1
|
Gong C, Yang Z, Hu Y, Wu Q, Wang S, Guo Z, Zhang Y. Silencing of the BtTPS genes by transgenic plant-mediated RNAi to control Bemisia tabaci MED. PEST MANAGEMENT SCIENCE 2022; 78:1128-1137. [PMID: 34796637 DOI: 10.1002/ps.6727] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/25/2021] [Accepted: 11/18/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Whitefly (Bemisia tabaci) is a typical pest that causes severe damage to hundreds of agricultural crops. The trehalose-6-phosphate synthase (TPS) genes, as the key genes in the insect trehalose synthesis pathway, are important for insect growth and development. The whitefly TPS genes may be a main reason for the severe damage and may represent potential targets for the control of whiteflies. RESULTS In this study, we identified and cloned three TPS genes from B. tabaci MED and found that the BtTPS1 and BtTPS2 genes showed higher expression levels than the BtTPS3 gene. Then, RNA interference (RNAi) of BtTPS1 and BtTPS2 resulted in significant mortality and influenced the expression of related genes involved in energy metabolism and chitin biosynthesis in whitefly adults. Finally, the transgenic tobacco plants showed a significant effect on B. tabaci, and knockdown of BtTPS1 or BtTPS2 led to retarded growth and low hatchability in whitefly nymphs, and caused 90% mortality and decreased the fecundity in whitefly adults. Additionally, the transgenic tobacco with combinatorial RNAi of BtTPS1 and BtTPS2 showed a better efficacy against whiteflies than individual silencing. CONCLUSION Our results suggest that silencing of the BtTPS genes can compromise the growth and development of whiteflies, offering not only a new option for whitefly control but also a secure and environmentally friendly management strategy.
Collapse
Affiliation(s)
- Cheng Gong
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zezhong Yang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan Hu
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingjun Wu
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaoli Wang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhaojiang Guo
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
2
|
Plasmids Expressing shRNAs Specific to the Nucleocapsid Gene Inhibit the Replication of Porcine Deltacoronavirus In Vivo. Animals (Basel) 2021; 11:ani11051216. [PMID: 33922444 PMCID: PMC8145914 DOI: 10.3390/ani11051216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 11/25/2022] Open
Abstract
Simple Summary Porcine deltacoronavirus (PDCoV) is an emerging enteropathogen distributed globally, which causes substantial economic losses in the swine industry. The characterization of the receptor promiscuity may pose a risk of cross-species transmission. However, the options for pharmaceutical interventions are limited. In this study, the vectors expressing shRNAs targeting the nucleocapsid gene were generated to assess the inhibition effect of PDCoV reproduction. Our preliminary results demonstrate that a dual shRNA expression system is an effective strategy in combating PDCoV infection without cytotoxicity, which would facilitate the ongoing development of RNAi-based therapeutic drugs against viral diseases. Abstract Porcine deltacoronavirus (PDCoV) is a novel enteric coronavirus and is becoming one of the major causative agents of diarrhea in pig herds in recent years. To date, there are no commercial vaccines or antiviral pharmaceutical agents available to control PDCoV infection. Therefore, developing a reliable strategy against PDCoV is urgently needed. In this study, to observe the antiviral activity of RNA interference (RNAi), four short hairpin RNAs (shRNAs) specific to the nucleocapsid (N) gene of PDCoV were designed and tested in vitro. Of these, a double-shRNA-expression vector, designated as pSil-double-shRNA-N1, was the most effectively expressed, and the inhibition of PDCoV replication was then further evaluated in neonatal piglets. Our preliminary results reveal that plasmid-based double-shRNA-expression targeting the N gene of PDCoV can significantly protect LLC-PK1 cells and piglets from pathological lesions induced by PDCoV. Our study could benefit the investigation of the specific functions of viral genes related to PDCoV infection and offer a possible methodology of RNAi-based therapeutics for PDCoV infection.
