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Mars JC, Culjkovic-Kraljacic B, Borden KL. eIF4E orchestrates mRNA processing, RNA export and translation to modify specific protein production. Nucleus 2024; 15:2360196. [PMID: 38880976 PMCID: PMC11185188 DOI: 10.1080/19491034.2024.2360196] [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: 02/12/2024] [Accepted: 05/22/2024] [Indexed: 06/18/2024] Open
Abstract
The eukaryotic translation initiation factor eIF4E acts as a multifunctional factor that simultaneously influences mRNA processing, export, and translation in many organisms. Its multifactorial effects are derived from its capacity to bind to the methyl-7-guanosine cap on the 5'end of mRNAs and thus can act as a cap chaperone for transcripts in the nucleus and cytoplasm. In this review, we describe the multifactorial roles of eIF4E in major mRNA-processing events including capping, splicing, cleavage and polyadenylation, nuclear export and translation. We discuss the evidence that eIF4E acts at two levels to generate widescale changes to processing, export and ultimately the protein produced. First, eIF4E alters the production of components of the mRNA processing machinery, supporting a widescale reprogramming of multiple mRNA processing events. In this way, eIF4E can modulate mRNA processing without physically interacting with target transcripts. Second, eIF4E also physically interacts with both capped mRNAs and components of the RNA processing or translation machineries. Further, specific mRNAs are sensitive to eIF4E only in particular mRNA processing events. This selectivity is governed by the presence of cis-acting elements within mRNAs known as USER codes that recruit relevant co-factors engaging the appropriate machinery. In all, we describe the molecular bases for eIF4E's multifactorial function and relevant regulatory pathways, discuss the basis for selectivity, present a compendium of ~80 eIF4E-interacting factors which play roles in these activities and provide an overview of the relevance of its functions to its oncogenic potential. Finally, we summarize early-stage clinical studies targeting eIF4E in cancer.
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Affiliation(s)
- Jean-Clément Mars
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Montréal, QC, Canada
| | - Biljana Culjkovic-Kraljacic
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Montréal, QC, Canada
| | - Katherine L.B. Borden
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Montréal, QC, Canada
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2
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Vukovic I, Barnada SM, Ruffin JW, Karlin J, Lokareddy RK, Cingolani G, McMahon SB. Non-redundant roles for the human mRNA decapping cofactor paralogs DCP1a and DCP1b. Life Sci Alliance 2024; 7:e202402938. [PMID: 39256052 PMCID: PMC11387620 DOI: 10.26508/lsa.202402938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 08/21/2024] [Accepted: 08/21/2024] [Indexed: 09/12/2024] Open
Abstract
Eukaryotic gene expression is regulated at the transcriptional and post-transcriptional levels, with disruption of regulation contributing significantly to human diseases. The 5' m7G mRNA cap is a central node in post-transcriptional regulation, participating in both mRNA stabilization and translation efficiency. In mammals, DCP1a and DCP1b are paralogous cofactor proteins of the mRNA cap hydrolase DCP2. As lower eukaryotes have a single DCP1 cofactor, the functional advantages gained by this evolutionary divergence remain unclear. We report the first functional dissection of DCP1a and DCP1b, demonstrating that they are non-redundant cofactors of DCP2 with unique roles in decapping complex integrity and specificity. DCP1a is essential for decapping complex assembly and interactions between the decapping complex and mRNA cap-binding proteins. DCP1b is essential for decapping complex interactions with protein degradation and translational machinery. DCP1a and DCP1b impact the turnover of distinct mRNAs. The observation that different ontological groups of mRNA molecules are regulated by DCP1a and DCP1b, along with their non-redundant roles in decapping complex integrity, provides the first evidence that these paralogs have qualitatively distinct functions.
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Affiliation(s)
- Ivana Vukovic
- https://ror.org/00ysqcn41 Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Samantha M Barnada
- https://ror.org/00ysqcn41 Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | | | - Jon Karlin
- https://ror.org/00ysqcn41 Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Ravi Kumar Lokareddy
- https://ror.org/008s83205 Academic Joint Departments - Biochemistry & Molecular Genetic, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Gino Cingolani
- https://ror.org/008s83205 Academic Joint Departments - Biochemistry & Molecular Genetic, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Steven B McMahon
- https://ror.org/00ysqcn41 Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
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3
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Jiang H, Liu G, Gao Y, Gan J, Chen D, Murchie AIH. Cofactor Binding Triggers Rapid Conformational Remodelling of the Active Site of a Methyltransferase Ribozyme. J Biol Chem 2024:107863. [PMID: 39374779 DOI: 10.1016/j.jbc.2024.107863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 09/18/2024] [Accepted: 09/29/2024] [Indexed: 10/09/2024] Open
Abstract
The methyltransferase ribozyme SMRZ-1 utilizes S-adenosyl-methionine (SAM) and Cu (II) ions to methylate RNA. Comparison of the SAM bound and unbound RNA structures has shown a conformational change in the RNA. However, the contribution of specific interactions and the role of a pseudo-triplex motif in the catalytic centre on the methylation reaction is not completely understood. In this study, we have used atomic substitutions and mutational analysis to investigate the reaction specificity and the key interactions required for catalysis. Substitution of the fluorescent nucleotide 2-aminopurine within the active ribozyme enabled the conformational dynamics of the RNA upon co-factor binding to be explored using fluorescence spectroscopy. We show that fast co-factor binding (t1/2 ∼ 0.7 seconds) drives a conformational change in the RNA to facilitate methyl group transfer. The importance of stacking interactions at the pseudo-triplex motif and chelation of the Cu (II) ion were shown to be essential for SAM binding.
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Affiliation(s)
- Hengyi Jiang
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Pudong, Shanghai 201399, China. And Institute of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai 200032, China. Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Getong Liu
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Pudong, Shanghai 201399, China. And Institute of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai 200032, China. Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yanqing Gao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jianhua Gan
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Dongrong Chen
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Pudong, Shanghai 201399, China. And Institute of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai 200032, China. Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
| | - Alastair I H Murchie
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Pudong, Shanghai 201399, China. And Institute of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai 200032, China. Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
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4
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Karimi-Sani I, Molavi Z, Naderi S, Mirmajidi SH, Zare I, Naeimzadeh Y, Mansouri A, Tajbakhsh A, Savardashtaki A, Sahebkar A. Personalized mRNA vaccines in glioblastoma therapy: from rational design to clinical trials. J Nanobiotechnology 2024; 22:601. [PMID: 39367418 PMCID: PMC11453023 DOI: 10.1186/s12951-024-02882-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 09/26/2024] [Indexed: 10/06/2024] Open
Abstract
Glioblastomas (GBMs) are the most common and aggressive malignant brain tumors, presenting significant challenges for treatment due to their invasive nature and localization in critical brain regions. Standard treatment includes surgical resection followed by radiation and adjuvant chemotherapy with temozolomide (TMZ). Recent advances in immunotherapy, including the use of mRNA vaccines, offer promising alternatives. This review focuses on the emerging use of mRNA vaccines for GBM treatment. We summarize recent advancements, evaluate current obstacles, and discuss notable successes in this field. Our analysis highlights that while mRNA vaccines have shown potential, their use in GBM treatment is still experimental. Ongoing research and clinical trials are essential to fully understand their therapeutic potential. Future developments in mRNA vaccine technology and insights into GBM-specific immune responses may lead to more targeted and effective treatments. Despite the promise, further research is crucial to validate and optimize the effectiveness of mRNA vaccines in combating GBM.
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Affiliation(s)
- Iman Karimi-Sani
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Molavi
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Samaneh Naderi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyedeh-Habibeh Mirmajidi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Iman Zare
- Research and Development Department, Sina Medical Biochemistry Technologies Co. Ltd., Shiraz, 7178795844, Iran
| | - Yasaman Naeimzadeh
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Atena Mansouri
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Amir Tajbakhsh
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.
- Infertility Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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5
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Cheng Z, Islam S, Kanlong JG, Sheppard M, Seo H, Nikolaitchik OA, Kearse MG, Pathak VK, Musier-Forsyth K, Hu WS. Translation of HIV-1 unspliced RNA is regulated by 5' untranslated region structure. J Virol 2024:e0116024. [PMID: 39315813 DOI: 10.1128/jvi.01160-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 09/03/2024] [Indexed: 09/25/2024] Open
Abstract
HIV-1 must generate infectious virions to spread to new hosts and HIV-1 unspliced RNA (HIV-1 RNA) plays two central roles in this process. HIV-1 RNA serves as an mRNA that is translated to generate proteins essential for particle production and replication, and it is packaged into particles as the viral genome. HIV-1 uses several transcription start sites to generate multiple RNAs that differ by a few nucleotides at the 5' end, including those with one (1G) or three (3G) 5' guanosines. The virus relies on host machinery to translate its RNAs in a cap-dependent manner. Here, we demonstrate that the 5' context of HIV-1 RNA affects the efficiency of translation both in vitro and in cells. Although both RNAs are competent for translation, 3G RNA is translated more efficiently than 1G RNA. The 5' untranslated region (UTR) of 1G and 3G RNAs has previously been shown to fold into distinct structural ensembles. We show that HIV-1 mutants in which the 5' UTR of 1G and 3G RNAs fold into similar structures were translated at similar efficiencies. Thus, the host machinery translates two 99.9% identical HIV-1 RNAs with different efficiencies, and the translation efficiency is regulated by the 5' UTR structure.IMPORTANCEHIV-1 unspliced RNA contains all the viral genetic information and encodes virion structural proteins and enzymes. Thus, the unspliced RNA serves distinct roles as viral genome and translation template, both critical for viral replication. HIV-1 generates two major unspliced RNAs with a 2-nt difference at the 5' end (3G RNA and 1G RNA). The 1G transcript is known to be preferentially packaged over the 3G transcript. Here, we showed that 3G RNA is favorably translated over 1G RNA based on its 5' untranslated region (UTR) RNA structure. In HIV-1 mutants in which the two major transcripts have similar 5' UTR structures, 1G and 3G RNAs are translated similarly. Therefore, HIV-1 generates two 9-kb RNAs with a 2-nt difference, each serving a distinct role dictated by differential 5' UTR structures.
