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Ozaki M, Kuwayama T, Shimotsuma M, Hirose T. Separation and purification of short-, medium-, and long-stranded RNAs by RP-HPLC using different mobile phases and C 18 columns with various pore sizes. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:1948-1956. [PMID: 38445900 DOI: 10.1039/d4ay00114a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Nucleic acids, which have been employed in medicines for various diseases, are attracting attention as a new pharmaceutical model. Depending on the target substances, nucleic acid medicines with various nucleic acid chain lengths (several tens of nucleotides [nt] to several thousands of nt) exist. The purification of synthesized nucleic acids is crucial as various impurities remain in the crude product after synthesis. Presently, reversed-phase high-performance liquid chromatography (RP-HPLC) represents an effective purification method for nucleic acids. However, the information regarding the HPLC conditions for separating and purifying nucleic acids of various chain lengths is insufficient. Thus, this technical note describes the separation and purification of short-, medium-, and long-stranded nucleic acids (several tens of nt to thousands of nt) by RP-HPLC with various mobile phases and octadecyl-based columns with various pore sizes, such as normal (9-12 nm), wide (30 nm), and super wide (>30 nm) pores.
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Affiliation(s)
- Makoto Ozaki
- Research and Development Department, Nacalai Tesque, Inc., Ishibashi Kaide-cho, Muko-shi, Kyoto 617-0004, Japan.
| | - Tomomi Kuwayama
- Research and Development Department, Nacalai Tesque, Inc., Ishibashi Kaide-cho, Muko-shi, Kyoto 617-0004, Japan.
| | - Motoshi Shimotsuma
- Research and Development Department, Nacalai Tesque, Inc., Ishibashi Kaide-cho, Muko-shi, Kyoto 617-0004, Japan.
| | - Tsunehisa Hirose
- Research and Development Department, Nacalai Tesque, Inc., Ishibashi Kaide-cho, Muko-shi, Kyoto 617-0004, Japan.
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Romoli O, Henrion-Lacritick A, Blanc H, Frangeul L, Saleh MC. Limitations in harnessing oral RNA interference as an antiviral strategy in Aedes aegypti. iScience 2024; 27:109261. [PMID: 38433898 PMCID: PMC10907830 DOI: 10.1016/j.isci.2024.109261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/09/2024] [Accepted: 02/14/2024] [Indexed: 03/05/2024] Open
Abstract
Mosquitoes, particularly Aedes aegypti, are critical vectors for globally significant pathogenic viruses. This study examines the limitations of oral RNA interference (RNAi) as a strategy to disrupt viral transmission by Ae. aegypti. We hypothesized that double-stranded RNA (dsRNA) targeting the Zika virus (ZIKV) or chikungunya virus (CHIKV) genomes produced by engineered bacterial symbionts could trigger an antiviral response. Mosquitoes mono-colonized with Escherichia coli producing dsZIK or dsCHIK did not display reduced viral titers following exposure to virus-contaminated bloodmeals and failed to generate dsZIK- or dsCHIK-derived small interfering RNAs. To address potential limitations of bacterial dsRNA release, we explored dsRNA inoculation via feeding and injection. Although viral replication was impeded in mosquitoes injected with dsZIK or dsCHIK, no antiviral effect was observed in dsRNA-fed mosquitoes. These findings highlight complexities of implementing oral RNAi as an antiviral strategy in Ae. aegypti and warrant further exploration of local and systemic RNAi mechanisms.
