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Webb RJ, Roberts AA, Rush C, Skerratt LF, Tizard ML, Berger L. Small Interfering RNA Mediated Messenger RNA Knockdown in the Amphibian Pathogen Batrachochytrium dendrobatidis. J Basic Microbiol 2024; 64:e2400081. [PMID: 39031701 DOI: 10.1002/jobm.202400081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/03/2024] [Accepted: 05/19/2024] [Indexed: 07/22/2024]
Abstract
RNA interference (RNAi) has not been tested in the pandemic amphibian pathogen, Batrachochytrium dendrobatidis, but developing this technology could be useful to elucidate virulence mechanisms, identify therapeutic targets, and may present a novel antifungal treatment option for chytridiomycosis. To manipulate and decipher gene function, rationally designed small interfering RNA (siRNA) can initiate the destruction of homologous messenger RNA (mRNA), resulting in the "knockdown" of target gene expression. Here, we investigate whether siRNA can be used to manipulate gene expression in B. dendrobatidis via RNAi using differing siRNA strategies to target genes involved in glutathione and ornithine synthesis. To determine the extent and duration of mRNA knockdown, target mRNA levels were monitored for 24-48 h after delivery of siRNA targeting glutamate-cysteine ligase, with a maximum of ~56% reduction in target transcripts occurring at 36 h. A second siRNA design targeting glutamate-cysteine ligase also resulted in ~53% knockdown at this time point. siRNA directed toward a different gene target, ornithine decarboxylase, achieved 17% reduction in target transcripts. Although no phenotypic effects were observed, these results suggest that RNAi is possible in B. dendrobatidis, and that gene expression can be manipulated in this pathogen. We outline ideas for further optimization steps to increase knockdown efficiency to better harness RNAi techniques for control of B. dendrobatidis.
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Affiliation(s)
- Rebecca J Webb
- One Health Research Group, Melbourne Veterinary School, University of Melbourne, Werribee, Victoria, Australia
- Australian Institute of Tropical Health and Medicine, James Cook Univiersity, Townsville, Queensland, Australia
| | - Alexandra A Roberts
- Australian Institute of Tropical Health and Medicine, James Cook Univiersity, Townsville, Queensland, Australia
| | - Catherine Rush
- Australian Institute of Tropical Health and Medicine, James Cook Univiersity, Townsville, Queensland, Australia
| | - Lee F Skerratt
- One Health Research Group, Melbourne Veterinary School, University of Melbourne, Werribee, Victoria, Australia
| | - Mark L Tizard
- Australian Centre for Disease Preparedness, CSIRO Health and Biosecurity, Geelong, Victoria, Australia
| | - Lee Berger
- One Health Research Group, Melbourne Veterinary School, University of Melbourne, Werribee, Victoria, Australia
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Mishra D, Reddy I, Dey CS. PKCα Isoform Inhibits Insulin Signaling and Aggravates Neuronal Insulin Resistance. Mol Neurobiol 2023; 60:6642-6659. [PMID: 37470970 DOI: 10.1007/s12035-023-03486-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/05/2023] [Indexed: 07/21/2023]
Abstract
Overexpression of PKCα has been linked to inhibit insulin signaling disrupting IRS-1 and Akt phosphorylations in skeletal muscle. PKCα inhibits IRS-1 and Akt phosphorylations, but not required for insulin-stimulated glucose transport in skeletal muscles. Inhibition of PKCα increased whereas in some studies decreased GLUT-4 levels at the plasma membrane in skeletal muscles and adipocytes. Controversial studies have reported opposite expression pattern of PKCα expression in insulin-resistant skeletal muscles. These findings indicate that the role of PKCα on insulin signaling is controversial and could be tissue specific. Evidently, studies are required to decipher the role of PKCα in regulating insulin signaling and preferably in other cellular systems. Utilizing neuronal cells, like Neuro-2a, SHSY-5Y and insulin-resistant diabetic mice brain tissues; we have demonstrated that PKCα inhibits insulin signaling, through IRS-Akt pathway in PP2A-dependent mechanism by an AS160-independent route involving 14-3-3ζ. Inhibition and silencing of PKCα improves insulin sensitivity by increasing GLUT-4 translocation to the plasma membrane and glucose uptake. PKCα regulates GSK3 isoforms in an opposite manner in insulin-sensitive and in insulin-resistant condition. Higher activity of PKCα aggravates insulin-resistant neuronal diabetic condition through GSK3β but not GSK3α. Our results mechanistically explored the contribution of PKCα in regulating neuronal insulin resistance and diabetes, which opens up new avenues in dealing with metabolic disorders and neurodegenerative disorders.
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Affiliation(s)
- Devanshi Mishra
- Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, New Delhi, Hauz Khas, -110016, India
| | - Ishitha Reddy
- Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, New Delhi, Hauz Khas, -110016, India
| | - Chinmoy Sankar Dey
- Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, New Delhi, Hauz Khas, -110016, India.
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3
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Yadav Y, Dey CS. PP2Cα positively regulates neuronal insulin signalling and aggravates neuronal insulin resistance. FEBS J 2022; 289:7561-7581. [PMID: 35810470 DOI: 10.1111/febs.16574] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/11/2022] [Accepted: 07/08/2022] [Indexed: 01/14/2023]
Abstract
PP2Cα is one of the newly identified isoforms of metal-dependent protein phosphatases (PPM). The role of this phosphatase in neuronal insulin signalling is completely unknown. In the present study, we show insulin-mediated rapid upregulation of a protein of the insulin signalling cascade, PP2Cα, in mouse N2a cells and human SH-SY5Y cells. By contrast, such PP2Cα upregulation is not observed in insulin-resistant conditions despite insulin stimulation. Here, we report that, under insulin-sensitive and insulin-resistant conditions, the translation of PP2Cα was regulated by insulin through c-Jun N-terminal kinase. PP2Cα in turn dephosphorylated a novel inhibitory site of insulin receptor substrate-1 at Ser522 and AMP-activated protein kinase, hence positively regulating neuronal insulin signalling and insulin resistance.
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Affiliation(s)
- Yamini Yadav
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India
| | - Chinmoy Sankar Dey
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India
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Jakutis G, Stainier DYR. Genotype-Phenotype Relationships in the Context of Transcriptional Adaptation and Genetic Robustness. Annu Rev Genet 2021; 55:71-91. [PMID: 34314597 DOI: 10.1146/annurev-genet-071719-020342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetic manipulations with a robust and predictable outcome are critical to investigate gene function, as well as for therapeutic genome engineering. For many years, knockdown approaches and reagents including RNA interference and antisense oligonucleotides dominated functional studies; however, with the advent of precise genome editing technologies, CRISPR-based knockout systems have become the state-of-the-art tools for such studies. These technologies have helped decipher the role of thousands of genes in development and disease. Their use has also revealed how limited our understanding of genotype-phenotype relationships is. The recent discovery that certain mutations can trigger the transcriptional modulation of other genes, a phenomenon called transcriptional adaptation, has provided an additional explanation for the contradicting phenotypes observed in knockdown versus knockout models and increased awareness about the use of each of these approaches. In this review, we first cover the strengths and limitations of different gene perturbation strategies. Then we highlight the diverse ways in which the genotype-phenotype relationship can be discordant between these different strategies. Finally, we review the genetic robustness mechanisms that can lead to such discrepancies, paying special attention to the recently discovered phenomenon of transcriptional adaptation. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Gabrielius Jakutis
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany;
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany; .,German Centre for Cardiovascular Research (DZHK), Partner site Rhine-Main, 60590 Frankfurt am Main, Germany.,Excellence Cluster Cardio-Pulmonary Institute (CPI), 35392 Giessen, Germany
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5
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Madureira TV, Pinheiro I, Malhão F, Castro LFC, Rocha E, Urbatzka R. Silencing of PPARαBb mRNA in brown trout primary hepatocytes: effects on molecular and morphological targets under the influence of an estrogen and a PPARα agonist. Comp Biochem Physiol B Biochem Mol Biol 2018; 229:1-9. [PMID: 30528668 DOI: 10.1016/j.cbpb.2018.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 12/01/2018] [Indexed: 12/23/2022]
Abstract
The crosstalk between peroxisome proliferator-activated receptor α (PPARα) and estrogenic pathways are shared from fish to humans. Salmonid fish had an additional genome duplication, and two PPARα isoforms (PPARαBa and PPARαBb) were previously identified. Since a negative regulation between estrogen signaling and PPARα was described, a post-transcriptional gene silencing for PPARαBb was designed in primary brown trout hepatocytes. The aims of the study were to: (i) decipher the effects of PPARαBb knock-down on peroxisome morphology and on mRNA expression of potential target genes, and (ii) to assess the cross-interferences caused by an estrogenic compound (17α-ethinylestradiol - EE2) and a PPARα agonist (Wy-14,643 - Wy) using the established knock-down model. A knock-down efficiency of 70% was achieved for PPARαBb and its silencing significantly reduced the volume density of peroxisomes, but did not alter mRNA levels of the studied genes. Exposure to Wy did not change peroxisome morphology or mRNA expression, but under silencing conditions Wy rescued the volume density of peroxisomes to control levels, and increased acyl-coenzyme A oxidase 1-3l (Acox1-3l) mRNA. Exposure to EE2 caused a reduction of peroxisome volume density, but under silencing conditions this effect was abolished and ApoA1 mRNA level was diminished. The morphological alterations of peroxisomes by WY and EE2 demonstrated that obtained results are PPARαBb dependent, and suggest the regulation of unknown downstream targets of PPARαBb. In summary, PPARαBb is involved in the control of peroxisome size and/or number, which opens future opportunities to explore its regulation and molecular targets.
