251
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Gebre MS, Brito LA, Tostanoski LH, Edwards DK, Carfi A, Barouch DH. Novel approaches for vaccine development. Cell 2021; 184:1589-1603. [PMID: 33740454 PMCID: PMC8049514 DOI: 10.1016/j.cell.2021.02.030] [Citation(s) in RCA: 139] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/01/2021] [Accepted: 02/12/2021] [Indexed: 02/07/2023]
Abstract
Vaccines are critical tools for maintaining global health. Traditional vaccine technologies have been used across a wide range of bacterial and viral pathogens, yet there are a number of examples where they have not been successful, such as for persistent infections, rapidly evolving pathogens with high sequence variability, complex viral antigens, and emerging pathogens. Novel technologies such as nucleic acid and viral vector vaccines offer the potential to revolutionize vaccine development as they are well-suited to address existing technology limitations. In this review, we discuss the current state of RNA vaccines, recombinant adenovirus vector-based vaccines, and advances from biomaterials and engineering that address these important public health challenges.
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Affiliation(s)
- Makda S. Gebre
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- co-first authors
| | | | - Lisa H. Tostanoski
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
- co-first authors
| | | | - Andrea Carfi
- Moderna, Inc., Cambridge, MA, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
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252
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Khabou B, Hsairi M, Gargouri L, Miled N, Barbu V, Fakhfakh F. Characterization of a novel ABCC2 mutation in infantile Dubin Johnson syndrome. Clin Chim Acta 2021; 518:43-50. [PMID: 33713692 DOI: 10.1016/j.cca.2021.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/06/2021] [Accepted: 03/07/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS The Dubin Johnson Syndrome (DJS) occurs mostly in young adults but an early-onset of the disease has been reported in less common forms (Neonatal DJS and Infantile DJS). In this case, the clinical findings are of limit for the DJS diagnosis. Hence, the genetic testing remains the method of choice to provide an accurate diagnosis. In our study, we aimed to perform a genetic analysis for two siblings presented with an intrahepatic cholestasis before the age of 1 year to provide a molecular explanation for the developed phenotype. PATIENTS & METHODS A Tunisian family, having two siblings, manifesting signs of a hepatopathy, was enrolled in our study. A molecular analysis was performed, using a panel-based next generation sequencing, supplying results that were the subject of computational analysis. Then, a clinical follow-up was carried out to assess the evolution of the disease. RESULTS The genetic analysis revealed the presence of a novel missense c.4179G > T, (p.M1393I) mutation in ABCC2 gene associated with a substitution c.2789G > A (R930Q) in ATP8B1 gene. Predictive results consolidated the pathogenic effect of both variants. These results confirmed the DJS diagnosis in the studied patients. The clinical course of both patients fit well with the benign nature of DJS. CONCLUSION We described here a novel ABCC2 mutation associated with a putative ATP8B1 modifier variant. This finding constituted the first report of a complex genotype in DJS. Hence, genetic analysis by a panel-based next generation sequencing permits an accurate diagnosis and the identification of putative variants that could influence the developed phenotype.
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Affiliation(s)
- Boudour Khabou
- Laboratory of Molecular and Functional Genetics, Faculty of Science, University of Sfax, Tunisia.
| | - Manel Hsairi
- Department of Pediatrics, Pediatric Emergency and Intensive Care, Hedi Chaker Hospital, Faculty of Medicine, Sfax, Tunisia
| | - Lamia Gargouri
- Department of Pediatrics, Pediatric Emergency and Intensive Care, Hedi Chaker Hospital, Faculty of Medicine, Sfax, Tunisia
| | - Nabil Miled
- University of Jeddah, College of Science, Department of Biological Sciences, Saudi Arabia; University of Sfax, Higher Institute of Biotechnology, Unit of Plant Physiology and Functional Genomics, Sfax, Tunisia
| | - Véronique Barbu
- LCBGM, Medical Biology and Pathology Department, APHP, HUEP, St Antoine Hospital, & Sorbonne University, 75012 Paris, France
| | - Faiza Fakhfakh
- Laboratory of Molecular and Functional Genetics, Faculty of Science, University of Sfax, Tunisia.
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253
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Datta S. Optimizing Granulocyte Colony-Stimulating Factor Transcript for Enhanced Expression in Escherichia coli. Front Bioeng Biotechnol 2021; 9:630367. [PMID: 33768088 PMCID: PMC7985328 DOI: 10.3389/fbioe.2021.630367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/02/2021] [Indexed: 11/13/2022] Open
Abstract
The human granulocyte colony-stimulating factor (G-CSF) is a hematopoietic growth factor used to prevent and treat neutropenia. G-CSF stimulates the bone marrow to produce infection-fighting granulocytes. Food and Drug Administration of the United States approved G-CSF in 1991 and its PEGylated version in 2002 as a prophylactic and therapeutic measure against neutropenia. Recombinant human G-CSF is produced in surrogate host Escherichia coli and is PEGylated at N-terminal. Besides neutropenia, G-CSF is also used in bone marrow transplantation for the mobilization and maturation of peripheral blood stem cells. Considering the requirement of producing G-CSF therapeutic in large quantities, construct designing for high expression is critical for the biopharmaceutical and industrial application. Earlier studies have employed approaches such as codon optimization, use of strong promoters, employment of protein tags, secretion signals, optimization of protein folding, etc., for increasing expression and yield of therapeutic proteins. In this study, it was observed that mRNA transcribed from the native human cDNA of G-CSF and the codon-optimized variant leads to low protein expression in E. coli. To understand the underlying reasons, the mRNA secondary structure of the 5′ end of the G-CSF transcript was analyzed. This analysis revealed the presence of stable secondary structures at the 5′ end of the G-CSF transcript, arising from the native human gene and even from the codon-optimized sequence. These secondary structures were disrupted through translationally silent mutations within the first 24 nucleotides of the transcript without affecting the protein sequence. Interestingly, through this approach, the G-CSF protein expression was increased 60 folds as compared to native G-CSF construct. We believe that these findings create a roadmap for optimization of G-CSF transcript for enhanced expression in E. coli and could be employed to increase the expression of other therapeutic proteins.
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Affiliation(s)
- Sonal Datta
- Council of Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh, India
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254
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Van Hoecke L, Verbeke R, Dewitte H, Lentacker I, Vermaelen K, Breckpot K, Van Lint S. mRNA in cancer immunotherapy: beyond a source of antigen. Mol Cancer 2021; 20:48. [PMID: 33658037 PMCID: PMC7926200 DOI: 10.1186/s12943-021-01329-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 02/01/2021] [Indexed: 02/08/2023] Open
Abstract
mRNA therapeutics have become the focus of molecular medicine research. Various mRNA applications have reached major milestones at high speed in the immuno-oncology field. This can be attributed to the knowledge that mRNA is one of nature's core building blocks carrying important information and can be considered as a powerful vector for delivery of therapeutic proteins to the patient.For a long time, the major focus in the use of in vitro transcribed mRNA was on development of cancer vaccines, using mRNA encoding tumor antigens to modify dendritic cells ex vivo. However, the versatility of mRNA and its many advantages have paved the path beyond this application. In addition, due to smart design of both the structural properties of the mRNA molecule as well as pharmaceutical formulations that improve its in vivo stability and selective targeting, the therapeutic potential of mRNA can be considered as endless.As a consequence, many novel immunotherapeutic strategies focus on the use of mRNA beyond its use as the source of tumor antigens. This review aims to summarize the state-of-the-art on these applications and to provide a rationale for their clinical application.