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Affiliation(s)
- Ottavia Romoli
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNAi Unit, F-75015 Paris, France
| | | | - Hervé Blanc
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNAi Unit, F-75015 Paris, France
| | - Lionel Frangeul
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNAi Unit, F-75015 Paris, France
| | - Maria-Carla Saleh
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNAi Unit, F-75015 Paris, France
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Camperi J, Lippold S, Ayalew L, Roper B, Shao S, Freund E, Nissenbaum A, Galan C, Cao Q, Yang F, Yu C, Guilbaud A. Comprehensive Impurity Profiling of mRNA: Evaluating Current Technologies and Advanced Analytical Techniques. Anal Chem 2024; 96:3886-3897. [PMID: 38377434 PMCID: PMC10918618 DOI: 10.1021/acs.analchem.3c05539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/24/2024] [Accepted: 02/12/2024] [Indexed: 02/22/2024]
Abstract
In vitro transcription (IVT) of mRNA is a versatile platform for a broad range of biotechnological applications. Its rapid, scalable, and cost-effective production makes it a compelling choice for the development of mRNA-based cancer therapies and vaccines against infectious diseases. The impurities generated during mRNA production can potentially impact the safety and efficacy of mRNA therapeutics, but their structural complexity has not been investigated in detail yet. This study pioneers a comprehensive profiling of IVT mRNA impurities, integrating current technologies with innovative analytical tools. We have developed highly reproducible, efficient, and stability-indicating ion-pair reversed-phase liquid chromatography and capillary gel electrophoresis methods to determine the purity of mRNA from different suppliers. Furthermore, we introduced the applicability of microcapillary electrophoresis for high-throughput (<1.5 min analysis time per sample) mRNA impurity profiling. Our findings revealed that impurities are mainly attributed to mRNA variants with different poly(A) tail lengths due to aborted additions or partial hydrolysis and the presence of double-stranded mRNA (dsRNA) byproducts, particularly the dsRNA 3'-loop back form. We also implemented mass photometry and native mass spectrometry for the characterization of mRNA and its related product impurities. Mass photometry enabled the determination of the number of nucleotides of different mRNAs with high accuracy as well as the detection of their size variants [i.e., aggregates and partial and/or total absence of the poly(A) tail], thus providing valuable information on mRNA identity and integrity. In addition, native mass spectrometry provided insights into mRNA intact mass, heterogeneity, and important sequence features such as poly(A) tail length and distribution. This study highlights the existing bottlenecks and opportunities for improvement in the analytical characterization of IVT mRNA, thus contributing to the refinement and streamlining of mRNA production, paving the way for continued advancements in biotechnological applications.
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Affiliation(s)
- Julien Camperi
- Cell
Therapy Engineering and Development, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Steffen Lippold
- Protein
Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Luladey Ayalew
- Cell
Therapy Engineering and Development, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Brian Roper
- Cell
Therapy Engineering and Development, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Stephanie Shao
- Cell
Therapy Engineering and Development, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Emily Freund
- Department
of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Ariane Nissenbaum
- Department
of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Carolina Galan
- Department
of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Qinjingwen Cao
- Protein
Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Feng Yang
- Protein
Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Christopher Yu
- Cell
Therapy Engineering and Development, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Axel Guilbaud
- Protein
Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
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Niu J, Chen R, Wang JJ. RNA interference in insects: the link between antiviral defense and pest control. INSECT SCIENCE 2024; 31:2-12. [PMID: 37162315 DOI: 10.1111/1744-7917.13208] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/27/2023] [Accepted: 04/10/2023] [Indexed: 05/11/2023]
Abstract
RNA interference (RNAi) is a form of gene silencing triggered by double-stranded RNA (dsRNA) that operates in all eukaryotic cells. RNAi has been widely investigated in insects to determine the underlying molecular mechanism, to investigate its role in systemic antiviral defense, and to develop strategies for pest control. When insect cells are infected by viruses, viral dsRNA signatures trigger a local RNAi response to block viral replication and generate virus-derived DNA that confers systemic immunity. RNAi-based insect pest control involves the application of exogenous dsRNA targeting genes essential for insect development or survival, but the efficacy of this approach has limited potency in many pests through a combination of rapid dsRNA degradation, inefficient dsRNA uptake/processing, and ineffective RNAi machinery. This could be addressed by dsRNA screening and evaluation, focusing on dsRNA design and off-target management, as well as dsRNA production and delivery. This review summarizes recent progress to determine the role of RNAi in antiviral defense and as a pest control strategy in insects, addressing gaps between our fundamental understanding of the RNAi mechanism and the exploitation of RNAi-based pest control strategies.
