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Cao D, Tian M, Liu Z, Guo K, Peng J, Ravichandra A, Ferrell C, Dong Y. Unlock the sustained therapeutic efficacy of mRNA. J Control Release 2025; 383:113837. [PMID: 40368188 PMCID: PMC12145234 DOI: 10.1016/j.jconrel.2025.113837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2025] [Revised: 05/01/2025] [Accepted: 05/10/2025] [Indexed: 05/16/2025]
Abstract
mRNA therapies have emerged as a transformative class of medicines, offering immense potential across a diverse array of applications. This progress has been particularly evident in the wake of the success of lipid nanoparticle (LNP)-based mRNA vaccines during the COVID-19 pandemic. As these applications expand, the demand for sustained protein production has become increasingly critical. However, conventional mRNA therapies face significant challenges, including inherent RNA instability and suboptimal expression efficiency, often requiring repeated dosing to maintain therapeutic efficacy over time. This review highlights recent advances in strategies to prolong the therapeutic efficacy of LNP-mRNA systems. We focus on preclinical and emerging approaches aimed at extending the period of protein translation by engineering both the mRNA molecule and the LNP delivery system. Sustained protein expression is a cornerstone of mRNA-based therapeutics, and addressing this challenge is vital for unlocking their therapeutic potential. We hope this review provides valuable insights to guide the development of optimized delivery platforms for LNP-mRNA therapeutics.
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Affiliation(s)
- Dinglingge Cao
- Icahn Genomics Institute, Precision Immunology Institute, Department of Immunology and Immunotherapy, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Meng Tian
- Icahn Genomics Institute, Precision Immunology Institute, Department of Immunology and Immunotherapy, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhengwei Liu
- Icahn Genomics Institute, Precision Immunology Institute, Department of Immunology and Immunotherapy, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kaiyuan Guo
- Icahn Genomics Institute, Precision Immunology Institute, Department of Immunology and Immunotherapy, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jonathan Peng
- Icahn Genomics Institute, Precision Immunology Institute, Department of Immunology and Immunotherapy, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anjali Ravichandra
- Icahn Genomics Institute, Precision Immunology Institute, Department of Immunology and Immunotherapy, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Caroline Ferrell
- Icahn Genomics Institute, Precision Immunology Institute, Department of Immunology and Immunotherapy, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yizhou Dong
- Icahn Genomics Institute, Precision Immunology Institute, Department of Immunology and Immunotherapy, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Faizi M, Sakharova H, Lareau LF. A generative language model decodes contextual constraints on codon choice for mRNA design. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.05.13.653614. [PMID: 40463199 PMCID: PMC12132368 DOI: 10.1101/2025.05.13.653614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 06/11/2025]
Abstract
The genetic code allows multiple synonymous codons to encode the same amino acid, creating a vast sequence space for protein-coding regions. Codon choice can impact mRNA function and protein output, a consideration newly relevant with advances in mRNA technology. Genomes preferentially use some codons, but simple optimization methods that select preferred codons miss complex contextual patterns. We present Trias, an encoder-decoder language model trained on millions of eukaryotic coding sequences. Trias learns codon usage rules directly from sequence data, integrating local and global dependencies to generate species-specific codon sequences that align with biological constraints. Without explicit training on protein expression, Trias generates sequences and scores that correlate strongly with experimental measurements of mRNA stability, ribosome load, and protein output. The model outperforms commercial codon optimization tools in generating sequences resembling high-expression codon sequence variants. By modeling codon usage in context, Trias offers a data-driven framework for synthetic mRNA design and for understanding the molecular and evolutionary principles behind codon choice.
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Mo O, Zhang Z, Cheng X, Zhu L, Zhang K, Zhang N, Li J, Li H, Fan S, Li X, Hao P. mRNAdesigner: an integrated web server for optimizing mRNA design and protein translation in eukaryotes. Nucleic Acids Res 2025:gkaf410. [PMID: 40384581 DOI: 10.1093/nar/gkaf410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2025] [Revised: 04/19/2025] [Accepted: 05/02/2025] [Indexed: 05/20/2025] Open
Abstract
Messenger RNA (mRNA) therapy has revolutionized modern medicine through its rapid development capabilities and ability to induce effective immune responses, becoming a powerful weapon against infectious diseases. The expression level of target proteins from mRNA sequences is primarily influenced by translational efficiency and stability, which can be significantly enhanced by modifying the 5' and 3' untranslated regions (UTRs), codon adaptation index, GC content, and secondary structure. To address the challenges of optimizing mRNA design, we have developed mRNAdesigner (https://www.biosino.org/mRNAdesigner/), a web server specifically designed to improve mRNA stability and translational efficiency in eukaryotes. Users can input a coding sequence (CDS) along with optional 5' UTR and 3' UTR, and the tool optimizes the CDS by reducing unpaired regions, minimizing complex stem-loop structures, and mitigating the use of rare codons while adhering to user-defined GC content preferences. Additionally, mRNAdesigner identifies optimal UTR sequences to enhance translation efficiency and stability. As an open-access computational resource, mRNAdesigner supports full-length mRNA design, enabling researchers to generate high-expression mRNA sequences for efficient protein production in eukaryotic expression systems, providing extra support for vaccine development and protein therapeutics. This is the first such tool that was made open accessible to the public.
