Natalia V Klementieva, Evgenii A Lunev, Anna A Shmidt, Elizaveta M Loseva, Irina M Savchenko, Ekaterina A Svetlova, Ivan I Galkin, Anna V Polikarpova, Evgeny V Usachev, Svetlana G Vassilieva, Valeria I Marina, Marina A Dzhenkova, Anna D Romanova, Anton V Agutin, Anna A Timakova, Denis A Reshetov, Tatiana V Egorova, Maryana V Bardina
{"title":"RNA Interference Effectors Selectively Silence the Pathogenic Variant <i>GNAO1</i> c.607 G > A <i>In Vitro</i>.","authors":"Natalia V Klementieva, Evgenii A Lunev, Anna A Shmidt, Elizaveta M Loseva, Irina M Savchenko, Ekaterina A Svetlova, Ivan I Galkin, Anna V Polikarpova, Evgeny V Usachev, Svetlana G Vassilieva, Valeria I Marina, Marina A Dzhenkova, Anna D Romanova, Anton V Agutin, Anna A Timakova, Denis A Reshetov, Tatiana V Egorova, Maryana V Bardina","doi":"10.1089/nat.2023.0043","DOIUrl":"10.1089/nat.2023.0043","url":null,"abstract":"<p><p>RNA interference (RNAi)-based therapeutics hold the potential for dominant genetic disorders, enabling sequence-specific inhibition of pathogenic gene products. We aimed to direct RNAi for the selective suppression of the heterozygous <i>GNAO1</i> c.607 G > A variant causing <i>GNAO1</i> encephalopathy. By screening short interfering RNA (siRNA), we showed that <i>GNAO1</i> c.607G>A is a druggable target for RNAi. The si1488 candidate achieved at least twofold allelic discrimination and downregulated mutant protein to 35%. We created vectorized RNAi by incorporating the si1488 sequence into the short hairpin RNA (shRNA) in the adeno-associated virus (AAV) vector. The shRNA stem and loop were modified to improve the transcription, processing, and guide strand selection. All tested shRNA constructs demonstrated selectivity toward mutant <i>GNAO1</i>, while tweaking hairpin structure only marginally affected the silencing efficiency. The selectivity of shRNA-mediated silencing was confirmed in the context of AAV vector transduction. To conclude, RNAi effectors ranging from siRNA to AAV-RNAi achieve suppression of the pathogenic <i>GNAO1</i> c.607G>A and discriminate alleles by the single-nucleotide substitution. For gene therapy development, it is crucial to demonstrate the benefit of these RNAi effectors in patient-specific neurons and animal models of the GNAO1 encephalopathy.</p>","PeriodicalId":19412,"journal":{"name":"Nucleic acid therapeutics","volume":" ","pages":"90-99"},"PeriodicalIF":4.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139432811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"\"Goldilocks Modifications\" for mRNA Therapeutics Won the Nobel Prize.","authors":"Li Li","doi":"10.1089/nat.2023.0062","DOIUrl":"10.1089/nat.2023.0062","url":null,"abstract":"","PeriodicalId":19412,"journal":{"name":"Nucleic acid therapeutics","volume":" ","pages":"1-3"},"PeriodicalIF":4.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11302211/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139575862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Falk Ehmann, Andreas Kuhn, Anna Maria Gerdina Pasmooij, Anthony Humphreys, Arjon Van Hengel, Brian Dooley, Brigitte Anliker, Camilla Svensson, Daniel Capaldi, David Henshall, Emer Cooke, Haiyan Zhou, Hilde Bastaerts, Jeske Smink, Joop Van Gerven, Leonor Enes, Lubomir Nechev, Marcel Hoefnagel, Mariëtte Driessens, Michael Wenger, Oriane Blanquie, Pawel Widomski, Ralf Herold, René Thürmer, Sol Ruiz, Steffen Thirstrup, Susan Goody, Tal Zaks, Valentina Cordò, Annemieke M Aartsma-Rus
{"title":"Report of the European Medicines Agency Conference on RNA-Based Medicines.","authors":"Falk Ehmann, Andreas Kuhn, Anna Maria Gerdina Pasmooij, Anthony Humphreys, Arjon Van Hengel, Brian Dooley, Brigitte Anliker, Camilla Svensson, Daniel Capaldi, David Henshall, Emer Cooke, Haiyan Zhou, Hilde Bastaerts, Jeske Smink, Joop Van Gerven, Leonor Enes, Lubomir Nechev, Marcel Hoefnagel, Mariëtte Driessens, Michael Wenger, Oriane Blanquie, Pawel Widomski, Ralf Herold, René Thürmer, Sol Ruiz, Steffen Thirstrup, Susan Goody, Tal Zaks, Valentina Cordò, Annemieke M Aartsma-Rus","doi":"10.1089/nat.2023.0021","DOIUrl":"10.1089/nat.2023.0021","url":null,"abstract":"<p><p>RNA-based medicines have potential to treat a large variety of diseases, and research in the field is very dynamic. Proactively, The European Medicines Agency (EMA) organized a virtual conference on February 2, 2023 to promote the development of RNA-based medicines. The initiative addresses the goal of the EMA Regulatory Science Strategy to 2025 to \"catalyse the integration of science and technology in medicines development.