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Oncolytic Adenoviruses: Strategies for Improved Targeting and Specificity. Cancers (Basel) 2020; 12:cancers12061504. [PMID: 32526919 PMCID: PMC7352392 DOI: 10.3390/cancers12061504] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/29/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
Cancer is a major health problem. Most of the treatments exhibit systemic toxicity, as they are not targeted or specific to cancerous cells and tumors. Adenoviruses are very promising gene delivery vectors and have immense potential to deliver targeted therapy. Here, we review a wide range of strategies that have been tried, tested, and demonstrated to enhance the specificity of oncolytic viruses towards specific cancer cells. A combination of these strategies and other conventional therapies may be more effective than any of those strategies alone.
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Cai W, Cao J, Ren X, Qiao L, Chen X, Li M, Zang W. shRNA mediated knockdown of Nav1.7 in rat dorsal root ganglion attenuates pain following burn injury. BMC Anesthesiol 2016; 16:59. [PMID: 27514860 PMCID: PMC4982321 DOI: 10.1186/s12871-016-0215-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 07/21/2016] [Indexed: 11/16/2022] Open
Abstract
Background Abnormal acute pain after burn injury still torments patients severely. In this study, we investigated that one voltage gated sodium channel Nav1.7 plays a vital role in lowering heat pain threshold after burn injury, and the hypothesis that knockdown of Nav1.7 attenuates pain following burn injury. Methods Sixty eight adult male Sprague–Dawley rats were divided into 4 treatment groups: (1) sham, which hind paw was put on the room temperature metal plate for 15 s (2) burn model, which hind paw was put on the 85 °C metal plate for 15 s. (3) Burn injury + lentiviral vector -SCN9AsiRNA-GFP (LV- SCN9AsiRNA-GFP group, n = 18), which receive the DRG microinjection of LV- SCN9AsiRNA-GFP on the zero day. (4) Burn injury + lentiviral vector negative control (LV-NC-GFP group, n = 18), which receive the DRG microinjection of empty lentiviral vector on the zero day. Results Both mechanical and heat threshold were measured from day 1 to 21. Meanwhile, expression of sodium channels Nav1.7 in injured dorsal root ganglia were measured on post-operative days 7(POD 7). Rats exhibited decreased thresholds on both mechanical allodynia and thermal withdrawl latency, accompanied by increased Nav1.7 and c-fos expression in dorsal root ganglion (DRG). And knockdown of Nav1.7 in L5DRG led to the attenuation of burn injury-induced mechanical allodynia and thermal hyperalgesia in the rats. Conclusion We provide evidence that shRNA mediated knockdown of Nav1.7 attenuates burn induced pain in rats as well as decreased the activiation of c-fos protein.
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Affiliation(s)
- Weihua Cai
- Department of Anatomy, School of Basic Medical Sciences, Zhengzhou University, Henan, China
| | - Jing Cao
- Department of Anatomy, School of Basic Medical Sciences, Zhengzhou University, Henan, China
| | - Xiuhua Ren
- Department of Anatomy, School of Basic Medical Sciences, Zhengzhou University, Henan, China
| | - Liang Qiao
- Department of E.N.T, Zhoukou Central Hospital, Henan, China
| | - Xuemei Chen
- Department of Anatomy, School of Basic Medical Sciences, Zhengzhou University, Henan, China
| | - Ming Li
- Department of Anatomy, School of Basic Medical Sciences, Zhengzhou University, Henan, China
| | - Weidong Zang
- Department of Anatomy, School of Basic Medical Sciences, Zhengzhou University, Henan, China.
