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Inagaki M. Cell Reprogramming and Differentiation Utilizing Messenger RNA for Regenerative Medicine. J Dev Biol 2023; 12:1. [PMID: 38535481 PMCID: PMC10971469 DOI: 10.3390/jdb12010001] [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: 10/30/2023] [Revised: 12/06/2023] [Accepted: 12/19/2023] [Indexed: 06/16/2024] Open
Abstract
The COVID-19 pandemic generated interest in the medicinal applications of messenger RNA (mRNA). It is expected that mRNA will be applied, not only to vaccines, but also to regenerative medicine. The purity of mRNA is important for its medicinal applications. However, the current mRNA synthesis techniques exhibit problems, including the contamination of undesired 5'-uncapped mRNA and double-stranded RNA. Recently, our group developed a completely capped mRNA synthesis technology that contributes to the progress of mRNA research. The introduction of chemically modified nucleosides, such as N1-methylpseudouridine and 5-methylcytidine, has been reported by Karikó and Weissman, opening a path for the practical application of mRNA for vaccines and regenerative medicine. Yamanaka reported the production of induced pluripotent stem cells (iPSCs) by introducing four types of genes using a retrovirus vector. iPSCs are widely used for research on regenerative medicine and the preparation of disease models to screen new drug candidates. Among the Yamanaka factors, Klf4 and c-Myc are oncogenes, and there is a risk of tumor development if these are integrated into genomic DNA. Therefore, regenerative medicine using mRNA, which poses no risk of genome insertion, has attracted attention. In this review, the author summarizes techniques for synthesizing mRNA and its application in regenerative medicine.
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Affiliation(s)
- Masahito Inagaki
- Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
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Khan D, Terenzi F, Liu G, Ghosh PK, Ye F, Nguyen K, China A, Ramachandiran I, Chakraborty S, Stefan J, Khan K, Vasu K, Dong F, Willard B, Karn J, Gack MU, Fox PL. A viral pan-end RNA element and host complex define a SARS-CoV-2 regulon. Nat Commun 2023; 14:3385. [PMID: 37296097 PMCID: PMC10250186 DOI: 10.1038/s41467-023-39091-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, generates multiple protein-coding, subgenomic RNAs (sgRNAs) from a longer genomic RNA, all bearing identical termini with poorly understood roles in regulating viral gene expression. Insulin and interferon-gamma, two host-derived, stress-related agents, and virus spike protein, induce binding of glutamyl-prolyl-tRNA synthetase (EPRS1), within an unconventional, tetra-aminoacyl-tRNA synthetase complex, to the sgRNA 3'-end thereby enhancing sgRNA expression. We identify an EPRS1-binding sarbecoviral pan-end activating RNA (SPEAR) element in the 3'-end of viral RNAs driving agonist-induction. Translation of another co-terminal 3'-end feature, ORF10, is necessary for SPEAR-mediated induction, independent of Orf10 protein expression. The SPEAR element enhances viral programmed ribosomal frameshifting, thereby expanding its functionality. By co-opting noncanonical activities of a family of essential host proteins, the virus establishes a post-transcriptional regulon stimulating global viral RNA translation. A SPEAR-targeting strategy markedly reduces SARS-CoV-2 titer, suggesting a pan-sarbecoviral therapeutic modality.
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Affiliation(s)
- Debjit Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Fulvia Terenzi
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - GuanQun Liu
- Florida Research and Innovation Center, Cleveland Clinic Foundation, Port St. Lucie, FL, 34987, USA
| | - Prabar K Ghosh
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Fengchun Ye
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Kien Nguyen
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Arnab China
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Iyappan Ramachandiran
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Shruti Chakraborty
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Jennifer Stefan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Krishnendu Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Kommireddy Vasu
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Franklin Dong
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Belinda Willard
- Lerner Research Institute Proteomics and Metabolomics Core, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Michaela U Gack
- Florida Research and Innovation Center, Cleveland Clinic Foundation, Port St. Lucie, FL, 34987, USA
| | - Paul L Fox
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA.