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Affiliation(s)
- Tânia Vieira Madureira
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto (U.Porto), Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; Department of Microscopy, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto (U.Porto), Laboratory of Histology and Embryology, Rua Jorge Viterbo Ferreira 228, P 4050-313 Porto, Portugal
| | - Ivone Pinheiro
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto (U.Porto), Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; Department of Microscopy, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto (U.Porto), Laboratory of Histology and Embryology, Rua Jorge Viterbo Ferreira 228, P 4050-313 Porto, Portugal
| | - Fernanda Malhão
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto (U.Porto), Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; Department of Microscopy, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto (U.Porto), Laboratory of Histology and Embryology, Rua Jorge Viterbo Ferreira 228, P 4050-313 Porto, Portugal
| | - L Filipe C Castro
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto (U.Porto), Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; Department of Biology, University of Porto (U.Porto), Rua do Campo Alegre, P 4169-007 Porto, Portugal
| | - Eduardo Rocha
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto (U.Porto), Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; Department of Microscopy, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto (U.Porto), Laboratory of Histology and Embryology, Rua Jorge Viterbo Ferreira 228, P 4050-313 Porto, Portugal
| | - Ralph Urbatzka
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto (U.Porto), Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal.
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Kang S, Shin D, Noh MY, Peters JS, Smartt CT, Han YS, Hong YS. Optimization of double-stranded RNAi intrathoracic injection method in Aedes aegypti. ENTOMOLOGICAL RESEARCH 2018; 48:269-278. [PMID: 30505333 PMCID: PMC6261502 DOI: 10.1111/1748-5967.12300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
RNA interference is widely used to analyze gene functions via phenotypic knockdown of target transcripts in mosquitoes, which transmit numerous mosquito-borne diseases. Functional analysis of mosquito genes is indispensable to understand and reduce transmission of mosquito-borne diseases in mosquitoes. Intrathoracic injection of double-stranded RNA (dsRNA) remains the simplest and most customizable method in mosquitoes for functional analysis of the genes of interest. However, achieving consistent and effective knockdown by dsRNAi is often elusive and may require extensive optimization. We tested the effectiveness of gene silencing by intrathoracic injection of four different quantities of dsRNA targeting two Ae. aegypti genes, cysteine desulfurylase (Nfs1) and short-chain dehydrogenase (SDH). We found that Nfs1 gene has a lower expression level upon silencing than SDH gene. In the case of the gene that is easier to silence, Nfs1 gene expression was significantly silenced by all four tested quantities of dsRNA up to 21 d.p.i., but silencing of SDH, the gene that is difficult to silence, was less effective, with knockdown lasting up to 9 d.p.i. only when 1,000 ng of dsRNA was used. Based on our observation, intrathoracic injection of 500 ng of dsRNAs per mosquito is recommended to achieve effective knockdown for well-silenced transcripts such as Nfs1 for up to 3 weeks. This includes most in vivo bioassays involving arboviral infections in Ae. aegypti. The estimated quantities of dsRNA described in this study should be applicable to most Ae. aegypti dsRNAi studies and thus provide a guideline to develop efficient dsRNAi in other experimental investigations.
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Affiliation(s)
- Seokyoung Kang
- Dept. of Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Dongyoung Shin
- Dept. of Nematology and Entomology, University of Florida, Vero Beach, FL32962, USA
| | - Mi Young Noh
- Dept. of Agricultural Biology, Chonnam National University, Gwang-ju, 500-757, Republic of Korea
| | - Jill S. Peters
- Dept. of Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Chelsea T Smartt
- Dept. of Nematology and Entomology, University of Florida, Vero Beach, FL32962, USA
| | - Yeon Soo Han
- Dept. of Agricultural Biology, Chonnam National University, Gwang-ju, 500-757, Republic of Korea
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Identification and application of exogenous dsRNA confers plant protection against Sclerotinia sclerotiorum and Botrytis cinerea. Sci Rep 2018; 8:7320. [PMID: 29743510 PMCID: PMC5943259 DOI: 10.1038/s41598-018-25434-4] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 04/16/2018] [Indexed: 12/20/2022] Open
Abstract
Sclerotinia sclerotiorum, the causal agent of white stem rot, is responsible for significant losses in crop yields around the globe. While our understanding of S. sclerotiorum infection is becoming clearer, genetic control of the pathogen has been elusive and effective control of pathogen colonization using traditional broad-spectrum agro-chemical protocols are less effective than desired. In the current study, we developed species-specific RNA interference-based control treatments capable of reducing fungal infection. Development of a target identification pipeline using global RNA sequencing data for selection and application of double stranded RNA (dsRNA) molecules identified single gene targets of the fungus. Using this approach, we demonstrate the utility of this technology through foliar applications of dsRNAs to the leaf surface that significantly decreased fungal infection and S. sclerotiorum disease symptoms. Select target gene homologs were also tested in the closely related species, Botrytis cinerea, reducing lesion size and providing compelling evidence of the adaptability and flexibility of this technology in protecting plants against devastating fungal pathogens.
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Cambon K, Zimmer V, Martineau S, Gaillard MC, Jarrige M, Bugi A, Miniarikova J, Rey M, Hassig R, Dufour N, Auregan G, Hantraye P, Perrier AL, Déglon N. Preclinical Evaluation of a Lentiviral Vector for Huntingtin Silencing. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2017; 5:259-276. [PMID: 28603746 PMCID: PMC5453866 DOI: 10.1016/j.omtm.2017.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 05/07/2017] [Indexed: 01/12/2023]
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder resulting from a polyglutamine expansion in the huntingtin (HTT) protein. There is currently no cure for this disease, but recent studies suggest that RNAi to downregulate the expression of both normal and mutant HTT is a promising therapeutic approach. We previously developed a small hairpin RNA (shRNA), vectorized in an HIV-1-derived lentiviral vector (LV), that reduced pathology in an HD rodent model. Here, we modified this vector for preclinical development by using a tat-independent third-generation LV (pCCL) backbone and removing the original reporter genes. We demonstrate that this novel vector efficiently downregulated HTT expression in vitro in striatal neurons derived from induced pluripotent stem cells (iPSCs) of HD patients. It reduced two major pathological HD hallmarks while triggering a minimal inflammatory response, up to 6 weeks after injection, when administered by stereotaxic surgery in the striatum of an in vivo rodent HD model. Further assessment of this shRNA vector in vitro showed proper processing by the endogenous silencing machinery, and we analyzed gene expression changes to identify potential off-targets. These preclinical data suggest that this new shRNA vector fulfills primary biosafety and efficiency requirements for further development in the clinic as a cure for HD.
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Affiliation(s)
- Karine Cambon
- CEA, DRF, Institute of Biology Francois Jacob, Molecular Imaging Research Center, F-92265 Fontenay-aux-Roses, France
- CNRS, CEA, Paris-Sud University, University Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265 Fontenay-aux-Roses, France
| | - Virginie Zimmer
- Department of Clinical Neurosciences, Laboratory of Cellular and Molecular Neurotherapies, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
- Neuroscience Research Center, Laboratory of Cellular and Molecular Neurotherapies, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Sylvain Martineau
- CEA, DRF, Institute of Biology Francois Jacob, Molecular Imaging Research Center, F-92265 Fontenay-aux-Roses, France
- CNRS, CEA, Paris-Sud University, University Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265 Fontenay-aux-Roses, France
| | - Marie-Claude Gaillard
- CEA, DRF, Institute of Biology Francois Jacob, Molecular Imaging Research Center, F-92265 Fontenay-aux-Roses, France
- CNRS, CEA, Paris-Sud University, University Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265 Fontenay-aux-Roses, France
| | - Margot Jarrige
- Institut National de la Santé et de la Recherche Médicale UMR861, I-Stem, AFM, 91100 Corbeil-Essonnes, France
- UEVE UMR861, I-STEM, AFM, 91100 Corbeil-Essonnes, France
- CECS, I-STEM, AFM, 91100 Corbeil-Essonnes, France
| | - Aurore Bugi
- CECS, I-STEM, AFM, 91100 Corbeil-Essonnes, France
| | - Jana Miniarikova
- Department of Research & Development, uniQure, 1105 Amsterdam, the Netherlands
| | - Maria Rey
- Department of Clinical Neurosciences, Laboratory of Cellular and Molecular Neurotherapies, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
- Neuroscience Research Center, Laboratory of Cellular and Molecular Neurotherapies, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Raymonde Hassig
- CEA, DRF, Institute of Biology Francois Jacob, Molecular Imaging Research Center, F-92265 Fontenay-aux-Roses, France
- CNRS, CEA, Paris-Sud University, University Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265 Fontenay-aux-Roses, France
| | - Noelle Dufour
- CEA, DRF, Institute of Biology Francois Jacob, Molecular Imaging Research Center, F-92265 Fontenay-aux-Roses, France
- CNRS, CEA, Paris-Sud University, University Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265 Fontenay-aux-Roses, France
| | - Gwenaelle Auregan
- CEA, DRF, Institute of Biology Francois Jacob, Molecular Imaging Research Center, F-92265 Fontenay-aux-Roses, France
- CNRS, CEA, Paris-Sud University, University Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265 Fontenay-aux-Roses, France
| | - Philippe Hantraye
- CEA, DRF, Institute of Biology Francois Jacob, Molecular Imaging Research Center, F-92265 Fontenay-aux-Roses, France
- CNRS, CEA, Paris-Sud University, University Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265 Fontenay-aux-Roses, France
| | - Anselme L. Perrier
- Institut National de la Santé et de la Recherche Médicale UMR861, I-Stem, AFM, 91100 Corbeil-Essonnes, France
- UEVE UMR861, I-STEM, AFM, 91100 Corbeil-Essonnes, France
| | - Nicole Déglon
- Department of Clinical Neurosciences, Laboratory of Cellular and Molecular Neurotherapies, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
- Neuroscience Research Center, Laboratory of Cellular and Molecular Neurotherapies, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
- Corresponding author: Nicole Déglon, Lausanne University Hospital (CHUV), Laboratory of Cellular and Molecular Neurotherapies (LNCM), Pavillon 3, Avenue de Beaumont, 1011 Lausanne, Switzerland.
