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Gilbert JW, Kennedy Z, Godinho BMDC, Summers A, Weiss A, Echeverria D, Bramato B, McHugh N, Cooper D, Yamada K, Hassler M, Tran H, Gao FB, Brown RH, Khvorova A. Identification of selective and non-selective C9ORF72 targeting in vivo active siRNAs. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102291. [PMID: 39233852 PMCID: PMC11372813 DOI: 10.1016/j.omtn.2024.102291] [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: 01/03/2024] [Accepted: 07/29/2024] [Indexed: 09/06/2024]
Abstract
A hexanucleotide (G4C2) repeat expansion (HRE) within intron one of C9ORF72 is the leading genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). C9ORF72 haploinsufficiency, formation of RNA foci, and production of dipeptide repeat (DPR) proteins have been proposed as mechanisms of disease. Here, we report the first example of disease-modifying siRNAs for C9ORF72 driven ALS/FTD. Using a combination of reporter assay and primary cortical neurons derived from a C9-ALS/FTD mouse model, we screened a panel of more than 150 fully chemically stabilized siRNAs targeting different C9ORF72 transcriptional variants. We demonstrate the lack of correlation between siRNA efficacy in reporter assay versus native environment; repeat-containing C9ORF72 mRNA variants are found to preferentially localize to the nucleus, and thus C9ORF72 mRNA accessibility and intracellular localization have a dominant impact on functional RNAi. Using a C9-ALS/FTD mouse model, we demonstrate that divalent siRNAs targeting C9ORF72 mRNA variants specifically or non-selectively reduce the expression of C9ORF72 mRNA and significantly reduce DPR proteins. Interestingly, siRNA silencing all C9ORF72 mRNA transcripts was more effective in removing intranuclear mRNA aggregates than targeting only HRE-containing C9ORF72 mRNA transcripts. Combined, these data support RNAi-based degradation of C9ORF72 as a potential therapeutic paradigm.
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Affiliation(s)
| | | | | | | | - Alexandra Weiss
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | | | | | | | - David Cooper
- RNA Therapeutic Institute, Worcester, MA 01655, USA
| | - Ken Yamada
- RNA Therapeutic Institute, Worcester, MA 01655, USA
| | | | - Hélène Tran
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Fen Biao Gao
- RNA Therapeutic Institute, Worcester, MA 01655, USA
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
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2
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Liu P, Li Y, Yao Y, Wang W, Jia H, Bai Y, Yuan Z, Yang Z. Intra-amniotic delivery of tropomodulin 3 rescues cell apoptosis induced by miR-200b-3p upregulation via non-canonical nuclear factor kappa B pathways in ethylene thiourea induced anorectal malformations fetal rat. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 284:116918. [PMID: 39191136 DOI: 10.1016/j.ecoenv.2024.116918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 08/18/2024] [Accepted: 08/20/2024] [Indexed: 08/29/2024]
Abstract
Ethylene thiourea (ETU), a metabolite of the fungicide ethylene bisdithiocarbamate (EBDC), has received great concern because of its harmful effects. ETU-induced anorectal malformations (ARMs) in rat models have been reported and widely used in the study of ARMs embryogenesis. Dysplasia of the lumbosacral spinal cord (LSSC), pelvic floor muscles (PFMs), and hindgut (HG) during intrauterine life affects postoperative defecation in patients with ARMs. However, the underlying toxic effects of ETU and pathological mechanisms in the three defecation-related tissues of fetuses with ARMs have not been reported. Thus, this study aimed to elucidate the molecular mechanisms involved in ARMs, with a focus on the dysregulation of miR-200b-3p and its downstream target tropomodulin 3 (TMOD3). The mRNA and protein levels of miR-200b-3p and TMOD3 in LSSC, PFMs, and HG of fetal rats with ARMs were evaluated by reverse transcription quantitative polymerase chain reaction and Western blotting (WB) on embryonic day 17 (E17). Further, a dual-luciferase reporter assay confirmed their targeting relationship. Gene silencing and overexpression of miR-200b-3p and TMOD3 were performed to verify their functions in HEK-293 T cells. Fetal rats with ARMs also received intra-amniotic microinjection of Ad-TMOD3 on E15, and key molecules in nuclear factor kappa (NF-κB) signaling and apoptosis were evaluated by WB on E21. Abnormally high levels of miR-200b-3p inhibited TMOD3 expression by binding with its 3'-untranslated region, leading to the activation of the non-canonical NF-κB signaling pathway, which is critical in the maldevelopment of LSSC, PFMs, and HG in ARMs rats. Furthermore, miR-200b-3p triggered apoptosis by directly targeting TMOD3. Notably, intra-amniotic Ad-TMOD3 microinjection revealed that the upregulation of TMOD3 expression mitigates the effects of miR-200b-3p on the activation of non-canonical NF-κB signaling and apoptosis in fetal rat model of ARMs. A novel miR-200b-3p/TMOD3/non-canonical NF-κB signaling axis triggered the massive apoptosis in LSSC, PFMs, and HG of ARMs, which was restored by the intra-amniotic injection of Ad-TMOD3 during embryogenesis. Our results indicate the potential of TMOD3 as a treatment target to restore defecation.
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Affiliation(s)
- Peiqi Liu
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yue Li
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yifan Yao
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Weilin Wang
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Huimin Jia
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yuzuo Bai
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
| | - Zhengwei Yuan
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
| | - Zhonghua Yang
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China; Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
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3
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Tarafder E, Nizamani MM, Karunarathna SC, Das D, Zeng X, Rind RA, Wang Y, Tian F. Advancements in genetic studies of mushrooms: a comprehensive review. World J Microbiol Biotechnol 2024; 40:275. [PMID: 39034336 DOI: 10.1007/s11274-024-04079-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 07/10/2024] [Indexed: 07/23/2024]
Abstract
Genetic studies in mushrooms, driven by innovations such as CRISPR-Cas9 genome editing and RNA interference, transform our understanding of these enigmatic fungi and their multifaceted roles in agriculture, medicine, and conservation. This comprehensive review explores the rationale and significance of genetic research in mushrooms, delving into the ethical, regulatory, and ecological dimensions of this field. CRISPR-Cas9 emerges as a game-changing technology, enabling precise genome editing, targeted gene knockouts, and pathway manipulation. RNA interference complements these efforts by downregulating genes for improved crop yield and enhanced pest and disease resistance. Genetic studies also contribute to the conservation of rare species and developing more robust mushroom strains, fostering sustainable cultivation practices. Moreover, they unlock the potential for discovering novel medicinal compounds, offering new horizons in pharmaceuticals and nutraceuticals. As emerging technologies and ethical considerations shape the future of mushroom research, these studies promise to revolutionize our relationship with these fungi, paving the way for a more sustainable and innovative world.
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Affiliation(s)
- Entaj Tarafder
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, Guizhou, 550025, People's Republic of China
| | - Mir Muhammad Nizamani
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, Guizhou, 550025, People's Republic of China
| | - Samantha C Karunarathna
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan, 655011, People's Republic of China
- National Institute of Fundamental Studies, Kandy, Sri Lanka
| | - Diptosh Das
- Molecular and Applied Mycology and Plant Pathology Laboratory, Centre of Advanced Study, Department of Botany, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, West Bengal, 700019, India
| | - Xiangyu Zeng
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, Guizhou, 550025, People's Republic of China
| | - Raza Ali Rind
- Department of Plant Breeding and Genetics, Sindh Agriculture University Tandojam, Hyderabad, Pakistan
| | - Yong Wang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, Guizhou, 550025, People's Republic of China.
| | - Fenghua Tian
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, Guizhou, 550025, People's Republic of China.
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Traber GM, Yu AM. The Growing Class of Novel RNAi Therapeutics. Mol Pharmacol 2024; 106:13-20. [PMID: 38719476 PMCID: PMC11187687 DOI: 10.1124/molpharm.124.000895] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/15/2024] [Indexed: 06/20/2024] Open
Abstract
The clinical use of RNA interference (RNAi) molecular mechanisms has introduced a novel, growing class of RNA therapeutics capable of treating diseases by controlling target gene expression at the posttranscriptional level. With the newly approved nedosiran (Rivfloza), there are now six RNAi-based therapeutics approved by the United States Food and Drug Administration (FDA). Interestingly, five of the six FDA-approved small interfering RNA (siRNA) therapeutics [patisiran (Onpattro), lumasiran (Oxlumo), inclisiran (Leqvio), vutrisiran (Amvuttra), and nedosiran] were revealed to act on the 3'-untranslated regions of target mRNAs, instead of coding sequences, thereby following the common mechanistic action of genome-derived microRNAs (miRNA). Furthermore, three of the FDA-approved siRNA therapeutics [patisiran, givosiran (Givlaari), and nedosiran] induce target mRNA degradation or cleavage via near-complete rather than complete base-pair complementarity. These features along with previous findings confound the currently held characteristics to distinguish siRNAs and miRNAs or biosimilars, of which all converge in the RNAi regulatory pathway action. Herein, we discuss the RNAi mechanism of action and current criteria for distinguishing between miRNAs and siRNAs while summarizing the common and unique chemistry and molecular pharmacology of the six FDA-approved siRNA therapeutics. The term "RNAi" therapeutics, as used previously, provides a coherently unified nomenclature for broader RNAi forms as well as the growing number of therapeutic siRNAs and miRNAs or biosimilars that best aligns with current pharmacological nomenclature by mechanism of action. SIGNIFICANCE STATEMENT: The common and unique chemistry and molecular pharmacology of six FDA-approved siRNA therapeutics are summarized, in which nedosiran is newly approved. We point out rather a surprisingly mechanistic action as miRNAs for five siRNA therapeutics and discuss the differences and similarities between siRNAs and miRNAs that supports using a general and unified term "RNAi" therapeutics to align with current drug nomenclature criteria in pharmacology based on mechanism of action and embraces broader forms and growing number of novel RNAi therapeutics.
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Affiliation(s)
- Gavin M Traber
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California - Davis, Sacramento, California
| | - Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California - Davis, Sacramento, California
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Ferguson CM, Godinho BMDC, Echeverria D, Hassler M, Vangjeli L, Sousa J, McHugh N, Alterman J, Hariharan V, Krishnamurthy P, Watts J, Rogaev E, Khvorova A. A combinatorial approach for achieving CNS-selective RNAi. Nucleic Acids Res 2024; 52:5273-5284. [PMID: 38348876 PMCID: PMC11109952 DOI: 10.1093/nar/gkae100] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 12/30/2023] [Accepted: 02/12/2024] [Indexed: 05/23/2024] Open
Abstract
RNA interference (RNAi) is an endogenous process that can be harnessed using chemically modified small interfering RNAs (siRNAs) to potently modulate gene expression in many tissues. The route of administration and chemical architecture are the primary drivers of oligonucleotide tissue distribution, including siRNAs. Independently of the nature and type, oligonucleotides are eliminated from the body through clearance tissues, where their unintended accumulation may result in undesired gene modulation. Divalent siRNAs (di-siRNAs) administered into the CSF induce robust gene silencing throughout the central nervous system (CNS). Upon clearance from the CSF, they are mainly filtered by the kidneys and liver, with the most functionally significant accumulation occurring in the liver. siRNA- and miRNA-induced silencing can be blocked through substrate inhibition using single-stranded, stabilized oligonucleotides called antagomirs or anti-siRNAs. Using APOE as a model target, we show that undesired di-siRNA-induced silencing in the liver can be mitigated through administration of liver targeting GalNAc-conjugated anti-siRNAs, without impacting CNS activity. Blocking unwanted hepatic APOE silencing achieves fully CNS-selective silencing, essential for potential clinical translation. While we focus on CNS/liver selectivity, coadministration of differentially targeting siRNA and anti-siRNAs can be adapted as a strategy to achieve tissue selectivity in different organ combinations.
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Affiliation(s)
- Chantal M Ferguson
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Bruno M D C Godinho
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Matthew Hassler
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Lorenc Vangjeli
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Jacquelyn Sousa
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Julia Alterman
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Vignesh Hariharan
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | | | - Jonathan Watts
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Eveny Rogaev
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
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6
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Tang Q, Khvorova A. RNAi-based drug design: considerations and future directions. Nat Rev Drug Discov 2024; 23:341-364. [PMID: 38570694 PMCID: PMC11144061 DOI: 10.1038/s41573-024-00912-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 04/05/2024]
Abstract
More than 25 years after its discovery, the post-transcriptional gene regulation mechanism termed RNAi is now transforming pharmaceutical development, proved by the recent FDA approval of multiple small interfering RNA (siRNA) drugs that target the liver. Synthetic siRNAs that trigger RNAi have the potential to specifically silence virtually any therapeutic target with unprecedented potency and durability. Bringing this innovative class of medicines to patients, however, has been riddled with substantial challenges, with delivery issues at the forefront. Several classes of siRNA drug are under clinical evaluation, but their utility in treating extrahepatic diseases remains limited, demanding continued innovation. In this Review, we discuss principal considerations and future directions in the design of therapeutic siRNAs, with a particular emphasis on chemistry, the application of informatics, delivery strategies and the importance of careful target selection, which together influence therapeutic success.
