1
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Bhatnagar D, Ladhe S, Kumar D. Discerning the Prospects of miRNAs as a Multi-Target Therapeutic and Diagnostic for Alzheimer's Disease. Mol Neurobiol 2023; 60:5954-5974. [PMID: 37386272 DOI: 10.1007/s12035-023-03446-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/14/2023] [Indexed: 07/01/2023]
Abstract
Although over the last few decades, numerous attempts have been made to halt Alzheimer's disease (AD) progression and mitigate its symptoms, only a few have been proven beneficial. Most medications available, still only cater to the symptoms of the disease rather than fixing the cause at the root level. A novel approach involving the use of miRNAs, which work on the principle of gene silencing, is being explored by scientists. Naturally present miRNAs in the biological system help to regulate various genes than may be implicated in AD-like BACE-1 and APP. One miRNA thus, holds the power to keep a check on several genes, conferring it the ability to be used as a multi-target therapeutic. With aging and the onset of diseased pathology, dysregulation of these miRNAs is observed. This flawed miRNA expression is responsible for the unusual buildup of amyloid proteins, fibrillation of tau proteins in the brain, neuronal death and other hallmarks leading to AD. The use of miRNA mimics and miRNA inhibitors provides an attractive perspective for fixing the upregulation and downregulation of miRNAs that led to abnormal cellular activities. Furthermore, the detection of miRNAs in the CSF and serum of diseased patients might be considered an earlier biomarker for the disease. While most of the therapies designed around AD have not succeeded completely, the targeting of dysregulated miRNAs in AD patients might give a new direction to scholars to develop an effective treatment for Alzheimer's disease.
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Affiliation(s)
- Devyani Bhatnagar
- Department of Pharmaceutical Chemistry, Poona College of Pharmacy, Bharati Vidyapeeth (Deemed to Be University), Erandwane, Pune, 411038, Maharashtra, India
| | - Shreya Ladhe
- Department of Pharmaceutical Chemistry, Poona College of Pharmacy, Bharati Vidyapeeth (Deemed to Be University), Erandwane, Pune, 411038, Maharashtra, India
| | - Dileep Kumar
- Department of Pharmaceutical Chemistry, Poona College of Pharmacy, Bharati Vidyapeeth (Deemed to Be University), Erandwane, Pune, 411038, Maharashtra, India.
- Department of Entomology, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA.
- UC Davis Comprehensive Cancer Center, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA.
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2
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Pang HH, Huang CY, Chen PY, Li NS, Hsu YP, Wu JK, Fan HF, Wei KC, Yang HW. Bioengineered Bacteriophage-Like Nanoparticles as RNAi Therapeutics to Enhance Radiotherapy against Glioblastomas. ACS NANO 2023; 17:10407-10422. [PMID: 37120837 DOI: 10.1021/acsnano.3c01102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Since glioblastomas (GBMs) are radioresistant malignancies and most GBM recurrences occur in radiotherapy, increasing the effectiveness of radiotherapy by gene-silencing has recently attracted attention. However, the difficulty in precisely tuning the composition and RNA loading in nanoparticles leads to batch-to-batch variations of the RNA therapeutics, thus significantly restricting their clinical translation. Here, we bioengineer bacteriophage Qβ particles with a designed broccoli light-up three-way junction (b-3WJ) RNA scaffold (contains two siRNA/miRNA sequences and one light-up aptamer) packaging for the silencing of genes in radioresistant GBM cells. The in vitro results demonstrate that the cleavage of de novo designed b-3WJ RNA by Dicer enzyme can be easily monitored in real-time using fluorescence microscopy, and the TrQβ@b-3WJLet-7gsiEGFR successfully knocks down EGFR and IKKα simultaneously and thereby inactivates NF-κB signaling to inhibit DNA repair. Delivery of TrQβ@b-3WJLet-7gsiEGFR through convection-enhanced delivery (CED) infusion followed by 2Gy X-ray irradiation demonstrated that the median survival was prolonged to over 60 days compared with the 2Gy X-ray irradiated group (median survival: 31 days). Altogether, the results of this study could be critical for the design of RNAi-based genetic therapeutics, and CED infusion serves as a powerful delivery system for promoting radiotherapy against GBMs without evidence of systemic toxicity.
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Affiliation(s)
- Hao-Han Pang
- Department of Biomedical Engineering, National Cheng Kung University, No. 1, University Rd., Tainan 70101, Taiwan
| | - Chiung-Yin Huang
- Department of Neurosurgery, Neuroscience Research Center, Chang Gung Memorial Hospital, Linkou, 5 Fuxing St., Guishan Dist., Taoyuan 33305, Taiwan
| | - Pin-Yuan Chen
- Department of Neurosurgery, Neuroscience Research Center, Chang Gung Memorial Hospital, Linkou, 5 Fuxing St., Guishan Dist., Taoyuan 33305, Taiwan
- School of Medicine, Chang Gung University, 259 Wenhua 1st Rd., Guishan Dist., Taoyuan 33302, Taiwan
- Department of Neurosurgery, Chang Gung Memorial Hospital, Keelung, 222 Maijin Rd., Keelung 20401, Taiwan
| | - Nan-Si Li
- Department of Biomedical Engineering, National Cheng Kung University, No. 1, University Rd., Tainan 70101, Taiwan
| | - Ying-Pei Hsu
- Department of Biomedical Engineering, National Cheng Kung University, No. 1, University Rd., Tainan 70101, Taiwan
- Department of Materials and Optoelectronic Science, National Sun Yat-sen University, 70 Lienhai Rd., Kaohsiung 80424, Taiwan
| | - Jan-Kai Wu
- Department of Chemistry, National Sun Yat-sen University, 70 Lienhai Rd., Kaohsiung 80424, Taiwan
| | - Hsiu-Fang Fan
- Department of Chemistry, National Sun Yat-sen University, 70 Lienhai Rd., Kaohsiung 80424, Taiwan
- Institute of Medical Science and Technology, National Sun Yat-sen University, 70 Lienhai Rd., Kaohsiung 80424, Taiwan
| | - Kuo-Chen Wei
- Department of Neurosurgery, Neuroscience Research Center, Chang Gung Memorial Hospital, Linkou, 5 Fuxing St., Guishan Dist., Taoyuan 33305, Taiwan
- School of Medicine, Chang Gung University, 259 Wenhua 1st Rd., Guishan Dist., Taoyuan 33302, Taiwan
- Department of Neurosurgery, New Taipei Municipal TuCheng Hospital, 6, Sec 2, JunCheng Rd., New Taipei City 23652, Taiwan
| | - Hung-Wei Yang
- Department of Biomedical Engineering, National Cheng Kung University, No. 1, University Rd., Tainan 70101, Taiwan
- Medical Device Innovation Center, National Cheng Kung University, No. 1, University Rd., Tainan 70101, Taiwan
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3
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Chen MJ, Gatignol A, Scarborough RJ. The discovery and development of RNA-based therapies for treatment of HIV-1 infection. Expert Opin Drug Discov 2023; 18:163-179. [PMID: 36004505 DOI: 10.1080/17460441.2022.2117296] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Long-term control of HIV-1 infection can potentially be achieved using autologous stem cell transplants with gene-modified cells. Non-coding RNAs represent a diverse class of therapeutic agents including ribozymes, RNA aptamers and decoys, small interfering RNAs, short hairpin RNAs, and U1 interference RNAs that can be designed to inhibit HIV-1 replication. They have been engineered for delivery as drugs to complement current HIV-1 therapies and as gene therapies for a potential HIV-1 functional cure. AREAS COVERED This review surveys the past three decades of development of these RNA technologies with a focus on their efficacy and safety for treating HIV-1 infections. We describe the mechanisms of each RNA-based agent, targets they have been developed against, efforts to enhance their stability and efficacy, and we evaluate their performance in past and ongoing preclinical and clinical trials. EXPERT OPINION RNA-based technologies are among the top candidates for gene therapies where they can be stably expressed for long-term suppression of HIV-1. Advances in both gene and drug delivery strategies and improvements to non-coding RNA stability and antiviral properties will cooperatively drive forward progress in improving drug therapy and engineering HIV-1 resistant cells.
