1
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Monroe J, Eyler DE, Mitchell L, Deb I, Bojanowski A, Srinivas P, Dunham CM, Roy B, Frank AT, Koutmou KS. N1-Methylpseudouridine and pseudouridine modifications modulate mRNA decoding during translation. Nat Commun 2024; 15:8119. [PMID: 39284850 PMCID: PMC11405884 DOI: 10.1038/s41467-024-51301-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/02/2024] [Indexed: 09/20/2024] Open
Abstract
The ribosome utilizes hydrogen bonding between mRNA codons and aminoacyl-tRNAs to ensure rapid and accurate protein production. Chemical modification of mRNA nucleobases can adjust the strength and pattern of this hydrogen bonding to alter protein synthesis. We investigate how the N1-methylpseudouridine (m1Ψ) modification, commonly incorporated into therapeutic and vaccine mRNA sequences, influences the speed and fidelity of translation. We find that m1Ψ does not substantially change the rate constants for amino acid addition by cognate tRNAs or termination by release factors. However, we also find that m1Ψ can subtly modulate the fidelity of amino acid incorporation in a codon-position and tRNA dependent manner in vitro and in human cells. Our computational modeling shows that altered energetics of mRNA:tRNA interactions largely account for the context dependence of the low levels of miscoding we observe on Ψ and m1Ψ containing codons. The outcome of translation on modified mRNA bases is thus governed by the sequence context in which they occur.
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Affiliation(s)
- Jeremy Monroe
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Daniel E Eyler
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Lili Mitchell
- RNA and Genome Editing, New England Biolabs Inc., Ipswich, MA, USA
| | - Indrajit Deb
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
| | | | - Pooja Srinivas
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | | | - Bijoyita Roy
- RNA and Genome Editing, New England Biolabs Inc., Ipswich, MA, USA
| | - Aaron T Frank
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
- Computational Chemistry, Arrakis Therapeutics, Waltham, MA, USA
| | - Kristin S Koutmou
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
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2
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Zhang P, Wang Y, Jiang J, Yang C, Liu X, Lei T, Meng X, Yang J, Ding P, Chen J, Li Q. Macrophage manufacturing and engineering with 5'-Cap1 and N1-methylpseudouridine-modified mRNA. Mol Ther Methods Clin Dev 2024; 32:101307. [PMID: 39229455 PMCID: PMC11369376 DOI: 10.1016/j.omtm.2024.101307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 07/26/2024] [Indexed: 09/05/2024]
Abstract
Macrophage-based cell therapeutics is an emerging modality to treat cancer and repair tissue damage. A reproducible manufacturing and engineering process is central to fulfilling their therapeutic potential. Here, we establish a robust macrophage-manufacturing platform (Mo-Mac) and demonstrate that macrophage functionality can be enhanced by N1-methylpseudouridine (m1Ψ)-modified mRNA. Using single-cell transcriptomic analysis as an unbiased approach, we found that >90% cells in the final product were macrophages while the rest primarily comprised T cells, B cells, natural killer cells, promyelocytes, promonocytes, and hematopoietic stem cells. This analysis also guided the development of flow-cytometry strategies to assess cell compositions in the manufactured product to meet requirements by the National Medical Products Administration. To modulate macrophage functionality, as an illustrative example we examined whether the engulfment capability of macrophages could be enhanced by mRNA technology. We found that efferocytosis was increased in vitro when macrophages were electroporated with m1Ψ-modified mRNA encoding CD300LF (CD300LF-mRNA-macrophage). Consistently, in a mouse model of acute liver failure, CD300LF-mRNA-macrophages facilitated organ recovery from acetaminophen-induced hepatotoxicity. These results demonstrate a GMP-compliant macrophage-manufacturing process and indicate that macrophages can be engineered by versatile mRNA technology to achieve therapeutic goals.