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Affiliation(s)
- Lien Van Hoecke
- VIB-UGent Center for Inflammation Research, Technologiepark 71, 9052 Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
| | - Rein Verbeke
- Ghent Research Group on Nanomedicines, Lab for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Heleen Dewitte
- Ghent Research Group on Nanomedicines, Lab for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Ine Lentacker
- Ghent Research Group on Nanomedicines, Lab for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Karim Vermaelen
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Tumor Immunology Laboratory, Department of Respiratory Medicine and Immuno-Oncology Network Ghent, Ghent University Hospital, Corneel Heymanslaan 10 MRB2, 9000 Ghent, Belgium
| | - Karine Breckpot
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103 Building E, 1090 Brussels, Belgium
| | - Sandra Van Lint
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Tumor Immunology Laboratory, Department of Respiratory Medicine and Immuno-Oncology Network Ghent, Ghent University Hospital, Corneel Heymanslaan 10 MRB2, 9000 Ghent, Belgium
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255
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Kim J, Eygeris Y, Gupta M, Sahay G. Self-assembled mRNA vaccines. Adv Drug Deliv Rev 2021; 170:83-112. [PMID: 33400957 PMCID: PMC7837307 DOI: 10.1016/j.addr.2020.12.014] [Citation(s) in RCA: 261] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/22/2020] [Accepted: 12/27/2020] [Indexed: 01/08/2023]
Abstract
mRNA vaccines have evolved from being a mere curiosity to emerging as COVID-19 vaccine front-runners. Recent advancements in the field of RNA technology, vaccinology, and nanotechnology have generated interest in delivering safe and effective mRNA therapeutics. In this review, we discuss design and self-assembly of mRNA vaccines. Self-assembly, a spontaneous organization of individual molecules, allows for design of nanoparticles with customizable properties. We highlight the materials commonly utilized to deliver mRNA, their physicochemical characteristics, and other relevant considerations, such as mRNA optimization, routes of administration, cellular fate, and immune activation, that are important for successful mRNA vaccination. We also examine the COVID-19 mRNA vaccines currently in clinical trials. mRNA vaccines are ready for the clinic, showing tremendous promise in the COVID-19 vaccine race, and have pushed the boundaries of gene therapy.
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Affiliation(s)
- Jeonghwan Kim
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Robertson Life Science Building, 2730 South Moody Avenue, Portland, Oregon 97201, USA
| | - Yulia Eygeris
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Robertson Life Science Building, 2730 South Moody Avenue, Portland, Oregon 97201, USA
| | - Mohit Gupta
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Robertson Life Science Building, 2730 South Moody Avenue, Portland, Oregon 97201, USA
| | - Gaurav Sahay
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Robertson Life Science Building, 2730 South Moody Avenue, Portland, Oregon 97201, USA; Department of Biomedical Engineering, Oregon Health & Science University, Robertson Life Science Building, 2730 South Moody Avenue, Portland, Oregon 97201, USA; Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, Oregon 97239, USA.
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256
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Chia JY, Khoo KS, Ling TC, Croft L, Manickam S, Yap YJ, Show PL. Description and detection of excludons as transcriptional regulators in gram-positive, gram-negative and archaeal strains of prokaryotes. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.101933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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257
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Lim S, Khoo R, Juang YC, Gopal P, Zhang H, Yeo C, Peh KM, Teo J, Ng S, Henry B, Partridge AW. Exquisitely Specific anti-KRAS Biodegraders Inform on the Cellular Prevalence of Nucleotide-Loaded States. ACS CENTRAL SCIENCE 2021; 7:274-291. [PMID: 33655066 PMCID: PMC7908030 DOI: 10.1021/acscentsci.0c01337] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Indexed: 05/05/2023]
Abstract
Mutations to RAS proteins (H-, N-, and K-RAS) are among the most common oncogenic drivers, and tumors harboring these lesions are some of the most difficult to treat. Although covalent small molecules against KRASG12C have shown promising efficacy against lung cancers, traditional barriers remain for drugging the more prevalent KRASG12D and KRASG12V mutants. Targeted degradation has emerged as an attractive alternative approach, but for KRAS, identification of the required high-affinity ligands continues to be a challenge. Another significant hurdle is the discovery of a hybrid molecule that appends an E3 ligase-recruiting moiety in a manner that satisfies the precise geometries required for productive polyubiquitin transfer while maintaining favorable druglike properties. To gain insights into the advantages and feasibility of KRAS targeted degradation, we applied a protein-based degrader (biodegrader) approach. This workflow centers on the intracellular expression of a chimeric protein consisting of a high-affinity target-binding domain fused to an engineered E3 ligase adapter. A series of anti-RAS biodegraders spanning different RAS isoform/nucleotide-state specificities and leveraging different E3 ligases provided definitive evidence for RAS degradability. Further, these established that the functional consequences of KRAS degradation are context dependent. Of broader significance, using the exquisite degradation specificity that biodegraders can possess, we demonstrated how this technology can be applied to answer questions that other approaches cannot. Specifically, application of the GDP-state specific degrader uncovered the relative prevalence of the "off-state" of WT and various KRAS mutants in the cellular context. Finally, if delivery challenges can be addressed, anti-RAS biodegraders will be exciting candidates for clinical development.
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258
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Derbis M, Kul E, Niewiadomska D, Sekrecki M, Piasecka A, Taylor K, Hukema RK, Stork O, Sobczak K. Short antisense oligonucleotides alleviate the pleiotropic toxicity of RNA harboring expanded CGG repeats. Nat Commun 2021; 12:1265. [PMID: 33627639 PMCID: PMC7904788 DOI: 10.1038/s41467-021-21021-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 12/24/2020] [Indexed: 01/31/2023] Open
Abstract
Fragile X-associated tremor/ataxia syndrome (FXTAS) is an incurable neurodegenerative disorder caused by expansion of CGG repeats in the FMR1 5'UTR. The RNA containing expanded CGG repeats (rCGGexp) causes cell damage by interaction with complementary DNA, forming R-loop structures, sequestration of nuclear proteins involved in RNA metabolism and initiation of translation of polyglycine-containing protein (FMRpolyG), which forms nuclear insoluble inclusions. Here we show the therapeutic potential of short antisense oligonucleotide steric blockers (ASOs) targeting directly the rCGGexp. In nuclei of FXTAS cells ASOs affect R-loop formation and correct miRNA biogenesis and alternative splicing, indicating that nuclear proteins are released from toxic sequestration. In cytoplasm, ASOs significantly decrease the biosynthesis and accumulation of FMRpolyG. Delivery of ASO into a brain of FXTAS mouse model reduces formation of inclusions, improves motor behavior and corrects gene expression profile with marginal signs of toxicity after a few weeks from a treatment.
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Affiliation(s)
- Magdalena Derbis
- grid.5633.30000 0001 2097 3545Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, Poznan, Poland
| | - Emre Kul
- grid.5807.a0000 0001 1018 4307Department of Genetics and Molecular Neurobiology, Institute of Biology, Otto von Guericke University, Magdeburg, Germany
| | - Daria Niewiadomska
- grid.5633.30000 0001 2097 3545Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, Poznan, Poland
| | - Michał Sekrecki
- grid.5633.30000 0001 2097 3545Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, Poznan, Poland
| | - Agnieszka Piasecka
- grid.5633.30000 0001 2097 3545Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, Poznan, Poland
| | - Katarzyna Taylor
- grid.5633.30000 0001 2097 3545Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, Poznan, Poland
| | - Renate K. Hukema
- grid.5645.2000000040459992XDepartment of Clinical Genetics, Erasmus MC, CA Rotterdam, The Netherlands ,grid.450253.50000 0001 0688 0318Present Address: Department of Health Care Studies, Rotterdam University of Applied Sciences, HR Rotterdam, The Netherlands
| | - Oliver Stork
- grid.5807.a0000 0001 1018 4307Department of Genetics and Molecular Neurobiology, Institute of Biology, Otto von Guericke University, Magdeburg, Germany
| | - Krzysztof Sobczak
- grid.5633.30000 0001 2097 3545Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, Poznan, Poland
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259
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Wayment-Steele HK, Kim DS, Choe CA, Nicol JJ, Wellington-Oguri R, Watkins AM, Sperberg RAP, Huang PS, Participants E, Das R. Theoretical basis for stabilizing messenger RNA through secondary structure design. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.08.22.262931. [PMID: 32869022 PMCID: PMC7457604 DOI: 10.1101/2020.08.22.262931] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
RNA hydrolysis presents problems in manufacturing, long-term storage, world-wide delivery, and in vivo stability of messenger RNA (mRNA)-based vaccines and therapeutics. A largely unexplored strategy to reduce mRNA hydrolysis is to redesign RNAs to form double-stranded regions, which are protected from in-line cleavage and enzymatic degradation, while coding for the same proteins. The amount of stabilization that this strategy can deliver and the most effective algorithmic approach to achieve stabilization remain poorly understood. Here, we present simple calculations for estimating RNA stability against hydrolysis, and a model that links the average unpaired probability of an mRNA, or AUP, to its overall hydrolysis rate. To characterize the stabilization achievable through structure design, we compare AUP optimization by conventional mRNA design methods to results from more computationally sophisticated algorithms and crowdsourcing through the OpenVaccine challenge on the Eterna platform. These computational tests were carried out on both model mRNAs and COVID-19 mRNA vaccine candidates. We find that rational design on Eterna and the more sophisticated algorithms lead to constructs with low AUP, which we term 'superfolder' mRNAs. These designs exhibit wide diversity of sequence and structure features that may be desirable for translation, biophysical size, and immunogenicity, and their folding is robust to temperature, choice of flanking untranslated regions, and changes in target protein sequence, as illustrated by rapid redesign of superfolder mRNAs for B.1.351, P.1, and B.1.1.7 variants of the prefusion-stabilized SARS-CoV-2 spike protein. Increases in in vitro mRNA half-life by at least two-fold appear immediately achievable.