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Affiliation(s)
- Michelle J Chen
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada.,Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Anne Gatignol
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada.,Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada.,Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Robert J Scarborough
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada.,Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
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4
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Semple SL, Au SKW, Jacob RA, Mossman KL, DeWitte-Orr SJ. Discovery and Use of Long dsRNA Mediated RNA Interference to Stimulate Antiviral Protection in Interferon Competent Mammalian Cells. Front Immunol 2022; 13:859749. [PMID: 35603190 PMCID: PMC9120774 DOI: 10.3389/fimmu.2022.859749] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/04/2022] [Indexed: 12/20/2022] Open
Abstract
In invertebrate cells, RNA interference (RNAi) acts as a powerful immune defense that stimulates viral gene knockdown thereby preventing infection. With this pathway, virally produced long dsRNA (dsRNA) is cleaved into short interfering RNA (siRNA) by Dicer and loaded into the RNA-induced silencing complex (RISC) which can then destroy/disrupt complementary viral mRNA sequences. Comparatively, in mammalian cells it is believed that the type I interferon (IFN) pathway is the cornerstone of the innate antiviral response. In these cells, dsRNA acts as a potent inducer of the IFN system, which is dependent on dsRNA length, but not sequence, to stimulate an antiviral state. Although the cellular machinery for RNAi is intact and functioning in mammalian cells, its role to trigger an antiviral response using long dsRNA (dsRNAi) remains controversial. Here we show that dsRNAi is not only functional but has a significant antiviral effect in IFN competent mammalian cells. We found that pre-soaking mammalian cells with concentrations of sequence specific dsRNA too low to induce IFN production could significantly inhibit vesicular stomatitis virus expressing green fluorescent protein (VSV-GFP), and the human coronaviruses (CoV) HCoV-229E and SARS-CoV-2 replication. This phenomenon was shown to be dependent on dsRNA length, was comparable in effect to transfected siRNAs, and could knockdown multiple sequences at once. Additionally, knockout cell lines revealed that functional Dicer was required for viral inhibition, revealing that the RNAi pathway was indeed responsible. These results provide the first evidence that soaking with gene-specific long dsRNA can generate viral knockdown in mammalian cells. We believe that this novel discovery provides an explanation as to why the mammalian lineage retained its RNAi machinery and why vertebrate viruses have evolved methods to suppress RNAi. Furthermore, demonstrating RNAi below the threshold of IFN induction has uses as a novel therapeutic platform, both antiviral and gene targeting in nature.
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Affiliation(s)
- Shawna L. Semple
- Department of Health Sciences, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Sarah K. W. Au
- Department of Health Sciences, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Rajesh A. Jacob
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
| | - Karen L. Mossman
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
| | - Stephanie J. DeWitte-Orr
- Department of Health Sciences, Wilfrid Laurier University, Waterloo, ON, Canada
- *Correspondence: Stephanie J. DeWitte-Orr,
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5
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The Effect of Dicer Knockout on RNA Interference Using Various Dicer Substrate Small Interfering RNA (DsiRNA) Structures. Genes (Basel) 2022; 13:genes13030436. [PMID: 35327991 PMCID: PMC8952432 DOI: 10.3390/genes13030436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 12/10/2022] Open
Abstract
Small interfering RNAs (siRNAs) are artificial molecules used to silence genes of interest through the RNA interference (RNAi) pathway, mediated by the endoribonuclease Dicer. Dicer-substrate small interfering RNAs (DsiRNAs) are an alternative to conventional 21-mer siRNAs, with an increased effectiveness of up to 100-fold compared to traditional 21-mer designs. DsiRNAs have a novel asymmetric design that allows them to be processed by Dicer into the desired conventional siRNAs. DsiRNAs are a useful tool for sequence-specific gene silencing, but the molecular mechanism underlying their increased efficacy is not precisely understood. In this study, to gain a deeper understanding of Dicer function in DsiRNAs, we designed nicked DsiRNAs with and without tetra-loops to target a specific mRNA sequence, established a Dicer knockout in the HCT116 cell line, and analyzed the efficacy of various DsiRNAs on RNAi-mediated gene silencing activity. The gene silencing activity of all DsiRNAs was reduced in Dicer knockout cells. We demonstrated that tetra-looped DsiRNAs exhibited increased efficacy for gene silencing, which was mediated by Dicer protein. Thus, this study improves our understanding of Dicer function, a key component of RNAi silencing, which will inform RNAi research and applications.
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6
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Wang P, Zhou Y, Richards AM. Effective tools for RNA-derived therapeutics: siRNA interference or miRNA mimicry. Am J Cancer Res 2021; 11:8771-8796. [PMID: 34522211 PMCID: PMC8419061 DOI: 10.7150/thno.62642] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/30/2021] [Indexed: 12/18/2022] Open
Abstract
The approval of the first small interfering RNA (siRNA) drug Patisiran by FDA in 2018 marks a new era of RNA interference (RNAi) therapeutics. MicroRNAs (miRNA), an important post-transcriptional gene regulator, are also the subject of both basic research and clinical trials. Both siRNA and miRNA mimics are ~21 nucleotides RNA duplexes inducing mRNA silencing. Given the well performance of siRNA, researchers ask whether miRNA mimics are unnecessary or developed siRNA technology can pave the way for the emergence of miRNA mimic drugs. Through comprehensive comparison of siRNA and miRNA, we focus on (1) the common features and lessons learnt from the success of siRNAs; (2) the unique characteristics of miRNA that potentially offer additional therapeutic advantages and opportunities; (3) key areas of ongoing research that will contribute to clinical application of miRNA mimics. In conclusion, miRNA mimics have unique properties and advantages which cannot be fully matched by siRNA in clinical applications. MiRNAs are endogenous molecules and the gene silencing effects of miRNA mimics can be regulated or buffered to ameliorate or eliminate off-target effects. An in-depth understanding of the differences between siRNA and miRNA mimics will facilitate the development of miRNA mimic drugs.
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7
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Vocelle D, Chan C, Walton SP. Endocytosis Controls siRNA Efficiency: Implications for siRNA Delivery Vehicle Design and Cell-Specific Targeting. Nucleic Acid Ther 2020; 30:22-32. [PMID: 31718426 PMCID: PMC6987736 DOI: 10.1089/nat.2019.0804] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 10/10/2019] [Indexed: 12/19/2022] Open
Abstract
While small interfering RNAs (siRNAs) are commonly used for laboratory studies, development of siRNA therapeutics has been slower than expected, due, in part, to a still limited understanding of the endocytosis and intracellular trafficking of siRNA-containing complexes. With the recent characterization of multiple clathrin-/caveolin-independent endocytic pathways, that is, those mediated by Graf1, Arf6, and flotillin, it has become clear that the endocytic mechanism influences subsequent intracellular processing of the internalized cargo. To explore siRNA delivery in light of these findings, we developed a novel assay that differentiates uptake by each of the endocytic pathways and can be used to determine whether endocytosis by a pathway leads to the initiation of RNA interference (RNAi). Using Lipofectamine 2000 (LF2K), we determined the endocytosis pathway leading to active silencing (whether by clathrin, caveolin, Arf6, Graf1, flotillin, or macropinocytosis) across multiple cell types (HeLa, H1299, HEK293, and HepG2). We showed that LF2K is internalized by Graf1-, Arf6-, or flotillin-mediated endocytosis for the initiation of RNAi, depending on cell type. In addition, we found that a portion of siRNA-containing complexes is internalized by pathways that do not lead to initiation of silencing. Inhibition of these pathways enhanced intracellular levels of siRNAs with concomitant enhancement of silencing.
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Affiliation(s)
- Daniel Vocelle
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan
| | - Christina Chan
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | - S. Patrick Walton
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan
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8
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Rai MF, Pan H, Yan H, Sandell LJ, Pham CTN, Wickline SA. Applications of RNA interference in the treatment of arthritis. Transl Res 2019; 214:1-16. [PMID: 31351032 PMCID: PMC6848781 DOI: 10.1016/j.trsl.2019.07.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/02/2019] [Accepted: 07/09/2019] [Indexed: 12/14/2022]
Abstract
RNA interference (RNAi) is a cellular mechanism for post-transcriptional gene regulation mediated by small interfering RNA (siRNA) and microRNA. siRNA-based therapy holds significant promise for the treatment of a wide-range of arthritic diseases. siRNA selectively suppresses the expression of a gene product and can thus achieve the specificity that is lacking in small molecule inhibitors. The potential use of siRNA-based therapy in arthritis, however, has not progressed to clinical trials despite ample evidence for efficacy in preclinical studies. One of the main challenges to clinical translation is the lack of a suitable delivery vehicle to efficiently and safely access diverse pathologies. Moreover, the ideal targets in treatment of arthritides remain elusive given the complexity and heterogeneity of these disease pathogeneses. Herein, we review recent preclinical studies that use RNAi-based drug delivery systems to mitigate inflammation in models of rheumatoid arthritis and osteoarthritis. We discuss a self-assembling peptide-based nanostructure that demonstrates the potential of overcoming many of the critical barriers preventing the translation of this technology to the clinic.
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Affiliation(s)
- Muhammad Farooq Rai
- Department of Orthopedic Surgery, Musculoskeletal Research Center, Washington University School of Medicine, St. Louis, Missouri; Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, Missouri
| | - Hua Pan
- Department of Cardiovascular Sciences, University of South Florida Health Heart Institute, Morsani School of Medicine, Tampa, Florida
| | - Huimin Yan
- Department of Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Linda J Sandell
- Department of Orthopedic Surgery, Musculoskeletal Research Center, Washington University School of Medicine, St. Louis, Missouri; Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, Missouri
| | - Christine T N Pham
- Department of Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, Missouri, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri.
| | - Samuel A Wickline
- Department of Cardiovascular Sciences, University of South Florida Health Heart Institute, Morsani School of Medicine, Tampa, Florida
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9
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Angart PA, Adu-Berchie K, Carlson RJ, Vocelle DB, Chan C, Walton SP. Relative Quantification of siRNA Strand Loading into Ago2 for Design of Highly Active siRNAs. Methods Mol Biol 2019; 1974:41-56. [PMID: 31098994 DOI: 10.1007/978-1-4939-9220-1_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In RNA interference (RNAi), silencing is achieved through the interaction of double-stranded small interfering RNAs (siRNAs) with essential RNAi pathway proteins, including Argonaute 2 (Ago2). Based on these interactions, one strand of the siRNA is loaded into Ago2 forming the active RNA-induced silencing complex (RISC). Optimal siRNAs maximize RISC activity against the intended target and minimize off-target silencing. To achieve the desired activity and specificity, selection of the appropriate siRNA strand for loading into Ago2 is essential. Here, we provide a protocol to quantify the relative loading of individual siRNA strands into Ago2, one factor in determining the capacity of a siRNA to achieve silencing activity and target specificity.
