, a thigh muscle, of strength trained athletes http://umu.diva-portal.org/smash/record.jsf?pid=diva2%3A144813&dswid=-2747 1:04:45 The challenges of being enhanced 1:16:14 Closing out the natural podcast

Stimulation of mRNA translation rescues hippocampal synaptic plasticity and memory in mouse models of Alzheimer's disease

Play Episode Listen Later Aug 3, 2023

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.08.03.551808v1?rss=1 Authors: Ribeiro, F. C., Cozachenco, D., Argyrousi, E. K., Staniszewski, A., Wiebe, S., Calixtro, J. D., Soares-Neto, R., Al-Chami, A., El Sayegh, F., Bermudez, S., Arsenault, E., Cossenza, M., Lacaille, J.-C., Nader, K., Sun, H., De Felice, F. G., Lourenco, M. V., Arancio, O., Aguilar-Valles, A., Sonenberg, N., Ferreira, S. T. Abstract: Impaired synaptic plasticity and progressive memory deficits are major hallmarks of Alzheimer's disease (AD). Hippocampal mRNA translation, required for memory consolidation, is defective in AD. Here, we show that genetic reduction of the translational repressors, Fragile X messenger ribonucleoprotein (FMRP) or eukaryotic initiation factor 4E (eIF4E)-binding protein 2 (4E-BP2), ameliorated the inhibition of hippocampal protein synthesis and memory impairment induced by AD-linked amyloid-b; oligomers (AbOs) in mice. Furthermore, systemic treatment with (2R,6R)-hydroxynorketamine (HNK), an active metabolite of the antidepressant ketamine, prevented deficits in hippocampal mRNA translation, long-term potentiation (LTP) and memory induced by AbOs in mice. HNK activated hippocampal signaling by extracellular signal-regulated kinase 1/2 (ERK1/2), mechanistic target of rapamycin (mTOR), and p70S6 kinase 1 (S6K1)/ribosomal protein S6 (S6), which promote protein synthesis and synaptic plasticity. S6 phosphorylation instigated by HNK was mediated by mTOR in hippocampal slices, while rescue of hippocampal LTP and memory in HNK-treated AbO-infused mice depended on ERK1/2 and, partially, on mTORC1. Remarkably, treatment with HNK corrected LTP and memory deficits in aged APP/PS1 mice. RNAseq analysis showed that HNK reversed aberrant signaling pathways that are upregulated in APP/PS1 mice, including inflammatory and hormonal responses and programmed cell death. Taken together, our findings demonstrate that upregulation of mRNA translation corrects deficits in hippocampal synaptic plasticity and memory in AD models. The results raise the prospect that HNK could serve as a therapeutic to reverse memory decline in AD. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Phenotypic screen-based discovery of a small molecule that can increase adult neurogenesis and improve memory

Play Episode Listen Later Jul 28, 2023

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.07.27.550845v1?rss=1 Authors: Davies, J., Hoerder-suabedissen, A., Musaelyan, K., Torroba, M., Daubney, J., Untermoser, N., Carter, T., Bauer, U., Walker, R., Harris, K. S., Bromhead, L., Suresh, M., Fouka, P., Li, Y., Davies, S., Webber, C., Bannerman, D., Terstappen, G., Russell, A., Szele, F. Abstract: Stem cells and neurogenesis persist in the postnatal and adult brain. Adult brain stem cells can be neuroprotective in disease and augment hippocampal-dependent cognitive function and thus are an important therapeutic target. Although many molecules have been discovered that regulate neurogenesis, few studies have attempted to amplify the process pharmacologically as a therapeutic goal. To address this gap, we used murine neurosphere cultures from the two major stem cell niches: the subventricular zone (SVZ) and the subgranular zone (SGZ). We screened compounds sharing pharmacophores with known inducers of neurogenesis and found several dozen proneurogenic compounds in an in vitro phenotypic screen. One, OXS-N1 was stable, and had acceptable absorption, distribution, metabolism, and excretion profiles in animal studies. OXS-N1 could increase neurogenesis in the SVZ and SGZ in WT mice after both intraperitoneal and oral administration. The number of newborn neurons (BrdU+/NeuN+) was increased; however, the number of activated stem cells (BrdU+/GFAP+) was not, suggesting an effect on neurogenesis independent of stem cell activation. This was supported by OXS-N1 increasing neurosphere differentiation but not proliferation. OXS-N1 also increased neurogenesis and improved performance in a Y maze cognitive task in PDGF-APPSw,Ind mice, a model of Alzheimer's disease. RNAseq of SVZ and SGZ neurospheres in turn showed that genes associated with synaptic function were significantly increased by OXS-N1. Our study demonstrates the utility of phenotypic screening for the identification of molecules that increase neurogenesis and might be of therapeutic relevance. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

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Investigating the basis of lineage decisions and developmental trajectories in the dorsal spinal cord through pseudotime analyses

Play Episode Listen Later Jul 26, 2023

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.07.24.550380v1?rss=1 Authors: Gupta, S., Heinrichs, E., Novitch, B. G., Butler, S. J. Abstract: Dorsal interneurons (dIs) in the spinal cord encode the perception of touch, pain, heat, itch, and proprioception. While previous studies using genetic strategies in animal models have revealed important insights into dI development, the molecular details by which dIs arise as distinct populations of neurons remain incomplete. We have developed a resource to investigate dI fate specification, by combining a single-cell RNA-Seq atlas of mouse ESC-derived dIs with pseudotime analyses. To validate this in silico resource as a useful tool, we have used it to first identify novel genes that are candidates for directing the transition states that lead to distinct dI lineage trajectories, and then validated them using in situ hybridization analyses in the developing mouse spinal cord in vivo. We have also identified a novel endpoint of the dI5 lineage trajectory, and found that dIs become more transcriptionally homogenous during terminal differentiation. Together, this study introduces a valuable tool for further discovery about the timing of gene expression during dI differentiation and uses it to clarify dI lineage relationships. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

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An integrated single-cell RNA-seq atlas of the mouse hypothalamic paraventricular nucleus links transcriptional and functional types

Play Episode Listen Later Jul 19, 2023

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.07.19.549666v1?rss=1 Authors: Berkhout, J., Poormoghadam, D., Yi, C.-X., Kalsbeek, A., Meijer, O., Mahfouz, A. Abstract: The hypothalamic paraventricular nucleus (PVN) is a highly complex brain region that is crucial for homeostatic regulation through neuroendocrine signalling, outflow of the autonomic nervous system, and projections to other brain areas. The past years, single-cell datasets of the hypothalamus have contributed immensely to the current understanding of the diverse hypothalamic cellular composition. While the PVN has been adequately classified functionally, its molecular classification is currently still insufficient. To address this, we created a detailed atlas of PVN transcriptional cell types by integrating various PVN single-cell datasets into a recently published hypothalamus single-cell transcriptome atlas. Furthermore, we functionally profiled transcriptional cell types, based on relevant literature, existing retrograde tracing data and existing single-cell data of a PVN-projection target region. In our PVN atlas dataset, we identify the well-known different neuropeptide types, each composed of multiple novel subtypes. We identify Avp-Tac1, Avp-Th, Oxt-Foxp1, Crh-Nr3c1 and Trh-Nfib as the most important neuroendocrine subtypes based on markers described in literature. To characterize the pre-autonomic functional population, we integrated a single-cell retrograde tracing study of spinally-projecting pre-autonomic neurons into our PVN atlas. We identify these (pre-sympathetic) neurons to co-cluster with the Adarb2+ clusters in our dataset. Finally, we identify expression of receptors for Crh, Oxt, Penk, Sst, and Trh in the dorsal motor nucleus of the vagus, a key region that pre-parasympathetic PVN neurons project to. Concluding, our study present a detailed overview of the transcriptional cell types of the murine PVN, and provides a first attempt to resolve functionality for the identified populations. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

llc types copy mouse functional integrated concluding meijer yi nucleus sst single cell trh hypothalamic biorxiv crh transcriptional rnaseq pvn oxt

Cannabidiol administration reduces the expression of genes involved in mitochondrial electron transport chain and ribosome biogenesis in mice CA1 neurons

Play Episode Listen Later Jul 11, 2023

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.07.10.548420v1?rss=1 Authors: Machado, J. P., Almeida, V., Zuardi, A. W., Hallak, J. E., Crippa, J. A., Schwambach Vieira, A. Abstract: Background: Cannabidiol (CBD), one of the main cannabinoids present in the female flowers of Cannabis sativa, has been a therapeutic alternative for a plurality of disorders. Previous investigation has already provided insights into the CBD molecular mechanism, however, there is no transcriptome data for CBD effects on hippocampal subfields. Here, we explore the transcriptomic changes in dorsal and ventral CA1 of adult mice hippocampus after 100 mg/kg of CBD administration (i.p.) for one or seven consecutive days. Methods: C57BL/6JUnib mice were divided into 4 groups treated with either vehicle or CBD for 1 or 7 days. The collected brains were sectioned and the hippocampal subregions were laser microdissected for RNA-Seq analysis. Data alignment, quantification and analysis were conducted with the STAR Aligner/DESeq2/clusterProfiler R-package pipeline. Results: We found changes in gene expression in CA1 neurons after single and multiple CBD administrations. Furthermore, the enrichment analysis of differentially expressed genes following 7 days of CBD administration indicates a widespread decrease in the expression levels of electron transport chain and ribosome biogenesis transcripts, while chromatin modifications and synapse organization transcripts were increased. Conclusion: This dataset provides a significant contribution toward advancing our comprehension of the mechanisms responsible for CBD effects on hippocampal neurons. The findings suggest that CBD prompts a significant reduction in energy metabolism genes and the protein translation machinery in CA1 neurons. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Single neuron analysis of aging associated changes in learning reveals progressive impairmentsin transcriptional plasticity

JCO Precision Oncology Conversations

Play Episode Listen Later Jun 25, 2023

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.06.23.546336v1?rss=1 Authors: Badal, K. K., Sadhu, A., McCracken, C., Raveendra, B. L., Lozano-Villada, S., Shetty, A. C., Gillette, P., Zhao, Y., Stommes, D., Fieber, L. A., Schmale, M. C., Mahurkar, A., Hawkins, R. D., Puthanveettil, S. V. Abstract: Molecular mechanisms underlying aging associated impairments in learning and long-term memory storage are poorly understood. Here we leveraged the single identified motor neuron L7 in Aplysia, which mediates a form of non-associative learning, sensitization of the siphon-withdraw reflex, to assess the transcriptomic correlates of aging associated changes in learning. RNAseq analysis of the single L7 motor neuron isolated following short-term or long-term sensitization training of 8,10 and 12 months old Aplysia, corresponding to mature, late mature and senescent stages, has revealed progressive impairments in transcriptional plasticity during aging. Specifically, we observed modulation of the expression of multiple lncRNAs and mRNAs encoding transcription factors, regulators of translation, RNA methylation, and cytoskeletal rearrangements during learning and their deficits during aging. Our comparative gene expression analysis also revealed the recruitment of specific transcriptional changes in two other neurons, the motor neuron L11 and the giant cholinergic neuron R2 whose roles in long-term sensitization were previously not known. Taken together, our analyses establish cell type specific progressive impairments in the expression of learning- and memory-related components of the transcriptome during aging. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

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Real-World NTRK Fusions and TRK Inhibitors in Veterans