Collapse
|
3
|
Monty MA, Islam MA, Nan X, Tan J, Tuhin IJ, Tang X, Miao M, Wu D, Yu L. Emerging role of RNA interference in immune cells engineering and its therapeutic synergism in immunotherapy. Br J Pharmacol 2021; 178:1741-1755. [PMID: 33608889 DOI: 10.1111/bph.15414] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 02/09/2021] [Accepted: 02/09/2021] [Indexed: 12/12/2022] Open
Abstract
RNAi effectors (e.g. siRNA, shRNA and miRNA) can trigger the silencing of specific genes causing alteration of genomic functions becoming a new therapeutic area for the treatment of infectious diseases, neurodegenerative disorders and cancer. In cancer treatment, RNAi effectors showed potential immunomodulatory actions by down-regulating immuno-suppressive proteins, such as PD-1 and CTLA-4, which restrict immune cell function and present challenges in cancer immunotherapy. Therefore, compared with extracellular targeting by antibodies, RNAi-mediated cell-intrinsic disruption of inhibitory pathways in immune cells could promote an increased anti-tumour immune response. Along with non-viral vectors, DNA-based RNAi strategies might be a more promising method for immunomodulation to silence multiple inhibitory pathways in T cells than immune checkpoint blockade antibodies. Thus, in this review, we discuss diverse RNAi implementation strategies, with recent viral and non-viral mediated RNAi synergism to immunotherapy that augments the anti-tumour immunity. Finally, we provide the current progress of RNAi in clinical pipeline.
Collapse
Affiliation(s)
- Masuma Akter Monty
- Institute of Biomedical Engineering and Technology, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Md Ariful Islam
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Xu Nan
- Institute of Biomedical Engineering and Technology, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Jingwen Tan
- Institute of Biomedical Engineering and Technology, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Israth Jahan Tuhin
- Institute of Biomedical Engineering and Technology, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Xiaowen Tang
- The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Miao Miao
- The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Depei Wu
- The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Lei Yu
- Institute of Biomedical Engineering and Technology, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| |
Collapse
|
4
|
Fry LE, Peddle CF, Stevanovic M, Barnard AR, McClements ME, MacLaren RE. Promoter Orientation within an AAV-CRISPR Vector Affects Cas9 Expression and Gene Editing Efficiency. CRISPR J 2020; 3:276-283. [PMID: 32833533 PMCID: PMC7469699 DOI: 10.1089/crispr.2020.0021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Adeno-associated virus (AAV) vectors have been widely adopted for delivery of CRISPR-Cas components, especially for therapeutic gene editing. For a single vector system, both the Cas9 and guide RNA (gRNA) are encoded within a single transgene, usually from separate promoters. Careful design of this bi-cistronic construct is required due to the minimal packaging capacity of AAV. We investigated how placement of the U6 promoter expressing the gRNA on the reverse strand to SaCas9 driven by a cytomegalovirus promoter affected gene editing rates compared to placement on the forward strand. We show that orientation in the reverse direction reduces editing rates from an AAV vector due to reduced transcription of both SaCas9 and guide RNA. This effect was observed only following AAV transduction; it was not seen following plasmid transfection. These results have implications for the design of AAV-CRISPR vectors, and suggest that results from optimizing plasmid transgenes may not translate when delivered via AAV.