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Affiliation(s)
- Phillip A Angart
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
- Office of Biotechnology Products, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Kwasi Adu-Berchie
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Rebecca J Carlson
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
- Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA, USA
| | - Daniel B Vocelle
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - Christina Chan
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - S Patrick Walton
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA.
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10
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Hochrein LM, Ge TJ, Schwarzkopf M, Pierce NA. Signal Transduction in Human Cell Lysate via Dynamic RNA Nanotechnology. ACS Synth Biol 2018; 7:2796-2802. [PMID: 30525469 PMCID: PMC6305621 DOI: 10.1021/acssynbio.8b00424] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
Dynamic
RNA nanotechnology with small conditional RNAs (scRNAs)
offers a promising conceptual approach to introducing synthetic regulatory
links into endogenous biological circuits. Here, we use human cell
lysate containing functional Dicer and RNases as a testbed for engineering
scRNAs for conditional RNA interference (RNAi). scRNAs perform signal
transduction via conditional shape change: detection
of a subsequence of mRNA input X triggers formation of a Dicer substrate
that is processed to yield small interfering RNA (siRNA) output anti-Y
targeting independent mRNA Y for destruction. Automated sequence design
is performed using the reaction pathway designer within NUPACK to
encode this conditional hybridization cascade into the scRNA sequence
subject to the sequence constraints imposed by X and Y. Because it
is difficult for secondary structure models to predict which subsequences
of mRNA input X will be accessible for detection, here we develop
the RNAhyb method to experimentally determine accessible windows within
the mRNA that are provided to the designer as sequence constraints.
We demonstrate the programmability of scRNA regulators by engineering scRNAs for transducing
in both directions between two full-length mRNAs X and Y, corresponding
to either the forward molecular logic “if X then not Y”
(X Y) or
the reverse molecular logic “if Y then not X” (Y X). In human cell lysate, we
observe a strong OFF/ON conditional response with low crosstalk, corresponding
to a ≈20-fold increase in production of the siRNA output in
response to the cognate versus noncognate full-length mRNA input.
2′OMe-RNA chemical modifications protect signal transduction
reactants and intermediates against RNase degradation while enabling
Dicer processing of signal transduction products. Because diverse
biological pathways interact with RNA, scRNAs that transduce between
detection of endogenous RNA inputs and production of biologically
active RNA outputs hold great promise as a synthetic regulatory paradigm.
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Affiliation(s)
| | | | | | - Niles A. Pierce
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom
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11
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Campillo-Davo D, Fujiki F, Van den Bergh JMJ, De Reu H, Smits ELJM, Goossens H, Sugiyama H, Lion E, Berneman ZN, Van Tendeloo V. Efficient and Non-genotoxic RNA-Based Engineering of Human T Cells Using Tumor-Specific T Cell Receptors With Minimal TCR Mispairing. Front Immunol 2018; 9:2503. [PMID: 30464762 PMCID: PMC6234959 DOI: 10.3389/fimmu.2018.02503] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/10/2018] [Indexed: 12/12/2022] Open
Abstract
Genetic engineering of T cells with tumor specific T-cell receptors (TCR) is a promising strategy to redirect their specificity against cancer cells in adoptive T cell therapy protocols. Most studies are exploiting integrating retro- or lentiviral vectors to permanently introduce the therapeutic TCR, which can pose serious safety issues when treatment-related toxicities would occur. Therefore, we developed a versatile, non-genotoxic transfection method for human unstimulated CD8+ T cells. We describe an optimized double sequential electroporation platform whereby Dicer-substrate small interfering RNAs (DsiRNA) are first introduced to suppress endogenous TCR α and β expression, followed by electroporation with DsiRNA-resistant tumor-specific TCR mRNA. We demonstrate that double sequential electroporation of human primary unstimulated T cells with DsiRNA and TCR mRNA leads to unprecedented levels of transgene TCR expression due to a strongly reduced degree of TCR mispairing. Importantly, superior transgenic TCR expression boosts epitope-specific CD8+ T cell activation and killing activity. Altogether, DsiRNA and TCR mRNA double sequential electroporation is a rapid, non-integrating and highly efficient approach with an enhanced biosafety profile to engineer T cells with antigen-specific TCRs for use in early phase clinical trials.
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Affiliation(s)
- Diana Campillo-Davo
- Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Fumihiro Fujiki
- Department of Cancer Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Johan M J Van den Bergh
- Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Hans De Reu
- Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Evelien L J M Smits
- Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium.,Center for Cell Therapy & Regenerative Medicine, Antwerp University Hospital, Edegem, Belgium.,Faculty of Medicine and Health Sciences, Center for Oncological Research (CORE), University of Antwerp, Antwerp, Belgium
| | - Herman Goossens
- Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium.,Division of Clinical Biology, Antwerp University Hospital, Edegem, Belgium
| | - Haruo Sugiyama
- Department of Cancer Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Eva Lion
- Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium.,Center for Cell Therapy & Regenerative Medicine, Antwerp University Hospital, Edegem, Belgium
| | - Zwi N Berneman
- Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium.,Center for Cell Therapy & Regenerative Medicine, Antwerp University Hospital, Edegem, Belgium.,Division of Hematology, Antwerp University Hospital, Edegem, Belgium
| | - Viggo Van Tendeloo
- Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
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12
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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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13
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Ye J, Liu E, Gong J, Wang J, Huang Y, He H, Yang VC. High-Yield Synthesis of Monomeric LMWP(CPP)-siRNA Covalent Conjugate for Effective Cytosolic Delivery of siRNA. Am J Cancer Res 2017; 7:2495-2508. [PMID: 28744330 PMCID: PMC5525752 DOI: 10.7150/thno.19863] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/17/2017] [Indexed: 12/22/2022] Open
Abstract
Because of the unparalleled efficiency and universal utility in treating a variety of disease types, siRNA agents have evolved as the future drug-of-choice. Yet, the inability of the polyanionic siRNA macromolecules to cross the cell membrane remains as the bottleneck of possible clinical applications. With the cell penetrating peptides (CPP) being discovered lately, the most effective tactic to achieve the highest intracellular siRNA delivery deems to be by covalently conjugating the drug to a CPP; for instance, the arginine-rich Tat or low molecular weight protamine (LMWP) peptides. However, construction of such a chemical conjugate has been referred by scientists in this field as the “Holy Grail” challenge due to self-assembly of the cationic CPP and anionic siRNA into insoluble aggregates that are deprived of the biological functions of both compounds. Based on the dynamic motion of PEG, we present herein a concise coupling strategy that is capable of permitting a high-yield synthesis of the cell-permeable, cytosol-dissociable LMWP-siRNA covalent conjugates. Cell culture assessment demonstrates that this chemical conjugate yields by far the most effective intracellular siRNA delivery and its corresponded gene-silencing activities. This work may offer a breakthrough advance towards realizing the clinical potential of all siRNA therapeutics and, presumably, most anionic macromolecular drugs such as anti-sense oligonucleotides, gene compounds, DNA vectors and proteins where conjugation with the CPP encounters with problems of aggregation and precipitation. To this end, the impact of this coupling technique is significant, far-reaching and wide-spread.
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Verjans R, van Bilsen M, Schroen B. MiRNA Deregulation in Cardiac Aging and Associated Disorders. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2017; 334:207-263. [PMID: 28838539 DOI: 10.1016/bs.ircmb.2017.03.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The prevalence of age-related diseases is increasing dramatically, among which cardiac disease represents the leading cause of death. Aging of the heart is characterized by various molecular and cellular hallmarks impairing both cardiomyocytes and noncardiomyocytes, and resulting in functional deteriorations of the cardiac system. The aging process includes desensitization of β-adrenergic receptor (βAR)-signaling and decreased calcium handling, altered growth signaling and cardiac hypertrophy, mitochondrial dysfunction and impaired autophagy, increased programmed cell death, low-grade inflammation of noncanonical inflammatory cells, and increased ECM deposition. MiRNAs play a fundamental role in regulating the processes underlying these detrimental changes in the cardiac system, indicating that MiRNAs are crucially involved in aging. Among others, MiR-34, MiR-146a, and members of the MiR-17-92 cluster, are deregulated during senescence and drive cardiac aging processes. It is therefore suggested that MiRNAs form possible therapeutic targets to stabilize the aged failing myocardium.
