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Hegde S, Tang Z, Zhao J, Wang J. Inhibition of SARS-CoV-2 by Targeting Conserved Viral RNA Structures and Sequences. Front Chem 2021; 9:802766. [PMID: 35004621 PMCID: PMC8733332 DOI: 10.3389/fchem.2021.802766] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/29/2021] [Indexed: 01/18/2023] Open
Abstract
The ongoing COVID-19/Severe Acute Respiratory Syndrome CoV-2 (SARS-CoV-2) pandemic has become a significant threat to public health and has hugely impacted societies globally. Targeting conserved SARS-CoV-2 RNA structures and sequences essential for viral genome translation is a novel approach to inhibit viral infection and progression. This new pharmacological modality compasses two classes of RNA-targeting molecules: 1) synthetic small molecules that recognize secondary or tertiary RNA structures and 2) antisense oligonucleotides (ASOs) that recognize the RNA primary sequence. These molecules can also serve as a "bait" fragment in RNA degrading chimeras to eliminate the viral RNA genome. This new type of chimeric RNA degrader is recently named ribonuclease targeting chimera or RIBOTAC. This review paper summarizes the sequence conservation in SARS-CoV-2 and the current development of RNA-targeting molecules to combat this virus. These RNA-binding molecules will also serve as an emerging class of antiviral drug candidates that might pivot to address future viral outbreaks.
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Affiliation(s)
| | | | | | - Jingxin Wang
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS, United States
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102
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Mollocana-Lara EC, Ni M, Agathos SN, Gonzales-Zubiate FA. The infinite possibilities of RNA therapeutics. J Ind Microbiol Biotechnol 2021; 48:kuab063. [PMID: 34463324 PMCID: PMC8788720 DOI: 10.1093/jimb/kuab063] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 08/24/2021] [Indexed: 12/13/2022]
Abstract
Although the study of ribonucleic acid (RNA) therapeutics started decades ago, for many years, this field of research was overshadowed by the growing interest in DNA-based therapies. Nowadays, the role of several types of RNA in cell regulation processes and the development of various diseases have been elucidated, and research in RNA therapeutics is back with force. This short literature review aims to present general aspects of many of the molecules currently used in RNA therapeutics, including in vitro transcribed mRNA (IVT mRNA), antisense oligonucleotides (ASOs), aptamers, small interfering RNAs (siRNAs), and microRNAs (miRNAs). In addition, we describe the state of the art of technologies applied for synthetic RNA manufacture and delivery. Likewise, we detail the RNA-based therapies approved by the FDA so far, as well as the ongoing clinical investigations. As a final point, we highlight the current and potential advantages of working on RNA-based therapeutics and how these could lead to a new era of accessible and personalized healthcare.
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Affiliation(s)
- Evelyn C Mollocana-Lara
- School of Biological Sciences and Engineering, Yachay Tech University, 100119, San Miguel de Urcuquí, Ecuador
| | - Ming Ni
- GenScript, Jiangsu Province, 212000, People's Republic of China
| | - Spiros N Agathos
- Bioengineering Laboratory, Earth and Life Institute, Catholic University of Louvain, Louvain-la-Neuve B-1348, Belgium
| | - Fernando A Gonzales-Zubiate
- School of Biological Sciences and Engineering, Yachay Tech University, 100119, San Miguel de Urcuquí, Ecuador
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103
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Guimaraes G, Yuan L, Li P. Antisense Oligonucleotide In Vitro Protein Binding Determination in Plasma, Brain and Cerebral Spinal Fluid Using Hybridization LC-MS/MS. Drug Metab Dispos 2021; 50:268-276. [PMID: 34921096 DOI: 10.1124/dmd.121.000751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/10/2021] [Indexed: 11/22/2022] Open
Abstract
The development of quantitative models for prediction of drug pharmacokinetics based on in vitro data has transformed early drug discovery. Drug unbound fraction (ƒu) characterization is a key consideration in pharmacokinetic (PK) and pharmacodynamic (PD) modeling, assuming only unbound drug can interact with the target, and therefore has direct implications in the efficacy and potential toxicity of the drug. The current study describes the implementation of a hybridization LC-MS/MS platform for the direct quantitation of antisense oligonucleotide (ASO) ƒu The method provides substantial improvements including minimal matrix effects and high specificity when compared to previously used oligonucleotide ƒu detection methods such as ligand binding assays or liquid scintillation. The hybridization LC-MS/MS platform was integrated with ultracentrifugation, ultrafiltration and equilibrium dialysis, and method performance for each technique was evaluated. While ASO protein binding has been previously characterized in plasma, there were no studies that quantitated ASO ƒu in brain or CSF. As ASOs continue to undergo clinical trials for neurological and neuromuscular indications, ƒu characterization in brain and CSF can provide invaluable information about ASO distribution and target engagement in the central nervous system, therefore providing support for in vivo PK-PD data characterization. Significance Statement A novel hybridization LC-MS/MS based approach was successfully developed for the determination of ASO in vitro protein binding in plasma, and for the first time brain and cerebral spinal fluid. Ultrafiltration, equilibrium dialysis, and ultracentrifugation were assessed for the separation of unbound ASO from biological matrices. The hybridization LC-MS/MS platform provided unique advantages, including minimal matrix effects and high specificity, comparing to traditional ligand binding assays or liquid scintillation approaches, which enabled efficient and reliable in vitro protein binding assay.
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104
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Cheng HL, Liu RR. [Regulation effect of siRNA on β-globin in erythrocytes of hemoglobin H disease]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2021; 42:1015-1020. [PMID: 35045673 PMCID: PMC8770884 DOI: 10.3760/cma.j.issn.0253-2727.2021.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Indexed: 11/30/2022]
Abstract
Objective: To investigate the regulatory effect of targeted siRNA on β-globin in erythroid cells cultured by targeted differentiation in vitro and provide new theoretical support for gene therapy for hemoglobin H (HbH) disease. Methods: Based on the β-globin gene expression results, the optimal siRNA sequence and its effective action dose were screened in erythroid cells, and the effect of the effective dose of the optimal siRNA on the regulation of β-globin expression and apoptosis in erythroid cells was examined. The effective dose of the optimal siRNA was applied to erythroid cells with HbH disease. The effects of transfected siRNAs on red line cells with HbH disease were comprehensively evaluated by measuring the expression of β-globin, reactive oxygen species (ROS) , and apoptosis rates. Results: Within 96 hours after transfection, siRNA2 significantly downregulated β-globin expression in in vitro cultured erythroid cells, but not α-globin. siRNA silencing effect and duration of effect were dose-dependent. siRNA2 downregulated β-globin expression, reduced intracellular ROS production, and decreased apoptosis rate in erythroid cells with HbH disease. Conclusion: Targeted siRNAs can downregulate β-globin expression, reduce intracellular ROS production, and downregulate apoptosis rate in erythroid cells with HbH disease.
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Affiliation(s)
- H L Cheng
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - R R Liu
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
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105
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Konč J, Brown L, Whiten DR, Zuo Y, Ravn P, Klenerman D, Bernardes GJL. A Platform for Site‐Specific DNA‐Antibody Bioconjugation by Using Benzoylacrylic‐Labelled Oligonucleotides. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Juraj Konč
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Libby Brown
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Daniel R. Whiten
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Yukun Zuo
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Peter Ravn
- AstraZeneca R&D BioPharmaceuticals Unit
- Antibody Discovery & Protein Engineering (ADPE) Milstein Building, Granta Park Cambridge CB21 6GH UK
- Current address: Department of Biotherapeutic Discovery H. Lundbeck A/S Ottiliavej 9, 2500 Valby Denmark
| | - David Klenerman
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- UK Dementia Research Institute University of Cambridge Cambridge CB2 0XY UK
| | - Gonçalo J. L. Bernardes
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- Instituto de Medicina Molecular João Lobo Antunes Faculdade de Medicina Universidade de Lisboa Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
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106
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Konč J, Brown L, Whiten DR, Zuo Y, Ravn P, Klenerman D, Bernardes GJL. A Platform for Site-Specific DNA-Antibody Bioconjugation by Using Benzoylacrylic-Labelled Oligonucleotides. Angew Chem Int Ed Engl 2021; 60:25905-25913. [PMID: 34555238 PMCID: PMC9297960 DOI: 10.1002/anie.202109713] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Indexed: 12/27/2022]
Abstract
Many bioconjugation strategies for DNA oligonucleotides and antibodies suffer limitations, such as site-specificity, stoichiometry and hydrolytic instability of the conjugates, which makes them unsuitable for biological applications. Here, we report a new platform for the preparation of DNA-antibody bioconjugates with a simple benzoylacrylic acid pentafluorophenyl ester reagent. Benzoylacrylic-labelled oligonucleotides prepared with this reagent can be site-specifically conjugated to a range of proteins and antibodies through accessible cysteine residues. The homogeneity of the prepared DNA-antibody bioconjugates was confirmed by a new LC-MS protocol and the bioconjugate probes were used in fluorescence or super-resolution microscopy cell imaging experiments. This work demonstrates the versatility and robustness of our bioconjugation protocol that gives site-specific, well-defined and plasma-stable DNA-antibody bioconjugates for biological applications.
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Affiliation(s)
- Juraj Konč
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Libby Brown
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Daniel R. Whiten
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Yukun Zuo
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Peter Ravn
- AstraZenecaR&D BioPharmaceuticals Unit|Antibody Discovery & Protein Engineering (ADPE)Milstein Building, Granta ParkCambridgeCB21 6GHUK
- Current address: Department of Biotherapeutic DiscoveryH. Lundbeck A/SOttiliavej 9, 2500ValbyDenmark
| | - David Klenerman
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- UK Dementia Research InstituteUniversity of CambridgeCambridgeCB2 0XYUK
| | - Gonçalo J. L. Bernardes
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Instituto de Medicina Molecular João Lobo AntunesFaculdade de MedicinaUniversidade de LisboaAvenida Professor Egas Moniz1649-028LisboaPortugal
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107
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Talap J, Zhao J, Shen M, Song Z, Zhou H, Kang Y, Sun L, Yu L, Zeng S, Cai S. Recent advances in therapeutic nucleic acids and their analytical methods. J Pharm Biomed Anal 2021; 206:114368. [PMID: 34571322 DOI: 10.1016/j.jpba.2021.114368] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/11/2022]
Abstract
Therapeutic nucleic acids are various chemically modified RNA or DNA with different functions, which mainly play roles at the gene level. Owing to its accurately targeting at pathogenic genes, nucleic acid based therapeutics have a wide range of application prospects. Recently, the improvement on chemical synthesis and delivery materials accelerated the development of therapeutic nucleic acids rapidly. Up to now, 17 nucleic acid based therapeutics approved by Food and Drug Administration (FDA) or European Medicines Agency (EMA). The development of therapeutics raised higher requirements for analytical methods, both in quality control and in clinical research. The first part of this review introduces different classes of therapeutic nucleic acids, including antisense oligonucleotide (ASO), RNA interference (RNAi) therapy, mRNA, aptamer and other classes which are under research. The second part reviews the therapeutic nucleic acids commercialized from 2019 to now. The third part discusses the analytical methods for nucleic acid based therapeutics, including liquid chromatography-based methods, capillary gel electrophoresis (CGE), hybridization enzyme-linked immunosorbent assay (ELISA) and other infrequently used methods. Finally, the advantages and shortcomings of these methods are summarized, and the future development of analysis methods are prospected.
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Affiliation(s)
- Jadera Talap
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jing Zhao
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao
| | - Minzhe Shen
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zihan Song
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yu Kang
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lianli Sun
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lushan Yu
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Cancer Center of Zhejiang University, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Hangzhou, China.
| | - Sheng Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Cancer Center of Zhejiang University, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Hangzhou, China.
