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Kim YA, Mousavi K, Yazdi A, Zwierzyna M, Cardinali M, Fox D, Peel T, Coller J, Aggarwal K, Maruggi G. Computational design of mRNA vaccines. Vaccine 2024; 42:1831-1840. [PMID: 37479613 DOI: 10.1016/j.vaccine.2023.07.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/23/2023] [Accepted: 07/10/2023] [Indexed: 07/23/2023]
Abstract
mRNA technology has emerged as a successful vaccine platform that offered a swift response to the COVID-19 pandemic. Accumulating evidence shows that vaccine efficacy, thermostability, and other important properties, are largely impacted by intrinsic properties of the mRNA molecule, such as RNA sequence and structure, both of which can be optimized. Designing mRNA sequence for vaccines presents a combinatorial problem due to an extremely large selection space. For instance, due to the degeneracy of the genetic code, there are over 10632 possible mRNA sequences that could encode the spike protein, the COVID-19 vaccines' target. Moreover, designing different elements of the mRNA sequence simultaneously against multiple objectives such as translational efficiency, reduced reactogenicity, and improved stability requires an efficient and sophisticated optimization strategy. Recently, there has been a growing interest in utilizing computational tools to redesign mRNA sequences to improve vaccine characteristics and expedite discovery timelines. In this review, we explore important biophysical features of mRNA to be considered for vaccine design and discuss how computational approaches can be applied to rapidly design mRNA sequences with desirable characteristics.
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Affiliation(s)
| | | | | | | | | | | | | | - Jeff Coller
- Johns Hopkins University, Baltimore, MD, USA
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Li X, Qi J, Wang J, Hu W, Zhou W, Wang Y, Li T. Nanoparticle technology for mRNA: Delivery strategy, clinical application and developmental landscape. Theranostics 2024; 14:738-760. [PMID: 38169577 PMCID: PMC10758055 DOI: 10.7150/thno.84291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024] Open
Abstract
The mRNA vaccine, a groundbreaking advancement in the field of immunology, has garnered international recognition by being awarded the prestigious Nobel Prize, which has emerged as a promising prophylactic and therapeutic modality for various diseases, especially in cancer, rare disease, and infectious disease such as COVID-19, wherein successful mRNA treatment can be achieved by improving the stability of mRNA and introducing a safe and effective delivery system. Nanotechnology-based delivery systems, such as lipid nanoparticles, lipoplexes, polyplexes, lipid-polymer hybrid nanoparticles and others, have attracted great interest and have been explored for mRNA delivery. Nanoscale platforms can protect mRNA from extracellular degradation while promoting endosome escape after endocytosis, hence improving the efficacy. This review provides an overview of diverse nanoplatforms utilized for mRNA delivery in preclinical and clinical stages, including formulation, preparation process, transfection efficiency, and administration route. Furthermore, the market situation and prospects of mRNA vaccines are discussed here.
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Affiliation(s)
- Xiang Li
- Formulation and Process Development (FPD), WuXi Biologics, 291 Fucheng Road, Hangzhou, 311106, China
| | - Jing Qi
- Formulation and Process Development (FPD), WuXi Biologics, 291 Fucheng Road, Hangzhou, 311106, China
| | - Juan Wang
- Formulation and Process Development (FPD), WuXi Biologics, 291 Fucheng Road, Hangzhou, 311106, China
| | - Weiwei Hu
- WuXi Biologics, 291 Fucheng Road, Hangzhou, 311106, China
| | - Weichang Zhou
- WuXi Biologics, Waigaoqiao Free Trade Zone, Shanghai, 200131, China
| | - Yi Wang
- Formulation and Process Development (FPD), WuXi Biologics, 291 Fucheng Road, Hangzhou, 311106, China
| | - Tao Li
- Formulation and Process Development (FPD), WuXi Biologics, 291 Fucheng Road, Hangzhou, 311106, China
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3
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Zhang W, Taheri-Ledari R, Ganjali F, Mirmohammadi SS, Qazi FS, Saeidirad M, KashtiAray A, Zarei-Shokat S, Tian Y, Maleki A. Effects of morphology and size of nanoscale drug carriers on cellular uptake and internalization process: a review. RSC Adv 2022; 13:80-114. [PMID: 36605676 PMCID: PMC9764328 DOI: 10.1039/d2ra06888e] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
In the field of targeted drug delivery, the effects of size and morphology of drug nanocarriers are of great importance and need to be discussed in depth. To be concise, among all the various shapes of nanocarriers, rods and tubes with a narrow cross-section are the most preferred shapes for the penetration of a cell membrane. In this regard, several studies have focused on methods to produce nanorods and nanotubes with controlled optimized size and aspect ratio (AR). Additionally, a non-spherical orientation could affect the cellular uptake process while a tangent angle of less than 45° is better at penetrating the membrane, and Ω = 90° is beneficial. Moreover, these nanocarriers show different behaviors when confronting diverse cells whose fields should be investigated in future studies. In this survey, a comprehensive classification based on carrier shape is first submitted. Then, the most commonly used methods for control over the size and shape of the carriers are reviewed. Finally, influential factors on the cellular uptake and internalization processes and related analytical methods for evaluating this process are discussed.