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siRNA delivery via electropulsation: a review of the basic processes. Methods Mol Biol 2014; 1121:81-98. [PMID: 24510814 DOI: 10.1007/978-1-4614-9632-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Due to their capacity for inducing strong and sequence specific gene silencing in cells, small interfering RNAs (siRNAs) are now recognized not only as powerful experimental tools for basic research in Molecular biology but with promising potentials in therapeutic development. Delivery is a bottleneck in many studies. There is a common opinion that full potential of siRNA as therapeutic agent will not be attained until better methodologies for its targeted intracellular delivery to cells and tissues are developed. Electropulsation (EP) is one of the physical methods successfully used to transfer siRNA into living cells in vitro and in vivo. This review will describe how siRNA electrotransfer obeys characterized biophysical processes (cell-size-dependent electropermeabilization, electrophoretic drag) with a strong control of a low loss of viability. Protocols can be easily adjusted by a proper setting of the electrical parameters and pulsing buffers. EP can be easily directly applied on animals. Preclinical studies showed that electropermeabilization brings a direct cytoplasmic distribution of siRNA and an efficient silencing of the targeted protein expression. EP appears as a promising tool for clinical applications of gene silencing. A panel of successful trials will be given.
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Videira M, Arranja A, Rafael D, Gaspar R. Preclinical development of siRNA therapeutics: towards the match between fundamental science and engineered systems. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2013; 10:689-702. [PMID: 24333589 DOI: 10.1016/j.nano.2013.11.018] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 11/21/2013] [Accepted: 11/24/2013] [Indexed: 12/14/2022]
Abstract
UNLABELLED The evolution of synthetic RNAi faces the paradox of interfering with the human biological environment. Due to the fact that all cell physiological processes can be target candidates, silencing a precise biological pathway could be challenging if target selectivity is not properly addressed. Molecular biology has provided scientific tools to suppress some of the most critical issues in gene therapy, while setting the standards for siRNA clinical application. However, the protein down-regulation through the mRNA silencing is intimately related to the sequence-specific siRNA ability to interact accurately with the potential target. Moreover, its in vivo biological fate is highly dependent on the successful design of a vehicle able to overcome both extracellular and intracellular barriers. Anticipating a great deal of innovation, crucial to meet the challenges involved in the RNAi therapeutics, the present review intends to build up a synopsis on the delivery strategies currently developed. FROM THE CLINICAL EDITOR This review discusses recent progress and pertinent limiting factors related to the use of siRNA-s as efficient protein-specific "silencing" agents, focusing on targeted delivery not only to cells of interest, but to the proper intracellular destination.
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Affiliation(s)
- M Videira
- iMed.UL - Research Institute for Medicines and Pharmaceutical Sciences, Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-003 Lisbon, Portugal.
| | - A Arranja
- iMed.UL - Research Institute for Medicines and Pharmaceutical Sciences, Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-003 Lisbon, Portugal
| | - D Rafael
- iMed.UL - Research Institute for Medicines and Pharmaceutical Sciences, Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-003 Lisbon, Portugal
| | - R Gaspar
- iMed.UL - Research Institute for Medicines and Pharmaceutical Sciences, Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-003 Lisbon, Portugal
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Wang Z, Ding Z, Ding C, Yu S, Dang Y, Guo Y, Yang J, Meng Q, Liu J, Cong Y. Inhibition of Newcastle Disease Virus Replication by Lentivirus-Mediated RNA Interference. Avian Dis 2013; 57:260-5. [DOI: 10.1637/10468-121612-reg.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Abstract
Gene silencing, via RNA interference (RNAi) technologies using small interfering RNA (siRNA), has been developed as an important tool for target identification and validation in drug discovery and has huge therapeutic potential. However, effective delivery into cells presents a major challenge to the use of siRNA. pH-responsive cell-penetrating peptides have attracted considerable attention in recent years as delivery vectors due to their ability to transport their cargos across the biological membrane and/or to promote endosomal escape and prevent lysosomal degradation. To evaluate the in vitro transfection efficiency of the pH-responsive peptide-based siRNA delivery system, the western blotting technique is commonly employed. This method offers a simple, efficient and economical way to study the gene silencing effect of the siRNA by analysing the protein of interest in a sample with minimum equipment requirement. This chapter provides a description of siRNA delivery and analysis by western blotting protocols for qualitatively and quantitatively assessing gene silencing efficiency and selectivity.