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108
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Antisense Oligonucleotide-Based Therapy of Viral Infections. Pharmaceutics 2021; 13:pharmaceutics13122015. [PMID: 34959297 PMCID: PMC8707165 DOI: 10.3390/pharmaceutics13122015] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/23/2021] [Accepted: 11/23/2021] [Indexed: 02/07/2023] Open
Abstract
Nucleic acid-based therapeutics have demonstrated their efficacy in the treatment of various diseases and vaccine development. Antisense oligonucleotide (ASO) technology exploits a single-strand short oligonucleotide to either cause target RNA degradation or sterically block the binding of cellular factors or machineries to the target RNA. Chemical modification or bioconjugation of ASOs can enhance both its pharmacokinetic and pharmacodynamic performance, and it enables customization for a specific clinical purpose. ASO-based therapies have been used for treatment of genetic disorders, cancer and viral infections. In particular, ASOs can be rapidly developed for newly emerging virus and their reemerging variants. This review discusses ASO modifications and delivery options as well as the design of antiviral ASOs. A better understanding of the viral life cycle and virus-host interactions as well as advances in oligonucleotide technology will benefit the development of ASO-based antiviral therapies.
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109
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Li D, Zhang Z, Xia C, Niu C, Zhou W. Non-Coding RNAs in Glioma Microenvironment and Angiogenesis. Front Mol Neurosci 2021; 14:763610. [PMID: 34803608 PMCID: PMC8595242 DOI: 10.3389/fnmol.2021.763610] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/11/2021] [Indexed: 12/17/2022] Open
Abstract
Glioma, especially glioblastoma, is the most common and lethal brain tumor. In line with the complicated vascularization processes and the strong intratumoral heterogeneity, tumor-associated blood vessels in glioma are regulated by multiple types of cells through a variety of molecular mechanisms. Components of the tumor microenvironment, including tumor cells and tumor-associated stromata, produce various types of molecular mediators to regulate glioma angiogenesis. As critical regulatory molecules, non-coding RNAs (ncRNAs) inside cells or secreted to the tumor microenvironment play essential roles in glioma angiogenesis. In this review, we briefly summarize recent studies about the production, delivery, and functions of ncRNAs in the tumor microenvironment, as well as the molecular mechanisms underlying the regulation of angiogenesis by ncRNAs. We also discuss the ncRNA-based therapeutic strategies in the anti-angiogenic therapy for glioma treatment.
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Affiliation(s)
- Dongxue Li
- Intelligent Pathology Institute, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Department of Neurosurgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Zhe Zhang
- Basic Medical College, Qingdao University, Qingdao, China
| | - Chengyu Xia
- Department of Neurosurgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Chaoshi Niu
- Department of Neurosurgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wenchao Zhou
- Intelligent Pathology Institute, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Department of Pathology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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110
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Chitrakar A, Solorio-Kirpichyan K, Prangley E, Rath S, Du J, Korennykh A. Introns encode dsRNAs undetected by RIG-I/MDA5/interferons and sensed via RNase L. Proc Natl Acad Sci U S A 2021; 118:e2102134118. [PMID: 34772806 PMCID: PMC8609619 DOI: 10.1073/pnas.2102134118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2021] [Indexed: 12/24/2022] Open
Abstract
Double-stranded RNA (dsRNA), a hallmark viral material that activates antiviral interferon (IFN) responses, can appear in human cells also in the absence of viruses. We identify phosphorothioate DNAs (PS DNAs) as triggers of such endogenous dsRNA (endo-dsRNA). PS DNAs inhibit decay of nuclear RNAs and induce endo-dsRNA via accumulation of high levels of intronic and intergenic inverted retroelements (IIIR). IIIRs activate endo-dsRNA responses distinct from antiviral defense programs. IIIRs do not turn on transcriptional RIG-I/MDA5/IFN signaling, but they trigger the dsRNA-sensing pathways of OAS3/RNase L and PKR. Thus, nuclear RNA decay and nuclear-cytosolic RNA sorting actively protect from these innate immune responses to self. Our data suggest that the OAS3/RNase L and PKR arms of innate immunity diverge from antiviral IFN responses and monitor nuclear RNA decay by sensing cytosolic escape of IIIRs. OAS3 provides a receptor for IIIRs, whereas RNase L cleaves IIIR-carrying introns and intergenic RNAs.
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Affiliation(s)
- Alisha Chitrakar
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | | | - Eliza Prangley
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Sneha Rath
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Jin Du
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Alexei Korennykh
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
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111
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Therapeutic Prospects of Exon Skipping for Epidermolysis Bullosa. Int J Mol Sci 2021; 22:ijms222212222. [PMID: 34830104 PMCID: PMC8621297 DOI: 10.3390/ijms222212222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/03/2021] [Accepted: 11/08/2021] [Indexed: 12/12/2022] Open
Abstract
Epidermolysis bullosa is a group of genetic skin conditions characterized by abnormal skin (and mucosal) fragility caused by pathogenic variants in various genes. The disease severity ranges from early childhood mortality in the most severe types to occasional acral blistering in the mildest types. The subtype and severity of EB is linked to the gene involved and the specific variants in that gene, which also determine its mode of inheritance. Current treatment is mainly focused on symptomatic relief such as wound care and blister prevention, because truly curative treatment options are still at the preclinical stage. Given the current level of understanding, the broad spectrum of genes and variants underlying EB makes it impossible to develop a single treatment strategy for all patients. It is likely that many different variant-specific treatment strategies will be needed to ultimately treat all patients. Antisense-oligonucleotide (ASO)-mediated exon skipping aims to counteract pathogenic sequence variants by restoring the open reading frame through the removal of the mutant exon from the pre-messenger RNA. This should lead to the restored production of the protein absent in the affected skin and, consequently, improvement of the phenotype. Several preclinical studies have demonstrated that exon skipping can restore protein production in vitro, in skin equivalents, and in skin grafts derived from EB-patient skin cells, indicating that ASO-mediated exon skipping could be a viable strategy as a topical or systemic treatment. The potential value of exon skipping for EB is supported by a study showing reduced phenotypic severity in patients who carry variants that result in natural exon skipping. In this article, we review the substantial progress made on exon skipping for EB in the past 15 years and highlight the opportunities and current challenges of this RNA-based therapy approach. In addition, we present a prioritization strategy for the development of exon skipping based on genomic information of all EB-involved genes.
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112
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Zhang R, Fu Y, Cheng M, Ma W, Zheng N, Wang Y, Wu Z. sEVs RVG selectively delivers antiviral siRNA to fetus brain, inhibits ZIKV infection and mitigates ZIKV-induced microcephaly in mouse model. Mol Ther 2021; 30:2078-2091. [PMID: 34762817 PMCID: PMC9092305 DOI: 10.1016/j.ymthe.2021.10.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/13/2021] [Accepted: 10/10/2021] [Indexed: 12/12/2022] Open
Abstract
Zika virus (ZIKV), a flavivirus associated with neurological disorders, constitutes a global health threat. During pregnancy, ZIKV traverses the placenta and causes congenital disease such as microcephaly and Guillain-Barré syndrome in newborns. To develop a specific antiviral therapy against ZIKV-induced microcephaly that could cross placental and blood-brain barriers, we designed targeted small extracellular vesicles (sEVs) encapsulating antiviral siRNA (small interfering RNA) to inhibit ZIKV. The neuro-specific targeting was achieved by engineering EVs membrane protein lamp2b fused with a neuron-specific rabies virus glycoprotein derived peptide (RVG). Intravenous administration of the RVG-engineered sEVs loaded with siRNA (ZIKV-specific siRNA) protected pregnant AG6 mice against vertical transmission of ZIKV. Particularly, sEVsRVG-siRNA traversed placental and blood-brain barriers and suppressed ZIKV infection in fetal brains. Moreover, sEVsRVG-siRNA alleviated the neuroinflammation and neurological damage caused by ZIKV in the fetal mouse model. In general, we developed a sEVs-based targeted system of antiviral therapy for brain and fetal brain infections.
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Affiliation(s)
- Rui Zhang
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, PR China
| | - Yuxuan Fu
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Min Cheng
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, PR China
| | - Wenyuan Ma
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, PR China
| | - Nan Zheng
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, PR China
| | - Yongxiang Wang
- Department of Orthopedics, Northern Jiangsu People's Hospital, the Affiliated Hospital of Nanjing University Medical School, Yangzhou, China.
| | - Zhiwei Wu
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, PR China; State Key Lab of Analytical Chemistry for Life Science, Nanjing University, Nanjing, PR China; Medical School and Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, PR China.
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113
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Gupta A, Andresen JL, Manan RS, Langer R. Nucleic acid delivery for therapeutic applications. Adv Drug Deliv Rev 2021; 178:113834. [PMID: 34492233 DOI: 10.1016/j.addr.2021.113834] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/25/2021] [Accepted: 06/11/2021] [Indexed: 02/07/2023]
Abstract
Recent medical advances have exploited the ability to address a given disease at the underlying level of transcription and translation. These treatment paradigms utilize nucleic acids - including short interfering RNA (siRNA), microRNA (miRNA), antisense oligonucleotides (ASO), and messenger RNA (mRNA) - to achieve a desired outcome ranging from gene knockdown to induced expression of a selected target protein. Towards this end, numerous strategies for encapsulation or stabilization of various nucleic acid structures have been developed in order to achieve intracellular delivery. In this review, we discuss several therapeutic applications of nucleic acids directed towards specific diseases and tissues of interest, in particular highlighting recent technologies which have reached late-stage clinical trials and received FDA approval.
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Affiliation(s)
- Akash Gupta
- David H Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02139, USA
| | - Jason L Andresen
- David H Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rajith S Manan
- David H Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert Langer
- David H Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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114
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Cherif C, Nguyen DT, Paris C, Le TK, Sefiane T, Carbuccia N, Finetti P, Chaffanet M, Kaoutari AE, Vernerey J, Fazli L, Gleave M, Manai M, Barthélémy P, Birnbaum D, Bertucci F, Taïeb D, Rocchi P. Menin inhibition suppresses castration-resistant prostate cancer and enhances chemosensitivity. Oncogene 2021; 41:125-137. [PMID: 34711954 PMCID: PMC8724010 DOI: 10.1038/s41388-021-02039-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 09/09/2021] [Accepted: 09/27/2021] [Indexed: 11/09/2022]
Abstract
Disease progression and therapeutic resistance of prostate cancer (PC) are linked to multiple molecular events that promote survival and plasticity. We previously showed that heat shock protein 27 (HSP27) acted as a driver of castration-resistant phenotype (CRPC) and developed an oligonucleotides antisense (ASO) against HSP27 with evidence of anti-cancer activity in men with CRPC. Here, we show that the tumor suppressor Menin (MEN1) is highly regulated by HSP27. Menin is overexpressed in high-grade PC and CRPC. High MEN1 mRNA expression is associated with decreased biochemical relapse-free and overall survival. Silencing Menin with ASO technology inhibits CRPC cell proliferation, tumor growth, and restores chemotherapeutic sensitivity. ChIP-seq analysis revealed differential DNA binding sites of Menin in various prostatic cells, suggesting a switch from tumor suppressor to oncogenic functions in CRPC. These data support the evaluation of ASO against Menin for CRPC. ![]()
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Affiliation(s)
- Chaïma Cherif
- Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille, Inserm UMR 1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille University, 27 Bd. Leï Roure, F-13009 Marseille, France.,Laboratory of Biochemistry and Molecular Biology, Science University of Tunis, 2092, El Manar, Tunis, Tunisia
| | - Dang Tan Nguyen
- Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille, Inserm UMR 1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille University, 27 Bd. Leï Roure, F-13009 Marseille, France
| | - Clément Paris
- Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille, Inserm UMR 1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille University, 27 Bd. Leï Roure, F-13009 Marseille, France
| | - Thi Khanh Le
- Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille, Inserm UMR 1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille University, 27 Bd. Leï Roure, F-13009 Marseille, France
| | - Thibaud Sefiane
- Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille, Inserm UMR 1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille University, 27 Bd. Leï Roure, F-13009 Marseille, France
| | - Nadine Carbuccia
- Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille, Inserm UMR 1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille University, 27 Bd. Leï Roure, F-13009 Marseille, France
| | - Pascal Finetti
- Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille, Inserm UMR 1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille University, 27 Bd. Leï Roure, F-13009 Marseille, France
| | - Max Chaffanet
- Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille, Inserm UMR 1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille University, 27 Bd. Leï Roure, F-13009 Marseille, France
| | - Abdessamad El Kaoutari
- Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille, Inserm UMR 1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille University, 27 Bd. Leï Roure, F-13009 Marseille, France
| | - Julien Vernerey
- Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille, Inserm UMR 1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille University, 27 Bd. Leï Roure, F-13009 Marseille, France
| | - Ladan Fazli
- The Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
| | - Martin Gleave
- The Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
| | - Mohamed Manai
- Laboratory of Biochemistry and Molecular Biology, Science University of Tunis, 2092, El Manar, Tunis, Tunisia
| | - Philippe Barthélémy
- ARNA Laboratory, INSERM U1212, CNRS UMR 5320, University of Bordeaux, F-33076 Bordeaux, France
| | - Daniel Birnbaum
- Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille, Inserm UMR 1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille University, 27 Bd. Leï Roure, F-13009 Marseille, France
| | - François Bertucci
- Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille, Inserm UMR 1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille University, 27 Bd. Leï Roure, F-13009 Marseille, France
| | - David Taïeb
- Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille, Inserm UMR 1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille University, 27 Bd. Leï Roure, F-13009 Marseille, France.,Biophysics and Nuclear Medicine Department, La Timone University Hospital, European Center for Research in Medical Imaging, Aix-Marseille University, F-13005 Marseille, France
| | - Palma Rocchi
- Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille, Inserm UMR 1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille University, 27 Bd. Leï Roure, F-13009 Marseille, France.
