151
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Niu K, Zhang J, Ge S, Li D, Sun K, You Y, Qiu J, Wang K, Wang X, Liu R, Liu Y, Li B, Zhu ZJ, Qu L, Jiang H, Liu N. ONE-seq: epitranscriptome and gene-specific profiling of NAD-capped RNA. Nucleic Acids Res 2022; 51:e12. [PMID: 36477375 PMCID: PMC9881147 DOI: 10.1093/nar/gkac1136] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 11/01/2022] [Accepted: 11/15/2022] [Indexed: 12/13/2022] Open
Abstract
The hub metabolite, nicotinamide adenine dinucleotide (NAD), can be used as an initiating nucleotide in RNA synthesis to result in NAD-capped RNAs (NAD-RNA). Since NAD has been heightened as one of the most essential modulators in aging and various age-related diseases, its attachment to RNA might indicate a yet-to-be discovered mechanism that impacts adult life-course. However, the unknown identity of NAD-linked RNAs in adult and aging tissues has hindered functional studies. Here, we introduce ONE-seq method to identify the RNA transcripts that contain NAD cap. ONE-seq has been optimized to use only one-step chemo-enzymatic biotinylation, followed by streptavidin capture and the nudix phosphohydrolase NudC-catalyzed elution, to specifically recover NAD-capped RNAs for epitranscriptome and gene-specific analyses. Using ONE-seq, we discover more than a thousand of previously unknown NAD-RNAs in the mouse liver and reveal epitranscriptome-wide dynamics of NAD-RNAs with age. ONE-seq empowers the identification of NAD-capped RNAs that are responsive to distinct physiological states, facilitating functional investigation into this modification.
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Affiliation(s)
| | | | | | | | - Kunfeng Sun
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Rd., Pudong, Shanghai 201210, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingnan You
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Rd., Pudong, Shanghai 201210, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaqian Qiu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Rd., Pudong, Shanghai 201210, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kun Wang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Rd., Pudong, Shanghai 201210, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueting Wang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Rd., Pudong, Shanghai 201210, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Liu
- Singlera Genomics, 500 Fu Rong Hua Rd., Pudong, Shanghai 201204, China
| | - Yandong Liu
- Department of Vascular and Endovascular Surgery, Chang Zheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Bing Li
- IH Bluex Technology, 58 Xiang Cheng Road, Shanghai 200122, China
| | - Zheng-Jiang Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Rd., Pudong, Shanghai 201210, China,Shanghai Key Laboratory of Aging Studies, 100 Hai Ke Rd., Pudong, Shanghai 201210, China
| | - Lefeng Qu
- Correspondence may also be addressed to Lefeng Qu. Tel: +86 21 6361 0109;
| | - Hong Jiang
- Correspondence may also be addressed to Hong Jiang. Tel: +86 21 6858 2396;
| | - Nan Liu
- To whom correspondence should be addressed. Tel: +86 21 6858 2308;
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152
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Okuyama R. Nurturing Deep Tech to Solve Social Problems: Learning from COVID-19 mRNA Vaccine Development. Pathogens 2022; 11:pathogens11121469. [PMID: 36558803 PMCID: PMC9781701 DOI: 10.3390/pathogens11121469] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 12/11/2022] Open
Abstract
In mRNA vaccines against COVID-19, a new technology that had never been used for approved drugs was applied and succeeded in rapid clinical use. The development and application of new technologies are critical to solving emerging public health problems therefore it is important to understand which factors enabled the rapid development of the COVID-19 mRNA vaccines. This review discusses administrative and technological aspects of rapid vaccine development. In the technological aspects, I carefully examined the technology and clinical development histories of BioNTech and Moderna by searching their publication, patent application and clinical trials. Compared to the case of Japanese company that has not succeeded in the rapid development of mRNA vaccine, years of in-depth technology research and clinical development experience with other diseases and viruses were found to have enhanced BioNTech and Moderna's technological readiness and contributed to rapid vaccine development against COVID-19 in addition to government administrative support. An aspect of the investments that supported the long-term research and development of mRNA vaccines is also discussed.
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Affiliation(s)
- Ryo Okuyama
- College of International Management, Ritsumeikan Asia Pacific University, Beppu 874-8577, Japan
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153
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Ginseng fermentation solution is associated with immune response in lung adenocarcinoma by modulating the differential expression of the m7G regulators. J Funct Foods 2022. [DOI: 10.1016/j.jff.2022.105337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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154
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Giant Viruses as a Source of Novel Enzymes for Biotechnological Application. Pathogens 2022; 11:pathogens11121453. [PMID: 36558786 PMCID: PMC9787589 DOI: 10.3390/pathogens11121453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
The global demand for industrial enzymes has been increasing in recent years, and the search for new sources of these biological products is intense, especially in microorganisms. Most known viruses have limited genetic machinery and, thus, have been overlooked by the enzyme industry for years. However, a peculiar group of viruses breaks this paradigm. Giant viruses of the phylum Nucleocytoviricota infect protists (i.e., algae and amoebae) and have complex genomes, reaching up to 2.7 Mb in length and encoding hundreds of genes. Different giant viruses have robust metabolic machinery, especially those in the Phycodnaviridae and Mimiviridae families. In this review, we present some peculiarities of giant viruses that infect protists and discuss why they should be seen as an outstanding source of new enzymes. We revisited the genomes of representatives of different groups of giant viruses and put together information about their enzymatic machinery, highlighting several genes to be explored in biotechnology involved in carbohydrate metabolism, DNA replication, and RNA processing, among others. Finally, we present additional evidence based on structural biology using chitinase as a model to reinforce the role of giant viruses as a source of novel enzymes for biotechnological application.
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155
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Delos Santos NP, Duttke S, Heinz S, Benner C. MEPP: more transparent motif enrichment by profiling positional correlations. NAR Genom Bioinform 2022; 4:lqac075. [PMID: 36267125 PMCID: PMC9575187 DOI: 10.1093/nargab/lqac075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/18/2022] [Accepted: 09/23/2022] [Indexed: 11/11/2022] Open
Abstract
Score-based motif enrichment analysis (MEA) is typically applied to regulatory DNA to infer transcription factors (TFs) that may modulate transcription and chromatin state in different conditions. Most MEA methods determine motif enrichment independent of motif position within a sequence, even when those sequences harbor anchor points that motifs and their bound TFs may functionally interact with in a distance-dependent fashion, such as other TF binding motifs, transcription start sites (TSS), sequencing assay cleavage sites, or other biologically meaningful features. We developed motif enrichment positional profiling (MEPP), a novel MEA method that outputs a positional enrichment profile of a given TF's binding motif relative to key anchor points (e.g. transcription start sites, or other motifs) within the analyzed sequences while accounting for lower-order nucleotide bias. Using transcription initiation and TF binding as test cases, we demonstrate MEPP's utility in determining the sequence positions where motif presence correlates with measures of biological activity, inferring positional dependencies of binding site function. We demonstrate how MEPP can be applied to interpretation and hypothesis generation from experiments that quantify transcription initiation, chromatin structure, or TF binding measurements. MEPP is available for download from https://github.com/npdeloss/mepp.
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Affiliation(s)
- Nathaniel P Delos Santos
- Department of Biomedical Informatics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0634, USA
| | - Sascha Duttke
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Sven Heinz
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0634, USA
| | - Christopher Benner
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0634, USA
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156
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He L, Vatsalya V, Ma X, Klinge CM, Cave MC, Feng W, McClain CJ, Zhang X. Metabolic Analysis of Nucleosides/Bases in the Urine and Serum of Patients with Alcohol-Associated Liver Disease. Metabolites 2022; 12:metabo12121187. [PMID: 36557225 PMCID: PMC9783452 DOI: 10.3390/metabo12121187] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/15/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Accumulating evidence supports the important role of RNA modifications in liver disease pathogenesis. However, RNA modifications in alcohol-associated liver disease (ALD) have not yet been reported. Modified ribonucleosides/bases are products of RNA degradation; therefore, we investigated whether modified ribonucleosides/bases in human urine and serum are changed and whether these changes are associated with the severity of ALD. Human urine and serum samples from patients with ALD and appropriate controls were collected. Free nucleosides/bases were extracted from these samples and quantified using untargeted and targeted metabolomic approaches. Thirty-nine and forty free nucleosides/bases were respectively detected in human urine and serum samples. Twelve and eleven modified nucleosides are significantly changed in patients’ urine and serum (q < 0.05 and fold-change > 20%). The abundance of modified nucleobase and ribonucleoside, 7,9-dimethylguanine in urine and 2-methylthio-N6-threonylcarbamoyladenosine (ms2t6A) in serum are strongly associated with the severity of ALD. Spearman’s rank correlation coefficient of these two metabolites with the Model for End-stage Liver Disease (MELD) score are 0.66 and 0.74, respectively. Notably, the abundance changes in these two metabolites are sufficiently large to distinguish severe alcohol-associate hepatitis (AH) from non-severe ALD and non-severe ALD from healthy controls.
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Affiliation(s)
- Liqing He
- Department of Chemistry, University of Louisville, Louisville, KY 40292, USA
- Alcohol Research Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Hepatobiology & Toxicology Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY 40292, USA
| | - Vatsalya Vatsalya
- Alcohol Research Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Xipeng Ma
- Department of Chemistry, University of Louisville, Louisville, KY 40292, USA
- Alcohol Research Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Hepatobiology & Toxicology Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY 40292, USA
| | - Carolyn M. Klinge
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Matthew C. Cave
- Alcohol Research Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Hepatobiology & Toxicology Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Wenke Feng
- Alcohol Research Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Hepatobiology & Toxicology Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Craig J. McClain
- Alcohol Research Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Hepatobiology & Toxicology Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Robley Rex Department of Veterans Affairs Medical Center, Louisville, KY 40206, USA
- Correspondence: (C.J.M.); (X.Z.)
| | - Xiang Zhang
- Department of Chemistry, University of Louisville, Louisville, KY 40292, USA
- Alcohol Research Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Hepatobiology & Toxicology Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY 40292, USA
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Correspondence: (C.J.M.); (X.Z.)
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157
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Ornelas MY, Thomas AY, Johnson Rosas LI, Scoville RO, Mehta AP. Synthetic Platforms for Characterizing and Targeting of SARS-CoV-2 Genome Capping Enzymes. ACS Synth Biol 2022; 11:3759-3771. [PMID: 36331143 PMCID: PMC9662071 DOI: 10.1021/acssynbio.2c00359] [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: 07/07/2022] [Indexed: 11/06/2022]
Abstract
Essential viral enzymes have been successfully targeted to combat the diseases caused by emerging pathogenic RNA viruses (e.g., viral RNA-dependent RNA polymerase). Because of the conserved nature of such viral enzymes, therapeutics targeting these enzymes have the potential to be repurposed to combat emerging diseases, e.g., remdesivir, which was initially developed as a potential Ebola treatment, then was repurposed for COVID-19. Our efforts described in this study target another essential and highly conserved, but relatively less explored, step in RNA virus translation and replication, i.e., capping of the viral RNA genome. The viral genome cap structure disguises the genome of most RNA viruses to resemble the mRNA cap structure of their host and is essential for viral translation, propagation, and immune evasion. Here, we developed a synthetic, phenotypic yeast-based complementation platform (YeRC0M) for molecular characterization and targeting of SARS-CoV-2 genome-encoded RNA cap-0 (guanine-N7)-methyltransferase (N7-MTase) enzyme (nsp14). In YeRC0M, the lack of yeast mRNA capping N7-MTase in yeast, which is an essential gene in yeast, is complemented by the expression of functional viral N7-MTase or its variants. Using YeRC0M, we first identified important protein domains and amino acid residues that are essential for SARS-CoV-2 nsp14 N7-MTase activity. We also expanded YeRC0M to include key nsp14 variants observed in emerging variants of SARS-CoV-2 (e.g., delta variant of SARS-CoV-2 encodes nsp14 A394V and nsp14 P46L). We also combined YeRC0M with directed evolution to identify attenuation mutations in SARS-CoV-2 nsp14. Because of the high sequence similarity of nsp14 in emerging coronaviruses, these observations could have implications on live attenuated vaccine development strategies. These data taken together reveal key domains in SARS-CoV-2 nsp14 that can be targeted for therapeutic strategies. We also anticipate that these readily tractable phenotypic platforms can also be used for the identification of inhibitors of viral RNA capping enzymes as antivirals.