Play Episode Listen Later Jun 21, 2023 28:15

JCO PO authors Dr. Michael J. Kelley and Dr. Katherine I. Zhou share insights into their JCO PO article, “Real-world Experience With Neurotrophic Tyrosine Receptor Kinase Fusion–positive Tumors and Tropomyosin Receptor Kinase Inhibitors in Veterans.” Host Dr. Rafeh Naqash, Dr. Kelley, and Dr. Zhou discuss the robust Veterans Affairs (VA) National Precision Oncology Program (NPOP), accurate identification of gene fusions, and toxicities landscape of TRK inhibitors. Click here to read the article! TRANSCRIPT Dr. Rafeh Naqash: Hello and welcome to JCO Precision Oncology Conversations, where we bring you engaging conversations with authors of clinically relevant and highly significant JCO PO articles. I'm your host, Dr. Rafeh Naqash, Social Media Editor for JCO Precision Oncology, and assistant professor at the OU Stephenson Cancer Center in the Division of Medical Oncology. Today, I'm thrilled to be joined by Dr. Michael J. Kelley. Dr. Kelley is the executive director of Oncology for the Department of Veterans Affairs. He's also the chief of Hematology-Oncology at the Durham VA Medical Center, and also a Professor of Medicine at the Duke University School of Medicine. And he's also a member of the Duke Cancer Institute. We are also joined by Dr. Katherine I. Zhou who is a Hematology-Oncology fellow at the Duke University. Dr. Zhou also spent time at the Duke Medical Center as part of her fellowship training, which I believe is how this project that was led by her came to fruition. So thank you both for joining today. This is going to be, hopefully, of very high interest to our listeners and I look forward to chatting with you both. Dr. Michael Kelley: Great, thanks for having us. Dr. Katherine Zhou: Thank you for having us. Dr. Rafeh Naqash: Thank you so much for joining. So I was very intrigued with this paper, and this paper follows a recent podcast that we had with Dr. Alexander Drilon, who's led some of the NTRK tropomyosin receptor kinase inhibitor studies that have been published in the last several years. And we had a very interesting discussion a couple of weeks back and I felt this was going to be a very interesting subsequent discussion into what was also an interesting discussion with Dr. Drilon. So what caught my attention is obviously the fact that you guys in this report, which is a real-world report, did not exactly see what we generally expect from clinical trials as far as response to target therapies in NTRK fusions. So before I ask you questions related to this project, one of the very interesting things at least I found was the fact is that the Veterans Health Administration is the largest integrated health system. Studies, whether conducted in the UK, for that matter European countries, or in Canada, they have integrated health systems which we do not. But we do have this advantage of the VA trying to do things in a very unique, centralized manner. So I wanted to ask Dr. Kelley first, how is it that you have implemented this National Precision Oncology Program, the NPOP as you call it, into the VA precision medicine workflow and how does it help in conducting research studies like the one that you published in the JCO Precision Oncology? Dr. Michael Kelley: Yeah, thanks for that question, Dr. Naqash. The NPOP started in 2016 as a national program and right from the beginning it grew out of an effort that was a joint collaboration between both clinical operations in the VA and the Research Office or the Office of Research and Development. It was designed from the very beginning to support discovery, new knowledge generation, and identifying patients for clinical trials in addition to bringing them best-in-class molecular testing and a consultation service. So it was initially funded out of the Cancer Moonshot 1 in 2016 when President Biden was then Vice President. The VA endorsed the model going forward in 2019 and now it's continued on and grown even bigger, it's expanded both in terms of scope and the complexity of the testing that's been done. So it was offered as services to facilities. They didn't have to do this, but I think they all saw the value of using NPOP to provide this group of services and that's what led to the generation of the robust underlying dataset that Dr. Zhou has used for this paper. Dr. Rafeh Naqash: Definitely. Thank you so much for that explanation. I did not know, and was not well aware, of how robust this program is. So I think it's a great learning opportunity for our listeners to know that a program like this exists. As we all know, there are different platforms, sequencing platforms, that each institution uses, whether it's commercial or whether it's in-house based. But the fact is, until and unless we have big pool datasets like the ones that you have generated or have access to, it's not easy to answer real-world questions. So first of all, I'd like to congratulate you and the rest of the VA administration to set up a program like this that hopefully is helping in matching the right patients to the right therapies and in clinical trial approvals. Now, before we take a deeper dive into the study that Dr. Zhou led, I did want to ask you, you have access to this amazing centralized platform, what are the kind of sequencing strategies or platforms that you use as part of this program? And is there an incorporation of molecular tumor boards to help understand some of these sequencing results that sometimes can be a little complicated to understand even for oncologists who look at these reports on a daily basis? So could you tell us a little bit more about that, Dr. Kelley? Dr. Michael Kelley: Yeah, certainly. So the VA contracts for the sequencing service, currently we're contracting with Foundation Medicine and Tempus for the comprehensive genomic profiling. There are some other services, and before we started using Foundation, there were two other companies that we used. There is a molecular tumor board. Our molecular oncology tumor board is designed primarily for case-based education. But there's also an asynchronous on-demand consultation service that occurs electronically because we have a unified electronic health record system. So any oncology provider in the country can enter a request through what's called an interfacility consult. It comes to a team, that team vets that, discusses it with the appropriate experts; that includes molecular oncologists, molecular pathologists. A lot of oncology pharmacists have been trained at a course that's at the University of Kentucky. And we have a lot of experience in doing this since that service was set up in 2016 as well, right from the beginning, because we understood the complexity of the data and the need for every oncologist across our enterprise to have access to the very best interpretation of that. We also have educational sessions that are integrated into the molecular tumor board time slot we call primers in terms of the underlying science of why you do the interpretations the way you do. And then there's also some additional education that we'll be endeavoring to offer to our staff and our oncologists coming up this year. Dr. Rafeh Naqash: Excellent. It sounds like you definitely have taken this into a very multidisciplinary approach where you're incorporating oncologists, pharmacists, and perhaps even genetic counselors and then, obviously, keeping the patient at the center and trying to find the best possible therapies that are most relevant for that individual. Now, going to Dr. Zhou's study here. Dr. Zhou, first of all, it's great to see a fellow lead a study and then especially, I think you're our first fellow on the podcast. We've had a lot of different individuals, but we have not had a fellow before. So thanks for coming. Could you tell us, for our listeners, what drove your interest into NTRK fusions? As we know, they are rare, something that is not commonly seen, and we do have clinical trial data in this space. So what was the idea behind looking at a real-world data set? Did you start out with a hypothesis or were you just interested to see how targeting these fusions in the real-world setting, actually, what kind of results does it lead to? Dr. Katherine Zhou: Yeah, well, first of all, thanks for the question. And I do just want to mention that although I did sort of bring this project to the finish line, it was started by another fellow, Vishal Vashistha. So just wanted to mention that. And I think the interest was really just that NTRK is such a rare fusion and just a difficult one to be able to study, like you said, in the real-world setting. And we have the advantage of having so much data through the VA and through NPOP, specifically. And so having seen such great results with the TRK inhibitors and clinical trials, I think there's this big question of how that translates into the real-world setting. We have the ability to do that with our large patient population. Dr. Rafeh Naqash: Excellent. And again, it's nice to acknowledge the support that you had from the other individual who co-led this study. Now, since you would have, I'm guessing, done most of the analysis here and looked into the whole idea of the kind of results that you saw—and from my understanding, you looked at the entire VA data set and tried to understand first the incidence or frequency of NTRK fusions and also responses to treatment, which I think is the main message—but could you tell us a little bit more about the data set? How did you acquire the data set, and what it took to analyze? Because obviously every project has a very unique story, and I'm guessing there's one very unique story here, since as a fellow you have limited time to do all this interesting work. So how did you navigate that and analyze and work with some of the things that you had to look at to get to the results? Dr. Katherine Zhou: Yeah, so again, this was work that was done with multiple people involved, of course. And we used what we had, the resources we had available, some tools we had available through the VA. So first, looking at NPOP and looking at patients who are sequenced through NPOP, we could just find all the ones who had an NTRK rearrangement of some kind. The second way we went about finding patients was through the CDW or the Corporate Data Warehouse where we could see which patients were prescribed larotrectinib or entrectinib and kind of go backwards from there and see which of those patients had NTRK alterations or specifically NTRK rearrangements. And so we combined the patients from both of those different methods to come up with our cohort at the end of 33 patients with NTRK rearrangements and 12 patients who are treated with TRK inhibitors. Dr. Rafeh Naqash: Excellent. Could you walk us through what was the subsequent analysis as far as how many NTRK fusions? I know you mentioned in the paper about DNA versus RNA-based testing. So how many were DNA-based, how many were RNA-based? I think there's some element of ctDNA-based testing also, or what tumor types those people had so that we get an understanding of what's the landscape of the findings that you had. Dr. Katherine Zhou: Sure. Since this is a real-world setting, as you may expect, the vast majority of the sequencing was done through tissue DNA sequencing, and that was the case. So for the 25 patients who were sequenced through NPOP that we found who had NTRK rearrangements, 23 of them had tissue DNA sequencing. And then one was tissue DNA RNA, and one was cell-free DNA sequencing. And so using that and being able to go back and look at how many patients have been sequenced in NPOP in total, we could kind of come up with a yield, although the numbers are very small. But we do see that there does seem to be probably a lower yield, for example, with cell-free DNA sequencing, as one might expect. And then looking at our total group of 33 patients, if we look at what types of cancers they had, we did have quite a few patients just based on prevalent tumors at the VA, I think, and in the population, prostate cancer was common, lung cancer, and then we had smaller numbers of colon and bladder, and I think there's a pancreatic cancer patient. We did have some of these rarer tumor types that more commonly have NTRK fusions as well, so like papillary thyroid carcinoma, and salivary gland cancers as well as soft tissue sarcomas. Dr. Rafeh Naqash: Question for you, Dr. Kelley, related to this data set: do you think that given that the denominator that you have is a unique population, the VA population, that's often males, they're usually above the age of 18, could the frequency have been influenced by that denominator where you may not have been able to capture, let's say, some of the rarer tumors that happen in the younger patient population, for that matter? Could that be a little bit of a bias here? Dr. Michael Kelley: Definitely. The population of veterans that have cancer that is treated in the Veterans Health Administration do represent generally adult males in the United States, but there is some skewing in certain regards. One of them is towards a higher frequency of smoking status. So not current smoking, which is actually about the same as the national average of about 11%, but the former smoking rate is about twice as high as it is in the rest of the United States. So we may have a lower frequency of some actionable variants in cancers in general because there's a higher etiological role for tobacco smoke in our population. But overall, looking at adult men if we look at like EGFR mutations, our incidence of EGFR mutations in adenocarcinoma is similar to what is reported in other real-world evidence bases from the United States, which is significantly lower than that which is found in academic medical centers. Dr. Rafeh Naqash: Thank you. I'm a big fan personally of real-world data sets. I do a lot of this with some other collaborators and generally, I do phase I trials, which is why I'm interested in precision medicine. And two weeks back, actually, I had a patient with prostate cancer, who ended up having NTRK fusion on a liquid biopsy. Now, you do talk about some of this related to in-frame or out-of-frame fusions and how that can have interesting aspects related to the kinase domain functionality and RNA expression. Dr. Zhou, for the sake of our listeners, could you briefly describe why understanding some of that is important and what implications it has? Dr. Katherine Zhou: Yeah, so I think the oncogenic NTRK fusion that we think of and that's being targeted by the TRK inhibitors is a fusion 5-prime of a protein that forms a dimer and on the 3-prime end is the kinase domain of the tropomyosin receptor kinase. And so you have to have some kind of a gene fusion that results in not only the transcription of that RNA fusion, RNA transcript, but then the translation of that fusion protein. So that needs to be, like you mentioned, that has to be in frame so that the entire protein is translated and expressed and it needs to include the kinase domain. It can't be the other end of the NTRK gene. And both of the genes need to be in the same orientation, of course. And then also the partner gene probably matters in that the ones that we know that actually cause activation of this oncogene are the ones that sort of spontaneously dimerize. And so that's a lot of requirements that we don't necessarily see when we just get, for example, a DNA sequencing result that says there's an NTRK rearrangement. Dr. Rafeh Naqash: Excellent way to describe the importance of understanding the functionality of the activated oncogenic fusion. Now, I know here in most of the patients that you have is DNA sequencing and I'm sure you'll talk about some of the results. And when you connect the results to the kind of data that you have, do you think not having the RNA assessment played a role in not knowing perhaps whether those fusions were functionally active? Dr. Katherine Zhou: Yes, I think we can't know for sure without having the RNA sequencing data. But certainly, that is a pattern in our small number of patients that we saw and something that makes sense just in terms of the mechanism of this oncogenic fusion protein. So I think that is a question of when should we be doing RNA sequencing to confirm that a fusion that we see on DNA sequencing is actually transcribed into RNA and how do we use RNA sequencing in a cost-effective and useful way to be able to detect more of these NTRK fusions that are actually clinically relevant. Dr. Rafeh Naqash: I absolutely agree with you and this is an ongoing debate. I know some platforms, commercial platforms that is, have incorporated RNA sequencing both bulk or whole transcriptome as part of their platform assessments, but it's still not made inroads into some other sequencing platforms that are commercially used. So it's an ongoing debate, but at the same time helping people understand that certain fusions need some level of RNA assessments to understand whether they're functionally active or not. Which again has implications, as you pointed out in terms of therapies are extremely relevant. Now, going to the results, which again was very interesting, could you tell us about the findings from the therapeutic standpoint that you observed and what your thoughts are about why you saw those results which were very different from what one would have expected? Dr. Katherine Zhou: Right. So in the clinical trials of larotrectinib and entrectinib, there were quite high objective response rates on the order of 60%, 70%, even almost 80%. In our very small real-world group of 12 patients who were treated with TRK inhibitors, nobody had an objective response and five patients had stable disease and everybody else, the other seven patients, progressed. And so the question is why did we see such a big difference compared to the trials? I sort of think of this as two big buckets. One is the population that we were looking at. So this is a real-world population. For example, in the clinical trials, there were almost no Black or African American patients, whereas here we had about 30%-40% Black or African American patients. Because it's a VA population, it was very heavily male, of course, the age groups are also different in that we didn't have children in the VA population whereas children were included in the trials. And the tumor types also differed because I think in the trials, which makes sense, there's a bias towards tumor types that have more NTRK fusions, and some of the tumor types we were looking at are just common tumor types like prostate and lung cancer where NTRK fusions are not common. But just because there are so many patients with these cancers, we did see them. And so certain of these groups, particularly certain racial and ethnic groups as well as certain tumor types, were not really represented in the trial to the extent that we can make conclusions about whether TRK inhibitors are effective in this population. So that's one. The second part, I think we've already talked about some, is just the method of detecting these NTRK fusions and how many of these NTRK fusions were actually truly producing oncogenic fusion proteins. And I tried to sort of categorize some of these fusions as being canonical in that they've been more studied. We know the partner gene, they are known to produce an oncogenic protein and to respond to TRK inhibitors. But actually of the four patients who had what we called canonical fusions, all four of them had stable disease at least, whereas the ones that were noncanonical mostly did not have a response or have even stable disease and mostly just progressed. And so then you wonder whether they even had the actual target protein we thought we were targeting. So this is where the real-world setting we're not doing the RNA sequencing or this additional testing to confirm that it's an oncogenic fusion protein. Dr. Rafeh Naqash: And I do see in your results there's a patient especially—you pointed out canonical and noncanonical fusions—you have a patient with a papillary thyroid cancer that I believe had a stable disease for close to two years plus. Is there anything interesting apart from an NTRK fusion in that specific patient where certain co-mutation could have played a role or certain other factors that do you think played into the fact that this patient had stable disease but didn't respond on the TRK inhibitor? Dr. Katherine Zhou: I don't have a great answer for that. I think this is one of the cancers that was well represented in the trials and that commonly has NTRK, or more likely has NTRK fusions. And this was a well-studied canonical NTRK fusion. So I think those are all reasons. The question of co-mutations I think is really interesting. We didn't have the data for every single patient, but for the ones we looked at a lot of the time, NTRK fusions are mutually exclusive with other driver mutations. So we didn't see a whole lot of commutations that we could sort of differentiate between responders or stable disease and progression. Dr. Rafeh Naqash: Thank you. Going to the toxicities, as a phase I trialist myself toxicity is the bane of my existence where we have to label toxicities, attribute toxicities, understand toxicities. The trial, obviously, as you very well know, that in the trials, they didn't have a lot of toxicities that caused patients to come off or required significant dose reductions, which is not the case compared to what you saw. Could you tell us a little bit about the landscape of toxicities for TRK inhibitors and what you saw in your cohort? That, again, I feel was interesting. Dr. Katherine Zhou: Of the 12 patients, I think two-thirds of them had either dose reduction or interruption or discontinuation, or some combination of the above. The toxicities we saw were more common than, or at least led to discontinuation and interruption and dose reduction more commonly than in the trials. But the toxicities we saw were also seen in the clinical trials. So LFT elevations, creatinine elevations, neurotoxicity, some cytopenias. We didn't actually see a whole lot of that, but those were present as well, and then some sort of nonspecific things like fatigue. And so, as much as we could tell from retrospective trial review, at least these were severe enough to lead to holding the drug. Dr. Rafeh Naqash: Thank you so much, Dr. Zhou. Question for you, Dr. Kelley. Putting this into perspective, the analysis that you did, how would you connect it to other real-world questions that one could answer using these kinds of data sets? So basically, what are the lessons learned from this amazing program that you guys have run successfully and are, I'm guessing, expanding in different directions? And how can you use a program like this to look at some of these unique questions using real-world data sets? Dr. Michael Kelley: There are a couple of, I guess, next steps for us that are based off this study and other information that we've gotten in other analyses from our NPOP data set. So, first of all, access to an RNA-Seq test. So that has been resolved to some extent, in that we now have two options for comprehensive genomic profiling, one of which does have RNA-Seq. And then the other approach that we're doing is to do more robust data generation. So we're going to be launching a study to collect prospective data on patients who are treated with off-label drugs. And as part of that, we will also have an on-label cohort for rare populations or any investigator in the VA who's interested in a particular drug or a particular genetic variant. They'll be able to tie into this protocol, and we will then collect data from across the system prospectively, which we think will improve the quality to some degree. And then thirdly, I think there's an opportunity to merge the initial generation of data in rare genetic types or other populations, which are highly selected by doing a distributed type of clinical trial where patients can be enrolled in prospective treatment trials. So we're not just generating data based on their real-world exposure to FDA-approved drugs, but we're generating data as we're developing the new drugs, we can have a much more heterogeneous and representative population of patients enrolled in clinical trials. So this is called the decentralized clinical trial model. We're starting to launch some trials with industry partners in this area to test out the model. If it works, I think we'll be able to help contribute to the knowledge that we all can use in terms of the patient types, the patient characteristics, but also some of the different tumor characteristics, and also to bring clinical trial opportunities to a more representative group. A lot of the initial clinical trials are done in urban areas, rural populations in VA are about a third of our patients live in rural areas, compared to only 14% of the country. So we think this is a very important diversity issue that should be addressed. Those are some of the ways that we're taking a lesson from this trial and other data that we have to sort of bring it forward. Dr. Rafeh Naqash: Those are excellent next steps and I think the kind of work that the VA is doing and this specific program, Precision Oncology Program, the NPOP program is doing, it's definitely setting up a unique standard in the United States where we have been limited by not having a centralized database. So setting something up of this sort hopefully will help answer a lot of these unique, interesting questions as you have access to data. And then the fact that you mentioned decentralized clinical trials and trying to cater to this access issue for patients in the VA system, I think that would be huge. And again, I congratulate you and your team on these efforts, and once again, thank you for joining us today and making JCO Precision Oncology a destination for your interesting work. We hope to see more of this work subsequently and hopefully, I get a chance to talk to you more about all the exciting stuff that you guys are leading within the VA health system. Thank you for listening to JCO Precision Oncology Conversations. Don't forget to give us a rating or review and be sure to subscribe so you never miss an episode. You can find all ASCO shows at asco.org/podcast. The purpose of this podcast is to educate and inform. This is not a substitute for professional medical care and is not intended for use in the diagnosis or treatment of individual conditions. Guests on this podcast express their own opinions, experience, and conclusions. Guest statements on the podcast do not express the opinions of ASCO. The mention of any product, service, organization, activity, or therapy should not be construed as an ASCO endorsement. Bios: Michael J. Kelley, MD, is Executive Director of Oncology for the Department of Veterans Affairs, Chief of Hematology-Oncology, Durham VA Medical Center, Professor of Medicine at Duke University School of Medicine and Member of the Duke Cancer Institute. Katherine I. Zhou, MD, PhD is a hematology-oncology fellow at Duke University. She also spends time at the Durham VA Medical Center as part of her fellowship training. COIs: Michael J. Kelley, MD Research Funding: Novartis (Inst), Bristol-Myers Squibb (Inst), Regeneron (Inst), Genentech (Inst), EQRx (Inst) Katherine I. Zhou, MD, PhD: No disclosures