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Affiliation(s)
- Qi Tang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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7
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Yang C, Lin ZI, Zhang X, Xu Z, Xu G, Wang YM, Tsai TH, Cheng PW, Law WC, Yong KT, Chen CK. Recent Advances in Engineering Carriers for siRNA Delivery. Macromol Biosci 2024; 24:e2300362. [PMID: 38150293 DOI: 10.1002/mabi.202300362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/29/2023] [Indexed: 12/28/2023]
Abstract
RNA interference (RNAi) technology has been a promising treatment strategy for combating intractable diseases. However, the applications of RNAi in clinical are hampered by extracellular and intracellular barriers. To overcome these barriers, various siRNA delivery systems have been developed in the past two decades. The first approved RNAi therapeutic, Patisiran (ONPATTRO) using lipids as the carrier, for the treatment of amyloidosis is one of the most important milestones. This has greatly encouraged researchers to work on creating new functional siRNA carriers. In this review, the recent advances in siRNA carriers consisting of lipids, polymers, and polymer-modified inorganic particles for cancer therapy are summarized. Representative examples are presented to show the structural design of the carriers in order to overcome the delivery hurdles associated with RNAi therapies. Finally, the existing challenges and future perspective for developing RNAi as a clinical modality will be discussed and proposed. It is believed that the addressed contributions in this review will promote the development of siRNA delivery systems for future clinical applications.
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Affiliation(s)
- Chengbin Yang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Zheng-Ian Lin
- Polymeric Biomaterials Laboratory, Department of Materials and Optoelectronic Science, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan
| | - Xinmeng Zhang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Zhourui Xu
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Gaixia Xu
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Yu-Min Wang
- Polymeric Biomaterials Laboratory, Department of Materials and Optoelectronic Science, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan
| | - Tzu-Hsien Tsai
- Division of Cardiology and Department of Internal Medicine, Ditmanson Medical Foundation Chiayi Christian Hospital, Chiayi, 60002, Taiwan
| | - Pei-Wen Cheng
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, 81362, Taiwan
- Department of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan
| | - Wing-Cheung Law
- Department of Industrial and Systems Engineering, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, 999077, P. R. China
| | - Ken-Tye Yong
- School of Biomedical Engineering, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Chih-Kuang Chen
- Polymeric Biomaterials Laboratory, Department of Materials and Optoelectronic Science, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan
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Tang Q, Gross KY, Fakih HH, Jackson SO, Zain U.I. Abideen M, Monopoli KR, Blanchard C, Bouix-Peter C, Portal T, Harris JE, Khvorova A, Alterman JF. Multispecies-targeting siRNAs for the modulation of JAK1 in the skin. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102117. [PMID: 38304729 PMCID: PMC10831156 DOI: 10.1016/j.omtn.2024.102117] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Identifying therapeutic oligonucleotides that are cross-reactive to experimental animal species can dramatically accelerate the process of preclinical development and clinical translation. Here, we identify fully chemically-modified small interfering RNAs (siRNAs) that are cross-reactive to Janus kinase 1 (JAK1) in humans and a large variety of other species. We validated the identified siRNAs in silencing JAK1 in cell lines and skin tissues of multiple species. JAK1 is one of the four members of the JAK family of tyrosine kinases that mediate the signaling transduction of many inflammatory cytokine pathways. Dysregulation of these pathways is often involved in the pathogenesis of various immune disorders, and modulation of JAK family enzymes is an effective strategy in the clinic. Thus, this work may open up unprecedented opportunities for evaluating the modulation of JAK1 in many animal models of human inflammatory skin diseases. Further chemical engineering of the optimized JAK1 siRNAs may expand the utility of these compounds for treating immune disorders in additional tissues.
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Affiliation(s)
- Qi Tang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Katherine Y. Gross
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Hassan H. Fakih
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Samuel O. Jackson
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | | | - Kathryn R. Monopoli
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | | | | | | | - John E. Harris
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Julia F. Alterman
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
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Nguyen TT, Nguyen Thi YV, Chu DT. RNA therapeutics: Molecular mechanisms, and potential clinical translations. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 203:65-82. [PMID: 38360006 DOI: 10.1016/bs.pmbts.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
RNA therapies involve the utilization of natural and artificial RNA molecules to control the expression and function of cellular genes and proteins. Initializing from 1990s, RNA therapies now show the rapid growth in the development and application of RNA therapeutics for treating various conditions, especially for undruggable diseases. The outstanding success of recent mRNA vaccines against COVID-19 infection again highlighted the important role of RNA therapies in future medicine. In this review, we will first briefly provide the crucial investigations on RNA therapy, from the first pieces of discovery on RNA molecules to clinical applications of RNA therapeutics. We will then classify the mechanisms of RNA therapeutics from various classes in the treatment of diseases. To emphasize the huge potential of RNA therapies, we also provide the key RNA products that have been on clinical trials or already FDA-approved. With comprehensive knowledge on RNA biology, and the advances in analysis, technology and computer-aid science, RNA therapies can bring a promise to be more expanding to the market in the future.
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Affiliation(s)
- Tiep Tien Nguyen
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Epibiotech Co. Ltd., Incheon, Republic of Korea
| | - Yen Vi Nguyen Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam
| | - Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam.
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10
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Redhwan MAM, M G H, Samaddar S, Hard SAAA, Yadav V, Mukherjee A, Kumar R. Small interference (RNAi) technique: Exploring its clinical applications, benefits and limitations. Eur J Clin Invest 2023; 53:e14039. [PMID: 37309221 DOI: 10.1111/eci.14039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/16/2023] [Accepted: 05/25/2023] [Indexed: 06/14/2023]
Abstract
BACKGROUND Small interference RNA (siRNA) has emerged as the most desired method for researchers and clinicians who wish to silence a specific gene of interest and has been extensively developed as a therapeutic agent. This review points to collecting all clinical trials on siRNA and understanding its benefits, pharmacokinetics and safety by reading articles published in the last 5 years. MATERIALS AND METHODS Searching in the PubMed database using 'siRNA' and 'in vivo' with limits to articles published in the previous 5 years, article type 'clinical trials' and language 'English' to acquire papers on in vivo studies on siRNA approaches. Features of siRNA clinical trials registered at https://clinicaltrials.gov/ were analysed. RESULTS So far, 55 clinical studies have been published on siRNA. Many published clinical trials on siRNA showed tolerability, safety and effectiveness in treating cancers like breast, lung, colon, and other organs and other diseases like viral infections and hereditary diseases. Many different routes of administration can silence many genes at the same time. Limitations and uncertainties associated with siRNA treatment include the effectiveness of cellular uptake, precise targeting of the intended tissue or cell and prompt elimination from the body. CONCLUSIONS The siRNA or RNAi method will be one of the most critical and influential techniques to fight against many different diseases. Although the RNAi approach has certain advantages, it also has limitations concerning clinical applications. Overcoming these limitations remains a daunting challenge.
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Affiliation(s)
- Moqbel Ali Moqbel Redhwan
- Department of Pharmacology, KLE College of Pharmacy, Bengaluru, India
- Basic Science Research Center (Off-Campus), KLE College of Pharmacy, Bengaluru, India
| | - Hariprasad M G
- Department of Pharmacology, KLE College of Pharmacy, Bengaluru, India
- Basic Science Research Center (Off-Campus), KLE College of Pharmacy, Bengaluru, India
| | - Suman Samaddar
- BGS GIMS Research Institute, BGS Global Institute of Medical Sciences, Bengaluru, India
| | - Sumaia Abdulbari Ahmed Ali Hard
- Basic Science Research Center (Off-Campus), KLE College of Pharmacy, Bengaluru, India
- Department of Pharmaceutics, KLE College of Pharmacy, Bengaluru, India
| | | | - Apurbo Mukherjee
- Department of Pharmacology, KLE College of Pharmacy, Bengaluru, India
| | - Rahul Kumar
- Department of Pharmacology, KLE College of Pharmacy, Bengaluru, India
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11
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Boileau C, Deforges S, Peret A, Scavarda D, Bartolomei F, Giles A, Partouche N, Gautron J, Viotti J, Janowitz H, Penchet G, Marchal C, Lagarde S, Trebuchon A, Villeneuve N, Rumi J, Marissal T, Khazipov R, Khalilov I, Martineau F, Maréchal M, Lepine A, Milh M, Figarella-Branger D, Dougy E, Tong S, Appay R, Baudouin S, Mercer A, Smith JB, Danos O, Porter R, Mulle C, Crépel V. GluK2 Is a Target for Gene Therapy in Drug-Resistant Temporal Lobe Epilepsy. Ann Neurol 2023; 94:745-761. [PMID: 37341588 DOI: 10.1002/ana.26723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/22/2023]
Abstract
OBJECTIVE Temporal lobe epilepsy (TLE) is characterized by recurrent seizures generated in the limbic system, particularly in the hippocampus. In TLE, recurrent mossy fiber sprouting from dentate gyrus granule cells (DGCs) crea an aberrant epileptogenic network between DGCs which operates via ectopically expressed GluK2/GluK5-containing kainate receptors (KARs). TLE patients are often resistant to anti-seizure medications and suffer significant comorbidities; hence, there is an urgent need for novel therapies. Previously, we have shown that GluK2 knockout mice are protected from seizures. This study aims at providing evidence that downregulating KARs in the hippocampus using gene therapy reduces chronic epileptic discharges in TLE. METHODS We combined molecular biology and electrophysiology in rodent models of TLE and in hippocampal slices surgically resected from patients with drug-resistant TLE. RESULTS Here, we confirmed the translational potential of KAR suppression using a non-selective KAR antagonist that markedly attenuated interictal-like epileptiform discharges (IEDs) in TLE patient-derived hippocampal slices. An adeno-associated virus (AAV) serotype-9 vector expressing anti-grik2 miRNA was engineered to specifically downregulate GluK2 expression. Direct delivery of AAV9-anti grik2 miRNA into the hippocampus of TLE mice led to a marked reduction in seizure activity. Transduction of TLE patient hippocampal slices reduced levels of GluK2 protein and, most importantly, significantly reduced IEDs. INTERPRETATION Our gene silencing strategy to knock down aberrant GluK2 expression demonstrates inhibition of chronic seizure in a mouse TLE model and IEDs in cultured slices derived from TLE patients. These results provide proof-of-concept for a gene therapy approach targeting GluK2 KARs for drug-resistant TLE patients. ANN NEUROL 2023;94:745-761.