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Brazeau DA, Brazeau GA. Integrating Genomics into Pharmacy Education and Practice. Pharmacogenomics 2013. [DOI: 10.1016/b978-0-12-391918-2.00013-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Guzman-Villanueva D, El-Sherbiny IM, Herrera-Ruiz D, Vlassov AV, Smyth HDC. Formulation approaches to short interfering RNA and MicroRNA: challenges and implications. J Pharm Sci 2012; 101:4046-66. [PMID: 22927140 DOI: 10.1002/jps.23300] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 07/10/2012] [Accepted: 08/02/2012] [Indexed: 11/09/2022]
Abstract
RNA interference has emerged as a potentially powerful tool in the treatment of genetic and acquired diseases by delivering short interfering RNA (siRNA) or microRNA (miRNA) to target genes, resulting in their silencing. However, many physicochemical and biological barriers have to be overcome to obtain efficient in vivo delivery of siRNA and miRNA molecules to the organ/tissue of interest, thereby enabling their effective clinical therapy. This review discusses the challenges associated with the use of siRNA and miRNA and describes the nonviral delivery strategies used in overcoming these barriers. More specifically, emphasis has been placed on those technologies that have progressed to clinical trials for both local and systemic siRNA and miRNA delivery.
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Affiliation(s)
- Diana Guzman-Villanueva
- Division of Pharmaceutics, College of Pharmacy, The University of Texas at Austin, Texas 78712-0120, USA
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Abe N, Abe H, Ito Y. Synthesis of dumbbell-shaped cyclic RNAs for RNA interference. ACTA ACUST UNITED AC 2012; Chapter 16:Unit 16.4.1-11. [PMID: 22395966 DOI: 10.1002/0471142700.nc1604s48] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
RNA interference (RNAi) is a potent and highly specific gene-silencing phenomenon that was first reported for the nematode Caenorhabditis elegans. It has been discovered that genes could be silenced by introducing double-stranded RNAs (dsRNAs) complementary to the messenger RNA sequences. Since then, RNAi has been shown as an evolutionarily well-conserved process that plays an important role in host defense and in regulation of gene expression. Much effort has been dedicated to the application of the short dsRNA species (short interfering RNAs; siRNAs) as therapeutic agents, as they were shown to be effective in mammalian cells. Recently, we altered the structure of a siRNA molecule and produced dumbbell-shaped nanocircular RNAs. RNA dumbbells were shown to be stabilized in serum compared with its siRNA counterpart, despite their natural RNA strand. It has also been found that RNA dumbbells containing a 23-bp stem and two 9-nt loops exhibit a prolonged RNAi effect in cultured mammalian cells. In this unit, we describe the synthesis of RNA dumbbells from the design, its enzymatic synthesis, and to the purification.
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Affiliation(s)
- Naoko Abe
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, Saitama, Japan
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Fauster K, Hartl M, Santner T, Aigner M, Kreutz C, Bister K, Ennifar E, Micura R. 2'-Azido RNA, a versatile tool for chemical biology: synthesis, X-ray structure, siRNA applications, click labeling. ACS Chem Biol 2012; 7:581-9. [PMID: 22273279 PMCID: PMC3307367 DOI: 10.1021/cb200510k] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
Chemical modification can significantly enrich the structural
and
functional repertoire of ribonucleic acids and endow them with new
outstanding properties. Here, we report the syntheses of novel 2′-azido
cytidine and 2′-azido guanosine building blocks and demonstrate
their efficient site-specific incorporation into RNA by mastering
the synthetic challenge of using phosphoramidite chemistry in the
presence of azido groups. Our study includes the detailed characterization
of 2′-azido nucleoside containing RNA using UV-melting profile
analysis and CD and NMR spectroscopy. Importantly, the X-ray crystallographic
analysis of 2′-azido uridine and 2′-azido adenosine
modified RNAs reveals crucial structural details of this modification
within an A-form double helical environment. The 2′-azido group
supports the C3′-endo ribose conformation
and shows distinct water-bridged hydrogen bonding patterns in the
minor groove. Additionally, siRNA induced silencing of the brain acid
soluble protein (BASP1) encoding gene in chicken fibroblasts demonstrated
that 2′-azido modifications are well tolerated in the guide
strand, even directly at the cleavage site. Furthermore, the 2′-azido
modifications are compatible with 2′-fluoro and/or 2′-O-methyl modifications to achieve siRNAs of rich modification
patterns and tunable properties, such as increased nuclease resistance
or additional chemical reactivity. The latter was demonstrated by
the utilization of the 2′-azido groups for bioorthogonal Click
reactions that allows efficient fluorescent labeling of the RNA. In
summary, the present comprehensive investigation on site-specifically
modified 2′-azido RNA including all four nucleosides provides
a basic rationale behind the physico- and biochemical properties of
this flexible and thus far neglected type of RNA modification.
