1
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Adesanya O, Das D, Kalsotra A. Emerging roles of RNA-binding proteins in fatty liver disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1840. [PMID: 38613185 PMCID: PMC11018357 DOI: 10.1002/wrna.1840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/08/2024] [Accepted: 03/05/2024] [Indexed: 04/14/2024]
Abstract
A rampant and urgent global health issue of the 21st century is the emergence and progression of fatty liver disease (FLD), including alcoholic fatty liver disease and the more heterogenous metabolism-associated (or non-alcoholic) fatty liver disease (MAFLD/NAFLD) phenotypes. These conditions manifest as disease spectra, progressing from benign hepatic steatosis to symptomatic steatohepatitis, cirrhosis, and, ultimately, hepatocellular carcinoma. With numerous intricately regulated molecular pathways implicated in its pathophysiology, recent data have emphasized the critical roles of RNA-binding proteins (RBPs) in the onset and development of FLD. They regulate gene transcription and post-transcriptional processes, including pre-mRNA splicing, capping, and polyadenylation, as well as mature mRNA transport, stability, and translation. RBP dysfunction at every point along the mRNA life cycle has been associated with altered lipid metabolism and cellular stress response, resulting in hepatic inflammation and fibrosis. Here, we discuss the current understanding of the role of RBPs in the post-transcriptional processes associated with FLD and highlight the possible and emerging therapeutic strategies leveraging RBP function for FLD treatment. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
| | - Diptatanu Das
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Cancer Center @ Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
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2
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Xu Z, Fisher DE. mRNA melanoma vaccine revolution spurred by the COVID-19 pandemic. Front Immunol 2023; 14:1155728. [PMID: 37063845 PMCID: PMC10101324 DOI: 10.3389/fimmu.2023.1155728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023] Open
Abstract
The advent of mRNA vaccines represents a significant advance in the field of vaccinology. While several vaccine approaches (mRNA, DNA, recombinant protein, and viral-vectored vaccines) had been investigated at the start of the COVID-19 pandemic, mRNA vaccines quickly gained popularity due to superior immunogenicity at a low dose, strong safety/tolerability profiles, and the possibility of rapid vaccine mass manufacturing and deployment to rural regions. In addition to inducing protective neutralizing antibody responses, mRNA vaccines can also elicit high-magnitude cytotoxic T-cell responses comparable to natural viral infections; thereby, drawing significant interest from cancer immunotherapy experts. This mini-review will highlight key developmental milestones and lessons we have learned from mRNA vaccines during the COVID-19 pandemic, with a specific emphasis on clinical trial data gathered so far for mRNA vaccines against melanoma and other forms of cancer.
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Affiliation(s)
- Ziyang Xu
- Department of Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - David E. Fisher
- Department of Dermatology, Massachusetts General Hospital, Boston, MA, United States
- *Correspondence: David E. Fisher,
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3
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Cheng F, Wang Y, Bai Y, Liang Z, Mao Q, Liu D, Wu X, Xu M. Research Advances on the Stability of mRNA Vaccines. Viruses 2023; 15:668. [PMID: 36992377 PMCID: PMC10051489 DOI: 10.3390/v15030668] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Compared to other vaccines, the inherent properties of messenger RNA (mRNA) vaccines and their interaction with lipid nanoparticles make them considerably unstable throughout their life cycles, impacting their effectiveness and global accessibility. It is imperative to improve mRNA vaccine stability and investigate the factors influencing stability. Since mRNA structure, excipients, lipid nanoparticle (LNP) delivery systems, and manufacturing processes are the primary factors affecting mRNA vaccine stability, optimizing mRNA structure and screening excipients can effectively improve mRNA vaccine stability. Moreover, improving manufacturing processes could also prepare thermally stable mRNA vaccines with safety and efficacy. Here, we review the regulatory guidance associated with mRNA vaccine stability, summarize key factors affecting mRNA vaccine stability, and propose a possible research path to improve mRNA vaccine stability.