Collapse
Affiliation(s)
- Lewis E. Fry
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences and NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Caroline F. Peddle
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences and NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Marta Stevanovic
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences and NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Alun R. Barnard
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences and NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Michelle E. McClements
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences and NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Robert E. MacLaren
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences and NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| |
Collapse
|
5
|
Tiuryn J, Szczurek E. Learning signaling networks from combinatorial perturbations by exploiting siRNA off-target effects. Bioinformatics 2020; 35:i605-i614. [PMID: 31510678 PMCID: PMC6612802 DOI: 10.1093/bioinformatics/btz334] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Motivation Perturbation experiments constitute the central means to study cellular networks. Several confounding factors complicate computational modeling of signaling networks from this data. First, the technique of RNA interference (RNAi), designed and commonly used to knock-down specific genes, suffers from off-target effects. As a result, each experiment is a combinatorial perturbation of multiple genes. Second, the perturbations propagate along unknown connections in the signaling network. Once the signal is blocked by perturbation, proteins downstream of the targeted proteins also become inactivated. Finally, all perturbed network members, either directly targeted by the experiment, or by propagation in the network, contribute to the observed effect, either in a positive or negative manner. One of the key questions of computational inference of signaling networks from such data are, how many and what combinations of perturbations are required to uniquely and accurately infer the model? Results Here, we introduce an enhanced version of linear effects models (LEMs), which extends the original by accounting for both negative and positive contributions of the perturbed network proteins to the observed phenotype. We prove that the enhanced LEMs are identified from data measured under perturbations of all single, pairs and triplets of network proteins. For small networks of up to five nodes, only perturbations of single and pairs of proteins are required for identifiability. Extensive simulations demonstrate that enhanced LEMs achieve excellent accuracy of parameter estimation and network structure learning, outperforming the previous version on realistic data. LEMs applied to Bartonella henselae infection RNAi screening data identified known interactions between eight nodes of the infection network, confirming high specificity of our model and suggested one new interaction. Availability and implementation https://github.com/EwaSzczurek/LEM Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Jerzy Tiuryn
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Ewa Szczurek
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| |
Collapse
|
6
|
Sack LM, Davoli T, Xu Q, Li MZ, Elledge SJ. Sources of Error in Mammalian Genetic Screens. G3 (BETHESDA, MD.) 2016; 6:2781-90. [PMID: 27402361 PMCID: PMC5015935 DOI: 10.1534/g3.116.030973] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 06/27/2016] [Indexed: 02/06/2023]
Abstract
Genetic screens are invaluable tools for dissection of biological phenomena. Optimization of such screens to enhance discovery of candidate genes and minimize false positives is thus a critical aim. Here, we report several sources of error common to pooled genetic screening techniques used in mammalian cell culture systems, and demonstrate methods to eliminate these errors. We find that reverse transcriptase-mediated recombination during retroviral replication can lead to uncoupling of molecular tags, such as DNA barcodes (BCs), from their associated library elements, leading to chimeric proviral genomes in which BCs are paired to incorrect ORFs, shRNAs, etc This effect depends on the length of homologous sequence between unique elements, and can be minimized with careful vector design. Furthermore, we report that residual plasmid DNA from viral packaging procedures can contaminate transduced cells. These plasmids serve as additional copies of the PCR template during library amplification, resulting in substantial inaccuracies in measurement of initial reference populations for screen normalization. The overabundance of template in some samples causes an imbalance between PCR cycles of contaminated and uncontaminated samples, which results in a systematic artifactual depletion of GC-rich library elements. Elimination of contaminating plasmid DNA using the bacterial endonuclease Benzonase can restore faithful measurements of template abundance and minimize GC bias.
Collapse
Affiliation(s)
- Laura Magill Sack
- Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115 Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115
| | - Teresa Davoli
- Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115 Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115
| | - Qikai Xu
- Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115 Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115
| | - Mamie Z Li
- Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115 Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115
| | - Stephen J Elledge
- Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115 Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115
| |
Collapse
|
7
|
Shahbazi R, Ozpolat B, Ulubayram K. Oligonucleotide-based theranostic nanoparticles in cancer therapy. Nanomedicine (Lond) 2016; 11:1287-308. [PMID: 27102380 DOI: 10.2217/nnm-2016-0035] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Theranostic approaches, combining the functionality of both therapy and imaging, have shown potential in cancer nanomedicine. Oligonucleotides such as small interfering RNA and microRNA, which are powerful therapeutic agents, have been effectively employed in theranostic systems against various cancers. Nanoparticles are used to deliver oligonucleotides into tumors by passive or active targeting while protecting the oligonucleotides from nucleases in the extracellular environment. The use of quantum dots, iron oxide nanoparticles and gold nanoparticles and tagging with contrast agents, like fluorescent dyes, optical or magnetic agents and various radioisotopes, has facilitated early detection of tumors and evaluation of therapeutic efficacy. In this article, we review the advantages of theranostic applications in cancer therapy and imaging, with special attention to oligonucleotide-based therapeutics.