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Affiliation(s)
- Marya Y. Ornelas
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, United States
| | - Angela Y. Thomas
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, United States
| | - L. Idalee Johnson Rosas
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, United States
| | - Riley O. Scoville
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, United States
| | - Angad P. Mehta
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, United States
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign
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158
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Arzumanian VA, Dolgalev GV, Kurbatov IY, Kiseleva OI, Poverennaya EV. Epitranscriptome: Review of Top 25 Most-Studied RNA Modifications. Int J Mol Sci 2022; 23:ijms232213851. [PMID: 36430347 PMCID: PMC9695239 DOI: 10.3390/ijms232213851] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
The alphabet of building blocks for RNA molecules is much larger than the standard four nucleotides. The diversity is achieved by the post-transcriptional biochemical modification of these nucleotides into distinct chemical entities that are structurally and functionally different from their unmodified counterparts. Some of these modifications are constituent and critical for RNA functions, while others serve as dynamic markings to regulate the fate of specific RNA molecules. Together, these modifications form the epitranscriptome, an essential layer of cellular biochemistry. As of the time of writing this review, more than 300 distinct RNA modifications from all three life domains have been identified. However, only a few of the most well-established modifications are included in most reviews on this topic. To provide a complete overview of the current state of research on the epitranscriptome, we analyzed the extent of the available information for all known RNA modifications. We selected 25 modifications to describe in detail. Summarizing our findings, we describe the current status of research on most RNA modifications and identify further developments in this field.
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Affiliation(s)
- Viktoriia A. Arzumanian
- Correspondence: (V.A.A.); (G.V.D.); Tel.: +7-960-889-7117 (V.A.A.); +7-967-236-36-79 (G.V.D.)
| | - Georgii V. Dolgalev
- Correspondence: (V.A.A.); (G.V.D.); Tel.: +7-960-889-7117 (V.A.A.); +7-967-236-36-79 (G.V.D.)
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159
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Guo P, Wang P, Liu L, Wang P, Qu Z, Yu Z, Liu N. A novel
N7
‐methylguanosine‐related long noncoding
RNAs
signature for predicting prognosis and immune microenvironment in gastric cancer patients. PRECISION MEDICAL SCIENCES 2022. [DOI: 10.1002/prm2.12087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Peisen Guo
- College of Public Health Zhengzhou University Zhengzhou People's Republic of China
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health, Jinming Avenue North Section Henan University Kaifeng People's Republic of China
| | - Panpan Wang
- College of Public Health Zhengzhou University Zhengzhou People's Republic of China
| | - Limin Liu
- College of Public Health Zhengzhou University Zhengzhou People's Republic of China
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health, Jinming Avenue North Section Henan University Kaifeng People's Republic of China
| | - Peixi Wang
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health, Jinming Avenue North Section Henan University Kaifeng People's Republic of China
| | - Zhi Qu
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health, Jinming Avenue North Section Henan University Kaifeng People's Republic of China
| | - Zengli Yu
- College of Public Health Zhengzhou University Zhengzhou People's Republic of China
| | - Nan Liu
- College of Public Health Zhengzhou University Zhengzhou People's Republic of China
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health, Jinming Avenue North Section Henan University Kaifeng People's Republic of China
- Institute of Environment and Health, South China Hospital, Health Science Center Shenzhen University Shenzhen People's Republic of China
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160
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Mattay J. Noncanonical metabolite RNA caps: Classification, quantification, (de)capping, and function. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1730. [PMID: 35675554 DOI: 10.1002/wrna.1730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 06/15/2023]
Abstract
The 5' cap of eukaryotic mRNA is a hallmark for cellular functions from mRNA stability to translation. However, the discovery of novel 5'-terminal RNA caps derived from cellular metabolites has challenged this long-standing singularity in both eukaryotes and prokaryotes. Reminiscent of the 7-methylguanosine (m7G) cap structure, these noncanonical caps originate from abundant coenzymes such as NAD, FAD, or CoA and from metabolites like dinucleoside polyphosphates (NpnN). As of now, the significance of noncanonical RNA caps is elusive: they differ for individual transcripts, occur in distinct types of RNA, and change in response to environmental stimuli. A thorough comparison of their prevalence, quantity, and characteristics is indispensable to define the distinct classes of metabolite-capped RNAs. This is achieved by a structured analysis of all present studies covering functional, quantitative, and sequencing data which help to uncover their biological impact. The biosynthetic strategies of noncanonical RNA capping and the elaborate decapping machinery reveal the regulation and turnover of metabolite-capped RNAs. With noncanonical capping being a universal and ancient phenomenon, organisms have developed diverging strategies to adapt metabolite-derived caps to their metabolic needs, but ultimately to establish noncanonical RNA caps as another intriguing layer of RNA regulation. This article is categorized under: RNA Processing > Capping and 5' End Modifications RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Johanna Mattay
- Institute of Biochemistry, University of Münster, Münster, Germany
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161
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Abstract
Messenger RNA (mRNA) is an emerging class of therapeutic agent for the prevention and treatment of a wide range of diseases. The recent success of the two highly efficacious mRNA vaccines produced by Moderna and Pfizer-BioNTech to protect against COVID-19 highlights the huge potential of mRNA technology for revolutionizing life science and medical research. Challenges related to mRNA stability and immunogenicity, as well as in vivo delivery and the ability to cross multiple biological barriers, have been largely addressed by recent progress in mRNA engineering and delivery. In this Review, we present the latest advances and innovations in the growing field of mRNA nanomedicine, in the context of ongoing clinical translation and future directions to improve clinical efficacy.
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162
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Lu L, Zheng J, Liu B, Wu H, Huang J, Wu L, Li D. The m7G Modification Level and Immune Infiltration Characteristics in Patients with COVID-19. J Multidiscip Healthc 2022; 15:2461-2472. [PMID: 36320552 PMCID: PMC9618243 DOI: 10.2147/jmdh.s385050] [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: 08/04/2022] [Accepted: 10/14/2022] [Indexed: 11/10/2022] Open
Abstract
Purpose The 7-methylguanosine (m7G)-related genes were used to identify the clinical severity and prognosis of patients with coronavirus disease 2019 (COVID-19) and to identify possible therapeutic targets. Patients and Methods The GSE157103 dataset provides the transcriptional spectrum and clinical information required to analyze the expression of m7G-related genes and the disease subtypes. R language was applied for immune infiltration analysis, functional enrichment analysis, and nomogram model construction. Results Most m7G-related genes were up-regulated in COVID-19 and were closely related to immune cell infiltration. Disease subtypes were grouped using a clustering algorithm. It was found that the m7G-cluster B was associated with higher immune infiltration, lower mechanical ventilation, lower intensive care unit (ICU) status, higher ventilator-free days, and lower m7G scores. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that differentially expressed genes (DEGs) between m7G-cluster A and B were enriched in viral infection and immune-related aspects, including COVID-19 infection; Th17, Th1, and Th2 cell differentiation, and human T-cell leukemia virus 1 infection. Finally, through machine learning, six disease characteristic genes, NUDT4B, IFIT5, LARP1, EIF4E, LSM1, and NUDT4, were screened and used to develop a nomogram model to estimate disease risk. Conclusion The expression of most m7G genes was higher in COVID-19 patients compared with that in non-COVID-19 patients. The m7G-cluster B showed higher immune infiltration and milder symptoms. The predictive nomogram based on the six m7G genes can be used to accurately assess risk.
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Affiliation(s)
- Lingling Lu
- Fuzong Clinical Medical College of Fujian Medical University, The 900th Hospital, Fuzhou, People’s Republic of China
| | - Jiaolong Zheng
- Fuzong Clinical Medical College of Fujian Medical University, The 900th Hospital, Fuzhou, People’s Republic of China,Department of Hepatobiliary Disease, The 900th Hospital of Joint Logistics Support Force, Fuzhou, People’s Republic of China
| | - Bang Liu
- Fuzong Clinical Medical College of Fujian Medical University, The 900th Hospital, Fuzhou, People’s Republic of China
| | - Haicong Wu
- Fuzong Clinical Medical College of Fujian Medical University, The 900th Hospital, Fuzhou, People’s Republic of China,Department of Hepatobiliary Disease, The 900th Hospital of Joint Logistics Support Force, Fuzhou, People’s Republic of China
| | - Jiaofeng Huang
- Fuzong Clinical Medical College of Fujian Medical University, The 900th Hospital, Fuzhou, People’s Republic of China
| | - Liqing Wu
- Department of Hepatobiliary Disease, The 900th Hospital of Joint Logistics Support Force, Fuzhou, People’s Republic of China
| | - Dongliang Li
- Fuzong Clinical Medical College of Fujian Medical University, The 900th Hospital, Fuzhou, People’s Republic of China,Department of Hepatobiliary Disease, The 900th Hospital of Joint Logistics Support Force, Fuzhou, People’s Republic of China,Correspondence: Dongliang Li, Fuzong Clinical Medical College of Fujian Medical University, The 900th Hospital of the People’s Liberation Army Joint Logistics Support Force, No. 156 Xierhuan Road, Fuzhou, Fujian, 350025, People’s Republic of China, Tel/Fax +86 591 22859128, Email
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163
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Russ A, Wittmann S, Tsukamoto Y, Herrmann A, Deutschmann J, Lagisquet J, Ensser A, Kato H, Gramberg T. Nsp16 shields SARS-CoV-2 from efficient MDA5 sensing and IFIT1-mediated restriction. EMBO Rep 2022; 23:e55648. [PMID: 36285486 PMCID: PMC9724656 DOI: 10.15252/embr.202255648] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 12/12/2022] Open
Abstract
Methylation of the mRNA 5' cap by cellular methyltransferases enables efficient translation and avoids recognition by innate immune factors. Coronaviruses encode viral 2'-O-methyltransferases to shield their RNA from host factors. Here, we generate recombinant SARS-CoV-2 harboring a catalytically inactive 2'-O-methyltransferase Nsp16, Nsp16mut, and analyze viral replication in human lung epithelial cells. Although replication is only slightly attenuated, we find SARS-CoV-2 Nsp16mut to be highly immunogenic, resulting in a strongly enhanced release of type I interferon upon infection. The elevated immunogenicity of Nsp16mut is absent in cells lacking the RNA sensor MDA5. In addition, we report that Nsp16mut is highly sensitive to type I IFN treatment and demonstrate that this strong antiviral effect of type I IFN is mediated by the restriction factor IFIT1. Together, we describe a dual role for the 2'-O-methyltransferase Nsp16 during SARS-CoV-2 replication in avoiding efficient recognition by MDA5 and in shielding its RNA from interferon-induced antiviral responses, thereby identifying Nsp16 as a promising target for generating attenuated and highly immunogenic SARS-CoV-2 strains and as a potential candidate for therapeutic intervention.