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Affiliation(s)
- Hannah K Wayment-Steele
- Department of Chemistry, Stanford University, Stanford, CA, 94305
- Eterna Massive Open Laboratory. Consortium authors listed in Table S1
| | - Do Soon Kim
- Eterna Massive Open Laboratory. Consortium authors listed in Table S1
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208
- Department of Biochemistry, Stanford University, Stanford, CA, 94305
| | - Christian A Choe
- Eterna Massive Open Laboratory. Consortium authors listed in Table S1
- Department of Bioengineering, Stanford University, Stanford, CA, 94305
| | - John J Nicol
- Eterna Massive Open Laboratory. Consortium authors listed in Table S1
| | | | - Andrew M Watkins
- Eterna Massive Open Laboratory. Consortium authors listed in Table S1
- Department of Biochemistry, Stanford University, Stanford, CA, 94305
| | | | - Po-Ssu Huang
- Department of Bioengineering, Stanford University, Stanford, CA, 94305
| | | | - Rhiju Das
- Eterna Massive Open Laboratory. Consortium authors listed in Table S1
- Department of Biochemistry, Stanford University, Stanford, CA, 94305
- Department of Physics, Stanford University, Stanford, CA, 94305
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260
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Tan X, Letendre JH, Collins JJ, Wong WW. Synthetic biology in the clinic: engineering vaccines, diagnostics, and therapeutics. Cell 2021; 184:881-898. [PMID: 33571426 PMCID: PMC7897318 DOI: 10.1016/j.cell.2021.01.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/17/2022]
Abstract
Synthetic biology is a design-driven discipline centered on engineering novel biological functions through the discovery, characterization, and repurposing of molecular parts. Several synthetic biological solutions to critical biomedical problems are on the verge of widespread adoption and demonstrate the burgeoning maturation of the field. Here, we highlight applications of synthetic biology in vaccine development, molecular diagnostics, and cell-based therapeutics, emphasizing technologies approved for clinical use or in active clinical trials. We conclude by drawing attention to recent innovations in synthetic biology that are likely to have a significant impact on future applications in biomedicine.
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Affiliation(s)
- Xiao Tan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Division of Gastroenterology, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA; Harvard Medical School, 25 Shattuck St., Boston, MA 02115, USA; Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
| | - Justin H Letendre
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA
| | - James J Collins
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Synthetic Biology Center, MIT, 77 Massachusetts Ave., Cambridge, MA 02139, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.
| | - Wilson W Wong
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA.
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261
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Deal CE, Carfi A, Plante OJ. Advancements in mRNA Encoded Antibodies for Passive Immunotherapy. Vaccines (Basel) 2021; 9:vaccines9020108. [PMID: 33572679 PMCID: PMC7910832 DOI: 10.3390/vaccines9020108] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 12/28/2022] Open
Abstract
Monoclonal antibodies are the fastest growing therapeutic class in medicine today. They hold great promise for a myriad of indications, including cancer, allergy, autoimmune and infectious diseases. However, the wide accessibility of these therapeutics is hindered by manufacturing and purification challenges that result in high costs and long lead times. Efforts are being made to find alternative ways to produce and deliver antibodies in more expedient and cost-effective platforms. The field of mRNA has made significant progress in the last ten years and has emerged as a highly attractive means of encoding and producing any protein of interest in vivo. Through the natural role of mRNA as a transient carrier of genetic information for translation into proteins, in vivo expression of mRNA-encoded antibodies offer many advantages over recombinantly produced antibodies. In this review, we examine both preclinical and clinical studies that demonstrate the feasibility of mRNA-encoded antibodies and discuss the remaining challenges ahead.
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262
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Rice AM, Castillo Morales A, Ho AT, Mordstein C, Mühlhausen S, Watson S, Cano L, Young B, Kudla G, Hurst LD. Evidence for Strong Mutation Bias toward, and Selection against, U Content in SARS-CoV-2: Implications for Vaccine Design. Mol Biol Evol 2021; 38:67-83. [PMID: 32687176 PMCID: PMC7454790 DOI: 10.1093/molbev/msaa188] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Large-scale re-engineering of synonymous sites is a promising strategy to generate vaccines either through synthesis of attenuated viruses or via codon-optimized genes in DNA vaccines. Attenuation typically relies on deoptimization of codon pairs and maximization of CpG dinucleotide frequencies. So as to formulate evolutionarily informed attenuation strategies that aim to force nucleotide usage against the direction favored by selection, here, we examine available whole-genome sequences of SARS-CoV-2 to infer patterns of mutation and selection on synonymous sites. Analysis of mutational profiles indicates a strong mutation bias toward U. In turn, analysis of observed synonymous site composition implicates selection against U. Accounting for dinucleotide effects reinforces this conclusion, observed UU content being a quarter of that expected under neutrality. Possible mechanisms of selection against U mutations include selection for higher expression, for high mRNA stability or lower immunogenicity of viral genes. Consistent with gene-specific selection against CpG dinucleotides, we observe systematic differences of CpG content between SARS-CoV-2 genes. We propose an evolutionarily informed approach to attenuation that, unusually, seeks to increase usage of the already most common synonymous codons. Comparable analysis of H1N1 and Ebola finds that GC3 deviated from neutral equilibrium is not a universal feature, cautioning against generalization of results.
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Affiliation(s)
- Alan M Rice
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Atahualpa Castillo Morales
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Alexander T Ho
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Christine Mordstein
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Stefanie Mühlhausen
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Samir Watson
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Laura Cano
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Bethan Young
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Grzegorz Kudla
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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263
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Abstract
The mRNA epitranscriptome imparts diversity to gene expression by installing chemical modifications. Advances in detection methods have identified chemical modifications in eukaryotic, bacterial, and viral messenger RNAs (mRNAs). The biological functions of modifications in mRNAs still remain to be understood. Chemical modifications are introduced in synthetic mRNAs meant for therapeutic applications to maximize expression from the synthetic mRNAs and to evade the host immune response. This overview provides a background of chemical modifications found in mRNAs, with an emphasis on pseudouridine and its known effects on the mRNA life cycle, its potential applications in synthetic mRNA, and the methods used to assess its effects on mRNA translation.
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Affiliation(s)
- Bijoyita Roy
- RNA and Genome Editing, New England Biolabs Inc, Ipswich, MA, USA.
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264
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Processing of coding and non-coding RNAs in plant development and environmental responses. Essays Biochem 2020; 64:931-945. [DOI: 10.1042/ebc20200029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/14/2022]
Abstract
Abstract
Precursor RNAs undergo extensive processing to become mature RNAs. RNA transcripts are subjected to 5′ capping, 3′-end processing, splicing, and modification; they also form dynamic secondary structures during co-transcriptional and post-transcriptional processing. Like coding RNAs, non-coding RNAs (ncRNAs) undergo extensive processing. For example, secondary small interfering RNA (siRNA) transcripts undergo RNA processing, followed by further cleavage to become mature siRNAs. Transcriptome studies have revealed roles for co-transcriptional and post-transcriptional RNA processing in the regulation of gene expression and the coordination of plant development and plant–environment interactions. In this review, we present the latest progress on RNA processing in gene expression and discuss phased siRNAs (phasiRNAs), a kind of germ cell-specific secondary small RNA (sRNA), focusing on their functions in plant development and environmental responses.