Effects of Zoledronic Acid on Senescence and SASP Markers

Play Episode Listen Later May 15, 2023 3:43

A new research paper was published on the cover of Aging (Aging-US) Volume 15, Issue 9, entitled, “In vitro and in vivo effects of zoledronic acid on senescence and senescence-associated secretory phenotype markers.” Zoledronic acid has been found to reduce fracture risk and, in some studies, to decrease mortality in humans and extend lifespan and healthspan in animals. Because senescent cells accumulate with aging and contribute to multiple comorbidities, the non-skeletal actions of zoledronic acid could be due to senolytic (killing of senescent cells) or senomorphic (inhibition of the secretion of the senescence-associated secretory phenotype (SASP)) actions. In this new study, researchers Parinya Samakkarnthai, Dominik Saul, Lei Zhang, Zaira Aversa, Madison L. Doolittle, Jad G. Sfeir, Japneet Kaur, Elizabeth J. Atkinson, James R. Edwards, Graham G. Russell, Robert J. Pignolo, James L. Kirkland, Tamar Tchkonia, Laura J. Niedernhofer, David G. Monroe, Nathan K. Lebrasseur, Joshua N. Farr, Paul D. Robbins, and Sundeep Khosla from the Mayo Clinic, Phramongkutklao Hospital and College of Medicine, Eberhard Karls University, University of Minnesota, University of Oxford, and University of Sheffield tested the above hypothesis using multiple complementary approaches (in vitro, in vivo, and in silico) to evaluate possible effects of zoledronic acid on modulating cellular senescence. The researchers first performed in vitro senescence assays using human lung fibroblasts and DNA repair-deficient mouse embryonic fibroblasts, which demonstrated that zoledronic acid killed senescent cells with minimal effects on non-senescent cells. Next, in aged mice treated with zoledronic acid or vehicle for 8 weeks, zoledronic acid significantly reduced circulating SASP factors, including CCL7, IL-1β, TNFRSF1A, and TGFβ1 and improved grip strength. Analysis of publicly available RNAseq data from CD115+ (CSF1R/c-fms+) pre-osteoclastic cells isolated from mice treated with zoledronic acid demonstrated a significant downregulation of senescence/SASP genes (SenMayo). To establish that these cells are potential senolytic/senomorphic targets of zoledronic acid, the team used single cell proteomic analysis (cytometry by time of flight [CyTOF]) and demonstrated that zoledronic acid significantly reduced the number of pre-osteoclastic (CD115+/CD3e-/Ly6G-/CD45R-) cells and decreased protein levels of p16, p21, and SASP markers in these cells without affecting other immune cell populations. “Collectively, our findings demonstrate that zoledronic acid has senolytic effects in vitro and modulates senescence/SASP biomarkers in vivo. These data point to the need for additional studies testing zoledronic acid and/or other bisphosphonate derivatives for senotherapeutic efficacy.” DOI - https://doi.org/10.18632/aging.204701 Corresponding author - Sundeep Khosla - khosla.sundeep@mayo.edu About Aging-US Launched in 2009, Aging-US publishes papers of general interest and biological significance in all fields of aging research and age-related diseases, including cancer—and now, with a special focus on COVID-19 vulnerability as an age-dependent syndrome. Topics in Aging-US go beyond traditional gerontology, including, but not limited to, cellular and molecular biology, human age-related diseases, pathology in model organisms, signal transduction pathways (e.g., p53, sirtuins, and PI-3K/AKT/mTOR, among others), and approaches to modulating these signaling pathways. Please visit our website at https://www.Aging-US.com and connect with us: SoundCloud - https://soundcloud.com/Aging-Us Facebook - https://www.facebook.com/AgingUS/ Twitter - https://twitter.com/AgingJrnl Instagram - https://www.instagram.com/agingjrnl/ YouTube - https://www.youtube.com/@AgingJournal LinkedIn - https://www.linkedin.com/company/aging/ Pinterest - https://www.pinterest.com/AgingUS/ Media Contact 18009220957 MEDIA@IMPACTJOURNALS.COM

Rapid effects of valproic acid on the fetal brain transcriptome: Implications for brain development and autism

Play Episode Listen Later May 2, 2023

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.05.01.538959v1?rss=1 Authors: Dorsey, S. G., Mocci, E., Lane, M. V., Krueger, B. K. Abstract: There is an increased incidence of autism among the children of women who take the anti-epileptic, mood stabilizing drug, valproic acid (VPA) during pregnancy, moreover, exposure to VPA in utero causes autistic-like symptoms in rodents and non-human primates. Analysis of RNAseq data ob-tained from fetal mouse brains 3 hr after VPA administration revealed that VPA significantly [p(FDR) less than or equal to 0.025] increased or decreased the expression of approximately 7,300 genes. No significant sex dif-ferences in VPA-induced gene expression were observed. Expression of genes associated with neurodevelopmental disorders such as autism as well as neurogenesis, axon growth and synapto-genesis, GABAergic, glutaminergic and dopaminergic synaptic transmission, perineuronal nets, and circadian rhythms was dysregulated by VPA. Moreover, expression of 400 autism risk genes was significantly altered by VPA. In addition, expression of 247 genes that have been reported to play fundamental roles in the development of the nervous system, but are not linked to autism by GWAS, was significantly increased or decreased by VPA. The goal of this study was to identify mouse genes that are: (a) significantly up- or down-regulated by VPA in the fetal brain and (b) known to be associated with autism and/or to play a role in embryonic neurodevelopmental processes, perturbation of which has the potential to alter brain connectivity in the postnatal and adult brain. The set of genes meeting these criteria provides potential targets for future hypothesis-driven approaches to elucidating the proximal underlying causes of defective brain connectivity in neuro-developmental disorders such as autism. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

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GraphComm: A Graph-based Deep Learning Method to Predict Cell-Cell Communication in single-cell RNAseq data

Play Episode Listen Later Apr 27, 2023

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.04.26.538432v1?rss=1 Authors: So, E., Hayat, S., Kadambat Nair, S., Wang, B., Haibe-Kains, B. Abstract: Cell-cell interactions coordinate various functions across cell-types in health and disease. Novel single-cell techniques allow us to investigate cellular crosstalk at single-cell resolution. Cell-cell interactions are mediated by underlying gene-gene networks, however most current methods are unable to account for complex inter-connections within the cell as well as incorporate the effect of pathway and protein complexes on interactions. Therefore, to utilise relations of cells to ligands and receptors as well as multiple annotations, we present GraphComm - a new graph-based deep learning method for predicting cell-cell communication in single-cell RNAseq datasets. By learning off of a prior model and fine-tuning a network on single-cell transcriptomic data, GraphComm is able to predict cell-cell communication (CCC) activity across cells, and its impact on downstream pathways, spatially adjacent cells and changes due to drug perturbations. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

data llc method copy wang predict ccc deep learning graphs hayat single cell biorxiv rnaseq

Ep 118: Continuous Glucose Monitors (CGM) with Dr. Michael Snyder, Chair of Genetics and Director of Genomics and Personalised Medicine at Stanford University

Run with Fitpage

Play Episode Listen Later Apr 26, 2023 55:37

In this episode of Run with Fitpage, we had the pleasure of hosting the world's leading genomicist - Dr. Michael Snyder. Vikas and Dr. Snyder talk about CGMs and other variables in one of the most insightful conversations of Run with Fitpage so far.Michael Snyder is the Stanford Ascherman Professor and Chair of Genetics and the Director of the Center of Genomics and Personalized Medicine. He received his Ph.D. training at the California Institute of Technology and carried out postdoctoral training at Stanford University. Dr. Snyder has pioneered the use of “big data” and multi-omics to advance scientific discovery and transform healthcare. His laboratory has invented many technologies that are widely used in medicine and research, including methods for characterizing genomes and their products (e.g. RNA-Seq, NGS paired-end sequencing, ChIP-Chip and later Chip-Seq, protein arrays, machine learning for disease gene discovery).Snyder Lab was the first to perform a large-scale functional genomics project in any organism and has developed many technologies in genomics and proteomics. He has also co-founded January AI and Iollo. Listen to this episode with a pen and paper to learn more about Continous Glucose Monitoring and much more!Important resources from the episode:innovations.stanford.edu/wearablesq.biowww.iollo.comwww.january.aiRead more about Dr. Snyder's Research here.About Vikas Singh:Vikas Singh, an MBA from Chicago Booth, worked at Goldman Sachs, Morgan Stanley, APGlobale, and Reliance before coming up with the idea of democratizing fitness knowledge and helping beginners get on a fitness journey. Vikas is an avid long-distance runner, building fitpage to help people learn, train, and move better.For more information on Vikas, or to leave any feedback and requests, you can reach out to him via the channels below:Instagram: @vikas_singhhLinkedIn: Vikas SinghGmail: vikas@fitpage.inTwitter: @vikashsingh1010Subscribe To Our Newsletter For Weekly Nuggets of Knowledge!