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Affiliation(s)
- Ouyang Mo
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuo Zhang
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiang Cheng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Synthetic Biology, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Liqi Zhu
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaixiang Zhang
- Key Laboratory of Synthetic Biology, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Niubing Zhang
- Key Laboratory of Synthetic Biology, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Justin Li
- Department of Mathematics, University of Connecticut, 352 Mansfield Road, Storrs, CT 06269, United States
| | - Honglin Li
- Innovation Center for AI and Drug Discovery, School of Pharmacy, East China Normal University, Shanghai 200237, China
| | - Shixin Fan
- ChemPartner PharmaTech Co., Ltd, Shanghai 200237, China
| | - Xuan Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Synthetic Biology, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Pei Hao
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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4
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Reimão-Pinto MM, Castillo-Hair SM, Seelig G, Schier AF. The regulatory landscape of 5' UTRs in translational control during zebrafish embryogenesis. Dev Cell 2025; 60:1498-1515.e8. [PMID: 39818206 DOI: 10.1016/j.devcel.2024.12.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 07/22/2024] [Accepted: 12/19/2024] [Indexed: 01/18/2025]
Abstract
The 5' UTRs of mRNAs are critical for translation regulation during development, but their in vivo regulatory features are poorly characterized. Here, we report the regulatory landscape of 5' UTRs during early zebrafish embryogenesis using a massively parallel reporter assay of 18,154 sequences coupled to polysome profiling. We found that the 5' UTR suffices to confer temporal dynamics to translation initiation and identified 86 motifs enriched in 5' UTRs with distinct ribosome recruitment capabilities. A quantitative deep learning model, Danio Optimus 5-Prime (DaniO5P), identified a combined role for 5' UTR length, translation initiation site context, upstream AUGs, and sequence motifs on ribosome recruitment. DaniO5P predicts the activities of maternal and zygotic 5' UTR isoforms and indicates that modulating 5' UTR length and motif grammar contributes to translation initiation dynamics. This study provides a first quantitative model of 5' UTR-based translation regulation in development and lays the foundation for identifying the underlying molecular effectors.
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Affiliation(s)
| | - Sebastian M Castillo-Hair
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA 98195, USA; eScience Institute, University of Washington, Seattle, WA 98195, USA
| | - Georg Seelig
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA 98195, USA; Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - Alexander F Schier
- Biozentrum, University of Basel, 4056 Basel, Switzerland; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA.
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Zhang Y, Deveikis M, Qiu Y, Björn L, Martinez ZA, Chou TF, Freemont PS, Murray RM. Optimizing Protein Production in the One-Pot PURE System: Insights into Reaction Composition and Expression Efficiency. ACS Synth Biol 2025; 14:1496-1508. [PMID: 40209036 DOI: 10.1021/acssynbio.4c00779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2025]
Abstract
The One-Pot PURE (Protein synthesis Using Recombinant Elements) system simplifies the preparation of traditional PURE systems by coculturing and purifying 36 essential proteins for gene expression in a single step, enhancing accessibility and affordability for widespread laboratory adoption and customization. However, replicating this protocol to match the productivity of traditional PURE systems can take considerable time and effort due to uncharacterized variability. In this work, we observed unstable PURE protein expression in the original One-Pot PURE strains, E. coli M15/pREP4 and BL21(DE3), and addressed this issue using glucose-mediated catabolite repression to minimize burdensome background expression. We also identified several limitations making the M15/pREP4 strain unsuitable for PURE protein expression, including coculture incompatibility with BL21(DE3) and uncharacterized proteolytic activity. We showed that consolidating all expression vectors into a protease-deficient BL21(DE3) strain minimized proteolysis, led to more uniform coculture cell growth at the time of induction, and improved the stoichiometry of critical translation initiation factors in the final PURE mixture for efficient cell-free protein production. In addition to optimizing the One-Pot PURE protein composition, we found that variations in commercial energy solution formulations could compensate for suboptimal PURE protein stoichiometry. Notably, altering the source of E. coli tRNAs in the energy solution alone led to significant differences in the expression capacity of cell-free reactions, highlighting the importance of tRNA codon usage in influencing protein expression yield. Taken together, this work systematically investigates the proteome and biochemical factors influencing the One-Pot PURE system productivity, offering insights to enhance its robustness and adaptability across laboratories.
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Affiliation(s)
- Yan Zhang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Matas Deveikis
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, U.K
| | - Yanping Qiu
- Proteome Exploration Laboratory, California Institute of Technology, Pasadena, California 91125, United States
| | - Lovisa Björn
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Zachary A Martinez
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Tsui-Fen Chou
- Proteome Exploration Laboratory, California Institute of Technology, Pasadena, California 91125, United States
| | - Paul S Freemont
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, U.K
| | - Richard M Murray
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
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6
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Rubtsova M, Mokrushina Y, Andreev D, Poteshnova M, Shepelev N, Koryagina M, Moiseeva E, Malabuiok D, Prokopenko Y, Terekhov S, Chernov A, Vodovozova E, Smirnov I, Dontsova O, Gabibov A, Rubtsov Y. A Luciferase-Based Approach for Functional Screening of 5' and 3' Untranslated Regions of the mRNA Component for mRNA Vaccines. Vaccines (Basel) 2025; 13:530. [PMID: 40432139 PMCID: PMC12115628 DOI: 10.3390/vaccines13050530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2025] [Revised: 05/05/2025] [Accepted: 05/12/2025] [Indexed: 05/29/2025] Open
Abstract
Background/Objectives: The recent COVID-19 pandemic caused by SARS-CoV-2 infection has highlighted the need for protocols for rapid development of efficient screening methods to search for the optimal mRNA vaccine structures against mutable viral agents. The unmatched success of mRNA vaccines by Pfizer and Moderna encoding the spike protein of SARS-CoV-2 confirms the potential of lipid nanoparticles for mRNA delivery for an accelerated development of new vaccines. The efficacy of vaccination and the production cost of mRNA-based vaccines largely depend on the composition of mRNA components, since the synthesis of an immunogenic protein requires precise and efficient translation in vivo. The composition of 5' and 3' UTR combinations of mRNA has a strong impact on the translation efficiency. The major objective of this study was to increase the probability of producing the immunogenic protein encoded by vaccine mRNA. For this purpose, we proposed to find a new combination of natural UTRs and, in parallel with that, to design and test the system for in vivo selection of translationally active UTRs. Methods: By using Ribo-Seq analysis, sets of candidate short UTRs were generated. These UTRs were tested both in cell cultures and in mice for effective production of secreted nanoluciferase (NLuc) and the S protein of SARS-CoV-2. A combination of the most effective UTRs was used to generate a prototype of an mRNA vaccine capable of inducing neutralizing antibodies against coronavirus. Results: The usefulness of the selected UTRs for vaccine development was tested by implicating the full-length coding sequence of SARS-CoV-2 S protein to produce the main immunogen. As a result, the system for functional screening of UTRs was created by using the NLuc gene. Conclusions: The proposed approach allows non-invasive quantitative assessment of the translational activity of UTRs in the blood serum of mice. By using the full-length sequence of SARS-CoV-2 S protein as a prototype, we demonstrated that the combination of UTRs selected using our luciferase-based reporter assay induces IgG titers and neutralization rates comparable to those obtained by using UTRs from commercial S-protein-based mRNA vaccines.