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265
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Neelagandan N, Lamberti I, Carvalho HJF, Gobet C, Naef F. What determines eukaryotic translation elongation: recent molecular and quantitative analyses of protein synthesis. Open Biol 2020; 10:200292. [PMID: 33292102 PMCID: PMC7776565 DOI: 10.1098/rsob.200292] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/10/2020] [Indexed: 12/14/2022] Open
Abstract
Protein synthesis from mRNA is an energy-intensive and tightly controlled cellular process. Translation elongation is a well-coordinated, multifactorial step in translation that undergoes dynamic regulation owing to cellular state and environmental determinants. Recent studies involving genome-wide approaches have uncovered some crucial aspects of translation elongation including the mRNA itself and the nascent polypeptide chain. Additionally, these studies have fuelled quantitative and mathematical modelling of translation elongation. In this review, we provide a comprehensive overview of the key determinants of translation elongation. We discuss consequences of ribosome stalling or collision, and how the cells regulate translation in case of such events. Next, we review theoretical approaches and widely used mathematical models that have become an essential ingredient to interpret complex molecular datasets and study translation dynamics quantitatively. Finally, we review recent advances in live-cell reporter and related analysis techniques, to monitor the translation dynamics of single cells and single-mRNA molecules in real time.
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Affiliation(s)
| | | | | | | | - Felix Naef
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
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266
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Shu H, Donnard E, Liu B, Jung S, Wang R, Richter JD. FMRP links optimal codons to mRNA stability in neurons. Proc Natl Acad Sci U S A 2020; 117:30400-30411. [PMID: 33199649 PMCID: PMC7720238 DOI: 10.1073/pnas.2009161117] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Fragile X syndrome (FXS) is caused by inactivation of the FMR1 gene and loss of encoded FMRP, an RNA binding protein that represses translation of some of its target transcripts. Here we use ribosome profiling and RNA sequencing to investigate the dysregulation of translation in the mouse brain cortex. We find that most changes in ribosome occupancy on hundreds of mRNAs are largely driven by dysregulation in transcript abundance. Many down-regulated mRNAs, which are mostly responsible for neuronal and synaptic functions, are highly enriched for FMRP binding targets. RNA metabolic labeling demonstrates that, in FMRP-deficient cortical neurons, mRNA down-regulation is caused by elevated degradation and is correlated with codon optimality. Moreover, FMRP preferentially binds mRNAs with optimal codons, suggesting that it stabilizes such transcripts through direct interactions via the translational machinery. Finally, we show that the paradigm of genetic rescue of FXS-like phenotypes in FMRP-deficient mice by deletion of the Cpeb1 gene is mediated by restoration of steady-state RNA levels and consequent rebalancing of translational homeostasis. Our data establish an essential role of FMRP in codon optimality-dependent mRNA stability as an important factor in FXS.
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Affiliation(s)
- Huan Shu
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605;
| | - Elisa Donnard
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Botao Liu
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Suna Jung
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Ruijia Wang
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Joel D Richter
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
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267
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Urquidi-Camacho RA, Lokdarshi A, von Arnim AG. Translational gene regulation in plants: A green new deal. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1597. [PMID: 32367681 PMCID: PMC9258721 DOI: 10.1002/wrna.1597] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 01/09/2023]
Abstract
The molecular machinery for protein synthesis is profoundly similar between plants and other eukaryotes. Mechanisms of translational gene regulation are embedded into the broader network of RNA-level processes including RNA quality control and RNA turnover. However, over eons of their separate history, plants acquired new components, dropped others, and generally evolved an alternate way of making the parts list of protein synthesis work. Research over the past 5 years has unveiled how plants utilize translational control to defend themselves against viruses, regulate translation in response to metabolites, and reversibly adjust translation to a wide variety of environmental parameters. Moreover, during seed and pollen development plants make use of RNA granules and other translational controls to underpin developmental transitions between quiescent and metabolically active stages. The economics of resource allocation over the daily light-dark cycle also include controls over cellular protein synthesis. Important new insights into translational control on cytosolic ribosomes continue to emerge from studies of translational control mechanisms in viruses. Finally, sketches of coherent signaling pathways that connect external stimuli with a translational response are emerging, anchored in part around TOR and GCN2 kinase signaling networks. These again reveal some mechanisms that are familiar and others that are different from other eukaryotes, motivating deeper studies on translational control in plants. This article is categorized under: Translation > Translation Regulation RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Ricardo A. Urquidi-Camacho
- UT-ORNL Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996
| | - Ansul Lokdarshi
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Albrecht G von Arnim
- Department of Biochemistry & Cellular and Molecular Biology and UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996
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268
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Gbotsyo YA, Rowarth NM, Weir LK, MacRae TH. Short-term cold stress and heat shock proteins in the crustacean Artemia franciscana. Cell Stress Chaperones 2020; 25:1083-1097. [PMID: 32794096 PMCID: PMC7591681 DOI: 10.1007/s12192-020-01147-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/02/2020] [Accepted: 07/28/2020] [Indexed: 01/09/2023] Open
Abstract
In their role as molecular chaperones, heat shock proteins (Hsps) mediate protein folding thereby mitigating cellular damage caused by physiological and environmental stress. Nauplii of the crustacean Artemia franciscana respond to heat shock by producing Hsps; however, the effects of cold shock on Hsp levels in A. franciscana have not been investigated previously. The effect of cold shock at 1 °C followed by recovery at 27 °C on the amounts of ArHsp90, Hsp70, ArHsp40, and ArHsp40-2 mRNA and their respective proteins in A. franciscana nauplii was examined by quantitative PCR (qPCR) and immunoprobing of western blots. The same Hsp mRNAs and proteins were also quantified during incubation of nauplii at their optimal growth temperature of 27 °C. qPCR analyses indicated that the abundance of ArHsp90, Hsp70, and ArHsp40 mRNA remained relatively constant during both cold shock and recovery and was not significantly different compared with levels at optimal temperature. Western blotting revealed that ArHsp90, ArHsp40, and ArHsp40-2 were generally below baseline, but at detectable levels during the 6 h of cold shock, and persisted in early recovery stages before declining. Hsp70 was the only protein that remained constant in quantity throughout cold shock and recovery. By contrast, all Hsps declined rapidly during 6 h when nauplii were incubated continuously at 27 °C optimal temperature. Generally, the amounts of ArHsp90, ArHsp40, and ArHsp40-2 were higher during cold shock/recovery than those during continuous incubation at 27 °C. Our data support the conclusion that low temperature preserves Hsp levels, making them available to assist in protein repair and recovery after cold shock.
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Affiliation(s)
- Yayra A Gbotsyo
- Department of Biology, Dalhousie University, Halifax, N. S., B3H 4R2, Canada
| | - Nathan M Rowarth
- Department of Biology, Dalhousie University, Halifax, N. S., B3H 4R2, Canada
| | - Laura K Weir
- Biology Department, Saint Mary's University Halifax, Halifax, N. S., B3H 3C3, Canada.
| | - Thomas H MacRae
- Department of Biology, Dalhousie University, Halifax, N. S., B3H 4R2, Canada
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269
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Hopfinger MC, Kirkpatrick CC, Znosko BM. Predictions and analyses of RNA nearest neighbor parameters for modified nucleotides. Nucleic Acids Res 2020; 48:8901-8913. [PMID: 32810273 PMCID: PMC7498315 DOI: 10.1093/nar/gkaa654] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/02/2020] [Accepted: 07/27/2020] [Indexed: 12/21/2022] Open
Abstract
The most popular RNA secondary structure prediction programs utilize free energy (ΔG°37) minimization and rely upon thermodynamic parameters from the nearest neighbor (NN) model. Experimental parameters are derived from a series of optical melting experiments; however, acquiring enough melt data to derive accurate NN parameters with modified base pairs is expensive and time consuming. Given the multitude of known natural modifications and the continuing use and development of unnatural nucleotides, experimentally characterizing all modified NNs is impractical. This dilemma necessitates a computational model that can predict NN thermodynamics where experimental data is scarce or absent. Here, we present a combined molecular dynamics/quantum mechanics protocol that accurately predicts experimental NN ΔG°37 parameters for modified nucleotides with neighboring Watson–Crick base pairs. NN predictions for Watson-Crick and modified base pairs yielded an overall RMSD of 0.32 kcal/mol when compared with experimentally derived parameters. NN predictions involving modified bases without experimental parameters (N6-methyladenosine, 2-aminopurineriboside, and 5-methylcytidine) demonstrated promising agreement with available experimental melt data. This procedure not only yields accurate NN ΔG°37 predictions but also quantifies stacking and hydrogen bonding differences between modified NNs and their canonical counterparts, allowing investigators to identify energetic differences and providing insight into sources of (de)stabilization from nucleotide modifications.