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115
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Cen Y, Wang Z, Ke P, Zhu W, Yuan Z, Feng S, Chen Y, Lin C, Liu X, Li Y, Yan P. Development of a novel ssDNA aptamer targeting cardiac troponin I and its clinical applications. Anal Bioanal Chem 2021; 413:7043-7053. [PMID: 34673993 DOI: 10.1007/s00216-021-03667-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/30/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
Cardiac troponin I (cTnI) is a specific biomarker of acute myocardial infarction (AMI). However, cTnI detection kits prepared with antibodies have many defects. Nucleic acid aptamers are sequences of single-strand DNA or RNA that can overcome the deficiency of antibodies. Herein, sandwich ELONA methods were established based on aptamers. Two selected ssDNA aptamers (Apt3 and Apt6) showed high binding affinity and sensibility (Apt3: Kd = 1.01 ± 0.07 nM, Apt6: k = 0.68 ± 0.05) and did not bind to the same domain of cTnI. Therefore, these two aptamers can be applied to the ELONA methods. The detection range of cTnI using the dual-aptamer sandwich ELONA method was 0.05-200 ng/mL, and the bioanalytical method verification results can meet the national standard of Chinese Pharmacopoeia (2020 Edition). There was no difference between results of the dual-aptamer sandwich ELONA method and the diagnostic results of serum obtained from 243 people (P = 0.39, P ˃ 0.05). The sensitivity and specificity of the ELONA with cTnI in serum were 96.46% and 93.85%, respectively. Compared with the FICA kit, which is clinically used, the consequences of ELONA method are closer to the diagnostic results. This study suggests that the aptamers Apt3 and Apt6 have high affinity and strong specificity and that the dual-aptamer sandwich ELONA method has a wide detection range and can be used to determine cTnI in serum, with potential applications in the diagnosis of AMIs.
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Affiliation(s)
- Yi Cen
- Department of Pharmacy, Biomedicine Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhongping Wang
- Tongpeng Zhongxu Pharmaceutical Technology Company, Guangzhou, Guangdong, China
| | - Peixiong Ke
- Department of Pharmacology, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wenting Zhu
- Department of Pharmacy, Biomedicine Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhongwen Yuan
- Department of Pharmacy, Biomedicine Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Senling Feng
- Department of Pharmacy, Biomedicine Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yiqing Chen
- Tongpeng Zhongxu Pharmaceutical Technology Company, Guangzhou, Guangdong, China
| | - Caiyan Lin
- Tongpeng Zhongxu Pharmaceutical Technology Company, Guangzhou, Guangdong, China
| | - Xiaomin Liu
- Department of Pharmacy, Biomedicine Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yuting Li
- Department of Pharmacy, Biomedicine Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Pengke Yan
- Department of Pharmacy, Biomedicine Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
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116
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Triana-Fonseca P, Parada-Márquez JF, Silva-Aldana CT, Zambrano-Arenas D, Arias-Gomez LL, Morales-Fonseca N, Medina-Méndez E, Restrepo CM, Silgado-Guzmán DF, Fonseca-Mendoza DJ. Genetic Profile of the Dystrophin Gene Reveals New Mutations in Colombian Patients Affected with Muscular Dystrophinopathy. APPLICATION OF CLINICAL GENETICS 2021; 14:399-408. [PMID: 34629887 PMCID: PMC8493106 DOI: 10.2147/tacg.s317721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/31/2021] [Indexed: 11/23/2022]
Abstract
Background Duchenne and Becker muscular dystrophies (DMD/BMD) are the most common human dystrophinopathies with recessive X-linked inheritance. Dystrophin gene deletions and duplications are the most common mutations, followed by point mutations. The aim of this study is to characterize the mutational profile of the dystrophin gene in Colombian patients with DMD/BMD. Material and Methods Mutational profiling was determined in 69 affected patients using Sanger sequencing, next-generation sequencing (NGS) and/or multiplex ligation dependent-probes amplification (MLPA). Genetic variants were classified according to molecular consequence and new variants were determined through database and literature analysis. Results Mutational profile in affected patients revealed that large deletions/duplications analyzed by MLPA accounted for 72.5% of all genetic variations. By using Sanger sequencing or NGS, we identified point mutations in 15.9% and small deletions in 11.6% of the patients. New mutations were found, most of them were point mutations or small deletions (10.1%). Conclusion Our results described the genetic profile of the dystrophin gene in Colombian patients with DMD and contribute to efforts to identify molecular variants in Latin American populations. For our population, 18.8% of cases could be treated with FDA or MDA approved molecular therapies based on specific mutations. These data contribute to the establishment of appropriate genetic counseling and potential treatment.
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Affiliation(s)
| | | | - Claudia T Silva-Aldana
- Department of Molecular Diagnosis, Genética Molecular de Colombia SAS, Bogotá, DC, Colombia
| | | | | | | | - Esteban Medina-Méndez
- Department of Molecular Diagnosis, Genética Molecular de Colombia SAS, Bogotá, DC, Colombia
| | - Carlos M Restrepo
- Center for Research in Genetics and Genomics - CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, DC, Colombia
| | | | - Dora Janeth Fonseca-Mendoza
- Center for Research in Genetics and Genomics - CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, DC, Colombia
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117
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Huber HF, Jaberi-Douraki M, DeVader S, Aparicio-Lopez C, Nava-Chavez J, Xu X, Millagaha Gedara NI, Gaudreault NN, Delong RK. Targeting SARS-CoV-2 Variants with Nucleic Acid Therapeutic Nanoparticle Conjugates. Pharmaceuticals (Basel) 2021; 14:1012. [PMID: 34681236 PMCID: PMC8539335 DOI: 10.3390/ph14101012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 12/19/2022] Open
Abstract
The emergence of SARS-CoV-2 variants is cause for concern, because these may become resistant to current vaccines and antiviral drugs in development. Current drugs target viral proteins, resulting in a critical need for RNA-targeted nanomedicines. To address this, a comparative analysis of SARS-CoV-2 variants was performed. Several highly conserved sites were identified, of which the most noteworthy is a partial homopurine palindrome site with >99% conservation within the coding region. This sequence was compared among recently emerged, highly infectious SARS-CoV-2 variants. Conservation of the site was maintained among these emerging variants, further contributing to its potential as a regulatory target site for SARS-CoV-2. RNAfold was used to predict the structures of the highly conserved sites, with some resulting structures being common among coronaviridae. An RNA-level regulatory map of the conserved regions of SARS-CoV-2 was produced based on the predicted structures, with each representing potential target sites for antisense oligonucleotides, triplex-forming oligomers, and aptamers. Additionally, homopurine/homopyrimidine sequences within the viral genome were identified. These sequences also demonstrate appropriate target sites for antisense oligonucleotides and triplex-forming oligonucleotides. An experimental strategy to investigate these is summarized along with potential nanoparticle types for delivery, and the advantages and disadvantages of each are discussed.
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Affiliation(s)
- Hanah F. Huber
- Nanotechnology Innovation Center, Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (H.F.H.); (S.D.); (C.A.-L.); (J.N.-C.)
| | - Majid Jaberi-Douraki
- 1DATA Consortium and Department of Mathematics, Kansas State University Olathe, Olathe, KS 66061, USA; (M.J.-D.); (X.X.); (N.I.M.G.)
| | - Sarah DeVader
- Nanotechnology Innovation Center, Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (H.F.H.); (S.D.); (C.A.-L.); (J.N.-C.)
| | - Cesar Aparicio-Lopez
- Nanotechnology Innovation Center, Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (H.F.H.); (S.D.); (C.A.-L.); (J.N.-C.)
| | - Juliet Nava-Chavez
- Nanotechnology Innovation Center, Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (H.F.H.); (S.D.); (C.A.-L.); (J.N.-C.)
| | - Xuan Xu
- 1DATA Consortium and Department of Mathematics, Kansas State University Olathe, Olathe, KS 66061, USA; (M.J.-D.); (X.X.); (N.I.M.G.)
| | - Nuwan Indika Millagaha Gedara
- 1DATA Consortium and Department of Mathematics, Kansas State University Olathe, Olathe, KS 66061, USA; (M.J.-D.); (X.X.); (N.I.M.G.)
| | - Natasha N. Gaudreault
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA;
| | - Robert K. Delong
- Nanotechnology Innovation Center, Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (H.F.H.); (S.D.); (C.A.-L.); (J.N.-C.)
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Bost JP, Barriga H, Holme MN, Gallud A, Maugeri M, Gupta D, Lehto T, Valadi H, Esbjörner EK, Stevens MM, El-Andaloussi S. Delivery of Oligonucleotide Therapeutics: Chemical Modifications, Lipid Nanoparticles, and Extracellular Vesicles. ACS NANO 2021; 15:13993-14021. [PMID: 34505766 PMCID: PMC8482762 DOI: 10.1021/acsnano.1c05099] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Indexed: 05/04/2023]
Abstract
Oligonucleotides (ONs) comprise a rapidly growing class of therapeutics. In recent years, the list of FDA-approved ON therapies has rapidly expanded. ONs are small (15-30 bp) nucleotide-based therapeutics which are capable of targeting DNA and RNA as well as other biomolecules. ONs can be subdivided into several classes based on their chemical modifications and on the mechanisms of their target interactions. Historically, the largest hindrance to the widespread usage of ON therapeutics has been their inability to effectively internalize into cells and escape from endosomes to reach their molecular targets in the cytosol or nucleus. While cell uptake has been improved, "endosomal escape" remains a significant problem. There are a range of approaches to overcome this, and in this review, we focus on three: altering the chemical structure of the ONs, formulating synthetic, lipid-based nanoparticles to encapsulate the ONs, or biologically loading the ONs into extracellular vesicles. This review provides a background to the design and mode of action of existing FDA-approved ONs. It presents the most common ON classifications and chemical modifications from a fundamental scientific perspective and provides a roadmap of the cellular uptake pathways by which ONs are trafficked. Finally, this review delves into each of the above-mentioned approaches to ON delivery, highlighting the scientific principles behind each and covering recent advances.