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Affiliation(s)
- Maria Rubtsova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.P.); (N.S.); (M.K.)
| | - Yuliana Mokrushina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
| | - Dmitry Andreev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
| | - Maria Poteshnova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.P.); (N.S.); (M.K.)
| | - Nikita Shepelev
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.P.); (N.S.); (M.K.)
| | - Mariya Koryagina
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.P.); (N.S.); (M.K.)
| | - Ekaterina Moiseeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
| | - Diana Malabuiok
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
| | - Yury Prokopenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
| | - Stanislav Terekhov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
| | - Aleksander Chernov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
| | - Elena Vodovozova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
| | - Ivan Smirnov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.P.); (N.S.); (M.K.)
- Endocrinology Research Center of the Ministry of Health of the Russian Federation, 117292 Moscow, Russia
| | - Olga Dontsova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.P.); (N.S.); (M.K.)
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143025 Moscow, Russia
| | - Alexander Gabibov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
| | - Yury Rubtsov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
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7
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VanInsberghe M, van Oudenaarden A. Sequencing technologies to measure translation in single cells. Nat Rev Mol Cell Biol 2025; 26:337-346. [PMID: 39833532 DOI: 10.1038/s41580-024-00822-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2024] [Indexed: 01/22/2025]
Abstract
Translation is one of the most energy-intensive processes in a cell and, accordingly, is tightly regulated. Genome-wide methods to measure translation and the translatome and to study the complex regulation of protein synthesis have enabled unprecedented characterization of this crucial step of gene expression. However, technological limitations have hampered our understanding of translation control in multicellular tissues, rare cell types and dynamic cellular processes. Recent optimizations, adaptations and new techniques have enabled these measurements to be made at single-cell resolution. In this Progress, we discuss single-cell sequencing technologies to measure translation, including ribosome profiling, ribosome affinity purification and spatial translatome methods.
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Affiliation(s)
- Michael VanInsberghe
- Oncode Institute, Utrecht, the Netherlands.
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, the Netherlands.
- University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Alexander van Oudenaarden
- Oncode Institute, Utrecht, the Netherlands
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, the Netherlands
- University Medical Center Utrecht, Utrecht, the Netherlands
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8
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Pan M, Cao W, Zhai J, Zheng C, Xu Y, Zhang P. mRNA-based vaccines and therapies - a revolutionary approach for conquering fast-spreading infections and other clinical applications: a review. Int J Biol Macromol 2025; 309:143134. [PMID: 40233916 DOI: 10.1016/j.ijbiomac.2025.143134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/10/2025] [Accepted: 04/11/2025] [Indexed: 04/17/2025]
Abstract
Since the beginning of the COVID-19 pandemic, the development of messenger RNA (mRNA) vaccines has made significant progress in the pharmaceutical industry. The two COVID-19 mRNA vaccines from Moderna and Pfizer/BioNTech have been approved for marketing and have made significant contributions to preventing the spread of SARS-CoV-2. In addition, mRNA therapy has brought hope to some diseases that do not have specific treatment methods or are difficult to treat, such as the Zika virus and influenza virus infections, as well as the prevention and treatment of tumors. With the rapid development of in vitro transcription (IVT) technology, delivery systems, and adjuvants, mRNA therapy has also been applied to hereditary diseases such as Fabry's disease. This article reviews the recent development of mRNA vaccines for structural modification, treatment and prevention of different diseases; delivery carriers and adjuvants; and routes of administration to promote the clinical application of mRNA therapies.
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Affiliation(s)
- Mingyue Pan
- Department of Pharmacy, The Third Affiliated Hospital (The Affiliated Luohu Hospital) of Shenzhen University, Shenzhen 518001, China
| | - Weiling Cao
- Department of Pharmacy, The Third Affiliated Hospital (The Affiliated Luohu Hospital) of Shenzhen University, Shenzhen 518001, China
| | - Jingbo Zhai
- Key Laboratory of Zoonose Prevention and Control at Universities of Inner Mongolia Autonomous Region, Medical College, Inner Mongolia Minzu University, Tongliao 028000, China
| | - Chunfu Zheng
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.
| | - Yingying Xu
- Department of Pharmaceutics, School of Pharmacy, Fujian Medical University, Fuzhou 350122, China.
| | - Peng Zhang
- Department of Pharmacy, The Third Affiliated Hospital (The Affiliated Luohu Hospital) of Shenzhen University, Shenzhen 518001, China.