Collapse
Affiliation(s)
- Reza Shahbazi
- Department of Nanotechnology & Nanomedicine, Institute for Graduate Studies in Science & Engineering, Hacettepe University, Ankara 06532, Turkey
| | - Bulent Ozpolat
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kezban Ulubayram
- Department of Nanotechnology & Nanomedicine, Institute for Graduate Studies in Science & Engineering, Hacettepe University, Ankara 06532, Turkey.,Department of Basic Pharmaceutical Sciences, Faculty of Pharmacy, Hacettepe University, Ankara 06100, Turkey.,Department of Bioengineering, Institute for Graduate Studies in Science & Engineering, Hacettepe University, Ankara 06532, Turkey
| |
Collapse
|
8
|
Delayed Newcastle disease virus replication using RNA interference to target the nucleoprotein. Biologicals 2015; 43:274-80. [PMID: 26050911 PMCID: PMC7106533 DOI: 10.1016/j.biologicals.2015.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 02/21/2015] [Accepted: 03/26/2015] [Indexed: 01/05/2023] Open
Abstract
Each year millions of chickens die from Newcastle disease virus (NDV) worldwide leading to severe economic and food losses. Current vaccination campaigns have limitations especially in developing countries, due to elevated costs, need of trained personnel for effective vaccine administration, and functional cold chain network to maintain vaccine viability. These problems have led to heightened interest in producing new antiviral strategies, such as RNA interference (RNAi). RNAi methodology is capable of substantially decreasing viral replication at a cellular level, both in vitro and in vivo. In this study, we utilize microRNA (miRNA)-expressing constructs (a type of RNA interference) in an attempt to target and knockdown five NDV structural RNAs for nucleoprotein (NP), phosphoprotein (P), matrix (M), fusion (F), and large (L) protein genes. Immortalized chicken embryo fibroblast cells (DF-1) that transiently expressed miRNA targeting NP mRNA, showed increased resistance to NDV-induced cytopathic effects, as determined by cell count, relative to the same cells expressing miRNA against alternative NDV proteins. Upon infection with NDV, DF-1 cells constitutively expressing the NP miRNA construct had improved cell survival up to 48 h post infection (h.p.i) and decreased viral yield up to 24 h.p.i. These results suggest that overexpression of the NP miRNA in cells and perhaps live animal may provide resistance to NDV.
Collapse
|
9
|
Progress of targeting transforming growth factor-β1 small interfering RNA in liver fibrosis. ACTA ACUST UNITED AC 2015; 29:231-5. [PMID: 25429748 DOI: 10.1016/s1001-9294(14)60076-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Liver fibrosis is a common pathological consequence of a variety of chronic stimuli, including viral, autoimmune, drug-induced, cholestatic and metabolic diseases. Fibrosis is driven by a dynamic process involving increased synthesis of matrix components and a failure of physiological mechanisms of matrix turnover. Activation of hepatic stellate cells (HSCs) remains a central event in fibrosis. HSCs are the main source of extracellular matrix (ECM). Transforming growth factor-beta (TGF-Β), which is the fibrogenic master cytokine, can induce the activation of HSCs to produce a large amount of ECM, and is capable of inducing apoptosis of liver cells. RNA interference (RNAi) is a novel gene disruption technology. Studies have shown that small interfering RNA (siRNA) targeting TGF-Β1 may inhibit the activation and proliferation of HSCs, suppress ECM synthesis and block liver fibrosis. TGF-Β1 siRNA-mediated gene silencing therapy provides a new avenue for liver fibrosis. This review summarizes recent progresses in research on HSCs, TGF-Β1 and TGF-Β1 siRNA in liver fibrosis.