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Affiliation(s)
- Zetao Cheng
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - Saiful Islam
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - Joseph G Kanlong
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, Center for RNA Biology, Ohio State University, Columbus, Ohio, USA
| | - Madeline Sheppard
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, Center for RNA Biology, Ohio State University, Columbus, Ohio, USA
| | - Heewon Seo
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, Center for RNA Biology, Ohio State University, Columbus, Ohio, USA
| | - Olga A Nikolaitchik
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - Michael G Kearse
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, Ohio State University, Columbus, Ohio, USA
| | - Vinay K Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, Center for RNA Biology, Ohio State University, Columbus, Ohio, USA
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
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6
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Pather S, Charpentier N, van den Ouweland F, Rizzi R, Finlayson A, Salisch N, Muik A, Lindemann C, Khanim R, Abduljawad S, Smith ER, Gurwith M, Chen RT. A Brighton Collaboration standardized template with key considerations for a benefit-risk assessment for the Comirnaty COVID-19 mRNA vaccine. Vaccine 2024; 42:126165. [PMID: 39197299 DOI: 10.1016/j.vaccine.2024.126165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 07/18/2024] [Indexed: 09/01/2024]
Abstract
The Brighton Collaboration Benefit-Risk Assessment of VAccines by TechnolOgy (BRAVATO) Working Group evaluates the safety and other key features of new platform technology vaccines, including nucleic acid (RNA and DNA) vaccines. This manuscript uses the BRAVATO template to report the key considerations for a benefit-risk assessment of the coronavirus disease 2019 (COVID-19) mRNA-based vaccine BNT162b2 (Comirnaty®, or Pfizer-BioNTech COVID-19 vaccine) including the subsequent Original/Omicron BA.1, Original/Omicron BA.4-5 and Omicron XBB.1.5 variant-adapted vaccines developed by BioNTech and Pfizer to protect against COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Initial Emergency Use Authorizations or conditional Marketing Authorizations for the original BNT162b2 vaccine were granted based upon a favorable benefit-risk assessment taking into account clinical safety, immunogenicity, and efficacy data, which was subsequently reconfirmed for younger age groups, and by real world evidence data. In addition, the favorable benefit-risk assessment was maintained for the bivalent vaccines, developed against newly arising SARS-CoV-2 variants, with accumulating clinical trial data.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Emily R Smith
- Brighton Collaboration, a program of the Task Force for Global Health, Decatur, GA, USA.
| | - Marc Gurwith
- Brighton Collaboration, a program of the Task Force for Global Health, Decatur, GA, USA
| | - Robert T Chen
- Brighton Collaboration, a program of the Task Force for Global Health, Decatur, GA, USA
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7
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Lisy S, Rothamel K, Perevalova-Pinzul Y, Ascano M. PAR-dCLIP: Enabling detection of RNA binding protein target transcripts bound at 5' termini through the incorporation of a decapping step. Methods Enzymol 2024; 705:159-222. [PMID: 39389663 DOI: 10.1016/bs.mie.2024.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
RNA binding proteins (RBPs) are responsible for facilitating a wealth of post-transcriptional gene regulatory functions. The role of an RBP on regulated transcripts can be investigated through a pull-down of the RBP and high-throughput sequencing (HTS) of the associated transcripts. Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP), is one such pull-down method that isolates, detects, and sequences the cDNA of RBP-associated transcripts. PAR-CLIP relies on a photoactivatable ribonucleoside analogue, 4-thiouridine, to facilitate covalent RNA-protein crosslinks at 365 nm. These crosslinks permit stringent wash conditions and result in T to C mismatch incorporations during reverse transcription, a unique parameter for the computational analysis of high-confidence binding sites. However, until now, RBPs that bind at the 5'-termini of RNAs have been uniquely restricted from the full potential bandwidth of autoradiographic detection and HTS library preparation. The 5'-termini of RNAs are highly modified, including the most common Pol-II derived modification: the 7-methylguanosine (m7G) cap. In the conventional PAR-CLIP protocol, cap-binding proteins protect the m7G cap from the RNase treatment that generates the necessary substrate for autoradiographic detection and 5' adapter ligation-thus occluding entire populations of RNA from visualization and HTS. Here, we introduce decapping-PAR-CLIP or PAR-dCLIP. We incorporate a decapping step into the PAR-CLIP protocol to generate the necessary substrate to sequence m7G capped transcripts. While PAR-dCLIP was originally targeted towards known m7G-cap binding proteins, we argue that all RBP inquiries, and particularly those suspected to regulate translation, should incorporate this decapping step to ensure that all possible populations of bound transcripts are identified.
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Affiliation(s)
- Samantha Lisy
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Katherine Rothamel
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States; Center for RNA Technologies and Therapeutics, University of California San Diego, La Jolla, CA, United States
| | - Yelena Perevalova-Pinzul
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Manuel Ascano
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States.
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8
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Schlusser N, González A, Pandey M, Zavolan M. Current limitations in predicting mRNA translation with deep learning models. Genome Biol 2024; 25:227. [PMID: 39164757 PMCID: PMC11337900 DOI: 10.1186/s13059-024-03369-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 08/07/2024] [Indexed: 08/22/2024] Open
Abstract
BACKGROUND The design of nucleotide sequences with defined properties is a long-standing problem in bioengineering. An important application is protein expression, be it in the context of research or the production of mRNA vaccines. The rate of protein synthesis depends on the 5' untranslated region (5'UTR) of the mRNAs, and recently, deep learning models were proposed to predict the translation output of mRNAs from the 5'UTR sequence. At the same time, large data sets of endogenous and reporter mRNA translation have become available. RESULTS In this study, we use complementary data obtained in two different cell types to assess the accuracy and generality of currently available models for predicting translational output. We find that while performing well on the data sets on which they were trained, deep learning models do not generalize well to other data sets, in particular of endogenous mRNAs, which differ in many properties from reporter constructs. CONCLUSIONS These differences limit the ability of deep learning models to uncover mechanisms of translation control and to predict the impact of genetic variation. We suggest directions that combine high-throughput measurements and machine learning to unravel mechanisms of translation control and improve construct design.
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Affiliation(s)
- Niels Schlusser
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland.
| | - Asier González
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain
| | - Muskan Pandey
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
- Current address: Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Mihaela Zavolan
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland.
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9
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Neill B, Romero AR, Fenton OS. Advances in Nonviral mRNA Delivery Materials and Their Application as Vaccines for Melanoma Therapy. ACS APPLIED BIO MATERIALS 2024; 7:4894-4913. [PMID: 37930174 PMCID: PMC11220486 DOI: 10.1021/acsabm.3c00721] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Messenger RNA (mRNA) vaccines are promising platforms for cancer immunotherapy because of their potential to encode for a variety of tumor antigens, high tolerability, and capacity to induce strong antitumor immune responses. However, the clinical translation of mRNA cancer vaccines can be hindered by the inefficient delivery of mRNA in vivo. In this review, we provide an overview of mRNA cancer vaccines by discussing their utility in treating melanoma. Specifically, we begin our review by describing the barriers that can impede mRNA delivery to target cells. We then review native mRNA structure and discuss various modification methods shown to enhance mRNA stability and transfection. Next, we outline the advantages and challenges of three nonviral carrier platforms (lipid nanoparticles, polymeric nanoparticles, and lipopolyplexes) frequently used for mRNA delivery. Last, we summarize preclinical and clinical studies that have investigated nonviral mRNA vaccines for the treatment of melanoma. In writing this review, we aim to highlight innovative nonviral strategies designed to address mRNA delivery challenges while emphasizing the exciting potential of mRNA vaccines as next-generation therapies for the treatment of cancers.
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Affiliation(s)
- Bevin Neill
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Adriana Retamales Romero
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Owen S. Fenton
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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10
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Fang N, Liu B, Pan Q, Gong T, Zhan M, Zhao J, Wang Q, Tang Y, Li Y, He J, Xiang T, Sun F, Lu L, Xia J. SMG5 Inhibition Restrains Hepatocellular Carcinoma Growth and Enhances Sorafenib Sensitivity. Mol Cancer Ther 2024; 23:1188-1200. [PMID: 38647536 DOI: 10.1158/1535-7163.mct-23-0729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/25/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
Hepatocellular carcinoma (HCC) has a pathogenesis that remains elusive with restricted therapeutic strategies and efficacy. This study aimed to investigate the role of SMG5, a crucial component in nonsense-mediated mRNA decay (NMD) that degrades mRNA containing a premature termination codon, in HCC pathogenesis and therapeutic resistance. We demonstrated an elevated expression of SMG5 in HCC and scrutinized its potential as a therapeutic target. Our findings revealed that SMG5 knockdown not only inhibited the migration, invasion, and proliferation of HCC cells but also influenced sorafenib resistance. Differential gene expression analysis between the control and SMG5 knockdown groups showed an upregulation of methionine adenosyltransferase 1A in the latter. High expression of methionine adenosyltransferase 1A, a catalyst for S-adenosylmethionine (SAM) production, as suggested by The Cancer Genome Atlas data, was indicative of a better prognosis for HCC. Further, an ELISA showed a higher concentration of SAM in SMG5 knockdown cell supernatants. Furthermore, we found that exogenous SAM supplementation enhanced the sensitivity of HCC cells to sorafenib alongside changes in the expression of Bax and Bcl-2, apoptosis-related proteins. Our findings underscore the important role of SMG5 in HCC development and its involvement in sorafenib resistance, highlighting it as a potential target for HCC treatment.
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Affiliation(s)
- Nan Fang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Clinical Medical College of Jinan University (Zhuhai People's Hospital), Zhuhai, P. R. China
| | - Bing Liu
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Clinical Medical College of Jinan University (Zhuhai People's Hospital), Zhuhai, P. R. China
| | - Qiuzhong Pan
- Department of Biotherapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Tingting Gong
- Department of Ultrasound, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, P. R. China
| | - Meixiao Zhan
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Clinical Medical College of Jinan University (Zhuhai People's Hospital), Zhuhai, P. R. China
| | - Jingjing Zhao
- Department of Biotherapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Qijing Wang
- Department of Biotherapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Yan Tang
- Department of Biotherapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Yongqiang Li
- Department of Biotherapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Jia He
- Department of Biotherapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Tong Xiang
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Fengze Sun
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Clinical Medical College of Jinan University (Zhuhai People's Hospital), Zhuhai, P. R. China
- Department of Biotherapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Ligong Lu
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Clinical Medical College of Jinan University (Zhuhai People's Hospital), Zhuhai, P. R. China
| | - Jianchuan Xia
- Department of Biotherapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
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11
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Tomecki R, Drazkowska K, Madaj R, Mamot A, Dunin-Horkawicz S, Sikorski PJ. Expanding the Available RNA Labeling Toolbox With CutA Nucleotidyltransferase for Efficient Transcript Labeling with Purine and Pyrimidine Nucleotide Analogs. Chembiochem 2024; 25:e202400202. [PMID: 38818670 DOI: 10.1002/cbic.202400202] [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: 03/05/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/01/2024]
Abstract
RNA labeling is an invaluable tool for investigation of the function and localization of nucleic acids. Labels are commonly incorporated into 3' end of RNA and the primary enzyme used for this purpose is RNA poly(A) polymerase (PAP), which belongs to the class of terminal nucleotidyltransferases (NTases). However, PAP preferentially adds ATP analogs, thus limiting the number of available substrates. Here, we report the use of another NTase, CutA from the fungus Thielavia terrestris. Using this enzyme, we were able to incorporate into the 3' end of RNA not only purine analogs, but also pyrimidine analogs. We engaged strain-promoted azide-alkyl cycloaddition (SPAAC) to obtain fluorescently labeled or biotinylated transcripts from RNAs extended with azide analogs by CutA. Importantly, modified transcripts retained their biological properties. Furthermore, fluorescently labeled mRNAs were suitable for visualization in cultured mammalian cells. Finally, we demonstrate that either affinity studies or molecular dynamic (MD) simulations allow for rapid screening of NTase substrates, what opens up new avenues in the search for the optimal substrates for this class of enzymes.
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Affiliation(s)
- 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
| | - Karolina Drazkowska
- Laboratory of Epitranscriptomics, Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Rafal Madaj
- Laboratory of Structural Bioinformatics, Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Adam Mamot
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Stanislaw Dunin-Horkawicz
- Laboratory of Structural Bioinformatics, Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Pawel J Sikorski
- Laboratory of Epitranscriptomics, Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
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12
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Hagino R, Kuwabara R, Komura N, Imamura A, Ishida H, Ando H, Tanaka HN. Protecting-Group-Free Synthesis of ADP-Ribose and Dinucleoside Di-/Triphosphate Derivatives via P(V)-P(V) Coupling Reaction. Chemistry 2024; 30:e202401302. [PMID: 38763895 DOI: 10.1002/chem.202401302] [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: 04/02/2024] [Revised: 05/07/2024] [Accepted: 05/15/2024] [Indexed: 05/21/2024]
Abstract
Biomolecules containing adenosine di- or triphosphate (ADP or ATP) are crucial for diverse biological processes. Synthesis of these biomolecules and development of their chemical probes are important to elucidate their functions. Enabling reproducible and high-yielding access to these ADP- and ATP-containing molecules via conventional P(III)-P(V) and P(V)-P(V) coupling reactions is challenging owing to water content in highly polar phosphate-containing substrates. Herein, we report an efficient and reliable method for protecting-group-free P(V)-P(V) coupling reaction through in situ activation of phosphates using hydrolysis-stable 2-[N-(2-methylimidazoyl)]-1,3-dimethylimidazolinium chloride (2-MeImIm-Cl), providing the corresponding electrophilic P(V) intermediates for subsequent nucleophilic attack using their coupling partners. This P(V)-P(V) coupling reaction proceeded even in a wet reaction medium and showed a broad substrate scope, accommodating protecting-group-free synthesis of ADP-ribose and nicotinamide adenine diphosphate analogs, ATP-containing biomolecules, and ADP-ribosyl peptides.
