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Engineering ‘smart’ viral RNA structures for stable and targeted siRNA delivery

English title Engineering ‘smart’ viral RNA structures for stable and targeted siRNA delivery
Applicant Hill Alyssa
Number 190865
Funding scheme Spark
Research institution Institut für Pharmazeutische Wissenschaften ETH Zürich
Institution of higher education ETH Zurich - ETHZ
Main discipline Biochemistry
Start/End 01.01.2020 - 31.12.2020
Approved amount 99'894.00
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All Disciplines (2)

Discipline
Biochemistry
Molecular Biology

Keywords (7)

delivery; RNAi; engineering; flavivirus; nanotechnology; cancer; siRNA

Lay Summary (German)

Lead
Small interfering RNA (siRNA) ist eine neue Klasse von therapeutischen Medikamenten mit außergewöhnlichem Potenzial in der Behandlung von Krankheiten. Allerdings haben wichtige physiologische Barrieren ihre Übertragung in die Klinik weitgehend verhindert. Dieses Spark-Projekt zielt darauf ab, die Herausforderungen der siRNA-Versorgung durch die Entwicklung einer modularen und verallgemeinerbaren RNA-basierten Plattform unter Verwendung einer viral abgeleiteten RNA-Struktur zu bewältigen.
Lay summary
Eine kleine eingreifende RNA (engl. «small interfering RNA»; abgekürzt siRNA) ist ein kurzes, doppelsträngiges RNA-Molekül, welches eine neue Klasse von therapeutischen Medikamenten darstellt, die den natürlichen Gen-Stillegungs-Pfad, die so genannte RNA-Interferenz (RNAi), ausnutzt. Im Gegensatz zu herkömmlichen niedermolekularen Medikamenten (z.B. Aspirin) und Biologika (z.B. Herceptin), die an Proteine binden und deren Aktivität verändern, arbeiten siRNAs mit der bereits in der Zelle vorhandenen RNAi-Maschinerie: Die Boten-RNAs (engl. «messenger RNA»; abgekürzt mRNAs) - also Moleküle, die helfen, die in der DNA gespeicherte genetische Information in Proteine umzuwandeln- werden abgebaut. Dies bedeutet, dass siRNA-Medikamente ihre therapeutische Wirkung auf einem Niveau entfalten, das über dem von herkömmlichen proteinbindenden Medikamenten liegt. Metaphorisch lässt sich eine Krankheit wie ein undichter Wasserhahn beschreiben, wobei herkömmliche Medikamente den Boden trocken wischen, während siRNAs den Wasserhahn zudrehen. Da sie sequenzspezifisch an mRNAs binden, können siRNA-Medikamente theoretisch so konzipiert werden, dass sie jedes bekannte krankheitsverursachende Gen regulieren. Daher haben siRNAs das Potenzial, Krankheiten zu behandeln, die derzeit noch nicht heilbar sind, wie zum Beispiel genetische Defekte, Autoimmunerkrankungen und Krebs.
Die außergewöhnliche Leistungsfähigkeit der siRNAs hat sich jedoch in der Klinik als schwierig zu realisieren erwiesen. Nach systemischer Verabreichung werden siRNAs durch Enzyme, die Nukleasen genannt werden, schnell abgebaut, was im Blut zu einer Halbwertszeit von weniger als fünf Minuten führt. Außerdem werden siRNAs nicht frei in die Zellen aufgenommen. Zusammenfassend stellen diese physiologischen Barrieren einen Engpass dar, siRNA-Medikamenten vom Labor zum Krankenbett zu übertragen. Tatsächlich wurden in den letzten 20 Jahren, seit der Entdeckung von RNAi, nur zwei siRNA-Medikamente (patisiran und givosiran) kommerzialisiert, die auf komplexen und veralteten Verabreichungsstrategien beruhen (im Fall von Lipid-Nanopartikeln oder LNPs; siehe patisiran) oder spezifisch für die Leber (im Fall von N-Acetylgalactosamin oder GalNAc; siehe givosiran). Um das therapeutische Potenzial der siRNA zu realisieren, ist demnach eine innovative Verabreichungsstrategie erforderlich. Unter Berücksichtigung von Prinzipien der RNA-Nanotechnologie wird in diesem Spark-Projekt ein viral abgeleitetes RNA-Motiv, das den Nukleaseabbau erschwert, mit einem synthetischen RNA-Aptamer kombiniert, das die Zellaufnahme antreibt, um eine verallgemeinerbare RNA-basierte Plattform zu generieren, die die Herausforderungen der siRNA-Abgabe ganzheitlich angeht.
Direct link to Lay Summary Last update: 23.12.2019