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Affiliation(s)
- Jeremy P. Bost
- Department
of Laboratory Medicine, Karolinska Institutet, Huddinge 14152, Sweden
| | - Hanna Barriga
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Margaret N. Holme
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Audrey Gallud
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, Gothenburg 41296, Sweden
- Advanced
Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg 43150, Sweden
| | - Marco Maugeri
- Department
of Rheumatology and Inflammation Research, Institute of Medicine,
Sahlgrenska Academy, University of Gothenburg, Gothenburg 41390, Sweden
| | - Dhanu Gupta
- Department
of Laboratory Medicine, Karolinska Institutet, Huddinge 14152, Sweden
| | - Taavi Lehto
- Department
of Laboratory Medicine, Karolinska Institutet, Huddinge 14152, Sweden
- Institute
of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
| | - Hadi Valadi
- Department
of Rheumatology and Inflammation Research, Institute of Medicine,
Sahlgrenska Academy, University of Gothenburg, Gothenburg 41390, Sweden
| | - Elin K. Esbjörner
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, Gothenburg 41296, Sweden
| | - Molly M. Stevens
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
- Department
of Materials, Department of Bioengineering, Institute of Biomedical
Engineering, Imperial College London, London SW7 2BU, United Kingdom
| | - Samir El-Andaloussi
- Department
of Laboratory Medicine, Karolinska Institutet, Huddinge 14152, Sweden
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119
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Chen BM, Cheng TL, Roffler SR. Polyethylene Glycol Immunogenicity: Theoretical, Clinical, and Practical Aspects of Anti-Polyethylene Glycol Antibodies. ACS NANO 2021; 15:14022-14048. [PMID: 34469112 DOI: 10.1021/acsnano.1c05922] [Citation(s) in RCA: 185] [Impact Index Per Article: 61.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Polyethylene glycol (PEG) is a flexible, hydrophilic simple polymer that is physically attached to peptides, proteins, nucleic acids, liposomes, and nanoparticles to reduce renal clearance, block antibody and protein binding sites, and enhance the half-life and efficacy of therapeutic molecules. Some naïve individuals have pre-existing antibodies that can bind to PEG, and some PEG-modified compounds induce additional antibodies against PEG, which can adversely impact drug efficacy and safety. Here we provide a framework to better understand PEG immunogenicity and how antibodies against PEG affect pegylated drug and nanoparticles. Analysis of published studies reveals rules for predicting accelerated blood clearance of pegylated medicine and therapeutic liposomes. Experimental studies of anti-PEG antibody binding to different forms, sizes, and immobilization states of PEG are also provided. The widespread use of SARS-CoV-2 RNA vaccines that incorporate PEG in lipid nanoparticles make understanding possible effects of anti-PEG antibodies on pegylated medicines even more critical.
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Affiliation(s)
- Bing-Mae Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Tian-Lu Cheng
- Center for Biomarkers and Biotech Drugs, Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Steve R Roffler
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
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120
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Lesman D, Rodriguez Y, Rajakumar D, Wein N. U7 snRNA, a Small RNA with a Big Impact in Gene Therapy. Hum Gene Ther 2021; 32:1317-1329. [PMID: 34139889 DOI: 10.1089/hum.2021.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The uridine-rich 7 (U7) small nuclear RNA (snRNA) is a component of a small nuclear ribonucleoprotein (snRNP) complex. U7 snRNA naturally contains an antisense sequence that identifies histone premessenger RNAs (pre-mRNAs) and is involved in their 3' end processing. By altering this antisense sequence, researchers have turned U7 snRNA into a versatile tool for targeting pre-mRNAs and modifying splicing. Encapsulating a modified U7 snRNA into a viral vector such as adeno-associated virus (also referred as vectorized exon skipping/inclusion, or VES/VEI) enables the delivery of this highly efficacious splicing modulator into a range of cell lines, primary cells, and tissues. In addition, and in contrast to antisense oligonucleotides, viral delivery of U7 snRNA enables long-term expression of antisense sequences in the nucleus as part of a stable snRNP complex. As a result, VES/VEI has emerged as a promising therapeutic platform for treating a large variety of human diseases caused by errors in pre-mRNA splicing or its regulation. Here we provide an overview of U7 snRNA's natural function and its applications in gene therapy.
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Affiliation(s)
- Daniel Lesman
- Center for Gene Therapy, The Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Yacidzohara Rodriguez
- Center for Gene Therapy, The Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Dhanarajan Rajakumar
- Center for Gene Therapy, The Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Nicolas Wein
- Center for Gene Therapy, The Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatric, The Ohio State University, Columbus, Ohio, USA
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121
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Li Y, Garcia G, Arumugaswami V, Guo F. Structure-based design of antisense oligonucleotides that inhibit SARS-CoV-2 replication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.08.23.457434. [PMID: 34462746 PMCID: PMC8404888 DOI: 10.1101/2021.08.23.457434] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Antisense oligonucleotides (ASOs) are an emerging class of drugs that target RNAs. Current ASO designs strictly follow the rule of Watson-Crick base pairing along target sequences. However, RNAs often fold into structures that interfere with ASO hybridization. Here we developed a structure-based ASO design method and applied it to target severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Our method makes sure that ASO binding is compatible with target structures in three-dimensional (3D) space by employing structural design templates. These 3D-ASOs recognize the shapes and hydrogen bonding patterns of targets via tertiary interactions, achieving enhanced affinity and specificity. We designed 3D-ASOs that bind to the frameshift stimulation element and transcription regulatory sequence of SARS-CoV-2 and identified lead ASOs that strongly inhibit viral replication in human cells. We further optimized the lead sequences and characterized structure-activity relationship. The 3D-ASO technology helps fight coronavirus disease-2019 and is broadly applicable to ASO drug development.
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Affiliation(s)
- Yan Li
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, U.S.A
- Molecular Biology Interdepartmental Ph.D. Program, University of California, Los Angeles, CA 90095, U.S.A
| | - Gustavo Garcia
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, U.S.A
| | - Vaithilingaraja Arumugaswami
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, U.S.A
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095, U.S.A
| | - Feng Guo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, U.S.A
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, U.S.A
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122
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Behl T, Kaur I, Kumar A, Mehta V, Zengin G, Arora S. Gene Therapy in the Management of Parkinson's Disease: Potential of GDNF as a Promising Therapeutic Strategy. Curr Gene Ther 2021; 20:207-222. [PMID: 32811394 DOI: 10.2174/1566523220999200817164051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/14/2020] [Accepted: 07/15/2020] [Indexed: 12/13/2022]
Abstract
The limitations of conventional treatment therapies in Parkinson's disorder, a common neurodegenerative disorder, lead to the development of an alternative gene therapy approach. Multiple treatment options targeting dopaminergic neuronal regeneration, production of enzymes linked with dopamine synthesis, subthalamic nucleus neurons, regulation of astrocytes and microglial cells and potentiating neurotrophic factors, were established. Viral vector-based dopamine delivery, prodrug approaches, fetal ventral mesencephalon tissue transplantation and dopamine synthesizing enzyme encoding gene delivery are significant therapies evidently supported by numerous trials. The review primarily elaborates on the significant role of glial cell-line derived neurotrophic factor in alleviating motor symptoms and the loss of dopaminergic neurons in Parkinson's disease. Neuroprotective and neuroregenerative effects of GDNF were established via preclinical and clinical study outcomes. The binding of GDNF family ligands with associated receptors leads to the formation of a receptor-ligand complex activating Ret receptor of tyrosine kinase family, which is only expressed in dopaminergic neurons, playing an important role in Parkinson's disease, via its association with the essential protein encoded genes. Furthermore, the review establishes delivery aspects, like ventricular delivery of recombinant GDNF, intraparenchymal and intraputaminal delivery using infusion catheters. The review highlights problems and challenges of GDNF delivery, and essential measures to overcome them, like gene therapy combinations, optimization of delivery vectors, newer targeting devices, motor symptoms curbing focused ultrasound techniques, modifications in patient selection criteria and development of novel delivery strategies based on liposomes and encapsulated cells, to promote safe and effective delivery of neurotrophic factor and establishment of routine treatment therapy for patients.
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Affiliation(s)
- Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, India
| | - Ishnoor Kaur
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, India
| | - Arun Kumar
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, India
| | | | - Gokhan Zengin
- Department of Biology, Faculty of Science, Selcuk University Campus, Konya, Turkey
| | - Sandeep Arora
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, India
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123
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Lu Q, Lou J, Cai R, Han W, Pan H. Emerging roles of a pivotal lncRNA SBF2-AS1 in cancers. Cancer Cell Int 2021; 21:417. [PMID: 34372871 PMCID: PMC8351094 DOI: 10.1186/s12935-021-02123-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/29/2021] [Indexed: 12/25/2022] Open
Abstract
Long non-coding RNAs refer to transcripts over 200 nt in length that lack the ability to encode proteins, which occupy the majority of the genome and play a crucial role in the occurrence and development of human diseases, especially cancers. SBF2-AS1, a newly identified long non-coding RNA, has been verified to be highly expressed in diversiform cancers, and is involved in processes promoting tumorigenesis, tumor progression and tumor metastasis. Moreover, upregulation of SBF2-AS1 expression was significantly related to disadvantageous clinicopathologic characteristics and indicated poor prognosis. In this review, we comprehensively summarize the up-to-date knowledge of the detailed mechanisms and underlying functions of SBF2-AS1 in diverse cancer types, highlighting the potential of SBF2-AS1 as a diagnostic and prognostic biomarker and even a therapeutic target.
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Affiliation(s)
- Qian Lu
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jun Lou
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ruyun Cai
- Department of Colorectal Surgery, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Weidong Han
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
| | - Hongming Pan
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
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124
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Varty K, O’Brien C, Ignaszak A. Breast Cancer Aptamers: Current Sensing Targets, Available Aptamers, and Their Evaluation for Clinical Use in Diagnostics. Cancers (Basel) 2021; 13:cancers13163984. [PMID: 34439139 PMCID: PMC8391819 DOI: 10.3390/cancers13163984] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/28/2021] [Accepted: 08/04/2021] [Indexed: 02/07/2023] Open
Abstract
Breast cancer is the most commonly occurring cancer in women worldwide, and the rate of diagnosis continues to increase. Early detection and targeted treatment towards histological type is crucial to improving outcomes, but current screening methods leave some patients at risk of late diagnosis. The risk of late diagnosis and progressed disease is of particular concern for young women as current screening methods are not recommended early in life. Aptamers are oligonucleotides that can bind with high specificity to target molecules such as proteins, peptides, and other small molecules. They are relatively cheap to produce and are invariable from batch to batch, making them ideal for use in large-scale clinical or screening programs. The use of aptamers for breast cancer screening, diagnosis, and therapeutics is promising, but comparison of these aptamers and their corresponding biomarkers for use in breast cancer is significantly lacking. Here, we compare the currently available aptamers for breast cancer biomarkers and their respective biomarkers, as well as highlight the electrochemical sensors that are in development.
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125
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Winkle M, El-Daly SM, Fabbri M, Calin GA. Noncoding RNA therapeutics - challenges and potential solutions. Nat Rev Drug Discov 2021; 20:629-651. [PMID: 34145432 PMCID: PMC8212082 DOI: 10.1038/s41573-021-00219-z] [Citation(s) in RCA: 812] [Impact Index Per Article: 270.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2021] [Indexed: 02/07/2023]
Abstract
Therapeutic targeting of noncoding RNAs (ncRNAs), such as microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), represents an attractive approach for the treatment of cancers, as well as many other diseases. Over the past decade, substantial effort has been made towards the clinical application of RNA-based therapeutics, employing mostly antisense oligonucleotides and small interfering RNAs, with several gaining FDA approval. However, trial results have so far been ambivalent, with some studies reporting potent effects whereas others demonstrated limited efficacy or toxicity. Alternative entities such as antimiRNAs are undergoing clinical testing, and lncRNA-based therapeutics are gaining interest. In this Perspective, we discuss key challenges facing ncRNA therapeutics - including issues associated with specificity, delivery and tolerability - and focus on promising emerging approaches that aim to boost their success.
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Affiliation(s)
- Melanie Winkle
- Translational Molecular Pathology, MD Anderson Cancer Center, Texas State University, Houston, TX, USA
| | - Sherien M El-Daly
- Medical Biochemistry Department, Medical Research Division - Cancer Biology and Genetics Laboratory, Centre of Excellence for Advanced Sciences - National Research Centre, Cairo, Egypt
| | - Muller Fabbri
- Cancer Biology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - George A Calin
- Translational Molecular Pathology, MD Anderson Cancer Center, Texas State University, Houston, TX, USA.
- The RNA Interference and Non-codingRNA Center, MD Anderson Cancer Center, Texas State University, Houston, TX, USA.