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Affiliation(s)
| | - Severine Deforges
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience IINS, UMR 5297, Bordeaux, France
| | | | - Didier Scavarda
- APHM, INSERM, Aix Marseille Univ, INS, Timone Hospital, Pediatric Neurosurgery, Marseille, France
| | - Fabrice Bartolomei
- APHM, INSERM, Aix Marseille Univ, INS, Timone Hospital, Epileptology Department, Marseille, France
| | | | - Nicolas Partouche
- Aix-Marseille Univ. INSERM, Marseille, France
- Corlieve Therapeutics SAS, uniQure NV, Paris, France
| | - Justine Gautron
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience IINS, UMR 5297, Bordeaux, France
- Corlieve Therapeutics SAS, uniQure NV, Paris, France
| | - Julio Viotti
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience IINS, UMR 5297, Bordeaux, France
| | | | | | - Cécile Marchal
- Pellegrin Hospital, Neurosurgery Department, Bordeaux, France
| | - Stanislas Lagarde
- APHM, INSERM, Aix Marseille Univ, INS, Timone Hospital, Epileptology Department, Marseille, France
| | - Agnès Trebuchon
- APHM, INSERM, Aix Marseille Univ, INS, Timone Hospital, Epileptology Department, Marseille, France
| | - Nathalie Villeneuve
- APHM, INSERM, Aix Marseille Univ, INS, Timone Hospital, Epileptology Department, Marseille, France
| | - Julie Rumi
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience IINS, UMR 5297, Bordeaux, France
| | | | | | | | | | - Marine Maréchal
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience IINS, UMR 5297, Bordeaux, France
| | - Anne Lepine
- APHM, INSERM, Aix Marseille Univ, INS, Timone Hospital, Epileptology Department, Marseille, France
| | - Mathieu Milh
- APHM, INSERM, Aix Marseille Univ, INS, Timone Hospital, Epileptology Department, Marseille, France
| | - Dominique Figarella-Branger
- APHM, CNRS, INP, Inst Neurophysiopathol, CHU Timone, Service d'Anatomie Pathologique et de Neuropathologie, Aix-Marseille Univ, Marseille, France
| | - Etienne Dougy
- APHM, CNRS, INP, Inst Neurophysiopathol, CHU Timone, Service d'Anatomie Pathologique et de Neuropathologie, Aix-Marseille Univ, Marseille, France
| | - Soutsakhone Tong
- APHM, CNRS, INP, Inst Neurophysiopathol, CHU Timone, Service d'Anatomie Pathologique et de Neuropathologie, Aix-Marseille Univ, Marseille, France
| | - Romain Appay
- APHM, CNRS, INP, Inst Neurophysiopathol, CHU Timone, Service d'Anatomie Pathologique et de Neuropathologie, Aix-Marseille Univ, Marseille, France
| | | | | | | | | | | | - Christophe Mulle
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience IINS, UMR 5297, Bordeaux, France
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Sufian MA, Ilies MA. Lipid-based nucleic acid therapeutics with in vivo efficacy. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2023; 15:e1856. [PMID: 36180107 PMCID: PMC10023279 DOI: 10.1002/wnan.1856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/22/2022] [Accepted: 08/30/2022] [Indexed: 03/09/2023]
Abstract
Synthetic vectors for therapeutic nucleic acid delivery are currently competing significantly with their viral counter parts due to their reduced immunogenicity, large payload capacity, and ease of manufacture under GMP-compliant norms. The approval of Onpattro, a lipid-based siRNA therapeutic, and the proven clinical success of two lipid-based COVID-19 vaccines from Pfizer-BioNTech, and Moderna heralded the specific advantages of lipid-based systems among all other synthetic nucleic acid carriers. Lipid-based systems with diverse payloads-plasmid DNA (pDNA), antisense oligonucleotide (ASO), small interfering RNA (siRNA), microRNA (miRNA), small activating RNA (saRNA), and messenger RNA (mRNA)-are now becoming a mature technology, with growing impact in the clinic. Research over four decades identified the key factors determining the therapeutic success of these multi-component systems. Here, we discuss the main nucleic acid-based technologies, presenting their mechanism of action, delivery barriers facing them, the structural properties of the payload as well as the component lipids that regulate physicochemical properties, pharmacokinetics and biodistribution, efficacy, and toxicity of the resultant nanoparticles. We further detail on the formulation parameters, evolution of the manufacturing techniques that generate reproducible and scalable outputs, and key manufacturing aspects that enable control over physicochemical properties of the resultant particles. Preclinical applications of some of these formulations that were successfully translated from in vitro studies to animal models are subsequently discussed. Finally, clinical success and failure of these systems starting from 1993 to present are highlighted, in a holistic literature review focused on lipid-based nucleic acid delivery systems. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease Toxicology and Regulatory Issues in Nanomedicine > Toxicology of Nanomaterials.
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Affiliation(s)
- Md Abu Sufian
- Department of Pharmaceutical Sciences and Moulder Center for Drug Discovery Research, School of Pharmacy, Temple University, 3307 North Broad Street, Philadelphia, PA 19140, USA
| | - Marc A. Ilies
- Department of Pharmaceutical Sciences and Moulder Center for Drug Discovery Research, School of Pharmacy, Temple University, 3307 North Broad Street, Philadelphia, PA 19140, USA
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Nsairat H, AlShaer W, Odeh F, Essawi E, Khater D, Bawab AA, El-Tanani M, Awidi A, Mubarak MS. Recent Advances in Using Liposomes for Delivery of Nucleic Acid-Based Therapeutics. OPENNANO 2023. [DOI: 10.1016/j.onano.2023.100132] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
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14
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Akbarimotlagh M, Azizi A, Shams-Bakhsh M, Jafari M, Ghasemzadeh A, Palukaitis P. Critical points for the design and application of RNA silencing constructs for plant virus resistance. Adv Virus Res 2023; 115:159-203. [PMID: 37173065 DOI: 10.1016/bs.aivir.2023.02.001] [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: 05/15/2023]
Abstract
Control of plant virus diseases is a big challenge in agriculture as is resistance in plant lines to infection by viruses. Recent progress using advanced technologies has provided fast and durable alternatives. One of the most promising techniques against plant viruses that is cost-effective and environmentally safe is RNA silencing or RNA interference (RNAi), a technology that could be used alone or along with other control methods. To achieve the goals of fast and durable resistance, the expressed and target RNAs have been examined in many studies, with regard to the variability in silencing efficiency, which is regulated by various factors such as target sequences, target accessibility, RNA secondary structures, sequence variation in matching positions, and other intrinsic characteristics of various small RNAs. Developing a comprehensive and applicable toolbox for the prediction and construction of RNAi helps researchers to achieve the acceptable performance level of silencing elements. Although the attainment of complete prediction of RNAi robustness is not possible, as it also depends on the cellular genetic background and the nature of the target sequences, some important critical points have been discerned. Thus, the efficiency and robustness of RNA silencing against viruses can be improved by considering the various parameters of the target sequence and the construct design. In this review, we provide a comprehensive treatise regarding past, present and future prospective developments toward designing and applying RNAi constructs for resistance to plant viruses.
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Affiliation(s)
- Masoud Akbarimotlagh
- Plant Pathology Department, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran, Iran
| | - Abdolbaset Azizi
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran.
| | - Masoud Shams-Bakhsh
- Plant Pathology Department, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran, Iran
| | - Majid Jafari
- Department of Plant Protection, Higher Education Complex of Saravan, Saravan, Iran
| | - Aysan Ghasemzadeh
- Plant Pathology Department, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran, Iran
| | - Peter Palukaitis
- Department of Horticulture Sciences, Seoul Women's University, Seoul, Republic of Korea.
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Yasmin T, Adiba M, Saba AA, Nabi AHMN. In Silico Design of siRNAs for Silencing CLEC5A Receptor as a Potential Therapeutic Approach Against Dengue and Japanese Encephalitis Virus Infection in Human. Bioinform Biol Insights 2022; 16:11779322221142122. [PMID: 36530559 PMCID: PMC9749047 DOI: 10.1177/11779322221142122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/09/2022] [Indexed: 09/04/2024] Open
Abstract
Dengue and Japanese encephalitis virus (JEV) are mosquito-borne RNA viruses that can cause severe illness leading to death in the tropics and subtropics. Both of these viruses interact directly with the C-type lectin domain family 5, member A receptor (CLEC5A) on human macrophages which stimulates the release of proinflammatory cytokines. Since blockade of this interaction has been shown to suppress the secretion of cytokines, CLEC5A is considered a potential target for the development of new treatments to reduce virus-induced brain damage. Developing a vaccine against dengue is challenging because this virus can cause disease through 4 different serotypes. Therefore, the vaccine must immunize against all 4 serotypes to be effective, while unvaccinated people still contract JEV and suffer from its complications. Small interfering RNAs (siRNAs) play an important role in regulating gene expression by causing the degradation of target mRNAs. In this study, we attempted to rationally design potential siRNA molecules using various software, targeting the CLEC5A gene. In total, 3 siRNAs were found to be potential candidates for CLEC5A silencing. They showed good target accessibility, optimum guanine-cytosine (GC) content, the least chance of off-target effects, positive energy of folding, and strong interaction with Argonaute2 protein as denoted by a negative docking energy score. In addition, molecular dynamics simulation of the siRNA-Ago2-docked complexes showed the stability of the complexes over 1.5 nanoseconds. These predicted siRNAs might effectively downregulate the expression of the CLEC5A receptor and thus prove vital in the treatment of dengue and JEV infections.
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Affiliation(s)
- Tahirah Yasmin
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Maisha Adiba
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Abdullah Al Saba
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - AHM Nurun Nabi
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
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Lin L, Zhu S, Huang H, Wu LP, Huang J. Chemically modified small interfering RNA targeting Hedgehog signaling pathway for rheumatoid arthritis therapy. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 31:88-104. [PMID: 36618268 PMCID: PMC9813581 DOI: 10.1016/j.omtn.2022.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]
Abstract
Rheumatoid arthritis (RA) is an inflammatory disease that leads to disability; however, existing therapies are still unsatisfactory. Activated fibroblast-like synoviocytes (FLSs) play an essential role in synovitis formation and joint destruction in RA. The Hedgehog signaling pathway is aberrantly activated and contributes to the aggressive phenotype of RA-FLSs. However, it remains uncertain whether inhibiting Smoothened (SMO), a critical component of the Hedgehog signaling pathway, is an effective treatment for RA. Here, we design a series of small interfering RNAs (siRNAs) that specifically target the SMO gene. With precise chemical modifications, siRNAs' efficacy and stability are significantly improved, and the off-target effects are minimized. The optimized chemically modified siRNA (si-S1A3-Chol) decreases RA-FLS proliferation and invasiveness without the transfection reagent. Furthermore, si-S1A3-Chol injected intra-articularly effectively alleviates joint destruction and improves motor function in collagen-induced arthritis mouse models. Consequently, our results demonstrate that chemically modified siRNA targeting the Hedgehog signaling pathway may be a potential therapy for RA.
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Affiliation(s)
- Lang Lin
- Department of Rheumatology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, People’s Republic of China
| | - Shangling Zhu
- Department of Rheumatology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, People’s Republic of China
| | - Hongyu Huang
- Division of Clinical Public Health and Institute for Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Lin-Ping Wu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, People’s Republic of China,Corresponding author: Lin-Ping Wu, Center for Chemical Biology and Drug Discovery, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, People’s Republic of China.
| | - Jianlin Huang
- Department of Rheumatology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, People’s Republic of China,Corresponding author: Jianlin Huang, Department of Rheumatology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, People’s Republic of China.
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Luo M, Lee LKC, Peng B, Choi CHJ, Tong WY, Voelcker NH. Delivering the Promise of Gene Therapy with Nanomedicines in Treating Central Nervous System Diseases. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2201740. [PMID: 35851766 PMCID: PMC9475540 DOI: 10.1002/advs.202201740] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/19/2022] [Indexed: 06/01/2023]
Abstract
Central Nervous System (CNS) diseases, such as Alzheimer's diseases (AD), Parkinson's Diseases (PD), brain tumors, Huntington's disease (HD), and stroke, still remain difficult to treat by the conventional molecular drugs. In recent years, various gene therapies have come into the spotlight as versatile therapeutics providing the potential to prevent and treat these diseases. Despite the significant progress that has undoubtedly been achieved in terms of the design and modification of genetic modulators with desired potency and minimized unwanted immune responses, the efficient and safe in vivo delivery of gene therapies still poses major translational challenges. Various non-viral nanomedicines have been recently explored to circumvent this limitation. In this review, an overview of gene therapies for CNS diseases is provided and describes recent advances in the development of nanomedicines, including their unique characteristics, chemical modifications, bioconjugations, and the specific applications that those nanomedicines are harnessed to deliver gene therapies.
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Affiliation(s)
- Meihua Luo
- Monash Institute of Pharmaceutics ScienceMonash UniversityParkville Campus, 381 Royal ParadeParkvilleVIC3052Australia
- Australian Institute for Bioengineering and Nanotechnologythe University of QueenslandSt LuciaQLD4072Australia
| | - Leo Kit Cheung Lee
- Department of Biomedical EngineeringThe Chinese University of Hong KongShatinNew TerritoriesHong Kong
| | - Bo Peng
- Monash Institute of Pharmaceutics ScienceMonash UniversityParkville Campus, 381 Royal ParadeParkvilleVIC3052Australia
- Frontiers Science Center for Flexible ElectronicsXi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical materials & EngineeringNorthwestern Polytechnical UniversityXi'an710072China
| | - Chung Hang Jonathan Choi
- Department of Biomedical EngineeringThe Chinese University of Hong KongShatinNew TerritoriesHong Kong
| | - Wing Yin Tong
- Monash Institute of Pharmaceutics ScienceMonash UniversityParkville Campus, 381 Royal ParadeParkvilleVIC3052Australia
| | - Nicolas H. Voelcker
- Monash Institute of Pharmaceutics ScienceMonash UniversityParkville Campus, 381 Royal ParadeParkvilleVIC3052Australia
- Commonwealth Scientific and Industrial Research Organization (CSIRO)ClaytonVIC3168Australia
- Melbourne Centre for NanofabricationVictorian Node of the Australian National Fabrication Facility151 Wellington RoadClaytonVIC3168Australia
- Materials Science and EngineeringMonash University14 Alliance LaneClaytonVIC3800Australia
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Abstract
The highly specific induction of RNA interference-mediated gene knockdown, based on the direct application of small interfering RNAs (siRNAs), opens novel avenues towards innovative therapies. Two decades after the discovery of the RNA interference mechanism, the first siRNA drugs received approval for clinical use by the US Food and Drug Administration and the European Medicines Agency between 2018 and 2022. These are mainly based on an siRNA conjugation with a targeting moiety for liver hepatocytes, N-acetylgalactosamine, and cover the treatment of acute hepatic porphyria, transthyretin-mediated amyloidosis, hypercholesterolemia, and primary hyperoxaluria type 1. Still, the development of siRNA therapeutics faces several challenges and issues, including the definition of optimal siRNAs in terms of target, sequence, and chemical modifications, siRNA delivery to its intended site of action, and the absence of unspecific off-target effects. Further siRNA drugs are in clinical studies, based on different delivery systems and covering a wide range of different pathologies including metabolic diseases, hematology, infectious diseases, oncology, ocular diseases, and others. This article reviews the knowledge on siRNA design and chemical modification, as well as issues related to siRNA delivery that may be addressed using different delivery systems. Details on the mode of action and clinical status of the various siRNA therapeutics are provided, before giving an outlook on issues regarding the future of siRNA drugs and on their potential as one emerging standard modality in pharmacotherapy. Notably, this may also cover otherwise un-druggable diseases, the definition of non-coding RNAs as targets, and novel concepts of personalized and combination treatment regimens.