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Affiliation(s)
- Peixuan Zhang
- Departments of Obstetrics & Gynecology and Pediatrics, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Center of Growth, Metabolism and Aging, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yantai Wang
- Department of General Surgery, Breast Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Jinfeng Jiang
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu 610500, Sichuan, China
| | - Chao Yang
- Departments of Obstetrics & Gynecology and Pediatrics, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Center of Growth, Metabolism and Aging, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, Sichuan, China
| | - Xianxia Liu
- Division of Cell Manufacturing, Sichuan Cunde Therapeutics, Chengdu 610093, Sichuan, China
| | - Tingjun Lei
- Division of Cell Manufacturing, Sichuan Cunde Therapeutics, Chengdu 610093, Sichuan, China
| | - Xiangjun Meng
- Division of Cell Manufacturing, Sichuan Cunde Therapeutics, Chengdu 610093, Sichuan, China
| | - Jihong Yang
- Division of Cell Manufacturing, Sichuan Cunde Therapeutics, Chengdu 610093, Sichuan, China
| | - Ping Ding
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu 610500, Sichuan, China
| | - Jie Chen
- Department of General Surgery, Breast Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Qintong Li
- Departments of Obstetrics & Gynecology and Pediatrics, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Center of Growth, Metabolism and Aging, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, Sichuan, China
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3
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Smith A, Zhang I, Trang P, Liu F. Engineering of RNase P Ribozymes for Therapy against Human Cytomegalovirus Infection. Viruses 2024; 16:1196. [PMID: 39205170 PMCID: PMC11360822 DOI: 10.3390/v16081196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/20/2024] [Accepted: 07/22/2024] [Indexed: 09/04/2024] Open
Abstract
Nucleic acid-based gene interference and editing strategies, such as antisense oligonucleotides, ribozymes, RNA interference (RNAi), and CRISPR/Cas9 coupled with guide RNAs, are exciting research tools and show great promise for clinical applications in treating various illnesses. RNase P ribozymes have been engineered for therapeutic applications against human viruses such as human cytomegalovirus (HCMV). M1 ribozyme, the catalytic RNA subunit of RNase P from Escherichia coli, can be converted into a sequence-specific endonuclease, M1GS ribozyme, which is capable of hydrolyzing an mRNA target base-pairing with the guide sequence. M1GS RNAs have been shown to hydrolyze essential HCMV mRNAs and block viral progeny production in virus-infected cell cultures. Furthermore, RNase P ribozyme variants with enhanced hydrolyzing activity can be generated by employing in vitro selection procedures and exhibit better ability in suppressing HCMV gene expression and replication in cultured cells. Additional studies have also examined the antiviral activity of RNase P ribozymes in mice in vivo. Using cytomegalovirus infection as an example, this review summarizes the principles underlying RNase P ribozyme-mediated gene inactivation, presents recent progress in engineering RNase P ribozymes for applications in vitro and in mice, and discusses the prospects of using M1GS technology for therapeutic applications against HCMV as well as other pathogenic viruses.
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Affiliation(s)
- Adam Smith
- Program in Comparative Biochemistry, University of California, Berkeley, CA 94720, USA
- School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Isadora Zhang
- School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Phong Trang
- School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Fenyong Liu
- Program in Comparative Biochemistry, University of California, Berkeley, CA 94720, USA
- School of Public Health, University of California, Berkeley, CA 94720, USA
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4
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Sioud M, Juzeniene A, Sæbøe-Larssen S. Exploring the Impact of mRNA Modifications on Translation Efficiency and Immune Tolerance to Self-Antigens. Vaccines (Basel) 2024; 12:624. [PMID: 38932353 PMCID: PMC11209393 DOI: 10.3390/vaccines12060624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Therapeutic modified mRNAs are being developed for a broad range of human diseases. However, the impact of potential miscoding of modified mRNAs on self-tolerance remains unknown. Additionally, more studies are needed to explore the effects of nucleoside alkylation on translation. While all six tested modifications are tolerated as substrates by T7 RNA polymerase and inhibited mRNA immunogenicity, the translation efficiency varied significantly depending on the type of modification. In contrast to methylation, ethylation at the N1 position of pseudouridine (Ψ) hindered translation, suggesting that the C5-C1' glycosidic bond alone is not a critical element for high translation. Inhibition of mRNA translation was also observed with 5-methoxyuridine modification. However, this inhibition was partially alleviated through the optimization of mRNA coding sequences. BALB/c mice immunized with syngeneic ψ-modified mRNA encoding for Wilms' tumor antigen-1 (WT1) developed a low but significant level of anti-WT1 IgG antibodies compared to those immunized with either unmodified or N1-methyl ψ-modified mRNA. Overall, the data indicate that adding a simple ethyl group (-CH2CH3) at the N1 position of ψ has a major negative effect on translation despite its reduced immunogenicity. Additionally, mRNA containing Ψ may alter translation fidelity at certain codons, which could lead to a breakdown of immune tolerance to self-antigens. This concern should be taken into account during gene replacement therapies, although it could benefit mRNA-based vaccines by generating a diverse repertoire of antigens.
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Affiliation(s)
- Mouldy Sioud
- Department of Cancer Immunology, Oslo University Hospital, Radiumhospitalet, Ullernchausseen 70, 0379 Oslo, Norway
| | - Asta Juzeniene
- Department of Radiation Biology, Oslo University Hospital, Radiumhospitalet, Ullernchausseen 70, 0379 Oslo, Norway;
| | - Stein Sæbøe-Larssen
- Department of cellular Therapy, Oslo University Hospital, Radiumhospitalet, Ullernchausseen 70, 0379 Oslo, Norway;
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5
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Malireddi RKS, Sharma BR, Kanneganti TD. Innate Immunity in Protection and Pathogenesis During Coronavirus Infections and COVID-19. Annu Rev Immunol 2024; 42:615-645. [PMID: 38941608 PMCID: PMC11373870 DOI: 10.1146/annurev-immunol-083122-043545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
The COVID-19 pandemic was caused by the recently emerged β-coronavirus SARS-CoV-2. SARS-CoV-2 has had a catastrophic impact, resulting in nearly 7 million fatalities worldwide to date. The innate immune system is the first line of defense against infections, including the detection and response to SARS-CoV-2. Here, we discuss the innate immune mechanisms that sense coronaviruses, with a focus on SARS-CoV-2 infection and how these protective responses can become detrimental in severe cases of COVID-19, contributing to cytokine storm, inflammation, long-COVID, and other complications. We also highlight the complex cross talk among cytokines and the cellular components of the innate immune system, which can aid in viral clearance but also contribute to inflammatory cell death, cytokine storm, and organ damage in severe COVID-19 pathogenesis. Furthermore, we discuss how SARS-CoV-2 evades key protective innate immune mechanisms to enhance its virulence and pathogenicity, as well as how innate immunity can be therapeutically targeted as part of the vaccination and treatment strategy. Overall, we highlight how a comprehensive understanding of innate immune mechanisms has been crucial in the fight against SARS-CoV-2 infections and the development of novel host-directed immunotherapeutic strategies for various diseases.