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Affiliation(s)
- Rui Hagino
- The United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Ryo Kuwabara
- Department of Applied Bioorganic Chemistry, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Naoko Komura
- Institute for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Akihiro Imamura
- Institute for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
- The United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
- Department of Applied Bioorganic Chemistry, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Hideharu Ishida
- Institute for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
- The United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
- Department of Applied Bioorganic Chemistry, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Hiromune Ando
- Institute for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
- The United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Hide-Nori Tanaka
- Institute for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
- The United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
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13
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Li Z, Bilic M, Nagar B. Isolation of short RNAs with homogeneous 3'-ends using quaternary-amine anion exchange chromatography. Biol Methods Protoc 2024; 9:bpae033. [PMID: 38855193 PMCID: PMC11162090 DOI: 10.1093/biomethods/bpae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/12/2024] [Accepted: 05/16/2024] [Indexed: 06/11/2024] Open
Abstract
Visualizing RNA-protein interactions through structural approaches requires the use of RNA molecules purified to homogeneity. We describe here a simple and effective method, free of acrylamide contamination and without using UV radiation, to separate in vitro synthesized, heterogeneous RNA transcripts (up to ∼15 nucleotides) at single-nucleotide resolution by quaternary-amine anion exchange chromatography. The quality of short RNAs isolated through this method is validated by gel electrophoresis, mass spectrometry, and crystallization with a protein-binding partner.
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Affiliation(s)
- Zixian Li
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montreal, QC H3G 0B1, Canada
| | - Mia Bilic
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montreal, QC H3G 0B1, Canada
| | - Bhushan Nagar
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montreal, QC H3G 0B1, Canada
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14
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Chen S, Jiang Z, Li Q, Pan W, Chen Y, Liu J. Viral RNA capping: Mechanisms and antiviral therapy. J Med Virol 2024; 96:e29622. [PMID: 38682614 DOI: 10.1002/jmv.29622] [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: 12/19/2023] [Revised: 03/25/2024] [Accepted: 04/11/2024] [Indexed: 05/01/2024]
Abstract
RNA capping is an essential trigger for protein translation in eukaryotic cells. Many viruses have evolved various strategies for initiating the translation of viral genes and generating progeny virions in infected cells via synthesizing cap structure or stealing the RNA cap from nascent host messenger ribonucleotide acid (mRNA). In addition to protein translation, a new understanding of the role of the RNA cap in antiviral innate immunity has advanced the field of mRNA synthesis in vitro and therapeutic applications. Recent studies on these viral RNA capping systems have revealed startlingly diverse ways and molecular machinery. A comprehensive understanding of how viruses accomplish the RNA capping in infected cells is pivotal for designing effective broad-spectrum antiviral therapies. Here we systematically review the contemporary insights into the RNA-capping mechanisms employed by viruses causing human and animal infectious diseases, while also highlighting its impact on host antiviral innate immune response. The therapeutic applications of targeting RNA capping against viral infections and the development of RNA-capping inhibitors are also summarized.
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Affiliation(s)
- Saini Chen
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhimin Jiang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Qiuchen Li
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Wenliang Pan
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yu Chen
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jinhua Liu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
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15
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Zhou KI, Pecot CV, Holley CL. 2'- O-methylation (Nm) in RNA: progress, challenges, and future directions. RNA (NEW YORK, N.Y.) 2024; 30:570-582. [PMID: 38531653 PMCID: PMC11019748 DOI: 10.1261/rna.079970.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
RNA 2'-O-methylation (Nm) is highly abundant in noncoding RNAs including ribosomal RNA (rRNA), transfer RNA (tRNA), and small nuclear RNA (snRNA), and occurs in the 5' cap of virtually all messenger RNAs (mRNAs) in higher eukaryotes. More recently, Nm has also been reported to occur at internal sites in mRNA. High-throughput methods have been developed for the transcriptome-wide detection of Nm. However, these methods have mostly been applied to abundant RNAs such as rRNA, and the validity of the internal mRNA Nm sites detected with these approaches remains controversial. Nonetheless, Nm in both coding and noncoding RNAs has been demonstrated to impact cellular processes, including translation and splicing. In addition, Nm modifications at the 5' cap and possibly at internal sites in mRNA serve to prevent the binding of nucleic acid sensors, thus preventing the activation of the innate immune response by self-mRNAs. Finally, Nm has been implicated in a variety of diseases including cancer, cardiovascular diseases, and neurologic syndromes. In this review, we discuss current challenges in determining the distribution, regulation, function, and disease relevance of Nm, as well as potential future directions for the field.
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Affiliation(s)
- Katherine I Zhou
- Division of Medical Oncology, Department of Medicine, Duke University, Durham, North Carolina 27710, USA
| | - Chad V Pecot
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Division of Hematology and Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, USA
- University of North Carolina RNA Discovery Center, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Christopher L Holley
- Division of Cardiology, Department of Medicine, Duke University, Durham, North Carolina 27710, USA
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16
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Giraud G, El Achi K, Zoulim F, Testoni B. Co-Transcriptional Regulation of HBV Replication: RNA Quality Also Matters. Viruses 2024; 16:615. [PMID: 38675956 PMCID: PMC11053573 DOI: 10.3390/v16040615] [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: 03/25/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Chronic hepatitis B (CHB) virus infection is a major public health burden and the leading cause of hepatocellular carcinoma. Despite the efficacy of current treatments, hepatitis B virus (HBV) cannot be fully eradicated due to the persistence of its minichromosome, or covalently closed circular DNA (cccDNA). The HBV community is investing large human and financial resources to develop new therapeutic strategies that either silence or ideally degrade cccDNA, to cure HBV completely or functionally. cccDNA transcription is considered to be the key step for HBV replication. Transcription not only influences the levels of viral RNA produced, but also directly impacts their quality, generating multiple variants. Growing evidence advocates for the role of the co-transcriptional regulation of HBV RNAs during CHB and viral replication, paving the way for the development of novel therapies targeting these processes. This review focuses on the mechanisms controlling the different co-transcriptional processes that HBV RNAs undergo, and their contribution to both viral replication and HBV-induced liver pathogenesis.
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Affiliation(s)
- Guillaume Giraud
- INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, 69008 Lyon, France (F.Z.)
- The Lyon Hepatology Institute EVEREST, 69003 Lyon, France
| | - Khadija El Achi
- INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, 69008 Lyon, France (F.Z.)
| | - Fabien Zoulim
- INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, 69008 Lyon, France (F.Z.)
- The Lyon Hepatology Institute EVEREST, 69003 Lyon, France
- Hospices Civils de Lyon, Hôpital Croix Rousse, Service d’Hépato-Gastroentérologie, 69004 Lyon, France
| | - Barbara Testoni
- INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, 69008 Lyon, France (F.Z.)
- The Lyon Hepatology Institute EVEREST, 69003 Lyon, France
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17
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Avila-Bonilla RG, Macias S. The molecular language of RNA 5' ends: guardians of RNA identity and immunity. RNA (NEW YORK, N.Y.) 2024; 30:327-336. [PMID: 38325897 PMCID: PMC10946433 DOI: 10.1261/rna.079942.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/01/2024] [Indexed: 02/09/2024]
Abstract
RNA caps are deposited at the 5' end of RNA polymerase II transcripts. This modification regulates several steps of gene expression, in addition to marking transcripts as self to enable the innate immune system to distinguish them from uncapped foreign RNAs, including those derived from viruses. Specialized immune sensors, such as RIG-I and IFITs, trigger antiviral responses upon recognition of uncapped cytoplasmic transcripts. Interestingly, uncapped transcripts can also be produced by mammalian hosts. For instance, 5'-triphosphate RNAs are generated by RNA polymerase III transcription, including tRNAs, Alu RNAs, or vault RNAs. These RNAs have emerged as key players of innate immunity, as they can be recognized by the antiviral sensors. Mechanisms that regulate the presence of 5'-triphosphates, such as 5'-end dephosphorylation or RNA editing, prevent immune recognition of endogenous RNAs and excessive inflammation. Here, we provide a comprehensive overview of the complexity of RNA cap structures and 5'-triphosphate RNAs, highlighting their roles in transcript identity, immune surveillance, and disease.
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Affiliation(s)
- Rodolfo Gamaliel Avila-Bonilla
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
| | - Sara Macias
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
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18
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Adesanya O, Das D, Kalsotra A. Emerging roles of RNA-binding proteins in fatty liver disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1840. [PMID: 38613185 PMCID: PMC11018357 DOI: 10.1002/wrna.1840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/08/2024] [Accepted: 03/05/2024] [Indexed: 04/14/2024]
Abstract
A rampant and urgent global health issue of the 21st century is the emergence and progression of fatty liver disease (FLD), including alcoholic fatty liver disease and the more heterogenous metabolism-associated (or non-alcoholic) fatty liver disease (MAFLD/NAFLD) phenotypes. These conditions manifest as disease spectra, progressing from benign hepatic steatosis to symptomatic steatohepatitis, cirrhosis, and, ultimately, hepatocellular carcinoma. With numerous intricately regulated molecular pathways implicated in its pathophysiology, recent data have emphasized the critical roles of RNA-binding proteins (RBPs) in the onset and development of FLD. They regulate gene transcription and post-transcriptional processes, including pre-mRNA splicing, capping, and polyadenylation, as well as mature mRNA transport, stability, and translation. RBP dysfunction at every point along the mRNA life cycle has been associated with altered lipid metabolism and cellular stress response, resulting in hepatic inflammation and fibrosis. Here, we discuss the current understanding of the role of RBPs in the post-transcriptional processes associated with FLD and highlight the possible and emerging therapeutic strategies leveraging RBP function for FLD treatment. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
| | - Diptatanu Das
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Cancer Center @ Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
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19
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Kamath D, Iwakuma T, Bossmann SH. Therapeutic potential of combating cancer by restoring wild-type p53 through mRNA nanodelivery. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2024; 56:102732. [PMID: 38199451 PMCID: PMC11108594 DOI: 10.1016/j.nano.2024.102732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024]
Abstract
Among the tumor suppressor genes, TP53 is the most frequently mutated in human cancers, and most mutations are missense mutations causing production of mutant p53 (mutp53) proteins. TP53 mutations not only results in loss of function (LOH) as a transcription factor and a tumor suppressor, but also gain wild-type p53 (WTp53)-independent oncogenic functions that enhance cancer metastasis and progression (Yamamoto and Iwakuma, 2018; Zhang et al., 2022). TP53 has extensively been studied as a therapeutic target as well as for drug development and therapies, however with limited success. Achieving targeted therapies for restoration of WTp53 function and depletion or repair of mutant p53 (mutp53) will have far reaching implication in cancer treatment and therapies. This review briefly discusses the role of p53 mutation in cancer and the therapeutic potential of restoring WTp53 through the advances in mRNA nanomedicine.