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Affiliation(s)
- Maik Friedrich
- Faculty of Leipzig, Institute of Clinical Immunology, Max-Bürger-Forschungszentrum (MBFZ), University of Leipzig, Leipzig, Germany.,Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Achim Aigner
- Rudolf-Boehm Institute for Pharmacology and Toxicology, Clinical Pharmacology, University of Leipzig, Haertelstrasse 16-18, 04107, Leipzig, Germany.
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Lewin AS, Smith WC. Gene Therapy for Rhodopsin Mutations. Cold Spring Harb Perspect Med 2022; 12:a041283. [PMID: 35940643 PMCID: PMC9435570 DOI: 10.1101/cshperspect.a041283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Mutations in RHO, the gene for rhodopsin, account for a large fraction of autosomal-dominant retinitis pigmentosa (adRP). Patients fall into two clinical classes, those with early onset, pan retinal photoreceptor degeneration, and those who experience slowly progressive disease. The latter class of patients are candidates for photoreceptor-directed gene therapy, while former may be candidates for delivery of light-responsive proteins to interneurons or retinal ganglion cells. Gene therapy for RHO adRP may be targeted to the mutant gene at the DNA or RNA level, while other therapies preserve the viability of photoreceptors without addressing the underlying mutation. Correcting the RHO gene and replacing the mutant RNA show promise in animal models, while sustaining viable photoreceptors has the potential to delay the loss of central vision and may preserve photoreceptors for gene-directed treatments.
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Affiliation(s)
- Alfred S Lewin
- Departments of Molecular Genetics and Microbiology and Ophthalmology, University of Florida College of Medicine, Gainesville, Florida 32610, USA
| | - W Clay Smith
- Departments of Molecular Genetics and Microbiology and Ophthalmology, University of Florida College of Medicine, Gainesville, Florida 32610, USA
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RNAi-based modulation of IFN-γ signaling in skin. Mol Ther 2022; 30:2709-2721. [PMID: 35477658 PMCID: PMC9372319 DOI: 10.1016/j.ymthe.2022.04.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/03/2022] [Accepted: 04/25/2022] [Indexed: 11/23/2022] Open
Abstract
Aberrant activation of interferon (IFN)-γ signaling plays a key role in several autoimmune skin diseases, including lupus erythematosus, alopecia areata, vitiligo, and lichen planus. Here, we identify fully chemically modified small interfering RNAs (siRNAs) that silence the ligand binding chain of the IFN-γ receptor (IFNGR1), for the modulation of IFN-γ signaling. Conjugating these siRNAs to docosanoic acid (DCA) enables productive delivery to all major skin cell types local to the injection site, with a single dose of injection supporting effective IFNGR1 protein reduction for at least 1 month in mice. In an ex vivo model of IFN-γ signaling, DCA-siRNA efficiently inhibits the induction of IFN-γ-inducible chemokines, CXCL9 and CXCL10, in skin biopsies from the injection site. Our data demonstrate that DCA-siRNAs can be engineered for functional gene silencing in skin and establish a path toward siRNA treatment of autoimmune skin diseases.
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Saba AA, Adiba M, Chakraborty S, Nabi AN. Prediction of putative potential siRNAs for inhibiting SARS-CoV-2 strains, including variants of concern and interest. Future Microbiol 2022; 17:449-463. [PMID: 35285248 PMCID: PMC8958991 DOI: 10.2217/fmb-2021-0130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Aim: To predict siRNAs as a therapeutic intervention for highly infectious new variants of SARS-CoV-2. Methods: Conserved coding sequence regions of 11 SARS-CoV-2 proteins were used to construct siRNAs through sampling of metadata comprising 214,256 sequences. Results: Predicted siRNAs S1: 5′-UCAUUGAGAAAUGUUUACGCA-3′ and S2: 5′-AAAGACAUCAGCAUACUCCUG-3′ against RdRp of SARS-CoV-2 satisfied all the stringent filtering processes and showed good binding characteristics. The designed siRNAs are expected to inhibit viral replication and transcription of various coronavirus strains encompassing variants of concern and interest. Conclusion: The predicted siRNAs are expected to be potent against SARS-CoV-2, and following in vitro and in vivo validations may be considered as potential therapeutic measures.
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Affiliation(s)
- Abdullah Al Saba
- Department of Biochemistry and Molecular Biology, Laboratory of Population Genetics, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Maisha Adiba
- Department of Biochemistry and Molecular Biology, Laboratory of Population Genetics, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Sajib Chakraborty
- Department of Biochemistry and Molecular Biology, Systems Cell-Signalling Laboratory, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Ahm Nurun Nabi
- Department of Biochemistry and Molecular Biology, Laboratory of Population Genetics, University of Dhaka, Dhaka, 1000, Bangladesh
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Novel approaches in cancer treatment: preclinical and clinical development of small non-coding RNA therapeutics. J Exp Clin Cancer Res 2021; 40:383. [PMID: 34863235 PMCID: PMC8642961 DOI: 10.1186/s13046-021-02193-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/23/2021] [Indexed: 11/20/2022] Open
Abstract
Short or small interfering RNAs (siRNAs) and microRNA (miRNAs) are molecules similar in size and function able to inhibit gene expression based on their complementarity with mRNA sequences, inducing the degradation of the transcript or the inhibition of their translation. siRNAs bind specifically to a single gene location by sequence complementarity and regulate gene expression by specifically targeting transcription units via posttranscriptional gene silencing. miRNAs can regulate the expression of different gene targets through their imperfect base pairing. This process - known as RNA interference (RNAi) - modulates transcription in order to maintain a correct physiological environment, playing a role in almost the totality of the cellular pathways. siRNAs have been evolutionary evolved for the protection of genome integrity in response to exogenous and invasive nucleic acids such as transgenes or transposons. Artificial siRNAs are widely used in molecular biology for transient silencing of genes of interest. This strategy allows to inhibit the expression of any target protein of known sequence and is currently used for the treatment of different human diseases including cancer. Modifications and rearrangements in gene regions encoding for miRNAs have been found in cancer cells, and specific miRNA expression profiles characterize the developmental lineage and the differentiation state of the tumor. miRNAs with different expression patterns in tumors have been reported as oncogenes (oncomirs) or tumor-suppressors (anti-oncomirs). RNA modulation has become important in cancer research not only for development of early and easy diagnosis tools but also as a promising novel therapeutic approach. Despite the emerging discoveries supporting the role of miRNAs in carcinogenesis and their and siRNAs possible use in therapy, a series of concerns regarding their development, delivery and side effects have arisen. In this review we report the biology of miRNAs and siRNAs in relation to cancer summarizing the recent methods described to use them as novel therapeutic drugs and methods to specifically deliver them to cancer cells and overcome the limitations in the use of these molecules.
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Rahman A, Gupta SD, Rahman MA, Tamanna S. An in-silico approach to design potential siRNAs against the ORF57 of Kaposi's sarcoma-associated herpesvirus. Genomics Inform 2021; 19:e47. [PMID: 35012290 PMCID: PMC8752988 DOI: 10.5808/gi.21057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/25/2021] [Accepted: 12/09/2021] [Indexed: 12/21/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is one of the few human oncogenic viruses, which causes a variety of malignancies, including Kaposi's sarcoma, multicentric Castleman disease, and primary effusion lymphoma, particularly in human immunodeficiency virus patients. The currently available treatment options cannot always prevent the invasion and dissemination of this virus. In recent times, siRNA-based therapeutics are gaining prominence over conventional medications as siRNA can be designed to target almost any gene of interest. The ORF57 is a crucial regulatory protein for lytic gene expression of KSHV. Disruption of this gene translation will inevitably inhibit the replication of the virus in the host cell. Therefore, the ORF57 of KSHV could be a potential target for designing siRNA-based therapeutics. Considering both sequence preferences and target site accessibility, several online tools (i-SCORE Designer, Sfold web server) had been utilized to predict the siRNA guide strand against the ORF57. Subsequently, off-target filtration (BLAST), conservancy test (fuzznuc), and thermodynamics analysis (RNAcofold, RNAalifold, and RNA Structure web server) were also performed to select the most suitable siRNA sequences. Finally, two siRNAs were identified that passed all of the filtration phases and fulfilled the thermodynamic criteria. We hope that the siRNAs predicted in this study would be helpful for the development of new effective therapeutics against KSHV.
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Affiliation(s)
- Anisur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Science, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Shipan Das Gupta
- Department of Biotechnology and Genetic Engineering, Faculty of Science, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Md. Anisur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Science, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Saheda Tamanna
- Department of Biotechnology and Genetic Engineering, Faculty of Science, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
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Massengill MT, Lewin AS. Gene Therapy for Rhodopsin-associated Autosomal Dominant Retinitis Pigmentosa. Int Ophthalmol Clin 2021; 61:79-96. [PMID: 34584046 PMCID: PMC8478325 DOI: 10.1097/iio.0000000000000383] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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25
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Clément F, Nougarède A, Combe S, Kermarrec F, Dey AK, Obeid P, Millet A, Navarro FP, Marche PN, Sulpice E, Gidrol X. Therapeutic siRNAs Targeting the JAK/STAT Signalling Pathway in Inflammatory Bowel Diseases. J Crohns Colitis 2021; 16:286-300. [PMID: 34286840 PMCID: PMC8864631 DOI: 10.1093/ecco-jcc/jjab129] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND AND AIMS Inflammatory bowel diseases are highly debilitating conditions that require constant monitoring and life-long medication. Current treatments are focused on systemic administration of immunomodulatory drugs, but they have a broad range of undesirable side-effects. RNA interference is a highly specific endogenous mechanism that regulates the expression of the gene at the transcript level, which can be repurposed using exogenous short interfering RNA [siRNA] to repress expression of the target gene. While siRNA therapeutics can offer an alternative to existing therapies, with a high specificity critical for chronically administrated drugs, evidence of their potency compared to chemical kinase inhibitors used in clinics is still lacking in alleviating an adverse inflammatory response. METHODS We provide a framework to select highly specific siRNA, with a focus on two kinases strongly involved in pro-inflammatory diseases, namely JAK1 and JAK3. Using western-blot, real-time quantitative PCR and large-scale analysis, we assessed the specificity profile of these siRNA drugs and compared their efficacy to the most recent and promising kinase inhibitors for Janus kinases [Jakinibs], tofacitinib and filgotinib. RESULTS siRNA drugs can reach higher efficiency and selectivity at lower doses [5 pM vs 1 µM] than Jakinibs. Moreover, JAK silencing lasted up to 11 days, even with 6 h pulse transfection. CONCLUSIONS The siRNA-based drugs developed hold the potential to develop more potent therapeutics for chronic inflammatory diseases.