Collapse
|
10
|
Ramos J, Rege K. Poly(aminoether)-gold nanorod assemblies for shRNA plasmid-induced gene silencing. Mol Pharm 2013; 10:4107-19. [PMID: 24066795 DOI: 10.1021/mp400080f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Gold nanorods (GNRs) have emerged as promising nanomaterials for biosensing, imaging, photothermal hyperthermia treatments, and therapeutic delivery for several diseases. We generated poly(aminoether)-GNR nanoassemblies using a layer-by-layer deposition approach based on the 1,4C-1,4Bis polymer from a library recently synthesized in our laboratory. Subtoxic concentrations of 1,4C-1,4Bis-GNR nanoassemblies were employed to deliver expression vectors that express shRNA ("shRNA plasmid") against firefly luciferase gene to knock down expression of the protein constitutively expressed in prostate cancer cells. The role of hydrodynamic size and zeta potential in determining nanoassembly mediated luciferase silencing was investigated. Finally, the theranostic potential of 1,4C-1,4Bis-GNR nanoassemblies was demonstrated using live cell two-photon induced luminescence bioimaging. Our results indicate that poly(aminoether)-GNR nanoassemblies are a promising theranostic platform for delivery of therapeutic payloads capable of simultaneous gene silencing and bioimaging.
Collapse
Affiliation(s)
- James Ramos
- Biomedical Engineering, School of Biological and Health Systems Engineering and ‡Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University , 501 E. Tyler Mall, ECG 303, Tempe, Arizona 85287-6106, United States
| | | |
Collapse
|
11
|
Baryshnikova A, Costanzo M, Myers CL, Andrews B, Boone C. Genetic Interaction Networks: Toward an Understanding of Heritability. Annu Rev Genomics Hum Genet 2013; 14:111-33. [DOI: 10.1146/annurev-genom-082509-141730] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anastasia Baryshnikova
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544
| | - Michael Costanzo
- Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto M5S 3E1, Canada
| | - Chad L. Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Brenda Andrews
- Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto M5S 3E1, Canada;
| | - Charles Boone
- Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto M5S 3E1, Canada;
| |
Collapse
|
12
|
Abstract
Since the first application of RNA interference (RNAi) in mammalian cells, the expression of short hairpin RNAs (shRNAs) for targeted gene silencing has become a benchmark technology. Using plasmid and viral vectoring systems, the transcription of shRNA precursors that are effectively processed by the RNAi pathway can lead to potent gene knockdown. The past decade has seen continual advancement and improvement to the various strategies that can be used for shRNA delivery, and the use of shRNAs for clinical applications is well underway. Driving these developments has been the many benefits afforded by shRNA technologies, including the stable integration of expression constructs for long-term expression, infection of difficult-to-target cell lines and tissues using viral vectors, and the temporal control of shRNA transcription by inducible promoters. The use of different effector molecule formats, promoters, and vector types, has meant that experiments can be tailored to target specific cell types and minimize cellular toxicities. Through the application of combinatorial RNAi (co-RNAi), multiple shRNA delivery strategies can improve gene knockdown, permit multiple transcripts to be targeted simultaneously, and curtail the emergence of viral escape mutants. This chapter reviews the history, cellular processing, and various applications of shRNAs in mammalian systems, including options for effector molecule design, vector and promoter types, and methods for multiple shRNA delivery.
Collapse
Affiliation(s)
- Luke S Lambeth
- Murdoch Childrens Research Institute, Royal Childrens Hospital, Melbourne, VIC, Australia.
| | | |
Collapse
|
13
|
Generation of genetic constructs that simultaneously express several shRNAs. Biotechniques 2012; 52:000113880. [DOI: 10.2144/000113880] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 05/08/2012] [Indexed: 11/23/2022] Open
Abstract
RNAi has potential as an antiviral gene therapy strategy. Cassette constructs simultaneously expressing several siRNAs could prove to be the most efficient technique in developing gene therapy approaches for highly mutable viruses such as HIV-1. Here we describe a rapid and cost-saving protocol to generate cassettes that simultaneously express three siRNAs for repression of HIV-1 and CCR5 transcripts. siRNA biological activity was tested in a non-viral system, and exhibited both efficiency and specificity. Our results suggest this protocol can be used to rapidly generate cassette constructs for antiviral gene therapy applications.