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Affiliation(s)
- Divya Kamath
- The University of Kansas Medical Center, Department of Cancer Biology, 3901 Rainbow Blvd, mailstop 1071, 66160 Kansas City, KS, USA.
| | - Tomoo Iwakuma
- Children's Mercy Hospital, Adele Hall Campus, 2401 Gillham Rd, Kansas City, MO 64108, USA.
| | - Stefan H Bossmann
- The University of Kansas Medical Center, Department of Cancer Biology, 3901 Rainbow Blvd, mailstop 1071, 66160 Kansas City, KS, USA.
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20
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Delaunay S, Helm M, Frye M. RNA modifications in physiology and disease: towards clinical applications. Nat Rev Genet 2024; 25:104-122. [PMID: 37714958 DOI: 10.1038/s41576-023-00645-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2023] [Indexed: 09/17/2023]
Abstract
The ability of chemical modifications of single nucleotides to alter the electrostatic charge, hydrophobic surface and base pairing of RNA molecules is exploited for the clinical use of stable artificial RNAs such as mRNA vaccines and synthetic small RNA molecules - to increase or decrease the expression of therapeutic proteins. Furthermore, naturally occurring biochemical modifications of nucleotides regulate RNA metabolism and function to modulate crucial cellular processes. Studies showing the mechanisms by which RNA modifications regulate basic cell functions in higher organisms have led to greater understanding of how aberrant RNA modification profiles can cause disease in humans. Together, these basic science discoveries have unravelled the molecular and cellular functions of RNA modifications, have provided new prospects for therapeutic manipulation and have led to a range of innovative clinical approaches.
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Affiliation(s)
- Sylvain Delaunay
- Deutsches Krebsforschungszentrum (DKFZ), Division of Mechanisms Regulating Gene Expression, Heidelberg, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Michaela Frye
- Deutsches Krebsforschungszentrum (DKFZ), Division of Mechanisms Regulating Gene Expression, Heidelberg, Germany.
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21
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Zhang Y, Lei Y, Dong Y, Chen S, Sun S, Zhou F, Zhao Z, Chen B, Wei L, Chen J, Meng Z. Emerging roles of RNA ac4C modification and NAT10 in mammalian development and human diseases. Pharmacol Ther 2024; 253:108576. [PMID: 38065232 DOI: 10.1016/j.pharmthera.2023.108576] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 11/29/2023] [Accepted: 12/01/2023] [Indexed: 01/13/2024]
Abstract
RNA ac4C modification is a novel and rare chemical modification observed in mRNA. Traditional biochemical studies had primarily associated ac4C modification with tRNA and rRNA until in 2018, Arango D et al. first reported the presence of ac4C modification on mRNA and demonstrated its critical role in mRNA stability and translation regulation. Furthermore, they established that the ac4C modification on mRNA is mediated by the classical N-acetyltransferase NAT10. Subsequent studies have underscored the essential implications of NAT10 and mRNA ac4C modification across both physiological and pathological regulatory processes. In this review, we aimed to explore the discovery history of RNA ac4C modification, its detection methods, and its regulatory mechanisms in disease and physiological development. We offer a forward-looking examination and discourse concerning the employment of RNA ac4C modification as a prospective therapeutic strategy across diverse diseases. Furthermore, we comprehensively summarize the functions and mechanisms of NAT10 in gene expression regulation and pathogenesis independent of RNA ac4C modification.
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Affiliation(s)
- Yigan Zhang
- Institute of Biomedical Research, Department of Infectious Diseases, Regulatory Mechanism and Targeted Therapy for Liver Cancer Shiyan Key Laboratory, Hubei rovincial Clinical Research Center for Precise Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, China; Hubei Key Laboratory of Embryonic Stem Cell Research, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, China
| | - Yumei Lei
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, China
| | - Yanbin Dong
- Institute of Biophysics, Chinese Academy of Sciences, Key Laboratory of Nucleic Acid Biology, Chinese Academy of Sciences, Beijing, China
| | - Shuwen Chen
- School of Biomedical Engineering, Hubei University of Medicine, Shiyan, China
| | - Siyuan Sun
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, China
| | - Fange Zhou
- The First Clinical School of Hubei University of Medicine, Shiyan, China
| | - Zhiwen Zhao
- Department of Emergency Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Bonan Chen
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Lv Wei
- Institute of Biophysics, Chinese Academy of Sciences, Key Laboratory of Nucleic Acid Biology, Chinese Academy of Sciences, Beijing, China.
| | - Juan Chen
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, China.
| | - Zhongji Meng
- Institute of Biomedical Research, Department of Infectious Diseases, Regulatory Mechanism and Targeted Therapy for Liver Cancer Shiyan Key Laboratory, Hubei rovincial Clinical Research Center for Precise Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, China; Hubei Key Laboratory of Embryonic Stem Cell Research, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, China.
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22
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Mir S, Mir M. The mRNA vaccine, a swift warhead against a moving infectious disease target. Expert Rev Vaccines 2024; 23:336-348. [PMID: 38369742 DOI: 10.1080/14760584.2024.2320327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/14/2024] [Indexed: 02/20/2024]
Abstract
INTRODUCTION The rapid development of mRNA vaccines against SARS-CoV-2 has revolutionized vaccinology, offering hope for swift responses to emerging infectious diseases. Initially met with skepticism, mRNA vaccines have proven effective and safe, reducing vaccine hesitancy amid the evolving COVID-19 pandemic. The COVID-19 pandemic has demonstrated that the time required to modify mRNA vaccines to counter new mutant strains is significantly shorter than the time it takes for pathogens to mutate and generate new variants that can thrive in vaccinated populations. This highlights the notion that mRNA vaccine technology appears to be outpacing viruses in the ongoing evolutionary race. AREAS COVERED This review article offers valuable insights into several crucial aspects of mRNA vaccine development and deployment, including the fundamentals of mRNA vaccine design and synthesis, the utilization of delivery systems, considerations regarding vaccine safety, the longevity of the immune response, strategies for modifying the original mRNA vaccine to address emerging mutant strains, as well as addressing vaccine hesitancy and potential approaches to mitigate reluctance. EXPERT OPINION Challenges such as stability, storage, manufacturing complexities, production capacity, allergic reactions, long-term effects, accessibility, and misinformation must be addressed. Despite these hurdles, mRNA vaccine technology holds promise for revolutionizing future vaccination strategies.
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Affiliation(s)
- Sheema Mir
- College of Veterinary Sciences, Western University of Health Sciences, Pomona, CA, USA
| | - Mohammad Mir
- College of Veterinary Sciences, Western University of Health Sciences, Pomona, CA, USA
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23
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Potužník JF, Cahova H. If the 5' cap fits (wear it) - Non-canonical RNA capping. RNA Biol 2024; 21:1-13. [PMID: 39007883 PMCID: PMC11253889 DOI: 10.1080/15476286.2024.2372138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 06/18/2024] [Indexed: 07/16/2024] Open
Abstract
RNA capping is a prominent RNA modification that influences RNA stability, metabolism, and function. While it was long limited to the study of the most abundant eukaryotic canonical m7G cap, the field recently went through a large paradigm shift with the discovery of non-canonical RNA capping in bacteria and ultimately all domains of life. The repertoire of non-canonical caps has expanded to encompass metabolite caps, including NAD, FAD, CoA, UDP-Glucose, and ADP-ribose, alongside alarmone dinucleoside polyphosphate caps, and methylated phosphate cap-like structures. This review offers an introduction into the field, presenting a summary of the current knowledge about non-canonical RNA caps. We highlight the often still enigmatic biological roles of the caps together with their processing enzymes, focusing on the most recent discoveries. Furthermore, we present the methods used for the detection and analysis of these non-canonical RNA caps and thus provide an introduction into this dynamic new field.
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Affiliation(s)
- Jiří František Potužník
- Institute of Organic Chemistry and Biochemistry of the CAS, Prague 6, Czechia
- Department of Cell Biology, Charles University, Faculty of Science, Prague 2, Czechia
| | - Hana Cahova
- Institute of Organic Chemistry and Biochemistry of the CAS, Prague 6, Czechia
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24
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Ziegenhals T, Frieling R, Wolf P, Göbel K, Koch S, Lohmann M, Baiersdörfer M, Fesser S, Sahin U, Kuhn AN. Formation of dsRNA by-products during in vitro transcription can be reduced by using low steady-state levels of UTP. Front Mol Biosci 2023; 10:1291045. [PMID: 38146535 PMCID: PMC10749352 DOI: 10.3389/fmolb.2023.1291045] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/27/2023] [Indexed: 12/27/2023] Open
Abstract
Introduction: Exogeneous messenger ribonucleic acid (mRNA) can be used as therapeutic and preventive medication. However, during the enzymatic production process, commonly called in vitro transcription, by-products occur which can reduce the therapeutic efficacy of mRNA. One such by-product is double-stranded RNA (dsRNA). We therefore sought to limit the generation of dsRNA by-products during in vitro transcription. Materials and methods: In vitro transcription was performed with a DNA template including a poly(A)-tail-encoding region, dinucleotide or trinucleotide cap analogs for cotranscriptional capping, and relevant nucleoside triphosphates. Concentrations of UTP or modified UTP (m1ΨTP) and GTP were reduced and fed over the course of the reaction. mRNA was analyzed for dsRNA contamination, yield of the reaction, RNA integrity, and capping efficiency before translational activity was assessed. Results: Limiting the steady-state level of UTP or m1ΨTP during the enzymatic reaction reduced dsRNA formation, while not affecting mRNA yield or RNA integrity. Capping efficiency was optimized with the use of a combined GTP and UTP or m1ΨTP feed, while still reducing dsRNA formation. Lower dsRNA levels led to higher protein expression from the corresponding mRNAs. Discussion: Low steady-state concentrations of UTP and GTP, fed in combination over the course of the in vitro transcription reaction, produce mRNA with high capping and low levels of dsRNA formation, resulting in high levels of protein expression. This novel approach may render laborious purification steps to remove dsRNA unnecessary.
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25
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Granata S, Stallone G, Zaza G. mRNA as a medicine in nephrology: the future is now. Clin Kidney J 2023; 16:2349-2356. [PMID: 38046026 PMCID: PMC10689145 DOI: 10.1093/ckj/sfad196] [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: 07/14/2023] [Indexed: 12/05/2023] Open
Abstract
The successful employment of messenger RNA (mRNA) as vaccine therapy for the prevention of COVID-19 infection has spotlighted the attention of scientific community onto the potential clinical application of these molecules as innovative and alternative therapeutic approaches in different fields of medicine. As therapy, mRNAs may be advantageous due to their unique biological properties of targeting almost any genetic component within the cell, many of which may be unreachable using other pharmacological/therapeutic approaches, and encoding any proteins and peptides without the need for their transport into the nuclei of the target cells. Additionally, these molecules may be rapidly designed/produced and clinically tested. Once the chemistry of the RNA and its delivery system are optimized, the cost of developing novel variants of these medications for new selected clinical disorders is significantly reduced. However, although potentially useful as new therapeutic weapons against several kidney diseases, the complex architecture of kidney and the inability of nanoparticles that accommodate oligonucleotides to cross the integral glomerular filtration barrier have largely decreased their potential employment in nephrology. However, in the next few years, the technical improvements in mRNA that increase translational efficiency, modulate innate and adaptive immunogenicity, and increase their delivery at the site of action will overcome these limitations. Therefore, this review has the scope of summarizing the key strengths of these RNA-based therapies and illustrating potential future directions and challenges of this promising technology for widespread therapeutic use in nephrology.