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Affiliation(s)
- R K Subbarao Malireddi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA;
| | - Bhesh Raj Sharma
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA;
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6
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Ho LLY, Schiess GHA, Miranda P, Weber G, Astakhova K. Pseudouridine and N1-methylpseudouridine as potent nucleotide analogues for RNA therapy and vaccine development. RSC Chem Biol 2024; 5:418-425. [PMID: 38725905 PMCID: PMC11078203 DOI: 10.1039/d4cb00022f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/10/2024] [Indexed: 05/12/2024] Open
Abstract
Modified nucleosides are integral to modern drug development, serving as crucial building blocks for creating safer, more potent, and more precisely targeted therapeutic interventions. Nucleobase modifications often confer antiviral and anti-cancer activity as monomers. When incorporated into nucleic acid oligomers, they increase stability against degradation by enzymes, enhancing the drugs' lifespan within the body. Moreover, modification strategies can mitigate potential toxic effects and reduce immunogenicity, making drugs safer and better tolerated. Particularly, N1-methylpseudouridine modification improved the efficacy of the mRNA coding for spike protein of COVID-19. This became a crucial step for developing COVID-19 vaccine applied during the 2020 pandemic. This makes N1-methylpseudouridine, and its "parent" analogue pseudouridine, potent nucleotide analogues for future RNA therapy and vaccine development. This review focuses on the structure and properties of pseudouridine and N1-methylpseudouridine. RNA has a greater structural versatility, different conformation, and chemical reactivity than DNA. Watson-Crick pairing is not strictly followed by RNA that has more unusual base pairs and base-triplets. This requires detailed structural studies and structure-activity relationship analyses for RNA, also when modifications are incorporated. Recent successes in this direction are revised in this review. We describe recent successes with using pseudouridine and N1-methylpseudouridine in mRNA drug candidates. We also highlight remaining challenges that need to be solved to develop new mRNA vaccines and therapies.
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Affiliation(s)
- Lyana L Y Ho
- Technical University of Denmark 2800 Kongens Lyngby Denmark
- The Hong Kong Polytechnic University 11 Yuk Choi Rd Hung Hom Hong Kong
| | - Gabriel H A Schiess
- Departamento de Física, Universidade Federal de Minas Gerais Belo Horizonte MG Brazil
| | - Pâmella Miranda
- Departamento de Física, Universidade Federal de Minas Gerais Belo Horizonte MG Brazil
- Programa Interunidades de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais Belo Horizonte MG Brazil
| | - Gerald Weber
- Departamento de Física, Universidade Federal de Minas Gerais Belo Horizonte MG Brazil
| | - Kira Astakhova
- Technical University of Denmark 2800 Kongens Lyngby Denmark
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7
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Zhang C, Wei G, Zhou N, Wang Y, Feng J, Wang X, Zhang A, Chen K. Systematic Engineering of Escherichia coli for Efficient Production of Pseudouridine from Glucose and Uracil. ACS Synth Biol 2024; 13:1303-1311. [PMID: 38529630 DOI: 10.1021/acssynbio.4c00028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
In this study, we proposed a biological approach to efficiently produce pseudouridine (Ψ) from glucose and uracil in vivo using engineered Escherichia coli. By screening host strains and core enzymes, E. coli MG1655 overexpressing Ψ monophosphate (ΨMP) glycosidase and ΨMP phosphatase was obtained, which displayed the highest Ψ concentration. Then, optimization of the RBS sequences, enhancement of ribose 5-phosphate supply in the cells, and overexpression of the membrane transport protein UraA were investigated. Finally, fed-batch fermentation of Ψ in a 5 L fermentor can reach 27.5 g/L with a yield of 89.2 mol % toward uracil and 25.6 mol % toward glucose within 48 h, both of which are the highest to date. In addition, the Ψ product with a high purity of 99.8% can be purified from the fermentation broth after crystallization. This work provides an efficient and environmentally friendly protocol for allowing for the possibility of Ψ bioproduction on an industrial scale.
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Affiliation(s)
- Chi Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Guoguang Wei
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Ning Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Yingying Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Jia Feng
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Xin Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Alei Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
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8
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Gilbert WV. Recent developments, opportunities, and challenges in the study of mRNA pseudouridylation. RNA (NEW YORK, N.Y.) 2024; 30:530-536. [PMID: 38531650 PMCID: PMC11019745 DOI: 10.1261/rna.079975.124] [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: 01/30/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
Pseudouridine is an abundant mRNA modification found in diverse organisms ranging from bacteria and viruses to multicellular plants and humans. New developments in pseudouridine profiling provide quantitative tools to map mRNA pseudouridylation sites. Sparse biochemical studies establish the potential for mRNA pseudouridylation to affect most stages of the mRNA life cycle from birth to death. This recent progress sets the stage for deeper investigations into the molecular and cellular functions of specific mRNA pseudouridines, including in disease.