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9
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Yamada K, Suga K, Abe N, Hashimoto K, Tsutsumi S, Inagaki M, Hashiya F, Abe H, Hamada M. Multi-objective computational optimization of human 5' UTR sequences. Brief Bioinform 2025; 26:bbaf225. [PMID: 40413870 DOI: 10.1093/bib/bbaf225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2024] [Revised: 03/26/2025] [Accepted: 04/07/2025] [Indexed: 05/27/2025] Open
Abstract
The computational design of messenger RNA (mRNA) sequences is a critical technology for both scientific research and industrial applications. Recent advances in prediction and optimization models have enabled the automatic scoring and optimization of $5^\prime $ UTR sequences, key upstream elements of mRNA. However, fully automated design of $5^\prime $ UTR sequences with more than two objective scores has not yet been explored. In this study, we present a computational pipeline that optimizes human $5^\prime $ UTR sequences in a multi-objective framework, addressing up to four distinct and conflicting objectives. Our work represents an important advancement in the multi-objective computational design of mRNA sequences, paving the way for more sophisticated mRNA engineering.
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Affiliation(s)
- Keisuke Yamada
- Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
- Department of Bioengineering, University of Pennsylvania, 210 South 33rd Street, Philadelphia, PA 19104, United States
| | - Kanta Suga
- Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
| | - Naoko Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi, Japan
| | - Koji Hashimoto
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi, Japan
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Susumu Tsutsumi
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi, Japan
| | - Masahito Inagaki
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi, Japan
| | - Fumitaka Hashiya
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi, Japan
| | - Hiroshi Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Aichi, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Aichi, Japan
| | - Michiaki Hamada
- Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
- Cellular and Molecular Biotechnology Research Institute (CMB), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7, Aomi, Koto-ku, Tokyo 135-0064, Japan
- Graduate School of Medicine, Nippon Medical School, 1-1-5, Sendagi, Bunkyo-ku, Tokyo 113-8602, Japan
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10
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Skerritt JH. Considerations for mRNA Product Development, Regulation and Deployment Across the Lifecycle. Vaccines (Basel) 2025; 13:473. [PMID: 40432085 PMCID: PMC12116195 DOI: 10.3390/vaccines13050473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2025] [Revised: 04/22/2025] [Accepted: 04/23/2025] [Indexed: 05/29/2025] Open
Abstract
With the successful deployment of several mRNA vaccines against SARS-CoV-2, an mRNA vaccine against RSV (respiratory syncytial virus) and a large pipeline of mRNA products against other infectious diseases, cancers and rare diseases, it is important to examine the whole product lifecycle. mRNA technology enables product design, testing and manufacturing systems to be rapidly developed, but these advantages can be lost if other factors that determine public access are not closely considered. This review analyzes key aspects of the mRNA product lifecycle including candidate design, manufacturing, quality systems and product safety and storage. Regulatory thinking is well advanced in some countries but not others, but more thought on the regulation of mRNA vaccines outside of a pandemic situation as well as mRNA therapeutics including individual neoantigen therapies and rare disease treatments is needed. Consumer acceptance-the "social license to operate" around mRNA products-is critical for their uptake, particularly outside of a pandemic.
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Affiliation(s)
- John H Skerritt
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC 3010, Australia
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11
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Camperi J, Chatla K, Freund E, Galan C, Lippold S, Guilbaud A. Current Analytical Strategies for mRNA-Based Therapeutics. Molecules 2025; 30:1629. [PMID: 40286229 PMCID: PMC11990077 DOI: 10.3390/molecules30071629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2025] [Revised: 04/02/2025] [Accepted: 04/03/2025] [Indexed: 04/29/2025] Open
Abstract
Recent advancements in mRNA technology, utilized in vaccines, immunotherapies, protein replacement therapies, and genome editing, have emerged as promising and increasingly viable treatments. The rapid, potent, and transient properties of mRNA-encoded proteins make them attractive tools for the effective treatment of a variety of conditions, ranging from infectious diseases to cancer and single-gene disorders. The capability for rapid and large-scale production of mRNA therapeutics fueled the global response to the COVID-19 pandemic. For effective clinical implementation, it is crucial to deeply characterize and control important mRNA attributes such as purity/integrity, identity, structural quality features, and functionality. This implies the use of powerful and advanced analytical techniques for quality control and characterization of mRNA. Improvements in analytical techniques such as electrophoresis, chromatography, mass spectrometry, sequencing, and functionality assessments have significantly enhanced the quality and detail of information available for product and process characterization, as well as for routine stability and release testing. Here, we review the latest advancements in analytical techniques for the characterization of mRNA-based therapeutics, typically employed by the biopharmaceutical industry for eventual market release.
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Affiliation(s)
- Julien Camperi
- Cell Therapy Engineering and Development, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA;
| | - Kamalakar Chatla
- Cell Therapy Engineering and Development, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA;
| | - Emily Freund
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA; (E.F.); (C.G.)
| | - Carolina Galan
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA; (E.F.); (C.G.)
| | - Steffen Lippold
- Protein Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA;
| | - Axel Guilbaud
- Protein Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA;
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12
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Cope AL, Schraiber JG, Pennell M. Macroevolutionary divergence of gene expression driven by selection on protein abundance. Science 2025; 387:1063-1068. [PMID: 40048509 DOI: 10.1126/science.ads2658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Accepted: 01/24/2025] [Indexed: 03/28/2025]
Abstract
The regulation of messenger RNA (mRNA) and protein abundances is well-studied, but less is known about the evolutionary processes shaping their relationship. To address this, we derived a new phylogenetic model and applied it to multispecies mammalian data. Our analyses reveal (i) strong stabilizing selection on protein abundances over macroevolutionary time, (ii) mutations affecting mRNA abundances minimally impact protein abundances, (iii) mRNA abundances evolve under selection to align with protein abundances, and (iv) mRNA abundances adapt faster than protein abundances owing to greater mutational opportunity. These conclusions are supported by comparisons of model parameters with independent functional genomic data. By decomposing mutational and selective influences on mRNA-protein dynamics, our approach provides a framework for discovering the evolutionary rules that drive divergence in gene expression.