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Affiliation(s)
- Wenjie Zhang
- Department of Nuclear Medicine, West China Hospital, Sichuan University No. 37, Guoxue Alley Chengdu 610041 Sichuan Province P. R. China
| | - Reza Taheri-Ledari
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology Tehran 16846-13114 Iran +98 21 73021584 +98 21 77240640-50
| | - Fatemeh Ganjali
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology Tehran 16846-13114 Iran +98 21 73021584 +98 21 77240640-50
| | - Seyedeh Shadi Mirmohammadi
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology Tehran 16846-13114 Iran +98 21 73021584 +98 21 77240640-50
| | - Fateme Sadat Qazi
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology Tehran 16846-13114 Iran +98 21 73021584 +98 21 77240640-50
| | - Mahdi Saeidirad
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology Tehran 16846-13114 Iran +98 21 73021584 +98 21 77240640-50
| | - Amir KashtiAray
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology Tehran 16846-13114 Iran +98 21 73021584 +98 21 77240640-50
| | - Simindokht Zarei-Shokat
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology Tehran 16846-13114 Iran +98 21 73021584 +98 21 77240640-50
| | - Ye Tian
- Department of Orthodontics, West China Hospital of Stomatology, Sichuan University No. 14, 3rd Section of South Renmin Road Chengdu 610041 P. R. China
| | - Ali Maleki
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology Tehran 16846-13114 Iran +98 21 73021584 +98 21 77240640-50
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mTOR- and LARP1-dependent regulation of TOP mRNA poly(A) tail and ribosome loading. Cell Rep 2022; 41:111548. [DOI: 10.1016/j.celrep.2022.111548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 08/30/2022] [Accepted: 09/30/2022] [Indexed: 11/20/2022] Open
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Abe N, Imaeda A, Inagaki M, Li Z, Kawaguchi D, Onda K, Nakashima Y, Uchida S, Hashiya F, Kimura Y, Abe H. Complete Chemical Synthesis of Minimal Messenger RNA by Efficient Chemical Capping Reaction. ACS Chem Biol 2022; 17:1308-1314. [PMID: 35608277 DOI: 10.1021/acschembio.1c00996] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Site-specific chemical modification of mRNA can improve its translational efficiency and stability. For this purpose, it is desirable to develop a complete chemical synthesis method for chemically modified mRNA. The key is a chemical reaction that introduces a cap structure into the chemically synthesized RNA. In this study, we developed a fast and quantitative chemical capping reaction between 5'-phosphorylated RNA and N7-methylated GDP imidazolide in the presence of 1-methylimidazole in the organic solvent dimethyl sulfoxide. It enabled quantitative preparation of capping RNA within 3 h. We prepared chemically modified 107-nucleotide mRNAs, including N6-methyladenosine, insertion of non-nucleotide linkers, and 2'-O-methylated nucleotides at the 5' end and evaluated their effects on translational activity in cultured HeLa cells. The results showed that mRNAs with non-nucleotide linkers in the untranslated regions were sufficiently tolerant to translation and that mRNAs with the Cap_2 structure had higher translational activity than those with the Cap_0 structure.
