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Wiley Interdisciplinary Reviews. RNA 2023With the advent of ever more sophisticated methods for the in vitro synthesis and the in vivo delivery of RNAs, synthetic mRNAs have gained substantial interest both for... (Review)
Review
With the advent of ever more sophisticated methods for the in vitro synthesis and the in vivo delivery of RNAs, synthetic mRNAs have gained substantial interest both for medical applications, as well as for biotechnology. However, in most biological systems exogeneous mRNAs possess only a limited half-life, especially in fast dividing cells. In contrast, viral RNAs can extend their lifetime by actively replicating inside their host. As such they may serve as scaffolds for the design of synthetic self-replicating RNAs (srRNA), which can be used to increase both the half-life and intracellular concentration of coding RNAs. Synthetic srRNAs may be used to enhance recombinant protein expression or induce the reprogramming of differentiated cells into pluripotent stem cells but also to create cell-free systems for research based on experimental evolution. In this article, we discuss the applications and design principles of srRNAs used for cellular reprogramming, mRNA-based vaccines and tools for synthetic biology. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.
Topics: Cellular Reprogramming; RNA, Messenger; RNA, Viral
PubMed: 37264531
DOI: 10.1002/wrna.1803 -
Nucleic Acids Research Aug 2023Removal of the mRNA 5' cap primes transcripts for degradation and is central for regulating gene expression in eukaryotes. The canonical decapping enzyme Dcp2 is...
Removal of the mRNA 5' cap primes transcripts for degradation and is central for regulating gene expression in eukaryotes. The canonical decapping enzyme Dcp2 is stringently controlled by assembly into a dynamic multi-protein complex together with the 5'-3'exoribonuclease Xrn1. Kinetoplastida lack Dcp2 orthologues but instead rely on the ApaH-like phosphatase ALPH1 for decapping. ALPH1 is composed of a catalytic domain flanked by C- and N-terminal extensions. We show that T. brucei ALPH1 is dimeric in vitro and functions within a complex composed of the trypanosome Xrn1 ortholog XRNA and four proteins unique to Kinetoplastida, including two RNA-binding proteins and a CMGC-family protein kinase. All ALPH1-associated proteins share a unique and dynamic localization to a structure at the posterior pole of the cell, anterior to the microtubule plus ends. XRNA affinity capture in T. cruzi recapitulates this interaction network. The ALPH1 N-terminus is not required for viability in culture, but essential for posterior pole localization. The C-terminus, in contrast, is required for localization to all RNA granule types, as well as for dimerization and interactions with XRNA and the CMGC kinase, suggesting possible regulatory mechanisms. Most significantly, the trypanosome decapping complex has a unique composition, differentiating the process from opisthokonts.
Topics: Endoribonucleases; RNA Caps; RNA Stability; RNA, Messenger; RNA-Binding Proteins; Trypanosoma
PubMed: 37309887
DOI: 10.1093/nar/gkad497 -
Advanced Materials (Deerfield Beach,... Apr 2024Messenger RNA (mRNA)-based therapeutic strategies have shown remarkable promise in preventing and treating a staggering range of diseases. Optimizing the structure and... (Review)
Review
Messenger RNA (mRNA)-based therapeutic strategies have shown remarkable promise in preventing and treating a staggering range of diseases. Optimizing the structure and delivery system of engineered mRNA has greatly improved its stability, immunogenicity, and protein expression levels, which has led to a wider range of uses for mRNA therapeutics. Herein, a thorough analysis of the optimization strategies used in the structure of mRNA is first provided and delivery systems are described in great detail. Furthermore, the latest advancements in biomedical engineering for mRNA technology, including its applications in combatting infectious diseases, treating cancer, providing protein replacement therapy, conducting gene editing, and more, are summarized. Lastly, a perspective on forthcoming challenges and prospects concerning the advancement of mRNA therapeutics is offered. Despite these challenges, mRNA-based therapeutics remain promising, with the potential to revolutionize disease treatment and contribute to significant advancements in the biomedical field.