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Affiliation(s)
- Feiran Cheng
- National Medical Products Administration Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
- National Health Commission Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing 102600, China
| | - Yiping Wang
- Center for Reference Materials and Standardization, National Institutes for Food and Drug Control, Beijing 102600, China
| | - Yu Bai
- National Medical Products Administration Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
- National Health Commission Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing 102600, China
| | - Zhenglun Liang
- National Medical Products Administration Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
- National Health Commission Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing 102600, China
| | - Qunying Mao
- National Medical Products Administration Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
- National Health Commission Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing 102600, China
| | - Dong Liu
- National Medical Products Administration Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
- National Health Commission Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing 102600, China
| | - Xing Wu
- National Medical Products Administration Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
- National Health Commission Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing 102600, China
| | - Miao Xu
- National Medical Products Administration Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
- National Health Commission Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing 102600, China
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4
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Kim B, Hosn RR, Remba T, Yun D, Li N, Abraham W, Melo MB, Cortes M, Li B, Zhang Y, Dong Y, Irvine DJ. Optimization of storage conditions for lipid nanoparticle-formulated self-replicating RNA vaccines. J Control Release 2023; 353:241-253. [PMID: 36414195 PMCID: PMC9708520 DOI: 10.1016/j.jconrel.2022.11.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 11/03/2022] [Accepted: 11/13/2022] [Indexed: 12/03/2022]
Abstract
The recent clinical success of multiple mRNA-based SARS-CoV-2 vaccines has proven the potential of RNA formulated in lipid nanoparticles (LNPs) in humans, and products based on base-modified RNA, sequence-optimized RNA, and self-replicating RNAs formulated in LNPs are all in various stages of clinical development. However, much remains to be learned about critical parameters governing the manufacturing and use of LNP-RNA formulations. One important issue that has received limited attention in the literature to date is the identification of optimal storage conditions for LNP-RNA that preserve long-term activity of the formulations. Here, we analyzed the physical structure, in vivo expression characteristics, and functional activity of alphavirus-derived self-replicating RNA (repRNA)-loaded LNPs encoding HIV vaccine antigens following storage in varying temperatures, buffers, and in the presence or absence of cryoprotectants. We found that for lipid nanoparticles with compositions similar to clinically-used LNPs, storage in RNAse-free PBS containing 10% (w/v) sucrose at -20 °C was able to maintain vaccine stability and in vivo potency at a level equivalent to freshly prepared vaccines following 30 days of storage. LNPs loaded with repRNA could also be lyophilized with retention of bioactivity.
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Affiliation(s)
- Byungji Kim
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ryan R Hosn
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tanaka Remba
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dongsoo Yun
- Nanotechnology Materials Core, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Na Li
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Wuhbet Abraham
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mariane B Melo
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Manuel Cortes
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Bridget Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yuebao Zhang
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Yizhou Dong
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Department of Biomedical Engineering, The Center for Clinical and Translational Science, The Comprehensive Cancer Center, Dorothy M. Davis Heart & Lung Research Institute, Department of Radiation Oncology, Center for Cancer Engineering, Center for Cancer Metabolism, Pelotonia Institute for Immune-Oncology, The Ohio State University, Columbus, OH 43210, United States
| | - Darrell J Irvine
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Departments of Biological Engineering and Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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5
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García-Machorro J, Ramírez-Salinas GL, Martinez-Archundia M, Correa-Basurto J. The Advantage of Using Immunoinformatic Tools on Vaccine Design and Development for Coronavirus. Vaccines (Basel) 2022; 10:1844. [PMID: 36366353 PMCID: PMC9693616 DOI: 10.3390/vaccines10111844] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/21/2022] [Accepted: 10/27/2022] [Indexed: 10/28/2023] Open
Abstract
After the outbreak of SARS-CoV-2 by the end of 2019, the vaccine development strategies became a worldwide priority. Furthermore, the appearances of novel SARS-CoV-2 variants challenge researchers to develop new pharmacological or preventive strategies. However, vaccines still represent an efficient way to control the SARS-CoV-2 pandemic worldwide. This review describes the importance of bioinformatic and immunoinformatic tools (in silico) for guide vaccine design. In silico strategies permit the identification of epitopes (immunogenic peptides) which could be used as potential vaccines, as well as nonacarriers such as: vector viral based vaccines, RNA-based vaccines and dendrimers through immunoinformatics. Currently, nucleic acid and protein sequential as well structural analyses through bioinformatic tools allow us to get immunogenic epitopes which can induce immune response alone or in complex with nanocarriers. One of the advantages of in silico techniques is that they facilitate the identification of epitopes, while accelerating the process and helping to economize some stages of the development of safe vaccines.