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Affiliation(s)
- Alina Russ
- Institute of Clinical and Molecular VirologyFriedrich‐Alexander University Erlangen‐NürnbergErlangenGermany
| | - Sabine Wittmann
- Institute of Clinical and Molecular VirologyFriedrich‐Alexander University Erlangen‐NürnbergErlangenGermany
| | - Yuta Tsukamoto
- Institute of Cardiovascular ImmunologyUniversity Hospital Bonn, University of BonnBonnGermany
| | - Alexandra Herrmann
- Institute of Clinical and Molecular VirologyFriedrich‐Alexander University Erlangen‐NürnbergErlangenGermany
| | - Janina Deutschmann
- Institute of Clinical and Molecular VirologyFriedrich‐Alexander University Erlangen‐NürnbergErlangenGermany
| | - Justine Lagisquet
- Institute of Clinical and Molecular VirologyFriedrich‐Alexander University Erlangen‐NürnbergErlangenGermany
| | - Armin Ensser
- Institute of Clinical and Molecular VirologyFriedrich‐Alexander University Erlangen‐NürnbergErlangenGermany
| | - Hiroki Kato
- Institute of Cardiovascular ImmunologyUniversity Hospital Bonn, University of BonnBonnGermany
| | - Thomas Gramberg
- Institute of Clinical and Molecular VirologyFriedrich‐Alexander University Erlangen‐NürnbergErlangenGermany
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164
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Kairuz D, Samudh N, Ely A, Arbuthnot P, Bloom K. Advancing mRNA technologies for therapies and vaccines: An African context. Front Immunol 2022; 13:1018961. [PMID: 36353641 PMCID: PMC9637871 DOI: 10.3389/fimmu.2022.1018961] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 10/10/2022] [Indexed: 09/26/2023] Open
Abstract
Synthetic mRNA technologies represent a versatile platform that can be used to develop advanced drug products. The remarkable speed with which vaccine development programs designed and manufactured safe and effective COVID-19 vaccines has rekindled interest in mRNA technology, particularly for future pandemic preparedness. Although recent R&D has focused largely on advancing mRNA vaccines and large-scale manufacturing capabilities, the technology has been used to develop various immunotherapies, gene editing strategies, and protein replacement therapies. Within the mRNA technologies toolbox lie several platforms, design principles, and components that can be adapted to modulate immunogenicity, stability, in situ expression, and delivery. For example, incorporating modified nucleotides into conventional mRNA transcripts can reduce innate immune responses and improve in situ translation. Alternatively, self-amplifying RNA may enhance vaccine-mediated immunity by increasing antigen expression. This review will highlight recent advances in the field of synthetic mRNA therapies and vaccines, and discuss the ongoing global efforts aimed at reducing vaccine inequity by establishing mRNA manufacturing capacity within Africa and other low- and middle-income countries.
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Affiliation(s)
| | | | | | | | - Kristie Bloom
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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165
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Borišek J, Aupič J, Magistrato A. Establishing the catalytic and regulatory mechanism of
RNA
‐based machineries. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jure Borišek
- Theory Department National Institute of Chemistry Ljubljana Slovenia
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166
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Walsh CT. Covalent Catalytic Strategies for Enzymes That Modify RNA Molecules on their Tripartite Building Blocks. ACS Chem Biol 2022; 17:2686-2703. [PMID: 36103129 DOI: 10.1021/acschembio.2c00584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The tripartite structures of the four 5'-nucleotide monophosphate (NMP) building blocks in all RNAs enable enzyme-catalyzed chemical modifications to three types of sites: the heterocyclic bases via N- and C-methylations and other alkylations, conversion of the N-glycoside linkages of the uridine moiety to the C-C glycoside link in pseudouridines, and the phosphodiester-mediated processes of 5'-capping, splicing, and 3'-tailing of premRNAs. We examine known cases for enzymatic covalent catalytic strategies that entail transient formation and breakdown of covalent enzyme-RNA adducts in each catalytic cycle. One case involves generation of the required carbon nucleophile during C5 methylation of cytosine residues in RNAs. A second examines the mechanism proposed for pseudouridine synthases and for replacement of a guanine residue in tRNAs by queuosine. The third category involves phosphoric anhydride and phosphodiester chemistry by which viral RNAs encode enzymes for making their own mRNA 5'-caps. This strategy includes the recent finding that the SARS-CoV2 proteins assemble a canonical 5',5'-GTP cap on their 28 900 nucleotide genomic RNA to enable its translation as an mRNA by host translational machinery by way of a covalent RNA-viral enzyme intermediate.
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Affiliation(s)
- Christopher T Walsh
- ChEM-H Institute, Stanford University, Palo Alto, California 94305, United States
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167
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Shannon A, Sama B, Gauffre P, Guez T, Debart F, Vasseur JJ, Decroly E, Canard B, Ferron F. A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome. Nucleic Acids Res 2022; 50:11186-11198. [PMID: 36265859 DOI: 10.1093/nar/gkac876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 09/29/2022] [Indexed: 11/12/2022] Open
Abstract
The order Nidovirales is a diverse group of (+)RNA viruses, with a common genome organization and conserved set of replicative and editing enzymes. In particular, RNA methyltransferases play a central role in mRNA stability and immune escape. However, their presence and distribution in different Nidovirales families is not homogeneous. In Coronaviridae, the best characterized family, two distinct methytransferases perform methylation of the N7-guanine and 2'-OH of the RNA-cap to generate a cap-1 structure (m7GpppNm). The genes of both of these enzymes are located in the ORF1b genomic region. While 2'-O-MTases can be identified for most other families based on conservation of both sequence motifs and genetic loci, identification of the N7-guanine methyltransferase has proved more challenging. Recently, we identified a putative N7-MTase domain in the ORF1a region (N7-MT-1a) of certain members of the large genome Tobaniviridae family. Here, we demonstrate that this domain indeed harbors N7-specific methyltransferase activity. We present its structure as the first N7-specific Rossmann-fold (RF) MTase identified for (+)RNA viruses, making it remarkably different from that of the known Coronaviridae ORF1b N7-MTase gene. We discuss the evolutionary implications of such an appearance in this unexpected location in the genome, which introduces a split-off in the classification of Tobaniviridae.
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Affiliation(s)
- Ashleigh Shannon
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13009, Marseille, France
| | - Bhawna Sama
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13009, Marseille, France
| | - Pierre Gauffre
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13009, Marseille, France
| | - Théo Guez
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | - Françoise Debart
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | | | - Etienne Decroly
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13009, Marseille, France
| | - Bruno Canard
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13009, Marseille, France.,European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - François Ferron
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13009, Marseille, France.,European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
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168
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Xu J, Pratt HE, Moore JE, Gerstein MB, Weng Z. Building integrative functional maps of gene regulation. Hum Mol Genet 2022; 31:R114-R122. [PMID: 36083269 PMCID: PMC9585680 DOI: 10.1093/hmg/ddac195] [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: 07/17/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
Every cell in the human body inherits a copy of the same genetic information. The three billion base pairs of DNA in the human genome, and the roughly 50 000 coding and non-coding genes they contain, must thus encode all the complexity of human development and cell and tissue type diversity. Differences in gene regulation, or the modulation of gene expression, enable individual cells to interpret the genome differently to carry out their specific functions. Here we discuss recent and ongoing efforts to build gene regulatory maps, which aim to characterize the regulatory roles of all sequences in a genome. Many researchers and consortia have identified such regulatory elements using functional assays and evolutionary analyses; we discuss the results, strengths and shortcomings of their approaches. We also discuss new techniques the field can leverage and emerging challenges it will face while striving to build gene regulatory maps of ever-increasing resolution and comprehensiveness.
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Affiliation(s)
- Jinrui Xu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Henry E Pratt
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Jill E Moore
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Mark B Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, New Haven, CT 06520, USA
- Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
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169
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Tian Y, Deng Z, Yang P. mRNA vaccines: A novel weapon to control infectious diseases. Front Microbiol 2022; 13:1008684. [PMID: 36267192 PMCID: PMC9576954 DOI: 10.3389/fmicb.2022.1008684] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/06/2022] [Indexed: 12/01/2022] Open
Abstract
Infectious diseases have always threatened human life, but with the development of vaccines, effective strategies for preventing and controlling these diseases have become available. The global outbreak of COVID-19 ushered in the advent of mRNA vaccine technologies, which quickly led to the introduction of mRNA vaccines effective against SARS-CoV-2. The success of this approach has stimulated research into the use of mRNA vaccines in the fight against other emerging as well as remerging infectious diseases. This review examines the constructive strategies and delivery systems used in mRNA vaccines and provides an overview of current clinical trials of those vaccines in the prevention of infectious diseases. The underlying mechanisms of mRNA vaccines are also discussed, including the double-edged sword of the innate immune response. Finally, the challenges but also the potential of mRNA vaccines are considered.
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Affiliation(s)
- Yuying Tian
- Faculty of Hepato-Pancreato-Biliary Surgery, Institute of Hepatobiliary Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
- Inner Mongolia Medical University, Hohhot, China
| | - Zhuoya Deng
- Faculty of Hepato-Pancreato-Biliary Surgery, Institute of Hepatobiliary Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Penghui Yang
- Faculty of Hepato-Pancreato-Biliary Surgery, Institute of Hepatobiliary Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
- Inner Mongolia Medical University, Hohhot, China
- *Correspondence: Penghui Yang,
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170
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Zha L, Wang J, Cheng X. The effects of
RNA
methylation on immune cells development and function. FASEB J 2022; 36:e22552. [DOI: 10.1096/fj.202200716r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/23/2022] [Accepted: 09/06/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Ling‐Feng Zha
- Department of Cardiology Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Key Laboratory of Biological Targeted Therapy, Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases Wuhan China
| | - Jing‐Lin Wang
- Department of Cardiology Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Key Laboratory of Biological Targeted Therapy, Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases Wuhan China
| | - Xiang Cheng
- Department of Cardiology Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Key Laboratory of Biological Targeted Therapy, Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases Wuhan China
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171
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Yang C, Xie W, Zhang H, Xie W, Tian T, Qin Z. Recent two-year advances in anti-dengue small-molecule inhibitors. Eur J Med Chem 2022; 243:114753. [PMID: 36167010 DOI: 10.1016/j.ejmech.2022.114753] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 11/04/2022]
Abstract
Dengue is an acute tropical infectious disease transmitted by mosquitoes, which has posed a major challenge to global public health. Unfortunately, there is a lack of clinically proven dengue-specific drugs for its prevention and treatment. As the pathogenesis of dengue has not been fully elucidated, the development of specific drugs is seriously hindered. This article briefly describes the pathogenesis of dengue fever, the molecular characteristics, and epidemiology of dengue virus, and focuses on the potential small-molecule inhibitors of dengue virus, including on-target and multi-targeted inhibitors, which have been reported in the past two years.
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Affiliation(s)
- Chao Yang
- State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health, Macao University of Science and Technology, Macao, 999078, China
| | - Wansheng Xie
- Hainan Center for Drug and Medical Device Evaluation and Service, Hainan Provincial Drug Administration, Haikou, Hainan, 570206, China
| | - Heqian Zhang
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai, Guangdong, 519087, China
| | - Wenjian Xie
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, SAR, PR China
| | - Tiantian Tian
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai, Guangdong, 519087, China.
| | - Zhiwei Qin
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai, Guangdong, 519087, China.