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Affiliation(s)
- Naoko Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Akihiro Imaeda
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Masahito Inagaki
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Zhenmin Li
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Daisuke Kawaguchi
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Kaoru Onda
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Yuko Nakashima
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Satoshi Uchida
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Fumitaka Hashiya
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Yasuaki Kimura
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Hiroshi Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- CREST, Japan Science and Technology Agency, 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
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To KKW, Cho WCS. An overview of rational design of mRNA-based therapeutics and vaccines. Expert Opin Drug Discov 2021; 16:1307-1317. [PMID: 34058918 DOI: 10.1080/17460441.2021.1935859] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/25/2021] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Messenger RNA (mRNA)-based therapeutics and vaccines have emerged as a disruptive new drug class for various applications, including regenerative medicine, cancer treatment, and prophylactic and therapeutic vaccinations. AREAS COVERED This review provides an update about the rational structure-based design of various formats of mRNA-based therapeutics. The authors discuss the recent advances in the mRNA modifications that have been used to enhance stability, promote translation efficiency and regulate immunogenicity for specific applications. EXPERT OPINION Extensive research efforts have been made to optimize mRNA constructs and preparation procedures to unleash the full potential of mRNA-based therapeutics and vaccines. Sequence optimization (untranslated region and codon usage), chemical engineering of nucleotides and modified 5'cap, and optimization of in vitro transcription and mRNA purification protocols have overcome the major obstacles (instability, delivery, immunogenicity and safety) hindering the clinical applications of mRNA therapeutics and vaccines. The optimized design parameters should not be applied as default to different biological systems, but rather individually optimized for each mRNA sequence and intended application. Further advancement in the mRNA design and delivery technologies for achieving cell type- and organ site-specificity will broaden the scope and usefulness of this new class of drugs.
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Affiliation(s)
- Kenneth K W To
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - William C S Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, China
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Sudheesh AP, Mohan N, Francis N, Laishram RS, Anderson RA. Star-PAP controlled alternative polyadenylation coupled poly(A) tail length regulates protein expression in hypertrophic heart. Nucleic Acids Res 2020; 47:10771-10787. [PMID: 31598705 PMCID: PMC6847588 DOI: 10.1093/nar/gkz875] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 09/08/2019] [Accepted: 10/05/2019] [Indexed: 12/31/2022] Open
Abstract
Alternative polyadenylation (APA)-mediated 3′-untranslated region (UTR) shortening is known to increase protein expression due to the loss of miRNA regulatory sites. Yet, mRNAs with longer 3′-UTR also show enhanced protein expression. Here, we identify a mechanism by which longer transcripts generated by the distal-most APA site leads to increased protein expression compared to the shorter transcripts and the longer transcripts are positioned to regulate heart failure (HF). A Star-PAP target gene, NQO1 has three poly(A) sites (PA-sites) at the terminal exon on the pre-mRNA. Star-PAP selects the distal-most site that results in the expression of the longest isoform. We show that the NQO1 distal-specific mRNA isoform accounts for the majority of cellular NQO1 protein. Star-PAP control of the distal-specific isoform is stimulated by oxidative stress and the toxin dioxin. The longest NQO1 transcript has increased poly(A) tail (PA-tail) length that accounts for the difference in translation potentials of the three NQO1 isoforms. This mechanism is involved in the regulation of cardiac hypertrophy (CH), an antecedent condition to HF where NQO1 downregulation stems from the loss of the distal-specific transcript. The loss of NQO1 during hypertrophy was rescued by ectopic expression of the distal- but not the proximal- or middle-specific NQO1 mRNA isoforms in the presence of Star-PAP expression, and reverses molecular events of hypertrophy in cardiomyocytes.