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Yuan S, Yu Z, Liu Q, Zhang M, Xiang Y, Wu N, Wu L, Hu Z, Xu B, Cai T, Ma X, Zhang Y, Liao C, Wang L, Yang P, Bai L, Li Y. GPC5, a novel epigenetically silenced tumor suppressor, inhibits tumor growth by suppressing Wnt/β-catenin signaling in lung adenocarcinoma. Oncogene 2016; 35:6120-6131. [DOI: 10.1038/onc.2016.149] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 03/19/2016] [Accepted: 03/25/2016] [Indexed: 02/06/2023]
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Shatizadeh Malekshahi S, Arefian E, Salimi V, Mokhtari Azad T, Yavarian J. Potential siRNA Molecules for Nucleoprotein and M2/L Overlapping Region of Respiratory Syncytial Virus: In Silico Design. Jundishapur J Microbiol 2016; 9:e34304. [PMID: 27303618 PMCID: PMC4902852 DOI: 10.5812/jjm.34304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/05/2015] [Accepted: 02/16/2016] [Indexed: 11/28/2022] Open
Abstract
Background Human respiratory syncytial virus (RSV) is a leading cause of severe lower respiratory tract disease in the pediatric population, elderly and in immunosuppressed individuals. Respiratory syncytial virus is also responsible for bronchiolitis, pneumonia, and chronic obstructive pulmonary infections in all age groups. With this high disease burden and the lack of an effective RSV treatment and vaccine, there is a clear need for discovery and development of novel, effective and safe drugs to prevent and treat RSV disease. The most innovative approach is the use of small interfering RNAs (siRNAs) which represent a revolutionary new concept in human therapeutics. The nucleoprotein gene of RSV which is known as the most conserved gene and the M2/L mRNA, which encompass sixty-eight overlapping nucleotides, were selected as suitable targets for siRNA design. Objectives The present study is aimed to design potential siRNAs for silencing nucleoprotein and an overlapping region of M2-L coding mRNAs by computational analysis. Materials and Methods Various computational methods (target alignment, similarity search, secondary structure prediction, and RNA interaction calculation) have been used for siRNA designing against different strains of RSV. Results In this study, seven siRNA molecules were rationally designed against the nucleoprotein gene and validated using various computational methods for silencing different strains of RSV. Additionally, three effective siRNA molecules targeting the overlapping region of M2/L mRNA were designed. Conclusions This approach provides insight and a validated strategy for chemical synthesis of an antiviral RNA molecule which meets many sequence features for efficient silencing and treatment at the genomic level.
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Affiliation(s)
| | - Ehsan Arefian
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, IR Iran
| | - Vahid Salimi
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Talat Mokhtari Azad
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Jila Yavarian
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran
- Corresponding author: Jila Yavarian, Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran. Tel/Fax: +98-2188962343, E-mail:
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Dornseifer S, Willkomm S, Far RKK, Liebschwager J, Beltsiou F, Frank K, Laufer SD, Martinetz T, Sczakiel G, Claussen JC, Restle T. RNAi revised--target mRNA-dependent enhancement of gene silencing. Nucleic Acids Res 2015; 43:10623-32. [PMID: 26578554 PMCID: PMC4678823 DOI: 10.1093/nar/gkv1200] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 10/26/2015] [Indexed: 01/11/2023] Open
Abstract
The discovery of RNA interference (RNAi) gave rise to the development of new nucleic acid-based technologies as powerful investigational tools and potential therapeutics. Mechanistic key details of RNAi in humans need to be deciphered yet, before such approaches take root in biomedicine and molecular therapy. We developed and validated an in silico-based model of siRNA-mediated RNAi in human cells in order to link in vitro-derived pre-steady state kinetic data with a quantitative and time-resolved understanding of RNAi on the cellular level. The observation that product release by Argonaute 2 is accelerated in the presence of an excess of target RNA in vitro inspired us to suggest an associative mechanism for the RNA slicer reaction where incoming target mRNAs actively promote dissociation of cleaved mRNA fragments. This novel associative model is compatible with high multiple turnover rates of RNAi-based gene silencing in living cells and accounts for target mRNA concentration-dependent enhancement of the RNAi machinery.
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Affiliation(s)
- Simon Dornseifer
- Institute of Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | - Sarah Willkomm
- Institute of Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | | | - Janine Liebschwager
- Institute of Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | - Foteini Beltsiou
- Institute of Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | - Kirsten Frank
- Institute of Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | - Sandra D Laufer
- Institute of Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | - Thomas Martinetz
- Institute for Neuro- and Bioinformatics, University of Lübeck, 23538 Lübeck, Germany
| | - Georg Sczakiel
- Institute of Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | | | - Tobias Restle
- Institute of Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
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12
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Doan CC, Doan NT, Nguyen QH, Nguyen MH, Do MS, Le VD. Downregulation of Kinesin spindle protein inhibits proliferation, induces apoptosis and increases chemosensitivity in hepatocellular carcinoma cells. IRANIAN BIOMEDICAL JOURNAL 2015; 19:1-16. [PMID: 25605484 PMCID: PMC4322227 DOI: 10.6091/ibj.1386.2014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Background: Kinesin spindle protein (KSP) plays a critical role in mitosis. Inhibition of KSP function leads to cell cycle arrest at mitosis and ultimately to cell death. The aim of this study was to suppress KSP expression by specific small-interfering RNA (siRNA) in Hep3B cells and evaluate its anti-tumor activity. Methods: Three siRNA targeting KSP (KSP-siRNA #1-3) and one mismatched-siRNA (Cont-siRNA) were transfected into cells. Subsequently, KSP mRNA and protein levels, cell proliferation, and apoptosis were examined in both Hep3B cells and THLE-3 cells. In addition, the chemosensitivity of KSP-siRNA-treated Hep3B cells with doxorubicin was also investigated using cell proliferation and clonogenic survival assays. Results: The expression of endogenous KSP at both mRNA and protein levels in Hep3B cells was higher than in THLE-3 cells. In Hep3B cells, KSP-siRNA #2 showed a further downregulation of KSP as compared to KSP-siRNA #1 or KSP-siRNA #3. It also exhibited greater suppression of cell proliferation and induction of apoptosis than KSP-siRNA #1 or KSP-siRNA #3; this could be explained by the significant downregulation of cyclin D1, Bcl-2, and survivin. In contrast, KSP-siRNAs had no or lower effects on KSP expression, cell proliferation and apoptosis in THLE-3 cells. We also noticed that KSP-siRNA transfection could increase chemosensitivity to doxorubicin in Hep3B cells, even at low doses compared to control. Conclusion: Reducing the expression level of KSP, combined with drug treatment, yields promising results for eradicating hepatocellular carcinoma (HCC) cells in vitro. This study opens a new direction for liver cancer treatment.
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Affiliation(s)
- Chinh Chung Doan
- Faculty of Biology, University of Science, Vietnam National University, 227 Nguyen Van Cu Street, Ward 4, District 5, Ho Chi Minh City, Vietnam
| | - Ngoc Trung Doan
- Faculty of Biology, University of Science, Vietnam National University, 227 Nguyen Van Cu Street, Ward 4, District 5, Ho Chi Minh City, Vietnam
| | - Quang Huy Nguyen
- Faculty of Biology, University of Science, Vietnam National University, 227 Nguyen Van Cu Street, Ward 4, District 5, Ho Chi Minh City, Vietnam
| | - Minh Hoa Nguyen
- Faculty of Biology, University of Science, Vietnam National University, 227 Nguyen Van Cu Street, Ward 4, District 5, Ho Chi Minh City, Vietnam
| | - Minh Si Do
- Faculty of Biology, University of Science, Vietnam National University, 227 Nguyen Van Cu Street, Ward 4, District 5, Ho Chi Minh City, Vietnam
| | - Van Dong Le
- Faculty of Biology, University of Science, Vietnam National University, 227 Nguyen Van Cu Street, Ward 4, District 5, Ho Chi Minh City, Vietnam.,Dept. of Immunology, Vietnam Military Medical University,
160 Phung Hung Street, Ha Dong District, Ha Noi City, Vietnam
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13
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Inhibition of mTOR with everolimus and silencing by vascular endothelial cell growth factor-specific siRNA induces synergistic antitumor activity in multiple myeloma cells. Cancer Gene Ther 2014; 21:275-82. [DOI: 10.1038/cgt.2014.27] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 05/10/2014] [Accepted: 05/12/2014] [Indexed: 11/08/2022]
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14
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Hong SW, Jiang Y, Kim S, Li CJ, Lee DK. Target gene abundance contributes to the efficiency of siRNA-mediated gene silencing. Nucleic Acid Ther 2014; 24:192-8. [PMID: 24527979 DOI: 10.1089/nat.2013.0466] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The gene-silencing activity of a small interfering RNA (siRNA) is determined by various factors. Considering that RNA interference (RNAi) is an unparalleled technology in both basic research and therapeutic applications, thorough understanding of the factors determining RNAi activity is critical. This report presents observations that siRNAs targeting KRT7 show cell-line-dependent activity, which correlates with the expression level of KRT7 mRNA. By modulating the target mRNA level, it was confirmed that highly expressed genes are more susceptible to siRNA-mediated gene silencing. Finally, several genes that show different expression levels in a cell-line dependent manner were tested, which verified the expression-level-dependent siRNA activities. These results strongly suggest that the abundance of target mRNA is a critical factor that determines the efficiency of the siRNA-mediated gene silencing in a given cellular context. This report should provide practical guidelines for designing RNAi experiments and for selecting targetable genes in RNAi therapeutics studies.
