Podcasts about lncrna

In the fall of 2024, Haya Therapeutics, based in Switzerland and San Diego, landed a $1bn deal with Eli Lilly to apply its long non-coding RNA (ncRNA) technology to obesity.The company's lead candidate, HTX-001, is making progress towards the clinic in cardiomyopathy. CEO Samir is one of the first researchers to publish on lncRNA – which is also known as the Dark GenomeThis week, our podcast guest is Samir Ounzain, CEO and co-founder of Haya Therapeutics. Ounzain was one of the first researchers to publish on lncRNA, also known as the ‘dark genome.'00:55-03:47: About Haya Therapeutics03:47-06:37: What is the dark genome?06:37-09:29: What is the connection between lncRNA and disease?09:30-13:22: How can disease be addressed via the dark genome?13:22-16:45: Which diseases are you tackling?16:45-18:02: What is the EchoHAYA platform?18:02-21:07: How does your lead candidate, HTX-001, work?21:07-22:00: Is the objective stopping fibrosis or reversing it?22:00-23:41: Other companies in the field23:41-24:52: Working with Eli Lilly24:52-27:15: A new frontier in medicine?27:15-28:43: Cost effectiveness28:43-30:07: Clinical trials30:07-31:48: Applications to other diseasesInterested in being a sponsor of an episode of our podcast? Discover how you can get involved here! Stay updated by subscribing to our newsletter

Timestamps: 5:22 - From the UK to Switzerland 11:29 - The dark genome and chronic diseases 17:35 - HTX001 and heart failure 26:44 - Sticking to grants at first 34:32 - Managing two separate teams This episode was sponsored by smzh, your independent go-to partner in all matters relating to finance. About Samir Ounzain: Samir Ounzain is the co-founder and CEO of HAYA Therapeutics, a precision medicines company targeting the regulatory genome for cardiovascular diseases, fibrosis and cancer. He holds a PhD from the University of Leicester and was previously a researcher at Imperial College London, University College London and CHUV Lausanne University Hospital before starting HAYA in 2019, together with his co-founder Daniel Blessing. Early on in his academic career Samir studied the so-called “dark genome” (also known as the “regulatory genome”), which at the time of discovery (2001) was considered “junk DNA”, i.e. the 98% of our DNA that apparently did not make or in any way affect our genes. More recent scientific research has discovered that this regulatory genome is key to understanding how our genes interact with our environment, and can therefore be useful in targeting environment-caused diseases like heart failure and cancer. HAYA's lead therapeutic candidate is HTX-001, an antisense oligonucleotide targeting Wisper, which is a tissue and cell-specific cardiac lncRNA known to play a role in heart failure. The company is also developing a pipeline of lncRNA-targeting candidates for the cell-specific treatment of diseases in other tissues, including the lungs and the microenvironment of solid tumor cancers. The added benefit of their drugs is that by targeting the “dark” 98%, instead of the 2%, they result in zero side effects: conventional drugs help patients treat their diseases but they also produce secondary unwanted effects because the proteins that they are targeting (in our 2%) are also responsible for other functions — this same issue does not exist when it comes to drugs which interact with the dark genome. HAYA Therapeutics is headquartered at the life sciences park Biopôle, in Lausanne, with additional laboratory facilities at JLABS, San Diego. They have raised a total of $25M in funding backed by a strong consortium of investors, including Broadview Ventures, Apollo Health Ventures, 4SeeVentures, BioInnovator, Bernina Bioinvest, Humboldt and Schroder Adveq. This cover portrait was edited by www.smartportrait.io Don't forget to give us a follow on⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠ Twitter⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠,⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠ Instagram⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠,⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠ Facebook⁠⁠⁠⁠⁠⁠⁠⁠⁠ ⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠and⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠ Linkedin⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠, so you can always stay up to date with our latest initiatives. That way, there's no excuse for missing out on live shows, weekly giveaways or founders' dinners.

References Front Endocrinol (Lausanne). 2022;13: 822221 Bach, J.S. 1721. Brandenburg Concert 2. BMV 1047 https://open.spotify.com/track/38OfejDZKqrUstmOpCw6D3?si=5e8eee6b6d974f97 --- Support this podcast: https://podcasters.spotify.com/pod/show/dr-daniel-j-guerra/support

Dr. Dechao Feng from the Department of Urology, Institute of Urology, West China Hospital, Sichuan University, discusses a research paper he co-authored that was published by Aging (Aging-US) in Volume 15, Issue 18, entitled, “Identification of senescence-related lncRNA prognostic index correlating with prognosis and radiosensitivity in prostate cancer patients.” DOI - https://doi.org/10.18632/aging.204888 Corresponding authors - Dechao Feng - fdcfenix@stu.scu.edu.cn, and Ping Han - hanping@scu.edu.cn Video interview - https://www.youtube.com/watch?v=zHiWwd5RlJw Transcription - https://aging-us.net/2023/10/26/behind-the-study-senescence-related-lncrna-prognostic-index-in-prostate-cancer/ Sign up for free Altmetric alerts about this article - https://aging.altmetric.com/details/email_updates?id=10.18632%2Faging.204888 Subscribe for free publication alerts from Aging - https://www.aging-us.com/subscribe-to-toc-alerts Keywords - aging, prostate cancer, senescence-related lncRNA prognostic index, biochemical recurrence, radiosensitivity, androgen response 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

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.07.22.550175v1?rss=1 Authors: Trewin, A. J., Weeks, K. L., Wadley, G. D., Lamon, S. Abstract: Cardiomyocyte calcium homeostasis is a tightly regulated process. The mitochondrial calcium uniporter (MCU) complex can buffer elevated cytosolic Ca2+ levels and consists of pore-forming proteins including MCU, and various regulatory proteins such as mitochondrial calcium uptake proteins 1 and 2 (MICU1/2). The stoichiometry of these proteins influences the sensitivity to Ca2+ and activity of the complex. However, the factors that regulate their gene expression remain incompletely understood. Long non-coding RNAs (lncRNAs) regulate gene expression through various mechanisms, and we recently found that the lncRNA Tug1 increased the expression of Mcu and associated genes. To further explore this, we performed antisense LNA knockdown of Tug1 (Tug1 KD) in H9c2 rat cardiomyocytes. Tug1 KD increased MCU protein expression, yet pyruvate dehydrogenase dephosphorylation, which is indicative of mitochondrial Ca2+ uptake was not enhanced. However, RNA-seq revealed that Tug1 KD increased Mcu along with differential expression of greater than 1000 genes including many related to Ca2+ regulation pathways in the heart. To understand the effect of this on Ca2+ signalling, we measured phosphorylation of Ca2+/calmodulin-dependent protein kinase II (CaMKII) and its downstream target cAMP Response Element-Binding protein (CREB), a transcription factor known to drive Mcu gene expression. In response a Ca2+ stimulus, the increase in CaMKII and CREB phosphorylation was attenuated by Tug1 KD. Inhibition of CaMKII, but not CREB, partially prevented the Tug1 KD-mediated increase in Mcu. Together, these data suggest that Tug1 modulates MCU expression via a mechanism involving CaMKII and regulates cardiomyocyte Ca2+ signalling which could have important implications for cardiac function. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.07.14.549055v1?rss=1 Authors: Samaddar, S., Srinivasan, B., Garg, K., Raj, N., Sultana, S., Mukherjee, U., Banerjee, D., Liau, W.-S., Palakodeti, D., Bredy, T. W., Banerjee, S. Abstract: Characterization of brain-enriched lncRNAs have predominantly been restricted to the nuclear compartment; with limited exploration of synaptic lncRNA functions. Our RNA-seq analysis of synaptoneurosomes identify 94 synaptically-enriched lncRNAs in the adult mouse hippocampus. Among these, we characterized the roles of Pantr1, Pvt1 and 2410006H16Rik (named SynLAMP) in glutamatergic synapse development, plasticity and memory. Pvt1 regulates dendritic arborization, spine morphology and glutamatergic synapse formation via a molecular framework of synaptogenic genes; as detected by RNA-seq analysis of the hippocampal trancriptome following Pvt1 knockdown. SynLAMP and Pantr1 modulate mEPSC amplitude and surface AMPA receptor distribution in mature synapses. We find activity-invoked redistribution of these synaptic lncRNAs and their concommitant reversible association with RNA binding proteins. The activity-dependent, transcript-specific synaptic localization of SynLAMP and Pantr1 indicate their synapse-centric function. SynLAMP specifically regulates basal and activity-invoked nascent translation in somato-dendritic compartments and its RNAi disrupts memory consolidation, underlining its input-specific role in synaptic translation. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.05.03.539260v1?rss=1 Authors: Irwin, A. B., Martina, V., Sint Jago, S. C., Bahabry, R., Schreiber, A. M., Lubin, F. D. Abstract: Dysregulation of long non-coding RNAs (lncRNAs) have been associated with Alzheimer's disease (AD). However, the functional role of lncRNAs in AD remains unclear. Here, we report a crucial role for the lncRNA Neat1 in astrocyte dysfunction and memory deficits associated with AD. Transcriptomics analysis show abnormally high expression levels of NEAT1 in the brains of AD patients relative to aged-matched healthy controls, with the most significantly elevated levels in glial cells. In a human transgenic APP-J20 (J20) mouse model of AD, RNA-fluorescent in situ hybridization characterization of Neat1 expression in hippocampal astrocyte versus non-astrocyte cell populations revealed a significant increase in Neat1 expression in astrocytes of male, but not female, mice. This corresponded with increased seizure susceptibility in J20 male mice. Interestingly, Neat1 deficiency in the dCA1 in J20 male mice did not alter seizure threshold. Mechanistically, Neat1 deficiency in the dorsal area CA1 of the hippocampus (dCA1) J20 male mice significantly improved hippocampus-dependent memory. Neat1 deficiency also remarkably reduced astrocyte reactivity markers suggesting that Neat1 overexpression is associated with astrocyte dysfunction induced by hAPP/A{beta} in the J20 mice. Together, these findings indicate that abnormal Neat1 overexpression may contribute to memory deficits in the J20 AD model not through altered neuronal activity, but through astrocyte dysfunction. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.04.21.537806v1?rss=1 Authors: Kumarswamy, R., Ravi, A. B. Abstract: Abdominal Aortic Aneurysms (AAAs) are asymptomatic vascular diseases with life threatening outcomes. Smooth-muscle cell (SMC) dysfunction plays an important role in AAA development. The contributions of non-coding genome, specifically the role of long non-coding RNAs (lncRNAs) in SMC dysfunction are relatively unexplored. We investigated the role of lncRNA TUG1 in the pathology of AAA. TUG1 was identified through lncRNA profiling in Angiotensin-II (Ang-II) treated SMCs. TUG1 was upregulated in Ang-II treated SMCs in vitro and its expression increased with progression of aneurysm in mouse model of Ang-II induced AAA. Ang-II induced TUG1 was blunted by inhibition of Notch signaling and TUG1 is demonstrated to be a transcriptional target of Notch. AAA tissues exhibited inversely correlated expression of TUG1 and SMC contractile markers. TUG1 knock-down via siRNA/shRNA increased SMC differentiation. ChIP, DNA-RNA IP, and RNA-IP experiments demonstrated that TUG1 interacts with transcriptional repressor KLF4 and aides in its recruitment to Myocardin promoter, thereby repressing SMC differentiation. In summary, we show a novel role for lncRNA TUG1 in Ang-II induced AAA wherein it modulates SMC differentiation via KLF4-Myocardin axis. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.04.19.537575v1?rss=1 Authors: Zink, J., Froemel, T., Boon, R. A., Fleming, I., Benz, P. M. Abstract: Endothelial tip cells are essential for VEGF-induced angiogenesis, but underlying mechanisms are elusive. Endothelial-specific deletion of EVL, a member of the mammalian Ena/VASP protein family, reduced the expression of the tip cell marker protein endothelial cell specific molecule-1 (Esm1) and compromised the radial sprouting of the vascular plexus in the postnatal mouse retina. The latter effects could at least partly be attributed to reduced VEGF receptor 2 (VEGFR2) internalization and signaling but the underlying mechanisms(s) are not fully understood. In the present study, we revealed that the expression of the long non-coding RNA H19 was significantly reduced in endothelial cells from postnatal EVL-/- mice and in siRNA-transfected human endothelial cells under hypoxic conditions. H19 was recently shown to promote VEGF expression and bioavailability via Esm1 and hypoxia inducible factor 1 (HIF-1). Similar to EVL-/- mice, the radial outgrowth of the vascular plexus was significantly delayed in the postnatal retina of H19-/- mice. In summary, our data suggests that loss of EVL not only impairs VEGFR2 internalization and downstream signaling, but also impairs VEGF expression and bioavailability in the hypoxic retina via downregulation of lncRNA H19. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.03.21.533694v1?rss=1 Authors: Dolivo, D. M., Rodrigues, A. E., Galiano, R. D., Mustoe, T. A., Hong, S. J. Abstract: Study of fibroblast biology, including the process of fibroblast activation, is critical to our understanding of wound healing, tissue fibrosis, and cancer. However, the rapid adoption of next-generation sequencing technologies, particularly single-cell RNA-seq and spatial transcriptomics, has revealed that fibroblast heterogeneity of both healthy and pathological tissues is more complicated than we currently understand. Therefore, a better understanding of molecular players that are not only indicative of but also that contribute to fibroblast activation is critical to piecing together the complete picture and to informing therapeutic strategies to combat associated pathologies. Here we focus on a long-noncoding RNA, LINC01013, recently implicated in pathological activation of cardiac fibroblasts and valvular interstitial cell. We analyze several sets of publicly available human transcriptomic data with the aim of determining whether LINC01013 correlates with fibroblast activation state, and whether compounds that affect fibroblast activation also modulate expression of LINC01013. We find that, in numerous independent datasets of healthy and diseased human fibroblasts, LINC01013 expression is associated with fibroblast activation. We also describe that, even in datasets comprised of small sample sizes, statistically significant correlations exist between expression of LINC01013 and expression of fibroblast activation markers ACTA2 and CCN2. This finding, while preliminary, suggests that changes in LINC01013 expression may be an indicator of changes in fibroblast activation state, and that LINC01013 might functionally contribute to fibroblast activation, lending potential rationale for greater exploration of this lncRNA in the context of tissue fibrosis or tumor stroma. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.03.04.531072v1?rss=1 Authors: Garza, R., Atacho, D., Adami, A., Gerdes, P., Vinod, M., Hsieh, P., Karlsson, O., Horvath, V., Johansson, P. A., Pandiloski, N., Matas, J., Quaegebeur, A., Kouli, A., Sharma, Y., Jonsson, M. E., Monni, E., Englund, E., Eichler, E. E., Gale Hammell, M., Barker, R. A., Kokaia, Z., Douse, C. H., Jakobsson, J. Abstract: The genetic mechanisms underlying the expansion in size and complexity of the human brain remains poorly understood. L1 retrotransposons are a source of divergent genetic information in hominoid genomes, but their importance in physiological functions and their contribution to human brain evolution is largely unknown. Using multi-omic profiling we here demonstrate that L1-promoters are dynamically active in the developing and adult human brain. L1s generate hundreds of developmentally regulated and cell-type specific transcripts, many which are co-opted as chimeric transcripts or regulatory RNAs. One L1-derived lncRNA, LINC01876, is a human-specific transcript expressed exclusively during brain development. CRISPRi-silencing of LINC01876 results in reduced size of cerebral organoids and premature differentiation of neural progenitors, implicating L1s in human-specific developmental processes. In summary, our results demonstrate that L1-derived transcripts provide a previously undescribed layer of primate- and human-specific transcriptome complexity that contributes to the functional diversification of the human brain. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.01.25.525483v1?rss=1 Authors: Zhang, C., Yi, X., Hou, M., Li, Q., Li, X., Lu, L., Qi, E., Wu, M., Qi, L., Huan, J., Qi, Z., Lv, Y., Kong, X., Bi, M., Feng, S., Zhou, H. Abstract: Cerebral ischaemia-reperfusion injury, during which neurons undergo oxygen-glucose deprivation/reoxygenation (OGD/R), is a notable pathological process in many neurological diseases. N1-methyladenosine (m1A) is an RNA modification that can affect gene expression and RNA stability. The m1A landscape and potential functions of m1A modification in neurons remain poorly understood. We explored RNA (mRNA, lncRNA, and circRNA) m1A modification in normal and OGD/R-treated neurons and the effect of m1A on diverse RNAs. We investigated the m1A landscape in primary neurons, identified m1A-modified RNAs, and found that OGD/R increased the number of m1A RNAs. m1A modification might also affect the regulatory mechanisms of noncoding RNAs, e.g., lncRNA-RBP interactions and circRNA translation. We showed that m1A modification mediates the circRNA/lncRNA-miRNA-mRNA ceRNA mechanism and that 3'UTR methylation of mRNAs can hinder miRNA-mRNA binding. Three methylation patterns were identified, and genes with different patterns had intrinsic mechanisms with potential m1A-regulatory specificity. Systematic analysis of the m1A landscape in normal and OGD/R neurons lays a critical foundation for understanding RNA methylation and provides new perspectives and a theoretical basis for treating and developing drugs for OGD/R pathology related diseases. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