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Affiliation(s)
- Wendy V Gilbert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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9
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Teng M, Xia ZJ, Lo N, Daud K, He HH. Assembling the RNA therapeutics toolbox. MEDICAL REVIEW (2021) 2024; 4:110-128. [PMID: 38680684 PMCID: PMC11046573 DOI: 10.1515/mr-2023-0062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/29/2024] [Indexed: 05/01/2024]
Abstract
From the approval of COVID-19 mRNA vaccines to the 2023 Nobel Prize awarded for nucleoside base modifications, RNA therapeutics have entered the spotlight and are transforming drug development. While the term "RNA therapeutics" has been used in various contexts, this review focuses on treatments that utilize RNA as a component or target RNA for therapeutic effects. We summarize the latest advances in RNA-targeting tools and RNA-based technologies, including but not limited to mRNA, antisense oligos, siRNAs, small molecules and RNA editors. We focus on the mechanisms of current FDA-approved therapeutics but also provide a discussion on the upcoming workforces. The clinical utility of RNA-based therapeutics is enabled not only by the advances in RNA technologies but in conjunction with the significant improvements in chemical modifications and delivery platforms, which are also briefly discussed in the review. We summarize the latest RNA therapeutics based on their mechanisms and therapeutic effects, which include expressing proteins for vaccination and protein replacement therapies, degrading deleterious RNA, modulating transcription and translation efficiency, targeting noncoding RNAs, binding and modulating protein activity and editing RNA sequences and modifications. This review emphasizes the concept of an RNA therapeutic toolbox, pinpointing the readers to all the tools available for their desired research and clinical goals. As the field advances, the catalog of RNA therapeutic tools continues to grow, further allowing researchers to combine appropriate RNA technologies with suitable chemical modifications and delivery platforms to develop therapeutics tailored to their specific clinical challenges.
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Affiliation(s)
- Mona Teng
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ziting Judy Xia
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Nicholas Lo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Kashif Daud
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Housheng Hansen He
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
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10
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Li L. "Goldilocks Modifications" for mRNA Therapeutics Won the Nobel Prize. Nucleic Acid Ther 2024; 34:1-3. [PMID: 38285523 PMCID: PMC11302211 DOI: 10.1089/nat.2023.0062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 12/12/2023] [Indexed: 01/31/2024] Open
Affiliation(s)
- Li Li
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, Massachusetts, USA
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11
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Dutta N, Sarzynska J, Deb I, Lahiri A. Predicting nearest neighbor free energies of modified RNA with LIE: results for pseudouridine and N1-methylpseudouridine within RNA duplexes. Phys Chem Chem Phys 2024; 26:992-999. [PMID: 38088148 DOI: 10.1039/d3cp02442c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Pseudouridine (Ψ) and N1-methylpseudouridine (m1Ψ) are among the key modifications in the field of mRNA therapeutics and vaccine research. The accuracy of the design and development of therapeutic RNAs containing such modifications depends on the accuracy of the secondary structure prediction, which in turn depends on the nearest neighbor (NN) thermodynamic parameters for the standard and modified residues. Here, we propose a simple approach based on molecular dynamics simulations and linear interaction energy (LIE) approximation that is able to predict the NN free energy parameters for U-A, Ψ-A and m1Ψ-A pairs in reasonable agreement with the recent experimental reports. We report the NN thermodynamic parameters for different U, Ψ and m1Ψ base pairs, which might be helpful for a deeper understanding of the effect of these modifications in RNA. The predicted NN free energy parameters in this study are able to closely reproduce the folding free energies of duplexes containing internal Ψ for which the thermodynamic data were available. Additionally, we report the predicted folding free energies for the duplexes containing internal m1Ψ.
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Affiliation(s)
- Nivedita Dutta
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata 700009, West Bengal, India.
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan 61-704, Poland
| | - Indrajit Deb
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata 700009, West Bengal, India.
| | - Ansuman Lahiri
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata 700009, West Bengal, India.
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12
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Schievelbein MJ, Resende C, Glennon MM, Kerosky M, Brown JA. Global RNA modifications to the MALAT1 triple helix differentially affect thermostability and weaken binding to METTL16. J Biol Chem 2024; 300:105548. [PMID: 38092148 PMCID: PMC10805700 DOI: 10.1016/j.jbc.2023.105548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 12/28/2023] Open
Abstract
Therapeutic mRNAs are generated using modified nucleotides, namely N1-methylpseudouridine (m1Ψ) triphosphate, so that the mRNA evades detection by the immune system. RNA modifications, even at a single-nucleotide position, perturb RNA structure, although it is not well understood how structure and function is impacted by globally modified RNAs. Therefore, we examined the metastasis-associated lung adenocarcinoma transcript 1 triple helix, a highly structured stability element that includes single-, double-, and triple-stranded RNA, globally modified with N6-methyladenosine (m6A), pseudouridine (Ψ), or m1Ψ. UV thermal denaturation assays showed that m6A destabilizes both the Hoogsteen and Watson-Crick faces of the RNA by ∼20 °C, Ψ stabilizes the Hoogsteen and Watson-Crick faces of the RNA by ∼12 °C, and m1Ψ has minimal effect on the stability of the Hoogsteen face of the RNA but increases the stability of the Watson-Crick face by ∼9 °C. Native gel-shift assays revealed that binding of the methyltransferase-like protein 16 to the metastasis-associated lung adenocarcinoma transcript 1 triple helix was weakened by at least 8-, 99-, and 23-fold, respectively, when RNA is globally modified with m6A, Ψ, or m1Ψ. These results demonstrate that a more thermostable RNA structure does not lead to tighter RNA-protein interactions, thereby highlighting the regulatory power of RNA modifications by multiple means.