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Affiliation(s)
- Sun Woo Hong
- 1 Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University , Suwon, Korea
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15
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Ling MHT, Ban Y, Wen H, Wang SM, Ge SX. Conserved expression of natural antisense transcripts in mammals. BMC Genomics 2013; 14:243. [PMID: 23577827 PMCID: PMC3635984 DOI: 10.1186/1471-2164-14-243] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 03/06/2013] [Indexed: 02/03/2023] Open
Abstract
Background Recent studies had found thousands of natural antisense transcripts originating from the same genomic loci of protein coding genes but from the opposite strand. It is unclear whether the majority of antisense transcripts are functional or merely transcriptional noise. Results Using the Affymetrix Exon array with a modified cDNA synthesis protocol that enables genome-wide detection of antisense transcription, we conducted large-scale expression analysis of antisense transcripts in nine corresponding tissues from human, mouse and rat. We detected thousands of antisense transcripts, some of which show tissue-specific expression that could be subjected to further study for their potential function in the corresponding tissues/organs. The expression patterns of many antisense transcripts are conserved across species, suggesting selective pressure on these transcripts. When compared to protein-coding genes, antisense transcripts show a lesser degree of expression conservation. We also found a positive correlation between the sense and antisense expression across tissues. Conclusion Our results suggest that natural antisense transcripts are subjected to selective pressure but to a lesser degree compared to sense transcripts in mammals.
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Affiliation(s)
- Maurice H T Ling
- Department of Mathematics and Statistics, South Dakota State University, Brookings, SD 57007, USA
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16
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Filhol O, Ciais D, Lajaunie C, Charbonnier P, Foveau N, Vert JP, Vandenbrouck Y. DSIR: assessing the design of highly potent siRNA by testing a set of cancer-relevant target genes. PLoS One 2012; 7:e48057. [PMID: 23118925 PMCID: PMC3484153 DOI: 10.1371/journal.pone.0048057] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 09/20/2012] [Indexed: 11/21/2022] Open
Abstract
Chemically synthesized small interfering RNA (siRNA) is a widespread molecular tool used to knock down genes in mammalian cells. However, designing potent siRNA remains challenging. Among tools predicting siRNA efficacy, very few have been validated on endogenous targets in realistic experimental conditions. We previously described a tool to assist efficient siRNA design (DSIR, Designer of siRNA), which focuses on intrinsic features of the siRNA sequence. Here, we evaluated DSIR’s performance by systematically investigating the potency of the siRNA it designs to target ten cancer-related genes. mRNA knockdown was measured by quantitative RT-PCR in cell-based assays, revealing that over 60% of siRNA sequences designed by DSIR silenced their target genes by at least 70%. Silencing efficacy was sustained even when low siRNA concentrations were used. This systematic analysis revealed in particular that, for a subset of genes, the efficiency of siRNA constructs significantly increases when the sequence is located closer to the 5′-end of the target gene coding sequence, suggesting the distance to the 5′-end as a new feature for siRNA potency prediction. A new version of DSIR incorporating these new findings, as well as the list of validated siRNA against the tested cancer genes, has been made available on the web (http://biodev.extra.cea.fr/DSIR).
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Affiliation(s)
- Odile Filhol
- CEA, DSV, iRTSV, Laboratoire de Biologie du Cancer et de l’Infection, Grenoble, France
- INSERM U1036, Grenoble, France
- Université Grenoble I, Grenoble, France
- * E-mail: (OF); (YV)
| | - Delphine Ciais
- CEA, DSV, iRTSV, Laboratoire de Biologie du Cancer et de l’Infection, Grenoble, France
- INSERM U1036, Grenoble, France
- Université Grenoble I, Grenoble, France
| | - Christian Lajaunie
- Mines ParisTech, Centre for Computational Biology, Fontainebleau, France
- Institut Curie, Paris, France
- INSERM U900, Paris, France
| | - Peggy Charbonnier
- Université Grenoble I, Grenoble, France
- CEA, DSV, iRTSV, Laboratoire de Biologie à Grande Echelle, Grenoble, France
- INSERM U1038, Grenoble, France
| | - Nicolas Foveau
- Université Grenoble I, Grenoble, France
- CEA, DSV, iRTSV, Laboratoire de Biologie à Grande Echelle, Grenoble, France
- INSERM U1038, Grenoble, France
| | - Jean-Philippe Vert
- Mines ParisTech, Centre for Computational Biology, Fontainebleau, France
- Institut Curie, Paris, France
- INSERM U900, Paris, France
| | - Yves Vandenbrouck
- Université Grenoble I, Grenoble, France
- CEA, DSV, iRTSV, Laboratoire de Biologie à Grande Echelle, Grenoble, France
- INSERM U1038, Grenoble, France
- * E-mail: (OF); (YV)
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17
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Jin X, Sun T, Zhao C, Zheng Y, Zhang Y, Cai W, He Q, Taira K, Zhang L, Zhou D. Strand antagonism in RNAi: an explanation of differences in potency between intracellularly expressed siRNA and shRNA. Nucleic Acids Res 2011; 40:1797-806. [PMID: 22039150 PMCID: PMC3287203 DOI: 10.1093/nar/gkr927] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Strategies to regulate gene function frequently use small interfering RNAs (siRNAs) that can be made from their shRNA precursors via Dicer. However, when the duplex components of these siRNA effectors are expressed from their respective coding genes, the RNA interference (RNAi) activity is much reduced. Here, we explored the mechanisms of action of shRNA and siRNA and found the expressed siRNA, in contrast to short hairpin RNA (shRNA), exhibits strong strand antagonism, with the sense RNA negatively and unexpectedly regulating RNAi. Therefore, we altered the relative levels of strands of siRNA duplexes during their expression, increasing the level of the antisense component, reducing the level of the sense component, or both and, in this way we were able to enhance the potency of the siRNA. Such vector-delivered siRNA attacked its target effectively. These findings provide new insight into RNAi and, in particular, they demonstrate that strand antagonism is responsible for making siRNA far less potent than shRNA.
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Affiliation(s)
- Xin Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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18
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Petrova NS, Meschaninova MI, Venyaminova AG, Zenkova MA, Vlassov VV, Chernolovskaya EL. Silencing activity of 2'-O-methyl modified anti-MDR1 siRNAs with mismatches in the central part of the duplexes. FEBS Lett 2011; 585:2352-6. [PMID: 21704032 DOI: 10.1016/j.febslet.2011.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 05/25/2011] [Accepted: 06/01/2011] [Indexed: 11/19/2022]
Abstract
The thermodynamic properties of siRNA duplexes are important for their silencing activity. siRNAs with high thermodynamic stability of both the central part of the duplex and in the whole, usually display low silencing activity. Destabilization of the central part of the siRNA duplex could increase its silencing activity. However, mismatches located in the central part of the duplex could substantially decrease the amount of RNAi efficacy, hindering active RISC formation and function. In this study, we examined the impact of duplex destabilization by nucleotide substitutions in the central part (7-10 nt counting from the 5'-end of the antisense strand) of the nuclease-resistant siRNA on its silencing activity.
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Affiliation(s)
- Natalya S Petrova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
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19
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Koldehoff M, Kordelas L, Beelen DW, Elmaagacli AH. Small interfering RNA against BCR-ABL transcripts sensitize mutated T315I cells to nilotinib. Haematologica 2010; 95:388-97. [PMID: 20207846 DOI: 10.3324/haematol.2009.016063] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Selective inhibition of the BCR-ABL tyrosine kinase by RNA interference has been demonstrated in leukemic cells. We, therefore, evaluated specific BCR-ABL small interfering RNA silencing in BCR-ABL-positive cell lines, including those resistant to imatinib and particularly those with the T315I mutation. DESIGN AND METHODS The factor-independent 32Dp210 BCR-ABL oligoclonal cell lines and human imatinib-resistant BCR-ABL-positive cells from patients with leukemic disorders were investigated. The effects of BCR-ABL small interfering RNA or the combination of BCR-ABL small interfering RNA with imatinib and nilotinib were compared with those of the ABL inhibitors imatinib and nilotinib. RESULTS Co-administration of BCR-ABL small interfering RNA with imatinib or nilotinib dramatically reduced BCR-ABL expression in wild-type and mutated BCR-ABL cells and increased the lethal capacity. BCR-ABL small interfering RNA significantly induced apoptosis and inhibited proliferation in wild-type (P<0.0001) and mutated cells (H396P, T315I, P<0.0001) versus controls. Co-treatment with BCR-ABL small interfering RNA and imatinib or nilotinib resulted in increased inhibition of proliferation and induction of apoptosis in T315I cells as compared to imatinib or nilotinib alone (P<0.0001). Furthermore, the combination of BCR-ABL small interfering RNA with imatinib or nilotinib significantly (P<0.01) reversed multidrug resistance-1 gene-dependent resistance of mutated cells. In T315I cells BCR-ABL small interfering RNA with nilotinib had powerful effects on cell cycle distribution. CONCLUSIONS Our data suggest that silencing by BCR-ABL small interfering RNA combined with imatinib or nilotinib may be associated with an additive antileukemic activity against tyrosine kinase inhibitor-sensitive and resistant BCR-ABL cells, and might be an alternative approach to overcome BCR-ABL mutations.
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Affiliation(s)
- Michael Koldehoff
- Department of Bone Marrow Transplantation, West German Cancer Center, University Hospital of Duisburg-Essen, Hufelandstr. 55 45122 Essen, Germany.