On today's episode: Why is it ancient roman buildings are still standing? Self-healing concrete! What's better than camouflage? Invisibility! All that and more today on All Around Science. LINKS: [ARTICLE] First-in-Class Honeybee Vaccine Receives Conditional License from the USDA Center for Veterinary Biologics | Business Wire Evolution References De novo genes with an lncRNA origin encode unique human brain developmental functionality How humans got a new gene that makes our brains larger Comparison of human and chimpanzee genomes reveals striking similarities and differences THEME MUSIC by Andrew Allen https://twitter.com/KEYSwithSOUL http://andrewallenmusic.com

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.12.07.519382v1?rss=1 Authors: Fraile-Bethencourt, E., Khou, S., Wilson, R., Baris, A., Ruhl, R., Espinosa-Diez, C., Anand, S. Abstract: Endothelial cells are highly responsive to environmental changes that allow them to adapt to intrinsic and extrinsic stimuli and switch their transcriptome accordingly to go back to vascular homeostasis. Our previous data demonstrated that small non-coding-RNAs respond quickly to genotoxic stressors and determined endothelial cell fate and DNA damage response. To further understand the contribution of non-coding-RNAs, we profiled differentially expressed long non-coding RNAs in response to genotoxic stress and compared them to pro-angiogenic growth factor signaling. We identified the Maternally expressed gene 9 (MEG9) as a cytoprotective lncRNA in the endothelium. Gain and Loss-of-function studies indicate that MEG9 prevents endothelial cells from cell death, suggesting that MEG9 responses to genotoxic stress can be an adaptive and protective mechanism. Consistent with this phenotype, the knockdown of MEG9 decreases growth factor-dependent angiogenesis in a 3D fibrin gel angiogenesis assay. Deletion of the MEG9 ortholog, Mirg, in mice results in increased vascular leak in Matrigel plugs and a sex and age-dependent decrease in platelets. Mechanistically, we observed that both MEG9 knockdown in vitro and Mirg-deleted mice in vivo activated common pathways, including apoptosis, clotting, and inflammation. Indeed, the proinflammatory adhesion molecule ICAM1 was significantly increased in human and mouse endothelial cells in a MEG9-dependent manner, supporting the increased vascular permeability observed on MEG9 deficient cells. Taken together, our findings illustrate how genotoxic stress responses through dynamic modulation of lncRNAs, such as MEG9, trigger adaptive mechanisms to maintain endothelial function, while loss of these molecules contributes to maladaptive responses and endothelial cell dysfunction. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.11.30.518576v1?rss=1 Authors: Dueck, A., Althaus, L., Heise, K., Esfandyari, D., Bayguen, S., Brandes, R. P., Gagneur, J., Jae, N., Knolle, P., Leisegang, M. S., Maegdefessel, L., Meitinger, T., Petzold, N., Ramanujam, D., Sager, H., Schulz, C., Theodorakis, E., Uzonyi, A., Weinberger, T., Bader, M., Schmidt-Supprian, M., Engelhardt, S. Abstract: Cardiac resident macrophages (crMPs) were recently shown to exert pivotal functions in cardiac homeostasis and disease, but the underlying molecular mechanisms are largely unclear. Long non-coding RNAs (lncRNAs) are increasingly recognized as important regulatory molecules in a number of cell types, but neither the identity nor the molecular mechanisms of lncRNAs in crMPs are known. Here, we have employed deep RNA-seq and single cell RNA sequencing to resolve the crMP lncRNA landscape from healthy and diseased murine myocardium. CrMPs express previously unknown and highly cell type-specific lncRNAs, among which one lncRNA, termed Schlafenlnc, was particularly abundant and enriched in crMPs. We found Schlafenlnc to be necessary for migration-associated gene expression in macrophages in vitro and in vivo and essential for their adhesion and migration. Collectively, our data provide a basis to the systematic characterization of lncRNAs in crMPs and establish Schlafenlnc as a critical regulator of macrophage migratory functions. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Article: CAN OF SPINACH, a novel long non-coding RNA, affects iron deficiency responses in Arabidopsis thaliana Journal: Frontiers in Plant Science Year: 2022 Guest: Ahmet Bakirbas Host: Arif Ashraf Abstract Long non-coding RNAs (lncRNAs) are RNA molecules with functions independent of any protein-coding potential. A whole transcriptome (RNA-seq) study of Arabidopsis shoots under iron sufficient and deficient conditions was carried out to determine the genes that are iron-regulated in the shoots. We identified two previously unannotated transcripts on chromosome 1 that are significantly iron-regulated. We have called this iron-regulated lncRNA, CAN OF SPINACH (COS). cos mutants have altered iron levels in leaves and seeds. Despite the low iron levels in the leaves, cos mutants have higher chlorophyll levels than WT plants. Moreover, cos mutants have abnormal development during iron deficiency. Roots of cos mutants are longer than those of WT plants, when grown on iron deficient medium. In addition, cos mutant plants accumulate singlet oxygen during iron deficiency. The mechanism through which COS affects iron deficiency responses is unclear, but small regions of sequence similarity to several genes involved in iron deficiency responses occur in COS, and small RNAs from these regions have been detected. We hypothesize that COS is required for normal adaptation to iron deficiency conditions. --- Send in a voice message: https://anchor.fm/no-time-to-read-podcast/message

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.10.07.511381v1?rss=1 Authors: Augustin, J. J., Takayangi, S., Hoang, T., Winer, B., Blackshaw, S., Goff, L. A. Abstract: Ablation of the long non-coding RNA (lncRNA) Pantr2 re- sults in microcephaly in a knockout murine model of cor- ticogenesis, however, the precise mechanisms used are un- known. We present evidence that Pantr2 is a trans-acting lncRNA that regulates gene expression and chromatin ac- cessibility both in vivo and in vitro. We demonstrate that ec- topic expression of Pantr2 in a neuroblastoma cell line alters gene expression under differentiating conditions, and that both loss and gain of function of Pantr2 results in changes to cell-cycle dynamics. We show that expression of both the transcription factor Nfix and the cell cycle regulator Rgcc are negatively regulated by Pantr2. Using RNA binding pro- tein motif analysis and existing CLIP-seq data, we annotate potential HuR and QKI binding sites on Pantr2, and demon- strate that HuR does not directly bind Pantr2 using RNA immunoprecipitation assay. Finally, using Gene Ontology enrichment analysis, we identify disruption of both Notch and Wnt signaling following loss of Pantr2 expression, indi- cating potential Pantr2-dependent regulation of these path- ways. Copy rights belong to original authors. Visit the link for more info Podcast created by PaperPlayer

In this episode of the Epigenetics Podcast, we caught up with John Rinn from the University of Colorado in Boulder to talk about his work on the role of lncRNAs in gene expression and nuclear organization. The Rinn Lab pioneered the approach of screening the human genome for long noncoding RNAs (lncRNAs). More recently, the lab has shifted focus from measuring the number of lncRNAs to finding lncRNAs that have a distinct biological function in human health and disease. One example of such a lncRNA is FIRRE, which is present in all animals, however the sequence is not conserved, except for in primates. FIRRE contains many interesting features, such as repeat sequences and CTCF binding sites. In absence of FIRRE, defects in the immune system can be observed and also some brain defects may also be observed.   References Carter, T., Singh, M., Dumbovic, G., Chobirko, J. D., Rinn, J. L., & Feschotte, C. (2022). Mosaic cis-regulatory evolution drives transcriptional partitioning of HERVH endogenous retrovirus in the human embryo. eLife, 11, e76257. Advance online publication. https://doi.org/10.7554/eLife.76257 Long, Y., Hwang, T., Gooding, A. R., Goodrich, K. J., Rinn, J. L., & Cech, T. R. (2020). RNA is essential for PRC2 chromatin occupancy and function in human pluripotent stem cells. Nature Genetics, 52(9), 931–938. https://doi.org/10.1038/s41588-020-0662-x Kelley, D., & Rinn, J. (2012). Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome biology, 13(11), R107. https://doi.org/10.1186/gb-2012-13-11-r107 Khalil, A. M., Guttman, M., Huarte, M., Garber, M., Raj, A., Rivea Morales, D., Thomas, K., Presser, A., Bernstein, B. E., van Oudenaarden, A., Regev, A., Lander, E. S., & Rinn, J. L. (2009). Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proceedings of the National Academy of Sciences, 106(28), 11667–11672. https://doi.org/10.1073/pnas.0904715106 Guttman, M., Amit, I., Garber, M., French, C., Lin, M. F., Feldser, D., Huarte, M., Zuk, O., Carey, B. W., Cassady, J. P., Cabili, M. N., Jaenisch, R., Mikkelsen, T. S., Jacks, T., Hacohen, N., Bernstein, B. E., Kellis, M., Regev, A., Rinn, J. L., & Lander, E. S. (2009). Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 458(7235), 223–227. https://doi.org/10.1038/nature07672   Related Episodes The Role of lncRNAs in Tumor Growth and Treatment (Sarah Diermeier) The Role of Small RNAs in Transgenerational Inheritance in C. elegans (Oded Rechavi) Chromatin Structure and Dynamics at Ribosomal RNA Genes (Tom Moss)   Contact Active Motif on Twitter Epigenetics Podcast on Twitter Active Motif on LinkedIn Active Motif on Facebook Email: podcast@activemotif.com