Coronary Artery Disease Risk Gene PRDM16 is Preferentially Expressed in Vascular Smooth Muscle Cells and a Potential Novel Regulator of Smooth Muscle Homeostasis

Play Episode Listen Later Apr 4, 2023

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.04.03.535461v1?rss=1 Authors: Dong, K., He, X., Hu, G., Yao, Y., Zhou, J. Abstract: Objective: Vascular smooth muscle cells (VSMCs) are the primary contractile component of blood vessels and can undergo phenotypic switching from a contractile to a synthetic phenotype in vascular diseases such as coronary artery disease (CAD). This process leads to decreased expression of SMC lineage genes and increased proliferative, migratory and secretory abilities that drive disease progression. Super-enhancers (SE) and occupied transcription factors are believed to drive expression of genes that maintain cell identify and homeostasis. The goal of this study is to identify novel regulator of VSMC homeostasis by screening for SE-regulated transcription factors in arterial tissues. Approach and Results: We characterized human artery SEs by analyzing the enhancer histone mark H3K27ac ChIP-seq data of multiple arterial tissues. We unexpectedly discovered the transcription factor PRDM16, a GWAS identified CAD risk gene with previously well-documented roles in brown adipocytes but with an unknown function in vascular disease progression, is enriched with artery-specific SEs. Further analysis of public bulk RNA-seq and scRNA-seq datasets, as well as qRT-PCR and Western blotting analysis, demonstrated that PRDM16 is preferentially expressed in arterial tissues and in contractile VSMCs but not in visceral SMCs, and down-regulated in phenotypically modulated VSMCs. To explore the function of Prdm16 in vivo, we generated Prdm16 SMC-specific knockout mice and performed histological and bulk RNA-Seq analysis of aortic tissues. SMC-deficiency of Prdm16 does not affect the aortic morphology but significantly alters expression of many CAD risk genes and genes involved in VSMC phenotypic modulation. Specifically, Prdm16 negatively regulates the expression of Tgfb2 that encodes for an upstream ligand of TGF-{beta} signaling pathway, potentially through binding to the promoter region of Tgfb2. These transcriptomic changes likely disrupt VSMC homeostasis and predispose VSMCs to a disease state. Conclusions: Our results suggest that the CAD risk gene PRDM16 is preferentially expressed in VSMCs and is a novel regulator of VSMC homeostasis. Future studies are warranted to investigate its role in VSMCs under pathological conditions such as atherosclerosis. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Avoiding false discoveries: Revisiting an Alzheimer's disease snRNA-Seq dataset

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Play Episode Listen Later Apr 2, 2023

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.04.01.535040v1?rss=1 Authors: Murphy, A. E., Fancy, N., Skene, N. G. Abstract: Arising From: Mathys, H. et al. Nature (2019). https://doi.org/10.1038/s41586-019-1195-2 Mathys et al., conducted the first single-nucleus RNA-Seq study (snRNA-Seq) of Alzheimer's disease (AD). The authors profiled the transcriptomes of approximately 80,000 cells from the prefrontal cortex, collected from 48 individuals - 24 of which presented with varying degrees of AD pathology. With bulk RNA-Seq, changes in gene expression across cell types can be lost, potentially masking the differentially expressed genes (DEGs) across different cell types. Through the use of single-cell techniques, the authors benefitted from increased resolution with the potential to uncover cell type-specific DEGs in AD for the first time. However, there were limitations in both their data processing and quality control and their differential expression analysis. Here, we correct these issues with best-practice approaches to snRNA-Seq processing and differential expression, resulting 892 times fewer differentially expressed genes at a false discovery rate (FDR) of 0.05. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Repeated exposure to high-THC Cannabis smoke during gestation alters sex ratio, behavior, and amygdala gene expression of Sprague Dawley rat offspring

Play Episode Listen Later Mar 25, 2023

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.03.23.533930v1?rss=1 Authors: Sandini, T. M., Onofrychuk, T. J., Roebuck, A. J., Hammond, A., Udenze, D., Hayat, S., Herdzik, M. A., McElroy, D. L., Orvold, S. N., Greba, Q., Laprairie, R. B., Howland, J. G. Abstract: Due to the recent legalization of Cannabis in many jurisdictions and the consistent trend of increasing THC content in Cannabis products, there is an urgent need to understand the impact of Cannabis use during pregnancy on fetal neurodevelopment and behavior. To this end, we repeatedly exposed female Sprague-Dawley rats to Cannabis smoke from gestational days 6 to 20 (n=12; Aphria Mohawk; 19.51% THC, less than 0.07% cannabidiol) or room-air as a control (n=10) using a commercially available system. Maternal reproductive parameters, behavior of the adult offspring, and gene expression in the offspring amygdala were assessed. Body temperature was decreased in dams following smoke exposure and more fecal boli were observed in the chambers before and after smoke exposure in those dams exposed to smoke. Maternal weight gain, food intake, gestational length, litter number, and litter weight were not altered by exposure to Cannabis smoke. A significant increase in the male-to-female ratio was noted in the Cannabis-exposed litters. In adulthood, both male and female Cannabis smoke-exposed offspring explored the inner zone of an open field significantly less than control offspring. Gestational Cannabis smoke exposure did not affect behavior on the elevated plus maze test or social interaction test in the offspring. Cannabis offspring were better at visual pairwise discrimination and reversal learning tasks conducted in touchscreen-equipped operant conditioning chambers. Analysis of gene expression in the adult amygdala using RNAseq revealed subtle changes in genes related to development, cellular function, and nervous system disease in a subset of the male offspring. These results demonstrate that repeated exposure to high-THC Cannabis smoke during gestation alters maternal physiological parameters, sex ratio, and anxiety-like behaviors in the adulthood offspring. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

A new vision in inflammatory disease: RNAseq led precision medicine, Tariq Kassum, CEO, Celsius Tx

Biotech 2050 Podcast

Play Episode Listen Later Mar 22, 2023 26:07

Synopsis: Tariq Kassum, M.D. is the CEO of Celsius Therapeutics, a company pioneering new precision medicines in inflammatory disease by harnessing the power of single-cell RNA sequencing and human biology at scale. Tariq shares his unique journey from med school, to working in Wall Street as a biotech investment banker and stock analyst, to the corporate side working at Millennium Pharmaceuticals and Takeda, and finally the innovative biotech world. He discusses the importance of learning to adapt to each environment in order to remain productive and successful, and building meaningful relationships with coworkers and mentors. He also talks about what it will take for the biopharma executive of the future to be successful. Biography: Tariq Kassum brings 20 years of experience in corporate development, strategy and business leadership to Celsius. He joined the company in 2019 from Obsidian Therapeutics, where he was a co-founder and served as chief operating officer and head of corporate development. During this time, Tariq helped build Obsidian into a leading platform technology company and played a central role in the company's strategic partnership with Celgene. Prior to Obsidian, Tariq spent seven years with Millennium Pharmaceuticals and Takeda, most recently as vice president, business development and strategy for Takeda Oncology, responsible for transactions, collaborations, alliance management and strategic planning. Before that, he led Takeda's global corporate development efforts, where he managed multiple acquisitions and divestitures in the U.S. and internationally. He was also part of the business development team at Millennium Pharmaceuticals. Prior to Takeda, Tariq was an analyst covering healthcare equities for institutional investment firms, where he led scientific due diligence and investment decisions on numerous companies and pharmaceutical compounds across multiple therapeutic areas. He began his career as an investment banker with CIBC World Markets, serving clients in the biotechnology and specialty pharmaceuticals industries.

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Spatial and single-cell transcriptomics reveal neuron-astrocyte interplay in long-term memory

Play Episode Listen Later Mar 21, 2023

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.03.20.533566v1?rss=1 Authors: Sun, W., Liu, Z., Jiang, X., Chen, M. B., Dong, H., Liu, J., Sudhof, T. C., Quake, S. R. Abstract: Memory encodes past experiences, thereby enabling future plans. The basolateral amygdala (BLA) is a center of salience networks that underlie emotional experience and thus plays a key role in long-term fear memory formation. Here we used spatial and single-cell transcriptomics to illuminate the cellular and molecular architecture of the role of the basolateral amygdala in long-term memory. We identified transcriptional signatures in subpopulations of neurons and astrocytes that were memory-specific and persisted for weeks. These transcriptional signatures implicate neuropeptide signaling, mitogen-activated protein kinase (MAPK), brain-derived neurotrophic factor (BDNF), cAMP response element-binding protein (CREB), ubiquitination pathways, and synaptic connectivity in long-term memory. We also discovered that a neuronal sub-population, defined by increased Penk expression and decreased Tac expression, constitutes the most prominent component of the BLA's memory engram. These transcriptional changes were observed both with single-cell RNAseq and with single-molecule spatial transcriptomics in intact slices, thereby providing a rich spatial map of a memory engram. The spatial data enabled us to show that this neuronal subpopulation further interacts with spatially related astrocytes that are essential for memory consolidation, indicating that neurons require interactions with astrocytes to encode long term memory. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

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Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing

Play Episode Listen Later Mar 18, 2023

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.03.16.532873v1?rss=1 Authors: Zhang, A., Jin, L., Yao, S., Matsuyama, M., Velthoven, C. v., Sullivan, H., Sun, N., Kellis, M., Tasic, B., Wickersham, I. R., Chen, X. Abstract: Mapping the connectivity of diverse neuronal types provides the foundation for understanding the structure and function of neural circuits. High-throughput and low-cost neuroanatomical techniques based on RNA barcode sequencing have the potential to achieve circuit mapping at cellular resolution and a brain-wide scale, but existing Sindbis virus-based techniques can only map long-range projections using anterograde tracing approaches. Rabies virus can complement anterograde tracing approaches by enabling either retrograde labeling of projection neurons or monosynaptic tracing of direct inputs to genetically targeted postsynaptic neurons. However, barcoded rabies virus has so far been only used to map non-neuronal cellular interactions in vivo and synaptic connectivity of cultured neurons. Here we combine barcoded rabies virus with single-cell and in situ sequencing to perform retrograde labeling and transsynaptic labeling in the mouse brain. We sequenced 96 retrogradely labeled cells and 232 transsynaptically labeled cells using single-cell RNAseq, and 4,130 retrogradely labeled cells and 2,914 transsynaptically labeled cells in situ. We determined the transcriptomic identities of rabies virus-infected cells robustly using both single-cell RNA-seq and in situ sequencing. We then distinguished long-range projecting cortical cell types from multiple cortical areas and identified cell types with converging or diverging synaptic connectivity. Combining in situ sequencing with barcoded rabies virus thus complements existing sequencing-based neuroanatomical techniques and provides a potential path for mapping synaptic connectivity of neuronal types at scale. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

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Single cell RNA sequencing in isogenic FUS and TARDBP mutant ALS lines reveals early mitochondrial dysfunction as a common pathway in motor neurons

Play Episode Listen Later Mar 16, 2023

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.03.16.531876v1?rss=1 Authors: Schweingruber, C., Nijssen, J., Mechtersheimer, J., Reber, S., Keuper, M., Mei, I., Aguila Benitez, J., O'Brien, N., Jastroch, M., Ruepp, M.-D., Hedlund, E. Abstract: Mutations in the RNA/DNA-binding proteins FUS and TDP-43 cause amyotrophic lateral sclerosis (ALS) with distinct neuropathological features. It is currently unclear how these gene mutations lead to selective motor neuron death and if there are common mechanisms across disease causations. Using single cell RNA sequencing of neurons derived from isogenic induced pluripotent stem cell lines, we show that motor neurons harbouring FUS P525L or FUS R495X mutations show a 4.9- to 15.5-fold larger transcriptional response than interneurons. About 20% (737 DEGs) of transcripts were coregulated across FUS R495X and P525L motor neurons and by comparing to a FUS knockout line we could discern that 48% (355 DEGs) were part of gain-of-function of FUS. Cross-comparing with isogenic TDP-43 M337V motor neurons, identified common mitochondrial dysfunction across FUS gain-of-function and TARDBP gene mutations, as did comparison with published RNA-Seq data from C9orf72-ALS motor neurons. Metabolic assessment confirmed a decrease in mitochondrial respiration and ATP turnover in mutant FUS and TARDBP lines and live cell microscopy showed a decrease in mitochondrial motility across ALS motor axons. Thus, we have identified early mitochondrial dysfunction in motor neurons shared across ALS-causative mutations, that could have major implications for their survival and which could be targeted therapeutically. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

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The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch.

Play Episode Listen Later Mar 14, 2023

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.03.14.532536v1?rss=1 Authors: Rolland, L., Faucherre, A., Mancilla Abaroa, J., Drouard, A., Jopling, C. Abstract: Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals, these changes trigger an adaptive cardiomyocyte hypertrophic response which, if the damage is extensive, will ultimately lead to pathological hypertrophy and heart failure. Conversely, in response to extensive myocardial damage, cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish, changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based, on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals, RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore, using a cyclic cell stretch assay, we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

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Crosstalk in skin: Loss of desmoglein 1 in keratinocytes inhibits BRAFV600E-induced cellular senescence in human melanocytes

Play Episode Listen Later Feb 17, 2023

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.02.16.528886v1?rss=1 Authors: Tong, X., Burks, H. E., Ren, Z., Koetsier, J. L., Roth-Carter, Q. R., Green, K. J. Abstract: Melanoma arises from transformation of melanocytes in the basal layer of the epidermis where they are surrounded by keratinocytes, with which they interact through cell contact and paracrine communication. Considerable effort has been devoted to determining how the accumulation of oncogene and tumor suppressor gene mutations in melanocytes drive melanoma development. However, the extent to which alterations in keratinocytes that occur in the developing tumor niche serve as extrinsic drivers of melanoma initiation and progression is poorly understood. We recently identified the keratinocyte-specific cadherin, desmoglein 1 (Dsg1), as an important mediator of keratinocyte:melanoma cell crosstalk, demonstrating that its chronic loss, which can occur through melanoma cell-dependent paracrine signaling, promotes behaviors that mimic a malignant phenotype. Here we address the extent to which Dsg1 loss affects early steps in melanomagenesis. RNA-Seq analysis revealed that paracrine signals from Dsg1-deficient keratinocytes mediate a transcriptional switch from a differentiated to undifferentiated cell state in melanocytes expressing BRAFV600E, a driver mutation commonly present in both melanoma and benign nevi and reported to cause growth arrest and oncogene-induced senescence (OIS). Of ~220 differentially expressed genes in BRAFV600E cells treated with Dsg1-deficient conditioned media (CM), the laminin superfamily member NTN4/Netrin-4, which inhibits senescence in endothelial cells, stood out. Indeed, while BRAFV600E melanocytes treated with Dsg1-deficient CM showed signs of senescence bypass as assessed by increased senescence-associated {beta}-galactosidase activity and decreased p16, knockdown of NTN4 reversed these effects. These results suggest that Dsg1 loss in keratinocytes provides an extrinsic signal to push melanocytes towards oncogenic transformation once an initial mutation has been introduced. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

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Endothelial Cells are Heterogeneous in Different Brain Regions and are Dramatically Altered in Alzheimer's Disease

Play Episode Listen Later Feb 16, 2023

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.02.16.528825v1?rss=1 Authors: Bryant, A. G., Li, Z., Jayakumar, R., Serrano-Pozo, A., Woost, B., Hu, M., Woodbury, M. E., Wachter, A., Lin, G., Kwon, T., Talanian, R. V., Biber, K., Karran, E. H., Hyman, B. T., Das, S., Bennett, R. E. Abstract: Vascular endothelial cells play an important role in maintaining brain health, but their contribution to Alzheimer's disease (AD) is obscured by limited understanding of the cellular heterogeneity in normal aged brain and in disease. To address this, we performed single nucleus RNAseq on tissue from 32 AD and non-AD donors each with five cortical regions: entorhinal cortex, inferior temporal gyrus, prefrontal cortex, visual association cortex and primary visual cortex. Analysis of 51,586 endothelial cell nuclei revealed unique gene expression patterns across the five regions in non-AD donors. Alzheimer's brain endothelial cell nuclei were characterized by upregulated protein folding genes and distinct transcriptomic differences in response to amyloid beta plaques and cerebral amyloid angiopathy. This dataset demonstrates previously unrecognized regional heterogeneity in the endothelial cell transcriptome in both aged non-AD and AD brain. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