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Affiliation(s)
- Jinzhi Niu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing, China
| | - Ruoyu Chen
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing, China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing, China
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Luo D, Wu Z, Wang D, Zhang J, Shao F, Wang S, Cestellos-Blanco S, Xu D, Cao Y. Lateral flow immunoassay for rapid and sensitive detection of dsRNA contaminants in in vitro-transcribed mRNA products. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:445-453. [PMID: 37181450 PMCID: PMC10173069 DOI: 10.1016/j.omtn.2023.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 04/04/2023] [Indexed: 05/16/2023]
Abstract
High purity is essential in mRNA-based therapeutic applications. A major contaminant of in vitro-transcribed (IVT) mRNA manufacturing is double-stranded RNA (dsRNA), which can induce severe anti-viral immune responses. Detection methods, such as agarose gel electrophoresis, ELISA, and dot-blot assay, are used to detect the existence of dsRNA in IVT mRNA products. However, these methods are either not sensitive enough or time-consuming. To overcome these challenges, we develop a rapid, sensitive, and easy-to-implement colloidal gold nanoparticle-based lateral flow strip assay (LFSA) with sandwich format for the detection of dsRNA from IVT process. dsRNA contaminant can be determined visually on the test strip or quantitatively with a portable optical detector. This method allows for a 15 min detection of N1-methyl-pseudouridine (m1Ψ)-containing dsRNA with a detection limit of 69.32 ng/mL. Furthermore, we establish the correlation between the LFSA test results and the immune response caused by dsRNA in mice. The LFSA platform allows the rapid, sensitive, and quantitative monitoring of purity in massive IVT mRNA products and aids for the prevention of immunogenicity by dsRNA impurities.
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Affiliation(s)
- Dengwang Luo
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhanfeng Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Daming Wang
- Academy for Engineering and Technology, Fudan University, Shanghai 200433, China
- Suzhou Institute of Biomedical Engineering and Technology (SIBET), Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
- Anbio Biotechnology Company, Xiamen, Fujian 361026, China
| | - Jieli Zhang
- Anbio Biotechnology Company, Xiamen, Fujian 361026, China
| | - Fei Shao
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuo Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Stefano Cestellos-Blanco
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Dawei Xu
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, China
- Corresponding author: Dawei Xu, CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, China.
| | - Yuhong Cao
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, China
- School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing 100049, China
- Corresponding author: Yuhong Cao, CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, China.
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Kuwayama T, Ozaki M, Shimotsuma M, Hirose T. Separation of long-stranded RNAs by RP-HPLC using an octadecyl-based column with super-wide pores. ANAL SCI 2023; 39:417-425. [PMID: 36566342 PMCID: PMC9789886 DOI: 10.1007/s44211-022-00253-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/14/2022] [Indexed: 12/25/2022]
Abstract
Messenger ribonucleic acids (mRNAs) have been used in vaccines for various diseases and are attracting attention as a new pharmaceutical paradigm. The purification of mRNAs is necessary because various impurities, such as template DNAs and transcription enzymes, remain in the crude product after mRNA synthesis. Among the various purification methods, reversed-phase high-performance liquid chromatography (RP-HPLC) is currently attracting attention. Herein, we optimized the pore size of the packing materials, the mobile phase composition, and the temperature of the process; we also evaluated changes in the separation patterns of RNA strands of various lengths via RP-HPLC. Additionally, single-stranded (50-1000 nucleotides in length) and double-stranded (80-500 base pairs in length) RNAs were separated while their non-denatured states were maintained by performing the analysis at 60 °C using triethylammonium acetate as the mobile phase and octadecyl-based RNA-RP1 with super-wide pores (> 30 nm) as the column. Furthermore, impurities in a long-stranded RNA of several thousand nucleotides synthesized by in vitro transcription were successfully separated using an RNA-RP1 column. The columns used in this study are expected to separate various RNA strands and the impurities contained in them.