Please join Guest Host Mercedes Carnethon along with first author Connie Hess and Guest Editor Gregory Lip as they discuss the article "Reduction in Acute Limb Ischemia With Rivaroxaban Versus Placebo in Peripheral Artery Disease After Lower Extremity Revascularization: Insights From VOYAGER PAD." Dr. Carolyn Lam: Welcome to Circulation on the Run, your weekly podcast summary and backstage pass to the journal and its editors. We're your co-hosts. I'm Dr. Carolyn Lam, associate editor from the National Heart Center and Duke National University of Singapore. Dr. Greg Hundley: And I'm Dr. Greg Hundley, associate editor, director of the Poly Heart Center at VCU Health in Richmond, Virginia. Dr. Carolyn Lam: Greg, our feature discussion is on a really important topic, peripheral artery disease. So important, so rampant, not talked about enough. And it's really insights from the VOYAGER-PAD trial telling us about the reduction in acute limb ischemia with Rivaroxaban versus placebo in peripheral artery disease after lower extremity revascularization. But before we get into all that, I want you to get your coffee while I tell you about my picks of today's issue. Should I start? Dr. Greg Hundley: Very good. Dr. Carolyn Lam: Okay. So the first paper deals with the residual ischemic risk following coronary artery bypass grafting surgery. We know that despite advances, patients following CABG still have significant risk. So this paper refers to a subgroup of patients from the REDUCE-IT trial with a history of CABG, which was analyzed to evaluate the efficacy of icosapent ethyl treatment in the reduction of cardiovascular events in this high risk patient population. Now, as a reminder, the REDUCE-IT trial was a multicenter, placebo controlled, double blind trial, where statin treated patients with controlled LDL cholesterol and mild to moderate hypertriglyceridemia were randomized to four grams daily of icosapent ethyl or placebo. They experienced a 25% reduction in risk of a primary efficacy endpoint, which was cardiovascular death, MI, stroke, coronary revascularization, or hospitalization for unstable angina. Now the current report tells us about the subgroup of patients from the trial with a history of CABG. Dr. Greg Hundley: Ah, Carolyn. So what did they find in this subgroup of patients? Dr. Carolyn Lam: So of the 8,179 patients randomized in REDUCE-IT, 22.5% had a history of CABG with 897 patients randomized to icosapent ethyl and 940 to placebo. Baseline characteristics were similar between the treatment groups and randomization to icosapent ethyl was associated with a significant reduction in the primary endpoint, as well as in key secondary endpoint and in total ischemic events compared to placebo. This yielded an absolute risk reduction of 6.2% in first events with a number needed to treat of 16 over a median follow up time of 4.8 years. So, Greg, I think you'll agree, icosapent ethyl may be an important pharmaco-therapeutic option to consider in eligible patients with a history of coronary artery bypass grafting surgery. Dr. Greg Hundley: Very nice, Carolyn. What an excellent summary. So Carolyn, for my first paper... And this study comes to us from Professor Judith Haendeler from the Leibniz Research Institute for Environmental Medicine. So Carolyn, this is a new type of quiz question. And as you listen to the presentation, help us predict the clinical implications. Okay, here we go. Dr. Greg Hundley: All right. So Carolyn, telomerase, also called terminal transferase, is a ribonuclear protein that adds a species dependent telomere repeat sequence to the three prime end of telomeres. And Carolyn, just to refresh our memories, a telomere is a region of repetitive sequences at each end of the chromosomes of most eukaryotes. And telomerase was discovered interestingly by Carol Greider and Elizabeth Blackburn in 1984. And together with some others, including Jack Szostak, they were awarded the 2009 Nobel Prize in physiology and medicine for discovery. Dr. Greg Hundley: So Carolyn, telomerase is active in gamuts and most cancer cells, but is normally absent from or at very low levels in most somatic cells. And the catalytic subunit of telomerase called telomerase reverse transcriptase or trt has protective functions in the cardiovascular system, particularly in regard to ischemia reperfusion injury. And interestingly trt or telomerase reverse transcriptase is not present in the nucleus, but also in mitochondria. However, for us in cardiovascular medicine, it is unclear whether nuclear or mitochondrial trt is responsible for the observed protection. Dr. Carolyn Lam: Wow, fascinating. So what did today's paper find? Dr. Greg Hundley: Right, Carolyn. So it was mitochondrial, but not nuclear telomerase reverse transcriptase that was found critical for mitochondrial respiration during ischemia reperfusion injury. And mitochondrial telomerase reverse transcriptase improves complex 1 subunit composition. And trt is present in human heart mitochondria and remote ischemic preconditioning increases its level in these organelles. Also, Carolyn TA65 was found to have comparable effects ex vivo and improved migratory capacity of endothelial cells and myofibroblast differentiation. So Carolyn, with this summary, can you help speculate on the clinical implications of this paper? Dr. Carolyn Lam: Oh, Greg. You set it up so nicely. So I would speculate that the clinical implications are that an increase in the mitochondrial telomerase reverse transcriptase or trt would be able to help with cardioprotection in ischaemic reperfusion injury, or at least that's what we hope and that's where we should be going with this. Am I right? Dr. Greg Hundley: Absolutely, Carolyn. So in the future, this research showing that trt and cardioprotection... Maybe we increase this and it could serve as a therapeutic strategy. Excellent job, Carolyn. Dr. Carolyn Lam: Thank you, Greg. All right. My next paper is a preclinical paper. I will spare you of difficult quizzes and maybe... This is just so neat. Let me tell you about it. So the study really provides novel insights into the mechanisms underlying smooth muscle cell phenotypic modulation that contributes to the development of vascular diseases like renal atherosclerosis and restenosis after angioplasty. So very important. Dr. Jiliang Zhou from Medical College of Georgia and colleagues basically used an in silico approach to probe unbiased, proprietary, and diverse, publicly available bulk RNA-Seq and scRNA-Seq datasets to search for smooth muscle cell specific long non-coding RNAs or lncRNAs. Dr. Carolyn Lam: The search ended up identifying CARMN, which stands for cardiac mesoderm enhancer-associated non-coding RNA, CARMN. As a highly abundant, highly conserved smooth muscle cell specific lncRNA, CARMN was recently reported to play roles in cardiac differentiation and was initially annotated as a host lncRNA for the microRNA, the MIR143145 cluster, which is the best characterized microRNAs in regulating smooth muscle cell differentiation and phenotypical modulation. Dr. Carolyn Lam: But in the current study, the authors confirmed the expression specificity of CARMN using a novel GFP knock-in reporter mouse model, and discovered that CARMN is downregulated in various vascular diseases. They further found that CARMN is critical for maintaining vascular smooth muscle cell contractile phenotype, both in vitro and in vivo by directly binding to the smooth muscle cell specific transcriptional cofactor known as myocardit. Dr. Greg Hundley: Okay. Carolyn, what a beautiful summary here. So what's the take home message here? Dr. Carolyn Lam: So these findings collectively suggest that CARMN is a key regulator of vascular smooth muscle cell phenotype, and therefore represents a potential therapeutic target for the treatment of smooth muscle cell related proliferative diseases. Dr. Carolyn Lam: Well, Greg, thanks for letting me to tell you about that one. But let me tell you also about other papers in today's issue. There's an exchange of letters between Dr's Lee and Chew on high rates of coronary events in the rapid troponin T0 one hour protocol. Is it a reality or illusion? There's an ECG Challenge by Dr. Liu on “Acute Inferior Wall Myocardial Infarction. What is the Culprit Artery? In Cardiology News, Bridget Kuehn writes on persistent heart effects of COVID-19 and how that emphasizes the need for prevention. Dr. Greg Hundley: Very nice, Carolyn. Well, I've got a Research Letter to tell you about from Professor Huang, entitled “High Prevalence of Unrecognized Congenital Heart Disease in School-Age Children in Rural China: A Population-Based Echocardiographic Screening Study.” Well, Carolyn, what a fantastic issue. And how about we get onto that feature discussion now and learn more out lower extremity revascularization and insights from the VOYAGER-PAD study? Dr. Carolyn Lam: Let's go, Greg. Dr. Mercedes Carnethon: Good morning, everyone. Welcome to this episode of Circulation on the Run podcast. I'm Mercedes Carnethon, Professor and Vice Chair of Preventive Medicine at the Northwestern University Feinberg School of Medicine and associate editor of the journal. Really excited today to hear from one of our authors of a particularly interesting piece that we'd like to discuss today about peripheral artery disease after lower extremity revascularization. Dr. Mercedes Carnethon: And we have with us today, the lead author, Dr. Connie Hess from the division of cardiology at the University of Colorado School of Medicine in Aurora. And we have Dr. Gregory Lip with us. So welcome to the both of you. Professor Gregory Lip: Hello there. Dr. Connie Hess: Thank you for having me. Dr. Mercedes Carnethon: Thank you both for joining us. This is really exciting. I know that when I read this piece, I was really excited to think about the implications that these study findings from this clinical trial will have for a very important clinical problem of peripheral arterial disease and those complications. So, Connie, would you be willing to start by telling us a little bit about what you found in this study? Dr. Connie Hess: Yeah, absolutely. I think maybe a good place to start first is, if that's okay, is just a little bit of the background and why we looked at this and thought to look at this. I think as you're both probably aware, peripheral artery disease is a very highly prevalent condition. It affects a lot of people, but there's not a lot of awareness about it. It's in some ways the forgotten manifestation of atherosclerosis. And so acute limb ischemia in particular is a very feared complication of peripheral artery disease. And unlike things like ST elevation, myocardial infarction, and stroke about which patients and providers have a lot of knowledge and understanding, many people don't know about acute limb ischemia. And in particular ALI, acute limb ischemia, is a complication of peripheral revascularization that many of us as proceduralists are very concerned about. Dr. Connie Hess: And so what we wanted to do was use this very unique clinical trial and dataset to look at acute limb ischemia, to describe it, to better understand it, especially after a peripheral revascularization. And then also to look at the effect of Rivaroxaban plus aspirin versus aspirin alone on this feared outcome. We're lacking therapies to effectively prevent ALI. Dr. Connie Hess: And so if I just briefly review the trial, VOYAGER-PAD randomized 6,564 patients undergoing peripheral revascularization, both surgical or endovascular to Rivaroxaban, 2.5 milligrams twice daily versus placebo on top of aspirin. And then providers could use prochidagril for up to six months per their discretion. Now, the primary outcome for VOYAGER-PAD was very unique. This was a five point composite that looked at acute limb ischemia, major amputation of vascular etiology, myocardial infarction, ischemic stroke, or cardiovascular death. Dr. Connie Hess: And so in this trial in the primary results, Rivaroxaban plus aspirin versus aspirin alone was highly effective in reducing the primary endpoint, that five point composite I just described. And so we were excited to look specifically at the effect of this combination therapy on acute limb ischemia alone. What we found to begin with, I think in terms of describing acute limb ischemia is important. So the three year cumulative incidence in the patients assigned a placebo was about 8% for ALI. So this is not an uncommon problem. And in fact, we found that there was incidents of ALI occurring quite early after the procedure and that the risk persisted, even three years out. Dr. Connie Hess: And Rivaroxaban plus aspirin versus aspirin alone was very effective in reducing ALI by about 33%. Beyond that, we also looked at ALI in terms of severity of these complications. And we found that about a third of patients had a very severe ALI event that we defined as ALI followed by death, major amputation, or requiring a prolonged hospitalization with time in the intensive care unit. And for those patients, Rivaroxaban plus aspirin was even more effective with almost a 55% reduction. Dr. Connie Hess: Lastly, I think we also looked at just the patients who are at risk for ALI after peripheral revascularization. And we did identify some patient and procedural factors that might help us identify these patients. For example, having a prior lower extremity revascularization, having more severe PAD as indicated by a low ankle brachial index, undergoing surgical revascularization, and having longer target lesions. So I think we were able to describe ALI in a way that some other trials and datasets have not been able to do. And then also beyond that to provide some evidence for effective therapy to prevent this complication. Dr. Mercedes Carnethon: All of that is so exciting. And for somebody coming to this outside of the initial field, I can certainly see a lot of innovations that you describe in what you've done and the importance to the population of people who experience this very debilitating illness. So it's really wonderful to see this in print. So tell me, Greg, what excited you as the editor about this particular paper? So what made it really stand out in your mind? Professor Gregory Lip: Thanks, Mercedes. And firstly, congratulations to Dr. Hess for a really nice paper. And I think that it's really important because many cardiologists tend to neglect looking at and managing peripheral artery disease, especially with the medical therapies. And I think VOYAGER-PAD was an important advancement of how we can have... You could say, dual blockade, both with low dose anticoagulation plus antiplatelets should improve the outcomes. Professor Gregory Lip: So I think it really brings to the forefront how we should optimize medical therapy and peripheral disease. It's not simply a matter of surgery or just intervention with stenting. And I think maybe the other important aspects in regard to this study, this trial is when you combine an antiplatelet with an anticoagulant, it's worth flagging up the potential for added risk of bleeding. And it's therefore the fact that your analysis included to identify the patients at high risk of acute limb ischemia, then we will actually facilitate risk stratification so that we can perhaps target the very high risk patients where that balance in terms of the net benefit for the combination therapy compared to aspirin alone would be there because you're balancing the thrombotic and limb ischemic outcome versus the potential for bleeding. Professor Gregory Lip: We are also using of course, in VOYAGER-PAD low dose Rivaroxaban, which is not the stroke prevention dose of Rivaroxaban in everyday clinical practice. And that's worth emphasizing. So we translate peripheral disease dosages or regimes versus what we see in other prothrombotic situations like atrial fibrillation, which leads to stroke. And that's probably worth emphasizing. And I think really what is most important is that we can hopefully identify the high risk subset of patients with peripheral artery disease at risk of acute limb ischemia, where they're going to particularly benefit from combination therapy. So an important advance for medical therapy for peripheral disease. So congratulations on this paper as well. Dr. Mercedes Carnethon: Yeah. I really echo that. One of the things that when we write original research papers, we are always encouraged not to speculate beyond the data that we're presenting. But one of the values of this podcast is that we get a chance to really needle the authors and challenge them to speculate about what does this mean? What does this mean for the field? And Connie in particular, what do you think the next steps are for patients and providers based on what you found today in this excellent study? Dr. Connie Hess: Mercedes, that's a great question. Certainly we always want to know what next? What are the implications of these findings? And so to me, I echo both of you. I'm personally very excited as someone in the field. And as a proceduralist, I'm very excited that for the first time, we actually have data to support a medical therapy post intervention. Although there's a lot of use of things like dual antiplatelet therapy and even anticoagulation, there's not a lot of data to support it after peripheral revascularization. So this really is the first large scale, high quality data to support a strategy. And so I do think that this is something that we should adopt. Dr. Connie Hess: I think what I didn't mention before is that actually, when you look at the cumulative incidence curves for ALI in the Rivaroxaban versus placebo groups, not only do you see that there is early risk for ALI after the procedure... And typically we think of this as potentially technical failure that we can't modify, but you saw a very early benefit for Rivaroxaban plus aspirin versus aspirin alone here, suggesting that the sooner you start, the better. Of course, it has to be when it's safe from a bleeding perspective and when the proceduralist feels comfortable with this. But I do think that the implications are that we should... We proceduralists, especially in this population and as professor Lip mentioned the high risk patients in particular, should be starting this therapy as soon as we feel safe. And so I think the data are there. The next step to me is really increasing awareness, in particular among providers who are treating these patients, but even among our other colleagues or cardiovascular colleagues who may not treat these peripheral artery disease patients primarily, but do see them in their clinic. Dr. Connie Hess: A lot of them have cardiovascular disease and other cardiovascular problems, but to increase awareness that this dual pathway inhibition with low dose factor 10, anticoagulation inhibition and low antiplatelet therapy is a viable and favorable combination and to continue this so that when they see this, they're not surprised and not questioning whether to stop it. Dr. Connie Hess: I think also of course now that we are getting more data to understand how morbid and bad ALI is, I do think we also need to educate patients. You both probably recall all the tremendous efforts that were made to increase awareness in the patient population about myocardial infarction and stroke. You have all those campaigns and understanding the importance of timely intervention and reperfusion. I think that actually should be done for acute limb ischemia as well. We need to have providers aware about this complication and understanding emergent treatment. We also need patients to understand it so they can come in sooner so that they're not having delayed presentation for which primary amputation is the only treatment option. So I think there's a lot of work to be done, but certainly very excited that we have a better understanding of ALI as well as preventive therapy. Dr. Mercedes Carnethon: I really appreciate that final word. And I really can't think of a better way to wrap up than the final words that you provided, Connie. Both the context that you provided around this piece and your thoughts as well, Greg, about what makes it innovative and exciting for our readership at Circulation are really invaluable. So I just really want to thank you for joining us as an author and thank you for selecting this, Greg. This is a really great piece. I've learned a good deal. Dr. Mercedes Carnethon: This is me, Mercedes Carnethon, wrapping up this addition of Circulation on the Run, following an outstanding discussion with Dr. Connie Hess from the University of Colorado and Greg Lip, the handling editor for the piece. Dr. Greg Hundley: This program is copyright of the American Heart Association, 2021. The opinions expressed by speakers in this podcast are their own and not necessarily those of the editors or of the American Heart Association. For more, visit ahajournals.org.

Mauro Calabrese, Associate Professor at UNC Chapel Hill and Director of Graduate Studies in the Department of Pharmacology, discusses the future of RNA-based therapeutics and the role of lncRNA in gene transcription. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, with a focus on genomics. https://www.bioinformaticscro.com/

In this episode, we are diving deep into the world of the non-coding genome and, more specifically, an exciting new class of biomolecules - the long non-coding RNAs (lncRNA). Welcome, Dr. Samir Ounzain, the co-founder and CEO of HAYA Therapeutics. Samir and his startup HAYA are developing first-in-class therapies to target lncRNA responsible for the manifestation of various diseases. Samir and HAYA are aiming at fibrosis first, but have in mind a plethora of other conditions that can be treated by their approach. Join us for an insightful conversation on the non-coding genome, the journey from basic science to entrepreneurship, and the future of precision therapeutics.Together with Samir, we discussed:◦ The founding story of HAYA Therapeutics◦ The role of non-coding genome in human health◦ Ability to tweak non-coding genome to treat diseases◦ Postponing aging using lncRNAs◦ Impact on the future of precision medicine◦ Prerequisites for founding a successful biotech companyGet in touch with Samir:◦ LinkedIn: https://www.linkedin.com/in/samirounzain/◦ Twitter: @ispiyou◦ Website: https://www.hayatx.com/Make sure to download the full show notes with our guest's bio, links to their most notable work, and our recommendations for further reads on the topic of the episode at pmedcast.com