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20
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Tesfaye D, Regassa A, Rings F, Ghanem N, Phatsara C, Tholen E, Herwig R, Un C, Schellander K, Hoelker M. Suppression of the transcription factor MSX1 gene delays bovine preimplantation embryo development in vitro. Reproduction 2010; 139:857-70. [DOI: 10.1530/rep-09-0312] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
This study was conducted to investigate the effect of suppressing transcription factor geneMSX1on the development ofin vitroproduced bovine oocytes and embryos, and identify its potential target genes regulated by this gene. Injection of long double-stranded RNA (LdsRNA) and small interfering RNA (siRNA) at germinal vesicle stage oocyte reducedMSX1mRNA expression by 73 and 37% respectively at metaphase II stage compared with non-injected controls. Similarly, injection of the same anti-sense oligomers at zygote stage reducedMSX1mRNA expression by 52 and 33% at 8-cell stage compared with non-injected controls. Protein expression was also reduced in LdsRNA- and siRNA-injected groups compared with non-injected controls at both stages. Blastocysts rates were 33, 28, 20 and 18% in non-injected control, scrambled RNA (scRNA), LdsRNA- and siRNA-injected groups respectively. Cleavage rates were also significantly reduced in Smartpool siRNA (SpsiRNA)-injected group (53.76%) compared with scRNA-injected group (57.76%) and non-injected control group (61%). Large-scale gene expression analysis showed that 135 genes were differentially regulated in SpsiRNA-injected group compared with non-injected controls, of which 54 and 81 were down- and up-regulated respectively due to suppression ofMSX1. Additionally, sequence homology mapping and gene enrichment analysis with known human pathway information identified several functional modules that were affected due to suppression ofMSX1. In conclusion, suppression ofMSX1affects oocyte maturation, embryo cleavage rate and the expression of several genes, suggesting its potential role in the development of bovine preimplantation embryos.
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21
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Piston F, Uauy C, Fu L, Langston J, Labavitch J, Dubcovsky J. Down-regulation of four putative arabinoxylan feruloyl transferase genes from family PF02458 reduces ester-linked ferulate content in rice cell walls. PLANTA 2010; 231:677-91. [PMID: 20012086 PMCID: PMC2806532 DOI: 10.1007/s00425-009-1077-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2009] [Accepted: 11/22/2009] [Indexed: 05/17/2023]
Abstract
Industrial processes to produce ethanol from lignocellulosic materials are available, but improved efficiency is necessary to make them economically viable. One of the limitations for lignocellulosic conversion to ethanol is the inaccessibility of the cellulose and hemicelluloses within the tight cell wall matrix. Ferulates (FA) can cross-link different arabinoxylan molecules in the cell wall of grasses via diferulate and oligoferulate bridges. This complex cross-linking is thought to be a key factor in limiting the biodegradability of grass cell walls and, therefore, the reduction in FA is an attractive target to improve enzyme accessibility to cellulose and hemicelluloses. Unfortunately, our knowledge of the genes responsible for the incorporation of FA to the cell wall is limited. A bioinformatics prediction based on the gene similarities and higher transcript abundance in grasses relative to dicot species suggested that genes from the pfam family PF02458 may act as arabinoxylan feruloyl transferases. We show here that the FA content in the cell walls and the transcript levels of rice genes Os05g08640, Os06g39470, Os01g09010 and Os06g39390, are both higher in the stems than in the leaves. In addition, an RNA interference (RNAi) construct that simultaneously down-regulates transcript levels of these four genes is associated with a significant reduction in FA of the cell walls from the leaves of the transgenic plants relative to the control (19% reduction, P < 0.0001). Therefore, our experimental results in rice support the bioinformatics prediction that members of family PF02458 are involved in the incorporation of FA into the cell wall in grasses.
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Affiliation(s)
- Fernando Piston
- Department of Plant Sciences, University of California, One Shields Avenue, Mail Stop 1, Davis, CA 95616 USA
- Present Address: Dept. de Agronomía y Mejora Genética Vegetal, Instituto de Agricultura Sostenible, CSIC, Alameda del Obispo s/n, 14080 Córdoba, Spain
| | - Cristobal Uauy
- Department of Plant Sciences, University of California, One Shields Avenue, Mail Stop 1, Davis, CA 95616 USA
- Present Address: Department of Crop Genetics, John Innes Centre, Colney Lane, Norwich, NR4 7UH UK
| | - Lianhai Fu
- Department of Plant Sciences, University of California, One Shields Avenue, Mail Stop 1, Davis, CA 95616 USA
| | - James Langston
- Department of Plant Sciences, University of California, One Shields Avenue, Mail Stop 1, Davis, CA 95616 USA
| | - John Labavitch
- Department of Plant Sciences, University of California, One Shields Avenue, Mail Stop 1, Davis, CA 95616 USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, One Shields Avenue, Mail Stop 1, Davis, CA 95616 USA
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YAMANAKA KI, BALBOULA AZ, SAKATANI M, TAKAHASHI M. Gene Silencing of DNA Methyltransferases by RNA Interference in Bovine Fibroblast Cells. J Reprod Dev 2010; 56:60-7. [DOI: 10.1262/jrd.09-105a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Ahmed Zaky BALBOULA
- National Agricultural Research Center for Kyushu Okinawa Region
- Theriogenology Department, Faculty of Veterinary Medicine, Mansoura University
| | - Miki SAKATANI
- National Agricultural Research Center for Kyushu Okinawa Region
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Klingelhoefer JW, Moutsianas L, Holmes C. Approximate Bayesian feature selection on a large meta-dataset offers novel insights on factors that effect siRNA potency. ACTA ACUST UNITED AC 2009; 25:1594-601. [PMID: 19420052 PMCID: PMC2940241 DOI: 10.1093/bioinformatics/btp284] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Motivation: Short interfering RNA (siRNA)-induced RNA interference is an endogenous pathway in sequence-specific gene silencing. The potency of different siRNAs to inhibit a common target varies greatly and features affecting inhibition are of high current interest. The limited success in predicting siRNA potency being reported so far could originate in the small number and the heterogeneity of available datasets in addition to the knowledge-driven, empirical basis on which features thought to be affecting siRNA potency are often chosen. We attempt to overcome these problems by first constructing a meta-dataset of 6483 publicly available siRNAs (targeting mammalian mRNA), the largest to date, and then applying a Bayesian analysis which accommodates feature set uncertainty. A stochastic logistic regression-based algorithm is designed to explore a vast model space of 497 compositional, structural and thermodynamic features, identifying associations with siRNA potency. Results: Our algorithm reveals a number of features associated with siRNA potency that are, to the best of our knowledge, either under reported in literature, such as anti-sense 5′ −3′ motif ‘UCU’, or not reported at all, such as the anti-sense 5′ -3′ motif ‘ACGA’. These findings should aid in improving future siRNA potency predictions and might offer further insights into the working of the RNA-induced silencing complex (RISC). Contact:cholmes@stats.ox.ac.uk Supplementary information:Supplementary data are available at Bioinformatics online.
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Zhou D, Zhang J, Wang C, Bliesath JR, He Q, Yu D, Li-He Z, Wong-Staal F. A method for detecting and preventing negative RNA interference in preparation of lentiviral vectors for siRNA delivery. RNA (NEW YORK, N.Y.) 2009; 15:732-40. [PMID: 19244361 PMCID: PMC2661825 DOI: 10.1261/rna.985209] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2007] [Accepted: 01/07/2009] [Indexed: 05/27/2023]
Abstract
The lentiviral vector is a useful tool for delivery of hairpin siRNA (shRNA) into mammalian cells. However, the efficiency of this system for carrying double-stranded siRNA (dsRNA) has not been explored. In this study we cloned the two forms of siRNA-coding sequence, a palindromic DNA with a spacer loop for shRNA and a double-stranded DNA with opposing Pol III promoters for dsRNA, into lentiviral DNA vectors, and compared their viral vector production yields. Our results indicate that sharply lower titer vector was obtained for dsRNA while much higher titer vector was produced for shRNA, posing a fundamental concern whether siRNA-carrying viral RNA itself is an inherent target of RNAi. Further experimental analyses using packaging cells that either allow or do not allow siRNA transcription indicate that the shRNA-carrying viral RNA is resistant to RNAi but the viral RNA carrier for dsRNA is not, offering a linker of RNAi bias-target secondary structure that causes shRNA vector to evade RNAi degradation. More importantly, the poor yield of dsRNA vector production was restored when a novel packaging cell line was used that blocks the antisense strand from dsRNA duplexes. This method has important implications for the RNAi field, especially for those who are using lentiviral dsRNA and dsRNA libraries for various biological discovery and therapeutic interventions.
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Brunner K, Omann M, Pucher ME, Delic M, Lehner SM, Domnanich P, Kratochwill K, Druzhinina I, Denk D, Zeilinger S. Trichoderma G protein-coupled receptors: functional characterisation of a cAMP receptor-like protein from Trichoderma atroviride. Curr Genet 2008; 54:283-99. [PMID: 18836726 DOI: 10.1007/s00294-008-0217-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2008] [Revised: 09/17/2008] [Accepted: 09/18/2008] [Indexed: 12/17/2022]
Abstract
Galpha subunits act to regulate vegetative growth, conidiation, and the mycoparasitic response in Trichoderma atroviride. To extend our knowledge on G protein signalling, we analysed G protein-coupled receptors (GPCRs). As the genome sequence of T. atroviride is not publicly available yet, we carried out an in silico exploration of the genome database of the close relative T. reesei. Twenty genes encoding putative GPCRs distributed over eight classes and additional 35 proteins similar to the Magnaporthe grisea PTH11 receptor were identified. Subsequently, four T. atroviride GPCR-encoding genes were isolated and affiliated to the cAMP receptor-like family by phylogenetic and topological analyses. All four genes showed lowest expression on glycerol and highest mRNA levels upon carbon starvation. Transcription of gpr3 and gpr4 responded to exogenously added cAMP and the shift from liquid to solid media. gpr3 mRNA levels also responded to the presence of fungal hyphae or cellulose membranes. Further characterisation of mutants bearing a gpr1-silencing construct revealed that Gpr1 is essential for vegetative growth, conidiation and conidial germination. Four genes encoding the first GPCRs described in Trichoderma were isolated and their expression characterized. At least one of these GPCRs is important for several cellular processes, supporting the fundamental role of G protein signalling in this fungus.