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Affiliation(s)
- Flora Clément
- Univ. Grenoble Alpes, CEA, INSERM, IRIG, Biomics, Grenoble, France,Univ. Grenoble Alpes, INSERM U1209, CNRS UMR5309, IAB, La Tronche, France
| | - Adrien Nougarède
- Univ. Grenoble Alpes, CEA, Leti, Division for Biology and Healthcare Technologies, Microfluidic Systems and Bioengineering Lab, Grenoble, France
| | - Stéphanie Combe
- Univ. Grenoble Alpes, CEA, INSERM, IRIG, Biomics, Grenoble, France
| | | | - Arindam K Dey
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR5309, IAB, La Tronche, France
| | - Patricia Obeid
- Univ. Grenoble Alpes, CEA, INSERM, IRIG, Biomics, Grenoble, France
| | - Arnaud Millet
- Univ. Grenoble Alpes, Inserm U1209, CNRS UMR5309, Team Mechanobiology, immunity and Cancer, Institute for Advanced Biosciences, La Tronche, France
| | - Fabrice P Navarro
- Univ. Grenoble Alpes, CEA, Leti, Division for Biology and Healthcare Technologies, Microfluidic Systems and Bioengineering Lab, Grenoble, France
| | - Patrice N Marche
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR5309, IAB, La Tronche, France
| | - Eric Sulpice
- Univ. Grenoble Alpes, CEA, INSERM, IRIG, Biomics, Grenoble, France
| | - Xavier Gidrol
- Univ. Grenoble Alpes, CEA, INSERM, IRIG, Biomics, Grenoble, France,Corresponding author: Xavier Gidrol, Univ. Grenoble Alpes, CEA, INSERM, IRIG, Biomics, F-38000, Grenoble, France. Tel: +(33)4 38 78 22 36; Fax: +(33)4 38 78 59 17;
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Alshaer W, Zureigat H, Al Karaki A, Al-Kadash A, Gharaibeh L, Hatmal MM, Aljabali AAA, Awidi A. siRNA: Mechanism of action, challenges, and therapeutic approaches. Eur J Pharmacol 2021; 905:174178. [PMID: 34044011 DOI: 10.1016/j.ejphar.2021.174178] [Citation(s) in RCA: 155] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 05/04/2021] [Accepted: 05/12/2021] [Indexed: 11/19/2022]
Abstract
Owing to specific and compelling gene silencing, RNA interference (RNAi) is expected to become an essential approach in treating a variety of infectious, hemato-oncological, cardiovascular, and neurodegenerative conditions. The mechanism of action of small interfering RNA (siRNA) is based on post-transcriptional gene silencing. siRNA molecules are usually specific and efficient in the knockdown of disease-related genes. However, they are characterized by low cellular uptake and are susceptible to nuclease-mediated degradation. Therefore, siRNAs require a carrier for their protection and efficient delivery into target cells. The current review highlights the siRNA-based mechanism of action, challanges, and recent advances in clinical applications.
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Affiliation(s)
- Walhan Alshaer
- Cell Therapy Center, The University of Jordan, Amman, 11942, Jordan.
| | - Hadil Zureigat
- Faculty of Medicine, The University of Jordan, Amman, 11942, Jordan
| | - Arwa Al Karaki
- Faculty of Medicine, The University of Jordan, Amman, 11942, Jordan
| | | | - Lobna Gharaibeh
- Faculty of Pharmacy, Al-Ahliyya Amman University, Amman, 19328, Jordan
| | - Ma'mon M Hatmal
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University, Zarqa 13133, Jordan
| | - Alaa A A Aljabali
- Faculty of Pharmacy, Department of Pharmaceutical Sciences, Yarmouk University, Irbid, 21163, Jordan
| | - Abdalla Awidi
- Cell Therapy Center, The University of Jordan, Amman, 11942, Jordan; Faculty of Medicine, The University of Jordan, Amman, 11942, Jordan; Department of Hematology and Oncology, Jordan University Hospital, The University of Jordan, Amman, 11942, Jordan.
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Ferguson CM, Echeverria D, Hassler M, Ly S, Khvorova A. Cell Type Impacts Accessibility of mRNA to Silencing by RNA Interference. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:384-393. [PMID: 32650236 PMCID: PMC7340969 DOI: 10.1016/j.omtn.2020.06.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/04/2020] [Accepted: 06/08/2020] [Indexed: 12/28/2022]
Abstract
RNA interference (RNAi) is a potent mechanism that silences mRNA and protein expression in all cells and tissue types. RNAi is known to exert many of its functional effects in the cytoplasm, and thus, the cellular localization of target mRNA may impact observed potency. Here, we demonstrate that cell identity has a profound impact on accessibility of apolipoprotein E (ApoE) mRNA to RNAi. We show that, whereas both neuronal and glial cell lines express detectable ApoE mRNA, in neuronal cells, ApoE mRNA is not targetable by RNAi. Screening of a panel of thirty-five chemically modified small interfering RNAs (siRNAs) did not produce a single hit in a neuronal cell line, whereas up to fifteen compounds showed strong efficacy in glial cells. Further investigation of the cellular localization of ApoE mRNA demonstrates that ApoE mRNA is partially spliced and preferentially localized to the nucleus (∼80%) in neuronal cells, whereas more than 90% of ApoE mRNA is cytoplasmic in glial cells. Such an inconsistency in intracellular localization and splicing might provide an explanation for functional differences in RNAi compounds. Thus, cellular origin might have an impact on accessibility of mRNA to RNAi and should be taken into account during the screening process.
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Affiliation(s)
- Chantal M Ferguson
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Matthew Hassler
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Socheata Ly
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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28
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Cristofolini T, Dalmina M, Sierra JA, Silva AH, Pasa AA, Pittella F, Creczynski-Pasa TB. Multifunctional hybrid nanoparticles as magnetic delivery systems for siRNA targeting the HER2 gene in breast cancer cells. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2019; 109:110555. [PMID: 32228895 DOI: 10.1016/j.msec.2019.110555] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/04/2019] [Accepted: 12/12/2019] [Indexed: 12/30/2022]
Abstract
Breast cancer is a major cause of death among women worldwide. Resistance to conventional therapies has been observed in HER2-positive breast cancer patients, indicating the need for more effective treatments. Small interfering RNA (siRNA) therapy is an attractive strategy against HER2-positive tumors, but its success depends largely on the efficient delivery of agents to target tissues. In this study, we prepared a magnetic hybrid nanostructure composed of iron oxide nanoparticles coated with caffeic acid and stabilized by layers of calcium phosphate and PEG-polyanion block copolymer for incorporation of siRNA. Transmission electron microscopy images showed monodisperse, neutrally charged compact spheres sized <100 nm. Dynamic light scattering and nanoparticle tracking analysis revealed that the nanostructure had an average hydrodynamic diameter of 130 nm. Nanoparticle suspensions remained stable over 42 days of storage at 4 and 25 °C. Unloaded caffeic acid-magnetic calcium phosphate (Caf-MCaP) nanoparticles were not cytotoxic, and loaded nanoparticles were successfully taken up by the HER2-positive breast cancer cell line HCC1954, even more so under magnetic guidance. Nanoparticles escaped endosomal degradation and delivered siRNA into the cytoplasm, inducing HER2 gene silencing.
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Affiliation(s)
- Tatiane Cristofolini
- GEIMM, Department of Pharmaceutical Sciences, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Milene Dalmina
- GEIMM, Department of Pharmaceutical Sciences, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Jelver A Sierra
- GEIMM, Department of Pharmaceutical Sciences, Federal University of Santa Catarina, Florianópolis, SC, Brazil; PGMAT, Department of Mechanical Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Adny H Silva
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - André A Pasa
- LFFS, Department of Physics, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Frederico Pittella
- GEIMM, Department of Pharmaceutical Sciences, Federal University of Santa Catarina, Florianópolis, SC, Brazil; Department of Pharmaceutical Sciences, Federal University of Juiz de Fora, Juiz de Fora, MG, Brazil
| | - Tânia B Creczynski-Pasa
- GEIMM, Department of Pharmaceutical Sciences, Federal University of Santa Catarina, Florianópolis, SC, Brazil.
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Russo E, Villa C. Poloxamer Hydrogels for Biomedical Applications. Pharmaceutics 2019; 11:E671. [PMID: 31835628 PMCID: PMC6955690 DOI: 10.3390/pharmaceutics11120671] [Citation(s) in RCA: 199] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/25/2019] [Accepted: 12/06/2019] [Indexed: 11/23/2022] Open
Abstract
This review article focuses on thermoresponsive hydrogels consisting of poloxamers which are of high interest for biomedical application especially in drug delivery for ophthalmic, injectable, transdermal, and vaginal administration. These hydrogels remain fluid at room temperature but become more viscous gel once they are exposed to body temperature. In this way, the gelling system remains at the topical level for a long time and the drug release is controlled and prolonged. Poloxamers are synthetic triblock copolymers of poly(ethylene oxide)-b-poly(propylene oxide)-b-poly(ethylene oxide) (PEO-PPO-PEO), also commercially known as Pluronics®, Synperonics® or Lutrol®. The different poloxamers cover a range of liquids, pastes, and solids, with molecular weights and ethylene oxide-propylene oxide weight ratios varying from 1100 to 14,000 and 1:9 to 8:2, respectively. Concentrated aqueous solutions of poloxamers form thermoreversible gels. In recent years this type of gel has arouse interest for tissue engineering. Finally, the use of poloxamers as biosurfactants is evaluated since they are able to form micelles in an aqueous environment above a concentration threshold known as critical micelle concentration (CMC). This property is exploited for drug delivery and different therapeutic applications.
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Affiliation(s)
- Eleonora Russo
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 16132 Genova, Italy;
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Bartoszewski R, Sikorski AF. Editorial focus: understanding off-target effects as the key to successful RNAi therapy. Cell Mol Biol Lett 2019; 24:69. [PMID: 31867046 PMCID: PMC6902517 DOI: 10.1186/s11658-019-0196-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/03/2019] [Indexed: 12/21/2022] Open
Abstract
With the first RNA interference (RNAi) drug (ONPATTRO (patisiran)) on the market, we witness the RNAi therapy field reaching a critical turning point, when further improvements in drug candidate design and delivery pipelines should enable fast delivery of novel life changing treatments to patients. Nevertheless, ignoring parallel development of RNAi dedicated in vitro pharmacological profiling aiming to identify undesirable off-target activity may slow down or halt progress in the RNAi field. Since academic research is currently fueling the RNAi development pipeline with new therapeutic options, the objective of this article is to briefly summarize the basics of RNAi therapy, as well as to discuss how to translate basic research into better understanding of related drug candidate safety profiles early in the process.
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Affiliation(s)
- Rafal Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Aleksander F. Sikorski
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
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Ryu J, Kwon DH, Choe N, Shin S, Jeong G, Lim YH, Kim J, Park WJ, Kook H, Kim YK. Characterization of Circular RNAs in Vascular Smooth Muscle Cells with Vascular Calcification. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 19:31-41. [PMID: 31790973 PMCID: PMC6909180 DOI: 10.1016/j.omtn.2019.11.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 10/09/2019] [Accepted: 11/05/2019] [Indexed: 02/06/2023]
Abstract
Circular RNAs (circRNAs) are generally formed by back splicing and are expressed in various cells. Vascular calcification (VC), a common complication of chronic kidney disease (CKD), is often associated with cardiovascular disease. The relationship between circRNAs and VC has not yet been studied. Inorganic phosphate (Pi) was used to treat rat vascular smooth muscle cells to induce VC. circRNAs were identified by analyzing RNA sequencing (RNA-seq) data, and their expression change during VC was validated. The selected circRNAs, including circSamd4a, circSmoc1-1, circMettl9, and circUxs1, were resistant to RNase R digestion and mostly localized in the cytoplasm. While silencing circSamd4a promoted VC, overexpressing it reduced VC in calcium assay and Alizarin red S (ARS) staining. In addition, microRNA (miRNA) microarray, luciferase reporter assay, and calcium assay suggested that circSamd4a could act as a miRNA suppressor. Our data show that circSamd4a has an anti-calcification role by functioning as a miRNA sponge. Moreover, mRNAs that can interact with miRNAs were predicted from RNA-seq and bioinformatics analysis, and the circSamd4a-miRNA-mRNA axis involved in VC was verified by luciferase reporter assay and calcium assay. Since circSamd4a is conserved in humans, it can serve as a novel therapeutic target in resolving VC.