This week's episode features author Aaron Baggish and Associate Editor & Editorialist Satyam "Tom" Sarma as they discuss the article "SARS-CoV-2 Cardiac Involvement in Young Competitive Athletes." Dr. Carolyn Lam: Welcome to Circulation on the Run, your weekly podcast summary and backstage pass to the Journal and its editors. We're your co-hosts ... I'm Dr. Carolyn Lam Associate Editor from the National Heart Center and Duke National University of Singapore. Dr. Greg Hundley: And I'm Dr. Greg Hundley, Associate Editor, Director of the Pauley Heart Center from VCU health in Richmond, Virginia. Dr. Carolyn Lam: Greg, this feature discussion is just so relevant to our current times. It talks about SARS-CoV-2 cardiac involvement in young competitive athletes. Oh, one that I'm sure we're all dying to get to. Very important. But first, let's tell you what's in this week's issue. Greg, you want to go first? Dr. Greg Hundley: You bet, Carolyn. I'm going to grab a cup of coffee, and we're going to dive into the world of preclinical science. Our first paper comes to us from Professor Naftali Kaminski from Yale University. Carolyn, these investigators reprocessed human control single-cell RNA-sequencing, or scRNA sequence data from six datasets to provide a reference atlas of human lung endothelial cells to facilitate a better understanding of the phenotypic diversity and composition of cells comprising the lung endothelium. Also, the signaling network between different lung cell types was studied. Dr. Carolyn Lam: Wow. Okay. So what did they find, Greg? Dr. Greg Hundley: Six lung single-cell RNA-sequencing datasets were reanalyzed and annotated to identify over 15,000 vascular endothelial cells from 73 individuals. Beyond the broad cellular categories of lymphatic, capillary, arterial and venous endothelial cells, the co-authors found two previously indistinguishable populations. Pulmonary venous endothelial cells, called COL15A1neg localized to the lung parenchyma and systemic venous endothelial cells, COL1581positive localized to the airways and visceral pleura. Dr. Greg Hundley: Now, among capillary endothelium cells, the authors confirmed their subclassification into recently discovered aerocytes characterized by EDNRB, SOSTDC1, and TBXX2 and general capillary endothelial cells. The authors confirmed that all six endothelial cell types, including the systemic venous endothelial cells and aerocytes, are present in mice and identified endothelial marker genes conserved in both humans and mice. Dr. Greg Hundley: So Carolyn, I'm going to take a question I bet you're getting ready to ask. What are the clinical implications of this research? Well, mainly that understanding the lung endothelial diversity is crucially important to identify new therapeutic approaches for vascular diseases such as pulmonary hypertension. Dr. Carolyn Lam: Wow. That was interesting, Greg. Thank you. I've got another one from basic science world as well, and this one talks about the initial functional characterization of an exercise-induced cardiac physiological hypertrophy associated novel long non-coding RNA or LncRNA. Dr. Greg Hundley: Okay, Carolyn. Quick quiz. Can you remind us what these long-coding RNAs are? Dr. Carolyn Lam: Ha. Sure. So long non-coding RNAs or LncRNA refers to RNAs that are longer than 200 nucleotides and lack the potential to encode proteins, but have still been closely related to the occurrence and development of many diseases. Dr. Carolyn Lam: The current paper comes from co-corresponding authors, Dr. Li from the First Affiliated Hospital of Nanjing Medical University and Dr. Xiao from Shanghai University. They identified a LncRNA in the heart named cardiac physiological hypertrophy associated regulator, or CPhar. This was increased following exercise training and was necessary for exercise-induced cardiac growth. In neonatal mouse cardiomyocytes, over expression of this LncRNA induced an increase in these cardiomyocytes' size and expression of proliferation markers while inhibition of the LncRNA reduced these neonatal mouse cardiomyocytes' size and the expression of proliferative markers. Over expression of the LncRNA led to a reduction in oxygen glucose deprivation reperfusion-induced cardiomyocyte apoptosis, while LncRNA knockdown aggravated the apoptosis. Dr. Carolyn Lam: In vivo over expression of that LncRNA prevented myocardial ischemia reperfusion injury and improved cardiac function. So mechanistically though, the transcription factor, ATF7, acted as the functional downstream effector of this cardiac physiological hypertrophy associated regulator, the LncRNA. Dr. Carolyn Lam: Now Greg, following your example, I'm going to ask what are the clinical implications and tell you. So these results provide new insights into the regulation of exercise-induced cardiac physiological growth, demonstrating the cardioprotective role of this LncRNA known as cardiac physiological hypertrophy associated regulator in the heart. It also expanded our knowledge and understanding of the functions and fundamental mechanisms of LncRNAs in general. Dr. Greg Hundley: Wow, Carolyn. Beautifully described. Well, my next paper comes to us from the world of clinical science and really it's kind of something that's going to get into spending. It comes to us from Dr. Brandon Bellows from Columbia University. Dr. Greg Hundley: So Carolyn, spending on cardiovascular disease and cardiovascular risk factors, in total cardiovascular spending, accounts for a significant portion of overall US healthcare spending. The author's objective was to describe US adult cardiovascular spending patterns in 2016 and changes from 1996 to 2016, and look at the factors associated with these changes over time. Dr. Carolyn Lam: Wow. Okay. So were the authors are viewing time-dependent changes in cardiovascular spending. Is that it? What did they find? Dr. Greg Hundley: Absolutely Carolyn. So a bunch of data. Just kind of some interesting facts here. So let's work through them. Adult cardiovascular spending increased from 212 billion in 1996 to 320 billion in 2016, a period when the US population increased by over 52 million people and the median age increased from 33 to 36.9 years. Dr. Greg Hundley: Next, over this period, public insurance was responsible for the majority of cardiovascular spending at 54% followed by private insurance at 37% and out-of-pocket spending at 9%. Dr. Greg Hundley: Next, health services for ischemic heart disease at about 80 billion and hypertension, 71 billion, led to the most spending in 2016. Dr. Greg Hundley: Next, increased spending between 1996 and 2016 was primarily driven by treatment of hypertension, hyperlipidemia, and atrial fibrillation flutter on which spending rose by $42 billion, $18 billion and $16 billion respectively. Increasing service price and intensity alone were associated with 51% or 88 billion, and cardiovascular spending increased from 1996 through 2016. Whereas, changes in disease prevalence was associated with a 37% or $36 billion spending reduction over the same period after taking into account population growth and population aging. Dr. Greg Hundley: So in summary, Carolyn, US adult cardiovascular spending increased by about $100 billion from 1996 to 2016. Maybe policies tailored to control service price and intensity and preferentially reimburse higher quality care, perhaps that could help counteract future spending increases due to population aging and growth. Dr. Carolyn Lam: Oh, wow. Those are staggering numbers. Thanks Greg. Now let's go through what else is in this week's issue. There's an exchange of letters between doctors Mehmood and Houser regarding the article, Cardiac Remodeling During Pregnancy with Metabolic Syndrome: A Prologue of Pathological Remodeling. There's an ECG challenge by Dr. Real on an unusual call from the urology ward. There's also a Research Letter from Dr. Molkentin on cardiac cell therapy failing to rejuvenate the chronically scarred rodent heart. And finally a Special Report by Dr. Althouse on Recommendations for Statistical Reporting in Cardiovascular Medicine: A Special Report from the American Heart Association. Dr. Greg Hundley: Great, Carolyn, and I've got a Perspective piece entitled, Intravenous Iron Therapy in Heart Failure with Reduced Ejection Fraction: Tackling the Deficiency. It's from Professor Ardehali. Dr. Greg Hundley: Well, Carolyn, how about we get on to that feature discussion and learn more about SARS-CoV-2 in young competitive athletes. Dr. Carolyn Lam: Ooh, let's go. In our current COVID-19 pandemic a huge question is, does cardiac involvement in athletes with COVID-19 preclude their further participation in sports? What is their involvement after they've recovered from COVID-19? Guess what? Today's feature discussion is really hitting the spot with this question. So pleased to have with us the corresponding author of the feature paper, Dr. Aaron Baggish from Massachusetts General Hospital, as well as Dr. Satyam Sarma also known as Tom Sarma, our dear Associate Editor from UT Southwestern, who is also an editorialist for today's paper. So welcome Aaron and Tom. Aaron, could you start us off by describing your study and what you found? Dr. Aaron Baggish: Sure. So just very briefly, some historical context. As everyone is quite aware, when we first started seeing COVID-19 in the hospital, there was a lot of concern about what the virus did to the hearts in people that were sick enough to be hospitalized. Those of us in the sports cardiology community were quite concerned that when young athletes that developed COVID-19 infection got sick and then returned to sport, that we'd be seeing the adverse events associated with cardiac involvement. So that was the impetus to start the ORCCA Registry, which was really an opportunity to try to capture the large-scale experience with collegiate athletes returning to sport after COVID-19 infection. Indeed, with roughly 19,000 student athletes across 42 universities, there were approximately 3,000 that developed COVID-19 infection and then went through some form of cardiac screening prior to return to play. The registry was really about telling that story of what we found and what we think the implications are. Dr. Carolyn Lam: Aaron, I mean, first of all, more than 19,000 athletes recruited in just ... What was it? September 1st to December 31, 2020? How did you accomplish this amazing registry so quickly? That's amazing. Dr. Aaron Baggish: I need to acknowledge the fact that this was an incredible team effort. I was joined and continue to be joined in this by my co-PIs, Dr. Jon Drezner and Kim Harmon, who are sports medicine physicians out of the Seattle area, and the combination of cardiology, expertise and sports medicine expertise really able to pull in many of the large universities and colleges around the country, including most of the Power Five schools to participate in this registry. Dr. Aaron Baggish: In short order, team physicians from all these schools understood the importance of this work and agreed to partner with us to work very hard to enroll their student athletes and to provide us with the information we needed. Dr. Carolyn Lam: Incredible. But with the foresight, congratulations, this in and of itself is amazing. Now, could you please tell us what you found? Dr. Aaron Baggish: Sure. So we found that indeed, as we expected, that these student athletes were undergoing a fair bit of cardiac testing prior to being allowed to return to sport, and that there was variability in terms of what type of testing they were getting. The majority of schools were following what at that point were the recommendations, which were do, what we call the cardiac triad testing, which includes an echocardiogram, a high-sensitivity troponin, and an ECG and to use that information to either clear athletes or send them through further clinically indicated tests. A small number of early adopters had decided to do mandatory cardiac MRIs. So within that, we were able to understand what the prevalence, if you will, of cardiac involvement in these COVID-19 student athletes looked like, and it varied as a function of what type of tests people were doing. Dr. Carolyn Lam: And? Give us a sneak peek. Dr. Aaron Baggish: As people would expect, the more sensitive tests you do, the more abnormalities you detect. So among the schools that were using a mandatory cardiac MRI approach, there was a 3% prevalence, if you will, of either definitive, probable or possible COVID-19 cardiac involvement. When schools were following the triad testing first followed by clinically indicated CMR that prevalence was much less. It was approximately 0.5 or 0.6%. So I would emphasize that on the whole, regardless of which test was being used, that the involvement was at a much lower rate than we expected based on what we saw early in the hospitalized patient experience. So I think it's a very good news story. Dr. Carolyn Lam: Indeed. That's exactly, I think the title almost of Tom's editorial. Tom, could I bring you in here, please? Could you give us the context of this and then tell us what as editors we thought of the paper when it kind of reached out doors at Circulation? Dr. Satyam “Tom” Sarma: Sure. No, this was, I actually remember almost exactly when I was asked to handle this paper from an editorial standpoint. Joe texted me, Joe, our editor-in-chief texted me ... I think, the night, actually it was a Friday night I think ... That we had a really important paper, would you be able to take care of it on an expedited basis? I said, "Of course." So took a look at it over the weekend, and it's one of those papers when you're reading it, you almost wish you had a time machine because you realize if we had known this information eight, nine, 10, 11 months ago, it would have totally changed how we handle the pandemic from an athlete and young person standpoint. So from that aspect, I thought this is obviously a very high impact paper. Dr. Satyam “Tom” Sarma: Which then led me to the second challenge is finding the right reviewers for this paper because obviously this is a very controversial topic. We wanted to make sure we had the best reviewers we can get. The challenge, unfortunately, was that a lot of my usual go-to reviewers were actually members of the ORCCA Registry. So there were some issues with conflict of interest there, and so from a reviewer standpoint, I looked to sort of leaders in the field who had done something similar. The first thing that came to mind was really how the field has handled ECG screenings for our young athletes. I think there's, again, a perspective there that I think is very similar to how do you handle patients or young athletes with COVID and then how do you emphasize shared decision making? So from that standpoint, I had a narrow list of experts in shared decision making in sports cardiology, and really leaned on them to help guide us through the process because this is a complex paper. Dr. Satyam “Tom” Sarma: I think their feedback was instrumental in really helping to kind of distill the message, to kind of phrase things in a way that allowed the message to be easily digested by both the lay media, but more importantly, by sports trainers and athletic directors around the country. From that standpoint we really work hard and again, really thank you to Aaron and Jonathan on this manuscript because they worked so hard with our reviewers. They were incredibly responsive to almost every review comment. From that standpoint, I think the end result was amazing to really see it in final format. Dr. Carolyn Lam: I love that behind-the-scenes look. Thank you so much, Tom. What is the strong clinical implication of this? If you have questions for Aaron, please go ahead. Dr. Satyam “Tom” Sarma: Sure. No, I think the biggest thing for us as editors and sort of from the public health impact was, as Aaron mentioned, some schools have unlimited resources to really throw as much money as they can at the problem or what they think is the best approach to the problem. Again, when you have unlimited resources, you can get the "best tests." I think, unfortunately not every school in this country, both from a collegiate or high school level, has a capacity and more importantly, around the world. That's a really important limiting factor. Dr. Satyam “Tom” Sarma: Is there a way to distill the algorithm in a way that's both safe for the athletes, but more importantly is feasible for most schools? For us, that was the most important public health message was really to get that out there. The second of course, was that thinking back to last summer, just how many COVID myocarditis papers we handled in Circulation. Looking back with the again, in the heat of the battle, things are always challenging, but just to sort of see how the pendulum shifted in such a 180 degree sort of manner. So that also I think was important to get out there as well. Dr. Carolyn Lam: Yeah. And exactly why this paper is so important. So thank you once again for publishing it with Circulation. Tom though ... Okay. I mean, not to underestimate the MRI findings and so on. I think you had a question for Aaron in relation to that? Dr. Satyam “Tom” Sarma: I do. One of the challenges, again, being on the myocardial side is that we're not always experts in the papers we're assigned, and it's obviously been an incredible learning process. For me, I was hoping to pick your brain a little bit about the MRIs and sort of how you think the field will evolve from a sports cardiology standpoint. Especially as scanners get more powerful, as scanners get more sensitive, the challenges I think the field's going to have is really detecting the tiniest fleck of an abnormality. Dr. Satyam “Tom” Sarma: I think the context here is really the recent paper out of the Big 10 where they MRI'd, I believe, everyone in that registry ... I want to say it was over 2,000 athletes. Just out of curiosity, how was that handled, again, amongst your co-authors in deciding how best to present the MRI data? I like how you use the probabilistic language of it's either definite, probable or possible. How do you see that sort of progressing in terms of is that something practical that can be used by sports trainers and sports medicine staff to help restratify your athletes or athletes? Dr. Aaron Baggish: Tom, there's so much packed into that question. Let me try to unpack it piece by piece. So first off in our registry, there were a few schools that were early adopters in mandatory CMR screening, and so we wanted to very much responsibly report that. Again, there was about a 3% prevalence of something being abnormal with the myocardium based on the scans. We also realized that not all abnormalities were created equal, and that's why we did come up with that definitive, possible, probable nomenclature to really capture the fact that there were a few people that looked like they had overt myocarditis. But the vast majority had non-specific findings that those of us as clinicians pre-COVID would not have considered myocarditis. Dr. Aaron Baggish: The issue with MRI is a complicated one. The way I like to think about this as, as you mentioned earlier, is to go back to the historical experience we had with ECG screening in which doing that before we understood how to use it as a screening tool caused more problems than it solved. Dr. Aaron Baggish: It was really back in the mid-2000s when the Italians published their first ECG screening paper that the Americans got interested in it. What we learned is that if you used ECG, and this applies to MR too, without having good normative data, without understanding the cost implications, without having the experts prepared to interpret the test and deal with the downstream findings, that you're just not ready for prime time. Dr. Aaron Baggish: While I think the use of MRI as a screening technique during COVID was done with the best of intentions, I think the Big 10 paper, which is a very important dataset in this discussion, highlighted why MRI is just simply not a useful screening tool right now. If you look across their schools, they had tremendously variable rates of cardiac involvement, which is not a function of pathobiology. This virus is not different in Virginia than it is in Tennessee than it is in Wisconsin. It's just simply that people are using the tool in different ways and coming up with different findings. What we're now seeing clinically is that all these MRIs are finding a lot of stuff that either we don't want to care about or we don't want to know, and we're stuck dealing with it. So a challenge ahead of us, for sure. Dr. Satyam “Tom” Sarma: No, I think that's a really important point, Aaron. I think looking back even from a clinical standpoint in those, didn't not necessarily look at athletes, I think what you bring up is really important. The cognitive bias. Find something abnormal. I do wonder if you could talk a little bit about ... One of the other concerns we had behind the scenes was if you know an athlete, if you're an MRI reader and you know an athlete or the scan in front of you says 19-year-old athlete with COVID, can you talk a little bit about the cognitive biases that kind of go into sort of assuming either the worst case scenario, especially with athletes, because again, these are young, robust, healthy people who may or may not be on TV or in a very public format. How do you handle that as a sports cardiology in general, just kind of overcoming the cognitive bias, both from a public policy standpoint, but also from a lay public standpoint? Dr. Aaron Baggish: Yeah. So I think bias is such an interesting word to me because bias has a negative connotation, but bias actually also has some positive attributes associated with it. Bias really pushes people to be, in this situation, to be conservative and to try to do what they think is best. Dr. Aaron Baggish: But what I think it boils down to is going back to a very simple tenet and that's understanding the pre-test probability of disease. So when we interpret imaging data or exercise testing data, it always goes back to the question of why did this person get the test done in the first hand and what is our pre-test probability of finding something wrong? I think what we've learned through the COVID pandemic is that just simply having COVID does not equate with a high pre-test probability of having myocarditis in this young population. That it's really the kids that present, and these are the rare few and far between, that present with clinical findings that any doctor would think of as being consistent with myocarditis, where the scan is really helpful. The vast majority of time it's just simply not that case. Dr. Satyam “Tom” Sarma: No, I agree. I think that's always the challenge as well, too clinically as well too, with the diagnostic creep of you get one test that's kind of abnormal and the next thing you know, you're doing a cardiac biopsy and trying to figure out how you got to where you got to. Dr. Satyam “Tom” Sarma: I wanted to circle back to Carolyn's comment. I guess obviously COVID kind of really was the dominant health story over the last 12 to 14 months. Has there been a similar rash, in other words, I'm thinking back to H5N1 or some other pandemics in the past, was there a similar concern historically from the sports cardiology community with those viral outbreaks? Dr. Aaron Baggish: No. Not to my knowledge, and that's simply because there wasn't as much of an experience with hospitalized patients in the US in those prior pandemics. Again, our concern in sports cardiology world really stemmed from a very different population than the one we deal with on a daily basis. I think we learned that, although we thought that was a well-intending way to approach it, that it turned out to be an overreaction. Dr. Aaron Baggish: Before we end, I want to return to Tom's comments about the process and just share with the listeners what a satisfying process this was as an author. Having been through the peer review process, many hundreds of times with different journals, I don't remember one that was as satisfying nor one that led to as high quality of paper based on the feedback we got from the reviewers. So very much appreciative. Dr. Aaron Baggish: I also want to acknowledge the American Heart Association that has become a long-term partner in this effort. As we move out of the pandemic, the ORCCA Registry will be pivoting to really capture what happens to young athletes that are diagnosed with genetic and congenital forms of heart disease. We're very appreciative that the AHA has agreed to partner with us on this. Dr. Carolyn Lam: Aw, my goodness. Thank you so much, Aaron and Tom, for this incredible discussion. I really want to end with, if I may Tom, citing your editorial. I love the way you ended it by saying, "As Nelson Mandela said, 'Sports has the power to change the world. It has the power to inspire. It has the power to unite people in a way that little else does.'" We got seriously scared with COVID-19, but this paper is just so important in providing some reassurance that there has not been a single case of cardiac complication to date, documented to be clearly related to COVID-19 in this population. It's a real testament to the hard work that you've put in. So thank you. Thank you very much for this paper. For all the effort. Thank you both for being here to discuss this. Dr. Carolyn Lam: Well, audience, you've been listening to Circulation on the Run. Thanks for joining us today, and don't forget to join us again next week. Dr. Greg Hundley: This program is copyright of the American Heart Association, 2021. The opinions expressed by speakers in this podcast are their own and not necessarily those of the editors or of the American Heart Association. For more, visit ahajournals.org.  