\" The conference focused on RNA technologies (excluding RNA vaccines) and involved different stakeholders, including representatives from academia, industry, regulatory authorities, and patient organizations. The conference comprised presentations and discussion sessions conducted by panels of subject matter experts. In this meeting report, we summarize the presentations and recap the main themes of the panel discussions.</p>","PeriodicalId":19412,"journal":{"name":"Nucleic acid therapeutics","volume":" ","pages":"4-11"},"PeriodicalIF":4.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139087866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Brenda F Baker, Shuting Xia, Wesley Partridge, Jeffery A Engelhardt, Sotirios Tsimikas, Stanley T Crooke, Sanjay Bhanot, Richard S Geary
{"title":"Safety and Tolerability of GalNAc<sub>3</sub>-Conjugated Antisense Drugs Compared to the Same-Sequence 2'-<i>O</i>-Methoxyethyl-Modified Antisense Drugs: Results from an Integrated Assessment of Phase 1 Clinical Trial Data.","authors":"Brenda F Baker, Shuting Xia, Wesley Partridge, Jeffery A Engelhardt, Sotirios Tsimikas, Stanley T Crooke, Sanjay Bhanot, Richard S Geary","doi":"10.1089/nat.2023.0026","DOIUrl":"10.1089/nat.2023.0026","url":null,"abstract":"<p><p>The triantennary <i>N</i>-acetylgalactosamine (GalNAc<sub>3</sub>) cluster has demonstrated the utility of receptor-mediated uptake of ligand-conjugated antisense drugs targeting RNA expressed by hepatocytes. GalNAc<sub>3</sub>-conjugated 2'-<i>O</i>-methoxyethyl (2'MOE) modified antisense oligonucleotides (ASOs) have demonstrated a higher potency than the unconjugated form to support lower doses for an equivalent pharmacological effect. We utilized the Ionis integrated safety database to compare four GalNAc<sub>3</sub>-conjugated and four same-sequence unconjugated 2'MOE ASOs. This assessment evaluated data from eight randomized placebo-controlled dose-ranging phase 1 studies involving 195 healthy volunteers (79 GalNAc<sub>3</sub> ASO, 24 placebo; 71 ASO, 21 placebo). No safety signals were identified by the incidence of abnormal threshold values in clinical laboratory tests for either ASO group. However, there was a significant increase in mean alanine transaminase levels compared with placebo in the upper dose range of the unconjugated 2'MOE ASO group. The mean percentage of subcutaneous injections leading to local cutaneous reaction was 30-fold lower in the GalNAc<sub>3</sub>-conjugated ASO group compared with the unconjugated ASO group (0.9% vs. 28.6%), with no incidence of flu-like reactions (0.0% vs. 0.7%). Three subjects (4.2%) in the unconjugated ASO group discontinued dosing. An improvement in the overall safety and tolerability profile of GalNAc<sub>3</sub>-conjugated 2'MOE ASOs is evident in this comparison of short-term clinical data in healthy volunteers.</p>","PeriodicalId":19412,"journal":{"name":"Nucleic acid therapeutics","volume":" ","pages":"18-25"},"PeriodicalIF":4.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139479072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Martin D Requena, Amy Yan, Telmo Llanga, Bruce A Sullenger
{"title":"Reversible Aptamer Staining, Sorting, and Cleaning of Cells (Clean FACS) with Antidote Oligonucleotide or Nuclease Yields Fully Responsive Cells.","authors":"Martin D Requena, Amy Yan, Telmo Llanga, Bruce A Sullenger","doi":"10.1089/nat.2023.0050","DOIUrl":"10.1089/nat.2023.0050","url":null,"abstract":"<p><p>The ability to reverse the binding of aptamers to their target proteins has received considerable attention for developing controllable therapeutic agents. Recently, use of aptamers as reversible cell-sorting ligands has also sparked interest. Antibodies are currently utilized for isolating cells expressing a particular cell surface receptor. The inability to remove antibodies from isolated cells following sorting greatly limits their utility for many applications. Previously, we described how a particular aptamer-antidote oligonucleotide pair can isolate cells and clean them. Here, we demonstrate that this approach is generalizable; aptamers can simultaneously recognize more than one cell type during fluorescent activated cell sorting (FACS). Moreover, we describe a novel approach to reverse aptamer binding following cell sorting using a nuclease. This alternative strategy represents a cleaning approach that does not require the generation of antidote oligonucleotides for each aptamer and will greatly reduce the cost and expand the utility of Clean FACS.</p>","PeriodicalId":19412,"journal":{"name":"Nucleic acid therapeutics","volume":" ","pages":"12-17"},"PeriodicalIF":4.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11302193/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139575909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tom Metz, Mick M Welling, Ernst Suidgeest, Esmée Nieuwenhuize, Thomas de Vlaam, Daniel Curtis, Tsinatkeab T Hailu, Louise van der Weerd, Willeke M C van Roon-Mom