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Affiliation(s)
- Mika J Schievelbein
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Carlos Resende
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Madeline M Glennon
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Matthew Kerosky
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA.
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13
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Mulroney TE, Pöyry T, Yam-Puc JC, Rust M, Harvey RF, Kalmar L, Horner E, Booth L, Ferreira AP, Stoneley M, Sawarkar R, Mentzer AJ, Lilley KS, Smales CM, von der Haar T, Turtle L, Dunachie S, Klenerman P, Thaventhiran JED, Willis AE. N 1-methylpseudouridylation of mRNA causes +1 ribosomal frameshifting. Nature 2024; 625:189-194. [PMID: 38057663 PMCID: PMC10764286 DOI: 10.1038/s41586-023-06800-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 10/31/2023] [Indexed: 12/08/2023]
Abstract
In vitro-transcribed (IVT) mRNAs are modalities that can combat human disease, exemplified by their use as vaccines for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). IVT mRNAs are transfected into target cells, where they are translated into recombinant protein, and the biological activity or immunogenicity of the encoded protein exerts an intended therapeutic effect1,2. Modified ribonucleotides are commonly incorporated into therapeutic IVT mRNAs to decrease their innate immunogenicity3-5, but their effects on mRNA translation fidelity have not been fully explored. Here we demonstrate that incorporation of N1-methylpseudouridine into mRNA results in +1 ribosomal frameshifting in vitro and that cellular immunity in mice and humans to +1 frameshifted products from BNT162b2 vaccine mRNA translation occurs after vaccination. The +1 ribosome frameshifting observed is probably a consequence of N1-methylpseudouridine-induced ribosome stalling during IVT mRNA translation, with frameshifting occurring at ribosome slippery sequences. However, we demonstrate that synonymous targeting of such slippery sequences provides an effective strategy to reduce the production of frameshifted products. Overall, these data increase our understanding of how modified ribonucleotides affect the fidelity of mRNA translation, and although there are no adverse outcomes reported from mistranslation of mRNA-based SARS-CoV-2 vaccines in humans, these data highlight potential off-target effects for future mRNA-based therapeutics and demonstrate the requirement for sequence optimization.
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Affiliation(s)
| | - Tuija Pöyry
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | | | - Maria Rust
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | | | - Lajos Kalmar
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Emily Horner
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Lucy Booth
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | | | - Mark Stoneley
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | | | | | - Kathryn S Lilley
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - C Mark Smales
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, UK
- National Institute for Bioprocessing Research and Training, University College Dublin, Foster Avenue, Mount Merrion, Dublin, Ireland
| | - Tobias von der Haar
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Susanna Dunachie
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NDM Centre for Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Paul Klenerman
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK.
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14
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Metkar M, Pepin CS, Moore MJ. Tailor made: the art of therapeutic mRNA design. Nat Rev Drug Discov 2024; 23:67-83. [PMID: 38030688 DOI: 10.1038/s41573-023-00827-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2023] [Indexed: 12/01/2023]
Abstract
mRNA medicine is a new and rapidly developing field in which the delivery of genetic information in the form of mRNA is used to direct therapeutic protein production in humans. This approach, which allows for the quick and efficient identification and optimization of drug candidates for both large populations and individual patients, has the potential to revolutionize the way we prevent and treat disease. A key feature of mRNA medicines is their high degree of designability, although the design choices involved are complex. Maximizing the production of therapeutic proteins from mRNA medicines requires a thorough understanding of how nucleotide sequence, nucleotide modification and RNA structure interplay to affect translational efficiency and mRNA stability. In this Review, we describe the principles that underlie the physical stability and biological activity of mRNA and emphasize their relevance to the myriad considerations that factor into therapeutic mRNA design.
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15
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Pan S, Fan R, Han B, Tong A, Guo G. The potential of mRNA vaccines in cancer nanomedicine and immunotherapy. Trends Immunol 2024; 45:20-31. [PMID: 38142147 DOI: 10.1016/j.it.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/25/2023]
Abstract
Owing to their outstanding performance against COVID-19, mRNA vaccines have brought great hope for combating various incurable diseases, including cancer. Differences in the encoded proteins result in different molecular and cellular mechanisms of mRNA vaccines. With the rapid development of nanotechnology and molecular medicine, personalized antigen-encoding mRNA vaccines that enhance antigen presentation can trigger effective immune responses and prevent off-target toxicities. Herein, we review new insights into the influence of encoded antigens, cytokines, and other functional proteins on the mechanisms of mRNA vaccines. We also highlight the importance of delivery systems and chemical modifications for mRNA translation efficiency, stability, and targeting, and we discuss the potential problems and application prospects of mRNA vaccines as versatile tools for combating cancer.