Oncotarget published "A novel E2F1-regulated lncRNA, LAPAS1, is required for S phase progression and cell proliferation" which reported that long non-coding RNAs are major regulators of many cellular processes, including cell cycle progression and cell proliferation. Inhibition of LAPAS1 expression increases the percentage of S phase cells, and its silencing in synchronized cells delays their progression through S phase. In agreement with its suggested role in cell cycle progression, prolonged inhibition of LAPAS1 attenuates proliferation of human cancer cells. Importantly, knockdown of SPNS2 rescues the effect of LAPAS1 silencing on cell cycle and cell proliferation. Summarily, they identify LAPAS1 as a novel E2F-regulated lncRNA that has a potential role in human cancer and regulates cell-cycle progression and cell proliferation, at least in part, via regulation of SPNS2. Dr. Doron Ginsberg from The Bar-Ilan University said, "The human genome expresses many thousands of long non-coding RNAs (lncRNAs), which are transcripts longer than 200 bases that lack a significant open reading frame." Increasing evidence indicates that lncRNAs are key regulators of important biological processes including cell cycle progression, cell proliferation and apoptosis. Specifically, some lncRNAs function in regulation of cell cycle progression via modulation of critical cell cycle players, such as the cyclins, CDKs, CDK inhibitors, pRB, and p53. Transcription factors that regulate mRNA transcription were shown to also regulate lncRNAs expression. Inhibition of LAPAS1 expression delays progression of cells through S phase and inhibits proliferation of human cancer cells. Thus, the authors identify LAPAS1 as a new E2F-regulated lncRNA that has a potential role in human cancer and regulates cell proliferation and cell-cycle progression, at least in part, via regulation of SPNS2. The Ginsberg Research Team concluded in their Oncotarget Research Output, "this study reports the identification of a novel lncRNA that affects cell cycle progression and cell proliferation and may affect cancer progression. Its initial characterization shows that it is transcriptionally regulated by E2F and it exerts its activity, at least in part, by regulating SPNS2." DOI - https://doi.org/10.18632/oncotarget.27962 Full text - https://www.oncotarget.com/article/27962/text/ Correspondence to - Doron Ginsberg - doron.ginsberg@biu.ac.il Keywords - lncRNA, E2F, cell cycle, cell proliferation About Oncotarget Oncotarget is a bi-weekly, peer-reviewed, open access biomedical journal covering research on all aspects of oncology. To learn more about Oncotarget, please visit https://www.oncotarget.com or connect with: SoundCloud - https://soundcloud.com/oncotarget Facebook - https://www.facebook.com/Oncotarget/ Twitter - https://twitter.com/oncotarget 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 please visit https://www.ImpactJournals.com or connect with @ImpactJrnls Media Contact MEDIA@IMPACTJOURNALS.COM 18009220957x105 Copyright © 2021 Impact Journals, LLC Impact Journals is a registered trademark of Impact Journals, LLC

Listen to the latest oncology-focused research published in this week’s issue of Oncotarget, Volume 12, Issue 11. View the complete issue: https://www.oncotarget.com/archive/v12/i11/ COVER PAPER: “CEA as a blood-based biomarker in anal cancer” https://doi.org/10.18632/oncotarget.27959 NEWS: “FGFR1, a novel biomarker for metastatic castration-resistant prostate cancer?” https://doi.org/10.18632/oncotarget.27957 (PDF Download) EDITORIAL: “Advances in innovative exosome-technology for real time monitoring of viable drugs in clinical translation, prognosis and treatment response” https://doi.org/10.18632/oncotarget.27927 (PDF Download) EDITORIAL: “Drug-development, dose-selection, rational combinations from bench-to-bedside: are there any lessons worth revisiting?” https://doi.org/10.18632/oncotarget.27931 (PDF Download) RESEARCH PAPER: “Occurence of RAS reversion in metastatic colorectal cancer patients treated with bevacizumab” https://doi.org/10.18632/oncotarget.27965 RESEARCH PAPER: “Caspase-11 and AIM2 inflammasome are involved in smoking-induced COPD and lung adenocarcinoma” https://doi.org/10.18632/oncotarget.27964 RESEARCH PAPER: “A novel E2F1-regulated lncRNA, LAPAS1, is required for S phase progression and cell proliferation” https://doi.org/10.18632/oncotarget.27962 RESEARCH PAPER: “Epigallocatechin-3-gallate modulates Tau Post-translational modifications and cytoskeletal network” https://doi.org/10.18632/oncotarget.27963 RESEARCH PAPER: “Ex vivo analysis of DNA repair targeting in extreme rare cutaneous apocrine sweat gland carcinoma” https://doi.org/10.18632/oncotarget.27961 REVIEW: “Evaluation of liver kinase B1 downstream signaling expression in various breast cancers and relapse free survival after systemic chemotherapy treatment” https://doi.org/10.18632/oncotarget.27929 CASE REPORT: “Immunotherapy in Xeroderma Pigmentosum: a case of advanced cutaneous squamous cell carcinoma treated with cemiplimab and a literature review” https://doi.org/10.18632/oncotarget.27966 Keywords - anal cancer, prostate cancer, colorectal cancer, lung cancer, breast cancer, exosomes, cell proliferation, Tau protein, Alzheimer’s disease, DNA repair, advanced squamous cell carcinoma, cancer, science, research, oncology About Oncotarget Oncotarget is a bi-weekly, peer-reviewed, open access biomedical journal covering research on all aspects of oncology. To learn more about Oncotarget, please visit https://www.oncotarget.com/ or connect with: SoundCloud - https://soundcloud.com/oncotarget Facebook - https://www.facebook.com/Oncotarget/ Twitter - https://twitter.com/oncotarget LinkedIn - https://www.linkedin.com/company/oncotarget Instagram - https://www.instagram.com/oncotargetjrnl/ YouTube - https://www.youtube.com/oncotargetyoutube Pinterest - https://www.pinterest.com/oncotarget/ Reddit - https://www.reddit.com/user/Oncotarget Oncotarget is published by Impact Journals, LLC. Please visit https://www.impactjournals.com/ or connect with @ImpactJrnls Media Contact MEDIA@IMPACTJOURNALS.COM 18009220957

This month on Episode 19 of the Discover CircRes podcast, host Cindy St. Hilaire highlights three featured articles from the December 4 issue of Circulation Research. This episode features an in-depth conversation with Drs Mete Civelek and Redouane Aherrahrou, from the University of Virginia regarding their study titled Genetic Regulation of Atherosclerosis-Relevant Phenotypes in Human Vascular Smooth Muscle Cells.   Article highlights:   Zahreddine, et al. Tamoxifen and E2 Effects On Reendothelialization   Zheng, et al. Arterial Stiffness Preceding Diabetes   Galang, et al. ATAC-seq Identifies Novel Isl1 SAN Enhancer   Cindy St. Hilaire:              Hi, welcome to Discover CircRes, the podcast to The American Heart Association’s journal, Circulation Research. I'm your host, Dr Cindy St. Hilaire from The Vascular Medicine Institute at the University of Pittsburgh, and today I will be highlighting three articles selected from the December 4’th issue of Circ Res. Drs Mete Civelek and Redouane Aherrahrou, from the University of Virginia, are here to discuss their study, Genetic Regulation of Atherosclerosis-Relevant Phenotypes in Human Vascular Smooth Muscle Cells. Cindy St. Hilaire:              The first article I want to share is titled, Tamoxifen Accelerates Endothelial Healing by Targeting Estrogen Receptor-alpha in Smooth Muscle Cells. The first author is Rana Zahreddine, and the corresponding author is John Francois Arnal and they're from INSERM and the University of Toulouse, France. For breast cancers that contain high levels of estrogen receptor, a standard treatment is to give drugs that block either estrogen production or the receptor itself, such as tamoxifen. However, estrogen can elicit beneficial vascular protective effects, so treatment with tamoxifen might increase the risk of cardiovascular disease. Depending on the tissue, tamoxifen can both antagonize or activate estrogen receptor, so it's role in cardiovascular disease is unclear. Cindy St. Hilaire:              Some evidence even suggest tamoxifen might have protective effects, such as promoting vascular endothelial healing. Zahreddine and colleagues now show that while might suffering damage to the endothelial lining of a blood vessel have improved healing when treated with tamoxifen, or with estrogen, those suffering perivascular injury, that is to say, the injury that affects both the endothelial layer as well as the surrounding smooth muscle cell layer, heal only in response to estrogen. This suggests tamoxifen's healing effects might require smooth muscle cells. In mice, lacking the estrogen receptor and smooth muscle cells, they found estrogen, but not tamoxifen, healed endovascular injuries. While in mice lacking estrogen receptor and endothelial cells alone, they found the opposite. This work reveals nuances in the molecular actions of tamoxifen that should inform further assessment of its risk and benefits for use in patients. Cindy St. Hilaire:              The second article I want to share is titled, Arterial Stiffness Proceeding Diabetes, A Longitudinal Study. The first authors are Mengyi Zheng and Xinyuan Zhang and the corresponding authors are Xiang Gao and Shouling Wu, from Pennsylvania State University and North China University of Science and Technology. As a person ages, their risk of developing diabetes and cardiovascular disease increases. Aging is also linked to increase in arterial stiffness and high blood pressure, but how all these individual conditions affect and influence each other is not entirely clear. For example, while arterial stiffness and diabetes tend to correlate, whether one increases the risk, or the other, or the risk relationship or whether the risk relationship is bi-directional, is unknown. Cindy St. Hilaire:              To assess the interplay between these disease states, Zheng and colleagues studied diabetes and arterial stiffness in a cohort of 8,956 Chinese people between 2010 and 2015, none of whom had had diabetes or cardiovascular disease at the outset of the study. With repeated measures of fasting glucose levels, which is an indicator of diabetes, and pulse wave velocity, which is a measure of arterial stiffness, the team found that participants with a higher baseline arterial stiffness were more likely to develop diabetes during the five-year period than those with lower stiffness levels. Out of the original cohort of just over 8,900 individuals, a total of 979 individuals developed diabetes during the study. Higher baseline glucose levels did not predict future arterial stiffness; this suggests a risk relationship that is a one-way street. While the results require confirmation in additional cohorts, this finding is the first to identify the pathological mechanisms linking arterial stiffness to diabetes.  Cindy St. Hilaire:             The third article I want to share is titled, ATAC-Seq Reveals an ISL1 Enhancer That Regulates Sinoatrial Node Development and Function. The first author is Giselle Galang, Ravi Mandla, and Hongmei Ruan. And the corresponding author is Vasanth Vedantham, from the University of California, San Francisco. Pacemaker cells, of the sinoatrial node, establish and control the rhythmic contractions of the heart. These cells differ from regular cardiomyocytes in their transcription profiles, but how this transcriptional profile is established and maintained is not fully understood. To investigate the epigenetic landscape defining pacemaker cell fate, Galang and colleagues have employed a technique called ATAC-Seq, which identifies areas of the genome with accessible open chromatin structures, which is an indication of transcriptional activity. The team compared the genomes of pacemaker cells with atrial cardiomyocytes, and found a number of pacemaker cell-specific accessible loci that had both large numbers of transcription factor binding sequences and enhancer activity, when assayed in mice. Cindy St. Hilaire:              The team went on to specifically characterize one novel enhancer upstream of the gene, encoding ISL1, which is a key transcription factor for pacemaker cell identity. They showed that deleting the enhancer caused under development of the Sinoatrial node and arrhythmias in mice. They also noted that single cell nucleotide polymorphisms at the equivalent loci in humans, have been linked to variations in resting heart rate. The report verifies ATAC-Seq as an effective tool for identifying pacemaker enhancers and will launch future studies into how such enhancers function in heart development and disease. Cindy St. Hilaire:              Okay, so today with me is Dr Mete Civelek and Dr Redouane Aherrahrou, from the University of Virginia, and they're here to discuss their paper titled, Genetic Regulation of Atherosclerosis-Relevant Phenotypes in Human Vascular Smooth Muscle Cells. And this article is featured in our December 4th issue. So thank you both so much for being here with me today. Mete Civelek:                   Great to talk to you Cindy. Thank you for choosing our paper. Cindy St. Hilaire:              Yeah, and seeing you over Zoom, I wish these were in person, but... Redouane Aherrahrou:  Thank you for having us. Cindy St. Hilaire:              Yeah. Great. So, before we dig into the details of this paper, which I think is a really nice paper, one of the things I like about it is that it couples GWAS with some functional things, which is obviously super important for figuring out what is important in that GWAS data. So, before we dig into the nitty-gritty of the paper, could you maybe explain what a GWAS study is, and what the strengths and weaknesses are, in terms of using that as an approach to figure out disease related pathophysiology? Mete Civelek:                   So, we know that coronary artery disease, or these cardio-metabolic diseases, have a genetic component, and in the past we used to do linkage studies, studying families, but in the last 15 years or so, because of the developments in technology, we can do these genome-wide association studies. And essentially what they do is they look at a population and some of the people in the population will have coronary artery disease and some people will not have coronary artery disease, will be otherwise healthy. And then you study the genetic variance across the entire genome and look for frequency differences in the people with the healthy phenotype and people who have the disease. And of course you do some statistical tests to find if this frequency differences is indeed statistic, the different between these two groups and you identify essentially loci that are associated with the disease. Mete Civelek:                   But I see GWAS as almost a detective work, you say something like, okay, let's say there was a murder in the United States, and then now you do GWAS of course to find the murder, right? But what that tells you is, okay, the murder occurred in, let's say Pittsburgh or Charlottesville or Washington DC, sure, it narrows down the scope of where you're going to look at, but it doesn't tell you exactly what happened and where it happened and things like that. And so after GWAS there many more questions to answer looking at the molecular mechanism of the locus, the tissue or cell type of action, the gene, which is being affected by the locus to affect the phenotype. So, it's very good at narrowing down possibilities and coming up with hypotheses, but then the real work begins. Cindy St. Hilaire:              I was wondering actually, as you were saying that, have there ever been... I guess like false discoveries, where people have really focused in, on a loci, because it came up maybe in one or multiple studies, but then maybe it didn't prove to be causative or they still can't figure it out. Are there examples of that? Mete Civelek:                   The most obvious example is actually the 9p21 locus. Cindy St. Hilaire:              Interesting. That's the one I was thinking of actually. Mete Civelek:                   Which has been associated with coronary artery disease susceptibility in all kinds of studies and in kinds of populations, this signal itself is real, what it's doing is been a lot of debate. Some people think that it's affecting the CDKN2A and 2B genes nearby. Cindy St. Hilaire:              Is that p21 or p16? Mete Civelek:                   One is p21 and one is p16, but I can't remember which one. Cindy St. Hilaire:              Yeah, I can't either. Mete Civelek:                   Right. And then there's a non-coding RNA in that region called lnRNA. Some people think it's affecting and lncRNA expression. Some people think it's affecting isoform abundance, so that's just probably the most famous locus in our field, in terms of figuring out what it's doing. Yeah. Cindy St. Hilaire:              Well, at least it's probably causing a lot of people to think of a lot of good questions to ask, so that's exciting. In your study, you state that you want to focus on the impact of coronary artery disease associated variants in atherosclerosis-relevant smooth muscle cell phenotypes, and the phenotypes you wanted to focus on were calcification, which is my personal favorite. So calcification, proliferation, and migration. So I was wondering why you wanted to focus on these phenotypes and then what kind of functional assays did you do? Redouane Aherrahrou:  So, the reason we choose those phenotypes because they are playing important role in the disease. So, for example, during the advanced stage of the disease, smooth muscles cells, they proliferate and migrate to make the fibrous cap. So the fibrous cap is actually stabilize the plaque against the rupture, and also during the advanced stage of the disease, the calcification also happening, a lot of people believe that the calcification also contribute to instability of the fibrous cap. So that's why we focus on those three phenotype, migration, proliferation, and calcification. Cindy St. Hilaire:              Interesting, and so I think you'd said you had about 150 patients in your study. Does that mean you did these functional assays in 150 different cell lines? Or how did you do that? Redouane Aherrahrou:  That's a good question. So we conducted actually, our assays from 150 healthy and multi-ethnic donors, so those people actually did die from motorcycle and car accidents, and the doctors actually use the chunk of the aorta where we'll actually isolate these cells from, and then they are actually healthy enough to use for the heart transplantation. Cindy St. Hilaire:              Wow. And so were you introducing known SNPs or SNPs that are pulled out of GWAS into the cells, or did the cells already have the SNPs available? How was the correlation done between functionality and SNPs? Redouane Aherrahrou:  That's a great question. So we actually use the natural SNPs that already exist in those donors. And we ask the question how the genetic variants of those donor affects migration, proliferation, and calcification phenotypes. Mete Civelek:                   So we essentially perform a GWAS in a dish- Cindy St. Hilaire:              Yeah, that's kind of what I was thinking- Mete Civelek:                   That's the bottom line, you just culture these cells and do these phenotypic characterizations, which you cannot do in healthy living human beings of course, and then just the naturally occurring genetic variation in these individuals, in these donors, to essentially calculate the association between the genetic variants and then these phenotypes. Cindy St. Hilaire:              And you were using aortic smooth muscle cells, right? Mete Civelek:                   Yes. Cindy St. Hilaire:              Do you think... this is one thing I always think about, especially because kind of harping back to Mark Majesky's early work with the chick embryo and developmental origins. Do you think if you had coronary arteries from the same individuals that the smooth muscle cells would respond similarly? Mete Civelek:                   This is a really good question, partially, yes and partially, no. I'll give you one specific example, for example, one of the loci that is associated with coronary artery disease is over a transcription factor called TCF21. And TCF21 is actually playing an important role in smooth muscle cell phenotypes, and that transcription factor is expressed only in coronary artery smooth muscle cells, but not in aortic smooth muscle cells. Cindy St. Hilaire:              Interesting. Mete Civelek:                   This was something that Dr Tom Quertermous from Stanford showed. So presumably we are capturing some of the genetic variation that's important in coronary artery disease as some of it was probably missing because we're using aortic smooth muscle cells. Cindy St. Hilaire:              Yeah. That is so neat. I really like that heat map you had, I think it was figure 4 because you really lined up along the SNPs that were identified in these patients you looked at the effect of that SNPs on a specific function test, you did, and you did, was it 11 functional tests? Mete Civelek:                   12 different functional tests. Cindy St. Hilaire:              12? Mete Civelek:                   Yes. Cindy St. Hilaire:              It's an amazing amount of work really. Well, how long have you been working on this project? Mete Civelek:                   Redouane, why don't you answer this question? Cindy St. Hilaire:              Or do you not want to talk about that? Redouane Aherrahrou:  Of course, it's not easy actually to culture and characterize 151 smooth muscle because you expect sometimes, you capture them, some of them, they will not grow, some of them they get contaminated, and you have to perform it again. And also, you cannot do the same experiment for all of them at the same time. So what we did actually, before we started the experiments, we decided to take a smooth muscle cell from one donor, and expanded many times and then we use the same donor to run each time for all the experiments, just to count for the batch and environment effects. Cindy St. Hilaire:              Yep. Redouane Aherrahrou:  So it took me actually almost one and a half year, to finish the characterization for all 151 smooth muscle cell. At that time I was also using also two incubators and then you can imagine, when you put the incubator- Cindy St. Hilaire:              It's full. Redouane Aherrahrou:  ...and I try to finish that, and then I again, start the experiment again to finish the other batch. Cindy St. Hilaire:              Oh God. Yeah, my lab also... we work only in primary human tissues from vessels, but also from valves. So my staff will certainly appreciate all your efforts for this paper. Mete Civelek:                   And you can also imagine there was this group of undergraduates, trailing- Cindy St. Hilaire:              An army yeah. Mete Civelek:                   Redouane wherever he goes….they were helping him out with many aspects. Cindy St. Hilaire:              Oh, sure that's amazing- Mete Civelek:                   He mentored, I think maybe five, six different undergraduate students throughout this project and they're all part of the paper. Yeah. Cindy St. Hilaire:              That's excellent. So towards the end of the study, you guys really focused on a gene, MIA3. So can we talk a little bit about that? What is this gene? What its normal function? Is it known? And then what did you find out in relation to smooth muscle cells? Mete Civelek:                   Well, I'll start and Redouane you can continue. So let me just walk back just a little bit to tell you how we kind of decided to focus on that. So we identified the 79 loci that are associated with smooth muscle cell phenotypes and coronary artery disease. So we wanted to show at least some kind of a validation and so we looked for loci that are not associated with lipids because we thought they will maybe not be important in smooth muscle cells. And then we then looked for loci out of those, who affect a nearby gene expression in aorta, in smooth muscle cells, but not in endothelial cells and in monocyte so we thought that will give us confidence- Cindy St. Hilaire:              So kind of enriching for this smooth muscle cell? Mete Civelek:                   And this MIA3 popped up and there was only one study actually that showed that, in codes for protein that localizes to the ER exit site and affects these COPII carriers, which secrete collagen into extracellular matrix. Well, collagen as you know, is important in cell stability and what smooth cell muscle cells produced. So, that's how we decided to focus on that gene. And I will let Redouane describe I guess, what we did with that gene. Redouane Aherrahrou:  Yeah. So after the function and mutation, we come up with this gene. So the first thing we did, because we found that the genetic variety in this locus affects actually proliferation in smooth muscle cell. So to what it did at least, this is actually SNP that's affecting the proliferation of smooth muscle cell by this gene, we down-regulate this gene actually in smooth muscle cell using two different shRNA, and we found actually the downregulation of this gene lead to affect the proliferation in sense that dominant regulation of this gene will affect the proliferation. Redouane Aherrahrou:  And also we found that the same genetic variance also in this gene lead to lower periphery, migration, sorry, the expression of this gene in small as I said, and then also in the aortic tissue. And interestingly, we did not see in the monocytes macrophages or other cell type, actually in the aortic tissue suggesting that this genetic variance affecting the coronary artery disease via smooth muscle cell. Mete Civelek:                   And we also collaborated with Renu Virmani's group at CVPath Institute, stained lesions, coronary artery lesions, which have these thick caps and thin caps as you very well know that is really relevant to plaque stability, and show that the thin caps have fewer smooth muscle cells which were positive for this protein MIA3, which was all in line with our genetic findings, because our genetic findings basically show that lower expression of this gene was associated with increased susceptibility to coronary artery disease. Cindy St. Hilaire:              Interesting. I wonder if it could be correlated with plaque rupture, right. If there's less smooth muscle cell, obviously, then a thin fibrous cap is nothing that anybody wants. So is the proliferation of the smooth muscle cell almost protective in a sense, that's one of the things people are starting to think about in calcification, [Alina has these amazing imaging studies, where she looks at matrix vesical accumulation and calcification mitosis. And really the field has noticed, with work by Linda Demer also, the field  has noticed that a large, huge chunk of calcification seems to be much less risky, I guess, compared to the microcalcifications, and I wonder if MIA3 might be like that too, if you can have just enough smooth muscle cell proliferation to kind of keep that cap thicker, is that more protective? Mete Civelek:                   I think that's a really good point that you are raising, because some of the answer is, in that figure 4 in the paper that you mentioned. What we find is that these loci, when people have the risk allele of these loci, so obviously people are at higher risk for coronary artery disease, some of them are associated with higher proliferation, but some of them associated with lower proliferation, same with calcification, same with migration. So it's really difficult to say, at least just looking at the genetic loci, yes, higher proliferation is always better. Cindy St. Hilaire:              Yeah. Mete Civelek:                   There's probably this really delicate balance that allows for plaque stability. Cindy St. Hilaire:              Yeah, it's reminisent, I guess, of the IO1-beta story, right? Mete Civelek:                   Exactly. Cindy St. Hilaire:              Gary Owens and colleagues have really shown that well. The role of it in early versus late plaque is different and it's complicated. That's what we learned. Mete Civelek:                   I agree. And it's specific to MIA3, that locus is also associated with myocardial infarction. Cindy St. Hilaire:              Oh, interesting. Mete Civelek:                   So indeed there is a possibility that really affects plaque stability. Cindy St. Hilaire:              Yeah. So Mete, say you and I are in the same faculty class in that we both started- Mete Civelek:                   Yes we are. We are classmates. Cindy St. Hilaire:              2015 we started our labs, and this is obviously a huge undertaking and really starting a project like this... when you're new, it's really a risk. You're proposing to collect 150 smooth muscle cell lines and characterize them all functionally and it turned out amazingly, but can you maybe talk about the early days in this project's development, and was there ever a moment where you're like, "What the heck am I doing? Is this going to work or..." Just kind of maybe talk to us a bit about that. Mete Civelek:                   That's a really excellent question. To be totally honest with you, I was really lucky to have recruited Redouane to the lab, but he and I worked together when I was a postdoc and when he was a PhD student, as part of this little consortium. So I knew he was going to work hard on his part and he was very driven- Cindy St. Hilaire:              He had magic hands. Mete Civelek:                   And he really want to do this project. So, I knew that it was going to work, but of course he and I both had these moments of, "Are we sure of what we're doing, and why are we doing this? Are we going to get something out of it?" And it was both of us kind of pumping each other, if you will say like, "Yep, this is going to work, we know it's going to work, we have faith in this," but I should also say that my lab also works on adipose tissue biology, and I already had another kind of a safe project going on in that realm. Cindy St. Hilaire:              So, that's funny, I started my lab that way too. I kind of had the project that was the direct continuation of my K grant, and then this kind of high risk, high reward project on valves and you know what, I think that's something that’s smart, it's kind of you have two tracks of research and hopefully one works and then the other one will work. And if they don't work at the same time, hopefully the other one can fill in the gaps, so... Mete Civelek:                   I totally agree with you, but truly, Redouane made a big difference in this project, imagine a postdoc, who's doing nothing but cell culture for two years, hoping that something is going to come out, that's a big risk for him too, it certainly paid off and it's paying off because he has two other papers in the pipeline from this project. Cindy St. Hilaire:              Wonderful. That's excellent. So what's the future for this project? What's kind of the next question you're going to ask if you don't mind sharing. Mete Civelek:                   Oh no, not at all. The most obvious one is looking at gene expression. So we have cultured these cells under two distinct conditions, one is the more contractile phenotype, one is the more productive phenotype. And we did RNA-Seq from, again 150 of these individuals in both conditions and we did what is known as eQTL mapping, so looking at the effect of the genetic loci on gene expression. In a separate project, we also actually collected media from these cells and looked at secreted proteins in the media and we're also finding the genetic loci that are affecting secreted protein, because as you very well know, smooth muscle cells secrete proteins to stabilize plaque stability. So those two papers are Redouane's next projects. And he's almost finished with one and has finished the analysis of the other ones, so hopefully- Cindy St. Hilaire:              That's exciting. Mete Civelek:                   ...more papers coming out in the next six months or so. Oh, I should have said the paper was chosen for the Genomic and Precision Medicine Counci; Young Investigator Award, so Redouane is competing- Cindy St. Hilaire:              Wonderful, also you are in that, excellent. Thank you both so much for joining me today. This was a lovely paper, it was actually inspiring. It made me think about some way to think about my calcification studies. Mete Civelek:                   Thank you so much, Cindy. This was really wonderful. Cindy St. Hilaire:              Absolutely. Thank you. That's it for the highlights from the December 4th issue of Circulation Research. Thank you very much for listening. Please check out the CircRes Facebook page and follow us on Twitter and Instagram with the handle @CircRes and #DiscoverCircRes. Thank you to our guests, Drs Mete Civelek and Redouane Aherrahrou. This podcast is produced by Rebecca McTavish and Ishara Ratnayaka, edited by Melissa Stoner and supported by the editorial team of Circulation Research. Some of the copy texts for highlighted articles is provided by Ruth Williams. I'm your host, Dr Cindy St. Hilaire. And this Discover CircRes, your on the go source, for the most up-to-date and exciting discoveries in basic cardiovascular research.  