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172
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RNA modifications: importance in immune cell biology and related diseases. Signal Transduct Target Ther 2022; 7:334. [PMID: 36138023 PMCID: PMC9499983 DOI: 10.1038/s41392-022-01175-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/23/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
RNA modifications have become hot topics recently. By influencing RNA processes, including generation, transportation, function, and metabolization, they act as critical regulators of cell biology. The immune cell abnormality in human diseases is also a research focus and progressing rapidly these years. Studies have demonstrated that RNA modifications participate in the multiple biological processes of immune cells, including development, differentiation, activation, migration, and polarization, thereby modulating the immune responses and are involved in some immune related diseases. In this review, we present existing knowledge of the biological functions and underlying mechanisms of RNA modifications, including N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A), N7-methylguanosine (m7G), N4-acetylcytosine (ac4C), pseudouridine (Ψ), uridylation, and adenosine-to-inosine (A-to-I) RNA editing, and summarize their critical roles in immune cell biology. Via regulating the biological processes of immune cells, RNA modifications can participate in the pathogenesis of immune related diseases, such as cancers, infection, inflammatory and autoimmune diseases. We further highlight the challenges and future directions based on the existing knowledge. All in all, this review will provide helpful knowledge as well as novel ideas for the researchers in this area.
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173
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Abstract
As one of the prevalent posttranscriptional modifications of RNA, N7-methylguanosine (m7G) plays essential roles in RNA processing, metabolism, and function, mainly regulated by the methyltransferase-like 1 (METTL1) and WD repeat domain 4 (WDR4) complex. Emerging evidence suggests that the METTL1/WDR4 complex promoted or inhibited the processes of many tumors, including head and neck, lung, liver, colon, bladder cancer, and teratoma, dependent on close m7G methylation modification of tRNA or microRNA (miRNA). Therefore, METTL1 and m7G modification can be used as biomarkers or potential intervention targets, providing new possibilities for early diagnosis and treatment of tumors. This review will mainly focus on the mechanisms of METTL1/WDR4 via m7G in tumorigenesis and the corresponding detection methods.
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Affiliation(s)
- Wenli Cheng
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Aili Gao
- Guangzhou Institution of Dermatology, Guangzhou, Guangdong 510095, P.R. China
| | - Hui Lin
- Department of Radiation Oncology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P. R. China
| | - Wenjuan Zhang
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, P.R. China
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174
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Mature Rotavirus Particles Contain Equivalent Amounts of 7meGpppG-Capped and Noncapped Viral Positive-Sense RNAs. J Virol 2022; 96:e0115122. [PMID: 36000838 PMCID: PMC9472601 DOI: 10.1128/jvi.01151-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viruses have evolved different strategies to overcome their recognition by the host innate immune system. The addition of caps at their 5' RNA ends is an efficient mechanism not only to ensure escape from detection by the innate immune system but also to ensure the efficient synthesis of viral proteins. Rotavirus mRNAs contain a type 1 cap structure at their 5' end that is added by the viral capping enzyme VP3, which is a multifunctional protein with all the enzymatic activities necessary to add the cap and also functions as an antagonist of the 2'-5'-oligoadenylate synthetase (OAS)/RNase L pathway. Here, the relative abundances of capped and noncapped viral RNAs during the replication cycle of rotavirus were determined. We found that both classes of rotaviral plus-sense RNAs (+RNAs) were encapsidated and that they were present in a 1:1 ratio in the mature infectious particles. The capping of viral +RNAs was dynamic, since different ratios of capped and noncapped RNAs were detected at different times postinfection. Similarly, when the relative amounts of capped and uncapped viral +RNAs produced in an in vitro transcription system were determined, we found that the proportions were very similar to those in the mature viral particles and in infected cells, suggesting that the capping efficiency of VP3, both in vivo and in vitro, might be close to 50%. Unexpectedly, when the effect of simultaneously knocking down the expression of VP3 and RNase L on the cap status of viral +RNAs was evaluated, we found that, even though at late times postinfection there was an increased proportion of capped viral RNAs in infected cells, the viral particles isolated from this condition contained equal ratios of capped and noncapped viral RNA, suggesting that there might be selective packaging of capped and noncapped RNAs. IMPORTANCE Rotaviruses have a genome composed of 11 segments of double-stranded RNA. Whether all 5' ends of the positive-sense genomic RNAs contained in the mature viral particles are modified by a cap structure is unknown. In this work, we characterized the relative proportions of capped and noncapped viral RNAs in rotavirus-infected cells and in viral particles by using a direct quantitative assay. We found that, independent of the relative proportions of capped/noncapped RNAs present in rotavirus-infected cells, there were similar proportions of these two kinds of 5'-modified positive-sense RNAs in the viral particles.
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175
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A Temperature-Sensitive Recombinant of Avian Coronavirus Infectious Bronchitis Virus Provides Complete Protection against Homologous Challenge. J Virol 2022; 96:e0110022. [PMID: 35972294 PMCID: PMC9472628 DOI: 10.1128/jvi.01100-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Avian coronavirus infectious bronchitis virus (IBV) is the etiological agent of infectious bronchitis, an acute highly contagious economically relevant respiratory disease of poultry. Vaccination is used to control IBV infections, with live-attenuated vaccines generated via serial passage of a virulent field isolate through embryonated hens' eggs. A fine balance must be achieved between attenuation and the retention of immunogenicity. The exact molecular mechanism of attenuation is unknown, and vaccines produced in this manner present a risk of reversion to virulence as few consensus level changes are acquired. Our previous research resulted in the generation of a recombinant IBV (rIBV) known as M41-R, based on a pathogenic strain M41-CK. M41-R was attenuated in vivo by two amino acid changes, Nsp10-Pro85Leu and Nsp14-Val393Leu; however, the mechanism of attenuation was not determined. Pro85 and Val393 were found to be conserved among not only IBV strains but members of the wider coronavirus family. This study demonstrates that the same changes are associated with a temperature-sensitive (ts) replication phenotype at 41°C in vitro, suggesting that the two phenotypes may be linked. Vaccination of specific-pathogen-free chickens with M41-R induced 100% protection against clinical disease, tracheal ciliary damage, and challenge virus replication following homologous challenge with virulent M41-CK. Temperature sensitivity has been used to rationally attenuate other viral pathogens, including influenza, and the identification of amino acid changes that impart both a ts and an attenuated phenotype may therefore offer an avenue for future coronavirus vaccine development. IMPORTANCE Infectious bronchitis virus is a pathogen of economic and welfare concern for the global poultry industry. Live-attenuated vaccines against are generated by serial passage of a virulent isolate in embryonated eggs until attenuation is achieved. The exact mechanisms of attenuation are unknown, and vaccines produced have a risk of reversion to virulence. Reverse genetics provides a method to generate vaccines that are rationally attenuated and are more stable with respect to back selection due to their clonal origin. Genetic populations resulting from molecular clones are more homogeneous and lack the presence of parental pathogenic viruses, which generation by multiple passage does not. In this study, we identified two amino acids that impart a temperature-sensitive replication phenotype. Immunogenicity is retained and vaccination results in 100% protection against homologous challenge. Temperature sensitivity, used for the development of vaccines against other viruses, presents a method for the development of coronavirus vaccines.
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176
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Ding P, Summers MF. Sequestering the 5′‐cap for viral RNA packaging. Bioessays 2022; 44:e2200104. [PMID: 36101513 DOI: 10.1002/bies.202200104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/28/2022] [Accepted: 08/31/2022] [Indexed: 11/11/2022]
Abstract
Many viruses evolved mechanisms for capping the 5'-ends of their plus-strand RNAs as a means of hijacking the eukaryotic messenger RNA (mRNA) splicing/translation machinery. Although capping is critical for replication, the RNAs of these viruses have other essential functions including their requirement to be packaged as either genomes or pre-genomes into progeny viruses. Recent studies indicate that human immunodeficiency virus type-1 (HIV-1) RNAs are segregated between splicing/translation and packaging functions by a mechanism that involves structural sequestration of the 5'-cap. Here, we examined studies reported for other viruses and retrotransposons that require both selective packaging of their RNAs and 5'-RNA capping for host-mediated translation. Our findings suggest that viruses and retrotransposons have evolved multiple mechanisms to control 5'-cap accessibility, consistent with the hypothesis that removal or sequestration of the 5' cap enables packageable RNAs to avoid capture by the cellular RNA processing and translation machinery.
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Affiliation(s)
- Pengfei Ding
- Department of Chemistry and Biochemistry and Howard Hughes Medical Institute University of Maryland Baltimore County Baltimore Maryland USA
| | - Michael F. Summers
- Department of Chemistry and Biochemistry and Howard Hughes Medical Institute University of Maryland Baltimore County Baltimore Maryland USA
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177
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Yu D, McKinley L, Nien Y, Prall W, Zvarick A. RNA biology takes root in plant systems. PLANT DIRECT 2022; 6:e445. [PMID: 36091875 PMCID: PMC9448652 DOI: 10.1002/pld3.445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Advances in RNA biology such as RNAi, CRISPR, and the first mRNA vaccine represent the enormous potential of RNA research to address current problems. Additionally, plants are a diverse and undeniably essential resource for life threatened by climate change, loss of arable land, and pollution. Different aspects of RNA such as its processing, modification and structure are intertwined with plant development, physiology and stress response. This report details the findings of researchers around the world during the 23rd Penn State Symposium in Plant Biology with a focus in RNA biology.
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Affiliation(s)
- David Yu
- Department of BiologyThe Pennsylvania State UniversityUniversity ParkPAUSA
| | - Lauren McKinley
- Department of ChemistryThe Pennsylvania State UniversityUniversity ParkPAUSA
| | - Yachi Nien
- Department of BiologyThe Pennsylvania State UniversityUniversity ParkPAUSA
| | - Wil Prall
- Department of BiologyThe University of PennsylvaniaPhiladelphiaPAUSA
| | - Allison Zvarick
- Department of BiologyThe Pennsylvania State UniversityUniversity ParkPAUSA
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178
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Weixler L, Feijs KLH, Zaja R. ADP-ribosylation of RNA in mammalian cells is mediated by TRPT1 and multiple PARPs. Nucleic Acids Res 2022; 50:9426-9441. [PMID: 36018800 PMCID: PMC9458441 DOI: 10.1093/nar/gkac711] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 07/29/2022] [Accepted: 08/11/2022] [Indexed: 12/24/2022] Open
Abstract
RNA function relies heavily on posttranscriptional modifications. Recently, it was shown that certain PARPs and TRPT1 can ADP-ribosylate RNA in vitro. Traditionally, intracellular ADP-ribosylation has been considered mainly as a protein posttranslational modification. To date, it is not clear whether RNA ADP-ribosylation occurs in cells. Here we present evidence that different RNA species are ADP-ribosylated in human cells. The modification of cellular RNA is mediated by several transferases such as TRPT1, PARP10, PARP11, PARP12 and PARP15 and is counteracted by different hydrolases including TARG1, PARG and ARH3. In addition, diverse cellular stressors can modulate the content of ADP-ribosylated RNA in cells. We next investigated potential consequences of ADP-ribosylation for RNA and found that ADPr-capped mRNA is protected against XRN1 mediated degradation but is not translated. T4 RNA ligase 1 can ligate ADPr-RNA in absence of ATP, resulting in the incorporation of an abasic site. We thus provide the first evidence of RNA ADP-ribosylation in mammalian cells and postulate potential functions of this novel RNA modification.