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Affiliation(s)
| | | | | | | | | | | | - Eric Ennifar
- Architecture et Réactivité
de l′ARN, Institut de Biologie Moléculaire et Cellulaire, CNRS/Université de Strasbourg, 67084 Strasbourg,
France
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Achazi K, Patel P, Paliwal R, Radonić A, Niedrig M, Donoso-Mantke O. RNA interference inhibits replication of tick-borne encephalitis virus in vitro. Antiviral Res 2011; 93:94-100. [PMID: 22086130 DOI: 10.1016/j.antiviral.2011.10.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 10/21/2011] [Accepted: 10/31/2011] [Indexed: 10/15/2022]
Abstract
Each year, up to 10,000 cases of infections with the flavivirus tick-borne encephalitis (TBE) virus that affect the central nervous system are reported in Europe and Asia. Due to the potentially severe adverse effects of post-exposure prophylaxis with TBE virus hyperimmunoglobulin, TBE can currently only be treated symptomatically. An RNA interference (RNAi) approach to inhibit TBE virus replication was therefore developed. In this study we demonstrate for the first time that small interfering RNAs (siRNAs) targeted at the TBE virus genome reduce the quantity of infectious TBE virus particles, TBE virus genome, and TBE virus protein in vitro by up to 85%. The 50% inhibitory dose (DI(50)) of the shRNA plasmid was only 0.05μg/ml. As RNAi-based therapeutics for other diseases are already being evaluated in phases II and III clinical trials, it is possible that RNAi could become valuable tool for controlling TBE virus infection.
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Affiliation(s)
- Katharina Achazi
- Centre for Biological Security 1 (ZBS 1), Robert Koch Institute, Nordufer 20, D-13353 Berlin, Germany.
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Gish RG, Satishchandran C, Young M, Pachuk C. RNA interference and its potential applications to chronic HBV treatment: results of a Phase I safety and tolerability study. Antivir Ther 2011; 16:547-54. [PMID: 21685542 DOI: 10.3851/imp1798] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND RNA interference (RNAi) provides an attractive tool to modulate biological systems, and ultimately, to treat human diseases. We describe early results from a Phase Ib, first-in-human safety and tolerability study of an RNAi-based therapy, NUC B1000, among patients with mild to moderate chronic HBV. METHODS Three subjects received a single 5 mg DNA dose of NUC B1000 as part of a planned dose escalation study. RESULTS All participants reported pharyngitis, chills, myalgia and fever approximately 4-7 h after dosing. All subjects were asymptomatic after a single antipyretic dose with no symptom recurrences. Measurements of interferon (IFN)-α and -γ, interleukin (IL)-10, 12 18, 8 and 6, and tumour necrosis factor-α performed before and after dosing revealed cytokine increases before study drug administration. After drug administration, IFN-γ and IL-10 increased in two patients; IL-8 increased in one. Most increases returned to pretreatment levels within 1 week. Two patients were subsequently successfully treated with entecavir indicating that NUC B1000 does not compromise subsequent antiviral therapy. CONCLUSIONS Thus far, NUC B1000 appears safe and well-tolerated; safety and efficacy studies across a larger, more diverse patient spectrum using increasing doses are needed to determine its appropriate role in the antiviral armamentarium.
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Affiliation(s)
- Robert G Gish
- Center for Hepatobiliary Disease and Abdominal Transplantation, UCSD Medical Center, San Diego, CA, USA.