In his Part 2, Chang introduces long noncoding RNAs, or lncRNAs. As their name suggests, lncRNAs are not translated into proteins, and initially their functions were poorly understood. Chang’s group has developed technologies to better understand the function of lncRNAs. For example, his lab characterized the protein partners that interact with Xist, a canonical lncRNA that mediates X chromosome inactivation. They found that the protein Spen is necessary for X chromosome silencing. Interestingly, Spen has likely been co-opted by mammalian cells to inactivate the X chromosome via viral mimicry.

In his Part 2, Chang introduces long noncoding RNAs, or lncRNAs. As their name suggests, lncRNAs are not translated into proteins, and initially their functions were poorly understood. Chang's group has developed technologies to better understand the function of lncRNAs. For example, his lab characterized the protein partners that interact with Xist, a canonical lncRNA that mediates X chromosome inactivation. They found that the protein Spen is necessary for X chromosome silencing. Interestingly, Spen has likely been co-opted by mammalian cells to inactivate the X chromosome via viral mimicry.

In his Part 3, Chang reminds us that every lncRNA gene has its own set of DNA regulatory elements, such as enhancers and promoters. These regulatory elements can confer functionality to lncRNA genes. Chang shares the research story of a mysterious lncRNA known as PVT1, which is frequently co-amplified with the proto-oncogene MYC in human cancers. His group found that PVT1 promoter activity is inversely correlated with MYC expression – when one is up, the other is down. Finally, Chang shows that the PVT1 and MYC promoters compete for four enhancers located within the PVT1 gene locus.

In his Part 3, Chang reminds us that every lncRNA gene has its own set of DNA regulatory elements, such as enhancers and promoters. These regulatory elements can confer functionality to lncRNA genes. Chang shares the research story of a mysterious lncRNA known as PVT1, which is frequently co-amplified with the proto-oncogene MYC in human cancers. His group found that PVT1 promoter activity is inversely correlated with MYC expression – when one is up, the other is down. Finally, Chang shows that the PVT1 and MYC promoters compete for four enhancers located within the PVT1 gene locus.

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.14.296921v1?rss=1 Authors: Olgun, G., Tastan, O. Abstract: The dysregulation of long non-coding RNAs' (lncRNAs) expressions has been implicated in cancer. Since most of the lncRNAs' are not functionally characterized well, investigating the set of perturbed lncRNAs are is challenging. Existing methods that inspect lncRNAs functionally rely on the co-expressed coding genes, which are far better characterized functionally. LncRNAs can be known to act as transcriptional regulators; they may activate or repress the neighborhood's coding genes on the genome. Based on this, in this work, we aim to analyze the deregulated lncRNAs in cancer by taking into account their ability to regulate nearby loci on the genome. We perform functional analysis on differentially expressed lncRNAs for 28 different cancers considering their adjacent coding genes. We identify that some deregulated lncRNAs are cancer-specific, but a substantial number of lncRNAs are shared across cancers. Next, we assess the similarities of the cancer types based on the functional enrichment of the deregulated lncRNA sets. We find some cancers are very similar in the functions and biological processes related to the deregulated lncRNAs. We observe that some of the cancers for which we find similarity can be linked through primary, metastatic site relations. We investigate the similarity of enriched functional terms for the deregulated lncRNAs and the mRNAs. We further assess the enriched functions' similarity to the functions and processes that the known cancer driver genes take place. We believe that our methodology help to understand the impact of the lncRNAs in cancer functionally. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.10.291526v1?rss=1 Authors: Puthanveettil, S., Grinman, E., Nakahata, Y., Avchalumov, Y., Swarnkar, S., Yasuda, R. Abstract: Activity dependent structural plasticity at the synapse requires specific changes in the neuronal transcriptome. While much is known about the role of coding elements in this process, the role of the long-noncoding transcriptome remains elusive. Here we report the discovery of an intronic long noncoding RNA (lncRNA),termed ADEPTR, whose expression is upregulated and is synaptically transported in a cAMP/PKA dependent manner in hippocampal neurons, independent of its protein-coding host gene. Loss of ADEPTR function suppresses activity-dependent changes in synaptic transmission and structural plasticity of dendritic spines. Mechanistically, dendritic localization of ADEPTR is mediated by molecular motor protein Kif2A. ADEPTR physically binds to actin-scaffolding regulators Ankyrin (AnkB) and Spectrin (Sptn1) and is required for their dendritic localization. Taken together, this study demonstrates that ADEPTR regulates the dendritic Spectrin-Ankyrin network for structural plasticity at the synapse and illuminates a novel role for lncRNAs at the synapse. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.10.236562v1?rss=1 Authors: Roule, T., Ariel, F., Hartmann, C., Crespi, M., Blein, T. Abstract: Clustered organization of biosynthetic non-homologous genes is emerging as a characteristic feature of plant genomes. The co-regulation of clustered genes seems to largely depend on epigenetic reprogramming and three-dimensional chromatin conformation. Here we identified the long noncoding RNA (lncRNA) MARneral Silencing (MARS), localized inside the Arabidopsis marneral cluster, and which controls the local epigenetic activation of its surrounding region in response to ABA. MARS modulates the POLYCOMB REPRESSIVE COMPLEX 1 (PRC1) component LIKE-HETEROCHROMATIN PROTEIN 1 (LHP1) binding throughout the cluster in a dose-dependent manner, determining H3K27me3 deposition and chromatin condensation. In response to ABA, MARS decoys LHP1 away from the cluster and promotes the formation of a chromatin loop bringing together the MARNERAL SYNTHASE 1 (MRN1) locus and a distal ABA-responsive enhancer. The enrichment of co-regulated lncRNAs in clustered metabolic genes in Arabidopsis suggests that the acquisition of novel noncoding transcriptional units may constitute an additional regulatory layer driving the evolution of biosynthetic pathways. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.07.28.225193v1?rss=1 Authors: Mendez, M., FANTOM Consortium Main Contributors,, Scott, M. S., Hoffman, M. M. Abstract: BACKGROUND: Exploratory analysis of complex transcriptomic data presents multiple challenges. Many methods often rely on preexisting gene annotations, impeding identification and characterization of new transcripts. Even for a single cell type, comprehending the diversity of RNA species transcribed at each genomic region requires combining multiple datasets, each enriched for specific types of RNA. Currently, examining combinatorial patterns in these data requires time-consuming visual inspection using a genome browser. METHOD: We developed a new SAGA method, SegRNA, that integrates data from multiple transcriptome profiling assays. SegRNA identifies recurring combinations of signals across multiple datasets measuring the abundance of transcribed RNAs. Using complementary techniques, SegRNA builds on the Segway SAGA framework by learning parameters from both the forward and reverse DNA strands. SegRNA's unsupervised approach allows exploring patterns in these data without relying on pre-existing transcript models. RESULTS: We used SegRNA to generate the first unsupervised transcriptome annotation of the K562 chronic myeloid leukemia cell line, integrating multiple types of RNA data. Combining RNA-seq, CAGE, and PRO-seq experiments together captured a diverse population of RNAs throughout the genome. As expected, SegRNA annotated patterns associated with gene components such as promoters, exons, and introns. Additionally, we identified a pattern enriched for novel small RNAs transcribed within intergenic, intronic, and exonic regions. We applied SegRNA to FANTOM6 CAGE data characterizing 285 lncRNA knockdowns. Overall, SegRNA efficiently summarizes diverse multi-experiment data. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.07.22.215855v1?rss=1 Authors: Luo, H., Bu, D., Shao, L., Li, Y., Sun, L., Wang, C., Wang, J., Yang, W., Yang, X., Dong, J., Zhao, Y., Li, F. Abstract: The development of new therapeutic targets for cancer immunotherapies and the development of new biomarkers require deep understanding of T cells. To date, the complete landscape and systematic characterization of long noncoding RNAs (lncRNAs) in T cells in cancer immunity are lacking. Here, by systematically analyzing full-length single-cell RNA sequencing (scRNA-seq) data of more than 20,000 T cell libraries across three cancer types, we provide the first comprehensive catalog and the functional repertoires of lncRNAs in human T cells. Specifically, we developed a custom pipeline for de novo transcriptome assembly obtaining 9,433 novel lncRNA genes that increased the number of current human lncRNA catalog by 16% and nearly doubled the number of lncRNAs expressed in T cells. We found that a portion of expressed genes in single T cells were lncRNAs which have been overlooked by the majority of previous studies. Based on metacell maps constructed by MetaCell algorithm that partition scRNA-seq datasets into disjointed and homogenous groups of cells (metacells), 154 signature lncRNAs associated with effector, exhausted, and regulatory T cell states are identified, 84 of which are functionally annotated based on co-expression network, indicating that lncRNAs might broadly participate in regulation of T cell functions. Our findings provide a new point of view and resource for investigating the mechanisms of T cell regulation in cancer immunity as well as for novel cancer-immune biomarker development and cancer immunotherapies. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.07.14.202143v1?rss=1 Authors: Keshavarz, M., Tautz, D. Abstract: Mammalian genomes include many maternally or paternally imprinted genes. Most of these are also expressed in the brain and several were previously implicated in regulating specific behavioral traits. We have used here a knockout approach to study the function of Peg13. Peg13 codes for a fast evolving lncRNA and is part of a complex of imprinted genes on chromosome 15 in the mouse and chromosome 8 in humans. Two knockout constructs were analyzed, one with a full deletion of the gene, the other with a deletion of the three prime-half. The full deletion is semi lethal, while the partial deletion is fully viable, but the mice show distinctive behavioral differences. They lose interest in the opposite sex and show instead a preference for wildtype animals of the same sex. Further, they show a higher level of anxiety, as well as lowered activity and curiosity and females have a deficiency in pup retrieval behavior. Brain RNA expression analysis reveals that genes involved in the serotonergic system, formation of glutamergic synapses, olfactory processing and estrogen signaling, as well as more than half of the other known imprinted genes are affected in Peg13 deficient mice. Intriguingly, the pathways are differentially affected in the sexes, with the result that the male and female brains of Peg13 deficient mice differ more from each other than those of wildtype mice. We conclude that Peg13 is part of a developmental pathway that regulates the neurobiology of social interactions. Copy rights belong to original authors. Visit the link for more info