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Affiliation(s)
- Simona Granata
- Nephrology, Dialysis and Transplantation Unit, Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Giovanni Stallone
- Nephrology, Dialysis and Transplantation Unit, Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Gianluigi Zaza
- Nephrology, Dialysis and Transplantation Unit, Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
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26
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Del Valle-Morales D, Romano G, Le P, Saviana M, Brown R, Micalo L, Li H, Ferlita AL, Nigita G, Nana-Sinkam P, Acunzo M. METTL3 alters capping enzyme expression and its activity on ribosomal proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.568301. [PMID: 38045284 PMCID: PMC10690260 DOI: 10.1101/2023.11.22.568301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The 5' cap, catalyzed by RNA guanylyltransferase and 5'-phosphatase (RNGTT), is a vital mRNA modification for the functionality of mRNAs. mRNA capping occurs in the nucleus for the maturation of the functional mRNA and in the cytoplasm for fine-tuning gene expression. Given the fundamental importance of RNGTT in mRNA maturation and expression there is a need to further investigate the regulation of RNGTT. N6-methyladenosine (m 6 A) is one of the most abundant RNA modifications involved in the regulation of protein translation, mRNA stability, splicing, and export. We sought to investigate whether m 6 A could regulate the expression and activity of RNGTT. A motif for the m 6 A writer methyltransferase 3 (METTL3) in the 3'UTR of RNGTT mRNA was identified. Knockdown of METTL3 resulted in destabilizing RNGTT mRNA, and reduced protein expression. Sequencing of capped mRNAs identified an underrepresentation of ribosomal protein mRNA overlapping with 5' terminal oligopyrimidine (TOP) mRNAs and genes are dysregulated when cytoplasmic capping is inhibited. Pathway analysis identified disruptions in the mTOR and p70S6K pathways. A reduction in RPS6 mRNA capping, protein expression, and phosphorylation was detected with METTL3 knockdown.
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27
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Knop K, Gomez-Moreira C, Galloway A, Ditsova D, Cowling VH. RAM is upregulated during T cell activation and is required for RNA cap formation and gene expression. DISCOVERY IMMUNOLOGY 2023; 3:kyad021. [PMID: 38572449 PMCID: PMC10989996 DOI: 10.1093/discim/kyad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/25/2023] [Accepted: 10/29/2023] [Indexed: 04/05/2024]
Abstract
On T cell activation, upregulation of gene expression produces the protein required for the differentiation and proliferation of effector cell populations. RAM (RNMT-Activating Mini protein/RAMAC/Fam103a1), the cofactor of the RNA cap methyltransferase RNMT (RNA guanosine N-7 cap methyltransferase), is upregulated following activation. Formation of the RNA cap protects RNA during synthesis and guides RNA processing and translation. Using conditional gene deletion, we found that Ram expression stabilizes RNMT protein in T cells and is required for its upregulation on activation. When the Ram gene is deleted in naïve T cells, there are major impacts on activation-induced RNA cap formation and gene expression. Activated T cell proliferation is dependent on increased ribosome production; in Ram knockout T cells, activation-induced expression of ribosomal protein genes and snoRNAs is most severely reduced. Consistent with these changes, Ram deletion resulted in reduced protein synthesis, and reduced growth and proliferation of CD4 T cells. Deletion of Ram results in a similar but milder phenotype to Rnmt deletion, supporting the role of RAM as a RNMT cofactor.
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Affiliation(s)
- Katarzyna Knop
- Cancer Research UK Scotland Institute, Glasgow, G61 1BD, UK
- School of Life Sciences, University of Dundee, DD1 5EH, Dundee, UK
| | | | - Alison Galloway
- Cancer Research UK Scotland Institute, Glasgow, G61 1BD, UK
- School of Life Sciences, University of Dundee, DD1 5EH, Dundee, UK
| | - Dimitrinka Ditsova
- Cancer Research UK Scotland Institute, Glasgow, G61 1BD, UK
- School of Life Sciences, University of Dundee, DD1 5EH, Dundee, UK
| | - Victoria H Cowling
- Cancer Research UK Scotland Institute, Glasgow, G61 1BD, UK
- School of Life Sciences, University of Dundee, DD1 5EH, Dundee, UK
- School of Cancer Sciences, University of Glasgow, G61 1QH, Glasgow, UK
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28
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Burdick JT, Comai A, Bruzel A, Sun G, Dedon PC, Cheung VG. Nanopore-based direct sequencing of RNA transcripts with 10 different modified nucleotides reveals gaps in existing technology. G3 (BETHESDA, MD.) 2023; 13:jkad200. [PMID: 37655917 PMCID: PMC10627276 DOI: 10.1093/g3journal/jkad200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 06/14/2023] [Accepted: 08/23/2023] [Indexed: 09/02/2023]
Abstract
RNA undergoes complex posttranscriptional processing including chemical modifications of the nucleotides. The resultant-modified nucleotides are an integral part of RNA sequences that must be considered in studying the biology of RNA and in the design of RNA therapeutics. However, the current "RNA-sequencing" methods primarily sequence complementary DNA rather than RNA itself, which means that the modifications present in RNA are not captured in the sequencing results. Emerging direct RNA-sequencing technologies, such as those offered by Oxford Nanopore, aim to address this limitation. In this study, we synthesized and used Nanopore technology to sequence RNA transcripts consisting of canonical nucleotides and 10 different modifications in various concentrations. The results show that direct RNA sequencing still has a baseline error rate of >10%, and although some modifications can be detected, many remain unidentified. Thus, there is a need to develop sequencing technologies and analysis methods that can comprehensively capture the total complexity of RNA. The RNA sequences obtained through this project are made available for benchmarking analysis methods.
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Affiliation(s)
- Joshua T Burdick
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Annelise Comai
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alan Bruzel
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Guangxin Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Vivian G Cheung
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109, USA
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29
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Shen S, Zhang LS. The regulation of antiviral innate immunity through non-m 6A RNA modifications. Front Immunol 2023; 14:1286820. [PMID: 37915585 PMCID: PMC10616867 DOI: 10.3389/fimmu.2023.1286820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/04/2023] [Indexed: 11/03/2023] Open
Abstract
The post-transcriptional RNA modifications impact the dynamic regulation of gene expression in diverse biological and physiological processes. Host RNA modifications play an indispensable role in regulating innate immune responses against virus infection in mammals. Meanwhile, the viral RNAs can be deposited with RNA modifications to interfere with the host immune responses. The N6-methyladenosine (m6A) has boosted the recent emergence of RNA epigenetics, due to its high abundance and a transcriptome-wide widespread distribution in mammalian cells, proven to impact antiviral innate immunity. However, the other types of RNA modifications are also involved in regulating antiviral responses, and the functional roles of these non-m6A RNA modifications have not been comprehensively summarized. In this Review, we conclude the regulatory roles of 2'-O-methylation (Nm), 5-methylcytidine (m5C), adenosine-inosine editing (A-to-I editing), pseudouridine (Ψ), N1-methyladenosine (m1A), N7-methylguanosine (m7G), N6,2'-O-dimethyladenosine (m6Am), and N4-acetylcytidine (ac4C) in antiviral innate immunity. We provide a systematic introduction to the biogenesis and functions of these non-m6A RNA modifications in viral RNA, host RNA, and during virus-host interactions, emphasizing the biological functions of RNA modification regulators in antiviral responses. Furthermore, we discussed the recent research progress in the development of antiviral drugs through non-m6A RNA modifications. Collectively, this Review conveys knowledge and inspiration to researchers in multiple disciplines, highlighting the challenges and future directions in RNA epitranscriptome, immunology, and virology.
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Affiliation(s)
- Shenghai Shen
- Division of Life Science, The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
| | - Li-Sheng Zhang
- Division of Life Science, The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
- Department of Chemistry, The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
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30
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Wang YS, Kumari M, Chen GH, Hong MH, Yuan JPY, Tsai JL, Wu HC. mRNA-based vaccines and therapeutics: an in-depth survey of current and upcoming clinical applications. J Biomed Sci 2023; 30:84. [PMID: 37805495 PMCID: PMC10559634 DOI: 10.1186/s12929-023-00977-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 09/29/2023] [Indexed: 10/09/2023] Open
Abstract
mRNA-based drugs have tremendous potential as clinical treatments, however, a major challenge in realizing this drug class will promise to develop methods for safely delivering the bioactive agents with high efficiency and without activating the immune system. With regard to mRNA vaccines, researchers have modified the mRNA structure to enhance its stability and promote systemic tolerance of antigenic presentation in non-inflammatory contexts. Still, delivery of naked modified mRNAs is inefficient and results in low levels of antigen protein production. As such, lipid nanoparticles have been utilized to improve delivery and protect the mRNA cargo from extracellular degradation. This advance was a major milestone in the development of mRNA vaccines and dispelled skepticism about the potential of this technology to yield clinically approved medicines. Following the resounding success of mRNA vaccines for COVID-19, many other mRNA-based drugs have been proposed for the treatment of a variety of diseases. This review begins with a discussion of mRNA modifications and delivery vehicles, as well as the factors that influence administration routes. Then, we summarize the potential applications of mRNA-based drugs and discuss further key points pertaining to preclinical and clinical development of mRNA drugs targeting a wide range of diseases. Finally, we discuss the latest market trends and future applications of mRNA-based drugs.
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Affiliation(s)
- Yu-Shiuan Wang
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Monika Kumari
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Guan-Hong Chen
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11571, Taiwan
| | - Ming-Hsiang Hong
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11571, Taiwan
| | - Joyce Pei-Yi Yuan
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11571, Taiwan
| | - Jui-Ling Tsai
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Han-Chung Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan.
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11571, Taiwan.
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31
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Kurpiejewski K, Jankowska-Anyszka M, Grzela R. N2 modified cap analogues as translation inhibitors and substrates for preparation of therapeutic mRNA. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:511-519. [PMID: 37656232 PMCID: PMC10618310 DOI: 10.1007/s00249-023-01676-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/04/2023] [Accepted: 07/21/2023] [Indexed: 09/02/2023]
Abstract
In recent years many scientists have begun to focus on the mRNA molecule's emeregence as a new type of drug. Its fast-moving and successful career as a vaccine technology cannot be underestimated. mRNA provides new opportunities and allows for the rapid preparation of effective drugs at low cost. These extensive possibilities stem from a number of factors, but the small cap structure located at the 5' end of the mRNA is one contributing factor. Cap protects mRNA and ensures efficient recruitment to the biosynthesis machinery. Furthermore, it allows for the easy introduction of various modifications that influence the activity of the entire mRNA. Among the many different cap analogues that have been reported, those modified at the N2 position of guanosine have been systematically developed. N2-modified caps in the form of nucleoside monophosphates or dinucleotides show favorable biological properties, as well as a high capacity to inhibit the translation process in the cell-free RRL system. Modified N2 dinucleotides are efficiently incorporated into the structure of the mRNA transcript, and in specific circumstances with the correct orientation, making them an interesting alternative for ARCA-type analogues. Moreover, mRNA transcripts containing cap structures modified within the exocyclic amino group show very high translational activity. Therefore, analogues modified at the N2 position may have future applications as therapeutics against various manifestations of cancer and as desirable tools in RNA engineering.
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Affiliation(s)
| | | | - Renata Grzela
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, 02-093, Warsaw, Poland.