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Affiliation(s)
- Robin Verjans
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Marc van Bilsen
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Blanche Schroen
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands.
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15
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Angart PA, Carlson RJ, Adu-Berchie K, Walton SP. Terminal Duplex Stability and Nucleotide Identity Differentially Control siRNA Loading and Activity in RNA Interference. Nucleic Acid Ther 2016; 26:309-317. [PMID: 27399870 PMCID: PMC5067871 DOI: 10.1089/nat.2016.0612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/06/2016] [Indexed: 01/17/2023] Open
Abstract
Efficient short interfering RNA (siRNA)-mediated gene silencing requires selection of a sequence that is complementary to the intended target and possesses sequence and structural features that encourage favorable functional interactions with the RNA interference (RNAi) pathway proteins. In this study, we investigated how terminal sequence and structural characteristics of siRNAs contribute to siRNA strand loading and silencing activity and how these characteristics ultimately result in a functionally asymmetric duplex in cultured HeLa cells. Our results reiterate that the most important characteristic in determining siRNA activity is the 5' terminal nucleotide identity. Our findings further suggest that siRNA loading is controlled principally by the hybridization stability of the 5' terminus (Nucleotides: 1-2) of each siRNA strand, independent of the opposing terminus. Postloading, RNA-induced silencing complex (RISC)-specific activity was found to be improved by lower hybridization stability in the 5' terminus (Nucleotides: 3-4) of the loaded siRNA strand and greater hybridization stability toward the 3' terminus (Nucleotides: 17-18). Concomitantly, specific recognition of the 5' terminal nucleotide sequence by human Argonaute 2 (Ago2) improves RISC half-life. These findings indicate that careful selection of siRNA sequences can maximize both the loading and the specific activity of the intended guide strand.
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Affiliation(s)
- Phillip A Angart
- Department of Chemical Engineering and Materials Science, Michigan State University , East Lansing, Michigan
| | - Rebecca J Carlson
- Department of Chemical Engineering and Materials Science, Michigan State University , East Lansing, Michigan
| | - Kwasi Adu-Berchie
- Department of Chemical Engineering and Materials Science, Michigan State University , East Lansing, Michigan
| | - S Patrick Walton
- Department of Chemical Engineering and Materials Science, Michigan State University , East Lansing, Michigan
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16
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Vocelle D, Chesniak OM, Malefyt AP, Comiskey G, Adu-Berchie K, Smith MR, Chan C, Walton SP. Dextran functionalization enhances nanoparticle-mediated siRNA delivery and silencing. TECHNOLOGY 2016; 4:42. [PMID: 27774502 PMCID: PMC5072529 DOI: 10.1142/s2339547816400100] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Understanding the endocytosis and intracellular trafficking of short interfering RNA (siRNA) delivery vehicle complexes remains a critical bottleneck in designing siRNA delivery vehicles for highly active RNA interference (RNAi)-based therapeutics. In this study, we show that dextran functionalization of silica nanoparticles enhanced uptake and intracellular delivery of siRNAs in cultured cells. Using pharmacological inhibitors for endocytotic pathways, we determined that our complexes are endocytosed via a previously unreported mechanism for siRNA delivery in which dextran initiates scavenger receptor-mediated endocytosis through a clathrin/caveolin-independent process. Our findings suggest that siRNA delivery efficiency could be enhanced by incorporating dextran into existing delivery platforms to activate scavenger receptor activity across a variety of target cell types.
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Affiliation(s)
- Daniel Vocelle
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824-1226, USA
| | - Olivia M Chesniak
- Department of Chemistry, Michigan State University, East Lansing, MI 48824-1226, USA
| | - Amanda P Malefyt
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824-1226, USA
| | - Georgina Comiskey
- Department of Chemistry, Michigan State University, East Lansing, MI 48824-1226, USA
| | - Kwasi Adu-Berchie
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824-1226, USA
| | - Milton R Smith
- Department of Chemistry, Michigan State University, East Lansing, MI 48824-1226, USA
| | - Christina Chan
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824-1226, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-1226, USA
| | - S Patrick Walton
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824-1226, USA
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17
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Olejniczak M, Urbanek MO, Jaworska E, Witucki L, Szczesniak MW, Makalowska I, Krzyzosiak WJ. Sequence-non-specific effects generated by various types of RNA interference triggers. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:306-14. [DOI: 10.1016/j.bbagrm.2015.11.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Revised: 10/26/2015] [Accepted: 11/17/2015] [Indexed: 12/16/2022]
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18
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Daniels SM, Sinck L, Ward NJ, Melendez-Peña CE, Scarborough RJ, Azar I, Rance E, Daher A, Pang KM, Rossi JJ, Gatignol A. HIV-1 RRE RNA acts as an RNA silencing suppressor by competing with TRBP-bound siRNAs. RNA Biol 2015; 12:123-35. [PMID: 25668122 DOI: 10.1080/15476286.2015.1014759] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Several proteins and RNAs expressed by mammalian viruses have been reported to interfere with RNA interference (RNAi) activity. We investigated the ability of the HIV-1-encoded RNA elements Trans-Activation Response (TAR) and Rev-Response Element (RRE) to alter RNAi. MicroRNA let7-based assays showed that RRE is a potent suppressor of RNAi activity, while TAR displayed moderate RNAi suppression. We demonstrate that RRE binds to TAR-RNA Binding Protein (TRBP), an essential component of the RNA Induced Silencing Complex (RISC). The binding of TAR and RRE to TRBP displaces small interfering (si)RNAs from binding to TRBP. Several stem-deleted RRE mutants lost their ability to suppress RNAi activity, which correlated with a reduced ability to compete with siRNA-TRBP binding. A lentiviral vector expressing TAR and RRE restricted RNAi, but RNAi was restored when Rev or GagPol were coexpressed. Adenoviruses are restricted by RNAi and encode their own suppressors of RNAi, the Virus-Associated (VA) RNA elements. RRE enhanced the replication of wild-type and VA-deficient adenovirus. Our work describes RRE as a novel suppressor of RNAi that acts by competing with siRNAs rather than by disrupting the RISC. This function is masked in lentiviral vectors co-expressed with viral proteins and thus will not affect their use in gene therapy. The potent RNAi suppressive effects of RRE identified in this study could be used to enhance the expression of RNAi restricted viruses used in oncolysis such as adenoviruses.
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Key Words
- Ago2, Argonaute-2
- EGFP, enhanced green fluorescent protein
- EMSA, electrophoresis mobility shift assay
- FL, firefly luciferase
- GAPDH, glyceraldehyde-3-phosphate dehydrogenase
- HIV, human immunodeficiency virus
- HIV-1
- IP, immunoprecipitation
- NC, nucleocapsid
- PAGE, polyacrylamide gel electrophoresis
- RISC, RNA-Induced Silencing Complex
- RL, Renilla luciferase
- RNA interference
- RNA silencing suppressor
- RNAi, RNA interference
- RRE, Rev Response Element
- RSS, RNA silencing suppressor
- RT, reverse transcription
- Rev-Response Element RNA
- TAR RNA Binding Protein (TRBP)
- TAR, trans-activation responsive element
- TRBP, TAR RNA Binding Protein
- Trans-Activation Response Element
- UTR, untranslated region
- VA, virus-associated
- WT, wild-type
- adenovirus
- ds, double-stranded
- lentiviral vectors
- miRNA, micro RNA
- pre-miRNA, precursor miRNA
- siRNA, small interfering RNA
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Affiliation(s)
- Sylvanne M Daniels
- a Virus-Cell Interactions Laboratory ; Lady Davis Institute for Medical Research ; Montréal , Québec , Canada
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19
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Hou KK, Pan H, Schlesinger PH, Wickline SA. A role for peptides in overcoming endosomal entrapment in siRNA delivery - A focus on melittin. Biotechnol Adv 2015; 33:931-40. [PMID: 26025036 PMCID: PMC4540690 DOI: 10.1016/j.biotechadv.2015.05.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 05/20/2015] [Accepted: 05/23/2015] [Indexed: 12/21/2022]
Abstract
siRNA has the possibility to revolutionize medicine by enabling highly specific and efficient silencing of proteins involved in disease pathogenesis. Despite nearly 20 years of research dedicated to translating siRNA from a research tool into a clinically relevant therapeutic, minimal success has been had to date. Access to RNA interference machinery located in the cytoplasm is often overlooked, but must be considered when designing the next generation of siRNA delivery strategies. Peptide transduction domains (PTDs) have demonstrated moderate siRNA transfection, which is primarily limited by endosomal entrapment. Strategies aimed at overcoming endosomal entrapment associated with peptide vectors are reviewed here, including osmotic methods, lipid conjugation, and fusogenic peptides. As an alternative to traditional PTD, the hemolytic peptide melittin exhibits the native capacity for endosomal disruption but causes cytotoxicity. However, appropriate packaging and protection of melittin with activation and release in the endosomal compartment has allowed melittin-based strategies to demonstrate both in vitro and in vivo safety and efficacy. These data suggest that melittin's membrane disruptive properties can enable safe and effective endosomolysis, building a case for melittin as a key component in a new generation of siRNA therapeutics.