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126
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Danielsen MB, Wengel J. Cationic oligonucleotide derivatives and conjugates: A favorable approach for enhanced DNA and RNA targeting oligonucleotides. Beilstein J Org Chem 2021; 17:1828-1848. [PMID: 34386102 PMCID: PMC8329367 DOI: 10.3762/bjoc.17.125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/14/2021] [Indexed: 12/20/2022] Open
Abstract
Antisense oligonucleotides (ASOs) have the ability of binding to endogenous nucleic acid targets, thereby inhibiting the gene expression. Although ASOs have great potential in the treatment of many diseases, the search for favorable toxicity profiles and distribution has been challenging and consequently impeded the widespread use of ASOs as conventional medicine. One strategy that has been employed to optimize the delivery profile of ASOs, is the functionalization of ASOs with cationic amine groups, either by direct conjugation onto the sugar, nucleobase or internucleotide linkage. The introduction of these positively charged groups has improved properties like nuclease resistance, increased binding to the nucleic acid target and improved cell uptake for oligonucleotides (ONs) and ASOs. The modifications highlighted in this review are some of the most prevalent cationic amine groups which have been attached as single modifications onto ONs/ASOs. The review has been separated into three sections, nucleobase, sugar and backbone modifications, highlighting what impact the cationic amine groups have on the ONs/ASOs physiochemical and biological properties. Finally, a concluding section has been added, summarizing the important knowledge from the three chapters, and examining the future design for ASOs.
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Affiliation(s)
- Mathias B Danielsen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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127
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DeLong RK, Swanson R, Niederwerder MC, Khanal P, Aryal S, Marasini R, Jaberi-Douraki M, Shakeri H, Mazloom R, Schneider S, Ensley S, Clarke LL, Woode RA, Young S, Rayamajhi S, Miesner T, Higginbotham ML, Lin Z, Shrestha T, Ghosh K, Glaspell G, Mathew EN. Zn-based physiometacomposite nanoparticles: distribution, tolerance, imaging, and antiviral and anticancer activity. Nanomedicine (Lond) 2021; 16:1857-1872. [PMID: 34282923 DOI: 10.2217/nnm-2021-0179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The aim of this study was to investigate the distribution, tolerance, and anticancer and antiviral activity of Zn-based physiometacomposites (PMCs). Manganese, iron, nickel and cobalt-doped ZnO, ZnS or ZnSe were synthesized. Cell uptake, distribution into 3D culture and mice, and biochemical and chemotherapeutic activity were studied by fluorescence/bioluminescence, confocal microscopy, flow cytometry, viability, antitumor and virus titer assays. Luminescence and inductively coupled plasma mass spectrometry analysis showed that nanoparticle distribution was liver >spleen >kidney >lung >brain, without tissue or blood pathology. Photophysical characterization as ex vivo tissue probes and LL37 peptide, antisense oligomer or aptamer delivery targeting RAS/Ras binding domain (RBD) was investigated. Treatment at 25 μg/ml for 48 h showed ≥98-99% cell viability, 3D organoid uptake, 3-log inhibition of β-Galactosidase and porcine reproductive respiratory virus infection. Data support the preclinical development of PMCs for imaging and delivery targeting cancer and infectious disease.
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Affiliation(s)
- Robert K DeLong
- Department of Anatomy & Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.,Nanotechnology Innovation Center, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Ryan Swanson
- Department of Anatomy & Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.,Nanotechnology Innovation Center, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Megan C Niederwerder
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Pratiksha Khanal
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Santosh Aryal
- Department of Chemistry, Kansas State University, Manhattan, KS 66506, USA.,Department of Pharmaceutical Sciences and Health Outcomes, The Ben and Maytee Fisch College of Pharmacy, University of Texas at Tyler, Tyler, TX 75799, USA
| | - Ramesh Marasini
- Nanotechnology Innovation Center, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.,Department of Chemistry, Kansas State University, Manhattan, KS 66506, USA
| | - Majid Jaberi-Douraki
- 1DATA Consortium, & Department of Mathematics, Kansas State University Olathe, Olathe, KS 66061, USA
| | - Heman Shakeri
- 1DATA Consortium, & Department of Mathematics, Kansas State University Olathe, Olathe, KS 66061, USA
| | - Reza Mazloom
- 1DATA Consortium, & Department of Mathematics, Kansas State University Olathe, Olathe, KS 66061, USA
| | - Sarah Schneider
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.,Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Steve Ensley
- Department of Anatomy & Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.,Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Lane L Clarke
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, USA.,Department of Biomedical Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Rowena A Woode
- Department of Biomedical Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Sarah Young
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Sagar Rayamajhi
- Department of Chemistry, Kansas State University, Manhattan, KS 66506, USA
| | - Tracy Miesner
- Comparative Medicine Group, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Mary L Higginbotham
- Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Zhoumeng Lin
- Department of Anatomy & Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.,Institute for Computational Comparative Medicine, Kansas State University Manhattan, KS 66061, USA
| | - Tej Shrestha
- Department of Anatomy & Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.,Nanotechnology Innovation Center, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Kartik Ghosh
- Department of Physics, Astronomy & Materials Science, Missouri State University, Springfield, MO 65897, USA
| | - Garry Glaspell
- US Army Corps of Engineers Engineer Research & Development Center, Alexandria, VA 22315, USA
| | - Elza N Mathew
- Department of Anatomy & Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.,University of Massachusetts Medical School, Worcester, MA 01605, USA
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128
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Binzel DW, Li X, Burns N, Khan E, Lee WJ, Chen LC, Ellipilli S, Miles W, Ho YS, Guo P. Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity. Chem Rev 2021; 121:7398-7467. [PMID: 34038115 PMCID: PMC8312718 DOI: 10.1021/acs.chemrev.1c00009] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA nanotechnology is the bottom-up self-assembly of nanometer-scale architectures, resembling LEGOs, composed mainly of RNA. The ideal building material should be (1) versatile and controllable in shape and stoichiometry, (2) spontaneously self-assemble, and (3) thermodynamically, chemically, and enzymatically stable with a long shelf life. RNA building blocks exhibit each of the above. RNA is a polynucleic acid, making it a polymer, and its negative-charge prevents nonspecific binding to negatively charged cell membranes. The thermostability makes it suitable for logic gates, resistive memory, sensor set-ups, and NEM devices. RNA can be designed and manipulated with a level of simplicity of DNA while displaying versatile structure and enzyme activity of proteins. RNA can fold into single-stranded loops or bulges to serve as mounting dovetails for intermolecular or domain interactions without external linking dowels. RNA nanoparticles display rubber- and amoeba-like properties and are stretchable and shrinkable through multiple repeats, leading to enhanced tumor targeting and fast renal excretion to reduce toxicities. It was predicted in 2014 that RNA would be the third milestone in pharmaceutical drug development. The recent approval of several RNA drugs and COVID-19 mRNA vaccines by FDA suggests that this milestone is being realized. Here, we review the unique properties of RNA nanotechnology, summarize its recent advancements, describe its distinct attributes inside or outside the body and discuss potential applications in nanotechnology, medicine, and material science.
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Affiliation(s)
- Daniel W Binzel
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Xin Li
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Nicolas Burns
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Eshan Khan
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wen-Jui Lee
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Li-Ching Chen
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Satheesh Ellipilli
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wayne Miles
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yuan Soon Ho
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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129
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Mansouri V, Beheshtizadeh N, Gharibshahian M, Sabouri L, Varzandeh M, Rezaei N. Recent advances in regenerative medicine strategies for cancer treatment. Biomed Pharmacother 2021; 141:111875. [PMID: 34229250 DOI: 10.1016/j.biopha.2021.111875] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 02/07/2023] Open
Abstract
Cancer stands as one of the most leading causes of death worldwide, while one of the most significant challenges in treating it is revealing novel alternatives to predict, diagnose, and eradicate tumor cell growth. Although various methods, such as surgery, chemotherapy, and radiation therapy, are used today to treat cancer, its mortality rate is still high due to the numerous shortcomings of each approach. Regenerative medicine field, including tissue engineering, cell therapy, gene therapy, participate in cancer treatment and development of cancer models to improve the understanding of cancer biology. The final intention is to convey fundamental and laboratory research to effective clinical treatments, from the bench to the bedside. Proper interpretation of research attempts helps to lessen the burden of treatment and illness for patients. The purpose of this review is to investigate the role of regenerative medicine in accelerating and improving cancer treatment. This study examines the capabilities of regenerative medicine in providing novel cancer treatments and the effectiveness of these treatments to clarify this path as much as possible and promote advanced future research in this field.
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Affiliation(s)
- Vahid Mansouri
- Gene Therapy Research Center, Digestive Diseases Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran; Regenerative Medicine group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Nima Beheshtizadeh
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Iran; School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia; Regenerative Medicine group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
| | - Maliheh Gharibshahian
- Department of Tissue Engineering, School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran; Regenerative Medicine group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Leila Sabouri
- Regenerative Medicine group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Mohammad Varzandeh
- Department of Materials Engineering, Isfahan University of Technology, Isfahan 84156-83111, Iran; Regenerative Medicine group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran; Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
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130
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Yu C, Li L, Hu P, Yang Y, Wei W, Deng X, Wang L, Tay FR, Ma J. Recent Advances in Stimulus-Responsive Nanocarriers for Gene Therapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2100540. [PMID: 34306980 PMCID: PMC8292848 DOI: 10.1002/advs.202100540] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/07/2021] [Indexed: 05/29/2023]
Abstract
Gene therapy provides a promising strategy for curing monogenetic disorders and complex diseases. However, there are challenges associated with the use of viral delivery vectors. The advent of nanomedicine represents a quantum leap in the application of gene therapy. Recent advances in stimulus-responsive nonviral nanocarriers indicate that they are efficient delivery systems for loading and unloading of therapeutic nucleic acids. Some nanocarriers are responsive to cues derived from the internal environment, such as changes in pH, redox potential, enzyme activity, reactive oxygen species, adenosine triphosphate, and hypoxia. Others are responsive to external stimulations, including temperature gradients, light irradiation, ultrasonic energy, and magnetic field. Multiple stimuli-responsive strategies have also been investigated recently for experimental gene therapy.
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Affiliation(s)
- Cheng Yu
- Department of StomatologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei Province430030China
| | - Long Li
- Department of OncologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei Province430030China
| | - Pei Hu
- Department of StomatologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei Province430030China
| | - Yan Yang
- Department of StomatologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei Province430030China
| | - Wei Wei
- Department of StomatologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei Province430030China
| | - Xin Deng
- Department of StomatologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei Province430030China
| | - Lu Wang
- Department of OncologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei Province430030China
| | | | - Jingzhi Ma
- Department of StomatologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei Province430030China
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131
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Copping NA, McTighe SM, Fink KD, Silverman JL. Emerging Gene and Small Molecule Therapies for the Neurodevelopmental Disorder Angelman Syndrome. Neurotherapeutics 2021; 18:1535-1547. [PMID: 34528170 PMCID: PMC8608975 DOI: 10.1007/s13311-021-01082-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2021] [Indexed: 02/07/2023] Open
Abstract
Angelman syndrome (AS) is a rare (~1:15,000) neurodevelopmental disorder characterized by severe developmental delay and intellectual disability, impaired communication skills, and a high prevalence of seizures, sleep disturbances, ataxia, motor deficits, and microcephaly. AS is caused by loss-of-function of the maternally inherited UBE3A gene. UBE3A is located on chromosome 15q11-13 and is biallelically expressed throughout the body but only maternally expressed in the brain due to an RNA antisense transcript that silences the paternal copy. There is currently no cure for AS, but advancements in small molecule drugs and gene therapies offer a promising approach for the treatment of the disorder. Here, we review AS and how loss-of-function of the maternal UBE3A contributes to the disorder. We also discuss the strengths and limitations of current animal models of AS. Furthermore, we examine potential small molecule drug and gene therapies for the treatment of AS and associated challenges faced by the therapeutic design. Finally, gene therapy offers the opportunity for precision medicine in AS and advancements in the treatment of this disorder can serve as a foundation for other single-gene neurodevelopmental disorders.
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Affiliation(s)
- Nycole A Copping
- School of Medicine, Department of Psychiatry and Behavioral Sciences, MIND Institute, University of California, Research II Building 96, 4625 2nd Avenue, Suite 1001B, Davis, Sacramento, CA, 95817, USA
- Stem Cell Program and Gene Therapy Center, Department of Neurology, MIND Institute, University of California, Davis, Sacramento, CA, USA
| | | | - Kyle D Fink
- Stem Cell Program and Gene Therapy Center, Department of Neurology, MIND Institute, University of California, Davis, Sacramento, CA, USA
| | - Jill L Silverman
- School of Medicine, Department of Psychiatry and Behavioral Sciences, MIND Institute, University of California, Research II Building 96, 4625 2nd Avenue, Suite 1001B, Davis, Sacramento, CA, 95817, USA.