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32
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Zhang G, Tang T, Chen Y, Huang X, Liang T. mRNA vaccines in disease prevention and treatment. Signal Transduct Target Ther 2023; 8:365. [PMID: 37726283 PMCID: PMC10509165 DOI: 10.1038/s41392-023-01579-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 07/01/2023] [Accepted: 07/30/2023] [Indexed: 09/21/2023] Open
Abstract
mRNA vaccines have emerged as highly effective strategies in the prophylaxis and treatment of diseases, thanks largely although not totally to their extraordinary performance in recent years against the worldwide plague COVID-19. The huge superiority of mRNA vaccines regarding their efficacy, safety, and large-scale manufacture encourages pharmaceutical industries and biotechnology companies to expand their application to a diverse array of diseases, despite the nonnegligible problems in design, fabrication, and mode of administration. This review delves into the technical underpinnings of mRNA vaccines, covering mRNA design, synthesis, delivery, and adjuvant technologies. Moreover, this review presents a systematic retrospective analysis in a logical and well-organized manner, shedding light on representative mRNA vaccines employed in various diseases. The scope extends across infectious diseases, cancers, immunological diseases, tissue damages, and rare diseases, showcasing the versatility and potential of mRNA vaccines in diverse therapeutic areas. Furthermore, this review engages in a prospective discussion regarding the current challenge and potential direction for the advancement and utilization of mRNA vaccines. Overall, this comprehensive review serves as a valuable resource for researchers, clinicians, and industry professionals, providing a comprehensive understanding of the technical aspects, historical context, and future prospects of mRNA vaccines in the fight against various diseases.
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Affiliation(s)
- Gang Zhang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, Zhejiang, China
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, Zhejiang, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, 310003, Hangzhou, Zhejiang, China
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, 310009, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Tianyu Tang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, Zhejiang, China
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, Zhejiang, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, 310003, Hangzhou, Zhejiang, China
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, 310009, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Yinfeng Chen
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, Zhejiang, China
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, Zhejiang, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, 310003, Hangzhou, Zhejiang, China
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, 310009, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Xing Huang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, Zhejiang, China.
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, Zhejiang, China.
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, 310003, Hangzhou, Zhejiang, China.
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, 310009, Hangzhou, Zhejiang, China.
- Cancer Center, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
| | - Tingbo Liang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, Zhejiang, China.
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, Zhejiang, China.
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, 310003, Hangzhou, Zhejiang, China.
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, 310009, Hangzhou, Zhejiang, China.
- Cancer Center, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
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33
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Zhang X, Zhu WY, Shen SY, Shen JH, Chen XD. Biological roles of RNA m7G modification and its implications in cancer. Biol Direct 2023; 18:58. [PMID: 37710294 PMCID: PMC10500781 DOI: 10.1186/s13062-023-00414-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/07/2023] [Indexed: 09/16/2023] Open
Abstract
M7G modification, known as one of the common post-transcriptional modifications of RNA, is present in many different types of RNAs. With the accurate identification of m7G modifications within RNAs, their functional roles in the regulation of gene expression and different physiological functions have been revealed. In addition, there is growing evidence that m7G modifications are crucial in the emergence of cancer. Here, we review the most recent findings regarding the detection techniques, distribution, biological functions and Regulators of m7G. We also summarize the connections between m7G modifications and cancer development, drug resistance, and tumor microenvironment as well as we discuss the research's future directions and trends.
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Affiliation(s)
- Xin Zhang
- Department of Dermatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Wen-Yan Zhu
- Department of Dermatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Shu-Yi Shen
- Department of Dermatology, the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Jia-Hao Shen
- Department of Dermatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Xiao-Dong Chen
- Department of Dermatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China.
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34
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Andrzejewska A, Grzela R, Stankiewicz-Drogon A, Rogujski P, Nagaraj S, Darzynkiewicz E, Lukomska B, Janowski M. Mesenchymal stem cell engineering by ARCA analog-capped mRNA. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:454-468. [PMID: 37588684 PMCID: PMC10425852 DOI: 10.1016/j.omtn.2023.07.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/11/2023] [Indexed: 08/18/2023]
Abstract
We previously have shown that mRNA-based engineering may enhance mesenchymal stem cell (MSC) trafficking. However, optimal conditions for in vitro mRNA engineering of MSCs are unknown. Here, we investigated several independent variables: (1) transfection factor (Lipofectamine 2000 vs. TransIT), (2) mRNA purification method (spin column vs. high-performance liquid chromatography [HPLC] column), and (3) mRNA capping (ARCA vs. β-S-ARCA D1 and β-S-ARCA D2). Dependent variables included protein production based on mRNA template (measured by the bioluminescence of reporter gene luciferase over hours), MSC metabolic activity corresponding with their wellbeing measured by CCK-8 over days, and endogenous expression of genes by RT-qPCR related to innate intracellular immune response and decapping at two time points: days 2 and 5. We have found that Lipofectamine 2000 outperforms TransIT, and used it throughout the study. Then, we showed that mRNA must be purified by HPLC to be relatively neutral to MSCs in terms of metabolic activity and endogenous protein production. Ultimately, we demonstrated that β-S-ARCA D1 enables higher protein production but at the cost of lower MSC metabolic activity, with no impact on RT-qPCR results. Thus Lipofectamine 2000-based in vitro transfection of HPLC-purified and ARCA- or β-S-ARCA D1-capped mRNA is optimal for MSC engineering.
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Affiliation(s)
- Anna Andrzejewska
- NeuroRepair Department, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland
- Center for Advanced Imaging Research, Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Renata Grzela
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
- Interdisciplinary Laboratory of Molecular Biology and Biophysics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Anna Stankiewicz-Drogon
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Piotr Rogujski
- NeuroRepair Department, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Siranjeevi Nagaraj
- Interdisciplinary Laboratory of Molecular Biology and Biophysics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Edward Darzynkiewicz
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
- Interdisciplinary Laboratory of Molecular Biology and Biophysics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Barbara Lukomska
- NeuroRepair Department, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Miroslaw Janowski
- Center for Advanced Imaging Research, Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland, Baltimore, MD 21201, USA
- Tumor Immunology and Immunotherapy Program, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD 21201, USA
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35
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Li C, Xu P, Huang Y, Wang Y, Wu Y, Li H, Peng Y, Wang X, Li G, He J, Miao C. RNA methylations in depression, from pathological mechanism to therapeutic potential. Biochem Pharmacol 2023; 215:115750. [PMID: 37595670 DOI: 10.1016/j.bcp.2023.115750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 08/13/2023] [Accepted: 08/15/2023] [Indexed: 08/20/2023]
Abstract
Depression is caused by a variety of factors such as genetic factors, biological factors, and psychosocial factors, and the pathogenesis is complex. RNA methylations and related downstream signaling pathways influence a variety of biological mechanisms, including cell differentiation, tumorigenesis, sex determination, and stress response. In this work, we searched the PubMed, Web of Science, National Library of Science and Technology (NSTL), and ScienceDirect Online (SDOL) databases to summarize the biological roles of RNA methylations and their impact on the pathological mechanisms of depression. RNA methylations play a key role in the development of many diseases, and current research shows that RNA methylations are also closely linked to depression. RNA methylations in depression mainly involve "writers" (mediating the methylation modification process of RNAs), "erasers" (mediating the demethylation modification process of RNA methylation). Fat Mass and Obesity Associated (FTO) influences the development of depression by increasing body mass index (BMI), decreases the dopamine level, inhibits the adrenoceptor beta 2 (ADRB2)-c-Myc-sirt1 pathway, results in the m6A/m6Am dysregulation in brain, and may be involved in the pathogenesis of depression. The study of RNA methylations in depression has further deepened our understanding of the pathogenesis and development process of depression, provides new perspectives for the study of the pathological mechanism of depression, and provides new targets for the prevention and treatment of this disease.
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Affiliation(s)
- Chen Li
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Pengfei Xu
- Department of Orthopedics, the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Yurong Huang
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Yuting Wang
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Yajie Wu
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Hui Li
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Yanhui Peng
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Xiao Wang
- Department of Clinical Nursing, Anhui University of Chinese Medicine, Hefei, Anhui, China.
| | - Guoying Li
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China.
| | - Juan He
- Department of Gynecology, Anhui Maternal and Child Health Hospital, Hefei, Anhui, China.
| | - Chenggui Miao
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China; Institute of Traditional Chinese Medicine for the Prevention and Treatment of Rheumatology, Anhui University of Chinese Medicine, Hefei, Anhui, China.
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36
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Kang DD, Li H, Dong Y. Advancements of in vitro transcribed mRNA (IVT mRNA) to enable translation into the clinics. Adv Drug Deliv Rev 2023; 199:114961. [PMID: 37321375 PMCID: PMC10264168 DOI: 10.1016/j.addr.2023.114961] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 06/02/2023] [Accepted: 06/08/2023] [Indexed: 06/17/2023]
Abstract
The accelerated progress and approval of two mRNA-based vaccines to address the SARS-CoV-2 virus were unprecedented. This record-setting feat was made possible through the solid foundation of research on in vitro transcribed mRNA (IVT mRNA) which could be utilized as a therapeutic modality. Through decades of thorough research to overcome barriers to implementation, mRNA-based vaccines or therapeutics offer many advantages to rapidly address a broad range of applications including infectious diseases, cancers, and gene editing. Here, we describe the advances that have supported the adoption of IVT mRNA in the clinics, including optimization of the IVT mRNA structural components, synthesis, and lastly concluding with different classes of IVT RNA. Continuing interest in driving IVT mRNA technology will enable a safer and more efficacious therapeutic modality to address emerging and existing diseases.
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Affiliation(s)
- Diana D Kang
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Genomics Institute, Precision Immunology Institute, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Haoyuan Li
- Genomics Institute, Precision Immunology Institute, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Yizhou Dong
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Department of Biomedical Engineering, The Center for Clinical and Translational Science, The Comprehensive Cancer Center; Dorothy M. Davis Heart & Lung Research Institute, Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, United States; Genomics Institute, Precision Immunology Institute, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
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37
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Solodushko V, Fouty B. Terminal hairpins improve protein expression in IRES-initiated mRNA in the absence of a cap and polyadenylated tail. Gene Ther 2023; 30:620-627. [PMID: 36828937 PMCID: PMC9951143 DOI: 10.1038/s41434-023-00391-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 01/31/2023] [Accepted: 02/08/2023] [Indexed: 02/26/2023]
Abstract
Synthesizing mRNA in vitro is a standard and simple procedure. Adding the 5' cap and 3' polyadenylated (poly(A)) tail to make this mRNA functional for use as a vaccine or therapy increases the time and cost of production and usually decreases the yield, however. We designed mRNA that lacked a cap and poly(A) tail but included an internal ribosomal entry site (IRES) to initiate protein translation. To protect the 5' and 3' ends of mRNA from exonucleases, we added stable terminal hairpins. When compared against typical mRNA (i.e., mRNA that contained a cap and poly(A) tail but lacked hairpins), expression of the delivered reporter protein in HEK293 cells was similar. Using a triple instead of a single hairpin at each end increased protein expression even more. This method has the potential to simplify the production and reduce the cost of synthesizing exogenous mRNA for use as biologics or vaccines.
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Affiliation(s)
- Victor Solodushko
- Department of Pharmacology, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
- The Center for Lung Biology, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
| | - Brian Fouty
- Department of Pharmacology, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
- The Center for Lung Biology, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
- Department of Internal Medicine, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
- The Division of Pulmonary and Critical Care Medicine, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
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38
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Shao X, Zhang H, Zhu Z, Ji F, He Z, Yang Z, Xia Y, Cai Z. DpCoA tagSeq: Barcoding dpCoA-Capped RNA for Direct Nanopore Sequencing via Maleimide-Thiol Reaction. Anal Chem 2023; 95:11124-11131. [PMID: 37439785 PMCID: PMC10372868 DOI: 10.1021/acs.analchem.3c02063] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/27/2023] [Indexed: 07/14/2023]
Abstract
Recent discoveries of noncanonical RNA caps, such as nicotinamide adenine dinucleotide (NAD+) and 3'-dephospho-coenzyme A (dpCoA), have expanded our knowledge of RNA caps. Although dpCoA has been known to cap RNAs in various species, the identities of its capped RNAs (dpCoA-RNAs) remained unknown. To fill this gap, we developed a method called dpCoA tagSeq, which utilized a thiol-reactive maleimide group to label dpCoA cap with a tag RNA serving as the 5' barcode. The barcoded RNAs were isolated using a complementary DNA strand of the tag RNA prior to direct sequencing by nanopore technology. Our validation experiments with model RNAs showed that dpCoA-RNA was efficiently tagged and captured using this protocol. To confirm that the tagged RNAs are capped by dpCoA and no other thiol-containing molecules, we used a pyrophosphatase NudC to degrade the dpCoA cap to adenosine monophosphate (AMP) moiety before performing the tagSeq protocol. We identified 44 genes that transcribe dpCoA-RNAs in mouse liver, demonstrating the method's effectiveness in identifying and characterizing the capped RNAs. This strategy provides a viable approach to identifying dpCoA-RNAs that allows for further functional investigations of the cap.