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Affiliation(s)
- A P Sudheesh
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum-014, India.,Manipal Academy of Higher Education, Manipal 576104, India
| | - Nimmy Mohan
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum-014, India.,Manipal Academy of Higher Education, Manipal 576104, India
| | - Nimmy Francis
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum-014, India.,Manipal Academy of Higher Education, Manipal 576104, India
| | - Rakesh S Laishram
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum-014, India
| | - Richard A Anderson
- School of Medicine and Public Health, University of Wisconsin, MD 53726, USA
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Jaïs PH, Decroly E, Jacquet E, Le Boulch M, Jaïs A, Jean-Jean O, Eaton H, Ponien P, Verdier F, Canard B, Goncalves S, Chiron S, Le Gall M, Mayeux P, Shmulevitz M. C3P3-G1: first generation of a eukaryotic artificial cytoplasmic expression system. Nucleic Acids Res 2019; 47:2681-2698. [PMID: 30726994 PMCID: PMC6412113 DOI: 10.1093/nar/gkz069] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 12/03/2018] [Accepted: 01/25/2019] [Indexed: 12/25/2022] Open
Abstract
Most eukaryotic expression systems make use of host-cell nuclear transcriptional and post-transcriptional machineries. Here, we present the first generation of the chimeric cytoplasmic capping-prone phage polymerase (C3P3-G1) expression system developed by biological engineering, which generates capped and polyadenylated transcripts in host-cell cytoplasm by means of two components. First, an artificial single-unit chimeric enzyme made by fusing an mRNA capping enzyme and a DNA-dependent RNA polymerase. Second, specific DNA templates designed to operate with the C3P3-G1 enzyme, which encode for the transcripts and their artificial polyadenylation. This system, which can potentially be adapted to any in cellulo or in vivo eukaryotic expression applications, was optimized for transient expression in mammalian cells. C3P3-G1 shows promising results for protein production in Chinese Hamster Ovary (CHO-K1) cells. This work also provides avenues for enhancing the performances for next generation C3P3 systems.
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Affiliation(s)
- Philippe H Jaïs
- Eukarÿs SAS, Génopole Campus 3, 4 rue Pierre Fontaine, 91058 Evry Cedex, France
| | - Etienne Decroly
- Architecture et Fonction des Macromolécules Biologiques (AFMB) UMR 7257 CNRS/AMU, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Marine Le Boulch
- Eukarÿs SAS, Génopole Campus 3, 4 rue Pierre Fontaine, 91058 Evry Cedex, France
| | - Aurélien Jaïs
- Eukarÿs SAS, Génopole Campus 3, 4 rue Pierre Fontaine, 91058 Evry Cedex, France
| | - Olivier Jean-Jean
- Sorbonne Université, CNRS-UMR8256, Biological Adaptation and Ageing, Institut de Biologie Paris Seine (B2A-IBPS), F-75252 Paris, France
| | - Heather Eaton
- Medical Microbiology and Immunology, University of Alberta, 6-142J Katz Group Centre for Pharmacy and Health Research, 114 Street NW, Edmonton, Alberta T6G 2E1, Canada
| | - Prishila Ponien
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Fréderique Verdier
- INSERM Unit 1016, Institut Cochin, Bâtiment Gustave Roussy, 27 rue du faubourg Saint-Jacques, 75014 Paris, France
| | - Bruno Canard
- Architecture et Fonction des Macromolécules Biologiques (AFMB) UMR 7257 CNRS/AMU, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Sergio Goncalves
- Eukarÿs SAS, Génopole Campus 3, 4 rue Pierre Fontaine, 91058 Evry Cedex, France
| | - Stéphane Chiron
- Eukarÿs SAS, Génopole Campus 3, 4 rue Pierre Fontaine, 91058 Evry Cedex, France
| | - Maude Le Gall
- Gastrointestinal and Metabolic Dysfunctions in Nutritional Pathologies, INSERM UMRS1149, 16 rue Henri Huchard, 75890 Paris Cedex 18, France
| | - Patrick Mayeux
- INSERM Unit 1016, Institut Cochin, Bâtiment Gustave Roussy, 27 rue du faubourg Saint-Jacques, 75014 Paris, France
| | - Maya Shmulevitz
- Medical Microbiology and Immunology, University of Alberta, 6-142J Katz Group Centre for Pharmacy and Health Research, 114 Street NW, Edmonton, Alberta T6G 2E1, Canada
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RNA-based therapy for osteogenesis. Int J Pharm 2019; 569:118594. [DOI: 10.1016/j.ijpharm.2019.118594] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/02/2019] [Accepted: 08/03/2019] [Indexed: 02/06/2023]