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Affiliation(s)
- Lisa Weixler
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen 52074, Germany
| | - Karla L H Feijs
- Correspondence may also be addressed to Karla L.H. Feijs. Tel: +49 2418080692; Fax: +49 2418082427;
| | - Roko Zaja
- To whom correspondence should be addressed. Tel: +49 2418037944; Fax: +49 2418082427;
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179
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Drazkowska K, Tomecki R, Warminski M, Baran N, Cysewski D, Depaix A, Kasprzyk R, Kowalska J, Jemielity J, Sikorski P. 2'-O-Methylation of the second transcribed nucleotide within the mRNA 5' cap impacts the protein production level in a cell-specific manner and contributes to RNA immune evasion. Nucleic Acids Res 2022; 50:9051-9071. [PMID: 36018811 PMCID: PMC9458431 DOI: 10.1093/nar/gkac722] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/02/2022] [Accepted: 08/16/2022] [Indexed: 12/24/2022] Open
Abstract
In mammals, m7G-adjacent nucleotides undergo extensive modifications. Ribose of the first or first and second transcribed nucleotides can be subjected to 2'-O-methylation to form cap1 or cap2, respectively. When the first transcribed nucleotide is 2'-O-methylated adenosine, it can be additionally modified to N6,2'-O-dimethyladenosine (m6Am). Recently, the crucial role of cap1 in distinguishing between 'self' and 'non-self' in mammalian cells during viral infection was revealed. Here, we attempted to understand the impact of cap methylations on RNA-related processes. Therefore, we synthesized tetranucleotide cap analogues and used them for RNA capping during in vitro transcription. Using this tool, we found that 2'-O-methylation of the second transcribed nucleotide within the mRNA 5' cap influences protein production levels in a cell-specific manner. This modification can strongly hamper protein biosynthesis or have no influence on protein production levels, depending on the cell line. Interestingly, 2'-O-methylation of the second transcribed nucleotide and the presence of m6Am as the first transcribed nucleotide serve as determinants that define transcripts as 'self' and contribute to transcript escape from the host innate immune response. Additionally, cap methylation status does not influence transcript affinity towards translation initiation factor eIF4E or in vitro susceptibility to decapping by DCP2; however, we observe the resistance of cap2-RNA to DXO (decapping exoribonuclease)-mediated decapping and degradation.
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Affiliation(s)
- Karolina Drazkowska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Rafal Tomecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Natalia Baran
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland,Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Dominik Cysewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland,Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland
| | - Anaïs Depaix
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Renata Kasprzyk
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Pawel J Sikorski
- To whom correspondence should be addressed. Tel: +48 22 55 43775; Fax: +48 22 55 43771;
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180
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Current Vaccine Platforms in Enhancing T-Cell Response. Vaccines (Basel) 2022; 10:vaccines10081367. [PMID: 36016254 PMCID: PMC9413345 DOI: 10.3390/vaccines10081367] [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: 06/24/2022] [Revised: 07/28/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
The induction of T cell-mediated immunity is crucial in vaccine development. The most effective vaccine is likely to employ both cellular and humoral immune responses. The efficacy of a vaccine depends on T cells activated by antigen-presenting cells. T cells also play a critical role in the duration and cross-reactivity of vaccines. Moreover, pre-existing T-cell immunity is associated with a decreased severity of infectious diseases. Many technical and delivery platforms have been designed to induce T cell-mediated vaccine immunity. The immunogenicity of vaccines is enhanced by controlling the kinetics and targeted delivery. Viral vectors are attractive tools that enable the intracellular expression of foreign antigens and induce robust immunity. However, it is necessary to select an appropriate viral vector considering the existing anti-vector immunity that impairs vaccine efficacy. mRNA vaccines have the advantage of rapid and low-cost manufacturing and have been approved for clinical use as COVID-19 vaccines for the first time. mRNA modification and nanomaterial encapsulation can help address mRNA instability and translation efficacy. This review summarizes the T cell responses of vaccines against various infectious diseases based on vaccine technologies and delivery platforms and discusses the future directions of these cutting-edge platforms.
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181
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Identification and Inhibition of the Druggable Allosteric Site of SARS-CoV-2 NSP10/NSP16 Methyltransferase through Computational Approaches. Molecules 2022; 27:molecules27165241. [PMID: 36014480 PMCID: PMC9416396 DOI: 10.3390/molecules27165241] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/24/2022] [Accepted: 07/04/2022] [Indexed: 11/28/2022] Open
Abstract
Since its emergence in early 2019, the respiratory infectious virus, SARS-CoV-2, has ravaged the health of millions of people globally and has affected almost every sphere of life. Many efforts are being made to combat the COVID-19 pandemic’s emerging and recurrent waves caused by its evolving and more infectious variants. As a result, novel and unexpected targets for SARS-CoV-2 have been considered for drug discovery. 2′-O-Methyltransferase (nsp10/nsp16) is a significant and appealing target in the SARS-CoV-2 life cycle because it protects viral RNA from the host degradative enzymes via a cap formation process. In this work, we propose prospective allosteric inhibitors that target the allosteric site, SARS-CoV-2 MTase. Four drug libraries containing ~119,483 compounds were screened against the allosteric site of SARS-CoV-2 MTase identified in our research. The identified best compounds exhibited robust molecular interactions and alloscore-score rankings with the allosteric site of SARS-CoV-2 MTase. Moreover, to further assess the dynamic stability of these compounds (CHEMBL2229121, ZINC000009464451, SPECS AK-91811684151, NCI-ID = 715319), a 100 ns molecular dynamics simulation, along with its holo-form, was performed to provide insights on the dynamic nature of these allosteric inhibitors at the allosteric site of the SARS-CoV-2 MTase. Additionally, investigations of MM-GBSA binding free energies revealed a good perspective for these allosteric inhibitor–enzyme complexes, indicating their robust antagonistic action on SARS-CoV-2 (nsp10/nsp16) methyltransferase. We conclude that these allosteric repressive agents should be further evaluated through investigational assessments in order to combat the proliferation of SARS-CoV-2.
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182
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Felix AS, Quillin AL, Mousavi S, Heemstra JM. Harnessing Nature's Molecular Recognition Capabilities to Map and Study RNA Modifications. Acc Chem Res 2022; 55:2271-2279. [PMID: 35900335 PMCID: PMC9388579 DOI: 10.1021/acs.accounts.2c00287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
RNA editing or "epitranscriptomic modification" refers to the processing of RNA that occurs after transcription to alter the sequence or structure of the nucleic acid. These chemical alterations can be found on either the ribose sugar or the nucleobase, and although many are "silent" and do not change the Watson-Crick-Franklin code of the RNA, others result in recoding events. More than 170 RNA modifications have been identified so far, each having a specific biological purpose. Additionally, dysregulated RNA editing has been linked to several types of diseases and disorders. As new modifications are discovered and our understanding of their functional impact grows, so does the need for selective methods of identifying and mapping editing sites in the transcriptome.The most common methods for studying RNA modifications rely on antibodies as affinity reagents; however, antibodies can be difficult to generate and often have undesirable off-target binding. More recently, selective chemical labeling has advanced the field by offering techniques that can be used for the detection, enrichment, and quantification of RNA modifications. In our method using acrylamide for inosine labeling, we demonstrated the versatility with which this approach enables pull-down or downstream functionalization with other tags or affinity handles. Although this method did enable the quantitative analysis of A-to-I editing levels, we found that selectivity posed a significant limitation, likely because of the similar reactivity profiles of inosine and pseudouridine or other nucleobases.Seeking to overcome the inherent limitations of antibodies and chemical labeling methods, a more recent approach to studying the epitranscriptome is through the repurposing of proteins and enzymes that recognize modified RNA. Our laboratory has used Endonuclease V, a repair enzyme that cleaves inosine-containing RNAs, and reprogrammed it to instead bind inosine. We first harnessed EndoV to develop a preparative technique for RNA sequencing that we termed EndoVIPER-seq. This method uses EndoV to enrich inosine-edited RNAs, providing better coverage in RNA sequencing and leading to the discovery of previously undetected A-to-I editing sites. We also leveraged EndoV to create a plate-based immunoassay (EndoVLISA) to quantify inosine in cellular RNA. This approach can detect differential A-to-I editing levels across tissue types or disease states while being independent of RNA sequencing, making it cost-effective and high-throughput. By harnessing the molecular recognition capabilities of this enzyme, we show that EndoV can be repurposed as an "anti-inosine antibody" to develop new methods of detecting and enriching inosine from cellular RNA.Nature has evolved a plethora of proteins and enzymes that selectively recognize and act on RNA modifications, and exploiting the affinity of these biomolecules offers a promising new direction for the field of epitranscriptomics.
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Affiliation(s)
- Ansley S. Felix
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Alexandria L. Quillin
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Shikufa Mousavi
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Jennifer M. Heemstra
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
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183
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Gyebi GA, Ogunyemi OM, Adefolalu AA, Rodríguez-Martínez A, López-Pastor JF, Banegas-Luna AJ, Pérez-Sánchez H, Adegunloye AP, Ogunro OB, Afolabi SO. African derived phytocompounds may interfere with SARS-CoV-2 RNA capping machinery via inhibition of 2'-O-ribose methyltransferase: An in silico perspective. J Mol Struct 2022; 1262:133019. [PMID: 35431328 PMCID: PMC9002684 DOI: 10.1016/j.molstruc.2022.133019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 02/07/2023]
Abstract
Despite the ongoing vaccination against the life-threatening COVID-19, there is need for viable therapeutic interventions. The S-adenosyl-l-Methionine (SAM) dependent 2-O'-ribose methyltransferase (2'-O-MTase) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents a therapeutic target against COVID-19 infection. In a bid to profile bioactive principles from natural sources, a custom-made library of 226 phytochemicals from African medicinal plants with especially anti-malarial activity was screened for direct interactions with SARS-CoV-2 2'-O-MTase (S2RMT) using molecular docking and molecular dynamics (MD) simulations as well as binding free energies methods. Based on minimal binding energy lower than sinefungin (a reference methyl-transferase inhibitor) and binding mode analysis at the catalytic site of S2RMT, a list of 26 hit phytocompounds was defined. The interaction of these phytocompounds was compared with the 2'-O-MTase of SARS-CoV and MERS-CoV. Among these compounds, the lead phytocompounds (LPs) viz: mulberrofuran F, 24-methylene cycloartenol, ferulate, 3-benzoylhosloppone and 10-hydroxyusambarensine interacted strongly with the conserved KDKE tetrad within the substrate binding pocket of the 2'-O-MTase of the coronavirus strains which is critical for substrate binding. The thermodynamic parameters analyzed from the MD simulation trajectories of the LPs-S2RMT complexes presented an eminent structural stability and compactness. These LPs demonstrated favorable druggability and in silico ADMET properties over a diverse array of molecular computing descriptors. The LPs show promising prospects in the disruption of S2RMT capping machinery in silico. However, these LPs should be validated via in vitro and in vivo experimental models.
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Affiliation(s)
- Gideon A. Gyebi
- Department of Biochemistry, Bingham University, Karu, Nigeria,Corresponding authors
| | - Oludare M. Ogunyemi
- Human Nutraceuticals and Bioinformatics Research Unit, Department of Biochemistry, Salem University, Lokoja, Nigeria
| | | | - Alejandro Rodríguez-Martínez
- Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), Universidad Católica de Murcia (UCAM), Spain
| | - Juan F. López-Pastor
- Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), Universidad Católica de Murcia (UCAM), Spain
| | - Antonio J. Banegas-Luna
- Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), Universidad Católica de Murcia (UCAM), Spain
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), Universidad Católica de Murcia (UCAM), Spain,Corresponding authors
| | | | - Olalekan B. Ogunro
- Department of Biological Sciences, KolaDaisi University, Ibadan, Nigeria
| | - Saheed O. Afolabi
- Department of Pharmacology and Therapeutics, Faculty of Basic Medical Sciences University of Ilorin, Ilorin, Nigeria
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184
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Zhao H, Liu J, He L, Zhang L, Yu R, Kang C. Virtual screening and molecular dynamics simulation for identification of natural antiviral agents targeting SARS-CoV-2 NSP10. Biochem Biophys Res Commun 2022; 626:114-120. [PMID: 35988295 PMCID: PMC9376029 DOI: 10.1016/j.bbrc.2022.08.029] [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: 07/29/2022] [Revised: 08/03/2022] [Accepted: 08/11/2022] [Indexed: 11/28/2022]
Abstract
New variations of SARS-CoV-2 continue to emerge in the global pandemic, which may be resistant to at least some vaccines in COVID-19, indicating that drug and vaccine development must be continuously strengthened. NSP10 plays an essential role in SARS-CoV-2 viral life cycle. It stimulates the enzymatic activities of NSP14-ExoN and NSP16-O-MTase by the formation of NSP10/NSP14 and NSP10/NSP16 complexes. Inhibiting NSP10 can block the binding of NSP10 to NSP14 and NSP16. This study has identified potential natural NSP10 inhibitors from ZINC database. The protein druggable pocket was identified for screening candidates. Molecular docking of the selected compounds was performed and MM-GBSA binding energy was calculated. After ADMET assessment, 4 hits were obtained for favorable druggability. The analysis of site interactions suggested that the hits all had excellent binding. Molecular dynamics studies revealed that selected natural compounds stably bind to NSP10. These compounds were identified as potential leads against NSP10 for the development of strategies to combat SARS-CoV-2 replication and could serve as the basis for further studies.