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Abe N, Abe H, Nagai C, Harada M, Hatakeyama H, Harashima H, Ohshiro T, Nishihara M, Furukawa K, Maeda M, Tsuneda S, Ito Y. Synthesis, structure, and biological activity of dumbbell-shaped nanocircular RNAs for RNA interference. Bioconjug Chem 2011; 22:2082-92. [PMID: 21899349 DOI: 10.1021/bc2003154] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
RNA interference (RNAi) is one of the most promising new approaches for disease therapy. The design of a dumbbell-shaped nanocircular RNA allows it to act as a short interfering RNA (siRNA) precursor. To optimize the design, we studied the relationship between the nanostructure and RNAi activity by synthesizing various RNA dumbbells. An RNA dumbbell with a 23-bp stem and 9-nt loops was the most potent. Sequence analysis by mass spectrometry showed that Dicer could edit RNA dumbbells to siRNA species. The reaction offered the slow release of siRNA species, which conferred prolonged RNAi activity. Introduction of DNA into the loop position significantly stabilized the dumbbell in biological fluid without any loss of RNAi activity. In-depth pharmacological evaluation was performed by introducing dumbbells into HeLa cells that stably express the target luciferase gene. The dumbbells provided a rapid silencing effect and retained this effect for a longer time even at a lower concentration than that at which standard siRNA completely lost RNAi activity. We conclude that an RNA dumbbell with DNA loops is the most promising design for in vivo applications for RNA medicine.
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Affiliation(s)
- Naoko Abe
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, Wako-shi, Saitama, Japan.
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16
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Hovey BM, Ward JE, Soo Hoo P, O'Hara CJ, Connors LH, Seldin DC. Preclinical development of siRNA therapeutics for AL amyloidosis. Gene Ther 2011; 18:1150-6. [PMID: 21562591 PMCID: PMC3155733 DOI: 10.1038/gt.2011.69] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Amyloid light chain (AL) amyloidosis is a rare hematologic disorder characterized by the accumulation of a misfolded monoclonal immunoglobulin (Ig) light chain (LC) as fibrillar protein deposits. Current treatments, including cytotoxic chemotherapy and immunomodulatory therapy, are directed at killing the plasma cells that produce the LCs, but have significant toxicity for other cell types. We have designed small interfering RNAs (siRNAs) targeting the amyloidogenic LC messenger RNA (mRNA) in order to reduce expression of the amyloid precursor protein. Using nanomolar concentrations of siRNAs, we have inhibited synthesis of LC in transfected cells in vitro in a dose-dependent fashion. Furthermore, in an in vivo plasmacytoma mouse model of AL amyloidosis, we have demonstrated that these siRNAs can significantly reduce local production and circulating levels of LC. This model system highlights the therapeutic potential of siRNA for AL amyloidosis.
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Affiliation(s)
- B M Hovey
- Amyloid Treatment and Research Program, Alan and Sandra Gerry Amyloid Research Laboratory, Boston University School of Medicine, Boston, MA 02118, USA
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Grijalvo S, Ocampo SM, Perales JC, Eritja R. Synthesis of oligonucleotides carrying amino lipid groups at the 3'-end for RNA interference studies. J Org Chem 2011; 75:6806-13. [PMID: 20863084 DOI: 10.1021/jo101143j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Novel lipid derivatives carrying amino and triazolyl groups were efficiently synthesized and covalently anchored at the 3'-termini of oligonucleotides. The desired amino-lipid conjugates were fully characterized by reversed-phase HPLC and MALDI-TOF mass spectrometry. The methodology was applied to the synthesis of lipid-siRNA designed to inhibit tumor necrosis factor (TNF-α) in order to obtain siRNAs with anti-inflammatory properties. The siRNA duplex carrying amino-lipids at the 3'-end of the passenger strand has inhibitory properties similar to those of unmodified RNA duplexes in HeLa cells, indicating that the new lipid derivatives are compatible with the RNA interference machinery.