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132
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Sutton JM, Kim J, El Zahar NM, Bartlett MG. BIOANALYSIS AND BIOTRANSFORMATION OF OLIGONUCLEOTIDE THERAPEUTICS BY LIQUID CHROMATOGRAPHY-MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2021; 40:334-358. [PMID: 32588492 DOI: 10.1002/mas.21641] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 05/05/2020] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
Since 2016, eight new oligonucleotide therapies have been approved which has led to increased interest in oligonucleotide analysis. There is a particular need for powerful bioanalytical tools to study the metabolism and biotransformation of these molecules. This review provides the background on the biological basis of these molecules as currently used in therapies. The article also reviews the current state of analytical methodology including state of the art sample preparation techniques, liquid chromatography-mass spectrometry methods, and the current limits of detection/quantitation. Finally, the article summarizes the challenges in oligonucleotide bioanalysis and provides future perspectives for this emerging field. © 2020 John Wiley & Sons Ltd.
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Affiliation(s)
- James Michael Sutton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, 250 West Green Street, Athens, GA, 30602-2352
| | - Jaeah Kim
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, 250 West Green Street, Athens, GA, 30602-2352
| | - Noha M El Zahar
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, 250 West Green Street, Athens, GA, 30602-2352
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Organization of African Unity Street, Cairo, 11566, Egypt
| | - Michael G Bartlett
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, 250 West Green Street, Athens, GA, 30602-2352
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133
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Fuster-García C, García-Bohórquez B, Rodríguez-Muñoz A, Aller E, Jaijo T, Millán JM, García-García G. Usher Syndrome: Genetics of a Human Ciliopathy. Int J Mol Sci 2021; 22:6723. [PMID: 34201633 PMCID: PMC8268283 DOI: 10.3390/ijms22136723] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 12/21/2022] Open
Abstract
Usher syndrome (USH) is an autosomal recessive syndromic ciliopathy characterized by sensorineural hearing loss, retinitis pigmentosa and, sometimes, vestibular dysfunction. There are three clinical types depending on the severity and age of onset of the symptoms; in addition, ten genes are reported to be causative of USH, and six more related to the disease. These genes encode proteins of a diverse nature, which interact and form a dynamic protein network called the "Usher interactome". In the organ of Corti, the USH proteins are essential for the correct development and maintenance of the structure and cohesion of the stereocilia. In the retina, the USH protein network is principally located in the periciliary region of the photoreceptors, and plays an important role in the maintenance of the periciliary structure and the trafficking of molecules between the inner and the outer segments of photoreceptors. Even though some genes are clearly involved in the syndrome, others are controversial. Moreover, expression of some USH genes has been detected in other tissues, which could explain their involvement in additional mild comorbidities. In this paper, we review the genetics of Usher syndrome and the spectrum of mutations in USH genes. The aim is to identify possible mutation associations with the disease and provide an updated genotype-phenotype correlation.
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Affiliation(s)
- Carla Fuster-García
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain; (C.F.-G.); (B.G.-B.); (A.R.-M.); (E.A.); (T.J.); (G.G.-G.)
- Unidad Mixta de Enfermedades Raras IIS La Fe-Centro de Investigación Príncipe Felipe, 46026 Valencia, Spain
- Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
| | - Belén García-Bohórquez
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain; (C.F.-G.); (B.G.-B.); (A.R.-M.); (E.A.); (T.J.); (G.G.-G.)
- Unidad Mixta de Enfermedades Raras IIS La Fe-Centro de Investigación Príncipe Felipe, 46026 Valencia, Spain
| | - Ana Rodríguez-Muñoz
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain; (C.F.-G.); (B.G.-B.); (A.R.-M.); (E.A.); (T.J.); (G.G.-G.)
- Unidad Mixta de Enfermedades Raras IIS La Fe-Centro de Investigación Príncipe Felipe, 46026 Valencia, Spain
| | - Elena Aller
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain; (C.F.-G.); (B.G.-B.); (A.R.-M.); (E.A.); (T.J.); (G.G.-G.)
- Unidad Mixta de Enfermedades Raras IIS La Fe-Centro de Investigación Príncipe Felipe, 46026 Valencia, Spain
- Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
- Genetics Unit, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
| | - Teresa Jaijo
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain; (C.F.-G.); (B.G.-B.); (A.R.-M.); (E.A.); (T.J.); (G.G.-G.)
- Unidad Mixta de Enfermedades Raras IIS La Fe-Centro de Investigación Príncipe Felipe, 46026 Valencia, Spain
- Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
- Genetics Unit, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
| | - José M. Millán
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain; (C.F.-G.); (B.G.-B.); (A.R.-M.); (E.A.); (T.J.); (G.G.-G.)
- Unidad Mixta de Enfermedades Raras IIS La Fe-Centro de Investigación Príncipe Felipe, 46026 Valencia, Spain
- Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
| | - Gema García-García
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain; (C.F.-G.); (B.G.-B.); (A.R.-M.); (E.A.); (T.J.); (G.G.-G.)
- Unidad Mixta de Enfermedades Raras IIS La Fe-Centro de Investigación Príncipe Felipe, 46026 Valencia, Spain
- Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
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Shahryari A, Burtscher I, Nazari Z, Lickert H. Engineering Gene Therapy: Advances and Barriers. ADVANCED THERAPEUTICS 2021. [DOI: 10.1002/adtp.202100040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alireza Shahryari
- Institute of Diabetes and Regeneration Research Helmholtz Zentrum München 85764 Neuherberg Germany
- School of Medicine Department of Human Genetics Technical University of Munich Klinikum Rechts der Isar 81675 München Germany
- Institute of Stem Cell Research Helmholtz Zentrum München 85764 Neuherberg Germany
- Stem Cell Research Center Golestan University of Medical Sciences Gorgan 49341‐74515 Iran
| | - Ingo Burtscher
- Institute of Diabetes and Regeneration Research Helmholtz Zentrum München 85764 Neuherberg Germany
- Institute of Stem Cell Research Helmholtz Zentrum München 85764 Neuherberg Germany
| | - Zahra Nazari
- Department of Biology School of Basic Sciences Golestan University Gorgan 49361‐79142 Iran
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research Helmholtz Zentrum München 85764 Neuherberg Germany
- School of Medicine Department of Human Genetics Technical University of Munich Klinikum Rechts der Isar 81675 München Germany
- Institute of Stem Cell Research Helmholtz Zentrum München 85764 Neuherberg Germany
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135
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Ye WC, Huang SF, Hou LJ, Long HJ, Yin K, Hu CY, Zhao GJ. Potential Therapeutic Targeting of lncRNAs in Cholesterol Homeostasis. Front Cardiovasc Med 2021; 8:688546. [PMID: 34179148 PMCID: PMC8224755 DOI: 10.3389/fcvm.2021.688546] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/19/2021] [Indexed: 12/19/2022] Open
Abstract
Maintaining cholesterol homeostasis is essential for normal cellular and systemic functions. Long non-coding RNAs (lncRNAs) represent a mechanism to fine-tune numerous biological processes by controlling gene expression. LncRNAs have emerged as important regulators in cholesterol homeostasis. Dysregulation of lncRNAs expression is associated with lipid-related diseases, suggesting that manipulating the lncRNAs expression could be a promising therapeutic approach to ameliorate liver disease progression and cardiovascular disease (CVD). However, given the high-abundant lncRNAs and the poor genetic conservation between species, much work is required to elucidate the specific role of lncRNAs in regulating cholesterol homeostasis. In this review, we highlighted the latest advances in the pivotal role and mechanism of lncRNAs in regulating cholesterol homeostasis. These findings provide novel insights into the underlying mechanisms of lncRNAs in lipid-related diseases and may offer potential therapeutic targets for treating lipid-related diseases.
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Affiliation(s)
- Wen-Chu Ye
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Shi-Feng Huang
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Lian-Jie Hou
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Hai-Jiao Long
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China.,Xiangya Hospital, Central South University, Changsha, China
| | - Kai Yin
- Guangxi Key Laboratory of Diabetic Systems Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Ching Yuan Hu
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Guo-Jun Zhao
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
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136
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Baisden JT, Childs-Disney JL, Ryan LS, Disney MD. Affecting RNA biology genome-wide by binding small molecules and chemically induced proximity. Curr Opin Chem Biol 2021; 62:119-129. [PMID: 34118759 PMCID: PMC9264282 DOI: 10.1016/j.cbpa.2021.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 01/08/2023]
Abstract
The ENCODE and genome-wide association projects have shown that much of the genome is transcribed into RNA and much less is translated into protein. These and other functional studies suggest that the druggable transcriptome is much larger than the druggable proteome. This review highlights approaches to define druggable RNA targets and structure-activity relationships across genomic RNA. Binding compounds can be identified and optimized into structure-specific ligands by using sequence-based design with various modes of action, for example, inhibiting translation or directing pre-mRNA splicing outcomes. In addition, strategies to direct protein activity against an RNA of interest via chemically induced proximity is a burgeoning area that has been validated both in cells and in preclinical animal models, and we describe that it may allow rapid access to new avenues to affect RNA biology. These approaches and the unique modes of action suggest that more RNAs are potentially amenable to targeting than proteins.
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Affiliation(s)
- Jared T Baisden
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458 USA
| | - Jessica L Childs-Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458 USA
| | - Lucas S Ryan
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458 USA
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458 USA.
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137
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Le Marois M, Tzavara E, Ibrahim EC, Blin O, Belzeaux R. RNA therapeutics for mood disorders: current evidence toward clinical trials. Expert Opin Investig Drugs 2021; 30:721-736. [PMID: 33966550 DOI: 10.1080/13543784.2021.1928073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Mood disorders are severe yet frequent psychiatric disorders worldwide, comprising major depressive disorder (MDD) and bipolar disorders (BD). Their treatment remains poorly effective. Recently, growing evidence for epigenetic mechanisms has emerged. Consequently, a great interest in a novel pharmacological class arose: RNA therapeutics. AREAS COVERED We conducted a systematic review of RNA therapeutics -antisense oligonucleotides (ASOs), small interfering RNAs (siRNAs), short hairpin RNAs (shRNAs), and micro-RNA (miRNA) therapeutics- for the treatment of mood disorders studied in pre-clinical animal models listed in PubMed, in clinical trials registered in ClinicalTrials.gov and available on the market by combining literature search and Food and Drug Administration and European Medicine Agency online databases. Eighteen pre-clinical studies investigated the antidepressant effects of RNA therapeutics. However, even though there is an increasing number of marketing authorizations and clinical trials for the past twenty years, no RNA therapeutic has reached the clinical development pipeline for the treatment of psychiatric disorders yet. EXPERT OPINION Several promising RNA therapeutics have been tested in pre-clinical studies for MDD, whereas no molecule has been developed for BD. There are several issues to address before reaching clinical development and new challenges include stratifying patient population and predicting therapeutic response.