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Affiliation(s)
- Kirk K Hou
- Computational and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Hua Pan
- Department of Medicine, Washington University School of Medicine, St Louis, MO 63108, USA
| | - Paul H Schlesinger
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Samuel A Wickline
- Department of Medicine, Washington University School of Medicine, St Louis, MO 63108, USA; Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO 63108, USA.
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20
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Méndez C, Ahlenstiel CL, Kelleher AD. Post-transcriptional gene silencing, transcriptional gene silencing and human immunodeficiency virus. World J Virol 2015; 4:219-244. [PMID: 26279984 PMCID: PMC4534814 DOI: 10.5501/wjv.v4.i3.219] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 01/24/2015] [Accepted: 04/29/2015] [Indexed: 02/05/2023] Open
Abstract
While human immunodeficiency virus 1 (HIV-1) infection is controlled through continuous, life-long use of a combination of drugs targeting different steps of the virus cycle, HIV-1 is never completely eradicated from the body. Despite decades of research there is still no effective vaccine to prevent HIV-1 infection. Therefore, the possibility of an RNA interference (RNAi)-based cure has become an increasingly explored approach. Endogenous gene expression is controlled at both, transcriptional and post-transcriptional levels by non-coding RNAs, which act through diverse molecular mechanisms including RNAi. RNAi has the potential to control the turning on/off of specific genes through transcriptional gene silencing (TGS), as well as fine-tuning their expression through post-transcriptional gene silencing (PTGS). In this review we will describe in detail the canonical RNAi pathways for PTGS and TGS, the relationship of TGS with other silencing mechanisms and will discuss a variety of approaches developed to suppress HIV-1 via manipulation of RNAi. We will briefly compare RNAi strategies against other approaches developed to target the virus, highlighting their potential to overcome the major obstacle to finding a cure, which is the specific targeting of the HIV-1 reservoir within latently infected cells.
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21
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Ghosh S, Kakumani PK, Kumar A, Malhotra P, Mukherjee SK, Bhatnagar RK. Genome wide screening of RNAi factors of Sf21 cells reveal several novel pathway associated proteins. BMC Genomics 2014; 15:775. [PMID: 25199785 PMCID: PMC4247154 DOI: 10.1186/1471-2164-15-775] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 08/29/2014] [Indexed: 12/18/2022] Open
Abstract
Background RNA interference (RNAi) leads to sequence specific knock-down of gene expression and has emerged as an important tool to analyse gene functions, pathway analysis and gene therapy. Although RNAi is a conserved cellular process involving common elements and factors, species-specific differences have been observed among different eukaryotes. Identification of components for RNAi pathway is pursued intensively and successful genome-wide screens have been performed for components of RNAi pathways in various organisms. Functional comparative genomics analysis offers evolutionary insight that forms basis of discoveries of novel RNAi-factors within related organisms. Keeping in view the academic and commercial utility of insect derived cell-line from Spodoptera frugiperda, we pursued the identification and functional analysis of components of RNAi-machinery of Sf21 cell-line using genome-wide application. Results The genome and transcriptome of Sf21 was assembled and annotated. In silico application of comparative genome analysis among insects allowed us to identify several RNAi factors in Sf21 line. The candidate RNAi factors from assembled genome were validated by knockdown analysis of candidate factors using the siRNA screens on the Sf21-gfp reporter cell-line. Forty two (42) potential factors were identified using the cell based assay. These include core RNAi elements including Dicer-2, Argonaute-1, Drosha, Aubergine and auxiliary modules like chromatin factors, RNA helicases, RNA processing module, signalling allied proteins and others. Phylogenetic analyses and domain architecture revealed that Spodoptera frugiperda homologs retained identity with Lepidoptera (Bombyx mori) or Coleoptera (Tribolium castaneum) sustaining an evolutionary conserved scaffold in post-transcriptional gene silencing paradigm within insects. Conclusion The database of RNAi-factors generated by whole genome association survey offers comprehensive outlook about conservation as well as specific differences of the proteins of RNAi machinery. Understanding the interior involved in different phases of gene silencing also offers impending tool for RNAi-based applications. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-775) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Pawan Malhotra
- Insect Resistance Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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22
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Bian XJ, Zhang GM, Gu CY, Cai Y, Wang CF, Shen YJ, Zhu Y, Zhang HL, Dai B, Ye DW. Down-regulation of Dicer and Ago2 is associated with cell proliferation and apoptosis in prostate cancer. Tumour Biol 2014; 35:11571-8. [DOI: 10.1007/s13277-014-2462-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Accepted: 08/06/2014] [Indexed: 12/20/2022] Open
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23
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Li T, Wu M, Zhu YY, Chen J, Chen L. Development of RNA Interference–Based Therapeutics and Application of Multi-Target Small Interfering RNAs. Nucleic Acid Ther 2014; 24:302-12. [DOI: 10.1089/nat.2014.0480] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Tiejun Li
- Department of Pathological Anatomy, Nantong University, Nantong, China
- Small RNA Technology and Application Institute, Nantong University, Nantong, China
- Department of Life Science Center, Biomics Biotechnologies Co., Ltd., Nantong, China
| | - Meihua Wu
- Department of Pathological Anatomy, Nantong University, Nantong, China
- Small RNA Technology and Application Institute, Nantong University, Nantong, China
- Department of Life Science Center, Biomics Biotechnologies Co., Ltd., Nantong, China
| | - York Yuanyuan Zhu
- Small RNA Technology and Application Institute, Nantong University, Nantong, China
- Department of Life Science Center, Biomics Biotechnologies Co., Ltd., Nantong, China
| | - Jianxin Chen
- Small RNA Technology and Application Institute, Nantong University, Nantong, China
- Department of Life Science Center, Biomics Biotechnologies Co., Ltd., Nantong, China
| | - Li Chen
- Department of Pathological Anatomy, Nantong University, Nantong, China
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Deep Sequencing Insights in Therapeutic shRNA Processing and siRNA Target Cleavage Precision. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e145. [PMID: 24496437 PMCID: PMC3951910 DOI: 10.1038/mtna.2013.73] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 11/29/2013] [Indexed: 01/17/2023]
Abstract
TT-034 (PF-05095808) is a recombinant adeno-associated virus serotype 8 (AAV8) agent expressing three short hairpin RNA (shRNA) pro-drugs that target the hepatitis C virus (HCV) RNA genome. The cytosolic enzyme Dicer cleaves each shRNA into multiple, potentially active small interfering RNA (siRNA) drugs. Using next-generation sequencing (NGS) to identify and characterize active shRNAs maturation products, we observed that each TT-034–encoded shRNA could be processed into as many as 95 separate siRNA strands. Few of these appeared active as determined by Sanger 5′ RNA Ligase-Mediated Rapid Amplification of cDNA Ends (5-RACE) and through synthetic shRNA and siRNA analogue studies. Moreover, NGS scrutiny applied on 5-RACE products (RACE-seq) suggested that synthetic siRNAs could direct cleavage in not one, but up to five separate positions on targeted RNA, in a sequence-dependent manner. These data support an on-target mechanism of action for TT-034 without cytotoxicity and question the accepted precision of substrate processing by the key RNA interference (RNAi) enzymes Dicer and siRNA-induced silencing complex (siRISC).
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25
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Angart P, Vocelle D, Chan C, Walton SP. Design of siRNA Therapeutics from the Molecular Scale. Pharmaceuticals (Basel) 2013; 6:440-68. [PMID: 23976875 PMCID: PMC3749788 DOI: 10.3390/ph6040440] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
While protein-based therapeutics is well-established in the market, development of nucleic acid therapeutics has lagged. Short interfering RNAs (siRNAs) represent an exciting new direction for the pharmaceutical industry. These small, chemically synthesized RNAs can knock down the expression of target genes through the use of a native eukaryotic pathway called RNA interference (RNAi). Though siRNAs are routinely used in research studies of eukaryotic biological processes, transitioning the technology to the clinic has proven challenging. Early efforts to design an siRNA therapeutic have demonstrated the difficulties in generating a highly-active siRNA with good specificity and a delivery vehicle that can protect the siRNA as it is transported to a specific tissue. In this review article, we discuss design considerations for siRNA therapeutics, identifying criteria for choosing therapeutic targets, producing highly-active siRNA sequences, and designing an optimized delivery vehicle. Taken together, these design considerations provide logical guidelines for generating novel siRNA therapeutics.
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Affiliation(s)
- Phillip Angart
- Department of Chemical Engineering and Materials Science, Michigan State University, 428 S. Shaw Lane, Room 2527, East Lansing, MI 48824, USA; (P.A.); (D.V.); (C.C.)
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26
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Abstract
RNA interference (RNAi) is an evolutionarily conserved, endogenous process for post-transcriptional regulation of gene expression. Although RNAi therapeutics have recently progressed through the pipeline toward clinical trials, the application of these as ideal, clinical therapeutics requires the development of safe and effective delivery systems. Inspired by the immense progress with nanotechnology in drug delivery, efforts have been dedicated to the development of nanoparticle-based RNAi delivery systems. For example, a precisely engineered, multifunctional nanocarrier with combined passive and active targeting capabilities may address the delivery challenges for the widespread use of RNAi as a therapy. Therefore, in this review, we introduce the major hurdles in achieving efficient RNAi delivery and discuss the current advances in applying nanotechnology-based delivery systems to overcome the delivery hurdles of RNAi therapeutics. In particular, some representative examples of nanoparticle-based delivery formulations for targeted RNAi therapeutics are highlighted.