  VIDEO WITH VISUAL AIDS ON YOUTUBE!!   How did you get so put together?  DNA is the blueprint, but it doesn't determine everything.  DNA gets turned into RNA, and then finally into proteins that help build your body and brain.  But there are SO many steps in that process that affect the final product- you.   The sum of these steps is a process called genetic regulation.  Genetic regulation makes sure that not all of our genes are expressed and turned into protein at the same time and same place- that would be a mess! This episode is all about genetic regulation by long, non-coding RNAs (lncRNAs, pronounced "link-R N A").  LncRNAs are long segments of RNA that serve non-traditional functions in the genome.  Although recently discovered, lncRNAs seem to be involved in everything from the genetic regulation of development to diseases like cancer.  LncRNAs could help rewrite the field of genetic regulation, and might be the biggest shift to understanding genetics since epigenetics became a hot topic. https://www.straightfromascientist.com/rachel-cherney/ Rachel is also highly involved in other forms of science communication!  Check out the Pipettepen and UNC SWAC for more info!  If you're at UNC, make sure to check TIBBS for career training and opportunities.    Specific visual references and their approximate timestamps are listed below.  Make sure to watch the Youtube Video for the full experience! 5:00: DNA vs RNA vs Protein - (image in video) 7:30: Alternative splicing - (image in video) 9:00: Jimena giudice lab at UNC  - http://giudicelab.web.unc.edu/ (Alternative splicing and intracellular trafficking in development and diseases) 9:30: It's estimated that >90% of proteins undergo alternative splicing 13:30: protein coding gene structure (image in video) 15:30: Additional note:  smaller ncRNAs have more defined structure than lncRNAs, their functions are better known 17:33: dosage compensation - calico cats (image in video) 20:50: An example of a motif that proteins recognize (http://www.rnajournal.org/cgi/pmidlookup?view=long&pmid=31097619, figure 3 ) 21:00: xist repeat structure (https://www.mdpi.com/2311-553X/4/4/28/htm, figure 2, human vs mouse xist) 23:00:in cis lncRNA function (https://dev.biologists.org/content/143/21/3882, figure 2 b and c) 25:05: Markers are placed on histones, rather than DNA. Histones are proteins that DNA wraps around to compact dna into cells (image in video) 25:30: A note: polycomb complexes are conserved to plants and even fungi.  lncRNAs can be found in plants* 28:15: immunoprecipitation pipeline (image in video) 31:30 -33:35: Examples of Single Nucleotide Polymorphisms (SNPs) (image in video) 35:00: Enhancer rnas (https://www.sciencedirect.com/science/article/pii/S1672022917300761 figure 1 38:30: single line RNA vs double line DNA, 3DRNA structure (image in video) 41:00: xist vs rsx  (http://www.rnajournal.org/cgi/pmidlookup?view=long&pmid=31097619, figure 6b ) 42:30: SWAC /pipettepen,com - link to swac article that prompted this podcast -http://www.thepipettepen.com/what-determines-our-complexity/ 44:30: TIBBS -https://tibbs.unc.edu/