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Affiliation(s)
- Kurt Brunner
- Vienna University of Technology, Institute for Chemical Engineering, Research Area of Gene Technology and Applied Biochemistry, Getreidemarkt 9/166, Vienna, Austria
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26
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Koldehoff M, Beelen DW, Elmaagacli AH. Small-molecule inhibition of proteasome and silencing by vascular endothelial cell growth factor-specific siRNA induce additive antitumor activity in multiple myeloma. J Leukoc Biol 2008; 84:561-76. [PMID: 18458152 DOI: 10.1189/jlb.0907632] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Angiogenesis plays an important role in the pathogenesis and progression in multiple myeloma (MM), and MM cells secrete vascular endothelial growth factor (VEGF), which further promotes proliferation of the tumor cells. Therefore, we evaluated the anti-myeloma effect of VEGF small interfering RNA (siRNA) silencing in MM cells and whether it can be augmented by the additional application of bortezomib directed against the 26S proteasome. After transfection with VEGF siRNA, we observed a reduction of VEGF expression in all studied cell lines: OPM-2, RPMI-8226, INA-6, Jurkat, Raji, and Karpas-299, as well as in cells of MM and lymphoma patients. VEGF siRNA significantly induced apoptosis and inhibited proliferation in OPM-2 cells (P<0.0001), RPMI-8226 (P<0.0001), and INA-6 (P<0.01) versus controls. Cotreatment with VEGF siRNA and bortezomib in MM cells resulted in an exaggerated inhibition of proliferation and induction of apoptosis compared with VEGF siRNA or bortezomib alone (P<0.001). In addition, the combination of VEGF siRNA and bortezomib significantly (P<0.01) reversed multidrug resistance gene 1-dependent resistance of MM cells. Our data suggest that small-molecule inhibition of proteasome and silencing by VEGF-specific siRNA may be associated with an additive antitumor activity and might be a suitable target for new, therapeutic strategies using RNA interference in MM.
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Affiliation(s)
- Michael Koldehoff
- Department of Bone Marrow Transplantation, University Hospital of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany.
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Krueger U, Bergauer T, Kaufmann B, Wolter I, Pilk S, Heider-Fabian M, Kirch S, Artz-Oppitz C, Isselhorst M, Konrad J. Insights into effective RNAi gained from large-scale siRNA validation screening. Oligonucleotides 2007; 17:237-50. [PMID: 17638527 DOI: 10.1089/oli.2006.0065] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Transfection of chemically synthesized short interfering RNAs (siRNAs) enables a high level of sequence-specific gene silencing. Although siRNA design algorithms have been improved in recent years, it is still necessary to prove the functionality of a given siRNA experimentally. We have functionally tested several thousand siRNAs for target genes from various gene families including kinases, phosphatases, and cancer-related genes (e.g., genes involved in apoptosis and the cell cycle). Some targets were difficult to silence above a threshold of 70% knockdown. By working with one design algorithm and a standardized validation procedure, we discovered that the level of silencing achieved was not exclusively dependent on the siRNA sequences. Here we present data showing that neither the gene expression level nor the cellular environment has a direct impact on the knockdown which can be achieved for a given target. Modifications of the experimental setting have been investigated with the aim of improving knockdown efficiencies for siRNA-target combinations that show only moderate knockdown. Use of higher siRNA concentrations did not change the overall performance of the siRNA-target combinations analyzed. Optimal knockdown at the mRNA level was usually reached 48-72 hours after transfection. Target gene-specific characteristics such as the accessibility of the corresponding target sequences to the RNAi machinery appear to have a significant influence on the knockdown observed, making certain targets easy or difficult to knock down using siRNA.
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Kayed H, Jiang X, Keleg S, Jesnowski R, Giese T, Berger MR, Esposito I, Löhr M, Friess H, Kleeff J. Regulation and functional role of the Runt-related transcription factor-2 in pancreatic cancer. Br J Cancer 2007; 97:1106-15. [PMID: 17876328 PMCID: PMC2360444 DOI: 10.1038/sj.bjc.6603984] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Recent evidence suggests that Runt-related transcription factors play a role in different human tumours. In the present study, the localisation of the Runt-related transcription factor-2 (Runx2), its transcriptional activity, as well as its regulation of expression was analysed in human pancreatic ductal adenocarcinoma (PDAC). Quantitative real-time PCR and immunohistochemistry were used for Runx2 expression and localisation analysis. Runt-related transcription factor-2 expression was silenced using specific siRNA oligonucleotides in pancreatic cancer cells (Panc-1) and immortalised pancreatic stellate cells (IPSCs). Overexpression of Runx2 was achieved using a full-length expression vector. TGF-β1, BMP2, and other cytokines were assessed for their potential to regulate Runx2 expression. There was a 6.1-fold increase in median Runx2 mRNA levels in PDAC tissues compared to normal pancreatic tissues (P<0.0001). Runt-related transcription factor-2 was localised in pancreatic cancer cells, tubular complexes, and PanIN lesions of PDAC tissues as well as in tumour-associated fibroblasts/stellate cells. Coculture of IPSCs and Panc-1 cells, as well as treatment with TGF-β1 and BMP2, led to increased Runx2 expression in Panc-1 cells. Runt-related transcription factor-2 overexpression was associated with decreased MMP1 release as well as decreased growth and invasion of Panc-1 cells. These effects were reversed by Runx2 silencing. In conclusion, Runx2 is overexpressed in PDAC, where it is regulated by certain cytokines such as TGF-β1 and BMP2 in an auto- and paracrine manner. In addition, Runx2 has the potential to regulate the transcription of extracellular matrix modulators such as SPARC and MMP1, thereby influencing the tumour microenvironment.
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Affiliation(s)
- H Kayed
- Department of General Surgery, University of Heidelberg, Heidelberg, Germany
| | - X Jiang
- Department of General Surgery, University of Heidelberg, Heidelberg, Germany
| | - S Keleg
- Department of General Surgery, University of Heidelberg, Heidelberg, Germany
| | - R Jesnowski
- Molecular Gastroenterology Unit, German Cancer Research Centre, Heidelberg, Germany
- Department of Medicine II, University of Heidelberg, Mannheim, Germany
| | - T Giese
- Institute of Immunology, University of Heidelberg, Heidelberg, Germany
| | - M R Berger
- Unit of Toxicology and Chemotherapy, German Cancer Research Centre, Heidelberg, Germany
| | - I Esposito
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - M Löhr
- Molecular Gastroenterology Unit, German Cancer Research Centre, Heidelberg, Germany
- Department of Medicine II, University of Heidelberg, Mannheim, Germany
| | - H Friess
- Department of General Surgery, University of Heidelberg, Heidelberg, Germany
| | - J Kleeff
- Department of General Surgery, University of Heidelberg, Heidelberg, Germany
- Department of Surgery, Technical University of Munich, Ismaningerstrasse 22, Munich 81675, Germany. E-mail:
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Zhang J, Wang C, Ke N, Bliesath J, Chionis J, He QS, Li QX, Chatterton JE, Wong-Staal F, Zhou D. A more efficient RNAi inducible system for tight regulation of gene expression in mammalian cells and xenograft animals. RNA (NEW YORK, N.Y.) 2007; 13:1375-83. [PMID: 17616554 PMCID: PMC1924899 DOI: 10.1261/rna.520707] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Two types of tetracycline-controlled inducible RNAi expression systems have been developed that generally utilize multiple tetracycline operators (TetOs) or repressor fusion proteins to overcome the siRNA leakiness. Here, we report a novel system that overexpresses the tetracycline repressor (TetR) via a bicistronic construct to control siRNA expression. The high level of TetR expression ensures that the inducible promoter is tightly bound, with minimal basal transcription, allowing for regulation solely dependent on TetR rather than a TetR fusion protein via a more complicated mechanism. At the same time, this system contains only a single TetO, thus minimizing the promoter impairment occurring in existing systems due to the incorporation of multiple TetOs, and maximizing the siRNA expression upon induction. In addition, this system combines all the components required for regulation of siRNA expression into a single lentiviral vector, so that stable cell lines can be generated by a single transduction and selection, with significant reduction in time and cost. Taken together, this all-in-one lentiviral vector with the feature of TetR overexpression provides a unique and more efficient tool for conditional gene knockdown that has wide applications. We have demonstrated the high degree of robustness and versatility of this system as applied to several mammalian cells and xenograft animals.
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Schellander K, Hoelker M, Tesfaye D. Selective degradation of transcripts in mammalian oocytes and embryos. Theriogenology 2007; 68 Suppl 1:S107-15. [PMID: 17573104 DOI: 10.1016/j.theriogenology.2007.05.054] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
During the last decade several gene expression analysis studies have been carried out to investigate the transcriptional profile of bovine embryos in response to various culture and treatments conditions. Despite this fact, the function of a large number of genes in mammalian embryogenesis has not yet been investigated or is not known. The conventional gene-knockout experiments have been used extensively to study the function of genes in mammalian embryogenesis. However, these studies are relatively slow and cannot keep pace with the rapid accumulation of new sequence information produced by various genome projects. For this, the posttranscriptional gene silencing (PTGS) by double-stranded RNA (dsRNA), or RNA interference (RNAi), has emerged as a new tool for studying gene function in an increasing number of organisms. The present review will focus on recent developments in the use of RNAi for selective degradation of transcripts in mammalian embryos to elucidate their function in early development.