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Affiliation(s)
- Jazmín García-Machorro
- Laboratorio de Medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Gema Lizbeth Ramírez-Salinas
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City 11340, Mexico
| | - Marlet Martinez-Archundia
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City 11340, Mexico
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City 11340, Mexico
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6
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Beyersdorf J, Bawage S, Iglesias N, Peck HE, Hobbs RA, Wroe JA, Zurla C, Gersbach CA, Santangelo PJ. Robust, Durable Gene Activation In Vivo via mRNA-Encoded Activators. ACS NANO 2022; 16:5660-5671. [PMID: 35357116 PMCID: PMC9047660 DOI: 10.1021/acsnano.1c10631] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Programmable control of gene expression via nuclease-null Cas9 fusion proteins has enabled the engineering of cellular behaviors. Here, both transcriptional and epigenetic gene activation via synthetic mRNA and lipid nanoparticle delivery was demonstrated in vivo. These highly efficient delivery strategies resulted in high levels of activation in multiple tissues. Finally, we demonstrate durable gene activation in vivo via transient delivery of a single dose of a gene activator that combines VP64, p65, and HSF1 with a SWI/SNF chromatin remodeling complex component SS18, representing an important step toward gene-activation-based therapeutics. This induced sustained gene activation could be inhibited via mRNA-encoded AcrIIA4, further improving the safety profile of this approach.
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Affiliation(s)
- Jared
P. Beyersdorf
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Krone Engineering Biosystems Building, 950 Atlantic Drive NW, Atlanta, Georgia 30332, United
States
| | - Swapnil Bawage
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Krone Engineering Biosystems Building, 950 Atlantic Drive NW, Atlanta, Georgia 30332, United
States
| | - Nahid Iglesias
- Department
of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Hannah E. Peck
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Krone Engineering Biosystems Building, 950 Atlantic Drive NW, Atlanta, Georgia 30332, United
States
| | - Ryan A. Hobbs
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Krone Engineering Biosystems Building, 950 Atlantic Drive NW, Atlanta, Georgia 30332, United
States
| | - Jay A. Wroe
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Krone Engineering Biosystems Building, 950 Atlantic Drive NW, Atlanta, Georgia 30332, United
States
| | - Chiara Zurla
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Krone Engineering Biosystems Building, 950 Atlantic Drive NW, Atlanta, Georgia 30332, United
States
| | - Charles A. Gersbach
- Department
of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
- Center
for Advanced Genomic Technologies, Duke
University, Durham, North Carolina 27708, United States
- Department
of Surgery, Duke University Medical Center, Durham, North Carolina 27708, United States
| | - Philip J. Santangelo
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Krone Engineering Biosystems Building, 950 Atlantic Drive NW, Atlanta, Georgia 30332, United
States
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7
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Pantelić I, Ilić T, Nikolić I, Savić S. Lipid nanoparticles employed in mRNA-based COVID-19 vaccines: An overview of materials and processes used for development and production. ARHIV ZA FARMACIJU 2022. [DOI: 10.5937/arhfarm72-33660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
In the light of the recommended application of the third dose, both public and professional community would benefit from a detailed report on the technological advances behind the developed messenger ribonucleic acid (mRNA) based COVID-19 vaccines. Although many vaccine developers are yet to reveal their precise formulations, it is apparent they are founded on nanotechnology platforms similar to the one successfully used for registered drug OnpattroTM (INN: patisiran). Optimal encapsulation of mRNA requires the presence of four lipids: an ionizable cationic lipid, a polyethylene-glycol (PEG)-lipid, a neutral phospholipid and cholesterol. Together with other excipients (mainly buffers, osmolytes and cryoprotectives), they enable the formation of lipid nanoparticles (LNPs) using rapid-mixing microfluidic or T-junction systems. However, some limitations of thermostability testing protocols, coupled with the companies' more or less cautious approach to predicting vaccine stability, led to rigorous storage conditions: -15° to -25°C or even -60° to -80°C. Nevertheless, some inventors recently announced their mRNA-LNP based vaccine candidates to be stable at both 25° and 37°C for a week. Within the formulation design space, further optimization of the ionizable lipids should be expected, especially in the direction of increasing their branching and optimizing pKa values, ultimately leading to the second generation of mRNA-LNP COVID-19 vaccines.