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Butyrate endows extraocular muscle stem cell-like transcriptomic patterns that ameliorate satellite cell depletion and denervation to slow ALS progression

Play Episode Listen Later Feb 13, 2023

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.02.12.528218v1?rss=1 Authors: Li, A., Yi, J., Li, X., Dong, L., Ostrow, L. W., Ma, J., Zhou, J. Abstract: Amyotrophic lateral sclerosis (ALS) is a fatal neuromuscular disease that affects all voluntary muscles in the body, leading to paralysis and respiratory failure, while the extraocular muscles (EOMs) are largely spared even at the end-stage of ALS. Through whole-mount muscle imaging, we detected severe denervation along with depletion of Pax7+ satellite cells (SCs) peri-neuromuscular junction (NMJ) in hindlimb and diaphragm muscles of end-stage SOD1G93A mice (a familial ALS mouse model), but not in EOMs. Upon isolating SCs from different muscles using fluorescence activated cell sorting (FACS), the FACS profiles of hindlimb and diaphragm SCs of G93A mice exhibited activation and depletion phenotypes but not in wildtype controls. Importantly, both wildtype and G93A EOM SCs exhibited spontaneous activation behavior without significant differences in abundance. Examination of Pax7+ and Ki67+ cell ratios and RNA-Seq of SCs cultured in growth and differentiation medium revealed that EOM SCs maintained renewability and stemness better than diaphragm and hindlimb counterparts, especially in differentiation-favoring environments. Comparative functional annotation analyses indicate enrichment of axon guidance molecules, such as Cxcl12, in cultured EOM SCs. In neuromuscular coculture experiments, overexpressing Cxcl12 in G93A hindlimb SC-derived myotubes enhanced motor neuron axon extension and improved innervation, partially replicating the multi-innervation property of EOM SC-derived myotubes. The unique SC homeostasis regulation and the production of axon guidance molecules including Cxcl12 may explain the ALS resistant nature of EOMs. Intriguingly, feeding G93A mice with sodium butyrate extended the life span of G93A mice, alleviated NMJ denervation and SCs depletion. Butyrate treatment promoted renewability and stemness of cultured G93A hindlimb and diaphragm SCs, as well as Cxcl12 expression. Thus, butyrate-induced EOM SC-like transcriptomic patterns may contribute to its beneficiary effects observed in G93A mice. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

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Severe neurometabolic phenotype in npc1-/- zebrafish with a C-terminal mutation

Play Episode Listen Later Feb 10, 2023

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.02.09.527822v1?rss=1 Authors: Quelle Regaldie, A., Gandoy Fieiras, N., R Villamayor, P., Maceiras, S., Losada, A. P., Folgueira, M., Cabezas, P., Barreiro-Iglesias, A., Villar-Lopez, M., Quiroga-Berdeal, M. I., Sanchez, L., Sobrido, M. J. Abstract: Niemann Pick disease type C (NPC) is an autosomal recessive neurodegenerative lysosomal disorder characterized by an accumulation of lipids in different organs. Clinical manifestations can start at any age and include hepatosplenomegaly, intellectual impairment, and cerebellar ataxia. NPC1 is the most common causal gene, with over 460 different mutations with heterogeneous pathological consequences. We generated a zebrafish NPC1 model by CRISPR/Cas9 carrying a homozygous mutation in exon 22, which encodes the end of the cysteine-rich luminal loop of the protein. This is the first zebrafish model with a mutation in this gene region, which is frequently involved in the human disease. We observed a high lethality in npc1 mutants, with all larvae dying before reaching the adult stage. Npc1 mutant larvae were smaller than wild type (wt) and their motor function was impaired. We observed vacuolar aggregations positive to cholesterol and sphingomyelin staining in the liver, intestine, renal tubules and cerebral gray matter of mutant larvae. RNAseq comparison between npc1 mutants and controls showed 249 differentially expressed genes, including genes with functions in neurodevelopment, lipid exchange and metabolism, muscle contraction, cytoskeleton, angiogenesis, and hematopoiesis. Lipidomic analysis revealed significant reduction of cholesteryl esters and increase of sphingomyelin in the mutants. Compared to previously available zebrafish models, our model seems to recapitulate better the early onset forms of the NPC disease. Thus, this new model of NPC will allow future research in the cellular and molecular causes/consequences of the disease and on the search for new treatments. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

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A Single-Cell RNA-Seq Analysis Unravels The Heterogeniety Of Primary Cultured Human Corneal Endothelial Cells

Play Episode Listen Later Feb 10, 2023

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.02.09.527872v1?rss=1 Authors: Catala, P., Groen, N., LaPointe, V., Dickman, M. M. Abstract: The primary culture of donor-derived human corneal endothelial cells (CECs) is a promising cell therapy. It confers the potential to treat multiple patients from a single donor, alleviating the global donor shortage. Nevertheless, this approach has limitations preventing its adoption, particularly culture protocols allow limited expansion of CECs and there is a lack of clear parameters to identify therapy-grade CECs. To address this limitation, a better understanding of the molecular changes arising from the primary culture of CECs is required. Using single-cell RNA sequencing on primary cultured CECs, we identify their variable transcriptomic fingerprint at the single cell level, provide a pseudo temporal reconstruction of the changes arising from primary culture, and suggest markers to assess the quality of primary CEC cultures. This research depicts a deep transcriptomic understanding of the cellular heterogeneity arising from the primary expansion of CECs and sets the basis for further improvement of culture protocols and therapies. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

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Dissecting 16p11.2 hemi-deletion to study sex-specific striatal phenotypes of neurodevelopmental disorders

Play Episode Listen Later Feb 9, 2023

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.02.09.527866v1?rss=1 Authors: Kim, J., Vanrobaeys, Y., Peterson, Z., Kelvington, B., Gaine, M. E., Nickl-Jockschat, T., Abel, T. Abstract: Neurodevelopmental disorders (NDDs) are polygenic in nature and copy number variants (CNVs) are ideal candidates to study the nature of this polygenic risk. The disruption of striatal circuits is considered a central mechanism in NDDs. The 16p11.2 hemi-deletion (16p11.2 del) is one of the most common CNVs associated with NDD, and 16p11.2 del/+ mice show sex-specific striatum-related behavioral phenotypes. However, the critical genes among the 27 genes in the 16p11.2 region that underlie these phenotypes remain unknown. Previously, we applied a novel strategy to identify candidate genes associated with the sex-specific phenotypes of 16p11.2 del/+ mice and identified 3 genes of particular importance within the deleted region: thousand and one amino acid protein kinase 2 (Taok2), seizure-related 6 homolog-like 2 (Sez6l2), and major vault protein (Mvp). Using the CRISPR/Cas9 technique, we generated 3 gene hemi-deletion (3g del/+) mice carrying null mutations inTaok2, Sez6l2, and Mvp. We assessed striatum-dependent phenotypes of these 3g del/+ mice in behavioral, molecular, and imaging studies. Hemi-deletion of Taok2, Sez6l2, and Mvp induces sex-specific behavioral alterations in striatum-dependent behavioral tasks, specifically male-specific hyperactivity and impaired motivation for reward seeking, resembling behavioral phenotypes of 16p11.2 del/+ mice. Moreover, RNAseq analysis revealed that 3g del/+ mice exhibit gene expression changes in the striatum similar to 16p11.2 del/+ mice, but only in males. Pathway analysis identified ribosomal dysfunction and translation dysregulation as molecular mechanisms underlying male-specific, striatum-dependent behavioral alterations. Together, the mutation of 3 genes within the 16p11.2 region phenocopies striatal sex-specific phenotypes of 16p11.2 del/+ mice, unlike single gene mutation studies. These results support the importance of a polygenic approach to study NDDs and our novel strategy to identify genes of interest using gene expression patterns in brain regions, such as the striatum, which are impacted in these disorders. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

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Co-Targeting IL-6 and EGFR signaling for the treatment of schwannomatosis and associated pain

Play Episode Listen Later Feb 6, 2023

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.02.06.527377v1?rss=1 Authors: Yin, Z., Wu, L., Zhang, Y., Sun, Y., Chen, J. W., Subudhi, S., Ho, W., Lee, G. Y., Wang, A., Gao, X., Ren, J., Zhu, C., Zhang, N., Ferraro, G. B., Muzikansky, A., Zhang, L., Stemmer-Rachamimov, A., Mao, J., Plotkin, S. R., Xu, L. Abstract: Patients with Schwannomatosis (SWN) overwhelmingly present with intractable, debilitating chronic pain. There are no effective therapies to treat SWN. The drivers of pain response and tumor progression in SWN are not clear. The pain is not proportionally linked to tumor size and is not always relieved by tumor resection, suggesting that mechanisms other than mechanical nerve compression exist to cause pain. SWN research is limited by the lack of clinically-relevant models. Here, we established novel patient-derived xenograft (PDX) models, dorsal root ganglia (DRG) imaging model, and combined with single-cell resolution intravital imaging and RNASeq, we discovered: i) schwannomas on the peripheral nerve cause macrophage influx into the DRG, via secreting HMGB1 to directly stimulate DRG neurons to express CCL2, the key macrophage chemokine, ii) once recruited, macrophages cause pain response via overproduction of IL-6, iii) IL-6 blockade in a therapeutic setting significantly reduces pain but has modest efficacy on tumor growth, iv) EGF signaling is a potential driver of schwannoma growth and escape mechanism from anti-IL6 treatment, and v) combined IL-6 and EGFR blockade simultaneously controlled pain and tumor growth in SWN models. Our findings prompted the initiation of phase II clinical trial (NCT05684692) for pain relief in patients with SWN. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Anti-PD-1 Immune Checkpoint Therapy Resistance, Macrophages and the Wnt Pathway

Play Episode Listen Later Jan 5, 2023 3:34

A new research paper was published in Oncotarget's Volume 13 on December 20, 2022, entitled, “Resistance of MMTV-NeuT/ATTAC mice to anti-PD-1 immune checkpoint therapy is associated with macrophage infiltration and Wnt pathway expression.” One of the central challenges for cancer therapy is the identification of factors in the tumor microenvironment that increase tumor progression and immune tolerance. In breast cancer, fibrosis is a histopathologic criterion for invasive cancer and poor survival that results from inflammatory factors and remodeling of the extracellular matrix to produce an immune-tolerant microenvironment. In this new study, researchers Hongyan Yuan, Lu Jin, Handan Xiang, Anannya Bhattacharya, Philip E. Brandish, Gretchen Baltus, Alexander Tong, Changyan Zhou, and Robert I. Glazer from Georgetown University Medical Center, Merck Research Institute and Bicycle Therapeutics aimed to determine whether tolerance is associated with the immune checkpoint, Programmed Cell Death 1 (PD-1). A conditional model of mammary fibrosis recently developed by this team, NeuT/ATTAC mice, were administered a murine-specific anti-PD-1 mAb related to pembrolizumab. The researchers monitored drug response by tumor development, imaging mass cytometry, immunohistochemistry, and tumor gene expression by RNAseq. “Utilizing this more stringent tumor model to test its susceptibility to anti-PD-1 immunotherapy, we report the signaling processes associated with its lack of responsiveness.” Tumor progression in NeuT/ATTAC mice was unaffected by weekly injection of anti-PD-1 over four months. Insensitivity to anti-PD-1 was associated with several processes, including increased tumor-associated macrophages (TAM), epithelial to mesenchymal transition (EMT), fibroblast proliferation, an enhanced extracellular matrix and the Wnt signaling pathway, including increased expression of Fzd5, Wnt5a, Vimentin, Mmp3, Col2a1, and Tgfβ1. These results suggest potential therapeutic avenues that may enhance PD-1 immune checkpoint sensitivity, including the use of tumor microenvironment targeted agents and Wnt pathway inhibitors. “Overall, the immune tolerant TME in NeuT/ATTAC mice was associated with tumor-infiltrating macrophages, Foxp3+/PD-1- Treg cells as well as upregulation of the Wnt signaling pathway, which may provide further insights into the therapeutic options that may enhance immune checkpoint therapy.” DOI: https://doi.org/10.18632/oncotarget.28330 Correspondence to: Robert I. Glazer - glazerr@georgetown.edu Keywords: PD-1, NeuT, Wnt, macrophages, mammary tumorigenesis About Oncotarget: Oncotarget (a primarily oncology-focused, peer-reviewed, open access journal) aims to maximize research impact through insightful peer-review; eliminate borders between specialties by linking different fields of oncology, cancer research and biomedical sciences; and foster application of basic and clinical science. To learn more about Oncotarget, visit Oncotarget.com and connect with us on social media: Twitter - https://twitter.com/Oncotarget Facebook - https://www.facebook.com/Oncotarget YouTube – www.youtube.com/c/OncotargetYouTube Instagram - https://www.instagram.com/oncotargetjrnl/ LinkedIn - https://www.linkedin.com/company/oncotarget/ Pinterest - https://www.pinterest.com/oncotarget/ LabTube - https://www.labtube.tv/channel/MTY5OA SoundCloud - https://soundcloud.com/oncotarget For media inquiries, please contact: media@impactjournals.com.