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Affiliation(s)
- Marguerite Le Marois
- Aix Marseille Univ, APHM, INSERM, Inst Neurosci Syst, University Hospital Federation DHUNE, Service de Pharmacologie Clinique et Pharmacovigilance, Marseille, France.,Aix Marseille Univ, CNRS, Inst Neurosci Timone, Marseille, France
| | - Eleni Tzavara
- Fondation FondaMental, Créteil, France.,Pôle De Psychiatrie, Hôpital Sainte-Marguerite, AP-HM, Marseille, France
| | - El Chérif Ibrahim
- Aix Marseille Univ, CNRS, Inst Neurosci Timone, Marseille, France.,Fondation FondaMental, Créteil, France
| | - Olivier Blin
- Aix Marseille Univ, APHM, INSERM, Inst Neurosci Syst, University Hospital Federation DHUNE, Service de Pharmacologie Clinique et Pharmacovigilance, Marseille, France
| | - Raoul Belzeaux
- Aix Marseille Univ, CNRS, Inst Neurosci Timone, Marseille, France.,Fondation FondaMental, Créteil, France.,Pôle De Psychiatrie, Hôpital Sainte-Marguerite, AP-HM, Marseille, France
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138
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Uppuladinne MVN, Dowerah D, Sonavane UB, Ray SK, Deka RC, Joshi RR. Structural insight into locked nucleic acid based novel antisense modifications: A DFT calculations at monomer and MD simulations at oligomer level. J Mol Graph Model 2021; 107:107945. [PMID: 34102527 DOI: 10.1016/j.jmgm.2021.107945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/04/2021] [Accepted: 05/17/2021] [Indexed: 11/25/2022]
Abstract
In the present study, five novel LNA based antisense modifications have been proposed. A conformational search was carried out using TANGO, followed by geometry optimization using MOPAC. Based on their electronic energies the most stable conformation for each modification was identified. Further, DFT based full geometry optimization on the most stable conformations at the gas phase B3LYP/6-31G(d,p) using a Gaussian03 and single point energy calculations on the optimized structures at the solvent phase B3LYP/6-311G(d,p) level of theory were done to derive their quantum chemical descriptors using the Gaussian09. A comparison of global reactivity descriptors confirmed that the LNA based modifications were the most reactive. Base-pair stability was recorded by observing the binding energies and base-pairing conformations of modified GC base pairs at the B3LYP/6-311G(d,p) level of theory. Molecular dynamics simulations have been performed at the oligomer duplex level by incorporating individual modifications on 20-mer RNA-RNA duplexes using AMBER16. Free energy calculations of duplex structures suggested that incorporation of A2 modification into the RNA-RNA duplex increased the duplex binding affinity similar to LNA. Whereas, the A3 modification showed less binding compared to LNA but improved binding compared to MOE. This computational approach using quantum chemical methods may be very useful to propose better modifications than the existing ones before performing the experiments in the area of antisense technology.
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Affiliation(s)
- Mallikarjunachari V N Uppuladinne
- HPC - Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchavati, Pashan, Pune, India.
| | - Dikshita Dowerah
- Department of Chemical Sciences, Tezpur University, Assam, India.
| | - Uddhavesh B Sonavane
- HPC - Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchavati, Pashan, Pune, India.
| | - Suvendra Kumar Ray
- Department of Molecular Biology and Biotechnology, Tezpur University, Assam, India.
| | - Ramesh C Deka
- Department of Chemical Sciences, Tezpur University, Assam, India.
| | - Rajendra R Joshi
- HPC - Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchavati, Pashan, Pune, India.
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139
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Demelenne A, Servais AC, Crommen J, Fillet M. Analytical techniques currently used in the pharmaceutical industry for the quality control of RNA-based therapeutics and ongoing developments. J Chromatogr A 2021; 1651:462283. [PMID: 34107400 DOI: 10.1016/j.chroma.2021.462283] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 01/21/2023]
Abstract
The number of RNA-based therapeutics has significantly grown in number on the market over the last 20 years. This number is expected to further increase in the coming years as many RNA therapeutics are being tested in late clinical trials stages. The first part of this paper considers the mechanism of action, the synthesis and the potential impurities resulting from synthesis as well as the strategies used to increase RNA-based therapeutics efficacy. In the second part of this review, the tests that are usually performed in the pharmaceutical industry for the quality testing of antisense oligonucleotides (ASOs), small-interfering RNAs (siRNAs) and messenger RNAs (mRNAs) will be described. In the last part, the remaining challenges and the ongoing developments to meet them are discussed.
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Affiliation(s)
- Alice Demelenne
- Laboratory for the Analysis of Medicines, Department of Pharmacy, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege, Quartier Hôpital, Avenue Hippocrate 15, CHU, B36, Liege 4000, Belgium
| | - Anne-Catherine Servais
- Laboratory for the Analysis of Medicines, Department of Pharmacy, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege, Quartier Hôpital, Avenue Hippocrate 15, CHU, B36, Liege 4000, Belgium
| | - Jacques Crommen
- Laboratory for the Analysis of Medicines, Department of Pharmacy, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege, Quartier Hôpital, Avenue Hippocrate 15, CHU, B36, Liege 4000, Belgium
| | - Marianne Fillet
- Laboratory for the Analysis of Medicines, Department of Pharmacy, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege, Quartier Hôpital, Avenue Hippocrate 15, CHU, B36, Liege 4000, Belgium.
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140
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Asada K, Sakaue F, Nagata T, Zhang JC, Yoshida-Tanaka K, Abe A, Nawa M, Nishina K, Yokota T. Short DNA/RNA heteroduplex oligonucleotide interacting proteins are key regulators of target gene silencing. Nucleic Acids Res 2021; 49:4864-4876. [PMID: 33928345 PMCID: PMC8136785 DOI: 10.1093/nar/gkab258] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 03/25/2021] [Accepted: 04/23/2021] [Indexed: 01/31/2023] Open
Abstract
Antisense oligonucleotide (ASO)-based therapy is one of the next-generation therapy, especially targeting neurological disorders. Many cases of ASO-dependent gene expression suppression have been reported. Recently, we developed a tocopherol conjugated DNA/RNA heteroduplex oligonucleotide (Toc-HDO) as a new type of drug. Toc-HDO is more potent, stable, and efficiently taken up by the target tissues compared to the parental ASO. However, the detailed mechanisms of Toc-HDO, including its binding proteins, are unknown. Here, we developed native gel shift assays with fluorescence-labeled nucleic acids samples extracted from mice livers. These assays revealed two Toc-HDO binding proteins, annexin A5 (ANXA5) and carbonic anhydrase 8 (CA8). Later, we identified two more proteins, apurinic/apyrimidinic endodeoxyribonuclease 1 (APEX1) and flap structure-specific endonuclease 1 (FEN1) by data mining. shRNA knockdown studies demonstrated that all four proteins regulated Toc-HDO activity in Hepa1-6, mouse hepatocellular cells. In vitro binding assays and fluorescence polarization assays with purified recombinant proteins characterized the identified proteins and pull-down assays with cell lysates demonstrated the protein binding to the Toc-HDO and ASO in a biological environment. Taken together, our findings provide a brand new molecular biological insight as well as future directions for HDO-based disease therapy.
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Affiliation(s)
- Ken Asada
- Department of Neurology and Neurological Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
- Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Fumika Sakaue
- Department of Neurology and Neurological Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
- Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Tetsuya Nagata
- Department of Neurology and Neurological Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
- Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Ji-chun Zhang
- Department of Neurology and Neurological Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
- Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Kie Yoshida-Tanaka
- Department of Neurology and Neurological Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
- Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Aya Abe
- Department of Neurology and Neurological Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
- Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Makiko Nawa
- Laboratory of Cytometry and Proteome Research, Nanken-Kyoten and Research Core Center, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Kazutaka Nishina
- Department of Neurology and Neurological Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
- Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Takanori Yokota
- Department of Neurology and Neurological Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
- Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
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Intranasal delivery of an antisense oligonucleotide to the RNA-binding protein HuR relieves nerve injury-induced neuropathic pain. Pain 2021; 162:1500-1510. [PMID: 33259457 DOI: 10.1097/j.pain.0000000000002154] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 11/17/2020] [Indexed: 01/10/2023]
Abstract
ABSTRACT Neuropathic pain remains an undertreated condition and there is a medical need to develop effective treatments. Accumulating evidence indicates that posttranscriptional regulation of gene expression is involved in neuropathic pain; however, RNA processing is not clearly investigated. Our study investigated the role of HuR, an RNA binding protein, in promoting neuropathic pain and trauma-induced microglia activation in the spared nerve injury mouse model. To this aim, an antisense oligonucleotide (ASO) knockdown of HuR gene expression was used. Antisense oligonucleotides poorly cross the blood-brain barrier and an intranasal (i.n.) administration was used to achieve central nervous system penetration through a noninvasive delivery. The efficacy of i.n. ASO administration was compared to an intrathecal (i.t.) delivery. I.n. administered ASO reduced spinal HuR protein and relieved pain hypersensitivity with a similar efficacy to i.t. administration. Immunofluorescence studies showed that HuR was expressed in activated microglia, colocalized with p38 and, partially, with extracellular signal-regulated kinase (ERK)1/2 within the spinal cord dorsal horn. An anti-HuR ASO inhibited the activation of spinal microglia by reducing the levels of proinflammatory cytokines, inducible nitric oxide synthase, the activation of nuclear factor-κB (NF-κB), and suppressed the spared nerve injury-induced overphosphorylation of spinal p38, ERK1/2 and c-Jun-N-terminal kinase (JNK)-1. In addition, HuR silencing increased the expression of the anti-inflammatory cytokine IL-10, promoting the shift of microglial M1 to M2 phenotype. Targeting HuR by i.n. anti-HuR ASO might represent a noninvasive promising perspective for neuropathic pain management by its powerful inhibition of microglia-mediated spinal neuroinflammation and promotion of an anti-inflammatory and neuroprotectant response.
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142
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Abstract
Antisense oligonucleotides (AON) are synthetic single-stranded fragments of nucleic acids that bind to a specific complementary messenger RNA (mRNA) sequence and change the final gene product. AON were initially approved for treating cytomegalovirus retinitis and have shown promise in treating Mendelian systemic disease. AON are currently being investigated as a treatment modality for many ophthalmic diseases, including inherited retinal disorders (IRD), inflammatory response and wound healing after glaucoma surgery, and macular degeneration. They provide a possible solution to gene therapy for IRD that are not candidates for adeno-associated virus (AAV) delivery. This chapter outlines the historical background of AON and reviews clinical applications and ongoing clinical trials.
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Affiliation(s)
- Kevin Ferenchak
- Inherited Retinal Disorders Service, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, United States
| | - Iris Deitch
- Inherited Retinal Disorders Service, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, United States
| | - Rachel Huckfeldt
- Inherited Retinal Disorders Service, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, United States
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143
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From Antisense RNA to RNA Modification: Therapeutic Potential of RNA-Based Technologies. Biomedicines 2021; 9:biomedicines9050550. [PMID: 34068948 PMCID: PMC8156014 DOI: 10.3390/biomedicines9050550] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 02/07/2023] Open
Abstract
Therapeutic oligonucleotides interact with a target RNA via Watson-Crick complementarity, affecting RNA-processing reactions such as mRNA degradation, pre-mRNA splicing, or mRNA translation. Since they were proposed decades ago, several have been approved for clinical use to correct genetic mutations. Three types of mechanisms of action (MoA) have emerged: RNase H-dependent degradation of mRNA directed by short chimeric antisense oligonucleotides (gapmers), correction of splicing defects via splice-modulation oligonucleotides, and interference of gene expression via short interfering RNAs (siRNAs). These antisense-based mechanisms can tackle several genetic disorders in a gene-specific manner, primarily by gene downregulation (gapmers and siRNAs) or splicing defects correction (exon-skipping oligos). Still, the challenge remains for the repair at the single-nucleotide level. The emerging field of epitranscriptomics and RNA modifications shows the enormous possibilities for recoding the transcriptome and repairing genetic mutations with high specificity while harnessing endogenously expressed RNA processing machinery. Some of these techniques have been proposed as alternatives to CRISPR-based technologies, where the exogenous gene-editing machinery needs to be delivered and expressed in the human cells to generate permanent (DNA) changes with unknown consequences. Here, we review the current FDA-approved antisense MoA (emphasizing some enabling technologies that contributed to their success) and three novel modalities based on post-transcriptional RNA modifications with therapeutic potential, including ADAR (Adenosine deaminases acting on RNA)-mediated RNA editing, targeted pseudouridylation, and 2′-O-methylation.