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Affiliation(s)
- Alexander L Cope
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Department of Genetics, Rutgers University, New Brunswick, NJ, USA
- Human Genetics Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
- Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
| | - Joshua G Schraiber
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Matt Pennell
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Department of Computational Biology, Cornell University, Ithaca, CA, USA
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13
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Akirtava C, May G, McManus CJ. Deciphering the landscape of cis-acting sequences in natural yeast transcript leaders. Nucleic Acids Res 2025; 53:gkaf165. [PMID: 40071932 PMCID: PMC11897887 DOI: 10.1093/nar/gkaf165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 02/16/2025] [Accepted: 02/20/2025] [Indexed: 03/15/2025] Open
Abstract
Protein synthesis is a vital process that is highly regulated at the initiation step of translation. Eukaryotic 5' transcript leaders (TLs) contain a variety of cis-acting features that influence translation and messenger RNA stability. However, the relative influences of these features in natural TLs are poorly characterized. To address this, we used massively parallel reporter assays (MPRAs) to quantify RNA levels, ribosome loading, and protein levels from 11,027 natural yeast TLs in vivo and systematically compared the relative impacts of their sequence features on gene expression. We found that yeast TLs influence gene expression over two orders of magnitude. While a leaky scanning model using Kozak contexts (-4 to +1 around the AUG start) and upstream AUGs (uAUGs) explained half of the variance in expression across TLs, the addition of other features explained ∼80% of gene expression variation. Our analyses detected key cis-acting sequence features, quantified their effects in vivo, and compared their roles to motifs reported from an in vitro study of ribosome recruitment. In addition, our work quantitated the effects of alternative transcription start site usage on gene expression in yeast. Thus, our study provides new quantitative insights into the roles of TL cis-acting sequences in regulating gene expression.
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Affiliation(s)
- Christina Akirtava
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, United States
- RNA Bioscience Initiative, University of Colorado – Anschutz, Aurora, CO 80045, United States
| | - Gemma E May
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, United States
| | - C Joel McManus
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, United States
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, United States
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14
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Khorshid Sokhangouy S, Behzadi M, Rezaei S, Farjami M, Haghshenas M, Sefidbakht Y, Mozaffari-Jovin S. mRNA Vaccines: Design Principles, Mechanisms, and Manufacturing-Insights From COVID-19 as a Model for Combating Infectious Diseases. Biotechnol J 2025; 20:e202400596. [PMID: 39989260 DOI: 10.1002/biot.202400596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2024] [Revised: 01/24/2025] [Accepted: 02/09/2025] [Indexed: 02/25/2025]
Abstract
The full approval of two SARS-CoV-2 mRNA vaccines, Comirnaty and Spikevax, has greatly accelerated the development of numerous mRNA vaccine candidates targeting infectious diseases and cancer. mRNA vaccines provide a rapid, safe, and versatile manufacturing process while eliciting strong humoral and cellular immune responses, making them particularly beneficial for addressing emerging pandemics. Recent advancements in modified nucleotides and lipid nanoparticle delivery systems have further emphasized the potential of this vaccine platform. Despite these transformative opportunities, significant improvements are needed to enhance vaccine efficacy, stability, and immunogenicity. This review outlines the fundamentals of mRNA vaccine design, the manufacturing process, and administration strategies, along with various optimization approaches. It also offers a comprehensive overview of the mRNA vaccine candidates developed since the onset of the COVID-19 pandemic, the challenges posed by emerging SARS-CoV-2 variants, and current strategies to address these variants. Finally, we discuss the potential of broad-spectrum and combined mRNA vaccines and examine the challenges and future prospects of the mRNA vaccine platform.
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Affiliation(s)
- Saeideh Khorshid Sokhangouy
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Biotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Matine Behzadi
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Shokuh Rezaei
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | - Mahsa Farjami
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maryam Haghshenas
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Yahya Sefidbakht
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | - Sina Mozaffari-Jovin
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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15
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Liu Y, Rao S, Hoskins I, Geng M, Zhao Q, Chacko J, Ghatpande V, Qi K, Persyn L, Wang J, Zheng D, Zhong Y, Park D, Cenik ES, Agarwal V, Ozadam H, Cenik C. Translation efficiency covariation across cell types is a conserved organizing principle of mammalian transcriptomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.08.11.607360. [PMID: 39149359 PMCID: PMC11326257 DOI: 10.1101/2024.08.11.607360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Characterization of shared patterns of RNA expression between genes across conditions has led to the discovery of regulatory networks and novel biological functions. However, it is unclear if such coordination extends to translation, a critical step in gene expression. Here, we uniformly analyzed 3,819 ribosome profiling datasets from 117 human and 94 mouse tissues and cell lines. We introduce the concept of Translation Efficiency Covariation (TEC), identifying coordinated translation patterns across cell types. We nominate potential mechanisms driving shared patterns of translation regulation. TEC is conserved across human and mouse cells and helps uncover gene functions. Moreover, our observations indicate that proteins that physically interact are highly enriched for positive covariation at both translational and transcriptional levels. Our findings establish translational covariation as a conserved organizing principle of mammalian transcriptomes.