Topics: RNA, Messenger; Gene Editing; Biomedical Engineering
PubMed: 37805865
DOI: 10.1002/adma.202308029 -
Seminars in Cell & Developmental Biology Feb 2024Translation is regulated spatiotemporally to direct protein synthesis when and where it is needed. RNA localization and local translation have been observed in various... (Review)
Review
Translation is regulated spatiotemporally to direct protein synthesis when and where it is needed. RNA localization and local translation have been observed in various subcellular compartments, allowing cells to rapidly and finely adjust their proteome post-transcriptionally. Local translation on membrane-bound organelles is important to efficiently synthesize proteins targeted to the organelles. Protein-RNA phase condensates restrict RNA spatially in membraneless organelles and play essential roles in translation regulation and RNA metabolism. In addition, the temporal translation kinetics not only determine the amount of protein produced, but also serve as an important checkpoint for the quality of ribosomes, mRNAs, and nascent proteins. Translation imaging provides a unique capability to study these fundamental processes in the native environment. Recent breakthroughs in imaging enabled real-time visualization of translation of single mRNAs, making it possible to determine the spatial distribution and key biochemical parameters of in vivo translation dynamics. Here we reviewed the recent advances in translation imaging methods and their applications to study spatiotemporal translation regulation in vivo.
Topics: Protein Biosynthesis; Ribosomes; RNA, Messenger; Organelles
PubMed: 36963991
DOI: 10.1016/j.semcdb.2023.03.006 -
International Journal of Molecular... Sep 2023In the last few decades, RNA-based drugs have emerged as a promising candidate in the treatment of various diseases. The introduction of messenger RNA (mRNA) as a... (Review)
Review
In the last few decades, RNA-based drugs have emerged as a promising candidate in the treatment of various diseases. The introduction of messenger RNA (mRNA) as a vaccine or therapeutic agent enables the production of almost any functional protein/peptide. The key to applying RNA therapy in clinical trials is developing safe and effective delivery systems. Exosomes and lipid nanoparticles (LNPs) have been exploited as promising vehicles for drug delivery. This review discusses the feasibility of exosomes and LNPs as vehicles for mRNA delivery. Cancer/testis antigens (CTAs) show restricted expression in normal tissues and widespread expression in cancer tissues. Many of these CTAs show expression in the sera of patients with cancers. These characteristics of CTAs make them excellent targets for cancer immunotherapy. This review summarizes the roles of CTAs in various life processes and current studies on mRNAs encoding CTAs. Clinical studies present the beneficial effects of mRNAs encoding CTAs in patients with cancers. This review highlight clinical studies employing mRNA-LNPs encoding CTAs.
Topics: Male; Humans; Antigens, Neoplasm; Testis; RNA; Neoplasms; RNA, Messenger
PubMed: 37834126
DOI: 10.3390/ijms241914679 -
Nature Sep 2023
Topics: RNA, Messenger; Biotechnology
PubMed: 37253980
DOI: 10.1038/d41586-023-01745-z -
American Journal of Physiology. Cell... Jan 2024Cardiac fibrosis remains an unmet clinical need that has so far proven difficult to eliminate using current therapies. As such, novel technologies are needed that can...
Cardiac fibrosis remains an unmet clinical need that has so far proven difficult to eliminate using current therapies. As such, novel technologies are needed that can target the pathological fibroblasts responsible for fibrosis and adverse tissue remodeling. mRNA encapsulated in lipid nanoparticles (LNPs) is an emerging technology that could offer a solution to this problem. Indeed, this strategy has already shown clinical success with the mRNA COVID-19 vaccines. In this AJP perspective, we discuss how this technology can be leveraged to specifically target cardiac fibrosis via several complementary strategies. First, we discuss the successful preclinical studies in a mouse model of cardiac injury to use T cell-targeted LNPs to produce anti-fibroblast chimeric antigen receptor T (CAR T) cells in vivo that could effectively reduce cardiac fibrosis. Next, we discuss how these T cell-targeted LNPs could be used to generate T regulatory cells (T-regs), which could migrate to areas of active fibrosis and dampen inflammation through paracrine effects as an alternative to active fibroblast killing by CAR T cells. Finally, we conclude with thoughts on directly targeting pathological fibroblasts to deliver RNAs that could interfere with fibroblast activation and activity. We hope this discussion serves as a catalyst for finding approaches that harness the power of mRNA and LNPs to eliminate cardiac fibrosis and treat other fibrotic diseases amenable to such interventions. Cardiac fibrosis has few specific interventions available for effective treatment. mRNA encapsulated in lipid nanoparticles could provide a novel solution for treating cardiac fibrosis. This AJP perspective discusses what possible strategies could rely on this technology, from in vivo-produced CAR T cells that kill pathological fibroblasts to in vivo-produced T regulatory cells that dampen the concomitant profibrotic inflammatory cells contributing to remodeling, directly targeting fibroblasts and eliminating them or silencing profibrotic pathways.