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Affiliation(s)
- Juhee Ryu
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Jeollanam-do, Republic of Korea; Department of Biomedical Sciences, Center for Creative Biomedical Scientists at Chonnam National University, Jeollanam-do, Republic of Korea; Department of Biochemistry, Chonnam National University Medical School, Jeollanam-do, Republic of Korea; Department of Pharmacology, Chonnam National University Medical School, Jeollanam-do, Republic of Korea
| | - Duk-Hwa Kwon
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Jeollanam-do, Republic of Korea; Department of Pharmacology, Chonnam National University Medical School, Jeollanam-do, Republic of Korea
| | - Nakwon Choe
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Jeollanam-do, Republic of Korea; Department of Pharmacology, Chonnam National University Medical School, Jeollanam-do, Republic of Korea
| | - Sera Shin
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Jeollanam-do, Republic of Korea; Department of Pharmacology, Chonnam National University Medical School, Jeollanam-do, Republic of Korea
| | - Geon Jeong
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Jeollanam-do, Republic of Korea; Department of Biomedical Sciences, Center for Creative Biomedical Scientists at Chonnam National University, Jeollanam-do, Republic of Korea; Department of Biochemistry, Chonnam National University Medical School, Jeollanam-do, Republic of Korea
| | - Yeong-Hwan Lim
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Jeollanam-do, Republic of Korea; Department of Biomedical Sciences, Center for Creative Biomedical Scientists at Chonnam National University, Jeollanam-do, Republic of Korea; Department of Biochemistry, Chonnam National University Medical School, Jeollanam-do, Republic of Korea
| | - Jaetaek Kim
- Division of Endocrinology and Metabolism, Department of Internal Medicine, College of Medicine, Chung-Ang University, Seoul, Republic of Korea
| | - Woo Jin Park
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Jeollanam-do, Republic of Korea; College of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Hyun Kook
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Jeollanam-do, Republic of Korea; Department of Biomedical Sciences, Center for Creative Biomedical Scientists at Chonnam National University, Jeollanam-do, Republic of Korea; Department of Pharmacology, Chonnam National University Medical School, Jeollanam-do, Republic of Korea.
| | - Young-Kook Kim
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Jeollanam-do, Republic of Korea; Department of Biomedical Sciences, Center for Creative Biomedical Scientists at Chonnam National University, Jeollanam-do, Republic of Korea; Department of Biochemistry, Chonnam National University Medical School, Jeollanam-do, Republic of Korea.
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Abstract
The RNA interference (RNAi) pathway regulates mRNA stability and translation in nearly all human cells. Small double-stranded RNA molecules can efficiently trigger RNAi silencing of specific genes, but their therapeutic use has faced numerous challenges involving safety and potency. However, August 2018 marked a new era for the field, with the US Food and Drug Administration approving patisiran, the first RNAi-based drug. In this Review, we discuss key advances in the design and development of RNAi drugs leading up to this landmark achievement, the state of the current clinical pipeline and prospects for future advances, including novel RNAi pathway agents utilizing mechanisms beyond post-translational RNAi silencing.
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Titze-de-Almeida R, Titze-de-Almeida SS, Ferreira NR, Fontanari C, Faccioli LH, Del Bel E. Suppressing nNOS Enzyme by Small-Interfering RNAs Protects SH-SY5Y Cells and Nigral Dopaminergic Neurons from 6-OHDA Injury. Neurotox Res 2019; 36:117-131. [PMID: 31041676 DOI: 10.1007/s12640-019-00043-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/27/2019] [Accepted: 04/04/2019] [Indexed: 01/11/2023]
Abstract
Nitric oxide (NO) has chemical properties that make it uniquely suitable as an intracellular and intercellular messenger. NO is produced by the activity of the enzyme nitric oxide synthases (NOS). There is substantial and mounting evidence that slight abnormalities of NO may underlie a wide range of neurodegenerative disorders. NO participates of the oxidative stress and inflammatory processes that contribute to the progressive dopaminergic loss in Parkinson's disease (PD). The present study aimed to evaluate in vitro and in vivo the effects of neuronal NOS-targeted siRNAs on the injury caused in dopaminergic neurons by the toxin 6-hidroxydopamine (6-OHDA). First, we confirmed (immunohistochemistry and Western blotting) that SH-SY5Y cell lineage expresses the dopaminergic marker tyrosine hydroxylase (TH) and the protein under analysis, neuronal NOS (nNOS). We designed four siRNAs by using the BIOPREDsi algorithm choosing the one providing the highest knockdown of nNOS mRNA in SH-SY5Y cells, as determined by qPCR. siRNA 4400 carried by liposomes was internalized into cells, caused a concentration-dependent knockdown on nNOS, and reduced the toxicity induced by 6-OHDA (p < 0.05). Regarding in vivo action in the dopamine-depleted animals, intra-striatal injection of siRNA 4400 at 4 days prior 6-OHDA produced a decrease in the rotational behavior induced by apomorphine. Finally, siRNA 4400 mitigated the loss of TH(+) cells in substantia nigra dorsal and ventral part. In conclusion, the suppression of nNOS enzyme by targeted siRNAs modified the progressive death of dopaminergic cells induced by 6-OHDA and merits further pre-clinical investigations as a neuroprotective approach for PD.
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Affiliation(s)
- Ricardo Titze-de-Almeida
- Technology for Gene Therapy Laboratory, Central Institute of Sciences, University of Brasília-FAV, Brasília, DF, 70910-900, Brazil
| | - Simoneide S Titze-de-Almeida
- Technology for Gene Therapy Laboratory, Central Institute of Sciences, University of Brasília-FAV, Brasília, DF, 70910-900, Brazil
| | - Nadia Rubia Ferreira
- Department of Basic and Oral Biology, Dental School, University of São Paulo (USP), Ribeirão Preto, SP, 14040-904, Brazil
| | - Caroline Fontanari
- Department of Clinical Analyses, Toxicology and Bromatology, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, 14040-903, Brazil
| | - Lúcia Helena Faccioli
- Department of Clinical Analyses, Toxicology and Bromatology, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, 14040-903, Brazil
| | - Elaine Del Bel
- Department of Basic and Oral Biology, Dental School, University of São Paulo (USP), Ribeirão Preto, SP, 14040-904, Brazil.
- Center for Interdisciplinary Research on Applied Neurosciences (NAPNA), University of São Paulo (USP), São Paulo, SP, Brazil.
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Abstract
Small silencing RNAs have provided powerful reverse genetics tools and have opened new areas of research. This introduction describes the use of RNAi to suppress expression of individual genes for loss-of-function analysis. It also summarizes methods for measuring specific and global changes in small RNA expression, as well as methods to inhibit the function of individual endogenous small RNA species such as miRNAs.
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Homologs of Human Dengue-Resistance Genes, FKBP1B and ATCAY, Confer Antiviral Resistance in Aedes aegypti Mosquitoes. INSECTS 2019; 10:insects10020046. [PMID: 30717390 PMCID: PMC6409984 DOI: 10.3390/insects10020046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 01/26/2019] [Accepted: 01/29/2019] [Indexed: 02/06/2023]
Abstract
Dengue virus (DENV) is transmitted by mosquitoes and is a major public health concern. The study of innate mosquito defense mechanisms against DENV have revealed crucial roles for the Toll, Imd, JAK-STAT, and RNAi pathways in mediating DENV in the mosquito. Often overlooked in such studies is the role of intrinsic cellular defense mechanisms that we hypothesize to work in concert with the classical immune pathways to affect organismal defense. Our understanding of the molecular interaction of DENV with mosquito host cells is limited, and we propose to expand upon the recent results from a genome-scale, small interfering RNA (siRNA)-based study that identified mammalian host proteins associated with resistance to dengue/West Nile virus (DENV/WNV) infection. The study identified 22 human DENV/WNV resistance genes (DVR), and we hypothesized that a subset would be functionally conserved in Aedes aegypti mosquitoes, imparting cellular defense against flaviviruses in this species. We identified 12 homologs of 22 human DVR genes in the Ae. aegypti genome. To evaluate their possible role in cellular resistance/antiviral defense against DENV, we used siRNA silencing targeted against each of the 12 homologs in an Ae. aegypti cell line (Aag2) infected with DENV2 and identified that silencing of the two candidates, AeFKBP1 and AeATCAY, homologs of human FKBP1B and ATCAY, were associated with a viral increase. We then used dsRNA to silence each of the two genes in adult mosquitoes to validate the observed antiviral functions in vivo. Depletion of AeFKBP1 or AeATCAY increased viral dissemination through the mosquito at 14 days post-infection. Our results demonstrated that AeFKBP1 and AeATCAY mediate resistance to DENV akin to what has been described for their homologs in humans. AeFKBP1 and AeATCAY provide a rare opportunity to elucidate a DENV-resistance mechanism that may be evolutionarily conserved between humans and Ae. aegypti.
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Turanov AA, Lo A, Hassler MR, Makris A, Ashar-Patel A, Alterman JF, Coles AH, Haraszti RA, Roux L, Godinho BMDC, Echeverria D, Pears S, Iliopoulos J, Shanmugalingam R, Ogle R, Zsengeller ZK, Hennessy A, Karumanchi SA, Moore MJ, Khvorova A. RNAi modulation of placental sFLT1 for the treatment of preeclampsia. Nat Biotechnol 2018; 36:nbt.4297. [PMID: 30451990 PMCID: PMC6526074 DOI: 10.1038/nbt.4297] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 10/05/2018] [Indexed: 12/14/2022]
Abstract
Preeclampsia is a placentally induced hypertensive disorder of pregnancy that is associated with substantial morbidity and mortality to mothers and fetuses. Clinical manifestations of preterm preeclampsia result from excess circulating soluble vascular endothelial growth factor receptor FLT1 (sFLT1 or sVEGFR1) of placental origin. Here we identify short interfering RNAs (siRNAs) that selectively silence the three sFLT1 mRNA isoforms primarily responsible for placental overexpression of sFLT1 without reducing levels of full-length FLT1 mRNA. Full chemical stabilization in the context of hydrophobic modifications enabled productive siRNA accumulation in the placenta (up to 7% of injected dose) and reduced circulating sFLT1 in pregnant mice (up to 50%). In a baboon preeclampsia model, a single dose of siRNAs suppressed sFLT1 overexpression and clinical signs of preeclampsia. Our results demonstrate RNAi-based extrahepatic modulation of gene expression with nonformulated siRNAs in nonhuman primates and establish a path toward a new treatment paradigm for patients with preterm preeclampsia.
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Affiliation(s)
- Anton A Turanov
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Agnes Lo
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Matthew R Hassler
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Angela Makris
- Heart Research Institute, Sydney, New South Wales, Australia
- School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- Renal Department, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Ami Ashar-Patel
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Julia F Alterman
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Andrew H Coles
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Reka A Haraszti
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Loic Roux
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Bruno M D C Godinho
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Suzanne Pears
- Heart Research Institute, Sydney, New South Wales, Australia
| | - Jim Iliopoulos
- School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
| | - Renuka Shanmugalingam
- Heart Research Institute, Sydney, New South Wales, Australia
- School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- Renal Department, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Robert Ogle
- Women's and Babies, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Zsuzsanna K Zsengeller
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Annemarie Hennessy
- Heart Research Institute, Sydney, New South Wales, Australia
- School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
| | - S Ananth Karumanchi
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Melissa J Moore
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Moderna Therapeutics, Cambridge, Massachusetts, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
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To accelerate the Zika beat: Candidate design for RNA interference-based therapy. Virus Res 2018; 255:133-140. [DOI: 10.1016/j.virusres.2018.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/11/2018] [Accepted: 07/17/2018] [Indexed: 12/12/2022]
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Gatta AK, Hariharapura RC, Udupa N, Reddy MS, Josyula VR. Strategies for improving the specificity of siRNAs for enhanced therapeutic potential. Expert Opin Drug Discov 2018; 13:709-725. [PMID: 29902093 DOI: 10.1080/17460441.2018.1480607] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION RNA interference has become a tool of choice in the development of drugs in various therapeutic areas of Post Transcriptional Gene Silencing (PTGS). The critical element in developing successful RNAi therapeutics lies in designing small interfering RNA (siRNA) using an efficient algorithm satisfying the designing criteria. Further, translation of siRNA from bench-side to bedside needs an efficient delivery system and/or chemical modification. Areas covered: This review emphasizes the importance of dicer, the criteria for efficient siRNA design, the currently available algorithms and strategies to overcome off-target effects, immune stimulatory effects and endosomal trap. Expert opinion: Specificity and stability are the primary concerns for siRNA therapeutics. The design criteria and algorithms should be chosen rationally to have a siRNA sequence that binds to the corresponding mRNA as it happens in the Watson and Crick base pairing. However, it must evade a few more hurdles (Endocytosis, Serum stability etc.) to be functional in the cytosol.