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Balzarini S, Van Ende R, Voet A, Geuten K. A widely applicable and cost-effective method for specific RNA-protein complex isolation. Sci Rep 2023; 13:6898. [PMID: 37106019 PMCID: PMC10140378 DOI: 10.1038/s41598-023-34157-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 04/24/2023] [Indexed: 04/29/2023] Open
Abstract
Although methodological advances have been made over the past years, a widely applicable, easily scalable and cost-effective procedure that can be routinely used to isolate specific ribonucleoprotein complexes (RNPs) remains elusive. We describe the "Silica-based Acidic Phase Separation (SAPS)-capture" workflow. This versatile method combines previously described techniques in a cost-effective, optimal and widely applicable protocol. The specific RNP isolation procedure is performed on a pre-purified RNP sample instead of cell lysate. This combination of protocols results in an increased RNP/bead ratio and by consequence a reduced experimental cost. To validate the method, the 18S rRNP of S. cerevisiae was captured and to illustrate its applicability we isolated the complete repertoire of RNPs in A. thaliana. The procedure we describe can provide the community with a powerful tool to advance the study of the ribonome of a specific RNA molecule in any organism or tissue type.
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Affiliation(s)
- Sam Balzarini
- Molecular Biotechnology of Plants and Micro-organisms, KU Leuven, 3001, Leuven, Belgium
| | - Roosje Van Ende
- Molecular Biotechnology of Plants and Micro-organisms, KU Leuven, 3001, Leuven, Belgium
| | - Arnout Voet
- Lab of biomolecular modelling and design, KU Leuven, 3001, Leuven, Belgium
| | - Koen Geuten
- Molecular Biotechnology of Plants and Micro-organisms, KU Leuven, 3001, Leuven, Belgium.
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Jiang M, Ning W, Wu S, Wang X, Zhu K, Li A, Li Y, Cheng S, Song B. Three-nucleotide periodicity of nucleotide diversity in a population enables the identification of open reading frames. Brief Bioinform 2022; 23:6607611. [PMID: 35698834 PMCID: PMC9294425 DOI: 10.1093/bib/bbac210] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/25/2022] [Accepted: 05/06/2022] [Indexed: 11/14/2022] Open
Abstract
Accurate prediction of open reading frames (ORFs) is important for studying and using genome sequences. Ribosomes move along mRNA strands with a step of three nucleotides and datasets carrying this information can be used to predict ORFs. The ribosome-protected footprints (RPFs) feature a significant 3-nt periodicity on mRNAs and are powerful in predicting translating ORFs, including small ORFs (sORFs), but the application of RPFs is limited because they are too short to be accurately mapped in complex genomes. In this study, we found a significant 3-nt periodicity in the datasets of populational genomic variants in coding sequences, in which the nucleotide diversity increases every three nucleotides. We suggest that this feature can be used to predict ORFs and develop the Python package ‘OrfPP’, which recovers ~83% of the annotated ORFs in the tested genomes on average, independent of the population sizes and the complexity of the genomes. The novel ORFs, including sORFs, identified from single-nucleotide polymorphisms are supported by protein mass spectrometry evidence comparable to that of the annotated ORFs. The application of OrfPP to tetraploid cotton and hexaploid wheat genomes successfully identified 76.17% and 87.43% of the annotated ORFs in the genomes, respectively, as well as 4704 sORFs, including 1182 upstream and 2110 downstream ORFs in cotton and 5025 sORFs, including 232 upstream and 234 downstream ORFs in wheat. Overall, we propose an alternative and supplementary approach for ORF prediction that can extend the studies of sORFs to more complex genomes.
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Affiliation(s)
- Mengyun Jiang
- Chinese Academy of Agricultural Sciences and Henan University, China
| | - Weidong Ning
- Chinese Academy of Agricultural Sciences and Huazhong Agricultural University, China
| | - Shishi Wu
- Chinese Academy of Agricultural Sciences and Henan University, China
| | - Xingwei Wang
- Chinese Academy of Agricultural Sciences and Henan University, China
| | - Kun Zhu
- Chinese Academy of Agricultural Sciences and Henan University, China
| | - Aomei Li
- Chinese Academy of Agricultural Sciences, China
| | - Yongyao Li
- Chinese Academy of Agricultural Sciences, China
| | | | - Bo Song
- Chinese Academy of Agricultural Sciences, China
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