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8
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Kim SC, Sekhon SS, Shin WR, Ahn G, Cho BK, Ahn JY, Kim YH. Modifications of mRNA vaccine structural elements for improving mRNA stability and translation efficiency. Mol Cell Toxicol 2021; 18:1-8. [PMID: 34567201 PMCID: PMC8450916 DOI: 10.1007/s13273-021-00171-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2021] [Indexed: 01/15/2023]
Abstract
Background mRNA vaccines hold great potential as therapeutic techniques against viral infections due to their efficacy, safety,
and large-scale production. mRNA vaccines offer flexibility in development as any protein can be produced from
mRNA without altering the production or application process. Objective This review highlights the iterative optimization of mRNA vaccine structural elements that impact the type,
specificity, and intensity of immune responses leading to higher translational potency and intracellular stability. Results Modifying the mRNA structural elements particularly the 5′ cap, 5′-and 3′-untranslated regions (UTRs), the coding region, and polyadenylation tail help reduce the excessive mRNA immunogenicity and consistently improve its
intracellular stability and translational efficiency. Conclusion Further studies regarding mRNA-structural elements and their optimization are needed to create new opportunities
for engineering mRNA vaccines.
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Affiliation(s)
- Sun Chang Kim
- Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 South Korea
| | - Simranjeet Singh Sekhon
- School of Biological Sciences, Chungbuk National University, Chungdae-ro, Seowon-gu, Cheongju, 28644 South Korea
| | - Woo-Ri Shin
- School of Biological Sciences, Chungbuk National University, Chungdae-ro, Seowon-gu, Cheongju, 28644 South Korea.,Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk 28644 South Korea
| | - Gna Ahn
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk 28644 South Korea
| | - Byung-Kwan Cho
- Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 South Korea
| | - Ji-Young Ahn
- School of Biological Sciences, Chungbuk National University, Chungdae-ro, Seowon-gu, Cheongju, 28644 South Korea.,Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk 28644 South Korea
| | - Yang-Hoon Kim
- School of Biological Sciences, Chungbuk National University, Chungdae-ro, Seowon-gu, Cheongju, 28644 South Korea.,Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk 28644 South Korea
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9
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Uddin MN, Roni MA. Challenges of Storage and Stability of mRNA-Based COVID-19 Vaccines. Vaccines (Basel) 2021; 9:1033. [PMID: 34579270 PMCID: PMC8473088 DOI: 10.3390/vaccines9091033] [Citation(s) in RCA: 141] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/08/2021] [Accepted: 09/13/2021] [Indexed: 01/14/2023] Open
Abstract
In December 2019, a new and highly pathogenic coronavirus emerged-coronavirus disease 2019 (COVID-19), a disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), quickly spread throughout the world. In response to this global pandemic, a few vaccines were allowed for emergency use, beginning in November 2020, of which the mRNA-based vaccines by Moderna (Moderna, Cambridge, MA, USA) and BioNTech (BioTech, Mainz, Germany)/Pfizer (Pfizer, New York, NY, USA) have been identified as the most effective ones. The mRNA platform allowed rapid development of vaccines, but their global use is limited by ultracold storage requirements. Most resource-poor countries do not have cold chain storage to execute mass vaccination. Therefore, determining strategies to increase stability of mRNA-based vaccines in relatively higher temperatures can be a game changer to address the current global pandemic and upcoming new waves. In this review, we summarized the current research strategies to enhance stability of the RNA vaccine delivery system.