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Affiliation(s)
- K Schellander
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany.
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Egerod KL, Holst B, Petersen PS, Hansen JB, Mulder J, Hökfelt T, Schwartz TW. GPR39 splice variants versus antisense gene LYPD1: expression and regulation in gastrointestinal tract, endocrine pancreas, liver, and white adipose tissue. Mol Endocrinol 2007; 21:1685-98. [PMID: 17488974 DOI: 10.1210/me.2007-0055] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
G protein-coupled receptor 39 (GPR39) is a constitutively active, orphan member of the ghrelin receptor family that is activated by zinc ions. GPR39 is here described to be expressed in a full-length, biologically active seven-transmembrane form, GPR39-1a, as well as in a truncated splice variant five-transmembrane form, GPR39-1b. The 3' exon of the GPR39 gene overlaps with an antisense gene called LYPD1 (Ly-6/PLAUR domain containing 1). Quantitative RT-PCR analysis demonstrated that GPR39-1a is expressed selectively throughout the gastrointestinal tract, including the liver and pancreas as well as in the kidney and adipose tissue, whereas the truncated GPR39-1b form has a more broad expression pattern, including the central nervous system but with highest expression in the stomach and small intestine. In contrast, the LYPD1 antisense gene is highly expressed throughout the central nervous system as characterized with both quantitative RT-PCR and in situ hybridization analysis. A functional analysis of the GPR39 promoter region identified sites for the hepatocyte nuclear factors 1alpha and 4alpha (HNF-1alpha and -4alpha) and specificity protein 1 (SP1) transcription factors as being important for the expression of GPR39. In vivo experiments in rats demonstrated that GPR39 is up-regulated in adipose tissue during fasting and in response to streptozotocin treatment, although its expression is kept constant in the liver from the same animals. GPR39-1a was expressed in white but not brown adipose tissue and was down-regulated during adipocyte differentiation of fibroblasts. It is concluded that the transcriptional control mechanism, the tissue expression pattern, and in vivo response to physiological stimuli all indicate that the GPR39 receptor very likely is of importance for the function of a number of metabolic organs, including the liver, gastrointestinal tract, pancreas, and adipose tissue.
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MESH Headings
- Adipose Tissue/metabolism
- Adipose Tissue, Brown/metabolism
- Alternative Splicing
- Amino Acid Sequence
- Animals
- Antisense Elements (Genetics)
- Base Sequence
- Cell Line
- DNA Primers/genetics
- Diabetes Mellitus, Experimental/genetics
- Diabetes Mellitus, Experimental/metabolism
- Gastrointestinal Tract/metabolism
- Gene Expression Regulation
- Humans
- In Situ Hybridization
- Islets of Langerhans/metabolism
- Liver/metabolism
- Male
- Models, Molecular
- Molecular Sequence Data
- Promoter Regions, Genetic
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Rats
- Rats, Wistar
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/genetics
- Receptors, G-Protein-Coupled/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Tissue Distribution
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Affiliation(s)
- Kristoffer L Egerod
- Laboratory for Molecular Pharmacology, Department of Neuroscience and Pharmacology, University of Copenhagen, DK-2200 Copenhagen, Denmark
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Borawski J, Lindeman A, Buxton F, Labow M, Gaither LA. Optimization Procedure for Small Interfering RNA Transfection in a 384-Well Format. ACTA ACUST UNITED AC 2007; 12:546-59. [PMID: 17435168 DOI: 10.1177/1087057107300172] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
High-throughput screening of RNAi libraries has become an essential part of functional analysis in academic and industrial settings. The transition of a cell-based RNAi assay into a 384-well format requires several optimization steps to ensure the phenotype being screened is appropriately measured and that the signal-to-background ratio is above a certain quantifiable threshold. Methods currently used to assess small interfering RNA (siRNA) efficacy after transfection, including quantitative PCR or branch DNA analysis, face several technical limitations preventing the accurate measurement of mRNA levels in a 384-well format. To overcome these difficulties, the authors developed an approach using a viral-based transfection system that measures siRNA efficacy in a standardized 384-well assay. This method allows measurement of siRNA activity in a phenotypically neutral manner by quantifying the knockdown of an exogenous luciferase gene delivered by a lentiviral vector. In this assay, the efficacy of a luciferase siRNA is compared to a negative control siRNA across many distinct assay parameters including cell type, cell number, lipid type, lipid volume, time of the assay, and concentration of siRNA. Once the siRNA transfection is optimized as a 384-well luciferase knockdown, the biologically relevant phenotypic analysis can proceed using the best siRNA transfection conditions. This approach provides a key technology for 384-well assay development when direct measurement of mRNA knockdown is not possible. It also allows for direct comparison of siRNA activity across cell lines from almost any mammalian species. Defining optimal conditions for siRNA delivery into mammalian cells will greatly increase the speed and quality of large-scale siRNA screening campaigns. ( Journal of Biomolecular Screening 2007:546-559)
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Affiliation(s)
- Jason Borawski
- Genome and Proteome Sciences Department Platform and Chemical Biology Unit Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
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Tesfaye D, Lonergan P, Hoelker M, Rings F, Nganvongpanit K, Havlicek V, Besenfelder U, Jennen D, Tholen E, Schellander K. Suppression of connexin 43 and E-cadherin transcripts in in vitro derived bovine embryos following culture in vitro or in vivo in the homologous bovine oviduct. Mol Reprod Dev 2007; 74:978-88. [PMID: 17219420 DOI: 10.1002/mrd.20678] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In this study, a combination of RNAi and endoscopic transfer to the oviduct of synchronized heifers has been used to investigate the effect of suppression of Cx43 and E-cadherin on the development, mRNA and protein expression of bovine blastocysts cultured in vitro or in vivo. In vitro matured and fertilized bovine zygotes were randomly assigned to one of four groups namely: Connexin43 dsRNA-injected (n = 790), E-cadherin dsRNA-injected (n = 775), water-injected (n = 774), and noninjected controls (n = 652). Following 2 days in vitro culture, 4- and 8-cell stage embryos from each treatment group were used for culture in vitro or in vivo. About half of the 4-8-cell stage embryos from each treatment group were transferred to the oviduct of synchronized heifers, while the remainder were further cultured in vitro. Embryos from in vivo culture were flushed from recipients on the fourth day post transfer (= Day 7 post insemination). Blastocyst stage embryos from both culture systems were used for mRNA and protein expression analysis. Irrespective of treatment or culture conditions, microinjection resulted in a decline in the proportion of embryos reaching the blastocyst stage. Significantly, lower blastocyst development was observed in E-cadherin and water-injected embryos following in vivo culture compared to the noninjected controls, while intermediate results were obtained following injection with Cx43 dsRNA. Both mRNA and protein products of the target genes were suppressed but the efficiency of suppression of the target genes varied depending on the initial level of transcript abundance, which is known to be greatly affected by the culture environment.
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Affiliation(s)
- Dawit Tesfaye
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, Bonn, Germany.
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Radke JR, Donald RG, Eibs A, Jerome ME, Behnke MS, Liberator P, White MW. Changes in the expression of human cell division autoantigen-1 influence Toxoplasma gondii growth and development. PLoS Pathog 2006; 2:e105. [PMID: 17069459 PMCID: PMC1626100 DOI: 10.1371/journal.ppat.0020105] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2005] [Accepted: 08/29/2006] [Indexed: 11/18/2022] Open
Abstract
Toxoplasma is a significant opportunistic pathogen in AIDS, and bradyzoite differentiation is the critical step in the pathogenesis of chronic infection. Bradyzoite development has an apparent tropism for cells and tissues of the central nervous system, suggesting the need for a specific molecular environment in the host cell, but it is unknown whether this environment is parasite directed or the result of molecular features specific to the host cell itself. We have determined that a trisubstituted pyrrole acts directly on human and murine host cells to slow tachyzoite replication and induce bradyzoite-specific gene expression in type II and III strain parasites but not type I strains. New mRNA synthesis in the host cell was required and indicates that novel host transcripts encode signals that were able to induce parasite development. We have applied multivariate microarray analyses to identify and correlate host gene expression with specific parasite phenotypes. Human cell division autoantigen-1 (CDA1) was identified in this analysis, and small interfering RNA knockdown of this gene demonstrated that CDA1 expression causes the inhibition of parasite replication that leads subsequently to the induction of bradyzoite differentiation. Overexpression of CDA1 alone was able to slow parasite growth and induce the expression of bradyzoite-specific proteins, and thus these results demonstrate that changes in host cell transcription can directly influence the molecular environment to enable bradyzoite development. Investigation of host biochemical pathways with respect to variation in strain type response will help provide an understanding of the link(s) between the molecular environment in the host cell and parasite development.
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Affiliation(s)
- Jay R Radke
- Department of Veterinary Molecular Biology, Montana State University, Bozeman, Montana, USA.