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144
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Hammond SM, Sergeeva OV, Melnikov PA, Goli L, Stoodley J, Zatsepin TS, Stetsenko DA, Wood MJA. Mesyl Phosphoramidate Oligonucleotides as Potential Splice-Switching Agents: Impact of Backbone Structure on Activity and Intracellular Localization. Nucleic Acid Ther 2021; 31:190-200. [PMID: 33989066 DOI: 10.1089/nat.2020.0860] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A series of 2'-deoxy and novel 2'-O-methyl and 2'-O-(2-methoxyethyl) (2'-MOE) oligonucleotides with internucleotide methanesulfonyl (mesyl, μ) or 1-butanesulfonyl (busyl, β) phosphoramidate groups has been synthesized for evaluation as potential splice-switching oligonucleotides. Evaluation of their splice-switching activity in spinal muscular atrophy patient-derived fibroblasts revealed no significant difference in splice-switching efficacy between 2'-MOE mesyl oligonucleotide and the corresponding phosphorothioate (nusinersen). Yet, a survival study with model neonatal mice has shown the antisense 2'-MOE mesyl oligonucleotide to be inferior to nusinersen at the highest dose of 40 mg/kg. A reason for their lower activity in vivo as ascertained by cellular uptake study by fluorescent confocal microscopy in HEK293 cell line could possibly be ascribed to compromised endosomal release and/or nuclear uptake of the 2'-OMe or 2'-MOE μ- and β-oligonucleotides compared to their phosphorothioate analog.
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Affiliation(s)
- Suzan M Hammond
- Department of Paediatrics and Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Olga V Sergeeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Pavel A Melnikov
- Serbsky National Medical Research Center for Psychiatry and Narcology, Moscow, Russia
| | - Larissa Goli
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Jessica Stoodley
- Department of Paediatrics and Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Timofei S Zatsepin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry A Stetsenko
- Department of Physics, Novosibirsk State University, Novosibirsk, Russia.,Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Matthew J A Wood
- Department of Paediatrics and Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
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145
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Stulz R, Milligan F, Stovold C, Love I, Strömberg R, Andersson S, Dahlén A. 34S-SIL of PCSK9-Active Oligonucleotide as Tools for Accurate Quantification by Mass Spectrometry. Nucleic Acid Ther 2021; 31:375-381. [PMID: 33978476 DOI: 10.1089/nat.2020.0915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Stable isotope labeling (SIL) of active pharmaceutical ingredients (API) is a well-established technique for the accurate quantification of small-molecule drugs. As the scope of active ingredients is expanding into areas of larger molecules, such as oligonucleotides (ONs), the development of new quantification techniques is critical. Herein, we describe the analysis of a 34S-SIL anti-PCSK9 gapmer-type antisense ON. A new method for the quantification of this API in complex biological matrices was developed and applied to mouse, dog, and monkey tissue homogenates, which gave improved accuracy and reproducibility compared with the use of auxiliary ONs as internal standard.
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Affiliation(s)
- Rouven Stulz
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.,Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal, and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.,Department of Biosciences and Nutrition, Karolinska Institutet, NEO, S-14183 Huddinge, Sweden
| | - Fiona Milligan
- Bioanalysis Department, Charles River Laboratories, Elphinstone Research Centre, Tranent, United Kingdom
| | - Craig Stovold
- Integrated Bioanalysis, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Iain Love
- Bioanalysis Department, Charles River Laboratories, Elphinstone Research Centre, Tranent, United Kingdom
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, S-14183 Huddinge, Sweden
| | - Shalini Andersson
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.,DMPK, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Anders Dahlén
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.,Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal, and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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146
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Honcharenko M, Honcharenko D, Stromberg R. Copper-Catalyzed Huisgen 1,3-Dipolar Cycloaddition Tailored for Phosphorothioate Oligonucleotides. ACTA ACUST UNITED AC 2021; 80:e102. [PMID: 31884728 DOI: 10.1002/cpnc.102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An efficient method for attachment of a variety of reporter groups to oligonucleotides (ONs) is copper (I) [Cu(I)]-catalyzed Huisgen azide-alkyne 1,3-dipolar cycloaddition ("click reaction"). However, in the case of ONs with phosphorothioate modifications as internucleosidic linkages (PS-ONs), this conjugation method has to be adjusted to be compatible with the sulfur-containing groups. The method described here is adapted for PS-ONs, utilizes solid-supported ONs, and implements the Cu(I) bromide dimethyl sulfide complex (CuBr × Me2 S) as a mediator for the click reaction. The solid-supported ONs can be readily transformed into "clickable ONs" by on-line addition of an alkyne-containing linker that subsequently can react with an azido-containing moiety (e.g., a peptide) in the presence of CuBr × Me2 S. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: Conjugation on solid support Support Protocol: Removal of 4,4'-dimethoxytrityl group from amino linker Basic Protocol 2: Removal of protecting groups and cleavage from solid support Basic Protocol 3: HPLC purification.
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Affiliation(s)
| | - Dmytro Honcharenko
- Karolinska Institutet, Department of Biosciences and Nutrition, Huddinge, Sweden
| | - Roger Stromberg
- Karolinska Institutet, Department of Biosciences and Nutrition, Huddinge, Sweden
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147
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Guo X, Wang T, Huang G, Li R, Da Costa C, Li H, Lv S, Li N. Rediscovering potential molecular targets for glioma therapy through the analysis of the cell of origin, microenvironment, and metabolism. Curr Cancer Drug Targets 2021; 21:558-574. [PMID: 33949933 DOI: 10.2174/1568009621666210504091722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 11/22/2022]
Abstract
Gliomas are the most common type of malignant brain tumors. Despite significant medical advances, gliomas remain incurable and are associated with high mortality. Although numerous biomarkers of diagnostic value have been identified and significant progress in the prognosis of the outcome has been made, the treatment has not been parallelly improved during the last three decades. This review summarizes and discusses three aspects of recent discoveries related to glioma, with the objective to highlight the advantages of glioma-specific drugs targeting the cell of origin, microenvironment, and metabolism. Given the heterogeneous nature of gliomas, various cell populations have been implicated as likely sources of the tumor. Depending on the mutation(s) acquired by the cells, it is believed that neuronal stem/progenitor cells, oligodendrocyte progenitor cells, mature neurons, and glial cells can initiate cell transformation into a malignant phenotype. The level of tumorigenicity appears to be inversely correlated with the maturation of a given cell population. The microenvironment of gliomas includes non-cancer cells such as immune cells, fibroblasts, and cells of blood vessels, as well as secreted molecules and the extracellular matrix, and all these components play a vital role during tumor initiation and progression. We will discuss in detail how the tumor microenvironment can stimulate and drive the transformation of non-tumor cell populations into tumor-supporting cells or glioma cells. Metabolic reprogramming is a key feature of gliomas and is thought to reflect the adaptation to the increased nutritional requirements of tumor cell proliferation, growth, and survival. Mutations in the IDH gene can shape metabolic reprogramming and may generate some vulnerabilities in glioma cells, such as abnormal lipid metabolism and sensitivity to endoplasmic reticulum stress (ERS). We will analyze the prominent metabolic features of malignant gliomas and the key pathways regulating glioma metabolism. This review is intended to provide a conceptual background for the development of glioma therapies based on the properties of tumor cell populations, microenvironment, and metabolism.
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Affiliation(s)
- Xiaoran Guo
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University (SYSU), No.628, Zhenyuan Rd, Guangming Dist., Shenzhen 518107. China
| | - Tao Wang
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University (SYSU), No.628, Zhenyuan Rd, Guangming Dist., Shenzhen 518107. China
| | - Guohao Huang
- Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University, No. 183 Xinqiao Street, Shapingba District, Chongqing City 400037. China
| | - Ruohan Li
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University (SYSU), No.628, Zhenyuan Rd, Guangming Dist., Shenzhen 518107. China
| | - Clive Da Costa
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT. United Kingdom
| | - Huafu Li
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University (SYSU), No.628, Zhenyuan Rd, Guangming Dist., Shenzhen 518107. China
| | - Shengqing Lv
- Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University, No. 183 Xinqiao Street, Shapingba District, Chongqing City 400037. China
| | - Ningning Li
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University (SYSU), No.628, Zhenyuan Rd, Guangming Dist., Shenzhen 518107. China
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148
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Huang M, Xu X, Qiu H, Li N. Analytical characterization of DNA and RNA oligonucleotides by hydrophilic interaction liquid chromatography-tandem mass spectrometry. J Chromatogr A 2021; 1648:462184. [PMID: 33991753 DOI: 10.1016/j.chroma.2021.462184] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/28/2021] [Accepted: 04/18/2021] [Indexed: 01/06/2023]
Abstract
Liquid chromatography-mass spectrometry has been widely implemented as a powerful tool for providing in-depth characterization of nucleic acid therapeutic modalities, such as anti-sense oligonucleotides and small interfering RNAs (siRNAs). In this study, we developed a generic hydrophilic interaction liquid chromatography (HILIC) hyphenated with tandem mass spectrometry method in the absence of ion-pairing reagents and demonstrated its capability as an attractive and robust alternative for oligonucleotide and siRNA analysis. HILIC separation of mixtures of unmodified and fully phosphorothioate-modified DNA oligonucleotides and their synthetic 3' exonuclease-digested metabolites were also assessed. High-resolution mass spectrometric (HRMS) analysis was used to determine the deconvoluted masses of oligonucleotide and siRNA standards and their impurities. To enable unbiased sequence characterization with tandem mass spectrometry (MS/MS), we also optimized higher-energy C-trap dissociation (HCD) on improving the sequence coverage of DNA and RNA oligonucleotides. Lastly, we evaluated on-column sensitivity for a phosphorothioate oligonucleotide by performing targeted analysis with either targeted selected ion monitoring (tSIM) or parallel reaction monitoring (PRM). Higher on-column sensitivity of 13 ng, equivalent to 2.0 pmol, of a phosphorothioate oligonucleotide was achieved by tSIM analysis as compared to PRM analysis.
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Affiliation(s)
- Ming Huang
- Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Xiaobin Xu
- Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA.
| | - Haibo Qiu
- Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA.
| | - Ning Li
- Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
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149
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Kelaini S, Chan C, Cornelius VA, Margariti A. RNA-Binding Proteins Hold Key Roles in Function, Dysfunction, and Disease. BIOLOGY 2021; 10:biology10050366. [PMID: 33923168 PMCID: PMC8146904 DOI: 10.3390/biology10050366] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 02/06/2023]
Abstract
RNA-binding proteins (RBPs) are multi-faceted proteins in the regulation of RNA or its RNA splicing, localisation, stability, and translation. Amassing proof from many recent and dedicated studies reinforces the perception of RBPs exerting control through differing expression levels, cellular localization and post-transcriptional alterations. However, since the regulation of RBPs is reliant on the micro-environment and events like stress response and metabolism, their binding affinities and the resulting RNA-RBP networks may be affected. Therefore, any misregulation and disruption in the features of RNA and its related homeostasis can lead to a number of diseases that include diabetes, cardiovascular disease, and other disorders such as cancer and neurodegenerative diseases. As such, correct regulation of RNA and RBPs is crucial to good health as the effect RBPs exert through loss of function can cause pathogenesis. In this review, we will discuss the significance of RBPs and their typical function and how this can be disrupted in disease.
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150
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Xu M, Zhang K, Song J. Targeted Therapy in Cardiovascular Disease: A Precision Therapy Era. Front Pharmacol 2021; 12:623674. [PMID: 33935716 PMCID: PMC8085499 DOI: 10.3389/fphar.2021.623674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
Targeted therapy refers to exploiting the specific therapeutic drugs against the pathogenic molecules (a protein or a gene) or cells. The drug specifically binds to disease-causing molecules or cells without affecting normal tissue, thus enabling personalized and precision treatment. Initially, therapeutic drugs included antibodies and small molecules, (e.g. nucleic acid drugs). With the advancement of the biology technology and immunotherapy, the gene editing and cell editing techniques are utilized for the disease treatment. Currently, targeted therapies applied to treat cardiovascular diseases (CVDs) mainly include protein drugs, gene editing technologies, nucleic acid drugs and cell therapy. Although targeted therapy has demonstrated excellent efficacy in pre-clinical and clinical trials, several limitations need to be recognized and overcome in clinical application, (e.g. off-target events, gene mutations, etc.). This review introduces the mechanisms of different targeted therapies, and mainly describes the targeted therapy applied in the CVDs. Furthermore, we made comparative analysis to clarify the advantages and disadvantages of different targeted therapies. This overview is expected to provide a new concept to the treatment of the CVDs.
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Affiliation(s)
- Mengda Xu
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kailun Zhang
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,*Correspondence: Kailun Zhang, ; Jiangping Song,
| | - Jiangping Song
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,*Correspondence: Kailun Zhang, ; Jiangping Song,
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