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Datasets

Engineering ‘smart’ viral RNA structures for stable and targeted siRNA delivery

Author Hill, Alyssa
Publication date 09.02.2021
Persistent Identifier (PID) https://doi.org/10.5061/dryad.x95x69phd
Repository Dryad Digital Repository
Abstract
Innovative delivery strategies are needed in order to realize the potential of small interfering RNA (siRNA) in medicine. SiRNAs are short, double-stranded RNA molecules that silence genes by co-opting an endogenous RNA interference (RNAi) pathway. Because they act on messenger RNA (mRNA) sequences via RNAi, siRNAs hold promise as potentially curative therapies for genetic defects, autoimmune disorders, cancers, and other diseases that cannot be treated with traditional, protein-binding small molecule drugs and biologics. However, key physiological barriers largely have precluded the translation of siRNA drugs into clinical practice. In vivo, naked siRNAs are degraded rapidly by nucleases and cleared by the kidneys, resulting in a half-life of less than five minutes. Moreover, by comparison to small molecule drugs, siRNA drugs are relatively large, hydrophilic molecules that do not distribute widely to tissues or passively cross the cell membrane. Therefore, without an effective strategy for delivery, the accumulation of siRNA drugs at target sites is minimal. Today, there are few prominent siRNA delivery approaches, and each has significant limitations. For example, chemical modifications can improve nuclease resistance, but with the increase in stability also come tradeoffs in potency and safety. Lipid nanoparticles (LNPs) physically shield siRNAs from degradation and can be modified to promote biodistribution and uptake; but as LNPs are optimized for efficacy, they become increasingly complex, posing quality assurance, cost, and evaluation problems. Finally, conjugation to the N-Acetylgalactosamine (GalNAc) ligand is a promising delivery strategy for the liver, but targeted delivery to other tissues is a problem that still remains to be solved. Advances in nucleic acid nanotechnology have shown that RNA is an emerging platform for drug delivery. In particular, a three-way junction (3WJ) derived from bacteriophage prohead RNA (pRNA) has gained prominence as a vector for small molecule, microRNA (miRNA), anti-miRNA, and siRNA delivery. As a delivery solution for siRNA, RNA-based platforms like the pRNA 3WJ have many notable advantages. For example, size and shape can be controlled to minimize clearance, and functionalization with aptamers can drive cell uptake. Also, RNA is a fundamentally biocompatible molecule that is simple, straightforward to produce, and multifunctional. However, its metabolic instability is limiting. Exciting new research has uncovered ‘smart’ RNA structures that are produced by flaviviruses (e.g., Zika, Dengue, West Nile) to thwart nuclease degradation. Compared to other RNA structures used for drug delivery, these nuclease-resistant structures (NRSs) may be uniquely positioned for in vivo applications. The aim of this project is to harness the inherent stability of flaviviral NRSs in the creation of a supramolecular platform for siRNA delivery. This project has the potential to address a critical need in the field of oligonucleotide therapeutics, which has few promising solutions for harnessing the power of RNAi in the clinic. Additionally, this project will validate new stable structures as building blocks for use in RNA nanotechnology and therefore will help researchers design supramolecular structures for a variety of applications well beyond those described in this proposal.

Communication with the public

Communication Title Media Place Year
Media relations: print media, online media Taking a page from the playbook of viruses EU Research, Blazon Publishing and Media Ltd International 2020

Abstract

Innovative delivery strategies are needed in order to realize the potential of small interfering RNA (siRNA) in medicine. SiRNAs are short, double-stranded RNA molecules that silence genes by co-opting an endogenous RNA interference (RNAi) pathway. Because they act on messenger RNA (mRNA) sequences via RNAi, siRNAs hold promise as potentially curative therapies for genetic defects, autoimmune disorders, cancers, and other diseases that cannot be treated with traditional, protein-binding small molecule drugs and biologics.However, key physiological barriers largely have precluded the translation of siRNA drugs into clinical practice. In vivo, naked siRNAs are degraded rapidly by nucleases and cleared by the kidneys, resulting in a half-life of less than five minutes. Moreover, by comparison to small molecule drugs, siRNA drugs are relatively large, hydrophilic molecules that do not distribute widely to tissues or passively cross the cell membrane. Therefore, without an effective strategy for delivery, the accumulation of siRNA drugs at target sites is minimal.Today, there are few prominent siRNA delivery approaches, and each has significant limitations. For example, chemical modifications can improve nuclease resistance, but with the increase in stability also come tradeoffs in potency and safety. Lipid nanoparticles (LNPs) physically shield siRNAs from degradation and can be modified to promote biodistribution and uptake; but as LNPs are optimized for efficacy, they become increasingly complex, posing quality assurance, cost, and evaluation problems. Finally, conjugation to the N-Acetylgalactosamine (GalNAc) ligand is a promising delivery strategy for the liver, but targeted delivery to other tissues is a problem that still remains to be solved.Advances in nucleic acid nanotechnology have shown that RNA is an emerging platform for drug delivery. In particular, a three-way junction (3WJ) derived from bacteriophage prohead RNA (pRNA) has gained prominence as a vector for small molecule, microRNA (miRNA), anti-miRNA, and siRNA delivery. As a delivery solution for siRNA, RNA-based platforms like the pRNA 3WJ have many notable advantages. For example, size and shape can be controlled to minimize clearance, and functionalization with aptamers can drive cell uptake. Also, RNA is a fundamentally biocompatible molecule that is simple, straightforward to produce, and multifunctional. However, its metabolic instability is limiting.Exciting new research has uncovered ‘smart’ RNA structures that are produced by flaviviruses (e.g., Zika, Dengue, West Nile) to thwart nuclease degradation. Compared to other RNA structures used for drug delivery, these nuclease-resistant structures (NRSs) may be uniquely positioned for in vivo applications. The aim of this project is to harness the inherent stability of flaviviral NRSs in the creation of a supramolecular platform for siRNA delivery. This project has the potential to address a critical need in the field of oligonucleotide therapeutics, which has few promising solutions for harnessing the power of RNAi in the clinic. Additionally, this project will validate new stable structures as building blocks for use in RNA nanotechnology and therefore will help researchers design supramolecular structures for a variety of applications well beyond those described in this proposal.
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