Treasures From Trash In Cancer Research

JCO Precision Oncology Conversations

Play Episode Listen Later Nov 22, 2022 3:26

A new research perspective was published in Oncotarget's Volume 13 on November 17, 2022, entitled, “Treasures from trash in cancer research.” Cancer research has significantly improved in recent years, primarily due to next-generation sequencing (NGS) technology. Consequently, an enormous amount of genomic and transcriptomic data has been generated. In most cases, the data needed for research goals are used, and unwanted reads are discarded. However, these eliminated data contain relevant information. Aiming to test this hypothesis, genomic and transcriptomic data were acquired from public datasets. In this new research perspective, researchers Fabiano Cordeiro Moreira, Dionison Pereira Sarquis, Jorge Estefano Santana de Souza, Daniel de Souza Avelar, Taíssa Maria Thomaz Araújo, André Salim Khayat, Sidney Emanuel Batista dos Santos, and Paulo Pimentel de Assumpção from Instituto Metrópole Digital at the Universidade Federal do Rio Grande do Norte and Núcleo de Pesquisas em Oncologia and Instituto de Ciências Biológicas at the Universidade Federal do Pará used metagenomic tools to explore genomic cancer data; additional annotations were used to explore differentially expressed ncRNAs from miRNA experiments, and variants in adjacent to tumor samples from RNA-seq experiments were also investigated. “Here, we demonstrate potential strategies to benefit from nontargeted information resulting from high-throughput cancer investigations.” In all analyses, new data were obtained: from DNA-seq data, microbiome taxonomies were characterized with a similar performance of dedicated metagenomic research; from miRNA-seq data, additional differentially expressed sncRNAs were found; and in tumor and adjacent to tumor tissue data, somatic variants were found. These findings indicate that unexplored data from NGS experiments could help elucidate carcinogenesis and discover putative biomarkers with clinical applications. Further investigations should be considered for experimental design, providing opportunities to optimize data, saving time and resources while granting access to multiple genomic perspectives from the same sample and experimental run. “Altogether, our results strengthen the hypothesis that abundant additional and potentially useful information can be extracted from NGS. Moreover, the integrated investigation of every available information should provide a broader and more robust interpretation of the molecular scenario from each experiment.” DOI: https://doi.org/10.18632/oncotarget.28308 Correspondence to: Paulo Pimentel de Assumpção - assumpcaopp@gmail.com Video: https://www.youtube.com/watch?v=etqlRWCdhI0 Keywords: cancer metagenomics, cancer sncRNA expression, RNA-Seq variant calling About Oncotarget: Oncotarget (a primarily oncology-focused, peer-reviewed, open access journal) aims to maximize research impact through insightful peer-review; eliminate borders between specialties by linking different fields of oncology, cancer research and biomedical sciences; and foster application of basic and clinical science. To learn more about Oncotarget, visit Oncotarget.com and connect with us on social media: Twitter – https://twitter.com/Oncotarget Facebook – https://www.facebook.com/Oncotarget YouTube – www.youtube.com/c/OncotargetYouTube Instagram – https://www.instagram.com/oncotargetjrnl/ LinkedIn – https://www.linkedin.com/company/oncotarget/ Pinterest – https://www.pinterest.com/oncotarget/ LabTube – https://www.labtube.tv/channel/MTY5OA SoundCloud – https://soundcloud.com/oncotarget For media inquiries, please contact: media@impactjournals.com

The Gary Null Show - 11.15.22

The Gary Null Show

Play Episode Listen Later Nov 16, 2022 61:34

VIDEOS: Niall Ferguson – Woke Totalitarianism (0:19 to 18:14) How Ukraine – Not Russia – Floods Social Media With War Propaganda (0:00 to 1:20) Here's why no one trusts CNN (3:35) The Green New Deal's Bad Science (8:14) JUST IN: Matt Gaetz Says Kevin McCarthy Could Ask Democrats To Help Make Him Speaker Forbes Breaking News 1.35M subscribers Subscribe (5:19) Neil Oliver asks why we should be expected to sweep Covid hysteria under the rug? (0:36 to 5:32) Jimmy Dore – Tim Robbins Apologizes To Unvaccinated For Being Wrong On Covid Policy (0:00 to 9:13) Grape Powder Could Extend Lifespan by 4-5 Years Long Island University, November 3, 2022 In a study the authors called “remarkable,” researchers found that giving grape powder to mice reduced the risk of non-alcoholic fatty liver disease and extended lifespan. To see if grape powder could modulate the harmful effects of a high-fat diet, researchers fed mice a typical Western (high-fat) diet. Half then received 5% standardized grape powder while the other half didn't. Compared to mice not fed the grape powder, the mice given grape powder saw beneficial increases in antioxidant genes, reductions in fatty liver, and extended lifespans. The lead author estimated that when translated to humans, the extended lifespan would correspond to an additional 4-5 years in the life of a human. The grape powder used in this study was composed of fresh red, green and black grapes that were freeze-dried to retain their bioactive compounds. The researchers concluded: “These results suggest the potential of dietary grapes to modulate hepatic gene expression, prevent oxidative damage, induce fatty acid metabolism, ameliorate NAFLD (non-alcoholic fatty liver disease), and increase longevity when co-administered with a high-fat diet.” Study: Neuroprotective Effect of Virgin Coconut Oil Helps Relieve ALS Katholieke University (Belgium), November 6, 2022 An animal study looked into the potential of coconut oil for preventing or reducing ALS symptoms. Coconut oil has already demonstrated safe efficacy for treating Alzheimer's disease symptoms, which is also a neurodegenerative disease for which mainstream medicine has no answer. 1H-magnetic resonance spectroscopy is ideal for ALS treatment diagnostics and research. It is used for many animal and human studies to isolate minute molecular changes in brain and nervous system studies without having to procure tissue and blood samples. Thus, it is non-invasive.[The study results] revealed that the coconut oil supplementation together with the regular diet delayed disease symptoms, enhanced motor performance, and prolonged survival in the SOD1G93A mouse model. Furthermore, MRS data showed stable metabolic profile at day 120 in the coconut oil diet group compared to the group receiving a standard diet without coconut oil supplementation. In addition, a positive correlation between survival and the neuronal marker NAA was found. … this is the first study that reports metabolic changes in the brainstem using in vivo MRS and effects of coconut oil supplementation as a prophylactic treatment in SOD1G93A mice.One of the major metabolites NAA (N-acetylaspartate), has been observed as an integral part of neuron loss, which is a major factor of onset ALS when it is diminished from the central nervous system. NAA reduction was greater in the non-coconut oil fed group of rats, indicating those on coconut oil were experiencing less neurodegeneration and neuronal destruction. Aerobic activity can reduce the risk of metastatic cancer by 72% Tel Aviv University (Israel), November 14, 2022 A new study at Tel Aviv University found that aerobic exercise can reduce the risk of metastatic cancer by 72%. According to the researchers, intensity aerobic exercise increases the glucose (sugar) consumption of internal organs, thereby reducing the availability of energy to the tumor. The study was led by two researchers from TAU's Sackler Faculty of Medicine. Prof. Levy and Dr. Gepner said, “Studies have demonstrated that physical exercise reduces the risk for some types of cancer by up to 35%. This positive effect is similar to the impact of exercise on other conditions, such as heart disease and diabetes. In this study we added new insight, showing that high-intensity aerobic exercise, which derives its energy from sugar, can reduce the risk of metastatic cancer by as much as 72%. If so far the general message to the public has been ‘be active, be healthy,' now we can explain how aerobic activity can maximize the prevention of the most aggressive and metastatic types of cancer.” The study combined an animal model in which mice were trained under a strict exercise regimen, with data from healthy human volunteers examined before and after running. The human data, obtained from an epidemiological study that monitored 3,000 individuals for about 20 years, indicated 72% less metastatic cancer in participants who reported regular aerobic activity at high intensity, compared to those who did not engage in physical exercise. They found that aerobic activity significantly reduced the development of metastatic tumors in the lymph nodes, lungs, and liver. The researchers hypothesized that in both humans and model animals, this favorable outcome is related to the enhanced rate of glucose consumption induced by exercise. Prof. Levy stated, “Our study is the first to investigate the impact of exercise on the internal organs in which metastases usually develop, like the lungs, liver, and lymph nodes. “Consequently, if cancer develops, the fierce competition over glucose reduces the availability of energy that is critical to metastasis. Moreover, when a person exercises regularly, this condition becomes permanent: the tissues of internal organs change and become similar to muscle tissue. We all know that sports and physical exercise are good for our health. Our study, examining the internal organs, discovered that exercise changes the whole body, so that the cancer cannot spread, and the primary tumor also shrinks in size.” Dr. Gepner adds, “Our results indicate that unlike fat-burning exercise, which is relatively moderate, it is a high-intensity aerobic activity that helps in cancer prevention. If the optimal intensity range for burning fat is 65–70% of the maximum pulse rate, sugar burning requires 80–85%—even if only for brief intervals. For example: a one-minute sprint followed by walking, then another sprint. Vegan diet best for weight loss even with carbohydrate consumption, study finds University of South Carolina, November 6, 2022 The month of November often brings about a sense of dread at the thought of food filled holiday parties and gatherings, but those who consume a plant based diet have little need for concern. A newstudy by the University of South Carolina confirms one big draw of saying no to all animal products: the ability to shed weight faster than those who consume a diet that contains meat and dairy. The study compared the amount of weight lost by those on vegan diets to those on a mostly plant-based diet, and those eating an omnivorous diet with a mix of animal products and plant based foods. At the end of six months, individuals on the vegan diet lost more weight than the other two groups by an average of 4.3%, or 16.5 pounds. The study followed participants who were randomly assigned to one of five diets on the dietary spectrum: vegan which excludes all animal products, semi-vegetarian with occasional meat intake; pesco-vegetarian which excludes all meat except seafood; vegetarian which excludes all meat and seafood but includes animal products, and omnivorous, which excludes no foods. Participants followed their assigned dietary restrictions for six months, with all groups except the omnivorous participating in weekly group meetings. Those who stuck to the vegan diet showed the greatest weight loss at the two and six month marks. The lead authornotes that the diet consumed by vegan participants was high in carbohydrates that rate low on the glycemic index. “We've gotten somewhat carb-phobic here in the U.S. when it comes to weight loss. This study might help alleviate the fears of people who enjoy pasta, rice, and other grains but want to lose weight,” she said. Weight loss was not the only positive outcome for participants in the strictly vegan group. They also showed the greatest amount of decrease in their fat and saturated fat levels at the two and six month checks, had lower BMIs, and improved macro nutrients more than other diets. Eschewing all animal products appears to be key for these positive results. Uterine fibroid growth activated by chemicals found in everyday products Northwestern University, November 14, 2022 For the first time, scientists at Northwestern Medicine have demonstrated a causal link between environmental phthalates (toxic chemicals found in everyday consumer products) and the increased growth of uterine fibroids, the most common tumors among women. Manufacturers use environmental phthalates in numerous industrial and consumer products, and they've also been detected in medical supplies and food. Although they are known to be toxic, they are currently unbanned in the U.S. “These toxic pollutants are everywhere, including food packaging, hair and makeup products, and more, and their usage is not banned,” said corresponding study author Dr. Serdar Bulun, chair of the department of obstetrics and gynecology at Northwestern University Feinberg School of Medicine and a Northwestern Medicine physician. “These are more than simply environmental pollutants. They can cause specific harm to human tissues.” Up to 80% of all women may develop a fibroid tumor during their lifetime, Bulun said. One-quarter of these women become symptomatic with excessive and uncontrolled uterine bleeding, anemia, miscarriages, infertility and large abdominal tumors necessitating technically difficult surgeries. The new study found women with a high exposure to certain phthalates such as DEHP (used as a plasticizer to increase the durability of products such as shower curtains, car upholstery, lunchboxes, shoes and more) and its metabolites have a high risk for having a symptomatic fibroid. The scientists discovered exposure to DEHP may activate a hormonal pathway that activates an environmentally responsive receptor (AHR) to bind to DNA and cause increased growth of fibroid tumors. Immune cells mistake heart attacks for viral infections University of California San Diego and Harvard University, November 12, 2022 A study led by Kevin King, a bioengineer and physician at the University of California San Diego, has found that the immune system plays a surprising role in the aftermath of heart attacks. The research could lead to new therapeutic strategies for heart disease. The team, which also includes researchers from the Center for Systems Biology at Massachusetts General Hospital (MGH), Brigham and Women's Hospital, Harvard Medical School, and the University of Massachusetts, presents the findings in Nature Medicine. Ischemic heart disease is the most common cause of death in the world and it begins with a heart attack. During this process, heart cells die, prompting immune cells to enter the dead tissue, clear debris and orchestrate stabilization of the heart wall. But what is it about dying cells in the heart that stimulates the immune system? To answer this, researchers looked deep inside thousands of individual cardiac immune cells and mapped their individual transcriptomes using a method called single cell RNA-Seq. This led to the discovery that after a heart attack, DNA from dying cells masquerades as a virus and activates an ancient antiviral program called the type I interferon response in specialized immune cells. The researchers named these “interferon inducible cells (IFNICs).” When investigators blocked the interferon response, either genetically or with a neutralizing antibody given after the heart attack, there was less inflammation, less heart dysfunction, and improved survival. Specifically, blocking antiviral responses in mice improved survival from 60 percent to over 95 percent. These findings reveal a new potential therapeutic opportunity to prevent heart attacks from progressing to heart failure in patients. “We are interested to learn whether interferons contribute to adverse cardiovascular outcomes after heart attacks in humans,” said King, who did most of the work on the study while he was a cardiology fellow at Brigham and Women's Hospital and at the Center for Systems Biology at MGH in Boston. Investigators found that surprisingly, the antiviral interferon response is also turned on after a heart attack despite the absence of any infection. Their results point to dying cell DNA as the cause of this confusion because the immune system interprets it as the molecular signature of a virus. Surprisingly, the immune cells participating in the interferon response were a previously unrecognized subset of cardiac macrophages. These cells could not be identified by conventional flow sorting because unique markers on the cell surface were not known. By using single cell RNA Seq, an emerging technique that combines microfluidic nanoliter droplet reactors with single cell barcoding and next generation sequencing, the researchers were able to examine expression of every gene in over 4,000 cardiac immune cells and found the specialized IFNIC population of responsible cells.