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Affiliation(s)
- Shulin Pan
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Rangrang Fan
- Department of Neurosurgery and Institute of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Bo Han
- School of Pharmacy, Shihezi University, and Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Shihezi, 832002, China
| | - Aiping Tong
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Gang Guo
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
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16
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Prokhorova D, Matveeva A, Zakabunin A, Ryabchenko A, Stepanov G. Influence of N1-Methylpseudouridine in Guide RNAs on CRISPR/Cas9 Activity. Int J Mol Sci 2023; 24:17116. [PMID: 38069437 PMCID: PMC10707292 DOI: 10.3390/ijms242317116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
At present, there are many strategies to improve the activity of CRISPR/Cas9. A well-known and effective approach is guide RNA modification. Many chemical guide RNA modifications have been studied, whereas naturally occurring RNA modifications are largely unexplored. N1-methylpseudouridine (m1Ψ) is an RNA base modification widely used in mRNA therapy, and it holds great promise for application in genome editing systems. The present study focuses on investigating the effect of N1-methylpseudouridine on the functioning of CRISPR/Cas9. In vitro cleavage assays helped determine the level of m1Ψ guide RNA modification that is sufficient to cleave the target substrate. By analyzing FAM-labeled dsDNA substrate cleavage, we calculated the kinetic parameters and the specificity scores of modified guide RNAs. Neon transfection and digital PCR enabled us to assess the activity of modified guide RNAs in mammalian cells. Our study shows that the presence of m1Ψ in guide RNAs can help preserve on-target genome editing while significantly reducing the off-target effects of CRISPR/Cas9 in vitro. We also demonstrate that Cas9 complexes with guide RNAs containing m1Ψ allow for genome editing in human cells. Thus, the incorporation of m1Ψ into guide RNAs supports CRISPR/Cas9 activity both in vitro and in cells.
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Affiliation(s)
| | | | | | | | - Grigory Stepanov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.P.); (A.Z.)
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17
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Monziani A, Ulitsky I. Noncoding snoRNA host genes are a distinct subclass of long noncoding RNAs. Trends Genet 2023; 39:908-923. [PMID: 37783604 DOI: 10.1016/j.tig.2023.09.001] [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: 07/17/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 10/04/2023]
Abstract
Mammalian genomes are pervasively transcribed into different noncoding (nc)RNA classes, each one with its own hallmarks and exceptions. Some of them are nested into each other, such as host genes for small nucleolar RNAs (snoRNAs), which were long believed to simply act as molecular containers strictly facilitating snoRNA biogenesis. However, recent findings show that noncoding snoRNA host genes (ncSNHGs) display features different from those of 'regular' long ncRNAs (lncRNAs) and, more importantly, they can exert independent and unrelated functions to those of the encoded snoRNAs. Here, we review and summarize past and recent evidence that ncSNHGs form a defined subclass among the plethora of lncRNAs, and discuss future research that can further elucidate their biological relevance.
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Affiliation(s)
- Alan Monziani
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, 7610001 Rehovot, Israel.
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18
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Kramer NJ, Prakash G, Isaac RS, Choquet K, Soto I, Petrova B, Merens HE, Kanarek N, Churchman LS. Regulators of mitonuclear balance link mitochondrial metabolism to mtDNA expression. Nat Cell Biol 2023; 25:1575-1589. [PMID: 37770567 PMCID: PMC11370000 DOI: 10.1038/s41556-023-01244-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 08/29/2023] [Indexed: 09/30/2023]
Abstract
Mitochondrial oxidative phosphorylation (OXPHOS) complexes are assembled from proteins encoded by both nuclear and mitochondrial DNA. These dual-origin enzymes pose a complex gene regulatory challenge for cells requiring coordinated gene expression across organelles. To identify genes involved in dual-origin protein complex synthesis, we performed fluorescence-activated cell-sorting-based genome-wide screens analysing mutant cells with unbalanced levels of mitochondrial- and nuclear-encoded subunits of Complex IV. We identified genes involved in OXPHOS biogenesis, including two uncharacterized genes: PREPL and NME6. We found that PREPL specifically impacts Complex IV biogenesis by acting at the intersection of mitochondrial lipid metabolism and protein synthesis, whereas NME6, an uncharacterized nucleoside diphosphate kinase, controls OXPHOS biogenesis through multiple mechanisms reliant on its NDPK domain. Firstly, NME6 forms a complex with RCC1L, which together perform nucleoside diphosphate kinase activity to maintain local mitochondrial pyrimidine triphosphate levels essential for mitochondrial RNA abundance. Secondly, NME6 modulates the activity of mitoribosome regulatory complexes, altering mitoribosome assembly and mitochondrial RNA pseudouridylation. Taken together, we propose that NME6 acts as a link between compartmentalized mitochondrial metabolites and mitochondrial gene expression.