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Affiliation(s)
- Xiaojian Shao
- State
Key Laboratory of Environmental and Biological Analysis, Department
of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Hailei Zhang
- Department
of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Zhou Zhu
- School
of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Fenfen Ji
- State
Key Laboratory of Environmental and Biological Analysis, Department
of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Zhao He
- State
Key Laboratory of Environmental and Biological Analysis, Department
of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Zhu Yang
- State
Key Laboratory of Environmental and Biological Analysis, Department
of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Yiji Xia
- Department
of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Zongwei Cai
- State
Key Laboratory of Environmental and Biological Analysis, Department
of Chemistry, Hong Kong Baptist University, Hong Kong, China
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39
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Nikolaitchik OA, Islam S, Kitzrow JP, Duchon A, Cheng Z, Liu Y, Rawson JMO, Shao W, Nikolaitchik M, Kearney MF, Maldarelli F, Musier-Forsyth K, Pathak VK, Hu WS. HIV-1 usurps transcription start site heterogeneity of host RNA polymerase II to maximize replication fitness. Proc Natl Acad Sci U S A 2023; 120:e2305103120. [PMID: 37252967 PMCID: PMC10266039 DOI: 10.1073/pnas.2305103120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 05/03/2023] [Indexed: 06/01/2023] Open
Abstract
HIV-1 relies on host RNA polymeraseII (Pol II) to transcribe its genome and uses multiple transcription start sites (TSS), including three consecutive guanosines located near the U3-R junction, to generate transcripts containing three, two, and one guanosine at the 5' end, referred to as 3G, 2G, and 1G RNA, respectively. The 1G RNA is preferentially selected for packaging, indicating that these 99.9% identical RNAs exhibit functional differences and highlighting the importance of TSS selection. Here, we demonstrate that TSS selection is regulated by sequences between the CATA/TATA box and the beginning of R. Furthermore, we have generated two HIV-1 mutants with distinct 2-nucleotide modifications that predominantly express 3G RNA or 1G RNA. Both mutants can generate infectious viruses and undergo multiple rounds of replication in T cells. However, both mutants exhibit replication defects compared to the wild-type virus. The 3G-RNA-expressing mutant displays an RNA genome-packaging defect and delayed replication kinetics, whereas the 1G-RNA-expressing mutant exhibits reduced Gag expression and a replication fitness defect. Additionally, reversion of the latter mutant is frequently observed, consistent with sequence correction by plus-strand DNA transfer during reverse transcription. These findings demonstrate that HIV-1 maximizes its replication fitness by usurping the TSS heterogeneity of host RNA Pol II to generate unspliced RNAs with different specialized roles in viral replication. The three consecutive guanosines at the junction of U3 and R may also maintain HIV-1 genome integrity during reverse transcription. These studies reveal the intricate regulation of HIV-1 RNA and complex replication strategy.
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Affiliation(s)
- Olga A. Nikolaitchik
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD21702
| | - Saiful Islam
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD21702
| | - Jonathan P. Kitzrow
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD21702
| | - Alice Duchon
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD21702
| | - Zetao Cheng
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD21702
| | - Yang Liu
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD21702
| | - Jonathan M. O. Rawson
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD21702
| | - Wei Shao
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD21702
| | - Maria Nikolaitchik
- Clinical Retrovirology Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD21702
| | - Mary F. Kearney
- Translation Research Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD21702
| | - Frank Maldarelli
- Clinical Retrovirology Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD21702
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, Ohio State University, Columbus, OH43210
| | - Vinay K. Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD21702
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD21702
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40
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Naesens L, Haerynck F, Gack MU. The RNA polymerase III-RIG-I axis in antiviral immunity and inflammation. Trends Immunol 2023; 44:435-449. [PMID: 37149405 PMCID: PMC10461603 DOI: 10.1016/j.it.2023.04.002] [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: 01/30/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 05/08/2023]
Abstract
Nucleic acid sensors survey subcellular compartments for atypical or mislocalized RNA or DNA, ultimately triggering innate immune responses. Retinoic acid-inducible gene-I (RIG-I) is part of the family of cytoplasmic RNA receptors that can detect viruses. A growing literature demonstrates that mammalian RNA polymerase III (Pol III) transcribes certain viral or cellular DNA sequences into immunostimulatory RIG-I ligands, which elicits antiviral or inflammatory responses. Dysregulation of the Pol III-RIG-I sensing axis can lead to human diseases including severe viral infection outcomes, autoimmunity, and tumor progression. Here, we summarize the newly emerging role of viral and host-derived Pol III transcripts in immunity and also highlight recent advances in understanding how mammalian cells prevent unwanted immune activation by these RNAs to maintain homeostasis.
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Affiliation(s)
- Leslie Naesens
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium; Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Filomeen Haerynck
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium; Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Michaela U Gack
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA.
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41
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Prall W, Ganguly DR, Gregory BD. The covalent nucleotide modifications within plant mRNAs: What we know, how we find them, and what should be done in the future. THE PLANT CELL 2023; 35:1801-1816. [PMID: 36794718 PMCID: PMC10226571 DOI: 10.1093/plcell/koad044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/16/2022] [Accepted: 01/09/2023] [Indexed: 05/30/2023]
Abstract
Although covalent nucleotide modifications were first identified on the bases of transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), a number of these epitranscriptome marks have also been found to occur on the bases of messenger RNAs (mRNAs). These covalent mRNA features have been demonstrated to have various and significant effects on the processing (e.g. splicing, polyadenylation, etc.) and functionality (e.g. translation, transport, etc.) of these protein-encoding molecules. Here, we focus our attention on the current understanding of the collection of covalent nucleotide modifications known to occur on mRNAs in plants, how they are detected and studied, and the most outstanding future questions of each of these important epitranscriptomic regulatory signals.
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Affiliation(s)
- Wil Prall
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, 433 S. University Ave., Philadelphia, PA 19104, USA
| | - Diep R Ganguly
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, 433 S. University Ave., Philadelphia, PA 19104, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, 433 S. University Ave., Philadelphia, PA 19104, USA
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42
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Liang S, Almohammed R, Cowling VH. The RNA cap methyltransferases RNMT and CMTR1 co-ordinate gene expression during neural differentiation. Biochem Soc Trans 2023:233029. [PMID: 37145036 DOI: 10.1042/bst20221154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 04/03/2023] [Accepted: 04/18/2023] [Indexed: 05/06/2023]
Abstract
Regulation of RNA cap formation has potent impacts on gene regulation, controlling which transcripts are expressed, processed and translated into protein. Recently, the RNA cap methyltransferases RNA guanine-7 methyltransferase (RNMT) and cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 (CMTR1) have been found to be independently regulated during embryonic stem (ES) cell differentiation controlling the expression of overlapping and distinct protein families. During neural differentiation, RNMT is repressed and CMTR1 is up-regulated. RNMT promotes expression of the pluripotency-associated gene products; repression of the RNMT complex (RNMT-RAM) is required for repression of these RNAs and proteins during differentiation. The predominant RNA targets of CMTR1 encode the histones and ribosomal proteins (RPs). CMTR1 up-regulation is required to maintain the expression of histones and RPs during differentiation and to maintain DNA replication, RNA translation and cell proliferation. Thus the co-ordinate regulation of RNMT and CMTR1 is required for different aspects of ES cell differentiation. In this review, we discuss the mechanisms by which RNMT and CMTR1 are independently regulated during ES cell differentiation and explore how this influences the co-ordinated gene regulation required of emerging cell lineages.
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Affiliation(s)
- Shang Liang
- Cancer Research UK Beatson Institute, Glasgow, U.K
- School of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, U.K
| | - Rajaei Almohammed
- Cancer Research UK Beatson Institute, Glasgow, U.K
- School of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, U.K
| | - Victoria H Cowling
- Cancer Research UK Beatson Institute, Glasgow, U.K
- School of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, U.K
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43
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Franco G, Taillebourg E, Delfino E, Homolka D, Gueguen N, Brasset E, Pandey RR, Pillai RS, Fauvarque MO. The catalytic-dead Pcif1 regulates gene expression and fertility in Drosophila. RNA (NEW YORK, N.Y.) 2023; 29:609-619. [PMID: 36754578 PMCID: PMC10158991 DOI: 10.1261/rna.079192.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 01/09/2023] [Indexed: 05/06/2023]
Abstract
Eukaryotic mRNAs are modified at the 5' end with a methylated guanosine (m7G) that is attached to the transcription start site (TSS) nucleotide. The TSS nucleotide is 2'-O-methylated (Nm) by CMTR1 in organisms ranging from insects to human. In mammals, the TSS adenosine can be further N 6 -methylated by RNA polymerase II phosphorylated CTD-interacting factor 1 (PCIF1) to create m6Am. Curiously, the fly ortholog of mammalian PCIF1 is demonstrated to be catalytic-dead, and its functions are not known. Here, we show that Pcif1 mutant flies display a reduced fertility which is particularly marked in females. Deep sequencing analysis of Pcif1 mutant ovaries revealed transcriptome changes with a notable increase in expression of genes belonging to the mitochondrial ATP synthetase complex. Furthermore, the Pcif1 protein is distributed along euchromatic regions of polytene chromosomes, and the Pcif1 mutation behaved as a modifier of position-effect-variegation (PEV) suppressing the heterochromatin-dependent silencing of the white gene. Similar or stronger changes in the transcriptome and PEV phenotype were observed in flies that expressed a cytosolic version of Pcif1. These results point to a nuclear cotranscriptional gene regulatory role for the catalytic-dead fly Pcif1 that is probably based on its conserved ability to interact with the RNA polymerase II carboxy-terminal domain.
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Affiliation(s)
- Giulia Franco
- Université Grenoble Alpes, CEA, INSERM, BGE, F-38000 Grenoble, France
| | | | - Elena Delfino
- Department of Molecular Biology, Science III, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - David Homolka
- Department of Molecular Biology, Science III, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Nathalie Gueguen
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
| | - Emilie Brasset
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
| | - Radha Raman Pandey
- Department of Molecular Biology, Science III, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Ramesh S Pillai
- Department of Molecular Biology, Science III, University of Geneva, CH-1211 Geneva 4, Switzerland
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44
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Garsetti DE, Sahay K, Wang Y, Rogers MB. Sex and the basal mRNA synthesis machinery. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1765. [PMID: 36195437 PMCID: PMC10070566 DOI: 10.1002/wrna.1765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/26/2022] [Accepted: 09/09/2022] [Indexed: 11/07/2022]
Abstract
Evolution and change generated an incredible diversity of organisms on this earth. Yet, some processes are so central to life that change is strongly selected against. Synthesis of the eukaryotic messenger RNA is one example. The assemblies that carry out transcription and processing (capping, polyadenylation, and splicing) are so conserved that most genes have recognizable orthologs in yeast and humans. Naturally, most would conclude transcription and processing are identical in both sexes. However, this is an assumption. Men and women vastly differ in their physiologies. The incidence of pathologies, symptom presentation, disease outcome, and therapeutic response in each sex vary enormously. Despite the harm ignorance causes women, biological research has been historically carried out without regard to sex. The male mouse was the default mammal. A cultured cell's sex was considered irrelevant. Attempts to fill this knowledge gap have revealed molecular dissimilarities. For example, the earliest embryonic male and female transcriptomes differ long before fetal sex hormones appear. We used public data to challenge the assumption of sameness by reviewing reports of sex-biased gene expression and gene targeting. We focused on 120 genes encoding nonregulatory proteins involved in mRNA synthesis. Remarkably, genes with recognizable orthologs in yeast and thus LEAST likely to differ, did differ between the sexes. The rapidly growing public databases can be used to compare the expression of any gene in male and female tissues. Appreciating the principles that drive sex differences will enrich our understanding of RNA biology in all humans-men and women. This article is categorized under: RNA in Disease and Development > RNA in Development RNA Evolution and Genomics > Computational Analyses of RNA.