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Beverly M, Hagen C, Slack O. Poly A tail length analysis of in vitro transcribed mRNA by LC-MS. Anal Bioanal Chem 2018; 410:1667-1677. [PMID: 29313076 DOI: 10.1007/s00216-017-0840-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 11/03/2017] [Accepted: 11/17/2017] [Indexed: 11/29/2022]
Abstract
The 3'-polyadenosine (poly A) tail of in vitro transcribed (IVT) mRNA was studied using liquid chromatography coupled to mass spectrometry (LC-MS). Poly A tails were cleaved from the mRNA using ribonuclease T1 followed by isolation with dT magnetic beads. Extracted tails were then analyzed by LC-MS which provided tail length information at single-nucleotide resolution. A 2100-nt mRNA with plasmid-encoded poly A tail lengths of either 27, 64, 100, or 117 nucleotides was used for these studies as enzymatically added poly A tails showed significant length heterogeneity. The number of As observed in the tails closely matched Sanger sequencing results of the DNA template, and even minor plasmid populations with sequence variations were detected. When the plasmid sequence contained a discreet number of poly As in the tail, analysis revealed a distribution that included tails longer than the encoded tail lengths. These observations were consistent with transcriptional slippage of T7 RNAP taking place within a poly A sequence. The type of RNAP did not alter the observed tail distribution, and comparison of T3, T7, and SP6 showed all three RNAPs produced equivalent tail length distributions. The addition of a sequence at the 3' end of the poly A tail did, however, produce narrower tail length distributions which supports a previously described model of slippage where the 3' end can be locked in place by having a G or C after the poly nucleotide region. Graphical abstract Determination of mRNA poly A tail length using magnetic beads and LC-MS.
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Affiliation(s)
- Michael Beverly
- Novartis Institutes of Biomedical Research, 700 Main Street, Cambridge, MA, 02139, USA.
| | - Caitlin Hagen
- Novartis Institutes of Biomedical Research, 700 Main Street, Cambridge, MA, 02139, USA
| | - Olga Slack
- Novartis Institutes of Biomedical Research, 700 Main Street, Cambridge, MA, 02139, USA
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Oh S, Kessler JA. Design, Assembly, Production, and Transfection of Synthetic Modified mRNA. Methods 2017; 133:29-43. [PMID: 29080741 DOI: 10.1016/j.ymeth.2017.10.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/11/2017] [Accepted: 10/12/2017] [Indexed: 10/18/2022] Open
Abstract
Proteins are drivers of cell functions and are targets of many therapies. Exogenous protein expression techniques, therefore, have been essential for research and medicine. The most common method for exogenous protein expression relies on DNA-based viral or non-viral vectors. However, DNA-based vectors have the potential to integrate into the host genome and cause permanent mutations. RNA-based vectors solve this shortcoming. In particular, synthetic modified mRNA provides non-viral, integration-free, zero-footprint method for expressing proteins. Modified mRNA can direct cell fate specification and cellular reprogramming faster and more efficiently than other methods. Furthermore, when simultaneously express multiple different proteins, mRNA vectors allow for greater flexibility and control over stoichiometric ratios, dose titrations, and complete silencing of expressions. Additionally, modified mRNAs have been shown to be viable and safe as therapeutic agents for gene therapy and vaccine, providing an alternative approach to address diseases. Despite these advantages, technical challenge, mRNA instability, and host immunogenicity have caused significant barriers to widespread use of this technology. The comprehensive method presented here addresses all of these shortcomings. This stepwise protocol describes every step necessary for the synthesis of modified mRNA from any coding DNA sequence of interest. The meticulously detailed protocol enables the users to make alterations to each component of modified mRNA for even more significant customization, allowing the researchers to apply this technology to a wide range of uses. This non-cytotoxic synthetic modified mRNA can be used for protein expression, regulation of cell reprogramming or differentiation, and drug delivery.