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Affiliation(s)
- Huilin Zhao
- School of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Jin Liu
- School of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Lei He
- School of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Lichuan Zhang
- School of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Rilei Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Congmin Kang
- School of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
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185
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Multiple Roles of m6A RNA Modification in Translational Regulation in Cancer. Int J Mol Sci 2022; 23:ijms23168971. [PMID: 36012237 PMCID: PMC9408962 DOI: 10.3390/ijms23168971] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/17/2022] Open
Abstract
Despite its discovery in the early 1970s, m6A modification within mRNA molecules has only powerfully entered the oncology field in recent years. This chemical modification can control all aspects of the maturation of mRNAs, both in the nucleus and in the cytoplasm. Thus, the alteration in expression levels of writers, erasers, and readers may significantly contribute to the alteration of gene expression observed in cancer. In particular, the activation of oncogenic pathways can lead to an alteration of the global rate of mRNA translation or the selective translation of specific mRNAs. In both cases, m6A can play an important role. In this review, we highlight the role of m6A in the regulation of translation by focusing on regulatory mechanisms and cancer-related functions of this novel but still controversial field.
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186
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Park GJ, Osinski A, Hernandez G, Eitson JL, Majumdar A, Tonelli M, Henzler-Wildman K, Pawłowski K, Chen Z, Li Y, Schoggins JW, Tagliabracci VS. The mechanism of RNA capping by SARS-CoV-2. Nature 2022; 609:793-800. [PMID: 35944563 PMCID: PMC9492545 DOI: 10.1038/s41586-022-05185-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 08/03/2022] [Indexed: 11/29/2022]
Abstract
The RNA genome of SARS-CoV-2 contains a 5′ cap that facilitates the translation of viral proteins, protection from exonucleases and evasion of the host immune response1–4. How this cap is made in SARS-CoV-2 is not completely understood. Here we reconstitute the N7- and 2′-O-methylated SARS-CoV-2 RNA cap (7MeGpppA2′-O-Me) using virally encoded non-structural proteins (nsps). We show that the kinase-like nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain5 of nsp12 transfers the RNA to the amino terminus of nsp9, forming a covalent RNA–protein intermediate (a process termed RNAylation). Subsequently, the NiRAN domain transfers the RNA to GDP, forming the core cap structure GpppA-RNA. The nsp146 and nsp167 methyltransferases then add methyl groups to form functional cap structures. Structural analyses of the replication–transcription complex bound to nsp9 identified key interactions that mediate the capping reaction. Furthermore, we demonstrate in a reverse genetics system8 that the N terminus of nsp9 and the kinase-like active-site residues in the NiRAN domain are required for successful SARS-CoV-2 replication. Collectively, our results reveal an unconventional mechanism by which SARS-CoV-2 caps its RNA genome, thus exposing a new target in the development of antivirals to treat COVID-19. Reconstitution of the SARS-CoV-2 RNA 5′ cap reveals the unconventional mechanism by which SARS-CoV-2 caps its RNA genome, providing a new target in the development of antiviral agents to treat COVID-19.
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Affiliation(s)
- Gina J Park
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Adam Osinski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Genaro Hernandez
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jennifer L Eitson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Abir Majumdar
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Marco Tonelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Zhe Chen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yang Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John W Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA. .,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA. .,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
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187
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Application of mRNA Technology in Cancer Therapeutics. Vaccines (Basel) 2022; 10:vaccines10081262. [PMID: 36016150 PMCID: PMC9415393 DOI: 10.3390/vaccines10081262] [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: 07/11/2022] [Revised: 07/31/2022] [Accepted: 08/01/2022] [Indexed: 11/18/2022] Open
Abstract
mRNA-based therapeutics pose as promising treatment strategies for cancer immunotherapy. Improvements in materials and technology of delivery systems have helped to overcome major obstacles in generating a sufficient immune response required to fight a specific type of cancer. Several in vivo models and early clinical studies have suggested that various mRNA treatment platforms can induce cancer-specific cytolytic activity, leading to numerous clinical trials to determine the optimal method of combinations and sequencing with already established agents in cancer treatment. Nevertheless, further research is required to optimize RNA stabilization, delivery platforms, and improve clinical efficacy by interacting with the tumor microenvironment to induce a long-term antitumor response. This review provides a comprehensive summary of the available evidence on the recent advances and efforts to overcome existing challenges of mRNA-based treatment strategies, and how these efforts play key roles in offering perceptive insights into future considerations for clinical application.
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188
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Shanmugasundaram M, Senthilvelan A, Kore AR. Recent Advances in Modified Cap Analogs: Synthesis, Biochemical Properties, and mRNA Based Vaccines. CHEM REC 2022; 22:e202200005. [PMID: 35420257 PMCID: PMC9111249 DOI: 10.1002/tcr.202200005] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/25/2022] [Indexed: 12/15/2022]
Abstract
The recent FDA approval of the mRNA vaccine for severe acute respiratory syndrome coronavirus (SARS-CoV-2) emphasizes the importance of mRNA as a powerful tool for therapeutic applications. The chemically modified mRNA cap analogs contain a unique cap structure, m7 G[5']ppp[5']N (where N=G, A, C or U), present at the 5'-end of many eukaryotic cellular and viral RNAs and several non-coding RNAs. The chemical modifications on cap analog influence orientation's nature, translational efficiency, nuclear stability, and binding affinity. The recent invention of a trinucleotide cap analog provides groundbreaking research in the area of mRNA analogs. Notably, trinucleotide cap analogs outweigh dinucleotide cap analogs in terms of capping efficiency and translational properties. This review focuses on the recent development in the synthesis of various dinucleotide cap analogs such as dinucleotide containing a triazole moiety, phosphorothiolate cap, biotinylated cap, cap analog containing N1 modification, cap analog containing N2 modification, dinucleotide containing fluorescence probe and TAT, bacterial caps, and trinucleotide cap analogs. In addition, the biological applications of these novel cap analogs are delineated.
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Affiliation(s)
| | - Annamalai Senthilvelan
- Life Sciences Solutions GroupThermo Fisher Scientific2130 Woodward StreetAustinTX 78744-1832US
| | - Anilkumar R. Kore
- Life Sciences Solutions GroupThermo Fisher Scientific2130 Woodward StreetAustinTX 78744-1832US
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189
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Xu M, Risse J, Kormelink R. Cap-snatching as a possible contributor to photosynthesis shut-off. J Gen Virol 2022; 103. [PMID: 35947091 DOI: 10.1099/jgv.0.001763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cap-snatching is a mechanism applied by segmented, negative strand (-) RNA viruses (NSVs) to initiate genome transcription. So far, the cap donor source of cytoplasmic-replicating NSVs has remained elusive. Recently, studies pointed to processing body (P body, PB) as the potential source for providing capped RNAs but conclusive evidence is still lacking. To attempt identifying these sources, here the 5' non-viral leader sequences of Tomato spotted wilt virus (TSWV) N mRNAs were analysed by high-throughput sequencing (HTS) from plants subjected to normal and heat-stress conditions, and subsequently mapped on host donor transcripts. The majority of non-viral heterogenous, host-derived leader sequences ranged in size between ~10-20 nt and contained A or AG residues at the cleavage site and the presence of certain sequence motifs. Mapping the capped-leader sequences to the 5' UTR region of genes encoded by the Nicotiana tabacum genome, identified 348 donor genes and which were specifically enriched in cellular photosynthesis pathway. Nineteen of those were clearly expressed differentially at normal condition versus heat-stress conditions. Although the results did not point towards snatching of capped-RNA leader sequences from certain cytoplasmic RNA granules in particular, they indicated photosynthesis downregulation (and development of disease symptoms) partially result from cap-snatching.
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Affiliation(s)
- Min Xu
- Laboratory of Virology, Department of Plant Sciences, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Judith Risse
- Laboratory of Bioinformatics, Department of Plant Sciences, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Richard Kormelink
- Laboratory of Virology, Department of Plant Sciences, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
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190
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Chan SH, Whipple JM, Dai N, Kelley TM, Withers K, Tzertzinis G, Corrêa IR, Robb GB. RNase H-based analysis of synthetic mRNA 5' cap incorporation. RNA (NEW YORK, N.Y.) 2022; 28:1144-1155. [PMID: 35680168 PMCID: PMC9297845 DOI: 10.1261/rna.079173.122] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Advances in mRNA synthesis and lipid nanoparticles technologies have helped make mRNA therapeutics and vaccines a reality. The 5' cap structure is a crucial modification required to functionalize synthetic mRNA for efficient protein translation in vivo and evasion of cellular innate immune responses. The extent of 5' cap incorporation is one of the critical quality attributes in mRNA manufacturing. RNA cap analysis involves multiple steps: generation of predefined short fragments from the 5' end of the kilobase-long synthetic mRNA molecules using RNase H, a ribozyme or a DNAzyme, enrichment of the 5' cleavage products, and LC-MS intact mass analysis. In this paper, we describe (1) a framework to design site-specific RNA cleavage using RNase H; (2) a method to fluorescently label the RNase H cleavage fragments for more accessible readout methods such as gel electrophoresis or high-throughput capillary electrophoresis; (3) a simplified method for post-RNase H purification using desthiobiotinylated oligonucleotides and streptavidin magnetic beads followed by elution using water. By providing a design framework for RNase H-based RNA 5' cap analysis using less resource-intensive analytical methods, we hope to make RNA cap analysis more accessible to the scientific community.
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Affiliation(s)
- S Hong Chan
- New England Biolabs, Ipswich, Massachusetts 01938, USA
| | | | - Nan Dai
- New England Biolabs, Ipswich, Massachusetts 01938, USA
| | | | | | | | - Ivan R Corrêa
- New England Biolabs, Ipswich, Massachusetts 01938, USA
| | - G Brett Robb
- New England Biolabs, Ipswich, Massachusetts 01938, USA
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191
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Perzanowska O, Smietanski M, Jemielity J, Kowalska J. Chemically Modified Poly(A) Analogs Targeting PABP: Structure Activity Relationship and Translation Inhibitory Properties. Chemistry 2022; 28:e202201115. [PMID: 35575378 PMCID: PMC9400960 DOI: 10.1002/chem.202201115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Indexed: 11/13/2022]
Abstract
Poly(A)‐binding protein (PABP) is an essential element of cellular translational machinery. Recent studies have revealed that poly(A) tail modifications can modulate mRNA stability and translational potential, and that oligoadenylate‐derived PABP ligands can act as effective translational inhibitors with potential applications in pain management. Although extensive research has focused on protein‐RNA and protein‐protein interactions involving PABPs, further studies are required to examine the ligand specificity of PABP. In this study, we developed a microscale thermophoresis‐based assay to probe the interactions between PABP and oligoadenylate analogs containing different chemical modifications. Using this method, we evaluated oligoadenylate analogs modified with nucleobase, ribose, and phosphate moieties to identify modification hotspots. In addition, we determined the susceptibility of the modified oligos to CNOT7 to identify those with the potential for increased cellular stability. Consequently, we selected two enzymatically stable oligoadenylate analogs that inhibit translation in rabbit reticulocyte lysates with a higher potency than a previously reported PABP ligand. We believe that the results presented in this study and the implemented methodology can be capitalized upon in the future development of RNA‐based biological tools.