{"title":"Biodistribution of Radioactively Labeled Splice Modulating Antisense Oligonucleotides After Intracerebroventricular and Intrathecal Injection in Mice.","authors":"Tom Metz, Mick M Welling, Ernst Suidgeest, Esmée Nieuwenhuize, Thomas de Vlaam, Daniel Curtis, Tsinatkeab T Hailu, Louise van der Weerd, Willeke M C van Roon-Mom","doi":"10.1089/nat.2023.0018","DOIUrl":"10.1089/nat.2023.0018","url":null,"abstract":"<p><p>Antisense oligonucleotides (AONs) are promising therapeutic candidates, especially for neurological diseases. Intracerebroventricular (ICV) injection is the predominant route of administration in mouse studies, while in clinical trials, intrathecal (IT) administration is mostly used. There is little knowledge on the differences in distribution of these injection methods within the same species over time. In this study, we compared the distribution of splice-switching AONs targeting exon 15 of amyloid precursor protein pre-mRNA injected via the ICV and IT route in mice. The AON was labeled with radioactive indium-111 and mice were imaged using single-photon emission computed tomography (SPECT) 0, 4, 24, 48, 72, and 96 h after injection. <i>In vivo</i> SPECT imaging showed <sup>111</sup>In-AON activity diffused throughout the central nervous system (CNS) in the first hours after injection. The <sup>111</sup>In-AON activity in the CNS persisted over the course of 4 days, while signal in the kidneys rapidly decreased. Postmortem counting in different organs and tissues showed very similar distribution of <sup>111</sup>In-AON activity throughout the body, while the signal in the different brain regions was higher with ICV injection. Overall, IT and ICV injection have very similar distribution patterns in the mouse, but ICV injection is much more effective in reaching the brain.</p>","PeriodicalId":19412,"journal":{"name":"Nucleic acid therapeutics","volume":"34 1","pages":"26-34"},"PeriodicalIF":4.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139932298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Brian J Thomas, Caitlyn Guldenpfennig, Mark A Daniels, Donald H Burke, David Porciani
{"title":"Multiplexed <i>In Vivo</i> Screening Using Barcoded Aptamer Technology to Identify Oligonucleotide-Based Targeting Reagents.","authors":"Brian J Thomas, Caitlyn Guldenpfennig, Mark A Daniels, Donald H Burke, David Porciani","doi":"10.1089/nat.2024.0010","DOIUrl":"10.1089/nat.2024.0010","url":null,"abstract":"<p><p>Recent FDA approvals of mRNA vaccines, short-interfering RNAs, and antisense oligonucleotides highlight the success of oligonucleotides as therapeutics. Aptamers are excellent affinity reagents that can selectively label protein biomarkers, but their clinical application has lagged. When formulating a given aptamer for <i>in vivo</i> use, molecular design details can determine biostability and biodistribution; therefore, extensive postselection manipulation is often required for each new design to identify clinically useful reagents harboring improved pharmacokinetic properties. Few methods are available to comprehensively screen such aptamers, especially <i>in vivo</i>, constituting a significant bottleneck in the field. In this study, we introduce barcoded aptamer technology (BApT) for multiplexed screening of predefined aptamer formulations <i>in vitro</i> and <i>in vivo</i>. We demonstrate this technology by simultaneously investigating 20 aptamer formulations, each harboring different molecular designs, for targeting Non-Small Cell Lung Cancer cells and tumors. Screening <i>in vitro</i> identified a 45 kDa bispecific formulation as the best cancer cell targeting reagent, whereas screening <i>in vivo</i> identified a 30 kDa monomeric formulation as the best tumor-specific targeting reagent. The multiplexed analysis pipeline also identified biodistribution phenotypes shared among formulations with similar molecular architectures. The BApT approach we describe here has the potential for broad application to fields where oligonucleotide-based targeting reagents are desired.