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Affiliation(s)
- Aditya Kiran Gatta
- a Cell and Molecular Biology lab, Department of Pharmaceutical Biotechnology , Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education , Manipal , Karnataka , India
| | - Raghu Chandrashekhar Hariharapura
- a Cell and Molecular Biology lab, Department of Pharmaceutical Biotechnology , Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education , Manipal , Karnataka , India
| | - Nayanabhirama Udupa
- b Research Directorate of Health Sciences , Manipal Academy of Higher Education , Manipal , Karnataka , India
| | - Meka Sreenivasa Reddy
- c Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences , Manipal Academy of Higher Education , Manipal , Karnataka , India
| | - Venkata Rao Josyula
- a Cell and Molecular Biology lab, Department of Pharmaceutical Biotechnology , Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education , Manipal , Karnataka , India
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RNA interference technology to improve the baculovirus-insect cell expression system. Biotechnol Adv 2018; 36:443-451. [DOI: 10.1016/j.biotechadv.2018.01.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 12/11/2017] [Accepted: 01/13/2018] [Indexed: 02/02/2023]
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Seok H, Lee H, Jang ES, Chi SW. Evaluation and control of miRNA-like off-target repression for RNA interference. Cell Mol Life Sci 2018; 75:797-814. [PMID: 28905147 PMCID: PMC11105550 DOI: 10.1007/s00018-017-2656-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 09/06/2017] [Accepted: 09/07/2017] [Indexed: 01/08/2023]
Abstract
RNA interference (RNAi) has been widely adopted to repress specific gene expression and is easily achieved by designing small interfering RNAs (siRNAs) with perfect sequence complementarity to the intended target mRNAs. Although siRNAs direct Argonaute (Ago), a core component of the RNA-induced silencing complex (RISC), to recognize and silence target mRNAs, they also inevitably function as microRNAs (miRNAs) and suppress hundreds of off-targets. Such miRNA-like off-target repression is potentially detrimental, resulting in unwanted toxicity and phenotypes. Despite early recognition of the severity of miRNA-like off-target repression, this effect has often been overlooked because of difficulties in recognizing and avoiding off-targets. However, recent advances in genome-wide methods and knowledge of Ago-miRNA target interactions have set the stage for properly evaluating and controlling miRNA-like off-target repression. Here, we describe the intrinsic problems of miRNA-like off-target effects caused by canonical and noncanonical interactions. We particularly focus on various genome-wide approaches and chemical modifications for the evaluation and prevention of off-target repression to facilitate the use of RNAi with secured specificity.
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Affiliation(s)
- Heeyoung Seok
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea
| | - Haejeong Lee
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea
| | - Eun-Sook Jang
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea
- EncodeGEN Co. Ltd, Seoul, 06329, Korea
| | - Sung Wook Chi
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea.
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Roderick H, Urwin PE, Atkinson HJ. Rational design of biosafe crop resistance to a range of nematodes using RNA interference. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:520-529. [PMID: 28703405 PMCID: PMC5787825 DOI: 10.1111/pbi.12792] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 07/05/2017] [Accepted: 07/05/2017] [Indexed: 05/31/2023]
Abstract
Double-stranded RNA (dsRNA) molecules targeting two genes have been identified that suppress economically important parasitic nematode species of banana. Proteasomal alpha subunit 4 (pas-4) and Actin-4 (act-4) were identified from a survey of sequence databases and cloned sequences for genes conserved across four pests of banana, Radopholus similis, Pratylenchus coffeae, Meloidogyne incognita and Helicotylenchus multicinctus. These four species were targeted with dsRNAs containing exact 21 nucleotide matches to the conserved regions. Potential off-target effects were limited by comparison with Caenorhabditis, Drosophila, rat, rice and Arabidopsis genomes. In vitro act-4 dsRNA treatment of R. similis suppressed target gene expression by 2.3-fold, nematode locomotion by 66 ± 4% and nematode multiplication on carrot discs by 49 ± 5%. The best transgenic carrot hairy root lines expressing act-4 or pas-4 dsRNA reduced transcript message abundance of target genes in R. similis by 7.9-fold and fourfold and nematode multiplication by 94 ± 2% and 69 ± 3%, respectively. The same act-4 and pas-4 lines reduced P. coffeae target transcripts by 1.7- and twofold and multiplication by 50 ± 6% and 73 ± 8%. Multiplication of M. incognita on the pas-4 lines was reduced by 97 ± 1% and 99 ± 1% while target transcript abundance was suppressed 4.9- and 5.6-fold. There was no detectable RNAi effect on nontarget nematodes exposed to dsRNAs targeting parasitic nematodes. This work defines a framework for development of a range of nonprotein defences to provide broad resistance to pests and pathogens of crops.
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Park J, Ahn SH, Cho KM, Gu D, Jang ES, Chi SW. siAbasic: a comprehensive database for potent siRNA-6Ø sequences without off-target effects. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:5122757. [PMID: 30321353 PMCID: PMC6183071 DOI: 10.1093/database/bay109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 09/24/2018] [Indexed: 11/15/2022]
Abstract
Small interfering RNA (siRNA) is widely used to specifically silence target gene expression, but its microRNA (miRNA)-like function inevitably suppresses hundreds of off-targets. Recently, complete elimination of the off-target repression has been achieved by introducing an abasic nucleotide to the pivot (position 6; siRNA-6Ø), of which impaired base pairing destabilizes transitional nucleation (positions 2–6). However, siRNA-6Ø varied in its conservation of on-target activity (∼80–100%), demanding bioinformatics to discover the principles underlying its on-target efficiency. Analyses of miRNA–target interactions (Ago HITS-CLIP) showed that the stability of transitional nucleation correlated with the target affinity of RNA interference. Furthermore, interrogated analyses of siRNA screening efficiency, experimental data and broadly conserved miRNA sequences showed that the free energy of transitional nucleation (positions 2–5) in siRNA-6Ø required the range of stability for effective on-target activity (−6 ≤ ΔG[2:5] ≤ −3.5 kcal mol−1). Taking into consideration of these features together with locations, guanine-cytosine content (GC content), nucleotide stretches, single nucleotide polymorphisms and repetitive elements, we implemented a database named ‘siAbasic’ that provided the list of potent siRNA-6Ø sequences for most of human and mouse genes (≥ ∼95%), wherein we experimentally validated some of their therapeutic potency. siAbasic will aid to ensure potency of siRNA-6Ø sequences without concerning off-target effects for experimental and clinical purposes.
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Affiliation(s)
- Jongyeun Park
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Seung Hyun Ahn
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Kwang Moon Cho
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Dowoon Gu
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Eun-Sook Jang
- Department of Life Sciences, Korea University, Seoul, Korea.,EncodeGEN Co. Ltd., Seoul, Korea
| | - Sung Wook Chi
- Department of Life Sciences, Korea University, Seoul, Korea
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Abstract
RNA interference (RNAi) is a biological process by which double-stranded RNA (dsRNA) induces sequence-specific gene silencing by targeting mRNA for degradation. As a tool for knocking down the expression of individual genes posttranscriptionally, RNAi has been widely used to study the cellular function of genes. In this chapter, I describe procedures for using gene-specific, synthetic, short interfering RNA (siRNA) to induce gene silencing in mammalian cells. Protocols for using lipid-based transfection reagents and electroporation techniques are provided. Potential challenges and problems associated with the siRNA technology are also discussed.
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Affiliation(s)
- Haiyong Han
- Translational Genomics Research Institute, 445. N. Fifth St., Suite 400, Phoenix, AZ, 85004, USA.
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44
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Safari F, Rahmani Barouji S, Tamaddon AM. Strategies for Improving siRNA-Induced Gene Silencing Efficiency. Adv Pharm Bull 2017; 7:603-609. [PMID: 29399550 PMCID: PMC5788215 DOI: 10.15171/apb.2017.072] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/24/2017] [Accepted: 10/25/2017] [Indexed: 11/29/2022] Open
Abstract
Purpose: Human telomerase reverse transcriptase (hTERT)
plays a crucial role in tumorigenesis and progression of cancers. Gene silencing of hTERT
by short interfering RNA (siRNA) is considered as a promising strategy for cancer gene
therapy. Various algorithms have been devised for designing a high efficient siRNA which
is a significant issue in the clinical usage. Thereby, in the present study, the relation
of siRNA designing criteria and the gene silencing efficiency was evaluated. Methods: The siRNA sequences were designed and
characterized by using on line soft wares. Cationic co-polymer (polyethylene
glycol-g-polyethylene imine (PEG-g-PEI)) was used for the construction of polyelectrolyte
complexes (PECs) containing siRNAs. The cellular uptake of the PECs was evaluated. The
gene silencing efficiency of different siRNA sequences was investigated and the effect of
observing the rational designing on the functionality of siRNAs was assessed. Results: The size of PEG-g-PEI siRNA with N/P
(Nitrogen/Phosphate) ratio of 2.5 was 114 ± 0.645 nm. The transfection efficiency of PECs
was desirable (95.5% ± 2.4%.). The results of Real-Time PCR showed that main sequence (MS)
reduced the hTERT expression up to 90% and control positive sequence (CPS) up to 63%.
These findings demonstrated that the accessibility to the target site has priority than
the other criteria such as sequence preferences and thermodynamic features. Conclusion: siRNA opens a hopeful window in cancer therapy
which provides a convenient and tolerable therapeutic approach. Thereby, using the set of
criteria and rational algorithms in the designing of siRNA remarkably affect the gene
silencing efficiency.
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Affiliation(s)
- Fatemeh Safari
- Medical Biotechnology Department, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.,Shiraz University of Medical Sciences, Shiraz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Solmaz Rahmani Barouji
- Department of Traditional Medicine, Faculty of Traditional Medicine, University of Medical Sciences, Tabriz, Iran
| | - Ali Mohammad Tamaddon
- Center for Pharmaceutical Nanotechnology and Biomaterials, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
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Mohanta TK, Bashir T, Hashem A, Abd Allah EF, Bae H. Genome Editing Tools in Plants. Genes (Basel) 2017; 8:E399. [PMID: 29257124 PMCID: PMC5748717 DOI: 10.3390/genes8120399] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/08/2017] [Accepted: 12/15/2017] [Indexed: 12/23/2022] Open
Abstract
Genome editing tools have the potential to change the genomic architecture of a genome at precise locations, with desired accuracy. These tools have been efficiently used for trait discovery and for the generation of plants with high crop yields and resistance to biotic and abiotic stresses. Due to complex genomic architecture, it is challenging to edit all of the genes/genomes using a particular genome editing tool. Therefore, to overcome this challenging task, several genome editing tools have been developed to facilitate efficient genome editing. Some of the major genome editing tools used to edit plant genomes are: Homologous recombination (HR), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), pentatricopeptide repeat proteins (PPRs), the CRISPR/Cas9 system, RNA interference (RNAi), cisgenesis, and intragenesis. In addition, site-directed sequence editing and oligonucleotide-directed mutagenesis have the potential to edit the genome at the single-nucleotide level. Recently, adenine base editors (ABEs) have been developed to mutate A-T base pairs to G-C base pairs. ABEs use deoxyadeninedeaminase (TadA) with catalytically impaired Cas9 nickase to mutate A-T base pairs to G-C base pairs.
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Affiliation(s)
| | - Tufail Bashir
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea.
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
- Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, Agriculture Research Center, Giza 12619, Egypt.
| | - Elsayed Fathi Abd Allah
- Plant Production Department, College of Food and Agriculture Science, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Hanhong Bae
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea.
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Inability of DNAzymes to cleave RNA in vivo is due to limited Mg[Formula: see text] concentration in cells. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 47:333-343. [PMID: 29248953 DOI: 10.1007/s00249-017-1270-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 11/18/2017] [Indexed: 10/18/2022]
Abstract
Sequence specific cleavage of RNA can be achieved by hammerhead ribozymes as well as DNAzymes. They comprise a catalytic core sequence flanked by regions that form double strands with complementary RNA. While different types of ribozymes have been discovered in natural organisms, DNAzymes derive from in vitro selection. Both have been used for therapeutic down-regulation of harmful proteins by reducing drastically the corresponding mRNA concentration. A priori DNAzymes appear advantageous because of the higher haemolytic stability and better cost effectiveness when compared to RNA. In the present work the 10-23 DNAzyme was applied to knockdown expression of the prion protein (PrP), the sole causative agent of transmissible spongiform encephalopathies. We selected accessible target sequences on the PrP mRNA based on a sequential folding algorithm. Very high effectivity of DNAzymes was found for cleavage of RNA in vitro, but activity in neuroblastoma cells was very low. However, siRNA directed to the identical target sequences reduced expression of PrP in the same cell type. According to our analysis, three Mg[Formula: see text] bind cooperatively to the DNAzyme to exert full activity. However, free ATP binds the Mg[Formula: see text] ions more strongly and already stoichiometric amounts of Mg[Formula: see text] and ATP inhibited the activity of DNAzymes drastically. In contrast, natural ribozymes form three-dimensional structures close to the cleavage site that stabilize the active conformation at much lower Mg[Formula: see text] concentrations. For DNAzymes, however, a similar stabilization is not known and therefore DNAzymes need higher free Mg[Formula: see text] concentrations than that available inside the cell.