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Affiliation(s)
- Sanders Oh
- Department of Neurology, Northwestern University, Chicago, IL, USA.
| | - John A Kessler
- Department of Neurology, Northwestern University, Chicago, IL, USA
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12
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An Mtr4/ZFC3H1 complex facilitates turnover of unstable nuclear RNAs to prevent their cytoplasmic transport and global translational repression. Genes Dev 2017; 31:1257-1271. [PMID: 28733371 PMCID: PMC5558927 DOI: 10.1101/gad.302604.117] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 06/22/2017] [Indexed: 12/12/2022]
Abstract
Ogami et al. highlight a critical role for Mtr4/ZFC3H1 in nuclear surveillance of naturally unstable lncRNAs to prevent their accumulation, transport to the cytoplasm, and resultant disruption of protein synthesis. Many long noncoding RNAs (lncRNAs) are unstable and rapidly degraded in the nucleus by the nuclear exosome. An exosome adaptor complex called NEXT (nuclear exosome targeting) functions to facilitate turnover of some of these lncRNAs. Here we show that knockdown of one NEXT subunit, Mtr4, but neither of the other two subunits, resulted in accumulation of two types of lncRNAs: prematurely terminated RNAs (ptRNAs) and upstream antisense RNAs (uaRNAs). This suggested a NEXT-independent Mtr4 function, and, consistent with this, we isolated a distinct complex containing Mtr4 and the zinc finger protein ZFC3H1. Strikingly, knockdown of either protein not only increased pt/uaRNA levels but also led to their accumulation in the cytoplasm. Furthermore, all pt/uaRNAs examined associated with active ribosomes, but, paradoxically, this correlated with a global reduction in heavy polysomes and overall repression of translation. Our findings highlight a critical role for Mtr4/ZFC3H1 in nuclear surveillance of naturally unstable lncRNAs to prevent their accumulation, transport to the cytoplasm, and resultant disruption of protein synthesis.
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Kiss DL, Waters CE, Ouda IM, Saldivar JC, Karras JR, Amin ZA, Mahrous S, Druck T, Bundschuh RA, Schoenberg DR, Huebner K. Identification of Fhit as a post-transcriptional effector of Thymidine Kinase 1 expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:374-382. [PMID: 28093273 DOI: 10.1016/j.bbagrm.2017.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 01/09/2017] [Accepted: 01/12/2017] [Indexed: 11/30/2022]
Abstract
FHIT is a genome caretaker gene that is silenced in >50% of cancers. Loss of Fhit protein expression promotes accumulation of DNA damage, affects apoptosis and epithelial-mesenchymal transition, though molecular mechanisms underlying these alterations have not been fully elucidated. Initiation of genome instability directly follows Fhit loss and the associated reduced Thymidine Kinase 1 (TK1) protein expression. The effects on TK1 of Fhit knockdown and Fhit induction in the current study confirmed the role of Fhit in regulating TK1 expression. Changes in Fhit expression did not impact TK1 protein turnover or transcription from the TK1 promoter, nor steady-state levels of TK1 mRNA or turnover. Polysome profile analysis showed that up-regulated Fhit expression resulted in decreased TK1 RNA in non-translating messenger ribonucleoproteins and increased ribosome density on TK1 mRNA. Fhit does not bind RNA but its expression increased luciferase expression from a transgene bearing the TK1 5'-UTR. Fhit has been reported to act as a scavenger decapping enzyme, and a similar result with a mutant (H96) that binds but does not cleave nucleoside 5',5'-triphosphates suggests the impact on TK1 translation is due to its ability to modulate the intracellular level of cap-like molecules. Consistent with this, cells expressing Fhit mutants with reduced activity toward cap-like dinucleotides exhibit DNA damage resulting from TK1 deficiency, whereas cells expressing wild-type Fhit or the H96N mutant do not. The results have implications for the mechanism by which Fhit regulates TK1 mRNA, and more broadly, for its modulation of multiple functions as tumor suppressor/genome caretaker.