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Affiliation(s)
- Diane E Garsetti
- Rutgers-New Jersey Medical School (NJMS), Department of Microbiology, Biochemistry, and Molecular Genetics, Newark, New Jersey, USA
| | - Khushboo Sahay
- Rutgers-New Jersey Medical School (NJMS), Department of Microbiology, Biochemistry, and Molecular Genetics, Newark, New Jersey, USA
| | - Yue Wang
- Rutgers-New Jersey Medical School (NJMS), Department of Microbiology, Biochemistry, and Molecular Genetics, Newark, New Jersey, USA
| | - Melissa B Rogers
- Rutgers-New Jersey Medical School (NJMS), Department of Microbiology, Biochemistry, and Molecular Genetics, Newark, New Jersey, USA
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45
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Turner M. Regulation and function of poised mRNAs in lymphocytes. Bioessays 2023; 45:e2200236. [PMID: 37009769 DOI: 10.1002/bies.202200236] [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: 12/07/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 04/04/2023]
Abstract
Pre-existing but untranslated or 'poised' mRNA exists as a means to rapidly induce the production of specific proteins in response to stimuli and as a safeguard to limit the actions of these proteins. The translation of poised mRNA enables immune cells to express quickly genes that enhance immune responses. The molecular mechanisms that repress the translation of poised mRNA and, upon stimulation, enable translation have yet to be elucidated. They likely reflect intrinsic properties of the mRNAs and their interactions with trans-acting factors that direct poised mRNAs away from or into the ribosome. Here, I discuss mechanisms by which this might be regulated.
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Affiliation(s)
- Martin Turner
- Immunology Programme, The Babraham Institute, Cambridge, UK
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46
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Kozarski M, Drazkowska K, Bednarczyk M, Warminski M, Jemielity J, Kowalska J. Towards superior mRNA caps accessible by click chemistry: synthesis and translational properties of triazole-bearing oligonucleotide cap analogs. RSC Adv 2023; 13:12809-12824. [PMID: 37114020 PMCID: PMC10126820 DOI: 10.1039/d3ra00026e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/01/2023] [Indexed: 04/29/2023] Open
Abstract
Messenger RNA (mRNA)-based gene delivery is a powerful strategy for the development of vaccines and therapeutics. Consequently, approaches that enable efficient synthesis of mRNAs with high purity and biological activity are in demand. Chemically modified 7-methylguanosine (m7G) 5' caps can augment the translational properties of mRNA; however, efficient synthesis of structurally complex caps, especially on a large scale, is challenging. Previously, we proposed a new strategy to assemble dinucleotide mRNA caps by replacing the traditional pyrophosphate bond formation by copper-catalyzed azide-alkyne cycloaddition (CuAAC). Here, we used CuAAC to synthesize 12 novel triazole-containing tri- and tetranucleotide cap analogs with the aim of exploring the chemical space around the first transcribed nucleotide in mRNA and overcoming some of the limitations previously reported for the triazole-containing dinucleotide analogs. We evaluated the efficiency of incorporation into RNA for these analogs and their influence on the translational properties of in vitro transcribed (IVT) mRNAs in rabbit reticulocyte lysate and JAWS II cultured cells. The incorporation of the triazole moiety within the 5',5'-oligophosphate of trinucleotide cap produced compounds that were well incorporated into RNA by T7 polymerase while replacing the 5',3'-phosphodiester bond with triazole impaired incorporation and translation efficiency, despite a neutral effect on the interaction with the translation initiation factor eIF4E. One of the compounds (m7Gppp-tr-C2H4pAmpG), had translational activity and other biochemical properties comparable to natural cap 1 structure, thus being a promising mRNA capping reagent for potential in cellulo and in vivo applications in the field of mRNA-based therapeutics.
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Affiliation(s)
- Mateusz Kozarski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw Pasteura 5 02-093 Warsaw Poland
- Centre of New Technologies, University of Warsaw Banacha 2c 02-097 Warsaw Poland
| | - Karolina Drazkowska
- Centre of New Technologies, University of Warsaw Banacha 2c 02-097 Warsaw Poland
| | - Marcelina Bednarczyk
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw Pasteura 5 02-093 Warsaw Poland
- Centre of New Technologies, University of Warsaw Banacha 2c 02-097 Warsaw Poland
| | - Marcin Warminski
- 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
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw Pasteura 5 02-093 Warsaw Poland
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47
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Sun Y, Shen W, Hu S, Lyu Q, Wang Q, Wei T, Zhu W, Zhang J. METTL3 promotes chemoresistance in small cell lung cancer by inducing mitophagy. J Exp Clin Cancer Res 2023; 42:65. [PMID: 36932427 PMCID: PMC10022264 DOI: 10.1186/s13046-023-02638-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 03/05/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND Small cell lung cancer (SCLC) is the most aggressive subtype of lung cancer. Although most patients are initially sensitive to first-line combination chemotherapy with cisplatin and etoposide, chemotherapy drug resistance easily develops and quickly leads to tumour progression. Therefore, understanding the mechanisms of chemotherapy drug resistance and how to reverse it is key to improving the prognosis of patients with SCLC. Moreover, N6-methyladenosine (m6A) is the most abundant mRNA modification and is catalysed by the methyltransferase complex, in which methyltransferase-like 3 (METTL3) is the sole catalytic subunit. METHODS The effects of METTL3 on chemoresistance in SCLC cells were determined using qRT-PCR, Western blotting, immunohistochemistry, cell counting kit (CCK-8) assays, flow cytometry, and tumorigenicity experiments. Methylated RNA immunoprecipitation sequencing (MeRIP-seq), MeRIP qPCR, immunofluorescence, and drug inhibitor experiments were performed to confirm the molecular mechanism of Decapping Protein 2 (DCP2), which is involved in the chemoresistance of SCLC. RESULTS In the present study, we found that METTL3 is a marker for poor SCLC prognosis, and it is highly expressed in chemoresistant SCLC cells. METTL3 promotes SCLC chemoresistance by positively regulating mitophagy. METTL3 induces m6A methylation of DCP2 and causes the degradation of DCP2, which promotes mitochondrial autophagy through the Pink1-Parkin pathway, leading to chemotherapy resistance. We also found that STM2457, a novel METTL3 inhibitor, can reverse SCLC chemoresistance. CONCLUSIONS The m6A methyltransferase METTL3 regulates Pink1-Parkin pathway-mediated mitophagy and mitochondrial damage in SCLC cells by targeting DCP2, thereby promoting chemotherapy resistance in patients with SCLC.
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Affiliation(s)
- Yueqin Sun
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Weitao Shen
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Shulu Hu
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Qiong Lyu
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Qiongyao Wang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Ting Wei
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
| | - Weiliang Zhu
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
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48
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Anreiter I, Tian YW, Soller M. The cap epitranscriptome: Early directions to a complex life as mRNA. Bioessays 2023; 45:e2200198. [PMID: 36529693 DOI: 10.1002/bies.202200198] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
Animal, protist and viral messenger RNAs (mRNAs) are most prominently modified at the beginning by methylation of cap-adjacent nucleotides at the 2'-O-position of the ribose (cOMe) by dedicated cap methyltransferases (CMTrs). If the first nucleotide of an mRNA is an adenosine, PCIF1 can methylate at the N6 -position (m6 A), while internally the Mettl3/14 writer complex can methylate. These modifications are introduced co-transcriptionally to affect many aspects of gene expression including localisation to synapses and local translation. Of particular interest, transcription start sites of many genes are heterogeneous leading to sequence diversity at the beginning of mRNAs, which together with cOMe and m6 Am could constitute an extensive novel layer of gene expression control. Given the role of cOMe and m6 A in local gene expression at synapses and higher brain functions including learning and memory, such code could be implemented at the transcriptional level for lasting memories through local gene expression at synapses.
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Affiliation(s)
- Ina Anreiter
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Canada
| | - Yuan W Tian
- Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK.,School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Matthias Soller
- Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK.,School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK
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Wolfram-Schauerte M, Höfer K. NAD-capped RNAs - a redox cofactor meets RNA. Trends Biochem Sci 2023; 48:142-155. [PMID: 36068130 DOI: 10.1016/j.tibs.2022.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/03/2022] [Accepted: 08/04/2022] [Indexed: 01/25/2023]
Abstract
RNA modifications immensely expand the diversity of the transcriptome, thereby influencing the function, localization, and stability of RNA. One prominent example of an RNA modification is the eukaryotic cap located at the 5' terminus of mRNAs. Interestingly, the redox cofactor NAD can be incorporated into RNA by RNA polymerase in vitro. The existence of NAD-modified RNAs in vivo was confirmed using liquid chromatography and mass spectrometry (LC-MS). In the past few years novel technologies and methods have characterized NAD as a cap-like RNA structure and enabled the investigation of NAD-capped RNAs (NAD-RNAs) in a physiological context. We highlight the identification of NAD-RNAs as well as the regulation and functions of this epitranscriptomic mark in all domains of life.
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Affiliation(s)
| | - Katharina Höfer
- Max-Planck-Institute for Terrestrial Microbiology, Marburg, 35043, Hessen, Germany.
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50
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Grzela R, Piecyk K, Stankiewicz-Drogon A, Pietrow P, Lukaszewicz M, Kurpiejewski K, Darzynkiewicz E, Jankowska-Anyszka M. N2 modified dinucleotide cap analogs as a potent tool for mRNA engineering. RNA (NEW YORK, N.Y.) 2023; 29:200-216. [PMID: 36418172 PMCID: PMC9891257 DOI: 10.1261/rna.079460.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
mRNA-based vaccines are relatively new technologies that have been in the field of interest of research centers and pharmaceutical companies in recent years. Such therapeutics are an attractive alternative for DNA-based vaccines since they provide material that can be used with no risk of genomic integration. Additionally, mRNA can be quite easily engineered to introduce modifications for different applications or to modulate its properties, for example, to increase translational efficiency or stability, which is not available for DNA vectors. Here, we describe the use of N2 modified dinucleotide cap analogs as components of mRNA transcripts. The compounds obtained showed very promising biological properties while incorporated into mRNA. The presented N2-guanine modifications within the cap structure ensure proper attachment of the dinucleotide to the transcripts in the IVT reaction, guarantees their incorporation only in the correct orientation, and enables highly efficient translation of mRNA both in the in vitro translation system and in human HEK293 cells.
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Affiliation(s)
- Renata Grzela
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Karolina Piecyk
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland
| | - Anna Stankiewicz-Drogon
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Paulina Pietrow
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland
| | - Maciej Lukaszewicz
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, 02-093 Warsaw, Poland
| | | | - Edward Darzynkiewicz
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, 02-093 Warsaw, Poland
- Center of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
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