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Affiliation(s)
- Olga Perzanowska
- Division of Biophysics Faculty of Physics University of Warsaw Ludwika Pasteura 5 02-093 Warsaw Poland
- Centre of New Technologies University of Warsaw Stefana Banacha 2c 02-097 Warsaw Poland
| | - Miroslaw Smietanski
- Centre of New Technologies University of Warsaw Stefana Banacha 2c 02-097 Warsaw Poland
| | - Jacek Jemielity
- Centre of New Technologies University of Warsaw Stefana Banacha 2c 02-097 Warsaw Poland
| | - Joanna Kowalska
- Division of Biophysics Faculty of Physics University of Warsaw Ludwika Pasteura 5 02-093 Warsaw Poland
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192
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Zhang K, Law MCY, Nguyen TM, Tan YB, Wirawan M, Law YS, Jeong LS, Luo D. Molecular basis of specific viral RNA recognition and 5'-end capping by the Chikungunya virus nsP1. Cell Rep 2022; 40:111133. [PMID: 35905713 DOI: 10.1016/j.celrep.2022.111133] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 06/15/2022] [Accepted: 07/01/2022] [Indexed: 11/17/2022] Open
Abstract
Many viruses encode RNA-modifying enzymes to edit the 5' end of viral RNA to mimic the cellular mRNA for effective protein translation, genome replication, and evasion of the host defense mechanisms. Alphavirus nsP1 synthesizes the 5' end Cap-0 structure of viral RNAs. However, the molecular basis of the capping process remains unclear. We determine high-resolution cryoelectron microscopy (cryo-EM) structures of Chikungunya virus nsP1 in complex with m7GTP/SAH, covalently attached m7GMP, and Cap-0 viral RNA. These structures reveal details of viral-RNA-capping reactions and uncover a sequence-specific virus RNA-recognition pattern that, in turn, regulates viral-RNA-capping efficiency to ensure optimal genome replication and subgenomic RNA transcription. This sequence-specific enzyme-RNA pairing is conserved across all alphaviruses.
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Affiliation(s)
- Kuo Zhang
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore; School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Michelle Cheok Yien Law
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Trinh Mai Nguyen
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Yaw Bia Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Melissa Wirawan
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Yee-Song Law
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Lak Shin Jeong
- College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 636921, Singapore.
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193
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Chen HM, Li H, Lin MX, Fan WJ, Zhang Y, Lin YT, Wu SX. Research Progress for RNA Modifications in Physiological and Pathological Angiogenesis. Front Genet 2022; 13:952667. [PMID: 35937999 PMCID: PMC9354963 DOI: 10.3389/fgene.2022.952667] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/20/2022] [Indexed: 12/04/2022] Open
Abstract
As a critical layer of epigenetics, RNA modifications demonstrate various molecular functions and participate in numerous biological processes. RNA modifications have been shown to be essential for embryogenesis and stem cell fate. As high-throughput sequencing and antibody technologies advanced by leaps and bounds, the association of RNA modifications with multiple human diseases sparked research enthusiasm; in addition, aberrant RNA modification leads to tumor angiogenesis by regulating angiogenesis-related factors. This review collected recent cutting-edge studies focused on RNA modifications (N6-methyladenosine (m6A), N5-methylcytosine (m5C), N7-methylguanosine (m7G), N1-methyladenosine (m1A), and pseudopuridine (Ψ)), and their related regulators in tumor angiogenesis to emphasize the role and impact of RNA modifications.
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Affiliation(s)
- Hui-Ming Chen
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
| | - Hang Li
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Meng-Xian Lin
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Wei-Jie Fan
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Yi Zhang
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Yan-Ting Lin
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
- *Correspondence: Shu-Xiang Wu, ; Yan-Ting Lin,
| | - Shu-Xiang Wu
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
- *Correspondence: Shu-Xiang Wu, ; Yan-Ting Lin,
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194
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Böldicke T. Therapeutic Potential of Intrabodies for Cancer Immunotherapy: Current Status and Future Directions. Antibodies (Basel) 2022; 11:antib11030049. [PMID: 35892709 PMCID: PMC9326752 DOI: 10.3390/antib11030049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/29/2022] [Accepted: 07/12/2022] [Indexed: 12/04/2022] Open
Abstract
Tumor cells are characterized by overexpressed tumor-associated antigens or mutated neoantigens, which are expressed on the cell surface or intracellularly. One strategy of cancer immunotherapy is to target cell-surface-expressed tumor-associated antigens (TAAs) with therapeutic antibodies. For targeting TAAs or neoantigens, adoptive T-cell therapies with activated autologous T cells from cancer patients transduced with novel recombinant TCRs or chimeric antigen receptors have been successfully applied. Many TAAs and most neoantigens are expressed in the cytoplasm or nucleus of tumor cells. As alternative to adoptive T-cell therapy, the mRNA of intracellular tumor antigens can be depleted by RNAi, the corresponding genes or proteins deleted by CRISPR-Cas or inactivated by kinase inhibitors or by intrabodies, respectively. Intrabodies are suitable to knockdown TAAs and neoantigens without off-target effects. RNA sequencing and proteome analysis of single tumor cells combined with computational methods is bringing forward the identification of new neoantigens for the selection of anti-cancer intrabodies, which can be easily performed using phage display antibody repertoires. For specifically delivering intrabodies into tumor cells, the usage of new capsid-modified adeno-associated viruses and lipid nanoparticles coupled with specific ligands to cell surface receptors can be used and might bring cancer intrabodies into the clinic.
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Affiliation(s)
- Thomas Böldicke
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
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195
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Gómez-Aguado I, Rodríguez-Castejón J, Beraza-Millor M, Rodríguez-Gascón A, Del Pozo-Rodríguez A, Solinís MÁ. mRNA delivery technologies: Toward clinical translation. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2022; 372:207-293. [PMID: 36064265 DOI: 10.1016/bs.ircmb.2022.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Messenger RNA (mRNA)-therapies have recently taken a huge step toward clinic thanks to the first mRNA-based medicinal products marketed. mRNA features for clinical purposes are improved by chemical modifications, but the inclusion in a delivery system is a regular requirement. mRNA nanomedicines must be designed for the specific therapeutic purpose, protecting the nucleic acid and facilitating the overcoming of biological barriers. Polymers, polypeptides, and cationic lipids are the main used materials to design mRNA delivery systems. Among them, lipid nanoparticles (LNPs) are the most advanced ones, and currently they are at the forefront of preclinical and clinical evaluation in several fields, including immunotherapy (against infectious diseases and cancer), protein replacement, gene editing and regenerative medicine. This chapter includes an overview on mRNA delivery technologies, with special interest in LNPs, and the most recent advances in their clinical application. Liposomes are the mRNA delivery technology with the highest clinical translation among LNPs, whereas the first clinical trial of a therapeutic mRNA formulated in exosomes has been recently approved for protein replacement therapy. The first mRNA products approved by the regulatory agencies worldwide are LNP-based mRNA vaccines against viral infections, specifically against the 2019 coronavirus disease (COVID-19). The clinical translation of mRNA-therapies for cancer is mainly focused on three strategies: anti-cancer vaccination by means of delivering cancer antigens or acting as an adjuvant, mRNA-engineered chimeric antigen receptors (CARs) and T-cell receptors (TCRs), and expression of antibodies and immunomodulators. Cancer immunotherapy and, more recently, COVID-19 vaccines spearhead the advance of mRNA clinical use.
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Affiliation(s)
- Itziar Gómez-Aguado
- Pharmacokinetic, Nanotechnology and Gene Therapy Group (PharmaNanoGene), Faculty of Pharmacy, Centro de investigación Lascaray ikergunea, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain; Bioaraba, Microbiology, Infectious Disease, Antimicrobial Agents, and Gene Therapy, Vitoria-Gasteiz, Spain
| | - Julen Rodríguez-Castejón
- Pharmacokinetic, Nanotechnology and Gene Therapy Group (PharmaNanoGene), Faculty of Pharmacy, Centro de investigación Lascaray ikergunea, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain; Bioaraba, Microbiology, Infectious Disease, Antimicrobial Agents, and Gene Therapy, Vitoria-Gasteiz, Spain
| | - Marina Beraza-Millor
- Pharmacokinetic, Nanotechnology and Gene Therapy Group (PharmaNanoGene), Faculty of Pharmacy, Centro de investigación Lascaray ikergunea, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain; Bioaraba, Microbiology, Infectious Disease, Antimicrobial Agents, and Gene Therapy, Vitoria-Gasteiz, Spain
| | - Alicia Rodríguez-Gascón
- Pharmacokinetic, Nanotechnology and Gene Therapy Group (PharmaNanoGene), Faculty of Pharmacy, Centro de investigación Lascaray ikergunea, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain; Bioaraba, Microbiology, Infectious Disease, Antimicrobial Agents, and Gene Therapy, Vitoria-Gasteiz, Spain
| | - Ana Del Pozo-Rodríguez
- Pharmacokinetic, Nanotechnology and Gene Therapy Group (PharmaNanoGene), Faculty of Pharmacy, Centro de investigación Lascaray ikergunea, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain; Bioaraba, Microbiology, Infectious Disease, Antimicrobial Agents, and Gene Therapy, Vitoria-Gasteiz, Spain
| | - María Ángeles Solinís
- Pharmacokinetic, Nanotechnology and Gene Therapy Group (PharmaNanoGene), Faculty of Pharmacy, Centro de investigación Lascaray ikergunea, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain; Bioaraba, Microbiology, Infectious Disease, Antimicrobial Agents, and Gene Therapy, Vitoria-Gasteiz, Spain.
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196
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Strezsak S, Pimentel AJ, Hill IT, Beuning PJ, Skizim NJ. Novel Mobile Phase to Control Charge States and Metal Adducts in the LC/MS for mRNA Characterization Assays. ACS OMEGA 2022; 7:22181-22191. [PMID: 35811888 PMCID: PMC9260895 DOI: 10.1021/acsomega.2c00185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Mass spectrometry is a widely used tool in the characterization of oligonucleotides. This analysis can be challenging due to the large number of possible charge states of oligonucleotides, which can limit the sensitivity of the assay, along with the propensity of oligonucleotides to readily form adducts with free alkali metals. To reduce the adduct formation, oligonucleotides are typically purified with desalting columns prior to analysis. We have developed a mobile phase that gives superior reduction in charge states and adduct formation compared to previously reported methods and, more importantly, obviates the requirement of desalting samples prior to mass spectrometric analysis, significantly decreasing the sample preparation time and amount of RNA required for analysis. We have applied this mobile phase to develop methods to quantify the 5'-capping efficiency and to characterize the polyadenosine (poly(A)) tail of mRNA synthesized in vitro: two critical quality attributes of mRNA therapeutics. Through this, we were able to demonstrate RNA that was co-transcriptionally capped to have capping efficiency equivalent (the percent total molecules that contain a cap) to other reports in the literature using materials that were generated using the same synthesis procedure. Furthermore, by using a mobile phase mixture comprised of hexafluoroisopropanol, triethylammonium acetate, triethylamine, and ethanol, we were able to determine the size distribution of the poly(A) tail in various mRNA samples from DNA templates that ranged from 50 to 150 nt poly(A) and verify that distribution with commercially available RNA standards, successfully demonstrating that this mobile phase composition could be used for characterization assays for both mRNA caps and tails.