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Affiliation(s)
- Tomomi Kuwayama
- Nacalai Tesque, Inc., Ishibashi Kaide-Cho, Muko, Kyoto, 617-0004, Japan
| | - Makoto Ozaki
- Nacalai Tesque, Inc., Ishibashi Kaide-Cho, Muko, Kyoto, 617-0004, Japan
| | | | - Tsunehisa Hirose
- Nacalai Tesque, Inc., Ishibashi Kaide-Cho, Muko, Kyoto, 617-0004, Japan.
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Hough J, Howard JD, Brown S, Portwood DE, Kilby PM, Dickman MJ. Strategies for the production of dsRNA biocontrols as alternatives to chemical pesticides. Front Bioeng Biotechnol 2022; 10:980592. [PMID: 36299286 PMCID: PMC9588923 DOI: 10.3389/fbioe.2022.980592] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/23/2022] [Indexed: 01/09/2023] Open
Abstract
Current crop pest control strategies rely on insecticidal and fungicidal sprays, plant genetic resistance, transgenes and agricultural practices. However, many insects, plant viruses, and fungi have no current means of control or have developed resistance against traditional pesticides. dsRNA is emerging as a novel sustainable method of plant protection as an alternative to traditional chemical pesticides. The successful commercialisation of dsRNA based biocontrols for effective pest management strategies requires the economical production of large quantities of dsRNA combined with suitable delivery methods to ensure RNAi efficacy against the target pest. A number of methods exist for the production and delivery of dsRNA based biocontrols and here we review alternative methods currently employed and emerging new approaches for their production. Additionally, we highlight potential challenges that will need to be addressed prior to widespread adoption of dsRNA biocontrols as novel sustainable alternatives to traditional chemical pesticides.
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Affiliation(s)
- James Hough
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingtom
| | - John D. Howard
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingtom
| | - Stephen Brown
- Sheffield RNAi Screening Facility, School of Biosciences, University of Sheffield, Sheffield, United Kingtom
| | - David E. Portwood
- Syngenta, Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | - Peter M. Kilby
- Syngenta, Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | - Mark J. Dickman
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingtom
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Analysis and purification of ssRNA and dsRNA molecules using asymmetrical flow field flow fractionation. J Chromatogr A 2022; 1683:463525. [DOI: 10.1016/j.chroma.2022.463525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/30/2022] [Accepted: 09/18/2022] [Indexed: 11/20/2022]
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RNA Interference Strategies for Future Management of Plant Pathogenic Fungi: Prospects and Challenges. PLANTS 2021; 10:plants10040650. [PMID: 33805521 PMCID: PMC8067263 DOI: 10.3390/plants10040650] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 12/11/2022]
Abstract
Plant pathogenic fungi are the largest group of disease-causing agents on crop plants and represent a persistent and significant threat to agriculture worldwide. Conventional approaches based on the use of pesticides raise social concern for the impact on the environment and human health and alternative control methods are urgently needed. The rapid improvement and extensive implementation of RNA interference (RNAi) technology for various model and non-model organisms has provided the initial framework to adapt this post-transcriptional gene silencing technology for the management of fungal pathogens. Recent studies showed that the exogenous application of double-stranded RNA (dsRNA) molecules on plants targeting fungal growth and virulence-related genes provided disease attenuation of pathogens like Botrytis cinerea, Sclerotinia sclerotiorum and Fusarium graminearum in different hosts. Such results highlight that the exogenous RNAi holds great potential for RNAi-mediated plant pathogenic fungal disease control. Production of dsRNA can be possible by using either in-vitro or in-vivo synthesis. In this review, we describe exogenous RNAi involved in plant pathogenic fungi and discuss dsRNA production, formulation, and RNAi delivery methods. Potential challenges that are faced while developing a RNAi strategy for fungal pathogens, such as off-target and epigenetic effects, with their possible solutions are also discussed.
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