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Affiliation(s)
- Yue Liu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Shilpa Rao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Ian Hoskins
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Michael Geng
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Qiuxia Zhao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jonathan Chacko
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Vighnesh Ghatpande
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Kangsheng Qi
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Logan Persyn
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jun Wang
- mRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA
| | - Dinghai Zheng
- mRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA
| | - Yochen Zhong
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Dayea Park
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Elif Sarinay Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Vikram Agarwal
- mRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA
| | - Hakan Ozadam
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
- Present address: Sail Biomedicines, Cambridge, MA, 02141, USA
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16
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Seephetdee C, Kiss DL. Codon optimality modulates cellular stress and innate immune responses triggered by exogenous RNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.26.625518. [PMID: 39651201 PMCID: PMC11623643 DOI: 10.1101/2024.11.26.625518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2024]
Abstract
The COVID-19 mRNA vaccines demonstrated the power of mRNA medicines. Despite advancements in sequence design, evidence regarding the preferential use of synonymous codons on cellular stress and innate immune responses is lacking. To this end, we developed a proprietary codon optimality matrix to re-engineer the coding sequences of three luciferase reporters. We demonstrate that optimal mRNAs elicited dramatic increases in luciferase activities compared to non-optimal sequences. Notably, transfecting an optimal RNA affects the translation of other RNAs in the cell including control transcripts in dual luciferase assays. This held true in multiple cell lines and for an unrelated reporter. Further, non-optimal mRNAs preferentially activated innate immune pathways and the phosphorylation of the translation initiation factor eIF2α, a central event of the integrated stress response. Using nucleoside-modified or circular RNAs partially or fully abrogated these responses. Finally, we show that circularizing RNAs enhances both RNA lifespan and durability of protein expression. Our results show that RNA sequence, composition, and structure all govern RNA translatability. However, we also show that RNA sequences with poor codon optimality are immunogenic and induce cellular stress. Hence, RNA sequence engineering, chemical, and topological modifications must all be combined to elicit favorable therapeutic outcomes.
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17
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Li J, Wang L, Yu B, Su J, Dong S. IL7R, GZMA and CD8A serve as potential molecular biomarkers for sepsis based on bioinformatics analysis. Front Immunol 2024; 15:1445858. [PMID: 39654893 PMCID: PMC11625646 DOI: 10.3389/fimmu.2024.1445858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 10/30/2024] [Indexed: 12/12/2024] Open
Abstract
Purpose Sepsis is an unusual systemic reaction to what is sometimes an otherwise ordinary infection, and it probably represents a pattern of response by the immune system to injury. However, the relationship between biomarkers and sepsis remains unclear. This study aimed to find potential molecular biomarkers, which could do some help to patients with sepsis. Methods The sepsis dataset GSE28750, GSE57065 was downloaded from the GEO database, and ten patients with or without sepsis from our hospital were admitted for RNA-seq and the differentially expressed genes (DEGs) were screened. The Metascape database was used for functional enrichment analysis and was used to found the differential gene list. Protein-protein interaction network was used and further analyzed by using Cytoscape and STRING. Logistic regression and Correlation analysis were used to find the potential molecular biomarkers. Results Taking the intersection of the three datasets yielded 287 differential genes. The enrichment results included Neutrophil degranulation, leukocyte activation, immune effectors process, positive regulation of immune response, regulation of leukocyte activation. The top 10 key genes of PPI connectivity were screened using cytoHubba plugin, which were KLRK1, KLRB1, IL7R, GZMA, CD27, PRF1, CD8A, CD2, IL2RB, and GZMB. All of the hub genes are higher expressed in health group of different databases. Logistic regression showed that IL7R, GZMA and CD8A proteins were analyzed and all of them were statistically significant. Correlation analysis showed that there was a statistically significant correlation between IL7R, GZMA and CD8A. Conclusion KLRK1, KLRB1, IL7R, GZMA, CD27, PRF1, CD8A, CD2, IL2RB, GZMB are key genes in sepsis, which associated with the development of sepsis. However, IL7R, GZMA and CD8A may serve as the attractively potential molecular biomarkers for sepsis.
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Affiliation(s)
- Jin Li
- Department of Emergency, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Lantao Wang
- Department of Emergency, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Bin Yu
- Department of Emergency, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Jie Su
- Department of Emergency, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Shimin Dong
- Department of Emergency, Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
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18
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Wei PS, Thota N, John G, Chang E, Lee S, Wang Y, Ma Z, Tsai YH, Mei KC. Enhancing RNA-lipid nanoparticle delivery: Organ- and cell-specificity and barcoding strategies. J Control Release 2024; 375:366-388. [PMID: 39179112 PMCID: PMC11972657 DOI: 10.1016/j.jconrel.2024.08.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 07/25/2024] [Accepted: 08/19/2024] [Indexed: 08/26/2024]
Abstract
Recent advancements in RNA therapeutics highlight the critical need for precision gene delivery systems that target specific organs and cells. Lipid nanoparticles (LNPs) have emerged as key vectors in delivering mRNA and siRNA, offering protection against enzymatic degradation, enabling targeted delivery and cellular uptake, and facilitating RNA cargo release into the cytosol. This review discusses the development and optimization of organ- and cell-specific LNPs, focusing on their design, mechanisms of action, and therapeutic applications. We explore innovations such as DNA/RNA barcoding, which facilitates high-throughput screening and precise adjustments in formulations. We address major challenges, including improving endosomal escape, minimizing off-target effects, and enhancing delivery efficiencies. Notable clinical trials and recent FDA approvals illustrate the practical applications and future potential of LNP-based RNA therapies. Our findings suggest that while considerable progress has been made, continued research is essential to resolve existing limitations and bridge the gap between preclinical and clinical evaluation of the safety and efficacy of RNA therapeutics. This review highlights the dynamic progress in LNP research. It outlines a roadmap for future advancements in RNA-based precision medicine.