</p>","PeriodicalId":19412,"journal":{"name":"Nucleic acid therapeutics","volume":" ","pages":"109-124"},"PeriodicalIF":4.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11250842/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140945568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Zelia Corradi, Rebekkah J Hitti-Malin, Laura A de Rooij, Alejandro Garanto, Rob W J Collin, Frans P M Cremers
{"title":"Antisense Oligonucleotide-Based Rescue of Complex Intronic Splicing Defects in <i>ABCA4</i>.","authors":"Zelia Corradi, Rebekkah J Hitti-Malin, Laura A de Rooij, Alejandro Garanto, Rob W J Collin, Frans P M Cremers","doi":"10.1089/nat.2024.0008","DOIUrl":"10.1089/nat.2024.0008","url":null,"abstract":"<p><p>The <i>ABCA4</i> gene, involved in Stargardt disease, has a high percentage of splice-altering pathogenic variants, some of which cause complex RNA defects. Although antisense oligonucleotides (AONs) have shown promising results in splicing modulation, they have not yet been used to target complex splicing defects. Here, we performed AON-based rescue studies on <i>ABCA4</i> complex splicing defects. Intron 13 variants c.1938-724A>G, c.1938-621G>A, c.1938-619A>G, and c.1938-514A>G all lead to the inclusion of different pseudo-exons (PEs) with and without an upstream PE (PE1). Intron 44 variant c.6148-84A>T results in multiple PE inclusions and/or exon skipping events. Five novel AONs were designed to target these defects. AON efficacy was assessed by <i>in vitro</i> splice assays using midigenes containing the variants of interest. All screened complex splicing defects were effectively rescued by the AONs. Although varying levels of efficacy were observed between AONs targeting the same PEs, for all variants at least one AON restored splicing to levels comparable or better than wildtype. In conclusion, AONs are a promising approach to target complex splicing defects in <i>ABCA4</i>.</p>","PeriodicalId":19412,"journal":{"name":"Nucleic acid therapeutics","volume":" ","pages":"125-133"},"PeriodicalIF":4.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141155286","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Adi Idris, Surya Shrivastava, Aroon Supramaniam, Roslyn M Ray, Galina Shevchenko, Dhruba Acharya, Nigel A J McMillan, Kevin V Morris
{"title":"Extracellular Vesicles Loaded with Long Antisense RNAs Repress Severe Acute Respiratory Syndrome Coronavirus 2 Infection.","authors":"Adi Idris, Surya Shrivastava, Aroon Supramaniam, Roslyn M Ray, Galina Shevchenko, Dhruba Acharya, Nigel A J McMillan, Kevin V Morris","doi":"10.1089/nat.2023.0078","DOIUrl":"10.1089/nat.2023.0078","url":null,"abstract":"<p><p>Long antisense RNAs (asRNAs) have been observed to repress HIV and other virus expression in a manner that is refractory to viral evolution. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19) disease, has a distinct ability to evolve resistance around antibody targeting, as was evident from the emergence of various SARS-CoV-2 spike antibody variants. Importantly, the effectiveness of current antivirals is waning due to the rapid emergence of new variants of concern, more recently the omicron variant. One means of avoiding the emergence of viral resistance is by using long asRNA to target SARS-CoV-2. Similar work has proven successful with HIV targeting by long asRNA. In this study, we describe a long asRNA targeting SARS-CoV-2 RNA-dependent RNA polymerase gene and the ability to deliver this RNA in extracellular vesicles (EVs) to repress virus expression. The observations presented in this study suggest that EV-delivered asRNAs are one means to targeting SARS-CoV-2 infection, which is both effective and broadly applicable as a means to control viral expression in the absence of mutation. This is the first demonstration of the use of engineered EVs to deliver long asRNA payloads for antiviral therapy.</p>","PeriodicalId":19412,"journal":{"name":"Nucleic acid therapeutics","volume":" ","pages":"101-108"},"PeriodicalIF":4.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11296208/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140288685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}