Hyperthermic Intraperitoneal Chemotherapy–Induced Molecular Changes in Humans Validate Preclinical Data in Ovarian Cancer with Dr. Thanh Dellinger

Play Episode Listen Later Oct 19, 2022 22:19

In this JCO Precision Oncology Conversations podcast, JCO PO author Dr. Thanh Dellinger of City of Hope National Medical Center shares insights into the research published in her article, “Hyperthermic Intraperitoneal Chemotherapy–Induced Molecular Changes in Humans Validate Preclinical Data in Ovarian Cancer.” Podcast host Dr. Abdul Rafeh Naqash talks with Dr. Dellinger about hyperthermic intraperitoneal chemotherapy (HIPEC) and the various challenges of the treatment of epithelial ovarian cancer (EOC). The study described in this JCO PO article discusses protein expression, RNAseq alterations and signature, and whole-transcriptome sequencing and signatures. Read here  https://ascopubs.org/doi/full/10.1200/PO.21.00239 TRANSCRIPT Dr. Abdul Rafeh Naqash: Welcome to ASCO's Precision Oncology Conversations where we bring you the highlights and overview of precision oncology. This podcast is here to provide interactive dialogue focusing on the excellent research published in the JCO Precision Oncology. Our episodes will feature engaging conversations regarding precision oncology with the authors of a clinically relevant and highly significant JCO Precision Oncology article. You can find all our shows including this one at asco.org/podcasts, or wherever you get your podcasts. Hello, I am Dr. Abdul Rafeh Naqash. I'm a medical oncologist and a phase one clinical trialist at the OU Stephenson Cancer Center. You're listening to JCO Precision Oncology Conversations. I have no conflicts of interest related to this podcast. A complete list of disclosures is available at the end of each episode. Today, I will be talking with Dr. Thanh Dellinger from the City of Hope Comprehensive Cancer Center, who's a gynecological oncologist, and we'll be talking about her JCO Precision Oncology article, ‘Hyperthermic Intraperitoneal Chemotherapy-Induced Molecular Changes in Humans Validate Preclinical Data in Ovarian Cancer.' Dr. Dellinger does not have any conflicts of interest. Hi, Dr. Dellinger, welcome to our podcast! Dr. Thanh Dellinger: Hi, Dr. Naqash! It's such a pleasure to be on with you. Dr. Abdul Rafeh Naqash: We recently saw your paper published. It's one of those interesting, clinical translational papers that we felt needed to be highlighted in our Precision Oncology Podcast series. So, we're really excited to have you here today to take a deeper dive into the findings and some of the novel approaches that you used in your recent publication. So, for starters, could you give our listeners a brief idea of what HIPEC is, where it's used, and when it's used in ovarian cancer? Dr. Thanh Dellinger: Right! Thank you very much for this great introduction. So, HIPEC or Hyperthermic Intraperitoneal Chemotherapy has been used in ovarian cancer for quite some time. The most relevant data giving us an indication for ovarian cancer was published by Dr. van Driel in the OVHIPEC-1 randomized trial several years ago in the New England Journal of Medicine, which demonstrated that in stage 3 ovarian cancer patients who undergo an interval tumor debulking with HIPEC, that those patients appear to enjoy both progression-free and overall survival benefit. In fact, the overall survival benefit is nearly 12 months for those patients. So, with this in mind and a number of other data, the HIPEC treatment for those patients that interval debulking has been incorporated into the NCCN guidelines. Nonetheless, there have been some criticisms of HIPEC and it still remains to be seen who those patients are, the ovarian cancer patients who really best benefit from HIPEC, given the morbidity of HIPEC. We now know also that HIPEC is probably equivalent to just cytoreductive surgery alone in terms of morbidity. Dr. Abdul Rafeh Naqash: Thank you for that explanation. And especially for people like myself, who are not surgeons or gynecological oncologists, that was very helpful. So, my next question, and you probably partly answered it, but I'm going to still ask the question is: what is the reason you think that intraperitoneal chemotherapy overall, has not been as widely adopted? Dr. Thanh Dellinger: You touch on a very good point there. As many of the listeners may understand, IP chemotherapy has demonstrated a lot of efficacies in multiple clinical trials over the last decade or two decades even. And part of why, despite its benefit, it has not been taken up in the overall community may really be the difficulty and the complexity of doing IP chemotherapy in the community, especially the side effects are difficult sometimes to take care of. There's increased abdominal pain and there are catheter issues. And so, especially with more recent data, that with the presence of Avastin, IP chemotherapy may not necessarily be as beneficial. Unfortunately, IP chemotherapy hasn't been really taken up in daily oncologic care with ovarian cancer. Nonetheless, we know that there are a lot of theoretical benefits because of the peritoneal metastasis not being as best treated with intravenous chemotherapy as with regional therapy. Dr. Abdul Rafeh Naqash: Thank you! So, now going to the data that you published. I was very intrigued with some of the findings. And from what I understood, your main aim was to understand predictive biomarkers to identify patients or basically identify molecular characteristics for patients' selection for HIPEC. So, could you tell us more about why you initiated this study? And I understand this is one of the, I believe the first study in humans to evaluate some of these interesting biomarkers, both pre- and post-. So, what was the background of doing this trial? And what led to this interesting study? Dr. Thanh Dellinger: Thank you for pointing out this aim. There's a lot of criticism of HIPEC and part of it is that we may not exactly understand the mechanisms of HIPEC, why is it that it works so well in some patients? There's a lot of preclinical data supporting hyperthermia, especially with cisplatin. There's synergy between cisplatin and hyperthermia, and improving the DNA adduct formation. There's increased cytotoxicity seen when the temperature increases up to 43 degrees. And there's also a T-cell activation and immune response that occurs during hyperthermia. So, a lot of this, however, has been done in preclinical studies, in vitro data as well as preclinical mouse models. There hasn't been much or really anything published that, as far as I know, has been done in humans. And so, this particular study looked at both pre-treatments, pre-HIPEC specimens, peritoneal biopsies, as well as immediate post-operative peritoneal biopsies, tumors, and normal samples, and we wanted to look both at the whole transcriptomic sequencing profile, but also at the tumor microenvironment. Dr. Abdul Rafeh Naqash: From a logistic standpoint, from a trial design standpoint, was this a phase 1 study? I know you use the term pilot in the publication. So, were you trying to look at safety also, or was this primarily I would say, a biomarker, pharmacodynamic biomarker-driven study that you were trying to evaluate? Dr. Thanh Dellinger: You're correct. This was essentially a feasibility study. But we additionally looked at safety and feasibility with HIPEC at our institution. And in some respects, we also looked at the feasibility of giving intraperitoneal chemotherapy normothermically early after HIPEC, and so it was also an endpoint to look at safety. Dr. Abdul Rafeh Naqash: Understand! I believe there was some difference in the dose for the cisplatin, I believe, is the chemotherapy that you use. What was the rationale for the difference in the dose for 75 milligrams per meter square that you use in your study? Dr. Thanh Dellinger: The study was initiated at a time before the OVHIPEC-1 trial was published. And so, at that time, the HIPEC dose for cisplatin was still not established. 75 milligrams per meter square for cisplatin was actually used in other trials, and has been noted to be effective in other clinical trials. Dr. Abdul Rafeh Naqash: Thank you! Now going to the patient population for this trial. What type of patients were you enrolling? Was it just epithelial ovarian cancer patients, did these patients need to have peritoneal metastases when you were doing this cytoreductive surgery? What was the patient population that you were targeting in this trial? Dr. Thanh Dellinger: The majority of the patients did have epithelial ovarian cancer. We did enroll a few, actually 5, uterine cancer patients as well, which were not included in this specific publication. But the majority of them were epithelial ovarian cancer patients. Dr. Abdul Rafeh Naqash: Going to the interesting translational analysis. So, you had three subsets of patients based on the biopsy collection. What were your hypotheses, and what drove some of those translational studies to understand the biomarkers? Dr. Thanh Dellinger: The first translational analysis we conducted was the whole transcriptomic sequencing, and specifically, we wanted to look, one, for any potential transcriptomic signatures that may correlate with survival or improved response to HIPEC. The second one was to look at whole exome sequencing. Thirdly, we looked at whole transcriptomic sequencing differences before and after HIPEC treatment. And lastly, we looked at the tumor microenvironment through multiplexing of certain markers associated with T-cell response. Dr. Abdul Rafeh Naqash: From a clinical outcome standpoint - and we'll discuss the biomarkers in more detail - from a clinical standpoint, when I briefly looked over the PFS curves, were the results, as far as expected outcomes, were they similar to what you see with the current standard? Or were there any unusual safety signals? Or would you attribute any of the adverse events that you saw to intraperitoneal chemotherapy specifically? Because I believe some patients did have some chemotherapy pre-surgery, neoadjuvant if I'm correct. So, how would you attribute some of those AEs, and if at all, did you see any interesting safety signals of concern and outcomes as far as PFS is concerned? Dr. Thanh Dellinger: So, one of the major toxicities that we saw in the first half of our trial were actually renal toxicities. In fact, there were actually two patients who could not go on to adjuvant chemotherapy because they suffered chronic renal failure. And because of that, halfway through the trial, we did actually add a nephro protectant called sodium thiosulfate. And this actually dramatically improved those renal toxicities. And for the second half of our study, no patients suffered grade three or grade four renal adverse events. And so, that did change significantly. Dr. Abdul Rafeh Naqash: From a genomic standpoint, it's very interesting that you were able to do all these very cool and interesting translational biomarker studies, including multiplex immunofluorescence. From a genomic standpoint, though, would you say it's fair to say that there was no significant correlation based on the baseline genomics for some of the patients and their outcomes? Is that a fair assessment? Dr. Thanh Dellinger: Yes, that is a very fair assessment. I think that our cohort was really too small to make those kinds of assessments. I don't know whether you saw there recently was a paper published by the OVHIPEC-1 group looking at their cohort of over 200 patients that underwent the interval cytoreductive surgery in HIPEC and they did actually demonstrate benefit in patients who are HIV-positive but BRCA wild-type, but not necessarily in BRCA mutated patients. So, I think that I would point to that study to look for genomic effects with HIPEC patients. Dr. Abdul Rafeh Naqash: Understand. Now, again, going to the biomarkers that your team evaluated, it seems from among good responders especially, you saw an increase in tumor necrosis factor, alpha signaling, NF-kappa B signaling, KRAS signaling, and then you also saw some pathways that were downregulated, especially the G2-M checkpoint, and Myc targets. What would you say the correlation of these is in terms of future drug development in this specific setting? Dr. Thanh Dellinger: I think that we did see some increase in immune pathways in patients who did better in the end. And also, our multiplex results did demonstrate that E1 expression was increased in patients who had better responses after HIPEC. So, our hypothesis is that potentially, there's an activation of T-cell response with HIPEC and that potentially PD-1 inhibitor could be added in the future. This is a hypothesis that certainly would need to have more work, but it's something that is interesting enough to really look at in ways of how to improve HIPEC. Dr. Abdul Rafeh Naqash: Going to your point on the PD-1, I found really intriguing that you were able to see an increase in PD-1 expression on CD8+ T cells but no actual increase in the number of CD8+ T cells suggesting there's some sort of activation of this marker and this may not necessarily be a marker for T-cell exhaustion. So, would you interpret it in a way that in a different setting, perhaps a new adjuvant approach with immunotherapy, would perhaps somehow augment this and then you could see more upregulation? Is there any work being done in that field? How would you put this in the context of your findings? Dr. Thanh Dellinger: You bring up a really great point because to date HIPEC has been demonstrated to have benefit in the interval setting. But there was a more recent study done by, well not recent, a more recently published study by a Korean group that demonstrated no benefit in the adjuvant setting for HIPEC and still some benefit in the interval setting. And the question is, are these really two different types of cohorts who respond differently because of potential differences in immune response and tumor microenvironment? I think that that would be a great way of delving further into this. What are really the differences in tumor microenvironment changes in those two different settings? Dr. Abdul Rafeh Naqash: Definitely! It's very exciting. You've also shown upregulation of, as you mentioned earlier, immune pathways, as well as upregulation of genes related to heat shock proteins. Does that play into future drug development as far as HSP Inhibitors are concerned? Dr. Thanh Dellinger: That is a really great question. Certainly, in preclinical models, heat shock proteins are known to be elevated and they do activate dendritic cells and result in T-cell activation. Now, whether that can be spelled out into actually some future drug therapy definitely remains to be seen. To date, there hasn't been any success in using heat shock types of agents or inhibitors, unfortunately. So, I think while this is of great interest, I'm not entirely sure that this will translate into any drug therapy in the future. Dr. Abdul Rafeh Naqash: And I totally connect with you there as a phase 1 trialist. I completely agree that we see a lot of translational data, more often than not, going into the phase 1 site because many of these targets are not actionable. Now, from a DNA repair standpoint, you did see that there was interference with DNA repair, as far as some of the analyses that you did, but I did not specifically see any markers for DNA damage that were assessed on the biopsies such as Gamma-H2AX, RAD 51, or Phospho-NBS. Was there a reason why that was not looked at? Dr. Thanh Dellinger: I think that we did look at that and there weren't really any significant results. We did put some of the data into the supplementary data. I think that in the end, our cohort was really too small to really make any meaningful data. But I absolutely agree with you looking at HSP and DNA repair is really important. And as I mentioned that most recently published paper does address that. Dr. Abdul Rafeh Naqash: Excellent! Do you think that there could be any confounders in this analysis that could have led to the upregulation of some of these pathways and may not necessarily have been the intraperitoneal chemotherapy? Could you think of some other reasons that this could have been a confounding factor? Or would it primarily be attributed to the intraperitoneal chemotherapy that you guys have looked at in this interesting paper? Dr. Thanh Dellinger: Yeah, it is a rather small cohort. So, I think that more data is required to potentially repeat this in the larger cohort. But what is interesting is that we did have paired analysis. So, we had matched peritoneal samples from the same patients looking before the HIPEC and after the HIPEC, which is very unique and hasn't really been done in the setting before. And while you couldn't necessarily repeat the same exact peritoneal tumor it was very close. And so, in the best setting, I think that we did have a good paired analysis. Dr. Abdul Rafeh Naqash: That was one of the very interesting aspects of this study that I very much appreciated, that you were able to get some of those paired biopsies and do the analyses on samples and look at all these markers. So, this was all excellent work and definitely intrigues the mind into what other ways one could use some of these findings to develop future combination-based approaches, whether it's the neoadjuvant or the adjuvant setting for patients with ovarian cancer. Are there any next steps as part of this project that you are excited about that you can share? Dr. Thanh Dellinger: Right! I'm definitely very excited about trying to build on this and essentially developing a much larger predictive study using hundreds of ovarian cancer HIPEC-treated tumors in collaboration with others. We have definitely developed a great community of HIPEC investigators who are very interested in developing somewhat of a predictive signature for ovarian cancer undergoing HIPEC. So, I'm very excited to hopefully be able to develop this consortium of HIPEC transcriptomic research. And so, I'm looking forward to collaborating with my co-investigators on that. Dr. Abdul Rafeh Naqash: It was definitely exciting to talk to you about your work. Now, I want to ask you about you as an investigator or as a researcher. How did you end up in this field? What was your background while you were pursuing science and medicine? How did you end up in this field and how are you mentoring the next generation? Dr. Thanh Dellinger: When I was a fellow at UCI, my mentor Robert Bristow introduced me to HIPEC and that has really stuck. As a GYN oncologist, it is hard to really do both chemo and be a good surgeon. And in many ways, I have really specialized in surgical oncology more than in medical oncology. And HIPEC is really a very nice blend of the two. It allows you to do clinical trials while still doing surgery and giving some chemotherapy. Really, it was for the introduction of my more recent mentor, Elena Rodriguez, who really introduced me to genomics and applying this to HIPEC samples that this all came about. And so, I think that there are a lot of opportunities for surgical oncologists who do not give chemo and may think that clinical research is not for them, but there are a lot of translational opportunities and clinical trial opportunities for those who don't give chemotherapy, but are surgical oncologists. Dr. Abdul Rafeh Naqash: Thank you so much. We are really excited for all the work that you're doing and will continue to do and hopefully, we'll see more of this evolve as time progresses. Dr. Thanh Dellinger: Thank you so much, Dr. Naqash. It was such a pleasure meeting you and talking to you. Dr. Abdul Rafeh Naqash: Same here. Thank you for listening to JCO Precision Oncology Conversations. To listen to more, visit asco.org/podcasts, or find them on Google Play Spotify and Apple podcasts. To stay up to date, be sure to follow and share JCO Precision Oncology content on Twitter. The Twitter handle is @JCOPO_ASCO. All JCO PO articles and series can be found at ascopubs.org/journals/PO. The purpose of this podcast is to educate and inform. This is not a substitute for professional medical care and is not intended for use in the diagnosis or treatment of individual conditions. Guests on this podcast express their own opinions, experience, and conclusions. Guest statements on the podcast do not express the opinions of ASCO. The mention of any product, service, organization, activity or therapy should not be construed as an ASCO endorsement. Guest Bio Dr. Thanh Dellinger, MD, is a gynecologic oncologist and physician-scientist who specializes in ovarian and uterine cancer. She is an expert in hyperthermic (HIPEC) and pressurized aerosolized intraperitoneal chemotherapy (PIPAC), and is the primary investigator of clinical and translational studies focusing on these therapies. She received her medical degree at University of California Irvine, where she also completed a gynecologic oncology fellowship. She is leading the first U.S. clinical trial in PIPAC (pressurized intraperitoneal aerosolized chemotherapy), a novel therapy using pressurized aerosolized chemotherapy for ovarian cancer. Her current research focuses on innovative therapies for ovarian cancer using intraoperative chemotherapy, and novel antibody and nanoparticle therapies.