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Affiliation(s)
- Nicholas J Kramer
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Gyan Prakash
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - R Stefan Isaac
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Karine Choquet
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Iliana Soto
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Boryana Petrova
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hope E Merens
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Naama Kanarek
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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19
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Wang YS, Kumari M, Chen GH, Hong MH, Yuan JPY, Tsai JL, Wu HC. mRNA-based vaccines and therapeutics: an in-depth survey of current and upcoming clinical applications. J Biomed Sci 2023; 30:84. [PMID: 37805495 PMCID: PMC10559634 DOI: 10.1186/s12929-023-00977-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 09/29/2023] [Indexed: 10/09/2023] Open
Abstract
mRNA-based drugs have tremendous potential as clinical treatments, however, a major challenge in realizing this drug class will promise to develop methods for safely delivering the bioactive agents with high efficiency and without activating the immune system. With regard to mRNA vaccines, researchers have modified the mRNA structure to enhance its stability and promote systemic tolerance of antigenic presentation in non-inflammatory contexts. Still, delivery of naked modified mRNAs is inefficient and results in low levels of antigen protein production. As such, lipid nanoparticles have been utilized to improve delivery and protect the mRNA cargo from extracellular degradation. This advance was a major milestone in the development of mRNA vaccines and dispelled skepticism about the potential of this technology to yield clinically approved medicines. Following the resounding success of mRNA vaccines for COVID-19, many other mRNA-based drugs have been proposed for the treatment of a variety of diseases. This review begins with a discussion of mRNA modifications and delivery vehicles, as well as the factors that influence administration routes. Then, we summarize the potential applications of mRNA-based drugs and discuss further key points pertaining to preclinical and clinical development of mRNA drugs targeting a wide range of diseases. Finally, we discuss the latest market trends and future applications of mRNA-based drugs.
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Affiliation(s)
- Yu-Shiuan Wang
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Monika Kumari
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Guan-Hong Chen
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11571, Taiwan
| | - Ming-Hsiang Hong
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11571, Taiwan
| | - Joyce Pei-Yi Yuan
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11571, Taiwan
| | - Jui-Ling Tsai
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Han-Chung Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan.
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11571, Taiwan.
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20
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Martínez J, Lampaya V, Larraga A, Magallón H, Casabona D. Purification of linearized template plasmid DNA decreases double-stranded RNA formation during IVT reaction. Front Mol Biosci 2023; 10:1248511. [PMID: 37842641 PMCID: PMC10570549 DOI: 10.3389/fmolb.2023.1248511] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/19/2023] [Indexed: 10/17/2023] Open
Abstract
After the COVID-19 pandemic, messenger RNA (mRNA) has revolutionized traditional vaccine manufacturing. With the increasing number of RNA-based therapeutics, valuable new scientific insights into these molecules have emerged. One fascinating area of study is the formation of double-stranded RNA (dsRNA) during in vitro transcription (IVT) which is considered a significant impurity, as it has been identified as a major trigger in the cellular immune response pathway. Therefore, there is a growing importance placed to develop and optimize purification processes for the removal of this by-product. Traditionally, efforts have primarily focused on mRNA purification after IVT through chromatographic separations, with anion exchange and reverse phase chromatography emerging as effective tools for this purpose. However, to the best of our knowledge, the influence and significance of the quality of the linearized plasmid have not been thoroughly investigated. Plasmids production involves the growth of bacterial cultures, bacterial harvesting and lysis, and multiple filtration steps for plasmid DNA purification. The inherent complexity of these molecules, along with the multitude of purification steps involved in their processing, including the subsequent linearization and the less-developed purification techniques for linearized plasmids, often result in inconsistent batches with limited control over by-products such as dsRNA. This study aims to demonstrate how the purification process employed for linearized plasmids can impact the formation of dsRNA. Several techniques for the purification of linearized plasmids based on both, resin filtration and chromatographic separations, have been studied. As a result of that, we have optimized a chromatographic method for purifying linearized plasmids using monolithic columns with C4 chemistry (butyl chains located in the surface of the particles), which has proven successful for mRNAs of various sizes. This chromatographic separation facilitates the generation of homogeneous linearized plasmids, leading to mRNA batches with lower levels of dsRNA during subsequent IVT processes. This finding reveals that dsRNA formation is influenced not only by RNA polymerase and IVT conditions but also by the quality of the linearized template. The results suggest that plasmid impurities may contribute to the production of dsRNA by providing additional templates that can be transcribed into sequences that anneal with the mRNA molecules. This highlights the importance of considering the quality of plasmid purification in relation to dsRNA generation during transcription. Further investigation is needed to fully understand the mechanisms and implications of plasmid-derived dsRNA. This discovery could shift the focus in mRNA vaccine production, placing more emphasis on the purification of linearized plasmids and potentially saving, in some instances, a purification step for mRNA following IVT.