Topics: Mice; Animals; Humans; COVID-19 Vaccines; RNA, Messenger; Cardiomyopathies; Fibroblasts; Fibrosis
PubMed: 38047297
DOI: 10.1152/ajpcell.00504.2023 -
Biochimica Et Biophysica Acta. General... Mar 2024The effectiveness of messenger RNA (mRNA) vaccines, especially those designed for COVID-19, relies heavily on sophisticated delivery systems that ensure efficient... (Review)
Review
The effectiveness of messenger RNA (mRNA) vaccines, especially those designed for COVID-19, relies heavily on sophisticated delivery systems that ensure efficient delivery of mRNA to target cells. A variety of nanoscale vaccine delivery systems (VDSs) have been explored for this purpose, including lipid nanoparticles (LNPs), liposomes, and polymeric nanoparticles made from biocompatible polymers such as poly(lactic-co-glycolic acid), as well as viral vectors and lipid-polymer hybrid complexes. Among these, LNPs are particularly notable for their efficiency in encapsulating and protecting mRNA. These nanoscale VDSs can be engineered to enhance stability and facilitate uptake by cells. The choice of delivery system depends on factors like the specific mRNA vaccine, target cell types, stability requirements, and desired immune response. In this review, we shed light on recent advances in delivery mechanisms for self-amplifying RNA (saRNA) vaccines, emphasizing groundbreaking studies on nanoscale delivery systems aimed at improving the efficacy and safety of mRNA/saRNA vaccines.
Topics: mRNA Vaccines; Vaccines; RNA; RNA, Messenger; Polymers
PubMed: 38185238
DOI: 10.1016/j.bbagen.2024.130558 -
Biochimica Et Biophysica Acta. Gene... Jun 2024RNA polymerase II (Pol II) is the multi-protein complex responsible for transcribing all protein-coding messenger RNA (mRNA). Most research on gene regulation is focused... (Review)
Review
RNA polymerase II (Pol II) is the multi-protein complex responsible for transcribing all protein-coding messenger RNA (mRNA). Most research on gene regulation is focused on the mechanisms controlling which genes are transcribed when, or on the mechanics of transcription. How global Pol II activity is determined receives comparatively less attention. Here, we follow the life of a Pol II molecule from 'assembly of the complex' to nuclear import, enzymatic activity, and degradation. We focus on how Pol II spends its time in the nucleus, and on the two-way relationship between Pol II abundance and activity in the context of homeostasis and global transcriptional changes.
Topics: RNA Polymerase II; Transcription, Genetic; Humans; Gene Expression Regulation; Cell Nucleus; RNA, Messenger; Active Transport, Cell Nucleus; Animals
PubMed: 38552781
DOI: 10.1016/j.bbagrm.2024.195024 -
Molecular Cell Dec 2023Reactive aldehydes are produced by normal cellular metabolism or after alcohol consumption, and they accumulate in human tissues if aldehyde clearance mechanisms are...
Reactive aldehydes are produced by normal cellular metabolism or after alcohol consumption, and they accumulate in human tissues if aldehyde clearance mechanisms are impaired. Their toxicity has been attributed to the damage they cause to genomic DNA and the subsequent inhibition of transcription and replication. However, whether interference with other cellular processes contributes to aldehyde toxicity has not been investigated. We demonstrate that formaldehyde induces RNA-protein crosslinks (RPCs) that stall the ribosome and inhibit translation in human cells. RPCs in the messenger RNA (mRNA) are recognized by the translating ribosomes, marked by atypical K6-linked ubiquitylation catalyzed by the RING-in-between-RING (RBR) E3 ligase RNF14, and subsequently resolved by the ubiquitin- and ATP-dependent unfoldase VCP. Our findings uncover an evolutionary conserved formaldehyde-induced stress response pathway that protects cells against RPC accumulation in the cytoplasm, and they suggest that RPCs contribute to the cellular and tissue toxicity of reactive aldehydes.
Topics: Humans; RNA; Ubiquitination; Ubiquitin-Protein Ligases; Formaldehyde; Aldehydes; RNA, Messenger
PubMed: 37951215
DOI: 10.1016/j.molcel.2023.10.011