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27
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Human RNAi pathway: crosstalk with organelles and cells. Funct Integr Genomics 2013; 14:31-46. [PMID: 24197738 DOI: 10.1007/s10142-013-0344-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 10/03/2013] [Accepted: 10/07/2013] [Indexed: 12/12/2022]
Abstract
Understanding gene regulation mechanisms has been a serious challenge in biology. As a novel mechanism, small non-coding RNAs are an alternative means of gene regulation in a specific and efficient manner. There are growing reports on regulatory roles of these RNAs including transcriptional gene silencing/activation and post-transcriptional gene silencing events. Also, there are several known small non-coding RNAs which all work through RNA interference pathway. Interestingly, these small RNAs are secreted from cells toward targeted cells presenting new communication approach in cell-cell or cell-organ signal transduction. In fact, understanding cellular and molecular basis of these pathways will strongly improve developing targeted therapies and potent and specific regulatory tools. This study will review some of the most recent findings in this subject and will introduce a super-pathway RNA interference-based small RNA silencing network.
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5' Unlocked Nucleic Acid Modification Improves siRNA Targeting. MOLECULAR THERAPY-NUCLEIC ACIDS 2013; 2:e103. [PMID: 23820891 PMCID: PMC3732871 DOI: 10.1038/mtna.2013.36] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 05/17/2013] [Indexed: 12/26/2022]
Abstract
Optimization of small interfering RNAs (siRNAs) is important in RNA interference (RNAi)-based therapeutic development. Some specific chemical modifications can control which siRNA strand is selected by the RNA-induced silencing complex (RISC) for gene silencing. Intended strand selection will increase potency and reduce off-target effects from the unintended strand. Sometimes, blocking RISC loading of the unintended strand leads to improved intended strand-silencing potency, but the generality of this phenomenon is unclear. Specifically, unlocked nucleic acid (UNA) modification of the 5′ end of canonical (i.e., 19+2) siRNAs abrogates gene silencing of the modified strand, but the fate and potency of the unmodified strand has not been investigated. Here, we show that 5′ UNA-modified siRNAs show improved silencing potency of the unmodified strand. We harness this advantageous property in a therapeutic context, where a limited target region in a conserved HIV 5′ long terminal repeat U5 region would otherwise yield siRNAs with undesired strand selection properties and poor silencing. Applying 5′ UNA modification to the unintended sense (S) strand of these otherwise poorly targeted siRNAs dramatically improves on-target silencing by the intended antisense (AS) strand in pNL4-3.luciferase studies. This study highlights the utility of 5′ UNA siRNA modification in therapeutic contexts where siRNA sequence selection is constrained.
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29
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Comparison between the repression potency of siRNA targeting the coding region and the 3'-untranslated region of mRNA. BIOMED RESEARCH INTERNATIONAL 2013; 2013:637850. [PMID: 23841081 PMCID: PMC3694366 DOI: 10.1155/2013/637850] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 05/29/2013] [Accepted: 05/29/2013] [Indexed: 01/23/2023]
Abstract
Small interfering RNAs (siRNAs) are applied for post-transcriptional gene silencing by binding target mRNA. A target coding region is usually chosen, although the 3'-untranslated region (3'-UTR) can also be a target. This study elucidates whether the coding region or 3'-UTR elicits higher repression. pFLuc and pRLuc are two reporter plasmids. A segment of FLuc gene was PCR-amplified and inserted behind the stop codon of the RLuc gene of the pRLuc. Similarly, a segment of RLuc gene was inserted behind the stop codon of FLuc. Two siFLuc and two siRLuc were siRNAs designed to target the central portions of these segments. Therefore, the siRNA encountered the same targets and flanking sequences. Results showed that the two siFLuc elicited higher repression when the FLuc segment resided in the coding region. Conversely, the two siRLuc showed higher repression when the RLuc segment was in the 3'-UTR. These results indicate that both the coding region and the 3'-UTR can be more effective targets. The thermodynamic stability of the secondary structures was analyzed. The siRNA elicited higher repression in the coding region when the target configuration was stable, and needed to be solved by translation. A siRNA may otherwise favor the target at 3'-UTR.
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Huang Y, Chen Z, Chen Y, Zhang H, Zhang Y, Zhao Y, Yang Z, Zhang L. Effects of conformational alteration induced by D-/L-isonucleoside incorporation in siRNA on their stability in serum and silencing activity. Bioconjug Chem 2013; 24:951-9. [PMID: 23682837 DOI: 10.1021/bc300642u] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We report here that all of the d- or l-isonucleoside (isoNA) modified siRNAs investigated showed the characteristic A-form conformation in the circular dichroism (CD) spectra compared to native siRNA. The d-isoNA modification had less influence on the thermal stability of siRNAs, but all l-isoNA modification displayed a significant tendency to decrease the thermal stability of siRNA. It was also found that the stabilities of d-/l-isoNA modified siMek1 in serum were different and d-isoNA modification was more potent, i.e., increase of serum stability of siRNA, than l-isoNA modification. When d-isoNA incorporated at position 4 and position 5 at antisense strand of siMek1 showed obvious improvement on serum stability, however, l-isoNA incorporated at positions 11 and 12 at antisense strand and position 9 at sense strand made the siMek1 duplex formed very unstable in serum. The silencing activities of modified siMek1s with d-/l-isoNA at position 1 of antisense strand also dropped dramatically; however, the modification at 3'-terminal of the sense strand with d- or l-isoNA significantly enhanced the silencing activity targeting the antisense strand as reporter and minimized the passenger strand-specific off-target effect. IsoNA modified in the seed area of siMek1, siMek1 A04D and siMek1 A05L, showed similar activity to the native one and better target selectivity. In the case of modification at the position near the cleavage area, it was found that d- or l-isoNA modified sense strand at position 8, 9, or 15 of siMek1 could retain the silencing activities targeting the antisense strand as reporter. Especially, both siMek1 S15D and siMek1 S15L showed good silencing activity and high target selectivity compared to native siMek1. The effects of conformational alteration of such isoNA modification of siRNA on their stability in serum and silencing activity are discussed based on computer simulation. Systematic investigation of the relationship between modified siRNA conformation and their physical and biological properties should provide a useful guideline for chemical modification and optimization of siRNA for further clinical application.
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Affiliation(s)
- Ye Huang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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Snead NM, Wu X, Li A, Cui Q, Sakurai K, Burnett JC, Rossi JJ. Molecular basis for improved gene silencing by Dicer substrate interfering RNA compared with other siRNA variants. Nucleic Acids Res 2013; 41:6209-21. [PMID: 23620279 PMCID: PMC3695504 DOI: 10.1093/nar/gkt200] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The canonical exogenous trigger of RNA interference (RNAi) in mammals is small interfering RNA (siRNA). One promising application of RNAi is siRNA-based therapeutics, and therefore the optimization of siRNA efficacy is an important consideration. To reduce unfavorable properties of canonical 21mer siRNAs, structural and chemical variations to canonical siRNA have been reported. Several of these siRNA variants demonstrate increased potency in downstream readout-based assays, but the molecular mechanism underlying the increased potency is not clear. Here, we tested the performance of canonical siRNAs and several sequence-matched variants in parallel in gene silencing, RNA-induced silencing complex (RISC) assembly, stability and Argonaute (Ago) loading assays. The commonly used 19mer with two deoxythymidine overhangs (19merTT) variant performed similarly to canonical 21mer siRNA. A shorter 16mer variant (16merTT) did not perform comparably in our assays. Dicer substrate interfering RNA (dsiRNA) demonstrated better gene silencing by the guide strand (target complementary strand), better RISC assembly, persistence of the guide strand and relatively more loading of the guide strand into Ago. Hence, we demonstrate the advantageous properties of dsiRNAs at upstream, intermediate and downstream molecular steps of the RNAi pathway.
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Affiliation(s)
- Nicholas M Snead
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
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Fu Q, Yuan YA. Structural insights into RISC assembly facilitated by dsRNA-binding domains of human RNA helicase A (DHX9). Nucleic Acids Res 2013; 41:3457-70. [PMID: 23361462 PMCID: PMC3597700 DOI: 10.1093/nar/gkt042] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 12/18/2012] [Accepted: 01/06/2013] [Indexed: 12/31/2022] Open
Abstract
Intensive research interest has focused on small RNA-processing machinery and the RNA-induced silencing complex (RISC), key cellular machines in RNAi pathways. However, the structural mechanism regarding RISC assembly, the primary step linking small RNA processing and RNA-mediated gene silencing, is largely unknown. Human RNA helicase A (DHX9) was reported to function as an RISC-loading factor, and such function is mediated mainly by its dsRNA-binding domains (dsRBDs). Here, we report the crystal structures of human RNA helicase A (RHA) dsRBD1 and dsRBD2 domains in complex with dsRNAs, respectively. Structural analysis not only reveals higher siRNA duplex-binding affinity displayed by dsRBD1, but also identifies a crystallographic dsRBD1 pair of physiological significance in cooperatively recognizing dsRNAs. Structural observations are further validated by isothermal titration calorimetric (ITC) assay. Moreover, co-immunoprecipitation (co-IP) assay coupled with mutagenesis demonstrated that both dsRBDs are required for RISC association, and such association is mediated by dsRNA. Hence, our structural and functional efforts have revealed a potential working model for siRNA recognition by RHA tandem dsRBDs, and together they provide direct structural insights into RISC assembly facilitated by RHA.