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Affiliation(s)
| | | | | | | | - Diego Casabona
- RNA Synthesis and Development Department, Certest Pharma, Certest Biotec, Zaragoza, Spain
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21
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Niu D, Wu Y, Lian J. Circular RNA vaccine in disease prevention and treatment. Signal Transduct Target Ther 2023; 8:341. [PMID: 37691066 PMCID: PMC10493228 DOI: 10.1038/s41392-023-01561-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 06/02/2023] [Accepted: 07/09/2023] [Indexed: 09/12/2023] Open
Abstract
CircRNAs are a class of single-stranded RNAs with covalently linked head-to-tail topology. In the decades since its initial discovery, their biogenesis, regulation, and function have rapidly disclosed, permitting a better understanding and adoption of them as new tools for medical applications. With the development of biotechnology and molecular medicine, artificial circRNAs have been engineered as a novel class of vaccines for disease treatment and prevention. Unlike the linear mRNA vaccine which applications were limited by its instability, inefficiency, and innate immunogenicity, circRNA vaccine which incorporate internal ribosome entry sites (IRESs) and open reading frame (ORF) provides an improved approach to RNA-based vaccination with safety, stability, simplicity of manufacture, and scalability. However, circRNA vaccines are at an early stage, and their optimization, delivery and applications require further development and evaluation. In this review, we comprehensively describe circRNA vaccine, including their history and superiority. We also summarize and discuss the current methodological research for circRNA vaccine preparation, including their design, synthesis, and purification. Finally, we highlight the delivery options of circRNA vaccine and its potential applications in diseases treatment and prevention. Considering their unique high stability, low immunogenicity, protein/peptide-coding capacity and special closed-loop construction, circRNA vaccine, and circRNA-based therapeutic platforms may have superior application prospects in a broad range of diseases.
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Affiliation(s)
- Dun Niu
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), 400038, Chongqing, China
- Department of Clinical Biochemistry, Army Medical University (Third Military Medical University), 400038, Chongqing, China
| | - Yaran Wu
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), 400038, Chongqing, China
- Department of Clinical Biochemistry, Army Medical University (Third Military Medical University), 400038, Chongqing, China
| | - Jiqin Lian
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), 400038, Chongqing, China.
- Department of Clinical Biochemistry, Army Medical University (Third Military Medical University), 400038, Chongqing, China.
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22
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Solodushko V, Fouty B. Terminal hairpins improve protein expression in IRES-initiated mRNA in the absence of a cap and polyadenylated tail. Gene Ther 2023; 30:620-627. [PMID: 36828937 PMCID: PMC9951143 DOI: 10.1038/s41434-023-00391-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 01/31/2023] [Accepted: 02/08/2023] [Indexed: 02/26/2023]
Abstract
Synthesizing mRNA in vitro is a standard and simple procedure. Adding the 5' cap and 3' polyadenylated (poly(A)) tail to make this mRNA functional for use as a vaccine or therapy increases the time and cost of production and usually decreases the yield, however. We designed mRNA that lacked a cap and poly(A) tail but included an internal ribosomal entry site (IRES) to initiate protein translation. To protect the 5' and 3' ends of mRNA from exonucleases, we added stable terminal hairpins. When compared against typical mRNA (i.e., mRNA that contained a cap and poly(A) tail but lacked hairpins), expression of the delivered reporter protein in HEK293 cells was similar. Using a triple instead of a single hairpin at each end increased protein expression even more. This method has the potential to simplify the production and reduce the cost of synthesizing exogenous mRNA for use as biologics or vaccines.
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Affiliation(s)
- Victor Solodushko
- Department of Pharmacology, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
- The Center for Lung Biology, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
| | - Brian Fouty
- Department of Pharmacology, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
- The Center for Lung Biology, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
- Department of Internal Medicine, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
- The Division of Pulmonary and Critical Care Medicine, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
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23
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Kramer NJ, Prakash G, Choquet K, Soto I, Petrova B, Merens HE, Kanarek N, Churchman LS. Genome-wide screens for mitonuclear co-regulators uncover links between compartmentalized metabolism and mitochondrial gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.11.528118. [PMID: 36798306 PMCID: PMC9934615 DOI: 10.1101/2023.02.11.528118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Mitochondrial oxidative phosphorylation (OXPHOS) complexes are assembled from proteins encoded by both nuclear and mitochondrial DNA. These dual-origin enzymes pose a complex gene regulatory challenge for cells, in which gene expression must be coordinated across organelles using distinct pools of ribosomes. How cells produce and maintain the accurate subunit stoichiometries for these OXPHOS complexes remains largely unknown. To identify genes involved in dual-origin protein complex synthesis, we performed FACS-based genome-wide screens analyzing mutant cells with unbalanced levels of mitochondrial- and nuclear-encoded subunits of cytochrome c oxidase (Complex IV). We identified novel genes involved in OXPHOS biogenesis, including two uncharacterized genes: PREPL and NME6 . We found that PREPL specifically regulates Complex IV biogenesis by interacting with mitochondrial protein synthesis machinery, while NME6, an uncharacterized nucleoside diphosphate kinase (NDPK), controls OXPHOS complex biogenesis through multiple mechanisms reliant on its NDPK domain. First, NME6 maintains local mitochondrial pyrimidine triphosphate levels essential for mitochondrial RNA abundance. Second, through stabilizing interactions with RCC1L, NME6 modulates the activity of mitoribosome regulatory complexes, leading to disruptions in mitoribosome assembly and mitochondrial RNA pseudouridylation. Taken together, we propose that NME6 acts as a link between compartmentalized mitochondrial metabolites and mitochondrial gene expression. Finally, we present these screens as a resource, providing a catalog of genes involved in mitonuclear gene regulation and OXPHOS biogenesis.
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