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Affiliation(s)
| | | | - Brent M Znosko
- Department of Chemistry, Saint Louis University, Saint Louis, MO 63103, USA
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270
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Toki N, Takahashi H, Zucchelli S, Gustincich S, Carninci P. Synthetic in vitro transcribed lncRNAs (SINEUPs) with chemical modifications enhance target mRNA translation. FEBS Lett 2020; 594:4357-4369. [PMID: 33012004 DOI: 10.1002/1873-3468.13928] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 08/24/2020] [Accepted: 08/24/2020] [Indexed: 01/14/2023]
Abstract
Chemically modified mRNAs are extensively studied with a view toward their clinical application. In particular, long noncoding RNAs (lncRNAs) containing SINE elements, which enhance the translation of their target mRNAs (i.e., SINEUPs), have potential as RNA therapies for various diseases, such as haploinsufficiencies. To establish a SINEUP-based system for efficient protein expression, we directly transfected chemically modified in vitro transcribed (mIVT) SINEUP RNAs to examine their effects on target mRNA translation. mIVT SINEUP RNAs enhanced translation of EGFP mRNA and endogenous target Sox9 mRNA in both cultured cells and a cell-free translation system. Our findings reveal the functional role of RNA modifications in SINEUPs and suggest several broad clinical applications of such an RNA regulatory system.
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Affiliation(s)
- Naoko Toki
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Functional Genomics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Hazuki Takahashi
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Functional Genomics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Silvia Zucchelli
- Department of Health Sciences, Center for Autoimmune and Allergic Diseases (CAAD) and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Stefano Gustincich
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), Genova, Italy.,Area of Neuroscience, International School for Advanced Studies (SISSA), Trieste, Italy
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Functional Genomics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
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271
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Corbett KS, Edwards DK, Leist SR, Abiona OM, Boyoglu-Barnum S, Gillespie RA, Himansu S, Schäfer A, Ziwawo CT, DiPiazza AT, Dinnon KH, Elbashir SM, Shaw CA, Woods A, Fritch EJ, Martinez DR, Bock KW, Minai M, Nagata BM, Hutchinson GB, Wu K, Henry C, Bahl K, Garcia-Dominguez D, Ma L, Renzi I, Kong WP, Schmidt SD, Wang L, Zhang Y, Phung E, Chang LA, Loomis RJ, Altaras NE, Narayanan E, Metkar M, Presnyak V, Liu C, Louder MK, Shi W, Leung K, Yang ES, West A, Gully KL, Stevens LJ, Wang N, Wrapp D, Doria-Rose NA, Stewart-Jones G, Bennett H, Alvarado GS, Nason MC, Ruckwardt TJ, McLellan JS, Denison MR, Chappell JD, Moore IN, Morabito KM, Mascola JR, Baric RS, Carfi A, Graham BS. SARS-CoV-2 mRNA vaccine design enabled by prototype pathogen preparedness. Nature 2020; 586:567-571. [PMID: 32756549 PMCID: PMC7581537 DOI: 10.1038/s41586-020-2622-0] [Citation(s) in RCA: 1016] [Impact Index Per Article: 254.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 07/29/2020] [Indexed: 12/11/2022]
Abstract
A vaccine for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is needed to control the coronavirus disease 2019 (COVID-19) global pandemic. Structural studies have led to the development of mutations that stabilize Betacoronavirus spike proteins in the prefusion state, improving their expression and increasing immunogenicity1. This principle has been applied to design mRNA-1273, an mRNA vaccine that encodes a SARS-CoV-2 spike protein that is stabilized in the prefusion conformation. Here we show that mRNA-1273 induces potent neutralizing antibody responses to both wild-type (D614) and D614G mutant2 SARS-CoV-2 as well as CD8+ T cell responses, and protects against SARS-CoV-2 infection in the lungs and noses of mice without evidence of immunopathology. mRNA-1273 is currently in a phase III trial to evaluate its efficacy.
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Affiliation(s)
- Kizzmekia S Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Sarah R Leist
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Olubukola M Abiona
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Seyhan Boyoglu-Barnum
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rebecca A Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Alexandra Schäfer
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cynthia T Ziwawo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Anthony T DiPiazza
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kenneth H Dinnon
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | | | - Ethan J Fritch
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David R Martinez
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kevin W Bock
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mahnaz Minai
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Bianca M Nagata
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Geoffrey B Hutchinson
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kai Wu
- Moderna Inc, Cambridge, MA, USA
| | | | | | | | | | | | - Wing-Pui Kong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Stephen D Schmidt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Emily Phung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Institute for Biomedical Sciences, George Washington University, Washington, DC, USA
| | - Lauren A Chang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rebecca J Loomis
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | | - Cuiping Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ande West
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kendra L Gully
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura J Stevens
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nianshuang Wang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Daniel Wrapp
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Gabriela S Alvarado
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Martha C Nason
- Biostatistics Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tracy J Ruckwardt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Mark R Denison
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - James D Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ian N Moore
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kaitlyn M Morabito
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ralph S Baric
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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272
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Khrustalev VV, Giri R, Khrustaleva TA, Kapuganti SK, Stojarov AN, Poboinev VV. Translation-Associated Mutational U-Pressure in the First ORF of SARS-CoV-2 and Other Coronaviruses. Front Microbiol 2020; 11:559165. [PMID: 33072018 PMCID: PMC7536284 DOI: 10.3389/fmicb.2020.559165] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 08/31/2020] [Indexed: 12/17/2022] Open
Abstract
Within 4 months of the ongoing COVID-19 pandemic caused by SARS-CoV-2, more than 250 nucleotide mutations have been detected in ORF1ab of the virus isolated from infected persons from different parts of the globe. These observations open up an obvious question about the rate and direction of mutational pressure for further vaccine and therapeutics designing. In this study, we did a comparative analysis of ORF1a and ORF1b by using the first isolate (Wuhan strain) as the parent sequence. We observed that most of the nucleotide mutations are C to U transitions. The rate of synonymous C to U transitions is significantly higher than the rate of non-synonymous ones, indicating negative selection on amino acid substitutions. Further, trends in nucleotide usage bias have been investigated in 49 coronaviruses species. A strong bias in nucleotide usage in fourfold degenerate sites toward uracil residues is seen in ORF1ab of all the studied coronaviruses: both in the ORF1a and in the ORF1b translated thanks to the programmed ribosomal frameshifting that has an efficiency of 14 – 45% in different species. A more substantial mutational U-pressure is observed in ORF1a than in ORF1b perhaps because ORF1a is translated more frequently than ORF1b. Mutational U-pressure is there even in ORFs that are not translated from genomic RNA plus strands, but the bias is weaker than in ORF1ab. Unlike other nucleotide mutations, mutational U-pressure caused by cytosine deamination, mostly occurring during the RNA plus strand replication and also translation, cannot be corrected by the proof-reading machinery of coronaviruses. The knowledge generated on the mutational U-pressure that becomes stronger during translation of viral RNA plus strands has implications for vaccine and nucleoside analog development for treating COVID-19 and other coronavirus infections.