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Affiliation(s)
- Daniel L Kiss
- Center for RNA Biology, 484 West 12th Ave., Columbus, OH 43210 USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, 1060 Carmack Rd., Columbus, OH 43210 USA
| | - Catherine E Waters
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12 Ave., Columbus, OH 43210 USA
| | - Iman M Ouda
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12 Ave., Columbus, OH 43210 USA
- Department of Clinical Pathology, Faculty of Medicine, 2nd floor, Surgery Hospital, Zagazig University, Zagazig 44519, Egypt
| | - Joshua C Saldivar
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12 Ave., Columbus, OH 43210 USA
| | - Jenna R Karras
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12 Ave., Columbus, OH 43210 USA
| | - Zaynab A Amin
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12 Ave., Columbus, OH 43210 USA
| | - Seham Mahrous
- Department of Clinical Pathology, Faculty of Medicine, 2nd floor, Surgery Hospital, Zagazig University, Zagazig 44519, Egypt
| | - Teresa Druck
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12 Ave., Columbus, OH 43210 USA
| | - Ralf A Bundschuh
- Center for RNA Biology, 484 West 12th Ave., Columbus, OH 43210 USA
- Department of Physics, Department of Chemistry and Biochemistry, and Division of Hematology, Department of Internal Medicine, The Ohio State University, 191 West Woodruff Ave., Columbus, OH 43210 USA
| | - Daniel R Schoenberg
- Center for RNA Biology, 484 West 12th Ave., Columbus, OH 43210 USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, 1060 Carmack Rd., Columbus, OH 43210 USA
| | - Kay Huebner
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12 Ave., Columbus, OH 43210 USA
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14
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Reautschnig P, Vogel P, Stafforst T. The notorious R.N.A. in the spotlight - drug or target for the treatment of disease. RNA Biol 2016; 14:651-668. [PMID: 27415589 PMCID: PMC5449091 DOI: 10.1080/15476286.2016.1208323] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
mRNA is an attractive drug target for therapeutic interventions. In this review we highlight the current state, clinical trials, and developments in antisense therapy, including the classical approaches like RNaseH-dependent oligomers, splice-switching oligomers, aptamers, and therapeutic RNA interference. Furthermore, we provide an overview on emerging concepts for using RNA in therapeutic settings including protein replacement by in-vitro-transcribed mRNAs, mRNA as vaccines and anti-allergic drugs. Finally, we give a brief outlook on early-stage RNA repair approaches that apply endogenous or engineered proteins in combination with short RNAs or chemically stabilized oligomers for the re-programming of point mutations, RNA modifications, and frame shift mutations directly on the endogenous mRNA.
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Affiliation(s)
- Philipp Reautschnig
- a Interfaculty Institute of Biochemistry, University of Tübingen Auf der Morgenstelle , Tübingen , Germany
| | - Paul Vogel
- a Interfaculty Institute of Biochemistry, University of Tübingen Auf der Morgenstelle , Tübingen , Germany
| | - Thorsten Stafforst
- a Interfaculty Institute of Biochemistry, University of Tübingen Auf der Morgenstelle , Tübingen , Germany
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15
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Kiss DL, Oman KM, Dougherty JA, Mukherjee C, Bundschuh R, Schoenberg DR. Cap homeostasis is independent of poly(A) tail length. Nucleic Acids Res 2015; 44:304-14. [PMID: 26673707 PMCID: PMC4705677 DOI: 10.1093/nar/gkv1460] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 11/28/2015] [Indexed: 12/02/2022] Open
Abstract
Cap homeostasis is a cyclical process of decapping and recapping that maintains the cap on a subset of the cytoplasmic transcriptome. Interfering with cytoplasmic capping results in the redistribution of target transcripts from polysomes to non-translating mRNPs, where they accumulate in an uncapped but nonetheless stable form. It is generally thought that decapping is preceded by shortening of the poly(A) tail to a length that can no longer support translation. Therefore recapped target transcripts would either have to undergo cytoplasmic polyadenylation or retain a reasonably long poly(A) tail if they are to return to the translating pool. In cells that are inhibited for cytoplasmic capping there is no change in the overall distribution of poly(A) lengths or in the elution profile of oligo(dT)-bound targets. Poly(A) tail lengths were similar for target mRNAs on polysomes or in non-translating mRNPs, and the presence of polyadenylated uncapped mRNA in mRNPs was confirmed by separation into capped and uncapped pools prior to assay. Finally, in silico analysis of cytoplasmic capping targets revealed significant correlations with genes encoding transcripts with uridylated or multiply modified 3′ ends, and genes possessing multiple 3′-untranslated regions (UTRs) generated by alternative cleavage and polyadenylation.