university apple data dna medicine md humans korean hiv ip rad pd molecular induced validate chemotherapy hsp uci new england journal ovarian cancer asco nf gyn aes brca california irvine thanh pfs kras guest bio dr eoc myc dellinger preclinical driel nccn avastin cd8 t hipec rnaseq hope national medical center intraperitoneal transcript dr google play spotify g2 m

Characterization of Epigenetic States in the Oligodendrocyte Lineage (Gonçalo Castelo-Branco)

Epigenetics Podcast

Play Episode Listen Later Jul 28, 2022 42:32

In this episode of the Epigenetics Podcast, we caught up with Goncalo Castelo-Branco from the Karolinska Institute to talk about his work on the characterization of epigenetic states in the Oligodendrocyte Lineage. The group from Gonçalo Castelo-Branco's lab focuses on characterizing epigenetic states of oligodendrocytes, with the aim to understand their contribution to diseases like multiple sclerosis. To do this the group used single-cell RNA-Seq to identify sub-populations of oligodendrocytes. Furthermore, the team pioneered improvements in CUT&Tag and applied it to the single-cell space, as well as developing spatial CUT&Tag. More recently they used nanobodies in an optimised version of single cell CUT&Tag that allows simultaneous probing of three epigenomic modalities at single-cell resolution, using nanobody-Tn5 fusion proteins. The three modalities encompass chromatin accessibility as measured via ATAC-Seq and two histone post-transcriptional modifications. References Deng Y, Bartosovic M, Kukanja P, Zhang D, Liu Y, Su G, Enninful A, Bai Z, Castelo-Branco G, Fan R. Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level. Science. 2022 Feb 11;375(6581):681-686. doi: 10.1126/science.abg7216. Epub 2022 Feb 10. PMID: 35143307. Winick-Ng W, Kukalev A, Harabula I, Zea-Redondo L, Szabó D, Meijer M, Serebreni L, Zhang Y, Bianco S, Chiariello AM, Irastorza-Azcarate I, Thieme CJ, Sparks TM, Carvalho S, Fiorillo L, Musella F, Irani E, Torlai Triglia E, Kolodziejczyk AA, Abentung A, Apostolova G, Paul EJ, Franke V, Kempfer R, Akalin A, Teichmann SA, Dechant G, Ungless MA, Nicodemi M, Welch L, Castelo-Branco G, Pombo A. Cell-type specialization is encoded by specific chromatin topologies. Nature. 2021 Nov;599(7886):684-691. doi: 10.1038/s41586-021-04081-2. Epub 2021 Nov 17. PMID: 34789882; PMCID: PMC8612935. Bartosovic M, Kabbe M, Castelo-Branco G. Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues. Nat Biotechnol. 2021 Jul;39(7):825-835. doi: 10.1038/s41587-021-00869-9. Epub 2021 Apr 12. PMID: 33846645; PMCID: PMC7611252. Marek Bartosovic, Gonçalo Castelo-Branco. Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag. bioRxiv. 2022.03.08.483459; doi: https://doi.org/10.1101/2022.03.08.483459 Related Episodes Multiple challenges of CUT&Tag (Cassidee McDonough, Kyle Tanguay) Chromatin Profiling: From ChIP to CUT&RUN, CUT&Tag and CUTAC (Steven Henikoff) Contact Active Motif on Twitter Epigenetics Podcast on Twitter Active Motif on LinkedIn Active Motif on Facebook Email: podcast@activemotif.com

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EULAR22 Lupus Podcast

Rheumnow Podcast

Play Episode Listen Later Jun 20, 2022 27:35

- Kathryn Dao: What Patients Want and Are Willing to Risk with SLE https://www.youtube.com/watch?v=lytObQy_UdQ&list=PLbd4uixNDSBSKgUojFF3dfPfHlN8QN2EP&index=13 - Yuz Yusof: What Symptoms or Targets Mattered Most to People with Lupus? https://www.youtube.com/watch?v=EJKPsegnpS0&list=PLbd4uixNDSBSKgUojFF3dfPfHlN8QN2EP&index=8&t=6s - Kathryn Dao: AURORA-2 Two-year Results Voclosporin For Lupus Nephritis https://www.youtube.com/watch?v=HZOFQi559S4&list=PLbd4uixNDSBSKgUojFF3dfPfHlN8QN2EP&index=14 - Kathryn Dao: Severe Hematologic Relapse Risk in SLE https://www.youtube.com/watch?v=j3S-BOhNhDE&list=PLbd4uixNDSBSKgUojFF3dfPfHlN8QN2EP&index=15 - Eric Dein: Let's Talk about Sex and Autoimmune Disease https://www.youtube.com/watch?v=hi_DqRiLPUw&list=PLbd4uixNDSBSKgUojFF3dfPfHlN8QN2EP&index=21 - Kathryn Dao: DMARDS, Prednisone, Pregnancy, OH MY! https://www.youtube.com/watch?v=kwzKrzFjIWM&list=PLbd4uixNDSBSKgUojFF3dfPfHlN8QN2EP&index=25 - Kathryn Dao: Belimumab Use in Pregnancy https://www.youtube.com/watch?v=14MUTorltoU&list=PLbd4uixNDSBSKgUojFF3dfPfHlN8QN2EP&index=26 - Peter Nash: Deucravacitinib at EULAR 2022 https://www.youtube.com/playlist?list=PLbd4uixNDSBSKgUojFF3dfPfHlN8QN2EP - Yuz Yusof: Interview with Dr. Lucy Carter on RNA-Seq analysis to determine who's at risk for SLE https://www.youtube.com/watch?v=PhQvt6IVPfY&list=PLbd4uixNDSBSKgUojFF3dfPfHlN8QN2EP&index=50

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EULAR22 Lupus Podcast

Rheumnow Podcast

Play Episode Listen Later Jun 20, 2022 27:35

talk sex risk pregnancy lupus autoimmune disease sle prednisone rnaseq eular

How ONC201 Kills Breast Cancer Cells

Play Episode Listen Later Apr 22, 2022 12:53

Dr. Stanley Lipkowitz and Dr. Yoshimi Endo Greer from the Women's Malignancies Branch at the National Cancer Institute discuss a research paper they co-authored that was published by Oncotarget in 2018, entitled, "ONC201 kills breast cancer cells in vitro by targeting mitochondria." DOI - https://doi.org/10.18632/oncotarget.24862 Correspondence to - lipkowis@mail.nih.gov Abstract We report a novel mechanism of action of ONC201 as a mitochondria-targeting drug in cancer cells. ONC201 was originally identified as a small molecule that induces transcription of TNF-related apoptosis-inducing ligand (TRAIL) and subsequently kills cancer cells by activating TRAIL death receptors. In this study, we examined ONC201 toxicity on multiple human breast and endometrial cancer cell lines. ONC201 attenuated cell viability in all cancer cell lines tested. Unexpectedly, ONC201 toxicity was not dependent on either TRAIL receptors nor caspases. Time-lapse live cell imaging revealed that ONC201 induces cell membrane ballooning followed by rupture, distinct from the morphology of cells undergoing apoptosis. Further investigation found that ONC201 induces phosphorylation of AMP-dependent kinase and ATP loss. Cytotoxicity and ATP depletion were significantly enhanced in the absence of glucose, suggesting that ONC201 targets mitochondrial respiration. Further analysis indicated that ONC201 indirectly inhibits mitochondrial respiration. Confocal and electron microscopic analysis demonstrated that ONC201 triggers mitochondrial structural damage and functional impairment. Moreover, ONC201 decreased mitochondrial DNA (mtDNA). RNAseq analysis revealed that ONC201 suppresses expression of multiple mtDNA-encoded genes and nuclear-encoded mitochondrial genes involved in oxidative phosphorylation and other mitochondrial functions. Importantly, fumarate hydratase deficient cancer cells and multiple cancer cell lines with reduced amounts of mtDNA were resistant to ONC201. These results indicate that cells not dependent on mitochondrial respiration are ONC201-resistant. Our data demonstrate that ONC201 kills cancer cells by disrupting mitochondrial function and further suggests that cancer cells that are dependent on glycolysis will be resistant to ONC201. Sign up for free Altmetric alerts about this article - https://oncotarget.altmetric.com/details/email_updates?id=10.18632%2Foncotarget.24862 Press release - https://www.oncotarget.com/index.php?journal=oncotarget&page=news&op=press&item=onc201-kills-breast-cancer-cells-in-vitro-by-targeting-mitochondria Keywords - ONC201, breast cancer, mitochondria About Oncotarget Oncotarget is a peer-reviewed, open access biomedical journal covering research on all aspects of oncology. To learn more about Oncotarget, please visit https://www.oncotarget.com and connect with us: SoundCloud - https://soundcloud.com/oncotarget Facebook - https://www.facebook.com/Oncotarget/ Twitter - https://twitter.com/oncotarget Instagram - https://www.instagram.com/oncotargetjrnl/ YouTube - https://www.youtube.com/OncotargetYouTube LinkedIn - https://www.linkedin.com/company/oncotarget Pinterest - https://www.pinterest.com/oncotarget/ Reddit - https://www.reddit.com/user/Oncotarget/ Oncotarget is published by Impact Journals, LLC: https://www.ImpactJournals.com Media Contact MEDIA@IMPACTJOURNALS.COM 18009220957

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Multimodal Characterization of Cellular Identity | CITE-Seq and Beyond (Peter Smibert, VP of 10X Genomics)

Epigenetics Podcast

Play Episode Listen Later Apr 14, 2022 48:12

In this episode of the Epigenetics Podcast, we speak with Peter Smibert, Vice President of Biology at 10X Genomics to talk about an exciting new method in Multimodal Characterization of Cellular Identity using Barcoding. During his time at the New York Genome Center, Peter Smibert was instrumental in the development of a new method called "Cellular Indexing of Transcriptomes and Epitopes by Sequencing" short CITE-Seq. This method enables the characterization of a cell's transcriptome, while at the same time, also allows the characterization of the cell's protein surface markers - at the single cell level. In CITE-Seq, sequencing adapters are coupled to antibodies that recognize surface proteins, which can then be detected by sequencing. Further advancements of the CITE-Seq method led to the launch of BioLegend's TOTAL-Seq and the integration of scATAC-Seq into the workflow. With the integration of scATAC-Seq in the CITE-Seq protocol, it is now possible to characterize single-cells along the path of the central dogma of biology, this is why the method called DOGMA-Seq. References https://cite-seq.com Baron, M., Yanai, I. New skin for the old RNA-Seq ceremony: the age of single-cell multi-omics. Genome Biol 18, 159 (2017). https://doi.org/10.1186/s13059-017-1300-5 Stoeckius, M., Zheng, S., Houck-Loomis, B. et al. Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics. Genome Biol 19, 224 (2018). https://doi.org/10.1186/s13059-018-1603-1 Stoeckius, M., Hafemeister, C., Stephenson, W. et al. Simultaneous epitope and transcriptome measurement in single cells. Nat Methods 14, 865–868 (2017). https://doi.org/10.1038/nmeth.4380 Mimitou, E.P., Cheng, A., Montalbano, A. et al. Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells. Nat Methods 16, 409–412 (2019). https://doi.org/10.1038/s41592-019-0392-0 Related Episodes Epigenome-based Precision Medicine (Eleni Tomazou) ATAC-Seq, scATAC-Seq and Chromatin Dynamics in Single-Cells Investigating the Dynamics of Epigenetic Plasticity in Cancer with Single Cell Technologies (Céline Vallot) Contact Active Motif on Twitter Epigenetics Podcast on Twitter Active Motif on LinkedIn Active Motif on Facebook Email: podcast@activemotif.com

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Down Syndrome iPSC Model: Endothelial Perspective on Tumor Development