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Affiliation(s)
| | - Monzurul A. Roni
- College of Medicine, University of Illinois, Peoria, IL 61605, USA
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10
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Minuesa G, Alsina C, Garcia-Martin JA, Oliveros J, Dotu I. MoiRNAiFold: a novel tool for complex in silico RNA design. Nucleic Acids Res 2021; 49:4934-4943. [PMID: 33956139 PMCID: PMC8136780 DOI: 10.1093/nar/gkab331] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/09/2021] [Accepted: 04/21/2021] [Indexed: 12/23/2022] Open
Abstract
Novel tools for in silico design of RNA constructs such as riboregulators are required in order to reduce time and cost to production for the development of diagnostic and therapeutic advances. Here, we present MoiRNAiFold, a versatile and user-friendly tool for de novo synthetic RNA design. MoiRNAiFold is based on Constraint Programming and it includes novel variable types, heuristics and restart strategies for Large Neighborhood Search. Moreover, this software can handle dozens of design constraints and quality measures and improves features for RNA regulation control of gene expression, such as Translation Efficiency calculation. We demonstrate that MoiRNAiFold outperforms any previous software in benchmarking structural RNA puzzles from EteRNA. Importantly, with regard to biologically relevant RNA designs, we focus on RNA riboregulators, demonstrating that the designed RNA sequences are functional both in vitro and in vivo. Overall, we have generated a powerful tool for de novo complex RNA design that we make freely available as a web server (https://moiraibiodesign.com/design/).
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Affiliation(s)
- Gerard Minuesa
- Moirai Biodesign, c/ Baldiri Reixach s/n, Parc Científic de Barcelona (PCB), 08028 Barcelona, Spain
| | - Cristina Alsina
- Moirai Biodesign, c/ Baldiri Reixach s/n, Parc Científic de Barcelona (PCB), 08028 Barcelona, Spain
| | - Juan Antonio Garcia-Martin
- Bioinformatics for Genomics and Proteomics. National Centre for Biotechnology (CNB-CSIC). c/ Darwin 3, 28049 Madrid, Spain
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Universidad Carlos III de Madrid, 28911 Madrid, Spain
| | - Juan Carlos Oliveros
- Bioinformatics for Genomics and Proteomics. National Centre for Biotechnology (CNB-CSIC). c/ Darwin 3, 28049 Madrid, Spain
| | - Ivan Dotu
- Moirai Biodesign, c/ Baldiri Reixach s/n, Parc Científic de Barcelona (PCB), 08028 Barcelona, Spain
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11
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Schoenmaker L, Witzigmann D, Kulkarni JA, Verbeke R, Kersten G, Jiskoot W, Crommelin DJA. mRNA-lipid nanoparticle COVID-19 vaccines: Structure and stability. Int J Pharm 2021; 601:120586. [PMID: 33839230 PMCID: PMC8032477 DOI: 10.1016/j.ijpharm.2021.120586] [Citation(s) in RCA: 620] [Impact Index Per Article: 206.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 02/06/2023]
Abstract
A drawback of the current mRNA-lipid nanoparticle (LNP) COVID-19 vaccines is that they have to be stored at (ultra)low temperatures. Understanding the root cause of the instability of these vaccines may help to rationally improve mRNA-LNP product stability and thereby ease the temperature conditions for storage. In this review we discuss proposed structures of mRNA-LNPs, factors that impact mRNA-LNP stability and strategies to optimize mRNA-LNP product stability. Analysis of mRNA-LNP structures reveals that mRNA, the ionizable cationic lipid and water are present in the LNP core. The neutral helper lipids are mainly positioned in the outer, encapsulating, wall. mRNA hydrolysis is the determining factor for mRNA-LNP instability. It is currently unclear how water in the LNP core interacts with the mRNA and to what extent the degradation prone sites of mRNA are protected through a coat of ionizable cationic lipids. To improve the stability of mRNA-LNP vaccines, optimization of the mRNA nucleotide composition should be prioritized. Secondly, a better understanding of the milieu the mRNA is exposed to in the core of LNPs may help to rationalize adjustments to the LNP structure to preserve mRNA integrity. Moreover, drying techniques, such as lyophilization, are promising options still to be explored.