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Affiliation(s)
- Pu-Sheng Wei
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, State University of New York at Binghamton, Johnson City, New York, NY 13790, USA
| | - Nagasri Thota
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, State University of New York at Binghamton, Johnson City, New York, NY 13790, USA
| | - Greshma John
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, State University of New York at Binghamton, Johnson City, New York, NY 13790, USA
| | - Evelyn Chang
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, State University of New York at Binghamton, Johnson City, New York, NY 13790, USA
| | - Sunjae Lee
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, State University of New York at Binghamton, Johnson City, New York, NY 13790, USA
| | - Yuanjun Wang
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, State University of New York at Binghamton, Johnson City, New York, NY 13790, USA
| | - Zitao Ma
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, State University of New York at Binghamton, Johnson City, New York, NY 13790, USA
| | - Yu-Hsuan Tsai
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, State University of New York at Binghamton, Johnson City, New York, NY 13790, USA
| | - Kuo-Ching Mei
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, State University of New York at Binghamton, Johnson City, New York, NY 13790, USA.
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19
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Tomuro K, Mito M, Toh H, Kawamoto N, Miyake T, Chow SYA, Doi M, Ikeuchi Y, Shichino Y, Iwasaki S. Calibrated ribosome profiling assesses the dynamics of ribosomal flux on transcripts. Nat Commun 2024; 15:7061. [PMID: 39187487 PMCID: PMC11347596 DOI: 10.1038/s41467-024-51258-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 08/02/2024] [Indexed: 08/28/2024] Open
Abstract
Ribosome profiling, which is based on deep sequencing of ribosome footprints, has served as a powerful tool for elucidating the regulatory mechanism of protein synthesis. However, the current method has substantial issues: contamination by rRNAs and the lack of appropriate methods to measure ribosome numbers in transcripts. Here, we overcome these hurdles through the development of "Ribo-FilterOut", which is based on the separation of footprints from ribosome subunits by ultrafiltration, and "Ribo-Calibration", which relies on external spike-ins of stoichiometrically defined mRNA-ribosome complexes. A combination of these approaches estimates the number of ribosomes on a transcript, the translation initiation rate, and the overall number of translation events before its decay, all in a genome-wide manner. Moreover, our method reveals the allocation of ribosomes under heat shock stress, during aging, and across cell types. Our strategy of modified ribosome profiling measures kinetic and stoichiometric parameters of cellular translation across the transcriptome.
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Grants
- JP20H05784 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP24H02307 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20H05782 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP24H02306 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20H05786 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP24H02307 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP21H05734 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP23H04268 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20gm1410001 Japan Agency for Medical Research and Development (AMED)
- JP20gm1410001 Japan Agency for Medical Research and Development (AMED)
- JP23gm6910005 Japan Agency for Medical Research and Development (AMED)
- JP22fk0108570 Japan Agency for Medical Research and Development (AMED)
- JP23H02415 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23H00095 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP21K15023 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23K05648 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP22K20765 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23K14173 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23KJ2178 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23KJ2175 MEXT | Japan Society for the Promotion of Science (JSPS)
- Pioneering Project MEXT | RIKEN
- RIKEN TRIP initiative "TRIP-AGIS" MEXT | RIKEN
- Pioneering Project MEXT | RIKEN
- JPMJBS2418 MEXT | Japan Science and Technology Agency (JST)
- JPMJFR226F MEXT | Japan Science and Technology Agency (JST)
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Affiliation(s)
- Kotaro Tomuro
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Hirotaka Toh
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Naohiro Kawamoto
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Takahito Miyake
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan
| | - Siu Yu A Chow
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan
| | - Masao Doi
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan
| | - Yoshiho Ikeuchi
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Institute for AI and Beyond, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan.
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20
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Kerkhofs K, Guydosh NR, Bayfield MA. Respiratory Syncytial Virus (RSV) optimizes the translational landscape during infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.02.606199. [PMID: 39131278 PMCID: PMC11312563 DOI: 10.1101/2024.08.02.606199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Viral infection often triggers eukaryotic initiator factor 2α (eIF2α) phosphorylation, leading to global 5'-cap-dependent translation inhibition. RSV encodes messenger RNAs (mRNAs) mimicking 5'-cap structures of host mRNAs and thus inhibition of cap-dependent translation initiation would likely also reduce viral translation. We confirmed that RSV limits widespread translation initiation inhibition and unexpectedly found that the fraction of ribosomes within polysomes increases during infection, indicating higher ribosome loading on mRNAs during infection. We found that AU-rich host transcripts that are less efficiently translated under normal conditions become more efficient at recruiting ribosomes, similar to RSV transcripts. Viral transcripts are transcribed in cytoplasmic inclusion bodies, where the viral AU-rich binding protein M2-1 has been shown to bind viral transcripts and shuttle them into the cytoplasm. We further demonstrated that M2-1 is found on polysomes, and that M2-1 might deliver host AU-rich transcripts for translation.