  This month on the Discover CircRes podcast, host Cindy St. Hilaire highlights three featured articles from recent issues of Circulation Research and talks with Denisa Wagner and Nicoletta Sorvillo about their article on how PAD4 in blood promotes VWF strings and thrombosis. Article highlights: Goodyer et al: ScRNA-seq of the Cardiac Conduction System   Xiong et al: Chemotaxis Mediated Second Heart Field Deployment   Ranchoux et al: Pulmonary Hypertension and Metabolic Syndrome   Rühl et al. Thrombin/APC Response in FVL and FII 20210G>A   Mahmoud et al. LncRNA SMILR’s Mechanism and Therapeutic Potential   Transcript   Cindy St. H:                         Hi, welcome to Discover CircRes, the monthly podcast of the American Heart Association's Journal, Circulation Research. I'm your host, Cindy St. Hilaire, and I'm an assistant professor at the University of Pittsburgh. My goal as host of this podcast is to share with you some highlights from the recent articles published in the August 2nd and August 16th issues of Circulation Research. Cindy St. H:                         After I discuss some highlights, we'll also have an in-depth conversation with Drs. Denisa Wagner and Nicoletta Sorvillo, from Boston Children's Hospital and Harvard Medical School, who are the lead authors of one of the exciting discoveries from the August 16th issue. Cindy St. H:                         The first article I want to share with you today is titled Transcriptomic Profiling of the Developing Cardiac Conduction System at Single-Cell Resolution. The first author is William R. Goodyer, and the corresponding author is Sean Wu. They are both located at the Cardiovascular Institute and the Department of Pediatrics at Stanford University. Cindy St. H:                         Have you ever wondered how your heart beats, and why there's always this glub-glub pattern, and where did it come from? How is the heart able to initiate that pattern, from cells that don't contract to cells that contract? Well, the beating of the heart is regulated by what's called the cardiac conduction system, and this is an area in the heart of specialized cells, and these cells establish the rhythmic beating by coordinating the contraction of the chambers of the heart. Cindy St. H:                         There's several components to the CSS. The sinoatrial node acts as the pacemaker in the right atrium. The arterial ventricle node is the electrical relay that slows down the pulse from the SA node. A His bundle helps to transmit those impulses, and the Purkinjie fibers are the terminus of the electrical signal. Between all of these different components are a heterogeneous population of what are called transitional cells. There are several studies that have linked these somewhat amorphous or heterogeneous transitional cells to different arrhythmic disorders. Cindy St. H:                         For the normal function of the heart, all of these parts must come together, and when they don't, there's severe clinical manifestations such as arrhythmias, like I said, but also you can get decreased cardiac output and even sudden cardiac death. While important, the cells of the CSS are rather elusive, and that's because they're in a relatively small number compared to the rest of the cells in the heart, and there also aren't very clear markers to identify the cells in the CSS. Cindy St. H:                         To address this, Goodyer and colleagues harvested cells from embryonic mouse hearts and performed single-cell RNA sequencing on 22,000 individually barcoded cells. What they were looking for is learning what type of cells they are, but more importantly, they had the goal of identifying what these elusive transitional cells are, and can we find a marker for these cells to study them? And in some, yes. Together, the sequencing and spatial data provided gene expression atlas of the mouse CSS. Hopefully, this atlas will guide future studies into the essential electrical system that regulates the heartbeat. Cindy St. H:                         The next article I'd like to highlight is titled Single-Cell Transcriptomics Reveals Chemotaxis-Mediated Intra-Organ Crosstalk During Cardiogenesis. We're really going to hit you over the head with some single-cell transcriptomics in this month's podcast. The first authors of this article are Halqing Xiong, Yingjie Lou, Yanzhu Yue, Jiejie Zhang and the corresponding author is Aibin He and they're all from the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine and the Peking-Tsinghua Center for Life Sciences, all at Peking University in Beijing, China. Cindy St. H:                         During development, the mammalian heart originates from two distinct areas in the early embryo and they're called the first heart field and the second heart field. Progenitor cells from these regions give rise to very different structures. From the first heart field comes the atria and the left ventricle, and the second heart field forms the right ventricle and the outflow tract. While we know the outcomes of these different developmental layers, a full understanding of how the first and second heart fields are regulated and how they actually interact with one another is actually lacking a lot of detail and we're not exactly sure how those structures can influence one another. Cindy St. H:                         So to learn more, Xiong and colleagues utilized two different murine models that were engineered to label cells coming from either the first or second heart fields red, and by labeling these cells red, it allows for their very pure isolation and then downstream studying at the single-cell level. So from each of these two models, they collected about 600 red-labeled cells and they collected these cells at four different time points, that were essentially at 12 hour intervals, and they did this starting at embryonic day 7.5, and that's because that's the time point in the mouse where these second and first heart fields are starting to develop. Cindy St. H:                         What they found, by using single-cell RNA sequencing, is that the first heart field cells differentiated into cardiomyocytes, in what they called a gradual, wave-like manner, while the second heart field cells differentiated in what they referred to as a more stepwise, defined pattern. The team also found high expression of migration factor MIF in first heart field cells and they found MIF's receptor CXCR2 in the second heart field progenitor cells. This suggests that perhaps the first heart field cells could regulate the migration of the second heart field cells. Sure enough, blocking MIF- CXCR2 interaction in cultured mouse embryos prevented second heart field cell migration and also prevented normal development of the right ventricular outflow tract structures. So together these results provide insight into both normal heart development and also suggest what might go awry in certain congenital heart malformations. Cindy St. H:                         The next paper I want to highlight is titled Metabolic Syndrome Exacerbates Pulmonary Hypertension due to Left Heart Disease. The first author is Benoit Ranchoux and the corresponding author is Francois Potus, and they are from the Pulmonary Hypertension Research Group at Laval University in Quebec City in Quebec, Canada. The disease pulmonary hypertension can arise from a number of causes, but one of the main drivers of what's called group two pulmonary hypertension is left heart disease. Left heart disease itself is caused by several conditions, such as diastolic dysfunction, aortic stenosis, which is a disease that I study, or mitral valve disease. All of these pathologies result in the left heart not beating efficiently or exerting too much energy. Cindy St. H:                         More than half of all group 2 PH patients also have metabolic syndrome, and metabolic syndrome is a condition that is ever increasing in the modern age, especially in America, and it's characterized by obesity coupled with pathology such as dyslipidemia, type 2 diabetes and high blood pressure. Metabolic syndrome is also marked by elevated levels of the inflammatory cytokine IL6. Rat studies have shown that IL6 can induce proliferation of the pulmonary artery smooth muscle cells and consequently, pulmonary hypertension. Cindy St. H:                         In this study Ranchoux and colleagues pulled together all these different pieces in a rat model and essentially want to test left heart disease coupled with metabolic syndrome coupled with does pulmonary hypertension happen or get worse? What they found was really interesting. Left heart disease was induced in a rat model using super coronary aortic banding and then metabolic syndrome was induced with a high fat diet feeding, or with treatment with Olanzapine, which is a second generation anti-psychotic agent, and it's known to induce metabolic syndrome not only in rats, but also in humans. The data from this paper show that inducing metabolic syndrome in rats coupled with left heart disease resulted in elevated IL6 levels and also greatly exacerbated pulmonary hypertension. Cindy St. H:                         Digging into this mechanism, they found that inhibition of IL6, using either an anti-IL6 antibody or by reducing IL6 secretion from macrophages, using the diabetes drug Metformin, ameliorated the pulmonary hypertension in the rats. They then went on and looked at human samples and they found that IL6 was higher in the lungs of pulmonary hypertension patients and that this IL6 could induce proliferation of human pulmonary artery smooth muscle cells. So together these data suggest that the observation in rats holds true for humans, but further goes on to suggest that perhaps Metformin, which is a well-known, well-used diabetic drug, could perhaps be used for the potential treatment of Group 2 pulmonary hypertension patients.   Cindy St. H:                           In the August 16th issue, we have an article titled Increased Activated Protein C Response Rates Reduce the Thrombotic Risk of Factor V Leiden Carriers but not of Prothrombin 20210G>A Carriers. That is some title. The first authors are Heiko Rühl, and Christina Berens, and Dr Rühl is also the corresponding author, and they are at the Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, in Bonn, Germany. Genetic studies have found two mutations that convey particularly increased risk for venous thrombo-embolism, and VTE is also more commonly referred to as deep vein thrombosis. These mutations are called factor five Leiden mutations, or FVL, and the prothrombin 20210G>A mutation we're just going to call F2. Interestingly, the penetrance of these mutations, or how likely they are to exhibit a phenotype, is variable. Some individuals with mutations never experience deep vein thrombosis, while others experience multiple episodes. Cindy St. H:                         As a group, the FVL carriers produce a higher than normal level of an anticoagulation factor called APC, or activated protein c. They also produce high levels of the pro-coagulation factor thrombin, and the authors of this study wondered if it was the balance, or rather perhaps an imbalance, of these factors that could explain the phenotypic variations in the patients that harbor the same mutation. To test this, they collected 58 patients. 30 were FVL and 28 were F2 carriers, and they injected these patients with clotting factors and examined their response rates. In both of the groups, about half of the individuals had no history of deep vein thrombosis, while the other half had had at least one episode. Cindy St. H:                         The team found that while both types of mutations were associated with increased APC and thrombin levels after coagulant injection compared with a control group, in the FVL group lower APC levels correlated with a much higher risk of deep vein thrombosis. In other words, the FVL carriers who had never experienced deep vein thrombosis produced higher levels of APC. Translating this to the clinic, perhaps APC testing could help identify individuals who are carriers of the FVL mutation and determine which of them are at higher risk due to lower levels of APC. Cindy St. H:                         The last paper we're going to highlight before switching to our interview is titled The Human- and Smooth Muscle Cell Enriched lncRNA, SMILR, Promotes Proliferation by Regulating Mitotic CENPF mRNA and Drives Cell Cycle Progression Which Can Be Targeted to Limit Vascular Remodeling. Now that is a crazy title! We’ve got to limit these names here this is difficult. The first authors are Amira Mahmoud and Margaret Ballantyne and the corresponding author is Andrew Baker, and they're all from Queens Medical Research Institute, BHF Center for Cardiovascular Sciences at University of Edinburgh in Edinburgh, UK. Cindy St. H:                         Before we dive into this article, I think it's important that we give a quick explanation of what is a lncRNA? lncRNA, or L-N-C RNA, stands for long non-coding RNA, and these are described as being transcripts which are made into RNA that are in lengths exceeding 200 nucleotides. So that differs them from micro RNAs or peewee RNAs or snRNAs, and they are classically or, I guess originally, considered not to be translated into protein. However, I think now more and more studies are finding that perhaps they are made into peptide sequences. However it's not fully clear what the function of those sequences are. Similar to micro RNAs, they also harbor regulatory functions that can control cellular functions by helping to fine tune the regulation of gene transcription and translation. Cindy St. H:                         Largely speaking, vascular smooth muscle cells are quiescent, but they can be stimulated to proliferate and migrate following injury to the vessel wall. While such activation of smooth muscle cells is essential for wound healing, these same processes are operative in vascular disease or after a cardiovascular procedure. Often what happens is an excess of proliferation of the smooth muscle cell wall can lead to dangerous occlusion of the blood vessel. The long non-coding RNA, SMILR, was recently identified as a promoter of smooth muscle cell proliferation and now in this article, Mahmoud and colleagues have defined its mechanism of action. Through transcriptome analysis of human smooth muscle cells, in which the levels of SMILR were either modulated to be increased or suppressed, the team found that lncRNA regulated expression of several genes involved in mitosis, or cell division. Furthermore, RNA interaction experiments revealed that the messenger RNA encoding the mitotic centromere protein, CENPF, was a direct interaction partner of SMILR. So just like the suppression of SMILR, the inhibition of CENPF resulted in reduced mitosis of the smooth muscle cells. Cindy St. H:                         The team then went on to show the inhibition of SMILR via RNA interference could block the smooth muscle cell proliferation ex-vivo, and they did this using intact sections of human saphenous vein. These results suggest that targeting this lncRNA could be a potential clinical treatment in situations where vessel occlusion is at risk. Cindy St. H:                       Okay, so now we're going to switch and have our interview with Drs Denisa Wagner and Nicoletta Sorvillo, and we're going to discuss their paper entitled Plasma Peptidylarginine Deiminase IV Promotes VWF-Platelet String Formation and Accelerates Thrombosis after Vessel Injury. Thank you Drs. Wagner and Sorvillo for joining us today. I think a funny thing is that between Nicoletta in Switzerland, me and you on the East coast and my producer on the West coast, I think we're spanning about nine hours of time zones here. Thank you all for taking the time, whatever time of day it is, wherever you are. Dr Wagner:                         Thank you. Cindy St. H:                         I was wondering, Denisa, if you could please introduce yourself and tell us a little bit about your background. Dr Wagner:                         I am a vascular biologist. I was always interested in platelets, endothelial cells, and leukocyte. I started with a background of von Willebrand factor research. Von Willebrand factor is the most important adhesion molecule for platelets and it is stored in endothelial cells as we have found very early on, in an organelle called Weibel-Palade bodies. So my work on this paper is actually related to the first observation I ever made scientifically of showing that von Willebrand factor is released from endothelium. Cindy St. H:                         Wow, that's wonderful. And Nicoletta, could you please introduce yourself and tell us a little bit about your background? Nicoletta:                            I'm Italian, I studied in Italy and I did my PhD in the Netherlands, and I've always worked on inflammation and thrombosis during my PhD. One of the major proteins I was working on is ADAMTS13. That is again a protagonist of our paper. Then I moved to Boston, where I had the pleasure to be able to work in Denisa Wagner's lab, and there I continued working on inflammation and ADAMTS13 and now currently I moved here to Bern and I'm bringing my expertise here, but I moved a little bit towards ischemia and reperfusion injury and transplantation. Cindy St. H:                         Interesting. Wow. Denisa, I want to circle back to this factor being one of the first findings that you worked on. How does it feel to still be working on it? Is it still exciting? Dr Wagner:                         It is nice and it's refreshing to come back to it. I did a lot of stuff in between. We did a lot of adhesion molecule work, leukocyte rolling. We made the early knockouts like b-selectin, p-selectin, and von Willebrand factor knockout as well. So it's fun. And by the way, since Nicoletta said that she was Italian, I am originally Czech, from Prague. Cindy St. H:                         Interesting. I did not know that. And actually, Denisa, I don't know if you remember, but when I was a graduate student in Katya Ravid’s lab, we collaborated with you to use some of this intravital imaging on one of our JCI papers. Dr Wagner:                         Oh right, right. I was wondering where I knew your name from. That's funny. Cindy St. H:                         Yes. Yeah, yeah. So it's wonderful to speak to you again. Really I wanted to interview you because I loved this paper, not only because it was a really interesting mechanism that actually I wasn't very well aware of, this citrullination and also because of the beautiful intravital imaging you could do and then link it to patient disease states. Maybe you can start by telling me what's the clinical unmet need or the question that your paper was trying to address? Nicoletta:                            So Denisa Wagner's lab always has worked on neutrophils and NETs and it has been shown that these NETs are involved in thrombosis. So we were curious what happens when even the enzyme that is important to make these NETs, this extracellular DNA, does when it's in the circulation. And this enzyme is of course PAD4 and it is known that it can modify our [inaudible] residues on protein through this process of citrullination. So we went to see if it could modify plasma proteins and as Denisa already said, an important molecule that initiates thrombotic processes is vWF that can be released during inflammation or when there's a damage to the endothelium .  So we went to see what happens if the enzyme that is involved in removing this vWF that is ADAMTS13 happens if it gets modified by this enzyme path. So our question was more like what happens if you have the release of an enzyme that is normally intracellular? What would happen if it gets outside of the cell? Cindy St. H:                         Interesting. So before we get too deep in the weeds, what is citrullinization and why is it important? What do these modifications do? Nicoletta:                            It changes the charge of a protein. It goes and modifies arginine, and it transforms it into citrulline. It changes the charge of a protein and therefore you can imagine if you change a charge of protein it can change even the structure of a protein and if you change the structure then you can change the function. So this is what this modification can do. Cindy St. H:                         And that's what it's doing on the ADAMTS13? It's essentially altering or inhibiting its function? Nicoletta:                            Yes. What we saw is that we can find these citrullinated residues on ADAMTS13 and we identify them by mass spectrometry and then we saw that if it is modified by citrullination, it loses its activity so it doesn't function anymore. Cindy St. H:                         Interesting. Very neat. Could you talk a little bit about the process of where this is happening naturally and where it goes wrong in a diseased state such as either sepsis or aging or just general clotting? Dr Wagner:                         These neutrophil extracellular traps are generated often more during a disease state when there is either an infection or exacerbated inflammation that would be like in sepsis or for example, in a metabolic disorder like diabetes. So there is a lot more of them being generated. Also, for example, in diabetes, PAD4 is elevated inside the neutrophil four-fold. If it's released from diabetic neutrophils , then there would be really a lot more of it. And in aging also, then a NETosis becomes much more prominent. We have done this only with mice, but I believe that it will be also, unfortunately, the case with humans that old mice make a lot more NETs than young mice. Therefore this is relevant to look. Since thrombosis increases both with aging, the incidence of thrombosis, thrombosis increases with a disease like diabetes or in sepsis, you will have micro thrombosis. We thought it would be interesting to study those processes as well, then. Cindy St. H:                         That's really neat. One of the techniques that you utilize heavily in this paper and several of your papers that I'm familiar with is this intravital imaging or intravital microscopy. Just so people can get a sense of what it is you're actually doing, could you maybe describe what that experiment is? Maybe Nicoletta, you could describe that for us? Nicoletta:                            During intravital microscopy, we are able to image in vivo, a vessel in a live mouse. And in this case we use mice and we can label leukocytes and platelets and then look at them in the vessel in vivo and you can then look for a thrombus forming or you can look at the [inaudible 00:23:43] already had leukocyte rolling and you can see what is happening inside the vessel during a proper blood flow and you can damage the vessel in some cases. In our case, in our paper, we do a ferric chloride injury where we damaged the vessel with ferric chloride and therefor you initiate a thrombus development and you can visualize it in vivo and real time. Cindy St. H:                         Excellent. Yes. And hopefully our listeners will look and see the beautiful pictures because those are some serious clots you get forming in the vessels. Yeah. Yeah. And so the other thing that you did was confirming the modification on ADAMTS13, you use mass spectrometry. How difficult was it to confirm that what you thought was happening was happening using that technique? Nicoletta:                            It was very difficult and challenging, I have to say. Dr Wagner:                         See, I would love to hear more about it because you often read, Oh, then we did mass spec and we got this beautiful whatever. Could you tell us a little bit about the struggles? Nicoletta:                            It was quite a struggle. I mean I think trying to identify such a modification that is very, first of all, novel and it changes the math only of one thousandth it's very difficult. To identify you can confuse it with a deiminasion again because of the increase of mass is the same. And another problem was that ADAMTS13, our plasma protein, is low abundance in plasma compared to other plasma proteins like Fibrinogen, that is very, very much abundant. It was a challenge for this reason. So trying to pinpoint out a small, tiny modification already in a protein that is not so abundant in plasma and therefore we have to use this probe, this Biosyn PG program. And we did this in collaboration with Paul Thompson's lab and we were able to then fish out what was modified by the citrullination, but it was very challenging. We tried several different types of techniques that were different types of approaches before being able to show that in vivo. So in human samples we can find this modification. Dr Wagner:                         Nicoletta grew a lot of gray hair during that period. (laughs) Dr Wagner:                         It took us about a year to figure out how we could detect it in vivo because also some antibodies to ADAMTS13 don't work so well. It's a minor protein, but she figured it out. Cindy St. H:                         Wow. That's amazing. Well, congratulations on that. That's excellent. I guess what I'm wondering now is what are the next steps and what might your findings mean in terms of future potential therapeutic options or treatment strategies for different detrimental thrombotic events? Dr Wagner:                         I think what we have really verified that the PAD4 remains active when it circulates in circulation, when the release, and there are several diseases in which PAD4 levels were found to be elevated, like rheumatoid arthritis and what it means in general. That is PAD4 is actually causing havoc. It is citrullinating probably quite indiscriminately. Several proteins may be finding the exposed parts. Maybe it could have some binding sites, but I think it just affects proteins in general and for some of them like, ADAMTS13, this had a very detrimental effect. So in diseases where there is a lot of PAD4, one has to worry about the consequences of citrullinating things and perhaps spot for inhibitors should be used. What do you think, Nicolleta? Nicoletta:                            I totally agree with you. Yes, I totally agree. I mean PAD4 outside the cell could be dangerous, of course. However, we never know if there's something good that it can do that protects by citrullinating proteins so there's so much more to discover about extracellular PAD4 and its effect on the environment. Dr Wagner:                         However, Nicoletta when she wrote a paper at the end she decided to talk about ADAMTS13 as a therapeutic because both she and I, we are convinced that ADAMTS13 it's a possible future therapeutic and it's already given to patients who are lucky in ADAMTS13 and may be given to patients who have thrombotic events in the future, like stroke or myocardial infarction. And these situations are highly pro-inflammatory. Therefore, we would anticipate that in these situations, NETs, and we know NETs are released and therefore, what Nicolleta suggests at the end, is that introducing together with ADAMTS13 an inhibitor of citrullination would be a good thing so that the protein, the ADAMTS13, remains active in circulation. Cindy St. H:                         Wow. So a two-hit strategy. I mean I can think of a handful of potential diseases this would be good for. You know, patients with sickle cell, there's a lot of NETs released then thrombotic events or even stroke. I mean, do you see that this is a potential mechanism that's common to all thrombotic disease or just kind of specific subsets? Nicoletta:                            All is a big word I think, but I think that there are many disorders where together with a thrombotic event, you can find also low levels or low activity of ADAMTS13 and in many of these disorders, nobody knew really why you have a reduction of ADAMTS13 activity, what is happening? Why do you lose this ADAMTS13? What we believe, but of course further studies are needed, is that maybe in these disorders, what is causing the loss of ADAMTS13 is this release of PAD4 because in stroke or in some DIC sepsis, you can find patients or many patients who do have low levels of ADAMTS13 activity and we believe that it's due to maybe citrullination by PAD4. So in that case, I agree with you maybe then that this therapy can be used in different thrombotic events as you suggested. Cindy St. H:                         So what does PAD4 normally do when it's intracellular? What is its, I guess healthy role, in a cell, if it has one? Nicoletta:                            So what is known now is that it really regulates transcription. So that's very important because it citrullinates transcription factors to facilitate transcription. And what Denisa Wagner's lab has identified is that it's extremely important to form these NETs because it citrullinates histone and allows the unraveling of the chromatin and then the NET release. However, it's extremely interesting. We are very interested to understand what else does it do within the cell. Cindy St. H:                         Interesting. That is so neat. I love this story. Dr Sorvillo and Dr Wagner, thank you so much for joining us and congratulations again on a wonderful paper. Dr Wagner:                         Thank you. Nicoletta:                            Thank you for having us and inviting us. Thank you. Cindy St. H:                         So that's it for the highlights from our August issues of Circulation Research. Thank you for listening. This podcast is produced by Rebecca McTavish and edited by Melissa Stoner and supported by the editorial team of Circulation Research. Copy text for the highlighted articles is provided by Ruth Williams. I'm your host, Cindy St Hilaire and this is Discover CircRes, your source for the most up-to-date and exciting discoveries in basic cardiovascular research.  

Medicine is often a race against time, to diagnose, to develop and to treat. This week we're looking at new research which speeds up the detection of Alzheimers in patients and provides a chance to test out potential treatments. We also find out how University of Sydney researchers may help deliver a quick antivenom to those stung by the deadly box jellyfish. Plus ways to turn leftover bits of junk in blood plasma, into useful diagnosis tools that may help save time and lives in treatment without wasting more time on tests.References: Man-Tat Lau, John Manion, Jamie B. Littleboy, Lisa Oyston, Thang M. Khuong, Qiao-Ping Wang, David T. Nguyen, Daniel Hesselson, Jamie E. Seymour, G. Gregory Neely. Molecular dissection of box jellyfish venom cytotoxicity highlights an effective venom antidote. Nature Communications, 2019; 10 (1) DOI: 10.1038/s41467-019-09681-1 Maria D Giraldez, Ryan M Spengler, Alton Etheridge, Annika J Goicochea, Missy Tuck, Sung Won Choi, David J Galas, Muneesh Tewari. Phospho-RNA-seq: a modified small RNA-seq method that reveals circulating mRNA and lncRNA fragments as potential biomarkers in human plasma. EMBO Journal, 2019 DOI: 10.15252/embj.2019101695 Andreas Nabers, Henning Hafermann, Jens Wiltfang, Klaus Gerwert. Aβ and tau structure-based biomarkers for a blood- and CSF-based two-step recruitment strategy to identify patients with dementia due to Alzheimer's disease. Alzheimer's & Dementia: Diagnosis, Assessment & Disease Monitoring, 2019; 11: 257 DOI: 10.1016/j.dadm.2019.01.008 Medicine is often a race against time, to diagnose, to develop and to treat. This week it's stories of scientists and doctors racing against the clock.New research which speeds up the detection of Alzheimer's in patients and provides a chance to test out potential treatments.We find out how University of Sydney researchers may help deliver a quick antivenom to those stung by the deadly box jellyfish.Plus ways to turn leftover bits of junk in blood plasma, into useful diagnosis tools that may help save time and lives in treatment without wasting more time on tests.There are whole bundles of random RNA fragments in blood plasma, but these can be used to help diagnose specific issues.The box jellyfish is just one of the many things in Australia that is trying to kill you, but now it's slightly less deadly thanks to University of Sydney researchers.

The ImmuNerds discuss how a cellular long non-coding RNA binds to an innate RNA sensor and regulates virus-induced interferon production to prevent damage to the host. Hosts: Vincent Racaniello, Stephanie Langel, and Cynthia Leifer Subscribe (free): iTunes, Google Podcasts. RSS, email Become a patron of Immune! Links for this episode Host lncRNA binds RIG-I (Cell) Microbe Art at virology blog Letters read on Immune 13 Time stamps by Jolene. Thanks! Weekly Science Picks Steph- That's Pediatrics Podcast Cindy- Trilobite Glassworks Vincent- Research!America Music by Steve Neal. Immune logo image by Blausen Medical. Send your immunology questions and comments to immune@microbe.tv

Nels joins the TWiV team to talk about his work on genomic accordions in vaccinia virus, hepatitis B virus in a 439 year old mummy, and viral induction of energy synthesis by a long noncoding RNA. Hosts: Vincent Racaniello, Dickson Despommier, Alan Dove, Rich Condit, and Kathy Spindler Guest: Nels Elde Click arrow to play Download TWiV 476 (63 MB .mp3, 105 min) Subscribe (free): iTunes, RSS, email Become a patron of TWiV! Links for this episode ASV 2018: asv.org, asv2018.umd.edu TWiV is a must-listen (WaPo) More on poxvirus accordions (bioRxiv) HBV from a 439 year old mummy (PLoS Path) lncRNA promotes viral replication by inducing metabolism (Science) Making Data Visual Letters read on TWiV 476 Weekly Science Picks Nels - Everyday Evolution Kathy - Paper-fold an ellipse Rich - Oxford Nanopore Technologies: YouTube channel; General technology; DNA sequencing; Sequencing singularity Dickson - Spiders that look like pelicans Alan - Guessing pool for China Spacelab reentry Vincent - How to take a picture of the stealth bomber over the rose bowl Listener Picks Gretchen - The Bearded Lady Project Intro music is by Ronald Jenkees. Send your virology questions and comments to twiv@microbe.tv

We’re back! It is grant season, so the podcast schedule is slowing down a bit, but we are still at it. Over an audio backdrop of torrential rain—which kept Anna Lisa from opening the show—we chat with Assistant Professor Adam Williams. We discuss his research into long noncoding RNAs and what they have to do with immune system function. We also talk about asthma, allergic reactions, 3D cell culture systems, the Hygiene Hypothesis, peanuts, English food and the Brexit.

Sharon Turcotte did research on lncRNAs with Williams Lab at the Jackson Laboratory for Genomic Medicine. She teaches us what a lncRNA is, its function in gene expression, diseases lncRNAs have been associated with, using the CRISPR-Cas system and her advice for students joining the biotech industry. If you want to learn more about RNAs, check out the database RNAcentral.org. You can also read more information about Williams Lab.