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Affiliation(s)
- Santiago Grijalvo
- Institute for Research in Biomedicine (IRB Barcelona), Networking Center on Bioengineering, Biomaterials and Biomedicine (CIBER-BBN) and Institute for Advanced Chemistry of Catalonia (IQAC), Spanish Research Council (CSIC), Cluster Building, Baldiri Reixac 10, E-08028 Barcelona, Spain
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Aigner M, Hartl M, Fauster K, Steger J, Bister K, Micura R. Chemical synthesis of site-specifically 2'-azido-modified RNA and potential applications for bioconjugation and RNA interference. Chembiochem 2011; 12:47-51. [PMID: 21171007 PMCID: PMC3193913 DOI: 10.1002/cbic.201000646] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 11/01/2010] [Indexed: 01/13/2023]
Affiliation(s)
- Michaela Aigner
- Institute of Organic Chemistry, Center for Molecular Biosciences CMBI, University of Innsbruck, 6020 Innsbruck, Austria
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Blakely K, Ketela T, Moffat J. Pooled lentiviral shRNA screening for functional genomics in mammalian cells. Methods Mol Biol 2011; 781:161-182. [PMID: 21877282 DOI: 10.1007/978-1-61779-276-2_9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Genome sequencing efforts have reformed the nature of biological inquiry, prompting the development of technologies for the functional annotation of mammalian genes. Based on methodologies originally discovered in plants and Caenorhabditis elegans, RNA interference has offered cell biologists an effective and reproducible approach to perturb gene function in mammalian cells and whole organisms. Initial application of RNA interference libraries targeting the human and mouse genomes relied on arrayed screening approaches, whereby each unique RNA interference reagent is arrayed into individual wells of a microtiter plate. These screens are not trivial to perform, requiring a substantial investment in infrastructure. In the past decade, many technological advances have been made that make genome-wide RNA interference screening more accessible to researchers and more feasible to perform in nonspecialized laboratories. Here, we describe a comprehensive protocol for pooled short-hairpin RNA screening, including methodologies for pooled lentivirus production, cell infection, genome-wide negative selection screening and resources for pooled screen deconvolution, and data analysis. As a technique, pooled shRNA screening is still in its infancy, but the methodology has already been successfully applied to probe diverse signaling pathways, as a means of drug target identification, and to identify essential genes in normal and cancer cell lines.
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Affiliation(s)
- Kim Blakely
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, ON, Canada
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Wanunu M, Dadosh T, Ray V, Jin J, McReynolds L, Drndić M. Rapid electronic detection of probe-specific microRNAs using thin nanopore sensors. NATURE NANOTECHNOLOGY 2010; 5:807-14. [PMID: 20972437 DOI: 10.1038/nnano.2010.202] [Citation(s) in RCA: 511] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Accepted: 09/14/2010] [Indexed: 05/24/2023]
Abstract
Small RNA molecules have an important role in gene regulation and RNA silencing therapy, but it is challenging to detect these molecules without the use of time-consuming radioactive labelling assays or error-prone amplification methods. Here, we present a platform for the rapid electronic detection of probe-hybridized microRNAs from cellular RNA. In this platform, a target microRNA is first hybridized to a probe. This probe:microRNA duplex is then enriched through binding to the viral protein p19. Finally, the abundance of the duplex is quantified using a nanopore. Reducing the thickness of the membrane containing the nanopore to 6 nm leads to increased signal amplitudes from biomolecules, and reducing the diameter of the nanopore to 3 nm allows the detection and discrimination of small nucleic acids based on differences in their physical dimensions. We demonstrate the potential of this approach by detecting picogram levels of a liver-specific miRNA from rat liver RNA.
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Affiliation(s)
- Meni Wanunu
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Abstract
RNA interference (RNAi) is an effective tool for genome-scale, high-throughput analysis of gene function. In the past five years, a number of genome-scale RNAi high-throughput screens (HTSs) have been done in both Drosophila and mammalian cultured cells to study diverse biological processes, including signal transduction, cancer biology, and host cell responses to infection. Results from these screens have led to the identification of new components of these processes and, importantly, have also provided insights into the complexity of biological systems, forcing new and innovative approaches to understanding functional networks in cells. Here, we review the main findings that have emerged from RNAi HTS and discuss technical issues that remain to be improved, in particular the verification of RNAi results and validation of their biological relevance. Furthermore, we discuss the importance of multiplexed and integrated experimental data analysis pipelines to RNAi HTS.