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Affiliation(s)
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Tatyana Aleksandrovna Khrustaleva
- Biochemical Group of Multidisciplinary Diagnostic Laboratory, Institute of Physiology of the National Academy of Sciences of Belarus, Minsk, Belarus
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273
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Borchardt EK, Martinez NM, Gilbert WV. Regulation and Function of RNA Pseudouridylation in Human Cells. Annu Rev Genet 2020; 54:309-336. [PMID: 32870730 DOI: 10.1146/annurev-genet-112618-043830] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recent advances in pseudouridine detection reveal a complex pseudouridine landscape that includes messenger RNA and diverse classes of noncoding RNA in human cells. The known molecular functions of pseudouridine, which include stabilizing RNA conformations and destabilizing interactions with varied RNA-binding proteins, suggest that RNA pseudouridylation could have widespread effects on RNA metabolism and gene expression. Here, we emphasize how much remains to be learned about the RNA targets of human pseudouridine synthases, their basis for recognizing distinct RNA sequences, and the mechanisms responsible for regulated RNA pseudouridylation. We also examine the roles of noncoding RNA pseudouridylation in splicing and translation and point out the potential effects of mRNA pseudouridylation on protein production, including in the context of therapeutic mRNAs.
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Affiliation(s)
- Erin K Borchardt
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, USA; , ,
| | - Nicole M Martinez
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, USA; , ,
| | - Wendy V Gilbert
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, USA; , ,
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274
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Li Z, Chen X, Liu Z, Ye W, Li L, Qian L, Ding H, Li P, Aung LHH. Recent Advances: Molecular Mechanism of RNA Oxidation and Its Role in Various Diseases. Front Mol Biosci 2020; 7:184. [PMID: 32850971 PMCID: PMC7413073 DOI: 10.3389/fmolb.2020.00184] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/13/2020] [Indexed: 12/11/2022] Open
Abstract
Compared with the research on DNA damage, there are fewer studies on RNA damage, and the damage mechanism remains mostly unknown. Recent studies have shown that RNA is more vulnerable to damage than DNA when the cells are exposed to endogenous and exogenous insults. RNA injury may participate in a variety of disease occurrence and development. RNA not only has important catalytic functions and other housekeeping functions, it also plays a decisive role in the translation of genetic information and protein biosynthesis. Various kinds of stressors, such as ultraviolet, reactive oxygen species and nitrogen, can cause damage to RNA. It may involve in the development and progression of diseases. In this review, we focused on the relationship between the RNA damage and disease as well as the research progress on the mechanism of RNA damage, which is of great significance for the pathogenesis, diagnosis, and treatment of related diseases.
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Affiliation(s)
- Zhe Li
- Center for Molecular Genetics, Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.,School of Basic Medicine, Qingdao University, Qingdao, China
| | - Xiatian Chen
- Center for Molecular Genetics, Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.,School of Basic Medicine, Qingdao University, Qingdao, China
| | - Ziqian Liu
- Center for Molecular Genetics, Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.,School of Basic Medicine, Qingdao University, Qingdao, China
| | - Wei Ye
- Jiangsu Provincial Engineering Research Center for Biomedical Materials and Advanced Medical Device, Huaiyin Institute of Technology, Huaian, China
| | - Ling Li
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Lili Qian
- Center for Molecular Genetics, Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Hongyan Ding
- Jiangsu Provincial Engineering Research Center for Biomedical Materials and Advanced Medical Device, Huaiyin Institute of Technology, Huaian, China
| | - Peifeng Li
- Center for Molecular Genetics, Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lynn Htet Htet Aung
- Center for Molecular Genetics, Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.,School of Basic Medicine, Qingdao University, Qingdao, China
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275
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Jones JD, Monroe J, Koutmou KS. A molecular-level perspective on the frequency, distribution, and consequences of messenger RNA modifications. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1586. [PMID: 31960607 PMCID: PMC8243748 DOI: 10.1002/wrna.1586] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/21/2019] [Accepted: 01/04/2020] [Indexed: 01/16/2023]
Abstract
Cells use chemical modifications to alter the sterics, charge, and conformations of large biomolecules, modulating their biogenesis, function, and stability. Until recently post-transcriptional RNA modifications were thought to be largely limited to nonprotein coding RNA species. However, this dogma has rapidly transformed with the discovery of a host of modifications in protein coding messenger RNAs (mRNAs). Recent advancements in genome-wide sequencing technologies have enabled the identification of mRNA modifications as a potential new frontier in gene regulation-leading to the development of the epitranscriptome field. As a result, there has been a flurry of multiple groundbreaking discoveries, including new modifications, nucleoside modifying enzymes ("writers" and "erasers"), and RNA binding proteins that recognize chemical modifications ("readers"). These discoveries opened the door to understanding how post-transcriptional mRNA modifications can modulate the mRNA lifecycle, and established a link between the epitranscriptome and human health and disease. Despite a rapidly growing recognition of their importance, fundamental questions regarding the identity, prevalence, and functional consequences of mRNA modifications remain to be answered. Here, we highlight quantitative studies that characterize mRNA modification abundance, frequency, and interactions with cellular machinery. As the field progresses, we see a need for the further integration of quantitative and reductionist approaches to complement transcriptome wide studies in order to establish a molecular-level framework for understanding the consequences of mRNA chemical modifications on biological processes. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Joshua D. Jones
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan
| | - Jeremy Monroe
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan
| | - Kristin S. Koutmou
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan
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276
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Kramer MC, Janssen KA, Palos K, Nelson ADL, Vandivier LE, Garcia BA, Lyons E, Beilstein MA, Gregory BD. N 6-methyladenosine and RNA secondary structure affect transcript stability and protein abundance during systemic salt stress in Arabidopsis. PLANT DIRECT 2020; 4:e00239. [PMID: 32724893 PMCID: PMC7379018 DOI: 10.1002/pld3.239] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/05/2020] [Accepted: 06/11/2020] [Indexed: 05/22/2023]
Abstract
After transcription, a messenger RNA (mRNA) is further post-transcriptionally regulated by several features including RNA secondary structure and covalent RNA modifications (specifically N6-methyladenosine, m6A). Both RNA secondary structure and m6A have been demonstrated to regulate mRNA stability and translation and have been independently linked to plant responses to soil salinity levels. However, the effect of m6A on regulating RNA secondary structure and the combinatorial interplay between these two RNA features during salt stress response has yet to be studied. Here, we globally identify RNA-protein interactions and RNA secondary structure during systemic salt stress. This analysis reveals that RNA secondary structure changes significantly during salt stress, and that it is independent of global changes in RNA-protein interactions. Conversely, we find that m6A is anti-correlated with RNA secondary structure in a condition-dependent manner, with salt-specific m6A correlated with a decrease in mRNA secondary structure during salt stress. Taken together, we suggest that salt-specific m6A deposition and the associated loss of RNA secondary structure results in increases in mRNA stability for transcripts encoding abiotic stress response proteins and ultimately increases in protein levels from these stabilized transcripts. In total, our comprehensive analyses reveal important post-transcriptional regulatory mechanisms involved in plant long-term salt stress response and adaptation.
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Affiliation(s)
- Marianne C. Kramer
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPAUSA
- Cell and Molecular Biology Graduate GroupPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Kevin A. Janssen
- Department of Biochemistry and BiophysicsPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
- Epigenetics InstitutePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
- Biochemistry and Molecular Biophysics Graduate GroupUniversity of PennsylvaniaPAUSA
| | - Kyle Palos
- School of Plant SciencesUniversity of ArizonaTucsonAZUSA
| | | | - Lee E. Vandivier
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPAUSA
- Cell and Molecular Biology Graduate GroupPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Benjamin A. Garcia
- Department of Biochemistry and BiophysicsPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
- Epigenetics InstitutePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Eric Lyons
- School of Plant SciencesUniversity of ArizonaTucsonAZUSA
- CyVerseUniversity of ArizonaTucsonAZUSA
| | | | - Brian D. Gregory
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPAUSA
- Cell and Molecular Biology Graduate GroupPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
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277
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Penn WD, Harrington HR, Schlebach JP, Mukhopadhyay S. Regulators of Viral Frameshifting: More Than RNA Influences Translation Events. Annu Rev Virol 2020; 7:219-238. [PMID: 32600156 DOI: 10.1146/annurev-virology-012120-101548] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Programmed ribosomal frameshifting (PRF) is a conserved translational recoding mechanism found in all branches of life and viruses. In bacteria, archaea, and eukaryotes PRF is used to downregulate protein production by inducing a premature termination of translation, which triggers messenger RNA (mRNA) decay. In viruses, PRF is used to drive the production of a new protein while downregulating the production of another protein, thus maintaining a stoichiometry optimal for productive infection. Traditionally, PRF motifs have been defined by the characteristics of two cis elements: a slippery heptanucleotide sequence followed by an RNA pseudoknot or stem-loop within the mRNA. Recently, additional cis and new trans elements have been identified that regulate PRF in both host and viral translation. These additional factors suggest PRF is an evolutionarily conserved process whose function and regulation we are just beginning to understand.