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Shaifta Y, MacKay CE, Irechukwu N, O'Brien KA, Wright DB, Ward JPT, Knock GA. Transforming growth factor-β enhances Rho-kinase activity and contraction in airway smooth muscle via the nucleotide exchange factor ARHGEF1. J Physiol 2017; 596:47-66. [PMID: 29071730 PMCID: PMC5746525 DOI: 10.1113/jp275033] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 10/19/2017] [Indexed: 01/16/2023] Open
Abstract
Key points Transforming growth‐factor‐β (TGF‐β) and RhoA/Rho‐kinase are independently implicated in the airway hyper‐responsiveness associated with asthma, but how these proteins interact is not fully understood. We examined the effects of pre‐treatment with TGF‐β on expression and activity of RhoA, Rho‐kinase and ARHGEF1, an activator of RhoA, as well as on bradykinin‐induced contraction, in airway smooth muscle. TGF‐β enhanced bradykinin‐induced RhoA translocation, Rho‐kinase‐dependent phosphorylation and contraction, but partially suppressed bradykinin‐induced RhoA activity (RhoA‐GTP content). TGF‐β enhanced the expression of ARHGEF1, while a small interfering RNA against ARHGEF1 and a RhoGEF inhibitor prevented the effects of TGF‐β on RhoA and Rho‐kinase activity and contraction, respectively. ARHGEF1 expression was also enhanced in airway smooth muscle from asthmatic patients and ovalbumin‐sensitized mice. ARHGEF1 is a key TGF‐β target gene, an important regulator of Rho‐kinase activity and therefore a potential therapeutic target for the treatment of asthmatic airway hyper‐responsiveness.
Abstract Transforming growth factor‐β (TGF‐β), RhoA/Rho‐kinase and Src‐family kinases (SrcFK) have independently been implicated in airway hyper‐responsiveness, but how they interact to regulate airway smooth muscle contractility is not fully understood. We found that TGF‐β pre‐treatment enhanced acute contractile responses to bradykinin (BK) in isolated rat bronchioles, and inhibitors of RhoGEFs (Y16) and Rho‐kinase (Y27632), but not the SrcFK inhibitor PP2, prevented this enhancement. In cultured human airway smooth muscle cells (hASMCs), TGF‐β pre‐treatment enhanced the protein expression of the Rho guanine nucleotide exchange factor ARHGEF1, MLC20, MYPT‐1 and the actin‐severing protein cofilin, but not of RhoA, ROCK2 or c‐Src. In hASMCs, acute treatment with BK triggered subcellular translocation of ARHGEF1 and RhoA and enhanced auto‐phosphorylation of SrcFK and phosphorylation of MYPT1 and MLC20, but induced de‐phosphorylation of cofilin. TGF‐β pre‐treatment amplified the effects of BK on RhoA translocation and MYPT1/MLC20 phosphorylation, but suppressed the effects of BK on RhoA‐GTP content, SrcFK auto‐phosphorylation and cofilin de‐phosphorylation. In hASMCs, an ARHGEF1 small interfering RNA suppressed the effects of BK and TGF‐β on RhoA‐GTP content, RhoA translocation and MYPT1 and MLC20 phosphorylation, but minimally influenced the effects of TGF‐β on cofilin expression and phosphorylation. ARHGEF1 expression was also enhanced in ASMCs of asthmatic patients and in lungs of ovalbumin‐sensitized mice. Our data indicate that TGF‐β enhances BK‐induced contraction, RhoA translocation and Rho‐kinase activity in airway smooth muscle largely via ARHGEF1, but independently of SrcFK and total RhoA‐GTP content. A role for smooth muscle ARHGEF1 in asthmatic airway hyper‐responsiveness is worthy of further investigation. Transforming growth‐factor‐β (TGF‐β) and RhoA/Rho‐kinase are independently implicated in the airway hyper‐responsiveness associated with asthma, but how these proteins interact is not fully understood. We examined the effects of pre‐treatment with TGF‐β on expression and activity of RhoA, Rho‐kinase and ARHGEF1, an activator of RhoA, as well as on bradykinin‐induced contraction, in airway smooth muscle. TGF‐β enhanced bradykinin‐induced RhoA translocation, Rho‐kinase‐dependent phosphorylation and contraction, but partially suppressed bradykinin‐induced RhoA activity (RhoA‐GTP content). TGF‐β enhanced the expression of ARHGEF1, while a small interfering RNA against ARHGEF1 and a RhoGEF inhibitor prevented the effects of TGF‐β on RhoA and Rho‐kinase activity and contraction, respectively. ARHGEF1 expression was also enhanced in airway smooth muscle from asthmatic patients and ovalbumin‐sensitized mice. ARHGEF1 is a key TGF‐β target gene, an important regulator of Rho‐kinase activity and therefore a potential therapeutic target for the treatment of asthmatic airway hyper‐responsiveness.
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Affiliation(s)
- Yasin Shaifta
- Division of Asthma, Allergy and Lung Biology, Faculty of Life Sciences and Medicine, King's College London, London, SE1 1UL, UK
| | - Charles E MacKay
- Division of Asthma, Allergy and Lung Biology, Faculty of Life Sciences and Medicine, King's College London, London, SE1 1UL, UK
| | - Nneka Irechukwu
- Division of Asthma, Allergy and Lung Biology, Faculty of Life Sciences and Medicine, King's College London, London, SE1 1UL, UK
| | - Katie A O'Brien
- Division of Asthma, Allergy and Lung Biology, Faculty of Life Sciences and Medicine, King's College London, London, SE1 1UL, UK
| | - David B Wright
- Division of Asthma, Allergy and Lung Biology, Faculty of Life Sciences and Medicine, King's College London, London, SE1 1UL, UK
| | - Jeremy P T Ward
- Division of Asthma, Allergy and Lung Biology, Faculty of Life Sciences and Medicine, King's College London, London, SE1 1UL, UK
| | - Greg A Knock
- Division of Asthma, Allergy and Lung Biology, Faculty of Life Sciences and Medicine, King's College London, London, SE1 1UL, UK
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Lu M, Xing H, Xun Z, Yang T, Ding P, Cai C, Wang D, Zhao X. Exosome-based small RNA delivery: Progress and prospects. Asian J Pharm Sci 2017; 13:1-11. [PMID: 32104373 PMCID: PMC7032220 DOI: 10.1016/j.ajps.2017.07.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/14/2017] [Accepted: 07/28/2017] [Indexed: 12/29/2022] Open
Abstract
RNA interfering (RNAi), mediated by small interfering RNAs and microRNAs, is currently one of the most promising tools of gene therapy. Small RNAs are capable of inducing specific post-transcriptional gene silencing, providing a potentially effective platform for the treatment of a wide array of diseases. However, similar to other nucleic acid-based drugs, the major hurdle of RNAi therapy is lack of efficient and non-immunogenic delivery vehicles. Currently, viruses, synthetic polymers, and lipid-based carriers are among the most widely studied vehicles for small RNA delivery. However, many drawbacks are reported to be associated with these delivery vehicles. There is a pressing need to replace them with more efficient and better-tolerated approaches. Exosomes secreted from the endocytic compartment of live cells, are a subtype of endogenous extracellular vesicles that transfer genetic and biochemical information among different cells, thus playing an important role in cell-cell communication. Recently, accumulating attention has been focused on harnessing exosomes as nanaocarriers for small RNAs delivery. Due to their natural role in shuttling endogenous nucleic acid in our body, exosomes may exhibit higher delivery efficiency, lower immunogenicity, and better compatibility than existing foreign RNA carriers. Importantly, exosomes own intrinsic homing capacity that can guide small RNAs across natural membranous barriers. Moreover, such a capacity can be further improved by adding appropriate targeting moieties. In this manuscript, we briefly review the progress and challenges of RNAi therapy, and discuss the potential of exosomes' applications in small RNA delivery with focus on the most recent advances in exosome-based small RNA delivery for disease therapy.
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Affiliation(s)
- Mei Lu
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, China
| | - Haonan Xing
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, China
| | - Zhe Xun
- Institute of Metabolic Disease Research and Drug Development, China Medical University, Shenyang, China
| | - Tianzhi Yang
- Department of Basic Pharmaceutical Sciences, School of Pharmacy, Husson University, Bangor, ME, USA
| | - Pingtian Ding
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, China
| | - Cuifang Cai
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, China
| | - Dongkai Wang
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, China
| | - Xiaoyun Zhao
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, China
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49
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Haraszti RA, Roux L, Coles AH, Turanov AA, Alterman JF, Echeverria D, Godinho BM, Aronin N, Khvorova A. 5΄-Vinylphosphonate improves tissue accumulation and efficacy of conjugated siRNAs in vivo. Nucleic Acids Res 2017; 45:7581-7592. [PMID: 28591791 PMCID: PMC5570069 DOI: 10.1093/nar/gkx507] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 05/23/2017] [Accepted: 05/31/2017] [Indexed: 12/20/2022] Open
Abstract
5΄-Vinylphosphonate modification of siRNAs protects them from phosphatases, and improves silencing activity. Here, we show that 5΄-vinylphosphonate confers novel properties to siRNAs. Specifically, 5΄-vinylphosphonate (i) increases siRNA accumulation in tissues, (ii) extends duration of silencing in multiple organs and (iii) protects siRNAs from 5΄-to-3΄ exonucleases. Delivery of conjugated siRNAs requires extensive chemical modifications to achieve stability in vivo. Because chemically modified siRNAs are poor substrates for phosphorylation by kinases, and 5΄-phosphate is required for loading into RNA-induced silencing complex, the synthetic addition of a 5΄-phosphate on a fully modified siRNA guide strand is expected to be beneficial. Here, we show that synthetic phosphorylation of fully modified cholesterol-conjugated siRNAs increases their potency and efficacy in vitro, but when delivered systemically to mice, the 5΄-phosphate is removed within 2 hours. The 5΄-phosphate mimic 5΄-(E)-vinylphosphonate stabilizes the 5΄ end of the guide strand by protecting it from phosphatases and 5΄-to-3΄ exonucleases. The improved stability increases guide strand accumulation and retention in tissues, which significantly enhances the efficacy of cholesterol-conjugated siRNAs and the duration of silencing in vivo. Moreover, we show that 5΄-(E)-vinylphosphonate stabilizes 5΄ phosphate, thereby enabling systemic delivery to and silencing in kidney and heart.
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Affiliation(s)
- Reka A. Haraszti
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Loic Roux
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Andrew H. Coles
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Anton A. Turanov
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Julia F. Alterman
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Bruno M.D.C. Godinho
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Department of Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
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50
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Hagedorn PH, Hansen BR, Koch T, Lindow M. Managing the sequence-specificity of antisense oligonucleotides in drug discovery. Nucleic Acids Res 2017; 45:2262-2282. [PMID: 28426096 PMCID: PMC5389529 DOI: 10.1093/nar/gkx056] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 01/21/2017] [Indexed: 01/06/2023] Open
Abstract
All drugs perturb the expression of many genes in the cells that are exposed to them. These gene expression changes can be divided into effects resulting from engaging the intended target and effects resulting from engaging unintended targets. For antisense oligonucleotides, developments in bioinformatics algorithms, and the quality of sequence databases, allow oligonucleotide sequences to be analyzed computationally, in terms of the predictability of their interactions with intended and unintended RNA targets. Applying these tools enables selection of sequence-specific oligonucleotides where no- or only few unintended RNA targets are expected. To evaluate oligonucleotide sequence-specificity experimentally, we recommend a transcriptomics protocol where two or more oligonucleotides targeting the same RNA molecule, but with entirely different sequences, are evaluated together. This helps to clarify which changes in cellular RNA levels result from downstream processes of engaging the intended target, and which are likely to be related to engaging unintended targets. As required for all classes of drugs, the toxic potential of oligonucleotides must be evaluated in cell- and animal models before clinical testing. Since potential adverse effects related to unintended targeting are sequence-dependent and therefore species-specific, in vitro toxicology assays in human cells are especially relevant in oligonucleotide drug discovery.
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Affiliation(s)
- Peter H Hagedorn
- Roche Pharmaceutical Discovery and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, Hørsholm 2970, Denmark.,Center for Computational and Applied Transcriptomics, Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
| | - Bo R Hansen
- Roche Pharmaceutical Discovery and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, Hørsholm 2970, Denmark
| | - Troels Koch
- Roche Pharmaceutical Discovery and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, Hørsholm 2970, Denmark
| | - Morten Lindow
- Roche Pharmaceutical Discovery and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, Hørsholm 2970, Denmark.,Center for Computational and Applied Transcriptomics, Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark.,The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
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