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Affiliation(s)
- Stephanie Mohr
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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22
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Shukla S, Sumaria CS, Pradeepkumar PI. Exploring chemical modifications for siRNA therapeutics: a structural and functional outlook. ChemMedChem 2010; 5:328-49. [PMID: 20043313 DOI: 10.1002/cmdc.200900444] [Citation(s) in RCA: 156] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
RNA interference (RNAi) is a post-transcriptional gene silencing mechanism induced by small interfering RNAs (siRNAs) and micro-RNAs (miRNAs), and has proved to be one of the most important scientific discoveries made in the last century. The robustness of RNAi has opened up new avenues in the development of siRNAs as therapeutic agents against various diseases including cancer and HIV. However, there had remained a lack of a clear mechanistic understanding of messenger RNA (mRNA) cleavage mediated by Argonaute2 of the RNA-induced silencing complex (RISC), due to inadequate structural data. The X-ray crystal structures of the Argonaute (Ago)-DNA-RNA complexes reported recently have proven to be a breakthrough in this field, and the structural details can provide guidelines for the design of the next generation of siRNA therapeutics. To harness siRNAs as therapeutic agents, the prudent use of various chemical modifications is warranted to enhance nuclease resistance, prevent immune activation, decrease off-target effects, and to improve pharmacokinetic and pharmacodynamic properties. The focus of this review is to interpret the tolerance of various chemical modifications employed in siRNAs toward RNAi by taking into account the crystal structures and biochemical studies of Ago-RNA complexes. Moreover, the challenges and recent progress in imparting druglike properties to siRNAs along with their delivery strategies are discussed.
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Affiliation(s)
- Siddharth Shukla
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Xiong M, Li S, Peng X, Feng Y, Yu G, Xin Q, Gong Y. Adipogenesis in ducks interfered by small interfering ribonucleic acids of peroxisome proliferator-activated receptor gamma gene. Poult Sci 2010; 89:88-95. [PMID: 20008806 PMCID: PMC7107157 DOI: 10.3382/ps.2009-00289] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Peroxisome proliferator-activated receptor γ (PPARγ) participates in adipocyte differentiation and maintenance, including the promotion of lipid storage in mammals. In the present study, 3 duck PPARγ small interfering RNA (siRNA) expression plasmids were constructed to investigate the effect of downregulating the expression of PPARγ on adipogenesis and fat accumulation in ducks. The results indicate that the 3 siRNA specific for conserved regions of PPARγ can effectively inhibit expression of PPARγ. It was demonstrated that the expression of lipoprotein lipase and adipocyte fatty acid-binding protein in duck adipose tissue is repressed when the expression of PPARγ is downregulated by siRNA. At the same time, the weight of abdominal fat at 21 and 35 d of age is decreased significantly (P < 0.05) compared with the control. However, the triglyceride levels in serum and muscle are not affected when the mRNA of PPARγ is repressed. The current study indicates that the suppression of PPARγ reduces abdominal fat deposition and regulates adipogenesis in ducks.
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Affiliation(s)
- M Xiong
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, P. R. China
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Bird MK, Lawrence AJ. The promiscuous mGlu5 receptor--a range of partners for therapeutic possibilities? Trends Pharmacol Sci 2009; 30:617-23. [PMID: 19892412 DOI: 10.1016/j.tips.2009.09.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 09/23/2009] [Accepted: 09/23/2009] [Indexed: 01/20/2023]
Abstract
The issue of non-specific effects for potential therapeutics is particularly salient in neurological/psychiatric disorders, where adverse drug reactions could impair critical brain functions. The issue of specificity is not limited to candidate molecules, as receptor targets themselves often influence physiological as well as pathological outcomes. Metabotropic glutamate receptor 5 (mGlu5) is an example of a "promiscuous" receptor target that has been implicated in addiction, but also many other processes. However, if receptor modulation could be restricted to specific pathways/brain regions, mGlu5 may still prove to be a viable therapeutic target for various indications. Using this premise, a number of possible methods to refine drug development strategy are discussed, including exploiting specific interactions of mGlu5 with other receptors to narrow the influence of pharmacological agents, and also the use of RNA interference targeted to specific cells/regions of the brain.
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Affiliation(s)
- Michael K Bird
- Florey Neuroscience Institutes, University of Melbourne, Parkville, Victoria, 3010, Australia
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