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Affiliation(s)
- Linde Schoenmaker
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, the Netherlands
| | - Dominik Witzigmann
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; NanoMedicines Innovation Network (NMIN), University of British Columbia, Vancouver, BC, Canada
| | - Jayesh A Kulkarni
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; NanoMedicines Innovation Network (NMIN), University of British Columbia, Vancouver, BC, Canada
| | - Rein Verbeke
- Ghent Research Group on Nanomedicines, Faculty of Pharmacy, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Gideon Kersten
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, the Netherlands; Coriolis Pharma, Fraunhoferstrasse 18b, 82152 Martinsried, Germany
| | - Wim Jiskoot
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, the Netherlands; Coriolis Pharma, Fraunhoferstrasse 18b, 82152 Martinsried, Germany.
| | - Daan J A Crommelin
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Faculty of Science, Utrecht University, Utrecht, the Netherlands.
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12
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Leppek K, Byeon GW, Kladwang W, Wayment-Steele HK, Kerr CH, Xu AF, Kim DS, Topkar VV, Choe C, Rothschild D, Tiu GC, Wellington-Oguri R, Fujii K, Sharma E, Watkins AM, Nicol JJ, Romano J, Tunguz B, Participants E, Barna M, Das R. Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.29.437587. [PMID: 33821271 PMCID: PMC8020971 DOI: 10.1101/2021.03.29.437587] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Therapeutic mRNAs and vaccines are being developed for a broad range of human diseases, including COVID-19. However, their optimization is hindered by mRNA instability and inefficient protein expression. Here, we describe design principles that overcome these barriers. We develop a new RNA sequencing-based platform called PERSIST-seq to systematically delineate in-cell mRNA stability, ribosome load, as well as in-solution stability of a library of diverse mRNAs. We find that, surprisingly, in-cell stability is a greater driver of protein output than high ribosome load. We further introduce a method called In-line-seq, applied to thousands of diverse RNAs, that reveals sequence and structure-based rules for mitigating hydrolytic degradation. Our findings show that "superfolder" mRNAs can be designed to improve both stability and expression that are further enhanced through pseudouridine nucleoside modification. Together, our study demonstrates simultaneous improvement of mRNA stability and protein expression and provides a computational-experimental platform for the enhancement of mRNA medicines.
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Affiliation(s)
- Kathrin Leppek
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Gun Woo Byeon
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Wipapat Kladwang
- Department of Biochemistry, Stanford University, California 94305, USA
| | | | - Craig H Kerr
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Adele F Xu
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Do Soon Kim
- Department of Biochemistry, Stanford University, California 94305, USA
| | - Ved V Topkar
- Program in Biophysics, Stanford University, Stanford, California 94305, USA
| | - Christian Choe
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | - Daphna Rothschild
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Gerald C Tiu
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | | | - Kotaro Fujii
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Eesha Sharma
- Department of Biochemistry, Stanford University, California 94305, USA
| | - Andrew M Watkins
- Department of Biochemistry, Stanford University, California 94305, USA
| | | | - Jonathan Romano
- Eterna Massive Open Laboratory
- Department of Computer Science and Engineering, State University of New York at Buffalo, Buffalo, New York, 14260, USA
| | - Bojan Tunguz
- Department of Biochemistry, Stanford University, California 94305, USA
| | | | - Maria Barna
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University, California 94305, USA
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13
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Blakney AK, Ip S, Geall AJ. An Update on Self-Amplifying mRNA Vaccine Development. Vaccines (Basel) 2021; 9:97. [PMID: 33525396 PMCID: PMC7911542 DOI: 10.3390/vaccines9020097] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/21/2021] [Accepted: 01/23/2021] [Indexed: 12/13/2022] Open
Abstract
This review will explore the four major pillars required for design and development of an saRNA vaccine: Antigen design, vector design, non-viral delivery systems, and manufacturing (both saRNA and lipid nanoparticles (LNP)). We report on the major innovations, preclinical and clinical data reported in the last five years and will discuss future prospects.
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Affiliation(s)
- Anna K. Blakney
- Michael Smith Laboratories, School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Shell Ip
- Precision NanoSystems Inc., Vancouver, BC V6P 6T7, Canada; (S.I.); (A.J.G.)
| | - Andrew J. Geall
- Precision NanoSystems Inc., Vancouver, BC V6P 6T7, Canada; (S.I.); (A.J.G.)
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