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Affiliation(s)
- Steven
R. Strezsak
- Department
of Chemistry & Chemical Biology, Northeastern
University, 102 Hurtig Hall, Boston, Massachusetts 02115, United States
- Greenlight
Biosciences, 200 Boston Avenue Suite 1000, Medford, Massachusetts 02155, United States
| | - Alyssa Jean Pimentel
- Greenlight
Biosciences, 200 Boston Avenue Suite 1000, Medford, Massachusetts 02155, United States
| | - Ian T. Hill
- Greenlight
Biosciences, 200 Boston Avenue Suite 1000, Medford, Massachusetts 02155, United States
| | - Penny J. Beuning
- Department
of Chemistry & Chemical Biology, Northeastern
University, 102 Hurtig Hall, Boston, Massachusetts 02115, United States
| | - Nicholas J. Skizim
- Greenlight
Biosciences, 200 Boston Avenue Suite 1000, Medford, Massachusetts 02155, United States
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197
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Wu X, Li C, Wang Z, Zhang Y, Liu S, Chen S, Chen S, Liu W, Liu X. A bioinformatic analysis study of m 7G regulator-mediated methylation modification patterns and tumor microenvironment infiltration in glioblastoma. BMC Cancer 2022; 22:729. [PMID: 35788194 PMCID: PMC9251941 DOI: 10.1186/s12885-022-09791-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 06/16/2022] [Indexed: 11/25/2022] Open
Abstract
Background Glioblastoma is one of the most common brain cancers in adults, and is characterized by recurrence and little curative effect. An effective treatment for glioblastoma patients remains elusive worldwide. 7-methylguanosine (m7G) is a common RNA modification, and its role in tumors has become a research hotspot. Methods By searching for differentially expressed genes related to m7G, we generated a prognostic signature via cluster analysis and established classification criteria of high and low risk scores. The effectiveness of classification was validated using the Non-negative matrix factorization (NMF) algorithm, and repeatedly verified using training and test groups. The dimension reduction method was used to clearly show the difference and clinical significance of the data. All analyses were performed via R (version 4.1.2). Results According to the signature that included four genes (TMOD2, CACNG2, PLOD3, and TMSB10), glioblastoma patients were divided into high and low risk score groups. The survival rates between the two groups were significantly different, and the predictive abilities for 1-, 3-, and 5-year survivals were effective. We further established a Nomogram model to further examine the signature,as well as other clinical factors, with remaining significant results. Our signature can act as an independent prognostic factor related to immune-related processes in glioblastoma. Conclusions Our research addresses the gap in knowledge in the m7G and glioblastoma research fields. The establishment of a prognostic signature and the extended analysis of the tumor microenvironment, immune correlation, and tumor mutation burden further suggest the important role of m7G in the development and development of this disease. This work will provide support for future research. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09791-y.
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Affiliation(s)
- Xinrui Wu
- Department of oncology and chemotherapy, Affiliated Hospital of Nantong University, Nantong, China.,Department of Clinical Medicine, Medical School of Nantong University, Nantong, China
| | - Chuanyu Li
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Zhisu Wang
- Department of Clinical Medicine, Medical School of Nantong University, Nantong, China
| | - Yundi Zhang
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shifan Liu
- Department of Medical imaging, Medical School of Nantong University, Nantong, China
| | - Siqi Chen
- Department of Medical imaging, Medical School of Nantong University, Nantong, China
| | - Shuai Chen
- Department of measurement and control technology and instruments, School of mechanical engineering, Nantong University, Nantong, China
| | - Wangrui Liu
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China. .,Department of Interventional Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Xiaoman Liu
- Department of oncology and chemotherapy, Affiliated Hospital of Nantong University, Nantong, China. .,Department of Clinical Medicine, Medical School of Nantong University, Nantong, China.
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198
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Zhou K, Yang J, Li X, Xiong W, Zhang P, Zhang X. N7-Methylguanosine Regulatory Genes Profoundly Affect the Prognosis, Progression, and Antitumor Immune Response of Hepatocellular Carcinoma. Front Surg 2022; 9:893977. [PMID: 35784919 PMCID: PMC9246272 DOI: 10.3389/fsurg.2022.893977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is a common abdominal cancer with poor survival outcomes. Although there is growing evidence that N7-methylguanosine (m7G) is closely associated with tumor prognosis, development, and immune response, few studies focus on this topic. Methods The novel m7G risk signature was constructed through the Lasso regression analysis. Its prognostic value was evaluated through a series of survival analyses and was tested in ICGC-LIRI, GSE14520, and GSE116174 cohorts. CIBERSORT, ssGSEA, and ESTIMATE methods were applied to explore the effects of the m7G risk score on tumor immune microenvironment (TIM). The GSEA method was used to evaluate the impacts of the m7G risk score on glycolysis, ferroptosis, and pyroptosis. The human protein atlas (HPA) database was used to clarify the histological expression levels of five m7G signature genes. The biofunctions of NCBP2 in hepatocellular cancer (HC) cells were confirmed through qPCR, CCK8, and transwell assays. Results Five m7G regulatory genes comprised the novel risk signature. The m7G risk score was identified as an independent prognostic factor of HCC and could increase the decision-making benefit of traditional prognostic models. Besides, we established a nomogram containing the clinical stage and m7G risk score to predict the survival rates of HCC patients. The prognostic value of the m7G model was successfully validated in ICGC and GSE116174 cohorts. Moreover, high m7G risk led to a decreased infiltration level of CD8+ T cells, whereas it increased the infiltration levels of Tregs and macrophages. The glycolysis and pyroptosis processes were found to be enriched in the HCC patients with high m7G risk. Finally, overexpression of NCBP2 could promote the proliferation, migration, and invasion of HC cells. Conclusions The m7G risk score was closely related to the prognosis, antitumor immune process, glycolysis, and malignant progression of HCC. NCBP2 has pro-oncogenic abilities, showing promise as a novel treatment target.
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Affiliation(s)
- Kexiang Zhou
- Department of Gastroenterology, The Third Affiliated Hospital of ChongQing Medical University, China
- ChongQing Medical University, Chongqing, China
| | - Jiaqun Yang
- Department of Gastroenterology, The Third Affiliated Hospital of ChongQing Medical University, China
| | - Xiaoyan Li
- Department of Gastroenterology, The Third Affiliated Hospital of ChongQing Medical University, China
| | - Wei Xiong
- Department of Gastroenterology, The Third Affiliated Hospital of ChongQing Medical University, China
| | - Pengbin Zhang
- Department of Gastroenterology, The Third Affiliated Hospital of ChongQing Medical University, China
| | - Xuqing Zhang
- ChongQing Medical University, Chongqing, China
- Department of Infectious Diseases, The Third Affiliated Hospital of ChongQing Medical University, China
- Correspondence: Xuqing Zhang
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199
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Lu F, Gao J, Hou Y, Cao K, Xia Y, Chen Z, Yu H, Chang L, Li W. Construction of a Novel Prognostic Model in Lung Adenocarcinoma Based on 7-Methylguanosine-Related Gene Signatures. Front Oncol 2022; 12:876360. [PMID: 35785179 PMCID: PMC9243265 DOI: 10.3389/fonc.2022.876360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
Increasing evidence has implicated the modification of 7-methylguanosine (m7G), a type of RNA modification, in tumor progression. However, no comprehensive analysis to date has summarized the predicted role of m7G-related gene signatures in lung adenocarcinoma (LUAD). Herein, we aimed to develop a novel prognostic model in LUAD based on m7G-related gene signatures. The LUAD transcriptome profiling data and corresponding clinical data were acquired from the Cancer Genome Atlas (TCGA) and two Gene Expression Omnibus datasets. After screening, we first obtained 29 m7G-related genes, most of which were upregulated in tumor tissues and negatively associated with overall survival (OS). According to the expression similarity of m7G-related genes, the combined samples from the TCGA-LUAD and GSE68465 datasets were further classified as two clusters that exhibit distinct OS rates and genetic heterogeneity. Then, we constructed a novel prognostic model involving four genes by using 130 differentially expressed genes among the two clusters. The combined samples were randomly divided into a training cohort and an internal validation cohort in a 1:1 ratio, and the GSE72094 dataset was used as an external validation cohort. The samples were divided into high- and low-risk groups. We demonstrated that a higher risk score was an independent negative prognostic factor and predicted poor OS. A nomogram was further constructed to better predict the survival of LUAD patients. Functional enrichment analyses indicated that cell cycle and DNA replication-related biological processes and pathways were enriched in the high-risk group. More importantly, the low-risk group had greater infiltration and enrichment of most immune cells, as well as higher ESTIMATE, immune, and stromal scores. In addition, the high-risk group had a lower TIDE score and higher expressions of most immune checkpoint-related genes. We finally noticed that patients in the high-risk group were more sensitive to chemotherapeutic agents commonly used in LUAD. In conclusion, we herein summarized for the first time the alterations and prognostic role of m7G-related genes in LUAD and then constructed a prognostic model based on m7G-related gene signatures that could accurately and stably predict survival and guide individualized treatment decision-making in LUAD patients.
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Affiliation(s)
- Fei Lu
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
- Department of Oncology and Hematology, Southern Central Hospital of Yunnan Province, The First People’s Hospital of Honghe State, Mengzi, China
| | - Jingyan Gao
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Yu Hou
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Ke Cao
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Yaoxiong Xia
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Zhengting Chen
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Hui Yu
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Li Chang
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
- *Correspondence: Wenhui Li, ; Li Chang,
| | - Wenhui Li
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
- *Correspondence: Wenhui Li, ; Li Chang,
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Qureischi M, Mohr J, Arellano-Viera E, Knudsen SE, Vohidov F, Garitano-Trojaola A. mRNA-based therapies: Preclinical and clinical applications. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2022; 372:1-54. [PMID: 36064262 DOI: 10.1016/bs.ircmb.2022.04.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
At the fundamental level, messenger RNA (mRNA)-based therapeutics involves the delivery of in vitro-transcribed (IVT) mRNA into the cytoplasm of a target cell, where it is translated into the desired protein. IVT mRNA presents various advantages compared to DNA and recombinant protein-based approaches that make it ideal for a broad range of therapeutic applications. IVT mRNA, which is translated in the cytoplasm after transfection into cells, can encode virtually any target protein. Notably, it does not enter the nucleus, which avoids its integration into the genome and the risk of insertional mutagenesis. The large-scale production of IVT mRNA is less complex than production of recombinant proteins, and Good Manufacturing Practice-compliant mRNA production is easily scalable, ideally poising mRNA for not only off-the-shelf, but more personalized treatment approaches. IVT mRNA's safety profile, pharmacokinetics, and pharmacodynamics, including its inherent immunostimulatory capacity, can be optimized for different therapeutic applications by harnessing a wide array of optimized sequence elements, chemical modifications, purification techniques, and delivery methods. The value of IVT mRNA was recently proved during the COVID-19 pandemic when mRNA-based vaccines outperformed the efficacy of established technologies, and millions of doses were rapidly deployed. In this review, we will discuss chemical modifications of IVT mRNA and highlight numerous preclinical and clinical applications including vaccines for cancer and infectious diseases, cancer immunotherapy, protein replacement, gene editing, and cell reprogramming.
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