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Affiliation(s)
- Wesley D Penn
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Haley R Harrington
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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278
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Corbett KS, Edwards D, Leist SR, Abiona OM, Boyoglu-Barnum S, Gillespie RA, Himansu S, Schäfer A, Ziwawo CT, DiPiazza AT, Dinnon KH, Elbashir SM, Shaw CA, Woods A, Fritch EJ, Martinez DR, Bock KW, Minai M, Nagata BM, Hutchinson GB, Bahl K, Garcia-Dominguez D, Ma L, Renzi I, Kong WP, Schmidt SD, Wang L, Zhang Y, Stevens LJ, Phung E, Chang LA, Loomis RJ, Altaras NE, Narayanan E, Metkar M, Presnyak V, Liu C, Louder MK, Shi W, Leung K, Yang ES, West A, Gully KL, Wang N, Wrapp D, Doria-Rose NA, Stewart-Jones G, Bennett H, Nason MC, Ruckwardt TJ, McLellan JS, Denison MR, Chappell JD, Moore IN, Morabito KM, Mascola JR, Baric RS, Carfi A, Graham BS. SARS-CoV-2 mRNA Vaccine Development Enabled by Prototype Pathogen Preparedness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.11.145920. [PMID: 32577634 PMCID: PMC7301911 DOI: 10.1101/2020.06.11.145920] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A SARS-CoV-2 vaccine is needed to control the global COVID-19 public health crisis. Atomic-level structures directed the application of prefusion-stabilizing mutations that improved expression and immunogenicity of betacoronavirus spike proteins. Using this established immunogen design, the release of SARS-CoV-2 sequences triggered immediate rapid manufacturing of an mRNA vaccine expressing the prefusion-stabilized SARS-CoV-2 spike trimer (mRNA-1273). Here, we show that mRNA-1273 induces both potent neutralizing antibody and CD8 T cell responses and protects against SARS-CoV-2 infection in lungs and noses of mice without evidence of immunopathology. mRNA-1273 is currently in a Phase 2 clinical trial with a trajectory towards Phase 3 efficacy evaluation.
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Affiliation(s)
- Kizzmekia S. Corbett
- Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | - Darin Edwards
- Moderna Inc., Cambridge, MA, 02139; United States of America
| | - Sarah R. Leist
- Department of Epidemiology; University of North Carolina at Chapel Hill; Chapel Hill, North Carolina, 27599; United States of America
| | - Olubukola M. Abiona
- Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | - Seyhan Boyoglu-Barnum
- Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | - Rebecca A. Gillespie
- Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | - Sunny Himansu
- Moderna Inc., Cambridge, MA, 02139; United States of America
| | - Alexandra Schäfer
- Department of Epidemiology; University of North Carolina at Chapel Hill; Chapel Hill, North Carolina, 27599; United States of America
| | - Cynthia T. Ziwawo
- Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | - Anthony T. DiPiazza
- Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | - Kenneth H. Dinnon
- Department of Epidemiology; University of North Carolina at Chapel Hill; Chapel Hill, North Carolina, 27599; United States of America
| | | | | | - Angela Woods
- Moderna Inc., Cambridge, MA, 02139; United States of America
| | - Ethan J. Fritch
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill; Chapel Hill, North Carolina, 27599; United States of America
| | - David R. Martinez
- Department of Epidemiology; University of North Carolina at Chapel Hill; Chapel Hill, North Carolina, 27599; United States of America
| | - Kevin W. Bock
- National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | - Mahnaz Minai
- National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | - Bianca M. Nagata
- National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | - Geoffrey B. Hutchinson
- Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | - Kapil Bahl
- Moderna Inc., Cambridge, MA, 02139; United States of America
| | | | - LingZhi Ma
- Moderna Inc., Cambridge, MA, 02139; United States of America
| | - Isabella Renzi
- Moderna Inc., Cambridge, MA, 02139; United States of America
| | - Wing-Pui Kong
- Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | - Stephen D. Schmidt
- Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | - Lingshu Wang
- Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | - Yi Zhang
- Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | - Laura J. Stevens
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, 37212; United States of America
| | - Emily Phung
- Institute for Biomedical Sciences, George Washington University, Washington, DC 20052, United States of America
| | - Lauren A. Chang
- Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | - Rebecca J. Loomis
- Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | | | | | - Mihir Metkar
- Moderna Inc., Cambridge, MA, 02139; United States of America
| | - Vlad Presnyak
- Moderna Inc., Cambridge, MA, 02139; United States of America
| | - Catherine Liu
- Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | - Mark K. Louder
- Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | - Wei Shi
- Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | - Kwanyee Leung
- Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | - Eun Sung Yang
- Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | - Ande West
- Department of Epidemiology; University of North Carolina at Chapel Hill; Chapel Hill, North Carolina, 27599; United States of America
| | - Kendra L. Gully
- Department of Epidemiology; University of North Carolina at Chapel Hill; Chapel Hill, North Carolina, 27599; United States of America
| | - Nianshuang Wang
- Department of Molecular Biosciences; University of Texas at Austin; Austin, Texas, 78712; United States of America
| | - Daniel Wrapp
- Department of Molecular Biosciences; University of Texas at Austin; Austin, Texas, 78712; United States of America
| | - Nicole A. Doria-Rose
- Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | | | | | - Martha C. Nason
- Biostatistics Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | - Tracy J. Ruckwardt
- Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | - Jason S. McLellan
- Department of Molecular Biosciences; University of Texas at Austin; Austin, Texas, 78712; United States of America
| | - Mark R. Denison
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, 37212; United States of America
| | - James D. Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, 37212; United States of America
| | - Ian N. Moore
- National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | - Kaitlyn M. Morabito
- Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | - John R. Mascola
- Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
| | - Ralph S. Baric
- Department of Epidemiology; University of North Carolina at Chapel Hill; Chapel Hill, North Carolina, 27599; United States of America
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill; Chapel Hill, North Carolina, 27599; United States of America
| | - Andrea Carfi
- Moderna Inc., Cambridge, MA, 02139; United States of America
| | - Barney S. Graham
- Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892; United States of America
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279
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Lee CH, Grey F. Systems Virology and Human Cytomegalovirus: Using High Throughput Approaches to Identify Novel Host-Virus Interactions During Lytic Infection. Front Cell Infect Microbiol 2020; 10:280. [PMID: 32587832 PMCID: PMC7298070 DOI: 10.3389/fcimb.2020.00280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/12/2020] [Indexed: 12/16/2022] Open
Abstract
Human Cytomegalovirus (HCMV) is a highly prevalent herpesvirus, persistently infecting between 30 and 100% of the population, depending on socio-economic status (Fields et al., 2013). HCMV remains an important clinical pathogen accounting for more than 60% of complications associated with solid organ transplant patients (Kotton, 2013; Kowalsky et al., 2013; Bruminhent and Razonable, 2014). It is also the leading cause of infectious congenital birth defects and has been linked to chronic inflammation and immune aging (Ballard et al., 1979; Griffith et al., 2016; Jergovic et al., 2019). There is currently no effective vaccine and HCMV antivirals have significant side effects. As current antivirals target viral genes, the virus can develop resistance, reducing drug efficacy. There is therefore an urgent need for new antiviral agents that are effective against HCMV, have better toxicity profiles and are less vulnerable to the emergence of resistant strains. Targeting of host factors that are critical to virus replication is a potential strategy for the development of novel antivirals that circumvent the development of viral resistance. Systematic high throughput approaches provide powerful methods for the identification of novel host-virus interactions. As well as contributing to our basic understanding of virus and cell biology, such studies provide potential targets for the development of novel antiviral agents. High-throughput studies, such as RNA sequencing, proteomics, and RNA interference screens, are useful tools to identify HCMV-induced global changes in host mRNA and protein expression levels and host factors important for virus replication. Here, we summarize new findings on HCMV lytic infection from high-throughput studies since 2014 and how screening approaches have evolved.