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35
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Xu P, Zhang Y, Kang L, Roossinck MJ, Mysore KS. Computational estimation and experimental verification of off-target silencing during posttranscriptional gene silencing in plants. PLANT PHYSIOLOGY 2006; 142:429-40. [PMID: 16920874 PMCID: PMC1586062 DOI: 10.1104/pp.106.083295] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Accepted: 08/07/2006] [Indexed: 05/11/2023]
Abstract
Successful application of posttranscriptional gene silencing (PTGS) for gene function study in both plants and animals depends on high target specificity and silencing efficiency. By computational analysis with genome and/or transcriptome sequences of 25 plant species, we predicted that about 50% to 70% of gene transcripts in plants have potential off-targets when used for PTGS that could obscure experimental results. We have developed a publicly available Web-based computational tool called siRNA Scan to identify potential off-targets during PTGS. Some of the potential off-targets obtained from this tool were tested by measuring the amount of off-target transcripts using quantitative reverse transcription-PCR. Up to 50% of the predicted off-target genes tested in plants were actually silenced when tested experimentally. Our results suggest that a high risk of off-target gene silencing exists during PTGS in plants. Our siRNA Scan tool is useful to design better constructs for PTGS by minimizing off-target gene silencing in both plants and animals.
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Affiliation(s)
- Ping Xu
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401, USA
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Abstract
GPR39, an orphan G protein-coupled receptor, has been recently identified as the receptor for the bioactive peptide obestatin. Obestatin is secreted from the stomach and acts as an anti-appetite hormone. This activity is induced whether obestatin is administered intraperitoneally or intracerebroventricularly. GPR39 is known to be expressed in the central nervous system but its precise localization is unknown. In view of the growing importance of this system, we decided to study the sites of GPR39 mRNA expression by in-situ hybridization. We find the highest levels of GPR39 mRNA in the amygdala, the hippocampus, and the auditory cortex and low levels in several other brain regions. Surprisingly, we find no expression of GPR39 in the hypothalamus, expected to be the site of the anorexigenic action of obestatin.
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Affiliation(s)
- Valerie R Jackson
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California 92697-4625, USA.
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Yu DH, Fan W, Liu G, Nguy V, Chatterton JE, Long S, Ke N, Meyhack B, Bruengger A, Brachat A, Wong-Staal F, Li QX. PHTS, a novel putative tumor suppressor, is involved in the transformation reversion of HeLaHF cells independently of the p53 pathway. Exp Cell Res 2006; 312:865-76. [PMID: 16413018 DOI: 10.1016/j.yexcr.2005.12.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2005] [Revised: 10/30/2005] [Accepted: 12/01/2005] [Indexed: 10/25/2022]
Abstract
HeLaHF is a non-transformed revertant of HeLa cells, likely resulting from the activation of a putative tumor suppressor(s). p53 protein was stabilized in this revertant and reactivated for certain transactivation functions. Although p53 stabilization has not conclusively been linked to the reversion, it is clear that the genes in p53 pathway are involved. The present study confirms the direct role of p53 in HeLaHF reversion by demonstrating that RNAi-mediated p53 silencing partially restores anchorage-independent growth potential of the revertant through the suppression of anoikis. In addition, we identified a novel gene, named PHTS, with putative tumor suppressor properties, and showed that this gene is also involved in HeLaHF reversion independently of the p53 pathway. Expression profiling revealed that PHTS is one of the genes that is up-regulated in HeLaHF but not in HeLa. It encodes a putative protein with CD59-like domains. RNAi-mediated PHTS silencing resulted in the partial restoration of transformation (anchorage-independent growth) in HeLaHF cells, similar to that of p53 gene silencing, implying its tumor suppressor effect. However, the observed increased transformation potential by PHTS silencing appears to be due to an increased anchorage-independent proliferation rate rather than suppression of anoikis, unlike the effect of p53 silencing. p53 silencing did not affect PHTS gene expression, and vice versa, suggesting PHTS may function in a new and p53-independent tumor suppressor pathway. Furthermore, over-expression of PHTS in different cancer cell lines, in addition to HeLa, reduces cell growth likely via induced apoptosis, confirming the broad PHTS tumor suppressor properties.
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Affiliation(s)
- De-Hua Yu
- Immusol, Inc. 10790 Roselle Street, San Diego, CA 92121, USA
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Shabalina SA, Spiridonov AN, Ogurtsov AY. Computational models with thermodynamic and composition features improve siRNA design. BMC Bioinformatics 2006; 7:65. [PMID: 16472402 PMCID: PMC1431570 DOI: 10.1186/1471-2105-7-65] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Accepted: 02/12/2006] [Indexed: 11/17/2022] Open
Abstract
Background Small interfering RNAs (siRNAs) have become an important tool in cell and molecular biology. Reliable design of siRNA molecules is essential for the needs of large functional genomics projects. Results To improve the design of efficient siRNA molecules, we performed a comparative, thermodynamic and correlation analysis on a heterogeneous set of 653 siRNAs collected from the literature. We used this training set to select siRNA features and optimize computational models. We identified 18 parameters that correlate significantly with silencing efficiency. Some of these parameters characterize only the siRNA sequence, while others involve the whole mRNA. Most importantly, we derived an siRNA position-dependent consensus, and optimized the free-energy difference of the 5' and 3' terminal dinucleotides of the siRNA antisense strand. The position-dependent consensus is based on correlation and t-test analyses of the training set, and accounts for both significantly preferred and avoided nucleotides in all sequence positions. On the training set, the two parameters' correlation with silencing efficiency was 0.5 and 0.36, respectively. Among other features, a dinucleotide content index and the frequency of potential targets for siRNA in the mRNA added predictive power to our model (R = 0.55). We showed that our model is effective for predicting the efficiency of siRNAs at different concentrations. We optimized a neural network model on our training set using three parameters characterizing the siRNA sequence, and predicted efficiencies for the test siRNA dataset recently published by Novartis. On this validation set, the correlation coefficient between predicted and observed efficiency was 0.75. Using the same model, we performed a transcriptome-wide analysis of optimal siRNA targets for 22,600 human mRNAs. Conclusion We demonstrated that the properties of the siRNAs themselves are essential for efficient RNA interference. The 5' ends of antisense strands of efficient siRNAs are U-rich and possess a content similarity to the pyrimidine-rich oligonucleotides interacting with the polypurine RNA tracks that are recognized by RNase H. The advantage of our method over similar methods is the small number of parameters. As a result, our method requires a much smaller training set to produce consistent results. Other mRNA features, though expensive to compute, can slightly improve our model.
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Affiliation(s)
- Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, MD 20894, USA
| | - Alexey N Spiridonov
- Department of Applied Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Aleksey Y Ogurtsov
- National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, MD 20894, USA
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Haindl M, Holler E. Use of the giant multinucleate plasmodium of Physarum polycephalum to study RNA interference in the myxomycete. Anal Biochem 2005; 342:194-9. [PMID: 15922285 DOI: 10.1016/j.ab.2005.03.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2004] [Revised: 03/14/2005] [Accepted: 03/16/2005] [Indexed: 10/25/2022]
Abstract
The plasmodium of Physarum polycephalum harbors billions of synchronized nuclei in a single cell of complex structure. Due to its synchrony and extreme size, it is used as a model to study events on a single cell level, such as cell cycle and differentiation. We show here for the first time that this model, despite its enormous size and structural complexity, is accessible to RNA interference by simple injection of dsRNA or siRNA. The targeted gene is that of polymalatase, an intracellular adapter of poly(beta-l-malate) involved in the maintenance of the synchrony and functioning as an extracellular hydrolase of this polymer. Real-time reverse transcriptase polymerase chain reaction analysis revealed that the specific mRNA was knocked down to about 10% of the original level. The suppression of a single injection lasted for approximately 14 cell cycles (144 h) and could be prolonged for any time by repeated dsRNA injections. Western blots indicated that the knockdown of RNA was paralleled by a strong reduction in polymalatase synthesis. However, a change in the phenotype of the plasmodium could not be clearly observed. In principle, the plasmodium offers an easy system for studying gene knockdown by RNA interference.
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Affiliation(s)
- Markus Haindl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
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Adams AM, Pratt SL, Stice SL. Knockdown of the Dnmt1s transcript using small interfering RNA in primary murine and bovine fibroblast cells. Mol Reprod Dev 2005; 72:311-9. [PMID: 16078273 DOI: 10.1002/mrd.20357] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
RNA interference (RNAi) has rapidly developed into one of the most widely applied technologies in molecular and cellular research, and although young, is now an essential experimental tool. The versatility of RNAi, especially in mammalian species, lends to its potential applications in a wide array of fields. Without having to genetically manipulate the genome, the ability to selectively reduce the level of a specific transcript using small interfering RNA (siRNA) molecules has great appeal in studying reprogramming issues in somatic cell nuclear transfer (SCNT) embryos. In such embryos, the aberrant expression of the somatic isoform of Dnmt1 (Dnmt1s), the enzyme responsible for maintaining DNA methylation in all somatic cells, has been implicated as one factor in the improper reprogramming of the donor genome. In the present study, the ability to develop a method allowing for the knockdown, or reduction, of Dnmt1s in primary fibroblast cells, like those commonly used as karyoplast donors in SCNT studies, was investigated in primary murine and bovine fibroblast cells as well as in a compromised cell line (NIH/3T3). Two Dnmt1s-specific siRNA candidates were designed and tested. Using optimized conditions, these siRNAs were transiently transfected into the cells with total RNA and nuclear protein being collected. A 56.5% knockdown in Dnmt1s was achieved in the compromised and primary murine cells whereas Dnmt1s was reduced by 15.4% in the primary bovine cells. A reduction in Dnmt1s mRNA did not correspond to a reduction in protein as determined by immunodetection of Western blots. Overall, this study demonstrated the ability of siRNA to knockdown Dnmt1s mRNA in primary fibroblast donor cells. In order to substantially increase the efficiency while decreasing the anomalies seen in SCNT, novel techniques, like the one proposed, are needed to assist the oocyte's ability to reprogram a differentiated genome.
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Affiliation(s)
- A M Adams
- Animal and Dairy Science Department, University of Georgia, 425 River Road, Athens, Georgia 30602, USA
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