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Affiliation(s)
| | - Y. Adam Yuan
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
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The multiple functions of TRBP, at the hub of cell responses to viruses, stress, and cancer. Microbiol Mol Biol Rev 2013; 76:652-66. [PMID: 22933564 DOI: 10.1128/mmbr.00012-12] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The TAR RNA binding protein (TRBP) has emerged as a key player in many cellular processes. First identified as a cellular protein that facilitates the replication of human immunodeficiency virus, TRBP has since been shown to inhibit the activation of protein kinase R (PKR), a protein involved in innate immune responses and the cellular response to stress. It also binds to the PKR activator PACT and regulates its function. TRBP also contributes to RNA interference as an integral part of the minimal RNA-induced silencing complex with Dicer and Argonaute proteins. Due to its multiple functions in the cell, TRBP is involved in oncogenesis when its sequence is mutated or its expression is deregulated. The depletion or overexpression of TRBP results in malignancy, suggesting that the balance of TRBP expression is key to normal cellular function. These studies show that TRBP is multifunctional and mediates cross talk between different pathways. Its activities at the molecular level impact the cellular function from normal development to cancer and the response to infections.
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Fukushima A, Kusano M. Recent progress in the development of metabolome databases for plant systems biology. FRONTIERS IN PLANT SCIENCE 2013; 4:73. [PMID: 23577015 PMCID: PMC3616245 DOI: 10.3389/fpls.2013.00073] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 03/15/2013] [Indexed: 05/19/2023]
Abstract
Metabolomics has grown greatly as a functional genomics tool, and has become an invaluable diagnostic tool for biochemical phenotyping of biological systems. Over the past decades, a number of databases involving information related to mass spectra, compound names and structures, statistical/mathematical models and metabolic pathways, and metabolite profile data have been developed. Such databases complement each other and support efficient growth in this area, although the data resources remain scattered across the World Wide Web. Here, we review available metabolome databases and summarize the present status of development of related tools, particularly focusing on the plant metabolome. Data sharing discussed here will pave way for the robust interpretation of metabolomic data and advances in plant systems biology.
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Affiliation(s)
- Atsushi Fukushima
- RIKEN Plant Science CenterYokohama, Kanagawa, Japan
- *Correspondence: Atsushi Fukushima, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. e-mail:
| | - Miyako Kusano
- RIKEN Plant Science CenterYokohama, Kanagawa, Japan
- Department of Genome System Sciences, Graduate School of Nanobioscience, Kihara Institute for Biological ResearchYokohama, Kanagawa, Japan
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Abstract
Small RNA molecules regulate eukaryotic gene expression during development and in response to stresses including viral infection. Specialized ribonucleases and RNA-binding proteins govern the production and action of small regulatory RNAs. After initial processing in the nucleus by Drosha, precursor microRNAs (pre-miRNAs) are transported to the cytoplasm, where Dicer cleavage generates mature microRNAs (miRNAs) and short interfering RNAs (siRNAs). These double-stranded products assemble with Argonaute proteins such that one strand is preferentially selected and used to guide sequence-specific silencing of complementary target mRNAs by endonucleolytic cleavage or translational repression. Molecular structures of Dicer and Argonaute proteins, and of RNA-bound complexes, have offered exciting insights into the mechanisms operating at the heart of RNA-silencing pathways.
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36
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Bae S, Yoon Y. Anti-Adipogenic Activity of Berberine is Not Mediated by the WNT/β-Catenin Pathway. Phytother Res 2012; 27:937-43. [DOI: 10.1002/ptr.4918] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 11/26/2012] [Accepted: 11/30/2012] [Indexed: 01/13/2023]
Affiliation(s)
- Sungmin Bae
- Department of Microbiology; Chung-Ang University College of Medicine; Seoul 156-756 Korea
| | - Yoosik Yoon
- Department of Microbiology; Chung-Ang University College of Medicine; Seoul 156-756 Korea
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Gibbings D, Mostowy S, Jay F, Schwab Y, Cossart P, Voinnet O. Selective autophagy degrades DICER and AGO2 and regulates miRNA activity. Nat Cell Biol 2012; 14:1314-21. [PMID: 23143396 PMCID: PMC3771578 DOI: 10.1038/ncb2611] [Citation(s) in RCA: 197] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 10/02/2012] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) form a class of short RNAs (∼ 21 nucleotides) that post-transcriptionally regulate partially complementary messenger RNAs. Each miRNA may target tens to hundreds of transcripts to control key biological processes. Although the biochemical reactions underpinning miRNA biogenesis and activity are relatively well defined and the importance of their homeostasis is increasingly evident, the processes underlying regulation of the miRNA pathway in vivo are still largely elusive. Autophagy, a degradative process in which cytoplasmic material is targeted into double-membrane vacuoles, is recognized to critically contribute to cellular homeostasis. Here, we show that the miRNA-processing enzyme, DICER (also known as DICER1), and the main miRNA effector, AGO2 (also known as eukaryotic translation initiation factor 2C, 2 (EIF2C2)), are targeted for degradation as miRNA-free entities by the selective autophagy receptor NDP52 (also known as calcium binding and coiled-coil domain 2 (CALCOCO2)). Autophagy establishes a checkpoint required for continued loading of miRNA into AGO2; accordingly, NDP52 and autophagy are required for homeostasis and activity of the tested miRNAs. Autophagy also engages post-transcriptional regulation of the DICER mRNA, underscoring the importance of fine-tuned regulation of the miRNA pathway. These findings have implications for human diseases linked to misregulated autophagy, DICER- and miRNA-levels, including cancer.
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Affiliation(s)
- Derrick Gibbings
- Swiss Federal Institute of Technology (ETH-Z), Department of Biology, Zürich 8092, Switzerland
- University of Ottawa, Department of Cellular and Molecular Medicine, Ottawa, Canada
| | - Serge Mostowy
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Département de Biologie Cellulaire et Infection, 75015 Paris, France
- Inserm, Unité 604, 75015 Paris, France
- INRA, USC2020, 75015 Paris, France
- Section of Microbiology, Centre for Molecular Microbiology and Infection, Imperial College London, Armstrong Road, London SW7 2AZ, UK
| | - Florence Jay
- Swiss Federal Institute of Technology (ETH-Z), Department of Biology, Zürich 8092, Switzerland
| | - Yannick Schwab
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7104, Institut National de la Santé et de la Recherche Médicale Unité 964, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Pascale Cossart
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Département de Biologie Cellulaire et Infection, 75015 Paris, France
- Inserm, Unité 604, 75015 Paris, France
- INRA, USC2020, 75015 Paris, France
| | - Olivier Voinnet
- Swiss Federal Institute of Technology (ETH-Z), Department of Biology, Zürich 8092, Switzerland
- Institut de Biologie Moléculaire des Plantes (IBMP), 12 rue du Général Zimmer, 67084 Strasbourg Cedex, France
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Loinger A, Shemla Y, Simon I, Margalit H, Biham O. Competition between small RNAs: a quantitative view. Biophys J 2012; 102:1712-21. [PMID: 22768926 DOI: 10.1016/j.bpj.2012.01.058] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 11/28/2011] [Accepted: 01/11/2012] [Indexed: 11/17/2022] Open
Abstract
Two major classes of small regulatory RNAs--small interfering RNAs (siRNAs) and microRNA (miRNAs)--are involved in a common RNA interference processing pathway. Small RNAs within each of these families were found to compete for limiting amounts of shared components, required for their biogenesis and processing. Association with Argonaute (Ago), the catalytic component of the RNA silencing complex, was suggested as the central mechanistic point in RNA interference machinery competition. Aiming to better understand the competition between small RNAs in the cell, we present a mathematical model and characterize a range of specific cell and experimental parameters affecting the competition. We apply the model to competition between miRNAs and study the change in the expression level of their target genes under a variety of conditions. We show quantitatively that the amount of Ago and miRNAs in the cell are dominant factors contributing greatly to the competition. Interestingly, we observe what to our knowledge is a novel type of competition that takes place when Ago is abundant, by which miRNAs with shared targets compete over them. Furthermore, we use the model to examine different interaction mechanisms that might operate in establishing the miRNA-Ago complexes, mainly those related to their stability and recycling. Our model provides a mathematical framework for future studies of competition effects in regulation mechanisms involving small RNAs.