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Affiliation(s)
- Daniel L Kiss
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Kenji M Oman
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Julie A Dougherty
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Chandrama Mukherjee
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Ralf Bundschuh
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA Department of Physics, The Ohio State University, Columbus, OH 43210, USA Department of Chemistry and Biochemistry, and Division of Hematology, The Ohio State University, Columbus, OH 43210, USA
| | - Daniel R Schoenberg
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
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16
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Abstract
Messenger RNA (mRNA) has recently emerged with remarkable potential as an effective alternative to DNA-based therapies because of several unique advantages. mRNA does not require nuclear entry for transfection activity and has a negligible chance of integrating into the host genome which excludes the possibility of potentially detrimental genomic alternations. Chemical modification of mRNA has further enhanced its stability and decreased its activation of innate immune responses. Additionally, mRNA has been found to have rapid expression and predictable kinetics. Nevertheless, the ubiquitous application of mRNA remains challenging given its unfavorable attributes, such as large size, negative charge and susceptibility to enzymatic degradation. Further refinement of mRNA delivery modalities is therefore essential for its development as a therapeutic tool. This review provides an exclusive overview of current state-of-the-art biomaterials and nanotechnology platforms for mRNA delivery, and discusses future prospects to bring these exciting technologies into clinical practice.
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Affiliation(s)
- Mohammad Ariful Islam
- Laboratory for Nanoengineering & Drug Delivery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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17
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Youn H, Chung JK. Modified mRNA as an alternative to plasmid DNA (pDNA) for transcript replacement and vaccination therapy. Expert Opin Biol Ther 2015; 15:1337-48. [PMID: 26125492 PMCID: PMC4696419 DOI: 10.1517/14712598.2015.1057563] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Introduction: Current gene therapy involves replacement of defective gene by delivery of healthy genetic material to precede normal function. Virus-mediated gene delivery is the most successful and efficient method for gene therapy, but it has been challenged due to serious safety concerns. Conversely, gene delivery using plasmid DNA (pDNA) is considered safer, but its transfection efficiency is much lower than virus-mediated gene transfer. Recently, mRNA has been suggested as an alternative option to avoid undesired insertion of delivered DNA sequences with higher transfection efficiency and stability. Area covered: In this review, we summarize the currently available strategies of mRNA modification to increase the therapeutic efficacy; we also highlight the recent improvements of mRNA delivery for in vivo applications of gene therapy. Expert opinion: The use of mRNA-based gene transfer could indeed be a promising new strategy for gene therapy. Notable advantages include no risk of integration into the genomic DNA, adjustable gene expression and easier modulation of the immune system. By reducing or utilizing the immunogenic properties, mRNA offers a promising tool for gene/or transcript replacement.
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Affiliation(s)
- Hyewon Youn
- Seoul National University, College of Medicine, Department of Nuclear Medicine , 103 Daehak-ro, Jongno-gu, Seoul 110-799 , Korea +82 2 2072 3341 ; +82 2 745 7690 ;
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18
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Tavernier G, Andries O, Demeester J, Sanders NN, De Smedt SC, Rejman J. mRNA as gene therapeutic: How to control protein expression. J Control Release 2011; 150:238-47. [DOI: 10.1016/j.jconrel.2010.10.020] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Accepted: 10/13/2010] [Indexed: 10/18/2022]
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