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Affiliation(s)
- Chen-Hsuin Lee
- Division of Infection and Immunity, Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Finn Grey
- Division of Infection and Immunity, Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
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280
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Chang KS, Kim J, Park H, Hong SJ, Lee CG, Jin E. Enhanced lipid productivity in AGP knockout marine microalga Tetraselmis sp. using a DNA-free CRISPR-Cas9 RNP method. BIORESOURCE TECHNOLOGY 2020; 303:122932. [PMID: 32058903 DOI: 10.1016/j.biortech.2020.122932] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/28/2020] [Accepted: 01/28/2020] [Indexed: 06/10/2023]
Abstract
A marine green microalga, Tetraselmis sp., has been studied for the production of biomass and lipids in seawater culture. Since carbohydrate and lipid biosynthesis are competitive metabolic pathways, we attempted to increase lipid synthesis in Tetraselmis by inhibiting carbohydrate synthesis. The main regulatory enzyme in the starch synthesis pathway is ADP-glucose pyrophosphorylase (AGP). AGP loss-of-function mutants were developed using the CRISPR-Cas9 ribonucleoprotein (RNP) delivery system. AGP mutants showed a slight decrease in growth. However, the lipid content in two AGP mutants was significantly enhanced by 2.7 and 3.1 fold (21.1% and 24.1% of DCW), respectively, compared to that in the wild type (7.68% of DCW) under nitrogen starvation. This study is an example of metabolic engineering by genetic editing using the CRISPR-Cas9 RNP method in marine green microalgae. Consequently, starchless Tetraselmis mutants might be considered potential producers of lipids in seawater cultures.
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Affiliation(s)
- Kwang Suk Chang
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Jongrae Kim
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Hanwool Park
- Department of Marine Science & Biological Engineering, Marine Bioenergy R&D Consortium, Inha University, Inchon 22212, Republic of Korea
| | - Seong-Joo Hong
- Department of Marine Science & Biological Engineering, Marine Bioenergy R&D Consortium, Inha University, Inchon 22212, Republic of Korea
| | - Choul-Gyun Lee
- Department of Marine Science & Biological Engineering, Marine Bioenergy R&D Consortium, Inha University, Inchon 22212, Republic of Korea
| | - EonSeon Jin
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea.
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281
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Weng Y, Li C, Yang T, Hu B, Zhang M, Guo S, Xiao H, Liang XJ, Huang Y. The challenge and prospect of mRNA therapeutics landscape. Biotechnol Adv 2020; 40:107534. [PMID: 32088327 DOI: 10.1016/j.biotechadv.2020.107534] [Citation(s) in RCA: 193] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 02/05/2020] [Accepted: 02/15/2020] [Indexed: 12/13/2022]
Abstract
Messenger RNA (mRNA)-based therapeutics hold the potential to cause a major revolution in the pharmaceutical industry because they can be used for precise and individualized therapy, and enable patients to produce therapeutic proteins in their own bodies without struggling with the comprehensive manufacturing issues associated with recombinant proteins. Compared with the current therapeutics, the production of mRNA is much cost-effective, faster and more flexible because it can be easily produced by in vitro transcription, and the process is independent of mRNA sequence. Moreover, mRNA vaccines allow people to develop personalized medications based on sequencing results and/or personalized conditions rapidly. Along with the great potential from bench to bedside, technical obstacles facing mRNA pharmaceuticals are also obvious. The stability, immunogenicity, translation efficiency, and delivery are all pivotal issues need to be addressed. In the recently published research results, these issues are gradually being overcome by state-of-the-art development technologies. In this review, we describe the structural properties and modification technologies of mRNA, summarize the latest advances in developing mRNA delivery systems, review the preclinical and clinical applications, and put forward our views on the prospect and challenges of developing mRNA into a new class of drug.
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Affiliation(s)
- Yuhua Weng
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, Key Laboratory of Molecular Medicine and Biotherapy, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, PR China
| | - Chunhui Li
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, Key Laboratory of Molecular Medicine and Biotherapy, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, PR China
| | - Tongren Yang
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, Key Laboratory of Molecular Medicine and Biotherapy, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, PR China
| | - Bo Hu
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, Key Laboratory of Molecular Medicine and Biotherapy, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, PR China
| | - Mengjie Zhang
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, Key Laboratory of Molecular Medicine and Biotherapy, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, PR China
| | - Shuai Guo
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, Key Laboratory of Molecular Medicine and Biotherapy, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, PR China
| | - Haihua Xiao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Xing-Jie Liang
- Chinese Academy of Sciences (CAS), Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, PR China
| | - Yuanyu Huang
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, Key Laboratory of Molecular Medicine and Biotherapy, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, PR China.
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282
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mRNA structure regulates protein expression through changes in functional half-life. Proc Natl Acad Sci U S A 2019; 116:24075-24083. [PMID: 31712433 PMCID: PMC6883848 DOI: 10.1073/pnas.1908052116] [Citation(s) in RCA: 275] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Despite widespread recognition that RNA is inherently structured, the interplay between local and global mRNA secondary structure (particularly in the coding region) and overall protein expression has not been thoroughly explored. Our work uses 2 approaches to disentangle the regulatory roles of mRNA primary sequence and secondary structure: global substitution with modified nucleotides and computational sequence design. By fitting detailed kinetic expression data to mathematical models, we show that secondary structure can increase mRNA half-life independent of codon usage. These findings have significant implications for both translational regulation of endogenous mRNAs and the emerging field of mRNA therapeutics. Messenger RNAs (mRNAs) encode information in both their primary sequence and their higher order structure. The independent contributions of factors like codon usage and secondary structure to regulating protein expression are difficult to establish as they are often highly correlated in endogenous sequences. Here, we used 2 approaches, global inclusion of modified nucleotides and rational sequence design of exogenously delivered constructs, to understand the role of mRNA secondary structure independent from codon usage. Unexpectedly, highly expressed mRNAs contained a highly structured coding sequence (CDS). Modified nucleotides that stabilize mRNA secondary structure enabled high expression across a wide variety of primary sequences. Using a set of eGFP mRNAs with independently altered codon usage and CDS structure, we find that the structure of the CDS regulates protein expression through changes in functional mRNA half-life (i.e., mRNA being actively translated). This work highlights an underappreciated role of mRNA secondary structure in the regulation of mRNA stability.
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283
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Abstract
Chemical modifications of RNAs have long been established as key modulators of nonprotein-coding RNA structure and function in cells. There is a growing appreciation that messenger RNA (mRNA) sequences responsible for directing protein synthesis can also be posttranscriptionally modified. The enzymatic incorporation of mRNA modifications has many potential outcomes, including changing mRNA stability, protein recruitment, and translation. We tested how one of the most common modifications present in mRNA coding regions, pseudouridine (Ψ), impacts protein synthesis using a fully reconstituted bacterial translation system and human cells. Our work reveals that replacing a single uridine nucleotide with Ψ in an mRNA codon impedes amino acid addition and EF-Tu GTPase activation. A crystal structure of the Thermus thermophilus 70S ribosome with a tRNAPhe bound to a ΨUU codon in the A site supports these findings. We also find that the presence of Ψ can promote the low-level synthesis of multiple peptide products from a single mRNA sequence in the reconstituted translation system as well as human cells, and increases the rate of near-cognate Val-tRNAVal reacting on a ΨUU codon. The vast majority of Ψ moieties in mRNAs are found in coding regions, and our study suggests that one consequence of the ribosome encountering Ψ can be to modestly alter both translation speed and mRNA decoding.
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