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Affiliation(s)
- Adiel Loinger
- Racah Institute of Physics, The Hebrew University, Jerusalem, Israel
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Spadaro PA, Bredy TW. Emerging role of non-coding RNA in neural plasticity, cognitive function, and neuropsychiatric disorders. Front Genet 2012; 3:132. [PMID: 22811697 PMCID: PMC3395882 DOI: 10.3389/fgene.2012.00132] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 06/28/2012] [Indexed: 11/18/2022] Open
Abstract
Non-coding RNAs (ncRNAs) have emerged as critical regulators of transcription, epigenetic processes, and gene silencing, which make them ideal candidates for insight into molecular evolution and a better understanding of the molecular pathways of neuropsychiatric disease. Here, we provide an overview of the current state of knowledge regarding various classes of ncRNAs and their role in neural plasticity and cognitive function, and highlight the potential contribution they may make to the development of a variety of neuropsychiatric disorders, including schizophrenia, addiction, and fear-related anxiety disorders.
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Affiliation(s)
- Paola A Spadaro
- Psychiatric Epigenomics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
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Human prion protein binds Argonaute and promotes accumulation of microRNA effector complexes. Nat Struct Mol Biol 2012; 19:517-24, S1. [PMID: 22484317 DOI: 10.1038/nsmb.2273] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 02/28/2012] [Indexed: 12/13/2022]
Abstract
Despite intense research in the context of neurodegenerative diseases associated with its misfolding, the endogenous human prion protein PrP(C) (or PRNP) has poorly understood physiological functions. Whereas most PrP(C) is exposed to the extracellular environment, conserved domains result in transmembrane forms of PrP(C) that traffic in the endolysosomal system and are linked to inherited and infectious neuropathologies. One transmembrane PrP(C) variant orients the N-terminal 'octarepeat' domain into the cytoplasm. Here we demonstrate that the octarepeat domain of human PrP(C) contains GW/WG motifs that bind Argonaute (AGO) proteins, the essential components of microRNA (miRNA)-induced silencing complexes (miRISCs). Transmembrane PrP(C) preferentially binds AGO, and PrP(C) promotes formation or stability of miRISC effector complexes containing the trinucleotide repeat-containing gene 6 proteins (TNRC6) and miRNA-repressed mRNA. Accordingly, effective repression of several miRNA targets requires PrP(C). We propose that dynamic interactions between PrP(C)-enriched endosomes and subcellular foci of AGO underpin these effects.
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Yuan Z, Wu X, Liu C, Xu G, Wu Z. Asymmetric siRNA: new strategy to improve specificity and reduce off-target gene expression. Hum Gene Ther 2012; 23:521-32. [PMID: 22229698 DOI: 10.1089/hum.2011.145] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Small interfering RNAs (siRNAs) have been used extensively in reverse genetic research, and many have made their way into clinical trials. The most widely used siRNA structure consists of double-stranded RNA with 19 base pairs and 2-nucleotide overhangs at the 3'-end of both strands (19+2). Although widely used, this symmetric structure bears inherent disadvantages in both research and clinical applications. One of the most common caveats is the off-target effect leading to adverse effects in clinical application. In the current study, using C-C chemokine receptor (CCR5) as a target, we have shown that 19+2 siRNA could still cause considerable global off-target effects regardless of rational design based on its thermodynamic asymmetry. However, we demonstrated that structurally asymmetric siRNA targeting CCR5 could be adopted to improve the strand specificity and greatly reduce the off-target effects without significantly compromising its on-target effects. Data from microarray analysis suggest that an unidentified mechanism resulting in global gene down-regulation might be avoided through strand shortening. Taken together, our work suggested a promising and simple way to improve strand specificity and overcome the off-target gene-expression effects without introducing more complications while retaining the efficacy of siRNA.
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Affiliation(s)
- Zhongping Yuan
- Center for Public Health Research, Medical School and Nanjing University, Nanjing 210093, P.R. China
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42
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Betancur JG, Tomari Y. Dicer is dispensable for asymmetric RISC loading in mammals. RNA (NEW YORK, N.Y.) 2012; 18:24-30. [PMID: 22106413 PMCID: PMC3261740 DOI: 10.1261/rna.029785.111] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
In flies, asymmetric loading of small RNA duplexes into Argonaute2-containing RNA-induced silencing complex (Ago2-RISC) requires Dicer-2/R2D2 heterodimer, which acts as a protein sensor for the thermodynamic stabilities of the ends of small RNA duplexes. However, the mechanism of small RNA asymmetry sensing in mammalian RISC assembly remains obscure. Here, we quantitatively examined RISC assembly and target silencing activity in the presence or absence of Dicer in mammals. Our data show that, unlike the well-characterized fly Ago2-RISC assembly pathway, mammalian Dicer is dispensable for asymmetric RISC loading in vivo and in vitro.
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Affiliation(s)
- Juan G. Betancur
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Medical Genome Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yukihide Tomari
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Medical Genome Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Corresponding author.E-mail .
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Koscianska E, Starega-Roslan J, Krzyzosiak WJ. The role of Dicer protein partners in the processing of microRNA precursors. PLoS One 2011; 6:e28548. [PMID: 22163034 PMCID: PMC3232248 DOI: 10.1371/journal.pone.0028548] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 11/10/2011] [Indexed: 01/13/2023] Open
Abstract
One of the cellular functions of the ribonuclease Dicer is to process microRNA precursors (pre-miRNAs) into mature microRNAs (miRNAs). Human Dicer performs this function in cooperation with its protein partners, AGO2, PACT and TRBP. The exact role of these accessory proteins in Dicer activity is still poorly understood. In this study, we used the northern blotting technique to investigate pre-miRNA cleavage efficiency and specificity after depletion of AGO2, PACT and TRBP by RNAi. The results showed that the inhibition of either Dicer protein partner substantially affected not only miRNA levels but also pre-miRNA levels, and it had a rather minor effect on the specificity of Dicer cleavage. The analysis of the Dicer cleavage products generated in vitro revealed the presence of a cleavage intermediate when pre-miRNA was processed by recombinant Dicer alone. This intermediate was not observed during pre-miRNA cleavage by endogenous Dicer. We demonstrate that AGO2, PACT and TRBP were required for the efficient functioning of Dicer in cells, and we suggest that one of the roles of these proteins is to assure better synchronization of cleavages triggered by two RNase III domains of Dicer.
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Affiliation(s)
- Edyta Koscianska
- Laboratory of Cancer Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Julia Starega-Roslan
- Laboratory of Cancer Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Wlodzimierz J. Krzyzosiak
- Laboratory of Cancer Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- * E-mail:
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Affiliation(s)
- Daniela Castanotto
- Division of Molecular Biology, Beckman Research Institute of City of Hope, Duarte, California 91010, USA.
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45
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Abstract
RNA interference (RNAi) is a powerful approach for reducing expression of endogenously expressed proteins. It is widely used for biological applications and is being harnessed to silence mRNAs encoding pathogenic proteins for therapy. Various methods - including delivering RNA oligonucleotides and expressing RNAi triggers from viral vectors - have been developed for successful RNAi in cell culture and in vivo. Recently, RNAi-based gene silencing approaches have been demonstrated in humans, and ongoing clinical trials hold promise for treating fatal disorders or providing alternatives to traditional small molecule therapies. Here we describe the broad range of approaches to achieve targeted gene silencing for therapy, discuss important considerations when developing RNAi triggers for use in humans, and review the current status of clinical trials.
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Affiliation(s)
- Beverly L Davidson
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA.
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46
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Ando Y, Maida Y, Morinaga A, Burroughs AM, Kimura R, Chiba J, Suzuki H, Masutomi K, Hayashizaki Y. Two-step cleavage of hairpin RNA with 5' overhangs by human DICER. BMC Mol Biol 2011; 12:6. [PMID: 21306637 PMCID: PMC3048551 DOI: 10.1186/1471-2199-12-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Accepted: 02/09/2011] [Indexed: 12/21/2022] Open
Abstract
Background DICER is an RNase III family endoribonuclease that processes precursor microRNAs (pre-miRNAs) and long double-stranded RNAs, generating microRNA (miRNA) duplexes and short interfering RNA duplexes with 20~23 nucleotides (nts) in length. The typical form of pre-miRNA processed by the Drosha protein is a hairpin RNA with 2-nt 3' overhangs. On the other hand, production of mature miRNA from an endogenous hairpin RNA with 5' overhangs has also been reported, although the mechanism for this process is unknown. Results In this study, we show that human recombinant DICER protein (rDICER) processes a hairpin RNA with 5' overhangs in vitro and generates an intermediate duplex with a 29 nt-5' strand and a 23 nt-3' strand, which was eventually cleaved into a canonical miRNA duplex via a two-step cleavage. The previously identified endogenous pre-miRNA with 5' overhangs, pre-mmu-mir-1982 RNA, is also determined to be a substrate of rDICER through the same two-step cleavage. Conclusions The two-step cleavage of a hairpin RNA with 5' overhangs shows that DICER releases double-stranded RNAs after the first cleavage and binds them again in the inverse direction for a second cleavage. These findings have implications for how DICER may be able to interact with or process differing precursor structures.
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Affiliation(s)
- Yoshinari Ando
- RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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