Collapse
|
14
|
Mohr SE, Perrimon N. RNAi screening: new approaches, understandings, and organisms. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:145-58. [PMID: 21953743 DOI: 10.1002/wrna.110] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
RNA interference (RNAi) leads to sequence-specific knockdown of gene function. The approach can be used in large-scale screens to interrogate function in various model organisms and an increasing number of other species. Genome-scale RNAi screens are routinely performed in cultured or primary cells or in vivo in organisms such as C. elegans. High-throughput RNAi screening is benefitting from the development of sophisticated new instrumentation and software tools for collecting and analyzing data, including high-content image data. The results of large-scale RNAi screens have already proved useful, leading to new understandings of gene function relevant to topics such as infection, cancer, obesity, and aging. Nevertheless, important caveats apply and should be taken into consideration when developing or interpreting RNAi screens. Some level of false discovery is inherent to high-throughput approaches and specific to RNAi screens, false discovery due to off-target effects (OTEs) of RNAi reagents remains a problem. The need to improve our ability to use RNAi to elucidate gene function at large scale and in additional systems continues to be addressed through improved RNAi library design, development of innovative computational and analysis tools and other approaches.
Collapse
Affiliation(s)
- Stephanie E Mohr
- Drosophila RNAi Screening Center, Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | |
Collapse
|
15
|
Wilson NH, Stoeckli ET. Cell type specific, traceable gene silencing for functional gene analysis during vertebrate neural development. Nucleic Acids Res 2011; 39:e133. [PMID: 21824915 PMCID: PMC3203593 DOI: 10.1093/nar/gkr628] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Many genes have several, sometimes divergent functions during development. Therefore, timing of gene knockdown for functional analysis during development has to be done with precise temporal control, as loss of a gene's function at early stages prevents its analysis later in development. RNAi, in combination with the accessibility of chicken embryos, is an effective approach for temporally controlled analysis of gene function during neural development. Here, we describe novel plasmid vectors that contain cell type-specific promoters/enhancers to drive the expression of a fluorescent marker, followed directly by a miR30-RNAi transcript for gene silencing. These vectors allow for direct tracing of cells experiencing gene silencing by the bright fluorescence. The level of knockdown is sufficient to reproduce the expected pathfinding defects upon perturbation of genes with known axon guidance functions. Mixing different vectors prior to electroporation enables the simultaneous knockdown of multiple genes in independent regions of the spinal cord. This permits complex cellular and molecular interactions to be examined during development, in a fast and precise manner. The advancements of the in ovo RNAi technique that we describe will not only markedly enhance functional gene analysis in the chicken, but also could be adapted to other organisms in developmental studies.
Collapse
Affiliation(s)
- Nicole H Wilson
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | | |
Collapse
|
16
|
Mcintyre GJ, Arndt AJ, Gillespie KM, Mak WM, Fanning GC. A comparison of multiple shRNA expression methods for combinatorial RNAi. GENETIC VACCINES AND THERAPY 2011; 9:9. [PMID: 21496330 PMCID: PMC3098768 DOI: 10.1186/1479-0556-9-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Accepted: 04/17/2011] [Indexed: 01/09/2023]
Abstract
RNAi gene therapies for HIV-1 will likely need to employ multiple shRNAs to counter resistant strains. We evaluated 3 shRNA co-expression methods to determine their suitability for present use; multiple expression vectors, multiple expression cassettes and single transcripts comprised of several dsRNA units (aka domains) with each being designed to a different target. Though the multiple vector strategy was effective with 2 shRNAs, the increasing number of vectors required is a major shortcoming. With single transcript configurations we only saw adequate activity from 1 of 10 variants tested, the variants being comprised of 2 - 3 different target domains. Whilst single transcript configurations have the most advantages on paper, these configurations can not yet be rapidly and reliably re-configured for new targets. However, our multiple cassette combinations of 2, 3 and 4 (29 bp) shRNAs were all successful, with suitable activity maintained in all positions and net activities comparable to that of the corresponding single shRNAs. We conclude that the multiple cassette strategy is the most suitably developed for present use as it is easy to design, assemble, is directly compatible with pre-existing shRNA and can be easily expanded.
Collapse
Affiliation(s)
- Glen J Mcintyre
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Allison J Arndt
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
| | - Kirsten M Gillespie
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
| | - Wendy M Mak
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
| | - Gregory C Fanning
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
- Tibotec BVBA, Gen De Wittelaan L 11 B3, 2800 Mechelen, Belgium
| |
Collapse
|