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Affiliation(s)
- Kyra Kerkhofs
- Department of Biology, Faculty of Science, York University, Toronto, Ontario N3J 1P3, Canada
| | - Nicholas R. Guydosh
- Section on mRNA Regulation and Translation, Laboratory of Biochemistry & Genetics. National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark A. Bayfield
- Department of Biology, Faculty of Science, York University, Toronto, Ontario N3J 1P3, Canada
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21
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Wu Z, Sun W, Qi H. Recent Advancements in mRNA Vaccines: From Target Selection to Delivery Systems. Vaccines (Basel) 2024; 12:873. [PMID: 39203999 PMCID: PMC11359327 DOI: 10.3390/vaccines12080873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/31/2024] [Accepted: 07/31/2024] [Indexed: 09/03/2024] Open
Abstract
mRNA vaccines are leading a medical revolution. mRNA technologies utilize the host's own cells as bio-factories to produce proteins that serve as antigens. This revolutionary approach circumvents the complicated processes involved in traditional vaccine production and empowers vaccines with the ability to respond to emerging or mutated infectious diseases rapidly. Additionally, the robust cellular immune response elicited by mRNA vaccines has shown significant promise in cancer treatment. However, the inherent instability of mRNA and the complexity of tumor immunity have limited its broader application. Although the emergence of pseudouridine and ionizable cationic lipid nanoparticles (LNPs) made the clinical application of mRNA possible, there remains substantial potential for further improvement of the immunogenicity of delivered antigens and preventive or therapeutic effects of mRNA technology. Here, we review the latest advancements in mRNA vaccines, including but not limited to target selection and delivery systems. This review offers a multifaceted perspective on this rapidly evolving field.
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Affiliation(s)
- Zhongyan Wu
- Newish Biological R&D Center, Beijing 100101, China;
| | - Weilu Sun
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK;
| | - Hailong Qi
- Newish Biological R&D Center, Beijing 100101, China;
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22
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Courvan EMC, Parker RR. Hypoxia and inflammation induce synergistic transcriptome turnover in macrophages. Cell Rep 2024; 43:114452. [PMID: 38968068 DOI: 10.1016/j.celrep.2024.114452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/24/2024] [Accepted: 06/21/2024] [Indexed: 07/07/2024] Open
Abstract
Macrophages are effector immune cells that experience substantial changes to oxygenation when transiting through tissues, especially when entering tumors or infected wounds. How hypoxia alters gene expression and macrophage effector function at the post-transcriptional level remains poorly understood. Here, we use TimeLapse-seq to measure how inflammatory activation modifies the hypoxic response in primary macrophages. Nucleoside recoding sequencing allows the derivation of steady-state transcript levels, degradation rates, and transcriptional synthesis rates from the same dataset. We find that hypoxia produces distinct responses from resting and inflammatory macrophages. Hypoxia induces destabilization of mRNA transcripts, though inflammatory macrophages substantially increase mRNA degradation compared to resting macrophages. Increased RNA turnover results in the upregulation of ribosomal protein genes and downregulation of extracellular matrix components in inflammatory macrophages. Pathways regulated by mRNA decay in vitro are differentially regulated in tumor-associated macrophages implying that mixed stimuli could induce post-transcriptional regulation of macrophage function in solid tumors.
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Affiliation(s)
- Edward M C Courvan
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA; Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80303, USA.
| | - Roy R Parker
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA; Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA.
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23
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Horvath A, Janapala Y, Woodward K, Mahmud S, Cleynen A, Gardiner E, Hannan R, Eyras E, Preiss T, Shirokikh N. Comprehensive translational profiling and STE AI uncover rapid control of protein biosynthesis during cell stress. Nucleic Acids Res 2024; 52:7925-7946. [PMID: 38721779 PMCID: PMC11260467 DOI: 10.1093/nar/gkae365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/21/2024] [Accepted: 04/25/2024] [Indexed: 07/23/2024] Open
Abstract
Translational control is important in all life, but it remains a challenge to accurately quantify. When ribosomes translate messenger (m)RNA into proteins, they attach to the mRNA in series, forming poly(ribo)somes, and can co-localize. Here, we computationally model new types of co-localized ribosomal complexes on mRNA and identify them using enhanced translation complex profile sequencing (eTCP-seq) based on rapid in vivo crosslinking. We detect long disome footprints outside regions of non-random elongation stalls and show these are linked to translation initiation and protein biosynthesis rates. We subject footprints of disomes and other translation complexes to artificial intelligence (AI) analysis and construct a new, accurate and self-normalized measure of translation, termed stochastic translation efficiency (STE). We then apply STE to investigate rapid changes to mRNA translation in yeast undergoing glucose depletion. Importantly, we show that, well beyond tagging elongation stalls, footprints of co-localized ribosomes provide rich insight into translational mechanisms, polysome dynamics and topology. STE AI ranks cellular mRNAs by absolute translation rates under given conditions, can assist in identifying its control elements and will facilitate the development of next-generation synthetic biology designs and mRNA-based therapeutics.
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Affiliation(s)
- Attila Horvath
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
| | - Yoshika Janapala
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
| | - Katrina Woodward
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
| | - Shafi Mahmud
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
| | - Alice Cleynen
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
- Institut Montpelliérain Alexander Grothendieck, Université de Montpellier, CNRS, Montpellier, France
| | - Elizabeth E Gardiner
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The National Platelet Research and Referral Centre, The Australian National University, Canberra, ACT 2601, Australia
| | - Ross D Hannan
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3010, Australia
- Peter MacCallum Cancer Centre, Melbourne 3000, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Australia
- School of Biomedical Sciences, University of Queensland, St Lucia 4067, Australia
| | - Eduardo Eyras
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Centre for Computational Biomedical Sciences, The Australian National University, Canberra, ACT 2601, Australia
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Preiss
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Nikolay E Shirokikh
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601, Australia
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